Functional Metagenomic Investigations of Microbial Communities in a Shallow-Sea Hydrothermal System

Abstract

Little is known about the functional capability of microbial communities in shallow-sea hydrothermal systems (water depth of <200 m). This study analyzed two high-throughput pyrosequencing metagenomic datasets from the vent and the surface water in the shallow-sea hydrothermal system offshore NE Taiwan. This system exhibited distinct geochemical parameters. Metagenomic data revealed that the vent and the surface water were predominated by Epsilonproteobacteria (Nautiliales-like organisms) and Gammaproteobacteria ( Thiomicrospira -like organisms), respectively. A significant difference in microbial carbon fixation and sulfur metabolism was found between the vent and the surface water. The chemoautotrophic microorganisms in the vent and in the surface water might possess the reverse tricarboxylic acid cycle and the Calvin−Bassham−Benson cycle for carbon fixation in response to carbon dioxide highly enriched in the environment, which is possibly fueled by geochemical energy with sulfur and hydrogen. Comparative analyses of metagenomes showed that the shallow-sea metagenomes contained some genes similar to those present in other extreme environments. This study may serve as a basis for deeply understanding the genetic network and functional capability of the microbial members of shallow-sea hydrothermal systems.

A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics

“…, and Sivaceros spp , and among early Antilopinae or stem Antilopinae, Caprotragoides potwaricus , Tethytragus spp., Gentrytragus spp. , and early forms assigned to ‘ Gazella ’ [25,83,85-88]. This pool of taxa indicates that the divergence of Bovinae and Antilopinae probably took place during the middle Miocene.…”

The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment

“…Sediment and X. testudinaria from the Kepulauan Seribu and Spermonde reefs, in turn, had the highest relative abundances of nitrate reductase beta subunit (K00371) a possible indication that sediment and sponge archaeal communities use nitrate as a nitrogen source or electron acceptor (Tang et al . ), suggesting relatively high rates of reduction of nitrate to nitrite (the first step of denitrification) in these biotopes (Liu et al . ).…”

“…Sediment and X. testudinaria from the Kepulauan Seribu and Spermonde reefs, in turn, had the highest relative abundances of nitrate reductase beta subunit (K00371) a possible indication that sediment and sponge archaeal communities use nitrate as a nitrogen source or electron acceptor (Tang et al 2013), suggesting relatively high rates of reduction of nitrate to nitrite (the first step of denitrification) in these biotopes . To the best of our knowledge, this enzyme has not been previously associated with Cenarchaealesrelated sequences that were responsible for almost all of the nitrate reductase beta subunit (K00371) counts in this study.…”

The 16S rRNA gene in the study of marine microbial communities

“…These communities are representative of extreme environments and do not show a high diversity. The members of the main taxonic groups, however, show greater variability in the 16S sequences, a reflection of the great evolutionary pressure exerted by the environment (Biddle et al 2006, Havelsrud et al 2011, Roussel et al 2011, Tang et al 2013, Shao et al 2014, Kato et al 2015.…”

“…Nonetheless, rRNA sequences have sufficient variability to differentiate not only the most distant ambiente extremo y no muestran gran diversidad. Sin embargo, como un reflejo de la gran presión evolutiva ejercida por el medio, los miembros de los principales grupos taxonómicos presentan mayor variación en sus secuencias del 16S (Biddle et al 2006, Havelsrud et al 2011, Roussel et al 2011, Tang et al 2013, Shao et al 2014, Kato et al 2015.…”