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Géoscience
Sciences de la Planète

Julie Cosmidis and Karim Benzerara

Why do microbes make minerals?

Volume 354, issue 1 (2022), p. 1-39

<https://doi.org/10.5802/crgeos.107>

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Comptes Rendus
Géoscience — Sciences de la Planète
2022, 354, n 1, p. 1-39
https://doi.org/10.5802/crgeos.107

Review Article — Petrology, Geochemistry

Why do microbes make minerals?

∗, a b
Julie Cosmidis and Karim Benzerara

a Department of Earth Sciences, University of Oxford, Oxford, UK

b Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne

Université, UMR CNRS 7590, Muséum National d’Histoire Naturelle, Paris, France
E-mails: julie.cosmidis@earth.ox.ac.uk (J. Cosmidis), karim.benzerara@upmc.fr
(K. Benzerara)

Abstract. Prokaryotes have been shaping the surface of the Earth and impacting geochemical cycles
for the past four billion years. Biomineralization, the capacity to form minerals, is a key process by
which microbes interact with their environment. While we keep improving our understanding of the
mechanisms of this process (“how?”), questions around its functions and adaptive roles (“why?”)
have been less intensively investigated. Here, we discuss biomineral functions for several examples
of prokaryotic biomineralization systems, and propose a roadmap for the study of microbial biomin-
eralization through the lens of adaptation. We also discuss emerging questions around the potential
roles of biomineralization in microbial cooperation and as important components of biofilm architec-
tures. We call for a shift of focus from mechanistic to adaptive aspects of biomineralization, in order
to gain a deeper comprehension of how microbial communities function in nature, and improve our
understanding of life co-evolution with its mineral environment.

Keywords. Biomineralization, Microbial evolution, Cooperation, Biofilms, Sulfur, Iron, Carbonates.

Note. Submission by invitation of the editorial board.
Manuscript received 8th October 2021, revised and accepted 30th November 2021.

1. Introduction the Earth, and hence are important drivers of geo-

chemical cycles [Falkowski et al., 2008]. Since the
Prokaryotes form an invisible yet major part of Earth’s origin of life about 4 billion years ago, microorgan-
biosphere. Although easy to overlook due to their isms have been influencing their geochemical en-
small sizes, bacteria and archaea contribute to a vironment, and have in turn been influenced by it.
significant fraction of modern biodiversity in terms Throughout this long co-evolutionary history, some
of species abundance, total biomass, and capacity prokaryotes have acquired the capability to form
to thrive in habitats inhospitable to more conspic- minerals, a process called biomineralization [Frankel
uous forms of life [Bar-On et al., 2018]. Moreover, and Bazylinski, 2003]. Prokaryotic biomineralization
due to their impressively diverse metabolic capabil- mirrors Eukaryotes’ capacity to form mineral skele-
ities, prokaryotes participate in transformations and tons, shells, or teeth, and has been evidenced as
fluxes of most elements present at the surface of early as the 19th century, with, for instance, the dis-
coveries of Fe-oxide biomineralization by Gallionella
[Ehrenberg, 1836] or Ca-carbonate biomineralization
∗ Corresponding author.
by Achromatium oxaliferum [Schewiakoff, 1893].

ISSN (electronic) : 1778-7025 https://comptes-rendus.academie-sciences.fr/geoscience/

2 Julie Cosmidis and Karim Benzerara

Under given conditions, certain prokaryotes depending on authors, serving different explanatory
biomineralize more intensively than others, while schemes [Donovan, 2019]. A function may relate to
many do not biomineralize at all, and thus we can how a trait contributes to the functioning of a bio-
define this capability as a biological trait*, i.e. a logical system, without discriminating adaptations*
phenotypic* characteristic that can be measured. from “fortuitous effects”. This is called a “causal role”
In this review, we focus on an often-overlooked as- function* and can be determined for example by
pect of this trait: its potential biological functions. observing how a microbial system responds to the
Much progress has been made in recent years on the removal or alteration of the trait [Klassen, 2018]. In
molecular-level mechanisms of microbial mineral a more teleological way, a function may be seen as
formation, due to combined advances in genomic the effect of a trait which has been responsible for its
approaches [e.g., Koeksoy et al., 2021, Uebe and selection upon evolution (i.e. referring to its causal
Schüler, 2016, Zhang et al., 2020] and microscopy history). This is called a “selected effect” function*.
techniques [e.g., Blondeau et al., 2018b, Comolli Last, the “fitness contribution” function* of a trait
et al., 2011, Li et al., 2017]. However, the question may be seen as the effect it presently contributes to
of the biological functions of biomineralization is the fitness* (or reproductive success) of the organ-
often relegated to the discussion section of articles ism, regardless of its history. The last two views imply
on the topic—when not completely ignored. As the- that the trait is adaptive. In this review, we will dis-
orized by the Nobel Prize laureate Nikolaas Tinber- cuss these different views when referring to potential
gen, ultimate causes (“why?”) need to be addressed functions of biominerals, while carefully avoiding
along proximate ones (“how?”) if a comprehensive the Panglossian paradigm as defined by Gould and
understanding of any biological phenomenon is to Lewontin [1979], in which all traits taken separately
be achieved [Tinbergen, 1963]. There is now a need are considered as adaptive.
to shed light on the ultimate causes of prokaryotic
biomineralization, including its potential functional
and adaptive* aspects. After presenting the classi- 2. Prokaryotic biomineralization processes
cal framework used to conceptualize prokaryotic and their functions: the classical framework
biominerals and their potential functions, we de-
scribe recent results and hypotheses about the bi- In this section, we present the conceptual framework
ological functions of prokaryotic biomineralization originally laid out by Lowenstam [1981] and later de-
by focussing on a few selected examples (elemental veloped by other authors to conceptualize biominer-
sulfur, extracellular Fe(III) minerals, and intracellu- alization, and describe how they intersect with the
lar carbonates). We then propose experimental ap- question of the biological functions of prokaryotic
proaches that may allow future progress on these “ul- biominerals (Figure 1).
timate” questions, before focussing on two emerging
roles for microbial biomineralization: cooperative
2.1. Controlled biomineralization
interactions and biofilm* architectures. The exam-
ples and concepts developed in this review finally Biologically controlled mineralization was intro-
allow us to propose a new framework to classify duced by Mann [1983], generalizing the “organic
biomineralization processes based on their adaptive matrix-mediated” notion coined by Lowenstam
value. [1981]. As its name implies, in controlled biominer-
Note that we will use the terms “microbes” and alization, the organism exerts strict genetic control
“microbial” interchangeably with “prokaryotes” and to direct the nucleation, growth, and final location
“prokaryotic” (respectively) in this review, leaving of the formed biominerals. Controlled mineraliza-
aside biomineralization by microbial Eukaryotes. tion can be intracellular* or extracellular* and/or
Terms specific to microbiology or evolutionary bi- start intracellularly with a final extracellular location
ology rarely used in the Earth science literature are of the biominerals. Many eukaryotic biominerals
defined in Table 1 and are indicated by an asterisk are formed by controlled mineralization and serve
on their first occurrence. Also note that the term clearly identified biological functions (in both “causal
‘biological function’ can have diverse meanings role” and “selected effect” views), such as structure

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 Julie Cosmidis and Karim Benzerara 3

Table 1. Definitions of some technical terms specific to microbiology and evolutionary biology

Term Definition
Adaptation Any change in the structure or functioning of successive generations of a
population that makes it better suited to its environment.
Adaptive Generally, providing, contributing to, or arising as a result to adaptation.
More specifically, refers to a heritable trait that serves a specific function
and improves an organism’s fitness or survival.
Aerotaxis The movement of a cell or microorganism driven by a dioxygen gradient.
Antagonistic pleiotropy Phenomenon in which versions of genes that are detrimental under certain
conditions (e.g., late in life) improve fitness under other conditions (e.g.,
earlier in life).
Autotroph(ic)* Refers to an organism that can build its own macromolecules from inor-
ganic molecules, such as carbon dioxide (carbon autotrophy) or ammonia
(nitrogen autotrophy).
Biofilm A complex aggregation of bacteria and other microorganisms, that adheres
to a substrate and is encased within a matrix of extracellular polymeric
substances (EPS).
Capsule A thick and relatively rigid gelatinous layer completely surrounding the cell
wall of certain bacteria.
Causal role function Contribution of a trait to the functioning of a biological system.
Chemotroph(ic)* Refers to an organism whose energy is the result of endogenous, light-
independent chemical reactions.
Clone, clonal Refers to a group of genetically identical cells or organisms all descended
from a single common ancestral cell or organism.
Convergent evolution The development of apparently similar structures in unrelated organisms,
usually because the organisms live in the same kind of environment.
Cytoplasm(ic) Refers to the content of the cell, located within the plasma membrane.
EPS Extracellular polymeric substances secreted by microorganisms. Some-
times used as a synonym for exopolysaccharides, a specific range of sug-
ars produced either as insoluble capsules or a soluble slimes in the extra-
cellular medium.
Exaptation A character that provides a selective advantage under current conditions
but had a different function at its origin.
Extracellular(ly) Located or occurring outside the cell.
Extracytoplasmic Located or occurring outside the cytoplasm.
Fitness A measure of the contribution of an individual to the genetic composition
of subsequent generations through its offspring.
Fitness contribution function The contribution of a trait to the fitness of the organism.
Heterotroph(ic)* Refers to an organism whose energy is derived from the intake and diges-
tion of organic substances
Homeostasis, homeostatic Refers to the regulation by an organism of the chemical composition of its
internal environment.
(continued on next page)

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4 Julie Cosmidis and Karim Benzerara

Table 1. (continued)

Term Definition
Homologous Referring to structures or processes in different organisms that show a funda-
mental similarity because of their having descended from a common ancestor.
Interspecific Occurring between members of different species.
Intracellular(ly) Located or occurring within cells.
Intraspecific Occurring between members of the same species.
Isogenic Genetically identical.
Knockout A technique for inactivating a particular gene or genes within an organism or
cell.
Lithotroph(ic)* Refers to an organism that uses an inorganic substance as a substrate in its
energy metabolism.
Magnetotaxis The movement of a cell or microorganism in response to a magnetic field.
Maladaptive Refers to a trait that does not lead to the highest relative fitness of the traits in
the allowed set
Microaerophilic Describes an aerobic environment with a lower partial pressure of dioxygen
than that under normal atmospheric conditions. Alternatively, describes an
organism whose maximal rate of growth occurs in such an environment.
Mixotroph(ic) Refers to an organism that can alternatively or simultaneously adopt both
autotrophic and heterotrophic growth modes.
Mucilage, mucilaginous Refers to abundant, complex polysaccharides formed by organisms. Mucilages
are typically slimy when wet.
Organelle A minute structure within a cell that has a particular function.
Periplasm(ic) Refers to the volume enclosed between the plasma membrane and the outer
membrane in Gram-negative bacteria.
Phenotype The observable characteristics of an organism. These are determined by its
genes and by the interaction of the genes with the environment.
Phototroph(ic)* Refers to an organism that uses light as the source of energy for metabolism and
growth.
Pleiotropy, pleiotropic Describes a situation in which a version of a gene has more than one effect in
an organism.
Recombinant DNA A composite DNA molecule created in vitro by joining a foreign DNA with a
vector molecule.
Selected effect function The effect of a trait which has been responsible for its selection upon evolution.
Symbiosis A long-term intimate relationship between individuals of different species. The
term is generally used to describe relationships in which both species benefit.
Syntrophy A relationship where the metabolic product of a partner is used by the other
partner as a metabolic substrate (and vice versa). A narrower definition is an
obligately mutualistic metabolism.
Trait A phenotypic characteristic of an organism that can be quantified. In particular,
a quantitative trait shows continuous variation and can be measured quantita-
tively.
Transformation A permanent heritable change in a cell that occurs as a result of its acquiring
foreign DNA.
(continued on next page)

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 Julie Cosmidis and Karim Benzerara 5

Table 1. (continued)

Term Definition
Transposon A small, mobile DNA sequence that can be replicated and inserted at other sites in the
genome.
Wild-type The phenotype that is characteristic of most of the members of a species occurring
naturally and contrasting with the phenotype of a mutant.
The definitions are adapted from [Cammack et al., 2006, Donovan, 2019, Hine, 2019, King et al., 2014, Morris
et al., 2013]. Asterisks indicate terms that may be combined, e.g., “chemolithoautotrophic”.

Figure 1. The classical framework of microbial biomineralization. In biologically controlled mineral-

ization (illustrated here by intracellular magnetite biomineralization), the bacteria exert a strict control
on mineral nucleation, growth, and final location of the biominerals. The involvement of molecular ma-
chineries to direct mineral formation is associated with an important physiological cost, compensated by
supposed fitness benefits for the organism. On the other hand, in biologically induced and biologically
influenced mineralization (illustrated here by extracellular calcium carbonate precipitation in a biofilm),
mineral precipitation respectively occurs as a result of local chemical changes caused by metabolic activ-
ity of the cells (here, a pH increase), or following passive nucleation on cellular or extracellular structures
(here, favored by adsorption of Ca2+ ions on negatively charged EPS). Mineral properties are typically
poorly controlled, and biomineral formation is thought to not necessarily provide fitness benefits (it may
in some cases be detrimental to the cells). See Section 2 for more details.

(e.g. apatite in bones), protection (e.g., aragonite or The best studied and most frequently cited exam-
silica in shells), or food acquisition (e.g., apatite in ple of biologically controlled (or directed) prokary-
teeth). The chemical, morphological and crystallo- otic biomineralization is the formation of intracellu-
graphic properties of the biominerals are under tight lar magnetic iron minerals by magnetotactic bacteria
genetic control, and they most often form within [Faivre and Schüler, 2008] (Figure 1). These biomin-
organic vesicles or matrices where mineralization erals, either magnetite (Fe3 O4 ) or greigite (Fe3 S4 ),
is precisely directed [Veis, 2003]. Such strict genetic are located within a specialized bacterial organelle*,
control on biomineral formation and properties also the magnetosome. The molecular-level machiner-
exists in prokaryotic systems, but it is thought to be ies involved in iron acquisition and transport, iron
rare. redox chemistry, and mineral formation and posi-

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6 Julie Cosmidis and Karim Benzerara

tioning have now been described [Komeili, 2007, ply biological functions (in a “selected effect” view)
Lower and Bazylinski, 2013, Uebe and Schüler, 2016]. or benefits to the cells, are often described [Benz-
Magnetic iron biominerals possess several defining erara et al., 2011, Dupraz et al., 2009, Lowenstam,
properties that sets them apart from abiotic “equiv- 1981]. As opposed to controlled biomineralization,
alent” mineral phases, which makes them of partic- which in bacteria is typically intracellular, these two
ular interest for paleobiology and astrobiology [Ben- modes of biomineralization often occur extracellu-
zerara et al., 2019, Li et al., 2020a]: they usually have larly (even at distance from the cells), or at least
few crystal defects; their trace element content and extracytoplasmically* within the cell wall. In a first
isotopic composition are different from that of mag- process termed “biologically induced” or “indirect”
netites forming extracellularly in the same environ- biomineralization, minerals precipitate as a result of
ment; they have restricted size and shape ranges so as local chemical changes (e.g. redox transformations
to form stable single-magnetic domains, and they are or shifts in pH) caused by the metabolic activity of
aligned into a chain within the microbial cell, stabi- the cells. In this case, the microorganisms play an ac-
lizing and maximizing their magnetic dipole moment tive role in mineral precipitation by causing or in-
[Amor et al., 2020, 2016, 2015, Martel et al., 2012]. As creasing solution supersaturation, but there is no or-
a result, magnetotactic bacteria are equipped with ganic control on crystal nucleation or growth. Biolog-
the equivalent of an efficient single magnet, allow- ically induced mineralization thus requires metabol-
ing them to align with and swim along Earth’s mag- ically active cells or enzymes. In the second mech-
netic field lines. Combined with aerotaxis*, mag- anism, called “biologically influenced” or “passive”
netotaxis* is thought to increase the bacteria’s effi- biomineralization, microbial cell walls or extracellu-
ciency to find and stay within their preferred oxygen lar organic structures such as extracellular polymeric
conditions in natural environments [Frankel et al., substances (EPS*) act as nucleation surfaces cat-
2007, Stephens, 2006], corresponding to a “causal alyzing mineral precipitation in supersaturated so-
role” and a “fitness contribution” function. Originally, lutions. By allowing heterogeneous nucleation, these
magnetosomes may have had another biological surfaces decrease the free energy barrier for mineral
function (a “selected effect” function), such as har- precipitation, which may become kinetically favored
vesting reactive oxygen species [Lefèvre and Bazylin- [e.g., Giuffre et al., 2013]. Biologically influenced
ski, 2013, Lin et al., 2020]. Interestingly, it has been biomineralization does not require cells to be alive or
shown that the navigation function of magnetite metabolically active. We note that some authors do
biominerals sometimes contribute to the onset of not refer to this process as biomineralization but use
symbioses* between magnetic bacteria and unicel- the term organomineralization instead [Dupraz et al.,
lular eukaryotes, adding another potential function 2009]. These two processes—induced and influenced
[Monteil et al., 2019]. An important idea associated biomineralization—can occur simultaneously. For
with biologically controlled mineralization is that example, in microbial mats, calcium carbonate min-
strict genetic control inevitably involves metabolic eral precipitation may occur as a result of (often pho-
costs (to produce the enzymes and organic matrices tosynthetic) metabolism, which increases alkalinity
directing biomineral formation). Such costs need to and hence solution saturation with respect to cal-
be compensated with beneficial effects for the organ- cium carbonate phases, while the EPS matrix acts as a
isms, and thus point toward the existence of impor- template for mineral nucleation [Dupraz et al., 2009,
tant biological functions. In magnetotactic bacteria, Iniesto et al., 2021] (Figure 1). It is often assumed
this idea is further supported by the observation of that biologically induced or influenced biominer-
frequent spontaneous losses of magnetotaxis under als do not necessarily serve a function (other than
non-selective cultivation conditions due to deletions “waste”), and their precipitation may even be de-
in the genomic “magnetosome island” [Ullrich et al., scribed as purely accidental or “unintended” [Frankel
2005]. and Bazylinski, 2003], when not detrimental to the
microorganisms (for instance if cells become com-
2.2. Induced and influenced biomineralization pletely entombed by the growing minerals). While
Two other mechanisms of prokaryotic biomineral- this does not mean that there is no genetic basis to
ization, which by contrast do not necessarily im- this kind of biomineralization (for instance, genes are

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 Julie Cosmidis and Karim Benzerara 7

needed to encode the production of EPS), it is meant physiological conditions [e.g., at a specific growth
that the effects of these biomineralization processes rate; Maharjan et al., 2013] and detrimental un-
do not increase the fitness of the microorganisms and der other conditions. Alternatively, the capability to
are therefore not adaptive, at least under the consid- biomineralize may be one trait under the control
ered environmental conditions. We will see later that of a pleiotropic gene, i.e. a gene controlling several
this view may be questioned based on recent results traits at the same time. One of the other traits might
on the potential benefits of extracellular biomineral- be beneficial to the overall fitness of the microor-
ization in biofilms (Section 8.2). ganism and therefore adaptive, while the biomin-
eralization trait might be indirectly selected [Lande
and Arnold, 1983]. We will further discuss this point
3. Does prokaryotic biomineralization need to
below.
have a function?
Phoenix and Konhauser [2008] proposed a list of
The apparently inadvertent and detrimental nature potential benefits of prokaryotic biomineralization.
of biologically induced or influenced mineralization While some proposed benefits were supported by
has led several authors to focus on the question of data (such as screening from detrimental solar ra-
how microorganisms can survive mineral precipita- diation, nutrient storage, or toxin immobilization),
tion and subsequent entombment (as reviewed for others were more speculative (such as physical pro-
instance in Benzerara et al. [2011] and Konhauser tection from grazing or desiccation, and participa-
et al. [2008]). However, the idea that non-controlled tion in biofilm strength and structural integrity). In
prokaryotic biomineralization is an accidental pro- a recent review, Mansor and Xu [2020] cited addi-
cess is somewhat unsatisfying. Indeed, life has been tional possible functions of prokaryotic biominer-
co-evolving with the mineral world for nearly 4 bil- als, such as extracellular electron transfer, detoxifica-
lion years [Hazen et al., 2008, Williams and Rick- tion of harmful metabolic products, or the conserva-
aby, 2012], and there is now experimental evidence tion of thermodynamic potentials for metabolic reac-
that microbial communities are uniquely adapted to tions. In the next sections, we will present several ex-
their mineral environment [e.g., Jones and Bennett, amples of microbial biomineralization systems with
2014]. Several habitats of the early Earth, such as hy- demonstrated or supposed biological functions, with
drothermal vents and stromatolite-supporting shal- no attempt to be exhaustive.
low waters, were particularly prone to mineral pre- Significant advances have been recently achieved
cipitation, and the geological record contains numer- regarding “proximate” questions (“how?”) on micro-
ous and clear evidence of rapid encrustation of bac- bial mineral formation, as we are learning about the
terial cells by minerals, a phenomenon which is at the genetic and enzymatic systems involved as well as
origin of their fossilization and preservation in rocks fine details of crystal nucleation and growth mech-
[Li et al., 2013, Javaux and Lepot, 2018]. Entombment anisms at the microbe–mineral interface. Here, we
within a mineral matrix is likely to greatly limit the are deliberately setting these details aside to focus
transport of essential nutrients and energy sources to on studies where “ultimate” questions (“why?”) have
the bacteria [e.g., Miot et al., 2015], while also lim- been addressed, or at least raised.
iting the transport of waste away from the cells and
preventing their motility. If overall detrimental, one 4. Elemental sulfur biominerals: energy stor-
can wonder why mineral encrustation has persisted age materials
through billions of years of microbial evolution. In
cases where mineral precipitation is triggered by the Several biominerals are proposed to serve a storage
bacteria themselves, we may ask ourselves whether function, either of nutrients or energy (i.e. electron
biomineralization could provide benefits that out- donors or acceptors for energy metabolism). Here we
weigh its potential detrimental effects to the cells. We will address elemental sulfur (S0 ) as an example of
may thus be led to take into account concepts such biomineral for which an energy storage function is
as antagonistic pleiotropy*, in which the same trait well established, and explain what observations are
(for instance here, the capability to biomineralize) supporting this proposed function (in a “causal role”
is beneficial under certain environmental and/or and a “fitness contribution” view).

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8 Julie Cosmidis and Karim Benzerara

4.1. Elemental sulfur storage and utilization genic photosynthesis in the absence of sulfide, re-
leasing sulfate, while in the dark S0 is used as an elec-
Elemental sulfur, or zero-valent sulfur (S0 ), is an in- tron acceptor, releasing sulfide [Mas and Gemerden,
termediate of the biogeochemical sulfur cycle that 1995]. S0 reduction to sulfide was also observed in
is found as a mineral in many natural environments the anaerobic growth of Beggiatoa in the presence of
such as marine sediments, water columns of lakes or an organic carbon source (acetate) [Nelson and Cas-
oceans, cold or hot springs, hydrothermal environ- tenholz, 1981]. Bacteria that precipitate S0 extracel-
ments, salt marshes and caves [Findlay et al., 2014, lularly may also utilize their own S0 biominerals for
Hamilton et al., 2015, Jørgensen et al., 2019, Lau et al., energy metabolism and growth in the absence of
2017, Zerkle et al., 2010]. S0 is formed by abiolog- other reduced sulfur sources. For example, the pur-
ical or biological oxidation of more reduced sulfur ple sulfur bacterium Ectothiorhodospira halochloris
species, although in low-temperature environments precipitates extracellular S0 from sulfide oxidation.
biological S-oxidation rates are typically more than During growth in the absence of sulfide, they reduce
three orders of magnitude faster than abiotic ones S0 back to sulfide [Then and Trüper, 1984]. More
[Luther et al., 2011]. A wide diversity of microor- recently, the green sulfur bacterium Chlorobaculum
ganisms can oxidize sulfide, polysulfides, or thiosul- tepidum was shown to form extracellular S0 globules
fate and precipitate S0 , through phototrophic* (pur- during sulfide oxidation, and then uses this biogenic
ple sulfur bacteria, green sulfur bacteria, cyanobac- S0 as an electron donor for photosynthesis when
teria) and chemotrophic* (colorless sulfur bacteria) sulfide is exhausted [Hanson et al., 2016, Marnocha
pathways [Dahl and Prange, 2006, Kleinjan et al., et al., 2016] (Figure 1C,E).
2003]. In turn, microbially formed S0 can be used as It is not clear what determines whether S0 is pro-
a source of energy for diverse S-oxidizers, S-reducers, duced intra- or extracellularly. From a functional
and microorganisms that perform S0 disproportion- perspective, the “choice” of external energy stor-
ation [Dahl, 2020] (Figure 2A). Some, such as the ther- age is problematic, since these stores are open to
moacidophile Acidianus, can grow from all three re- piracy by other cells within the same population.
actions [Amenabar and Boyd, 2018]. As further explained below, some S0 -forming bacte-
The enzymatic machinery involved in microbial ria may have developed strategies to prevent such
S-oxidation has been described for many known S- piracy. One possible advantage of the extracellular
oxidizers [Dahl et al., 2008, Friedrich et al., 2001, storage strategy is that an unlimited amount of S0 can
Ghosh and Dam, 2009, Gregersen et al., 2011, Koch be stored by an individual microorganism, since ac-
and Dahl, 2018] and will not be detailed here. El- cumulation is not limited by the dimensions of the
emental sulfur formed through S-oxidation can be cell. Indeed, sulfur content is the main determinant
found either intracellularly or extracellularly [Dahl of volume variation in cells of Allochromatium vi-
and Prange, 2006, Kleinjan et al., 2003, Maki, 2013] nosum [Mas and Gemerden, 1995]. Moreover, Beg-
(Figure 2B,C). In both cases, S0 may serve an energy giatoa filaments grown with a high-sulfide flux can
storage function. Indeed, S0 produced under favor- accumulate so much intracellular S0 that they even-
able environmental conditions can then be used as tually burst [Berg et al., 2014], showing that cell di-
an electron donor or an electron acceptor if condi- mensions are clearly limiting S0 storage capacities
tions change. For instance, the S-oxidizer Thiobacil- in microorganisms biomineralizing S0 intracellularly.
lus denitrificans accumulates intracellular S0 from the Intracellular S0 accumulation furthermore increases
oxidation of thiosulfate, but the transiently stored S0 cell density which may negatively impact the buoy-
can later be further oxidized to sulfate for energy pro- ancy of microorganisms with planktonic lifestyles
duction when thiosulfate is depleted in the medium [Mas and van Gemerden, 1987].
[Schedel and Trüper, 1980]. Beggiatoa oxidizes sul-
fide to intracellular S0 under high-sulfide conditions, 4.2. The properties of biogenic S0 : adaptation to
while under low-sulfide conditions this stored S0 is the energy storage function?
oxidized to sulfate [Berg et al., 2014]. Purple sulfur
bacteria such as Achromatium vinosum use intra- It has been known for several decades that both intra-
cellular S0 as a source of reducing power for anoxy- and extracellular biomineralized S0 possess proper-

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 Julie Cosmidis and Karim Benzerara 9

Figure 2. Elemental sulfur biominerals as energy storage materials. (A) Simplified biogeochemical sulfur
cycle, adapted from Zopfi et al. [2004]. Elemental sulfur (S0 ) occupies a central ecological role in the
S cycle. It is produced by oxidation of more reduced S species, and can be consumed by S reduction,
oxidation, or disproportionation. (B) Intracellular S0 storage in Thiothrix sp. (Image: C. Nims, University
of Michigan). (C) Extracellular S0 formation by Chlorobaculum tepidum [Marnocha et al., 2016]. Image
reproduced with permission from the Microbiology Society. (D) Extracellular S0 stores stabilized by EPS
in a Sulfurovum-rich biofilm [Cron et al., 2021] (Image: B. Cron, Northwest Indian College). (E) Multiple C.
tepidum cells degrading a S0 globule, illustrating “mutualistic” S0 utilization [Hanson et al., 2016]. Image
reproduced with permission from John Wiley and Sons. (F) Thiobacillus ferrooxidans retaining S0 colloids
within its organic capsule, illustrating “selfish” S0 utilization [Rojas et al., 1995]. Inset: after cell division,
the S0 stores are shared with the daughter cell. Images reproduced with permission from Springer Nature.

ties that significantly differ from those of inorgani- not been systematically determined, but it is thought
cally precipitated S0 minerals [Steudel, 1989]. Micro- to be either liquid-like [Hageae et al., 1970], solid
bial S0 can be stored under different forms depending amorphous [Nims et al., 2019], or microcrystalline
on the biological species, which suggests some level [Pasteris et al., 2001]. Extracellularly biomineralized
of genetic control on S0 chemical and mineralogi- S0 may also exist in different forms and structures.
cal properties. For instance, some chemotrophic S- For instance, S0 globules produced by Acidithiobacil-
oxidizers such as Thiomargarita, Thioploca, Beggia- lus ferroxidans are composed mostly of polythion-
toa and Thiothrix store sulfur as intracellular glob- ates [Prange et al., 2002, Steudel et al., 1987], while
ules of cyclo-octasulfur (S8 ) [Nims et al., 2019, Pas- extracellular S0 produced by the phototrophic green
teris et al., 2001, Prange et al., 2002], possibly in com- sulfur bacterium Chlorobium vibrioforme is com-
bination with polysulfides (S2− n ) [Berg et al., 2014], posed mostly of sulfur chains terminated by or-
while purple (phototrophic) S-oxidizers and some ganic residues [Prange et al., 2002]. Another green
chemotrophic S-oxidizers from the Firmicutes phy- sulfur bacterium, C. tepidum, produces extracellu-
lum store S0 intracellularly as sulfur chains, possibly lar globules composed of amorphous and nanocrys-
terminated by organic end groups (i.e., organic poly- talline S8 , and they were found to be less stiff and
sulfanes) [Lee et al., 2007, Prange et al., 2002]. The more elastic than commercial S0 [Marnocha et al.,
crystal structure of S0 in intracellular globules has 2019]. Sulfuricurvum kujiense, a chemoautotrophic*

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10 Julie Cosmidis and Karim Benzerara

S-oxidizing bacterium, produces extracellular S0 un- tion during consumption, showing an adaptation
der a metastable crystalline form, the monoclinic al- of the S0 biomineral properties to their biological
lotropes β- and γ-S8 [Cron et al., 2019]. Extracel- function. For instance, when grown on S0 provided
lular metastable monoclinic S8 allotropes were also extracellularly, A. vinosum cells show a preference
found in the environment in Sulfurovum-dominated for polymeric sulfur over commercial crystalline S8 ,
biofilms [Cron et al., 2021] (Figure 2D). which they are unable to uptake [Franz et al., 2007].
The stable form for S0 under ambient temperature Preference for polymeric sulfur utilization over S8
and pressure conditions is crystalline orthorhom- was also evidenced in natural mats of chemotrophic
bic α-S8 [Steudel and Eckert, 2003], and it is likely S-oxidizers [Engel et al., 2007]. Particle size, surface
that unstable S0 forms need to be stabilized by area, and S0 composition and structure affects S0 ox-
close interaction with organic structures. Internal idation rate by Thiobacillus albertis [Laishley et al.,
S0 is typically periplasmic*, nested in an invagina- 1986]. Incubation experiments of natural freshwater
tion of the cytoplasmic membrane [e.g., Larkin and communities with different sulfur sources showed a
Strohl, 1983, Prange et al., 2004]. Protein membranes preference for the utilization of a reactive form of col-
were identified around the intracellular S0 glob- loidal S0 —possibly polythionates—over S8 [Findlay
ules in diverse S-oxidizers including Beggiatoa, Thio- and Kamyshny, 2017]. The structure of the enzymes
thrix, Thiovulum and different purple sulfur bacte- involved in sulfur utilization may provide a clue to
ria [Maki, 2013]. Three proteins forming an enve- the relationship between S0 form or structure and its
lope around the S0 globules were identified (SgpA, utilization. For instance, sulfur oxygenase reductase
SgpB, SgpC) in the purple sulfur bacterium Allochro- (SOR) enzymes present in some archaea possess an
matium vinosum, and their critical role in intracel- elongated active site that accommodates linear poly-
lular S0 formation and storage was demonstrated sulfides but not S8 [Li et al., 2008, Urich et al., 2006].
[Brune, 1995, Prange et al., 2004]. Similarly, organic The presence of an organic envelope around biomin-
envelopes were observed at the surface of extracellu- eralized S0 may also be important for S0 utilization,
lar S0 globules formed by Thiobacillus sp. W5 [Klein- by making S0 hydrophilic and thus allowing inter-
jan et al., 2005], C. tepidum [Hanson et al., 2016, action with the cell surface. Indeed, it was recently
Marnocha et al., 2019], and S. kujiense [Cron et al., shown that C. tepidum can grow on its own biogenic
2019], as well as in natural biofilms [Cron et al., S0 globules but not on commercial S0 , crystalline S0 ,
2021]. These organic envelopes contain polysaccha- or inorganically precipitated colloidal S0 , which is
rides and proteins [Cron et al., 2019, Marnocha et al., mineralogically very similar to biogenic S0 but does
2019], which are not homologous to the Sgp proteins not have an organic coating [Marnocha et al., 2019,
forming the envelope around intracellular S0 glob- 2016].
ules in A. vinosum [Hanson et al., 2016]. The pres-
ence of this organic coating allows extracellular S0
to exist in a metastable form [Cosmidis et al., 2019, 4.3. Selfish versus mutualist utilization of S0
Cron et al., 2019, 2021] and slows down its crystal- stores
lization to stable α-S8 [Marnocha et al., 2019, Steudel,
2003]. Organically coated S0 globules may be formed As pointed out earlier, extracellular location of S0
through a self-assembly process, in which soluble resources exposes to the risk of piracy by “free rid-
organic molecules react with extracellular sulfide or ers” benefiting from their utilization without par-
polysulfides to form sulfurized polymers assembling ticipating in their production. Different strategies
into vesicles around S0 minerals [Cosmidis et al., have been developed to privatize S0 stores by phys-
2019, Cron et al., 2019]. Alternatively, the mechanism ically excluding nonproducers. For instance, the
of secretion of organically coated S0 globules could green sulfur bacterium Chlorobium limicola, which
involve the production of outer membrane vesicles forms extracellular S0 globules adjacent to the cell
in some species [Li et al., 2020b]. wall in the presence of sulfide, grows tubular sur-
There is now ample evidence that S0 storage un- face appendages called spinae and surrounds it-
der a metastable form (e.g., polymeric sulfur, or self with a mucilaginous* capsule* when subjected
amorphous or monoclinic S8 ) favors its mobiliza- to sulfide starvation periods (i.e. under conditions

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 Julie Cosmidis and Karim Benzerara 11

where S0 may be used as an electron donor) [Piber- not always seem to require physical contact with
nat and Abella, 1996]. The spinae and capsule may the minerals [Amenabar and Boyd, 2018, Blumentals
favor the retention of the S0 globules near the cells et al., 1990, Boyd and Druschel, 2013]. Potential roles
and their attachment to the outer membrane, ef- of biomineralization in intra-* and interspecific* co-
fectively excluding utilization by other bacteria operation will be further developed later in this
[Mas and Gemerden, 1995, van Gemerden, 1986]. review.
Similarly, transient extracellular colloidal S0 parti-
cles produced by Acidithiobacillus ferrooxidans are
retained within a thick organic capsule which may 5. Extracellular iron minerals: a biomineral
play a similar role in the privatization of S0 resources type with multiple functions
[Rojas et al., 1995] (Figure 2F). In other cases, even if
Iron biominerals can be formed extracellularly by
no such physical barriers exist, S0 consumption by
bacteria, as the end product of various iron-cycling
rival cells may be limited by the fact that S0 utiliza-
metabolisms [Kappler et al., 2021]. Iron mostly ex-
tion requires intimate physical contact with the S0
ists in the environments under two redox states:
globules, as for instance with A. vinosum [Franz et al.,
Fe(II) (or ferrous iron) and Fe(III) (ferric iron). Fer-
2007], Acidithiobacillus thiooxidans [Knickerbocker
ric iron is relatively insoluble under circumneutral
et al., 2000], or different strains of Acidithiobacillus
pH conditions, so iron oxidation may often result
and Acidiphilium spp. [Rohwerder and Sand, 2003].
in the precipitation of Fe(III)-bearing phases such
In biofilms where cell motility is limited, utilization
as Fe(III)-(oxyhydr)oxides and Fe(III)-phosphates, or
of S0 would thus be limited to the producer and its
mixed valence Fe(II)-Fe(III) phases such as magnetite
immediate neighbors, which typically belong to the
or green rusts. Bacteria can oxidize ferrous to ferric
same clonal* cluster [Nadell et al., 2016].
iron via different metabolic pathways, namely: mi-
Interestingly, for some species, a mutualistic uti-
croaerophilic* Fe(II) oxidation (whereby O2 is used
lization of S0 could be demonstrated. In the case of
as the electron acceptor and Fe(II) the electron donor
C. tepidum, both S0 formation and consumption are
for lithoautotrophic* growth), phototrophic Fe(II) ox-
cooperative processes (Figure 2E). Indeed, multiple
idation (whereby light and electrons from Fe(II) are
cells contribute to the formation of a single globule,
used to fix inorganic carbon into organics), and
and during the utilization phase, cells attached to
nitrate-dependent Fe(II) oxidation (whereby Fe(II)
the S0 globules and unattached cells have compara-
oxidation is coupled with nitrate reduction, either
ble growth rates, suggesting that attached cells could
through a chemolithoautotrophic* pathway leading
be solubilizing S0 as diffusing polysulfides, “feeding”
to energy generation and inorganic carbon fixation,
the free cells [Marnocha et al., 2016]. A similar co-
or, more often, through abiotic Fe(II) oxidation by re-
operative solubilization mechanism could exist for
active nitrogen species produced as a result of het-
Acidithiobacillus ferrooxidans. Indeed, while adsorp-
erotrophic* denitrification; in the latter case, Fe(II)
tion of some cells to the surface of the minerals seems
oxidation is not an energy-generating process) [Bryce
necessary for growth of S0 , free cells also participate
et al., 2018, Emerson et al., 2010, Kappler et al., 2021].
in sulfur oxidation and growth [Ceskova et al., 2002].
Ultimately, S0 can be traded in mutualistic re-
lationships between members of different bacterial 5.1. Extracellular biomineralized structures of
species. For instance, the S0 -producing green sulfur microaerophilic iron oxidizers: adaptation
bacterium Chlorobium virbrioforme can be grown in to life at a redox interface?
a syntrophic* co-culture with the S0 -reducing Desul-
furomonas acetoxidans [Warthmann et al., 1992]. In Parallel to the diversity of metabolic pathways lead-
these cultures, S0 produced as a result of sulfide oxi- ing to Fe(II) oxidation, there is a variety of proposed
dation by Chlorobium is used as an electron accep- functions of the Fe(III) biominerals formed as prod-
tor by Desulfuromonas for acetate oxidation, lead- ucts of these microbial oxidation processes. The
ing to the regeneration of sulfide. Syntrophic inter- question of the biological functions of Fe biomin-
actions may be facilitated by the fact that S0 uti- eralization has often been raised in the case of mi-
lization by reduction and disproportionation does croaerophilic iron oxidizers (Figure 3). Some of them

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12 Julie Cosmidis and Karim Benzerara

Figure 3. Biomineralized iron architectures: adaptation to life at a redox interface. (A) SEM image of a
Mariprofundus ferrooxydans PV-1 cell and biomineralized twisted stalk [Chan et al., 2016b]. (B) Differ-
ential interference contrast image of M. ferrooxydans growing in the presence of an oxygen gradient in a
microslide experiment. The corresponding radial plot shows directional orientation of the stalks in the
oxygen gradient [Krepski et al., 2013]. (C) SEM of the biomineralized sheath of Leptothrix ochracea [Chan
et al., 2016b]. (D) Confocal image of a mat of sheath-forming cells. The cells are shown in green, while
the Fe-(oxyhydr)oxides of the sheaths are shown in red. Living cells occupy the edge of the mat. Cell fil-
aments and sheaths are mostly parallel to the growth direction of the mat (white arrow) [Chan et al.,
2016a]. (E) SEM image of dreadlock-like iron structures produced by the pelagic Zetaproteobacterium
strain CP-8. The biomineralized structures are easily shed, which may help cells maintain suspension in
the water column. The likely location of the missing cell is denoted as a yellow oval. (F) Gradient tube cul-
tures inoculated by Zetaproteobacteria strains CP-5 and CP-8, displaying distinct orange growth bands
(white arrows). The cells occupy a narrow zone of the tubes, corresponding to optimal oxygen conditions
[Chiu et al., 2017]. Images (A), (B), and (C) are reproduced with permission from John Wiley and Sons.
Images (D), (E), and (F) are under Creative Commons Attribution License (CC BY).

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 Julie Cosmidis and Karim Benzerara 13

direct Fe(III) precipitation onto organic extracellu- and Fe(II) conditions [McAllister et al., 2019] (Fig-
lar structures, which may consist in tubular sheaths ure 3F). Interestingly, we note here a convergence
around the cells [e.g., the betaproteobacterium Lep- of functions with extracellular sulfur filaments pro-
tothrix ochracea; Chan et al., 2009], twisted stalks duced by Candidatus Arcobacter sulfidicus, a mi-
[e.g., the freshwater betaproteobacterium Gal- croaerophilic sulfur oxidizer affiliated to Epsilonpro-
lionella ferruginea or the marine zetaproteobac- teobacteria. These microorganisms thrive in deep-
terium Mariprofundus ferrooxydans; Chan et al., sea hydrothermal vents [Taylor and Wirsen, 1997]
2011], or structures resembling “dreadlocks” [e.g., and form mat-like biomineralized architectures at
the Mariprofundus strains CP-5 and CP-8; Chiu et al., interfaces between oxygen and sulfide gradients,
2017] (Figure 3A,C,E). These extracellular structures permitting retainment within their specialized niche
are mostly composed of acidic polysaccharides and [Sievert et al., 2007].
saturated aliphatic chains (probably lipids) [Chan Another potential function of mineralized extra-
et al., 2011, 2009, Laufer et al., 2017], and serve as cellular structures of microaerophilic iron oxidizers
templates for the nucleation of poorly crystalline was proposed by Hallbeck and Pedersen [1995]. Us-
Fe(III)-(oxyhydr)oxides. The organic structures di- ing competition experiments between stalk-forming
rect Fe(III) precipitation away from the cells, pre- Galionella ferruginea and a spontaneous non-stalk
venting their encrustation by iron minerals [Chan forming mutant, they showed that the capacity of
et al., 2011], a function that is further aided by spe- stalk formers to direct iron oxidation onto the stalks
cific mineral-repelling properties of the cell surface and away from the cells conferred them competitive
such as low charge and hydrophilicity [Saini and advantage in iron-rich environments, by protecting
Chan, 2013]. In addition, sheaths and stalks appear them from toxic oxygen species (e.g., hydroxyl radi-
to serve as attachment and support structures that cals) produced by the chemical reduction of oxygen
help the microbes occupy niches where O2 and Fe(II) by ferrous iron.
gradients overlap [Chan et al., 2016a], an impor-
tant requirement for these microaerophilic iron ox- 5.2. Other potential functions of extracellular
idizers [Emerson et al., 2010, Maisch et al., 2019]
iron biominerals
(Figure 3D). Indeed, when Mariprofundus ferrooxy-
dans is grown in opposing O2 and Fe(II) concen- Potential functions of Fe(III) biominerals in other
tration gradients, their stalks, forming rigid hold- types of iron-oxidizing bacteria have more rarely
fasts anchoring them to surfaces, grow direction- been discussed. It has been proposed that bio-
ally toward higher oxygen concentrations, allowing genic ferrihydrite minerals forming at the sur-
the bacteria (living at the end of stalks) to orient face of anoxygenic phototrophic Fe(II) oxidizers
themselves within the redox gradient and colonize a Rhodopseudomonas palustris and Rhodobacter
narrow band with well-defined O2 and Fe(II) condi- ferrooxidans may act like “sunscreen”, protecting
tions [Krepski et al., 2013] (Figure 3B). On the other them from harmful UV radiation and DNA dam-
hand, the marine Zetaproteobacteria Mariprofun- age [Gauger et al., 2015]. Note that shielding from
dus strains CP-5 and CP-8 are pelagic, occupying the UV-induced DNA damage by minerals has also been
oxic–anoxic transition zone of a stratified estuary suggested for silicifying cyanobacteria [Phoenix
[Chiu et al., 2017], and thus do not appear to need et al., 2006, 2001], although it remains to be for-
anchoring or support structures. However, their iron mally proven that this protection is not coincidental
“dreadlocks” can easily be shed (Figure 3E), which but rather results from an adaptation to high-UV
may help the cells maintain suspension and adjust environments.
buoyancy in the water column. The correlation be- Although somewhat speculative, a possible bene-
tween the morphology of biomineralized iron struc- fit of Fe(III) biomineralization in general may be the
tures (sheaths and stalks versus “dreadlocks”) and establishment of an energy-generating proton mo-
microbial lifestyle (benthic vs. planktonic) reinforces tive force in the vicinity of the cells [Mansor and Xu,
the hypothesis that biomineralized structures of mi- 2020]. Indeed, as shown by Equations 1 and 2, Fe(II)
croaerophilic iron oxidizers are used by the cells to oxidation and Fe(III)-oxyhydroxide precipitation re-
colonize environmental niches with adequate O2 lease protons. Fe(III) biomineralization, if occurring

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14 Julie Cosmidis and Karim Benzerara

close to the cells, may thus result in the formation of sensu) syntrophic relationship between Fe-reducing
a proton gradient across the cell wall, which may be Geobacter and methanogenic Methanosarcina, by
harnessed for ATP production. promoting extracellular electron transfer between
the two partners [Tang et al., 2016]. Other examples
Fe2+ + 2H2 O→Fe(III)(OH)+ +
2 + 2H + e
−
(1)
for the role of (potentially biogenic) Fe minerals in
Fe(OH)+
2 →FeOOH + H
+
(2) the mediation of electron transfers supporting meta-
While it has been proposed by Chan et al. [2004] bolic networks are provided in the recent review by
for microaerophilic iron oxidizers, this mechanism Mansor and Xu [2020].
may apply to any iron-oxidizing bacteria locating
Fe(III) precipitation near the cell wall. However, it re- 5.3. Adaptation to mineralizing environments:
mains to be experimentally demonstrated that bacte- avoiding iron encrustation
ria indeed harvest this proton motive force for energy
generation. It is possible that in some cases, iron biominerals
Finally, an interesting, and probably underex- are just accumulated as metabolic waste products
plored function of Fe(III) biomineralization may be of ferrous iron oxidation and do not serve any other
the establishment of syntrophic relationships be- biological function. However, an absence of function
tween Fe-oxidizers and Fe-reducers. In a broad sense (other than “waste”) does not necessarily imply a
of the term, syntrophy can be used as a synonym complete lack of control on mineral formation, since
for mutual co-feeding, i.e. a relationship where the some iron oxidizers may have evolved strategies to
metabolic product of a partner is used by the other locate mineral precipitation away from the cells,
partner as a metabolic substrate (and vice versa) avoiding formation of Fe(III) minerals intracellularly
[Morris et al., 2013]. Several studies have shown a or on the cell surface, which would be damaging
coupling between Fe-oxidation and Fe-reduction in to the bacteria. This control on mineral location is
the environment, i.e. situations in which biogenic achieved through different strategies, evidenced in
Fe(III) minerals produced by Fe-oxidizing bacteria several phototrophic iron oxidizers [e.g., Schädler
are used as substrates for Fe-reducers [Blöthe and et al., 2009]. For instance, some bacteria produce
Roden, 2009, Emerson et al., 2010]. Interestingly, ex- extracellular polymeric fibers nucleating Fe(III) min-
periments have shown that biogenic Fe(III) min- erals [e.g., Rhodobacter sp.; Miot et al., 2009a], while
erals are more easily colonized and reduced than others lower the pH around the cells, which de-
abiogenic ones [e.g., Glodowska et al., 2021], sug- creases the rate of Fe(III) absorption to the cell sur-
gesting that Fe-reducers may rely on Fe-oxidizers to face and increases its solubility [e.g., Thiodictyon sp.;
supply bioavailable Fe(III) substrates in some envi- Hegler et al., 2010], or secrete Fe(III)-complexing EPS
ronments. Such cooperative metabolic relationships [e.g., Rhodovulum iodosum; Swanner et al., 2015,
may be particularly relevant to environments where Wu et al., 2014]. On the one hand, encrustation of
Fe-reduction and Fe-oxidation processes spatially the cells by precipitation of Fe(III) minerals at the
overlap [e.g., Laufer et al., 2016]. In some cases, Fe cell surface and/or within the periplasm* was fre-
redox cycling may even occur within mineral par- quently observed in the case of iron oxidizers per-
ticles containing both Fe(II) and Fe(III) [e.g., mag- forming heterotrophic or mixotrophic* nitrate re-
netite; Byrne et al., 2015], effectively acting as min- duction [e.g., Acidovorax sp. strain BoFeN1; Miot
eral “biogeobatteries” sustaining Fe-cycling bacte- et al., 2009b, Schädler et al., 2009]. On the other
rial communities [Peiffer et al., 2021]. It would be hand, in chemolithoautotrophic nitrate-reducing Fe-
interesting to test whether metabolic relationships oxidizers [e.g., the enrichment culture KS; Blöthe and
based on the formation and consumption of biogenic Roden, 2009], no Fe(III) encrustation is observed,
Fe(III) minerals fall within a stricter definition of syn- possibly evidencing the existence of strategies to
trophy, i.e. an “obligately mutualistic metabolism” in avoid cell entombment [Nordhoff et al., 2017]. There
which otherwise endergonic reactions become ex- thus appears to be a divide between chemolithoau-
ergonic through the removal of reaction products totrophic nitrate oxidizers, for which Fe(II) oxida-
by the other partner [Morris et al., 2013]. Biogenic tion is an enzymatically catalyzed, energy-generating
magnetite has been shown to facilitate the (stricto process, and which may have evolved adaptations

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 Julie Cosmidis and Karim Benzerara 15

to avoid the damaging effects of Fe(III) encrustation, biominerals is, intracellular ACC formation must
and heterotrophic or mixotrophic nitrate oxidizers, impact cell physiology and/or ecology [Couradeau
for which Fe(II) oxidation does not generate en- et al., 2012, Monteil et al., 2021].
ergy, and for which such adaptations may not exist. Bacterial intracellular biomineralization of ACC
However, Nordhoff et al. [2017] note that even het- can occur in undersaturated extracellular solutions,
erotrophic nitrate oxidizers do not become encrusted where carbonate precipitation would not occur oth-
under environmentally relevant, relatively low Fe(II) erwise [Cam et al., 2018, Head et al., 2000]. Biominer-
concentrations, or when these organisms are present alization thus involves some energy expense (hence,
in co-culture with autotrophic nitrate reducers, it is an active process), possibly in relation with the
suggesting that Fe(III) entombment may not be a transport of alkaline earth elements and/or C, in-
problem for nitrate-reducing bacteria in nature re- creasing the saturation of the intracellular solution
gardless of the mechanism. in contact with the nascent precipitates. It has been
pointed out that intracellular ACC formation was not
6. Intracellular carbonates: a controlled consistent with the chemical composition of a bac-
biomineralization process with unidenti- terial cytoplasm which is typically inferred as under-
saturated with respect to calcium carbonate phases
fied functions
[Cam et al., 2015]. However, this apparent paradox
Bacterial calcium carbonate precipitation is often is solved by the existence of dedicated intracellular
considered a non-controlled, extracellular process. compartments within the bacteria, where chemical
However, an increasing diversity of bacteria has conditions are appropriate for mineral precipitation
been shown to biomineralize amorphous calcium without being detrimental to the functioning of the
carbonates (ACC) intracellularly [Segovia-Campos rest of the cells. The nature of the envelope delimiting
et al., 2021] (Figure 4). The giant uncultured sulfur- these compartments differ in nature between phyla:
oxidizing Achromatium, affiliated to the Gammapro- an envelope composed of a protein shell or a lipid
teobacteria, was the first bacterium identified among monolayer in Cyanobacteria [Blondeau et al., 2018b]
them [Schewiakoff, 1893]. More recently, biominer- vs. a lipid bilayer in Proteobacteria [Gray, 2006, Mon-
alization of intracellular ACC was also discovered teil et al., 2021] (Figure 4E). This suggests that at least
in several species of Cyanobacteria (Figure 4A–C) part of the process of intracellular ACC biomineral-
[Benzerara et al., 2014, Couradeau et al., 2012] as well ization may have evolved convergently* in different
as several undescribed members of the Alphapro- bacterial groups.
teobacteria [Monteil et al., 2021, Liu et al., 2021]. Apart from these facts, the molecular mecha-
Interestingly, the latter are magnetotactic bacteria, nisms of intracellular ACC formation remain cur-
controlling the intracellular mineralization of mag- rently unknown. Several of these bacteria contain
netite crystals (Figure 4D). Some of these intracel- RuBisCO or a homologous* gene and can fix inor-
lularly calcifying bacteria had been studied before ganic carbon. Consistently, fixation of CO2 favors
but their biomineralization capability had been over- carbonate precipitation. However, this may not be a
looked, suggesting that intracellular ACC biomin- requirement since some Achromatium populations
eralization may be much more widespread than do not contain any of these genes, while being able to
presently acknowledged [Li et al., 2016a]. The ca- biomineralize ACC [Gray, 2006]. Moreover, calcium
pability to biomineralize intracellular carbonates is transporters were targeted in the genomes of
found in certain taxa only, and is sometimes shared intracellular-ACC-forming bacteria as possible im-
by all the members of a clade, showing that it is a portant actors but no specificity was particularly
heritable trait [Benzerara et al., 2014]. evidenced compared with bacteria not biomineraliz-
Cells may contain significant volumes or masses ing ACC [Wever et al., 2019]. The mechanism of the
of intracellular ACC (Figure 4F,G), accounting for up stabilization of ACC as a reactive amorphous solid
to ∼2/3 of the total cell volume in Alphaproteobac- remains to be understood. It may be due to confine-
teria and leading to a 12% cell density increase in ment within intracellular compartments [Cavanaugh
the cyanobacterium Gloeomargarita lithophora. It et al., 2019, Zeng et al., 2018]. The genes involved
has been argued that whatever the function of these in the formation of the compartments remain to be

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16 Julie Cosmidis and Karim Benzerara

Figure 4. Diversity and function of intracellular ACC biomineralization. (A) SEM image in the secondary
electron (SE) mode of the cyanobacterium Neosynechococcus sphagnicola forming numerous ACC
inclusions (brightest spots) together with polyphosphate granules (bright grey). (B) Overlay of Ca (red)

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 Julie Cosmidis and Karim Benzerara 17

Figure 4. (cont.) and P (green) chemical maps obtained by energy dispersive X-ray spectrometry over the
SEM image shown in (A). (C) SEM image of the cyanobacterium Synechococcus sp. PCC 6717 forming in-
tracellular ACC mostly located at the poles of the cells. (D) SEM image in the SE mode of a magnetotactic
alphaproteobacterium forming intracellular ACC. Two large ACC granules are observed as well as a small
one close to the middle of the cell. Bright spots appearing in the bottom part of the cell correspond to a
magnetite chain. (E) Cryo-transmission electron microscopy image of a cryo-ultramicrotomy section in
a magnetotactic cell forming intracellular ACC. The ACC granule appears in dark and is surrounded by
a thin feature which corresponds to a lipid bilayer. (F) Light microscopy image of an Achromatium oxal-
iferum cell. The refringent granules correspond to ACC. (G) SEM image of an Achromatium cell showing
the numerous ACC granules paving the whole volume of the cell. (H) Diversity of the functions postulated
for intracellular ACC in bacteria. One function (Fct 1) relates to buffering of intracellular pH upon carbon
fixation by e.g., oxygenic photosynthesis and/or the use of inorganic C stored in ACC for C fixation. A sec-
ond function (Fct 2) relates to intracellular pH buffering upon S-oxidation (e.g., in Achromatium and/or
magnetotactic alphaproteobacteria). Oxidation of sulfides to elemental sulfur is associated with ACC for-
mation. Oxidation of elemental sulfur to sulfates or reduction of elemental sulfur to sulfides are associ-
ated with ACC dissolution. Last, a third function (Fct 3) is related to cell buoyancy modification, allowed
by the relatively high density of ACC compared to the rest of the cells. (Images: KB).

identified in all these bacteria. tion of the term (see Section 2.1).

Intracellular carbonate phases formed by bacte- Several functions have been speculated for in-
ria display several features that differ from those of tracellular bacterial carbonates (Figure 4H). We
abiotically precipitated carbonates. First, they are in- note that these different potential functions are not
variably amorphous and therefore unstable due to exclusive and intracellular ACC biominerals may
their high solubility relative to crystalline forms such have varying functions in different microorganisms:
as calcite or aragonite [Addadi et al., 2003]. Diverging (i) they may serve as a storage reservoir for inor-
conclusions were reached over time about the iden- ganic C for C-fixating organisms. Some authors have
tity of the formed CaCO3 phase in Achromatium but also proposed that ACC may serve as an electron
the early identifications as an amorphous calcium acceptor [Gray, 2006]. As mentioned, some of these
carbonate phase were recently confirmed by Raman autotrophic organisms need large amounts of inor-
spectroscopy analyzes [Benzerara et al., 2021]. ACC ganic C for their metabolism. The large reactivity of
is widespread among eukaryotic biominerals and ACC inclusions conferred by their non-crystalline
it has been suggested that their high reactivity fa- structure, allowing a rapid remobilization, could be
cilitates the homeostatic* function that was attrib- consistent with such a function. (ii) They may buffer
uted to them [Addadi et al., 2003, Gower, 2008]. Sec- intracellular pH variations, which are expected to be
ond, in some cases, intracellular carbonates formed important in these bacteria due to their metabolisms.
by bacteria contain relatively high proportions of Achromatium is a S-oxidizing bacterium and can ox-
heavy alkaline earth elements such as Sr or Ba, in- idize sulfide to S0 or S0 to sulfate. The first oxidation
dicating the existence of a fractionation mechanism process consumes protons, while the second one
favoring the uptake of these elements over Ca in the produces protons. On the other hand, the formation
biominerals [Blondeau et al., 2018a, Cam et al., 2016, of ACC produces protons, whereas its dissolution
Mehta et al., 2019]. Part of the enrichment of ACC in consumes protons. Consistently with a pH buffer
trace elements might be related to some particle-size role, ACC inclusions precipitate when cells oxidize
effects. However, overall, the different characteristics sulfide to S0 and dissolve when cells are exposed to
observed for intracellular ACC, in addition to an in- O2 and S0 is oxidized to sulfate [Yang et al., 2019].
tracellular localization and the presence of an enve- Similarly, photosynthesizing bacteria tend to con-
lope around the carbonate inclusions, point toward a sume protons when fixing CO2 by RuBisCO and for-
biologically controlled process in the classical defini- mation of ACC may contribute to pH buffering in

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18 Julie Cosmidis and Karim Benzerara

addition to other molecular pH-buffering systems on the adaptive functions of the biominerals may be
such as proton pumps [Görgen et al., 2021]. (iii) Last, formulated and tested in the laboratory. We give fur-
it has been suggested that ACC inclusions, owing ther details on the different steps of this roadmap be-
to their density (>2 g·cm−3 ), serve as ballasts for low (Figure 5).
cells, and thus represent an adaptation to a benthic
lifestyle [Couradeau et al., 2012, Gray and Head, 2014,
7.1. Discovering functional genes in microbial
Monteil et al., 2021]. However, this has been ques-
biomineralization systems
tioned for some microorganisms based on ecological
considerations showing an inverse relationship be- In recent decades, DNA sequencing techniques have
tween the quantity of ACC and the depth within the allowed important progress in our understanding
sediments [Head et al., 2000]. of the genetic mechanisms of microbial biominer-
Overall, although the genetic basis of intracellular alization. We have learned about specific genes in-
calcium carbonate biomineralization is not known, volved in the formation of different biominerals [e.g.,
it is likely that this is a controlled process which im- Keffer et al., 2021], discovered how they are dis-
pacts cell fitness and has been selected by evolution. tributed in the environment [e.g., Macalady et al.,
Yet, this example illustrates the difficulty to infer the 2013], and how they may interact in complex net-
genuine function of biominerals. The next section works in ecosystems [e.g., Hamilton et al., 2015].
will describe some approaches and strategies that However, there has been a clear bias toward the study
may be employed to make progress on this funda- of metabolic genes, involved for instance in energy-
mental question. generating oxidation–reduction processes, which are
often the primary drivers of microbial mineral for-
7. A roadmap for functional studies of micro- mation. A functional understanding of biomineral-
bial biominerals ization now requires turning our attention to genes
that are involved in controlling biomineral proper-
A deeper understanding of the functions of micro- ties such as morphology, structure, texture, chemi-
bial biomineralization in a teleological view requires cal composition, or localization. Indeed, in the same
to shift our focus from descriptive and mechanis- way that the structures of proteins determine their
tic (“How?”) to evolutionary and adaptive (“Why?”) functions, properties of adaptive biominerals are in-
questions. Importantly, it is crucial to discriminate timately linked with their biological functions (see
biominerals which are adaptive traits, i.e. pheno- for instance Section 2.1 for our description of the
types* with genetically encoded (heritable) varia- properties of intracellular biominerals in magneto-
tion, which evolved through natural selection for tactic bacteria and their role in magnetotaxis). On
a specific function, from non-adaptive ones, which the other hand, it is unlikely that cellular resources
are only the “unintended and uncontrolled conse- are spent to control mineral properties in the case of
quence of metabolic activities” [Frankel and Bazylin- non-adaptive biominerals, i.e. minerals that are only
ski, 2003]. Non-adaptive minerals may precipitate formed as metabolic by-products or as a result of “ac-
“accidentally” because of geochemical changes in the cidental” precipitation.
local environment, as a result of metabolism, or fol- Biomineralization processes typically involve
lowing heterogeneous nucleation on microbial sur- a great number of genes acting together to con-
faces or EPS, and do not serve any function that is trol mineral nucleation and growth. These genetic
beneficial to the cell. As we will explain below, in or- pathways remain to be discovered for most micro-
der to demonstrate that the formation of a biomin- bial biomineralization systems. Microbiology ap-
eral is an adaptive trait, the first necessary (but not proaches based on high-throughput sequencing
sufficient) step is to demonstrate that variation of this techniques now allow to improve our understanding
trait is genetically encoded (and therefore heritable). of the genetic basis of phenotypic variations, i.e. to
Secondly, it must be established that the biomin- determine how mutations (i.e. changes to encoding
eralization phenotype is beneficial to the organism, DNA sequences) can alter gene functions and phe-
which means that it is associated with increased fit- notypes [Kobras et al., 2021]. These methods may
ness (or reproductive success). Finally, hypotheses now be applied to discover new genes involved in

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 Julie Cosmidis and Karim Benzerara 19

Figure 5. A roadmap for functional studies of microbial biomineralization. The figure illustrates some
of the experimental approaches described in the respective sub-sections of Section 7 (please refer to the
main text for more details). Some drawings are adapted from Kobras et al. [2021] and McDonald [2019].

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20 Julie Cosmidis and Karim Benzerara

controlling the “mineral phenotype”. Genome-wide These libraries can then be screened to identify mu-
association studies (Figure 5) have been used to iden- tants with altered mineral phenotypes, and their
tify genes associated with traits of interest in natu- whole genomes sequenced to locate the mutations
ral microbial populations [Mallawaarachchi et al., and identify affected genes [e.g., Faivre and Baum-
2021]. In these methods, genomes from hundreds of gartner, 2015, Rahn-Lee et al., 2015] (Figure 5). In
isolates from different environments are sequenced the last decade, new methods based on transposon*
and compared to identify genomic elements that insertion mutagenesis have been developed [Cain
are statistically associated with a given phenotype et al., 2020, van Opijnen and Camilli, 2013]. These
[Chen and Shapiro, 2015, Read and Massey, 2014]. methods require the construction of libraries of mu-
This comparative genomic approach can be used to tants for which most non-essential genes contain
understand the genetic basis of the production of transposon insertions. After a screening process
some biominerals with specific properties. For in- aimed at selecting mutants displaying the phenotype
stance, comparisons of whole genomes of stalk- of interest, sequencing of the transposon–genome
forming and stalk-less microaerophilic iron oxidiz- junctions allows for the determination of the in-
ers allowed for the identification of genes clusters sertion location of each transposon. Regions of the
involved in the formation of these organic-mineral genome where transposon insertions are statisti-
structures in Betaproteobacteria and Zetaproteobac- cally underrepresented in selected mutants are likely
teria [Kato et al., 2015, Koeksoy et al., 2021]. As noted to contain genes that are essential for the pheno-
by Kobras et al. [2021], in the case of complex traits type of interest. Whole-genome mutant libraries can
(such as biomineralization), genome-wide associ- also now be obtained using technologies based on
ation studies may return thousands of genetic ele- CRISPR-Cas systems [e.g., Vo et al., 2021]. In the fu-
ments associated with the phenotype of interest, and ture, the more widespread use of these new technolo-
it may be difficult to identify the role of individual gies is likely to bring important progress in our un-
genes and understand their interactions. Another derstanding of the genotype–phenotype relationship
important limitation of this approach is the need in biomineralization systems.
to assemble large genome databases comprehend- We see that the methods described above rely
ing both biomineralizing, poorly biomineralizing both on high-throughput sequencing methods, al-
or non-biomineralizing bacteria, which often relies lowing for the obtention and processing of large DNA
on culture-dependent approaches to test mineral- sequence datasets, and high-throughput screening
ization capabilities. Increasing use of single-cell ge- techniques, allowing for the selection of microbial
nomic sequencing of environmental samples may strains displaying phenotypes of interest among en-
facilitate this endeavor [e.g., Mansor et al., 2015]. vironmental populations or mutant libraries. While
Application of genome-wide association studies also falling costs have massively democratized sequenc-
requires that the genes of interest are relatively well ing approaches, screening may remain a major bot-
conserved. Last but not least, this strategy relies on tleneck for the implementation of next-generation
the assumption that the biomineralization capabil- microbiology methods to biomineralization studies.
ity is encoded by a same set of genes shared by the Indeed, analytical tools for the identification and
different microorganisms and does not result from characterization of biominerals classically include
convergent evolution, i.e. phylogenetically unrelated crystallography approaches such as X-ray diffrac-
molecular systems. tion, or microscopy techniques such as electron
It may be necessary to study the importance and microscopy or X-ray (micro)spectroscopy [Cosmidis
functions of specific genes involved in biomineral- and Benzerara, 2014, Miot et al., 2014], which re-
ization under more carefully controlled conditions. quire time-intensive sample preparation and cannot
Other approaches may be employed to observe how be used to process hundreds of samples at a time.
small genetic differences in otherwise genetically There is thus a need for the development of high-
identical (i.e., isogenic*) strains influence microbial throughput characterization methods for the charac-
phenotypes. Random chemical or physical (e.g., UV) terization of biominerals, that could be implemented
mutagenesis can be used to generate mutant libraries for instance directly in vivo, with minimal sample
of a specific microbial strain [e.g., Achal et al., 2009]. preparation, on microplates where different mutants

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 Julie Cosmidis and Karim Benzerara 21

or environmental strains have been separated. These the rest of the necessary cellular machinery is avail-
methods would not only need to determine whether able in this bacterium (Figure 5). The genetically en-
or not biominerals are present in each well of the mi- gineered E. coli strains can then be used to study
croplate, but also to characterize the functional prop- how altering different factors such as the activity of
erties of these biominerals, such as morphology or the recombinant enzyme [Heveran et al., 2019] or
crystal structure. Raman spectromicroscopy may be its cellular sublocation [Cosmidis et al., 2015] affects
a very powerful tool in this context, since it allows for biomineralization. In some cases, it may be relevant
in vivo identification of biominerals and characteri- to determine the intra- or extracellular localizations
zation of their structures at a micron of sub-micron of the proteins of interest, and determine whether
scale [e.g., Nims et al., 2019]. Coupling spectroscopic they coincide with biomineral localization. Separa-
analyzes with confocal microscopy imaging, data on tion of different cell fractions (e.g., cytoplasm, cell
mineral morphology (e.g., size distribution, aspect wall, membranes) followed by western blotting can
ratios) could be acquired simultaneously with miner- be used to localize proteins at the sub-cellular level
alogical and crystallographic information in a single [e.g., Schüler, 2004]. Protein localization can also be
step. For intracellular biominerals, it may be possible achieved using fluorescence microscopy after fusion
to screen cells using flow sorting techniques based with a fluorescent reporter, an approach that was for
on the light-scattering or fluorescent properties of instance used to localize proteins involved in silica
the biominerals [e.g., Bawazer et al., 2012]. Screening biomineralization in diatoms [Scheffel et al., 2011].
techniques based on more specific properties such as Fine details of the genotype–mineral phenotype
mineral magnetism may also be implemented [e.g., relationship may be revealed through mutation and
Liu et al., 2016]. screening in synthetic biomineralization systems.
Different methods such as error-prone PCR or DNA
shuffling (i.e., random recombination* with a simi-
lar gene, or “molecular sex”) can be used to induce
7.2. Validating the functions of genes involved in random mutations in the sequence of the gene of in-
biomineralization terest and obtain a mutant library. These mutant se-
quences may be expressed in genetically engineered
Once genes involved in biomineralization have been microbial cells [Liu et al., 2016] or biomimetic vesi-
identified, their specific role in controlling mineral cles [Bawazer et al., 2012] and screened for specific
formation and properties must be confirmed and re- biomineral properties. Mutant sequences resulting in
fined. “Knockout”* studies consist in deleting or in- biominerals with altered properties can then be se-
activating a gene of interest and investigating the ef- quenced to localize the mutations and determine the
fect of the gene loss by comparing the resulting mu- relative importance of specific gene regions or amino
tant phenotypes with that of a “wild-type”* strain. acids in the biomineralization process (Figure 5).
This approach was for instance used to demon-
strate that filaments formed by the actin-like pro-
tein mamK are crucial to align and position intra- 7.3. How to determine whether a biomineral is
cellular iron biominerals in magnetotactic bacteria. beneficial?
Indeed, while these biominerals are organized into
a chain in the wild-type strain, they were randomly The discovery of genes controlling the formation and
ordered in a mamK deletion mutant [Komeili et al., properties of a biomineral is a useful step toward
2006, Scheffel et al., 2006]. However, many bacterial demonstrating that the biomineralization process is
strains are currently not amenable to genetic ma- a functional, adaptive trait. However, it is not suffi-
nipulation [e.g., Chenebault et al., 2020, Corts et al., cient, since even the formation of non-adaptive min-
2019]. Another possible approach consists in trans- erals is encoded in pleiotropic genes. For instance,
forming* the model bacterium Escherichia coli, in or- genetically encoded changes in EPS composition or
der to test whether the expression of a gene (e.g. cod- abundance can alter the morphology or structure of
ing for an enzyme of interest) induces biomineral- (non-adaptive) minerals forming under the influence
ization [e.g., Bachmeier et al., 2002], considering that of these substances [Tourney and Ngwenya, 2009,

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22 Julie Cosmidis and Karim Benzerara

Yin et al., 2020]. In fact, a trait can only be consid- in the laboratory [e.g., Krepski et al., 2013]. Ideally, ex-
ered to be adaptive if both its variation is genetically periments should be conducted using adequate con-
encoded (heritable trait), and if it helps an organ- trols, such as isogenic strains that do not produce the
ism to maximize its fitness. In microbial experiments, biominerals [e.g., Gauger et al., 2015], or that produce
fitness is often measured as a growth rate [Kussell, biominerals with different properties or at different
2013]. It is particularly useful to perform competi- rates.
tion experiments, in which a bacterial strain express- Microbial evolution experiments may be partic-
ing the trait of interest (here, certain property or a ularly useful to demonstrate biomineral functions,
biomineral) is grown in co-culture (in a 50:50 mix- although, to our best knowledge, these approaches
ture) with an isogenic strain for which this trait was have yet to be used in this context. Microbial evo-
suppressed or has a different value (e.g., for which lution experiments are designed to study how mi-
the biomineral property of interest is altered). Mea- crobial populations adapt to different environmen-
suring the relative growth rates of these two strains tal pressures. These experiments consist in propa-
gives a quantitative measure of the benefit of the gating microbial populations over a large number
trait (the mineral property) with respect to the fit- of generations (typically thousands or tens of thou-
ness of the bacteria (Figure 5). Competition exper- sands) under controlled conditions, allowing for nu-
iments require both strains to be labeled, using for merous “rounds of evolution”, using for instance se-
instance, fluorescent protein expression constructs, rial dilutions in batch cultures or continuous cul-
so that they can both be counted on plates or us- tures in chemostats [Kussell, 2013, Lenski et al., 1991,
ing flow cytometry. Obviously, determining the fit- McDonald, 2019] (Figure 5). The evolved strains can
ness benefits of biomineralization is complicated in be sampled at different times throughout the exper-
the case where mineral formation is correlated with iments (which may be continued over many months
important metabolic functions (under the control of or years) and compared with the founder strains, to
pleiotropic gene systems). For this reason, we stress identify new phenotypes and associated mutations
on the fact that the trait we are proposing to test in through DNA sequencing. Microbial evolution ap-
these competition experiments is not mineral forma- proaches are thus also powerful tools for the dis-
tion itself, but a specific property of the biomineral covery of new gene functions. Once a hypothesis on
(for instance, a certain morphology of structure). It biomineralization function has been formulated, i.e.
may also be useful to measure the relationship be- once it has been proposed that a biomineral with
tween fitness and certain quantitative values of the specific properties is an adaptation to a particular
correlated traits among variable populations in or- niche or lifestyle, then it should be possible to make
der to disentangle their respective selection effects predictions on how biomineralization should evolve
[Lande and Arnold, 1983]. when environmental conditions are altered. For in-
stance, if the extracellular accumulation of bioavail-
able S0 is an adaptation to life under fluctuating re-
dox conditions (Section 4.1), then it can be predicted
7.4. Testing the functions of microbial that S0 biomineralization may be lost, or that S0
biominerals properties are altered in a way that reduces bioavail-
ability, in a cell lineage evolving with a constant sup-
Once it has been established that the formation of a ply of reduced sulfur [through the accumulation of
biomineral with specific properties is an adaptation, loss-of-function mutations; Hottes et al., 2013, Mc-
we may formulate and test hypotheses regarding its Donald, 2019].
biological function. This final step of our roadmap is
difficult to describe in general terms, since the details 8. New roles for biominerals
are likely to vary significantly from one biomineral
function to another. However, as a general rule, hy- Here we describe new conceptual frameworks for fu-
potheses on biomineral functions should preferably ture functional studies of biomineralization. We con-
be formulated from field observations [e.g., Chan sider prokaryotic biominerals as potential “public
et al., 2016a], and tested under controlled conditions goods”, and interrogate their role in building biofilm

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 Julie Cosmidis and Karim Benzerara 23

architectures. While more speculative, this section overcome the public good problem, i.e. how exploita-
describes how future research may be conducted tion of the public goods is averted.
within these frameworks to shine light on potential In order to remain evolutionarily stable against
roles of biomineralization in microbial social interac- exploitation, the benefits of a cooperative behav-
tions in natural biofilm habitats. ior must be directed toward other cooperating in-
dividuals (as compared to toward “cheaters”). Bac-
teria may adopt different strategies to solve public
8.1. Are extracellular biominerals “public good problems, for instance by privatizing the goods
goods”? through uptake strategies that exclude competitive
strains [e.g., Niehus et al., 2017], or through negative
When they are extracellular, biominerals are in prin- frequency-dependent selection mechanisms making
ciple available to microorganisms other than their cheating beneficial only when rare but not when
producers, and their potential benefits are thus common [Ross-Gillespie et al., 2007]. An important
shared with neighboring cells. Cooperative behav- mechanism to avert exploitation of public goods
iors in which a good produced by one individual is consists in increasing the spatial structure of the pop-
available to neighbors may be problematic when the ulation by producing biofilm-building EPS, which
production of this good comes with a physiological limits both the motility of cells and the diffusion of
cost. Indeed, “cheating” nonproducers may emerge their goods. As a result, the distance over which pro-
and rapidly outcompete producers, as they do not duction by one individual benefits its neighbors is re-
pay the fitness cost associated with production. Thus, duced, and thus the benefits of the public goods are
it has to be explained how such individually costly preferentially provided to nearby clonemates, who
cooperative behavior can be selected and sustained are more likely to be cooperative producers than
in a population, a puzzle often termed the “public cheaters. This mechanism has been described for
good problem” in evolutionary biology [Smith and bacterial public goods such as extracellular enzymes
Schuster, 2019]. Different types of extracellular sub- [Drescher et al., 2014] and siderophores [Julou et al.,
stances produced by bacteria have been described as 2013], and is likely to be relevant in the case of extra-
public goods, including siderophores [Kramer et al., cellular biominerals which are poorly diffusible, and
2020], digestive enzymes [Drescher et al., 2014], and thus for which spatial segregation between produc-
EPS structuring biofilms [Nadell and Bassler, 2011]. ers and nonproducers is likely to have major effects
It may be interesting to figure out whether in cer- on availability.
tain systems, extracellular biomineralization may be The study of biominerals as public goods, and
considered as a public good (i.e., an exploitable and more generally all “social” aspects of microbial
costly cooperative behavior), and, if so, how this trait biomineralization, are topics that remain largely
can be maintained in microbial populations (i.e., unexplored. Given the importance of population
how exploitation can be averted). spatial structure for the evolution of cooperation and
We do not expect all extracellular biominerals to competition in natural communities, it is unfortu-
be public goods. However, this concept may be use- nate that microbial biomineralization experiments
ful for instance in the case of extracellular S0 biomin- are in the immense majority of cases performed in
erals, the formation of which seems to require the liquid cultures, where bacterial populations are uni-
(costly) production of S0 -stabilizing organics [e.g., formly mixed, and thus where structure is nonexis-
Cron et al., 2019], and which may be used as en- tent. Future studies on the adaptive functions of mi-
ergy resources by neighboring cells (Section 4). To crobial biominerals may thus benefit from working
fully demonstrate this, it would be necessary to show with colonies growing on agar plates or on mineral
that biomineral production (or the control of certain surfaces. Aside from any consideration of social be-
biomineral properties, such as a metastable struc- haviors, biofilms are a major form of bacterial habitat
ture increasing bioavailability) carries a fitness cost, [Hall-Stoodley et al., 2004, Nadell et al., 2016], where
which can be achieved through competition experi- many biomineralization processes actually occur in
ments with isogenic nonproducers. Then, it would be nature [e.g., Cron et al., 2021]. In the next section, we
interesting to determine how bacterial populations will discuss the idea that some functions of biomin-

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24 Julie Cosmidis and Karim Benzerara

erals may be specific to microbial populations living to their ureolytic activity [the enzymatically catalyzed
in biofilms. hydrolysis of urea, which locally increases pH and
favors CaCO3 supersaturation; Castro-Alonso et al.,
2019, Görgen et al., 2021]. A growing body of liter-
8.2. Biominerals and biofilm architecture
ature now suggests that CaCO3 minerals may be a
As explained in the previous section, it is important previously overlooked component of the extracellu-
that questions around the roles of biominerals in lar matrix of microbial biofilms containing ureolytic
cooperation and competition behaviors are investi- bacteria [reviewed in Keren-Paz and Kolodkin-Gal,
gated using experiments with microbial biofilm com- 2020] (Figure 6). Different lines of evidence suggest
munities rather than liquid cultures, given the im- that this mechanism confers important fitness ben-
portance of surface adhesion and population struc- efits to the bacteria, as shown for instance by com-
ture in such interactions [Kees et al., 2021, Kim et al., petition experiments using dual-species biofilms [Li
2014, Nadell et al., 2016, Schluter et al., 2015]. More- et al., 2016b] (Figure 6A), or studies using defec-
over, as speculated by Phoenix and Konhauser [2008], tive mutants [Oppenheimer-Shaanan et al., 2016].
some possible benefits of biominerals may mirror The extracellular CaCO3 minerals are indeed thought
those afforded by EPS in biofilms, such as screening to form a framework structuring and strengthening
from detrimental radiation, physical protection from the biofilm, and protecting the bacteria from antibi-
grazing or desiccation, and participation in biofilm otics and other harmful environmental substances
strength and structural integrity. However, an advan- [Dade-Robertson et al., 2017, Keren-Paz et al., 2018]
tage of biominerals over EPS would be that they can (Figure 6B). CaCO3 precipitation may also be used
be produced at a smaller energetic cost [Phoenix and as a detoxification mechanism preventing the ac-
Konhauser, 2008]. cumulation of CO2 in non-photosynthetic biofilms
Extracellular precipitation of calcium carbonates [Oppenheimer-Shaanan et al., 2016]. It thus appears
in microbial mats has been extensively studied by that it may now be time to reconsider extracellular
geobiologists, in part due to its role in the formation calcification not as an “unintended” consequence of
of microbialites and stromatolites [e.g., Couradeau microbial metabolisms and passive Ca2+ adsorption
et al., 2013, Ferrer et al., 2022], which are important onto EPS, but as an adaptive process and important
archives of microbial life on early Earth [Bosak et al., feature of the extracellular matrix of biofilms, play-
2013]. The primary driver for calcification in biofilms ing a crucial role in bacterial fitness and interspecies
is the local increase in calcium carbonate supersat- competition [Keren-Paz and Kolodkin-Gal, 2020].
uration, which may result from specific microbial
metabolisms, for instance, photosynthesis, ureolysis, 9. Conclusions
or sulfate reduction [e.g., Saghaï et al., 2016, White
et al., 2016]. This active, biologically induced CaCO3 We have reviewed functional aspects of several
mineralization process occurs concurrently with pas- prokaryotic biomineralization systems (see a sum-
sive binding of Ca2+ ions on the EPS matrix of the mary in Table 2), and described approaches that may
biofilm, which may favor CaCO3 heterogeneous nu- be used to discover or test new functions of biomin-
cleation, and influence mineral properties such as erals. Many “ultimate” questions around microbial
morphology, size, or structure [Dupraz et al., 2009, biomineralization remain to be understood. Funda-
Görgen et al., 2021, Lyu et al., 2020]. Interestingly, it mentally, it is still not clear in many systems whether
is now recognized that microbially induced CaCO3 biomineralization increases an organism’s fitness,
precipitation may not be limited to heavily calcify- and whether producing biominerals with specific
ing, mat-building environmental communities such properties contributes to adaptation to certain en-
as those forming stromatolites, but can also occur in vironmental conditions. Moreover, we note that the
biofilms of bacteria previously studied as pathogens term “function” should be taken with caution as it
in a medical context [e.g., Pseudomonas aeruginosa encompasses diverse meanings. As we have seen
or Proteus mirabilis; Li et al., 2016a, 2015]. A vari- here, these questions can be addressed through ex-
ety of both gram-negative and gram-positive bacte- perimentation, but the use of these experimental ap-
ria can induce calcium carbonate precipitation due proaches often requires prior understanding of the

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 Julie Cosmidis and Karim Benzerara 25

Figure 6. Roles of extracellular CaCO3 biomineralization in biofilms. (A) Competition experiment in

a dual-species biofilm between non-biomineralizing P. aeruginosa (fluorescently stained in green) and
biomineralizing P. mirabilis (fluorescently stained in red), expressing the urease. The confocal fluo-
rescence micrographs show the distribution of CaCO3 minerals (blue) as well as of both types of cells

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26 Julie Cosmidis and Karim Benzerara

Figure 6. (cont.) during the experiments in the presence of a non-buffered medium, where CaCO3
biomineralization can occur (left), or in a buffered medium where CaCO3 precipitation is inhibited
(right). When it can occur, biomineralization is responsible for the fitness advantage of P. mirabilis in the
biofilm [Li et al., 2016a]. Figure reproduced with permission from Oxford University Press. (B) B. subtilis
colonies and cross-sections of colonies after application of a fluorescein dye. The colonies were grown
either with (+Ca) or without (−Ca) calcium (left and middle panels). The colonies on the right panel
were grown in the presence of acetohydroxamic acid (AHA), a known inhibitor of the urease enzyme.
Precipitation of CaCO3 minerals, mediated by urease activity, is crucial to form the complex structure
of the biofilm and creates a diffusion barrier sheltering the inner cell mass of the colony. Scale bars:
0.5 mm [Keren-Paz et al., 2018]. Figure under a Creative Commons Attribution 4.0 International License
(http://creativecommons.org/licenses/by/4.0/).

genetic pathways controlling biomineral formation of biomineralization. Indeed, while “controlled”

and properties. It should be noted that genes control- biomineralization is sometimes used as a synonym
ling biomineralization may not always be found, es- for adaptive biomineralization (i.e., a trait with vari-
pecially in microbial species that are not amenable to ation under genetic control, which serves a specific
culture or genetic manipulation. Moreover, the idea function that increases fitness), “induced” and “in-
of specific genes for biomineralization should also fluenced” biomineralization processes refer to the
be viewed as too restrictive or misleading, especially mechanisms leading to mineral precipitation (re-
in cases when these genes are pleiotropic. Despite spectively: increased saturation due to metabolic
these difficulties, a deeper knowledge of these ge- activity, or mineral nucleation on organic surfaces).
netic controls is crucial to allow us to reconstruct the The variation of the latter two processes may or
phylogenetic and evolutionary history of microbial may not be under genetic control (and therefore, be
biomineralization, which, in conjunction with a bet- heritable traits), and they may or may not be adap-
ter understanding of the geological record, will assist tive and increase fitness, leading to blurry bound-
efforts to decipher the history of life co-evolution aries between the three classical categories. For in-
with its mineral environment. stance, until recently, extracellular CaCO3 precip-
Among emerging questions around the functions itation as a result of the activity of the urease en-
of microbial biomineralization, it will be particularly zyme may have been viewed as a typical example
interesting to address the roles of biominerals in “so- of “induced” biomineralization. However, ureolytic
cial” interactions between prokaryotes, at both intra- CaCO3 biomineralization is clearly a heritable trait
and interspecific levels, in particular in biofilm habi- under genetic control [consistently, an E. coli strain
tats. Indeed, cooperative formation and utilization of transformed with the urease genes of an ureolytic
biominerals may be important to sustain microbial Bacillus pasteurii strain acquires strong biominer-
communities in the environment. From a practical alization capabilities; Bachmeier et al., 2002]. More-
point of view, new knowledge on adaptive aspects of over, with the discovery of important fitness benefits
microbial biomineralization may be used in the fu- of extracellular CaCO3 biominerals due to their roles
ture to develop and improve microbial bioremedia- in interspecies competition, biofilm structure, and
tion strategies [Gadd, 2010], identify therapeutic tar- limitation of antibiotics diffusion [Keren-Paz and
gets to fight against pathogens [e.g., Keren-Paz et al., Kolodkin-Gal, 2020, Li et al., 2016a, Oppenheimer-
2018], or design new biomaterials through directed Shaanan et al., 2016] (Figure 6), ureolytic calcium
evolution approaches [e.g., Liu et al., 2016]. carbonate biomineralization can be described as
As we shift our focus from “proximate” to “ul- an adaptation to certain biofilm habitats. Often,
timate” questions, we may consider revisiting the the use of “controlled” biomineralization conveys
classical framework used to categorize biominer- the idea that the properties of the biominerals are
alization processes (Section 2). An issue with the tightly regulated by genes, so that the biominerals
“controlled”/“induced”/“influenced” categories is differ (e.g., in morphology, structure, or composi-
that they combine mechanistic and adaptive aspects tion) from equivalent minerals precipitated through

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 Julie Cosmidis and Karim Benzerara 27

Table 2. Summary of biomineral functions described in this review

Function Biomineral example Reference

Protection:
From UV radiation Silica Phoenix et al. [2001, 2006]
Fe(III)-(oxyhydr)oxides Gauger et al. [2015]
From grazing ? (hypothetical) Phoenix and Konhauser [2008]
From dehydration ? (hypothetical) Phoenix and Konhauser [2008]
From encrustation Fe(III)-(oxyhydr)oxides Chan et al. [2011], Miot et al. [2009a]
From antibiotics Extracellular carbonates Dade-Robertson et al. [2017], Keren-Paz
et al. [2018]
Detoxification:
Of reactive oxygen species Magnetite, greigite Lefèvre and Bazylinski [2013], Lin et al.
[2020]
Fe(III)-(oxyhydr)oxides Hallbeck and Pedersen [1995]
Of organic toxins Clays Habte and Barrion [1984], Phoenix and
Konhauser [2008]
Of toxic metals Metal nanoparticles Hulkoti and Taranath [2014]
Of CO2 Extracellular carbonates Oppenheimer-Shaanan et al. [2016]
Storage:
Of nutrients Iron phosphates Konhauser et al. [1994]
Clays Phoenix and Konhauser [2008], Stotzky
and Rem [1966]
Of energy (electron donors or Elemental sulfur Dahl [2020]; numerous references in the
acceptors) present review (Section 4)
Of inorganic carbon Intracellular carbonates This review (Section 6)
Structure:
Biofilm strength and integrity ? (hypothetical) Phoenix and Konhauser [2008]
Attachment and support Fe(III)-(oxyhydr)oxides Chan et al. [2016a]
Magnetotaxis magnetite, greigite Frankel et al. [2007], Stephens [2006]
Positioning in redox gradients Fe(III)-(oxyhydr)oxides Chan et al. [2016a], Krepski et al. [2013]
Elemental sulfur Sievert et al. [2007]
Buoyancy adjustment Fe(III)-(oxyhydr)oxides Chiu et al. [2017]
Intracellular carbonates Couradeau et al. [2012], Gray and Head
[2014], Monteil et al. [2021]
Interspecific interactions:
Symbiosis magnetite Monteil et al. [2019]
Syntrophy Elemental sulfur Warthmann et al. [1992]
Magnetite Tang et al. [2016]
Fe(III)-(oxyhydr)oxides Blöthe and Roden [2009], Emerson et al.
[2010]
Public goods ? (hypothetical) This review (Section 8.1)
Competition in biofilms Extracellular carbonates Li et al. [2016a]
(continued on next page)

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28 Julie Cosmidis and Karim Benzerara

Table 2. (continued)

Function Biomineral example Reference

Intraspecific interactions:
Cooperative use of resources Elemental sulfur Ceskova et al. [2002], Marnocha
et al. [2016];
Extracellular electron transfer Conductive or semi-conductive Mansor and Xu [2020], Tang et al.
iron nanoparticles [2016]
Establishment of an energy- Fe(III)-(oxyhydr)oxides Chan et al. [2004], Mansor and Xu
generating proton motive force [2020]
pH homeostasis Intracellular carbonates This review (Section 6)

abiotic processes under similar conditions [Frankel pates in renewing curiosity for this interesting issue,
and Bazylinski, 2003]. However, it may be argued and provides some foundation for future studies fo-
that this is also likely to be the case of any mineral cussing on this topic.
precipitating in the presence of organic substances
[e.g., Cosmidis et al., 2019]. Unusual mineral proper-
Conflicts of interest
ties thus do not say anything about whether or not
biomineralization is adaptive. Furthermore, when Authors have no conflict of interest to declare.
tight control on biomineral properties indeed exists,
it operates through microbially induced changes in
mineral saturation and/or under the templating ef- Acknowledgments
fect of organic matrices, further blurring the lines
Karim Benzerara thanks the French National Re-
between “controlled”, “induced”, and “influenced”
search Agency (HARLEY: ANR-19-CE44-0017) for fi-
classical biomineralization categories.
nancial support. Both authors thank Emmanuelle
We propose that microbial biomineralization Porcher for helpful comments and suggestions on the
processes should be described either according to manuscript.
their adaptive value (e.g., adaptive or maladaptive*,
based on whether or not they increase the organ-
ism’s fitness), or according to their mechanism (in- References
duced and/or influenced biomineralization, both of
Achal, V., Mukherjee, A., Basu, P. C., and Reddy, M. S.
which may occur concurrently, and in both adap-
(2009). Strain improvement of Sporosarcina pas-
tive and maladaptive processes). Actually, in cases
teurii for enhanced urease and calcite production.
where biomineralization results from the activity of a
J. Ind. Microbiol. Biotechnol., 36, 981–988.
pleiotropic gene (such as the gene coding for the ure-
Addadi, L., Raz, S., and Weiner, S. (2003). Taking ad-
ase, which is involved in both C and N metabolism
vantage of disorder: amorphous calcium carbonate
and CaCO3 precipitation), biomineralization may be
and its roles in biomineralization. Adv. Mater., 15,
described as an exaptation*, i.e. a feature that now in-
959–970.
creases fitness but was not built by natural selection
Amenabar, M. J. and Boyd, E. S. (2018). Mecha-
for its current goal [Gould and Vrba, 1982]. Further
nisms of mineral substrate acquisition in a ther-
complicating this categorization problem, the adap-
moacidophile. Appl. Environ. Microbiol., 84, arti-
tive value of some biominerals may depend on the
cle no. e00334-18.
environment (i.e., biomineralization may increase or
Amor, M., Busigny, V., Durand-Dubief, M., Tharaud,
decrease fitness based on external conditions).
M., Ona-Nguema, G., Gélabert, A., Alphandéry, E.,
Overall, we hope that this review, rather than pro- Menguy, N., Benedetti, M. F., Chebbi, I., and Guyot,
viding definitive answers to the fundamental ques- F. (2015). Chemical signature of magnetotactic bac-
tion “why do microbes make minerals?”, partici- teria. Proc. Natl. Acad. Sci. USA, 112, 1699–1703.

C. R. Géoscience — 2022, 354, n 1, 1-39

 Julie Cosmidis and Karim Benzerara 29

Amor, M., Busigny, V., Louvat, P., Gelabert, A., Car- intermediates in the oxidation of sulfide to sulfate
tigny, P., Durand-Dubief, M., Ona-Nguema, G., Al- by beggiatoa spp. Appl. Environ. Microbiol., 80,
phandery, E., Chebbi, I., and Guyot, F. (2016). Mass- 629–636.
dependent and -independent signature of Fe iso- Blondeau, M., Benzerara, K., Ferard, C., Guigner, J.-
topes in magnetotactic bacteria. Science, 352, 705– M., Poinsot, M., Coutaud, M., Tharaud, M., Cordier,
708. L., and Skouri-Panet, F. (2018a). Impact of the
Amor, M., Mathon, F. P., Monteil, C. L., Busigny, V., cyanobacterium Gloeomargarita lithophora on the
and Lefevre, C. T. (2020). Iron-biomineralizing geochemical cycles of Sr and Ba. Chem. Geol., 483,
organelle in magnetotactic bacteria: function, 88–97.
synthesis and preservation in ancient rock sam- Blondeau, M., Sachse, M., Boulogne, C., Gillet, C.,
ples. Environ. Microbiol., 22, 3611–3632. Guigner, J.-M., Skouri-Panet, F., Poinsot, M., Ferard,
Bachmeier, K. L., Williams, A. E., Warmington, C., Miot, J., and Benzerara, K. (2018b). Amorphous
J. R., and Bang, S. S. (2002). Urease activity calcium carbonate granules form within an intra-
in microbiologically-induced calcite precipitation. cellular compartment in calcifying cyanobacteria.
J. Biotechnol., 93, 171–181. Front. Microbiol., 9, article no. 1768.
Bar-On, Y. M., Phillips, R., and Milo, R. (2018). The Blöthe, M. and Roden, E. E. (2009). Composition and
biomass distribution on earth. Proc. Natl. Acad. Sci. activity of an autotrophic Fe(II)-oxidizing, nitrate-
USA, 115, 6506–6511. reducing enrichment culture. Appl. Environ. Mi-
Bawazer, L. A., Izumi, M., Kolodin, D., Neilson, J. R., crobiol., 75, 6937–6940.
Schwenzer, B., and Morse, D. E. (2012). Evolution- Blumentals, I. I., Itoh, M., Olson, G. J., and Kelly, R. M.
ary selection of enzymatically synthesized semi- (1990). Role of polysulfides in reduction of el-
conductors from biomimetic mineralization vesi- emental sulfur by the hyperthermophilic archae-
cles. Proc. Natl. Acad. Sci. USA, 109, E1705–E1714. bacterium pyrococcus furiosus. Appl. Environ. Mi-
Benzerara, K., Bernard, S., and Miot, J. (2019). Miner- crobiol., 56, 1255–1262.
alogical identification of traces of life. In Cavalazzi, Bosak, T., Knoll, A. H., and Petroff, A. P. (2013). The
B. and Westall, F., editors, Biosignatures for Astrobi- meaning of stromatolites. Annu. Rev. Earth Planet.
ology, Advances in Astrobiology and Biogeophysics, Sci., 41, 21–44.
pages 123–144. Springer International Publishing, Boyd, E. S. and Druschel, G. K. (2013). Involvement
Cham, Switzerland. of intermediate sulfur species in biological reduc-
Benzerara, K., Bolzoni, R., Monteil, C., Beyssac, O., tion of elemental sulfur under acidic, hydrother-
Forni, O., Alonso, B., Asta, M. P., and Lefevre, C. mal conditions. Appl. Environ. Microbiol., 79,
(2021). The gammaproteobacterium Achromatium 2061–2068.
forms intracellular amorphous calcium carbonate Brune, D. C. (1995). Isolation and characterization of
and not (crystalline) calcite. Geobiology, 19, 199– sulfur globule proteins from Chromatium vinosum
213. and Thiocapsa roseopersicina. Arch. Microbiol.,
Benzerara, K., Miot, J., Morin, G., Ona-Nguema, G., 163, 391–399.
Skouri-Panet, F., and Férard, C. (2011). Signifi- Bryce, C., Blackwell, N., Schmidt, C., Otte, J., Huang,
cance, mechanisms and environmental implica- Y.-M., Kleindienst, S., Tomaszewski, E., Schad, M.,
tions of microbial biomineralization. C. R. Geosci., Warter, V., Peng, C., Byrne, J. M., and Kappler, A.
343, 160–167. (2018). Microbial anaerobic Fe(II) oxidation – ecol-
Benzerara, K., Skouri-Panet, F., Li, J., Ferard, C., Gug- ogy, mechanisms and environmental implications.
ger, M., Laurent, T., Couradeau, E., Ragon, M., Cos- Environ. Microbiol., 20, 3462–3483.
midis, J., Menguy, N., Margaret-Oliver, I., Tavera, R., Byrne, J. M., Klueglein, N., Pearce, C., Rosso, K. M.,
Lopez-Garcia, P., and Moreira, D. (2014). Intracellu- Appel, E., and Kappler, A. (2015). Redox cycling of
lar Ca-carbonate biomineralization is widespread Fe(II) and Fe(III) in magnetite by Fe-metabolizing
in cyanobacteria. Proc. Natl. Acad. Sci. USA, 111, bacteria. Science, 347, 1473–1476.
10933–10938. Cain, A. K., Barquist, L., Goodman, A. L., Paulsen, I. T.,
Berg, J. S., Schwedt, A., Kreutzmann, A.-C., Kuypers, Parkhill, J., and van Opijnen, T. (2020). A decade
M. M. M., and Milucka, J. (2014). Polysulfides as of advances in transposon-insertion sequencing.

C. R. Géoscience — 2022, 354, n 1, 1-39

30 Julie Cosmidis and Karim Benzerara

Nat. Rev. Genet., 21, 526–540. formation. ISME J., 5, 717–727.

Cam, N., Benzerara, K., Georgelin, T., Jaber, M., Chan, C. S., McAllister, S. M., Leavitt, A. H., Glazer,
Lambert, J.-F., Poinsot, M., Skouri-Panet, F., and B. T., Krepski, S. T., and Emerson, D. (2016a). The
Cordier, L. (2016). Selective uptake of alkaline earth architecture of iron microbial mats reflects the
metals by cyanobacteria forming intracellular car- adaptation of chemolithotrophic iron oxidation in
bonates. Environ. Sci. Technol., 50, 11654–11662. freshwater and marine environments. Front. Mi-
Cam, N., Benzerara, K., Georgelin, T., Jaber, M., Lam- crobiol., 7, article no. 796.
bert, J.-F., Poinsot, M., Skouri-Panet, F., Moreira, Chan, C. S., Stasio, G. D., Welch, S. A., Girasole, M.,
D., López-García, P., Raimbault, E., Cordier, L., and Frazer, B. H., Nesterova, M. V., Fakra, S., and Ban-
Jézéquel, D. (2018). Cyanobacterial formation of field, J. F. (2004). Microbial polysaccharides tem-
intracellular Ca-carbonates in undersaturated so- plate assembly of nanocrystal fibers. Science, 303,
lutions. Geobiology, 16, 49–61. 1656–1658.
Cam, N., Georgelin, T., Jaber, M., Lambert, J.-F., Chen, P. E. and Shapiro, B. J. (2015). The advent
and Benzerara, K. (2015). In vitro synthesis of of genome-wide association studies for bacteria.
amorphous Mg-, Ca-, Sr- and Ba-carbonates: What Curr. Opin. Microbiol. Environ. Microbiol. Extrem.,
do we learn about intracellular calcification by 25, 17–24.
cyanobacteria? Geochim. Cosmochim. Acta, 161, Chenebault, C., Diaz-Santos, E., Kammerscheit, X.,
36–49. Görgen, S., Ilioaia, C., Streckaite, S., Gall, A., Robert,
Cammack, R., Atwood, T., Campbell, P., Parish, H., B., Marcon, E., Buisson, D.-A., Benzerara, K., Sassi,
Smith, A., Vella, F., and Stirling, J., editors (2006). J.-F., Cassier-Chauvat, C., and Chauvat, F. (2020). A
Oxford Dictionary of Biochemistry and Molecular genetic toolbox for the new model cyanobacterium
Biology. Oxford University Press, Oxford, UK. cyanothece PCC 7425: a case study for the photo-
Castro-Alonso, M. J., Montañez Hernandez, L. E., synthetic production of limonene. Front. Micro-
Sanchez-Muñoz, M. A., Macias Franco, M. R., biol., 11, article no. 2335.
Narayanasamy, R., and Balagurusamy, N. (2019). Chiu, B. K., Kato, S., McAllister, S. M., Field, E. K., and
Microbially Induced Calcium Carbonate Precip- Chan, C. S. (2017). Novel pelagic iron-oxidizing
itation (MICP) and its potential in bioconcrete: zetaproteobacteria from the chesapeake bay oxic–
microbiological and molecular concepts. Front. anoxic transition zone. Front. Microbiol., 8, article
Mater., 6, article no. 126. no. 1280.
Cavanaugh, J., Whittaker, M. L., and Joester, D. (2019). Comolli, L. R., Luef, B., and Chan, C. S. (2011). High-
Crystallization kinetics of amorphous calcium car- resolution 2D and 3D cryo-TEM reveals structural
bonate in confinement. Chem. Sci., 10, 5039–5043. adaptations of two stalk-forming bacteria to an Fe-
Ceskova, P., Mandl, M., Helanova, S., and Kas- oxidizing lifestyle. Environ. Microbiol., 13, 2915–
parovska, J. (2002). Kinetic studies on elemental 2929.
sulfur oxidation by Acidithiobacillus ferrooxidans: Corts, A. D., Thomason, L. C., Gill, R. T., and Gral-
sulfur limitation and activity of free and adsorbed nick, J. A. (2019). A new recombineering system
bacteria. Biotechnol. Bioeng., 78, 24–30. for precise genome-editing in Shewanella onei-
Chan, C. S., Emerson, D., and Luther, G. W. (2016b). densis strain MR-1 using single-stranded oligonu-
The role of microaerophilic Fe-oxidizing micro- cleotides. Sci. Rep., 9, article no. 39.
organisms in producing banded iron formations. Cosmidis, J. and Benzerara, K. (2014). Soft X-
Geobiology, 14, 509–528. ray scanning transmission spectromicroscopy. In
Chan, C. S., Fakra, S. C., Edwards, D. C., Emerson, D., Biomineralization Sourcebook: Characterization of
and Banfield, J. F. (2009). Iron oxyhydroxide min- Biominerals and Biomimetic Materials, pages 115–
eralization on microbial extracellular polysaccha- 133. E. DiMasi and L. B. Gower, London, UK.
rides. Geochim. Cosmochim. Acta, 73, 3807–3818. Cosmidis, J., Benzerara, K., Guyot, F., Skouri-Panet,
Chan, C. S., Fakra, S. C., Emerson, D., Fleming, E. J., F., Duprat, E., Férard, C., Guigner, J.-M., Babon-
and Edwards, K. J. (2011). Lithotrophic iron- neau, F., and Coelho, C. (2015). Calcium-
oxidizing bacteria produce organic stalks to con- phosphate biomineralization induced by alkaline
trol mineral growth: implications for biosignature phosphatase activity in escherichia coli: localiza-

C. R. Géoscience — 2022, 354, n 1, 1-39

 Julie Cosmidis and Karim Benzerara 31

tion, kinetics, and potential signatures in the fossil Dupraz, C., Reid, R. P., Braissant, O., Decho, A. W.,
record. Front. Earth Sci., 3, article no. 84. Norman, R. S., and Visscher, P. T. (2009). Pro-
Cosmidis, J., Nims, C. W., Diercks, D., and Templeton, cesses of carbonate precipitation in modern micro-
A. S. (2019). Formation and stabilization of elemen- bial mats. Earth Sci. Rev., 96, 141–162.
tal sulfur through organomineralization. Geochim. Ehrenberg, C. G. (1836). Vorläufige Mitteilungen
Cosmochim. Acta, 247, 59–82. über das wirkliche Vorkommen fossiler Infusorien
Couradeau, E., Benzerara, K., Gérard, E., Estève, und ihre groBe Verbreitung. Poggend.’s Ann. Phys.
I., Moreira, D., Tavera, R., and López-García, P. Chem., 38, 213–227.
(2013). Cyanobacterial calcification in modern mi- Emerson, D., Fleming, E. J., and McBeth, J. M. (2010).
crobialites at the submicrometer scale. Biogeo- Iron-oxidizing bacteria: an environmental and ge-
sciences, 10, 5255–5266. nomic perspective. Annu. Rev. Microbiol., 64, 561–
Couradeau, E., Benzerara, K., Gerard, E., Moreira, 583.
D., Bernard, S., Brown, G. E., and Lopez-Garcia, P. Engel, A. S., Lichtenberg, H., Prange, A., and Hormes,
(2012). An early-branching microbialite cyanobac- J. (2007). Speciation of sulfur from filamentous mi-
terium forms intracellular carbonates. Science, 336, crobial mats from sulfidic cave springs using X-ray
459–462. absorption near-edge spectroscopy. FEMS Micro-
Cron, B., Henri, P., Chan, C. S., Macalady, J. L., and biol. Lett., 269, 54–62.
Cosmidis, J. (2019). Elemental sulfur formation by Faivre, D. and Baumgartner, J. (2015). The combina-
Sulfuricurvum kujiense is mediated by extracellu- tion of random mutagenesis and sequencing high-
lar organic compounds. Front. Microbiol., 10, arti- light the role of unexpected genes in an intractable
cle no. 2710. organism. PLoS Genet., 11, article no. e1004895.
Cron, B., Macalady, J. L., and Cosmidis, J. (2021). Or- Faivre, D. and Schüler, D. (2008). Magnetotactic bac-
ganic stabilization of extracellular elemental sulfur teria and magnetosomes. Chem. Rev., 108, 4875–
in a Sulfurovum-rich biofilm: a new role for EPS? 4898.
Front. Microbiol., 12, article no. 720101. Falkowski, P. G., Fenchel, T., and Delong, E. F. (2008).
Dade-Robertson, M., Keren-Paz, A., Zhang, M., and The microbial engines that drive earth’s biogeo-
Kolodkin-Gal, I. (2017). Architects of nature: grow- chemical cycles. Science, 320, 1034–1039.
ing buildings with bacterial biofilms. Microb. Ferrer, F. M., Rosen, M. R., Feyhl-Buska, J., Russell,
Biotechnol., 10, 1157–1163. V. V., Sønderholm, F., Loyd, S., Shapiro, R., Stamps,
Dahl, C. (2020). A biochemical view on the biological B. W., Petryshyn, V., Demirel-Floyd, C., Bailey, J. V.,
sulfur cycle. In Environmental Technologies to Treat Johnson, H. A., Spear, J. R., and Corsetti, F. A. (2022).
Sulfur Pollution: Principles and Engineering, pages Potential role for microbial ureolysis in the rapid
55–96. IWA Publishing, London, UK. formation of carbonate tufa mounds. Geobiology,
Dahl, C., Friedrich, C., and Kletzin, A. (2008). Sulfur 20, 79–97.
oxidation in prokaryotes. In Encyclopedia of Life Findlay, A. J., Gartman, A., MacDonald, D. J., Hanson,
Sciences. John Wiley & Sons, Chichester, UK. T. E., Shaw, T. J., and Luther, G. W. (2014). Distri-
Dahl, C. and Prange, A. (2006). Bacterial sulfur bution and size fractionation of elemental sulfur in
globules: occurrence, structure and metabolism. aqueous environments: The Chesapeake Bay and
In Shively, J. M., editor, Inclusions in Prokaryotes, Mid-Atlantic Ridge. Geochim. Cosmochim. Acta,
pages 21–51. Springer-Verlag, Berlin, Germany. 142, 334–348.
Donovan, C. (2019). Biological function. In Shack- Findlay, A. J. and Kamyshny, A. (2017). Turnover rates
elford, T. K. and Weekes-Shackelford, V. A., ed- of intermediate sulfur species (Sx2-, S0, S2O32-
itors, Encyclopedia of Evolutionary Psychological , S4O62-, SO32-) in anoxic freshwater and sedi-
Science, pages 1–4. Springer International Publish- ments. Front. Microbiol., 8, article no. 2551.
ing, Cham, Switzerland. Frankel, R. B. and Bazylinski, D. A. (2003). Biologically
Drescher, K., Nadell, C. D., Stone, H. A., Wingreen, induced mineralization by bacteria. Rev. Mineral.
N. S., and Bassler, B. L. (2014). Solutions to the Geochem., 54, 95–114.
public goods dilemma in bacterial biofilms. Curr. Frankel, R. B., Williams, T. J., and Bazylinski, D. A.
Biol., 24, 50–55. (2007). Magnetoreception and Magnetosomes in

C. R. Géoscience — 2022, 354, n 1, 1-39

32 Julie Cosmidis and Karim Benzerara

Bacteria, Microbiology Monographs. Springer, Gower, L. B. (2008). Biomimetic model systems for in-
Berlin, Germany. vestigating the amorphous precursor pathway and
Franz, B., Lichtenberg, H., Hormes, J., Modrow, H., its role in biomineralization. Chem. Rev., 108, 4551–
Dahl, C., and Prange, A. (2007). Utilization of solid 4627.
“elemental” sulfur by the phototrophic purple sul- Gray, N. and Head, I. (2014). The family achro-
fur bacterium Allochromatium vinosum: a sulfur matiaceae. In Rosenberg, E., DeLong, E. F., Lory,
K-edge X-ray absorption spectroscopy study. Mi- S., Stackebrandt, E., and Thompson, F., editors,
crobiology, 153, 1268–1274. The Prokaryotes: Gammaproteobacteria, pages 1–
Friedrich, C. G., Rother, D., Bardischewsky, F., Quent- 14. Springer, Berlin, Germany.
meier, A., and Fischer, J. (2001). Oxidation of re- Gray, N. D. (2006). The unique role of intracellular
duced inorganic sulfur compounds by bacteria: calcification in the genus achromatium. In Shiv-
emergence of a common mechanism? Appl. Env- ely, J. M., editor, Inclusions in Prokaryotes, Microbi-
iron. Microbiol., 67, 2873–2882. ology Monographs, pages 299–309. Springer, Berlin,
Gadd, G. M. (2010). Metals, minerals and microbes: Germany.
geomicrobiology and bioremediation. Microbiol- Gregersen, L. H., Bryant, D. A., and Frigaard, N.-U.
ogy, 156, 609–643. (2011). Mechanisms and evolution of oxidative
Gauger, T., Konhauser, K., and Kappler, A. (2015). Pro- sulfur metabolism in green sulfur bacteria. Front.
tection of phototrophic iron(II)-oxidizing bacteria Microbiol., 2, article no. 116.
from UV irradiation by biogenic iron(III) minerals: Habte, M. and Barrion, M. (1984). Interaction of rhi-
Implications for early Archean banded iron forma- zobium sp. with toxin-producing fungus in culture
tion. Geology, 43, 1067–1070. medium and in a tropical soil. Appl. Environ. Mi-
Ghosh, W. and Dam, B. (2009). Biochemistry and crobiol., 47, 1080–1083.
molecular biology of lithotrophic sulfur oxidation Hageae, G. J., Eanes, E. D., and Gherna, R. L. (1970). X-
by taxonomically and ecologically diverse bacteria ray diffraction studies of the sulfur globules accu-
and archaea. FEMS Microbiol. Rev., 33, 999–1043. mulated by chromatium species. J. Bacteriol., 101,
Giuffre, A. J., Hamm, L. M., Han, N., De Yoreo, J. J., and 464–469.
Dove, P. M. (2013). Polysaccharide chemistry regu- Hall-Stoodley, L., Costerton, J. W., and Stoodley, P.
lates kinetics of calcite nucleation through compe- (2004). Bacterial biofilms: from the natural envi-
tition of interfacial energies. Proc. Natl. Acad. Sci. ronment to infectious diseases. Nat. Rev. Micro-
USA, 110, 9261–9266. biol., 2, 95–108.
Glodowska, M., Schneider, M., Eiche, E., Kontny, A., Hallbeck, L. and Pedersen, K. (1995). Benefits associ-
Neumann, T., Straub, D., Kleindienst, S., and Kap- ated with the stalk of Gallionella ferruginea, evalu-
pler, A. (2021). Microbial transformation of bio- ated by comparison of a stalk-forming and a non-
genic and abiogenic Fe minerals followed by in- stalk-forming strain and biofilm studies in situ. Mi-
situ incubations in an As-contaminated vs. non- crob. Ecol., 30, 257–268.
contaminated aquifer. Environ. Pollut., 281, article Hamilton, T. L., Jones, D. S., Schaperdoth, I., and
no. 117012. Macalady, J. L. (2015). Metagenomic insights
Görgen, S., Benzerara, K., Skouri-Panet, F., Gugger, into S(0) precipitation in a terrestrial subsurface
M., Chauvat, F., and Cassier-Chauvat, C. (2021). lithoautotrophic ecosystem. Front. Microbiol., 5,
The diversity of molecular mechanisms of carbon- article no. 756.
ate biomineralization by bacteria. Discov. Mater., 1, Hanson, T. E., Bonsu, E., Tuerk, A., Marnocha, C. L.,
article no. 2. Powell, D. H., and Chan, C. S. (2016). Chlorobacu-
Gould, S. J. and Lewontin, R. C. (1979). The spandrels lum tepidum growth on biogenic S(0) as the sole
of San Marco and the Panglossian paradigm: a cri- photosynthetic electron donor. Environ. Micro-
tique of the adaptationist programme. Proc. R. Soc. biol., 18, 2856–2867.
Lond. B. Biol. Sci., 205, 581–598. Hazen, R. M., Papineau, D., Bleeker, W., Downs, R. T.,
Gould, S. J. and Vrba, E. S. (1982). Exaptation-a miss- Ferry, J. M., McCoy, T. J., Sverjensky, D. A., and Yang,
ing term in the science of form. Paleobiology, 8, 4– H. (2008). Mineral evolution. Am. Mineral., 93,
15. 1693–1720.

C. R. Géoscience — 2022, 354, n 1, 1-39

 Julie Cosmidis and Karim Benzerara 33

Head, I. M., Gray, N. D., Howarth, R., Pickup, R. W., on biogeochemical cycling of iron. Nat. Rev. Micro-
Clarke, K. J., and Jones, J. G. (2000). Achro- biol., 19, 360–374.
matium oxaliferum Understanding the Unmistak- Kato, S., Ohkuma, M., Powell, D. H., Krepski, S. T.,
able. In Schink, B., editor, Advances in Microbial Oshima, K., Hattori, M., Shapiro, N., Woyke, T.,
Ecology, Advances in Microbial Ecology, pages 1–40. and Chan, C. S. (2015). Comparative genomic
Springer US, Boston, MA, USA. insights into ecophysiology of neutrophilic, mi-
Hegler, F., Schmidt, C., Schwarz, H., and Kappler, A. croaerophilic iron oxidizing bacteria. Front. Micro-
(2010). Does a low-pH microenvironment around biol., 6, article no. 1265.
phototrophic Fe(II)-oxidizing bacteria prevent cell Kees, E. D., Levar, C. E., Miller, S. P., Bond, D. R.,
encrustation by Fe(III) minerals? FEMS Microbiol. Gralnick, J. A., and Dean, A. M. (2021). Survival
Ecol., 74, 592–600. of the first rather than the fittest in a Shewanella
Heveran, C. M., Liang, L., Nagarajan, A., Hubler, electrode biofilm. Commun. Biol., 4, 1–9.
M. H., Gill, R., Cameron, J. C., Cook, S. M., and Keffer, J. L., McAllister, S. M., Garber, A. I., Hallahan,
Srubar, W. V. (2019). Engineered ureolytic microor- B. J., Sutherland, M. C., Rozovsky, S., and Chan, C. S.
ganisms can tailor the morphology and nanome- (2021). Iron oxidation by a fused cytochrome-porin
chanical properties of microbial-precipitated cal- common to diverse iron-oxidizing bacteria. mBio,
cium carbonate. Sci. Rep., 9, article no. 14721. 0, article no. e01074-21.
Hine, R., editor (2019). A Dictionary of Biology. Ox- Keren-Paz, A., Brumfeld, V., Oppenheimer-Shaanan,
ford University Press, Oxford, UK. Y., and Kolodkin-Gal, I. (2018). Micro-CT X-
Hottes, A. K., Freddolino, P. L., Khare, A., Donnell, ray imaging exposes structured diffusion barriers
Z. N., Liu, J. C., and Tavazoie, S. (2013). Bacterial within biofilms. NPJ Biofilms Microbiomes, 4, 1–4.
adaptation through loss of function. PLOS Genet., Keren-Paz, A. and Kolodkin-Gal, I. (2020). A brick in
9, article no. e1003617. the wall: discovering a novel mineral component of
Hulkoti, N. I. and Taranath, T. C. (2014). Biosynthe- the biofilm extracellular matrix. New Biotechnol.,
sis of nanoparticles using microbes—a review. Col- 56, 9–15.
loids Surf. B, 121, 474–483. Kim, W., Racimo, F., Schluter, J., Levy, S. B., and Fos-
Iniesto, M., Moreira, D., Reboul, G., Deschamps, P., ter, K. R. (2014). Importance of positioning for mi-
Benzerara, K., Bertolino, P., Saghaï, A., Tavera, R., crobial evolution. Proc. Natl. Acad. Sci. USA, 111,
and López-García, P. (2021). Core microbial com- E1639–E1647.
munities of lacustrine microbialites sampled along King, R. C., Mulligan, P. K., and Stansfield, W. D.
an alkalinity gradient. Environ. Microbiol., 23, 51– (2014). A Dictionary of Genetics. Oxford University
68. Press, Oxford, UK.
Javaux, E. J. and Lepot, K. (2018). The Paleoprotero- Klassen, J. L. (2018). Defining microbiome function.
zoic fossil record: Implications for the evolution of Nat. Microbiol., 3, 864–869.
the biosphere during Earth’s middle-age. Earth Sci. Kleinjan, W. E., de Keizer, A., and Janssen, A. J. H.
Rev., 176, 68–86. (2005). Equilibrium of the reaction between dis-
Jones, A. A. and Bennett, P. C. (2014). Mineral mi- solved sodium sulfide and biologically produced
croniches control the diversity of subsurface mi- sulfur. Colloids Surf. B, 43, 228–237.
crobial populations. Geomicrobiol. J., 31, 246–261. Kleinjan, W. E., Keizer, A., and Janssen, A. J. H. (2003).
Jørgensen, B. B., Findlay, A. J., and Pellerin, A. (2019). Biologically produced sulfur. In Steudel, R., edi-
The biogeochemical sulfur cycle of marine sedi- tor, Elemental Sulfur and Sulfur-Rich Compounds
ments. Front. Microbiol., 10, article no. 849. I, pages 167–188. Springer, Berlin, Germany.
Julou, T., Mora, T., Guillon, L., Croquette, V., Schalk, Knickerbocker, C., Nordstrom, D. K., and Southam,
I. J., Bensimon, D., and Desprat, N. (2013). Cell– G. (2000). The role of “blebbing” in overcoming
cell contacts confine public goods diffusion inside the hydrophobic barrier during biooxidation of el-
Pseudomonas aeruginosa clonal microcolonies. emental sulfur by Thiobacillus thiooxidans. Chem.
Proc. Natl. Acad. Sci. USA, 110, 12577–12582. Geol., 169, 425–433.
Kappler, A., Bryce, C., Mansor, M., Lueder, U., Byrne, Kobras, C. M., Fenton, A. K., and Sheppard, S. K.
J. M., and Swanner, E. D. (2021). An evolving view (2021). Next-generation microbiology: from com-

C. R. Géoscience — 2022, 354, n 1, 1-39

34 Julie Cosmidis and Karim Benzerara

parative genomics to gene function. Genome Biol., presence of organic carbon at a sulfur-rich glacial
22, article no. 123. site in the Canadian High Arctic. Geochim. Cos-
Koch, T. and Dahl, C. (2018). A novel bacterial sulfur mochim. Acta, 200, 218–231.
oxidation pathway provides a new link between the Laufer, K., Nordhoff, M., Halama, M., Martinez, R. E.,
cycles of organic and inorganic sulfur compounds. Obst, M., Nowak, M., Stryhanyuk, H., Richnow,
ISME J., 12, 2479–2491. H. H., and Kappler, A. (2017). Microaerophilic
Koeksoy, E., Bezuidt, O. M., Bayer, T., Chan, C. S., Fe(II)-oxidizing Zetaproteobacteria isolated from
and Emerson, D. (2021). Zetaproteobacteria pan- low-Fe marine coastal sediments: physiology and
genome reveals candidate gene cluster for twisted composition of their twisted stalks. Appl. Environ.
stalk biosynthesis and export. Front. Microbiol., 12. Microbiol., 83, article no. e03118-16.
Komeili, A. (2007). Molecular mechanisms of magne- Laufer, K., Nordhoff, M., Røy, H., Schmidt, C.,
tosome formation. Annu. Rev. Biochem., 76, 351– Behrens, S., Jørgensen, B. B., and Kappler, A. (2016).
366. Coexistence of Microaerophilic, nitrate-reducing,
Komeili, A., Li, Z., Newman, D. K., and Jensen, G. J. and phototrophic Fe(II) oxidizers and Fe(III) reduc-
(2006). Magnetosomes are cell membrane invagi- ers in coastal marine sediment. Appl. Environ. Mi-
nations organized by the actin-like protein MamK. crobiol., 82, 1433–1447.
Science, 311, 242–245. Lee, Y.-J., Prange, A., Lichtenberg, H., Rohde, M.,
Konhauser, K. O., Fyfe, W. S., Schultze-Lam, S., Ferris, Dashti, M., and Wiegel, J. (2007). In situ analysis
F. G., and Beveridge, T. J. (1994). Iron phosphate of sulfur species in sulfur globules produced from
precipitation by epilithic microbial biofilms in Arc- thiosulfate by Thermoanaerobacter sulfurigignens
tic Canada. Can. J. Earth Sci., 31, 1320–1324. and Thermoanaerobacterium thermosulfurigenes.
Konhauser, K. O., Lalonde, S. V., and Phoenix, V. R. J. Bacteriol., 189, 7525–7529.
(2008). Bacterial biomineralization: where to from Lefèvre, C. T. and Bazylinski, D. A. (2013). Ecology,
here? Geobiology, 6, 298–302. diversity, and evolution of magnetotactic bacteria.
Kramer, J., Özkaya, O., and Kümmerli, R. (2020). Bac- Microbiol. Mol. Biol. Rev., 77, 497–526.
terial siderophores in community and host interac- Lenski, R. E., Rose, M. R., Simpson, S. C., and Tadler,
tions. Nat. Rev. Microbiol., 18, 152–163. S. C. (1991). Long-term experimental evolution
Krepski, S. T., Emerson, D., Hredzak-Showalter, P. L., in Escherichia coli. I. Adaptation and divergence
Luther, G. W., and Chan, C. S. (2013). Morphology during 2,000 generations. Am. Nat., 138, 1315–
of biogenic iron oxides records microbial physiol- 1341.
ogy and environmental conditions: toward inter- Li, J., Benzerara, K., Bernard, S., and Beyssac, O.
preting iron microfossils. Geobiology, 11, 457–471. (2013). The link between biomineralization and
Kussell, E. (2013). Evolution in Microbes. Annu. Rev. fossilization of bacteria: insights from field and ex-
Biophys., 42, 493–514. perimental studies. Chem. Geol., 359, 49–69.
Laishley, E. J., Bryant, R. D., Kobryn, B. W., and Hyne, Li, J., Liu, Y., Liu, S., Roberts, A. P., Pan, H., Xiao, T., and
J. B. (1986). Microcrystalline structure and surface Pan, Y. (2020a). Classification of a complexly mixed
area of elemental sulphur as factors influencing its magnetic mineral assemblage in pacific ocean sur-
oxidation by Thiobacillus albertis. Can. J. Micro- face sediment by electron microscopy and super-
biol., 32, 237–242. vised magnetic unmixing. Front. Earth Sci., 8, arti-
Lande, R. and Arnold, S. J. (1983). The measurement cle no. 609058.
of selection on correlated characters. Evolution, 37, Li, J., Margaret Oliver, I., Cam, N., Boudier, T., Blon-
1210–1226. deau, M., Leroy, E., Cosmidis, J., Skouri-Panet, F.,
Larkin, J. M. and Strohl, W. R. (1983). Beggiatoa, Guigner, J.-M., Férard, C., Poinsot, M., Moreira,
Thiothrix, and Thioploca. Annu. Rev. Microbiol., D., Lopez-Garcia, P., Cassier-Chauvat, C., Chau-
37, 341–367. vat, F., and Benzerara, K. (2016a). Biomineraliza-
Lau, G. E., Cosmidis, J., Grasby, S. E., Trivedi, C. B., tion patterns of intracellular carbonatogenesis in
Spear, J. R., and Templeton, A. S. (2017). Low- cyanobacteria: molecular hypotheses. Minerals, 6,
temperature formation and stabilization of rare al- article no. 10.
lotropes of cyclooctasulfur (β-S8 and γ-S8 in the Li, J., Zhang, H., Menguy, N., Benzerara, K., Wang, F.,

C. R. Géoscience — 2022, 354, n 1, 1-39

 Julie Cosmidis and Karim Benzerara 35

Lin, X., Chen, Z., and Pan, Y. (2017). Single-cell res- ticle accumulation in microbial induced carbonate
olution of uncultured magnetotactic bacteria via precipitation: the crucial role of extracellular poly-
fluorescence-coupled electron microscopy. Appl. meric substance. Geomicrobiol. J., 37, 837–847.
Environ. Microbiol., 83, article no. e00409-17. Macalady, J. L., Hamilton, T. L., Grettenberger, C. L.,
Li, M., Chen, Z., Zhang, P., Pan, X., Jiang, C., An, X., Jones, D. S., Tsao, L. E., and Burgos, W. D. (2013).
Liu, S., and Chang, W. (2008). Crystal structure Energy, ecology and the distribution of microbial
studies on sulfur oxygenase reductase from Acidi- life. Philos. Trans. R. Soc. B: Biol. Sci., 368, article
anus tengchongensis. Biochem. Biophys. Res. Com- no. 20120383.
mun., 369, 919–923. Maharjan, R., McKenzie, C., Yeung, A., and Ferenci, T.
Li, W., Zhang, M., Kang, D., Chen, W., Yu, T., Xu, D., (2013). The basis of antagonistic pleiotropy in hfq
Zeng, Z., Li, Y., and Zheng, P. (2020b). Mechanisms mutations that have opposite effects on fitness at
of sulfur selection and sulfur secretion in a biologi- slow and fast growth rates. Heredity (Edinb), 110,
cal sulfide removal (BISURE) system. Environ. Int., 10–18.
137, article no. 105549. Maisch, M., Lueder, U., Laufer, K., Scholze, C., Kap-
Li, X., Chopp, D. L., Russin, W. A., Brannon, pler, A., and Schmidt, C. (2019). Contribution of
P. T., Parsek, M. R., and Packman, A. I. (2015). Microaerophilic Iron(II)-Oxidizers to Iron(III) min-
Spatial patterns of carbonate biomineralization eral formation. Environ. Sci. Technol., 53, 8197–
in biofilms. Appl. Environ. Microbiol., 81, 7403– 8204.
7410. Maki, J. S. (2013). Bacterial intracellular sulfur glob-
Li, X., Lu, N., Brady, H. R., and Packman, A. I. (2016b). ules: structure and function. J. Mol. Microbiol.
Biomineralization strongly modulates the forma- Biotechnol., 23, 270–280.
tion of Proteus mirabilis and Pseudomonas aerugi- Mallawaarachchi, S., Tonkin-Hill, G., Croucher, N. J.,
nosa dual-species biofilms. FEMS Microbiol. Ecol., Turner, P., Speed, D., Corander, J., and Balding, D.
92, article no. fiw189. (2021). Genome-wide association, prediction and
Lin, W., Kirschvink, J. L., Paterson, G. A., Bazylinski, heritability in bacteria. https://arxiv.org/abs/2021.
D. A., and Pan, Y. (2020). On the origin of microbial 10.04.462983. Preprint.
magnetoreception. Nat. Sci. Rev., 7, 472–479. Mann, S. (1983). Mineralization in biological sys-
Liu, P., Liu, Y., Ren, X., Zhang, Z., Zhao, X., Roberts, tems. In Connett, P. H., Folłmann, H., Lammers,
A. P., Pan, Y., and Li, J. (2021). A novel magneto- M., Mann, S., Odom, J. D., and Wetterhahn, K. E.,
tactic alphaproteobacterium producing intracellu- editors, Inorganic Elements in Biochemistry, Struc-
lar magnetite and calcium-bearing minerals. Appl. ture and Bonding, pages 125–174. Springer, Berlin,
Environ. Microbiol., 87, article no. e01556-21. Germany.
Liu, X., Lopez, P. A., Giessen, T. W., Giles, M., Way, J. C., Mansor, M., Hamilton, T. L., Fantle, M. S., and Macal-
and Silver, P. A. (2016). Engineering genetically- ady, J. (2015). Metabolic diversity and ecological
encoded mineralization and magnetism via di- niches of Achromatium populations revealed with
rected evolution. Sci. Rep., 6, article no. 38019. single-cell genomic sequencing. Front. Microbiol.,
Lowenstam, H. (1981). Minerals formed by organ- 6, article no. 822.
isms. Science, 211, 1126–1131. Mansor, M. and Xu, J. (2020). Benefits at the
Lower, B. H. and Bazylinski, D. A. (2013). The bacte- nanoscale: a review of nanoparticle-enabled pro-
rial magnetosome: a unique prokaryotic organelle. cesses favouring microbial growth and functional-
J. Mol. Microbiol. Biotechnol., 23, 63–80. ity. Environ. Microbiol., 22, 3633–3649.
Luther, G. W., Findlay, A. J., MacDonald, D. J., Ow- Marnocha, C. L., Levy, A. T., Powell, D. H., Hanson,
ings, S. M., Hanson, T. E., Beinart, R. A., and Gir- T. E., and Chan, C. S. (2016). Mechanisms of extra-
guis, P. R. (2011). Thermodynamics and kinetics cellular S0 globule production and degradation in
of sulfide oxidation by oxygen: a look at inorgan- Chlorobaculum tepidum via dynamic cell–globule
ically controlled reactions and biologically medi- interactions. Microbiology, 162, 1125–1134.
ated processes in the environment. Front. Micro- Marnocha, C. L., Sabanayagam, C. R., Modla, S., Pow-
biol., 2, article no. 62. ell, D. H., Henri, P. A., Steele, A. S., Hanson, T. E.,
Lyu, J., Qin, W., Zhang, C., and Li, F. (2020). Nanopar- Webb, S. M., and Chan, C. S. (2019). Insights into

C. R. Géoscience — 2022, 354, n 1, 1-39

36 Julie Cosmidis and Karim Benzerara

the mineralogy and surface chemistry of extracel- mirrors individual metabolic activity in a nitrate-
lular biogenic S0 globules produced by chlorobac- dependent Fe(II)-oxidizer. Front. Microbiol., 6, ar-
ulum tepidum. Front. Microbiol., 10, article no. 271. ticle no. 879.
Martel, J., Young, D., Peng, H.-H., Wu, C.-Y., and Monteil, C. L., Benzerara, K., Menguy, N., Bidaud,
Young, J. D. (2012). Biomimetic properties of min- C. C., Michot-Achdjian, E., Bolzoni, R., Mathon,
erals and the search for life in the Martian Mete- F. P., Coutaud, M., Alonso, B., Garau, C., Jézéquel,
orite ALH84001. Annu. Rev. Earth Planet. Sci., 40, D., Viollier, E., Ginet, N., Floriani, M., Swaraj, S.,
167–193. Sachse, M., Busigny, V., Duprat, E., Guyot, F., and
Mas, J. and Gemerden, H. (1995). Storage products Lefevre, C. T. (2021). Intracellular amorphous
in purple and green sulfur bacteria. In Anoxygenic Ca-carbonate and magnetite biomineralization by
Photosynthetic Bacteria, pages 973–990. Kluwer a magnetotactic bacterium affiliated to the Al-
Academic Publishers, Dordrecht, The Netherlands. phaproteobacteria. ISME J., 15, 1–18.
Mas, J. and van Gemerden, H. (1987). Influence Monteil, C. L., Vallenet, D., Menguy, N., Benzerara, K.,
of sulfur accumulation and composition of sul- Barbe, V., Fouteau, S., Cruaud, C., Floriani, M., Vi-
fur globule on cell volume and buoyant density of ollier, E., Adryanczyk, G., Leonhardt, N., Faivre, D.,
Chromatium vinosum. Arch. Microbiol., 146, 362– Pignol, D., López-García, P., Weld, R. J., and Lefevre,
369. C. T. (2019). Ectosymbiotic bacteria at the origin of
McAllister, S. M., Moore, R. M., Gartman, A., Luther, magnetoreception in a marine protist. Nat. Micro-
G. W., III, Emerson, D., and Chan, C. S. (2019). biol., 4, 1088–1095.
The Fe(II)-oxidizing Zetaproteobacteria: historical, Morris, B. E. L., Henneberger, R., Huber, H., and
ecological and genomic perspectives. FEMS Micro- Moissl-Eichinger, C. (2013). Microbial syntrophy:
biol. Ecol., 95, article no. fiz015. interaction for the common good. FEMS Microbiol.
McDonald, M. J. (2019). Microbial experimental evo- Rev., 37, 384–406.
lution – a proving ground for evolutionary theory Nadell, C. D. and Bassler, B. L. (2011). A fitness trade-
and a tool for discovery. EMBO Rep., 20, article off between local competition and dispersal in Vib-
no. e46992. rio cholerae biofilms. Proc. Natl. Acad. Sci. USA,
Mehta, N., Benzerara, K., Kocar, B. D., and Chapon, 108, 14181–14185.
V. (2019). Sequestration of Radionuclides Radium- Nadell, C. D., Drescher, K., and Foster, K. R. (2016).
226 and Strontium-90 by Cyanobacteria forming Spatial structure, cooperation and competition in
intracellular calcium carbonates. Environ. Sci. biofilms. Nat. Rev. Microbiol., 14, 589–600.
Technol., 53, 12639–12647. Nelson, D. C. and Castenholz, R. W. (1981). Use of re-
Miot, J., Benzerara, K., and Kappler, A. (2014). In- duced sulfur compounds by Beggiatoa sp. J. Bacte-
vestigating microbe-mineral interactions: recent riol., 147, 140–154.
advances in X-Ray and electron microscopy and Niehus, R., Picot, A., Oliveira, N. M., Mitri, S., and
redox-sensitive methods. Annu. Rev. Earth Planet. Foster, K. R. (2017). The evolution of siderophore
Sci., 42, 271–289. production as a competitive trait: the competitive
Miot, J., Benzerara, K., Morin, G., Kappler, A., evolution of siderophores. Evolution, 71, 1443–
Bernard, S., Obst, M., Férard, C., Skouri-Panet, F., 1455.
Guigner, J.-M., Posth, N., Galvez, M., Brown, G. E., Nims, C., Cron, B., Wetherington, M., Macalady, J.,
and Guyot, F. (2009a). Iron biomineralization and Cosmidis, J. (2019). Low frequency Raman
by anaerobic neutrophilic iron-oxidizing bacteria. Spectroscopy for micron-scale and in vivo charac-
Geochim. Cosmochim. Acta, 73, 696–711. terization of elemental sulfur in microbial samples.
Miot, J., Benzerara, K., Obst, M., Kappler, A., Hegler, Sci. Rep., 9, article no. 7971.
F., Schadler, S., Bouchez, C., Guyot, F., and Morin, Nordhoff, M., Tominski, C., Halama, M., Byrne, J. M.,
G. (2009b). Extracellular iron biomineralization Obst, M., Kleindienst, S., Behrens, S., and Kap-
by photoautotrophic iron-oxidizing bacteria. Appl. pler, A. (2017). Insights into nitrate-reducing Fe(II)
Environ. Microbiol., 75, 5586–5591. oxidation mechanisms through analysis of cell-
Miot, J., Remusat, L., Duprat, E., Gonzalez, A., Pont, mineral associations, cell encrustation, and min-
S., and Poinsot, M. (2015). Fe biomineralization eralogy in the chemolithoautotrophic enrichment

C. R. Géoscience — 2022, 354, n 1, 1-39

 Julie Cosmidis and Karim Benzerara 37

culture KS. Appl. Environ. Microbiol., 83, article Glenn, D. R., Milbourne, T., Walsworth, R. L.,
no. e00752-17. Vali, H., and Komeili, A. (2015). A genetic strat-
Oppenheimer-Shaanan, Y., Sibony-Nevo, O., Bloom- egy for probing the functional diversity of mag-
Ackermann, Z., Suissa, R., Steinberg, N., Kartvel- netosome formation. PLOS Genet., 11, article
ishvily, E., Brumfeld, V., and Kolodkin-Gal, I. (2016). no. e1004811.
Spatio-temporal assembly of functional mineral Read, T. D. and Massey, R. C. (2014). Characteriz-
scaffolds within microbial biofilms. NPJ Biofilms ing the genetic basis of bacterial phenotypes using
Microbiomes, 2, 1–10. genome-wide association studies: a new direction
Pasteris, J. D., Freeman, J. J., Goffredi, S. K., and Buck, for bacteriology. Genome Med., 6, article no. 109.
K. R. (2001). Raman spectroscopic and laser scan- Rohwerder, T. and Sand, W. (2003). The sulfane
ning confocal microscopic analysis of sulfur in liv- sulfur of persulfides is the actual substrate of
ing sulfur-precipitating marine bacteria. Chem. the sulfur-oxidizing enzymes from Acidithiobacil-
Geol., 180, 3–18. lus and Acidiphilium spp. Microbiology, 149, 1699–
Peiffer, S., Kappler, A., Haderlein, S. B., Schmidt, 1710.
C., Byrne, J. M., Kleindienst, S., Vogt, C., Rich- Rojas, J., Giersig, M., and Tributsch, H. (1995). Sul-
now, H. H., Obst, M., Angenent, L. T., Bryce, C., fur colloids as temporary energy reservoirs for
McCammon, C., and Planer-Friedrich, B. (2021). Thiobacillus ferrooxidans during pyrite oxidation.
A biogeochemical–hydrological framework for the Arch. Microbiol., 163, 352–356.
role of redox-active compounds in aquatic sys- Ross-Gillespie, A., Gardner, A., West, S. A., and Griffin,
tems. Nat. Geosci., 14, 264–272. A. S. (2007). Frequency dependence and coopera-
Phoenix, V. R., Bennett, P. C., Engel, A. S., Tyler, S. W., tion: theory and a test with bacteria. Am. Nat., 170,
and Ferris, F. G. (2006). Chilean high-altitude hot- 331–342.
spring sinters: a model system for UV screening Saghaï, A., Zivanovic, Y., Moreira, D., Benzerara, K.,
mechanisms by early Precambrian cyanobacteria. Bertolino, P., Ragon, M., Tavera, R., López-Archilla,
Geobiology, 4, 15–28. A. I., and López-García, P. (2016). Compara-
Phoenix, V. R. and Konhauser, K. O. (2008). Benefits tive metagenomics unveils functions and genome
of bacterial biomineralization. Geobiology, 6, 303– features of microbialite-associated communities
308. along a depth gradient. Environ. Microbiol., 18,
Phoenix, V. R., Konhauser, K. O., Adams, D. G., and 4990–5004.
Bottrell, S. H. (2001). Role of biomineralization as Saini, G. and Chan, C. S. (2013). Near-neutral surface
an ultraviolet shield: implications for Archean life. charge and hydrophilicity prevent mineral encrus-
Geology, 29, 823–826. tation of Fe-oxidizing micro-organisms. Geobiol-
Pibernat, I. V. and Abella, C. A. (1996). Sulfide puls- ogy, 11, 191–200.
ing as the controlling factor of spinae production Schädler, S., Burkhardt, C., Hegler, F., Straub, K. L.,
in Chlorobium limicola strain UdG 6038. Arch. Mi- Miot, J., Benzerara, K., and Kappler, A. (2009). For-
crobiol., 165, 272–278. mation of cell-iron-mineral aggregates by pho-
Prange, A., Chauvistré, R., Modrow, H., Hormes, J., totrophic and nitrate-reducing anaerobic Fe(II)-
Trüper, H. G., and Dahl, C. (2002). Quantitative oxidizing bacteria. Geomicrobiol. J., 26, 93–103.
speciation of sulfur in bacterial sulfur globules: X- Schedel, M. and Trüper, H. G. (1980). Anaerobic
ray absorption spectroscopy reveals at least three oxidation of thiosulfate and elemental sulfur in
different species of sulfur. Microbiology (Reading, Thiobacillus denitrificans. Arch. Microbiol., 124,
English), 148, 267–276. 205–210.
Prange, A., Engelhardt, H., Trüper, H. G., and Dahl, Scheffel, A., Gruska, M., Faivre, D., Linaroudis, A.,
C. (2004). The role of the sulfur globule proteins Plitzko, J. M., and Schüler, D. (2006). An acidic
of Allochromatium vinosum: mutagenesis of the protein aligns magnetosomes along a filamentous
sulfur globule protein genes and expression studies structure in magnetotactic bacteria. Nature, 440,
by real-time RT-PCR. Arch. Microbiol., 182, 165– 110–114.
174. Scheffel, A., Poulsen, N., Shian, S., and Kröger, N.
Rahn-Lee, L., Byrne, M. E., Zhang, M., Sage, D. L., (2011). Nanopatterned protein microrings from a

C. R. Géoscience — 2022, 354, n 1, 1-39

38 Julie Cosmidis and Karim Benzerara

diatom that direct silica morphogenesis. Proc. Natl. and kaolinite on bacteria. Can. J. Microbiol., 12,
Acad. Sci. USA, 108, 3175–3180. 547–563.
Schewiakoff, W. (1893). Über einen neuen bakterien- Swanner, E. D., Wu, W., Schoenberg, R., Byrne, J.,
nähnlichen Organismus des Süßwassers (Habilita- Michel, F. M., Pan, Y., and Kappler, A. (2015). Frac-
tionsschrift). University of Heidelberg, Heidelberg, tionation of Fe isotopes during Fe(II) oxidation by a
Germany. marine photoferrotroph is controlled by the forma-
Schluter, J., Nadell, C. D., Bassler, B. L., and Foster, tion of organic Fe-complexes and colloidal Fe frac-
K. R. (2015). Adhesion as a weapon in microbial tions. Geochim. Cosmochim. Acta, 165, 44–61.
competition. ISME J., 9, 139–149. Tang, J., Zhuang, L., Ma, J., Tang, Z., Yu, Z., and Zhou,
Schüler, D. (2004). Molecular analysis of a subcellu- S. (2016). Secondary mineralization of ferrihydrite
lar compartment: the magnetosome membrane in affects microbial methanogenesis in geobacter-
Magnetospirillum gryphiswaldense. Arch. Micro- methanosarcina cocultures. Appl. Environ. Micro-
biol., 181, 1–7. biol., 82, 5869–5877.
Segovia-Campos, I., Martignier, A., Filella, M., Jaquet, Taylor, C. D. and Wirsen, C. O. (1997). Microbiology
J.-M., and Ariztegui, D. (2021). Micropearls and and ecology of filamentous sulfur formation. Sci-
other intracellular inclusions of amorphous cal- ence, 277, 1483–1485.
cium carbonate: an unsuspected biomineraliza- Then, J. and Trüper, H. G. (1984). Utilization of sul-
tion capacity shared by diverse microorganisms. fide and elemental sulfur by Ectothiorhodospira
Environ. Microbiol. halochloris. Arch. Microbiol., 139, 295–298.
Sievert, S. M., Wieringa, E. B. A., Wirsen, C. O., and Tinbergen, N. (1963). On aims and methods of ethol-
Taylor, C. D. (2007). Growth and mechanism of ogy. Z. Tierpsychol., 20, 410–433.
filamentous-sulfur formation by Candidatus Ar- Tourney, J. and Ngwenya, B. T. (2009). Bacterial
cobacter sulfidicus in opposing oxygen-sulfide gra- extracellular polymeric substances (EPS) mediate
dients. Environ. Microbiol., 9, 271–276. CaCO3 morphology and polymorphism. Chem.
Smith, P. and Schuster, M. (2019). Public goods and Geol., 262, 138–146.
cheating in microbes. Curr. Biol., 29, R442–R447. Uebe, R. and Schüler, D. (2016). Magnetosome bio-
Stephens, C. (2006). Bacterial cell biology: managing genesis in magnetotactic bacteria. Nat. Rev. Micro-
magnetosomes. Curr. Biol., 16, R363–R365. biol., 14, 621–637.
Steudel, R. (1989). On the Nature of the “Elemen- Ullrich, S., Kube, M., Schübbe, S., Reinhardt, R.,
tal Sulfur” (S◦ ) Produced by Sulfur-oxidizing Bac- and Schüler, D. (2005). A hypervariable 130-
teria – a Model fror S◦ Globules. In Biology of Au- kilobase genomic region of Magnetospirillum
totrophic Bacteria, pages 289–303. Springer, Berlin, gryphiswaldense comprises a magnetosome island
Germany. which undergoes frequent rearrangements during
Steudel, R. (2003). Aqueous sulfur sols. In Steudel, stationary growth. J. Bacteriol., 187, 7176–7184.
R., editor, Elemental Sulfur and Sulfur-Rich Com- Urich, T., Gomes, C. M., Kletzin, A., and
pounds I, pages 153–166. Springer, Berlin, Ger- Frazão, C. (2006). X-ray structure of a self-
many. compartmentalizing sulfur cycle metalloenzyme.
Steudel, R. and Eckert, B. (2003). Solid sulfur al- Science, 311, 996–1000.
lotropes. In Steudel, R., editor, Elemental Sul- van Gemerden, H. (1986). Production of elemental
fur and Sulfur-Rich Compounds I, pages 1–80. sulfur by green and purple sulfur bacteria. Arch.
Springer, Berlin, Germany. Microbiol., 146, 52–56.
Steudel, R., Holdt, G., Göbel, T., and Hazeu, W. (1987). van Opijnen, T. and Camilli, A. (2013). Transposon
Chromatographic separation of higher polythion- insertion sequencing: a new tool for systems-level
ates SnO (n = 3. . . 22) and their detection in cultures analysis of microorganisms. Nat. Rev. Microbiol.,
of thiobacillus ferroxidans; molecular composition 11, 435–442.
of bacterial sulfur secretions. Angew. Chem. Int. Veis, A. (2003). Mineralization in organic matrix
Ed., 26, 151–153. frameworks. Rev. Mineral. Geochem., 54, 249–289.
Stotzky, G. and Rem, L. T. (1966). Influence of clay Vo, P. L. H., Ronda, C., Klompe, S. E., Chen, E. E.,
minerals on microorganisms. I. Montmorillonite Acree, C., Wang, H. H., and Sternberg, S. H. (2021).

C. R. Géoscience — 2022, 354, n 1, 1-39

 Julie Cosmidis and Karim Benzerara 39

CRISPR RNA-guided integrases for high-efficiency, V., Bagnell, R., and Nielsen, L. P. (2019). Intracel-
multiplexed bacterial genome engineering. Nat. lular calcite and sulfur dynamics of Achromatium
Biotechnol., 39, 480–489. cells observed in a lab-based enrichment and aero-
Warthmann, R., Cypionka, H., and Pfennig, N. (1992). bic incubation experiment. Antonie Leeuwenhoek,
Photoproduction of H2 from acetate by syn- 112, 263–274.
trophic cocultures of green sulfur bacteria and Yin, X., Weitzel, F., Jiménez-López, C., Griesshaber, E.,
sulfur-reducing bacteria. Arch. Microbiol., 157, Fernández-Díaz, L., Rodríguez-Navarro, A., Ziegler,
343–348. A., and Schmahl, W. W. (2020). Directing effect of
Wever, A. D., Benzerara, K., Coutaud, M., Caumes, G., bacterial extracellular polymeric substances (EPS)
Poinsot, M., Skouri-Panet, F., Laurent, T., Duprat, on calcite organization and EPS–carbonate com-
E., and Gugger, M. (2019). Evidence of high Ca up- posite aggregate formation. Cryst. Growth Des., 20,
take by cyanobacteria forming intracellular CaCO3 1467–1484.
and impact on their growth. Geobiology, 17, 676– Zeng, Y., Cao, J., Wang, Z., Guo, J., Zhou, Q., and Lu,
690. J. (2018). Insights into the confined crystallization
White, R. A., Chan, A. M., Gavelis, G. S., Leander, in microfluidics of amorphous calcium carbonate.
B. S., Brady, A. L., Slater, G. F., Lim, D. S. S., and Cryst. Growth Des., 18, 6538–6546.
Suttle, C. A. (2016). Metagenomic analysis suggests Zerkle, A. L., Kamyshny, A., Kump, L. R., Farquhar,
modern freshwater microbialites harbor a distinct J., Oduro, H., and Arthur, M. A. (2010). Sulfur cy-
core microbial community. Front. Microbiol., 6, cling in a stratified euxinic lake with moderately
article no. 1531. high sulfate: constraints from quadruple S iso-
Williams, R. J. P. and Rickaby, R. (2012). Evolution’s topes. Geochim. Cosmochim. Acta, 74, 4953–4970.
Destiny: Co-evolving Chemistry of the Environment Zhang, J., Liu, R., Xi, S., Cai, R., Zhang, X., and Sun,
and Life. Royal Society of Chemistry, London, UK. C. (2020). A novel bacterial thiosulfate oxidation
Wu, W., Swanner, E. D., Hao, L., Zeitvogel, F., Obst, M., pathway provides a new clue about the formation
Pan, Y., and Kappler, A. (2014). Characterization of zero-valent sulfur in deep sea. ISME J., 14, 2261–
of the physiology and cell–mineral interactions of 2274.
the marine anoxygenic phototrophic Fe(II) oxidizer Zopfi, J., Ferdelman, T. G., and Fossing, H. (2004).
Rhodovulum iodosum – implications for Precam- Distribution and fate of sulfur intermediates—
brian Fe(II) oxidation. FEMS Microbiol. Ecol., 88, sulfite, tetrathionate, thiosulfate, and elemental
503–515. sulfur—in marine sediments. In Special Paper 379:
Yang, T., Teske, A., Ambrose, W., Salman-Carvalho, Sulfur Biogeochemistry - Past and Present, pages
97–116. Geological Society of America, Boulder,
CO, USA.

C. R. Géoscience — 2022, 354, n 1, 1-39