Fullerton Heather, Moyer Craig L
Department of Biology, Western Washington University, Bellingham, Washington, USA.
Department of Biology, Western Washington University, Bellingham, Washington, USA
Appl Environ Microbiol. 2016 May 2;82(10):3000-3008. doi: 10.1128/AEM.00624-16. Print 2016 May 15.
Chloroflexi small-subunit (SSU) rRNA gene sequences are frequently recovered from subseafloor environments, but the metabolic potential of the phylum is poorly understood. The phylum Chloroflexi 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 Chloroflexi 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 Chloroflexi single amplified genomes (SAGs) suggested heterotrophic or lithotrophic metabolisms and provided no evidence for growth by reductive dehalogenation. Our nine Chloroflexi SAGs (seven of which are from the order Anaerolineales) 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 Chloroflexi SAGs. This protein can provide a link between the Wood-Ljungdahl pathway and other carbon anabolic pathways. Finally, one of the seven Anaerolineales SAGs contains a distinct reductive dehalogenase homologous (rdhA) gene.
Through the use of single amplified genomes (SAGs), we have extended the metabolic potential of an understudied group of subsurface microbes, the Chloroflexi These microbes are frequently detected in the subsurface biosphere, though their metabolic capabilities have remained elusive. In contrast to previously examined Chloroflexi SAGs, our genomes (several are from the order Anaerolineales) 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 (rdhA) has been directly linked to marine subsurface Chloroflexi, suggesting that reductive dehalogenation is not limited to the class Dehalococcoidia This discovery expands the nutrient-cycling and metabolic potential present within the deep subsurface and provides functional gene information relating to this enigmatic group.
绿弯菌门小亚基（SSU）rRNA基因序列经常在海底以下环境中被发现，但对该门的代谢潜力了解甚少。绿弯菌门由具有多种代谢策略的分离株代表，包括厌氧光合作用、发酵和还原性脱卤作用；因此，不能仅根据系统发育将功能归因于这些生物体。单细胞基因组学可以提供对未培养生物体的代谢见解，例如从冲绳海槽伊平屋北热液场采集的全圆岩芯材料的单细胞分选物中鉴定出9个SSU rRNA基因序列，这是综合大洋钻探计划（IODP）第331航次（深部热生物圈）的一部分。先前对地下绿弯菌门单扩增基因组（SAG）的研究表明其具有异养或无机营养代谢，且没有提供还原性脱卤生长的证据。我们的9个绿弯菌门SAG（其中7个来自厌氧绳菌目）表明，除了伍德-Ljungdahl途径的基因外，外源碳源可以被主动转运到细胞中。在4个绿弯菌门SAG中发现了至少一个丙酮酸铁氧化还原酶亚基。这种蛋白质可以在伍德-Ljungdahl途径和其他碳合成途径之间建立联系。最后，7个厌氧绳菌目SAG中的一个包含一个独特的还原性脱卤酶同源（rdhA）基因。
通过使用单扩增基因组（SAG），我们扩展了对一组研究较少的地下微生物——绿弯菌门的代谢潜力的认识。这些微生物在地下生物圈中经常被检测到，但其代谢能力仍然难以捉摸。与之前研究的绿弯菌门SAG不同，我们的基因组（几个来自厌氧绳菌目）是从一个热液驱动系统中获得的，因此为了解这种类型栖息地的代谢潜力提供了一个独特的窗口。此外，一个还原性脱卤酶基因（rdhA）已直接与海洋地下绿弯菌门相关联，这表明还原性脱卤作用并不局限于脱卤球菌纲。这一发现扩展了深部地下存在的营养循环和代谢潜力，并提供了与这个神秘类群相关的功能基因信息。
