Enumeration of citrus endophytic bacterial communities based on illumine metagenomics technique
Citrus is a valuable crop in Pakistan. It is rich in vitamin C, other nutrients and antioxidants. Huanglongbing (HLB) caused by a bacterium "Candidatus liberibacter asiaticus" (CLas), africanus and americanus has an influence on citrus production around the world. Beside HLB there exist se...
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| creator | Mushtaq, Sehrish Shafiq, Muhammad Ashraf, Tehseen Haider, Muhammad Saleem Atta, Sagheer Almaary, Khalid S Elshikh, Mohammad Soliman |
| description | Citrus is a valuable crop in Pakistan. It is rich in vitamin C, other nutrients and antioxidants. Huanglongbing (HLB) caused by a bacterium "Candidatus liberibacter asiaticus" (CLas), africanus and americanus has an influence on citrus production around the world. Beside HLB there exist several other bacterial species in citrus groves in Pakistan. The structure and diversity of bacterial species in various ecosystems can be quickly examined using NGS. This approach is considerably quicker and more precise than outdated methods. Healthy or citrus greening infected leaf samples of Grapefruit (Citrus paradisi), C. aurantifolia, and C. reticulata Blanco were used for diversity analysis. In this study high throughput, NGS technique was used to access the population of both cultivable and non-cultivable bacterial endophytes from citrus leaves, by using PCR amplicons of 16S rDNA sequences (V5-V7 regions) with Illumina Hi seq. As a result, a total number of 68,722 sequences were produced from the test samples. According to the NGS-based diversity classification, the most common genera of exploited bacterial endophytes were Proteobacteria, Firmicutes, Bacteroides, Cyanobacteria, and Actinobacteria. C. aurantifolia and C. paradisi showed almost equal diversity, whereas C. reticulata Blanco had a higher proportion of Proteobacteria and Cyanobacteria in their leaves. To determine alpha diversity (AD), additional data was analyzed using statistical indices such as Shannon, Chao1, and Simpson. According to the inverse Simpson diversity index, the abundance of the microbial population in six different citrus samples was 0.48, 0.567, and 0.163, respectively. The metagenomics of microbiota in plant tissues was successfully recorded by NGS technology, which can help us learn more about the interactions between plants and microbes. This research is the first step toward a better understanding of 16SrRNA-based metagenomics from citrus in Pakistan using Illumina (Hi seq) Technology. |
| doi_str_mv | 10.1371/journal.pone.0263144 |
| format | Article |
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It is rich in vitamin C, other nutrients and antioxidants. Huanglongbing (HLB) caused by a bacterium "Candidatus liberibacter asiaticus" (CLas), africanus and americanus has an influence on citrus production around the world. Beside HLB there exist several other bacterial species in citrus groves in Pakistan. The structure and diversity of bacterial species in various ecosystems can be quickly examined using NGS. This approach is considerably quicker and more precise than outdated methods. Healthy or citrus greening infected leaf samples of Grapefruit (Citrus paradisi), C. aurantifolia, and C. reticulata Blanco were used for diversity analysis. In this study high throughput, NGS technique was used to access the population of both cultivable and non-cultivable bacterial endophytes from citrus leaves, by using PCR amplicons of 16S rDNA sequences (V5-V7 regions) with Illumina Hi seq. As a result, a total number of 68,722 sequences were produced from the test samples. According to the NGS-based diversity classification, the most common genera of exploited bacterial endophytes were Proteobacteria, Firmicutes, Bacteroides, Cyanobacteria, and Actinobacteria. C. aurantifolia and C. paradisi showed almost equal diversity, whereas C. reticulata Blanco had a higher proportion of Proteobacteria and Cyanobacteria in their leaves. To determine alpha diversity (AD), additional data was analyzed using statistical indices such as Shannon, Chao1, and Simpson. According to the inverse Simpson diversity index, the abundance of the microbial population in six different citrus samples was 0.48, 0.567, and 0.163, respectively. The metagenomics of microbiota in plant tissues was successfully recorded by NGS technology, which can help us learn more about the interactions between plants and microbes. This research is the first step toward a better understanding of 16SrRNA-based metagenomics from citrus in Pakistan using Illumina (Hi seq) Technology.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0263144</identifier><identifier>PMID: 35417473</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Actinobacteria ; Antioxidants ; Ascorbic acid ; Bacteria ; Bacterial diseases ; Bacteroides ; Biology and Life Sciences ; Candidatus Liberibacter africanus ; Candidatus Liberibacter americanus ; Candidatus Liberibacter asiaticus ; Citrus ; Citrus - microbiology ; Citrus aurantifolia ; Citrus fruits ; Citrus greening ; Citrus paradisi ; Citrus reticulata ; College campuses ; Computer and Information Sciences ; Cyanobacteria ; Disease ; DNA sequencing ; Ecology and Environmental Sciences ; Ecosystem ; Endophytes ; Endophytes - genetics ; Enumeration ; Ethanol ; Firmicutes ; Fruits ; Genera ; Genetic aspects ; Genetic testing ; Health aspects ; Horticulture ; Laboratories ; Leaves ; Metagenomics ; Microbiota ; Microorganisms ; Nutrients ; Phylogenetics ; Plant bacterial diseases ; Plant diseases ; Plant Diseases - microbiology ; Plant genetics ; Plant pathology ; Plant sciences ; Plant tissues ; Proteobacteria ; Research and Analysis Methods ; Research methodology ; Rhizobiaceae - genetics ; rRNA 16S ; Sequences ; Species diversity ; Statistical methods ; Technology</subject><ispartof>PloS one, 2022-04, Vol.17 (4), p.e0263144-e0263144</ispartof><rights>COPYRIGHT 2022 Public Library of Science</rights><rights>2022 Mushtaq et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 Mushtaq et al 2022 Mushtaq et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c622t-1431845bc23cc2da152659c0706b67820a0715951dfbd525d11cf567df52f0373</citedby><cites>FETCH-LOGICAL-c622t-1431845bc23cc2da152659c0706b67820a0715951dfbd525d11cf567df52f0373</cites><orcidid>0000-0001-9537-2007</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9007379/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9007379/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,2103,2929,23871,27929,27930,53796,53798</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35417473$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Khan, Khalid Ali</contributor><creatorcontrib>Mushtaq, Sehrish</creatorcontrib><creatorcontrib>Shafiq, Muhammad</creatorcontrib><creatorcontrib>Ashraf, Tehseen</creatorcontrib><creatorcontrib>Haider, Muhammad Saleem</creatorcontrib><creatorcontrib>Atta, Sagheer</creatorcontrib><creatorcontrib>Almaary, Khalid S</creatorcontrib><creatorcontrib>Elshikh, Mohammad Soliman</creatorcontrib><title>Enumeration of citrus endophytic bacterial communities based on illumine metagenomics technique</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Citrus is a valuable crop in Pakistan. It is rich in vitamin C, other nutrients and antioxidants. Huanglongbing (HLB) caused by a bacterium "Candidatus liberibacter asiaticus" (CLas), africanus and americanus has an influence on citrus production around the world. Beside HLB there exist several other bacterial species in citrus groves in Pakistan. The structure and diversity of bacterial species in various ecosystems can be quickly examined using NGS. This approach is considerably quicker and more precise than outdated methods. Healthy or citrus greening infected leaf samples of Grapefruit (Citrus paradisi), C. aurantifolia, and C. reticulata Blanco were used for diversity analysis. In this study high throughput, NGS technique was used to access the population of both cultivable and non-cultivable bacterial endophytes from citrus leaves, by using PCR amplicons of 16S rDNA sequences (V5-V7 regions) with Illumina Hi seq. As a result, a total number of 68,722 sequences were produced from the test samples. According to the NGS-based diversity classification, the most common genera of exploited bacterial endophytes were Proteobacteria, Firmicutes, Bacteroides, Cyanobacteria, and Actinobacteria. C. aurantifolia and C. paradisi showed almost equal diversity, whereas C. reticulata Blanco had a higher proportion of Proteobacteria and Cyanobacteria in their leaves. To determine alpha diversity (AD), additional data was analyzed using statistical indices such as Shannon, Chao1, and Simpson. According to the inverse Simpson diversity index, the abundance of the microbial population in six different citrus samples was 0.48, 0.567, and 0.163, respectively. The metagenomics of microbiota in plant tissues was successfully recorded by NGS technology, which can help us learn more about the interactions between plants and microbes. This research is the first step toward a better understanding of 16SrRNA-based metagenomics from citrus in Pakistan using Illumina (Hi seq) Technology.</description><subject>Actinobacteria</subject><subject>Antioxidants</subject><subject>Ascorbic acid</subject><subject>Bacteria</subject><subject>Bacterial diseases</subject><subject>Bacteroides</subject><subject>Biology and Life Sciences</subject><subject>Candidatus Liberibacter africanus</subject><subject>Candidatus Liberibacter americanus</subject><subject>Candidatus Liberibacter asiaticus</subject><subject>Citrus</subject><subject>Citrus - microbiology</subject><subject>Citrus aurantifolia</subject><subject>Citrus fruits</subject><subject>Citrus greening</subject><subject>Citrus paradisi</subject><subject>Citrus reticulata</subject><subject>College campuses</subject><subject>Computer and Information Sciences</subject><subject>Cyanobacteria</subject><subject>Disease</subject><subject>DNA sequencing</subject><subject>Ecology and 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of citrus endophytic bacterial communities based on illumine metagenomics technique</title><author>Mushtaq, Sehrish ; Shafiq, Muhammad ; Ashraf, Tehseen ; Haider, Muhammad Saleem ; Atta, Sagheer ; Almaary, Khalid S ; Elshikh, Mohammad Soliman</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c622t-1431845bc23cc2da152659c0706b67820a0715951dfbd525d11cf567df52f0373</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Actinobacteria</topic><topic>Antioxidants</topic><topic>Ascorbic acid</topic><topic>Bacteria</topic><topic>Bacterial diseases</topic><topic>Bacteroides</topic><topic>Biology and Life Sciences</topic><topic>Candidatus Liberibacter africanus</topic><topic>Candidatus Liberibacter americanus</topic><topic>Candidatus Liberibacter asiaticus</topic><topic>Citrus</topic><topic>Citrus - microbiology</topic><topic>Citrus aurantifolia</topic><topic>Citrus 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metagenomics technique</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2022-04-13</date><risdate>2022</risdate><volume>17</volume><issue>4</issue><spage>e0263144</spage><epage>e0263144</epage><pages>e0263144-e0263144</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Citrus is a valuable crop in Pakistan. It is rich in vitamin C, other nutrients and antioxidants. Huanglongbing (HLB) caused by a bacterium "Candidatus liberibacter asiaticus" (CLas), africanus and americanus has an influence on citrus production around the world. Beside HLB there exist several other bacterial species in citrus groves in Pakistan. The structure and diversity of bacterial species in various ecosystems can be quickly examined using NGS. This approach is considerably quicker and more precise than outdated methods. Healthy or citrus greening infected leaf samples of Grapefruit (Citrus paradisi), C. aurantifolia, and C. reticulata Blanco were used for diversity analysis. In this study high throughput, NGS technique was used to access the population of both cultivable and non-cultivable bacterial endophytes from citrus leaves, by using PCR amplicons of 16S rDNA sequences (V5-V7 regions) with Illumina Hi seq. As a result, a total number of 68,722 sequences were produced from the test samples. According to the NGS-based diversity classification, the most common genera of exploited bacterial endophytes were Proteobacteria, Firmicutes, Bacteroides, Cyanobacteria, and Actinobacteria. C. aurantifolia and C. paradisi showed almost equal diversity, whereas C. reticulata Blanco had a higher proportion of Proteobacteria and Cyanobacteria in their leaves. To determine alpha diversity (AD), additional data was analyzed using statistical indices such as Shannon, Chao1, and Simpson. According to the inverse Simpson diversity index, the abundance of the microbial population in six different citrus samples was 0.48, 0.567, and 0.163, respectively. The metagenomics of microbiota in plant tissues was successfully recorded by NGS technology, which can help us learn more about the interactions between plants and microbes. This research is the first step toward a better understanding of 16SrRNA-based metagenomics from citrus in Pakistan using Illumina (Hi seq) Technology.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>35417473</pmid><doi>10.1371/journal.pone.0263144</doi><tpages>e0263144</tpages><orcidid>https://orcid.org/0000-0001-9537-2007</orcidid><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2022-04, Vol.17 (4), p.e0263144-e0263144 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2649986026 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Actinobacteria Antioxidants Ascorbic acid Bacteria Bacterial diseases Bacteroides Biology and Life Sciences Candidatus Liberibacter africanus Candidatus Liberibacter americanus Candidatus Liberibacter asiaticus Citrus Citrus - microbiology Citrus aurantifolia Citrus fruits Citrus greening Citrus paradisi Citrus reticulata College campuses Computer and Information Sciences Cyanobacteria Disease DNA sequencing Ecology and Environmental Sciences Ecosystem Endophytes Endophytes - genetics Enumeration Ethanol Firmicutes Fruits Genera Genetic aspects Genetic testing Health aspects Horticulture Laboratories Leaves Metagenomics Microbiota Microorganisms Nutrients Phylogenetics Plant bacterial diseases Plant diseases Plant Diseases - microbiology Plant genetics Plant pathology Plant sciences Plant tissues Proteobacteria Research and Analysis Methods Research methodology Rhizobiaceae - genetics rRNA 16S Sequences Species diversity Statistical methods Technology |
| title | Enumeration of citrus endophytic bacterial communities based on illumine metagenomics technique |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-15T04%3A10%3A05IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Enumeration%20of%20citrus%20endophytic%20bacterial%20communities%20based%20on%20illumine%20metagenomics%20technique&rft.jtitle=PloS%20one&rft.au=Mushtaq,%20Sehrish&rft.date=2022-04-13&rft.volume=17&rft.issue=4&rft.spage=e0263144&rft.epage=e0263144&rft.pages=e0263144-e0263144&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0263144&rft_dat=%3Cgale_plos_%3EA700337436%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2649986026&rft_id=info:pmid/35417473&rft_galeid=A700337436&rft_doaj_id=oai_doaj_org_article_0c6d06a4aca94cedb8ef682efc81edac&rfr_iscdi=true |