{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T06:19:25Z","timestamp":1790317165247,"version":"4.1.0"},"reference-count":37,"publisher":"American Society for Microbiology","issue":"9","license":[{"start":{"date-parts":[[2008,5,1]],"date-time":"2008-05-01T00:00:00Z","timestamp":1209600000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2008,5]]},"abstract":"ABSTRACT<\/jats:title>\n \n Quantitative PCR (qPCR) was coupled with reverse transcription (RT) to analyze both gene copy numbers and transcripts of the 16S rRNA gene and three reductive dehalogenase (RDase) genes (\n tceA<\/jats:italic>\n ,\n vcrA<\/jats:italic>\n , and\n bvcA<\/jats:italic>\n ) as biomarkers of \u201c\n Dehalococcoides<\/jats:italic>\n \u201d spp. in the groundwater of a trichloroethene-dense nonaqueous-phase liquid site at Fort Lewis, WA, that was sequentially subjected to biostimulation and bioaugmentation.\n Dehalococcoides<\/jats:italic>\n cells carrying the\n tceA<\/jats:italic>\n ,\n vcrA<\/jats:italic>\n , and\n bvcA<\/jats:italic>\n genes were indigenous to the site. The sum of the three identified RDase gene copy numbers closely correlated to 16S rRNA gene copy numbers throughout the biostimulation and bioaugmentation activity, suggesting that these RDase genes represented the major\n Dehalococcoides<\/jats:italic>\n metabolic functions at this site. Biomarker quantification revealed an overall increase of more than 3 orders of magnitude in the total\n Dehalococcoides<\/jats:italic>\n population through the 1-year monitoring period (spanning biostimulation and bioaugmentation), and measurement of the respective RDase gene concentrations indicated different growth dynamics among\n Dehalococcoides<\/jats:italic>\n cells. The\n Dehalococcoides<\/jats:italic>\n cells containing the\n tceA<\/jats:italic>\n gene consistently lagged behind other\n Dehalococcoides<\/jats:italic>\n cells in population numbers and made up less than 5% of the total\n Dehalococcoides<\/jats:italic>\n population, whereas the\n vcrA<\/jats:italic>\n - and\n bvcA<\/jats:italic>\n -containing cells represented the dominant fractions. Quantification of transcripts in groundwater samples verified that the 16S rRNA gene and the\n bvcA<\/jats:italic>\n and\n vcrA<\/jats:italic>\n genes were consistently highly expressed in all samples examined, while the\n tceA<\/jats:italic>\n transcripts were detected inconsistently, suggesting a less active physiological state of the cells with this gene. The production of vinyl chloride and ethene toward the end of treatment supported the physiological activity of the\n bvcA<\/jats:italic>\n - and\n vcrA<\/jats:italic>\n -carrying cells. A clone library of the expressed RDase genes in field samples produced with degenerate primers revealed the expression of two putative RDase genes that were not previously monitored with RT-qPCR. The level of abundance of one of the putative RDase genes (\n FtL-RDase-1638<\/jats:italic>\n ) identified in the cDNA clone library tracked closely in field samples with abundance of the\n bvcA<\/jats:italic>\n gene, suggesting that the\n FtL-RDase-1638<\/jats:italic>\n gene was likely colocated in genomes containing the\n bvcA<\/jats:italic>\n gene. Overall, results from this study demonstrate that quantification of biomarker dynamics at field sites can provide useful information about the in situ physiology of\n Dehalococcoides<\/jats:italic>\n strains and their associated activity.\n <\/jats:p>","DOI":"10.1128\/aem.02199-07","type":"journal-article","created":{"date-parts":[[2008,3,8]],"date-time":"2008-03-08T02:09:58Z","timestamp":1204942198000},"page":"2728-2739","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":142,"title":["Quantifying Genes and Transcripts To Assess the In Situ Physiology of \u201c\n Dehalococcoides<\/i>\n \u201d spp. in a Trichloroethene-Contaminated Groundwater Site"],"prefix":"10.1128","volume":"74","author":[{"given":"Patrick K. H.","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tamzen W.","family":"Macbeth","sequence":"additional","affiliation":[{"name":"North Wind Inc., 1425 Higham St., Idaho Falls, Idaho 83402"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Jr.","given":"Kent S.","family":"Sorenson","sequence":"additional","affiliation":[{"name":"CDM, 1331 17th Street, Suite 1200, Denver, Colorado 80202"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rula A.","family":"Deeb","sequence":"additional","affiliation":[{"name":"Malcolm Pirnie, Inc., 2000 Powell Street, Suite 1180, Emeryville, California 94608"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa","family":"Alvarez-Cohen","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710"},{"name":"Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 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