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      Leafcutter ants enhance microbial drought resilience in tropical forest soil

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          Abstract

          We conducted a research campaign in a neotropical rainforest in Costa Rica throughout the drought phase of an El‐Nino Southern Oscillation event to determine microbial community dynamics and soil C fluxes. Our study included nests of the leafcutter ant Atta cephalotes, as soil disturbances made by these ecosystem engineers may influence microbial drought response. Drought decreased the diversity of microbes and the abundance of core microbiome taxa, including Verrucomicrobial bacteria and Sordariomycete fungi. Despite initial responses of decreasing diversity and altered composition, 6 months post‐drought the microbiomes were similar to pre‐drought conditions, demonstrating the resilience of soil microbial communities to drought events. A. cephalotes nests altered fungal composition in the surrounding soil, and reduced both fungal mortality and growth of Acidobacteria post‐drought. Drought increased CH 4 consumption in soils due to lower soil moisture, and A. cephalotes nests decrease the variability of CH 4 emissions in some soil types. CH 4 emissions were tracked by the abundance of methanotrophic bacteria and fungal composition. These results characterize the microbiome of tropical soils across both time and space during drought and provide evidence for the importance of leafcutter ant nests in shaping soil microbiomes and enhancing microbial resilience during climatic perturbations.

          Abstract

          We carried out an eight‐month investigation on a tropical soil microbial community in the aftermath of a severe drought event, which resulted in changes to soil moisture levels and methane emissions. Our study reveals that the leafcutter ant, Atta cephalotes, plays a crucial role in stabilizing the microbial community and enhancing its resilience by mitigating the mortality rates of fungi and methanotrophs. The findings underscore the significance of multi‐trophic interactions in bolstering ecosystem resilience in the face of extreme climatic occurrences.

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          Most cited references48

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          The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

          SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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            Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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              phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

              Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.
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                Author and article information

                Contributors
                hshulman@utk.edu
                Journal
                Environ Microbiol Rep
                Environ Microbiol Rep
                10.1111/(ISSN)1758-2229
                EMI4
                Environmental Microbiology Reports
                John Wiley & Sons, Inc. (Hoboken, USA )
                1758-2229
                23 May 2024
                June 2024
                : 16
                : 3 ( doiID: 10.1111/emi4.v16.3 )
                : e13251
                Affiliations
                [ 1 ] Department of Microbiology and Plant Pathology University of California Riverside California USA
                [ 2 ] Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee USA
                [ 3 ] Center for Conservation Biology University of California Riverside California USA
                [ 4 ] Department of Biological Sciences Florida International University Miami Florida USA
                [ 5 ] Centro De Investigación En Estructuras Microscópicas Universidad de Costa Rica San José Costa Rica
                Author notes
                [*] [* ] Correspondence

                Hannah B. Shulman, Department of Ecology and Evolutionary Biology, University of Tennessee, 573 Dabney Hall, Knoxville, TN 37996‐1610, USA.

                Email: hshulman@ 123456utk.edu

                Author information
                https://orcid.org/0000-0002-9959-9417
                Article
                EMI413251
                10.1111/1758-2229.13251
                11112399
                38778789
                5df2e1c5-0d66-43e4-98fd-d039866db06d
                © 2024 The Authors. Environmental Microbiology Reports published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 19 December 2023
                : 15 March 2024
                Page count
                Figures: 4, Tables: 0, Pages: 9, Words: 6600
                Funding
                Funded by: Directorate for Biological Sciences , doi 10.13039/100000076;
                Award ID: 1624623
                Categories
                Brief Report
                Brief Reports
                Custom metadata
                2.0
                June 2024
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.4.3 mode:remove_FC converted:23.05.2024

                Microbiology & Virology
                Microbiology & Virology

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