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

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          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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          Most cited references 36

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            Ecological intensification: harnessing ecosystem services for food security.

            Rising demands for agricultural products will increase pressure to further intensify crop production, while negative environmental impacts have to be minimized. Ecological intensification entails the environmentally friendly replacement of anthropogenic inputs and/or enhancement of crop productivity, by including regulating and supporting ecosystem services management in agricultural practices. Effective ecological intensification requires an understanding of the relations between land use at different scales and the community composition of ecosystem service-providing organisms above and below ground, and the flow, stability, contribution to yield, and management costs of the multiple services delivered by these organisms. Research efforts and investments are particularly needed to reduce existing yield gaps by integrating context-appropriate bundles of ecosystem services into crop production systems. Copyright © 2012 Elsevier Ltd. All rights reserved.
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              Microbial diversity and function in soil: from genes to ecosystems.

              Soils sustain an immense diversity of microbes, which, to a large extent, remains unexplored. A range of novel methods, most of which are based on rRNA and rDNA analyses, have uncovered part of the soil microbial diversity. The next step in the era of microbial ecology is to extract genomic, evolutionary and functional information from bacterial artificial chromosome libraries of the soil community genomes (the metagenome). Sophisticated analyses that apply molecular phylogenetics, DNA microarrays, functional genomics and in situ activity measurements will provide huge amounts of new data, potentially increasing our understanding of the structure and function of soil microbial ecosystems, and the interactions that occur within them. This review summarizes the recent progress in studies of soil microbial communities with focus on novel methods and approaches that provide new insight into the relationship between phylogenetic and functional diversity.

                Author and article information

                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                04 March 2015
                : 6
                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.

                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
                Original Research Article


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