Climate warming threatens Arctic permafrost with seasonal cycles of freezing and thawing. Arctic soil microorganisms regulate carbon stocks and greenhouse gas exchanges with the atmosphere, yet their precise seasonal growth and dormancy dynamics, and their responses to permafrost thaw, are not well understood. We thawed frozen Svalbard active layer soil and traced microbial growth using DNA quantitative stable isotope probing with H218O. We observed temporal growth patterns resulting in distinct early (21-day) and late-stage (98-day) growing microbial populations. In particular, Acidobacteriota, Actinobacteriota, Bacteroidota, Proteobacteria, and predatory and epibiont bacterial taxa (such as those affiliated to Bdellovibrionota and Patescibacteria) were identified in the soil active layer as clades that were growing following thawing. Methane concentrations in our microcosms remained low, yet pmoA genes were 18O-labeled, indicating growth of aerobic methane-oxidizing bacteria. Approximately half of the microbial taxa detected did not grow, suggesting that Arctic soils constitute sizeable reservoirs of dormant microorganisms. Our results reveal complex and temporal microbial dormancy, growth, death, predation, and parasitism dynamics in seasonally changing Arctic soils. These processes likely regulate the exchange and storage of soil carbon across the increasingly vulnerable Arctic region.IMPORTANCEMicroorganisms play key roles in transforming soil carbon into greenhouse gases. As Arctic soils warm as a result of climate change, greater depths and expanses of permanently frozen soil are experiencing seasonal thaw. Despite the importance of active soil microorganisms in transforming soil carbon, the seasonal freezing and thawing of Arctic soils and associated dormancy and re-activation of microbial populations are not well constrained. Here, we thawed and incubated active layer (i.e., seasonally thawing) Arctic soil with a stable isotope to directly label the DNA of growing soil microorganisms. We found that half of the microbial diversity did not grow after thaw and that some groups, including the Bacteroidota and predatory bacteria, grew disproportionately. The growing microbial community shifted over time, and bacteria capable of oxidizing methane grew more after prolonged thaw. These findings highlight that dormancy, predation, and variable growth dynamics are important factors determining ecological and biogeochemical processes in thawing Arctic soil.
We investigate patterns of phylogenetic selectivity of extinction in early aquatic vertebrates from the Silurian to the Carboniferous, an interval punctuated by one of the "Big Five" mass extinctions and marked by many critical anatomical (e.g., jaws, limbs) and ecological (e.g., macrophagy, terrestrialization) vertebrate evolutionary innovations. Using a new > 1300 taxon, formally inferred supertree, we show that phylogenetic extinction clustering in early vertebrates varied through time and between major ecomorphological divisions of the tree. At the end of the Silurian and into the Early Devonian, jawless fishes became marginalized components of vertebrate faunas and show more strongly clustered extinction than jawed fishes, which became ecologically dominant during this interval. Clustered extinction (contemporaneous extinction of close relatives) is typical of most stages of the Devonian, particularly during the Late Devonian extinctions. By contrast, the subsequent early Carboniferous interval of putative recovery is characterized by overdispersed extinction (contemporaneous extinction of distant relatives), consistent with widespread persistence of phylogenetically distinct lineages. This work shows how varying patterns of extinction selectivity pruned the vertebrate tree at the time when the first-order patterns of diversity apparent in modern aquatic vertebrate faunas were first established.
The greening of electronics remains a grand societal challenge, with no radical improvement within sight. Sustainable solutions for electronics, such as biobased and transient materials, are hence receiving growing attention. Presently, there are no biobased alternatives to conventional conductors such as metals and organic polymers, as their conductivity is too low. The discovery of cable bacteria, which are filamentous microorganisms capable of conducting electricity over centimeter-scale distances, has the potential to change this. In cable bacteria, conductivity occurs through thin wires embedded in the cell envelope, displaying conductivities comparable to those of the best highly doped organic polymers. However, exposure to ambient air leads to a gradual loss of their conductivity. To enhance stability, a bioderived protective coating could be useful, thus retaining a fully biobased system. To this end, we investigated pullulan, a polysaccharide polymer primarily used in food packaging that is known for its excellent oxygen-barrier properties. Cable bacterium filaments protected with a film derived from a 10 wt % pullulan solution exhibited a 10-fold increase in conduction stability under ambient conditions compared to uncoated controls. Reducing ambient moisture also preserved the long-term conductivity of the cable bacteria, even in the absence of a protective coating, indicating that humidity plays a critical role in conductance deterioration. Our findings provide an important step toward further technological implementation of the highly conductive wires of cable bacteria and offer practical guidelines for developing biobased coatings for O2-sensitive materials in electronics, thus contributing to the advancement of next-generation green technologies.
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Antimicrobial resistance studies have focused on clinical bacteria, neglecting the role of resistant isolates in natural environments. However, oceans are daily contaminated with high loads of antimicrobials and resistant bacteria from agro-industrial and urban activities. Deep-sea sediment is a challenging environment that may select microbial strains with resistance to chemicals and ability to form biofilms, becoming a potential reservoir of resistance genes. We evaluated the susceptibility to antimicrobials of six Pseudomonas sp., five Bacillus sp., two Brevibacillus sp. and two Paenibacillus sp. from deep-sea sediments of the Pelotas Basin (Brazil) by the disk diffusion and microdilution tests. Pseudomonas and Bacillales were tested against 11 and 7 antimicrobials, respectively. Biofilms of susceptible isolates were exposed to antimicrobials to determine the minimum biofilm inhibitory concentration (MBIC) and the minimum biofilm eradication concentration (MBEC). All Pseudomonas were resistant to aztreonam at very high concentrations (up to 2048 μg/mL). MBIC values were significantly higher than respective MICs, and only one third of biofilms were eradicated. These results underscore the importance of the study, as one of the first reporting antimicrobial tolerance of biofilms of cultivable bacteria from deep-sea sediments, contributing to the knowledge of bacterial resistance in these environments, concerning One Health issues.
The rate of evolution of a single morphological character is not homogeneous across the phylogeny and this rate heterogeneity varies between morphological characters. However, traditional models of morphological character evolution often assume that all characters evolve according to a time-homogeneous Markov process, which applies uniformly across the entire phylogeny. While models incorporating among-character rate variation alleviate the assumption of the same rate for all characters, they still fail to address lineage-specific rate variation for individual characters. The covarion model, originally developed for molecular data to model the invariability of some sites for parts of the phylogeny, provides a promising framework for addressing this issue in morphological phylogenetics. In this study, we extend the covarion model in RevBayes to morphological character evolution, which we call the covariomorph model, and apply it to a diverse range of morphological datasets. Our covariomorph model utilizes multiple rate categories derived from a discretized probability distribution, which scales rate matrices accordingly. Characters are allowed to evolve within any of these rate categories, with the possibility of switching between rate categories during the evolutionary process. We verified our implementation of the covariomorph model with the help of simulations. Additionally, we examined 164 empirical datasets, finding patterns of rate heterogeneity compatible with covarion-like dynamics in approximately half of them. Upon further examination of two focal datasets that exhibited covarion-like rate variation, we found that the covariomorph model provides a more nuanced approach to incorporate rate variation across lineages, significantly affecting the resulting tree topology and branch lengths compared to traditional models. The observed sensitivity of branch lengths to model choice underscores potential implications of this approach for divergence time estimation and evolutionary rate calculations. By accounting for lineage- and character-specific rate shifts, the covariomorph model offers a robust framework to improve the accuracy of morphological phylogenetic inference.
Demosponge classification is notoriously challenged by the paucity of informative morphological characters with sufficient complexity to discriminate between apomorphies and convergences. Molecular data, preferably from type material, helps shed light on phylogenetic relationships. In the following, we review, based on the results of DNA barcoding of type (and other) material, the classification of several demosponge species and genera with either eminent or previously uncertain classification. We report that the aster-bearing genus Leptosastra Topsent, 1904, is a poecilosclerid, unlike Clathria faviformis Lehnert & van Soest, 1996, which should be classified as Raspailiidae. The genus transfers of Eurypon laughlini Díaz, Alvarez & van Soest, 1987 to Prosuberites Topsent, and Leucophloeus lewisi Van Soest & Stentoft, 1988, to Axinyssa Lendenfeld are supported, unlike the transfer of Halichondria almae (Carballo, Uriz & García-Gómez, 1996) from Ciocalapata de Laubenfels. The new sequences are the first to be published in the new version of the Sponge Barcoding Database (SBDv2) of the Sponge Barcoding Project (www.spongebarcoding.org). Our findings underline the benefits of sequencing historic reference material, even if it is centuries old, and emphasises that type material should always be considered in answering systematic questions, particularly with challenging taxa such as sponges.
The nitrogen metabolism genes and associated microorganisms in polar oceans and hydrothermal vents remain insufficiently studied. In this study, metagenomic data were analyzed to characterize the geographical and biological features of 16 key nitrogen-cycling genes. NasA/B, narG, and nxrB were consistently abundant in both environments. Polar oceans were dominated by common nitrogen-cycling taxa, whereas hydrothermal vents hosted species linked to sulfur and methane metabolism. Environmental extremes exerted a stronger influence on nitrogen cycling than depth. Distinct co-occurrence networks (centralized vs. redundant) and accurate habitat classification (>95 %) highlighted strong environmental shaping. Differences in amino acid preferences and enzyme thermal stability reflected evolutionary divergence and adaptation to extreme temperatures. Overall, depth and environmental conditions structured community networks, while genetic variation supported ecological adaptation. These findings reveal contrasting nitrogen-cycling strategies and adaptations, with potential implications for biotechnological applications.
Microbially mediated manganese (Mn) oxidation is a key process in the biogeochemical cycling of Mn. While Shewanella is widely recognized for its metal-reducing capabilities, recent studies have shown that certain terrestrial strains can also oxidize Mn2+ during aerobic respiration. Nevertheless, the Mn2+-oxidizing capacity of marine Shewanella strains, which are ubiquitous in oceanic settings, has remained largely unexplored, and the influence of environmental factors on this capacity has not been systematically evaluated. Here, we investigated the ability of the deep-sea bacterium S. piezotolerans WP3 to oxidize Mn2+ under aerobic conditions and examined the effects of temperature (4°C-20°C) and hydrostatic pressure (0.1-20 MPa). We found that S. piezotolerans WP3 efficiently oxidizes Mn2+ to Mn oxides, predominantly forming bixbyite-like minerals and amorphous mixed-valence nanoparticles. This oxidation process was not attributable to a Mn2+-specific enzyme but to bacterially generated reactive oxygen species (ROS), with superoxide (O2 •-) playing the primary role. Both temperature and hydrostatic pressure significantly affected the final extent of Mn2+ oxidation by altering the production of O2 •-. Transcriptomic analysis revealed that exposure to high hydrostatic pressure induced the upregulation of genes involved in antioxidative stress, which likely accounts for the enhanced ROS-mediated Mn2+ oxidation observed in cultures incubated at 20 MPa. Under alternating aerobic and anaerobic conditions, strain WP3 mediated successive Mn oxidation and reduction, ultimately forming rhodochrosite as a secondary mineral. These results suggest that S. piezotolerans WP3 has the potential to mediate Mn redox cycling in marine sediments, coupling ROS-dependent oxidation with anaerobic Mn reduction.
The history of Earth's atmospheric oxygen is a cornerstone of evolutionary biology. While unequivocal evidence for an increase in atmospheric O2 marks the Great Oxidation Event (GOE) roughly 2.4 billion years ago, evidence underlying proposals for pre-GOE O2 accumulation is debated. Here we have investigated the distribution of genes for oxygen reductases, the enzymes that consume O2 in respiratory chains, across independently generated molecular timescales of prokaryotic evolution. The data indicate that cytochrome bd-oxidases, heme-copper oxidases and alternative oxidases arose in the wake of the GOE ca. 2.4 billion years ago, after which the genes were subjected to abundant lateral gene transfer, a reflection of their utility in redox balance and membrane bioenergetics. The data lead us to propose a straightforward four-stage model for O2 accumulation surrounding the GOE: (i) Negligible O2 existed prior to the GOE. (ii) Cyanobacterial O2 production started at the GOE, yet was capped at 2 % [v/v] atmospheric O2, the threshold at which cyanobacterial nitrogenase is inhibited by O2. (iii) Production of 0.02 atm of O2 (2 % [v/v]) at the GOE buried roughly the entire atmospheric CO2 inventory, causing sudden enrichment of 13C in dissolved inorganic carbon (the Lomagundi 13C anomaly), through RuBisCO isotope discrimination, without atmospheric O2 exceeding 2 % [v/v]. (iv) High atmospheric 12C at the end of the Lomagundi excursion marks the origin of oxygen reductases, their rapid spread via function in respiratory CO2 liberation, and the onset of equilibrium between photosynthetic O2 production and respiratory O2 consumption at 2 % atmospheric O2.
Sponges harbor complex and diverse microbiomes that contribute to the host's fitness and, ultimately, the health of the ecosystems sponges inhabit. Using high-throughput 16S and 18S rRNA amplicon sequencing, we explore the prokaryotic and eukaryotic communities associated with three sympatric Mediterranean demosponges, namely Tethya aurantium, Tethya meloni, and Tethya citrina. We found species-specific prokaryotic and eukaryotic communities despite the close sympatry of the three Mediterranean Tethya species studied. This offers further support for the phylogenetic nature of the sponge microbiome, where microbial communities reflect the evolutionary ancestry of their host species. These patterns are both present in the eukaryotic and prokaryotic sponge-associated communities, since both display similar levels of host species specificity.
We present a genome assembly from a specimen of Phakellia ventilabrum (Porifera; Demospongiae; Bubarida; Bubaridae). The genome sequence has a total length of 211.92 megabases. Most of the assembly (99.97%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.36 kilobases in length. Gene annotation of this assembly by Ensembl identified 21 622 protein-coding genes. Thirty-three binned genomes were generated from the metagenome assembly, of which eight were classified as high-quality metagenome assembled genomes (MAGs) and of which four of the MAGs are fully circular. The MAGs were taxonomically assigned to Pseudomonadota (i.e. Candidatus Poriferihabitaceae), Nitrospirota, Nitrospinota, and the archaeal Nitrosopumilus clade.
BACKGROUND: Cable bacteria are filamentous, sulphur-oxidizing microorganisms of the Desulfobulbaceae family that conduct electrons over centimetre-scale distances, coupling sulphide oxidation in deeper sediments to oxygen reduction near the surface. Geochemical evidence demonstrates high rates of aerobic sulphide oxidation in sediments inhabited by cable bacteria. Still, the underlying physiological and molecular basis of this electrogenic sulphur metabolism remains unresolved. Previous genomic analysis proposed that cable bacteria oxidize sulphide by reversing the canonical dissimilatory sulphite reduction (Dsr) pathway. RESULTS: We evaluated the sulphur metabolism of cable bacteria and related Desulfobulbales through comparative genomics, using an expanded set of 31 quality-filtered cable bacteria genomes, including 7 closed assemblies. We showed that cable bacteria encode a complete Dsr pathway, including the previously missing dsrD and dsrT genes, as well as a novel gene cluster with DsrOP homologues. All Dsr genes were classified as reductive-type, and phylogenetic analyses indicated a close affiliation with those of other Desulfobulbaceae (sulphate-reducing and/or sulphur-disproportionating bacteria). In addition, several other previously unrecognized sulphur-metabolism genes were identified in both cable bacteria and closely related Desulfobulbales, including a novel subtype of sulphide:quinone oxidoreductase (SQR), a putative rhodanese–persulphide dioxygenase fusion (Rho–PDO), and a YTD gene cluster (consisting of five genes) previously proposed to be characteristic of sulphur-disproportionation lineages. Structural predictions indicate that three uncharacterized YTD-encoded proteins assemble into a DsrEFH-like double heterotrimer, albeit with highly divergent, non-orthologous sequences. Finally, we integrated publicly available transcriptomic and proteomic data to confirm the in vivo expression of these genes, with expression patterns mirroring those of Desulfolithobacter dissulfuricans and Desulfurivibrio alkaliphilus. CONCLUSION: Cable bacteria show minimal genetic divergence and little differential expression in their sulphur-metabolism genes compared to related organisms. Together, our findings challenge the idea that sulphide oxidation occurs via a reversed Dsr pathway. We propose a unique sulphur metabolism model for cable bacteria, in which a canonical reductive/disproportionating sulphur-metabolism repertoire (similar to Desulfolithobacter dissulfuricans and Desulfurivibrio alkaliphilus) is coupled to net sulphide oxidation through long-distance electron transport. Key steps include sulphide oxidation to polysulphide by SQR, putative conversion to sulphite via Rho–PDO and/or proteins encoded in the YTD cluster, and subsequent disproportionation through the Dsr pathway, where sulphide re-enters the cycle. Net sulphide oxidation and sulphate production arise because electrons are efficiently drained via long-distance electron transport, effectively coupling the metabolism to oxygen reduction.
Microorganisms have profoundly shaped Earth's biological and geological history, from the origins of oxygenic photosynthesis to present-day global biogeochemical cycles. Metagenomics-through its ability to recover genomic information directly from environmental samples-has revolutionized our understanding of microbial evolution by uncovering unbeknownst lineages, revealing functional adaptations, and reshaping our view of the Tree of Life. By bypassing the need for cultivation, shotgun metagenomics and metabarcoding approaches have enabled researchers to investigate microbial diversity, ecology, and evolutionary processes across aquatic, terrestrial, extreme, and host-associated environments. This review highlights recent advances in evolutionary biology driven by metagenomics, including studies on deep evolutionary branching events, microbial adaptation to extreme environments, the evolution of host-associated microbiomes, and the emergence and spread of pathogens and antimicrobial resistance. The integration of ancient DNA has expanded our ability to reconstruct past ecosystems and disease dynamics, offering insights into long-term microbial evolution. In parallel, studies of microbial domestication and urban settings reveal how human practices have shaped microbial genomes over millennia. Despite significant progress, key challenges remain-including improving bioinformatic tools for degraded ancient DNA, resolving deep phylogenetic relationships, identifying adaptive variants, and linking genomic shifts to ecosystem-level processes. The future of microbial evolutionary research will depend on combining longitudinal metagenomic data, experimental evolution, functional assays, and predictive modeling to better understand microbial responses to climate change and anthropogenic pressures. Together, these approaches will deepen our understanding of microbial evolution and its consequences for life on Earth-past, present, and future.
The Ediacaran-Cambrian boundary, which precedes one of the most significant biotic diversification events in Earth's history, is associated with a global negative carbon isotope excursion termed the BAsal Cambrian carbon isotope Excursion (BACE). Late Ediacaran and early Cambrian changes in shallow marine oxygenation have been proposed to relate to the BACE as well as metazoan extinction and radiation. However, reconstructing paleoredox conditions at the Ediacaran-Cambrian boundary is limited by challenges in correlating carbonate strata due to sparse stratigraphic markers and non-unique chemostratigraphic correlations. These imprecise correlations have led to uncertainty in how redox changes across the BACE should be interpreted in relation to broader regional and global environmental patterns. Here, we present redox reconstructions from southwestern Laurentian carbonate successions that record the BACE, including the limestone-dominated Deep Spring Formation, southwestern USA, and the dolostone-dominated La Ciénega Formation, northern Mexico. We combine local (carbonate-bound iodine, I/(Ca + Mg) and cerium anomaly, Ce/Ce*) and global (carbonate-associated uranium isotopes, δ238Ucarb) redox proxies to investigate marine oxygenation in relation to the BACE. Contrary to previous suggestions that a global ocean oxygenation event coincided with the BACE, we do not observe a shift in δ238Ucarb concurrent with the carbon isotope excursion in either section. The δ238Ucarb values differ between two sections, likely reflecting distinct diagenetic offsets attributed to different diagenetic U reduction, but together provide a minimal constraint on the carbonate δ238U value and suggest a more anoxic ocean compared to today. The local proxy results at both sites suggest widespread low-oxygen surface waters with a transient and localized interval of shallow marine oxygenation at one site that coincides with the nadir of the BACE. Persistently low I/(Ca + Mg) ratios, below values observed in today's oxygenated oceans, suggest a broadly redox-stratified surface ocean. Negative Ce anomalies in the La Ciénega Formation were recorded during the BACE nadir, suggesting a short-lived interval of local oxygenation within otherwise low-oxygen conditions. In sum, we do not find evidence for major, widespread oxygenation coincident with the BACE, but a continuation of low-oxygen conditions punctuated by a short-lived oxygenation event in the shallow oceans. These brief fluctuations in oxygen levels, in turn, may have played a role in the onset of behavioral complexity among bilaterian invertebrates during this critical transition.
Phylogenetic comparative methods are a major tool for evaluating macroevolutionary hypotheses. Methods based on the mean-reverting stochastic Ornstein-Uhlenbeck process allow for modelling adaptation on a phenotypic adaptive landscape that itself evolves and where fitness peaks depend on measured characteristics of the external environment and/or other organismal traits. Here, we give an overview of the conceptual framework for the many implementations of these methods and discuss how we might interpret estimated parameters. We emphasize that the ability to model a changing adaptive landscape sets these methods apart from other approaches and discuss why this aspect captures long-term trait evolution more realistically. Recent multivariate extensions of these methods provide a powerful framework for testing evolutionary hypotheses but are also more complicated to use and interpret. We provide some guidance on their usage and put recent literature on the topic in biological rather than mathematical terms. We further show how these methods provide a starting point for modelling reciprocal selection (i.e., coevolution) between interacting lineages. We then briefly review some critiques of the methodologies. Finally, we provide some ideas for future developments that we think will be useful to evolutionary biologists.
Continuous characters have received comparatively little attention in Bayesian phylogenetic estimation. This is predominantly because they cannot be modeled by a standard phylogenetic Q-matrix approach due to their non-discrete nature. In this paper, we explore the use of continuous traits under two Brownian motion models to estimate a phylogenetic tree for Dicynodontia, a well-studied group of early synapsids (stem mammals) in which both discrete and continuous characters have been extensively used in parsimony-based tree reconstruction. We examine the differences in phylogenetic signal between a continuous trait partition, a discrete trait partition, and a joint analysis with both types of characters. We find that continuous and discrete traits contribute substantially different signal to the analysis, even when other parts of the model (clock and tree) are held constant. Tree topologies resulting from the new analyses differ strongly from the established phylogeny for dicynodonts, highlighting continued difficulty in incorporating truly continuous data in a Bayesian phylogenetic framework.
Strong disparity in species richness among organisms is well documented, but heterogeneity in the underlying diversification process is less understood. Using novel probabilistic methods, we investigate clade-specific diversification rate shifts in several species-rich phylogenies, together representing over 300,000 species across the Tree of Life. We find that diversification rate shifts are extremely prevalent across all clades, with more frequent changes in younger clades and an overall excess of upshifts, resulting in an apparent acceleration of net diversification rates. We also reveal that heterogeneity in diversification rates is related to the tempo of diversification itself. While we find support for more prevalent shifts in speciation rates than extinction rates and more upshifts than downshifts, this is partially due to data insufficiency and inference challenges. Our insights are fundamentally enabled by studying numerous large phylogenies with rigorous statistical methods, showing widespread prevalence of diversification rate shifts across the Tree of Life.
Time-calibrating a phylogenetic tree is a fundamental step in phylogenetic inference, as it allows the study of macroevolutionary processes such as lineage diversification, trait evolution and historical biogeography. To this end, the fossilized birth-death (FBD) process, a stochastic process that coherently integrates fossils into phylogenies, is increasingly used as an alternative to traditional ad hoc node-calibration densities. However, the effective prior distribution on node ages induced by the FBD has never been investigated before, hindering an informed choice between the two approaches. Here, we analyse two empirical datasets (crocodylians and fireflies) by applying several models of time-calibration, including traditional node calibrations and FBD. We show that the effective node age priors induced by the FBD process in the absence of morphological data are comparable to those induced by flat node calibrations when only the oldest fossil occurrence per calibrated clade is included in the FBD analysis. However, effective node age priors become more informative when several fossil occurrences per calibrated clade are included. Our exploration sheds light on how palaeontological information is translated to node ages by the FBD process, and suggests that node calibration approaches remain an important alternative when the fossil record of the studied group is scarce and other prior information can be used to devise informative calibration densities.
Sulfate-reducing bacteria (SRB) drive the process of sulfate reduction in low-temperature sedimentary environments. Through the production of sulfide, they promote the formation of iron-sulfide (Fe-S) minerals when Fe(II) is available. The negative charge of the cell surface of bacteria can promote the binding of Fe(II), leading to the precipitation of Fe-S minerals at the surface of SRB when sulfide is released from cells. We evaluated interactions between Fe-S minerals and the surface of SRB using transmission electron microscopy (TEM) in cultures of Maridesulfovibrio hydrothermalis AM13 grown with 4 mM of Fe(II) over 1 month of incubation. On average, 18% ± 10% of cells were encrusted in cultures collected during the exponential phase. Fe-S mineral deposition occurred at the surface of cells while cells were growing and producing sulfide in the presence of Fe(II), but mineral crusts were removed from most cells shortly after deposition. Cells removed crusts from their surface through the formation of membrane vesicles, which were apparently only produced during growth. Mineralized and non-mineralized membrane vesicles were preserved in mineral aggregates in stationary-phase cultures. On average, 17% ± 7% of cells were encrusted in cultures collected during the stationary phase, indicating that Fe-S minerals precipitated during the exponential phase and removed from the cell surface did not aggregate back onto cells. On the contrary, they formed large aggregates away from cells. When Fe-S mineral precipitation occurred in non-growing cell suspensions that were first exposed to Fe(II) then to sulfide, the proportion of encrusted cells increased to 95% ± 6%, indicating that resting or non-growing cells were not able to remove mineral crusts from their surface. The metabolic status of SRB therefore plays a role in their ability to escape Fe-S mineral entombment.