Archaea in Yellowstone Lake

Abstract

The Yellowstone geothermal complex has yielded foundational discoveries that have significantly enhanced our understanding of the Archaea. This study continues on this theme, examining Yellowstone Lake and its lake floor hydrothermal vents. Significant Archaea novelty and diversity were found associated with two near-surface photic zone environments and two vents that varied in their depth, temperature and geochemical profile. Phylogenetic diversity was assessed using 454-FLX sequencing (B51 000 pyrosequencing reads; V1 and V2 regions) and Sanger sequencing of 200 near-full-length polymerase chain reaction (PCR) clones. Automated classifiers (Ribosomal Database Project (RDP) and Greengenes) were problematic for the 454-FLX reads (wrong domain or phylum), although BLAST analysis of the 454-FLX reads against the phylogenetically placed fulllength Sanger sequenced PCR clones proved reliable. Most of the archaeal diversity was associated with vents, and as expected there were differences between the vents and the near-surface photic zone samples. Thaumarchaeota dominated all samples: vent-associated organisms corresponded to the largely uncharacterized Marine Group I, and in surface waters, B69-84% of the 454-FLX reads matched archaeal clones representing organisms that are Nitrosopumilus maritimus-like (96-97% identity). Importance of the lake nitrogen cycling was also suggested by 45% of the alkaline vent phylotypes being closely related to the nitrifier Candidatus Nitrosocaldus yellowstonii. The Euryarchaeota were primarily related to the uncharacterized environmental clones that make up the Deep Sea Euryarchaeal Group or Deep Sea Hydrothermal Vent Group-6. The phylogenetic parallels of Yellowstone Lake archaea to marine microorganisms provide opportunities to examine interesting evolutionary tracks between freshwater and marine lineages.

Pyrosequencing of mcrA and Archaeal 16S rRNA Genes Reveals Diversity and Substrate Preferences of Methanogen Communities in Anaerobic Digesters

“…gDNA was amplified with primers specific to the mcrA gene (8) and the archaeal 16S rRNA gene (25) according to the PCR protocols indicated in these references. To enable sample multiplexing during sequencing, barcodes were incorporated between the adapter and forward primer.…”

Hot Spring Microbial Community Composition, Morphology, and Carbon Fixation: Implications for Interpreting the Ancient Rock Record

“…Woesearchaeota (formerly in the Euryarchaeota DHVEG-6 cluster) (Castelle et al, 2015) OTUs were most abundant in samples from Sites 1 and 2, accounting for 50-75% of the total sequences recovered from these samples ( Figure 3B). Sequences affiliated with Woesearchaeota have been recovered from diverse environments ranging from surface waters of oligotrophic high-altitude lakes (Ortiz-Alvarez and Casamayor, 2016), stratified microbial mats (Saghaï et al, 2017), sediments, plankton and hydrothermal vents (Robertson et al, 2009;Pachiadaki et al, 2011), and hot springs (Kan et al, 2011). A single Woesearchaeota OTU accounted for 45-50% of the sequences recovered from the green and orange mats from Site 1.…”

Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India

“…elevated Na, Ca and SiO 2 (Siangbood and Ramanujam 2011; Rakshak et al 2013). Compared to many studies on hot springs at lower elevations such as Yellowstone National Park (Kan et al 2011), Kamchatka in Russia (Reigstad et al 2010), Iceland (Mirete et al 2011) Indonesia (Aditiawati et al 2009), Tunisia (Sayeh et al 2010) and north-eastern Australia (Weidler et al 2007), very little is known about the microbial diversity of high elevation Himalayan hot springs. Hot springs present in high elevation HGB are less explored in terms of biotic components (Ghosh et al 2003).…”