Linking extracellular enzymes to phylogeny indicates a predominantly particle-associated lifestyle of deep-sea prokaryotes

Community differences and potential function along the particle size spectrum of microbes in the twilight zone

BACKGROUND

The twilight zone, which extends from the base of the euphotic zone to a depth of 1000 m, is the major area of particulate organic carbon (POC) remineralization in the ocean. However, little is known about the microbial community and metabolic activity that are directly associated with POC remineralization in this consistently underexplored realm. Here, we utilized a large-volume in situ water transfer system to collect the microbes on different-sized particles from the twilight zone in three regions and analyzed their composition and metabolic function by metagenomic analysis.

RESULTS

Distinct prokaryotic communities with significantly lower diversity and less endemic species were detected on particles in the South East Asian Time-series Study (SEATS) compared with the other two regions, perhaps due to the in situ physicochemical conditions and low labile nutrient availability in this region. Observable transitions in community composition and function at the upper and lower boundaries of the twilight zone suggest that microbes respond differently to (and potentially drive the transformation of) POC through this zone. Substantial variations among different particle sizes were observed, with smaller particles typically exhibiting lower diversity but harboring a greater abundance of carbon degradation-associated genes than the larger particles. Such a pattern might arise due to the relatively larger surface area of the smaller particles relative to their volume, which likely provides more sites for microbial colonization, increasing their chance of being remineralized. This makes them less likely to be transferred to the deep ocean, and thus, they contribute more to carbon recycling than to long-term sequestration. Both contig-based and metagenome-assembled genome-(MAG-) based analyses revealed a high diversity of the Carbohydrate-Active enZymes (CAZy) family. This indicates the versatile carbohydrate metabolisms of the microbial communities associated with sinking particles that modulate the remineralization and export of POC in the twilight zone.

CONCLUSION

Our study reveals significant shifts in microbial community composition and function in the twilight zone, with clear differences among the three particle sizes. Microbes with diverse metabolic potential exhibited different responses to the POC entering the twilight zone and also collectively drove the transformation of POC through this zone. These findings provided insights into the diversity of prokaryotes in sinking particles and their roles in POC remineralization and export in marine ecosystems. Video Abstract.

Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach

BACKGROUND

Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.

RESULTS

Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).

CONCLUSIONS

Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.

Collaborative metabolic curation of an emerging model marine bacterium, Alteromonas macleodii ATCC 27126

Inferring the metabolic capabilities of an organism from its genome is a challenging process, relying on computationally-derived or manually curated metabolic networks. Manual curation can correct mistakes in the draft network and add missing reactions based on the literature, but requires significant expertise and is often the bottleneck for high-quality metabolic reconstructions. Here, we present a synopsis of a community curation workshop for the model marine bacterium Alteromonas macleodii ATCC 27126 and its genome database in BioCyc, focusing on pathways for utilizing organic carbon and nitrogen sources. Due to the scarcity of biochemical information or gene knock-outs, the curation process relied primarily on published growth phenotypes and bioinformatic analyses, including comparisons with related Alteromonas strains. We report full pathways for the utilization of the algal polysaccharides alginate and pectin in contrast to inconclusive evidence for one-carbon metabolism and mixed acid fermentation, in accordance with the lack of growth on methanol and formate. Pathways for amino acid degradation are ubiquitous across Alteromonas macleodii strains, yet enzymes in the pathways for the degradation of threonine, tryptophan and tyrosine were not identified. Nucleotide degradation pathways are also partial in ATCC 27126. We postulate that demonstrated growth on nitrate as sole nitrogen source proceeds via a nitrate reductase pathway that is a hybrid of known pathways. Our evidence highlights the value of joint and interactive curation efforts, but also shows major knowledge gaps regarding Alteromonas metabolism. The manually-curated metabolic reconstruction is available as a "Tier-2" database on BioCyc.

Impact of salinity gradients on nitric oxide emissions and functional microbes in estuarine wetland sediments

Estuarine wetland sediments are hotspots for nitrogen cycling and critical sources of atmospheric nitric oxide (NO). Yet studies on the impact of sediment salinity gradients on NO emissions and associated functional microbes at the land-ocean interface remain limited. Here, we measured sediment NO emission rates from incubated sediment samples that were collected from an estuarine wetland in Qingdao, China. Our findings indicate that sediment salinity is a pivotal factor shaping NO emission rates, by altering the community composition and gene abundance of functional microbes involved in NO emissions, with rates ranging from 0.04 to 0.25 μg N kg-1 dry soil h-1. Metagenomic analysis of the sediment samples reveals that greater NO emission rates (+486 %) under salinity changes are linked to a higher abundance of the nirS gene (+26 %) responsible for NO formation and a lower abundance of norBC genes (-23 %) responsible for NO consumption. Accordingly, the increase of NO emissions may be attributed to the accumulation of denitrifying NO, which could improve plant salt tolerance through co-evolutionary interactions between plants and sediment-dwelling microbes. Taken together, these findings contribute to a richer understanding of how biochemical NO emissions in estuarine wetland sediments respond to salinity gradients.

Ayu: a machine intelligence tool for identification of extracellular proteins in the marine secretome

Microbes are the engines driving the elemental cycles. In order to interact with their environment and the community, microbes secrete proteins into the environment (known collectively as the secretome), where they remain active for prolonged periods of time. Despite the environmental relevance of microbes, our knowledge of the marine secretome remains limited due to a lack of effective in silico methods for the study of secreted proteins. An alternative approach to characterise the secretome is to combine modern machine learning tools with the evolutionary adaptation changes of the proteome to the marine environment. In this study, we identify and describe adaptations of marine extracellular proteins, which vary between phyla, resulting in differences in ATP costs, amino acid composition and nitrogen and sulphur content. We develop 'Ayu', a machine prediction tool that does not employ homology-based predictors and achieves better and quicker performance than current state-of-the-art software. When applied to oceanic samples (Tara Oceans dataset), our method was able to recover more than double the proteins compared to the most widely used method to identify secreted proteins. The application of this tool to open ocean samples allows better characterisation of the composition of the marine secretome.

Decrypting the phylogeny and metabolism of microbial dark matter in green and red Antarctic snow

Antarctic snow harbors diverse microorganisms, including pigmented algae and bacteria, which create colored snow patches and influence global climate and biogeochemical cycles. However, the genomic diversity and metabolic potential of colored snow remain poorly understood. We conducted a genome-resolved study of microbiomes in colored snow from 13 patches (7 green and 6 red) on the Fildes Peninsula, Antarctica. Using metagenome assembly and binning, we reconstructed 223 metagenome-assembled genomes (MAGs), with 91% representing previously unexplored microbes. Green snow (GS) and red snow (RS) showed distinct MAGs profile, with Polaromonas and Ferruginibacter as the most abundant genera, respectively. GS exhibited higher alpha diversity with more unique and enriched MAGs, while RS showed greater variability with higher beta diversity. All MAGs contained genes encoding auxiliary activities (AAs), carbohydrate esterases (CEs), glycoside hydrolases (GHs), and glycosyl transferases (GTs), indicating microbial degradation of complex carbon substrates. The most abundant enzymes included GT2 (cellulose synthase), GT4 (sucrose synthase), CE1 (acetyl xylan esterase), GT41 (peptide beta-N-acetylglucosaminyltransferase), and CE10 (arylesterase). GS had a higher abundance of GTs, whereas RS was enriched in GHs. Furthermore, 56% of MAGs contained genes for inorganic nitrogen cycling, with 18 gene families involved in assimilatory nitrate reduction, dissimilatory nitrate reduction, and denitrification. Potential coupling of nitrogen cycling and carbohydrate metabolism was observed at both genome and community levels, suggesting close links between these pathways, particularly through nitrate reduction during carbohydrate degradation. This study enhances our understanding of microbial metabolic functions in polar ecosystems and highlights their roles in maintaining Antarctic ecological stability.

Revealing the metabolic potential and environmental adaptation of nematophagous fungus, Purpureocillium lilacinum, derived from hadal sediment

The extreme environment shapes fungi in deep-sea sediments with novel metabolic capabilities. The ubiquity of fungi in deep-sea habitats supports their significant roles in these ecosystems. However, there is limited research on the metabolic activities and adaptive mechanisms of filamentous fungi in deep-sea ecosystems. In this study, we investigated the biological activities, including antibacterial, antitumor and nematicidal activity of Purpureocillium lilacinum FDZ8Y1, isolated from sediments of the Mariana Trench. A key feature of P. lilacinum FDZ8Y1 was its tolerance to high hydrostatic pressure (HHP), up to 110 MPa. We showed that HHP affected its vegetative growth, development, and production of secondary metabolites, indicating the potential for discovering novel natural products from hadal fungi. Whole-genome sequencing of P. lilacinum FDZ8Y1 revealed the metabolic potential of this piezotolerant fungus in carbon (carbohydrate metabolism), nitrogen (assimilatory nitrate reduction and protein degradation) and sulfur cycling processes (assimilatory sulfate reduction). Transcriptomic analysis under elevated HHP showed that P. lilacinum FDZ8Y1 may activate several metabolic pathways and stress proteins to cope with HHP, including fatty acid metabolism, the antioxidant defense system, the biosynthetic pathway for secondary metabolites, extracellular enzymes and membrane transporters. This study provides valuable insights into the metabolic potential and adaptation mechanisms of hadal fungi to the challenging conditions of the hadal environment.

Organic matter composition fluctuations disrupt free-living bacterial communities more than particle-associated bacterial communities in coastal waters

Marine organic matter fuels the growth of microbial communities, shaping the composition of bacteria that specialize in its breakdown. However, responses of free-living (FL) and particle-associated (PA) bacterial communities to the changing pools of dissolved organic matter (DOM) and particulate organic matter (POM) remained unclear. This study investigates the composition of size-fractionated bacterial communities, DOM and POM in coastal waters over a 22-day period that includes a diatom bloom. Co-occurrence analysis showed that the FL bacterial communities were significantly less stable than PA communities. During the diatom bloom, we observed a significant increase in DOM molecules, particularly those derived from amino acids and peptides. In contrast, the relative intensities of major POM molecule classes remained stable despite the algal bloom's influence. Our study revealed a strong negative correlation between bacterial alpha-diversity and the amount of molecules in the organic matter pool. Similarly, bacterial community beta-diversity was found to be related to the composition of organic matter pool. However, the composition of organic matter was more strongly related to the composition of FL bacterial communities compared to PA communities. This suggests that FL bacteria exhibit greater variations in temporal dynamics and higher sensitivity to the specific structure of organic matter molecules.

Insights into prokaryotic communities and their potential functions in biogeochemical cycles in cold seep

Microorganisms are significant drivers of organic matter mineralization and are essential in marine biogeochemical cycles. However, the variations and influencing factors in prokaryotic communities from cold-seep sediments to the water column and the specific role of these microorganisms in biogeochemical cycles in the water column above cold seep remain unclear. Here, we investigated prokaryotic communities and their roles in nitrogen/sulfur cycling processes and conducted in situ dissolved organic matter (DOM) enrichment experiments to explore the effects of diverse sources of DOM on prokaryotic communities. Field investigations showed that the prokaryotic communities in the near-bottom water were more similar to those in the deep layer of the euphotic zone (44.60%) and at a depth of 400 m (50.89%) than those in the sediment (18.00%). DOM enrichment experiments revealed that adding dissolved organic nitrogen (DON) and phosphorus DOP caused a notable increase in the relative abundances of Rhodobacterales and Vibrionales, respectively. A remarkable increase was observed in the relative abundance of Alteromonadales and Pseudomonadales after the addition of dissolved organic sulfur (DOS). The metagenomic results revealed that Proteobacteria served as the keystone taxa in mediating the biogeochemical cycles of nitrogen, phosphorus, and sulfur in the Haima cold seep. This study highlights the responses of prokaryotes to DOM with different components and the microbially driven elemental cycles in cold seeps, providing a foundational reference for further studies on material energy metabolism and the coupled cycling of essential elements mediated by deep-sea microorganisms.

IMPORTANCE

Deep-sea cold seeps are among the most productive ecosystems, sustaining unique fauna and microbial communities through the release of methane and other hydrocarbons. Our study revealed that the influence of seepage fluid on the prokaryotic community in the water column is surprisingly limited, which challenges conventional views regarding the impact of seepage fluids. In addition, we identified that different DOM compositions play a crucial role in shaping the prokaryotic community composition, providing new insights into the factors driving microbial diversity in cold seeps. Furthermore, the study highlighted Proteobacteria as key and multifaceted drivers of biogeochemical cycles in cold seeps, emphasizing their significant contribution to complex interactions and processes. These findings offer a fresh perspective on the dynamics of cold-seep environments and their microbial communities, advancing our understanding of the biogeochemical functions in deep-sea environments.

Significant response of coral-associated bacteria and their carbohydrate-active enzymes diversity to coral bleaching

Analysis of bacterial carbohydrate-active enzymes (CAZymes) contributes significantly to comprehending the response exhibited by coral symbionts to the external environment. This study explored the impact of bleaching on the bacteria and their CAZymes in coral Favites sp. through metagenomic sequencing. Notably, principal coordinates analysis (PCoA) unveiles substantial difference in bacterial communities between bleached and unbleached corals. Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidota, and Chloroflexi, exhibit noteworthy alterations during coral bleaching. CAZymes profiles in bleached coral disclosed a significant increase in Glycosyltransferases (GTs) abundance, suggesting an intensified biosynthesis of polysaccharides. Conversely, there is a marked reduction in other CAZymes abundance in bleached coral. Proteobacteria, Bacteroidota, Chlorobi, and Planctomycetota exhibit greater contributions to CAZymes in bleached corals, with Rhodobacterales, Cytophagales, Burkholderiales, Caulobacterales, and Hyphomicrobiales being the main contributors. While Acidobacteria, Actinobacteria, and Chloroflexi demonstrate higher contributions to CAZymes in unbleached corals. The changes in bacteria and their CAZymes reflect the ecological adaptability of coral holobionts when facing environmental stress. The alterations in CAZymes composition caused by bleaching events may have profound impacts on coral nutrient absorption and ecosystem stability. Therefore, understanding the dynamic changes in CAZymes is crucial for assessing the health and recovery potential of coral ecosystems.

EXCRETE workflow enables deep proteomics of the microbial extracellular environment

Extracellular proteins play a significant role in shaping microbial communities which, in turn, can impact ecosystem function, human health, and biotechnological processes. Yet, for many ubiquitous microbes, there is limited knowledge regarding the identity and function of secreted proteins. Here, we introduce EXCRETE (enhanced exoproteome characterization by mass spectrometry), a workflow that enables comprehensive description of microbial exoproteomes from minimal starting material. Using cyanobacteria as a case study, we benchmark EXCRETE and show a significant increase over current methods in the identification of extracellular proteins. Subsequently, we show that EXCRETE can be miniaturized and adapted to a 96-well high-throughput format. Application of EXCRETE to cyanobacteria from different habitats (Synechocystis sp. PCC 6803, Synechococcus sp. PCC 11901, and Nostoc punctiforme PCC 73102), and in different cultivation conditions, identified up to 85% of all potentially secreted proteins. Finally, functional analysis reveals that cell envelope maintenance and nutrient acquisition are central functions of the predicted cyanobacterial secretome. Collectively, these findings challenge the general belief that cyanobacteria lack secretory proteins and suggest that multiple functions of the secretome are conserved across freshwater, marine, and terrestrial species.

Dynamic patterns of carbohydrate metabolism genes in bacterioplankton during marine algal blooms

Carbohydrates play a pivotal role in nutrient recycling and regulation of algal-bacterial interactions. Despite their ecological significance, the intricate molecular mechanisms governing regulation of phycosphere carbohydrates by bacterial taxa linked with natural algal bloom have yet to be fully elucidated. Here, a comprehensive temporal metagenomic analysis was conducted to explore the carbohydrate-active enzyme (CAZyme) genes in two discrete algal bloom microorganisms (Gymnodinium catenatum and Phaeocystis globosa) across three distinct bloom stages: pre-bloom, peak bloom, and post-bloom. Elevated levels of extracellular carbohydrates, primarily rhamnose, galactose, glucose, and arabinose, were observed during the initial and post-peak stages. The prominent CAZyme families identified-glycoside hydrolases (GH) and carbohydrate-binding modules (CBMs)-were present in both algal bloom occurrences. In the G. catenatum bloom, GH23/24 and CBM13/14 were prevalent during the pre-bloom and peak bloom stages, whereas GH2/3/30 and CBM12/24 exhibited increased prevalence during the post-bloom phase. In contrast, the P. globosa bloom had a dominance of GH13/23 and CBM19 in the initial phase, and this was succeeded by GH3/19/24/30 and CBM54 in the later stages. This gene pool variation-observed distinctly in specific genera-highlighted the dynamic structural shifts in functional resources driven by temporal alterations in available substrates. Additionally, ecological linkage analysis underscored a correlation between carbohydrates (or their related genes) and phycospheric bacteria, hinting at a pattern of bottom-up control. These findings contribute to understanding of the dynamic nature of CAZymes, emphasizing the substantial influence of substrate availability on the metabolic capabilities of algal symbiotic bacteria, especially in terms of carbohydrates.

Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean

Proteins in the open ocean represent a significant source of organic matter, and their profiles reflect the metabolic activities of marine microorganisms. Here, by analyzing metaproteomic samples collected from the Pacific, Atlantic and Southern Ocean, we reveal size-fractionated patterns of the structure and function of the marine microbiota protein pool in the water column, particularly in the dark ocean (>200 m). Zooplankton proteins contributed three times more than algal proteins to the deep-sea community metaproteome. Gammaproteobacteria exhibited high metabolic activity in the deep-sea, contributing up to 30% of bacterial proteins. Close virus-host interactions of this taxon might explain the dominance of gammaproteobacterial proteins in the dissolved fraction. A high urease expression in nitrifiers suggested links between their dark carbon fixation and zooplankton urea production. In summary, our results uncover the taxonomic contribution of the microbiota to the oceanic protein pool, revealing protein fluxes from particles to the dissolved organic matter pool.

Functional vertical connectivity of microbial communities in the ocean

Sinking particles are a critical conduit for the transport of surface microbes to the ocean's interior. Vertical connectivity of phylogenetic composition has been shown; however, the functional vertical connectivity of microbial communities has not yet been explored in detail. We investigated protein and taxa profiles of both free-living and particle-attached microbial communities from the surface to 3000 m depth using a combined metaproteomic and 16S rRNA amplicon sequencing approach. A clear compositional and functional vertical connectivity of microbial communities was observed throughout the water column with Oceanospirillales, Alteromonadales, and Rhodobacterales as key taxa. The surface-derived particle-associated microbes increased the expression of proteins involved in basic metabolism, organic matter processing, and environmental stress response in deep waters. This study highlights the functional vertical connectivity between surface and deep-sea microbial communities via sinking particles and reveals that a considerable proportion of the deep-sea microbes might originate from surface waters and have a major impact on the biogeochemical cycles in the deep sea.

Substrate uptake patterns shape niche separation in marine prokaryotic microbiome

Marine heterotrophic prokaryotes primarily take up ambient substrates using transporters. The patterns of transporters targeting particular substrates shape the ecological role of heterotrophic prokaryotes in marine organic matter cycles. Here, we report a size-fractionated pattern in the expression of prokaryotic transporters throughout the oceanic water column due to taxonomic variations, revealed by a multi-"omics" approach targeting ATP-binding cassette (ABC) transporters and TonB-dependent transporters (TBDTs). Substrate specificity analyses showed that marine SAR11, Rhodobacterales, and Oceanospirillales use ABC transporters to take up organic nitrogenous compounds in the free-living fraction, while Alteromonadales, Bacteroidetes, and Sphingomonadales use TBDTs for carbon-rich organic matter and metal chelates on particles. The expression of transporter proteins also supports distinct lifestyles of deep-sea prokaryotes. Our results suggest that transporter divergency in organic matter assimilation reflects a pronounced niche separation in the prokaryote-mediated organic matter cycles.

Decoupling between the genetic potential and the metabolic regulation and expression in microbial organic matter cleavage across microbiomes

Metagenomics, metatranscriptomics, and metaproteomics are used to explore the microbial capability of enzyme secretion, but the links between protein-encoding genes and corresponding transcripts/proteins across ecosystems are underexplored. By conducting a multi-omics comparison focusing on key enzymes (carbohydrate-active enzymes [CAZymes] and peptidases) cleaving the main biomolecules across distinct microbiomes living in the ocean, soil, and human gut, we show that the community structure, functional diversity, and secretion mechanisms of microbial secretory CAZymes and peptidases vary drastically between microbiomes at metagenomic, metatranscriptomic, and metaproteomic levels. Such variations lead to decoupled relationships between CAZymes and peptidases from genetic potentials to protein expressions due to the different responses of key players toward organic matter sources and concentrations. Our results highlight the need for systematic analysis of the factors shaping patterns of microbial cleavage on organic matter to better link omics data to ecosystem processes.

IMPORTANCE

Omics tools are used to explore adaptive mechanism of microbes in diverse systems, but the advantages and limitations of different omics tools remain skeptical. Here, we reported distinct profiles in microbial secretory enzyme composition revealed by different omics methods. In general, the predicted function from metagenomic analysis decoupled from the expression of corresponding transcripts/proteins. Linking omics results to taxonomic origin, functional capability, substrate specificity, secretion preference, and enzymatic activity measurement suggested the substrate's source, concentration and stoichiometry impose strong filtering on the expression of extracellular enzymes, which may overwrite the genetic potentials. Our results present an integrated perspective on the need for multi-dimensional characterization of microbial adaptation in a changing environment.

Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench

BACKGROUND

The deep sea represents the largest marine ecosystem, driving global-scale biogeochemical cycles. Microorganisms are the most abundant biological entities and play a vital role in the cycling of organic matter in such ecosystems. The primary food source for abyssal biota is the sedimentation of particulate organic polymers. However, our knowledge of the specific biopolymers available to deep-sea microbes remains largely incomplete. One crucial rate-limiting step in organic matter cycling is the depolymerization of particulate organic polymers facilitated by extracellular enzymes (EEs). Therefore, the investigation of active EEs and the microbes responsible for their production is a top priority to better understand the key nutrient sources for deep-sea microbes.

RESULTS

In this study, we conducted analyses of extracellular enzymatic activities (EEAs), metagenomics, and metatranscriptomics from seawater samples of 50-9305 m from the Mariana Trench. While a diverse array of microbial groups was identified throughout the water column, only a few exhibited high levels of transcriptional activities. Notably, microbial populations actively transcribing EE genes involved in biopolymer processing in the abyssopelagic (4700 m) and hadopelagic zones (9305 m) were primarily associated with the class Actinobacteria. These microbes actively transcribed genes coding for enzymes such as cutinase, laccase, and xyloglucanase which are capable of degrading phytoplankton polysaccharides as well as GH23 peptidoglycan lyases and M23 peptidases which have the capacity to break down peptidoglycan. Consequently, corresponding enzyme activities including glycosidases, esterase, and peptidases can be detected in the deep ocean. Furthermore, cell-specific EEAs increased at 9305 m compared to 4700 m, indicating extracellular enzymes play a more significant role in nutrient cycling in the deeper regions of the Mariana Trench.

CONCLUSIONS

Transcriptomic analyses have shed light on the predominant microbial population actively participating in organic matter cycling in the deep-sea environment of the Mariana Trench. The categories of active EEs suggest that the complex phytoplankton polysaccharides (e.g., cutin, lignin, and hemicellulose) and microbial peptidoglycans serve as the primary nutrient sources available to deep-sea microbes. The high cell-specific EEA observed in the hadal zone underscores the robust polymer-degrading capacities of hadal microbes even in the face of the challenging conditions they encounter in this extreme environment. These findings provide valuable new insights into the sources of nutrition, the key microbes, and the EEs crucial for biopolymer degradation in the deep seawater of the Mariana Trench. Video Abstract.

Increasing transposase abundance with ocean depth correlates with a particle-associated lifestyle

Transposases are mobile genetic elements that move within and between genomes, promoting genomic plasticity in microorganisms. In marine microbial communities, the abundance of transposases increases with depth, but the reasons behind this trend remain unclear. Our analysis of metagenomes from the Tara Oceans and Malaspina Expeditions suggests that a particle-associated lifestyle is the main covariate for the high occurrence of transposases in the deep ocean, and this trend holds true for individual genomes as well as in a community-wide sense. We observed a strong and depth-independent correlation between transposase abundance and the presence of biofilm-associated genes, as well as the prevalence of secretory enzymes. This suggests that mobile genetic elements readily propagate among microbial communities within crowded biofilms. Furthermore, we show that particle association positively correlates with larger genome size, which is in turn associated with higher transposase abundance. Cassette sequences associated with transposons are enriched with genes related to defense mechanisms, which are more highly expressed in the deep sea. Thus, while transposons spread at the expense of their microbial hosts, they also introduce novel genes and potentially benefit the hosts in helping to compete for limited resources. Overall, our results suggest a new understanding of deep ocean particles as highways for gene sharing among defensively oriented microbial genomes.IMPORTANCEGenes can move within and between microbial genomes via mobile genetic elements, which include transposases and transposons. In the oceans, there is a puzzling increase in transposase abundance in microbial genomes as depth increases. To gain insight into this trend, we conducted an extensive analysis of marine microbial metagenomes and metatranscriptomes. We found a significant correlation between transposase abundance and a particle-associated lifestyle among marine microbes at both the metagenome and genome-resolved levels. We also observed a link between transposase abundance and genes related to defense mechanisms. These results suggest that as microbes become densely packed into crowded particles, mobile genes are more likely to spread and carry genetic material that provides a competitive advantage in crowded habitats. This may enable deep sea microbes to effectively compete in such environments.

Archaeal blooms and busts in an estuarine time series

Coastal bays, such as Delaware Bay, are highly productive, ecologically important transitions between rivers and the coastal ocean. They offer opportunities to investigate archaeal assemblages across seasons, with the exchange of water masses that occurs with tidal cycles, and in the context of variable organic matter quality. For a year-long estuarine, size-fractionated time series, we used amplicon sequencing, chemical measurements, and qPCR to follow archaeal groups through the seasons. We detected seasonally high abundances of Marine Group II archaea in summer months which correlate with indicators of phytoplankton production, although not phytoplankton biomass. Although previous studies have reported associations between Marine Group II archaea and particles, here they are almost entirely found in very small particles (0.22-0.7 μm), suggesting they are free-living cells. Populations of Nitrososphaeria did not vary with particle size or environmental conditions. Methanogens were significant fractions of archaeal sequences in large particles at low tide during winter months. Contrary to expectations, Nanoarchaeia were found predominantly in the free-living fraction despite the previous observation that they require an association with hosts. These results underscore the utility of time series studies in shallow, tidally mixed estuarine environments that capture variable conditions for understanding the ecology and biogeochemistry of planktic archaea.

Functional guilds and drivers of diversity in seaweed-associated bacteria

Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.

Planktonic microbial signatures of sinking particle export in the open ocean's interior

A considerable amount of particulate carbon produced by oceanic photosynthesis is exported to the deep-sea by the "gravitational pump" (~6.8 to 7.7 Pg C/year), sequestering it from the atmosphere for centuries. How particulate organic carbon (POC) is transformed during export to the deep sea however is not well understood. Here, we report that dominant suspended prokaryotes also found in sinking particles serve as informative tracers of particle export processes. In a three-year time series from oceanographic campaigns in the Pacific Ocean, upper water column relative abundances of suspended prokaryotes entrained in sinking particles decreased exponentially from depths of 75 to 250 m, conforming to known depth-attenuation patterns of carbon, energy, and mass fluxes in the epipelagic zone. Below ~250 m however, the relative abundance of suspended prokaryotes entrained in sinking particles increased with depth. These results indicate that microbial entrainment, colonization, and sinking particle formation are elevated at mesopelagic and bathypelagic depths. Comparison of suspended and sinking particle-associated microbes provides information about the depth-variability of POC export and biotic processes, that is not evident from biogeochemical data alone.

Microbial carbohydrate-active enzymes influence soil carbon by regulating the of plant- and fungal-derived biomass decomposition in plateau peat wetlands under differing water conditions

Peatlands are important carbon sinks and water sources in terrestrial ecosystems. It is important to explore their microbial-driven water-carbon synergistic mechanisms to understand the driving mechanisms of carbon processes in peatlands. Based on macrogenomic sequencing techniques, located on the peatland of the eastern margin of the Tibetan Plateau with similar stand and different water conditions, we taken soil properties, microbiome abundance, CAZyme abundance and enzyme gene pathways as the object of study, investigated the characterization of soil microbial carbohydrate-active enzymes (CAZymes) under different water gradients in peatland. According to the results, these three phyla (Chloroflexi, Gemmatimonadetes, and Verrucomicrobia) differed significantly between water gradients. Under dried wetlands, the abundance of CAZymes involved in hemicellulose and glucan degradation increased by 3.0 × 10-5 and 3.0 × 10-6, respectively. In contrast, the abundance of CAZymes involved in chitin degradation decreased by 1.1 × 10-5 (p < 0.05). It highlights that regulating plant- and fungus-derived carbon metabolism processes by soil microorganisms in highland peatlands is a crucial mechanism for their response to water changes. Most plant-derived carbon fractions are regulated by soil enzymes (endo-beta 1,4-xylanase, alpha-L-arabinofuranosidase, and alpha-L-fucosidase) containing CAZymes functional genes. Additional findings in this enzyme gene pathway indicate that water changes that affect soil carbon fractions indirectly influence the three enzyme gene metabolic pathways related to plant carbon sources (the glycolysis/gluconeogenesis, other glycan degradation and amino sugar, and nucleotide sugar metabolism). Overall, this study highlights the significance of microbial CAZymes in highland peatland soil carbon processes and indicates that microbial conversion of plant and fungal biomass carbon is more sensitive to water changes.

The largely neglected ecological role of oceanic pelagic fungi

Most investigations into ocean ecology and biogeochemistry have tended to focus on marine bacteria, archaea, and protists, while pelagic fungi (mycoplankton) have traditionally been neglected and considered to reside only in association with benthic solid substrates. Nevertheless, recent studies have revealed that pelagic fungi are distributed ubiquitously throughout the water column in every ocean basin and play an active role in the degradation of organic matter and the cycling of nutrients. We review the current status of knowledge on the ecology of mycoplankton and highlight knowledge gaps and challenges. These findings underscore the need to recognize this neglected kingdom as significant contributors to the organic matter cycling and ecology of the oceans.

Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean

BACKGROUND

Heterotrophic microbes in the Southern Ocean are challenged by the double constraint of low concentrations of organic carbon (C) and iron (Fe). These essential elements are tightly coupled in cellular processes; however, the prokaryotic requirements of C and Fe under varying environmental settings remain poorly studied. Here, we used a combination of metatranscriptomics and metaproteomics to identify prokaryotic membrane transporters for organic substrates and Fe in naturally iron-fertilized and high-nutrient, low-chlorophyll waters of the Southern Ocean during spring and late summer.

RESULTS

Pronounced differences in membrane transporter profiles between seasons were observed at both sites, both at the transcript and protein level. When specific compound classes were considered, the two approaches revealed different patterns. At the transcript level, seasonal patterns were only observed for subsets of genes belonging to each transporter category. At the protein level, membrane transporters of organic compounds were relatively more abundant in spring as compared to summer, while the opposite pattern was observed for Fe transporters. These observations suggest an enhanced requirement for organic C in early spring and for Fe in late summer. Mapping transcripts and proteins to 50 metagenomic-assembled genomes revealed distinct taxon-specific seasonal differences pointing to potentially opportunistic clades, such as Pseudomonadales and Nitrincolaceae, and groups with a more restricted repertoire of expressed transporters, such as Alphaproteobacteria and Flavobacteriaceae.

CONCLUSION

The combined investigations of C and Fe membrane transporters suggest seasonal changes in the microbial requirements of these elements under different productivity regimes. The taxon-specific acquisition strategies of different forms of C and Fe illustrate how diverse microbes could shape transcript and protein expression profiles at the community level at different seasons. Our results on the C- and Fe-related metabolic capabilities of microbial taxa provide new insights into their potential role in the cycling of C and Fe under varying nutrient regimes in the Southern Ocean. Video Abstract.

Deep-sea Bacteroidetes from the Mariana Trench specialize in hemicellulose and pectin degradation typically associated with terrestrial systems

BACKGROUND

Hadal trenches (>6000 m) are the deepest oceanic regions on Earth and depocenters for organic materials. However, how these enigmatic microbial ecosystems are fueled is largely unknown, particularly the proportional importance of complex polysaccharides introduced through deposition from the photic surface waters above. In surface waters, Bacteroidetes are keystone taxa for the cycling of various algal-derived polysaccharides and the flux of carbon through the photic zone. However, their role in the hadal microbial loop is almost unknown.

RESULTS

Here, culture-dependent and culture-independent methods were used to study the potential of Bacteroidetes to catabolize diverse polysaccharides in Mariana Trench waters. Compared to surface waters, the bathypelagic (1000-4000 m) and hadal (6000-10,500 m) waters harbored distinct Bacteroidetes communities, with Mesoflavibacter being enriched at ≥ 4000 m and Bacteroides and Provotella being enriched at 10,400-10,500 m. Moreover, these deep-sea communities possessed distinct gene pools encoding for carbohydrate active enzymes (CAZymes), suggesting different polysaccharide sources are utilised in these two zones. Compared to surface counterparts, deep-sea Bacteroidetes showed significant enrichment of CAZyme genes frequently organized into polysaccharide utilization loci (PULs) targeting algal/plant cell wall polysaccharides (i.e., hemicellulose and pectin), that were previously considered an ecological trait associated with terrestrial Bacteroidetes only. Using a hadal Mesoflavibacter isolate (MTRN7), functional validation of this unique genetic potential was demonstrated. MTRN7 could utilize pectic arabinans, typically associated with land plants and phototrophic algae, as the carbon source under simulated deep-sea conditions. Interestingly, a PUL we demonstrate is likely horizontally acquired from coastal/land Bacteroidetes was activated during growth on arabinan and experimentally shown to encode enzymes that hydrolyze arabinan at depth.

CONCLUSIONS

Our study implies that hadal Bacteroidetes exploit polysaccharides poorly utilized by surface populations via an expanded CAZyme gene pool. We propose that sinking cell wall debris produced in the photic zone can serve as an important carbon source for hadal heterotrophs and play a role in shaping their communities and metabolism. Video Abstract.

Jellyfish detritus supports niche partitioning and metabolic interactions among pelagic marine bacteria

BACKGROUND

Jellyfish blooms represent a significant but largely overlooked source of labile organic matter (jelly-OM) in the ocean, characterized by a high protein content. Decaying jellyfish are important carriers for carbon export to the ocean's interior. To accurately incorporate them into biogeochemical models, the interactions between microbes and jelly-OM have yet to be fully characterized. We conducted jelly-OM enrichment experiments in microcosms to simulate the scenario experienced by the coastal pelagic microbiome after the decay of a jellyfish bloom. We combined metagenomics, endo- and exo-metaproteomic approaches to obtain a mechanistic understanding on the metabolic network operated by the jelly-OM degrading bacterial consortium.

RESULTS

Our analysis revealed that OM released during the decay of jellyfish blooms triggers a rapid shuffling of the taxonomic and functional profile of the pelagic bacterial community, resulting in a significant enrichment of protein/amino acid catabolism-related enzymes in the jelly-OM degrading community dominated by Pseudoalteromonadaceae, Alteromonadaceae and Vibrionaceae, compared to unamended control treatments. In accordance with the proteinaceous character of jelly-OM, Pseudoalteromonadaceae synthesized and excreted enzymes associated with proteolysis, while Alteromonadaceae contributed to extracellular hydrolysis of complex carbohydrates and organophosphorus compounds. In contrast, Vibrionaceae synthesized transporter proteins for peptides, amino acids and carbohydrates, exhibiting a cheater-type lifestyle, i.e. benefiting from public goods released by others. In the late stage of jelly-OM degradation, Rhodobacteraceae and Alteromonadaceae became dominant, growing on jelly-OM left-overs or bacterial debris, potentially contributing to the accumulation of dissolved organic nitrogen compounds and inorganic nutrients, following the decay of jellyfish blooms.

CONCLUSIONS

Our findings indicate that specific chemical and metabolic fingerprints associated with decaying jellyfish blooms are substantially different to those previously associated with decaying phytoplankton blooms, potentially altering the functioning and biogeochemistry of marine systems. We show that decaying jellyfish blooms are associated with the enrichment in extracellular collagenolytic bacterial proteases, which could act as virulence factors in human and marine organisms' disease, with possible implications for marine ecosystem services. Our study also provides novel insights into niche partitioning and metabolic interactions among key jelly-OM degraders operating a complex metabolic network in a temporal cascade of biochemical reactions to degrade pulses of jellyfish-bloom-specific compounds in the water column. Video Abstract.

Polymeric carbohydrates utilization separates microbiomes into niches: insights into the diversity of microbial carbohydrate-active enzymes in the inner shelf of the Pearl River Estuary, China

Polymeric carbohydrates are abundant and their recycling by microbes is a key process of the ocean carbon cycle. A deeper analysis of carbohydrate-active enzymes (CAZymes) can offer a window into the mechanisms of microbial communities to degrade carbohydrates in the ocean. In this study, metagenomic genes encoding microbial CAZymes and sugar transporter systems were predicted to assess the microbial glycan niches and functional potentials of glycan utilization in the inner shelf of the Pearl River Estuary (PRE). The CAZymes gene compositions were significantly different between in free-living (0.2-3 μm, FL) and particle-associated (>3 μm, PA) bacteria of the water column and between water and surface sediments, reflecting glycan niche separation on size fraction and selective degradation in depth. Proteobacteria and Bacteroidota had the highest abundance and glycan niche width of CAZymes genes, respectively. At the genus level, Alteromonas (Gammaproteobacteria) exhibited the greatest abundance and glycan niche width of CAZymes genes and were marked by a high abundance of periplasmic transporter protein TonB and members of the major facilitator superfamily (MFS). The increasing contribution of genes encoding CAZymes and transporters for Alteromonas in bottom water contrasted to surface water and their metabolism are tightly related with particulate carbohydrates (pectin, alginate, starch, lignin-cellulose, chitin, and peptidoglycan) rather than on the utilization of ambient-water DOC. Candidatus Pelagibacter (Alphaproteobacteria) had a narrow glycan niche and was primarily preferred for nitrogen-containing carbohydrates, while their abundant sugar ABC (ATP binding cassette) transporter supported the scavenging mode for carbohydrate assimilation. Planctomycetota, Verrucomicrobiota, and Bacteroidota had similar potential glycan niches in the consumption of the main component of transparent exopolymer particles (sulfated fucose and rhamnose containing polysaccharide and sulfated-N-glycan), developing considerable niche overlap among these taxa. The most abundant CAZymes and transporter genes as well as the widest glycan niche in the abundant bacterial taxa implied their potential key roles on the organic carbon utilization, and the high degree of glycan niches separation and polysaccharide composition importantly influenced bacterial communities in the coastal waters of PRE. These findings expand the current understanding of the organic carbon biotransformation, underlying the size-fractionated glycan niche separation near the estuarine system.

The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules

BACKGROUND

Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-independent biosphere. However, the type of metabolism that dominates the deep subseafloor of the gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas hydrate-rich sediments up to 49 m below the seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions and performed metagenomic and metatranscriptomic analyses to characterize microbial communities and their role in carbon mineralization.

RESULTS

Comparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones were clearly distinguished from those below the SMI. Chloroflexota were most abundant above the SMI, whereas Caldatribacteriota dominated below the SMI. Verrucomicrobiota, Bathyarchaeia, and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest an important role in the fermentation of macromolecules. In contrast, sulfate reducers and methanogens that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs and alkanotrophs that anaerobically grow on alkanes were also identified to be at low abundances. The ANME-1 group actively thrived in or slightly below the current SMI. Members from Heimdallarchaeia were found to encode the potential for anaerobic oxidation of short-chain hydrocarbons.

CONCLUSIONS

These findings indicate that the fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes. Video Abstract.

Prokaryotic Life in the Deep Ocean's Water Column

The oceanic waters below a depth of 200 m represent, in terms of volume, the largest habitat of the biosphere, harboring approximately 70% of the prokaryotic biomass in the oceanic water column. These waters are characterized by low temperature, increasing hydrostatic pressure, and decreasing organic matter supply with depth. Recent methodological advances in microbial oceanography have refined our view of the ecology of prokaryotes in the dark ocean. Here, we review the ecology of prokaryotes of the dark ocean, present data on the biomass distribution and heterotrophic and chemolithoautotrophic prokaryotic production in the major oceanic basins, and highlight the phylogenetic and functional diversity of this part of the ocean. We describe the connectivity of surface and deep-water prokaryotes and the molecular adaptations of piezophilic prokaryotes to high hydrostatic pressure. We also highlight knowledge gaps in the ecology of the dark ocean's prokaryotes and their role in the biogeochemical cycles in the largest habitat of the biosphere.

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.

Characterization of membrane vesicles in Alteromonas macleodii indicates potential roles in their copiotrophic lifestyle

Bacterial membrane vesicles (MVs) are abundant in the oceans, but their potential functional roles remain unclear. In this study we characterized MV production and protein content of six strains of Alteromonas macleodii, a cosmopolitan marine bacterium. Alteromonas macleodii strains varied in their MV production rates, with some releasing up to 30 MVs per cell per generation. Microscopy imaging revealed heterogenous MV morphologies, including some MVs aggregated within larger membrane structures. Proteomic characterization revealed that A. macleodii MVs are rich in membrane proteins related to iron and phosphate uptake, as well as proteins with potential functions in biofilm formation. Furthermore, MVs harbored ectoenzymes, such as aminopeptidases and alkaline phosphatases, which comprised up to 20% of the total extracellular enzymatic activity. Our results suggest that A. macleodii MVs may support its growth through generation of extracellular 'hotspots' that facilitate access to essential substrates. This study provides an important basis to decipher the ecological relevance of MVs in heterotrophic marine bacteria.

Global Distribution of Carbohydrate Utilization Potential in the Prokaryotic Tree of Life

Microorganisms dominate all ecosystems on Earth and play a key role in the turnover of organic matter. By producing enzymes, they degrade complex carbohydrates, facilitating the recycling of nutrients and controlling the carbon cycle. Despite their importance, our knowledge regarding microbial carbohydrate utilization has been limited to genome-sequenced taxa and thus heavily biased to specific groups and environments. Here, we used the Genomes from Earth's Microbiomes (GEM) catalog to describe the carbohydrate utilization potential in >7000 bacterial and archaeal taxa originating from a range of terrestrial, marine and host-associated habitats. We show that the production of carbohydrate-active enzymes (CAZymes) is phylogenetically conserved and varies significantly among microbial phyla. High numbers of carbohydrate-active enzymes were recorded in phyla known for their versatile use of carbohydrates, such as Firmicutes, Fibrobacterota, and Armatimonadota, but also phyla without cultured representatives whose carbohydrate utilization potential was so far unknown, such as KSB1, Hydrogenedentota, Sumerlaeota, and UBP3. Carbohydrate utilization potential reflected the specificity of various habitats: the richest complements of CAZymes were observed in MAGs of plant microbiomes, indicating the structural complexity of plant biopolymers. IMPORTANCE This study expanded our knowledge of the phylogenetic distribution of carbohydrate-active enzymes across prokaryotic tree of life, including new phyla where the carbohydrate-active enzymes composition have not been described until now and demonstrated the potential for carbohydrate utilization of numerous yet uncultured phyla. Profiles of carbohydrate-active enzymes are largely habitat-specific and reflect local carbohydrate availability by selecting taxa with appropriate complements of these enzymes. This information should aid in the prediction of functions in microbiomes of known taxonomic composition and helps to identify key components of habitat-specific carbohydrate pools. In addition, these findings have a high relevance for the understanding of carbohydrate utilization and carbon cycling in the environment, the process that is closely link to the carbon storage potential of Earth habitats and the production of greenhouse gasses.

Bioprospecting for Novel Bacterial Sources of Hydrolytic Enzymes and Antimicrobials in the Romanian Littoral Zone of the Black Sea

Marine microorganisms have evolved a large variety of metabolites and biochemical processes, providing great opportunities for biotechnologies. In the search for new hydrolytic enzymes and antimicrobial compounds with enhanced characteristics, the current study explored the diversity of cultured and uncultured marine bacteria in Black Sea water from two locations along the Romanian coastline. Microbial cell density in the investigated samples varied between 65 and 12.7 × 10³ CFU·mL^-1. The total bacterial community identified by Illumina sequencing of 16S rRNA gene comprised 185 genera belonging to 46 classes, mainly Gammaproteobacteria, Alphaproteobacteria, Flavobacteriia, and 24 phyla. The 66 bacterial strains isolated on seawater-based culture media belonged to 33 genera and showed variable growth temperatures, growth rates, and salt tolerance. A great fraction of these strains, including Pseudoalteromonas and Flavobacterium species, produced extracellular proteases, lipases, and carbohydrases, while two strains belonging to the genera Aquimarina and Streptomyces exhibited antimicrobial activity against human pathogenic bacteria. This study led to a broader view on the diversity of microbial communities in the Black Sea, and provided new marine strains with hydrolytic and antimicrobial capabilities that may be exploited in industrial and pharmaceutical applications.

Limited carbon cycling due to high-pressure effects on the deep-sea microbiome

Deep-sea microbial communities are exposed to high-pressure conditions, which has a variable impact on prokaryotes depending on whether they are piezophilic (that is, pressure-loving), piezotolerant or piezosensitive. While it has been suggested that elevated pressures lead to higher community-level metabolic rates, the response of these deep-sea microbial communities to the high-pressure conditions of the deep sea is poorly understood. Based on microbial activity measurements in the major oceanic basins using an in situ microbial incubator, we show that the bulk heterotrophic activity of prokaryotic communities becomes increasingly inhibited at higher hydrostatic pressure. At 4,000 m depth, the bulk heterotrophic prokaryotic activity under in situ hydrostatic pressure was about one-third of that measured in the same community at atmospheric pressure conditions. In the bathypelagic zone-between 1,000 and 4,000 m depth-~85% of the prokaryotic community was piezotolerant and ~5% of the prokaryotic community was piezophilic. Despite piezosensitive-like prokaryotes comprising only ~10% (mainly members of Bacteroidetes, Alteromonas) of the deep-sea prokaryotic community, the more than 100-fold metabolic activity increase of these piezosensitive prokaryotes upon depressurization leads to high apparent bulk metabolic activity. Overall, the heterotrophic prokaryotic activity in the deep sea is likely to be substantially lower than hitherto assumed, with major impacts on the oceanic carbon cycling.

Asynchronous responses of microbial CAZymes genes and the net CO2 exchange in alpine peatland following 5 years of continuous extreme drought events

Peatlands act as an important sink of carbon dioxide (CO2). Yet, they are highly sensitive to climate change, especially to extreme drought. The changes in the net ecosystem CO2 exchange (NEE) under extreme drought events, and the driving function of microbial enzymatic genes involved in soil organic matter (SOM) decomposition, are still unclear. Herein we investigated the effects of extreme drought events in different periods of plant growth season at Zoige peatland on NEE and microbial enzymatic genes of SOM decomposition after 5 years. The results showed that the NEE of peatland decreased significantly by 48% and 26% on average (n = 12, P < 0.05) under the early and midterm extreme drought, respectively. The microbial enzymatic genes abundance of SOM decomposition showed the same decreasing trend under early and midterm extreme drought, but an increasing trend under late extreme drought. The microbial community that contributes to these degradation genes mainly derives from Proteobacteria and Actinobacteria. NEE was mainly affected by soil hydrothermal factors and gross primary productivity but weakly correlated with SOM enzymatic decomposition genes. Soil microbial respiration showed a positive correlation with microbial enzymatic genes involved in the decomposition of labile carbon (n = 18, P < 0.05). This study provided new insights into the responses of the microbial decomposition potential of SOM and ecosystem CO2 sink function to extreme drought events in the alpine peatland.

Microbe Profile: Alteromonas macleodii - a widespread, fast-responding, 'interactive' marine bacterium

Alteromonas macleodii is a marine heterotrophic bacterium with widespread distribution - from temperate to tropical oceans, and from surface to deep waters. Strains of A. macleodii exhibit considerable genomic and metabolic variability, and can grow rapidly on diverse organic compounds. A. macleodii is a model organism for the study of population genomics, physiological adaptations and microbial interactions, with individual genomes encoding diverse phenotypic traits influenced by recombination and horizontal gene transfer.

Particles act as ‘specialty centers’ with expanded enzymatic function throughout the water column in the western North Atlantic

Heterotrophic bacteria initiate the degradation of high molecular weight organic matter by producing an array of extracellular enzymes to hydrolyze complex organic matter into sizes that can be taken up into the cell. These bacterial communities differ spatially and temporally in composition, and potentially also in their enzymatic complements. Previous research has shown that particle-associated bacteria can be considerably more active than bacteria in the surrounding bulk water, but most prior studies of particle-associated bacteria have been focused on the upper ocean - there are few measurements of enzymatic activities of particle-associated bacteria in the mesopelagic and bathypelagic ocean, although the bacterial communities in the deep are dependent upon degradation of particulate organic matter to fuel their metabolism. We used a broad suite of substrates to compare the glucosidase, peptidase, and polysaccharide hydrolase activities of particle-associated and unfiltered seawater microbial communities in epipelagic, mesopelagic, and bathypelagic waters across 11 stations in the western North Atlantic. We concurrently determined bacterial community composition of unfiltered seawater and of samples collected via gravity filtration (&gt;3 μm). Overall, particle-associated bacterial communities showed a broader spectrum of enzyme activities compared with unfiltered seawater communities. These differences in enzymatic activities were greater at offshore than at coastal locations, and increased with increasing depth in the ocean. The greater differences in enzymatic function measured on particles with depth coincided with increasing differences in particle-associated community composition, suggesting that particles act as ‘specialty centers’ that are essential for degradation of organic matter even at bathypelagic depths.

Efficient carbon and nitrogen transfer from marine diatom aggregates to colonizing bacterial groups

Bacterial degradation of sinking diatom aggregates is key for the availability of organic matter in the deep-ocean. Yet, little is known about the impact of aggregate colonization by different bacterial taxa on organic carbon and nutrient cycling within aggregates. Here, we tracked the carbon (C) and nitrogen (N) transfer from the diatom Leptocylindrus danicus to different environmental bacterial groups using a combination of 13C and 15N isotope incubation (incubated for 72 h), CARD-FISH and nanoSIMS single-cell analysis. Pseudoalteromonas bacterial group was the first colonizing diatom-aggregates, succeeded by the Alteromonas group. Within aggregates, diatom-attached bacteria were considerably more enriched in 13C and 15N than non-attached bacteria. Isotopic mass balance budget indicates that both groups showed comparable levels of diatom C in their biomass, accounting for 19 ± 7% and 15 ± 11%, respectively. In contrast to C, bacteria of the Alteromonas groups showed significantly higher levels of N derived from diatoms (77 ± 28%) than Pseudoalteromonas (47 ± 17%), suggesting a competitive advantage for Alteromonas in the N-limiting environments of the deep-sea. Our results imply that bacterial succession within diatom aggregates may largely impact taxa-specific C and N uptake, which may have important consequences for the quantity and quality of organic matter exported to the deep ocean.

Global contribution of pelagic fungi to protein degradation in the ocean

BACKGROUND

Fungi are important degraders of organic matter responsible for reintegration of nutrients into global food chains in freshwater and soil environments. Recent evidence suggests that they are ubiquitously present in the oceanic water column where they play an active role in the degradation of carbohydrates. However, their role in processing other abundant biomolecules in the ocean in comparison with that of prokaryotes remains enigmatic. Here, we performed a global-ocean multi-omics analysis of all fungal-affiliated peptidases (main enzymes responsible for cleaving proteins), which constitute the major fraction (> 50%) of marine living and detrital biomass. We determined the abundance, expression, diversity, taxonomic affiliation, and functional classification of the genes encoding all pelagic fungal peptidases from the epi- and mesopelagic layers.

RESULTS

We found that pelagic fungi are active contributors to protein degradation and nitrogen cycling in the global ocean. Dothideomycetes are the main fungi responsible for protease activity in the surface layers, whereas Leotiomycetes dominate in the mesopelagic realm. Gene abundance, diversity, and expression increased with increasing depth, similar to fungal CAZymes. This contrasts with the total occurrence of prokaryotic peptidases and CAZymes which are more uniformly distributed in the oceanic water column, suggesting potentially different ecological niches of fungi and prokaryotes. In-depth analysis of the most widely expressed fungal protease revealed the potentially dominating role of saprotrophic nutrition in the oceans.

CONCLUSIONS

Our findings expand the current knowledge on the role of oceanic fungi in the carbon cycle (carbohydrates) to the so far unknown global participation in nitrogen (proteins) degradation, highlighting potentially different ecological niches occupied by fungi and prokaryotes in the global ocean. Video Abstract.

Genomic insights into versatile lifestyle of three new bacterial candidate phyla

Metagenomic explorations of the Earth's biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance. Here, we retrieved 11 metagenomic-assembled genomes (MAGs) affiliated to three new monophyletic bacterial lineages from the seawater of the Yap Trench. Phylogenomic analysis revealed that each lineage is a new bacterial candidate phylum, subsequently named Candidatus Qinglongiota, Candidatus Heilongiota, and Candidatus Canglongiota. Metabolic reconstruction of genomes from the three phyla suggested that they adopt a versatile lifestyle, with the potential to utilize various types of sugars, proteins, and/or short-chain fatty acids through anaerobic pathways. This was further confirmed by a global distribution map of the three phyla, indicating a preference for oxygen-limited or particle-attached niches, such as anoxic sedimentary environments. Of note, Candidatus Canglongiota genomes harbor genes for the complete Wood- Ljungdahl pathway and sulfate reduction that are similar to those identified in some sulfate-reducing bacteria. Evolutionary analysis indicated that gene gain and loss events, and horizontal gene transfer (HGT) play important roles in shaping the genomic and metabolic features of the three new phyla. This study presents the genomic insight into the ecology, metabolism, and evolution of three new phyla, which broadens the phylum-level diversity within the domain Bacteria.

Ecological dynamics of the gut microbiome in response to dietary fiber

Dietary fibers are generally thought to benefit intestinal health. Their impacts on the composition and metabolic function of the gut microbiome, however, vary greatly across individuals. Previous research showed that each individual's response to fibers depends on their baseline gut microbiome, but the ecology driving microbiota remodeling during fiber intake remained unclear. Here, we studied the long-term dynamics of the gut microbiome and short-chain fatty acids (SCFAs) in isogenic mice with distinct microbiota baselines fed with the fermentable fiber inulin and resistant starch compared to the non-fermentable fiber cellulose. We found that inulin produced a generally rapid response followed by gradual stabilization to new equilibria, and those dynamics were baseline-dependent. We parameterized an ecology model from the time-series data, which revealed a group of bacteria whose growth significantly increased in response to inulin and whose baseline abundance and interspecies competition explained the baseline dependence of microbiome density and community composition dynamics. Fecal levels of SCFAs, such as propionate, were associated with the abundance of inulin responders, yet inter-individual variation of gut microbiome impeded the prediction of SCFAs by machine learning models. We showed that our methods and major findings were generalizable to dietary resistant starch. Finally, we analyzed time-series data of synthetic and natural human gut microbiome in response to dietary fiber and validated the inferred interspecies interactions in vitro. This study emphasizes the importance of ecological modeling to understand microbiome responses to dietary changes and the need for personalized interventions.

Diverse Genomic Traits Differentiate Sinking-Particle-Associated versus Free-Living Microbes throughout the Oligotrophic Open Ocean Water Column

Bacteria and archaea are central to the production, consumption, and remineralization of dissolved and particulate organic matter and contribute critically to carbon delivery, nutrient availability, and energy transformations in the deep ocean. To explore environmentally relevant genomic traits of sinking-particle-associated versus free-living microbes, we compared habitat-specific metagenome-assembled genomes recovered throughout the water column in the North Pacific Subtropical Gyre. The genomic traits of sinking-particle-associated versus free-living prokaryotes were compositionally, functionally, and phylogenetically distinct. Substrate-specific transporters and extracellular peptidases and carbohydrate-active enzymes were more enriched and diverse in particle-associated microbes at all depths than in free-living counterparts. These data indicate specific roles for particle-attached microbes in particle substrate hydrolysis, uptake, and remineralization. Shallow-water particle-associated microbes had elevated genomic GC content and proteome nitrogen content and reduced proteome carbon content in comparison to abyssal particle-associated microbes. An inverse trend was observed for their sympatric free-living counterparts. These different properties of attached microbes are postulated to arise in part due to elevated organic and inorganic nitrogen availability inside sinking particles. Particle-attached microbes also were enriched in genes for environmental sensing via two-component regulatory systems, and cell-cell interactions via extracellular secretion systems, reflecting their surface-adapted lifestyles. Finally, particle-attached bacteria had greater predicted maximal growth efficiencies than free-living bacterioplankton at all depths. All of these particle-associated specific genomic and proteomic features appear to be driven by microhabitat-specific elevated nutrient and energy availability as well as surface-associated competitive and synergistic ecological interactions. Although some of these characteristics have been previously postulated or observed individually, we report them together here in aggregate via direct comparisons of cooccurring free-living and sinking-particle-attached microbial genomes from the open ocean.

Phylogeny and Metabolic Potential of the Candidate Phylum SAR324

The bacterial SAR324 cluster is ubiquitous and abundant in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 30% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding genes (instead of the previously used 16S rRNA single gene marker), the former Deltaproteobacteria cluster SAR324 has been classified since 2018 as its own phylum. Yet, very little is known about its phylogeny and metabolic potential. We downloaded all publicly available SAR324 genomes (65) from all natural environments and reconstructed 18 new genomes using publicly available oceanic metagenomic data and unpublished data from the waters underneath the Ross Ice Shelf. We calculated a global SAR324 phylogenetic tree and identified six clusters (namely 1A, 1B, 2A, 2B, 2C and 2D) within this clade. Genome annotation and metatranscriptome read mapping showed that SAR324 clades possess a flexible array of genes suited for survival in various environments. Clades 2A and 2C are mostly present in the surface mesopelagic layers of global oceans, while clade 2D dominates in deeper regions. Our results show that SAR324 has a very versatile and broad metabolic potential, including many heterotrophic, but also autotrophic pathways. While one surface water associated clade (2A) seems to use proteorhodopsin to gain energy from solar radiation, some deep-sea genomes from clade 2D contain the complete Calvin-Benson-Bassham cycle gene repertoire to fix carbon. This, in addition to a variety of other genes and pathways for both oxic (e.g., dimethylsulfoniopropionate degradation) and anoxic (e.g., dissimilatory sulfate reduction, anaerobic benzoate degradation) conditions, can help explain the ubiquitous presence of SAR324 in aquatic habitats.

Metaexoproteomics Reveals Microbial Behavior in the Ocean's Interior

The proteins present in the extracellular environment of cells, named the "exoproteome," are critical for microbial survival, growth, and interaction with their surroundings. However, little is known about microbial exoproteomes in natural marine environments. Here, we used a metaproteomic approach to characterize the exoprotein profiles (10 kDa-0.2 μm) throughout a water column in the South China Sea. Viruses, together with Alpha- and Gammaproteobacteria were the predominant contributors. However, the exoprotein-producing microbial communities varied with depth: SAR11 in the shallow waters, Pseudomonadales and Nitrososphaeria in the mesopelagic layer, and Alteromonadales, Rhizobiales, and Betaproteobacteria in the bathypelagic layer. Besides viral and unknown proteins, diverse transporters contributed substantially to the exoproteomes and varied vertically in their microbial origins, but presented similar patterns in their predicted substrate identities throughout the water column. Other microbial metabolic processes subject to vertical zonation included proteolysis, the oxidation of ammonia, nitrite and carbon monoxide, C1 metabolism, and the degradation of sulfur-containing dissolved organic matter (DOM). Our metaexoproteomic study provides insights into the depth-variable trends in the in situ ecological traits of the marine microbial community hidden in the non-cellular world, including nutrient cycling, niche partitioning and DOM remineralization.

Taxon-Specific Shifts in Bacterial and Archaeal Transcription of Dissolved Organic Matter Cycling Genes in a Stratified Fjord

A considerable fraction of organic matter derived from photosynthesis in the euphotic zone settles into the ocean’s interior and, as it progresses, is degraded by diverse microbial consortia that utilize a suite of extracellular enzymes and membrane transporters. Still, the molecular details that regulate carbon cycling across depths remain little explored. As stratification in fjords has made them attractive models to explore patterns in biological oceanography, we here analyzed bacterial and archaeal transcription in samples from five depth layers in the Gullmar Fjord, Sweden. Transcriptional variation over depth correlated with gradients in chlorophyll a and nutrient concentrations. Differences in transcription between sampling dates (summer and early autumn) were strongly correlated with ammonium concentrations, which potentially was linked with a stronger influence of (micro-)zooplankton grazing in summer. Transcriptional investment in carbohydrate-active enzymes (CAZymes) decreased with depth and shifted toward peptidases, partly a result of elevated CAZyme transcription by Flavobacteriales, Cellvibrionales, and Synechococcales at 2 to 25 m and a dominance of peptidase transcription by Alteromonadales and Rhodobacterales from 50 m down. In particular, CAZymes for chitin, laminarin, and glycogen were important. High levels of transcription of ammonium transporter genes by Thaumarchaeota at depth (up to 18% of total transcription), along with the genes for ammonia oxidation and CO₂ fixation, indicated that chemolithoautotrophy contributed to the carbon flux in the fjord. The taxon-specific expression of functional genes for processing of the marine pool of dissolved organic matter and inorganic nutrients across depths emphasizes the importance of different microbial foraging mechanisms over spatiotemporal scales for shaping biogeochemical cycles.

IMPORTANCE It is generally recognized that stratification in the ocean strongly influences both the community composition and the distribution of ecological functions of microbial communities, which in turn are expected to shape the biogeochemical cycling of essential elements over depth. Here, we used metatranscriptomics analysis to infer molecular detail on the distribution of gene systems central to the utilization of organic matter in a stratified marine system. We thereby uncovered that pronounced shifts in the transcription of genes encoding CAZymes, peptidases, and membrane transporters occurred over depth among key prokaryotic orders. This implies that sequential utilization and transformation of organic matter through the water column is a key feature that ultimately influences the efficiency of the biological carbon pump.

Hydrothermal plumes as hotspots for deep-ocean heterotrophic microbial biomass production

Carbon budgets of hydrothermal plumes result from the balance between carbon sinks through plume chemoautotrophic processes and carbon release via microbial respiration. However, the lack of comprehensive analysis of the metabolic processes and biomass production rates hinders an accurate estimate of their contribution to the deep ocean carbon cycle. Here, we use a biogeochemical model to estimate the autotrophic and heterotrophic production rates of microbial communities in hydrothermal plumes and validate it with in situ data. We show how substrate limitation might prevent net chemolithoautotrophic production in hydrothermal plumes. Elevated prokaryotic heterotrophic production rates (up to 0.9 gCm^-2y^-1) compared to the surrounding seawater could lead to 0.05 GtCy^-1 of C-biomass produced through chemoorganotrophy within hydrothermal plumes, similar to the Particulate Organic Carbon (POC) export fluxes reported in the deep ocean. We conclude that hydrothermal plumes must be accounted for as significant deep sources of POC in ocean carbon budgets.

Sea ice presence is linked to higher carbon export and vertical microbial connectivity in the Eurasian Arctic Ocean

Arctic Ocean sea ice cover is shrinking due to warming. Long-term sediment trap data shows higher export efficiency of particulate organic carbon in regions with seasonal sea ice compared to regions without sea ice. To investigate this sea-ice enhanced export, we compared how different early summer phytoplankton communities in seasonally ice-free and ice-covered regions of the Fram Strait affect carbon export and vertical dispersal of microbes. In situ collected aggregates revealed two-fold higher carbon export of diatom-rich aggregates in ice-covered regions, compared to Phaeocystis aggregates in the ice-free region. Using microbial source tracking, we found that ice-covered regions were also associated with more surface-born microbial clades exported to the deep sea. Taken together, our results showed that ice-covered regions are responsible for high export efficiency and provide strong vertical microbial connectivity. Therefore, continuous sea-ice loss may decrease the vertical export efficiency, and thus the pelagic-benthic coupling, with potential repercussions for Arctic deep-sea ecosystems.

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

The deep sea, the largest ocean's compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

Potential and expression of carbohydrate utilization by marine fungi in the global ocean

BACKGROUND

Most of the research on the cycling of carbon in the open-ocean has focused on heterotrophic prokaryotes and eukaryotic phytoplankton, but the role of pelagic fungi remains largely enigmatic.

METHODS

Here, we performed a global-ocean multi-omics analysis of all pelagic fungal carbohydrate-active enzymes (CAZymes), key enzymes in the carbon cycling. We studied the occurrence, expression, diversity, functional classification, and taxonomic affiliation of the genes encoding all pelagic fungal CAZymes from the epi- and mesopelagic realm.

RESULTS

Pelagic fungi are active in carbohydrate degradation as indicated by a high ratio of CAZymes transcripts per gene. Dothideomycetes in epipelagic and the Leotiomycetes in mesopelagic waters (both from the phylum Ascomycota) are the main pelagic fungi responsible for carbohydrate degradation in the ocean. The abundance, expression, and diversity of fungal CAZymes were higher in the mesopelagic than in the epipelagic waters, in contrast to the distribution pattern of prokaryotic CAZymes.

CONCLUSIONS

Our results reveal a widespread utilization of different types of CAZymes by pelagic fungi, uncovering an active and hitherto largely unexplored participation of fungi in the pelagic C cycling, where pelagic prokaryotes and fungi occupy different ecological niches, and fungi becoming relatively more important with depth. Video abstract.

Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses

Heterotrophic bacteria such as those from the Roseobacter group and genus Alteromonas dominate the hadal zones of oceans; however, we know little about the genomic characteristics and potential metabolic adaptations of hadal trench-dwelling bacteria. Here, we report multiple single amplified genomes (SAGs) belonging to Roseobacter and Alteromonas, recovered from the hadal zone of the Mariana Trench. While phylogenetic analyses show that these hadal SAGs cluster with their surface relatives, an analysis of genomic recruitment indicates that they have higher relative abundances in the hadal zone of the Mariana Trench. Comparative genomic analyses between the hadal SAGs and reference genomes of closely related shallow-water relatives indicate that genes involved in the mobilome (prophages and transposons) are overrepresented among the unique genes of the hadal Roseobacter and Alteromonas SAGs; the functional proteins encoded by this category of genes also shows higher amino acid sequence variation than those encoded by other gene sets within the Roseobacter SAGs. We also found that genes involved in cell wall/membrane/envelope biogenesis, transcriptional regulation, and metal transport may be important for the adaptation of hadal Roseobacter and Alteromonas lineages. These results imply that the modification of cell surface-related proteins and transporters is the major direction of genomic evolution in Roseobacter and Alteromonas bacteria adapting to the hadal environment, and that prophages and transposons may be the key factors driving this process.