Comparative 16S rRNA Analysis of Lake Bacterioplankton Reveals Globally Distributed Phylogenetic Clusters Including an Abundant Group of Actinobacteria

Abstract

In a search for cosmopolitan phylogenetic clusters of freshwater bacteria, we recovered a total of 190 full and partial 16S ribosomal DNA (rDNA) sequences from three different lakes (Lake Gossenköllesee, Austria; Lake Fuchskuhle, Germany; and Lake Baikal, Russia). The phylogenetic comparison with the currently available rDNA data set showed that our sequences fall into 16 clusters, which otherwise include bacterial rDNA sequences of primarily freshwater and soil, but not marine, origin. Six of the clusters were affiliated with the ␣, four were affiliated with the ␤, and one was affiliated with the ␥ subclass of the Proteobacteria; four were affiliated with the Cytophaga-Flavobacterium-Bacteroides group; and one was affiliated with the class Actinobacteria (formerly known as the high-G؉C gram-positive bacteria). The latter cluster (hgcI) is monophyletic and so far includes only sequences directly retrieved from aquatic environments. Fluorescence in situ hybridization (FISH) with probes specific for the hgcI cluster showed abundances of up to 1.7 ؋ 10 5 cells ml ؊1 in Lake Gossenköllesee, with strong seasonal fluctuations, and high abundances in the two other lakes investigated. Cell size measurements revealed that Actinobacteria in Lake Gossenköllesee can account for up to 63% of the bacterioplankton biomass. A combination of phylogenetic analysis and FISH was used to reveal 16 globally distributed sequence clusters and to confirm the broad distribution, abundance, and high biomass of members of the class Actinobacteria in freshwater ecosystems.

Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria

“…Collectively, these environmental sequence data in Figure 3 show that similar ActR genes are present among diverse freshwater habitats. Such observations verify our initial prediction based on our previous findings in Sharma et al (2008) and the knowledge that many environmental SSU rRNA studies show that members of the Actinobacteria are widespread in fresh waters (Glockner et al, 2000;Warnecke et al, 2004;Allgaier and Grossart, 2006).…”

Phenology of high-elevation pelagic bacteria: the roles of meteorologic variability, catchment inputs and thermal stratification in structuring communities

“…In combination with a companion study conducted in the same lake (Glockner et al, 2000), their work demonstrated strong and predictable seasonal changes in the relative abundances of dominant bacterial groups (Actinobacteria, b-Proteobacteria and Bacteroidetes; aka CFB) similar to those detailed here for Emerald Lake. In both studies, a maximum in the relative abundance of the b-Proteobacteria was associated with snowmelt, ice-off and spring mixing, followed by a midsummer peak in Actinobacteria, with peaks in the relative abundances of the Bacteroidetes occurring during periods of mixing, including fall overturn and ice-off (Table 3).…”

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

“…We demonstrated by FISH the presence of free-living PnecC cells in the pelagic zone of a freshwater habitat. This indicates that many or all of the environmental PnecC sequences collected from the pelagic zones of freshwater habitats (7,10,11,21,27,50) originate from free-living cells; however, it is still not known if these cells represent completely free-living strains or facultative endosymbionts of ciliates. The numerically significant contribution of free-living stages of facultative endosymbionts or facultative parasites of protists (e.g., Legionella spp.)…”

“…The monophyletic PnecC cluster is characterized by a high minimum sequence similarity of 98.5% (23) and resembles in this feature the microdiverse clusters of marine bacteria (1, 42). Sequences affiliated with PnecC were previously obtained from endosymbionts of aquatic ciliates (40,44), from many freshwater habitats investigated with culture-independent methods (11,21,27,50), and from strains isolated from several freshwater habitats (23). Reports on the detection of PnecC bacteria in soil or marine systems are lacking.…”