Intra‐ and inter‐lake variability of free‐living and particle‐associated Actinobacteria communities

Abstract

We have analysed the inter- and intra-lake variability of free-living and particle-associated freshwater Actinobacteria communities in four limnological different lakes of the Mecklenburg Lake District, Northeastern Germany. Denaturing gradient gel electrophoresis (DGGE) specific for Actinobacteria was used to investigate phylogenetic diversity and seasonal dynamics of actinobacterial communities in the epilimnion of all lakes (inter-lake variability) and to assess differences between Actinobacteria communities of the epi-, meta- and hypolimnion of a single lake (intra-lake variability) respectively. DGGE analyses showed significant inter- and intra-lake differences between Actinobacteria communities of all lakes and water layers as well as between free-living and particle-associated Actinobacteria. Phylogenetic inferences of 16S rRNA gene sequences suggest that particular members of particle-associated Actinobacteria were exclusively affiliated to certain actinobacterial lineages. The phylogenetic comparison of 16S rRNA gene sequences of all lakes and water layer, however, indicated the occurrence of almost similar phylogenetic lineages in all studied habitats and suggest high intracluster diversity within already known actinobacterial lineages. Non-metric multidimensional scaling (NMS) ordination analyses and Pearson's product moment correlations revealed several strong correlations between the investigated Actinobacteria communities and various limnological parameters, such as conductivity, total phosphorous, alkalinity or primary production. However, no uniform correlation patterns were found between lakes, water layers and bacterial fractions. These heterogeneous correlation patterns together with the phylogenetic similarities of Actinobacteria communities from different lakes indicate that particular Actinobacteria represent various ecotypes or exhibit a pronounced ecophysiological plasticity.

Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake

“…Actinobacteria remained a major part of the bacterial community during periods of high cyanobacterial biovolume, with clear increases in the relative abundance of the acIV taxon (Figure 4b). Studies have pointed to a number of actinobacteria as associated with particles, with several demonstrating the acI-C and acIV lineages form speciesspecific associations with cyanobacteria (Allgaier et al, 2007). Similar increases were observed for the particle-associated betI and betIV (Figure 4g), which have been noted for their attachment to prokaryotic (Bagatini et al, 2014) and eukaryotic phytoplankton (Paver et al, 2013), as well as the metabolism of the cyanobacterial toxin microcystin (Mou et al, 2013).…”

“…The Verrucomicrobia have previously been reported in cyanobacterial blooms and metagenomic analysis, suggesting that they possess numerous pathways for the assimilation of cyanobacterial extracellular polymeric substances, as well as exudates (Mou et al, 2013;Bagatini et al, 2014). The bacterial groups associated with the cyanobacteria Microcystis, Oscillatoria, Sphaerospermopsis and Cuspidothrix were overrepresented by particleassociated groups, including betI, acI-C, acIV-C (Allgaier et al, 2007;Paver et al, 2013;Bagatini et al, 2014) and the methylotrophic taxon betIV, and Methylophiliaceae .…”

“…Freshwater microbial communities exhibit high compositional and functional variability across spatial and temporal scales (Newton et al, 2011), reflecting changes in water chemistry and nutrient concentrations (Allgaier et al, 2007;Newton et al, 2007;Dennis et al, 2013), hydrodynamic stability of the water column (Salcher et al, 2011) and climatological impacts . Periods of high cyanobacterial biovolume are associated with elevated rates of denitrification (McCarthy et al, 2007) and carbon sequestration (Becker et al, 2011;Sandrini et al, 2014), applying additional perturbations to the water column that in turn contribute to already highly variable systems .…”

A Guide to the Natural History of Freshwater Lake Bacteria

“…Journal abbreviations are as follows: AEM, Applied and Environmental Microbiology; AME, Aquatic Microbial Ecology; EM, Environmental Microbiology; FEMS ME, FEMS Microbiology Ecology; FW Bio, Freshwater Biology; GeoMicro J, Geomicrobiology Journal; Mikro, Mikrobiologiia; L&O, Limnology and Oceanography; ME, Microbial Ecology; Micro, Microbiology; FEMS ML, FEMS Microbiology Letters; IJSEM, International Journal of Systematics and Evolutionary Microbiology; Polar Bio, Polar Biology; SAM, Systematic and Applied Microbiology. 1 , manuscript in press at Environmental Microbiology (141a) (includes GenBank accession numbers FJ827781 to FJ828505); 2 , GenBank accession numbers for the sequenced clones are HQ386253 to HQ386631; 3 , GenBank accession numbers for the sequenced clones are FJ916807 to FJ916903 and HQ530565 to HQ532908, except HQ530583, HQ531638, and HQ532521. (Based on data from references 2, 3,4,11,20,22,24,27,35,38,41,42,44,45,46,48,49,52,61,63,69,73,74,82,83,84,85,89,93,95,101,105,106,108,116,124,126,127,134,135,…”

Spatiotemporal pattern of bacterioplankton in Donghu Lake

“…The TN, very interestingly, showed no signifi cant infl uence on the Actinobacteria, but did infl uence the seven other bacterial groups (Table 3). However, the TP showed strong correlations to the Actinobacteria communities, in common with results from freshwater lakes in Germany (Allgaier et al, 2007). Therefore, TP was one of the major nutrient factors that could infl uence the Actinobacteria.…”