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      Soil-Borne Bacterial Structure and Diversity Does Not Reflect Community Activity in Pampa Biome

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          Abstract

          The Pampa biome is considered one of the main hotspots of the world’s biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated.

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          The diversity and biogeography of soil bacterial communities.

          For centuries, biologists have studied patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible for microorganisms, arguably the most diverse and abundant group of organisms on Earth. Here, we present a continental-scale description of soil bacterial communities and the environmental factors influencing their biodiversity. We collected 98 soil samples from across North and South America and used a ribosomal DNA-fingerprinting method to compare bacterial community composition and diversity quantitatively across sites. Bacterial diversity was unrelated to site temperature, latitude, and other variables that typically predict plant and animal diversity, and community composition was largely independent of geographic distance. The diversity and richness of soil bacterial communities differed by ecosystem type, and these differences could largely be explained by soil pH (r(2) = 0.70 and r(2) = 0.58, respectively; P < 0.0001 in both cases). Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in our study. Our results suggest that microbial biogeography is controlled primarily by edaphic variables and differs fundamentally from the biogeography of "macro" organisms.
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            Beyond the Venn diagram: the hunt for a core microbiome.

            Discovering a core microbiome is important for understanding the stable, consistent components across complex microbial assemblages. A core is typically defined as the suite of members shared among microbial consortia from similar habitats, and is represented by the overlapping areas of circles in Venn diagrams, in which each circle contains the membership of the sample or habitats being compared. Ecological insight into core microbiomes can be enriched by 'omics approaches that assess gene expression, thereby extending the concept of the core beyond taxonomically defined membership to community function and behaviour. Parameters defined by traditional ecology theory, such as composition, phylogeny, persistence and connectivity, will also create a more complex portrait of the core microbiome and advance understanding of the role of key microorganisms and functions within and across ecosystems. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.
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              Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.

              We constructed error-correcting DNA barcodes that allow one run of a massively parallel pyrosequencer to process up to 1,544 samples simultaneously. Using these barcodes we processed bacterial 16S rRNA gene sequences representing microbial communities in 286 environmental samples, corrected 92% of sample assignment errors, and thus characterized nearly as many 16S rRNA genes as have been sequenced to date by Sanger sequencing.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2013
                16 October 2013
                : 8
                : 10
                : e76465
                Affiliations
                [1 ]Departamento de Solos, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
                [2 ]Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO/KANW), Wageningen, The Netherlands
                [3 ]Departamento de Solos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
                [4 ]Universidade Federal do PAMPA, Campus São Gabriel, São Gabriel, Rio Grande do Sul, Brazil
                Dowling College, United States of America
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: ML RJSJ ZIA FAOC LFWR. Performed the experiments: ML AKAS. Analyzed the data: ML AKAS EEK LFWR. Contributed reagents/materials/analysis tools: RJSJ ZIA FAOC LFWR. Wrote the paper: ML EEK LFWR.

                Article
                PONE-D-13-25427
                10.1371/journal.pone.0076465
                3797755
                24146873
                d1f475f8-e1be-4496-9ed0-8fbcaa483a7e
                Copyright @ 2013

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 18 June 2013
                : 23 August 2013
                Page count
                Pages: 9
                Funding
                This work was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq – grant numbers 479133/2012-3 and 476121/2010-8). RJS Jacques, ZI Antoniolli, FAO Camargo and LFW Roesch receive research fellowships from the CNPq. M Lupatini and AKA Suleiman receive research fellowships from the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES - Brazil). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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