Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench

Alkane degradation mechanism of Mixta calida HXX308 isolated from sediment of the Mariana Trench

The Challenger Deep of the Mariana Trench, which is the deepest site in the ocean, contains rich deposits of n-alkanes in its sediments. However, the alkane metabolic processes of the bacteria in this extreme environment were not well understood. In this study, we isolated a strain Mixta calida HXX308 (Proteobacteria) from sediment samples of the Challenger Deep (10,816 meters below sea level). HXX308 grows under pressures ranging from 0 to 40 MPa, with optimal growth at lower pressures. Additionally, it degrades approximately 20% of eicosane at both atmospheric pressure (0.1 MPa) and 20 MPa. Metabolic profiling indicated that HXX308 possesses a complete aerobic alkane metabolism pathway, along with nitrate reduction and sulfate reduction pathways, which support its adaptation to the trench's anoxic environment. Comparative genomic studies showed that most strains in the genus Mixta contain the alkane-degrading gene LadB. Characterization of the LadB gene in HXX308 confirmed its role in the degradation of medium-to long-chain alkanes (C18-36). HXX308 is the first Mixta strain isolated from marine environment. Although this strain originated from the trench, its hydrocarbon metabolic characteristics are similar to those of cultures of terrestrial origin, suggesting that the alkanes in these sediments are likely from the terrestrial environment. Our study enhances the understanding of alkane-degrading in the phylum Proteobacteria and provides insights into the environmental adaptation of M. calida HXX308 in the Mariana Trench.

Microbial ecosystems and ecological driving forces in the deepest ocean sediments

Systematic exploration of the hadal zone, Earth's deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6-11 km in the Mariana Trench, Yap Trench, and Philippine Basin for the Mariana Trench Environment and Ecology Research (MEER) project. Metagenomic and 16S rRNA gene amplicon sequencing generated the 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike in reported environments, neutral drift played a minimal role, while homogeneous selection (HoS, 50.5%) and dispersal limitation (DL, 43.8%) emerged as dominant ecological drivers. HoS favored streamlined genomes with key functions for hadal adaptation, e.g., aromatic compound utilization (oligotrophic adaptation) and antioxidation (high-pressure adaptation). Conversely, DL promoted versatile metabolism with larger genomes. These findings indicated that environmental factors drive the high taxonomic novelty in the hadal zone, advancing our understanding of the ecological mechanisms governing microbial ecosystems in such an extreme oceanic environment.

Unlocking the transcriptional profiles of an oily waste-degrading bacterial consortium

This study investigates the transcriptional profile of a novel oil-degrading microbial consortium (MC1) composed of four bacterial isolates from Brazilian oil reservoirs: Acinetobacter baumannii subsp. oleum ficedula, Bacillus velezensis, Enterobacter asburiae, and Klebsiella pneumoniae. Genomic analysis revealed an enrichment of genes associated with xenobiotic degradation, particularly for aminobenzoate, atrazine, and aromatic compounds, compared to reference genomes. The consortium demonstrated superior growth and complete oil degradation relative to individual strains. Transcriptional profiling during growth on oil indicated that key subsystems involved membrane transport, stress response, and dehydrogenase complexes, crucial for hydrocarbon uptake. Notably, genes for degrading aromatics, naphthalene, and chloroalkanes were significantly expressed during the initial oil growth phase. The dominant gene expressed was alkane 1-monooxygenase, particularly in the late growth phase. While A. baumannii exhibited the highest transcriptional activity, B. velezensis showed lower activity despite possessing numerous hydrocarbon degradation genes. The synergistic interactions among strains, confirmed by complementary gene expression patterns, position MC1 as a promising bioremediation agent for hydrocarbon-contaminated environments. However, more than collaboration, competition for nutrient uptake and resistance to stress drive gene expression and adaptation in the presence of oil as the carbon source.

Genomic evidence on the distribution and ecological function of Pseudomonas in hadal zone

The hadal zone is the deepest region on Earth. It serves as a depositional zone for the sinking matter from surface ocean and continental margin, aided by its unique V-shaped structure. Due to extreme depth (over 6000 m), normally only organic matter with low degradability typically reaches the bottom of the trench. Concurrently, reports have indicated highly active carbon turnover and dense bacterial cells in the Mariana Trench. There remains a cognitive gap in understanding the connection between this phenomenon and the microbial taxa along with their metabolic activities. Here, we surveyed the Pseudomonas, one of the most widely distributed bacterial genera on Earth. The result revealed widespread distribution of Pseudomonas in the hadal zones. We obtained 21 metagenome-assembled genomes (MAGs) from seawater and sediment samples of the Mariana Trench, including three novel species. Comparative genomic analysis showed that hadal Pseudomonas possess more unique ortholog groups of genes related to energy generation and substances transport, distinct from those in other marine zones. These bacteria exhibit the ability to utilize diverse electron acceptors and accumulate compatible solutes, indicating two key strategies for adaptation for high hydrostatic pressure conditions. Furthermore, predicted genomic capabilities suggest that Pseudomonas could decompose various components of organic matter, particularly aromatics, as supported by metatranscriptomic datasets. These findings significantly enhance our understanding of Pseudomonas diversity and metabolic potential, providing valuable insights into the carbon and nitrogen cycles in hadal trench ecosystems.

High hydrostatic pressure stimulates n-C16 mineralization to CO2 by deep-ocean bacterium Alcanivorax xenomutans A28

Medium-chain alkanes have strong ecological impacts on marine ecosystems due to their persistence, toxicity, and ability to travel long distances. Microbial degradation is the dominant and ultimate removal process for n-alkanes in the deep ocean, where high hydrostatic pressure (HHP) regulates microbial activity. To gain insight into the impact of hydrostatic pressure (HP) on n-alkane degradation, we applied the deep-ocean experimental simulation to culture Alcanivorax xenomutans A28, a novel piezotolerant bacterium strain from trench sediment, with n-C16 as the sole carbon source under different HPs (0.1, 40, and 80 MPa). Activity analysis demonstrated that HHP stimulated the n-C16 complete mineralization ratio. Transcriptomic and metabolomic analyses showed that HHP induced the intracellular oxidative stress and accelerated the tricarboxylic acid (TCA) cycle. These results indicate a shift of n-alkanes biodegradation pattern regulated by HP, elucidating the fate and ecological risk of n-alkanes in the deep ocean.

Nutrient amendments enrich microbial hydrocarbon degradation metagenomic potential in freshwater coastal wetland microcosm experiments

Biostimulating native microbes with fertilizers has proven to be a highly effective strategy to speed up biodegradation rates in microbial communities. This study investigates the genetic potential of microbes to degrade light synthetic crude oil in a freshwater coastal wetland. Experimental sediment microcosms were exposed to a variety of conditions (biological control, a light synthetic crude oil amendment, and light synthetic crude oil with nutrient amendment) and incubated for 30 days before volatile organic compounds (BTEX) were quantified and DNA was sequenced for metagenomic analysis. The resulting DNA sequences were binned into metagenome-assembled genomes (MAGs). Analyses of MAGs uncovered a 13-fold significant increase in the abundance of rate-limiting hydrocarbon degrading monooxygenases and dioxygenases, identified only in MAGs from the light synthetic crude oil with nutrient amendments. Further, complete degradation pathways for BTEX compounds were found only in MAGs resulting from the light synthetic crude with nutrient amendment. Moreover, volatile organic compounds (BTEX, cyclohexane, and naphthalene) analyses of microcosm sediments in the presence of nutrients documented that benzene was degraded below detection limits, toluene (98%) and ethylbenzene (67%) were predominantly reduced within 30 days. Results indicate that the genetic potential to degrade BTEX compounds in this freshwater wetland can be linked to the functional potential for bioremediation. BTEX compounds are typically more recalcitrant and tougher to degrade than alkanes. This study demonstrated that stimulating a microbial community with nutrients to enhance its ability to biodegrade hydrocarbons, even in a relatively nutrient-rich habitat like a freshwater wetland, is an effective remediation tactic.

IMPORTANCE

The impact of oil spills in a freshwater aquatic environment can pose dire social, economic, and ecological effects on the region. An oil spill in the Laurentian Great Lakes region has the potential to affect the drinking water of more than 30 million people. The light synthetic crude oil used in this experimental microcosm study is transported through an underground pipeline crossing the waterway between two Laurentian Great Lakes. This study collected metagenomic data (experiments in triplicate) and assessed the quantity of BTEX compounds, which connected microbial degradation function to gene potential. The resulting data documented the bioremediation capabilities of native microbes in a freshwater coastal wetland. This study also provided evidence for this region that bioremediation can be a viable remediation strategy instead of invasive physical methods.

Niche Partitioning and Intraspecific Variation of Thaumarchaeota in Deep Ocean Sediments

Deep-sea sediments contain a large number of Thaumarchaeota that are phylogenetically distinct from their pelagic counterparts. However, their ecology and evolutionary adaptations are not well understood. Metagenomic analyses were conducted on samples from various depths of a 750-cm sediment core collected from the Mariana Trench Challenger Deep. The abundance of Thaumarchaeota and archaeal amoA generally decreased with depth, except for an unexpected peak midway through the core. The thaumarchaeotal metagenome-assembled genomes were classified into diverse phylogenetic clusters associated with amoA-NP-γ, amoA-NP-θ, and amoA-NP-δ of ammonia-oxidising Thaumarchaeota and non-ammonia-oxidising lineages. The most abundant group was within amoA-NP-γ, which is usually found in coastal and shallow habitats, indicating potential niche expansion from marine shallow to hadal environments. This benthic group showed within-species genomic variations compared to the previously identified Hadal water group, suggesting microdiversification of hadal Thaumarchaeota along with niche separation between benthic and pelagic environments. Evolutionary adaptations associated with the benthic-to-pelagic transition included reduced genome size, loss of motility/cell adhesion, altered energy metabolism, and different mechanisms for substrate acquisition and regulation (e.g., ammonium). These findings offer new insights into the evolution of hadal Thaumarchaeota and demonstrate, for the first time, intraspecies-level genomic variation in Thaumarchaeota related to the benthic-versus-pelagic niche partitioning in the deep ocean.

A novel virus potentially evolved from the N4-like viruses represents a unique viral family: Poorviridae

Pseudoalteromonas are widely distributed in marine extreme habitats and exhibit diverse extracellular protease activity, which is essential for marine biogeochemical cycles. However, our understanding of viruses that infect Pseudoalteromonas remains limited. This study isolated a virus infecting Pseudoalteromonas nigrifaciens from Xiaogang in Qingdao, China. vB_PunP_Y3 comprises a linear, double-strand DNA genome with a length of 48,854 bp, encoding 52 putative open reading frames. Transmission electron microscopy demonstrates the short-tailed morphology of vB_PunP_Y3. Phylogenetic and genome-content-based analysis indicate that vB_PunP_Y3 represents a novel virus family named as Poorviridae, along with three high-quality uncultivated viral genomes. Biogeographical analyses show that Poorviridae is distributed across five viral ecological zones, and is predominantly detected in the Antarctic, Arctic, and bathypelagic zones. Comparative genomics analyses identified three of the seven hallmark proteins of N4-like viruses (DNA polymerase, major capsid protein, and virion-encapsulated RNA polymerase) from vB_PunP_Y3, combing with the protein tertiary structures of the major capsid protein, suggesting that vB_PunP_Y3 might evolve from the N4-like viruses.

IMPORTANCE

vB_PunP_Y3 is a unique strain containing three of the seven hallmark proteins of N4-like viruses, but is grouped into a novel family-level viral cluster with three uncultured viruses from metagenomics, named Poorviridae. This study enhanced the understanding about the genetic diversity, evolution, and distribution of Pseudoalteromonas viruses and provided insights into the novel evolution mechanism of marine viruses.

Novel, active, and uncultured hydrocarbon-degrading microbes in the ocean

Given the vast quantity of oil and gas input to the marine environment annually, hydrocarbon degradation by marine microorganisms is an essential ecosystem service. Linkages between taxonomy and hydrocarbon degradation capabilities are largely based on cultivation studies, leaving a knowledge gap regarding the intrinsic ability of uncultured marine microbes to degrade hydrocarbons. To address this knowledge gap, metagenomic sequence data from the Deepwater Horizon (DWH) oil spill deep-sea plume was assembled to which metagenomic and metatranscriptomic reads were mapped. Assembly and binning produced new DWH metagenome-assembled genomes that were evaluated along with their close relatives, all of which are from the marine environment (38 total). These analyses revealed globally distributed hydrocarbon-degrading microbes with clade-specific substrate degradation potentials that have not been reported previously. For example, methane oxidation capabilities were identified in all Cycloclasticus. Furthermore, all Bermanella encoded and expressed genes for non-gaseous n-alkane degradation; however, DWH Bermanella encoded alkane hydroxylase, not alkane 1-monooxygenase. All but one previously unrecognized DWH plume member in the SAR324 and UBA11654 have the capacity for aromatic hydrocarbon degradation. In contrast, Colwellia were diverse in the hydrocarbon substrates they could degrade. All clades encoded nutrient acquisition strategies and response to cold temperatures, while sensory and acquisition capabilities were clade specific. These novel insights regarding hydrocarbon degradation by uncultured planktonic microbes provides missing data, allowing for better prediction of the fate of oil and gas when hydrocarbons are input to the ocean, leading to a greater understanding of the ecological consequences to the marine environment.IMPORTANCEMicrobial degradation of hydrocarbons is a critically important process promoting ecosystem health, yet much of what is known about this process is based on physiological experiments with a few hydrocarbon substrates and cultured microbes. Thus, the ability to degrade the diversity of hydrocarbons that comprise oil and gas by microbes in the environment, particularly in the ocean, is not well characterized. Therefore, this study aimed to utilize non-cultivation-based 'omics data to explore novel genomes of uncultured marine microbes involved in degradation of oil and gas. Analyses of newly assembled metagenomic data and previously existing genomes from other marine data sets, with metagenomic and metatranscriptomic read recruitment, revealed globally distributed hydrocarbon-degrading marine microbes with clade-specific substrate degradation potentials that have not been previously reported. This new understanding of oil and gas degradation by uncultured marine microbes suggested that the global ocean harbors a diversity of hydrocarbon-degrading bacteria, which can act as primary agents regulating ecosystem health.

Global marine microbial diversity and its potential in bioprospecting

The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems1,2. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications3,4. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR-Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR-Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine.

Microbial communities reveal niche partitioning across the slope and bottom zones of the challenger deep

Widespread marine microbiomes exhibit compositional and functional differentiation as a result of adaptation driven by environmental characteristics. We investigated the microbial communities in both seawater and sediments on the slope (7-9 km) and the bottom (9-11 km) of the Challenger Deep of the Mariana Trench to explore community differentiation. Both metagenome-assembled genomes (MAGs) and 16S rRNA amplicon sequence variants (ASVs) showed that the microbial composition in the seawater was similar to that of sediment on the slope, while distinct from that of sediment in the bottom. This scenario suggested a potentially stronger community interaction between seawater and sediment on the slope, which was further confirmed by community assembly and population movement analyses. The metagenomic analysis also indicates a specific stronger potential of nitrate reduction and sulphate assimilation in the bottom seawater, while more versatile nitrogen and sulphur cycling pathways occur on the slope, reflecting functional differentiations among communities in conjunction with environmental features. This work implies that microbial community differentiation occurred in the different hadal niches, and was likely an outcome of microbial adaptation to the extreme hadal trench environment, especially the associated hydrological and geological conditions, which should be considered and measured in situ in future studies.

Distinct microbial nitrogen cycling processes in the deepest part of the ocean

The Mariana Trench (MT) is the deepest part of the ocean on Earth. Previous studies have described the microbial community structures and functional potential in the seawater and surface sediment of MT. Still, the metabolic features and adaptation strategies of the microorganisms involved in nitrogen cycling processes are poorly understood. In this study, comparative metagenomic approaches were used to study microbial nitrogen cycling in three MT habitats, including hadal seawater [9,600-10,500 m below sea level (mbsl)], surface sediments [0-46 cm below seafloor (cmbsf) at a water depth between 7,143 and 8,638 mbsl], and deep sediments (200-306 cmbsf at a water depth of 8,300 mbsl). We identified five new nitrite-oxidizing bacteria (NOB) lineages that had adapted to the oligotrophic MT slope sediment, via their CO2 fixation capability through the reductive tricarboxylic acid (rTCA) or Calvin-Benson-Bassham (CBB) cycle; an anammox bacterium might perform aerobic respiration and utilize sedimentary carbohydrates for energy generation because it contains genes encoding type A cytochrome c oxidase and complete glycolysis pathway. In seawater, abundant alkane-oxidizing Ketobacter species can fix inert N2 released from other denitrifying and/or anammox bacteria. This study further expands our understanding of microbial life in the largely unexplored deepest part of the ocean.

IMPORTANCE

The metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O2 fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing Ketobacter species could fix N2 in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean.

Biofilms on Plastic Debris and the Microbiome

Plastic pollution has become a global environmental problem, and the large number of microorganisms attached to plastic debris in the environment has become a hot topic due to their rapid response to pollutants and environmental changes. In this study, we used high-throughput sequencing to investigate the microbial community structure of and explore the metagenome in the biofilm of two types of plastic debris, polystyrene (PS) and polyethylene terephthalate (PET), and compared them with a water sample collected at the sampling site. The phylum Proteobacteria dominated both the PET and PS samples, at 93.43% and 65.95%, respectively. The metagenome data indicated that the biofilm is enriched with a number of hydrocarbon (petroleum, microplastics, etc.) degrading genes. Our results show that the type of plastic determined the bacterial community structure of the biofilm, while the environment had relatively little effect.

Unravelling biosynthesis and biodegradation potentials of microbial dark matters in hypersaline lakes

Biosynthesis and biodegradation of microorganisms critically underpin the development of biotechnology, new drugs and therapies, and environmental remediation. However, most uncultured microbial species along with their metabolic capacities in extreme environments, remain obscured. Here we unravel the metabolic potential of microbial dark matters (MDMs) in four deep-inland hypersaline lakes in Xinjiang, China. Utilizing metagenomic binning, we uncovered a rich diversity of 3030 metagenome-assembled genomes (MAGs) across 82 phyla, revealing a substantial portion, 2363 MAGs, as previously unclassified at the genus level. These unknown MAGs displayed unique distribution patterns across different lakes, indicating a strong correlation with varied physicochemical conditions. Our analysis revealed an extensive array of 9635 biosynthesis gene clusters (BGCs), with a remarkable 9403 being novel, suggesting untapped biotechnological potential. Notably, some MAGs from potentially new phyla exhibited a high density of these BGCs. Beyond biosynthesis, our study also identified novel biodegradation pathways, including dehalogenation, anaerobic ammonium oxidation (Anammox), and degradation of polycyclic aromatic hydrocarbons (PAHs) and plastics, in previously unknown microbial clades. These findings significantly enrich our understanding of biosynthesis and biodegradation processes and open new avenues for biotechnological innovation, emphasizing the untapped potential of microbial diversity in hypersaline environments.

Genome-based taxonomic analysis of the genus Pseudoalteromonas reveals heterotypic synonyms

The Pseudoalteromonas genus comprises members that have been demonstrated to play significant ecological roles and produce enzymes, natural products, and activities that are beneficial to the environment and economy. A comprehensive evaluation of the genus revealed that the genomes of several Pseudoalteromonas species are highly similar to each other, exceeding species cutoff values. This evaluation involved determining and comparing the average nucleotide identity, in silico DNA-DNA hybridization, average amino acid identity, and the difference in G + C% between Pseudoalteromonas type strains with publicly available genomes. The genome of the Pseudoalteromonas elyakovii type strain was further assessed through additional sequencing and genomic comparisons to historical sequences. These findings suggest that six Pseudoalteromonas species, namely P. mariniglutinosa, P. donghaensis, P. maricaloris, P. elyakovii, P. profundi, and P. issachenkonii, should be reclassified as later heterotypic synonyms of the following validly published species: P. haloplanktis, P. lipolytica, P. flavipulchra, P. distincta, P. gelatinilytica, and P. tetraodonis. Furthermore, two names without valid standing, 'P. telluritireducens' and 'P. spiralis', should be associated with the validly published Pseudoalteromonas species P. agarivorans and P. tetraodonis, respectively.

Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes

Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggested a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (-5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.

Widespread and active piezotolerant microorganisms mediate phenolic compound degradation under high hydrostatic pressure in hadal trenches

Phenolic compounds, as well as other aromatic compounds, have been reported to be abundant in hadal trenches. Although high-throughput sequencing studies have hinted at the potential of hadal microbes to degrade these compounds, direct microbiological, genetic and biochemical evidence under in situ pressures remain absent. Here, a microbial consortium and a pure culture of Pseudomonas, newly isolated from Mariana Trench sediments, efficiently degraded phenol under pressures up to 70 and 60 MPa, respectively, with concomitant increase in biomass. By analyzing a high-pressure (70 MPa) culture metatranscriptome, not only was the entire range of metabolic processes under high pressure generated, but also genes encoding complete phenol degradation via ortho- and meta-cleavage pathways were revealed. The isolate of Pseudomonas also contained genes encoding the complete degradation pathway. Six transcribed genes (dmpKLMNOPsed) were functionally identified to encode a multicomponent hydroxylase catalyzing the hydroxylation of phenol and its methylated derivatives by heterogeneous expression. In addition, key catabolic genes identified in the metatranscriptome of the high-pressure cultures and genomes of bacterial isolates were found to be all widely distributed in 22 published hadal microbial metagenomes. At microbiological, genetic, bioinformatics, and biochemical levels, this study found that microorganisms widely found in hadal trenches were able to effectively drive phenolic compound degradation under high hydrostatic pressures. This information will bridge a knowledge gap concerning the microbial aromatics degradation within hadal trenches.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00224-2.

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.

A unique subseafloor microbiosphere in the Mariana Trench driven by episodic sedimentation

Hadal trenches are characterized by enhanced and infrequent high-rate episodic sedimentation events that likely introduce not only labile organic carbon and key nutrients but also new microbes that significantly alter the subseafloor microbiosphere. Currently, the role of high-rate episodic sedimentation in controlling the composition of the hadal subseafloor microbiosphere is unknown. Here, analyses of carbon isotope composition in a ~ 750 cm long sediment core from the Challenger Deep revealed noncontinuous deposition, with anomalous 14C ages likely caused by seismically driven mass transport and the funneling effect of trench geomorphology. Microbial community composition and diverse enzyme activities in the upper ~ 27 cm differed from those at lower depths, probably due to sudden sediment deposition and differences in redox condition and organic matter availability. At lower depths, microbial population numbers, and composition remained relatively constant, except at some discrete depths with altered enzyme activity and microbial phyla abundance, possibly due to additional sudden sedimentation events of different magnitude. Evidence is provided of a unique role for high-rate episodic sedimentation events in controlling the subsurface microbiosphere in Earth's deepest ocean floor and highlight the need to perform thorough analysis over a large depth range to characterize hadal benthic populations. Such depositional processes are likely crucial in shaping deep-water geochemical environments and thereby the deep subseafloor biosphere.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00212-y.

Isolation and Structure Elucidation of New Metabolites from the Mariana-Trench-Associated Fungus Aspergillus sp. SY2601

Fungi are important resource for the discovery of novel bioactive natural products. This study investigated the metabolites produced by Mariana-Trench-associated fungus Aspergillus sp. SY2601 in EY liquid and rice solid media, resulting in the isolation and structure determination of 28 metabolites, including five new compounds, asperindopiperazines A-C (1-3), 5-methoxy-8,9-dihydroxy-8,9-deoxyaspyrone (21), and 12S-aspertetranone D (26). Structures of the new compounds were elucidated based on extensive NMR spectral analyses, HRESIMS data, optical rotation, ECD, and 13C NMR calculations. The new compound 12S-aspertetranone D (26) exhibited antibacterial activity against both methicillin-resistant Staphylococcus aureus and Escherichia coli with MIC values of 3.75 and 5 μg/mL, respectively.

Depth shapes microbiome assembly and network stability in the Mariana Trench

IMPORTANCE

Exploring microbial interactions and their stability/resilience from the surface to the hadal ocean is critical for further understanding of the microbiome structure and ecosystem function in the Mariana Trench. Vertical gradients did not destabilize microbial communities after long-term evolution and adaption. The uniform niche breadth, diversity, community complexity, and stability of microbiomes in both upper bathypelagic and hadal waters suggest the consistent roles of microbiomes in elemental cycling and adaptive strategies to overcome extreme environmental conditions. Compared with microeukaryotes, bacteria and archaea play a pivotal role in shaping the stability of the hadal microbiome. The consistent co-occurrence stability of microbiomes across vertical gradients was observed in the Mariana Trench. These results illuminate a key principle of microbiomes inhabiting the deepest trench: although distinct microbial communities occupy specific habitats, the interactions within microbial communities remain consistently stable from the upper bathypelagic to the hadal waters.

Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments

Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.

Vertical dynamics of free-living and particle-associated vibrio communities in the eastern tropical Indian Ocean

Members of the family Vibrionaceae (vibrios) are widely distributed in estuarine, offshore, and marginal seas and perform an important ecological role in the marine organic carbon cycle. Nevertheless, there is little knowledge about whether vibrios play ecological roles in the oligotrophic pelagic area, which occupies a larger water volume. In this study, we investigated the abundance, diversity, and composition of free-living and particle-associated vibrios and their relationships with environmental factors along the water depth in the eastern tropical Indian Ocean (ETIO). The abundance of vibrios in free-living fractions was significantly higher than that of particle-associated fractions on the surface. Still, both were similar at the bottom, indicating that vibrios may shift from free-living lifestyles on the surface to mixed lifestyles at the bottom. Vibrio-specific 16S rRNA gene amplicon sequencing revealed that Paraphotobacterium marinum and Vibrio rotiferianus were dominant species in the water column, and Vibrio parahaemolyticus (a clinically important pathogen) was recorded in 102 samples of 111 seawater samples in 10 sites, which showed significant difference from the marginal seas. The community composition also shifted, corresponding to different depths in the water column. Paraphotobacterium marinum decreased with depth, and V. rotiferianus OTU1528 was mainly distributed in deeper water, which significantly correlated with the alteration of environmental factors (e.g., temperature, salinity, and dissolved oxygen). In addition to temperature and salinity, dissolved oxygen (DO) was an important factor that affected the composition and abundance of Vibrio communities in the ETIO. Our study revealed the vertical dynamics and preferential lifestyles of vibrios in the ETIO, helping to fill a knowledge gap on their ecological distribution in oligotrophic pelagic areas and fully understanding the response of vibrios in a global warming environment.

Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m

Viruses play crucial roles in the ecosystem by modulating the host community structure, mediating biogeochemical cycles, and compensating for the metabolism of host cells. Mariana Trench, the world's deepest hadal habitat, harbors a variety of unique microorganisms that have adapted to its extreme conditions of low temperatures, high pressure, and nutrient scarcity. However, our knowledge about isolated hadal phage strains in the hadal trench is still limited. This study reported the discovery of a temperate phage, vB_HmeY_H4907, infecting Halomonas meridiana H4907, isolated from surface sediment from the Mariana Trench at a depth of 8,900 m. To our best knowledge, it is the deepest isolated siphovirus from the ocean. Its 40,452 bp linear dsDNA genome has 57.64% GC content and 55 open reading frames, and it is highly homologous to its host. Phylogenetic analysis and average nucleotide sequence identification reveal that vB_HmeY_H4907 is separated from the isolated phages and represents a new family, Suviridae, with eight predicted proviruses and six uncultured viral genomes. They are widely distributed in the ocean, suggesting a prevalence of this viral family in the deep sea. These findings expand our understanding of the phylogenetic diversity and genomic features of hadal lysogenic phages, provide essential information for further studies of phage-host interactions and evolution, and may reveal new insights into the lysogenic lifestyles of viruses inhabiting the hadal ocean. IMPORTANCE Halomonas phage vB_HmeY_H4907 is the deepest isolated siphovirus from the ocean, and it represents a novel abundant viral family in the ocean. This study provides insights into the genomic, phylogenetic, and ecological characteristics of the new viral family, namely, Suviridae.

A moderately thermophilic origin of a novel family of marine group II euryarchaeota from deep ocean

Marine group II (MGII) is the most abundant planktonic heterotrophic archaea in the ocean. The evolutionary history of MGII archaea is elusive. In this study, 13 new MGII metagenome-assembled genomes were recovered from surface to the hadal zone in Challenger Deep of the Mariana Trench; four of them from the deep ocean represent a novel group. The optimal growth temperature (OGT) of the common ancestor of MGII has been estimated to be at about 60°C and OGTs of MGIIc, MGIIb, and MGIIa at 47°C-50ºC, 37°C-44ºC, and 30°C-37ºC, respectively, suggesting the adaptation of these species to different temperatures during evolution. The estimated OGT range of MGIIc was supported by experimental measurements of cloned β-galactosidase that showed optimal enzyme activity around 50°C. These results indicate that MGIIc may have originated from a common ancestor that lived in warm or even hot marine environment, such as hydrothermal vents.

Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole

The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted. The 16S rRNA genes/transcripts analyses showed that the microbial community structures associated with the sulfur cycling in each zone had distinctive features. Sulfur-oxidizing bacteria were mostly constituted by Gammaproteobacteria, Alphaproteobacteria, Campylobacterota, and Chlorobia above the anoxic zone I and sulfate-reducing bacteria were dominated by Desulfobacterota in anoxic zones. Metagenomic analyses showed that the sulfide-oxidation-related gene sqr and genes encoding the Sox system were mainly distributed in the anoxic zone I, while genes related to dissimilatory sulfate reduction and sulfur intermediate metabolite reduction were mainly distributed in the anoxic zone II, indicating different sulfur metabolic processes between these two zones. Moreover, sulfur-metabolism-related genes were identified in 81 metagenome-assembled genomes (MAGs), indicating a high diversity of microbial communities involved in sulfur cycling. Among them, three MAGs from the candidate phyla JdFR-76 and AABM5-125-24 with genes related to dissimilatory sulfate reduction exhibited distinctive metabolic features. Our results showed unique and novel microbial populations in the SYBH sulfur cycle correlated to the sharp redox gradients, revealing complex biogeochemical processes in this extreme environment. IMPORTANCE Oxygen-deficient regions in the global ocean are expanding rapidly and affect the growth, reproduction and ecological processes of marine organisms. The anaerobic water body of about 150 m in the Sansha Yongle Blue Hole (SYBH) provided a suitable environment to study the specific microbial metabolism in anaerobic seawater. Here, we found that the vertical distributions of the total and active communities of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were different in each water layer of the SYBH according to the dissolved oxygen content. Genes related to sulfur metabolism also showed distinct stratification characteristics. Furthermore, we have obtained diverse metagenome-assembled genomes, some of which exhibit special sulfur metabolic characteristics, especially candidate phyla JdFR-76 and AABM5-125-24 were identified as potential novel SRB. The results of this study will promote further understanding of the sulfur cycle in extreme environments, as well as the environmental adaptability of microorganisms in blue holes.

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.

Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench

BACKGROUND

The Kuril-Kamchatka Trench (maximum depth 9604 m), located in the NW Pacific Ocean, is among the top seven deepest hadal trenches. The work aimed to investigate the unexplored abyssal-hadal prokaryotic communities of this fascinating, but underrated environment.

RESULTS

As for the bacterial communities, we found that Proteobacteria (56.1-74.5%), Bacteroidetes (6.5-19.1%), and Actinobacteria (0.9-16.1%) were the most represented bacterial phyla over all samples. Thaumarchaeota (52.9-91.1%) was the most abundant phylum in the archaeal communities. The archaeal diversity was highly represented by the ammonia-oxidizing Nitrosopumilus, and the potential hydrocarbon-degrading bacteria Acinetobacter, Zhongshania, and Colwellia were the main bacterial genera. The α-diversity analysis evidenced that both prokaryotic communities were characterized by low evenness, as indicated by the high Gini index values (> 0.9). The β-diversity analysis (Redundancy Analysis) indicated that, as expected, the depth significantly affected the structure of the prokaryotic communities. The co-occurrence network revealed seven prokaryotic groups that covaried across the abyssal-hadal zone of the Kuril-Kamchatka Trench. Among them, the main group included the most abundant archaeal and bacterial OTUs (Nitrosopumilus OTU A2 and OTU A1; Acinetobacter OTU B1), which were ubiquitous across the trench.

CONCLUSIONS

This manuscript represents the first attempt to characterize the prokaryotic communities of the KKT abyssal-hadal zone. Our results reveal that the most abundant prokaryotes harbored by the abyssal-hadal zone of Kuril-Kamchatka Trench were chemolithotrophic archaea and heterotrophic bacteria, which did not show a distinctive pattern distribution according to depth. In particular, Acinetobacter, Zhongshania, and Colwellia (potential hydrocarbon degraders) were the main bacterial genera, and Nitrosopumilus (ammonia oxidizer) was the dominant representative of the archaeal diversity.

Profundirhabdus halotolerans gen. nov., sp. nov., an haloalkaliphilic actinobacterium isolated from seawater of the Mariana Trench

A Gram-stain-positive, strictly aerobic, rod-shaped actinobacterium, designated strain ZYF776T, was isolated from seawater of the Mariana Trench collected at a depth of 4000 m. Results of 16S rRNA gene sequence analysis indicated that strain ZYF776T was a member of the class Nitriliruptoria and closely related to Nitriliruptor alkaliphilus DSM 45188T (member of the order Nitriliruptorales, 94.94 % sequence similarity) and Egicoccus halophilus KCTC 33612T (member of the order Egicoccales, 94.46 %). Strain ZYF776T was catalase-positive and oxidase-negative. Growth occurred at 16-37 °C (optimum, 28 °C), in the presence of 0-13 % NaCl (w/v; optimum, 4 %) and at pH 7.0-10.0 (optimum, pH 8.0). Cell-wall hydrolysates of strain ZYF776T contained meso-diaminopimelic (peptidoglycan type A1γ), with ribose, rhamnose and a smaller amount of xylose as the cell-wall sugars. The major menaquinone was MK-10. The predominant fatty acids (>10 %) were C16:0, C17:1 ω8c and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The polar lipid profile mainly contained diphosphatidylglycerol, phosphatidylglycerol and phosphoglycolipid. The genomic DNA G+C content of strain ZYF776T was 68.7 mol%. The genome of strain ZYF776T was about 5.61 Mbp in size, which was larger than those of the reference strains N. alkaliphilus DSM45188T (5.56 Mbp) and E. halophilus KCTC 33612T (3.98 Mbp). The average nucleotide identity and digital DNA-DNA hybridization values between ZYF776T and the related strains N. alkaliphilus DSM 45188T and E. halophilus KCTC 33612T were 76.7 and 20.3 % and 75.8 and 20.0 %, respectively. Based on the polyphasic evidence, a novel genus and species with the name Profundirhabdus halotolerans gen. nov., sp. nov. is proposed. The type strain is ZYF776T (=JCM 33008T=MCCC 1K03555T).

Genomic diversity and ecological distribution of marine Pseudoalteromonas phages

Pseudoalteromonas, with a ubiquitous distribution, is one of the most abundant marine bacterial genera. It is especially abundant in the deep sea and polar seas, where it has been found to have a broad metabolic capacity and unique co-existence strategies with other organisms. However, only a few Pseudoalteromonas phages have so far been isolated and investigated and their genomic diversity and distribution patterns are still unclear. Here, the genomes, taxonomic features and distribution patterns of Pseudoalteromonas phages are systematically analyzed, based on the microbial and viral genomes and metagenome datasets. A total of 143 complete or nearly complete Pseudoalteromonas-associated phage genomes (PSAPGs) were identified, including 34 Pseudoalteromonas phage isolates, 24 proviruses, and 85 Pseudoalteromonas-associated uncultured viral genomes (UViGs); these were assigned to 47 viral clusters at the genus level. Many integrated proviruses (n = 24) and filamentous phages were detected (n = 32), suggesting the prevalence of viral lysogenic life cycle in Pseudoalteromonas. PSAPGs encoded 66 types of 249 potential auxiliary metabolic genes (AMGs) relating to peptidases and nucleotide metabolism. They may also participate in marine biogeochemical cycles through the manipulation of the metabolism of their hosts, especially in the phosphorus and sulfur cycles. Siphoviral and filamentous PSAPGs were the predominant viral lineages found in polar areas, while some myoviral and siphoviral PSAPGs encoding transposase were more abundant in the deep sea. This study has expanded our understanding of the taxonomy, phylogenetic and ecological scope of marine Pseudoalteromonas phages and deepens our knowledge of viral impacts on Pseudoalteromonas. It will provide a baseline for the study of interactions between phages and Pseudoalteromonas in the ocean.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00160-z.

Bacteria and Archaea Regulate Particulate Organic Matter Export in Suspended and Sinking Marine Particle Fractions

The biological carbon pump (BCP) in the Southern Ocean is driven by phytoplankton productivity and is a significant organic matter sink. However, the role of particle-attached (PA) and free-living (FL) prokaryotes (bacteria and archaea) and their diversity in influencing the efficiency of the BCP is still unclear. To investigate this, we analyzed the metagenomes linked to suspended and sinking marine particles from the Sub-Antarctic Southern Ocean Time Series (SOTS) by deploying a Marine Snow Catcher (MSC), obtaining suspended and sinking particulate material, determining organic carbon and nitrogen flux, and constructing metagenome-assembled genomes (MAGs). The suspended and sinking particle-pools were dominated by bacteria with the potential to degrade organic carbon. Bacterial communities associated with the sinking fraction had more genes related to the degradation of complex organic carbon than those in the suspended fraction. Archaea had the potential to drive nitrogen metabolism via nitrite and ammonia oxidation, altering organic nitrogen concentration. The data revealed several pathways for chemoautotrophy and the secretion of recalcitrant dissolved organic carbon (RDOC) from CO₂, with bacteria and archaea potentially sequestering particulate organic matter (POM) via the production of RDOC. These findings provide insights into the diversity and function of prokaryotes in suspended and sinking particles and their role in organic carbon/nitrogen export in the Southern Ocean. IMPORTANCE The biological carbon pump is crucial for the export of particulate organic matter in the ocean. Recent studies on marine microbes have shown the profound influence of bacteria and archaea as regulators of particulate organic matter export. Yet, despite the importance of the Southern Ocean as a carbon sink, we lack comparable insights regarding microbial contributions. This study provides the first insights regarding prokaryotic contributions to particulate organic matter export in the Southern Ocean. We reveal evidence that prokaryotic communities in suspended and sinking particle fractions harbor widespread genomic potential for mediating particulate organic matter export. The results substantially enhance our understanding of the role played by microorganisms in regulating particulate organic matter export in suspended and sinking marine fractions in the Southern Ocean.

The phylogeny and metabolic potentials of an n-alkane-degrading Venatorbacter bacterium isolated from deep-sea sediment of the Mariana Trench

Recently, several reports showed that n-alkanes were abundant in the hadal zone, suggesting that n-alkanes could be an important source of nutrients for microorganisms in hadal ecosystems. To date, most of the published studies on the microbial capacity to degrade hydrocarbons were conducted only at atmospheric temperature and pressure (0.1 MPa), and little is known about whether and which microbes could utilize n-alkanes at in situ environmental conditions in the hadal zone, including low temperature and high hydrostatic pressure (especially >30 MPa). In this study, a piezotolerant bacterium, strain C2-1, was isolated from a Mariana Trench sediment at depth of 5,800 m. Strain C2-1 was able to grow at in situ temperature (4°C) and pressure (58 MPa) with n-alkanes as the sole carbon source. Phylogenetically, strain C2-1 and related strains (TMPB967, ST750PaO-4, IMCC1826, and TTBP476) should be classified into the genus Venatorbacter. Metagenomic analysis using ~5,000 publicly available datasets showed that Venatorbacter has a wide environmental distribution in seawater (38), marine sediments (3), hydrothermal vent plumes (2), Antarctic ice (1), groundwater (13), and marine sponge ecosystems (1). Most Venatorbacter species are non-obligate n-alkane degraders that could utilize, at a minimal, C16-C18 n-alkanes, as well as other different types of carbon substrates, including carbohydrates, amino acids, peptides, and phospholipids. The type II secretion system, extracellular proteases, phospholipase, and endonuclease of Venatorbacter species were robustly expressed in the metatranscriptomes of deep-sea hydrothermal vents, suggesting their important contribution to secondary productivity by degrading extracellular macromolecules. The identification of denitrifying genes suggested a genus-specific ecological potential that allowed Venatorbacter species to be active in anoxic environments, e.g., the oxygen-minimal zone (OMZ) and the deeply buried marine sediments. Our results show that Venatorbacter species are responsible for the degradation of hydrocarbon and extracellular macromolecules, suggesting that they may play an important role in the biogeochemistry process in the Trench ecosystems.

Microbial community structure and exploration of bioremediation enzymes: functional metagenomics insight into Arabian Sea sediments

Deep-sea sediments provide important information on oceanic biogeochemical processes mediated by the microbiome and their functional roles which could be unravelled using genomic tools. The present study aimed to delineate microbial taxonomic and functional profiles from Arabian Sea sediment samples through whole metagenome sequencing using Nanopore technology. Arabian Sea is considered as a major microbial reservoir with significant bio-prospecting potential which needs to be explored extensively using recent advances in genomics. Assembly, co-assembly, and binning methods were used to predict Metagenome Assembled Genomes (MAGs) which were further characterized by their completeness and heterogeneity. Nanopore sequencing of Arabian Sea sediment samples generated around 1.73 tera basepairs of data. Proteobacteria (78.32%) was found to be the most dominant phylum followed by Bacteroidetes (9.55%) and Actinobacteria (2.14%) in the sediment metagenome. Further, 35 MAGs from assembled and 38 MAGs of co-assembled reads were generated from long-read sequence dataset with major representations from the genera Marinobacter, Kangiella, and Porticoccus. RemeDB analysis revealed a high representation of pollutant-degrading enzymes involved in hydrocarbon, plastic and dye degradation. Validation of enzymes with long nanopore reads using BlastX resulted in better characterization of complete gene signatures involved in hydrocarbon (6-monooxygenase and 4-hydroxyacetophenone monooxygenase) and dye degradation (Arylsulfatase). Enhancing the cultivability of deep-sea microbes predicted from the uncultured WGS approaches by I-tip method resulted in isolation of facultative extremophiles. This study presents a comprehensive insight into the taxonomic and functional profiles of Arabian Sea sediments, indicating a potential hotspot for bioprospection.

Influence of Extremely High Pressure and Oxygen on Hydrocarbon-Enriched Microbial Communities in Sediments from the Challenger Deep, Mariana Trench

Recent studies reported that highly abundant alkane content exists in the ~11,000 m sediment of the Mariana Trench, and a few key alkane-degrading bacteria were identified in the Mariana Trench. At present, most of the studies on microbes for degrading hydrocarbons were performed mainly at atmospheric pressure (0.1 MPa) and room temperature; little is known about which microbes could be enriched with the addition of n-alkanes under in-situ environmental pressure and temperature conditions in the hadal zone. In this study, we conducted microbial enrichments of sediment from the Mariana Trench with short-chain (SCAs, C7–C17) or long-chain (LCAs, C18–C36) n-alkanes and incubated them at 0.1 MPa/100 MPa and 4 °C under aerobic or anaerobic conditions for 150 days. Microbial diversity analysis showed that a higher microbial diversity was observed at 100 MPa than at 0.1 MPa, irrespective of whether SCAs or LCAs were added. Non-metric multidimensional scaling (nMDS) and hierarchical cluster analysis revealed that different microbial clusters were formed according to hydrostatic pressure and oxygen. Significantly different microbial communities were formed according to pressure or oxygen (p < 0.05). For example, Gammaproteobacteria (Thalassolituus) were the most abundant anaerobic n-alkanes-enriched microbes at 0.1 MPa, whereas the microbial communities shifted to dominance by Gammaproteobacteria (Idiomarina, Halomonas, and Methylophaga) and Bacteroidetes (Arenibacter) at 100 MPa. Compared to the anaerobic treatments, Actinobacteria (Microbacterium) and Alphaproteobacteria (Sulfitobacter and Phenylobacterium) were the most abundant groups with the addition of hydrocarbon under aerobic conditions at 100 MPa. Our results revealed that unique n-alkane-enriched microorganisms were present in the deepest sediment of the Mariana Trench, which may imply that extremely high hydrostatic pressure (100 MPa) and oxygen dramatically affected the processes of microbial-mediated alkane utilization.

The effect of Alcanivorax borkumensis SK2, a hydrocarbon-metabolising organism, on gas holdup in a 4-phase bubble column bioprocess

To design bioprocesses utilising hydrocarbon-metabolising organisms (HMO) as biocatalysts, the effect of the organism on the hydrodynamics of bubble column reactor (BCR), such as gas holdup, needs to be investigated. Therefore, this study investigates the first use of an HMO, Alcanivorax borkumensis SK2, as a solid phase in the operation and hydrodynamics of a BCR. The study investigated the gas holdup in 3-phase and 4-phase systems in a BCR under ranges of superficial gas velocities (U_G) from 1 to 3 cm/s, hydrocarbon (chain length C₁₃-₂₁) concentrations (H_C) of 0, 5, and 10% v/v and microbial concentrations (M_C) of 0, 0.35, 0.6 g/l. The results indicated that U_G was the most significant parameter, as gas holdup increases linearly with increasing U_G from 1 to 3 cm/s. Furthermore, the addition of hydrocarbons into the air-deionized water -SK2 system showed the highest increase in the gas holdup, particularly at high U_G (above 2 cm/s). The solids (yeast, cornflour, and SK2) phases had differing effects on gas holdup, potentially due to the difference in surface activity. In this work, SK2 addition caused a reduction in the fluid surface tension in the bioprocess which therefore resulted in an increase in the gas holdup in BCR. This work builds upon previous investigations in optimising the hydrodynamics for bubble column hydrocarbon bioprocesses for the application of alkane bioactivation.

Vibrio amylolyticus sp. nov. and Vibrio gelatinilyticus sp. nov., two marine bacteria isolated from surface seawater of Qingdao

Two Gram-stain-negative, oxidase-positive, facultative anaerobic and rod-shaped motile bacteria, designated strains ZSDZ34 and ZSDE26, were isolated from offshore surface seawater collected near Qingdao. Phylogenetic analysis based on 16S rRNA gene sequences placed ZSDE26^T and ZSDZ34^T within the genus Vibrio, family Vibrionaceae, class Gammaproteobacteria. Strain ZSDE26^T was most closely related to Vibrio gallaecicus VB 8.9^T with 97.3 % sequence similarity, whereas ZSDZ34^T was most closely related to Vibrio aestuarianus subsp. cardii DSM 109723^T with 97.8 % sequence similarity. Strain ZSDE26^T grew with 1-5 % (w/v) NaCl (optimum, 4 %), at 16-28 °C (optimum, 28 °C) and at pH 6.0-9.0 (optimum, pH 7.0). Growth of strain ZSDZ34^T occurred with 1-6 % (w/v) NaCl (optimum, 3 %), at 16-37 °C (optimum, 28 °C) and at pH 6.0-9.0 (optimum, pH 7.0). Both strains shared the same major fatty acid components (more than 10 % of total fatty acids) of summed feature 3 (C_16 : 1 ω7c and/or C_16 : 1 ω6c), summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c) and C_16 : 0. Additionally, strain ZSDZ34^T contained a higher proportion of iso-C_16 : 0. The DNA G+C contents of strains ZSDE26^T and ZSDZ34^T were 42.8 and 44.5 mol%, respectively. On the basis of the results of polyphasic analysis, ZSDE26^T and ZSDZ34^T are considered to represent novel species within the genus Vibrio, for which the names Vibrio amylolyticus sp. nov. (type strain, ZSDE26^T=KCTC 82890^T=MCCC 1K06290^T) and Vibrio gelatinilyticus sp. nov. (type strain, ZSDZ34^T=KCTC 82888^T=MCCC 1K06292^T) are proposed, respectively.

Bacterial taxonomic and functional profiles from Bohai Sea to northern Yellow Sea

Microbial distribution patterns are the result of a combination of biotic and abiotic factors, which are the core issues in microbial ecology research. To better understand the biogeographic pattern of bacteria in water environments from the Bohai Sea to the northern Yellow Sea, the effects of environmental factors, and spatial distance on the structure of bacterial communities in marine water were investigated using high-throughput sequencing technology based on 16S rRNA genes. The results showed that Proteobacteria, Bacteroidetes, Actinobacteri, Desulfobacterota, and Bdellovibrionota were the dominant phyla in the study area. A clear spatial pattern in the bacterial community was observed, and environmental factors, including salinity, nutrient concentration, carbon content, total phosphorus, dissolved oxygen, and seawater turbidity emerged as the central environmental factors regulating the variation in bacterial communities. In addition, the study provides direct evidence of the existence of dispersal limitation in this strongly connected marine ecological system. Therefore, these results revealed that the variation in bacterial community characteristics was attributed to environmental selection, accompanied by the regulation of stochastic diffusion. The network analysis demonstrated a nonrandom co-occurrence pattern in the microbial communities with distinct spatial distribution characteristics. It is implied that the biogeography patterns of bacterial community may also be associated with the characteristics of co-occurrence characterize among bacterial species. Furthermore, the PICRUSt analysis indicated a clear spatial distribution of functional characteristics in bacterial communities. This functional variation was significantly modulated by the environmental characteristics of seawater but uncoupled from the taxonomic characteristics of bacterial communities (e.g., diversity characteristics, community structure, and co-occurrence relationships). Together, this findings represent a significant advance in linking seawater to the mechanisms underlying bacterial biogeographic patterns and community assembly, co-occurrence patterns, and ecological functions, providing new insights for identifying the microbial ecology as well as the biogeochemical cycle in the marine environment.

Genome-based taxonomic rearrangement of Oceanobacter-related bacteria including the description of Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. and emended description of the genus Thalassolituus

Oceanobacter-related bacteria (ORB) are a group of oligotrophic marine bacteria play an underappreciated role in carbon cycling. They have been frequently described as one of the dominant bacterial groups with a wide distribution in coastal and deep seawater of global oceans. To clarify their taxonomic affiliation in relation to alkane utilization, phylogenomic and comparative genomics analyses were performed based on currently available genomes from GenBank and four newly isolated strains, in addition to phenotypic and chemotaxonomic characteristics. Consistently, phylogenomic analysis robustly separated them into two groups, which are accordingly hydrocarbon-degrading (HD, Thalassolituus and Oleibacter) and non-HD (NHD, Oceanobacter). In addition, the two groups can also be readily distinguished by several polyphasic taxonomic characteristics. Furthermore, both AAI and POCP genomic indices within the HD group support the conclusion that the members of the genus Oleibacter should be transferred into the genus Thalassolituus. Moreover, HD and NHD bacteria differed significantly in terms of genome size, G + C content and genes involved in alkane utilization. All HD bacteria contain the key gene alkB encoding an alkane monooxygenase, which can be used as a marker gene to distinguish the members of closely related genera Oceanobacter and Thalassolituus. Pangenome analysis revealed that the larger accessory genome may endow Thalassolituus with the flexibility to cope with the dynamics of marine environments and thrive therein, although they possess smaller pan, core- and unique-genomes than Oceanobacter. Within the HD group, twelve species were clearly distinguished from each other by both dDDH and ANI genomic indices, including two novel species represented by the newly isolated strains alknpb1M-1 ^T and 59MF3M-4 ^T , for which the names Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. are proposed. Collectively, these findings build a phylogenetic framework for the ORB and contribute to understanding of their role in marine carbon cycling.

High-Resolution Small RNAs Landscape Provides Insights into Alkane Adaptation in the Marine Alkane-Degrader Alcanivorax dieselolei B-5

Alkanes are widespread in the ocean, and Alcanivorax is one of the most ubiquitous alkane-degrading bacteria in the marine ecosystem. Small RNAs (sRNAs) are usually at the heart of regulatory pathways, but sRNA-mediated alkane metabolic adaptability still remains largely unknown due to the difficulties of identification. Here, differential RNA sequencing (dRNA-seq) modified with a size selection (~50-nt to 500-nt) strategy was used to generate high-resolution sRNAs profiling in the model species Alcanivorax dieselolei B-5 under alkane (n-hexadecane) and non-alkane (acetate) conditions. As a result, we identified 549 sRNA candidates at single-nucleotide resolution of 5'-ends, 63.4% of which are with transcription start sites (TSSs), and 36.6% of which are with processing sites (PSSs) at the 5'-ends. These sRNAs originate from almost any location in the genome, regardless of intragenic (65.8%), antisense (20.6%) and intergenic (6.2%) regions, and RNase E may function in the maturation of sRNAs. Most sRNAs locally distribute across the 15 reference genomes of Alcanivorax, and only 7.5% of sRNAs are broadly conserved in this genus. Expression responses to the alkane of several core conserved sRNAs, including 6S RNA, M1 RNA and tmRNA, indicate that they may participate in alkane metabolisms and result in more actively global transcription, RNA processing and stresses mitigation. Two novel CsrA-related sRNAs are identified, which may be involved in the translational activation of alkane metabolism-related genes by sequestering the global repressor CsrA. The relationships of sRNAs with the characterized genes of alkane sensing (ompS), chemotaxis (mcp, cheR, cheW2), transporting (ompT1, ompT2, ompT3) and hydroxylation (alkB1, alkB2, almA) were created based on the genome-wide predicted sRNA-mRNA interactions. Overall, the sRNA landscape lays the ground for uncovering cryptic regulations in critical marine bacterium, among which both the core and species-specific sRNAs are implicated in the alkane adaptive metabolisms.

Stress-responses of microbes in oil reservoir under high tetracycline exposure and their environmental risks

As the groundwater ecosystem is connected with surface, antibiotics and antibiotic resistance genes (ARGs) in aquatic environments will gradually infiltrate into the deep environment, posing a potential threat to groundwater ecosystem. However, knowledge on the environmental risk of antibiotics and ARGs in groundwater ecosystem and their ecological process still remains unexplored. In this study, lab-scale oil reservoirs under high tetracycline stress were performed to evaluate the dynamics of microbial communities, ARGs and potential functions by using 16S rRNA gene sequencing and metagenomics analysis. Although the presence of antibiotics remarkably reduced the microbial abundance and diversity in a short term, but remain stable or even increased after a long-term incubation. Antibiotic stress caused a greater diversity and abundance of ARGs, and higher numbers of ARGs-related species with the capacity to transfer ARGs to other microbes through horizontal gene transfer. Thus, a much more frequent associations of microbial community at both node- and network-level and a selective pressure on enrichment of antibiotic resistant bacteria related to "anaerobic n-alkane degradation" and "methylotrophic methanogenesis" were observed. It is important to emphasize that high antibiotic stress could also prevent some microbes related to "Sulfate reduction", "Fe(II) oxidation", "Nitrate reduction", and "Xylene and Toluene degradation". This study provides an insight into the long-term stress-responses of microbial communities and functions in oil reservoir under tetracycline exposure, which may help to elucidate the effect of antibiotic stress on biogeochemical cycling with microbial involvement in groundwater ecosystem.

Fine-Scale Structuring of Planktonic Vibrio spp. in the Chinese Marginal Seas

Vibrio is ubiquitous in marine environments with high metabolism flexibility and genome plasticity. Studies have investigated the ecological distribution of Vibrio spp. in several narrow zones, but a broad scale pattern of distribution and community assembly is still lacking. Here, we elucidated the distribution of Vibrio spp. in seawater along the Chinese marginal seas with a high spatial range. Comparison of Vibrio abundance between 3- and 0.2-μm-pore-size membranes showed distinction in preferential lifestyle. Vibrio spp. in the Yellow Sea (YS) was low in abundance and adopted a particle-associated lifestyle, whereas that in the East China Sea (ECS) and South China Sea (SCS) was more abundant and was likely in a temporary free-living state as a strategy to cope with nutrient limitation. Vibrio community compositions were also separated by sampling area, with different dominant groups in YS (Vibrio chagasii and Vibrio harveyi), ECS and SCS (Vibrio japonicus and V. chagasii). The community niche breadth was significantly wider in ECS and SCS than that of YS. Among species, V. chagasii and V. harveyi had the largest niche breadths likely reflecting strong competitive positions. Stochastic processes played important roles in shaping the geographical pattern of the vibrionic community. Environmental selection (e.g., temperature, salinity, and dissolved oxygen) had a much greater impact on the community in surface than in bottom water. The large proportions of unexplained variations (78.9%) imply complex mechanisms in their community assembly. Our study provides insights into the spatial distribution patterns and underlying assembly mechanisms of Vibrio at a broad spatial scale. IMPORTANCE Vibrio spp. may exert large impacts on biogeochemical cycling in coastal habitats, and their ecological importance has drawn increasing attention. Here, we investigated the spatial distribution pattern and community assembly of Vibrio populations along the Chinese marginal seas, spanning a wide spatial scale. Our results showed that the abundances of the Vibrio population increased with decreasing latitude and their preferential lifestyle differed among adjacent coastal areas. The compositions of Vibrio spp. were also separated by geographical location, which was mainly attributable to stochastic processes. Overall, this work contributes to the understanding of the ecological distribution patterns and the community assembly mechanisms of marine vibrios at a high spatial range. The large proportion of unexplained variations indicates the existence of complex mechanisms in the assembly of vibrionic community which should be considered comprehensively in future.

Comparison of prokaryotes between Mount Everest and the Mariana Trench

BACKGROUND

Mount Everest and the Mariana Trench represent the highest and deepest places on Earth, respectively. They are geographically separated, with distinct extreme environmental parameters that provide unique habitats for prokaryotes. Comparison of prokaryotes between Mount Everest and the Mariana Trench will provide a unique perspective to understanding the composition and distribution of environmental microbiomes on Earth.

RESULTS

Here, we compared prokaryotic communities between Mount Everest and the Mariana Trench based on shotgun metagenomic analysis. Analyzing 25 metagenomes and 1176 metagenome-assembled genomes showed distinct taxonomic compositions between Mount Everest and the Mariana Trench, with little taxa overlap, and significant differences in genome size, GC content, and predicted optimal growth temperature. However, community metabolic capabilities exhibited striking commonality, with > 90% of metabolic modules overlapping among samples of Mount Everest and the Mariana Trench, with the only exception for CO2 fixations (photoautotrophy in Mount Everest but chemoautotrophy in the Mariana Trench). Most metabolic pathways were common but performed by distinct taxa in the two extreme habitats, even including some specialized metabolic pathways, such as the versatile degradation of various refractory organic matters, heavy metal metabolism (e.g., As and Se), stress resistance, and antioxidation. The metabolic commonality indicated the overall consistent roles of prokaryotes in elemental cycling and common adaptation strategies to overcome the distinct stress conditions despite the intuitively huge differences in Mount Everest and the Mariana Trench.

CONCLUSION

Our results, the first comparison between prokaryotes in the highest and the deepest habitats on Earth, may highlight the principles of prokaryotic diversity: although taxa are habitat-specific, primary metabolic functions could be always conserved. Video abstract.

Genomic Analysis Reveals Adaptation of Vibrio campbellii to the Hadal Ocean

The genus Vibrio is characterized by high metabolic flexibility and genome plasticity and is widely distributed in the ocean from euphotic layers to deep-sea environments. The relationship between genome features and environmental adaptation strategies of Vibrio has been extensively investigated in coastal environments, yet very little is known about their survival strategies in oligotrophic deep-sea. In this study, we compared genomes of five Vibrio campbellii strains isolated from the Mariana and Yap Trenches at different water depths, including two epipelagic strains and three hadopelagic strains, to identify genomic characteristics that facilitate survival in the deep sea. Genome streamlining is found in pelagic strains, such as smaller genome sizes, lower G+C contents, and higher gene densities, which might be caused by long-term residence in an oligotrophic environment. Phylogenetic results showed that these five Vibrio strains are clustered into two clades according to their collection depth. Indeed, hadopelagic isolates harbor more genes involved in amino acid metabolism and transport, cell wall/membrane/envelope biogenesis, and inorganic ion transport and metabolism through comparative genomics analysis. Specific macrolide export gene and more tellurite resistance genes present in hadopelagic strains by the annotation of antibiotic and metal resistance genes. In addition, several genes related to substrate degradation are enriched in hadopelagic strains, such as chitinase genes, neopullulanase genes, and biopolymer transporter genes. In contrast, epipelagic strains are unique in their capacity for assimilatory nitrate reduction. The genomic characteristics investigated here provide insights into how Vibrio adapts to the deep-sea environment through genomic evolution. IMPORTANCE With the development of deep-sea sampling technology, an increasing number of deep-sea Vibrio strains have been isolated, but the adaptation mechanism of these eutrophic Vibrio strains to the deep-sea environment is unclear. Here, our results show that the genome of pelagic Vibrio is streamlined to adapt to a long-term oligotrophic environment. Through a phylogenomic analysis, we find that genomic changes in marine Vibrio campbellii strains are related to water depth. Our data suggest that an increase in genes related to antibiotic resistance, degradation of macromolecular and refractory substrates, and utilization of rare ions is related to the adaptation of V. campbellii strains to adapt to hadal environments, and most of the increased genes were acquired by horizontal gene transfer. These findings may deepen our understanding of adaptation strategies of marine bacteria to the extreme environment in hadal zones.

Virioplankton assemblages from challenger deep, the deepest place in the oceans

Hadal ocean biosphere, that is, the deepest part of the world's oceans, harbors a unique microbial community, suggesting a potential uncovered co-occurring virioplankton assemblage. Herein, we reveal the unique virioplankton assemblages of the Challenger Deep, comprising 95,813 non-redundant viral contigs from the surface to the hadal zone. Almost all of the dominant viral contigs in the hadal zone were unclassified, potentially related to Alteromonadales and Oceanospirillales. 2,586 viral auxiliary metabolic genes from 132 different KEGG orthologous groups were mainly related to the carbon, nitrogen, sulfur, and arsenic metabolism. Lysogenic viral production and integrase genes were augmented in the hadal zone, suggesting the prevalence of viral lysogenic life strategy. Abundant rve genes in the hadal zone, which function as transposase in the caudoviruses, further suggest the prevalence of viral-mediated horizontal gene transfer. This study provides fundamental insights into the virioplankton assemblages of the hadal zone, reinforcing the necessity of incorporating virioplankton into the hadal biogeochemical cycles.

Functional microbiome strategies for the bioremediation of petroleum-hydrocarbon and heavy metal contaminated soils: A review

Petroleum hydrocarbons and heavy metals are the two major soil contaminants that are released into the environment in the forms of industrial effluents. These contaminants exert serious impacts on human health and the sustainability of the environment. In this context, remediation of these pollutants via a biological approach can be effective, low-cost, and eco-friendly approach. The implementation of microorganisms and metagenomics are regarded as the advanced solution for remediating such pollutants. Further, microbiomes can overcome this issue via adopting specific structural, functional and metabolic pathways involved in the microbial community to degrade these pollutants. Genomic sequencing and library can effectively channelize the degradation of these pollutants via microbiomes. Nevertheless, more advanced technology and reliable strategies are required to develop. The present review provides insights into the role of microbiomes to effectively remediate/degrade petroleum hydrocarbons and heavy metals in contaminated soil. The possible degradation mechanisms of these pollutants have also been discussed in detail along with their existing limitations. Finally, prospects of the bioremediation strategies using microbiomes are discussed.

Spatial Variability of Bacterial Community Compositions in the Mariana Trench

Hadal microorganisms play an important role in the biogeochemical processes in marine ecosystems and act as a valuable resource for industrial applications. This paper presents the bacterial community analysis of samples taken from the Challenger Deep within the Mariana Trench, which is the deepest site in the ocean. High-throughput 16S rRNA gene amplicon sequencing was used to reveal that the vertically sampled bacterial populations at eight stations varied at the surface to 10 km depth. The surface water samples harbored a distinct bacterial assemblage, while the mesopelagic and bathyal samples manifested different bacterial community composition, which was not consistent with previous studies. Gammaproteobacteria was the most abundant bacteria in the bathyal and hadal water. The hadal bacterial community consisted mostly of Alteromonadales and Oceanospirillales. The former was widely spread in the water column, which might suggest habitat partitioning at the genus and OTU levels, while the latter might represent hadal-enriched hydrocarbon degraders. The present work complements the current knowledge and understanding of the bathyal and hadal bacterial communities of the Mariana Trench.

Extremophiles in Earth's Deep Seas: A View Toward Life in Exo-Oceans

Humanity's search for extraterrestrial life is a modern manifestation of the exploratory and curious nature that has led us through millennia of scientific discoveries. With the ongoing exploration of extraterrestrial bodies, the potential for discovery of extraterrestrial life has expanded. We may better inform this search through an understanding of how life persists and flourishes on Earth in a myriad of environmental extremes. A significant proportion of our knowledge of extremophiles on Earth comes from studies on deep ocean life. Here, we review and synthesize the range of environmental extremes observed in the deep sea, the life that persists in these extreme conditions, and the biological adaptations utilized by these remarkable life-forms. We also review confirmed and predicted extraterrestrial oceans in our solar system and propose deep-sea sites that may serve as planetary field analog environments. We show that the clever ingenuity of evolution under deep-sea conditions suggests that the plausibility of extraterrestrial life is much greater than previously thought.

Composition and Ecological Roles of the Core Microbiome along the Abyssal-Hadal Transition Zone Sediments of the Mariana Trench

The unique geological features of hadal trenches are known to influence both the structure and ecological function of microbial communities. It is also well known that heterotrophs and chemoautotrophs dominate the hadal and abyssal pelagic zones, respectively. Here, a metagenomic investigation was conducted on sediment samples obtained from the abyssal-hadal transition zone in the Mariana Trench to gain a better understanding of the general diversity and potential function of the core microbiome in this zone. A high level of cosmopolitanism existed in the core microbiome referred from a high community similarity among different stations. Niche differentiation along the fine-scale of different sediment layers was observed, especially for major archaeal groups, largely due to sediment depth and the source of organic matter. A prevalence of nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation in the abyssal-hadal biosphere was also demonstrated. The predominance of heterotrophic over chemolithoautotrophic pathways in this transition zone was found, and a high abundance of genes related to respiration and carbon fixation (i.e., the intact Calvin and rTCA cycles) were detected as well, which might reflect the intensive microbial activities known to occur in this deep biosphere. The presence of those metabolic processes and associated microbes were reflected by functional and genetic markers generated from the metagenomic data in the current study. However, their roles and contributions to the nitrogen/carbon biogeochemical cycles and flux in the abyssal-hadal transition zone still need further analysis. IMPORTANCE The Mariana Trench is the deepest oceanic region on earth, its microbial ecological exploration has become feasible with the rapid progress of submersible and metagenomic sequencing. We investigated the community compositions and metabolic functions of the core microbiome along the abyssal-hadal transition zone of the Mariana Trench, although most studies by far were focused on the pelagic zone. We found a predominance of heterotrophic groups and related metabolic pathways, which were closely associated with nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation.

Emulating Deep-Sea Bioremediation: Oil Plume Degradation by Undisturbed Deep-Sea Microbial Communities Using a High-Pressure Sampling and Experimentation System

Hydrocarbon biodegradation rates in the deep-sea have been largely determined under atmospheric pressure, which may lead to non-representative results. In this work, we aim to study the response of deep-sea microbial communities of the Eastern Mediterranean Sea (EMS) to oil contamination at in situ environmental conditions and provide representative biodegradation rates. Seawater from a 600 to 1000 m depth was collected using a high-pressure (HP) sampling device equipped with a unidirectional check-valve, without depressurization upon retrieval. The sample was then passed into a HP-reactor via a piston pump without pressure disruption and used for a time-series oil biodegradation experiment at plume concentrations, with and without dispersant application, at 10 MPa and 14 °C. The experimental results demonstrated a high capacity of indigenous microbial communities in the deep EMS for alkane degradation regardless of dispersant application (>70%), while PAHs were highly degraded when oil was dispersed (>90%) and presented very low half-lives (19.4 to 2.2 days), compared to published data. To our knowledge, this is the first emulation study of deep-sea bioremediation using undisturbed deep-sea microbial communities.