Title: Successional trajectories of rhizosphere bacterial communities over consecutive seasons

Abstract

ABSTRACT It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grassAvena fatuaover two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative to background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance ofAlphaproteobacteria,Betaproteobacteria, andBacteroidetesbut reduced the abundance ofAcidobacteria,Actinobacteria, andFirmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. IMPORTANCEWe document the successional patterns ofmore » rhizosphere bacterial communities associated with a “wild” annual grass,Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address “domesticated” plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal succession that was consistent and repeatable over two growing seasons. There are few studies assessing the reproducibility over multiple seasons. Through the growing season, the rhizosphere community became progressively less diverse, likely reflecting root homogenization of soil microniches. Phylogenetic clustering of the rhizosphere dynamic taxa suggests evolutionary adaptation toAvenaroots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence.« less

Authors:

Shi, Shengjing ^[1]; Nuccio, Erin ^[2]; Herman, Donald J. ^[3]; Rijkers, Ruud ^[4]; Estera, Katerina ^[4]; Li, Jiabao ^[5]; da Rocha, Ulisses Nunes ^[6]; He, Zhili ^[5]; Pett-Ridge, Jennifer ^[7]; Brodie, Eoin L. ^[3]; Zhou, Jizhong ^[8]; Firestone, Mary ^[3]

---

+ Show Author Affiliations

1. Univ. of California, Berkeley, CA (United States); Univ. of Oklahoma, Norman, OK (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); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
4. Univ. of California, Berkeley, CA (United States)
5. Univ. of Oklahoma, Norman, OK (United States)
6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
7. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
8. Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Tsinghua Univ., Beijing (China)

Publication Date:

Tue Aug 04 00:00:00 EDT 2015

Research Org.:

Lawrence Berkeley National Laboratory (LBNL), 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)

OSTI Identifier:

1215423

Alternate Identifier(s):

OSTI ID: 1324516; OSTI ID: 1512225

Report Number(s):

LLNL-JRNL-671995
Journal ID: ISSN 2150-7511

Grant/Contract Number:  

AC02-05CH11231; SA-DOE-29318; SC0004730; SC0010570; AC52-07NA27344

Resource Type:

Accepted Manuscript

Journal Name:

mBio (Online)

Additional Journal Information:

Journal Name: mBio (Online); Journal Volume: 6; Journal Issue: 4; Journal ID: ISSN 2150-7511

Publisher:

American Society for Microbiology

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; 54 ENVIRONMENTAL SCIENCES; 58 GEOSCIENCES