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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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.
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.
In 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.
Abstract:The growing complexity and interdependence of water management processes requires the involvement of multiple stakeholders in water governance. Multi-party collaboration is increasingly vital at both the strategy development and implementation levels. Multi-party collaboration involves a process of joint decision-making among key stakeholders in a problem domain directed towards the future of that domain. However, the common goal is not present from the beginning; rather, the common goal emerges during the process of collaboration. Unfortunately, when the conflicting interests of different actors are at stake, the large majority of environmental multi-party efforts often do not reliably deliver sustainable improvements to policy and/or practice. One of the reasons for this, which has been long established by many case studies, is that social learning with a focus on relational practices is missing. The purpose of this paper is to present the design and initial results of a pilot study that utilized a game-based approach to explore the effects of relational practices on the effectiveness of water governance. This paper verifies the methods used by addressing the following question: are game mechanisms, protocols for facilitation and observation, the recording of decisions and results, and participant surveys adequate to reliably test hypotheses about behavioral decisions related to water governance? We used the "Lords of the Valley" (LOV) game, which focuses on the local-level management of a hypothetical river valley involving many stakeholders. We used an observation protocol to collect data on the quality of relational practices and compared this data with the quantitative outcomes achieved by participants in the game. In this pilot study, we ran the game three times with different groups of participants, and here we provide the outcomes within the context of verifying and improving the methods.
Viruses are the most abundant biological entities on Earth and perform essential ecological functions in aquatic environments by mediating biogeochemical cycling and lateral gene transfer. Cellular life as well as viruses have been found in deep subseafloor sediment. However, the study of deep sediment viruses has been hampered by the complexities involved in efficiently extracting viruses from a sediment matrix. Here, we developed a new method for the extraction of viruses from sediment based on density separation using a Nycodenz density step gradient. The density separation method resulted in up to 2 orders of magnitude greater recovery of viruses from diverse subseafloor sediments compared to conventional methods. The density separation method also showed more consistent performance between samples of different sediment lithology, whereas conventional virus extraction methods were highly inconsistent. Using this new method, we show that previously published virus counts have underestimated viral abundances by up to 2 orders of magnitude. These improvements suggest that the carbon contained within viral biomass in the subseafloor environment may potentially be revised upward to 0.8–3.7 Gt from current estimates of 0.2 Gt. The vastly improved recovery of viruses indicate that viruses represent a far larger pool of organic carbon in subseafloor environments than previously estimated.
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