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      Soil Organic Carbon Attenuates the Influence of Plants on Root-Associated Bacterial Community

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          Abstract

          Plant-derived carbon (PDC) released by roots has a strong effect on root-associated bacterial community, which is critical for plant fitness in natural environments. However, the freshly exuded PDC can be diluted by the ancient soil-derived carbon (SDC) at a short distance from root apices. Thus, the rhizosphere C pools are normally dominated by SDC rather than PDC. Yet, how PDC and SDC interact to regulate root-associated bacterial community is largely unknown. In this study, a grass species and a legume species were planted in two contrasting matrixes, quartz sand and soil, to assess the role of PDC and SDC in regulating root-associated bacterial community, and to explore whether SDC affects the influence of PDC on bacterial community in soil. Our results indicated that the legume plant showed significantly positive priming effect on soil organic matter decomposition but the grass plant did not. PDC significantly shaped bacterial community in sand culture as indicated by PCR-DGGE and high-throughput sequencing of bacterial 16S rRNA gene. Intriguingly, we found that dissimilarity of bacterial communities associated with two plant species and the percentage of specific OTUs in quartz sand were significantly higher than those in soil. Moreover, several biomarkers enriched by plants in quartz sand turned to be general taxa in soil, which indicated that SDC attenuated the regulation of bacterial community by PDC. Taken together, these results suggest that SDC interacted with PDC and the root-associated microbial community, thus acted as soil buffering component of biological process contributing to soil resilience. The importance of PDC in structuring rhizosphere bacterial community needs to be reconsidered in the context of wider contribution of other C pool, such as SDC.

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          Most cited references 57

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          QIIME allows analysis of high-throughput community sequencing data.

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            UPARSE: highly accurate OTU sequences from microbial amplicon reads.

             Robert Edgar (2013)
            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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              UCHIME improves sensitivity and speed of chimera detection

              Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments. Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer. Contact: robert@drive5.com Availability: Source, binaries and data: http://drive5.com/uchime. Supplementary information: Supplementary data are available at Bioinformatics online.
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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
                09 November 2020
                2020
                : 11
                Affiliations
                1State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences , Guangzhou, China
                2College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science , Guangzhou, China
                Author notes

                Edited by: Carmen R. Beuzón, University of Málaga, Spain

                Reviewed by: Arjun Kafle, North Carolina State University, United States; Marco Zaccaria, Boston College, United States

                *Correspondence: Qing Yao, yaoqscau@ 123456scau.edu.cn

                This article was submitted to Microbe and Virus Interactions with Plants, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2020.594890
                7680919
                Copyright © 2020 Zhou, Yao and Zhu.

                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.

                Page count
                Figures: 6, Tables: 2, Equations: 0, References: 60, Pages: 12, Words: 0
                Funding
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Funded by: Guangdong Academy of Sciences 10.13039/501100009075
                Funded by: Science and Technology Planning Project of Guangdong Province 10.13039/501100012245
                Categories
                Microbiology
                Original Research

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