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      Temperature mediates continental-scale diversity of microbes in forest soils

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          Abstract

          Climate warming is increasingly leading to marked changes in plant and animal biodiversity, but it remains unclear how temperatures affect microbial biodiversity, particularly in terrestrial soils. Here we show that, in accordance with metabolic theory of ecology, taxonomic and phylogenetic diversity of soil bacteria, fungi and nitrogen fixers are all better predicted by variation in environmental temperature than pH. However, the rates of diversity turnover across the global temperature gradients are substantially lower than those recorded for trees and animals, suggesting that the diversity of plant, animal and soil microbial communities show differential responses to climate change. To the best of our knowledge, this is the first study demonstrating that the diversity of different microbial groups has significantly lower rates of turnover across temperature gradients than other major taxa, which has important implications for assessing the effects of human-caused changes in climate, land use and other factors.

          Abstract

          Climate warming has a wide range of effects on biodiversity. Here, Zhou et al. show that although variation in environmental temperature is a primary driver of soil microbial biodiversity, microbes show much lower rates of turnover across temperature gradients than other major taxa.

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          Most cited references26

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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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            The diversity and biogeography of soil bacterial communities.

            For centuries, biologists have studied patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible for microorganisms, arguably the most diverse and abundant group of organisms on Earth. Here, we present a continental-scale description of soil bacterial communities and the environmental factors influencing their biodiversity. We collected 98 soil samples from across North and South America and used a ribosomal DNA-fingerprinting method to compare bacterial community composition and diversity quantitatively across sites. Bacterial diversity was unrelated to site temperature, latitude, and other variables that typically predict plant and animal diversity, and community composition was largely independent of geographic distance. The diversity and richness of soil bacterial communities differed by ecosystem type, and these differences could largely be explained by soil pH (r(2) = 0.70 and r(2) = 0.58, respectively; P < 0.0001 in both cases). Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in our study. Our results suggest that microbial biogeography is controlled primarily by edaphic variables and differs fundamentally from the biogeography of "macro" organisms.
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              Microbial biogeography: putting microorganisms on the map.

              We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity. However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group
                2041-1723
                05 July 2016
                2016
                : 7
                : 12083
                Affiliations
                [1 ]State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University , Beijing 100084, China
                [2 ]Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, USA
                [3 ]Earth Science Division, Lawrence Berkeley National Laboratory , Berkeley, California 94270, USA
                [4 ]CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences , Beijing, 100085, China
                [5 ]Department of Ecology and Evolutionary Biology, University of Arizona , Tucson, Arizona 85721, USA
                [6 ]The Santa Fe Institute, USA , 1399 Hyde Park Rd, Santa Fe, New Mexico 87501, USA
                [7 ]EEB Graduate Program, Department of Biology, University of Oklahoma , Norman, OK 73019, USA
                [8 ]Smithsonian Tropical Research Institute , Balboa 0843-03092, Republic of Panama
                [9 ]Department of Biology, University of New Mexico , Albuquerque, New Mexico 87131, USA
                Author notes
                Author information
                http://orcid.org/0000-0002-7584-0632
                Article
                ncomms12083
                10.1038/ncomms12083
                4935970
                27377774
                b927f7ee-a82d-478b-8d8d-b5a618bb5667
                Copyright © 2016, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 11 June 2015
                : 27 May 2016
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