scholarly journals Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol

2019 ◽  
Vol 10 ◽  
Author(s):  
Zhou Li ◽  
Qiuming Yao ◽  
Xuan Guo ◽  
Alexander Crits-Christoph ◽  
Melanie A. Mayes ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Stable Isotope Probing ◽  
Soil Microbial

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.

scholarly journals Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil

mSphere ◽  
2021 ◽  
Author(s):  
Evan P. Starr ◽  
Shengjing Shi ◽  
Steven J. Blazewicz ◽  
Benjamin J. Koch ◽  
Alexander J. Probst ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Microbial Communities ◽  
Rhizosphere Soil ◽  
Soil Microbial Communities ◽  
Plant Productivity ◽  
Rhizosphere Bacteria ◽  
Soil Microbial ◽  
Intimate Association

Plants grow in intimate association with soil microbial communities; these microbes can facilitate the availability of essential resources to plants. Thus, plant productivity commonly depends on interactions with rhizosphere bacteria, viruses, and eukaryotes.

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.

Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Lucas Dantas Lopes ◽  
Jingjie Hao ◽  
Daniel P Schachtman
Keyword(s):  
Microbial Communities ◽  
Plant Species ◽  
Soil Ph ◽  
Soil Microbial Communities ◽  
Bulk Soil ◽  
Strong Impact ◽  
Alkaline Soil ◽  
Alkaline Soils ◽  
Soil Microbial ◽  
Soil Rhizosphere

ABSTRACT Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.

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