3
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Bacterioplankton community variation in Bohai Bay (China) is explained by joint effects of environmental and spatial factors

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Parsing the relative importance of environmental (recent disturbances) and spatial factors (historical processes) in determining community structure is a core issue in ecology. The Bohai Bay is a typical semi‐enclosed bay located in the north of China, surrounding by the metropolitan area with anthropogenic disturbances made it a complex marine coastal system with pollution gradients, where the distributions and determinants of bacterioplankton communities remain unclear. In this study, we collected surface water samples from 19 sites across Bohai Bay at about 100 km scale to investigate the relative roles of local environments and regional spatial factors in shaping bacterioplankton community composition (BCC). The environmental parameters in the sampling region showed gradient change according to the geographic variation. Several abundant OTUs were significantly correlated with the pollution parameters in the studied area, and 16 OTUs of them showed distinct distribution pattern in different polluted regions with obvious geographic segmentation, which indicated the effects of pollution gradient and dispersal limitation on specific taxon. The BCCs did not show obviously clustering effect between different polluted regions, which indicated the complexity for explaining the BCC variation in the studied region. The partial Mantel test revealed stronger spatial effects on beta diversity than those of local environmental factors, which indicated that dispersal limitation accounted more for the beta diversity than environmental heterogeneity. Furthermore, variation partitioning analysis (VPA) conducted by combining the environmental variables, linear trends, and principal coordinates of the variables from neighbor matrices (PCNM) showed that it was the joint effects of environmental and spatial factors contributed to the explained variation of BCC in the studied area. Considering the special human geography characteristics of Bohai Bay, the unmeasured biotic/abiotic factors, stochastic factors, and anthropogenic disturbances may be responsible for the unexplained variation of the BCC.

          Abstract

          Parsing the relative importance of environmental and spatial factors in determining community structure in anthropogenic disturbed semi‐enclosed bay environment is rarely few. This study found that the joint effects of environmental and spatial factors contributed to the explained variation of bacterioplankton community composition in Bohai Bay (China), in which stronger spatial effects on bacterial beta diversity than those of local environmental factors were detected, which indicated that dispersal limitation accounted more for the bacterial community variation than environmental heterogeneity.

          Related collections

          Most cited references50

          • Record: found
          • Abstract: found
          • Article: not found

          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.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            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.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              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.
                Bookmark

                Author and article information

                Contributors
                huang_zy@tib.cas.cn
                Journal
                Microbiologyopen
                Microbiologyopen
                10.1002/(ISSN)2045-8827
                MBO3
                MicrobiologyOpen
                John Wiley and Sons Inc. (Hoboken )
                2045-8827
                05 February 2020
                April 2020
                : 9
                : 4 ( doiID: 10.1002/mbo3.v9.4 )
                : e997
                Affiliations
                [ 1 ] Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin China
                [ 2 ] Core Facility Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin China
                Author notes
                [*] [* ] Correspondence

                Zhiyong Huang, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, No. 32, XiQiDao, Tianjin Airport Economic Area, Tianjin 300308, China.

                Email: huang_zy@ 123456tib.cas.cn

                Author information
                https://orcid.org/0000-0002-9026-4717
                Article
                MBO3997
                10.1002/mbo3.997
                7142376
                32022464
                b95954e3-835e-4885-891c-7fbc431de65e
                © 2020 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 21 August 2019
                : 23 December 2019
                : 31 December 2019
                Page count
                Figures: 11, Tables: 9, Pages: 20, Words: 14200
                Funding
                Funded by: Science and Technology Support Program of Tianjin Municipality
                Award ID: 16YFXTSY00580
                Award ID: 18YFZCNC01180
                Award ID: 18ZXSZSF00100
                Funded by: The Key Programs of Chinese Academy of Sciences
                Award ID: KFZD‐SW‐219
                Categories
                Original Article
                Original Articles
                Custom metadata
                2.0
                April 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.7.9 mode:remove_FC converted:09.04.2020

                Microbiology & Virology
                16s rrna v4 region gene,bacterioplankton community composition,bohai bay,marine environment,multivariate analysis,spatial factors

                Comments

                Comment on this article