Grazing exclusion alters soil methane flux and methanotrophic and methanogenic communities in alpine meadows on the Qinghai–Tibet Plateau – ScienceOpen
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      Grazing exclusion alters soil methane flux and methanotrophic and methanogenic communities in alpine meadows on the Qinghai–Tibet Plateau

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          Abstract

          Grazing exclusion (GE) is an effective measure for restoring degraded grassland ecosystems. However, the effect of GE on methane (CH 4) uptake and production remains unclear in dominant bacterial taxa, main metabolic pathways, and drivers of these pathways. This study aimed to determine CH 4 flux in alpine meadow soil using the chamber method. The in situ composition of soil aerobic CH 4-oxidizing bacteria (MOB) and CH 4-producing archaea (MPA) as well as the relative abundance of their functional genes were analyzed in grazed and nongrazed (6 years) alpine meadows using metagenomic methods. The results revealed that CH 4 fluxes in grazed and nongrazed plots were −34.10 and −22.82 μg‧m −2‧h −1, respectively. Overall, 23 and 10 species of Types I and II MOB were identified, respectively. Type II MOB comprised the dominant bacteria involved in CH 4 uptake, with Methylocystis constituting the dominant taxa. With regard to MPA, 12 species were identified in grazed meadows and 3 in nongrazed meadows, with Methanobrevibacter constituting the dominant taxa. GE decreased the diversity of MPA but increased the relative abundance of dominated species Methanobrevibacter millerae from 1.47 to 4.69%. The proportions of type I MOB, type II MOB, and MPA that were considerably affected by vegetation and soil factors were 68.42, 21.05, and 10.53%, respectively. Furthermore, the structural equation models revealed that soil factors (available phosphorus, bulk density, and moisture) significantly affected CH 4 flux more than vegetation factors (grass species number, grass aboveground biomass, grass root biomass, and litter biomass). CH 4 flux was mainly regulated by serine and acetate pathways. The serine pathway was driven by soil factors (0.84, p < 0.001), whereas the acetate pathway was mainly driven by vegetation (−0.39, p < 0.05) and soil factors (0.25, p < 0.05). In conclusion, our findings revealed that alpine meadow soil is a CH 4 sink. However, GE reduces the CH 4 sink potential by altering vegetation structure and soil properties, especially soil physical properties.

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          Kraken: ultrafast metagenomic sequence classification using exact alignments

          Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.
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            Quality control and preprocessing of metagenomic datasets

            Summary: Here, we present PRINSEQ for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets. Summary statistics of FASTA (and QUAL) or FASTQ files are generated in tabular and graphical form and sequences can be filtered, reformatted and trimmed by a variety of options to improve downstream analysis. Availability and Implementation: This open-source application was implemented in Perl and can be used as a stand alone version or accessed online through a user-friendly web interface. The source code, user help and additional information are available at http://prinseq.sourceforge.net/. Contact: rschmied@sciences.sdsu.edu; redwards@cs.sdsu.edu
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              Bracken: estimating species abundance in metagenomics data

              Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.
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                Author and article information

                Contributors
                URI : https://loop.frontiersin.org/people/1866967/overviewRole: Role: Role: Role: Role: Role:
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                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                18 December 2023
                2023
                : 14
                : 1293720
                Affiliations
                [1] 1Key Laboratory of Grassland Ecosystem, Ministry of Education, College of Pratacultural Science, Gansu Agricultural University , Lanzhou, China
                [2] 2Key Laboratory of Development of Forage Germplasm in the Qinghai-Tibetan Plateau of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University , Xining, China
                [3] 3Institute of Grassland Research, Chinese Academy of Agricultural Sciences , Hohhot, China
                Author notes

                Edited by: Marika Pellegrini, University of L’Aquila, Italy

                Reviewed by: Cuijing Zhang, Institute for Advanced Study, Shenzhen University, China; Rihab Djebaili, Consorzio Interuniversitario Nazionale per le Scienze Ambientali, Italy

                *Correspondence: Wenxia Cao, caowx@ 123456gsau.edu.cn
                Article
                10.3389/fmicb.2023.1293720
                10757936
                38164400
                57e2362b-880f-4138-8f28-f4146e17a62d
                Copyright © 2023 Wang, Chen, Li, Gong, Wang and Cao.

                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
                : 13 September 2023
                : 04 December 2023
                Page count
                Figures: 7, Tables: 2, Equations: 1, References: 74, Pages: 14, Words: 10697
                Funding
                Funded by: Fostering Foundation for the Excellent Ph.D. Dissertation of Gansu Agricultural University
                Award ID: YB2020004
                Funded by: National Natural Science Foundation of China, doi 10.13039/501100001809;
                Award ID: 32060269
                The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the Fostering Foundation for the Excellent Ph.D. Dissertation of Gansu Agricultural University [grant number YB2020004] and the National Natural Science Foundation of China [grant number 32060269].
                Categories
                Microbiology
                Original Research
                Custom metadata
                Terrestrial Microbiology

                Microbiology & Virology
                grazing management,greenhouse gas,alpine meadow,methane flux,methane sink,methane-oxidizing bacteria

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