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      Seasonal Changes in a Maize-Based Polyculture of Central Mexico Reshape the Co-occurrence Networks of Soil Bacterial Communities

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          Abstract

          The milpa is a traditional maize-based polyculture in Mexico that is typically practiced as rainfed agriculture. Because milpa cultivation has been practiced over a vast range of environmental and cultural conditions, this agroecosystem is recognized as an important repository of biological and cultural diversity. As for any agroecosystem, the relationship between plant development and the biogeochemical processes of the soil is critical. Although the milpa has been studied from different perspectives, the diversity and structure of microbial communities within milpa soils remain largely unexplored. In this study, we surveyed a milpa system in Central Mexico across cropping season: before planting (dry season; t1), during the early growth of plants (onset of the rainy season; t2), and before harvest (end of the rainy season; t3). In order to examine changes in community structure through time, we characterized bacterial diversity through high-throughput sequencing of 16S rRNA gene amplicons and recorded the nutrient status of multiple (5–10) soil samples from our milpa plots. We estimated microbial diversity from a total of 90 samples and constructed co-occurrence networks. Although we did not find significant changes in diversity or composition of bacterial communities across time, we identified significant rearrangements in their co-occurrence network structure. We found particularly drastic changes between the first and second time points. Co-occurrence analyses showed that the bacterial community changed from a less structured network at ( t1) into modules with a non-random composition of taxonomic groups at ( t2). We conclude that changes in bacterial communities undetected by standard diversity analyses can become evident when performing co-occurrence network analyses. We also postulate possible functional associations among keystone groups suggested by biogeochemical processes. This study represents the first contribution on soil microbial diversity of a maize-based polyculture and shows its dynamic nature in short-term scales.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            QIIME allows analysis of high-throughput community sequencing data.

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              Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

              The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                18 December 2017
                2017
                : 8
                : 2478
                Affiliations
                [1] 1Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México , Mexico City, Mexico
                [2] 2Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México , Mexico City, Mexico
                [3] 3Department of Ecology and Evolutionary Biology, University of California, Irvine , Irvine, CA, United States
                [4] 4Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México , Mexico City, Mexico
                [5] 5Facultad de Ciencias, Universidad Nacional Autónoma de México , Mexico City, Mexico
                Author notes

                Edited by: David Berry, University of Vienna, Austria

                Reviewed by: Alessio Mengoni, University of Florence, Italy; Angel Valverde, University of the Free State, South Africa

                *Correspondence: Ana E. Escalante, aescalante@ 123456iecologia.unam.mx Mariana Benítez, mbenitez@ 123456iecologia.unam.mx

                These authors have contributed equally to this work.

                This article was submitted to Microbial Symbioses, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2017.02478
                5741676
                29326663
                5c53a69a-37ac-4e7c-b068-68c47293e729
                Copyright © 2017 Rebollar, Sandoval-Castellanos, Roessler, Gaut, Alcaraz, Benítez and Escalante.

                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.

                History
                : 29 August 2017
                : 29 November 2017
                Page count
                Figures: 4, Tables: 2, Equations: 0, References: 70, Pages: 13, Words: 0
                Funding
                Funded by: Consejo Nacional de Ciencia y Tecnología 10.13039/501100003141
                Award ID: 221341
                Award ID: 247672
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                milpa,bacterial diversity,co-occurrence networks,seasonal agriculture,actinobacteria,proteobacteria,chloroflexi

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