This study presents an original 18S rRNA PCR survey of the freshwater picoeukaryote community, and was designed to detect unidentified heterotrophic picoflagellates (size range 0.6-5 microm) which are prevalent throughout the year within the heterotrophic flagellate assemblage in Lake Pavin. Four clone libraries were constructed from samples collected in two contrasting zones in the lake. Computerized statistic tools have suggested that sequence retrieval was representative of the in situ picoplankton diversity. The two sampling zones exhibited similar diversity patterns but shared only about 5% of the operational taxonomic units (OTUs). Phylogenetic analysis clustered our sequences into three taxonomic groups: Alveolates (30% of OTUs), Fungi (23%) and Cercozoa (19%). Fungi thus substantially contributed to the detected diversity, as was additionally supported by direct microscopic observations of fungal zoospores and sporangia. A large fraction of the sequences belonged to parasites, including Alveolate sequences affiliated to the genus Perkinsus known as zooparasites, and chytrids that include host-specific parasitic fungi of various freshwater phytoplankton species, primarily diatoms. Phylogenetic analysis revealed five novel clades that probably include typical freshwater environmental sequences. Overall, from the unsuspected fungal diversity unveiled, we think that fungal zooflagellates have been misidentified as phagotrophic nanoflagellates in previous studies. This is in agreement with a recent experimental demonstration that zoospore-producing fungi and parasitic activity may play an important role in aquatic food webs.

The Bacteria and Archaea from the meromictic Lake Pavin were analyzed in samples collected along a vertical profile in the anoxic monimolimnion and were compared to those in samples from the oxic mixolimnion. Nine targeted 16S rRNA oligonucleotide probes were used to assess the distribution of Bacteria and Archaea and to investigate the in situ occurrence of sulfate-reducing bacteria and methane-producing Archaea involved in the terminal steps of the anaerobic degradation of organic material. The diversity of the complex microbial communities was assessed from the 16S rRNA polymorphisms present in terminal restriction fragment (TRF) depth patterns. The densities of the microbial community increased in the anoxic layer, and Archaea detected with probe ARCH915 represented the largest microbial group in the water column, with a mean Archaea/ Eubacteria ratio of 1.5. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed an elevated archaeal and bacterial phylotype richness in anoxic bottom-water samples. The structure of the Archaea community remained rather homogeneous, while TRFLP patterns for the eubacterial community revealed a heterogeneous distribution of eubacterial TRFs.Permanent anoxic basins are of great interest to microbial ecologists, and during the last decade several papers have been published on microbial assemblages from different marine anoxic basins (e.g., see references 42 and 36). Among permanent anoxic aquatic systems, meromictic lakes are unusual and provide a special opportunity for research in aquatic biology for several reasons, e.g., the high physical stability of the water masses, clearly separated compartments, a relatively constant vertical stratification of bacterial populations, a compact and stable transition zone between the oxic mixolimnion and the anoxic monimolimnion, and in many cases the presence of a dense microbial community at the redox transition zone (6). These small and well-defined ecosystems can be useful for studying anaerobic microbial community structure and diversity and providing information on global carbon cycling and biogeochemical processes. Although molecular characterizations of microbial communities from Lake Saelenvannet (31, 41), Lake Cadagno (6), Mono Lake (18), and Mariager Fjord (34, 40) have been reported, the microbial populations and communities living in anaerobic zones of meromictic lakes remain largely unexplored.This paper focuses on the in situ distribution, abundance, and diversity of the Bacteria and Archaea communities in the anoxic zone of Lake Pavin, which has the advantage of being in a steady state (28). We have conducted culture-independent studies of the anoxic water column of Lake Pavin and of samples collected from the oxic zone to provide comparative information. Terminal restriction fragment length polymorphism (TRFLP) and fluorescent in situ hybridization analyses were performed on samples from between 50-and 90-m depths to characterize the microbial assemblages using 16S rRNA genes. Because previous geochemic...

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