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.

Download full-text


Available from: Jinjun Kan,
  • Source
    • "The transcribed bacterial V1 – V3 and archaeal V1 – V2 16S rRNA regions were amplified from template cDNA and gDNA ( bacterial only ) with the 27F / 534R ( Wu et al . , 2010 ) and A2Fa / A571R ( Kan et al . , 2011 ) primer pairs respectively , with PCR ingredients and conditions per the cited studies for 30 amplification cycles in triplicate reactions . To enable multiplexed 454 pyrosequencing , barcode sequences were incorporated between the adaptors and forward primers ( Hamady et al . , 2008 ) . Amplicons were pooled and purified with the Agen"
    [Show abstract] [Hide abstract]
    ABSTRACT: Anaerobic digestion (AD) is a widespread microbial technology used to treat organic waste and recover energy in the form of methane ("biogas"). While most AD systems have been designed to treat a single input, mixtures of digester sludge and solid organic waste are emerging as a means to improve efficiency and methane yield. We examined laboratory anaerobic cultures of AD sludge from two sources amended with food waste, xylose, and xylan at mesophilic temperatures, and with cellulose at meso- and thermophilic temperatures, to determine whether and how the inoculum and substrate affect biogas yield and community composition. All substrate and inoculum combinations yielded methane, with food waste most productive by mass. Pyrosequencing of transcribed bacterial and archaeal 16S rRNA showed that community composition varied across substrates and inocula, with differing ratios of hydrogenotrophic/acetoclastic methanogenic archaea associated with syntrophic partners. While communities did not cluster by either inoculum or substrate, additional sequencing of the bacterial 16S rRNA gene in the source sludge revealed that the bacterial communities were influenced by their inoculum. These results suggest that complete and efficient AD systems could potentially be assembled from different microbial inocula and consist of taxonomically diverse communities that nevertheless perform similar functions.
    Frontiers in Microbiology 10/2015; 6(1114):1-11. DOI:10.3389/fmicb.2015.01114 · 3.99 Impact Factor
  • Source
    • "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). "
    [Show abstract] [Hide abstract]
    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
  • Source
    • "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). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Considerable Nanoarchaeota novelty and diversity were encountered in Yellowstone Lake, Yellowstone National Park (YNP), where sampling targeted lake floor hydrothermal vent fluids, streamers and sediments associated with these vents, and in planktonic photic zones in three different regions of the lake. Significant homonucleotide repeats (HR) were observed in pyrosequence reads and in near full-length Sanger sequences, averaging 112 HR per 1349 bp clone and could confound diversity estimates derived from pyrosequencing, resulting in false nucleotide insertions or deletions (indels). However, Sanger sequencing of two different sets of PCR clones (110 bp, 1349 bp) demonstrated that at least some of these indels are real. The majority of the Nanoarchaeota PCR amplicons were vent associated; however, curiously, one relatively small Nanoarchaeota OTU (71 pyrosequencing reads) was only found in photic zone water samples obtained from a region of the lake furthest removed from the hydrothermal regions of the lake. Extensive pyrosequencing failed to demonstrate the presence of an Ignicoccus lineage in this lake, suggesting the Nanoarchaeota in this environment are associated with novel Archaea hosts. Defined phylogroups based on near full-length PCR clones document the significant Nanoarchaeota 16S rRNA gene diversity in this lake and firmly establish a terrestrial clade distinct from the marine Nanoarcheota as well as from other geographical locations.
    Frontiers in Microbiology 09/2013; 4:274. DOI:10.3389/fmicb.2013.00274 · 3.99 Impact Factor
Show more