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Community RNA-Seq: Multi-kingdom responses to living versus decaying root inputs in soil

View ORCID ProfileErin E. Nuccio, Nhu H. Nguyen, Ulisses Nunes da Rocha, Xavier Mayali, Jeremy Bougoure, Peter Weber, Eoin Brodie, Mary Firestone, Jennifer Pett-Ridge
doi: https://doi.org/10.1101/2021.01.12.426429
Erin E. Nuccio
1Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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  • For correspondence: nuccio1@llnl.gov pettridge2@llnl.gov
Nhu H. Nguyen
2Department of Tropical Plant and Soil Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI, USA
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Ulisses Nunes da Rocha
3Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
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Xavier Mayali
1Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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Jeremy Bougoure
4Centre for Microscopy, Characterisation & Analysis, The University of Western Australia, Perth, Australia
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Peter Weber
1Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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Eoin Brodie
5Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
6Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
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Mary Firestone
5Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
6Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
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Jennifer Pett-Ridge
1Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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  • For correspondence: nuccio1@llnl.gov pettridge2@llnl.gov
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ABSTRACT

Roots are the primary source of organic carbon inputs to most soils. Decomposition is a multi-trophic process involving multiple kingdoms of microbial life, but typically microbial ecology studies focus on one or two major lineages in isolation. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis (“community RNA-Seq”) to simultaneously study the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in 13CO2-labeled microcosms amended with 15N-root litter. We identified rhizosphere substrate preferences for 13C-exudates versus 15N-litter using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group’s more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving cross-kingdom interactions, and the trajectory of carbon through this soil food web likely impacts the fate of carbon in soil.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.
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Posted January 13, 2021.
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Community RNA-Seq: Multi-kingdom responses to living versus decaying root inputs in soil
Erin E. Nuccio, Nhu H. Nguyen, Ulisses Nunes da Rocha, Xavier Mayali, Jeremy Bougoure, Peter Weber, Eoin Brodie, Mary Firestone, Jennifer Pett-Ridge
bioRxiv 2021.01.12.426429; doi: https://doi.org/10.1101/2021.01.12.426429
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Community RNA-Seq: Multi-kingdom responses to living versus decaying root inputs in soil
Erin E. Nuccio, Nhu H. Nguyen, Ulisses Nunes da Rocha, Xavier Mayali, Jeremy Bougoure, Peter Weber, Eoin Brodie, Mary Firestone, Jennifer Pett-Ridge
bioRxiv 2021.01.12.426429; doi: https://doi.org/10.1101/2021.01.12.426429

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