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      Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities

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          Abstract

          Drylands’ poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities’ assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change.

          Abstract

          Salinity and aridity shape the assembly and structures, but not the potential functionality, of microbial communities from Southern African dryland soils.

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          Cutadapt removes adapter sequences from high-throughput sequencing reads

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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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                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: SoftwareRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: SoftwareRole: ValidationRole: Writing - review & editing
                Role: SoftwareRole: Validation
                Role: ResourcesRole: Writing - review & editing
                Role: ResourcesRole: Writing - review & editing
                Role: Writing - review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: Writing - original draftRole: Writing - review & editing
                Journal
                FEMS Microbiol Ecol
                FEMS Microbiol Ecol
                femsec
                FEMS Microbiology Ecology
                Oxford University Press
                0168-6496
                1574-6941
                December 2024
                20 November 2024
                20 November 2024
                : 100
                : 12
                : fiae157
                Affiliations
                Extreme Ecosystem Microbiomics & Ecogenomics (E²ME) Laboratory, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile , Santiago 8331150, Chile
                Microbial Ecology of Extreme Systems Laboratory, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile , Santiago 8331150, Chile
                Millennium Institute Center for Genome Regulation (CGR) , Santiago 8331150, Chile
                Microbial Ecology of Extreme Systems Laboratory, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile , Santiago 8331150, Chile
                Millennium Institute Center for Genome Regulation (CGR) , Santiago 8331150, Chile
                Center for Climate and Resilience Research (CR)2 , Santiago 8370449, Chile
                Microbial Ecology of Extreme Systems Laboratory, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile , Santiago 8331150, Chile
                Millennium Institute Center for Genome Regulation (CGR) , Santiago 8331150, Chile
                Center for Climate and Resilience Research (CR)2 , Santiago 8370449, Chile
                Scientific Services Kimberley, South African National Parks , Kimberley 8306, South Africa
                Applied Behavioural Ecology & Ecosystem Research Unit , UNISA, P/Bag X6, Florida 1710, South Africa
                Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria , P/Bag X20, Pretoria 0028, South Africa
                Extreme Ecosystem Microbiomics & Ecogenomics (E²ME) Laboratory, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile , Santiago 8331150, Chile
                Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria , P/Bag X20, Pretoria 0028, South Africa
                Author notes
                Corresponding author. Tomás Sauma-Sánchez, Extreme Ecosystem Microbiomics & Ecogenomics (E²ME) Laboratory, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile. E-mail: tomasauma@ 123456gmail.com
                Corresponding author. Jean-Baptiste Ramond, Extreme Ecosystem Microbiomics & Ecogenomics (E²ME) Laboratory, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile. E-mail: jbramond@ 123456uc.cl
                Author information
                https://orcid.org/0009-0006-2596-449X
                https://orcid.org/0000-0001-7662-239X
                https://orcid.org/0000-0002-6519-7321
                https://orcid.org/0000-0001-8059-861X
                https://orcid.org/0000-0003-4790-6232
                Article
                fiae157
                10.1093/femsec/fiae157
                11636270
                39568064
                5e723aa0-6134-4a9c-9fba-fba678e69854
                © The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 25 February 2024
                : 09 October 2024
                : 19 November 2024
                : 12 December 2024
                Page count
                Pages: 14
                Funding
                Funded by: National Research Foundation, DOI 10.13039/501100001321;
                Award ID: FBIS160422162807
                Funded by: Fondo Nacional de Desarrollo Científico y Tecnológico, DOI 10.13039/501100002850;
                Award ID: 1210912
                Categories
                Research Article
                AcademicSubjects/SCI01150

                Microbiology & Virology
                dryland soils,edaphic microbial communities,functional redundancy,metabarcoding,niche partitioning,shotgun metagenomics

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