scholarly journals Methane-derived carbon flow through host-virus trophic networks in soil

2020 ◽  
Author(s):  
Sungeun Lee ◽  
Ella T. Sieradzki ◽  
Alexa M. Nicolas ◽  
Robin L. Walker ◽  
Mary K. Firestone ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Stable Isotope Probing ◽  
Metagenomic Sequencing ◽  
Atmospheric Methane ◽  
Diverse Range ◽  
Soil Microbial ◽  
Trophic Networks ◽  
Predatory Bacteria ◽  
And Function

AbstractThe concentration of atmospheric methane continues to increase with microbial communities controlling soil-atmosphere fluxes. While there is substantial knowledge of the diversity and function of organisms regulating methane production and consumption, the frequency and impact of interactions with viruses on their activity in soil is unknown. Metagenomic sequencing of soil microbial communities has enabled identification of linkages between viruses and hosts. However, determining host-virus linkages through sequencing does not determine whether a virus or a host are active. In this study, we identified active individual interactions in situ by following the transfer of assimilated carbon from active hosts to viruses. Using DNA stable-isotope probing combined with metagenomic analyses, we characterized methane-fueled microbial networks in acidic and neutral pH soils, specifically primary and secondary utilisers of carbon, together with the recent transfer of methane-derived carbon to viruses. Sixty-three percent of viral contigs from replicated soil incubations contained genes associated with known methanotrophic bacteria. Genomic sequences from 13C-enriched viruses were present in clustered regularly interspaced short palindromic repeats (CRISPR) arrays of multiple, closely-related Methylocystis populations, revealing differences in their history of viral interaction. Viruses infecting non-methanotrophic methylotrophs and heterotrophic predatory bacteria were also identified through the analysis of shared homologous genes, demonstrating that carbon is transferred to a diverse range of viruses associated with methane-fueled microbial food networks.

scholarly journals Methane-derived carbon flows into host–virus networks at different trophic levels in soil

2021 ◽  
Vol 118 (32) ◽  
pp. e2105124118
Author(s):  
Sungeun Lee ◽  
Ella T. Sieradzki ◽  
Alexa M. Nicolas ◽  
Robin L. Walker ◽  
Mary K. Firestone ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Stable Isotope Probing ◽  
Trophic Levels ◽  
Methylotrophic Bacteria ◽  
Metagenomic Sequencing ◽  
Atmospheric Methane ◽  
Diverse Range ◽  
Soil Microbial ◽  
Predatory Bacteria

The concentration of atmospheric methane (CH4) continues to increase with microbial communities controlling soil–atmosphere fluxes. While there is substantial knowledge of the diversity and function of prokaryotes regulating CH4 production and consumption, their active interactions with viruses in soil have not been identified. Metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts. However, this does not determine if these represent current or historical interactions nor whether a virus or host are active. In this study, we identified active interactions between individual host and virus populations in situ by following the transfer of assimilated carbon. Using DNA stable-isotope probing combined with metagenomic analyses, we characterized CH4-fueled microbial networks in acidic and neutral pH soils, specifically primary and secondary utilizers, together with the recent transfer of CH4-derived carbon to viruses. A total of 63% of viral contigs from replicated soil incubations contained homologs of genes present in known methylotrophic bacteria. Genomic sequences of 13C-enriched viruses were represented in over one-third of spacers in CRISPR arrays of multiple closely related Methylocystis populations and revealed differences in their history of viral interaction. Viruses infecting nonmethanotrophic methylotrophs and heterotrophic predatory bacteria were also identified through the analysis of shared homologous genes, demonstrating that carbon is transferred to a diverse range of viruses associated with CH4-fueled microbial food networks.

Structure and function of alpine and arctic soil microbial communities

2005 ◽  
Vol 156 (7) ◽  
pp. 775-784 ◽  
Author(s):  
Diana R. Nemergut ◽  
Elizabeth K. Costello ◽  
Allen F. Meyer ◽  
Monte Y. Pescador ◽  
Michael N. Weintraub ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Structure And Function ◽  
Soil Microbial ◽  
Arctic Soil ◽  
And Function

scholarly journals Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2

mBio ◽  
2011 ◽  
Vol 2 (4) ◽  
Author(s):  
Jizhong Zhou ◽  
Ye Deng ◽  
Feng Luo ◽  
Zhili He ◽  
Yunfeng Yang
Keyword(s):  
Microbial Communities ◽  
Microbial Ecology ◽  
High Throughput ◽  
Network Topology ◽  
Ecosystem Functioning ◽  
Soil Microbial Communities ◽  
Microbial Populations ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Soil Microbial

ABSTRACT Understanding the interactions among different species and their responses to environmental changes, such as elevated atmospheric concentrations of CO2, is a central goal in ecology but is poorly understood in microbial ecology. Here we describe a novel random matrix theory (RMT)-based conceptual framework to discern phylogenetic molecular ecological networks using metagenomic sequencing data of 16S rRNA genes from grassland soil microbial communities, which were sampled from a long-term free-air CO2 enrichment experimental facility at the Cedar Creek Ecosystem Science Reserve in Minnesota. Our experimental results demonstrated that an RMT-based network approach is very useful in delineating phylogenetic molecular ecological networks of microbial communities based on high-throughput metagenomic sequencing data. The structure of the identified networks under ambient and elevated CO2 levels was substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher-order organization, topological roles of individual nodes, and network hubs, suggesting that the network interactions among different phylogenetic groups/populations were markedly changed. Also, the changes in network structure were significantly correlated with soil carbon and nitrogen contents, indicating the potential importance of network interactions in ecosystem functioning. In addition, based on network topology, microbial populations potentially most important to community structure and ecosystem functioning can be discerned. The novel approach described in this study is important not only for research on biodiversity, microbial ecology, and systems microbiology but also for microbial community studies in human health, global change, and environmental management. IMPORTANCE The interactions among different microbial populations in a community play critical roles in determining ecosystem functioning, but very little is known about the network interactions in a microbial community, owing to the lack of appropriate experimental data and computational analytic tools. High-throughput metagenomic technologies can rapidly produce a massive amount of data, but one of the greatest difficulties is deciding how to extract, analyze, synthesize, and transform such a vast amount of information into biological knowledge. This study provides a novel conceptual framework to identify microbial interactions and key populations based on high-throughput metagenomic sequencing data. This study is among the first to document that the network interactions among different phylogenetic populations in soil microbial communities were substantially changed by a global change such as an elevated CO2 level. The framework developed will allow microbiologists to address research questions which could not be approached previously, and hence, it could represent a new direction in microbial ecology research.

scholarly journals ATMOSPHERIC CO2AND THE COMPOSITION AND FUNCTION OF SOIL MICROBIAL COMMUNITIES

2000 ◽  
Vol 10 (1) ◽  
pp. 47-59 ◽  
Author(s):  
Donald R. Zak ◽  
Kurt S. Pregitzer ◽  
Peter S. Curtis ◽  
William E. Holmes
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
And Function

The diversity and function of soil microbial communities exposed to different disturbances

2002 ◽  
Vol 44 (1) ◽  
pp. 49-58 ◽  
Author(s):  
A. K. Müller ◽  
K. Westergaard ◽  
S. Christensen ◽  
S. J. Sørensen
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
And Function

scholarly journals Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities

2014 ◽  
Vol 114 (5) ◽  
pp. 1011-1021 ◽  
Author(s):  
N. Legay ◽  
C. Baxendale ◽  
K. Grigulis ◽  
U. Krainer ◽  
E. Kastl ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Plant Traits ◽  
Soil Microbial Communities ◽  
Structure And Function ◽  
Grassland Soil ◽  
Soil Microbial ◽  
Below Ground ◽  
And Function

scholarly journals Fatty Acid-Oxidizing Consortia along a Nutrient Gradient in the Florida Everglades

2006 ◽  
Vol 72 (4) ◽  
pp. 2400-2406 ◽  
Author(s):  
Ashvini Chauhan ◽  
Andrew Ogram
Keyword(s):  
Soil Microbial Communities ◽  
Stable Isotope Probing ◽  
Florida Everglades ◽  
Rrna Gene ◽  
Clone Libraries ◽  
Fermentation Products ◽  
Bacterial Phyla ◽  
Soil Microbial ◽  
Nutrient Gradient ◽  
And Function

ABSTRACT The Florida Everglades is one of the largest freshwater marshes in North America and has been subject to eutrophication for decades. A gradient in P concentrations extends for several kilometers into the interior of the northern regions of the marsh, and the structure and function of soil microbial communities vary along the gradient. In this study, stable isotope probing was employed to investigate the fate of carbon from the fermentation products propionate and butyrate in soils from three sites along the nutrient gradient. For propionate microcosms, 16S rRNA gene clone libraries from eutrophic and transition sites were dominated by sequences related to previously described propionate oxidizers, such as Pelotomaculum spp. and Syntrophobacter spp. Significant representation was also observed for sequences related to Smithella propionica, which dismutates propionate to butyrate. Sequences of dominant phylotypes from oligotrophic samples did not cluster with known syntrophs but with sulfate-reducing prokaryotes (SRP) and Pelobacter spp. In butyrate microcosms, sequences clustering with Syntrophospora spp. and Syntrophomonas spp. dominated eutrophic microcosms, and sequences related to Pelospora dominated the transition microcosm. Sequences related to Pelospora spp. and SRP dominated clone libraries from oligotrophic microcosms. Sequences from diverse bacterial phyla and primary fermenters were also present in most libraries. Archaeal sequences from eutrophic microcosms included sequences characteristic of Methanomicrobiaceae, Methanospirillaceae, and Methanosaetaceae. Oligotrophic microcosms were dominated by acetotrophs, including sequences related to Methanosarcina, suggesting accumulation of acetate.

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