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      Enhanced lignin degradation by Irpex lacteus through expanded sterilization further improved the fermentation quality and microbial community during the silage preservation process

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          Abstract

          Traditional autoclaving, slow degradation rate and preservation of biomass treated by fungi are the main factors restricting biological treatment. In our previous studies, strains with high efficiency and selective lignin degradation ability were obtained. To further solve the limiting factors of biological treatment, this paper proposed a composite treatment technology, which could replace autoclaves for fungal treatment and improve the preservation and utilization of fungal-pretreated straw. The autoclaved and expanded buckwheat straw were, respectively, degraded by Irpex lacteus for 14 days (CIL, EIL), followed by ensiling of raw materials (CK) and biodegraded straw of CIL and EIL samples with Lactobacillus plantarum for different days, respectively (CP, CIP, EIP). An expansion led to lactic acid bacteria, mold, and yeast of the samples below the detection line, and aerobic bacteria was significantly reduced, indicating a positive sterilization effect. Expansion before I. lacteus significantly enhanced lignin selective degradation by about 6%, and the absolute content of natural detergent solute was about 5% higher than that of the CIL. Moreover, EIL decreased pH by producing higher organic acids. The combination treatment created favorable conditions for ensiling. During ensiling, EIP silage produced high lactic acid about 26.83 g/kg DM and the highest acetic acid about 22.35 g/kg DM, and the pH value could be stable at 4.50. Expansion before I. lacteus optimized the microbial community for ensiling, resulting in EIP silage co-dominated by Lactobacillus, Pediococcus and Weissella, whereas only Lactobacillus was always dominant in CP and CIP silage. Clavispora gradually replaced Irpex in EIP silage, which potentially promoted lactic acid bacteria growth and acetic acid production. In vitro gas production (IVGP) in EIL was increased by 30% relative to CK and was higher than 24% in CIL. The role of expansion was more significant after ensiling, the IVGP in EIP was increased by 22% relative to CP, while that in CIP silage was only increased by 9%. Silage of fungal-treated samples reduced methane emissions by 28% to 31%. The study demonstrated that expansion provides advantages for fungal colonization and delignification, and further improves the microbial community and fermentation quality for silage, enhancing the nutrition and utilization value. This has practical application value for scaling up biological treatment and preserving the fungal-treated lignocellulose.

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          The online version contains supplementary material available at 10.1186/s40643-024-00730-2.

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          PICRUSt2 for prediction of metagenome functions

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            A practical guide to amplicon and metagenomic analysis of microbiome data

            Advances in high-throughput sequencing (HTS) have fostered rapid developments in the field of microbiome research, and massive microbiome datasets are now being generated. However, the diversity of software tools and the complexity of analysis pipelines make it difficult to access this field. Here, we systematically summarize the advantages and limitations of microbiome methods. Then, we recommend specific pipelines for amplicon and metagenomic analyses, and describe commonly-used software and databases, to help researchers select the appropriate tools. Furthermore, we introduce statistical and visualization methods suitable for microbiome analysis, including alpha- and beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, and common visualization styles to help researchers make informed choices. Finally, a step-by-step reproducible analysis guide is introduced. We hope this review will allow researchers to carry out data analysis more effectively and to quickly select the appropriate tools in order to efficiently mine the biological significance behind the data.
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              Current perspective on pretreatment technologies using lignocellulosic biomass: An emerging biorefinery concept

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                Author and article information

                Contributors
                xucc@cau.edu.cn
                Journal
                Bioresour Bioprocess
                Bioresour Bioprocess
                Bioresources and Bioprocessing
                Springer Nature Singapore (Singapore )
                2197-4365
                22 January 2024
                22 January 2024
                December 2024
                : 11
                : 1
                : 14
                Affiliations
                [1 ]College of Engineering, China Agricultural University, (East Campus), ( https://ror.org/04v3ywz14) 17 Qing-Hua-Dong-Lu, Haidian District, Beijing, 100083 People’s Republic of China
                [2 ]School of Environmental Science and Engineering, Huazhong University of Science and Technology, ( https://ror.org/00p991c53) Wuhan, 430074 Hubei Province China
                [3 ]Changzhou Key Laboratory of Biomass Green, Safe and High Value Utilization Technology, Institute of Urban and Rural Mining, Changzhou University, ( https://ror.org/04ymgwq66) Changzhou, 213164 China
                [4 ]College of Grassland Science and Technology, China Agricultural University, ( https://ror.org/04v3ywz14) Beijing, 100093 People’s Republic of China
                Author information
                http://orcid.org/0000-0003-0219-3304
                Article
                730
                10.1186/s40643-024-00730-2
                10992542
                c6538bc6-a8bc-4b37-8e37-c3ede2dac997
                © The Author(s) 2024

                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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 12 November 2023
                : 10 January 2024
                Funding
                Funded by: Modern Agro-industry Technology Research System of China
                Award ID: CARS-07-E-3
                Award Recipient :
                Categories
                Research
                Custom metadata
                © State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology 2024

                expansion,irpex lacteus,lignin,ensiling,microbial community,in vitro production

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