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]; Hungate, Bruce A.  ^[4]; Pett-Ridge, Jennifer  ^[3]; Firestone, Mary K.  ^[6]; Banfield, Jillian F.  ^[7]; Young, ed., Vincent B.

---

1. Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
2. Lincoln Science Centre, AgResearch Ltd., Christchurch, New Zealand
3. Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
4. Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA, Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
5. Biofilm Center, University of Duisburg—Essen, Essen, Germany
6. Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
7. 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

The functioning, health, and productivity of soil are intimately tied to a complex network of interactions, particularly in plant root-associated rhizosphere soil. We conducted a stable-isotope-informed, genome-resolved metagenomic study to trace carbon from Avena fatua grown in a ¹³CO₂ atmosphere into soil. We collected paired rhizosphere and nonrhizosphere soil at 6 and 9 weeks of plant growth and extracted DNA that was then separated by density using ultracentrifugation. Thirty-two fractions from each of five samples were grouped by density, sequenced, assembled, and binned to generate 55 unique bacterial genomes that were ≥70% complete. We also identified complete 18S rRNA sequences of several ¹³C-enriched microeukaryotic bacterivores and fungi. We generated 10 circularized bacteriophage (phage) genomes, some of which were the most labeled entities in the rhizosphere, suggesting that phage may be important agents of turnover of plant-derived C in soil. CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen. Another highly labeled phage is predicted to replicate in a Catenulispora sp., a possible plant growth-promoting bacterium. We searched the genome bins for traits known to be used in interactions involving bacteria, microeukaryotes, and plant roots and found DNA from heavily ¹³C-labeled bacterial genes thought to be involved in modulating plant signaling hormones, plant pathogenicity, and defense against microeukaryote grazing. Stable-isotope-informed, genome-resolved metagenomics indicated that phage can be important agents of turnover of plant-derived carbon in soil. 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. Our work is significant because we identified the organisms that took up plant-derived organic C in rhizosphere soil and determined that many of the active bacteria are plant pathogens or can impact plant growth via hormone modulation. Further, by showing that bacteriophage accumulate CO₂-derived carbon, we demonstrated their vital roles in redistribution of plant-derived C into the soil environment through bacterial cell lysis. The use of stable-isotope probing (SIP) to identify consumption (or lack thereof) of root-derived C by key microbial community members within highly complex microbial communities opens the way for assessing manipulations of bacteria and phage with potentially beneficial and detrimental traits, ultimately providing a path to improved plant health and soil carbon storage.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER); German Science Foundation; National Science Foundation (NSF); USDOE National Nuclear Security Administration (NNSA)
• Grant/Contract Number: SC0010570; SC0016247; SC10010566; SC0020172; SCW1589; SCW1632; AC02-05CH11231; DFG1603-1/1; AC52-07NA27344; CZO EAR-1331940; SC0010566; EAR-1331940
• 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 Vol. 6 Journal Issue: 5; ISSN 2379-5042
• Publisher: American Society for Microbiology
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
plant growth
labeling
density separation
sequencing
enrichment
growth
58 GEOSCIENCES
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
54 ENVIRONMENTAL SCIENCES