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      Compared to conventional, ecological intensive management promotes beneficial proteolytic soil microbial communities for agro-ecosystem functioning under climate change-induced rain regimes

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          Abstract

          Projected climate change and rainfall variability will affect soil microbial communities, biogeochemical cycling and agriculture. Nitrogen (N) is the most limiting nutrient in agroecosystems and its cycling and availability is highly dependent on microbial driven processes. In agroecosystems, hydrolysis of organic nitrogen (N) is an important step in controlling soil N availability. We analyzed the effect of management (ecological intensive vs. conventional intensive) on N-cycling processes and involved microbial communities under climate change-induced rain regimes. Terrestrial model ecosystems originating from agroecosystems across Europe were subjected to four different rain regimes for 263 days. Using structural equation modelling we identified direct impacts of rain regimes on N-cycling processes, whereas N-related microbial communities were more resistant. In addition to rain regimes, management indirectly affected N-cycling processes via modifications of N-related microbial community composition. Ecological intensive management promoted a beneficial N-related microbial community composition involved in N-cycling processes under climate change-induced rain regimes. Exploratory analyses identified phosphorus-associated litter properties as possible drivers for the observed management effects on N-related microbial community composition. This work provides novel insights into mechanisms controlling agro-ecosystem functioning under climate change.

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          FLASH: fast length adjustment of short reads to improve genome assemblies.

          Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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            Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine and terrestrial ecosystems.

            The cycles of the key nutrient elements nitrogen (N) and phosphorus (P) have been massively altered by anthropogenic activities. Thus, it is essential to understand how photosynthetic production across diverse ecosystems is, or is not, limited by N and P. Via a large-scale meta-analysis of experimental enrichments, we show that P limitation is equally strong across these major habitats and that N and P limitation are equivalent within both terrestrial and freshwater systems. Furthermore, simultaneous N and P enrichment produces strongly positive synergistic responses in all three environments. Thus, contrary to some prevailing paradigms, freshwater, marine and terrestrial ecosystems are surprisingly similar in terms of N and P limitation.
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              Vive la différence: plant functional diversity matters to ecosystem processes

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                Author and article information

                Contributors
                gabinpiton@gmail.com
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                29 April 2020
                29 April 2020
                2020
                : 10
                : 7296
                Affiliations
                [1 ]ISNI 0000 0004 0511 762X, GRID grid.424520.5, Department of Soil Sciences, , Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, ; 5070 Frick, Switzerland
                [2 ]ISNI 0000 0001 2165 8627, GRID grid.8664.c, Organic Farming with focus on Sustainable Soil Use, Karl-Glöckner-Str. 21 C, Justus-Liebig University Giessen, ; 35394 Giessen, Germany
                [3 ]ISNI 0000 0004 0609 8934, GRID grid.462909.0, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, ; 38000 Grenoble, France
                [4 ]ISNI 0000 0001 1898 0762, GRID grid.503168.9, École de la Nature et du Paysage, INSA Centre Val de Loire, 41000 Blois - CNRS, CITERES, UMR 7324, 37200, ; Tours, France
                [5 ]ISNI 0000 0001 0791 5666, GRID grid.4818.5, Soil Biology Group, Wageningen University & Research, P.O. Box 47, 6700 AA, ; Wageningen, The Netherlands
                [6 ]ISNI 0000 0001 2165 8627, GRID grid.8664.c, Bioinformatics and Systems Biology, Heinrich-Buff-Ring 58, Justus-Liebig-University Giessen, ; 35392 Giessen, Germany
                [7 ]ISNI 0000 0000 9511 4342, GRID grid.8051.c, Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, ; 3000-456 Coimbra, Portugal
                [8 ]Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-Les-Bains, France
                Article
                64279
                10.1038/s41598-020-64279-8
                7190635
                32350402
                723687e3-54af-417d-b9a8-2e1fcbfda1e4
                © The Author(s) 2020

                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
                : 19 September 2019
                : 13 April 2020
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                © The Author(s) 2020

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                ecology,agroecology,climate-change ecology,ecosystem ecology,grassland ecology,microbial ecology,molecular ecology

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