Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

Anantharaman, Karthik; Duhaime, Melissa B.; Breier, J. A.; Wendt, Kathleen A.; Toner, Brandy M.; Dick, Gregory J.

doi:10.1126/science.1252229

Cited by 235 publications

(236 citation statements)

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“…Four AMGs (i.e. similar to a domain from the "metabolism" category) were then selected for further study because of their central role in sulfur (dsrC and soxYZ) or nitrogen (P-II, amoC) cycle, and the fact that these had never been detected in a surface ocean viral genome so far (dsrC/tusE-like genes have been detected in deep water viruses 14,29 ). To evaluate if an AMG was "known", a list of PFAM domain detected in NCBI RefSeqVirus and Environmental Phages was computed based on a similar hmmsearch comparison (threshold of 40 on bit score and 0.001 on e-value), and augmented by manual annotation of AMGs from 24,82 .…”

Section: Identification and Annotation Of Putative Amgs Detection Of mentioning

confidence: 99%

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Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Roux

Brum

Dutilh

et al. 2016

Nature

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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

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Section: Identification and Annotation Of Putative Amgs Detection Of mentioning

confidence: 99%

“…Conserved residues are indicated below the alignment, and the two conserved C residues representing the active sites of "true dsrC" (Cys-B and Cys-A) are named as in 33 . Viral AMGs are highlighted in bold, with previously described anoxic SUP05 viruses sequences in red (from 14,29 ) and epipelagic GOV sequences in black. …”

Section: Supplementary Figurementioning

confidence: 99%

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Roux

Brum

Dutilh

et al. 2016

Nature

Self Cite

641

881

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“…The chemistry of nearby seawater is defined to represent 'typical' deep-sea water. Initial plume chemistry is prescribed using an existing reaction-path model (Breier et al, 2012;Anantharaman et al, 2014), which accounts for the rapid abiotic precipitation of minerals and chemical speciation in the vicinity of the chimney that results from the mixing of vent fluid (Mottl et al, 2011;Flores et al, 2012) and background seawater (Supplementary Table S3); details of this model for the A1 vent are described in Anantharaman et al (2014).…”

Section: Methodsmentioning

confidence: 99%

“…Microbial data used to drive and validate the model were collected from the ABE hydrothermal vent field, Lau basin, during cruises TN235 and TN236 aboard the R/V Thomas G Thompson in May-July 2009 (Supplementary Table S4; Anantharaman et al, 2014). Sampling was undertaken using a suspended-particle rosette multi-sampler (Breier et al, 2009) with 0.8 mm filters.…”

Section: Metagenomic Datamentioning

confidence: 99%

“…Given that energy drives deep-sea autotrophy, thermodynamic mixing models have been used extensively over the past 20 years to estimate primary production in chimney walls, plumes and low-temperature diffuse flow regions of submarine hydrothermal systems (for example, Shock et al, 1995;McCollom and Shock, 1997;McCollom, 2000McCollom, , 2007Amend et al, 2011;Anantharaman et al, 2013;Boettger et al, 2013;Anantharaman et al, 2014;Nakamura and Takai, 2014). These models calculate the amount of energy that is potentially available through a wide range of pathways, thus predicting the prevalence of these metabolisms.…”

Section: Introductionmentioning

confidence: 99%

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Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents

et al. 2015

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Submarine hydrothermal vents perturb the deep-ocean microbiome by injecting reduced chemical species into the water column that act as an energy source for chemosynthetic organisms. These systems thus provide excellent natural laboratories for studying the response of microbial communities to shifts in marine geochemistry. The present study explores the processes that regulate coupled microbial-geochemical dynamics in hydrothermal plumes by means of a novel mathematical model, which combines thermodynamics, growth and reaction kinetics, and transport processes derived from a fluid dynamics model. Simulations of a plume located in the ABE vent field of the Lau basin were able to reproduce metagenomic observations well and demonstrated that the magnitude of primary production and rate of autotrophic growth are largely regulated by the energetics of metabolisms and the availability of electron donors, as opposed to kinetic parameters. Ambient seawater was the dominant source of microbes to the plume and sulphur oxidisers constituted almost 90% of the modelled community in the neutrally-buoyant plume. Data from drifters deployed in the region allowed the different time scales of metabolisms to be cast in a spatial context, which demonstrated spatial succession in the microbial community. While growth was shown to occur over distances of tens of kilometers, microbes persisted over hundreds of kilometers. Given that high-temperature hydrothermal systems are found less than 100 km apart on average, plumes may act as important vectors between different vent fields and other environments that are hospitable to similar organisms, such as oil spills and oxygen minimum zones.

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The Architecture of Microbial Genomes

2018

Genomic Approaches in Earth and Environmental Sciences

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Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

Abstract: Viruses are the most abundant biological entities in the oceans and a pervasive cause of mortality of microorganisms that drive biogeochemical cycles. Although the ecological and evolutionary

Cited by 235 publications

References 74 publications

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents

The Architecture of Microbial Genomes

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