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      Biocrust reduces the soil erodibility of coral calcareous sand by regulating microbial community and extracellular polymeric substances on tropical coral island, South China Sea

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          Abstract

          Tropical coral islands assume a pivotal role in the conservation of oceanic ecosystem biodiversity. However, their distinctive environmental attributes and limited vegetation render them highly susceptible to soil erosion. The biological soil crust (biocrust), owing to its significant ecological role in soil stabilization and erosion prevention, is deemed an effective means of mitigating soil erosion on coral island. However, existing research on the mechanisms through which biocrusts resist soil erosion has predominantly concentrated on arid and semi-arid regions. Consequently, this study will specifically delve into elucidating the erosion-resistant mechanisms of biocrusts in tropical coral island environments, South China Sea. Specifically, we collected 16 samples of biocrusts and bare soil from Meiji Island. High-throughput amplicon sequencing was executed to analyze the microbial community, including bacteria, fungi, and archaea. Additionally, quantitative PCR was utilized to assess the abundance of the bacterial 16S rRNA, fungal ITS, archaeal 16S rRNA, and cyanobacterial 16S rRNA genes within these samples. Physicochemical measurements and assessments of extracellular polymeric substances (EPSs) were conducted to characterize the soil properties. The study reported a significantly decreased soil erodibility factor after biocrust formation. Compared to bare soil, soil erodibility factor decreased from 0.280 to 0.190 t h MJ −1 mm −1 in the biocrusts. Mechanistically, we measured the microbial EPS contents and revealed a negative correlation between EPS and soil erodibility factor. Consistent with increased EPS, the abundance of bacteria, fungi, archaea, and cyanobacteria were also detected significantly increased with biocrust formation. Correlation analysis detected Cyanobacteria, Chloroflexi, Deinococcota, and Crenarchaeota as potential microbials promoting EPSs and reducing soil erosion. Together, our study presents the evidence that biocrust from tropical coral island in the South China Sea promotes resistance to soil erosion, pinpointing key EPSs-producing microbials against soil erosion. The findings would provide insights for island soil restoration.

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          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.
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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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              Colorimetric Method for Determination of Sugars and Related Substances

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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
                13 December 2023
                2023
                : 14
                : 1283073
                Affiliations
                [1] 1CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou, China
                [2] 2University of Chinese Academy of Sciences , Beijing, China
                [3] 3Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) , Guangzhou, China
                Author notes

                Edited by: Hua Li, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences (CAS), China

                Reviewed by: Federico Rossi, University of Pisa, Italy; Weibo Wang, Wuhan Botanical Garden, Chinese Academy of Sciences (CAS), China

                *Correspondence: Jie Li, lijietaren@ 123456scsio.ac.cn

                These authors have contributed equally to this work

                Article
                10.3389/fmicb.2023.1283073
                10751374
                38152373
                414ae517-5537-400d-9793-ae6fe360fb0b
                Copyright © 2023 Wang, Huang, Yang, Mai, Xie, Lyu, Zhang and Li.

                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
                : 04 September 2023
                : 27 November 2023
                Page count
                Figures: 8, Tables: 0, Equations: 2, References: 93, Pages: 15, Words: 10056
                Funding
                The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The work was supported by the National Natural Science Foundation of China (grant nos. 41890853 and 42206155), the National Key Research and Development Project of China (grant no. 2022YFC3102103), the Natural Science Foundation of Guangdong Province, China (grant no. 2022A1515011889), and Guangzhou Science and Technology Plan Project (grant no. 202201010499).
                Categories
                Microbiology
                Original Research
                Custom metadata
                Terrestrial Microbiology

                Microbiology & Virology
                tropical coral island,biological soil crust,microbial community,extracellular polymeric substances,soil erodibility factor,soil nutrients

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