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      Effects of Delayed Harvest and Additives on Fermentation Quality and Bacterial Community of Corn Stalk Silage

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          Abstract

          This study aimed to investigate the effects of delayed harvest and additives on the fermentation quality and bacterial community of corn stalk silage in South China. The corn stalks after ear harvest at the 0 day (D0), 7 days (D7), and 15 days (D15) were used to produce small-bale silages. The silages at each harvest time were treated without (control, CK) or with Lactobacillus plantarum (LP) and sodium benzoate (BF). The results showed that delayed harvest increased pH and acetic acid content and reduced lactic acid content in corn stalk silage ( p < 0.05). Compared with CK, the additives decreased the contents of butyric acid and ammonia nitrogen (NH 3-N; p < 0.05). The silage treated with LP increased the content of lactic acid and decreased pH ( p < 0.05); the silage treated with BF decreased counts of coliform bacteria and yeasts and increased residual water soluble carbohydrates (WSC) content ( p < 0.05). Single Molecule, Real-Time sequencing (SMRT) revealed that the abundance of L. plantarum increased, while the abundance of Lactobacillus brevis and Lactobacillus ginsenosidimutans decreased with the delayed harvest. Additives influenced the bacterial community structure of corn stalk silage, revealed by enhanced bacterial diversity on D0 and reduced on D7 ( p < 0.05). Our research indicated that delayed harvest could exert a positive effect on acetic acid production, and additives could inhibit the butyric acid fermentation and protein degradation of corn stalk silage by shifting bacterial community composition.

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          The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

          SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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            UPARSE: highly accurate OTU sequences from microbial amplicon reads.

            Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.
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              Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.

              The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (> or = 95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                07 July 2021
                2021
                : 12
                : 687481
                Affiliations
                [1] 1College of Animal Science, Guizhou University , Guiyang, China
                [2] 2College of Grassland Science and Technology, China Agricultural University , Beijing, China
                [3] 3Sichuan Academy of Grassland Sciences , Chengdu, China
                Author notes

                Edited by: Yimin Cai, Japan International Research Center for Agricultural Sciences (JIRCAS), Japan

                Reviewed by: Qing Zhang, South China Agricultural University, China; Mao Li, Chinese Academy of Tropical Agricultural Sciences, China

                *Correspondence: Ping Li, lpyzm@ 123456sina.cn

                This article was submitted to Microbiotechnology, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2021.687481
                8294468
                efad8942-2b98-4bb1-b385-920ef1434715
                Copyright © 2021 Guo, Lu, Li, Chen, Gou and Zhang.

                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
                : 29 March 2021
                : 19 April 2021
                Page count
                Figures: 4, Tables: 4, Equations: 0, References: 53, Pages: 9, Words: 7147
                Funding
                Funded by: Sichuan Program for Key Research and Development
                Award ID: 18ZDYF1385
                Funded by: Guizhou Talent Base of Grassland Ecological Animal Husbandry
                Award ID: RCJD2018-13
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                corn stalk silage,delayed harvest,sodium benzoate,lactobacillus plantarum,bacterial community

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