Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: Comparison by microscopy and denaturing gradient gel electrophoresis

The microbial assemblages of Lake Cis6 and Lake Vilar (Banyoles, northeast Spain) were analyzed in space and time by microscopy and by performing PCR- denaturing gradient gel electrophoresis (DGGE)and sequence analysis of 16S rRNA gene fragments. Samples obtained from different water depths and at tw o different times of the year (in the winter during holomixis and in the ea rly spring during a phytoplankton bloom) were analyzed. Although the lakes have the same climatic conditions and the same water source, the limnologic al parameters were different, as were most of the morphologically distingui shable photosynthetic bacteria enumerated by microscopy. The phylogenetic a ffiliations of the predominant DGGE bands were inferred by performing a com parative 16S rRNA sequence analysis. Sequences obtained from Lake Cis6 samp les were related to gram-positive bacteria and to members of the division P roteobacteria. Sequences obtained from Lake Vilar samples were related to m embers of the Cytophaga-Flavobacterium-Bacteroides phylum and to cyanobacte ria. Thus, we found that like the previously reported differences between m orphologically distinct inhabitants of the two lakes, there were also diffe rences among the community members whose morphologies did not differ conspi cuously. The changes in the species composition from winter to spring were also marked. The two lakes both contained sequences belonging to phototroph ic green sulfur bacteria, which is consistent with microscopic observations , but these sequences were different from the sequences of cultured strains previously isolated from the lakes. Euryarchaeal sequences (i.e., methanog en- and thermoplasma-related sequences) also were present in both lakes. Th ese euryarchaeal group sequences dominated the archaeal sequences in Lake C is6 but not in Lake Vilar. In Lake Vilar, a new planktonic population relat ed to the crenarchaeota produced the dominant archaeal band. The phylogenet ic analysis indicated that new bacterial and archaeal lineages were present and that the microbial diversity of these assemblages was greater than pre viously known. We evaluated the correspondence between the abundances of se veral morphotypes and DGGE bands by comparing microscopy and sequencing res ults. Our data provide evidence that the sequences obtained from the DGGE f ingerprints correspond to the microorganisms that are actually present at h igher concentrations in the natural system.