title: Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons.
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 grass Avena fatua over 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 of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. 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.
  
  
  OBJECTIVE
  We document the successional patterns of 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 to Avena 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.
authors.affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
authors.forename: Shengjing
authors.initials: S
authors.lastname: Shi
authors.affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA.
authors.forename: Erin
authors.initials: E
authors.lastname: Nuccio
authors.affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Donald J
authors.initials: DJ
authors.lastname: Herman
authors.affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA.
authors.forename: Ruud
authors.initials: R
authors.lastname: Rijkers
authors.affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA.
authors.forename: Katerina
authors.initials: K
authors.lastname: Estera
authors.affiliation: Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
authors.forename: Jiabao
authors.initials: J
authors.lastname: Li
authors.affiliation: Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Ulisses Nunes
authors.initials: UN
authors.lastname: da Rocha
authors.affiliation: Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.affiliation: Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Pett-Ridge
authors.affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Eoin L
authors.initials: EL
authors.lastname: Brodie
authors.affiliation: Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA mkfstone@berkeley.edu.
authors.forename: Mary
authors.initials: M
authors.lastname: Firestone
mesh_terms: D018554:Avena / Q000382:microbiology*; D058448:Biota; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D058441:Rhizosphere; D012621:Seasons; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S