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

      Depth-dependent influence of biochar application on the abundance and community structure of diazotrophic under sugarcane growth

      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

          Despite progress in understanding diazotrophic distribution in surface soils, few studies have investigated the distribution of diazotrophic bacteria in deeper soil layers. Here, we leveraged high-throughput sequencing (HTS) of nifH genes obtained to assess the influence of biochar amended soil (BC) and control (CK), and soil depths (0–20, 20–40 and 40–60 cm) on diazotrophic abundance and community structures, soil enzyme activities and physio-chemical properties. Multivariate ANOVA analysis revealed that soil depth had profound impact on majority of the soil parameters measured than fertilization. Although soil physio-chemical properties, enzymes activities, diazotrophic genera and enriched operational taxonomic units (OTUs) were significantly influenced across the entire soil profiles, we also observed that BC amended soil significantly increased cane stalk height and weight, nitrate (NO 3 -), ammonium (NH 4 +), organic matter (OM), total carbon (TC) and available potassium (AK), and enhanced diazotrophic genera in soil depth 0–20 cm compared to CK treatment. Soil TC, total nitrogen (TN), OM and NH 4 + were the major impact factors shifting diazotrophic community structures in soil depth 0–20 cm. Overall, these results were more pronounced in 0–20 cm soil depth in BC than CK treatment.

          Related collections

          Most cited references69

          • 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: found
            Is Open Access

            Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

            DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.
              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              Bio-char Sequestration in Terrestrial Ecosystems – A Review

                Bookmark

                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: InvestigationRole: MethodologyRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: InvestigationRole: Resources
                Role: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: Data curationRole: ResourcesRole: Software
                Role: Resources
                Role: Project administrationRole: Supervision
                Role: ResourcesRole: Software
                Role: Data curation
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: ResourcesRole: Supervision
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                19 July 2021
                2021
                : 16
                : 7
                : e0253970
                Affiliations
                [1 ] Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
                [2 ] College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
                Government College University Faisalabad, Pakistan, PAKISTAN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0001-6923-9755
                Article
                PONE-D-20-39341
                10.1371/journal.pone.0253970
                8289083
                34280207
                1dc0f283-f23d-4f82-b48e-2e3d0b4ba9d2
                © 2021 Fallah et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 15 December 2020
                : 16 June 2021
                Page count
                Figures: 8, Tables: 2, Pages: 19
                Funding
                Funded by: public welfare industrial research project of china
                Award ID: 20150311904-01
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100010038, earmarked fund for china agriculture research system;
                Award ID: CARS-17
                We would like to acknowledge that this research was funded by Public Welfare Industrial Research Project of China (grant number 20150311904-01) and Earmarked Fund for China Agriculture Research System (CARS-17). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Physical Sciences
                Chemistry
                Chemical Compounds
                Organic Compounds
                Diazo Compounds
                Physical Sciences
                Chemistry
                Organic Chemistry
                Organic Compounds
                Diazo Compounds
                Biology and Life Sciences
                Ecology
                Community Ecology
                Community Structure
                Ecology and Environmental Sciences
                Ecology
                Community Ecology
                Community Structure
                Biology and Life Sciences
                Agriculture
                Agricultural Soil Science
                Earth Sciences
                Soil Science
                Agricultural Soil Science
                Biology and Life Sciences
                Agriculture
                Crop Science
                Crops
                Sugarcane
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Grasses
                Sugarcane
                Biology and Life Sciences
                Agriculture
                Agrochemicals
                Fertilizers
                Biology and Life Sciences
                Ecology
                Ecological Metrics
                Species Diversity
                Ecology and Environmental Sciences
                Ecology
                Ecological Metrics
                Species Diversity
                Physical sciences
                Chemistry
                Environmental chemistry
                Soil chemistry
                Soil pH
                Ecology and environmental sciences
                Environmental chemistry
                Soil chemistry
                Soil pH
                Earth sciences
                Soil science
                Soil chemistry
                Soil pH
                Biology and Life Sciences
                Biochemistry
                Enzymology
                Enzymes
                Ureases
                Biology and Life Sciences
                Biochemistry
                Proteins
                Enzymes
                Ureases
                Custom metadata
                All relevant data are within the manuscript and its Supporting Information files.

                Uncategorized
                Uncategorized

                Comments

                Comment on this article