{"id":7804,"date":"2016-06-14T23:58:26","date_gmt":"2016-06-14T23:58:26","guid":{"rendered":"https:\/\/www.darkenergybiosphere.org\/?post_type=publication&#038;p=7792"},"modified":"2016-10-14T19:06:51","modified_gmt":"2016-10-14T19:06:51","slug":"comparative-single-cell-genomics-of-chloroflexi-from-the-okinawa-trough-deep-subsurface-biosphere","status":"publish","type":"publication","link":"https:\/\/www.darkenergybiosphere.org\/publication\/comparative-single-cell-genomics-of-chloroflexi-from-the-okinawa-trough-deep-subsurface-biosphere\/","title":{"rendered":"Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep-Subsurface Biosphere"},"content":{"rendered":"<p><em>Chloroflexi<\/em> small-subunit (SSU) rRNA gene sequences are frequently recovered from subseafloor environments, but the metabolic potential of the phylum is poorly understood. The phylum <em>Chloroflexi<\/em> is represented by isolates with diverse metabolic strategies, including anoxic phototrophy, fermentation, and reductive dehalogenation; therefore, function cannot be attributed to these organisms based solely on phylogeny. Single-cell genomics can provide metabolic insights into uncultured organisms, like the deep-subsurface <em>Chloroflexi<\/em>. Nine SSU rRNA gene sequences were identified from single-cell sorts of whole-round core material collected from the Okinawa Trough at Iheya North hydrothermal field as part of Integrated Ocean Drilling Program (IODP) expedition 331 (Deep Hot Biosphere). Previous studies of subsurface <em>Chloroflexi<\/em> single amplified genomes (SAGs) suggested heterotrophic or lithotrophic metabolisms and provided no evidence for growth by reductive dehalogenation. Our nine <em>Chloroflexi<\/em> SAGs (seven of which are from the order <em>Anaerolineales<\/em>) indicate that, in addition to genes for the Wood-Ljungdahl pathway, exogenous carbon sources can be actively transported into cells. At least one subunit for pyruvate ferredoxin oxidoreductase was found in four of the <em>Chloroflexi<\/em> SAGs. This protein can provide a link between the Wood-Ljungdahl pathway and other carbon anabolic pathways. Finally, one of the seven <em>Anaerolineales<\/em> SAGs contains a distinct reductive dehalogenase homologous (<em>rdhA<\/em>) gene.<\/p>\n<p><strong>IMPORTANCE<\/strong> Through the use of single amplified genomes (SAGs), we have extended the metabolic potential of an understudied group of subsurface microbes, the <em>Chloroflexi<\/em>. These microbes are frequently detected in the subsurface biosphere, though their metabolic capabilities have remained elusive. In contrast to previously examined <em>Chloroflexi<\/em> SAGs, our genomes (several are from the order <em>Anaerolineales<\/em>) were recovered from a hydrothermally driven system and therefore provide a unique window into the metabolic potential of this type of habitat. In addition, a reductive dehalogenase gene (<em>rdhA<\/em>) has been directly linked to marine subsurface <em>Chloroflexi<\/em>, suggesting that reductive dehalogenation is not limited to the class <em>Dehalococcoidia<\/em>. This discovery expands the nutrient-cycling and metabolic potential present within the deep subsurface and provides functional gene information relating to this enigmatic group.<\/p>\n","protected":false},"template":"","tags":[],"publication_type":[19],"_links":{"self":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/publication\/7804"}],"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=7804"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/tags?post=7804"},{"taxonomy":"publication_type","embeddable":true,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/publication_type?post=7804"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}