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.

Microorganisms in marine subsurface sediments substantially contribute to global biomass. Sediments warmer than 40°C account for roughly half the marine sediment volume, but the processes mediated by microbial populations in these hard-to-access environments are poorly understood. We investigated microbial life in up to 1.2-kilometer-deep and up to 120°C hot sediments in the Nankai Trough subduction zone. Above 45°C, concentrations of vegetative cells drop two orders of magnitude and endospores become more than 6000 times more abundant than vegetative cells. Methane is biologically produced and oxidized until sediments reach 80° to 85°C. In 100° to 120°C sediments, isotopic evidence and increased cell concentrations demonstrate the activity of acetate-degrading hyperthermophiles. Above 45°C, populated zones alternate with zones up to 192 meters thick where microbes were undetectable.

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ABSTRACT. Although several frameworks for assessing the resilience of social-ecological systems (SESs) have been developed, some practitioners may not have sufficient time and information to conduct extensive resilience assessments. We have presented a simplified approach to resilience assessment that reviews the scientific, historical, and social literature to rate the resilience of an SES with respect to nine resilience properties: ecological variability, diversity, modularity, acknowledgement of slow variables, tight feedbacks, social capital, innovation, overlap in governance, and ecosystem services. We evaluated the effects of two large-scale projects, the construction of a major dam and the implementation of an ecosystem recovery program, on the resilience of the central Platte River SES (Nebraska, United States). We used this case study to identify the strengths and weaknesses of applying a simplified approach to resilience assessment. Although social resilience has increased steadily since the predam period for the central Platte River SES, ecological resilience was greatly reduced in the postdam period as compared to the predam and ecosystem recovery program time periods.

A variety of microbially mediated metabolic pathways impact biogeochemical cycling in terrestrial subsurface environments. However, the role that viruses have in influencing microbial mortality and microbial community structure is poorly understood. Here we investigated the production of viruses and change in microbial community structure within shallow alluvial aquifer sediment slurries amended with 13 C-labeled acetate and nitrate. Biostimulation resulted in production of viruses concurrent with acetate oxidation, 13 CO 2 production and nitrate reduction. Interestingly, change in viral abundance was positively correlated to acetate consumption (r 2 ¼ 0.6252, Po0.05) and 13 CO 2 production (r 2 ¼ 0.6572, Po0.05); whereas change in cell abundance was not correlated to acetate consumption or 13 CO 2 production. Viral-mediated cell lysis has implications for microbial community structure. Betaproteobacteria predominated microbial community composition (62% of paired-end reads) upon inoculation but decreased in relative abundance and was negatively correlated to changes in viral abundance (r 2 ¼ 0.5036, Po0.05). As members of the Betaproteobacteria decreased, Gammaproteobacteria, specifically Pseudomonas spp., increased in relative abundance (82% of paired-end reads) and was positively correlated with the change in viral abundance (r 2 ¼ 0.5368, Po0.05). A nitrate-reducing bacterium, Pseudomonas sp. strain Alda10, was isolated from these sediments and produced viral-like particles with a filamentous morphology that did not result in cell lysis. Together, these results indicate that viruses are linked to carbon biogeochemistry and community structure in terrestrial subsurface sediments. The subsequent cell lysis has the potential to alter available carbon pools in subsurface environments, additionally controlling microbial community structure from the bottom-up.