Article

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

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 (~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

Full-text

Available from: Jinjun Kan
  • Source
    • "The primary advantage of this approach is that it provides high throughput data which can, in turn, be analyzed and produce evidence in order to test ecological hypotheses. Since the onset of pyrosequencing, it has been widely used as the state-of-the-art approach in the field of microbial ecology, on samples from the deep sea (e.g.Sogin et al., 2006), soil (e.g.Roesch et al., 2007), deep mines (e.g.Edwards et al., 2006), extreme environments (e.g.Kan et al., 2011), open sea (e.g.Andersson et al., 2010), estuaries (e.g.Campbell and Kirchman, 2012), lakes (e.g.Monchy et al., 2011) and other habitats. Despite the fact the coastal lagoons are highly productive ecosystems, only a few studies have investigated the microbial diversity of this habitat type using pyrosequencing (e.g.Ghai et al., 2012;Thompson et al., 2011). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Lagoons are naturally enriched habitats, with unstable environmental conditions caused by their confinement, shallow depth and state of saprobity. The frequent fluctuations of the abiotic variables cause severe changes in the abundance and distribution of biota. This relationship has been studied extensively for the macrofaunal communities, but not sufficiently so for the bacterial ones. The aim of the present study was to explore the biodiversity patterns of bacterial assemblages and to examine whether these patterns are associated with biogeographic and environmental factors. For this purpose, sediment samples were collected fromfive lagoons located in the Amvrakikos Gulf (Ionian Sea, Western Greece). DNA was extracted from the sediment and was further processed through 16S rRNA pyrosequencing. The results of this exploratory study imply that salinity is the environmental factor best correlated with the bacterial community pattern, which has also been suggested in similar studies but for macrofaunal community patterns. In addition, the bacterial community of the brackish lagoons is differentiated from that of the brackish-marine lagoons. The findings of this study indicate that the studied lagoons have distinct bacterial communities.
    Full-text · Article · Jan 2016 · Marine Genomics
    • "Pacearchaeota and Woesearchaeota had been frequently reported in the literature since the 90s (Dojka et al., 1998;Großkopf et al., 1998) but barely discussed. Most sequences available in SILVA database are widely distributed in saline aquatic environments both marine or inland waters, mainly in microbial mats, sediments, plankton and hydrothermal vents (Robertson et al., 2009;Pachiadaki et al., 2011), followed by hot springs and freshwater (Kan et al., 2011), and very few in soils (specially Woesearchaeota). Thus, apparently, we could rule out that these populations found in surface waters may have been originated from soil contamination. "
    [Show abstract] [Hide abstract]
    ABSTRACT: We carried out a regional survey on the archaea composition from surface waters of > 300 high altitude Pyrenean lakes (average altitude 2300 m, pH range 4.4-10.1) by 16S rRNA gene tag-sequencing. Relative Archaea abundances ranged between 0 and 6.3% of total prokaryotes amplicons in the PCR mixture, and we detected 769 OTUs (grouped at 97% identity) that split into 13 different lineages, with altitude and pH having a significant effect on the community composition. Woesearchaeota and Pacearchaeota (formerly Euryarchaeota DHVEG-6 cluster) dominated the dataset (83% of total OTUS), showed a high occurrence (presence in c. 75% of the lakes), and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota-Diapherotrites (formerly Euryarchaeota MEG cluster), Methanomicrobia, Thermoplasmata, and AOA showed relative abundances between 1-3% and occurrences between 14-26%. Minor lineages were SM1K20, Aenigmarchaeota (formerly Euryarchaeota DSEG cluster), Methanobacteria, MCG, and SCG. Environmental preferences substantially differed among lineages, with Aenigmarchaeota and Methanomicrobia having the largest habitat breadth, and Thermoplasmata, AOA and Micrarchaeota the lowest. Pacearchaeota and Woesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.
    No preview · Article · Dec 2015 · Environmental Microbiology Reports
  • 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.
    Full-text · Article · Oct 2015 · Frontiers in Microbiology
Show more