Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring

Abstract

A culture-independent molecular phylogenetic survey was carried out for the bacterial community in Obsidian Pool (OP), a Yellowstone National Park hot spring previously shown to contain remarkable archaeal diversity (S. M. Barns, R. E. Fundyga, M. W. Jeffries, and N. R. Page, Proc. Natl. Acad. Sci. USA 91:1609–1613, 1994). Small-subunit rRNA genes (rDNA) were amplified directly from OP sediment DNA by PCR with universally conserved orBacteria-specific rDNA primers and cloned. Unique rDNA types among >300 clones were identified by restriction fragment length polymorphism, and 122 representative rDNA sequences were determined. These were found to represent 54 distinct bacterial sequence types or clusters (≥98% identity) of sequences. A majority (70%) of the sequence types were affiliated with 14 previously recognized bacterial divisions (main phyla; kingdoms); 30% were unaffiliated with recognized bacterial divisions. The unaffiliated sequence types (represented by 38 sequences) nominally comprise 12 novel, division level lineages termed candidate divisions. Several OP sequences were nearly identical to those of cultivated chemolithotrophic thermophiles, including the hydrogen-oxidizing Calderobacterium and the sulfate reducers Thermodesulfovibrio andThermodesulfobacterium, or belonged to monophyletic assemblages recognized for a particular type of metabolism, such as the hydrogen-oxidizing Aquificales and the sulfate-reducing δ-Proteobacteria. The occurrence of such organisms is consistent with the chemical composition of OP (high in reduced iron and sulfur) and suggests a lithotrophic base for primary productivity in this hot spring, through hydrogen oxidation and sulfate reduction. Unexpectedly, no archaeal sequences were encountered in OP clone libraries made with universal primers. Hybridization analysis of amplified OP DNA with domain-specific probes confirmed that the analyzed community rDNA from OP sediment was predominantly bacterial. These results expand substantially our knowledge of the extent of bacterial diversity and call into question the commonly held notion that Archaea dominate hydrothermal environments. Finally, the currently known extent of division level bacterial phylogenetic diversity is collated and summarized.

Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester

“…Members of this phylum include phototrophic and chemotrophic genera (Holt and Lewin, 1968;Oyaizu et al, 1987). Cultivation-independent 16S rRNA studies suggest that many species of the Chloroflexi thrive in certain natural habitats such as freshwater lakes and anaerobic dechlorinating enrichments (Von Wintzingerode et al, 1997;Chandler et al, 1998;Hugenholtz et al, 1998;Gich et al, 2001). Our finding is corroborated by other studies like those of Bjornsson and colleagues (2002).…”

The Wood–Ljungdahl pathway as a key component of metabolic versatility in candidate phylum Bipolaricaulota (Acetothermia, OP1)

“…Candidatus Bipolaricaulota (phylum Acetothermia) have originally been encountered in a seminal 16S rRNA gene survey of the Obsidian Pool (OP) in Yellowstone National Park, Wyoming, USA and given the alphanumeric designation OP1 (Hugenholtz et al, 1998). Subsequently, OP1-affiliated sequences have been identified in a wide range of environments ( Fig.…”

“…Candidate phylum Bipolaricaulota (Hao et al, 2018), previously referred to as candidate division OP1 (Hugenholtz et al, 1998) and Candidatus Acetothermia (Takami et al, 2012), represents one of the yetuncultured bacterial phyla, where the occurrence of WL pathway has previously been reported (Takami et al, 2012;Hao et al, 2018). However, as the WL pathway could be involved in a wide range of anabolic and catabolic processes; its mere identification in the genomes of uncultured microbial lineages does not provide adequate information regarding its exact role in the organisms' overall metabolic capacities.…”

Molecular phylogenetic analyses of reverse‐transcribed bacterial rRNA obtained from deep‐sea cold seep sediments

“…The 42 clones recovered from the library of the 2-4 cm layer belonged to five lineages: the a-Proteobacteria (four clones; 9.5%), g-Proteobacteria (one clone; 2.4%), d-Proteobacteria (19 clones; 45.2%), e-Proteobacteria (17 clones; 40.5%) and Gram-positive bacteria (one clone; 2.4%). In the 8-10 cm layer, cloned 48 crDNA sequences fell into five lineages: g-Proteobacteria (seven clones; 14.6%), d-Proteobacteria (18 clones; 37.5%), e-Proteobacteria (18 clones; 37.5%), Gram-positive bacteria (two clones; 4.2%) and candidate division OP8 (one clone; 2.1%) (Hugenholz et al, 1998). In the 14-16 cm layer, 47 crDNA sequences belonged to five lineages: b-Proteobacteria (five clones; 10.6%), g- Proteobacteria (two clones; 4.3%), d-Proteobacteria (12 clones; 25.5%), e-Proteobacteria (23 clones; 48.9%), and Gram-positive bacteria (three clones; 6.4%).…”