Picocyanobacterial community structure of freshwater lakes and the Baltic Sea revealed by phylogenetic analyses and clade-specific quantitative PCR

Abstract

Phylogenetic relationships among picocyanobacteria from the Syn/Pro clade sensu Sá nchez- Baracaldo et al. (2005) were determined using small subunit (ssu) rDNA sequences from novel culture isolates together with environmental samples from the Baltic Sea and seven freshwater lakes. The picocyanobacterial community comprised members of previously identified clades and of two previously undescribed clades. The number of well-supported clades suggests that freshwater picocyanobacterial communities encompass much greater diversity than is found in marine systems. To allow the quantification of community structure and temporal succession, clade-specific ssu rDNA TaqMan assays were designed and implemented. These assays were used to assess picocyanobacterial community structure in two lakes over an annual cycle in 2003/4, and in a small number of Baltic Sea samples collected in July 2003. In the lake-water samples, picocyanobacteria were found to be scarce during most of the year, with members of each clade reaching their peak abundance over a relatively short period during the summer (June to September), although representatives of the Cyanobium clade also developed an autumn peak extending towards the end of October. All four freshwater clades were present in the Baltic Sea, but their distribution was patchy over relatively short spatial scales. The use of molecular tools for describing and quantifying community structures reveals previously unexplored complexity in the phytoplankton and will facilitate the development of a more sophisticated understanding of community dynamics at the base of the food chains in lakes.

Periodic picophytoplankton predominance in a large, shallow alkaline lake (Lake Fertő, Neusiedlersee)

“…This could be the result of differences in the specificity of the two primer sets that may result in the preferential amplification of taxa (Sipos et al, 2007). We cannot rule out the possibility that the members of group C were presented among the 16S rDNA clones (one of the ungrouped sequences), but they cannot be clearly assigned to this group since no 16S rDNA sequences are available to date from group C. We should emphazise that genetic composition of picocyanobacteria could also have an annual cycle in freshwater ecosystems with the periodic dominance of certain phylotypes (Becker et al, 2007;Ivanikova et al, 2007;Sa´nchez-Baracaldo et al, 2008). Therefore it is likely that the groups reported here as major types of picocyanobacteria have only seasonal dominance in Lake Fertő in the open water.…”

“…3 and 4). Although group B and group C picocyanbacteria seemed to have limited distribution (Robertson et al, 2001;Ernst et al, 2003), increased picoplankton investigations revealed a more widespread occurrence of these groups (Crosbie et al, 2003;Ivanikova et al, 2007;Haverkamp et al, 2008;Sa´nchez-Baracaldo et al, 2008;this study). This widespread dispersal of some closely related picocyanobacterial phylotypes may confirm the high adaptive potential of these groups.…”

“…Some of them (e.g. the cpcBA-IGS clone St1c6) may unique for Lake Fertő , as new picocyanobacterial clusters were also reported from Lake Superior (Ivanikova et al, 2007) or from freshwater lakes in England (Sa´nchez-Baracaldo et al, 2008), but increased sampling may reduce the number of unique picoalgal groups.…”

Picocyanobacterial community structure and space-time dynamics in the subalpine Lake Maggiore (N. Italy)

“…The information given by ITS fragment length varies among taxa so that Pcy microdiversity can be studied with ARISA to identify different ecotypes, even if the data obtained are not quantitative (Brown et al 2005). A rapid succession of individual Pcy clades, illustrating the patchy structure of the Pcy community, was described over a quite small spatial/temporal scale for lakes in the English Lake District using quantitative PCR (Sánchez-Baracaldo et al 2008). Although we did not perform quantitative PCR, we still obtained a fairly detailed picture of OTU succession in Lake Maggiore.…”

Do acid-tolerant picocyanobacteria exist? A study of two strains isolated from humic lakes in Poland

“…Molecular analysis of 16S rRNA genes has resulted in the division of picocyanobacteria into several marine and freshwater clusters (Herdman et al, 2001). Among them, cosmopolitan and unique clusters and sequences have been identified (Crosbie et al, 2003a;Haverkamp et al, 2008;Sánchez-Baracaldo et al, 2008;Jasser et al, 2011), although the ecophysiological differences between strains belonging to various clusters often remain uncharacterized.…”