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

Starr, Evan P.; Shi, Shengjing; Blazewicz, Steven J.; Koch, Benjamin J.; Probst, Alexander J.; Hungate, Bruce A.; Pett-Ridge, Jennifer; Firestone, Mary K.; Banfield, Jillian F.; Young, ed., Vincent B.

doi:10.1128/mSphere.00085-21

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

Journal Article · Wed Oct 27 00:00:00 EDT 2021 · mSphere

DOI:https://doi.org/10.1128/mSphere.00085-21· OSTI ID:1818172

Starr, Evan P. ^[1]; Shi, Shengjing ^[2]; Blazewicz, Steven J. ^[3]; Koch, Benjamin J. ^[4]; Probst, Alexander J. ^[5]; ^[4]; ^[3]; ^[6]; ^[7]; Young, ed., Vincent B.

Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
Lincoln Science Centre, AgResearch Ltd., Christchurch, New Zealand
Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA, Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
Biofilm Center, University of Duisburg—Essen, Essen, Germany
Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA, Department of Earth and Planetary Science, University of California, Berkeley, California, USA, Innovative Genomics Institute, Berkeley, California, USA, Chan Zuckerberg Biohub, San Francisco, California, USA

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: German Science Foundation; National Science Foundation (NSF); USDOE; USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC52-07NA27344; SC0010566; SC0010570; SC0016247; SC0020172

OSTI ID:: 1818172

Alternate ID(s):: OSTI ID: 1855191
OSTI ID: 1867551

Report Number(s):: LLNL-JRNL-814137; e00085-21

Journal Information:: mSphere, Journal Name: mSphere Journal Issue: 5 Vol. 6; ISSN 2379-5042

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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The Ecological Role of Type Three Secretion Systems in the Interaction of Bacteria with Fungi in Soil and Related Habitats Is Diverse and Context-Dependent Nazir, Rashid; Mazurier, Sylvie; Yang, Pu Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00038	journal	January 2017
Microbial Phosphorus Solubilization and Its Potential for Use in Sustainable Agriculture Alori, Elizabeth T.; Glick, Bernard R.; Babalola, Olubukola O. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00971	journal	June 2017
New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes Kroeger, Marie E.; Delmont, Tom O.; Eren, A. M. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01635	journal	July 2018
Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development Raveh-Sadka, Tali; Thomas, Brian C.; Singh, Andrea eLife, Vol. 4 https://doi.org/10.7554/eLife.05477	journal	March 2015
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities Kang, Dongwan D.; Froula, Jeff; Egan, Rob PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1165	journal	January 2015
Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone Butterfield, Cristina N.; Li, Zhou; Andeer, Peter F. PeerJ, Vol. 4 https://doi.org/10.7717/peerj.2687	journal	January 2016
VirSorter: mining viral signal from microbial genomic data Roux, Simon; Enault, Francois; Hurwitz, Bonnie L. PeerJ, Vol. 3 https://doi.org/10.7717/peerj.985	journal	January 2015

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
54 ENVIRONMENTAL SCIENCES
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59 BASIC BIOLOGICAL SCIENCES
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Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil

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