Bacterial community structures in rhizosphere microsites of ryegrass (Lolium perenne var. Nui) as revealed by pyrosequencing

Management of soils to facilitate plant beneficial microbial interactions requires basic knowledge of the species composition and microbial community structures in the plant rhizosphere. Here, we examined composition of bacterial communities associated with rhizosphere microsites located at the root tips and mature root zones of Lolium perenne when grown in Chilean ash-derived volcanic soils (Andisols: Freire and Piedras Negras soil series). Community structures were analyzed by pyrosequencing of 16S ribosomal RNA (rRNA) genes followed by in silico analysis for phylogenetic assignments (MOTHUR and Visualization tool for Taxonomic Compositions of Microbial Community (VITCOMIC)). Analysis of the community structure revealed significant differences in community structures in relation to the soil series, which differed particularly in the relative abundance of Cyanobacteria and Firmicutes. However, no significant differences were observed with respect to root microsite location in the same Andisol series. Predominant taxa included members of the Proteobacteria, Actinobacteria, and Acidobacteria. Analysis by VITCOMIC showed that dominant bacterial groups comprised only 5 to 10 % of the total bacterial community and the remaining majority of bacteria included low-abundant taxa (Fusobacteria, Thermotogae, Lentisphaerae, Tenericutes, Deferribacteres Spirochaetes, Planctomycetes, Thermotogae, and Deinococcus-Thermus), most of which have not been previously reported or associated with the plant rhizosphere according to GenBank database. The results indicate that most of bacteria in the Chilean Andisols have not been described to the rhizosphere plants and their functional traits are still largely unknown.

[1]  I. Good THE POPULATION FREQUENCIES OF SPECIES AND THE ESTIMATION OF POPULATION PARAMETERS , 1953 .

[2]  J. P. Riley,et al.  A modified single solution method for the determination of phosphate in natural waters , 1962 .

[3]  D. Sparks,et al.  Methods of soil analysis. Part 3 - chemical methods. , 1996 .

[4]  S. Dakota Recommended Chemical Soil Test Procedures for the North Central Region , 1998 .

[5]  M. L. Mora,et al.  Effect of calcitic and dolomitic lime on physicochemical properties of a Chilean Andisol , 1999 .

[6]  M. Firestone,et al.  Mapping of Sugar and Amino Acid Availability in Soil around Roots with Bacterial Sensors of Sucrose and Tryptophan , 1999, Applied and Environmental Microbiology.

[7]  D. Crowley,et al.  Rhizosphere Microbial Community Structure in Relation to Root Location and Plant Iron Nutritional Status , 2000, Applied and Environmental Microbiology.

[8]  D. Crowley,et al.  Arbuscular mycorrhizal infection changes the bacterial 16 S rDNA community composition in the rhizosphere of maize , 2001, Mycorrhiza.

[9]  D. Crowley,et al.  Soil and plant specific effects on bacterial community composition in the rhizosphere , 2001 .

[10]  J. Kelly,et al.  In situ dynamics of phosphorus in the rhizosphere solution of five species. , 2004, Journal of environmental quality.

[11]  D. Crowley,et al.  Development of specific rhizosphere bacterial communities in relation to plant species, nutrition and soil type , 2004, Plant and Soil.

[12]  P. Garbeva,et al.  Microbial diversity in soil: selection microbial populations by plant and soil type and implications for disease suppressiveness. , 2004, Annual review of phytopathology.

[13]  Xiaohan Yang,et al.  The role of root exudates and allelochemicals in the rhizosphere , 2003, Plant and Soil.

[14]  Ji‐Zheng He,et al.  Pre-lysis washing improves DNA extraction from a forest soil , 2005 .

[15]  Peter J. Gregory,et al.  Rhizosphere geometry and heterogeneity arising from root-mediated physical and chemical processes. , 2005, The New phytologist.

[16]  P. Janssen Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes , 2006, Applied and Environmental Microbiology.

[17]  J. Passioura,et al.  Rates of root and organism growth, soil conditions, and temporal and spatial development of the rhizosphere. , 2006, Annals of botany.

[18]  Z. Rengel,et al.  Isolation of culturable phosphobacteria with both phytate-mineralization and phosphate-solubilization activity from the rhizosphere of plants grown in a volcanic soil , 2008, Biology and Fertility of Soils.

[19]  C. Nautiyal,et al.  Molecular mechanisms of plant and microbe coexistence , 2008 .

[20]  J. Ascher,et al.  Effects of Root Exudates in Microbial Diversity and Activity in Rhizosphere Soils , 2008 .

[21]  J. Ascher,et al.  Recent Advances in Functional Genomics and Proteomics of Plant Associated Microbes , 2008 .

[22]  F. Bastida,et al.  Soil metaproteomics: a review of an emerging environmental science. Significance, methodology and perspectives , 2009 .

[23]  Chika Suzuki,et al.  Bacterial communities are more dependent on soil type than fertilizer type, but the reverse is true for fungal communities , 2009 .

[24]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[25]  Eoin L. Brodie,et al.  Selective progressive response of soil microbial community to wild oat roots , 2009, The ISME Journal.

[26]  G. Chaer,et al.  Comparative Resistance and Resilience of Soil Microbial Communities and Enzyme Activities in Adjacent Native Forest and Agricultural Soils , 2009, Microbial Ecology.

[27]  M. L. Mora,et al.  Detection of aluminium tolerance plasmids and microbial diversity in the rhizosphere of plants grown in acidic volcanic soil , 2010 .

[28]  Hiroshi Mori,et al.  VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences , 2010, BMC Bioinformatics.

[29]  Safdar Ali,et al.  Soil beneficial bacteria and their role in plant growth promotion: a review , 2010, Annals of Microbiology.

[30]  W. Whitman,et al.  Change in Bacterial Community Structure in Response to Disturbance of Natural Hardwood and Secondary Coniferous Forest Soils in Central Taiwan , 2011, Microbial Ecology.

[31]  D. Crowley,et al.  Influence of nitrogen fertilisation on pasture culturable rhizobacteria occurrence and the role of environmental factors on their potential PGPR activities , 2011, Biology and Fertility of Soils.

[32]  Rob Knight,et al.  UCHIME improves sensitivity and speed of chimera detection , 2011, Bioinform..

[33]  D. Crowley,et al.  Rhizosphere interactions between microorganisms and plants govern iron and phosphorus acquisition along the root axis – model and research methods , 2011 .

[34]  J. Arjun,et al.  Metagenomic analysis of bacterial diversity in the rice rhizosphere soil microbiome , 2011 .

[35]  J. V. van Elsas,et al.  Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. , 2011, FEMS microbiology ecology.

[36]  D. Crowley,et al.  Identification of β-propeller phytase-encoding genes in culturable Paenibacillus and Bacillus spp. from the rhizosphere of pasture plants on volcanic soils. , 2011, FEMS microbiology ecology.

[37]  F. O'Gara,et al.  Functional genomics analysis of plant growth-promoting rhizobacterial traits involved in rhizosphere competence , 2011, Biology and Fertility of Soils.

[38]  Amy M. Sheflin,et al.  Manipulating the soil microbiome to increase soil health and plant fertility , 2012, Biology and Fertility of Soils.

[39]  Chaofei Yang,et al.  Pyrosequencing reveals how pulses influence rhizobacterial communities with feedback on wheat growth in the semiarid Prairie , 2012, Plant and Soil.

[40]  Elmar Pruesse,et al.  SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes , 2012, Bioinform..

[41]  A. Goesmann,et al.  Changes in Root Bacterial Communities Associated to Two Different Development Stages of Canola (Brassica napus L. var oleifera) Evaluated through Next-Generation Sequencing Technology , 2012, Microbial Ecology.

[42]  J. Setubal,et al.  Metagenomic Analysis of a Tropical Composting Operation at the São Paulo Zoo Park Reveals Diversity of Biomass Degradation Functions and Organisms , 2013, PloS one.

[43]  J. D. Elsas,et al.  Back to the basics: The need for ecophysiological insights to enhance our understanding of microbial behaviour in the rhizosphere , 2013, Plant and Soil.

[44]  P. Baldrian,et al.  The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses , 2013, PloS one.

[45]  W. Boer,et al.  Do genetic modifications in crops affect soil fungi? a review , 2014, Biology and Fertility of Soils.