Unique microbial communities often develop in different habitats found in many aquatic systems. Most aquatic geochemists agree that overlapping vertical gradients of some molecules in sediments are the outcome of competition for suitable electron acceptors by microorganisms. These gradients are responsible for the stratification of bacterial communities that demonstrate different metabolisms. Yet, surprisingly few studies exist on the structural diversity, especially genetic diversity, of similar communities in the water columns of lakes where most aquatic production is degraded. There are also physical and chemical gradients in the waters of most oceans and freshwater lakes that affect the abundance and distribution of microorganisms. Gradients of dissolved oxygen, dissolved organic matter, and phytoplankton are usually present, especially during the summer. Previous studies have focused on the functional responses of bacterioplankton along these gradients but have not adequately addressed differences in the structural diversity of bacterial communities.

Microbial Community DNA Similarity in Lake Ecosystems

Community DNA similarity provides a convenient way of comparing bacterial communities based on genomic abundance. We used this technique to investigate the diversity of bacterioplankton communities at two spatial scales in the North American Great Lakes (Pascoe and Hicks, in revision). The genetic complexity of bacterioplankton communities was estimated to determine if hypolimnetic communities were more diverse than bacterial communities in the epilimnia of these lakes. Similarities between bacterioplankton communities present after the epilimnia formed were calculated to compare epilimnetic bacterioplankton in these different lakes. Our objective was to evaluate whether environmental gradients may control community diversity of aerobic bacterioplankton communities. Bacterioplankton communities were collected from Lakes Erie, Ontario, Huron, Michigan, and Superior during July and August. The genetic similarity of these communities was estimated by pairwise hybridization of heterogeneous DNA samples. This similarity is an estimate of the fraction of DNA shared in common between two communities. Epilimnetic bacterial communities of similar genetic composition were present after the epilimnia formed in these lakes but these communities were usually different from communities of free bacterioplankton in the hypolimnia. Epilimnetic and hypolimnetic bacterial communities were genetically similar in Lake Erie, probably at one site in Lake Ontario, and during the early stratification of Lake Superior (July). Bacterioplankton communities from the epilimnion and hypolimnion were different at the other sites examined in the Great Lakes. The DNAs from bacterial communities in the epilimnia of these lakes were similar during August, except for comparisons to Lake Superior. This investigation demonstrated that the structures of bacterial communities in oxic portions of large lakes are not homogeneous but vary from lake to lake and even over short distances if physical gradients like thermoclines are seasonally present.

Relationship Between Microbial Nucleic Acids and Numerical Dominance

Different phytoplankton communities have been reported in different North American Great Lakes. Phytoplankton and bacterial production are tightly coupled in most oceans and lakes, but the structural similarity of bacterial communities has only been investigated in some aquatic environments. Initially, these investigations depended on identifying bacterial strains that were isolated on media. Subsequently, it has been recognized that many environmental strains of bacteria have not yet been cultured in the laboratory and thus our understanding of bacterial communities may be biased when only culture-based approaches are used. Ribosomal RNA-based probes have been successfully used to determine the relative abundances of 16S ribosomal RNA (rRNA) genes from different prokaryotic taxa within the picoplankton (0.2 to 2 µm size range) in freshwater and marine habitats. Even the relative abundances of as yet uncultured microorganisms have been estimated using this method. Rarely, however, have previous investigators tried to verify these nucleic acid-based estimates of prokaryotic dominance with other independent methods.

The abundances of rRNAs in microbial communities are a function of the species composition, cell biomasses, and cellular productivities of microorganisms. Although the abundance of 16S rRNA is not directly proportional to cell abundance or biomass alone, picoplanktonic cyanobacteria provide the opportunity to compare nucleic acid-based and microscopic estimates of abundance because there are 16S rRNA-based probes specific for cyanobacteria and cyanobacterial cells can be easily counted with an epifluorescence microscope due to the autofluorescence of their photosynthetic pigments. Thus, we described the phylogenetic diversity of picoplankton in the North American Great Lakes by quantitatively hybridizing rRNA-based probes for cyanobacteria and the major evolutionary lineages of life (Bacteria, Eucarya, Archaea) to picoplanktonic nucleic acids (Hicks and Pascoe, 2001). Our goal was to compare 16S rRNA probe-based hybridization estimates of cyanobacterial dominance with direct count measurements of autofluorescent picoplankton in these great lakes. The majority of picoplanktonic nucleic acids were from bacteria (91% to 98%). Cyanobacterial nucleic acids dominated the bacterial nucleic acids from picoplankton in the epilimnion of Lake Ontario. The percentage of cyanobacterial relative to picoplanktonic nucleic acids was correlated with the relative abundance of autofluorescent picoplanktonic cells. Results from this investigation supported the concept that quantitative hybridizations with rRNA-based oligonucleotide probes can reveal differences in the dominance of specific microbial taxa within picoplanktonic communities and that nucleic acid dominance is related to numerical dominance, at least for cyanobacteria populations.

Presence and Phylogenetic Affiliation of Archaeal Nucleic Acids from Picoplankton of Great Lakes

Recent surveys of microbial diversity worldwide have revealed the global distribution of a poorly understood group of prokaryotes, the Archaea. Archaeons were thought to be primarily extremophilic but evidence now suggests they are common in many terrestrial and aquatic habitats. Our work has revealed that up to 10% of picoplanktonic nucleic acid may be of archaeal origin in the Laurentian Great Lakes, Lakes Ladoga and Onega in Russia, and Lake Victoria in Africa (Keough and Hicks, in prep.). The presence of these archaeal nucleic acids was independently verified for most lakes by archaeal-specific PCR amplification of rDNA. Two approaches, top-down hybridization and sequencing of rDNA clones, were used to identify the phylogenetic affiliations of the archaeal nucleic acids. In most lakes, a very small amount of nucleic acid from the Group I non-thermophilic crenarchaeotal marine cluster was detected but the top-down hybridization analysis failed to account for the majority of archaeal nucleic acids detected at the Domain level. Sequence analysis of rDNA clones confirmed the presence of similar non-thermophilic crenarchaeotes in great lakes on all these continents, some of which appear to form a distinct undescribed cluster of archaeons. The results of this study extend the range of archaeons to picoplankton in oxic parts of large lake ecosystems worldwide.

Collaborator on this project:

Dr. Thomas Schmidt (Dept. of Microbiology, Michigan State University, East Lansing, MI)