Nearly Identical 16S rRNA Sequences Recovered from Lakes in North America and Europe Indicate the Existence of Clades of Globally Distributed Freshwater Bacteria

Abstract

We compared bacterial 16S ribosomal RNA gene sequences recovered from Lake Loosdrecht, the Netherlands, to reported sequences from lakes in Alaska and New York State. In each of the three lake systems, which differ in pH and trophic state, some sequence types were found without related sequences (sequence identity < 90%) in the data sets from the other two systems. Two sequences in the Actinomycetes and Verrucomicrobia radiations were more closely related to sequences from the New York lakes data set than to any other sequence in the global databases. However, the most striking similarities were found in the subdivisions alpha and beta of the Proteobacteria. In these subdivisions three different clusters of highly related bacteria were identified (97-100% sequence identity) that were represented in all three lake regions. The clusters contained no members other than freshwater bacteria. One cluster falls within a monophyletic aquatic supergroup that apparently diverged early in evolution into an exclusive freshwater cluster and an exclusive marine cluster, the so-called SAR11 cluster. The detection of these three bacterial clades in lakes distinguished by geographic distance as well as physical and chemical diversity suggests that these organisms are dispersed globally and that they possess unique functional capabilities enabling successful competition in a wide range of freshwater environments.

Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems

“…However, there are amino-acid differences between the PRs in this clade. This echoes similar findings of Zwart et al (1998), describing 16S rRNA clades consisting of highly related proteobacteria isolated from different continents. The similarity of PRs isolated from lakes in different parts of the world suggests that these genes are dispersed globally and that they may encode unique functional capabilities enabling successful competition in a wide range of freshwater environments.…”

“…We, therefore, assigned clades 6 and 7 as SAR11-related clades (Figure 1). Non-marine SAR11s (alphaproteobacterial cluster LD12) were first reported in an arctic lake (Bahr et al, 1996) and are readily detected in other freshwater systems (Zwart et al, 1998(Zwart et al, , 2003Crump et al, 1999). PRs from clades 6 and 7 could be from bacteria related to alphaproteobacterial cluster LD12.…”

Developing SSU rDNA metagenomic profiles of aquatic microbial communities for environmental assessments

“…This idea has been supported by studies of aquatic systems (e.g. [Zwart et al, 1998], [Glöckner et al, 2000] and [Zwart et al, 2002]), although there is also evidence that at least some extremophiles have much more restricted distributions ( [Papke et al, 2003] and [Whitaker et al, 2003]). Our ability to detect three OTUs across lakes using Q-PCR, even at low abundance, is consistent with the idea of widespread species distribution.…”

“…Similar approaches have revealed a considerable number of unidentified prokaryotes and eukaryotes in freshwater sources (e.g. [Bahr et al, 1996], [Zwart et al, 1998], [Glöckner et al, 2000] and [Crump et al, 2003]), confirming that most microbial species are not routinely cultured ( [Ward et al, 1990] and [Torsvik et al, 2002]). …”

“…In fact, several recent papers have discussed the possibility that microbial species are globally distributed (e.g. [Zwart et al, 1998], [Zwart et al, 2002], [Finlay, 2002], [Fenchel, 2003], [Papke et al, 2003] and [Whitaker et al, 2003]). …”