scholarly journals Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

2021 ◽  
Author(s):  
Zexin Li ◽  
Donald Pan ◽  
Guangshan Wei ◽  
Weiling Pi ◽  
Chuwen Zhang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Deep Sea ◽  
Cold Seep ◽  
Hydrocarbon Biodegradation ◽  
Viral Diversity ◽  
Cold Seeps ◽  
Host Interaction ◽  
Deep Sea Sediments ◽  
Subsurface Reservoir ◽  
Network Comparisons

AbstractIn marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans to assess viral diversity, virus–host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.

scholarly journals Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

2020 ◽  
Author(s):  
Zexin Li ◽  
Donald Pan ◽  
Guangshan Wei ◽  
Weiling Pi ◽  
Jiang-Hai Wang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Deep Sea ◽  
Cold Seep ◽  
Hydrocarbon Biodegradation ◽  
Viral Diversity ◽  
Cold Seeps ◽  
Host Interaction ◽  
Deep Sea Sediments ◽  
Subsurface Reservoir ◽  
Network Comparisons

AbstractIn marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, thus influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans, to assess viral diversity, virus-host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations, with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.

scholarly journals Deep-sea ophiuroids (Echinodermata) from reducing and non-reducing environments in the North Atlantic Ocean

2005 ◽  
Vol 85 (2) ◽  
pp. 383-402 ◽  
Author(s):  
Sabine Stöhr ◽  
Michel Segonzac
Keyword(s):  
South Carolina ◽  
Gulf Of Mexico ◽  
Deep Sea ◽  
Hydrothermal Vents ◽  
Cold Seep ◽  
Chemical Compositions ◽  
Cold Seeps ◽  
Additional Species ◽  
Blake Ridge ◽  
Reducing Environment

The animal communities associated with the deep-sea reducing environment have been studied for almost 30 years, but until now only a single species of ophiuroid, Ophioctenella acies, has been found at both hydrothermal vents and methane cold seeps. Since the faunal overlap between vent and seep communities is small and many endemic species have been found among other taxa (e.g. Mollusca, Crustacea), additional species of ophiuroids were expected at previously unstudied sites. Chemical compositions at reducing sites differ greatly from the nearby bathyal environment. Generally, species adapted to chemosynthetic environments are not found in non-chemosynthetic habitats, but occasional visitors of other bathyal species to vent and seep sites have been recorded among many taxa except ophiuroids. This paper presents an analysis of the ophiuroid fauna found at hydrothermal vents and non-reducing nearby sites on the Mid-Atlantic Ridge and on methane cold seeps in the Gulf of Mexico, at Blake Ridge off South Carolina and south of Barbados. In addition to O. acies, four species were found at vents, Ophiactis tyleri sp. nov., Ophiocten centobi, Ophiomitra spinea and Ophiotreta valenciennesi rufescens. While Ophioctenella acies appears to be restricted to chemosynthetic areas, the other four species were also found in other bathyal habitats. They also occur in low numbers (mostly single individuals), whereas species adapted to hydrothermal areas typically occur in large numbers. Ophioscolex tripapillatus sp. nov. and Ophiophyllum atlanticum sp. nov. are described from nearby non-chemosynthetic sites. In a cold seep south of Barbados, three species of ophiuroids were found, including Ophioctenella acies, Amphiura sp., Ophiacantha longispina sp. nov. and Ophioplinthaca chelys. From the cold seeps at Blake Ridge and the Gulf of Mexico, Ophienigma spinilimbatum gen. et sp. nov. is described, likely restricted to the reducing environment. Ophiotreta valenciennesi rufescens occurred abundantly among Lophelia corals in the Gulf of Mexico seeps, which is the first record of this species from the West Atlantic. Habitat descriptions complement the taxonomic considerations, and the distribution of the animals in reducing environments is discussed.

scholarly journals Thermogenic hydrocarbons fuel a redox stratified subseafloor microbiome in deep sea cold seep sediments

2020 ◽  
Author(s):  
Xiyang Dong ◽  
Jayne E. Rattray ◽  
D. Calvin Campbell ◽  
Jamie Webb ◽  
Anirban Chakraborty ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrogen Oxidation ◽  
Sulfide Oxidation ◽  
Cold Seep ◽  
Reductive Dehalogenation ◽  
Cold Seeps ◽  
Community Members ◽  
Metabolic Potential ◽  
Near Surface ◽  
Fumarate Addition

AbstractAt marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. In this work, we combined geochemical, metagenomic and metabolomic measurements in distinct sediment redox regimes to profile microbial activities within the uppermost 350 cm of a newly discovered cold seep in the NW Atlantic deep sea (2.3 km water depth). Depth-resolved metagenomic profiling revealed compositional and functional differentiation between near-surface sediments (dominated by Proteobacteria) and deeper subsurface layers (dominated by Atribacteria, Chloroflexi, Euryarchaeota and Lokiarchaeota). Metabolic capabilities of community members were inferred from 376 metagenome-assembled genomes spanning 46 phyla (including five novel candidate phyla). In deeper sulfate-reducing and methanogenic sediments, various community members are capable of anaerobically oxidizing short-chain alkanes (alkyl-CoM reductase pathway), longer-chain alkanes (fumarate addition pathway), and aromatic hydrocarbons (fumarate addition and subsequent benzoyl-CoA pathways). Geochemical profiling demonstrated that hydrocarbon substrates are abundant in this location, thermogenic in origin, and subject to biodegradation. The detection of alkyl-/arylalkylsuccinate metabolites, together with carbon isotopic signatures of ethane, propane and carbon dioxide, support that microorganisms are actively degrading hydrocarbons in these sediments. Hydrocarbon oxidation pathways operate alongside other deep seabed metabolisms such as sulfide oxidation, hydrogen oxidation, carbon fixation, fermentation and reductive dehalogenation. Upward migrated thermogenic hydrocarbons thus sustain diverse microbial communities with activities that affect subseafloor biogeochemical processes across the redox spectrum in deep sea cold seeps.

scholarly journals A deep-sea sulfate reducing bacterium directs the formation of zero-valent sulfur via sulfide oxidation

2021 ◽  
Author(s):  
Rui Liu ◽  
Yeqi Shan ◽  
Shichuan Xi ◽  
Xin Zhang ◽  
Chaomin Sun
Keyword(s):  
Deep Sea ◽  
Sulfide Oxidation ◽  
Sulfur Cycle ◽  
Cold Seep ◽  
Cold Seeps ◽  
Protein Activity ◽  
Quinone Oxidoreductase ◽  
Sulfate Reducing ◽  
Thiosulfate Reductase ◽  
Reducing Bacteria

Zero-valent sulfur (ZVS) is a critical intermediate in the biogeochemical sulfur cycle. Up to date, sulfur oxidizing bacteria have been demonstrated to dominate the formation of ZVS. In contrast, formation of ZVS mediated by sulfate reducing bacteria (SRB) has been rarely reported. Here, we report for the first time that a typical sulfate reducing bacterium Desulfovibrio marinus CS1 directs the formation of ZVS via sulfide oxidation. In combination with proteomic analysis and protein activity assays, thiosulfate reductase (PhsA) and sulfide: quinone oxidoreductase (SQR) were demonstrated to play key roles in driving ZVS formation. In this process, PhsA catalyzed thiosulfate to form sulfide, which was then oxidized by SQR to form ZVS. Consistently, the expressions of PhsA and SQR were significantly up-regulated in strain CS1 when cultured in the deep-sea cold seep, strongly indicating strain CS1 might form ZVS in its real inhabiting niches. Notably, homologs of phsA and sqr widely distributed in the metagenomes of deep-sea SRB. Given the high abundance of SRB in cold seeps, it is reasonable to propose that SRB might greatly contribute to the formation of ZVS in the deep-sea environments. Our findings add a new aspect to the current understanding of the source of ZVS.

scholarly journals Phosphorus Species in Deep-Sea Carbonate Deposits: Implications for Phosphorus Cycling in Cold Seep Environments

Minerals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 645
Author(s):  
Junlie Zhou ◽  
Mengran Du ◽  
Jiwei Li ◽  
Hengchao Xu ◽  
Kaiwen Ta ◽  
...  
Keyword(s):  
Deep Sea ◽  
Cold Seep ◽  
Anaerobic Oxidation Of Methane ◽  
Cold Seeps ◽  
Organic P ◽  
Anaerobic Oxidation ◽  
Phosphorus Species ◽  
China Sea ◽  
Oxidation Of Methane ◽  
Deep Sediments

Phosphorus (P) is an important nutrient for biological communities in cold seeps. However, our knowledge on the source, species, and cycling of P in cold seep environments is limited. In this study, the concentration, species, and micro to nanometer scale distribution of P in seep carbonates were examined at three deep-sea cold seeps in the South China Sea and East China Sea. The Ca-P accounts for the largest proportion of P—followed by detrital-P, Fe-P, organic-P, and exchangeable-P. The distribution patterns of Ca-P, detrital-P, and organic-P in the seep carbonates differ from one another, as shown by elemental mapping with NanoSIMS and scanning electron microscopy. The covariation of P with Ca and C reveals that Ca-P co-precipitates with Ca-carbonate, which is linked to the process of sulfate-driven anaerobic oxidation of methane. Organic-P is also observed within biofilm-like organic carbon aggregates, revealing the microbial enrichment of P by fluids in the process of anaerobic oxidation of methane. P with a granulated morphology was identified as detrital-P derived from deep sediments. Most importantly, it is evident that Ca-P is positively correlated to the Fe content in all the seep carbonates. This indicates the likelihood that the dissolved P in cold-seep fluids is released primarily from Fe oxides through Fe-driven anaerobic oxidation of methane in deep sediments. These processes associated with different species of P may have significant implications for P geochemical cycling and anaerobic oxidation of methane impelled by Fe and sulfate reduction in cold seep environments.

scholarly journals Cultivation and characterization of a novel clade of deep-sea Chloroflexi: providing a glimpse of the phylum Chloroflexi involved in sulfur cycling

2021 ◽  
Author(s):  
Rikuan Zheng ◽  
Ruining Cai ◽  
Rui Liu ◽  
Yeqi Shan ◽  
Ge Liu ◽  
...  
Keyword(s):  
Sulfate Reduction ◽  
Deep Sea ◽  
Phylogenetic Analyses ◽  
Cold Seep ◽  
Sulfur Cycling ◽  
Rrna Gene ◽  
Dissimilatory Sulfate Reduction ◽  
Operational Taxonomic Units ◽  
Deep Sea Sediments ◽  
Genes Encoding

AbstractChloroflexi bacteria are abundant and globally distributed in various unexplored biospheres on Earth. However, only few Chloroflexi members have been cultivated, hampering further understanding of this important group. In the current study, we firstly clarify the high abundance of the phylum Chloroflexi in deep-sea sediments via the operational taxonomic units analysis. We further successfully isolate a novel Chloroflexi strain ZRK33 from cold seep sediments by using an enrichment medium constantly supplemented with rifampicin. Phylogenetic analyses based on 16S rRNA gene, genome, RpoB and EF-tu proteins indicate that strain ZRK33 represents a novel class, and the class is designated as Sulfochloroflexia because whole set of genes encoding key enzymes responsible for assimilatory sulfate reduction are identified in the genome of strain ZRK33. Indeed, assimilation of sulfate or thiosulfate by strain ZRK33 evidently benefits its growth and morphogenesis. Proteomic results suggest that metabolization of sulfate or thiosulfate significantly promotes the transport and degradation of various macromolecules and thereby stimulating the energy production. Notably, the putative genes associated with assimilatory and dissimilatory sulfate reduction ubiquitously distribute in the metagenome-assembled genomes of 27 Chloroflexi members derived from deep-sea sediments, strongly suggesting that Chloroflexi bacteria play undocumented key roles in deep-sea sulfur cycling.

scholarly journals Chemosynthesis in the deep-sea: life without the sun

2012 ◽  
Vol 9 (12) ◽  
pp. 17037-17052 ◽  
Author(s):  
C. Smith
Keyword(s):  
Organic Matter ◽  
Surface Waters ◽  
Deep Sea ◽  
Hydrothermal Vents ◽  
Cold Seep ◽  
Cold Seeps ◽  
The Sun ◽  
Life Stages ◽  
Way Of Life ◽  
Use Of Resources

Abstract. Chemosynthetic communities in the deep-sea can be found at hydrothermal vents, cold seeps, whale falls and wood falls. While these communities have been suggested to exist in isolation from solar energy, much of the life associated with them relies either directly or indirectly on photosynthesis in the surface waters of the oceans. The sun indirectly provides oxygen, a byproduct of photosynthesis, which aerobic chemosynthetic microorganisms require to synthesize organic carbon from CO2. Planktonic life stages of many vent and cold seep invertebrates also directly feed on photosynthetically produced organic matter as they disperse to new vent and seep systems. While a large portion of the life at deep-sea chemosynthetic habitats can be linked to the sun and so could not survive without it, a small portion of anaerobically chemosynthetic microorganisms can persist in its absence. These small and exotic organisms have developed a way of life in the deep-sea which involves the use of resources originating in their entirety from terrestrial sources.

Sign in / Sign up

Export Citation Format

Share Document