Archaea in Yellowstone Lake

Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089-0740, USA.
The ISME Journal (Impact Factor: 9.3). 05/2011; 5(11):1784-95. DOI: 10.1038/ismej.2011.56
Source: PubMed


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 (~51,000 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 full-length 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, ~69-84% 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 >5% 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.

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Available from: Jinjun Kan, Oct 03, 2015
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    • "The DNA and cDNA samples were amplified with the primer sets 27F/534R (Wu et al., 2010) and A2Fa/A571R (Kan et al., 2011) to target the bacterial 16S rRNA gene (V1–V3 region) and archaeal 16S rRNA gene (V1–V2 region), respectively. The reported PCR thermocycling conditions and mastermix protocols (Kan et al., 2011; Wu et al., 2010) were used and each sample was amplified for 30 cycles. Barcodes allowing sample multiplexing during sequencing were incorporated between the adapter and forward primer (Hamady et al., 2008). "
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    ABSTRACT: This study analyzed the composition of a methane-generating microbial community and the corresponding active members during the transformation of three target substrates (food waste, cellulose or xylan) by barcoded 454 pyrosequencing of the bacterial and archaeal 16S rRNA genes in the DNA and RNA. The number of operational taxonomic units at 97% similarity for bacteria and archaea ranged from 162-261 and 31-166, respectively. Principal coordinates analysis and Venn diagram revealed that there were significant differences in the microbial community structure between the active members transforming each substrate and the inoculum. The active bacterial populations detected were those required for the hydrolysis of the amended substrate. The active archaeal populations were methanogens but the ratio of Methanosarcinales and Methanomicrobiales varied between the cultures. Overall, results of this study showed that a subset of the populations became active and altered in relative abundance during methane production according to the amended substrate.
    Bioresource Technology 09/2013; 148C:517-524. DOI:10.1016/j.biortech.2013.09.017 · 4.49 Impact Factor
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    • "Lake location and brief description of each site and of within-site samples are described below, and the relative and approximate lake locations are shown in Figure 1. Vent fluids and streamer samples were collected using a boat-tethered ROV previously described (Lovalvo et al., 2010; Clingenpeel et al., 2011; Kan et al., 2011). Characterization for aqueous solutes and gases were as recently described (Clingenpeel et al., 2011). "
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    Frontiers in Microbiology 09/2013; 4:274. DOI:10.3389/fmicb.2013.00274 · 3.99 Impact Factor
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    • "For rRNA gene-based taxonomic characterization of the three synthetic communities, multiple, variable-length fragments of the SSU rRNA genes spanning most hypervariable regions were amplified and sequenced using the 454 platform. The selection of primers was based on their use in prior Sanger and 454 sequencing studies and included five pairs for Bacteria, three pairs for Archaea and a pair that we developed to simultaneously capture both domains (Frank et al., 2008; Engelbrektson et al., 2010; Porat et al., 2010; Wu et al., 2010; Bates et al., 2011; Haas et al., 2011; Kan et al., 2011). Because some were limited in taxonomic coverage, we introduced modifications or supplemental variants employed in primer mixtures, to expand their breadth (Fig. S6 and Table S3). "
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