Microbial ecology of the dark ocean above, at, and below the seafloor

Microbial diversity and oil biodegradation potential of northern Barents Sea sediments

The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet. Here we combined geochemical analyses, incubation experiments, and microbial community profiling to detail the biogeography and biodegradation potential of Arctic sedimentary microbiomes in the northern Barents Sea. The results revealed a predominance of bacterial and archaea phyla typically found in the deep marine biosphere, such as Chloroflexi, Atribacteria, and Bathyarcheaota. The topmost benthic communities were spatially structured by sedimentary organic carbon, lacking a clear distinction among geographic regions. With increasing sediment depth, the community structure exhibited stratigraphic variability that could be correlated to redox geochemistry of sediments. The benthic microbiomes harbored multiple taxa capable of oxidizing hydrocarbons using aerobic and anaerobic pathways. Incubation of surface sediments with crude oil led to proliferation of several genera from the so-called rare biosphere. These include Alkalimarinus and Halioglobus, previously unrecognized as hydrocarbon-degrading genera, both harboring the full genetic potential for aerobic alkane oxidation. These findings increase our understanding of the taxonomic inventory and functional potential of unstudied benthic microbiomes in the Arctic.

Microbial oases in the ice: A state-of-the-art review on cryoconite holes as diversity hotspots and their scientific connotations

Cryoconite holes, small meltwater pools on the surface of glaciers and ice sheets, represent extremely cold ecosystems teeming with diverse microbial life. Cryoconite holes exhibit greater susceptibility to the impacts of climate change, underlining the imperative nature of investigating microbial communities as an essential module of polar and alpine ecosystem monitoring efforts. Microbes in cryoconite holes play a critical role in nutrient cycling and can produce bioactive compounds, holding promise for industrial and pharmaceutical innovation. Understanding microbial diversity in these delicate ecosystems is essential for effective conservation strategies. Therefore, this review discusses the microbial diversity in these extreme environments, aiming to unveil the complexity of their microbial communities. The current study envisages that cryoconite holes as distinctive ecosystems encompass a multitude of taxonomically diverse and functionally adaptable microorganisms that exhibit a rich microbial diversity and possess intricate ecological functions. By investigating microbial diversity and ecological functions of cryoconite holes, this study aims to contribute valuable insights into the broader field of environmental microbiology and enhance further understanding of these ecosystems. This review seeks to provide a holistic overview regarding the formation, evolution, characterization, and molecular adaptations of cryoconite holes. Furthermore, future research directions and challenges underlining the need for long-term monitoring, and ethical considerations in preserving these pristine environments are also provided. Addressing these challenges and resolutely pursuing future research directions promises to enrich our comprehension of microbial diversity within cryoconite holes, revealing the broader ecological and biogeochemical implications. The inferences derived from the present study will provide researchers, ecologists, and policymakers with a profound understanding of the significance and utility of cryoconite holes in unveiling the microbial diversity and its potential applications.

Single-cell analysis reveals an active and heterotrophic microbiome in the Guaymas Basin deep subsurface with significant inorganic carbon fixation by heterotrophs

The marine subsurface is a long-term sink of atmospheric carbon dioxide with significant implications for climate on geologic timescales. Subsurface microbial cells can either enhance or reduce carbon sequestration in the subsurface, depending on their metabolic lifestyle. However, the activity of subsurface microbes is rarely measured. Here, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to quantify anabolic activity in 3,203 individual cells from the thermally altered deep subsurface in the Guaymas Basin, Mexico (3-75 m below the seafloor, 0-14°C). We observed that a large majority of cells were active (83%-100%), although the rates of biomass generation were low, suggesting cellular maintenance rather than doubling. Mean single-cell activity decreased with increasing sediment depth and temperature and was most strongly correlated with porewater sulfate concentrations. Intracommunity heterogeneity in microbial activity decreased with increasing sediment depth and age. Using a dual-isotope labeling approach, we determined that all active cells analyzed were heterotrophic, deriving the majority of their cellular carbon from organic sources. However, we also detected inorganic carbon assimilation in these heterotrophic cells, likely via processes such as anaplerosis, and determined that inorganic carbon contributes at least 5% of the total biomass carbon in heterotrophs in this community. Our results demonstrate that the deep marine biosphere at Guaymas Basin is largely active and contributes to subsurface carbon cycling primarily by not only assimilating organic carbon but also fixing inorganic carbon. Heterotrophic assimilation of inorganic carbon may be a small yet significant and widespread underappreciated source of labile carbon in the global subsurface.

IMPORTANCE

The global subsurface is the largest reservoir of microbial life on the planet yet remains poorly characterized. The activity of life in this realm has implications for long-term elemental cycling, particularly of carbon, as well as how life survives in extreme environments. Here, we recovered cells from the deep subsurface of the Guaymas Basin and investigated the level and distribution of microbial activity, the physicochemical drivers of activity, and the relative significance of organic versus inorganic carbon to subsurface biomass. Using a sensitive single-cell assay, we found that the majority of cells are active, that activity is likely driven by the availability of energy, and that although heterotrophy is the dominant metabolism, both organic and inorganic carbon are used to generate biomass. Using a new approach, we quantified inorganic carbon assimilation by heterotrophs and highlighted the importance of this often-overlooked mode of carbon assimilation in the subsurface and beyond.

Environmental specificity of karst cave habitats evidenced by diverse symbiotic bacteria in Opiliones

BACKGROUND

Karst caves serve as natural laboratories, providing organisms with extreme and constant conditions that promote isolation, resulting in a genetic relationship and living environment that is significantly different from those outside the cave. However, research on cave creatures, especially Opiliones, remains scarce, with most studies focused on water, soil, and cave sediments.

RESULTS

The structure of symbiotic bacteria in different caves were compared, revealing significant differences. Based on the alpha and beta diversity, symbiotic bacteria abundance and diversity in the cave were similar, but the structure of symbiotic bacteria differed inside and outside the cave. Microorganisms in the cave play an important role in material cycling and energy flow, particularly in the nitrogen cycle. Although microbial diversity varies inside and outside the cave, Opiliones in Beijing caves and Hainan Island exhibited a strong similarity, indicating that the two environments share commonalities.

CONCLUSIONS

The karst cave environment possesses high microbial diversity and there are noticeable differences among different caves. Different habitats lead to significant differences in the symbiotic bacteria in Opiliones inside and outside the cave, and cave microorganisms have made efforts to adapt to extreme environments. The similarity in symbiotic bacteria community structure suggests a potential similarity in host environments, providing an explanation for the appearance of Sinonychia martensi in caves in the north.

Insights into phage-bacteria interaction in cold seep Gigantidas platifrons through metagenomics and transcriptome analyses

Viruses are crucial for regulating deep-sea microbial communities and biogeochemical cycles. However, their roles are still less characterized in deep-sea holobionts. Bathymodioline mussels are endemic species inhabiting cold seeps and harboring endosymbionts in gill epithelial cells for nutrition. This study unveiled a diverse array of viruses in the gill tissues of Gigantidas platifrons mussels and analyzed the viral metagenome and transcriptome from the gill tissues of Gigantidas platifrons mussels collected from a cold seep in the South Sea. The mussel gills contained various viruses including Baculoviridae, Rountreeviridae, Myoviridae and Siphovirdae, but the active viromes were Myoviridae, Siphoviridae, and Podoviridae belonging to the order Caudovirales. The overall viral community structure showed significant variation among environments with different methane concentrations. Transcriptome analysis indicated high expression of viral structural genes, integrase, and restriction endonuclease genes in a high methane concentration environment, suggesting frequent virus infection and replication. Furthermore, two viruses (GP-phage-contig14 and GP-phage-contig72) interacted with Gigantidas platifrons methanotrophic gill symbionts (bathymodiolin mussels host intracellular methanotrophic Gammaproteobacteria in their gills), showing high expression levels, and have huge different expression in different methane concentrations. Additionally, single-stranded DNA viruses may play a potential auxiliary role in the virus-host interaction using indirect bioinformatics methods. Moreover, the Cro and DNA methylase genes had phylogenetic similarity between the virus and Gigantidas platifrons methanotrophic gill symbionts. This study also explored a variety of viruses in the gill tissues of Gigantidas platifrons and revealed that bacteria interacted with the viruses during the symbiosis with Gigantidas platifrons. This study provides fundamental insights into the interplay of microorganisms within Gigantidas platifrons mussels in deep sea.

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.

Metagenomic analysis of carbohydrate-active enzymes and their contribution to marine sediment biodiversity

Marine sediments constitute the world's most substantial long-term carbon repository. The microorganisms dwelling in these sediments mediate the transformation of fixed oceanic carbon, but their contribution to the carbon cycle is not fully understood. Previous culture-independent investigations into sedimentary microorganisms have underscored the significance of carbohydrates in the carbon cycle. In this study, we employ a metagenomic methodology to investigate the distribution and abundance of carbohydrate-active enzymes (CAZymes) in 37 marine sediments sites. These sediments exhibit varying oxygen availability and were isolated in diverse regions worldwide. Our comparative analysis is based on the metabolic potential for oxygen utilisation, derived from genes present in both oxic and anoxic environments. We found that extracellular CAZyme modules targeting the degradation of plant and algal detritus, necromass, and host glycans were abundant across all metagenomic samples. The analysis of these results indicates that the oxic/anoxic conditions not only influence the taxonomic composition of the microbial communities, but also affect the occurrence of CAZyme modules involved in the transformation of necromass, algae and plant detritus. To gain insight into the sediment microbial taxa, we reconstructed metagenome assembled genomes (MAG) and examined the presence of primary extracellular carbohydrate active enzyme (CAZyme) modules. Our findings reveal that the primary CAZyme modules and the CAZyme gene clusters discovered in our metagenomes were prevalent in the Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria classes. We compared those MAGs to organisms from the same taxonomic classes found in soil, and we found that they were similar in its CAZyme repertoire, but the soil MAG contained a more abundant and diverse CAZyme content. Furthermore, the data indicate that abundant classes in our metagenomic samples, namely Alphaproteobacteria, Bacteroidia and Gammaproteobacteria, play a pivotal role in carbohydrate transformation within the initial few metres of the sediments.

Seafloor incubation experiments at deep-sea hydrothermal vents reveal distinct biogeographic signatures of autotrophic communities

The discharge of hydrothermal vents on the seafloor provides energy sources for dynamic and productive ecosystems, which are supported by chemosynthetic microbial populations. These populations use the energy gained by oxidizing the reduced chemicals contained within the vent fluids to fix carbon and support multiple trophic levels. Hydrothermal discharge is ephemeral and chemical composition of such fluids varies over space and time, which can result in geographically distinct microbial communities. To investigate the foundational members of the community, microbial growth chambers were placed within the hydrothermal discharge at Axial Seamount (Juan de Fuca Ridge), Magic Mountain Seamount (Explorer Ridge), and Kama'ehuakanaloa Seamount (Hawai'i hotspot). Campylobacteria were identified within the nascent communities, but different amplicon sequence variants were present at Axial and Kama'ehuakanaloa Seamounts, indicating that geography in addition to the composition of the vent effluent influences microbial community development. Across these vent locations, dissolved iron concentration was the strongest driver of community structure. These results provide insights into nascent microbial community structure and shed light on the development of diverse lithotrophic communities at hydrothermal vents.

Diversities and interactions of phages and bacteria in deep-sea sediments as revealed by metagenomics

Phages are found virtually everywhere, even in extreme environments, and are extremely diverse both in their virion structures and in their genomic content. They are thought to shape the taxonomic and functional composition of microbial communities as well as their stability. A number of studies on laboratory culture and viral metagenomic research provide deeper insights into the abundance, diversity, distribution, and interaction with hosts of phages across a wide range of ecosystems. Although most of these studies focus on easily accessible samples, such as soils, lakes, and shallow oceans, little is known about bathypelagic phages. In this study, through analyzing the 16S rRNA sequencing and viral metagenomic sequencing data of 25 samples collected from five different bathypelagic ecosystems, we detected a high diversity of bacteria and phages, particularly in the cold seep and hydrothermal vent ecosystems, which have stable chemical energy. The relative abundance of phages in these ecosystems was higher than in other three abyssal ecosystems. The low phage/host ratios obtained from host prediction were different from shallow ecosystems and indicated the prevalence of prophages, suggesting the complexity of phage-bacteria interactions in abyssal ecosystems. In the correlation analysis, we revealed several phages-bacteria interaction networks of potential ecological relevance. Our study contributes to a better understanding of the interactions between bathypelagic bacteria and their phages.

Unexpected carbon utilization activity of sulfate-reducing microorganisms in temperate and permanently cold marine sediments

Significant amounts of organic carbon in marine sediments are degraded, coupled with sulfate reduction. However, the actual carbon and energy sources used in situ have not been assigned to each group of diverse sulfate-reducing microorganisms (SRM) owing to the microbial and environmental complexity in sediments. Here, we probed microbial activity in temperate and permanently cold marine sediments by using potential SRM substrates, organic fermentation products at very low concentrations (15-30 μM), with RNA-based stable isotope probing. Unexpectedly, SRM were involved only to a minor degree in organic fermentation product mineralization, whereas metal-reducing microbes were dominant. Contrastingly, distinct SRM strongly assimilated 13C-DIC (dissolved inorganic carbon) with H2 as the electron donor. Our study suggests that canonical SRM prefer autotrophic lifestyle, with hydrogen as the electron donor, while metal-reducing microorganisms are involved in heterotrophic organic matter turnover, and thus regulate carbon fluxes in an unexpected way in marine sediments.

Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments

Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their niche separation and of the processes controlling their population structure in hadal and abyssal surface sediments is still limited. Here, we reconstructed 47 AOA metagenome-assembled genomes (MAGs) from surface sediments of the Atacama and Kermadec trench systems. They formed deep-sea-specific groups within the family Nitrosopumilaceae and were assigned to six amoA gene-based clades. MAGs from different clades had distinct distribution patterns along oxygen-ammonium counter gradients in surface sediments. At the species level, MAGs thus seemed to form different ecotypes and follow deterministic niche-based distributions. In contrast, intraspecific population structure, defined by patterns of Single Nucleotide Variants (SNV), seemed to reflect more complex contributions of both deterministic and stochastic processes. Firstly, the bathymetric range had a strong effect on population structure, with distinct populations in abyssal plains and hadal trenches. Then, hadal populations were clearly separated by trench system, suggesting a strong isolation-by-topography effect, whereas abyssal populations were rather controlled by sediment depth or geographic distances, depending on the clade considered. Interestingly, genetic variability between samples was lowest in sediment layers where the mean MAG coverage was highest, highlighting the importance of selective pressure linked with each AOA clade's ecological niche. Overall, our results show that deep-sea AOA genome distributions seem to follow both deterministic and stochastic processes, depending on the genomic variability scale considered.

Distinct diversity patterns and assembly mechanisms of prokaryotic microbial sub-community in the water column of deep-sea cold seeps

Methane leakage from deep-sea cold seeps has a major impact on marine ecosystems. Microbes sequester methane in the water column of cold seeps and can be divided into abundant and rare groups. Both abundant and rare groups play an important role in cold seep ecosystems, and the environmental heterogeneity in cold seeps may enhance conversion between taxa with different abundances. Yet, the environmental stratification and assembly mechanisms of these microbial sub-communities remain unclear. We investigated the diversities and assembly mechanisms in microbial sub-communities with distinct abundance in the deep-sea cold seep water column, from 400 m to 1400 m. We found that bacterial β-diversity, as measured by Sørensen dissimilarities, exhibited a significant species turnover pattern that was influenced by several environmental factors including depth, temperature, SiO32-, and salinity. In contrast, archaeal β-diversity showed a relatively high percentage of nestedness pattern, which was driven by the levels of soluble reactive phosphate and SiO32-. During the abundance dependency test, abundant taxa of both bacteria and archaea showed a significant species turnover, while the rare taxa possessed a higher percentage of nestedness. Stochastic processes were prominent in shaping the prokaryotic community, but deterministic processes were more pronounced for the abundant taxa than rare ones. Furthermore, the metagenomics results revealed that the abundances of methane oxidation, sulfur oxidation, and nitrogen fixation-related genes and related microbial groups were significantly higher in the bottom water. Our results implied that the carbon, sulfur, and nitrogen cycles were potentially strongly coupled in the bottom water. Overall, the results obtained in this study highlight taxonomic and abundance-dependent microbial community diversity patterns and assembly mechanisms in the water column of cold seeps, which will help understand the impacts of fluid seepage from the sea floor on the microbial community in the water column and further provide guidance for the management of cold seep ecosystem under future environmental pressures.

The role of hydrodynamics for the spatial distribution of high-temperature hydrothermal vent-endemic fauna in the deep ocean environment

Active hydrothermal vents provide the surrounding submarine environment with substantial amounts of matter and energy, thus serving as important habitats for diverse megabenthic communities in the deep ocean and constituting a unique, highly productive chemosynthetic ecosystem on Earth. Vent-endemic biological communities gather near the venting site and are usually not found beyond a distance of the order of 100 m from the vent. This is surprising because one would actually expect matter ejected from high-temperature vents, which generate highly turbulent buoyancy plumes, to be suspended and carried far away by the plume flows and deep-sea currents. Here, we study this problem from a fluid dynamics perspective by simulating the vent hydrodynamics using a numerical model that couples the plume flow with induced matter and energy transport. We find that both low- and high-temperature vents deposit most vent matter relatively close to the plume. In particular, the tendency of turbulent buoyancy plumes to carry matter far away is strongly counteracted by generated entrainment flows back into the plume stem. The deposition ranges of organic and inorganic hydrothermal particles obtained from the simulations for various natural high-temperature vents are consistent with the observed maximum spatial extent of biological communities, evidencing that plume hydrodynamics exercises strong control over the spatial distribution of vent-endemic fauna. While other factors affecting the spatial distribution of vent-endemic fauna, such as geology and geochemistry, are site-specific, the main physical features of plume hydrodynamics unraveled in this study are largely site-unspecific and therefore universal across vent sites on Earth.

Superoxide-Mediated Extracellular Mercury Reduction by Aerobic Marine Bacterium Alteromonas sp. KD01

Microbial reduction plays a crucial role in Hg redox and the global cycle. Although intracellular Hg(II) reduction mediated by MerA protein is well documented, it is still unclear whether or how bacteria reduce Hg(II) extracellularly without its internalization. Herein, for the first time, we discovered the extracellular reduction of Hg(II) by a widely distributed aerobic marine bacterium Alteromonas sp. KD01 through a superoxide-dependent mechanism. The generation of superoxide by Alteromonas sp. KD01 was determined using 3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide and methyl cypridina luciferin analogue as probes via UV-vis and chemiluminescence detection, respectively. The results demonstrated that Hg(II) reduction was inhibited by superoxide scavengers (superoxide dismutase (SOD) and Cu(NO3)2) or inhibitors of reduced nicotinamide adenine dinucleotide (NADH) oxidoreductases. In contrast, the addition of NADH significantly improved superoxide generation and, in turn, Hg(II) reduction. Direct evidence of superoxide-mediated Hg(II) reduction was provided by the addition of superoxide using KO2 in deionized water and seawater. Moreover, we observed that even superoxide at an environmental concentration of 9.6 ± 0.5 nM from Alteromonas sp. KD01 (5.4 × 106 cells mL-1) was capable of significantly reducing Hg(II). Our findings provide a greater understanding of Hg(II) reduction by superoxide from heterotrophic bacteria and eukaryotic phytoplankton in diverse aerobic environments, including surface water, sediment, and soil.

The diversity, community dynamics, and interactions of the microbiome in the world's deepest blue hole: insights into extreme environmental response patterns and tolerance of marine microorganisms

IMPORTANCE

This study comprehensively examined the community dynamics, functional profiles, and interactions of the microbiome in the world's deepest blue hole. The findings revealed a positive correlation between the α-diversities of Symbiodiniaceae and archaea, indicating the potential reliance of Symbiodiniaceae on archaea in an extreme environment resulting from a partial niche overlap. The negative association between the α-diversity and β-diversity of the bacterial community suggested that the change rule of the bacterial community was consistent with the Anna Karenina effects. The core microbiome comprised nine microbial taxa, highlighting their remarkable tolerance and adaptability to sharp environmental gradient variations. Bacteria and archaea played significant roles in carbon, nitrogen, and sulfur cycles, while fungi contributed to carbon metabolism. This study advanced our understanding of the community dynamics, response patterns, and resilience of microorganisms populating the world's deepest blue hole, thereby facilitating further ecological and evolutional exploration of microbiomes in diverse extreme environments.

Microbiomes respond predictably to built habitats on the seafloor

The seafloor contains complex ecosystems where habitat heterogeneity influences biodiversity. Natural biological and geological features including vents, seeps and reefs create habitats that select for distinct populations of micro- and macrofauna. While largely studied for macrobiological diversity, built habitats may also select distinct microbiomes. Built habitat density on the seafloor is increasing with ocean sprawl expanding in the continental shelf and slope, potentially having widespread effects on benthic communities. This study addresses one type of built habitat, shipwrecks, on microbiomes in surrounding sediment. Using deep-sea sediment samples (762 total) from the Gulf of Mexico, we report elevated diversity and a predictable core microbiome around nine shipwrecks. We show the sphere of influence of built habitats extends up to 300 m onto the seafloor. Supervised learning made predictions of sample proximity to structures based on frequency of taxa. Strongest predictions occurred in sediments nearest and furthest from sites for archaea and mid-transect for bacteria. The response of archaea to built habitats was consistent across sites, while bacteria showed greater between site variability. The archaeal core shipwreck microbiome was enriched in taxa (e.g., Bathyarchaeia, Lokiarchaeia, Thermoplasmata) not present in the surrounding seafloor. Shipwrecks shaped microbiomes in expected ways, providing insight on how built habitats impact microbiome biodiversity in the Anthropocene.

First shotgun metagenomics study of Juan de Fuca deep-sea sediments reveals distinct microbial communities above, within, between, and below sulfate methane transition zones

The marine deep subsurface is home to a vast microbial ecosystem, affecting biogeochemical cycles on a global scale. One of the better-studied deep biospheres is the Juan de Fuca (JdF) Ridge, where hydrothermal fluid introduces oxidants into the sediment from below, resulting in two sulfate methane transition zones (SMTZs). In this study, we present the first shotgun metagenomics study of unamplified DNA from sediment samples from different depths in this stratified environment. Bioinformatic analyses showed a shift from a heterotrophic, Chloroflexota-dominated community above the upper SMTZ to a chemolithoautotrophic Proteobacteria-dominated community below the secondary SMTZ. The reintroduction of sulfate likely enables respiration and boosts active cells that oxidize acetate, iron, and complex carbohydrates to degrade dead biomass in this low-abundance, low-diversity environment. In addition, analyses showed many proteins of unknown function as well as novel metagenome-assembled genomes (MAGs). The study provides new insights into microbial communities in this habitat, enabled by an improved DNA extraction protocol that allows a less biased view of taxonomic composition and metabolic activities, as well as uncovering novel taxa. Our approach presents the first successful attempt at unamplified shotgun sequencing samples from beyond 50 meters below the seafloor and opens new ways for capturing the true diversity and functional potential of deep-sea sediments.

Marine nitrogen-fixers in the Canadian Arctic Gateway are dominated by biogeographically distinct noncyanobacterial communities

We describe diazotrophs present during a 2015 GEOTRACES expedition through the Canadian Arctic Gateway (CAG) using nifH metabarcoding. In the less studied Labrador Sea, Bradyrhizobium sp. and Vitreoscilla sp. nifH variants were dominant, while in Baffin Bay, a Stutzerimonas stutzeri variant was dominant. In comparison, the Canadian Arctic Archipelago (CAA) was characterized by a broader set of dominant variants belonging to Desulfobulbaceae, Desulfuromonadales, Arcobacter sp., Vibrio spp., and Sulfuriferula sp. Although dominant diazotrophs fell within known nifH clusters I and III, only a few of these variants were frequently recovered in a 5-year weekly nifH times series in the coastal NW Atlantic presented herein, notably S. stutzeri and variants belonging to Desulfobacterales and Desulfuromonadales. In addition, the majority of dominant Arctic nifH variants shared low similarity (< 92% nucleotide identities) to sequences in a global noncyanobacterial diazotroph catalog recently compiled by others. We further detected UCYN-A throughout the CAG at low-levels using quantitative-PCR assays. Temperature, depth, salinity, oxygen, and nitrate were most strongly correlated to the Arctic diazotroph diversity observed, and we found a stark division between diazotroph communities of the Labrador Sea versus Baffin Bay and the CAA, hence establishing that a previously unknown biogeographic community division can occur for diazotrophs in the CAG.

Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin

Deep marine sediments (>1mbsf) harbor ~26% of microbial biomass and are the largest reservoir of methane on Earth. Yet, the deep subsurface biosphere and controls on its contribution to methane production remain underexplored. Here, we use a multidisciplinary approach to examine methanogenesis in sediments (down to 295 mbsf) from sites with varying degrees of thermal alteration (none, past, current) at Guaymas Basin (Gulf of California) for the first time. Traditional (13C/12C and D/H) and multiply substituted (13CH3D and 12CH2D2) methane isotope measurements reveal significant proportions of microbial methane at all sites, with the largest signal at the site with past alteration. With depth, relative microbial methane decreases at differing rates between sites. Gibbs energy calculations confirm methanogenesis is exergonic in Guaymas sediments, with methylotrophic pathways consistently yielding more energy than the canonical hydrogenotrophic and acetoclastic pathways. Yet, metagenomic sequencing and cultivation attempts indicate that methanogens are present in low abundance. We find only one methyl-coenzyme M (mcrA) sequence within the entire sequencing dataset. Also, we identify a wide diversity of methyltransferases (mtaB, mttB), but only a few sequences phylogenetically cluster with methylotrophic methanogens. Our results suggest that the microbial methane in the Guaymas subsurface was produced over geologic time by relatively small methanogen populations, which have been variably influenced by thermal sediment alteration. Higher resolution metagenomic sampling may clarify the modern methanogen community. This study highlights the importance of using a multidisciplinary approach to capture microbial influences in dynamic, deep subsurface settings like Guaymas Basin.

Biofilm-a Syntrophic Consortia of Microbial Cells: Boon or Bane?

Biofilm is the conglomeration of microbial cells which is associated with a surface. In the recent times, the study of biofilm has gained popularity and vivid research is being done to know about the effects of biofilm and that it consists of many organisms which are symbiotic in nature, some of which are human pathogens. Here, in this study, we have discussed about biofilms, its formation, relevance of its presence in the biosphere, and the possible remediations to cope up with its negative effects. Since removal of biofilm is difficult, emphasis has been made to suggest ways to prevent biofilm formation and also to devise ways to utilize biofilm in an economically and environment-friendly method.

Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments

BACKGROUND

Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques.

RESULTS

Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle.

CONCLUSIONS

The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.

Spatiotemporal dynamics of high and low nucleic acid-content bacterial communities in Chinese coastal seawater: assembly process, co-occurrence relationship and the ecological functions

Studies of high nucleic acid-content (HNA) and low nucleic acid-content (LNA) bacterial communities are updating our view of their distributions and taxonomic composition. However, there are still large gaps in our knowledge of the composition, assembly processes, co-occurrence relationships and ecological functions of HNA and LNA bacterial communities. Here, using 16S rRNA gene amplicon sequencing, we investigated the spatiotemporal dynamics, assembly processes, co-occurrence relationships and ecological functions of HNA and LNA bacterial communities in the samples collected in summer and winter in Chinese coastal seas. The communities of HNA and LNA bacteria had clear spatiotemporal patterns and LNA bacteria was phylogenetically less diverse than HNA bacteria in both seasons. The distribution of HNA and LNA bacteria were significantly affected by the environmental factors and a significant seasonal-consistent distance-decay patterns were found in HNA and LNA bacteria. Furthermore, a quantitative assessment of ecological processes revealed that dispersal limitation, homogeneous selection exerted important roles in the community assembly of HNA and LNA bacteria. More importantly, we observed seasonality in the co-occurrence relationships: closer inter-taxa connections of HNA bacterial communities in winter than in summer and the opposite is true in the LNA bacterial communities. Some ecological functions, such as: phototrophy, photoautotrophy, oxygenic photoautotrophy, were different between HNA and LNA bacteria. These results provide a better understanding of spatiotemporal patterns, processes, and the ecological functions of HNA and LNA bacterial communities in Chinese coastal seawater.

Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities

Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.

Sulphate-reducing bacteria-mediated pyrite formation in the Dachang Tongkeng tin polymetallic deposit, Guangxi, China

Mediation by sulphate-reducing bacteria (SRB) is responsible for pyrite (FeS₂) formation. The origin of the Dachang tin polymetallic ore field is related to the mineralisation of submarine hydrothermal vent sediments. Here, we investigated SRB in these ores via morphological, chemical, and isotopic analyses. Polarised and scanning electron microscopy indicated that trace SRB fossils in the metal sulphide ore were present in the form of tubular, beaded, and coccoidal bodies comprising FeS₂ and were enclosed within a pyrrhotite (FeS) matrix in the vicinity of micro-hydrothermal vents. The carbon (C), nitrogen (N), and oxygen (O) contents in the FeS₂ synthesised by SRB were high, and a clear biological Raman signal was detected. No such signals were discerned in the peripheral FeS. This co-occurrence of FeS, FeS₂, and the remains of bacteria (probably chemoautotrophic bacteria) was interpreted as the coprecipitation process of SRB-mediated FeS₂ formation, which has, to the best of our knowledge, not been reported before. Our study also illustrates that combined energy-dispersive X-ray spectroscopy, Raman spectroscopy, and isotopic analysis can be used as a novel methodology to document microbial-mediated processes of mineral deposition in submarine hydrothermal vent ecology on geological time scales.

Traces of Ancient Life in Oceanic Basalt Preserved as Iron-Mineralized Ultrastructures: Implications for Detecting Extraterrestrial Biosignatures

Benefiting from their adaptability to extreme environments, subsurface microorganisms have been discovered in sedimentary and igneous rock environments on Earth and have been advocated as candidates in the search for extraterrestrial life. In this article, we study iron-mineralized microstructures in calcite-filled veins within basaltic pillows of the late Ladinian Fernazza group (Middle Triassic, 239 Ma) in Italy. These microstructures represent diverse morphologies, including filaments, globules, nodules, and micro-digitate stromatolites, which are similar to extant iron-oxidizing bacterial communities. In situ analyses including Raman spectroscopy have been used to investigate the morphological, elemental, mineralogical, and bond-vibrational modes of the microstructures. According to the Raman spectral parameters, iron minerals preserve heterogeneous ultrastructures and crystallinities, coinciding with the morphologies and precursor microbial activities. The degree of crystallinity usually represents a microscale gradient decreasing toward previously existing microbial cells, revealing a decline of mineralization due to microbial activities. This study provides an analog of possible rock-dwelling subsurface life on Mars or icy moons and advocates Raman spectroscopy as an efficient tool for in situ analyses. We put forward the concept that ultrastructural characteristics of minerals described by Raman spectral parameters corresponding to microscale morphologies could be employed as carbon-lean biosignatures in future space missions.

Taxonomic diversity of microbial communities in sub-seafloor hydrothermal sediments of the active Santorini-Kolumbo volcanic field

Introduction

Active hydrothermal vents of volcanic origin provide a remarkable manifestation of life on Earth under extreme conditions, which may have consequences for our understanding of habitability on other terrestrial bodies as well.

Methods

Here, we performed for the first time Illumina sequencing of bacterial and archaeal communities on sub-seafloor samples collected from the Santorini-Kolumbo volcanic field. A total of 19 (3-m long) gravity corers were collected and processed for microbial community analysis.

Results

From a total of 6,46,671 produced V4 sequences for all samples, a total of 10,496 different Operational Taxonomic Units (OTUs) were identified that were assigned to 40 bacterial and 9 archaeal phyla and 14 candidate divisions. On average, the most abundant phyla in all samples were Chloroflexi (Chloroflexota) (24.62%), followed by Proteobacteria (Pseudomonadota) (11.29%), Firmicutes (Bacillota) (10.73%), Crenarchaeota (Thermoproteota) (8.55%), and Acidobacteria (Acidobacteriota) (8.07%). At the genus level, a total of 286 known genera and candidate genera were mostly dominated by members of Bacillus, Thermoflexus, Desulfatiglans, Pseudoalteromonas, and Pseudomonas.

Discussion

In most of the stations, the Chao1 values at the deeper layers were comparable to the surface sediment samples denoting the high diversity in the subsurface of these ecosystems. Heatmap analysis based on the 100 most abundant OTUs, grouped the sampling stations according to their geographical location, placing together the two hottest stations (up to 99°C). This result indicates that this specific area within the active Kolumbo crater create a distinct niche, where microorganisms with adaptation strategies to withstand heat stresses can thrive, such as the endospore-forming Firmicutes.

Expansion of Armatimonadota through marine sediment sequencing describes two classes with unique ecological roles

Marine sediments comprise one of the largest environments on the planet, and their microbial inhabitants are significant players in global carbon and nutrient cycles. Recent studies using metagenomic techniques have shown the complexity of these communities and identified novel microorganisms from the ocean floor. Here, we obtained 77 metagenome-assembled genomes (MAGs) from the bacterial phylum Armatimonadota in the Guaymas Basin, Gulf of California, and the Bohai Sea, China. These MAGs comprise two previously undescribed classes within Armatimonadota, which we propose naming Hebobacteria and Zipacnadia. They are globally distributed in hypoxic and anoxic environments and are dominant members of deep-sea sediments (up to 1.95% of metagenomic raw reads). The classes described here also have unique metabolic capabilities, possessing pathways to reduce carbon dioxide to acetate via the Wood-Ljungdahl pathway (WLP) and generating energy through the oxidative branch of glycolysis using carbon dioxide as an electron sink, maintaining the redox balance using the WLP. Hebobacteria may also be autotrophic, not previously identified in Armatimonadota. Furthermore, these Armatimonadota may play a role in sulfur and nitrogen cycling, using the intermediate compounds hydroxylamine and sulfite. Description of these MAGs enhances our understanding of diversity and metabolic potential within anoxic habitats worldwide.

A dataset of micro biodiversity in benthic sediment at a global scale

Microorganisms, occupying the largest biomass in deep sea, play essential roles in deep-sea ecosystem. It is believed that the microbes in deep-sea sediments are more representative of deep-sea microbial communities, the microbial composition of which is seldom affected by ocean currents. However, the community of benthic microbes on a global scale has not been adequately explored. Herein, we build a comprehensive global dataset determined by 16S rRNA gene sequencing to characterize the biodiversity of microorganisms in benthic sediment. The dataset comprised 212 records from 106 sites, included sequencing of bacteria and archaea for each site and yielded 4,766,502 and 1,562,989 reads, respectively. Through annotation, a total of 110,073 and 15,795 OTUs of bacteria and archaea were obtained, and 61 bacterial phyla and 15 archaeal phyla were identified, of which the dominant phyla were Proteobacteria and Thaumarchaeota in deep-sea sediment. Therefore, our findings provided a biodiversity data of microbial communities in deep-sea sediment at global-scale and laid a foundation to further reveal the structures of microorganism communities in deep sea.

Genome characterization of two novel deep-sea sediment fungi, Penicillium pacificagyrus sp. nov. and Penicillium pacificasedimenti sp. nov., from South Pacific Gyre subseafloor sediments, highlights survivability

BACKGROUND

Marine deep subsurface sediments were once thought to be devoid of eukaryotic life, but advances in molecular technology have unlocked the presence and activity of well-known closely related terrestrial and marine fungi. Commonly detected fungi in deep marine sediment environments includes Penicillium, Aspergillus, Cladosporium, Fusarium, and Schizophyllum, which could have important implications in carbon and nitrogen cycling in this isolated environment. In order to determine the diversity and unknown metabolic capabilities of fungi in deep-sea sediments, their genomes need to be fully analyzed. In this study, two Penicillium species were isolated from South Pacific Gyre sediment enrichments during Integrated Ocean Drilling Program Expedition 329. The inner gyre has very limited productivity, organic carbon, and nutrients.

RESULTS

Here, we present high-quality genomes of two proposed novel Penicillium species using Illumina HiSeq and PacBio sequencing technologies. Single-copy homologues within the genomes were compared to other closely related genomes using OrthoMCL and maximum-likelihood estimation, which showed that these genomes were novel species within the genus Penicillium. We propose to name isolate SPG-F1 as Penicillium pacificasedimenti sp. nov. and SPG-F15 as Penicillium pacificagyrus sp. nov. The resulting genome sizes were 32.6 Mbp and 36.4 Mbp, respectively, and both genomes were greater than 98% complete as determined by the presence of complete single-copy orthologs. The transposable elements for each genome were 4.87% for P. pacificasedimenti and 10.68% for P. pacificagyrus. A total of 12,271 genes were predicted in the P. pacificasedimenti genome and 12,568 genes in P. pacificagyrus. Both isolates contained genes known to be involved in the degradation of recalcitrant carbon, amino acids, and lignin-derived carbon.

CONCLUSIONS

Our results provide the first constructed genomes of novel Penicillium isolates from deep marine sediments, which will be useful for future studies of marine subsurface fungal diversity and function. Furthermore, these genomes shed light on the potential impact fungi in marine sediments and the subseafloor could have on global carbon and nitrogen biogeochemical cycles and how they may be persisting in the most energy-limited sedimentary biosphere.

Anaerobic degradation of organic carbon supports uncultured microbial populations in estuarine sediments

BACKGROUND

A large proportion of prokaryotic microbes in marine sediments remains uncultured, hindering our understanding of their ecological functions and metabolic features. Recent environmental metagenomic studies suggested that many of these uncultured microbes contribute to the degradation of organic matter, accompanied by acetogenesis, but the supporting experimental evidence is limited.

RESULTS

Estuarine sediments were incubated with different types of organic matters under anaerobic conditions, and the increase of uncultured bacterial populations was monitored. We found that (1) lignin stimulated the increase of uncultured bacteria within the class Dehalococcoidia. Their ability to metabolize lignin was further supported by the presence of genes associated with a nearly complete degradation pathway of phenolic monomers in the Dehalococcoidia metagenome-assembled genomes (MAGs). (2) The addition of cellulose stimulated the increase of bacteria in the phylum Ca. Fermentibacterota and family Fibrobacterales, a high copy number of genes encoding extracellular endoglucanase or/and 1,4-beta-cellobiosidase for cellulose decomposition and multiple sugar transporters were present in their MAGs. (3) Uncultured lineages in the order Bacteroidales and the family Leptospiraceae were enriched by the addition of casein and oleic acid, respectively, a high copy number of genes encoding extracellular peptidases, and the complete β-oxidation pathway were found in those MAGs of Bacteroidales and Leptospiraceae, respectively. (4) The growth of unclassified bacteria of the order Clostridiales was found after the addition of both casein and cellulose. Their MAGs contained multiple copies of genes for extracellular peptidases and endoglucanase. Additionally, ¹³C-labeled acetate was produced in the incubations when ¹³C-labeled dissolved inorganic carbon was provided.

CONCLUSIONS

Our results provide new insights into the roles of microorganisms during organic carbon degradation in anaerobic estuarine sediments and suggest that these macro and single molecular organic carbons support the persistence and increase of uncultivated bacteria. Acetogenesis is an additional important microbial process alongside organic carbon degradation. Video Abstract.

Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

Cold seeps, where cold hydrocarbon-rich fluid escapes from the seafloor, show strong enrichment of toxic metalloid arsenic (As). The toxicity and mobility of As can be greatly altered by microbial processes that play an important role in global As biogeochemical cycling. However, a global overview of genes and microbes involved in As transformation at seeps remains to be fully unveiled. Using 87 sediment metagenomes and 33 metatranscriptomes derived from 13 globally distributed cold seeps, we show that As detoxification genes (arsM, arsP, arsC1/arsC2, acr3) were prevalent at seeps and more phylogenetically diverse than previously expected. Asgardarchaeota and a variety of unidentified bacterial phyla (e.g. 4484-113, AABM5-125-24 and RBG-13-66-14) may also function as the key players in As transformation. The abundances of As cycling genes and the compositions of As-associated microbiome shifted across different sediment depths or types of cold seep. The energy-conserving arsenate reduction or arsenite oxidation could impact biogeochemical cycling of carbon and nitrogen, via supporting carbon fixation, hydrocarbon degradation and nitrogen fixation. Overall, this study provides a comprehensive overview of As cycling genes and microbes at As-enriched cold seeps, laying a solid foundation for further studies of As cycling in deep sea microbiome at the enzymatic and processual levels.

Long-term warming modulates diversity, vertical structuring of microbial communities, and sulfate reduction in coastal Baltic Sea sediments

Coastal waters such as those found in the Baltic Sea already suffer from anthropogenic related problems including increased algal blooming and hypoxia while ongoing and future climate change will likely worsen these effects. Microbial communities in sediments play a crucial role in the marine energy- and nutrient cycling, and how they are affected by climate change and shape the environment in the future is of great interest. The aims of this study were to investigate potential effects of prolonged warming on microbial community composition and nutrient cycling including sulfate reduction in surface (∼0.5 cm) to deeper sediments (∼ 24 cm). To investigate this, 16S rRNA gene amplicon sequencing was performed, and sulfate concentrations were measured and compared between sediments in a heated bay (which has been used as a cooling water outlet from a nearby nuclear power plant for approximately 50 years) and a nearby but unaffected control bay. The results showed variation in overall microbial diversity according to sediment depth and higher sulfate flux in the heated bay compared to the control bay. A difference in vertical community structure reflected increased relative abundances of sulfur oxidizing- and sulfate reducing bacteria along with a higher proportion of archaea, such as Bathyarchaeota, in the heated compared to the control bay. This was particularly evident closer to the sediment surface, indicating a compression of geochemical zones in the heated bay. These results corroborate findings in previous studies and additionally point to an amplified effect of prolonged warming deeper in the sediment, which could result in elevated concentrations of toxic compounds and greenhouse gases closer to the sediment surface.

Abiotic selection of microbial genome size in the global ocean

Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.

The Early Microbial Colonizers of a Short-Lived Volcanic Island in the Kingdom of Tonga

The island of Hunga Tonga Hunga Ha'apai (HTHH) in the Kingdom of Tonga was formed by Surtseyan eruptions and persisted for 7 years before being obliterated by a massive volcanic eruption on 15 January 2022. Before it was destroyed, HTHH was an unparalleled natural laboratory to study primary succession on a newly formed landmass. We characterized the microbial communities found on the surface sediments of HTHH using a combination of quantitative PCR, marker gene sequencing, and shotgun metagenomic analyses. Contrary to expectations, photosynthetic cyanobacteria were not detected in these sediments, even though they are typically dominant in the earliest stages of primary succession in other terrestrial environments. Instead, our results suggest that the early sediment communities were composed of a diverse array of bacterial taxa, including trace gas oxidizers, anoxygenic photosynthesizers, and chemolithotrophs capable of metabolizing inorganic sulfur, with these bacteria likely sourced from nearby active geothermal environments. While the destruction of HTHH makes it impossible to revisit the site to conduct in situ metabolic measurements or observe how the microbial communities might have continued to change over time, our results do suggest that the early microbial colonizers have unique origins and metabolic capabilities. IMPORTANCE The volcanic island of Hunga Tonga Hunga Ha'apai in the Kingdom of Tonga represents a very rare example of new island formation and thus a unique opportunity to study how organisms colonize a new landmass. We found that the island was colonized by diverse microbial communities shortly after its formation in 2015, with these microbes likely originating from nearby geothermal environments. Primary succession in this system was distinct from that typically observed in other terrestrial environments, with the early microbial colonizers relying on unique metabolic strategies to survive on the surface of this newly formed island, including the capacity to generate energy via sulfur and trace gas metabolism.

Microbial Diversity, Community Turnover, and Putative Functions in Submarine Canyon Sediments under the Action of Sedimentary Geology

Sampling challenges in deep-sea ecosystems lead to a lack of knowledge about the distribution of microbes in different submarine canyons. To study microbial diversity and community turnover under different ecological processes, we performed 16S/18S rRNA gene amplicon sequencing for sediment samples from a submarine canyon in the South China Sea. Bacteria, archaea, and eukaryotes made up 57.94% (62 phyla), 41.04% (12 phyla), and 1.02% (4 phyla) of the sequences, respectively. Thaumarchaeota, Planctomycetota, Proteobacteria, Nanoarchaeota, and Patescibacteria are the five most abundant phyla. Heterogeneous community composition was mainly observed in vertical profiles rather than horizontal geographic locations, and microbial diversity in the surface layer was much lower than that in deep layers. According to the null model tests, homogeneous selection dominated community assembly within each sediment layer, whereas heterogeneous selection and dispersal limitation dominated community assembly between distant layers. Different sedimentation processes of sediments, i.e., rapid deposition caused by turbidity currents or slow sedimentation, seem to be primarily responsible for these vertical variations. Finally, functional annotation through shotgun-metagenomic sequencing found that glycosyl transferases and glycoside hydrolases are the most abundant carbohydrate-active enzyme categories. The most likely expressed sulfur cycling pathways include assimilatory sulfate reduction, the link between inorganic and organic sulfur transformation, and organic sulfur transformation, while the potentially activated methane cycling pathways include aceticlastic methanogenesis and aerobic and anaerobic oxidation of methane. Overall, our study revealed high levels of microbial diversity and putative functions in canyon sediments and the important influence of sedimentary geology on microbial community turnover between vertical sediment layers. IMPORTANCE Deep-sea microbes have received growing attention due to their contribution to biogeochemical cycles and climate change. However, related research lags due to the difficulty of collecting samples. Based on our previous study, which revealed the formation of sediments under the dual action of turbidity currents and seafloor obstacles in a submarine canyon in the South China Sea, this interdisciplinary research provides new insights into how sedimentary geology influences microbial community assembly in sediments. We proposed some uncommon or new findings, including the following: (i) microbial diversity was much lower on the surface than in deeper layers (ii) archaea and bacteria dominated the surface and deep layers, respectively; (iii) sedimentary geology played key roles in vertical community turnover; and (iv) the microbes have great potential to catalyze sulfur, carbon, and methane cycling. This study may lead to extensive discussion of the assembly and function of deep-sea microbial communities in the context of geology.

Microbial survival mechanisms within serpentinizing Mariana forearc sediments

Marine deep subsurface sediment is often a microbial environment under energy-limited conditions. However, microbial life has been found to persist and even thrive in deep subsurface environments. The Mariana forearc represents an ideal location for determining how microbial life can withstand extreme conditions including pH 10-12.5 and depleted nutrients. The International Ocean Discovery Program Expedition 366 to the Mariana Convergent Margin sampled three serpentinizing seamounts located along the Mariana forearc chain with elevated concentrations of methane, hydrogen, and sulfide. Across all three seamount summits, the most abundant transcripts were for cellular maintenance such as cell wall and membrane repair, and the most abundant metabolic pathways were the Entner-Doudoroff pathway and tricarboxylic acid cycle. At flank samples, sulfur cycling involving taurine assimilation dominated the metatranscriptomes. The in situ activity of these pathways was supported by the detection of their metabolic intermediates. All samples had transcripts from all three domains of Bacteria, Archaea, and Eukarya, dominated by Burkholderiales, Deinococcales, and Pseudomonales, as well as the fungal group Opisthokonta. All samples contained transcripts for aerobic methane oxidation (pmoABC) and denitrification (nirKS). The Mariana forearc microbial communities show activity not only consistent with basic survival mechanisms, but also coupled metabolic reactions.

Structure and metabolic potential of the prokaryotic communities from the hydrothermal system of Paleochori Bay, Milos, Greece

Introduction

Shallow hydrothermal systems share many characteristics with their deep-sea counterparts, but their accessibility facilitates their study. One of the most studied shallow hydrothermal vent fields lies at Paleochori Bay off the coast of Milos in the Aegean Sea (Greece). It has been studied through extensive mapping and its physical and chemical processes have been characterized over the past decades. However, a thorough description of the microbial communities inhabiting the bay is still missing.

Methods

We present the first in-depth characterization of the prokaryotic communities of Paleochori Bay by sampling eight different seafloor types that are distributed along the entire gradient of hydrothermal influence. We used deep sequencing of the 16S rRNA marker gene and complemented the analysis with qPCR quantification of the 16S rRNA gene and several functional genes to gain insights into the metabolic potential of the communities.

Results

We found that the microbiome of the bay is strongly influenced by the hydrothermal venting, with a succession of various groups dominating the sediments from the coldest to the warmest zones. Prokaryotic diversity and abundance decrease with increasing temperature, and thermophilic archaea overtake the community.

Discussion

Relevant geochemical cycles of the Bay are discussed. This study expands our limited understanding of subsurface microbial communities in acidic shallow-sea hydrothermal systems and the contribution of their microbial activity to biogeochemical cycling.

Ganga River sediments of India predominate with aerobic and chemo-heterotrophic bacteria majorly engaged in the degradation of xenobiotic compounds

Sediment provides a stagnant habitat to microbes that accumulate organic matter and other industrial pollutants from the upper layer of the water. The sediment of the Ganga River of India is overlooked for exploring the bacterial diversity despite their taxon richness over the water counterpart. To enrich the limited information on the bacterial diversity of the Ganga River sediment, the present study was planned that relies on amplicon-based bacterial diversity of the Ganga River sediment by using bacterial-specific 16S hypervariable region (V₃-V₄). The Illumina MiSeq2500 platform generated 1,769,226 raw reads from the metagenomes of various samples obtained from ten sites in five major cities of Uttar Pradesh and Uttarakhand regions traversing the Ganga River. Taxonomy level analysis assigned 58 phyla, 366 order, and 715 genera of bacterial type. The high values of various diversity indices (Chao1, Shannon, and Simpson) in Kanpur sediment indicate the high bacterial richness compared to the Rishikesh sediment. However, several other ecological parameters (Shannon index, Simpson index, enspie _vector, and Faith_pd) were comparatively higher in Rishikesh sediment which is a comparatively less disturbed region by human activities over the other sediments samples studied here. Ganga River sediment dominates with Gram-negative, chemo-heterotrophic, and aerobic bacteria that chiefly belong to Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidota. The abundance of Nitrospira, Hydrogenophaga, Thauera, Vicinamibacteraceae, and Latescibacterota in the Ganga River sediment could be considered as the ecological indicators that find a significant role in the degradation of xenobiotic compounds. The PICRUSt-based analysis showed that ~ 35% of genes were involved in benzoate and aminobenzoate degradation where a significant portion of genes belong to nitrotoluene degradation (14%). Thus, the study uncovers a new perspective in the lineage of bacterial communities and their functional characterization of the Ganga River sediment.

Geographic Scale Influences the Interactivities Between Determinism and Stochasticity in the Assembly of Sedimentary Microbial Communities on the South China Sea Shelf

Determinism and stochasticity in microbial community composition decisions have attracted wide attention. However, there is no consensus on their interrelationships and relative importance, and the mechanism controlling the interaction between the two ecological processes remains to be revealed. The interaction of the two ecological processes on the continental shelf of the South China Sea was studied by performing 16S rRNA gene amplicon sequencing on 90 sediments at multiple depths in five sites. Three nearshore sites have higher microbial diversity than those two close to the shelf margin. Different microbial composition was observed between sites and microbial composition of nearshore sites was positively correlated with total nitrogen, total sulfur, total organic carbon, and dissolved oxygen, while that of offshore was positively correlated with total carbon, salinity, and photosynthetically active radiation. The null model test showed that the community composition among layers of the same site and between nearby sites was mainly dominated by the homogeneous selection, while that between distant sites was mainly affected by dispersal limitation, which indicates that geographic scale influences the interactivities of determinism and stochasticity. Our research indicates that the balance of these two ecological processes along the geographic scale is mainly determined by the dispersal ability of microbes and environmental heterogeneity between areas. The study provides new insights into how deterministic and stochastic processes shape microbial community composition on the continental shelf.

Single-cell view of deep-sea microbial activity and intracommunity heterogeneity

Microbial activity in the deep sea is cumulatively important for global elemental cycling yet is difficult to quantify and characterize due to low cell density and slow growth. Here, we investigated microbial activity off the California coast, 50-4000 m water depth, using sensitive single-cell measurements of stable-isotope uptake and nucleic acid sequencing. We observed the highest yet reported proportion of active cells in the bathypelagic (up to 78%) and calculated that deep-sea cells (200-4000 m) are responsible for up to 34% of total microbial biomass synthesis in the water column. More cells assimilated nitrogen derived from amino acids than ammonium, and at higher rates. Nitrogen was assimilated preferentially to carbon from amino acids in surface waters, while the reverse was true at depth. We introduce and apply the Gini coefficient, an established equality metric in economics, to quantify intracommunity heterogeneity in microbial anabolic activity. We found that heterogeneity increased with water depth, suggesting a minority of cells contribute disproportionately to total activity in the deep sea. This observation was supported by higher RNA/DNA ratios for low abundance taxa at depth. Intracommunity activity heterogeneity is a fundamental and rarely measured ecosystem parameter and may have implications for community function and resilience.

Ancestral reconstruction reveals catalytic inactivation of activation-induced cytidine deaminase concomitant with cold water adaption in the Gadiformes bony fish

BACKGROUND

Antibody affinity maturation in vertebrates requires the enzyme activation-induced cytidine deaminase (AID) which initiates secondary antibody diversification by mutating the immunoglobulin loci. AID-driven antibody diversification is conserved across jawed vertebrates since bony and cartilaginous fish. Two exceptions have recently been reported, the Pipefish and Anglerfish, in which the AID-encoding aicda gene has been lost. Both cases are associated with unusual reproductive behavior, including male pregnancy and sexual parasitism. Several cold water fish in the Atlantic cod (Gadinae) family carry an aicda gene that encodes for a full-length enzyme but lack affinity-matured antibodies and rely on antibodies of broad antigenic specificity. Hence, we examined the functionality of their AID.

RESULTS

By combining genomics, transcriptomics, immune responsiveness, and functional enzymology of AID from 36 extant species, we demonstrate that AID of that Atlantic cod and related fish have extremely lethargic or no catalytic activity. Through ancestral reconstruction and functional enzymology of 71 AID enzymes, we show that this enzymatic inactivation likely took place relatively recently at the emergence of the true cod family (Gadidae) from their ancestral Gadiformes order. We show that this AID inactivation is not only concordant with the previously shown loss of key adaptive immune genes and expansion of innate and cell-based immune genes in the Gadiformes but is further reflected in the genomes of these fish in the form of loss of AID-favored sequence motifs in their immunoglobulin variable region genes.

CONCLUSIONS

Recent demonstrations of the loss of the aicda gene in two fish species challenge the paradigm that AID-driven secondary antibody diversification is absolutely conserved in jawed vertebrates. These species have unusual reproductive behaviors forming an evolutionary pressure for a certain loss of immunity to avoid tissue rejection. We report here an instance of catalytic inactivation and functional loss of AID rather than gene loss in a conventionally reproducing vertebrate. Our data suggest that an expanded innate immunity, in addition to lower pathogenic pressures in a cold environment relieved the pressure to maintain robust secondary antibody diversification. We suggest that in this unique scenario, the AID-mediated collateral genome-wide damage would form an evolutionary pressure to lose AID function.

Frequent Occurrence and Metabolic Versatility of Marinifilaceae Bacteria as Key Players in Organic Matter Mineralization in Global Deep Seas

Transfer of animal and plant detritus of both terrestrial and marine origins to the deep sea occurs on a global scale. Microorganisms play an important role in mineralizing them therein, but these are yet to be identified in situ. To observe key bacteria involved, we conducted long-term in situ incubation and found that members of the family Marinifilaceae (MF) occurred as some of the most predominant bacteria thriving on the new inputs of plant and animal biomasses in the deep sea in both marginal and oceanic areas. This taxon is diverse and ubiquitous in marine environments. A total of 11 MAGs belonging to MF were retrieved from metagenomic data and diverged into four subgroups in the phylogenomic tree. Based on metagenomic and metatranscriptomic analyses, we described the metabolic features and in situ metabolizing activities of different subgroups. The MF-2 subgroup, which dominates plant detritus-enriched cultures, specializes in polysaccharide degradation and lignin oxidation and has high transcriptional activities of related genes in situ. Intriguingly, members of this subgroup encode a nitrogen fixation pathway to compensate for the shortage of nitrogen sources inside the plant detritus. In contrast, other subgroups dominating the animal tissue-supported microbiomes are distinguished from MF-2 with regard to carbon and nitrogen metabolism and exhibit high transcriptional activity for proteolysis in situ. Despite these metabolic divergences of MF lineages, they show high in situ transcriptional activities for organic fermentation and anaerobic respiration (reductions of metal and/or dimethyl sulfoxide). These results highlight the role of previously unrecognized Marinifilaceae bacteria in organic matter mineralization in marine environments by coupling carbon and nitrogen cycling with metal and sulfur. IMPORTANCE Microbial mineralization of organic matter has a significant impact on the global biogeochemical cycle. This report confirms the role of Marinifilaceae in organic degradation in the oceans, with a contribution to ocean carbon cycling that has previously been underestimated. It was the dominant taxon thriving on plant and animal biomasses in our in situ incubator, as well as in whale falls and wood falls. At least 9 subgroups were revealed, and they were widely distributed in oceans globally but predominant in organic-matter-rich environments, with an average relative abundance of 8.3%. Different subgroups display a preference for the degradation of different macromolecules (polysaccharides, lignin, and protein) and adapt to their environments via special metabolic mechanisms.

Fast-growing Arctic Fe-Mn deposits from the Kara Sea as the refuges for cosmopolitan marine microorganisms

The impact of biomineralization and redox processes on the formation and growth of ferromanganese deposits in the World Ocean remains understudied. This problem is particularly relevant for the Arctic marine environment where sharp seasonal variations of temperature, redox conditions, and organic matter inflow significantly impact the biogenic and abiotic pathways of ferromanganese deposits formation. The microbial communities of the fast-growing Arctic Fe-Mn deposits have not been reported so far. Here, we describe the microbial diversity, structure and chemical composition of nodules, crust and their underlying sediments collected from three different sites of the Kara Sea. Scanning electron microscopy revealed a high abundance of microfossils and biofilm-like structures within the nodules. Phylogenetic profiling together with redundancy and correlation analyses revealed a positive selection for putative metal-reducers (Thermodesulfobacteriota), iron oxidizers (Hyphomicrobiaceae and Scalinduaceae), and Fe-scavenging Nitrosopumilaceae or Magnetospiraceae in the microenvironments of the Fe-Mn deposits from their surrounding benthic microbial populations. We hypothesize that in the Kara Sea, the nodules provide unique redox-stable microniches for cosmopolitan benthic marine metal-cycling microorganisms in an unsteady environment, thus focusing the overall geochemical activity of nodule-associated microbial communities and accelerating processes of ferromanganese deposits formation to uniquely high rates.

Effects of Different Types of Human Disturbance on Total and Nitrogen-Transforming Bacteria in Haihe River

Haihe River is the largest water system in North China and is injected into the Bohai Sea in Tianjin City. In this study, different types of human disturbance (urban sewage, industrial pollution, ship disturbance) were selected from the upper reaches of Haihe river Tianjin section down to the estuary that connected with Bohai Sea for evaluation. By metagenomic sequencing, the effects of different types of disturbances on bacteria communities in Haihe sediments were studied, with a special focus on the function of nitrogen-cycling bacteria that were further analyzed through KEGG comparison. By analyzing the physical and chemical characteristics of sediments, results showed that human disturbance caused a large amount of nitrogen input into Haihe River, and different types of human disturbance led to distinct spatial heterogeneity in different sections of Haihe River. The bacteria community was dominated by Proteobacteria, followed by Chloroflexi, Bacteroidetes, Actinobacteria and Acidobacteria. The relative abundance of each phylum varied at different sites as a response to different types of human disturbances. In nitrogen cycling, microorganisms including nitrogen fixation and removal were detected at each site, which indicated the active potential for nitrogen transformation in Haihe River. In addition, a large number of metabolic pathways relating to human diseases were also revealed in urban and pollution sites by function potential, which provided an important basis for the indicative role of urban river ecosystem for public health security. In summary, by evaluating both the ecological role and function potential of bacteria in Haihe River under different types of human disturbance, the knowledge of microorganisms for healthy and disturbed river ecosystems has been broadened, which is also informative for further river management and bioremediation.

Distribution pattern of N-damo bacteria along an anthropogenic nitrogen input gradient from the coastal mangrove wetland to the South China sea sediments

Microbial nitrite-dependent anaerobic methane oxidation (n-damo) process is important for mitigating methane emission and anthropogenic nitrogen inputs in the marine environment. However, the distribution pattern of n-damo bacteria along an anthropogenic N-input gradient from the coastal wetland to the pristine South China Sea is poorly understood. This study investigated the diversity and abundance of n-damo bacteria in samples collected along a N-input gradient from Mai Po (MP) mangrove wetland sediments of the Pearl River Estuary (PRE) to the deep ocean sediments of the South China Sea (SCS). Retrieved 16S rDNA sequences showed a shift of n-damo community composition of complex structures with both freshwater and marine n-damo lineages in MP intertidal sediments to marine dominated characteristic in SCS sediments. The observed variation of Shannon and Chao1 indexes of n-damo bacteria shared a similar trend of a decrease at first followed by an increase along the targeting gradient with previously investigated methanogens, anaerobic methanotrophic archaea, ammonia-oxidizing archaea and ammonia-oxidizing bacteria, but had a reverse pattern with anammox bacteria. The community structure of pmoA gene sequences contained freshwater lineages only in SCS continental shelf sediments closer to the PRE, and turned to group with other marine samples in deeper and pristine sediments. Results suggested that n-damo bacteria might be a major contributor to anaerobic denitrification in the SCS sediments because their abundances were much higher than previously studied anammox bacteria in the same sample set. The distribution pattern of n-damo bacterial diversity, richness and abundance along the anthropogenic N-input gradient implies that they could be used as a bio-indicator for monitoring the anthropogenic/terrestrial inputs in marine environments.

Biogeography and Population Divergence of Microeukaryotes Associated with Fluids and Chimneys in the Hydrothermal Vents of the Southwest Indian Ocean

Deep-sea hydrothermal vents have been proposed as oases for microbes, but microeukaryotes as key components of the microbial loop have not been well studied. Based on high-throughput sequencing and network analysis of the 18S rRNA gene, distinct biogeographical distribution patterns and impacting factors were revealed from samples in the three hydrothermal fields of the southwest Indian Ocean, where higher gene abundance of microeukaryotes appeared in chimneys. The microeukaryotes in the fluids might be explained by hydrogeochemical heterogeneity, especially that of the nitrate and silicate concentrations, while the microeukaryotes in the chimneys coated with either Fe oxides or Fe-Si oxyhydroxides might be explained by potentially different associated prokaryotic groups. Population divergence of microeukaryotes, especially clades of parasitic Syndiniales, was observed among different hydrothermal fluids and chimneys and deserves further exploration to gain a deeper understanding of the trophic relationships and potential ecological function of microeukaryotes in the deep-sea extreme ecosystems, especially in the complex deep-sea chemoautotrophic habitats. IMPORTANCE Deep-sea hydrothermal vents have been proposed as oases for microbes, but microeukaryotes as key components of the microbial loop have not been well studied. Based on high-throughput sequencing and network analysis of the 18S rRNA gene, population divergence of microeukaryotes, especially clades of parasitic Syndiniales, was observed among different hydrothermal fields. This might be attributed to the hydrogeochemical heterogeneity of fluids and to the potentially different associated prokaryotic groups in chimneys.

An Ancient Respiratory System in the Widespread Sedimentary Archaea Thermoprofundales

Thermoprofundales, formerly Marine Benthic Group D (MBG-D), is a ubiquitous archaeal lineage found in sedimentary environments worldwide. However, its taxonomic classification, metabolic pathways, and evolutionary history are largely unexplored because of its uncultivability and limited number of sequenced genomes. In this study, phylogenomic analysis and average amino acid identity values of a collection of 146 Thermoprofundales genomes revealed five Thermoprofundales subgroups (A-E) with distinct habitat preferences. Most of the microorganisms from Subgroups B and D were thermophiles inhabiting hydrothermal vents and hot spring sediments, whereas those from Subgroup E were adapted to surface environments where sunlight is available. H2 production may be featured in Thermoprofundales as evidenced by a gene cluster encoding the ancient membrane-bound hydrogenase (MBH) complex. Interestingly, a unique structure separating the MBH gene cluster into two modular units was observed exclusively in the genomes of Subgroup E, which included a peripheral arm encoding the [NiFe] hydrogenase domain and a membrane arm encoding the Na+/H+ antiporter domain. These two modular structures were confirmed to function independently by detecting the H2-evolving activity in vitro and salt tolerance to 0.2 M NaCl in vivo, respectively. The peripheral arm of Subgroup E resembles the proposed common ancestral respiratory complex of modern respiratory systems, which plays a key role in the early evolution of life. In addition, molecular dating analysis revealed that Thermoprofundales is an early emerging archaeal lineage among the extant MBH-containing microorganisms, indicating new insights into the evolution of this ubiquitous archaea lineage.

A miniaturized bionic ocean-battery mimicking the structure of marine microbial ecosystems

Marine microbial ecosystems can be viewed as a huge ocean-battery charged by solar energy. It provides a model for fabricating bio-solar cell, a bioelectrochemical system that converts light into electricity. Here, we fabricate a bio-solar cell consisting of a four-species microbial community by mimicking the ecological structure of marine microbial ecosystems. We demonstrate such ecological structure consisting of primary producer, primary degrader, and ultimate consumers is essential for achieving high power density and stability. Furthermore, the four-species microbial community is assembled into a spatial-temporally compacted cell using conductive hydrogel as a sediment-like anaerobic matrix, forming a miniaturized bionic ocean-battery. This battery directly converts light into electricity with a maximum power of 380 μW and stably operates for over one month. Reproducing the photoelectric conversion function of marine microbial ecosystems in this bionic battery overcomes the sluggish and network-like electron transfer, showing the biotechnological potential of synthetic microbial ecology.

Spatial patterns of microbial diversity in Fe-Mn deposits and associated sediments in the Atlantic and Pacific oceans

Mining of deep-sea Fe-Mn deposits will remove crusts and nodules from the seafloor. The growth of these minerals takes millions of years, yet little is known about their microbiome. Besides being key elements of the biogeochemical cycles and essential links of food and energy to deep-sea, microbes have been identified to affect manganese oxide formation. In this study, we determined the composition and diversity of Bacteria and Archaea in deep-sea Fe-Mn crusts, nodules, and associated sediments from two areas in the Atlantic Ocean, the Tropic Seamount and the Rio Grande Rise. Samples were collected using ROV and dredge in 2016 and 2018 oceanographic campaigns, and the 16S rRNA gene was sequenced using Illumina platform. Additionally, we compared our results with microbiome data of Fe-Mn crusts, nodules, and sediments from Clarion-Clipperton Zone and Takuyo-Daigo Seamount in the Pacific Ocean. We found that Atlantic seamounts harbor an unusual and unknown Fe-Mn deposit microbiome with lower diversity and richness compared to Pacific areas. Crusts and nodules from Atlantic seamounts have unique taxa (Alteromonadales, Nitrospira, and Magnetospiraceae) and a higher abundance of potential metal-cycling bacteria, such as Betaproteobacteriales and Pseudomonadales. The microbial beta-diversity from Atlantic seamounts was clearly grouped into microhabitats according to sediments, crusts, nodules, and geochemistry. Despite the time scale of million years for these deposits to grow, a combination of environmental settings played a significant role in shaping the microbiome of crusts and nodules. Our results suggest that microbes of Fe-Mn deposits are key in biogeochemical reactions in deep-sea ecosystems. These findings demonstrate the importance of microbial community analysis in environmental baseline studies for areas within the potential of deep-sea mining.