Differentiation and Variability in the Rhizosphere and Endosphere Microbiomes of Healthy and Diseased Cotton (Gossypium sp.)

The plant microbiome is a key determinant of health and productivity. However, it is still difficult to understand the structural composition of the bacterial and fungal microbiomes of diseased and healthy plants, especially the spatial dynamics and phylogenies of endophytic and rhizosphere microbia...

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Veröffentlicht in:Frontiers in microbiology 2021-12, Vol.12, p.765269-765269, Article 765269
Hauptverfasser: Shi, Yingwu, Yang, Hongmei, Chu, Ming, Niu, Xinxiang, Wang, Ning, Lin, Qing, Lou, Kai, Zuo, Changgeng, Wang, Jingyi, Zou, Qiang, Zhang, Yumeng
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creator Shi, Yingwu
Yang, Hongmei
Chu, Ming
Niu, Xinxiang
Wang, Ning
Lin, Qing
Lou, Kai
Zuo, Changgeng
Wang, Jingyi
Zou, Qiang
Zhang, Yumeng
description The plant microbiome is a key determinant of health and productivity. However, it is still difficult to understand the structural composition of the bacterial and fungal microbiomes of diseased and healthy plants, especially the spatial dynamics and phylogenies of endophytic and rhizosphere microbial communities. We studied the differentiation and variability in the rhizosphere and endosphere microbiomes of healthy and diseased cotton from north and south of the Tianshan Mountains using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. The endophytic and rhizosphere bacterial abundances in the diseased plants were greater than those of healthy plants. The numbers of endophytic and rhizosphere fungi associated with diseased plants were greater than those associated healthy plants (p < 0.05). Endophytic and rhizosphere bacteria did not share common OTUs. The dominant rhizosphere bacteria were Proteobacteria (29.70%), Acidobacteria (23.14%), Gemmatimonadetes (15.17%), Actinobacteria (8.31%), Chloroflexi (7.99%), and Bacteroidetes (5.15%). The dominant rhizosphere fungi were Ascomycota (83.52%), Mortierellomycota (7.67%), Basidiomycota (2.13%), Chytridiomycota (0.39%), and Olpidiomycota (0.08%). The distribution of dominant bacteria in different cotton rhizosphere soils and roots differed, with the dominant bacteria Pseudomonas (15.54%) and Pantoea (9.19%), and the dominant fungi Alternaria (16.15%) and Cephalotrichum (9.10%) being present in the greatest numbers. At sampling points in different ecological regions, the total numbers of cotton endophytic and rhizosphere microbiome OTUs from southern to northern Xinjiang showed an increasing trend. There were significant differences in the composition and diversity of rhizosphere microbes and endophytes during the entire cotton growth period and in representative ecological regions (p < 0.01), whereas rhizosphere microbes and endophytes showed no significant differences among the four growth periods and in representative ecological regions. RB41, H16, Nitrospira, and Sphingomonas play important roles in the microbial ecology of cotton rhizosphere soil. Pseudomonas accounted for a large proportion of the microbes in the cotton rhizosphere soil. This study provides an in-depth understanding of the complex microbial composition and diversity associated with cotton north and south of the Tianshan Mountains.
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However, it is still difficult to understand the structural composition of the bacterial and fungal microbiomes of diseased and healthy plants, especially the spatial dynamics and phylogenies of endophytic and rhizosphere microbial communities. We studied the differentiation and variability in the rhizosphere and endosphere microbiomes of healthy and diseased cotton from north and south of the Tianshan Mountains using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. The endophytic and rhizosphere bacterial abundances in the diseased plants were greater than those of healthy plants. The numbers of endophytic and rhizosphere fungi associated with diseased plants were greater than those associated healthy plants (p &lt; 0.05). Endophytic and rhizosphere bacteria did not share common OTUs. The dominant rhizosphere bacteria were Proteobacteria (29.70%), Acidobacteria (23.14%), Gemmatimonadetes (15.17%), Actinobacteria (8.31%), Chloroflexi (7.99%), and Bacteroidetes (5.15%). The dominant rhizosphere fungi were Ascomycota (83.52%), Mortierellomycota (7.67%), Basidiomycota (2.13%), Chytridiomycota (0.39%), and Olpidiomycota (0.08%). The distribution of dominant bacteria in different cotton rhizosphere soils and roots differed, with the dominant bacteria Pseudomonas (15.54%) and Pantoea (9.19%), and the dominant fungi Alternaria (16.15%) and Cephalotrichum (9.10%) being present in the greatest numbers. At sampling points in different ecological regions, the total numbers of cotton endophytic and rhizosphere microbiome OTUs from southern to northern Xinjiang showed an increasing trend. There were significant differences in the composition and diversity of rhizosphere microbes and endophytes during the entire cotton growth period and in representative ecological regions (p &lt; 0.01), whereas rhizosphere microbes and endophytes showed no significant differences among the four growth periods and in representative ecological regions. RB41, H16, Nitrospira, and Sphingomonas play important roles in the microbial ecology of cotton rhizosphere soil. Pseudomonas accounted for a large proportion of the microbes in the cotton rhizosphere soil. 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However, it is still difficult to understand the structural composition of the bacterial and fungal microbiomes of diseased and healthy plants, especially the spatial dynamics and phylogenies of endophytic and rhizosphere microbial communities. We studied the differentiation and variability in the rhizosphere and endosphere microbiomes of healthy and diseased cotton from north and south of the Tianshan Mountains using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. The endophytic and rhizosphere bacterial abundances in the diseased plants were greater than those of healthy plants. The numbers of endophytic and rhizosphere fungi associated with diseased plants were greater than those associated healthy plants (p &lt; 0.05). Endophytic and rhizosphere bacteria did not share common OTUs. 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This study provides an in-depth understanding of the complex microbial composition and diversity associated with cotton north and south of the Tianshan Mountains.</description><subject>cotton</subject><subject>diversity</subject><subject>endophytic microbiome</subject><subject>healthy and diseased</subject><subject>Illumina MiSeq</subject><subject>Life Sciences &amp; Biomedicine</subject><subject>Microbiology</subject><subject>rhizosphere microbiome</subject><subject>Science &amp; Technology</subject><issn>1664-302X</issn><issn>1664-302X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>HGBXW</sourceid><sourceid>DOA</sourceid><recordid>eNqNkk1v1DAQhiMEolXpD-CCciyqdok_41yQUPopFSEhQNyssTPuukriJfaCtuLH491tV-0NH-yx_cw71vgtirekmjOmmg9u8NbMaUXJvJaCyuZFcUik5DNW0Z8vn8QHxXGMd1UevKJ5fl0cMN4wRWt1WPw9887hhGPykHwYSxi78gdMHozvfVqXfizTAsuvC38f4nKR0S1yPnaP28_eTsH4MGAsgyuvEPq0WG-pMx8RInZlG1LK4ieXIcb10q-GMi7n798Urxz0EY8f1qPi-8X5t_ZqdvPl8rr9dDOzXIo0E6bpDGfKca4Mc9QwhZJxIgHqznHbABDHBXNCMJACMlp3AMKqigpGOnZUXO90uwB3ejn5Aaa1DuD19iBMtxqm5G2PunISbYMVMdZwIrhCKrjojMrdQ8lp1vq401quzICdzZ2boH8m-vxm9At9G35rJZVgimWBkweBKfxaYUx68NFi38OIYRU1lYTRhhO6qUV2aG5wjBO6fRlS6Y0J9NYEemMCvTNBznn39H37jMcvz8DpDviDJrhoPY4W91j2R82YZKTeGIZkWv0_3fq0NVEbVmNi_wCF-dDY</recordid><startdate>20211206</startdate><enddate>20211206</enddate><creator>Shi, Yingwu</creator><creator>Yang, Hongmei</creator><creator>Chu, Ming</creator><creator>Niu, Xinxiang</creator><creator>Wang, Ning</creator><creator>Lin, Qing</creator><creator>Lou, Kai</creator><creator>Zuo, Changgeng</creator><creator>Wang, Jingyi</creator><creator>Zou, Qiang</creator><creator>Zhang, Yumeng</creator><general>Frontiers Media Sa</general><general>Frontiers Media S.A</general><scope>BLEPL</scope><scope>DTL</scope><scope>HGBXW</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0003-2511-2386</orcidid></search><sort><creationdate>20211206</creationdate><title>Differentiation and Variability in the Rhizosphere and Endosphere Microbiomes of Healthy and Diseased Cotton (Gossypium sp.)</title><author>Shi, Yingwu ; Yang, Hongmei ; Chu, Ming ; Niu, Xinxiang ; Wang, Ning ; Lin, Qing ; Lou, Kai ; Zuo, Changgeng ; Wang, Jingyi ; Zou, Qiang ; Zhang, Yumeng</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c465t-5b9db438f448b3f2b38e63416aa7df4c9aa1f453f553a65a4387daa5c802531d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>cotton</topic><topic>diversity</topic><topic>endophytic microbiome</topic><topic>healthy and diseased</topic><topic>Illumina MiSeq</topic><topic>Life Sciences &amp; Biomedicine</topic><topic>Microbiology</topic><topic>rhizosphere microbiome</topic><topic>Science &amp; Technology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Shi, Yingwu</creatorcontrib><creatorcontrib>Yang, Hongmei</creatorcontrib><creatorcontrib>Chu, Ming</creatorcontrib><creatorcontrib>Niu, Xinxiang</creatorcontrib><creatorcontrib>Wang, Ning</creatorcontrib><creatorcontrib>Lin, Qing</creatorcontrib><creatorcontrib>Lou, Kai</creatorcontrib><creatorcontrib>Zuo, Changgeng</creatorcontrib><creatorcontrib>Wang, Jingyi</creatorcontrib><creatorcontrib>Zou, Qiang</creatorcontrib><creatorcontrib>Zhang, Yumeng</creatorcontrib><collection>Web of Science Core Collection</collection><collection>Science Citation Index Expanded</collection><collection>Web of Science - Science Citation Index Expanded - 2021</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>Frontiers in microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shi, Yingwu</au><au>Yang, Hongmei</au><au>Chu, Ming</au><au>Niu, Xinxiang</au><au>Wang, Ning</au><au>Lin, Qing</au><au>Lou, Kai</au><au>Zuo, Changgeng</au><au>Wang, Jingyi</au><au>Zou, Qiang</au><au>Zhang, Yumeng</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Differentiation and Variability in the Rhizosphere and Endosphere Microbiomes of Healthy and Diseased Cotton (Gossypium sp.)</atitle><jtitle>Frontiers in microbiology</jtitle><stitle>FRONT MICROBIOL</stitle><addtitle>Front Microbiol</addtitle><date>2021-12-06</date><risdate>2021</risdate><volume>12</volume><spage>765269</spage><epage>765269</epage><pages>765269-765269</pages><artnum>765269</artnum><issn>1664-302X</issn><eissn>1664-302X</eissn><abstract>The plant microbiome is a key determinant of health and productivity. However, it is still difficult to understand the structural composition of the bacterial and fungal microbiomes of diseased and healthy plants, especially the spatial dynamics and phylogenies of endophytic and rhizosphere microbial communities. We studied the differentiation and variability in the rhizosphere and endosphere microbiomes of healthy and diseased cotton from north and south of the Tianshan Mountains using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. The endophytic and rhizosphere bacterial abundances in the diseased plants were greater than those of healthy plants. The numbers of endophytic and rhizosphere fungi associated with diseased plants were greater than those associated healthy plants (p &lt; 0.05). Endophytic and rhizosphere bacteria did not share common OTUs. 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subjects cotton
diversity
endophytic microbiome
healthy and diseased
Illumina MiSeq
Life Sciences & Biomedicine
Microbiology
rhizosphere microbiome
Science & Technology
title Differentiation and Variability in the Rhizosphere and Endosphere Microbiomes of Healthy and Diseased Cotton (Gossypium sp.)
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