Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches
Abstract
Soil bacteria and fungi are known to form niche-specific communities that differ between actively growing and decaying roots. Yet almost nothing is known about the cross-kingdom interactions that frame these communities and the environmental filtering that defines these potentially friendly or competing neighbors. We explored the temporal and spatial patterns of soil fungal (mycorrhizal and nonmycorrhizal) and bacterial cooccurrence near roots of wild oat grass, Avena fatua, growing in its naturalized soil in a greenhouse experiment. Amplicon sequences of the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA genes from rhizosphere and bulk soils collected at multiple plant growth stages were used to construct covariation-based networks as a step toward identifying fungal-bacterial associations. Corresponding stable-isotope-enabled metagenome-assembled genomes (MAGs) of bacteria identified in cooccurrence networks were used to inform potential mechanisms underlying the observed links. Bacterial-fungal networks were significantly different in rhizosphere versus bulk soils and between arbuscular mycorrhizal fungi (AMF) and nonmycorrhizal fungi. Over 12 weeks of plant growth, nonmycorrhizal fungi formed increasingly complex networks with bacteria in rhizosphere soils, while AMF more frequently formed networks with bacteria in bulk soils. Analysis of network-associated bacterial MAGs suggests that some of the fungal-bacterial links that we identified are potential indicatorsmore »
- Authors:
-
[4];
[6]
- Univ. of California, Berkeley, CA (United States)
- Univ. of Hawaii at Manoa, Honolulu, HI (United States)
- AgResearch Ltd., Lincoln Science Centre, Christchurch (New Zealand)
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- University of California, Berkeley, CA (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE National Nuclear Security Administration (NNSA)
- OSTI Identifier:
- 1780928
- Alternate Identifier(s):
- OSTI ID: 1902596
- Report Number(s):
- LLNL-JRNL-826080
Journal ID: ISSN 2150-7511
- Grant/Contract Number:
- SC0020163; SC0010570; AC52-07NA27344
- Resource Type:
- Accepted Manuscript
- Journal Name:
- mBio (Online)
- Additional Journal Information:
- Journal Name: mBio (Online); Journal Volume: 12; Journal Issue: 2; Journal ID: ISSN 2150-7511
- Publisher:
- American Society for Microbiology (ASM)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES; Arbuscular Mycorrhizal Fungi (AMF); metagenome-assembled genome (MAG); cooccurrance network; rhizosphere; detritusphere; hyphosphere; stable-isotope probing (SIP); spatial heterogeneity
Citation Formats
Yuan, Mengting Maggie, Kakouridis, Anne, Starr, Evan, Nguyen, Nhu, Shi, Shengjing, Pett-Ridge, Jennifer, Nuccio, Erin, Zhou, Jizhong, and Firestone, Mary. Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches. United States: N. p., 2021.
Web. doi:10.1128/mbio.03509-20.
Yuan, Mengting Maggie, Kakouridis, Anne, Starr, Evan, Nguyen, Nhu, Shi, Shengjing, Pett-Ridge, Jennifer, Nuccio, Erin, Zhou, Jizhong, & Firestone, Mary. Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches. United States. https://doi.org/10.1128/mbio.03509-20
Yuan, Mengting Maggie, Kakouridis, Anne, Starr, Evan, Nguyen, Nhu, Shi, Shengjing, Pett-Ridge, Jennifer, Nuccio, Erin, Zhou, Jizhong, and Firestone, Mary. Tue .
"Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches". United States. https://doi.org/10.1128/mbio.03509-20. https://www.osti.gov/servlets/purl/1780928.
@article{osti_1780928,
title = {Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches},
author = {Yuan, Mengting Maggie and Kakouridis, Anne and Starr, Evan and Nguyen, Nhu and Shi, Shengjing and Pett-Ridge, Jennifer and Nuccio, Erin and Zhou, Jizhong and Firestone, Mary},
abstractNote = {Soil bacteria and fungi are known to form niche-specific communities that differ between actively growing and decaying roots. Yet almost nothing is known about the cross-kingdom interactions that frame these communities and the environmental filtering that defines these potentially friendly or competing neighbors. We explored the temporal and spatial patterns of soil fungal (mycorrhizal and nonmycorrhizal) and bacterial cooccurrence near roots of wild oat grass, Avena fatua, growing in its naturalized soil in a greenhouse experiment. Amplicon sequences of the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA genes from rhizosphere and bulk soils collected at multiple plant growth stages were used to construct covariation-based networks as a step toward identifying fungal-bacterial associations. Corresponding stable-isotope-enabled metagenome-assembled genomes (MAGs) of bacteria identified in cooccurrence networks were used to inform potential mechanisms underlying the observed links. Bacterial-fungal networks were significantly different in rhizosphere versus bulk soils and between arbuscular mycorrhizal fungi (AMF) and nonmycorrhizal fungi. Over 12 weeks of plant growth, nonmycorrhizal fungi formed increasingly complex networks with bacteria in rhizosphere soils, while AMF more frequently formed networks with bacteria in bulk soils. Analysis of network-associated bacterial MAGs suggests that some of the fungal-bacterial links that we identified are potential indicators of bacterial breakdown and consumption of fungal biomass, while others intimate shared ecological niches.},
doi = {10.1128/mbio.03509-20},
journal = {mBio (Online)},
number = 2,
volume = 12,
place = {United States},
year = {Tue Apr 20 00:00:00 EDT 2021},
month = {Tue Apr 20 00:00:00 EDT 2021}
}
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