Unusual bacterioplankton community structure in ultra‐oligotrophic Crater Lake

Abstract

The bacterioplankton assemblage in Crater Lake, Oregon (U.S.A.), is different from communities found in other oxygenated lakes, as demonstrated by four small subunit ribosomal ribonucleic acid (SSU rRNA) gene clone libraries and oligonucleotide probe hybridization to RNA from lake water. Populations in the euphotic zone of this deep (589 m), oligotrophic caldera lake are dominated by two phylogenetic clusters of currently uncultivated bacteria: CL120-10, a newly identified cluster in the verrucomicrobiales, and ACK4 actinomycetes, known as a minor constituent of bacterioplankton in other lakes. Deep-water populations at 300 and 500 m are dominated by a different pair of uncultivated taxa: CL500-11, a novel cluster in the green nonsulfur bacteria, and group I marine crenarchaeota. ␤-Proteobacteria, dominant in most other freshwater environments, are relatively rare in Crater Lake (Յ16% of nonchloroplast bacterial rRNA at all depths). Other taxa identified in Crater Lake libraries include a newly identified candidate bacterial division, ABY1, and a newly identified subcluster, CL0-1, within candidate division OP10. Probe analyses confirmed vertical stratification of several microbial groups, similar to patterns observed in open-ocean systems. Additional similarities between Crater Lake and ocean microbial populations include aphotic zone dominance of group I marine crenarchaeota and green nonsulfur bacteria. Comparison of Crater Lake to other lakes studied by rRNA methods suggests that selective factors structuring Crater Lake bacterioplankton populations may include low concentrations of available trace metals and dissolved organic matter, chemistry of infiltrating hydrothermal waters, and irradiation by high levels of ultraviolet light.

Low Intraspecific Diversity in a Polynucleobacter Subcluster Population Numerically Dominating Bacterioplankton of a Freshwater Pond

“…The coexistence of different bacterial genotypes belonging to the same species-like phylogenetic group is well documented for marine (1,18,19,35,45) and freshwater habitats (8,9,10,11,27,30,43). Recently, Acinas et al (1) demonstrated by the construction and analysis of 16S rRNA clone libraries that a coastal bacterioplankton community contained a very high diversity of ribotypes, the vast majority of which fell into phylogenetically microdiverse sequence clusters (Ͻ1% divergent 16S rRNA sequences).…”

Physical constraints in the deep hypolimnion of a subalpine lake driving planktonicBacteriaandArchaeadistribution

“…The comparison cannot be extended to hypolimnion as no information is provided on the hypolimetic bacterioplankton of Lake Constance. A decrease of prokaryotic cell abundance was found in other deep lakes such as Lake Baikal [36], Crater Lake [14], Lake Tanganyika [34]. Nevertheless, as far as we know, long-term (decades) data on prokaryote abundance along the water column of deep lakes have not yet been published.…”

“…Among other factors affecting microbial diversity, depth gradient resulted in various marine systems to be a modulator of relative abundance of Bacteria and Archaea [11][12][13]. So far, few data have been published on distinguishing between Bacteria and Archaea in the hypolimnion of deep lakes with the exception of the high altitude ultraoligotrophic Crater Lake, USA [14,15] and the subalpine Lake Maggiore, Italy [16]. In Crater Lake the Group I marine Crenarchaeota accounted for 16-27% of deep-water populations, showing a similarity between ocean microbial populations and those living in an ultraoligotrophic deep lake [14].…”

“…So far, few data have been published on distinguishing between Bacteria and Archaea in the hypolimnion of deep lakes with the exception of the high altitude ultraoligotrophic Crater Lake, USA [14,15] and the subalpine Lake Maggiore, Italy [16]. In Crater Lake the Group I marine Crenarchaeota accounted for 16-27% of deep-water populations, showing a similarity between ocean microbial populations and those living in an ultraoligotrophic deep lake [14]. The existence of populations of Crenarchaeota have been also demonstrated among picoplankton of great lakes from three continents (North America, Africa, Eurasia) extending their known habitat range [17].…”

Identity of epibiotic bacteria on symbiontid euglenozoans in O2-depleted marine sediments: evidence for symbiont and host co-evolution

“…For the 341F/1492R primer pair amplification was: 95 1C for 5 min followed by 35 cycles of 95 1C for 1 min, 50 1C for 1 min and 72 1C for 2.5 min, and a final cycle of 72 1C for 10 min. Archaeal amplification was tested with Arch25F (Urbach et al, 2001) paired with U1492R. Amplified DNA was checked for quality by agarose gel electrophoresis, bands were gel purified using the Qiaquick Gel Extraction Kit (Qiagen, Valencia, CA, USA), and cloned into the vector pCR4-TOPO using the TOPO TA Cloning Kit (Invitrogen, CA, USA) following the manufacturer's instructions.…”