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Mark Lever

Methane-cycling Archaeal Diversity in Hydrothermal Sediment Investigated by General and Group-Specific PCR Primers

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The zonation of anaerobic methane-cycling Archaea in hydrothermal sediment of Guaymas Basin was studied by general primer pairs (mcrI, ME1/ME2, mcrIRD), targeting the alpha subunit of methyl coenzyme M reductase gene (mcrA), and by new group-specific mcrA and 16S rRNA gene primer pairs. The mcrIRD outperformed the other general mcrA primer pairs in detection sensitivity and phylogenetic coverage. Methanotrophic ANME-1 Archaea were the only group only detected with group-specific primers. The detection of 14 mcrA lineages surpasses the diversity previously found in this location. Most phylotypes have high sequence similarities to hydrogenotrophs, methylotrophs and anaerobic methanotrophs previously detected at Guaymas Basin or at hydrothermal vents, cold seeps, and oil reservoirs worldwide. Additionally, five mcrA phylotypes belonging to newly defined lineages are detected. Two of these belong to deeply-branching new orders, while the others are new species or genera of Methanopyraceae and Methermicoccaceae. Downcore diversity decreases, from all groups detected in the upper 6 cm (∼2-40°C, sulfate measurable to 4 cm), to only two groups below 6 cm (>40°C). Despite the presence of hyperthermophilic genera (Methanopyrus, -caldococcus) in cooler surface strata, no genes were detected below 10 cm (≥60°C). While mcrA and 16S rRNA gene-based community composition are generally congruent, the deeply-branching mcrA cannot be assigned to specific 16S rRNA gene lineages. Our study indicates that even among well-studied metabolic groups, and in previously characterized model environments, major evolutionary branches are overlooked. Detecting these groups by improved molecular biological methods is a crucial first step toward understanding their roles in nature.
Original languageEnglish
JournalApplied and Environmental Microbiology
Volume81
Issue4
Pages (from-to)1426-1441
Number of pages16
ISSN0099-2240
DOIs
Publication statusPublished - 2015

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