Outlook

Cultivation-independent molecular methods have opened new windows into the microbial world. Microbial ecologists can now investigate elusive bacteria, which are abundant in many ecosystems but have so far resisted all attempts of isolation and cultivation. However, many currently used molecular methods are too slow and laborintensive for broad ecological studies, which require comparative analyses of many environmental samples. Recent technical progress includes the development of DNA microarrays that detect particular phylogenetic groups of bacteria in the environment (so-called "PhyloChips").103-106 PhyloChips, isotope arrays, and functional gene arrays make it possible to analyze the structure and function of microbial communities faster and in more samples than achievable with nonparallelized techniques.

What else can be done to investigate uncultured bacteria? The term "environmental genomics" comprises methods to clone and analyze genome fragments, or even whole genomes, of yet uncultured microbes.107-111 Genes found by this approach may encode ecologically important or even completely novel physiological properties. Methods like the isotope array and FISH-MAR can be used to link the genetic data to the phenotype of the corresponding organisms. In addition, transkriptom-ics and proteomics will offer a wide range of possibilities to study the responses of uncultured bacteria to changing environmental conditions, and to discover the details of novel biochemical pathways.

Insight into the ecology of uncultured bacteria has many practical applications. For example, the biodiversity of nitrifying bacteria in wastewater treatment plants may have significant impact on the stability and performance of these systems. A high diversity of nitrifiers could guarantee that nitrification does not collapse during shifts of environmental conditions. The more the different populations of ammonia and nitrite oxidizers, the higher the chance that at least one population of each group will adapt to new conditions and will continue oxidizing ammonia or nitrite, respectively. Strategies to influence the diversity of nitrifiers and of other microbial guilds in engineered and agricultural habitats could be developed. Detailed insight into the ecology and physiology of the involved microorganisms is needed to achieve this goal.

Biological, chemical, and physical processes influence the formation and stability of flocs. In order to understand flocculation, physical, chemical, and microbiological approaches must be integrated. A task for the near future of flocculation research is to bring the methods and views of these disciplines together, and to strengthen the role of microbial ecology in this fascinating and promising field.

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