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Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture

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      Abstract

      Tropical smallholder agriculture is undergoing rapid transformation in nutrient cycling pathways as international development efforts strongly promote greater use of mineral fertilizers to increase crop yields. These changes in nutrient availability may alter the composition of microbial communities with consequences for rates of biogeochemical processes that control nutrient losses to the environment. Ecological theory suggests that altered microbial diversity will strongly influence processes performed by relatively few microbial taxa, such as denitrification and hence nitrogen losses as nitrous oxide, a powerful greenhouse gas. Whether this theory helps predict nutrient losses from agriculture depends on the relative effects of microbial community change and increased nutrient availability on ecosystem processes. We find that mineral and organic nutrient addition to smallholder farms in Kenya alters the taxonomic and functional diversity of soil microbes. However, we find that the direct effects of farm management on both denitrification and carbon mineralization are greater than indirect effects through changes in the taxonomic and functional diversity of microbial communities. Changes in functional diversity are strongly coupled to changes in specific functional genes involved in denitrification, suggesting that it is the expression, rather than abundance, of key functional genes that can serve as an indicator of ecosystem process rates. Our results thus suggest that widely used broad summary statistics of microbial diversity based on DNA may be inappropriate for linking microbial communities to ecosystem processes in certain applied settings. Our results also raise doubts about the relative control of microbial composition compared to direct effects of management on nutrient losses in applied settings such as tropical agriculture.

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      QIIME allows analysis of high-throughput community sequencing data.

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        Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

        DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.
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          Solutions for a cultivated planet.

          Increasing population and consumption are placing unprecedented demands on agriculture and natural resources. Today, approximately a billion people are chronically malnourished while our agricultural systems are concurrently degrading land, water, biodiversity and climate on a global scale. To meet the world's future food security and sustainability needs, food production must grow substantially while, at the same time, agriculture's environmental footprint must shrink dramatically. Here we analyse solutions to this dilemma, showing that tremendous progress could be made by halting agricultural expansion, closing 'yield gaps' on underperforming lands, increasing cropping efficiency, shifting diets and reducing waste. Together, these strategies could double food production while greatly reducing the environmental impacts of agriculture.
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            Author and article information

            Affiliations
            1Department of Ecology, Evolution and Environmental Biology, Columbia University New York, NY, USA
            2Agriculture and Food Security Center, The Earth Institute, Columbia University New York, NY, USA
            3Department of Ecology and Evolutionary Biology, Brown University Providence, RI, USA
            4School of Forestry and Environmental Studies, Yale University New Haven, CT, USA
            5Department of Biology, Barnard College of Columbia University New York, NY, USA
            6The Ecosystems Center, Marine Biological Laboratory Woods Hole, MA, USA
            7Department of Plant Science and Landscape Architecture, University of Maryland College Park, MD, USA
            8Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
            9Earth Science Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
            10State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University Beijing, China
            Author notes

            Edited by: Silvia Pajares Moreno, University of Oregon, USA

            Reviewed by: Trevor Carlos Charles, University of Waterloo, Canada; Ming Nie, University of Aberdeen, UK

            *Correspondence: Stephen A. Wood, Department of Ecology, Evolution and Environmental Biology, Columbia University, Schermerhorn Extension, 10th Floor, 1200 Amsterdam Avenue, New York, NY 10027, USA e-mail: saw2177@ 123456columbia.edu

            This article was submitted to Terrestrial Microbiology, a section of the journal Frontiers in Microbiology.

            Contributors
            Journal
            Front Microbiol
            Front Microbiol
            Front. Microbiol.
            Frontiers in Microbiology
            Frontiers Media S.A.
            1664-302X
            04 March 2015
            2015
            : 6
            4396515 10.3389/fmicb.2015.00090
            Copyright © 2015 Wood, Almaraz, Bradford, McGuire, Naeem, Neill, Palm, Tully and Zhou.

            This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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            Figures: 4, Tables: 2, Equations: 0, References: 44, Pages: 10, Words: 0
            Categories
            Microbiology
            Original Research Article

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