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      Interaction between dissolved organic carbon and fungal network governs carbon mineralization in paddy soil under co-incorporation of green manure and biochar

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          Abstract

          Legume crops in rice cultivation are typically rotated and incorporated into the soil as green manure to improve soil fertility. Biochar has recently been co-incorporated with green manure to simultaneously stimulate soil organic carbon (SOC) mineralization and increase carbon (C) sequestration. However, few studies examine the effects of the co-incorporation of biochar and green manure on C cycling and the underlying microbial mechanisms in paddy fields. In this study, the effects of the co-incorporation of green manure and biochar on C mineralization, dissolved organic carbon (DOC) characteristics, and microbial community structures were investigated. A pot study was conducted with three treatments: inorganic NPK (NPK), inorganic NPK + green manure (GM), and inorganic NPK + green manure + biochar (GMC). Organic amendments significantly increased cumulative C mineralization, with amounts in the order GMC (3,434 mg·kg −1) > GM (2,934 mg·kg −1) > NPK (2,592 mg·kg −1). Fertilizer treatments had similar effects on DOC concentrations, with amounts in the order GMC (279 mg·kg −1) > GM (255 mg·kg −1) > NPK (193 mg·kg −1). According to fluorescence spectra, the highest microbial humic acid-like fraction and biological index were also in GMC. Co-incorporation of green manure and biochar shifted the composition of bacterial and fungal communities but more importantly, increased fungal network complexity and decreased bacterial network complexity. The increase in fungal network complexity with the increase in DOC concentrations and microbially derived components was the dominant factor in promoting C mineralization. Overall, this study reveals the underlying biochemical mechanism, the interaction between DOC and fungal network of C cycling in paddy soil under the co-incorporation of green manure and biochar management, and provides fundamental knowledge for exploring effective approaches to improve soil fertility and health in the future.

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          ITS primers with enhanced specificity for basidiomycetes--application to the identification of mycorrhizae and rusts.

          M Gardes, T D Bruns (1993)
          We have designed two taxon-selective primers for the internal transcribed spacer (ITS) region in the nuclear ribosomal repeat unit. These primers, ITS1-F and ITS4-B, were intended to be specific to fungi and basidiomycetes, respectively. We have tested the specificity of these primers against 13 species of ascomycetes, 14 of basidiomycetes, and 15 of plants. Our results showed that ITS4-B, when paired with either a 'universal' primer ITS1 or the fungal-specific primer ITS1-F, efficiently amplified DNA from all basidiomycetes and discriminated against ascomycete DNAs. The results with plants were not as clearcut. The ITS1-F/ITS4-B primer pair produced a small amount of PCR product for certain plant species, but the quantity was in most cases less than that produced by the 'universal' ITS primers. However, under conditions where both plant and fungal DNAs were present, the fungal DNA was amplified to the apparent exclusion of plant DNA. ITS1-F/ITS4-B preferential amplification was shown to be particularly useful for detection and analysis of the basidiomycete component in ectomycorrhizae and in rust-infected tissues. These primers can be used to study the structure of ectomycorrhizal communities or the distribution of rusts on alternate hosts.
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            SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

            Elmar Pruesse, Christian Quast, Katrin Knittel … (2007)
            Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs.
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              Towards a unified paradigm for sequence-based identification of fungi.

              Urmas Kõljalg, R Nilsson, Kessy Abarenkov … (2013)
              The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE. © 2013 John Wiley & Sons Ltd.
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                Author and article information

                Contributors
                Journal
                Journal ID (nlm-ta): Front Microbiol
                Journal ID (iso-abbrev): Front Microbiol
                Journal ID (publisher-id): Front. Microbiol.
                Title: Frontiers in Microbiology
                Publisher: Frontiers Media S.A.
                ISSN (Electronic): 1664-302X
                Publication date (Electronic): 22 August 2023
                Publication date Collection: 2023
                Volume: 14
                Electronic Location Identifier: 1233465
                Affiliations
                [1] 1Key Laboratory of Poyang Lake Basin Agricultural Resource and Ecology of Jiangxi Province, College of Land Resource and Environment, Jiangxi Agricultural University , Nanchang, China
                [2] 2State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences , Nanjing, China
                [3] 3Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences , Kunming, China
                Author notes

                Edited by: Juntao Wang, Western Sydney University, Australia

                Reviewed by: Xu Liu, Chinese Academy of Sciences (CAS), China; Ziting Wang, Guangxi University, China; Jia Liu, Jiangxi Academy of Agricultural Sciences (CAAS), China

                *Correspondence: Xiaoyue Wang, wangxy@ 123456issas.ac.cn
                Article
                DOI: 10.3389/fmicb.2023.1233465
                PMC ID: 10477716
                PubMed ID: 37675431
                SO-VID: df3536bc-725b-47eb-8167-5702bb21b4b9
                Copyright © Copyright © 2023 Cheng, Wang, Fu, Wang, Liu and Sun.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                Date received : 02 June 2023
                Date accepted : 31 July 2023
                Page count
                Figures: 6, Tables: 3, Equations: 2, References: 61, Pages: 12, Words: 8228
                Funding
                Funded by: Chinese Academy of Sciences, doi 10.13039/501100002367;
                Award ID: XDA28030102
                Categories
                Subject: Microbiology
                Subject: Original Research
                Custom metadata
                section-at-acceptance Terrestrial Microbiology

                ScienceOpen disciplines: Microbiology & Virology
                Keywords: c mineralization,dissolved organic carbon,green manure,biochar,fluorescence spectra,microbial communities,co-occurrence network
                Data availability:
                ScienceOpen disciplines: Microbiology & Virology
                Keywords: c mineralization, dissolved organic carbon, green manure, biochar, fluorescence spectra, microbial communities, co-occurrence network

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