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      Long-term combined application of manure and chemical fertilizer sustained higher nutrient status and rhizospheric bacterial diversity in reddish paddy soil of Central South China

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          Abstract

          Bacteria, as the key component of soil ecosystems, participate in nutrient cycling and organic matter decomposition. However, how fertilization regime affects the rhizospheric bacterial community of reddish paddy soil remains unclear. Here, a long-term fertilization experiment initiated in 1982 was employed to explore the impacts of different fertilization regimes on physicochemical properties and bacterial communities of reddish paddy rhizospheric soil in Central South China by sequencing the 16S rRNA gene. The results showed that long-term fertilization improved the soil nutrient status and shaped the distinct rhizospheric bacterial communities. Particularly, chemical NPK fertilizers application significantly declined the richness of the bacterial community by 7.32%, whereas the application of manure alone or combined with chemical NPK fertilizers significantly increased the biodiversity of the bacterial community by 1.45%, 1.87% compared with no fertilization, respectively. Moreover, LEfSe indicated that application of chemical NPK fertilizers significantly enhanced the abundances of Verrucomicrobia and Nitrospiraceae, while manure significantly increased the abundances of Deltaproteobacteria and Myxococcales, but the most abundant Actinobacteria and Planctomycetes were detected in the treatment that combined application of manure and chemical NPK fertilizers. Furthermore, canonical correspondence analysis (CCA) and the Mantel test clarified that exchangeable Mg 2+ (E-Mg 2+), soil organic carbon (SOC) and alkali-hydrolyzable nitrogen (AN) are the key driving factors for shaping bacterial communities in the rhizosphere. Our results suggested that long-term balanced using of manure and chemical fertilizers not only increased organic material pools and nutrient availability but also enhanced the biodiversity of the rhizospheric bacterial community and the abundance of Actinobacteria, which contribute to the sustainable development of agro-ecosystems.

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          Most cited references45

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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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              The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms

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                Author and article information

                Contributors
                zhangyangzhu2006@163.com
                gjusheng@163.com
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                8 November 2018
                8 November 2018
                2018
                : 8
                : 16554
                Affiliations
                [1 ]GRID grid.257160.7, College of Resources and Environment, , Hunan Agricultural University, ; Changsha, 410128 China
                [2 ]Red Soil Experimental Station of Chinese Academy of Agricultural Sciences, Qiyang, Hunan 426182 China
                [3 ]ISNI 0000 0004 4911 9766, GRID grid.410598.1, Institute of Agro-Environment and Ecology, , Hunan Academy of Agricultural Sciences, ; Changsha, 410125 China
                Article
                34685
                10.1038/s41598-018-34685-0
                6224536
                30410029
                138d3c2e-ed0b-4335-8cb6-c89baaa07443
                © 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
                : 16 July 2018
                : 19 October 2018
                Funding
                Funded by: the National Science and Technology Basic Work Program of China (2014FY110200A15); the National Science and Technology Support Plan Program of China (2012BAD14B17)
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