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The program allows a rapid identification of the most polymorphic enzymes, creates a collection of T-RFs for the data set, and can potentially identify specific T-RFs in T-RF length polymorphism (T-RFLP) patterns by comparing theoretical and experimental results. TRiFLE was used for analyzing T-RFLP data generated for the amoA and pmoA genes. The peaks identified in the T-RFLP patterns show an overlap of ammonia- and methane-oxidizing bacteria in the metalimnion of a subtropical lake.", "publicationTitle": "Applied and Environmental Microbiology", "publisher": "", "place": "", "date": "2008-10", "volume": "74", "issue": "20", "section": "", "partNumber": "", "partTitle": "", "pages": "6452-6456", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Appl Environ Microbiol", "DOI": "10.1128/AEM.01394-08", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570284/", "accessDate": "2015-04-23T17:53:29Z", "PMID": "", "PMCID": "", "ISSN": "0099-2240", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 18757578\nPMCID: PMC2570284", "tags": [], "collections": [ "77IHXJE3" ], "relations": {}, "dateAdded": "2015-04-23T17:53:29Z", "dateModified": "2015-04-23T17:53:29Z" } }, { "key": "BE4K2AFF", "version": 70, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/BE4K2AFF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/BE4K2AFF", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/335962/items/XJTW6V8G", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } } }, "data": { "key": "BE4K2AFF", "version": 70, "parentItem": "XJTW6V8G", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2015-04-23T17:53:29Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570284/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2015-04-23T17:53:29Z", "dateModified": "2015-04-23T17:53:29Z" } }, { "key": "G8QPCJ4Z", "version": 69, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/G8QPCJ4Z", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/G8QPCJ4Z", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/335962/items/4CPSXVQU", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "G8QPCJ4Z", "version": 69, "parentItem": "4CPSXVQU", "itemType": "attachment", "linkMode": "imported_url", "title": "PubMed Central Full Text PDF", "accessDate": "2015-04-23T14:58:44Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965158/pdf/1471-2180-10-262.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Fernàndez-Guerra et al. - 2010 - T-RFPred a nucleotide sequence size prediction to.pdf", "md5": "d45e05a678b68c12db56ff55b26c919d", "mtime": 1429801140259, "tags": [], "relations": {}, "dateAdded": "2015-04-23T14:58:44Z", "dateModified": "2015-04-23T14:59:00Z" } }, { "key": "4CPSXVQU", "version": 69, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/4CPSXVQU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/4CPSXVQU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } }, "creatorSummary": "Fernàndez-Guerra et al.", "parsedDate": "2010-10-15", "numChildren": 2 }, "data": { "key": "4CPSXVQU", "version": 69, "itemType": "journalArticle", "title": "T-RFPred: a nucleotide sequence size prediction tool for microbial community description based on terminal-restriction fragment length polymorphism chromatograms", "creators": [ { "creatorType": "author", "firstName": "Antonio", "lastName": "Fernàndez-Guerra" }, { "creatorType": "author", "firstName": "Alison", "lastName": "Buchan" }, { "creatorType": "author", "firstName": "Xiaozhen", "lastName": "Mou" }, { "creatorType": "author", "firstName": "Emilio O", "lastName": "Casamayor" }, { "creatorType": "author", "firstName": "José M", "lastName": "González" } ], "abstractNote": "Background\nTerminal-Restriction Fragment Length Polymorphism (T-RFLP) is a technique used to analyze complex microbial communities. It allows for the quantification of unique or numerically dominant phylotypes in amplicon pools and it has been used primarily for comparisons between different communities. T-RFPred, Terminal-Restriction Fragment Prediction, was developed to identify and assign taxonomic information to chromatogram peaks of a T-RFLP fingerprint for a more comprehensive description of microbial communities. The program estimates the expected fragment size of representative 16S rRNA gene sequences (either from a complementary clone library or from public databases) for a given primer and restriction enzyme(s) and provides candidate taxonomic assignments.\n\nResults\nTo show the accuracy of the program, T-RFLP profiles of a marine bacterial community were described using artificial bacterioplankton clone libraries of sequences obtained from public databases. For all valid chromatogram peaks, a phylogenetic group could be assigned.\n\nConclusions\nT-RFPred offers enhanced functionality of T-RFLP profile analysis over current available programs. In particular, it circumvents the need for full-length 16S rRNA gene sequences during taxonomic assignments of T-RF peaks. Thus, large 16S rRNA gene datasets from environmental studies, including metagenomes, or public databases can be used as the reference set. Furthermore, T-RFPred is useful in experimental design for the selection of primers as well as the type and number of restriction enzymes that will yield informative chromatograms from natural microbial communities.", "publicationTitle": "BMC Microbiology", "publisher": "", "place": "", "date": "2010-10-15", "volume": "10", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "262", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "BMC Microbiol", "DOI": "10.1186/1471-2180-10-262", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965158/", "accessDate": "2015-04-23T14:58:44Z", "PMID": "", "PMCID": "", "ISSN": "1471-2180", "archive": "", "archiveLocation": "", "shortTitle": "T-RFPred", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 20950425\nPMCID: PMC2965158", "tags": [], "collections": [ "77IHXJE3" ], "relations": {}, "dateAdded": "2015-04-23T14:58:44Z", 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share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/NHECZ2CF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/NHECZ2CF", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/335962/items/BWRPDFBR", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "NHECZ2CF", "version": 63, "parentItem": "BWRPDFBR", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text PDF", "accessDate": "2015-04-09T21:19:56Z", "url": "http://jxb.oxfordjournals.org/content/60/6/1729.full.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Micallef et al. - 2009 - Influence of Arabidopsis thaliana accessions on rh.pdf", "md5": "e951265710f14fa649d07e5959804077", "mtime": 1428614399786, "tags": [], "relations": {}, "dateAdded": "2015-04-09T21:19:56Z", "dateModified": "2015-04-09T21:19:59Z" } }, { "key": "BWRPDFBR", "version": 67, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/BWRPDFBR", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/BWRPDFBR", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } }, "creatorSummary": "Micallef et al.", "parsedDate": "2009-04-01", "numChildren": 4 }, "data": { "key": "BWRPDFBR", "version": 67, "itemType": "journalArticle", "title": "Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates", "creators": [ { "creatorType": "author", "firstName": "Shirley A.", "lastName": "Micallef" }, { "creatorType": "author", "firstName": "Michael P.", "lastName": "Shiaris" }, { "creatorType": "author", "firstName": "Adán", "lastName": "Colón-Carmona" } ], "abstractNote": "Plant species is considered to be one of the most important factors in shaping rhizobacterial communities, but specific plant–microbe interactions in the rhizosphere are still not fully understood. Arabidopsis thaliana, for which a large number of naturally occurring ecotype accessions exist, lacks mycorrhizal associations and is hence an ideal model for rhizobacterial studies. Eight Arabidopsis accessions were found to exert a marked selective influence on bacteria associated with their roots, as determined by terminal-restriction fragment length polymorphism (T-RFLP) and ribosomal intergenic spacer analysis (RISA). Community differences in species composition and relative abundance were both significant (P <0.001). The eight distinct and reproducible accession-dependent community profiles also differed from control bulk soil. Root exudates of these variants were analysed by high performance liquid chromatography (HPLC) to try to establish whether the unique rhizobacterial assemblages among accessions could be attributed to plant-regulated chemical changes in the rhizosphere. Natural variation in root exudation patterns was clearly exhibited, suggesting that differences in exudation patterns among accessions could be influencing bacterial assemblages. Other factors such as root system architecture are also probably involved. Finally, to investigate the Arabidopsis rhizosphere further, the phylogenetic diversity of rhizobacteria from accession Cvi-0 is described.", "publicationTitle": "Journal of Experimental Botany", "publisher": "", "place": "", "date": "2009-04-01", "volume": "60", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "1729-1742", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Exp. 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"href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } } }, "data": { "key": "RMNRV7NQ", "version": 59, "parentItem": "G32KF6Q8", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2015-04-02T17:37:01Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/19561189", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2015-04-02T17:37:01Z", "dateModified": "2015-04-02T17:37:01Z" } }, { "key": "G32KF6Q8", "version": 59, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/G32KF6Q8", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/G32KF6Q8", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } }, "creatorSummary": "Feinstein et al.", "parsedDate": "2009-08", "numChildren": 2 }, "data": { "key": "G32KF6Q8", "version": 59, "itemType": "journalArticle", "title": "Assessment of bias associated with incomplete extraction of microbial DNA from soil", "creators": [ { "creatorType": "author", "firstName": "Larry M.", "lastName": "Feinstein" }, { "creatorType": "author", "firstName": "Woo Jun", "lastName": "Sul" }, { "creatorType": "author", "firstName": "Christopher B.", "lastName": "Blackwood" } ], "abstractNote": "DNA extraction bias is a frequently cited but poorly understood limitation of molecular characterizations of environmental microbial communities. To assess the bias of a commonly used soil DNA extraction kit, we varied the cell lysis protocol and conducted multiple extractions on subsamples of clay, sand, and organic soils. DNA, as well as bacterial and fungal ribosomal gene copies as measured by quantitative PCR, continued to be isolated in successive extractions. When terminal restriction fragment length polymorphism was used, a significant shift in community composition due to extraction bias was detected for bacteria but not for fungi. Pyrosequencing indicated that the relative abundances of sequences from rarely cultivated groups such as Acidobacteria, Gemmatimonades, and Verrucomicrobia were higher in the first extraction than in the sixth but that the reverse was true for Proteobacteria and Actinobacteria. This suggests that the well-known phylum-level bacterial cultivation bias may be partially exaggerated by DNA extraction bias. We conclude that bias can be adequately reduced in many situations by pooling three successive extractions, and additional measures should be considered when divergent soil types are compared or when comprehensive community analysis is necessary.", "publicationTitle": "Applied and Environmental Microbiology", "publisher": "", "place": "", "date": "Aug 2009", "volume": "75", "issue": "16", "section": "", "partNumber": "", "partTitle": "", "pages": "5428-5433", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Appl. Environ. Microbiol.", "DOI": "10.1128/AEM.00120-09", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1098-5336", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 19561189\nPMCID: PMC2725469", "tags": [ { "tag": "Bacteria", "type": 1 }, { "tag": "Bias (Epidemiology)", "type": 1 }, { "tag": "DNA, Bacterial", "type": 1 }, { "tag": "DNA, Fungal", "type": 1 }, { "tag": "Ecosystem", "type": 1 }, { "tag": "Electrophoresis, Gel, Pulsed-Field", "type": 1 }, { "tag": "Fungi", "type": 1 }, { "tag": "Genes, rRNA", "type": 1 }, { "tag": "Molecular Sequence Data", "type": 1 }, { "tag": "Polymerase Chain Reaction", "type": 1 }, { "tag": "Polymorphism, Restriction Fragment Length", "type": 1 }, { "tag": "Sequence Analysis, DNA", "type": 1 }, { "tag": "Soil", "type": 1 }, { "tag": "Soil Microbiology", "type": 1 } ], "collections": [ "77IHXJE3" ], "relations": {}, "dateAdded": "2015-04-02T17:37:01Z", "dateModified": "2015-04-02T17:37:01Z" } }, { "key": "TU32SNZ6", "version": 58, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/TU32SNZ6", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/TU32SNZ6", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/335962/items/2BUQVPNM", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "TU32SNZ6", "version": 58, "parentItem": "2BUQVPNM", "itemType": "attachment", "linkMode": "imported_file", "title": "TRFLP_Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "TRFLP_Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.pdf", "md5": "7fb571f1d95523070f35bf8cf0fa3eb1", "mtime": 1427934693015, "tags": [], "relations": {}, "dateAdded": "2015-04-02T00:39:43Z", "dateModified": "2015-04-02T00:39:43Z" } }, { "key": "PPJAWUK2", "version": 56, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/PPJAWUK2", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/PPJAWUK2", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/335962/items/2BUQVPNM", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "PPJAWUK2", "version": 56, "parentItem": "2BUQVPNM", "itemType": "attachment", "linkMode": "imported_url", "title": "PubMed Central Full Text PDF", "accessDate": "2015-04-02T00:39:19Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168770/pdf/634516.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Liu et al. - 1997 - Characterization of microbial diversity by determi.pdf", "md5": "8823af3ddb72861f8fdb811142b9a63b", "mtime": 1427935175511, "tags": [], "relations": {}, "dateAdded": "2015-04-02T00:39:19Z", "dateModified": "2015-04-02T00:39:35Z" } }, { "key": "2BUQVPNM", "version": 67, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/2BUQVPNM", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/2BUQVPNM", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } }, "creatorSummary": "Liu et al.", "parsedDate": "1997-11", "numChildren": 3 }, "data": { "key": "2BUQVPNM", "version": 67, "itemType": "journalArticle", "title": "Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.", "creators": [ { "creatorType": "author", "firstName": "W T", "lastName": "Liu" }, { "creatorType": "author", "firstName": "T L", "lastName": "Marsh" }, { "creatorType": "author", "firstName": "H", "lastName": "Cheng" }, { "creatorType": "author", "firstName": "L J", "lastName": "Forney" } ], "abstractNote": "A quantitative molecular technique was developed for rapid analysis of microbial community diversity in various environments. The technique employed PCR in which one of the two primers used was fluorescently labeled at the 5' end and was used to amplify a selected region of bacterial genes encoding 16S rRNA from total community DNA. The PCR product was digested with restriction enzymes, and the fluorescently labeled terminal restriction fragment was precisely measured by using an automated DNA sequencer. Computer-simulated analysis of terminal restriction fragment length polymorphisms (T-RFLP) for 1,002 eubacterial sequences showed that with proper selection of PCR primers and restriction enzymes, 686 sequences could be PCR amplified and classified into 233 unique terminal restriction fragment lengths or \"ribotypes.\" Using T-RFLP, we were able to distinguish all bacterial strains in a model bacterial community, and the pattern was consistent with the predicted outcome. Analysis of complex bacterial communities with T-RFLP revealed high species diversity in activated sludge, bioreactor sludge, aquifer sand, and termite guts; as many as 72 unique ribotypes were found in these communities, with 36 ribotypes observed in the termite guts. The community T-RFLP patterns were numerically analyzed and hierarchically clustered. The pattern derived from termite guts was found to be distinctly different from the patterns derived from the other three communities. Overall, our results demonstrated that T-RFLP is a powerful tool for assessing the diversity of complex bacterial communities and for rapidly comparing the community structure and diversity of different ecosystems.", "publicationTitle": "Applied and Environmental Microbiology", "publisher": "", "place": "", "date": "1997-11", "volume": "63", "issue": "11", "section": "", "partNumber": "", "partTitle": "", "pages": "4516-4522", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Appl Environ Microbiol", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168770/", "accessDate": "2015-04-02T00:39:19Z", "PMID": "", "PMCID": "", "ISSN": "0099-2240", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 9361437\nPMCID: PMC168770", "tags": [], "collections": [ "2JKWXWBG", "77IHXJE3" ], "relations": {}, "dateAdded": "2015-04-02T00:39:19Z", "dateModified": "2015-04-02T00:39:19Z" } }, { "key": "QPNVUFVW", "version": 55, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/QPNVUFVW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/QPNVUFVW", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/335962/items/2BUQVPNM", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } } }, "data": { "key": "QPNVUFVW", "version": 55, "parentItem": "2BUQVPNM", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2015-04-02T00:39:19Z", "url": 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"version": 52, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/62R7KBN4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/62R7KBN4", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/335962/items/FU6DZFIB", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "62R7KBN4", "version": 52, "parentItem": "FU6DZFIB", "itemType": "attachment", "linkMode": "imported_url", "title": "ScienceDirect Full Text PDF", "accessDate": "2015-04-01T17:01:19Z", "url": "http://www.sciencedirect.com/science/article/pii/S016770129700105X/pdfft?md5=7a30f1cd016d300c19a4334c6d6feda1&pid=1-s2.0-S016770129700105X-main.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Clement et al. - 1998 - Terminal restriction fragment patterns (TRFPs), a .pdf", "md5": "b40d17e024ea545d5d4b40a15ead2832", "mtime": 1427907680453, "tags": [], "relations": {}, "dateAdded": "2015-04-01T17:01:19Z", "dateModified": "2015-04-01T17:01:21Z" } }, { "key": "FU6DZFIB", "version": 67, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/FU6DZFIB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/FU6DZFIB", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } }, "creatorSummary": "Clement et al.", "parsedDate": "1998-01", "numChildren": 3 }, "data": { "key": "FU6DZFIB", "version": 67, "itemType": "journalArticle", "title": "Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities", "creators": [ { "creatorType": "author", "firstName": "Brian G", "lastName": "Clement" }, { "creatorType": "author", "firstName": "Lucia E", "lastName": "Kehl" }, { "creatorType": "author", "firstName": "Kristin L", "lastName": "DeBord" }, { "creatorType": "author", "firstName": "Christopher L", "lastName": "Kitts" } ], "abstractNote": "Microbial populations in complex environmental samples are difficult to characterize; current techniques are incomplete and time consuming. We investigated a polymerase chain reaction (PCR)-based method for rapidly comparing bacterial communities independent of culture or cloning. Community 16S rRNA genes were amplified and fluorescently labeled by PCR. The labeled products were digested by a restriction enzyme and the labeled, terminal restriction fragments (TRFs) were separated by electrophoresis and detected by laser-induced fluorescence on an automated gene sequencer. PCR parameters were optimized using an in vitro model community of known organisms. Community comparisons were made between deer fecal pellets, petroleum hydrocarbon-contaminated sands and pristine sand. Principal components analysis (PCA) was used to compare the resulting TRF patterns (TRFPs). Patterns derived from a single enzyme digest did not result in accurate community characterizations. Accurate characterizations reflecting the expected bacterial community biology were only achieved by combining TRFP data derived from different enzyme digestions. Suggestions are offered for future use of this technique.", "publicationTitle": "Journal of Microbiological Methods", "publisher": "", "place": "", "date": "January 1998", "volume": "31", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "135-142", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Journal of Microbiological Methods", "DOI": "10.1016/S0167-7012(97)00105-X", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S016770129700105X", "accessDate": "2015-04-01T17:01:19Z", "PMID": "", "PMCID": "", "ISSN": "0167-7012", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "16S rRNA", "type": 1 }, { "tag": "PCR", "type": 1 }, { "tag": "Principal components analysis", "type": 1 }, { "tag": "Restriction analysis", "type": 1 }, { "tag": "TRFP", "type": 1 }, { "tag": "bacterial communities", "type": 1 } ], "collections": [ "2JKWXWBG", "77IHXJE3" ], "relations": {}, "dateAdded": "2015-04-01T17:01:19Z", "dateModified": "2015-04-01T17:01:19Z" } }, { "key": "UXPTRHT7", "version": 50, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/UXPTRHT7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/UXPTRHT7", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/335962/items/X4W2TX4B", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "UXPTRHT7", "version": 50, "parentItem": "X4W2TX4B", "itemType": "attachment", "linkMode": "imported_file", "title": "Rhizosphere_bacterial communities in rhizosphere of vitis under distinct agricultural practices.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Rhizosphere_bacterial communities in rhizosphere of vitis under distinct agricultural practices.pdf", "md5": "15ab17c625ce707aac27b37f4ee1322c", "mtime": 1427859754823, "tags": [], "relations": {}, "dateAdded": "2015-04-01T03:51:12Z", "dateModified": "2015-04-01T03:51:12Z" } }, { "key": "X4W2TX4B", "version": 49, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/X4W2TX4B", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/X4W2TX4B", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } }, "creatorSummary": "Vega-Avila et al.", "parsedDate": "2015-02", "numChildren": 2 }, "data": { "key": "X4W2TX4B", "version": 49, "itemType": "journalArticle", "title": "Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina", "creators": [ { "creatorType": "author", "firstName": "A. D.", "lastName": "Vega-Avila" }, { "creatorType": "author", "firstName": "T.", "lastName": "Gumiere" }, { "creatorType": "author", "firstName": "P. a. M.", "lastName": "Andrade" }, { "creatorType": "author", "firstName": "J. E.", "lastName": "Lima-Perim" }, { "creatorType": "author", "firstName": "A.", "lastName": "Durrer" }, { "creatorType": "author", "firstName": "M.", "lastName": "Baigori" }, { "creatorType": "author", "firstName": "F.", "lastName": "Vazquez" }, { "creatorType": "author", "firstName": "F. D.", "lastName": "Andreote" } ], "abstractNote": "Plants interact with a myriad of microbial cells in the rhizosphere, an environment that is considered to be important for plant development. However, the differential structuring of rhizosphere microbial communities due to plant cultivation under differential agricultural practices remains to be described for most plant species. Here we describe the rhizosphere microbiome of grapevine cultivated under conventional and organic practices, using a combination of cultivation-independent approaches. The quantification of bacterial 16S rRNA and nifH genes, by quantitative PCR (qPCR), revealed similar amounts of these genes in the rhizosphere in both vineyards. PCR-DGGE was used to detect differences in the structure of bacterial communities, including both the complete whole communities and specific fractions, such as Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and those harboring the nitrogen-fixing related gene nifH. When analyzed by a multivariate approach (redundancy analysis), the shifts observed in the bacterial communities were poorly explained by variations in the physical and chemical characteristics of the rhizosphere. These approaches were complemented by high-throughput sequencing (67,830 sequences) based on the V6 region of the 16S rRNA gene, identifying the major bacterial groups present in the rhizosphere of grapevines: Proteobacteria, Actinobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Cloroflexi, Verrucomicrobia and Planctomycetes, which occur in distinct proportions in the rhizosphere from each vineyard. The differences might be related to the selection of plant metabolism upon distinct reservoirs of microbial cells found in each vineyard. The results fill a gap in the knowledge of the rhizosphere of grapevines and also show distinctions in these bacterial communities due to agricultural practices.", "publicationTitle": "Antonie Van Leeuwenhoek", "publisher": "", "place": "", "date": "Feb 2015", "volume": "107", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "575-588", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Antonie Van Leeuwenhoek", "DOI": "10.1007/s10482-014-0353-7", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1572-9699", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 25527391", "tags": [], "collections": [ "77IHXJE3" ], "relations": {}, "dateAdded": "2015-04-01T03:50:59Z", "dateModified": "2015-04-01T03:50:59Z" } }, { "key": "FN37HXQI", "version": 49, "library": { "type": "group", "id": 335962, "name": "Papers to share", "links": { "alternate": { "href": "https://www.zotero.org/groups/papers_to_share", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/335962/items/FN37HXQI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/papers_to_share/items/FN37HXQI", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/335962/items/X4W2TX4B", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2370577, "username": "divyaravichandar", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/divyaravichandar", "type": "text/html" } } } }, "data": { "key": "FN37HXQI", "version": 49, "parentItem": "X4W2TX4B", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2015-04-01T03:50:59Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/25527391", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2015-04-01T03:50:59Z", "dateModified": "2015-04-01T03:50:59Z" } } ]