The future of environmental microbiology will be shaped by the current advances in genome sequence analysis of cultured and uncultured microbes. This appears to create a favorable conceptual environment for a population-based perspective in aquatic microbial ecology. Already, the analysis of genomic information has strengthened the interest in the cultivation of abundant heterotrophic microbes from the water column (39
). Such activities will probably draw increased attention to the unique physiological features of different genotypes and thus to the potential ecological differences between cooccurring microbial populations in mixed assemblages.
Some genomic information will moreover doubtlessly be of direct interest for the study of aquatic microbial populations in situ. Emerging techniques such as a combined FISH staining of mRNA and rRNA (208) will allow us to detect the expression of metabolic genes within bacterioplankton populations defined at the level of single ecotypes (41). Ideally, such gene-specific probing could be applied in combination with other ecologically relevant features of bacterial cells, e.g., morphology (223), proliferation (213), substrate uptake and turnover (324), motility (104), exoenzyme activity (195), or polysaccharide sheath formation (288). Moreover, a more complete knowledge of microbial genomes will allow us to detect far more subtle phylogenetic differences between bacteria than what can presently be derived from the analysis of 16S rRNA genes (315). Questions addressing the biogeography (43, 315) and physiological or evolutionary adaptation of microbial ecotypes (27, 109, 128) might therefore form another area of future research in environmental microbiology.
However, the ties between environmental genomics and microbial population ecology should not be overstated. The population sizes of different microbes in the environment cannot be predicted from their genomic constitutions only, and the success of different bacterial taxa is codetermined by their interactions with competitors and predators in the context of the physicochemical environment. Moreover, while the existence of microbial biogeography arguably is debatable (66), this controversy cannot be a central concern of population ecology. Even if in principle "everything is everywhere" (18), it is known that different groups of heterotrophic aquatic microbes exhibit distinct temporal, spatial, and geographic distribution optima. Thus, a major challenge of the coming decade will be to understand the underlying reasons for the heterogenous distribution patterns of different microbial populations in marine and freshwater plankton.
We thank our students and colleagues for all the fruitful discussions and controversies that helped to shape our ideas and David Kirchman and two anonymous reviewers for their helpful comments on the manuscript.
We acknowledge the institutions that have supported our research on the topics discussed here, in particular the European Union (EVK3-2001-00194 BASICS), the German Ministry of Education and Research (BMBF01 LC0021/TP4), the German Research Foundation (PE-918/2-1), and the Max Planck Society.
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