Abstract:At 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. Here we combined geophysical, geochemical, metagenomic and metabolomic measurements to profile microbial activities at a newly discovered cold seep in the deep sea. Metagenomic … Show more
“…These genes have been increasingly recovered as putative AMGs in viruses, which may contribute to nucleotide and energy production during infection [ 75 , 81 , 82 ]. Deep sea sediment microorganisms associated with cold seeps were reported to be involved in a variety of carbohydrate degradation reactions for processing detrital organic matter supplied from the overlying water column [ 31 , 32 ]. Infection by viruses containing genes related to carbohydrate degradation in general is consistent with their supportive role in host metabolism during the infection cycle [ 13 ].…”
Section: Resultsmentioning
confidence: 99%
“…Except for EGM and SB, metagenomic data sets along with metadata were downloaded from NCBI Sequence Read Archive and NCBI BioSample databases ( https://www.ncbi.nlm.nih.gov ). Sample collection and DNA sequencing of samples from EGM and SB are described in detail elsewhere [ 31 , 32 ]. Fig.…”
Section: Methodsmentioning
confidence: 99%
“…nlm.nih.gov). Sample collection and DNA sequencing of samples from EGM and SB are described in detail elsewhere [31,32].…”
Section: Collection Of Metagenomic Data Sets For Deep Sea Cold Seepsmentioning
In 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.
“…These genes have been increasingly recovered as putative AMGs in viruses, which may contribute to nucleotide and energy production during infection [ 75 , 81 , 82 ]. Deep sea sediment microorganisms associated with cold seeps were reported to be involved in a variety of carbohydrate degradation reactions for processing detrital organic matter supplied from the overlying water column [ 31 , 32 ]. Infection by viruses containing genes related to carbohydrate degradation in general is consistent with their supportive role in host metabolism during the infection cycle [ 13 ].…”
Section: Resultsmentioning
confidence: 99%
“…Except for EGM and SB, metagenomic data sets along with metadata were downloaded from NCBI Sequence Read Archive and NCBI BioSample databases ( https://www.ncbi.nlm.nih.gov ). Sample collection and DNA sequencing of samples from EGM and SB are described in detail elsewhere [ 31 , 32 ]. Fig.…”
Section: Methodsmentioning
confidence: 99%
“…nlm.nih.gov). Sample collection and DNA sequencing of samples from EGM and SB are described in detail elsewhere [31,32].…”
Section: Collection Of Metagenomic Data Sets For Deep Sea Cold Seepsmentioning
In 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.
“…Hydrogenase activity can be predicted based on primary sequence ( Søndergaard et al, 2016 ). The HydDB database has been widely utilized to classify hydrogenases ( Dong, 2020 ; Mei, 2020 ; Panwar, 2020 ; Park et al, 2020 ; Picone et al, 2020 ; Stairs et al, 2020 ; Wong, 2020 ; Yu et al, 2020 ). We confirmed the reliability of gene annotations in the HydDB database using a simulated metagenomic dataset of hydrogenase-containing and hydrogenase-free genomes (see Materials and methods for details).…”
The composition of gut-associated microbial communities changes during intestinal inflammation, including an expansion of Enterobacteriaceae populations. The mechanisms underlying microbiota changes during inflammation are incompletely understood. Here, we analyzed previously published metagenomic datasets with a focus on microbial hydrogen metabolism. The bacterial genomes in the inflamed murine gut and in patients with inflammatory bowel disease contained more genes encoding predicted hydrogen-utilizing hydrogenases compared to communities found under non-inflamed conditions. To validate these findings, we investigated hydrogen metabolism of Escherichia coli, a representative Enterobacteriaceae, in mouse models of colitis. E. coli mutants lacking hydrogenase-1 and hydrogenase-2 displayed decreased fitness during colonization of the inflamed cecum and colon. Utilization of molecular hydrogen was in part dependent on respiration of inflammation-derived electron acceptors. This work highlights the contribution of hydrogenases to alterations of the gut microbiota in the context of non-infectious colitis.
“…Metagenomes representing diverse environments such as petroleum reservoirs (36)(37)(38)(39), oil spill experimental microcosms (40,41), marine systems (42)(43)(44)(45), host-associated microbiomes (46)(47)(48) and other environments (49,50), were downloaded either as unassembled raw data from the NCBI SRA or as predicted gene sequences from the JGI Genome Portal (Supplementary Table ST4). Raw reads from unassembled metagenomes were filtered using BBDuk (sourceforge.net/projects/bbmap/) for a minimum quality of 15 and a minimum read length of 150bp.…”
Section: Analysis Of Diverse Metagenomes Using Cant-hydmentioning
Discovery of microbial hydrocarbon degradation pathways has traditionally relied on laboratory isolation and characterization of microorganisms. Although many metabolic pathways for hydrocarbon degradation have been discovered, the absence of tools dedicated to their annotation makes it difficult to identify the relevant genes and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Furthermore, sequence homology between hydrocarbon degradation genes and genes with other functions often results in misannotation. A tool that systematically identifies hydrocarbon metabolic potential is therefore needed. We present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database containing HMMs of 37 marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we show that hydrocarbon metabolic potential is widespread in the tree of life and identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate scalability by analyzing large metagenomic datasets for the prediction of hydrocarbon utilization in diverse environments. To the best of our knowledge, CANT-HYD is the first comprehensive tool for robust and accurate identification of marker genes associated with aerobic and anaerobic hydrocarbon degradation.
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