Diversity and seasonal dynamics of Actinobacteria populations in four lakes in northeastern Germany

Abstract

The phylogenetic diversity and seasonal dynamics of freshwater Actinobacteria populations in four limnologically different lakes of the Mecklenburg-Brandenburg Lake District (northeastern Germany) were investigated. Fluorescence in situ hybridization was used to determine the seasonal abundances and dynamics of total Actinobacteria (probe HGC69a) and the three actinobacterial subclusters acI, acI-A, and acI-B (probes AcI-852, AcI-840-1, and AcI-840-2). Seasonal means of total Actinobacteria abundances in the epilimnia of the lakes varied from 13 to 36%, with maximum values of 30 to 58%, of all DAPI (4',6'-diamidino-2-phenylindole)-stained cells. Around 80% of total Actinobacteria belonged to the acI cluster. The two subclusters acI-A and acI-B accounted for 60 to 91% of the acI cluster and showed seasonal means of 49% (acI-B) and 23% (acI-A) in relation to the acI cluster. Total Actinobacteria and members of the clusters acI and acI-B showed distinct seasonal changes in their absolute abundances, with maxima in late spring and fall/winter. In eight clone libraries constructed from the lakes, a total of 76 actinobacterial 16S rRNA gene sequences were identified from a total of 177 clones. The majority of the Actinobacteria sequences belonged to the acI and acIV cluster. Several new clusters and subclusters were found (acSTL, scB1-4, and acIVA-D). The majority of all obtained 16S rRNA gene sequences are distinct from those of already-cultured freshwater Actinobacteria.

FIG. 1.

Seasonal means of abundances of total Actinobacteria (probe HGC69a) and members of the actinobacterial subgroups acI (AcI-852), acI-A (AcI-840-1), and acI-B (AcI-840-2) in relation to total bacterial numbers determined by direct microscopic counts.

FIG. 2.

Seasonal dynamics of the abundance of Actinobacteria determined by the oligonucleotide probes HGC69a (Actinobacteria), AcI-852 (acI), AcI-840-1 (acI-A), and AcI-840-2 (acI-B). The upper panels show the total bacterial numbers as enumerated by DAPI direct microscopic counts in comparison to Eubacteria determined by using the oligonucleotide probe mix EUB I-III. The arrows mark the peaks in abundances of Actinobacteria in late spring (gray arrows) and fall/winter (white arrows). Error bars represent standard deviations determined from absolute cell numbers in 10 independently counted microscopic fields. ST, Lake Stechlin; BL, Lake Breiter Luzin; TW, Lake Tiefwaren; FU, Lake Grosse Fuchskuhle; HL, hypolimnion.

FIG.3.

Phylogenetic trees of freshwater actinobacterial 16S rRNA gene sequences. Solid lines indicate sequences that were included in the primary analyses (sequences of >1,400 nucleotides), whereas dotted lines indicate partial sequences (<1,400 nucleotides). Sequences produced during this study are shown in boldface. GenBank accession numbers are given in parentheses. The scale bar correspond to 10 base substitutions per 100 nucleotide positions. Bootstrap values at the main branching points are given. (A) Detailed view of phylogenetic relationships within the acI cluster. (B) Phylogeny of other actinobacterial freshwater clusters.

FIG.3.

Phylogenetic trees of freshwater actinobacterial 16S rRNA gene sequences. Solid lines indicate sequences that were included in the primary analyses (sequences of >1,400 nucleotides), whereas dotted lines indicate partial sequences (<1,400 nucleotides). Sequences produced during this study are shown in boldface. GenBank accession numbers are given in parentheses. The scale bar correspond to 10 base substitutions per 100 nucleotide positions. Bootstrap values at the main branching points are given. (A) Detailed view of phylogenetic relationships within the acI cluster. (B) Phylogeny of other actinobacterial freshwater clusters.