Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole
Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial comm...
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| creator | Zhang, Xuwang Qu, Yuanyuan Ma, Qiao Zhang, Zhaojing Li, Duanxing Wang, Jingwei Shen, Wenli Shen, E Zhou, Jiti |
| description | Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1), phenol plus indole (G2) and indole only (G3), were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA) and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P |
| doi_str_mv | 10.1371/journal.pone.0125732 |
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The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1), phenol plus indole (G2) and indole only (G3), were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA) and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P<0.05). Nevertheless, the bacteria assigned to phylum Proteobacteria, family Comamonadaceae, and genera Diaphorobacter, Comamonas and Aquamicrobium were commonly shared dominant populations. Pearson correlations were calculated to discern the relationship between microbial communities and indigo yields. The typical indigo-producing populations Comamonas and Pseudomonas showed no positive correlations with indigo yields, while there emerged many other genera that exhibited positive relationships, such as Aquamicrobium, Truepera and Pusillimonas, which had not been reported for indigo production previously. The present study should provide new insights into indigo bio-production by microbial communities from indole.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0125732</identifier><identifier>PMID: 25928424</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Activated sludge ; Analysis ; Aromatic compounds ; Aromatics ; Biodegradation ; Biosynthesis ; Coking ; Comamonadaceae - metabolism ; Comamonas - metabolism ; Community structure ; Correlation ; Ecology ; Education ; Engineering ; Environmental engineering ; Environmental science ; Gene sequencing ; Genomes ; Heterocyclic compounds ; Hydrocarbons ; Indigo ; Indole ; Indoles ; Laboratories ; Microbial activity ; Microbiomes ; Microorganisms ; Naphthalene ; Phenols ; Pollutants ; Populations ; Proteobacteria - metabolism ; RNA ; rRNA 16S ; Sewage ; Sludge ; Wastewater ; Water treatment ; Yield</subject><ispartof>PloS one, 2015-04, Vol.10 (4), p.e0125732-e0125732</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Zhang 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>2015 Zhang et al 2015 Zhang et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-726c80467e2ff486c2511ffeb491caef77461e6fbf025be139b74f74cc5a7e2a3</citedby><cites>FETCH-LOGICAL-c692t-726c80467e2ff486c2511ffeb491caef77461e6fbf025be139b74f74cc5a7e2a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4416020/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4416020/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79569,79570</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25928424$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Xuwang</creatorcontrib><creatorcontrib>Qu, Yuanyuan</creatorcontrib><creatorcontrib>Ma, Qiao</creatorcontrib><creatorcontrib>Zhang, Zhaojing</creatorcontrib><creatorcontrib>Li, Duanxing</creatorcontrib><creatorcontrib>Wang, Jingwei</creatorcontrib><creatorcontrib>Shen, Wenli</creatorcontrib><creatorcontrib>Shen, E</creatorcontrib><creatorcontrib>Zhou, Jiti</creatorcontrib><title>Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1), phenol plus indole (G2) and indole only (G3), were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA) and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P<0.05). Nevertheless, the bacteria assigned to phylum Proteobacteria, family Comamonadaceae, and genera Diaphorobacter, Comamonas and Aquamicrobium were commonly shared dominant populations. Pearson correlations were calculated to discern the relationship between microbial communities and indigo yields. The typical indigo-producing populations Comamonas and Pseudomonas showed no positive correlations with indigo yields, while there emerged many other genera that exhibited positive relationships, such as Aquamicrobium, Truepera and Pusillimonas, which had not been reported for indigo production previously. The present study should provide new insights into indigo bio-production by microbial communities from indole.</description><subject>Activated sludge</subject><subject>Analysis</subject><subject>Aromatic compounds</subject><subject>Aromatics</subject><subject>Biodegradation</subject><subject>Biosynthesis</subject><subject>Coking</subject><subject>Comamonadaceae - metabolism</subject><subject>Comamonas - metabolism</subject><subject>Community structure</subject><subject>Correlation</subject><subject>Ecology</subject><subject>Education</subject><subject>Engineering</subject><subject>Environmental engineering</subject><subject>Environmental science</subject><subject>Gene sequencing</subject><subject>Genomes</subject><subject>Heterocyclic compounds</subject><subject>Hydrocarbons</subject><subject>Indigo</subject><subject>Indole</subject><subject>Indoles</subject><subject>Laboratories</subject><subject>Microbial activity</subject><subject>Microbiomes</subject><subject>Microorganisms</subject><subject>Naphthalene</subject><subject>Phenols</subject><subject>Pollutants</subject><subject>Populations</subject><subject>Proteobacteria - metabolism</subject><subject>RNA</subject><subject>rRNA 16S</subject><subject>Sewage</subject><subject>Sludge</subject><subject>Wastewater</subject><subject>Water treatment</subject><subject>Yield</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk99v0zAQxyMEYqPwHyCwhITgoSV2HCd5QSrjV6WhSSvwajnOOfXk2MN2Kvrn8J_irt3Uoj2gKEp097nv-e58WfYc5zNcVPjdlRu9FWZ27SzMckzKqiAPslPcFGTKSF48PPg_yZ6EcJXnZVEz9jg7IWVDakroafZnYcw4aCvQN72EXyi9I1ipbY8uYQ3CBPRRr8EHSID0rtXCoDM3DKPVUUNATqG5jHotInRoacauB7TchAhDQMuoh9HceNpN0lEKPNiI5t4NImoZkHIeLWyne4c-aBc2Nq4g6GRPxNbhDDzNHql0DHi2_06yH58_fT_7Oj2_-LI4m59PJWtInFaEyTqnrAKiFK2ZJCXGKWFLGywFqKqiDANTrcpJ2QIumraiqqJSliLFiGKSvdzpXhsX-L67gWNWVUXFypImYrEjOieu-LXXg_Ab7oTmNwbney58KssAZ03XdiTHEgSmrSxaDNC1NZWUNUIokrTe77ON7QCdTG3xwhyJHnusXvHerTmlmOVppJPszV7AuzSyEPmggwRjhAU3bs9d57iqGlYm9NU_6P3V7alepAK0VS7llVtRPqe4yYuyqbfU7B4qPR0MWqarqHSyHwW8PQpITITfsRdjCHyxvPx_9uLnMfv6gF2lmxpXwZkxamfDMUh3YLq9IXhQd03GOd9u0m03-HaT-H6TUtiLwwHdBd2uTvEXPoccsQ</recordid><startdate>20150430</startdate><enddate>20150430</enddate><creator>Zhang, Xuwang</creator><creator>Qu, Yuanyuan</creator><creator>Ma, Qiao</creator><creator>Zhang, Zhaojing</creator><creator>Li, Duanxing</creator><creator>Wang, Jingwei</creator><creator>Shen, Wenli</creator><creator>Shen, E</creator><creator>Zhou, Jiti</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20150430</creationdate><title>Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole</title><author>Zhang, Xuwang ; Qu, Yuanyuan ; Ma, Qiao ; Zhang, Zhaojing ; Li, Duanxing ; Wang, Jingwei ; Shen, Wenli ; Shen, E ; Zhou, Jiti</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-726c80467e2ff486c2511ffeb491caef77461e6fbf025be139b74f74cc5a7e2a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Activated sludge</topic><topic>Analysis</topic><topic>Aromatic compounds</topic><topic>Aromatics</topic><topic>Biodegradation</topic><topic>Biosynthesis</topic><topic>Coking</topic><topic>Comamonadaceae - metabolism</topic><topic>Comamonas - metabolism</topic><topic>Community structure</topic><topic>Correlation</topic><topic>Ecology</topic><topic>Education</topic><topic>Engineering</topic><topic>Environmental engineering</topic><topic>Environmental science</topic><topic>Gene sequencing</topic><topic>Genomes</topic><topic>Heterocyclic compounds</topic><topic>Hydrocarbons</topic><topic>Indigo</topic><topic>Indole</topic><topic>Indoles</topic><topic>Laboratories</topic><topic>Microbial activity</topic><topic>Microbiomes</topic><topic>Microorganisms</topic><topic>Naphthalene</topic><topic>Phenols</topic><topic>Pollutants</topic><topic>Populations</topic><topic>Proteobacteria - metabolism</topic><topic>RNA</topic><topic>rRNA 16S</topic><topic>Sewage</topic><topic>Sludge</topic><topic>Wastewater</topic><topic>Water treatment</topic><topic>Yield</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhang, Xuwang</creatorcontrib><creatorcontrib>Qu, Yuanyuan</creatorcontrib><creatorcontrib>Ma, Qiao</creatorcontrib><creatorcontrib>Zhang, Zhaojing</creatorcontrib><creatorcontrib>Li, Duanxing</creatorcontrib><creatorcontrib>Wang, Jingwei</creatorcontrib><creatorcontrib>Shen, Wenli</creatorcontrib><creatorcontrib>Shen, E</creatorcontrib><creatorcontrib>Zhou, Jiti</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Xuwang</au><au>Qu, Yuanyuan</au><au>Ma, Qiao</au><au>Zhang, Zhaojing</au><au>Li, Duanxing</au><au>Wang, Jingwei</au><au>Shen, Wenli</au><au>Shen, E</au><au>Zhou, Jiti</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2015-04-30</date><risdate>2015</risdate><volume>10</volume><issue>4</issue><spage>e0125732</spage><epage>e0125732</epage><pages>e0125732-e0125732</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1), phenol plus indole (G2) and indole only (G3), were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA) and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P<0.05). Nevertheless, the bacteria assigned to phylum Proteobacteria, family Comamonadaceae, and genera Diaphorobacter, Comamonas and Aquamicrobium were commonly shared dominant populations. Pearson correlations were calculated to discern the relationship between microbial communities and indigo yields. The typical indigo-producing populations Comamonas and Pseudomonas showed no positive correlations with indigo yields, while there emerged many other genera that exhibited positive relationships, such as Aquamicrobium, Truepera and Pusillimonas, which had not been reported for indigo production previously. The present study should provide new insights into indigo bio-production by microbial communities from indole.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25928424</pmid><doi>10.1371/journal.pone.0125732</doi><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
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| issn | 1932-6203 1932-6203 |
| language | eng |
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| subjects | Activated sludge Analysis Aromatic compounds Aromatics Biodegradation Biosynthesis Coking Comamonadaceae - metabolism Comamonas - metabolism Community structure Correlation Ecology Education Engineering Environmental engineering Environmental science Gene sequencing Genomes Heterocyclic compounds Hydrocarbons Indigo Indole Indoles Laboratories Microbial activity Microbiomes Microorganisms Naphthalene Phenols Pollutants Populations Proteobacteria - metabolism RNA rRNA 16S Sewage Sludge Wastewater Water treatment Yield |
| title | Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-13T14%3A28%3A15IST&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=Illumina%20MiSeq%20Sequencing%20Reveals%20Diverse%20Microbial%20Communities%20of%20Activated%20Sludge%20Systems%20Stimulated%20by%20Different%20Aromatics%20for%20Indigo%20Biosynthesis%20from%20Indole&rft.jtitle=PloS%20one&rft.au=Zhang,%20Xuwang&rft.date=2015-04-30&rft.volume=10&rft.issue=4&rft.spage=e0125732&rft.epage=e0125732&rft.pages=e0125732-e0125732&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0125732&rft_dat=%3Cgale_plos_%3EA419035984%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=1677376554&rft_id=info:pmid/25928424&rft_galeid=A419035984&rft_doaj_id=oai_doaj_org_article_69dbd201cea14bc3b1eedb84c469aaf2&rfr_iscdi=true |