Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep.
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), sulfate-reducing 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.
Heijs
Sander K
SK
Department of Microbiology, Laboratory of Microbial Ecology, Center for Ecological and Evolutionary Studies, University of Groningen, P.O. Box 14, 9750 AA Haren, The Netherlands. sander@house-of-media.nl
Haese
Ralf R
RR
van der Wielen
Paul W J J
PW
Forney
Larry J
LJ
van Elsas
Jan Dirk
JD
D001105:Archaea / Q000145:classification* / Q000235:genetics; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D001483:Base Sequence; D044822:Biodiversity; D017931:DNA Primers / Q000737:chemistry; D019641:DNA, Archaeal / Q000737:chemistry / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification; D004275:DNA, Ribosomal / Q000737:chemistry; D017753:Ecosystem; D004783:Environmental Microbiology; D015723:Gene Library; D019015:Geologic Sediments / Q000737:chemistry / Q000382:microbiology*; D008055:Lipids / Q000032:analysis; D008522:Mediterranean Sea; D008697:Methane / Q000378:metabolism; D019640:Methanosarcinales / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*
D017931:DNA Primers; D019641:DNA, Archaeal; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D008055:Lipids; D012336:RNA, Ribosomal, 16S; D008697:Methane