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Title: Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass

Journal Article · · Ecology
DOI:https://doi.org/10.1890/15-0882.1· OSTI ID:1581117
 [1];  [2];  [3];  [4];  [3];  [5];  [5]
  1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Physical and Life Sciences Directorate; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
  2. Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
  3. Univ. of California, Berkeley, CA (United States). Dept. of Environmental Science, Policy and Management
  4. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Physical and Life Sciences Directorate
  5. Univ. of California, Berkeley, CA (United States). Dept. of Environmental Science, Policy and Management; Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Earth and Environmental Sciences
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The interface between roots and soil, known as the rhizosphere, is a dynamic habitat in the soil ecosystem. Unraveling the factors that control rhizosphere community assembly is a key starting point for understanding the diversity of plant-microbial interactions that occur in soil. The goals of this study were to determine how environmental factors shape rhizosphere microbial communities, such as local soil characteristics and the regional climate, and to determine the relative influence of the rhizosphere on microbial community assembly compared to the pressures imposed by the local and regional environment. We identified the bacteria present in the soil immediately adjacent to the roots of wild oat (Avena spp.) in three California grasslands using deep Illumina 16S sequencing. Rhizosphere communities were more similar to each other than to the surrounding soil communities from which they were derived, despite the fact that the grasslands studied were separated by hundreds of kilometers. The rhizosphere was the dominant factor structuring bacterial community composition (38% variance explained), and was comparable in magnitude to the combined local and regional effects (22% and 21%, respectively). Rhizosphere communities were most influenced by factors related to the regional climate (soil moisture and temperature), while background soil communities were more influenced by soil characteristics (pH, CEC, exchangeable cations, clay content). The Avena core microbiome was strongly phylogenetically clustered according to the metrics NRI and NTI, which indicates that selective processes likely shaped these communities. Furthermore, 17% of these taxa were not detectable in the background soil, even with a robust sequencing depth of approximately 70,000 sequences per sample. These results support the hypothesis that roots select less abundant or possibly rare populations in the soil microbial community, which appear to be lineages of bacteria that have made a physiological tradeoff for rhizosphere competence at the expense of their competitiveness in non-rhizosphere soil.

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)
Grant/Contract Number:
AC02-05CH11231; AC52-07NA27344; SC0004730; SC0010570; SCW1421
OSTI ID:
1581117
Alternate ID(s):
OSTI ID: 1325886; OSTI ID: 1400974; OSTI ID: 1440928
Report Number(s):
LLNL-JRNL-670998; ark:/13030/qt4rp9k2qg
Journal Information:
Ecology, Vol. 97, Issue 5; ISSN 0012-9658
Publisher:
Ecological Society of America (ESA)Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 85 works
Citation information provided by
Web of Science

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Cited By (25)

Plants exhibit significant effects on the rhizospheric microbiome across contrasting soils in tropical and subtropical China journal July 2019
Where less may be more: how the rare biosphere pulls ecosystems strings text January 2017
Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome journal August 2019
Plant selection initiates alternative successional trajectories in the soil microbial community after disturbance journal March 2019
A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization journal May 2017
Where less may be more: how the rare biosphere pulls ecosystems strings journal January 2017
Niche differentiation is spatially and temporally regulated in the rhizosphere journal January 2020
Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands journal October 2019
Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat (Triticum aestivum) Cultivars journal February 2017
The Fate of Chemical Pollutants with Soil Properties and Processes in the Climate Change Paradigm—A Review journal September 2018
Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities journal July 2017
Leaf endophytic fungus interacts with precipitation to alter belowground microbial communities in primary successional dunes journal March 2017
Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality journal January 2018
Vegetation-Dependent Response to Drought in Salt Marsh Ammonia-Oxidizer Communities journal December 2019
Drought Stress and Root-Associated Bacterial Communities journal January 2018
Microbiome Dynamics Associated With the Atacama Flowering Desert journal January 2020
Eighty years of maize breeding alters plant nitrogen acquisition but not rhizosphere bacterial community composition journal July 2018
Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly journal March 2018
Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils journal January 2019
Highly reproducible 16S sequencing facilitates measurement of host genetic influences on the stickleback gut microbiome posted_content December 2018
The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages journal June 2016
Insights Into Culturomics of the Rumen Microbiome journal August 2018
Microbial communities associated with distance- and density-dependent seedling mortality in a tropical rainforest journal November 2019
Transmission of Bacterial Endophytes journal November 2017
Belowground microbial communities respond to water deficit and are shaped by decades of maize hybrid breeding journal June 2019

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Related Subjects

54 ENVIRONMENTAL SCIENCES
59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
rhizosphere
microbiome
plant-microbial interactions
community assembly
soil
climate
Avena