Use of 16S rRNA Gene Based Clone Libraries to Assess Microbial Communities Potentially Involved in Anaerobic Methane Oxidation in a Mediterranean Cold Seep

Abstract

This study provides data on the diversities of bacterial and archaeal communities in an active methane seep at the Kazan mud volcano in the deep Eastern Mediterranean sea. Layers of varying depths in the Kazan sediments were investigated in terms of (1) chemical parameters and (2) DNA-based microbial population structures. The latter was accomplished by analyzing the sequences of directly amplified 16S rRNA genes, resulting in the phylogenetic analysis of the prokaryotic communities. Sequences of organisms potentially associated with processes such as anaerobic methane oxidation and sulfate reduction were thus identified. Overall, the sediment layers revealed the presence of sequences of quite diverse bacterial and archaeal communities, which varied considerably with depth. Dominant types revealed in these communities are known as key organisms involved in the following processes: (1) anaerobic methane oxidation and sulfate reduction, (2) sulfide oxidation, and (3) a range of (aerobic) heterotrophic processes. In the communities in the lowest sediment layer sampled (22-34 cm), sulfatereducing bacteria and archaea of the ANME-2 cluster (likely involved in anaerobic methane oxidation) were prevalent, whereas heterotrophic organisms abounded in the top sediment layer (0-6 cm). Communities in the middle layer (6-22 cm) contained organisms that could be linked to either of the aforementioned processes. We discuss how these phylogeny (sequence)-based findings can support the ongoing molecular work aimed at unraveling both the functioning and the functional diversities of the communities under study.

Diverse and Novel nifH and nifH -Like Gene Sequences in the Deep-Sea Methane Seep Sediments of the Okhotsk Sea

“…3). The diversity of archaeal 16S rRNA gene sequences from the Okhotsk Sea is comparable to or higher than those of some of other deep-sea methane seeps or like environments (13,14,17).…”

Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments

“…MCG are present in terrestrial hot springs , deep oceanic subsurface sediments (Parkes et al, 2005), deep terrestrial subsurface (Inagaki et al, 2003), continental shelf sediments (Vetriani et al, 1998), ancient marine sapropels (Coolen et al, 2002), petroleum-contaminated soil (Kasai et al, 2005), termite guts (Friedrich et al, 2001), mud volcanoes (Heijs et al, 2007), methane hydrate-containing marine sediments (Inagaki et al, 2006), landfill leachate (Huang et al, 2003), anaerobic wastewater reactors (Collins et al, 2005), sulfidic springs (Elshahed et al, 2003), brackish lakes (Hershberger et al, 1996) and coastal salt marshes (Castro et al, 2004). Only 28 out of 4720 MCG sequences were retrieved from potentially oxic habitats (for example, database releases EU370096 and FJ560325).…”

Anaerobic degradation of propane and butane by sulfate-reducing bacteria enriched from marine hydrocarbon cold seeps

“…Prop12-GMe clone 235 and But12-HyR clone 303 shared 95.5% sequence identity and were closely related to strain BuS5 (93.1% and 94.5%,respectively) and to the dominant phylotype in the enrichment culture But12-GMe (94.3% and 95.3%, respectively;Kniemeyer et al, 2007) (Figure 4). Other close relatives include phylotypes retrieved from marine mud volcanoes (Heijs et al, 2007;Lö sekann et al, 2007), hydrocarbon seep-associated sediments (Orphan et al, 2001;Lloyd et al, 2006;Kleindienst et al, 2012) or marine sediments associated with gas hydrates Orcutt et al, 2010) (Figure 4). The high abundance of a distinct phylotype in each enrichment culture suggests that the corresponding microorganisms were most likely responsible for the degradation of propane or butane.…”