Seasonal Community and Population Dynamics of Pelagic Bacteria and Archaea in a High Mountain Lake

The seasonal variations in community structure and cell morphology of pelagic procaryotes from a high mountain lake (Gossenköllesee, Austria) were studied by in situ hybridization with rRNA-targeted fluorescently labeled oligonucleotide probes (FISH) and image-analyzed microscopy. Compositional changes and biomass fluctuations within the assemblage were observed both in summer and beneath the winter ice cover and are discussed in the context of physicochemical and biotic parameters. Proteobacteria of the beta subclass (beta-proteobacteria) formed a dominant fraction of the bacterioplankton (annual mean, 24% of the total counts), whereas alpha-proteobacteria were of similar relative importance only during spring (mean, 11%). Bacteria of the Cytophaga-Flavobacterium cluster, although less abundant, constituted the largest fraction of the filamentous morphotypes during most of the year, thus contributing significantly to the total microbial biomass. Successive peaks of threadlike and rod-shaped archaea were observed during autumn thermal mixing and the period of ice cover formation, respectively. A set of oligonucleotide probes targeted to single phylotypes was constructed from 16S rRNA-encoding gene clone sequences. Three distinct populations of uncultivated microbes, affiliated with the alpha- and beta-proteobacteria, were subsequently monitored by FISH. About one-quarter of all of the beta-proteobacteria (range, 6 to 53%) could be assigned to only two phylotypes. The bacterial populations studied were annually recurrent, seasonally variable, and vertically stratified, except during the periods of lake overturn. Their variability clearly exceeded the fluctuations of the total microbial assemblage, suggesting that the apparent stability of total bacterioplankton abundances may mask highly dynamic community fluctuations.Until recently, microbial ecologist studying aquatic bacteria faced a basic dilemma: they could either measure the abundance, biomass, growth rates, activity, etc. of the “average” bacterium under in situ conditions (e.g., see reference 13), ignoring the phylogenetic and physiological diversity of microbial communities, or they could isolate and ecophysiologically characterize individual bacterial strains (e.g., see reference 36) but were then not able to tell if these microorganisms were also common in the environment. Consequently, little knowledge has been gathered about the spatial and temporal abundance fluctuations of defined phylogenetic groups and of individual bacterial species in natural habitats. Molecular biological techniques used to identify microbes in environmental samples have recently provided new tools to study bacterioplankton biodiversity (e.g., see references 1, 9, 14, 15, and 19) and the in situ abundances of bacteria and archaea that could not be adequately distinguished before (2, 4, 5, 25). Microbiologists are now in a position to potentially elucidate the biogeography (24), population dynamics, and successions (28) not only of a few morphologically conspicuous microbes but of a large number of species, most of which might still be uncharacterized.Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes selectively visualizes bacterial cells with defined phylogenetic affiliations (3, 5). Based on a rapidly growing set of 16S (and, to a lesser extend, 23S) rRNA sequence data, it is probably the phylogenetically most sophisticated (22) approach for whole-cell in situ identification. On the other hand, FISH of plankton samples can be performed with minimal laboratory requirements (16), and evaluation relies on epifluorescence microscopy, which is a standard technique of aquatic microbial ecologists, e.g., for counting (30) and sizing (33) of picoplankton. In contrast to other identification approaches, FISH largely conserves the gestalt of the targeted microorganisms, i.e., their morphologies, cell sizes (26, 34), and cellular rRNA content (7, 32). So, despite the limitations of the method (as discussed in reference 5), its potential for the identification and cytometric analysis of planktonic microbes is just about to be recognized.Recent investigations have reported that various freshwater microbial communities are dominated by bacteria which are phylogenetically affiliated with the alpha and beta subclasses of the class Proteobacteria (alpha- and beta-proteobacteria, respectively) and with members of the Cytophaga-Flavobacterium cluster (2, 6, 16, 19). These observations were based on single or short-term sampling schemes. The instantaneous community composition of the bacterioplankton, however, may not be representative for different seasons, and the typical ranges of annual community variability remain to be established.The size distribution of planktonic bacteria, and particularly the appearance of filamentous cells, has come into the focus of aquatic microbial ecology in the context of studies of predator-prey interactions. It has been shown both in the laboratory (18, 37) and in field experiments (20) that the filamentous morphotype is a phenotypic adaptation of some microbes to protistan grazing, but there are probably numerous other causes for bacteria to elongate far beyond their typical sizes (e.g., see reference 23). Threadlike bacteria have been observed throughout the year in the plankton of a hypertrophic lake (41) but were also found in midwinter in an oligotropic alpine lake (31).In earlier studies, we demonstrated FISH to be an appropriate tool for the monitoring of spatial (2) and short-term temporal (26) dynamics of different phylogenetic groups of the planktonic microbial community in a high mountain lake. Here we report on the seasonal and vertical abundance distributions of pelagic members of Bacteria and Archaea in Gossenköllesee and analysis of the community structure at different levels of taxonomic resolution. We applied published domain- and group-specific oligonucleotide probes (5) but also used the sequence information from a 16S rRNA-encoding gene (rDNA) library obtained from Gossenköllesee bacterioplankton 1 year earlier to construct specific probes targeted at individual bacterial populations. Particular attention was paid to the changes in abundance and taxonomic composition of the filamentous bacterial morphotypes which were recognized as a permanently important fraction of the planktonic procaryotes in Gossenköllesee. Additionally, we monitored the seasonal changes in the biomass size distributions of the nonfilamentous fraction of the pelagic microbial community.