Diversity of Methane-Cycling Archaea in Hydrothermal Sediment Investigated by General and Group-Specific PCR Primers

Abstract

bThe 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 groupspecific mcrA and 16S rRNA gene primer pairs. The mcrIRD primer pair outperformed the other general mcrA primer pairs in detection sensitivity and phylogenetic coverage. Methanotrophic ANME-1 Archaea were the only group detected with groupspecific primers only. 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 (ϳ2 to 40°C, sulfate measurable to 4 cm) to only two groups below 6 cm (>40°C). Despite the presence of hyperthermophilic genera (Methanopyrus, Methanocaldococcus) in cooler surface strata, no genes were detected below 10 cm (>60°C). While mcrAbased and 16S rRNA gene-based community compositions 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.H ydrothermal surface sediments in Guaymas Basin support exceptionally high microbial activity and microbial diversity (1-4). The highly productive overlying water column, combined with terrestrial runoff, leads to sedimentation rates exceeding 1 mm yr Ϫ1 (5) and organic carbon contents of 2 to 4% by weight (6). In addition, the upward flow of hydrothermal fluids supplies hydrocarbons (methane, petroleum) and volatile fatty acids produced by thermal degradation of buried organic matter in deeper sediment layers to surface sediments and their microbial communities (1, 7-9).Methanogenesis and sulfate-dependent methane oxidation in Guaymas Basin are carried out by diverse microbial lineages. 16S rRNA gene-based surveys have detected known methane-cycling groups (Methanococcoides, Methanocorpusculum, Methanoculleus, Methermicoccus, ANME-1, ANME-2) (4, 10Ϫ12), a new lineage of ANME-1, ANME-1Guaymas (12), and unknown deeply branching euryarchaeotal groups within the phylogenetic vicinity of known methane-cycling Archaea (4, 10). Phylogenetic analyses of mcrA, a gene diagnostic of methanogenic and anaerobic methanotrophic Archaea (13,14), indicate an even higher diversity of methane-cycling Archaea than those detected by 16S rRNA gene surveys (Methanoco...

Comparative Study of Guaymas Basin Microbiomes: Cold Seeps vs. Hydrothermal Vents Sediments

“…Therefore, the Guaymas Basin represents a unique opportunity to directly compare hydrothermal vent and cold seep ecosystems. Previous investigations on the sedimentary microbial community compositions of the Guaymas Basin, from either but not both of these ecosystems, suggested that analogous microbial processes might occur, despite contrasted temperatures (Teske et al, 2002;Dhillon et al, 2003;McKay et al, 2012;Vigneron et al, 2013;Cruaud et al, 2015;Lever and Teske, 2015). However, these results remain hardly comparable since different methodologies were used.…”

Diverse anaerobic methane‐ and multi‐carbon alkane‐metabolizing archaea coexist and show activity in Guaymas Basin hydrothermal sediment

“…GB is the first hydrothermal vent habitat where the MAO process was detected (Teske et al, 2002). Diverse methane-oxidizing archaea belonging to ANME-1 and ANME-2 have been frequently detected by 16S rRNA and mcrA gene surveys at GB (Holler et al, 2011;Biddle et al, 2012;Vigneron et al, 2013;Lever and Teske, 2015;Dowell et al, 2016;McKay et al, 2016). Although, the archaeal multi-carbon alkane oxidizer Ca.…”

High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high‐altitude lakes

“…However, our current knowledge on the whole archaeal biology and ecology potentials is yet strongly biased by the difficulties in culturing, the still limited use of powerful metagenomic approaches (Rinke et al ., ; Castelle et al ., ) and the very few properly compiling studies homogeneously focused on a key functional archaeal gene of major ecological interest (e.g. the amoA gene, Pester et al ., , Fernàndez‐Guerra and Casamayor, ; or the mcrA gene Lever and Teske ). Large environmental surveys may also add clues on the ecology and biology of the uncultured archaea and unveil ecological patterns and environmental preferences.…”