Patterns and ecological drivers of ocean viral communities

Brum, Jennifer R.; Ignacio‐Espinoza, J. Cesar; Roux, Simon; Doulcier, Guilhem; Acinas, Silvia G.; Alberti, Adriana; Chaffron, Samuel; Cruaud, Corinne; Vargas, Colomban de; Gasol, Josep M.; Gorsky, Gabriel; Gregory, Ann C.; Guidi, Lionel; Hingamp, Pascal; Iudicone, Daniele; Not, Fabrice; Ogata, Hiroyuki; Pesant, Stéphane; Poulos, Bonnie T.; Schwenck, Sarah M.; Speich, Sabrina; Dimier, Céline; Kandels‐Lewis, Stefanie; Picheral, Marc; Searson, Sarah; Coordinators, Tara Oceans; Bork, Peer; Bowler, Chris; Sunagawa, Shinichi; Wincker, Patrick; Karsenti, Eric; Sullivan, Matthew B.

doi:10.1126/science.1261498

Cited by 644 publications

(764 citation statements)

References 66 publications

Supporting

Mentioning

716

Contrasting

Unclassified

Order By: Relevance

“…Similar contigs shared across time points, or between Utica and Marcellus shales, were identified by comparing contigs using the criteria of >95% ANI over 80% of the contig length, analogous to the clustering in ref. 48. Contigs within clusters were then individually aligned and manually inspected to confirm identical contig sequences.…”

Section: Methodsmentioning

confidence: 99%

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

et al. 2016

View full text Add to dashboard Cite

Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here, the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that many of the persisting organisms play roles in methylamine cycling, ultimately supporting methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while thiosulfate reduction could produce sulfide, contributing to reservoir souring and infrastructure corrosion. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface. S hale gas accounts for one-third of natural gas energy resources worldwide. It has been estimated that shale gas will provide half of the natural gas in the USA, annually, by 2040, with the Marcellus shale in the Appalachian Basin projected to produce three times more than any other formation 1 . Recovery of these hydrocarbons is dependent on hydraulic fracturing technologies, where the high-pressure injection of water and chemical additives generates extensive fractures in the shale matrix. Hydrocarbons trapped in tiny pore spaces are subsequently released and collected at the wellpad surface, together with a portion of the injected fluids that have reacted with the shale formation. The mixture of injected fluids and hydrocarbons collected is referred to as 'produced fluids'.Microbial metabolism and growth in hydrocarbon reservoirs has both positive and negative impacts on energy recovery. Whereas stimulation of methanogens in coal beds enhances energy recovery 2 , bacterial hydrogen sulfide production ('reservoir souring') decreases profits and contributes to corrosion and the risk of environmental contamination 3 . Additionally, biomass accumulation within newly generated fractures may reduce their permeability, decreasing natural gas recovery. Despite these potential microbial impacts, little is known about the function and activity of microorganisms in hydraulically fractured shale.Initial work by our group and others 4-9 used single marker gene analyses to identify microorganisms from several geographically distinct shale formations. These analyses showed similar halotolerant taxa in produced fluids several months after hydraulic fracturing. To assign functional roles to these organisms, we conducted metagenomic and metabolite analyses on input and produced fluids up to a year after hydraulic fracturing (HF) from two Appala...

show abstract

Section: Methodsmentioning

confidence: 99%

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

et al. 2016

View full text Add to dashboard Cite

show abstract

“…A very recent survey of various oceanic water samples distributed in all the major oceans (the circumglobal Tara Oceans expedition) provided a comprehensive overview of the Eukaryotic plankton diversity and of the global ocean microbiome . Dispite the in-depth analysis carried out, this project failed to uncover any mycoviruses because taxa in the eukaryotic plankton fraction (the one containing fungi) were detected through amplification of V9 region of the 18S rRNA gene therefore excluding the possibility of detecting their symbiotic viruses ( Brum et al, 2015.…”

Section: Discussionmentioning

confidence: 99%

“…Specifically, most marine viruses are cyanophages and have been shown to be major players in biogeochemical cycles and drivers of evolution of their algal hosts (Brussaard et al, 2008 andFuhrman, 1999) by influencing microbial population size through their lytic capacity, altering their metabolic output and providing an immensely diverse pool of genetic material available for horizontal gene transfer (Brum et al, 2015). Till now, no virus associated to marine fungi has been reported, probably because the presence and ecological role of fungi in marine environment has been neglected till few years ago.…”

Section: Introductionmentioning

confidence: 99%

Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi

Nerva¹,

et al. 2016

View full text Add to dashboard Cite

Highlights• First report of mycoviruses isolated from fungi from marine environment.• Survey of mycoviruses using multiple approaches for both DNA and RNA genomes.• RNAseq analysis is superior to sRNA for de novo assembly of mycoviruses.• Twelve new virus species were characterized molecularly.• Expression of a viral RNA from an endogenized cDNA segment. AbstractThe number of reported mycoviruses is increasing exponentially due to the current ability to detect mycoviruses using next-generation sequencing (NGS) approaches, with a large number of viral genomes built in-silico using data from fungal transcriptome projects. We decided to screen a collection of fungi originating from a specific marine environment (associated with the seagrass Posidonia oceanica) for the presence of mycoviruses: our findings reveal a wealth of diversity among these symbionts and this complexity will require further studies to address their specific role in this ecological niche. In specific, we identified twelve new virus species belonging to nine distinct lineages: they are members of megabirnavirus, totivirus, chrysovirus, partitivirus and five still undefined clades. We showed evidence of an endogenized virus ORF, and evidence of accumulation of dsRNA from metaviridae retroviral elements. We applied different techniques for detecting the presence of mycoviruses including (i) dsRNA extraction and cDNA cloning, (ii) small and total RNA sequencing through NGS techniques, (iii) rolling circle amplification (RCA) and total DNA extraction analyses, (iv) virus purifications and electron microscopy. We tried also to critically evaluate the intrinsic value and limitations of each of these techniques. Based on the samples we could compare directly, RNAseq analysis is superior to sRNA for de novo assembly of mycoviruses. To our knowledge this is the first report on the virome of fungi isolated from marine environment.

show abstract

“…1). This expands the number of known ocean viral populations nearly 3-fold over the prior TOV dataset 10 , while also improving the genomic context for these TOV-known populations by a 2.5-fold increase in contig length on average (Supplementary Table 2). Rarefaction analyses show that while mesopelagic viral communities remain undersampled, epipelagic viral communities now appear near-completely sampled (Extended Data Fig.…”

mentioning

confidence: 99%

“…4B). This suggests that, likely because of the global distribution of ocean viruses 10,22 , widespread and abundant hosts that are minimally diverse (e.g. Cyanobacteria) provide few viral niches, whereas more diverse host groups, even at lower abundance (e.g.…”

mentioning

confidence: 99%

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Roux

Brum

Dutilh

et al. 2016

Nature

Self Cite

692

885

View full text Add to dashboard Cite

Tara Oceans CoordinatorsInternational audienceOcean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups. This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks

show abstract

Patterns and ecological drivers of ocean viral communities

Cited by 644 publications

References 66 publications

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Contact Info

Product

Resources

About