{"id":11920,"date":"2017-10-31T16:47:52","date_gmt":"2017-10-31T23:47:52","guid":{"rendered":"https:\/\/www.darkenergybiosphere.org\/?post_type=publication&#038;p=11920"},"modified":"2017-11-10T14:15:14","modified_gmt":"2017-11-10T22:15:14","slug":"estimating-population-turnover-rates-from-relative-quantification-methods-reveals-microbial-dynamics-in-marine-sediment","status":"publish","type":"publication","link":"https:\/\/www.darkenergybiosphere.org\/publication\/estimating-population-turnover-rates-from-relative-quantification-methods-reveals-microbial-dynamics-in-marine-sediment\/","title":{"rendered":"Estimating population turnover rates from relative quantification methods reveals microbial dynamics in marine sediment"},"content":{"rendered":"<p>Difficulty quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina USA, anoxically at 21\u00b0C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentration consistent with predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, for fraction of read abundance times cells), to estimate population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply-branching uncultured groups and \u223c 98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured\u00a0<em>Methanomicrobiales<\/em>\u00a0and\u00a0<em>Methanosarcinales<\/em>\u00a0increased at the onset of methanogenesis with population turnover times estimated from quantitative PCR (qPCR) at 9.7 \u00b1 3.9 and 12.6 \u00b1 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 \u00b1 5.8 and 9.2 \u00b1 3.5 days, respectively. Uncultured\u00a0<em>Syntrophaceae<\/em>, which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis with FRAxC turnover times of 14.7 \u00b1 6.9 and 10.6 \u00b1 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate reducing bacteria,\u00a0<em>Desulfovibrio<\/em>\u00a0sp.,\u00a0<em>Desulfobacter<\/em>\u00a0sp., and\u00a0<em>Desulfobacterium<\/em>\u00a0sp. increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions only stimulates growth in a few clades directly involved in methanogenesis, rather than the whole microbial community.<\/p>\n","protected":false},"template":"","tags":[],"publication_type":[19],"_links":{"self":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/publication\/11920"}],"collection":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/publication"}],"about":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/types\/publication"}],"wp:attachment":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/media?parent=11920"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/tags?post=11920"},{"taxonomy":"publication_type","embeddable":true,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/publication_type?post=11920"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}