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      Soil bacterial networks are less stable under drought than fungal networks

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          Abstract

          Soil microbial communities play a crucial role in ecosystem functioning, but it is unknown how co-occurrence networks within these communities respond to disturbances such as climate extremes. This represents an important knowledge gap because changes in microbial networks could have implications for their functioning and vulnerability to future disturbances. Here, we show in grassland mesocosms that drought promotes destabilising properties in soil bacterial, but not fungal, co-occurrence networks, and that changes in bacterial communities link more strongly to soil functioning during recovery than do changes in fungal communities. Moreover, we reveal that drought has a prolonged effect on bacterial communities and their co-occurrence networks via changes in vegetation composition and resultant reductions in soil moisture. Our results provide new insight in the mechanisms through which drought alters soil microbial communities with potential long-term consequences, including future plant community composition and the ability of aboveground and belowground communities to withstand future disturbances.

          Abstract

          Drought conditions can alter the composition of soil microbial communities, but the effects of drought on network properties have not been tested. Here, de Vries and colleagues show that co-occurrence networks are destabilised under drought for bacteria but not fungi.

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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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            Notes on the characterization of prokaryote strains for taxonomic purposes.

            Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers.
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              Responses of soil bacterial and fungal communities to extreme desiccation and rewetting.

              The microbial response to summer desiccation reflects adaptation strategies, setting the stage for a large rainfall-induced soil CO2 pulse upon rewetting, an important component of the ecosystem carbon budget. In three California annual grasslands, the present (DNA-based) and potentially active (RNA-based) soil bacterial and fungal communities were tracked over a summer season and in response to controlled rewetting of intact soil cores. Phylogenetic marker genes for bacterial (16S) and fungal (28S) RNA and DNA were sequenced, and the abundances of these genes and transcripts were measured. Although bacterial community composition differed among sites, all sites shared a similar response pattern of the present and potentially active bacterial community to dry-down and wet-up. In contrast, the fungal community was not detectably different among sites, and was largely unaffected by dry-down, showing marked resistance to dessication. The potentially active bacterial community changed significantly as summer dry-down progressed, then returned to pre-dry-down composition within several hours of rewetting, displaying spectacular resilience. Upon rewetting, transcript copies of bacterial rpoB genes increased consistently, reflecting rapid activity resumption. Acidobacteria and Actinobacteria were the most abundant phyla present and potentially active, and showed the largest changes in relative abundance. The relative increase (Actinobacteria) and decrease (Acidobacteria) with dry-down, and the reverse responses to rewetting reflected a differential response, which was conserved at the phylum level and consistent across sites. These contrasting desiccation-related bacterial life-strategies suggest that predicted changes in precipitation patterns may affect soil nutrient and carbon cycling by differentially impacting activity patterns of microbial communities.
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                Author and article information

                Contributors
                franciska.devries@manchester.ac.uk
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                2 August 2018
                2 August 2018
                2018
                : 9
                : 3033
                Affiliations
                [1 ]ISNI 0000000121662407, GRID grid.5379.8, School of Earth and Environmental Sciences, , The University of Manchester, ; Oxford Road, Manchester, M13 9PT UK
                [2 ]Centre for Ecology & Hydrology Wallingford, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire OX10 8BB UK
                [3 ]ISNI 0000 0001 2336 6580, GRID grid.7605.4, Department of Life Sciences and Systems Biology, , University of Torino, ; Viale Mattioli 25, 10125 Torino, Italy
                [4 ]CNR—Institute for Sustainable Plant Protection, UOS Turin, Viale Mattioli 25, 10125 Torino, Italy
                [5 ]ISNI 0000 0000 8578 2742, GRID grid.6341.0, Department of Forest Mycology and Plant Pathology, , Swedish University of Agricultural Sciences, ; 750 07 Uppsala, Sweden
                [6 ]ISNI 0000000094781573, GRID grid.8682.4, Centre for Ecology & Hydrology Lancaster, ; Library Avenue, Bailrigg, Lancaster LA1 4AP UK
                [7 ]ISNI 0000 0001 2298 9313, GRID grid.5613.1, Agroécologie, AgroSup Dijon, INRA, , Univ. Bourgogne Franche-Comté, ; F-21000 Dijon, France
                [8 ]ISNI 0000 0000 8190 6402, GRID grid.9835.7, Lancaster Environment Centre, , Lancaster University, ; Library Avenue, Bailrigg, Lancaster LA1 4AP UK
                [9 ]ISNI 0000 0004 1936 7291, GRID grid.7107.1, School of Biological Sciences, , University of Aberdeen, ; Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU UK
                Author information
                http://orcid.org/0000-0002-6822-8883
                http://orcid.org/0000-0002-3341-4547
                http://orcid.org/0000-0002-6218-6301
                http://orcid.org/0000-0002-9069-9024
                http://orcid.org/0000-0001-9619-1320
                http://orcid.org/0000-0001-5864-8561
                http://orcid.org/0000-0003-3426-3178
                http://orcid.org/0000-0003-1757-5102
                http://orcid.org/0000-0002-8532-3700
                http://orcid.org/0000-0002-5131-0127
                Article
                5516
                10.1038/s41467-018-05516-7
                6072794
                30072764
                9af83ee9-a0cf-48d8-9013-a5699bdb9db3
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 4 September 2017
                : 11 July 2018
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council (BBSRC);
                Award ID: BB/L02456X/1
                Award Recipient :
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