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Title: Microbial community assembly differs across minerals in a rhizosphere microcosm

Abstract

Mineral–associated microbes drive many critical soil processes, including mineral weathering, soil aggregation and cycling of mineral–sorbed organic matter. To investigate the interactions between soil minerals and microbes in the rhizosphere, we incubated three types of minerals (ferrihydrite, kaolinite and quartz) and a native soil mineral fraction near roots of a common Californian annual grass, Avena barbata, growing in its resident soil. We followed microbial colonization of these minerals for up to 2.5 months – the plant's lifespan. Bacteria and fungi that colonized mineral surfaces during this experiment differed across mineral types and differed from those in the background soil, implying that microbial colonization was the result of processes in addition to passive movement with water to mineral surfaces. Null model analysis revealed that dispersal limitation was a dominant factor structuring mineral–associated microbial communities for all mineral types. Once bacteria arrived at a mineral surface, capacity for rapid growth appeared important, as ribosomal copy number was significantly correlated with relative enrichment on minerals. Glomeromycota (a phylum associated with arbuscular mycorrhizal fungi) appeared to preferentially associate with ferrihydrite surfaces. In conclusion, the mechanisms enabling the colonization of soil minerals may be foundational in shaping the overall soil microbiome composition and development ofmore » persistent organic matter in soils.« less

Authors:
ORCiD logo [1];  [2];  [3];  [3];  [4];  [5];  [6];  [7];  [8]
  1. Univ. of California, Berkeley, CA (United States); Univ. of Wisconsin, Madison, WI (United States)
  2. Univ. of California, Berkeley, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  3. Univ. of California, Berkeley, CA (United States)
  4. Univ. of Oklahoma, Norman, OK (United States)
  5. Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Tsinghua Univ., Beijing (China)
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  7. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  8. Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1479071
Alternate Identifier(s):
OSTI ID: 1469402; OSTI ID: 1563985
Report Number(s):
LLNL-JRNL-729889
Journal ID: ISSN 1462-2912; 880806
Grant/Contract Number:  
AC52-07NA27344; SC0010570; AC52‐07NA27344; AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Volume: 20; Journal Issue: 12; Journal ID: ISSN 1462-2912
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Whitman, Thea, Neurath, Rachel, Perera, Adele, Chu-Jacoby, Ilexis, Ning, Daliang, Zhou, Jizhong, Nico, Peter, Pett-Ridge, Jennifer, and Firestone, Mary. Microbial community assembly differs across minerals in a rhizosphere microcosm. United States: N. p., 2018. Web. doi:10.1111/1462-2920.14366.
Whitman, Thea, Neurath, Rachel, Perera, Adele, Chu-Jacoby, Ilexis, Ning, Daliang, Zhou, Jizhong, Nico, Peter, Pett-Ridge, Jennifer, & Firestone, Mary. Microbial community assembly differs across minerals in a rhizosphere microcosm. United States. doi:10.1111/1462-2920.14366.
Whitman, Thea, Neurath, Rachel, Perera, Adele, Chu-Jacoby, Ilexis, Ning, Daliang, Zhou, Jizhong, Nico, Peter, Pett-Ridge, Jennifer, and Firestone, Mary. Wed . "Microbial community assembly differs across minerals in a rhizosphere microcosm". United States. doi:10.1111/1462-2920.14366. https://www.osti.gov/servlets/purl/1479071.
@article{osti_1479071,
title = {Microbial community assembly differs across minerals in a rhizosphere microcosm},
author = {Whitman, Thea and Neurath, Rachel and Perera, Adele and Chu-Jacoby, Ilexis and Ning, Daliang and Zhou, Jizhong and Nico, Peter and Pett-Ridge, Jennifer and Firestone, Mary},
abstractNote = {Mineral–associated microbes drive many critical soil processes, including mineral weathering, soil aggregation and cycling of mineral–sorbed organic matter. To investigate the interactions between soil minerals and microbes in the rhizosphere, we incubated three types of minerals (ferrihydrite, kaolinite and quartz) and a native soil mineral fraction near roots of a common Californian annual grass, Avena barbata, growing in its resident soil. We followed microbial colonization of these minerals for up to 2.5 months – the plant's lifespan. Bacteria and fungi that colonized mineral surfaces during this experiment differed across mineral types and differed from those in the background soil, implying that microbial colonization was the result of processes in addition to passive movement with water to mineral surfaces. Null model analysis revealed that dispersal limitation was a dominant factor structuring mineral–associated microbial communities for all mineral types. Once bacteria arrived at a mineral surface, capacity for rapid growth appeared important, as ribosomal copy number was significantly correlated with relative enrichment on minerals. Glomeromycota (a phylum associated with arbuscular mycorrhizal fungi) appeared to preferentially associate with ferrihydrite surfaces. In conclusion, the mechanisms enabling the colonization of soil minerals may be foundational in shaping the overall soil microbiome composition and development of persistent organic matter in soils.},
doi = {10.1111/1462-2920.14366},
journal = {Environmental Microbiology},
issn = {1462-2912},
number = 12,
volume = 20,
place = {United States},
year = {2018},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 11 works
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Figures / Tables:

Figure 6 Figure 6: Relative influence of different bacterial / archaeal community assembly processes on spatial turnover among soil communities and between soil communities and those on different mineral surfaces. The governing processes were determined using RCBray and βNTI (Stegen et al., 2013). Different colors represent different the fraction of community turnoversmore » governed by each process.« less

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