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      Distinct effects of short-term reconstructed topsoil on soya bean and corn rhizosphere bacterial abundance and communities in Chinese Mollisol

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          Abstract

          Eroded black soils (classified as Mollisols) lead to a thinner topsoil layer, reduced organic carbon storage and declined crop productivity. Understanding the changes in soil microbial communities owing to soil erosion is of vital importance as soil microbial communities are sensitive indicators of soil condition and are essential in soil nutrient cycling. This study used the reconstructed facility with 10, 20 and 30 cm topsoil thickness under no-till soya bean–corn rotation in black soil region of Northeast China. Illumina MiSeq sequencing targeting 16S rRNA, qPCR and soil respiration measurement were performed to assess the changes in soya bean and corn rhizosphere bacterial communities, as well as their abundance and activities due to the topsoil thickness. The results showed that soil bacterial communities from both soya bean and corn were more sensitive to topsoil removal than to soil biogeochemical characteristics. Topsoil depths significantly influenced both soya bean and corn bacterial communities, while they only significantly influenced the bacterial abundance and respiration in corn. We also found that the topsoil depths significantly induced the changes in phyla and genera from both soya bean and corn rhizosphere bacterial community, which aid further understandings on how topsoil layer influences the global nutrient cycling of Mollisols by influencing the change in microbial communities.

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          An extraction method for measuring soil microbial biomass C

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            Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment.

            The subseafloor marine biosphere may be one of the largest reservoirs of microbial biomass on Earth and has recently been the subject of debate in terms of the composition of its microbial inhabitants, particularly on sediments from the Peru Margin. A metagenomic analysis was made by using whole-genome amplification and pyrosequencing of sediments from Ocean Drilling Program Site 1229 on the Peru Margin to further explore the microbial diversity and overall community composition within this environment. A total of 61.9 Mb of genetic material was sequenced from sediments at horizons 1, 16, 32, and 50 m below the seafloor. These depths include sediments from both primarily sulfate-reducing methane-generating regions of the sediment column. Many genes of the annotated genes, including those encoding ribosomal proteins, corresponded to those from the Chloroflexi and Euryarchaeota. However, analysis of the 16S small-subunit ribosomal genes suggests that Crenarchaeota are the abundant microbial member. Quantitative PCR confirms that uncultivated Crenarchaeota are indeed a major microbial group in these subsurface samples. These findings show that the marine subsurface is a distinct microbial habitat and is different from environments studied by metagenomics, especially because of the predominance of uncultivated archaeal groups.
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              Polyphasic evidence supporting the reclassification of Bradyrhizobium japonicum group Ia strains as Bradyrhizobium diazoefficiens sp. nov.

              Bradyrhizobium japonicum was described from soybean root-nodule bacterial isolates. Since its description, several studies have revealed heterogeneities among rhizobia assigned to this species. Strains assigned to B. japonicum group Ia have been isolated in several countries, and many of them are outstanding soybean symbionts used in inoculants worldwide, but they have also been isolated from other legume hosts. Here, we summarize published studies that indicate that group Ia strains are different from the B. japonicum type strain USDA 6(T) and closely related strains, and present new morphophysiological, genotypic and genomic evidence to support their reclassification into a novel species, for which the name Bradyrhizobium diazoefficiens sp. nov. is proposed. The type strain of the novel species is the well-studied strain USDA 110(T) ( =IAM 13628(T)  =CCRC 13528(T)  =NRRL B-4361(T)  =NRRL B-4450(T)  =TAL 102(T)  =BCRC 13528(T)  =JCM 10833(T)  =TISTR 339(T)  =SEMIA 5032(T)  =3I1B110(T)  =ACCC 15034(T)  =CCT 4249(T)  = NBRC 14792(T)  = R-12974(T)  = CNPSo 46(T)).

                Author and article information

                Journal
                R Soc Open Sci
                R Soc Open Sci
                RSOS
                royopensci
                Royal Society Open Science
                The Royal Society
                2054-5703
                January 2019
                30 January 2019
                30 January 2019
                : 6
                : 1
                : 181054
                Affiliations
                Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences , Harbin 150081, People's Republic of China
                Author notes
                Author for correspondence: Xiaobing Liu e-mail: liuxb@ 123456iga.ac.cn

                Electronic supplementary material is available online at https://dx.doi.org/10.6084/m9.figshare.c.4365650.

                Author information
                http://orcid.org/0000-0002-5312-1258
                Article
                rsos181054
                10.1098/rsos.181054
                6366214
                88b5ab7a-1cbc-4f3e-a35c-c4fec6f6d009
                © 2019 The Authors.

                Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

                History
                : 6 July 2018
                : 17 December 2018
                Funding
                Funded by: National Key Research and Development Program of China;
                Award ID: 2017YFD0300300
                Funded by: Key Program of the Natural Science Foundation of Heilongjiang Province of China;
                Award ID: ZD2016009
                Funded by: Natural Science Foundation of Heilongjiang Province of China;
                Award ID: D2018008, QC2015027
                Funded by: Ministry of Science and Technology of China;
                Award ID: 2014BAD11B01-A01
                Funded by: National Natural Science Foundation of China;
                Award ID: 41671274
                Categories
                1004
                69
                1001
                200
                Earth Science
                Research Article
                Custom metadata
                January, 2019

                soil erosion,topsoil thickness,mollisol,bacterial community,16s rrna gene sequencing

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