In-situincubation of iron-sulfur mineral reveals a diverse chemolithoautotrophic community and a new biogeochemical role forThiomicrospira

Sulfur cycling likely obscures dynamic biologically-driven iron redox cycling in contemporary methane seep environments

Deep-sea methane seeps are amongst the most biologically productive environments on Earth and are often characterised by stable, low oxygen concentrations and microbial communities that couple the anaerobic oxidation of methane to sulfate reduction or iron reduction in the underlying sediment. At these sites, ferrous iron (Fe2+) can be produced by organoclastic iron reduction, methanotrophic-coupled iron reduction, or through the abiotic reduction by sulfide produced by the abundant sulfate-reducing bacteria at these sites. The prevalence of Fe2+in the anoxic sediments, as well as the availability of oxygen in the overlying water, suggests that seeps could also harbour communities of iron-oxidising microbes. However, it is unclear to what extent Fe2+ remains bioavailable and in solution given that the abiotic reaction between sulfide and ferrous iron is often assumed to scavenge all ferrous iron as insoluble iron sulfides and pyrite. Accordingly, we searched the sea floor at methane seeps along the Cascadia Margin for microaerobic, neutrophilic iron-oxidising bacteria, operating under the reasoning that if iron-oxidising bacteria could be isolated from these environments, it could indicate that porewater Fe2+ can persist is long enough for biology to outcompete pyritisation. We found that the presence of sulfate in our enrichment media muted any obvious microbially-driven iron oxidation with most iron being precipitated as iron sulfides. Transfer of enrichment cultures to sulfate-depleted media led to dynamic iron redox cycling relative to abiotic controls and sulfate-containing cultures, and demonstrated the capacity for biogenic iron (oxyhydr)oxides from a methane seep-derived community. 16S rRNA analyses revealed that removing sulfate drastically reduced the diversity of enrichment cultures and caused a general shift from a Gammaproteobacteria-domainated ecosystem to one dominated by Rhodobacteraceae (Alphaproteobacteria). Our data suggest that, in most cases, sulfur cycling may restrict the biological "ferrous wheel" in contemporary environments through a combination of the sulfur-adapted sediment-dwelling ecosystems and the abiotic reactions they influence.

To live or die: "Fine-tuning" adaptation revealed by systemic analyses in symbiotic bathymodiolin mussels from diverse deep-sea extreme ecosystems

Hydrothermal vents (HVs) and cold seeps (CSs) are typical deep-sea extreme ecosystems with their own geochemical characteristics to supply the unique living conditions for local communities. Once HVs or CSs stop emission, the dramatic environmental change would pose survival risks to deep-sea organisms. Up to now, limited knowledge has been available to understand the biological responses and adaptive strategy to the extreme environments and their transition from active to extinct stage, mainly due to the technical difficulties and lack of representative organisms. In this study, bathymodiolin mussels, the dominant and successful species surviving in diverse deep-sea extreme ecosystems, were collected from active and extinct HVs (Southwest Indian Ocean) or CSs (South China Sea) via two individual cruises. The transcriptomic analysis and determination of multiple biological indexes in stress defense and metabolic systems were conducted in both gills and digestive glands of mussels, together with the metagenomic analysis of symbionts in mussels. The results revealed the ecosystem- and tissue-specific transcriptional regulation in mussels, addressing the autologous adaptations in antioxidant defense, energy utilization and key compounds (i.e. sulfur) metabolism. In detail, the successful antioxidant defense contributed to conquering the oxidative stress induced during the unavoidable metabolism of xenobiotics commonly existing in the extreme ecosystems; changes in metabolic rate functioned to handle toxic matters in different surroundings; upregulated gene expression of sulfide:quinone oxidoreductase indicated an active sulfide detoxification in mussels from HVs and active stage of HVs & CSs. Coordinately, a heterologous adaptation, characterized by the functional compensation between symbionts and mussels in energy utilization, sulfur and carbon metabolism, was also evidenced by the bacterial metagenomic analysis. Taken together, a new insight was proposed that symbiotic bathymodiolin mussels would develop a "finetuning" strategy combining the autologous and heterologous regulations to fulfill the efficient and effective adaptations for successful survival.

Linking Zetaproteobacterial diversity and substratum type in iron-rich microbial mats from the Lucky Strike hydrothermal field (EMSO-Azores observatory)

Zetaproteobacteria have been reported in different marine and terrestrial environments all over the globe. They play an essential role in marine iron-rich microbial mats, as one of their autotrophic primary producers, oxidizing Fe(II) and producing Fe-oxyhydroxides with different morphologies. Here, we study and compare the Zetaproteobacterial communities of iron-rich microbial mats from six different sites of the Lucky Strike Hydrothermal Field through the use of the Zetaproteobacterial operational taxonomic unit (ZetaOTU) classification. We report for the first time the Zetaproteobacterial core microbiome of these iron-rich microbial mats, which is composed of four ZetaOTUs that are cosmopolitan and essential for the development of the mats. The study of the presence and abundance of different ZetaOTUs among sites reveals two clusters, which are related to the lithology and permeability of the substratum on which they develop. The Zetaproteobacterial communities of cluster 1 are characteristic of poorly permeable substrata, with little evidence of diffuse venting, while those of cluster 2 develop on hydrothermal slabs or deposits that allow the percolation and outflow of diffuse hydrothermal fluids. In addition, two NewZetaOTUs 1 and 2 were identified, which could be characteristic of anthropic iron and unsedimented basalt, respectively. We also report significant correlations between the abundance of certain ZetaOTUs and that of iron oxide morphologies, indicating that their formation could be taxonomically and/or environmentally driven. We identified a new morphology of Fe(III)-oxyhydroxides that we named "corals." Overall, our work contributes to the knowledge of the biogeography of this bacterial class by providing additional data from the Atlantic Ocean, a lesser-studied ocean in terms of Zetaproteobacterial diversity.IMPORTANCEUp until now, Zetaproteobacterial diversity studies have revealed possible links between Zetaproteobacteria taxa, habitats, and niches. Here, we report for the first time the Zetaproteobacterial core microbiome of iron-rich mats from the Lucky Strike Hydrothermal Field (LSHF), as well as two new Zetaproteobacterial operational taxonomic units (NewZetaOTUs) that could be substratum specific. We highlight that the substratum on which iron-rich microbial mats develop, especially because of its permeability to diffuse hydrothermal venting, has an influence on their Zetaproteobacterial communities. Moreover, our work adds to the knowledge of the biogeography of this bacterial class by providing additional data from the hydrothermal vent sites along the Mid-Atlantic Ridge. In addition to the already described iron oxide morphologies, we identify in our iron-rich mats a new morphology that we named corals. Finally, we argue for significant correlations between the relative abundance of certain ZetaOTUs and that of iron oxide morphologies, contributing to the understanding of the drivers of iron oxide production in iron-oxidizing bacteria.

Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field

IMPORTANCE

Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron- and hydrogen-oxidizing Zetaproteobacteria representative belonging to Zetaproteobacteria operational taxonomic unit 9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.

Aerobic iron-oxidizing bacteria secrete metabolites that markedly impede abiotic iron oxidation

Iron is one of the Earth's most abundant elements and is required for essentially all forms of life. Yet, iron's reactivity with oxygen and poor solubility in its oxidized form (Fe3+) mean that it is often a limiting nutrient in oxic, near-neutral pH environments like Earth's ocean. In addition to being a vital nutrient, there is a diversity of aerobic organisms that oxidize ferrous iron (Fe2+) to harness energy for growth and biosynthesis. Accordingly, these organisms rely on access to co-existing Fe2+ and O2 to survive. It is generally presumed that such aerobic iron-oxidizing bacteria (FeOB) are relegated to low-oxygen regimes where abiotic iron oxidation rates are slower, yet some FeOB live in higher oxygen environments where they cannot rely on lower oxygen concentrations to overcome abiotic competition. We hypothesized that FeOB chemically alter their environment to limit abiotic interactions between Fe2+ and O2. To test this, we incubated the secreted metabolites (collectively known as the exometabolome) of the deep-sea iron- and hydrogen-oxidizing bacterium Ghiorsea bivora TAG-1 with ferrous iron and oxygen. We found that this FeOB's iron-oxidizing exometabolome markedly impedes the abiotic oxidation of ferrous iron, increasing the half-life of Fe2+ 100-fold from ∼3 to ∼335 days in the presence of O2, while the exometabolome of TAG-1 grown on hydrogen had no effect. Moreover, the few precipitates that formed in the presence of TAG-1's iron-oxidizing exometabolome were poorly crystalline, compared with the abundant iron particles that mineralized in the absence of abiotic controls. We offer an initial exploration of TAG-1's iron-oxidizing exometabolome and discuss potential key contributors to this process. Overall, our findings demonstrate that the exometabolome as a whole leads to a sustained accumulation of ferrous iron in the presence of oxygen, consequently altering the redox equilibrium. This previously unknown adaptation likely enables these microorganisms to persist in an iron-oxidizing and iron-precipitating world and could have impacts on the bioavailability of iron to FeOB and other life in iron-limiting environments.

Metagenomic Features Characterized with Microbial Iron Oxidoreduction and Mineral Interaction in Southwest Indian Ridge

The Southwest Indian Ridge (SWIR) is one of the typical representatives of deep-sea ultraslow-spreading ridges, and has increasingly become a hot spot of studying subsurface geological activities and deep-sea mining management. However, the understanding of microbial activities is still limited on active hydrothermal vent chimneys in SWIR. In this study, samples from an active black smoker and a diffuse vent located in the Longqi hydrothermal region were collected for deep metagenomic sequencing, which yielded approximately 290 GB clean data and 295 mid-to-high-quality metagenome-assembled genomes (MAGs). Sulfur oxidation conducted by a variety of Gammaproteobacteria, Alphaproteobacteria, and Campylobacterota was presumed to be the major energy source for chemosynthesis in Longqi hydrothermal vents. Diverse iron-related microorganisms were recovered, including iron-oxidizing Zetaproteobacteria, iron-reducing Deferrisoma, and magnetotactic bacterium. Twenty-two bacterial MAGs from 12 uncultured phyla harbored iron oxidase Cyc2 homologs and enzymes for organic carbon degradation, indicated novel chemolithoheterotrophic iron-oxidizing bacteria that affected iron biogeochemistry in hydrothermal vents. Meanwhile, potential interactions between microbial communities and chimney minerals were emphasized as enriched metabolic potential of siderophore transportation, and extracellular electron transfer functioned by multi-heme proteins was discovered. Composition of chimney minerals probably affected microbial iron metabolic potential, as pyrrhotite might provide more available iron for microbial communities. Collectively, this study provides novel insights into microbial activities and potential mineral-microorganism interactions in hydrothermal vents. IMPORTANCE Microbial activities and interactions with minerals and venting fluid in active hydrothermal vents remain unclear in the ultraslow-spreading SWIR (Southwest Indian Ridge). Understanding about how minerals influence microbial metabolism is currently limited given the obstacles in cultivating microorganisms with sulfur or iron oxidoreduction functions. Here, comprehensive descriptions on microbial composition and metabolic profile on 2 hydrothermal vents in SWIR were obtained based on cultivation-free metagenome sequencing. In particular, autotrophic sulfur oxidation supported by minerals was presumed, emphasizing the role of chimney minerals in supporting chemosynthesis. Presence of novel heterotrophic iron-oxidizing bacteria was also indicated, suggesting overlooked biogeochemical pathways directed by microorganisms that connected sulfide mineral dissolution and organic carbon degradation in hydrothermal vents. Our findings offer novel insights into microbial function and biotic interactions on minerals in ultraslow-spreading ridges.

Conservation of Energetic Pathways for Electroautotrophy in the Uncultivated Candidate Order Tenderiales

Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb₃ oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO₂ fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.

Niche differentiation of sulfur-oxidizing bacteria (SUP05) in submarine hydrothermal plumes

Hydrothermal plumes transport reduced chemical species and metals into the open ocean. Despite their considerable spatial scale and impact on biogeochemical cycles, niche differentiation of abundant microbial clades is poorly understood. Here, we analyzed the microbial ecology of two bathy- (Brothers volcano; BrV-cone and northwest caldera; NWC) and a mesopelagic (Macauley volcano; McV) plumes on the Kermadec intra-oceanic arc in the South Pacific Ocean. The microbial community structure, determined by a combination of 16S rRNA gene, fluorescence in situ hybridization and metagenome analysis, was similar to the communities observed in other sulfur-rich plumes. This includes a dominance of the vent characteristic SUP05 clade (up to 22% in McV and 51% in BrV). In each of the three plumes analyzed, the community was dominated by a different yet uncultivated chemoautotrophic SUP05 species, here, provisionally named, Candidatus Thioglobus vadi (McV), Candidatus Thioglobus vulcanius (BrV-cone) and Candidatus Thioglobus plumae (BrV-NWC). Statistical analyses, genomic potential and mRNA expression profiles suggested a SUP05 niche partitioning based on sulfide and iron concentration as well as water depth. A fourth SUP05 species was present at low frequency throughout investigated plume samples and may be capable of heterotrophic or mixotrophic growth. Taken together, we propose that small variations in environmental parameters and depth drive SUP05 niche partitioning in hydrothermal plumes.

Pseudemcibacter aquimaris gen. nov., sp. nov., isolated from an aquaculture farm

A rod-shaped, Gram-stain-negative, aerobic and non-motile bacterium, designated strain Y4T, was isolated from an aquaculture farm in Xiamen, PR China. Strain Y4T had 94.8, 93.3 and 91.8 % 16S rRNA gene sequence similarity to Paremcibacter congregatus ZYLT, Emcibacter nanhaiensis HTCJW17T and Luteithermobacter gelatinilyticus MEBiC09520T, respectively. The genomic DNA G+C content of strain Y4T was 42.7 mol%. The average amino acid identity and percentage of conserved proteins values between strain Y4T and type strains of the family Emcibacteraceae were 57.9–58.6 % and 44.5–47.6 %, respectively. Optimal growth was observed at 28 °C, at pH 7.0 and with 2 % (w/v) NaCl. The novel strain Y4T required Ca2+, K+ and Mg2+ ions in addition to NaCl for growth. The dominant fatty acids of strain Y4T were summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c), summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c) and C14 : 0 2-OH. The polar lipid profile contained phosphatidylethanolamine, phosphatidyglycerol, three unidentified aminolipids, four unidentified aminophospholipids and two unidentified lipids. Cells contained exclusively ubiquinone Q-10. On the basis of the polyphasic analysis, strain Y4T (=MCCC 1K06278T=KCTC 82926T) is considered to represent a novel species in a novel genus of the family Emcibacteraceae , for which the name Pseudemcibacter aquimaris gen. nov., sp. nov. is proposed.

Thiomicrorhabdus heinhorstiae sp. nov. and Thiomicrorhabdus cannonii sp. nov.: novel sulphur-oxidizing chemolithoautotrophs isolated from the chemocline of Hospital Hole, an anchialine sinkhole in Spring Hill, Florida, USA

Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anchialine sinkhole located within the Weeki Wachee River of Florida. Gram-stain-negative cells of both strains were motile, chemotactic rods. Phylogenetic analysis of the 16S rRNA gene and predicted amino acid sequences of ribosomal proteins, average nucleotide identities, and alignment fractions suggest the strains HH1^T and HH3^T represent novel species belonging to the genus Thiomicrorhabdus. The genome G+C fraction of HH1^T is 47.8 mol% with a genome length of 2.61 Mb, whereas HH3^T has a G+C fraction of 52.4 mol% and 2.49 Mb genome length. Major fatty acids of the two strains included C_16 : 1, C_18 : 1 and C_16 : 0, with the addition of C_10:0 3-OH in HH1^T and C_12 : 0 in HH3^T. Chemolithoautotrophic growth of both strains was supported by elemental sulphur, sulphide, tetrathionate, and thiosulphate, and HH1^T was also able to use molecular hydrogen. Neither strain was capable of heterotrophic growth or use of nitrate as a terminal electron acceptor. Strain HH1^T grew from pH 6.5 to 8.5, with an optimum of pH 7.4, whereas strain HH3^T grew from pH 6 to 8 with an optimum of pH 7.5. Growth was observed between 15-35 °C with optima of 32.8 °C for HH1^T and 32 °C for HH3^T. HH1^T grew in media with [NaCl] 80-689 mM, with an optimum of 400 mM, while HH3^T grew at 80-517 mM, with an optimum of 80 mM. The name Thiomicrorhabdus heinhorstiae sp. nov. is proposed, and the type strain is HH1^T (=DSM 111584^T=ATCC TSD-240^T). The name Thiomicrorhabdus cannonii sp. nov is proposed, and the type strain is HH3^T (=DSM 111593^T=ATCC TSD-241^T).

One-Year In Situ Incubation of Pyrite at the Deep Seafloor and Its Microbiological and Biogeochemical Characterizations

In this study, we performed a year-long in situ incubation experiment on a common ferrous sulfide (Fe-S) mineral, pyrite, at the oxidative deep seafloor in the hydrothermal vent field in the Izu-Bonin arc, Japan, and characterized its microbiological and biogeochemical properties to understand the microbial alteration processes of the pyrite, focusing on Fe(II) oxidation. The microbial community analysis of the incubated pyrite showed that the domain Bacteria heavily dominated over Archaea compared with that of the ambient seawater, and Alphaproteobacteria and Gammaproteobacteria distinctively codominated at the class level. The mineralogical characterization by surface-sensitive Fe X-ray absorption near-edge structure (XANES) analysis revealed that specific Fe(III) hydroxides (schwertmannite and ferrihydrite) were locally formed at the pyrite surface as the pyrite alteration products. Based on the Fe(III) hydroxide species and proportion, we thermodynamically calculated the pH value at the pyrite surface to be pH 4.9 to 5.7, indicating that the acidic condition derived from pyrite alteration was locally formed at the surface against neutral ambient seawater. This acidic microenvironment at the pyrite surface might explain the distinct microbial communities found in our pyrite samples. Also, the acidity at the pyrite surface indicates that the abiotic Fe(II) oxidation rate was much limited at the pyrite surface kinetically, 3.9 × 103- to 1.6 × 105-fold lower than that in the ambient seawater. Moreover, nanoscale characterization of microbial biomolecules using carbon near-edge X-ray absorption fine-structure (NEXAFS) analysis showed that the sessile cells attached to pyrite excreted the acidic polysaccharide-rich extracellular polymeric substances at the pyrite surface, which can lead to the promotion of biogenic Fe(II) oxidation and pyrite alteration. IMPORTANCE Pyrite is one of the most common Fe-S minerals found in submarine hydrothermal environments. Previous studies demonstrated that the Fe-S mineral can be a suitable host for Fe(II)-oxidizing microbes in hydrothermal environments; however, the details of microbial Fe(II) oxidation processes with Fe-S mineral alteration are not well known. The spectroscopic and thermodynamic examination in the present study suggests that a moderately acidic pH condition was locally formed at the pyrite surface during pyrite alteration at the seafloor due to proton releases with Fe(II) and sulfidic S oxidations. Following previous studies, the abiotic Fe(II) oxidation rate significantly decreases with a decrease in pH, but the biotic (microbial) Fe(II) oxidation rate is not sensitive to the pH decrease. Thus, our findings clearly suggest that the pyrite surface is a unique microenvironment where abiotic Fe(II) oxidation is limited and biotic Fe(II) oxidation is more prominent than that in neutral ambient seawater.

Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats

Microbial iron cycling influences the flux of major nutrients in the environment (e.g., through the adsorptive capacity of iron oxides) and includes biotically induced iron oxidation and reduction processes. The ecological extent of microbial iron cycling is not well understood, even with increased sequencing efforts, in part due to limitations in gene annotation pipelines and limitations in experimental studies linking phenotype to genotype. This is particularly true for the marine subseafloor, which remains undersampled, but represents the largest contiguous habitat on Earth. To address this limitation, we used FeGenie, a database and bioinformatics tool that identifies microbial iron cycling genes and enables the development of testable hypotheses on the biogeochemical cycling of iron. Herein, we survey the microbial iron cycle in diverse subseafloor habitats, including sediment-buried crustal aquifers, as well as surficial and deep sediments. We inferred the genetic potential for iron redox cycling in 32 of the 46 metagenomes included in our analysis, demonstrating the prevalence of these activities across underexplored subseafloor ecosystems. We show that while some processes (e.g., iron uptake and storage, siderophore transport potential, and iron gene regulation) are near-universal, others (e.g., iron reduction/oxidation, siderophore synthesis, and magnetosome formation) are dependent on local redox and nutrient status. Additionally, we detected niche-specific differences in strategies used for dissimilatory iron reduction, suggesting that geochemical constraints likely play an important role in dictating the dominant mechanisms for iron cycling. Overall, our survey advances the known distribution, magnitude, and potential ecological impact of microbe-mediated iron cycling and utilization in sub-benthic ecosystems.

Functional diversity of microbial communities in inactive seafloor sulfide deposits

The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.

Microorganisms from deep-sea hydrothermal vents

With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-020-00086-4.

Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community

The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.

Genomic Insights into Two Novel Fe(II)-Oxidizing Zetaproteobacteria Isolates Reveal Lifestyle Adaption to Coastal Marine Sediments

The discovery of the novel Zetaproteobacteria class greatly expanded our understanding of neutrophilic, microaerophilic microbial Fe(II) oxidation in marine environments. Despite molecular techniques demonstrating their global distribution, relatively few isolates exist, especially from low-Fe(II) environments. Furthermore, the Fe(II) oxidation pathways used by Zetaproteobacteria remain poorly understood. Here, we present the genomes (>99% genome completeness) of two Zetaproteobacteria, which are the only cultivated isolates originating from typical low-Fe [porewater Fe(II), 70 to 100 μM] coastal marine sediments. The two strains share <90% average nucleotide identity (ANI) with each other and <80% ANI with any other Zetaproteobacteria genome. The closest relatives were Mariprofundus aestuarium strain CP-5 and Mariprofundus ferrinatatus strain CP-8 (96 to 98% 16S rRNA gene sequence similarity). Fe(II) oxidation of strains KV and NF is most likely mediated by the putative Fe(II) oxidase Cyc2. Interestingly, the genome of strain KV also encodes a putative multicopper oxidase, PcoAB, which could play a role in Fe(II) oxidation, a pathway found only in two other Zetaproteobacteria genomes (Ghiorsea bivora TAG-1 and SCGC AB-602-C20). The strains show potential adaptations to fluctuating O₂ concentrations, indicated by the presence of both cbb ₃- and aa ₃-type cytochrome c oxidases, which are adapted to low and high O₂ concentrations, respectively. This is further supported by the presence of several oxidative-stress-related genes. In summary, our results reveal the potential Fe(II) oxidation pathways employed by these two novel chemolithoautotrophic Fe(II)-oxidizing species and the lifestyle adaptations which enable the Zetaproteobacteria to survive in coastal environments with low Fe(II) and regular redox fluctuations.IMPORTANCE Until recently, the importance and relevance of Zetaproteobacteria were mainly thought to be restricted to high-Fe(II) environments, such as deep-sea hydrothermal vents. The two novel Mariprofundus isolates presented here originate from typical low-Fe(II) coastal marine sediments. As well as being low in Fe(II), these environments are often subjected to fluctuating O₂ concentrations and regular mixing by wave action and bioturbation. The discovery of two novel isolates highlights the importance of these organisms in such environments, as Fe(II) oxidation has been shown to impact nutrients and trace metals. Genome analysis of these two strains further supported their lifestyle adaptation and therefore their potential preference for coastal marine sediments, as genes necessary for surviving dynamic O₂ concentrations and oxidative stress were identified. Furthermore, our analyses also expand our understanding of the poorly understood Fe(II) oxidation pathways used by neutrophilic, microaerophilic Fe(II) oxidizers.

Description of Luteithermobacter gelatinilyticus gen. nov., sp. nov., and Paremcibacter congregatus gen. nov., comb. nov. via reclassification of the genus Emcibacter

Strain MEBiC09520^T, which was isolated from a tidal sediment in Incheon, Korea, is a pale yellow, rod-shaped bacterium, cells of which are 0.4-0.5 µm in width and 1.5-2 µm in length. Strain MEBiC09520^T shared 95.17 and 92.57% 16S rRNA gene sequence similarity with Emcibacter nanhaiensis and E. congregatus, respectively. It grew optimally at pH 6.0, at 55 °C and with 2.5-3.5% (w/v) NaCl. Its polar lipid components included phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), an unidentified phospholipid (PL), three unidentified aminolipids (ALs) and two unidentified lipids (L). The fatty acids C_16:0, C_19:0 cyclo ω8c, C_14:0 2-OH and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c) were predominantly present in its cell wall. Strain MEBiC09520^T was thermophilic, while E. nanhaiensis and E. congregatus were mesophilic. Although E. nanhaiensis showed no nitrate reduction activity, MEBiC09520^T and E. congregatus showed a positive reaction. These strains differed in carbohydrate utilization. In particular, E. congregatus was able to thrive on various carbohydrate substrates as compared to the other strains. The average nucleotide identity value was 69.92% between strain MEBiC09520^T and E. congregatus ZYL^T, 70.38% between E. congregatus ZYL^T and E. nanhaiensis HTCJW17^T, and 72.83% between strain MEBiC09520 and E. nanhaiensis HTCJW17^T. Considering these differences, strain MEBiC09520^T (=KCCM 43320^T=MCCC 1K03920^T) is suggested to represent and novel species of a new genus, Luteithermobacter gelatinilyticus gen. nov., sp. nov., and E. congregatus should be reclassified as Paremcibacter congregatus gen. nov., comb. nov.

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys

BACKGROUND

Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-temperature hydrothermal fluids. While several studies have investigated the microbial diversity in both active and inactive sulfide chimneys that have been extinct for up to thousands of years, little is known about chimneys that have ceased activity more recently, as well as the microbial succession occurring during the transition from active to inactive chimneys.

RESULTS

Genome-resolved metagenomics was applied to an active and a recently extinct (~ 7 years) sulfide chimney from the 9-10° N hydrothermal vent field on the East Pacific Rise. Full-length 16S rRNA gene and a total of 173 high-quality metagenome assembled genomes (MAGs) were retrieved for comparative analysis. In the active chimney (L-vent), sulfide- and/or hydrogen-oxidizing Campylobacteria and Aquificae with the potential for denitrification were identified as the dominant community members and primary producers, fixing carbon through the reductive tricarboxylic acid (rTCA) cycle. In contrast, the microbiome of the recently extinct chimney (M-vent) was largely composed of heterotrophs from various bacterial phyla, including Delta-/Beta-/Alphaproteobacteria and Bacteroidetes. Gammaproteobacteria were identified as the main primary producers, using the oxidation of metal sulfides and/or iron oxidation coupled to nitrate reduction to fix carbon through the Calvin-Benson-Bassham (CBB) cycle. Further analysis revealed a phylogenetically distinct Nitrospirae cluster that has the potential to oxidize sulfide minerals coupled to oxygen and/or nitrite reduction, as well as for sulfate reduction, and that might serve as an indicator for the early stages of chimneys after venting has ceased.

CONCLUSIONS

This study sheds light on the composition, metabolic functions, and succession of microbial communities inhabiting deep-sea hydrothermal vent sulfide chimneys. Collectively, microbial succession during the life span of a chimney could be described to proceed from a "fluid-shaped" microbial community in newly formed and actively venting chimneys supported by the oxidation of reductants in the hydrothermal fluid to a "mineral-shaped" community supported by the oxidation of minerals after hydrothermal activity has ceased. Remarkably, the transition appears to occur within the first few years, after which the communities stay stable for thousands of years. Video Abstract.

Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents

Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans However, Cyc2 function is not well verified in neutrophilic Fe oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-quality metagenome-assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions and in incubations. The putative Fe oxidase gene cyc2 was highly expressed in situ, often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments.IMPORTANCE Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron oxidation gene, cyc2, in iron-rich hydrothermal vents, where iron-oxidizing microbes dominate. We pieced together diverse Zetaproteobacteria genomes, compared these genomes, and analyzed expression of cyc2 and other hypothetical iron oxidation genes. We show that cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity. These findings will help us understand and potentially quantify the impacts of neutrophilic iron oxidizers in a wide variety of marine and terrestrial environments.

Diet shapes cold-water corals bacterial communities

Different cold-water coral (CWC) species harbour distinct microbial communities and the community composition is thought to be linked to the ecological strategies of the host. Here we test whether diet shapes the composition of bacterial communities associated with CWC. We compared the microbiomes of two common CWC species in aquaria, Lophelia pertusa and Madrepora oculata, when they were either starved, or fed respectively with a carnivorous diet, two different herbivorous diets, or a mix of the 3. We targeted both the standing stock (16S rDNA) and the active fraction (16S rRNA) of the bacterial communities and showed that in both species, the corals' microbiome was specific to the given diet. A part of the microbiome remained, however, species-specific, which indicates that the microbiome's plasticity is framed by the identity of the host. In addition, the storage lipid content of the coral tissue showed that different diets had different effects on the corals' metabolisms. The combined results suggest that L. pertusa may be preying preferentially on zooplankton while M. oculata may in addition use phytoplankton and detritus. The results cast a new light on coral microbiomes as they indicate that a portion of the CWC's bacterial community could represent a food influenced microbiome.

Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO2 Fixation and 16S Tags of the Transcriptome in Incubation Experiments

The microbial community composition and its functionality was assessed for hydrothermal fluids and volcanic ash sediments from Haungaroa and hydrothermal fluids from the Brothers volcano in the Kermadec island arc (New Zealand). The Haungaroa volcanic ash sediments were dominated by epsilonproteobacterial Sulfurovum sp. Ratios of electron donor consumption to CO₂ fixation from respective sediment incubations indicated that sulfide oxidation appeared to fuel autotrophic CO₂ fixation, coinciding with thermodynamic estimates predicting sulfide oxidation as the major energy source in the environment. Transcript analyses with the sulfide-supplemented sediment slurries demonstrated that Sulfurovum prevailed in the experiments as well. Hence, our sediment incubations appeared to simulate environmental conditions well suggesting that sulfide oxidation catalyzed by Sulfurovum members drive biomass synthesis in the volcanic ash sediments. For the Haungaroa fluids no inorganic electron donor and responsible microorganisms could be identified that clearly stimulated autotrophic CO₂ fixation. In the Brothers hydrothermal fluids Sulfurimonas (49%) and Hydrogenovibrio/Thiomicrospira (15%) species prevailed. Respective fluid incubations exhibited highest autotrophic CO₂ fixation if supplemented with iron(II) or hydrogen. Likewise catabolic energy calculations predicted primarily iron(II) but also hydrogen oxidation as major energy sources in the natural fluids. According to transcript analyses with material from the incubation experiments Thiomicrospira/Hydrogenovibrio species dominated, outcompeting Sulfurimonas. Given that experimental conditions likely only simulated environmental conditions that cause Thiomicrospira/Hydrogenovibrio but not Sulfurimonas to thrive, it remains unclear which environmental parameters determine Sulfurimonas’ dominance in the Brothers natural hydrothermal fluids.

Genome Sequence of Mariprofundus sp. Strain EBB-1, a Novel Marine Autotroph Isolated from an Iron-Sulfur Mineral

Mariprofundus sp. strain EBB-1 was isolated from a pyrrhotite biofilm incubated in seawater from East Boothbay (ME, USA). Strain EBB-1 is an autotrophic member of the class Zetaproteobacteria with the ability to form iron oxide biominerals. Here, we present the 2.88-Mb genome sequence of EBB-1, which contains 2,656 putative protein-coding sequences.

Mariprofundus sp. strain EBB-1 was isolated from a pyrrhotite biofilm incubated in seawater from East Boothbay (ME, USA). Strain EBB-1 is an autotrophic member of the class Zetaproteobacteria with the ability to form iron oxide biominerals. Here, we present the 2.88-Mb genome sequence of EBB-1, which contains 2,656 putative protein-coding sequences.

Ecology of Subseafloor Crustal Biofilms

The crustal subseafloor is the least explored and largest biome on Earth. Interrogating crustal life is difficult due to habitat inaccessibility, low-biomass and contamination challenges. Subseafloor observatories have facilitated the study of planktonic life in crustal aquifers, however, studies of life in crust-attached biofilms are rare. Here, we investigate biofilms grown on various minerals at different temperatures over 1-6 years at subseafloor observatories in the Eastern Pacific. To mitigate potential sequence contamination, we developed a new bioinformatics tool - TaxonSluice. We explore ecological factors driving community structure and potential function of biofilms by comparing our sequence data to previous amplicon and metagenomic surveys of this habitat. We reveal that biofilm community structure is driven by temperature rather than minerology, and that rare planktonic lineages colonize the crustal biofilms. Based on 16S rRNA gene overlap, we partition metagenome assembled genomes into planktonic and biofilm fractions and suggest that there are functional differences between these community types, emphasizing the need to separately examine each to accurately describe subseafloor microbe-rock-fluid processes. Lastly, we report that some rare lineages present in our warm and anoxic study site are also found in cold and oxic crustal fluids in the Mid-Atlantic Ridge, suggesting global crustal biogeography patterns.

Time-dependent gut microbiota analysis of juvenile Oreochromis niloticus by dietary supplementation of resveratrol

To evaluate the changes in bacterial diversity at various time points under resveratrol supplementation, we aimed to investigate the diversification of gut microbiota and the changes in total genetic diversity. We performed 16S rDNA gene sequencing at different time points (15, 30, and 45 days) to analyze the gut microbiota of tilapia. Fusobacteria, Proteobacteria, and Bacteroidetes (15 days) or Cyanobacteria (30 and 45 days) were found to be the three most abundant phyla. Cyanobacteria (15 and 30 days), Proteobacteria (15 days), Firmicutes and Chlamydiae (30 and 45 days), Planctomycetes (30 days), Bacteroidetes, Actinobacteria, and Fusobacteria (45 days) in the 0.05 g/kg RES group increased as compared to that in the controls. Proteobacteria and Cyanobacteria significantly decreased and increased at 30 and 45 days, respectively, while the reverse pattern was observed at 15 days. The Bacteroidetes:Firmicutes and Proteobacteria:Cyanobacteria ratios were significantly increased (15 and 45 days, P < 0.05) and decreased (30 days, P < 0.05). RES supplementation did not affect the richness and diversity of the gut microbiota in tilapia. Our findings may contribute to the development of strategies for the management of diseases.

Environmental Evidence for and Genomic Insight into the Preference of Iron-Oxidizing Bacteria for More-Corrosion-Resistant Stainless Steel at Higher Salinities

Iron-oxidizing bacteria (FeOB) are some of the initial colonizing organisms during microbially influenced corrosion of steel infrastructure. To better understand the abiotic conditions under which FeOB colonize steel, an environmental study was conducted to determine the effects of salinity, temperature, dissolved oxygen levels, and steel type on FeOB colonization. Stainless steel (304 and 316 [i.e., 304SS and 316SS]) was used to determine the potential susceptibility of these specialized corrosion-resistant steels. Steel coupon deployments along salinity gradients in two river systems revealed attachment by FeOB at all sites, with greater abundance of FeOB at higher salinities and on 316SS, compared to 304SS. This may be due to the presence of molybdenum in 316SS, potentially providing a selective advantage for FeOB colonization. A novel Zetaproteobacteria species, Mariprofundus erugo, was isolated from these stainless steel samples. Genes for molybdenum utilization and uptake and reactive oxygen species protection were found within its genome, supporting the evidence from our FeOB abundance data; they may represent adaptations of FeOB for colonization of surfaces of anthropogenic iron sources such as stainless steel. These results reveal environmental conditions under which FeOB colonize steel surfaces most abundantly, and they provide the framework needed to develop biocorrosion prevention strategies for stainless steel infrastructure in coastal estuarine areas.IMPORTANCE Colonization of FeOB on corrosion-resistant stainless steel types (304SS and 316SS) has been quantified from environmental deployments along salinity gradients in estuarine environments. Greater FeOB abundance at higher salinities and on the more-corrosion-resistant 316SS suggests that there may be a higher risk of biocorrosion at higher salinities and there may be a selective advantage from certain stainless steel alloy metals, such as molybdenum, for FeOB colonization. A novel species of FeOB described here was isolated from our stainless steel coupon deployments, and its genome sequence supports our environmental data, as genes involved in the potential selectiveness toward surface colonization of stainless steel might lead to higher rates of biocorrosion of manmade aquatic infrastructure. These combined results provide environmental constraints for FeOB colonization on anthropogenic iron sources and build on previous frameworks for biocorrosion prevention strategies.

Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

Background

Obligate sulfur oxidizing chemolithoauthotrophic strains of Hydrogenovibrio crunogenus have been isolated from multiple hydrothermal vent associated habitats. However, a hydrogenase gene cluster (encoding the hydrogen converting enzyme and its maturation/assembly machinery) detected on the first sequenced H. crunogenus strain (XCL-2) suggested that hydrogen conversion may also play a role in this organism. Yet, numerous experiments have underlined XCL-2’s inability to consume hydrogen under the tested conditions. A recent study showed that the closely related strain SP-41 contains a homolog of the XCL-2 hydrogenase (a group 1b [NiFe]-hydrogenase), but that it can indeed use hydrogen. Hence, the question remained unresolved, why SP-41 is capable of using hydrogen, while XCL-2 is not.

Results

Here, we present the genome sequence of the SP-41 strain and compare it to that of the XCL-2 strain. We show that the chromosome of SP-41 codes for a further hydrogenase gene cluster, including two additional hydrogenases: the first appears to be a group 1d periplasmic membrane-anchored hydrogenase, and the second a group 2b sensory hydrogenase. The region where these genes are located was likely acquired horizontally and exhibits similarity to other Hydrogenovibrio species (H. thermophilus MA2-6 and H. marinus MH-110 ^T) and other hydrogen oxidizing Proteobacteria (Cupriavidus necator H16 and Ghiorsea bivora TAG-1 ^T). The genomes of XCL-2 and SP-41 show a strong conservation in gene order. However, several short genomic regions are not contained in the genome of the other strain. These exclusive regions are often associated with signs of DNA mobility, such as genes coding for transposases. They code for transport systems and/or extend the metabolic potential of the strains.

Conclusions

Our results suggest that horizontal gene transfer plays an important role in shaping the genomes of these strains, as a likely mechanism for habitat adaptation, including, but not limited to the transfer of the hydrogen conversion ability.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5710-5) contains supplementary material, which is available to authorized users.

The Fe(II)-oxidizing Zetaproteobacteria: historical, ecological and genomic perspectives

The Zetaproteobacteria are a class of bacteria typically associated with marine Fe(II)-oxidizing environments. First discovered in the hydrothermal vents at Loihi Seamount, Hawaii, they have become model organisms for marine microbial Fe(II) oxidation. In addition to deep sea and shallow hydrothermal vents, Zetaproteobacteria are found in coastal sediments, other marine subsurface environments, steel corrosion biofilms and saline terrestrial springs. Isolates from a range of environments all grow by autotrophic Fe(II) oxidation. Their success lies partly in their microaerophily, which enables them to compete with abiotic Fe(II) oxidation at Fe(II)-rich oxic/anoxic transition zones. To determine the known diversity of the Zetaproteobacteria, we have used 16S rRNA gene sequences to define 59 operational taxonomic units (OTUs), at 97% similarity. While some Zetaproteobacteria taxa appear to be cosmopolitan, others are enriched by specific habitats. OTU networks show that certain Zetaproteobacteria co-exist, sharing compatible niches. These niches may correspond with adaptations to O2, H2 and nitrate availability, based on genomic analyses of metabolic potential. Also, a putative Fe(II) oxidation gene has been found in diverse Zetaproteobacteria taxa, suggesting that the Zetaproteobacteria evolved as Fe(II) oxidation specialists. In all, studies suggest that Zetaproteobacteria are widespread, and therefore may have a broad influence on marine and saline terrestrial Fe cycling.

Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses

Metal‐sulfides are wide‐spread in marine benthic habitats. At deep‐sea hydrothermal vents, they occur as massive sulfide chimneys formed by mineral precipitation upon mixing of reduced vent fluids with cold oxygenated sea water. Although microorganisms inhabiting actively venting chimneys and utilizing compounds supplied by the venting fluids are well studied, only little is known about microorganisms inhabiting inactive chimneys. In this study, we combined 16S rRNA gene‐based community profiling of sulfide chimneys from the Manus Basin (SW Pacific) with radiometric dating, metagenome (n = 4) and metaproteome (n = 1) analyses. Our results shed light on potential lifestyles of yet poorly characterized bacterial clades colonizing inactive chimneys. These include sulfate‐reducing Nitrospirae and sulfide‐oxidizing Gammaproteobacteria dominating most of the inactive chimney communities. Our phylogenetic analysis attributed the gammaproteobacterial clades to the recently described Woeseiaceae family and the SSr‐clade found in marine sediments around the world. Metaproteomic data identified these Gammaproteobacteria as autotrophic sulfide‐oxidizers potentially facilitating metal‐sulfide dissolution via extracellular electron transfer. Considering the wide distribution of these gammaproteobacterial clades in marine environments such as hydrothermal vents and sediments, microbially accelerated neutrophilic mineral oxidation might be a globally relevant process in benthic element cycling and a considerable energy source for carbon fixation in marine benthic habitats.

Variation in electrode redox potential selects for different microorganisms under cathodic current flow from electrodes in marine sediments

Extracellular electron transport (EET) is a microbial process that allows microorganisms to transport electrons to and from insoluble substrates outside of the cell. Although progress has been made in understanding how microbes transfer electrons to insoluble substrates, the process of receiving electrons has largely remained unexplored. We investigated redox potentials favourable for donating electrons to dissolved and insoluble components in Catalina Harbor marine sediment by combining electrochemical techniques with geochemistry and molecular methods. Working electrodes buried in sediment microcosms were poised at seven redox potentials between -300 and -750 mV versus Ag/AgCl using a three-electrode system. In electrode biofilms recovered after 2-month incubations, overall community diversity increased with more negative redox potentials. Abundances of known EET-capable groups (e.g., Alteromonadales and Desulfuromonadales) varied with redox potential. Motility and chemotaxis genes were found in greater abundance in electrode communities, suggesting a possible selective advantage of these pathways for colonization and utilization of the electrode. Our enrichments demonstrated the validity of this approach in capturing groups known, as well as novel groups (e.g., Campylobacterales) that perform EET. The diverse nature of the enriched cathode communities suggest that insoluble substrate oxidation may be a critical, although poorly described microbial metabolic process in marine sediment.

Hydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits

To assess the risk that mining of seafloor massive sulfides (SMS) from extinct hydrothermal vent environments has for changing the ecosystem irreversibly, we sampled SMS analogous habitats from the Kairei and the Pelagia vent fields along the Indian Ridge. In total 19.8 million 16S rRNA tags from 14 different sites were analyzed and the microbial communities were compared with each other and with publicly available data sets from other marine environments. The chimneys appear to provide habitats for microorganisms that are not found or only detectable in very low numbers in other marine habitats. The chimneys also host rare organisms and may function as a vital part of the ocean’s seed bank. Many of the reads from active and inactive chimney samples were clustered into OTUs, with low or no resemblance to known species. Since we are unaware of the chemical reactions catalyzed by these unknown organisms, the impact of this diversity loss and bio-geo-coupling is hard to predict. Given that chimney structures can be considered SMS analogues, removal of sulfide deposits from the seafloor in the Kairei and Pelagia fields will most likely alter microbial compositions and affect element cycling in the benthic regions and probably beyond.

Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments

Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2.1-3.1 Mbp). An array of sulfur-oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2-6, acquired via horizontal gene transfer. In addition to high-affinity cbb₃ cytochrome c oxidase, some also encode cytochrome bd-type quinol oxidase or ba₃ -type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO₂ concentrating mechanisms. These adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms.

Genome Sequence of Hydrogenovibrio sp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer

Hydrogenovibrio sp. strain SC-1 was isolated from pyrrhotite incubated in situ in the marine surface sediment of Catalina Island, CA. Strain SC-1 has demonstrated autotrophic growth through the oxidation of thiosulfate and iron. Here, we present the 2.45-Mb genome sequence of SC-1, which contains 2,262 protein-coding genes.

Biological rejuvenation of iron oxides in bioturbated marine sediments

The biogeochemical cycle of iron is intricately linked to numerous element cycles. Although biological processes that catalyze the reductive side of the iron cycle are established, little is known about microbial oxidative processes on iron cycling in sedimentary environments-resulting in the formation of iron oxides. Here we show that a potential source of sedimentary iron oxides originates from the metabolic activity of iron-oxidizing bacteria from the class Zetaproteobacteria, presumably enhanced by burrowing animals in coastal sediments. Zetaproteobacteria were estimated to be a global total of 10²⁶ cells in coastal, bioturbated sediments, and predicted to annually produce 8 × 10¹⁵ g of Fe in sedimentary iron oxides-55 times larger than the annual flux of iron oxides deposited by rivers. These data suggest that iron-oxidizing Zetaproteobacteria are keystone organisms in marine sedimentary environments-despite their low numerical abundance-yet exert a disproportionate impact via the rejuvenation of iron oxides.

Sulfur Metabolism of Hydrogenovibrio thermophilus Strain S5 and Its Adaptations to Deep-Sea Hydrothermal Vent Environment

Hydrogenovibrio bacteria are ubiquitous in global deep-sea hydrothermal vents. However, their adaptations enabling survival in these harsh environments are not well understood. In this study, we characterized the physiology and metabolic mechanisms of Hydrogenovibrio thermophilus strain S5, which was first isolated from an active hydrothermal vent chimney on the Southwest Indian Ridge. Physiological characterizations showed that it is a microaerobic chemolithomixotroph that can utilize sulfide, thiosulfate, elemental sulfur, tetrathionate, thiocyanate or hydrogen as energy sources and molecular oxygen as the sole electron acceptor. During thiosulfate oxidation, the strain produced extracellular sulfur globules 0.7–6.0 μm in diameter that were mainly composed of elemental sulfur and carbon. Some organic substrates including amino acids, tryptone, yeast extract, casamino acids, casein, acetate, formate, citrate, propionate, tartrate, succinate, glucose and fructose can also serve as carbon sources, but growth is weaker than under CO₂ conditions, indicating that strain S5 prefers to be chemolithoautotrophic. None of the tested organic carbons could function as energy sources. Growth tests under various conditions confirmed its adaption to a mesophilic mixing zone of hydrothermal vents in which vent fluid was mixed with cold seawater, preferring moderate temperatures (optimal 37°C), alkaline pH (optimal pH 8.0), microaerobic conditions (optimal 4% O₂), and reduced sulfur compounds (e.g., sulfide, optimal 100 μM). Comparative genomics showed that strain S5 possesses more complex sulfur metabolism systems than other members of genus Hydrogenovibrio. The genes encoding the intracellular sulfur oxidation protein (DsrEF) and assimilatory sulfate reduction were first reported in the genus Hydrogenovibrio. In summary, the versatility in energy and carbon sources, and unique physiological properties of this bacterium have facilitated its adaptation to deep-sea hydrothermal vent environments.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb₃- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.

Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU) rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity.

Oxidative Weathering and Microbial Diversity of an Inactive Seafloor Hydrothermal Sulfide Chimney

When its hydrothermal supply ceases, hydrothermal sulfide chimneys become inactive and commonly experience oxidative weathering on the seafloor. However, little is known about the oxidative weathering of inactive sulfide chimneys, nor about associated microbial community structures and their succession during this weathering process. In this work, an inactive sulfide chimney and a young chimney in the early sulfate stage of formation were collected from the Main Endeavor Field of the Juan de Fuca Ridge. To assess oxidative weathering, the ultrastructures of secondary alteration products accumulating on the chimney surface were examined and the presence of possible Fe-oxidizing bacteria (FeOB) was investigated. The results of ultrastructure observation revealed that FeOB-associated ultrastructures with indicative morphologies were abundantly present. Iron oxidizers primarily consisted of members closely related to Gallionella spp. and Mariprofundus spp., indicating Fe-oxidizing species likely promote the oxidative weathering of inactive sulfide chimneys. Abiotic accumulation of Fe-rich substances further indicates that oxidative weathering is a complex, dynamic process, alternately controlled by FeOB and by abiotic oxidization. Although hydrothermal fluid flow had ceased, inactive chimneys still accommodate an abundant and diverse microbiome whose microbial composition and metabolic potential dramatically differ from their counterparts at active vents. Bacterial lineages within current inactive chimney are dominated by members of α-, δ-, and γ-Proteobacteria and they are deduced to be closely involved in a diverse set of geochemical processes including iron oxidation, nitrogen fixation, ammonia oxidation and denitrification. At last, by examining microbial communities within hydrothermal chimneys at different formation stages, a general microbial community succession can be deduced from early formation stages of a sulfate chimney to actively mature sulfide structures, and then to the final inactive altered sulfide chimney. Our findings provide valuable insights into the microbe-involved oxidative weathering process and into microbial succession occurring at inactive hydrothermal sulfide chimney after high-temperature hydrothermal fluids have ceased venting.