The ecology of CytophagaâFlavobacteria in aquatic environments

Culture-dependent and -independent studies have found that prokaryotic assemblages are quite diverse in aquatic habitats and contain representatives of virtually all of the roughly 40 divisions of bacteria and the major archaeal groups found so far in the biosphere 1. Fortunately, not all of these prokaryotic groups are abundant in the plankton nor important in all biogeochemical cycles. Autotrophic and heterotrophic bacteria dominate the prokaryotic biomass in surface waters, as Archaea appear to be abundant only in the plankton of the deep oceans 2. Among the heterotrophic bacteria, the two most abundant groups are often the Proteobacteria and the subject of this review, the Cytophaga–Flavobacteria cluster (Table 1). View this table: 1 The relative abundance of the major heterotrophic bacterial groups in aquatic ecosystems, as determined by FISH with oligonucleotide probes This paper reviews recent studies that have applied molecular methods to examine uncultured Cytophaga–Flavobacteria in freshwaters and the oceans, with the ultimate goal of using this information to better understand the role of heterotrophic bacteria in carbon cycles and other biogeochemical processes. The importance of heterotrophic bacteria in biogeochemical processes is now well appreciated, but until recently geochemists and field-orientated microbial ecologists considered these microbes as if they were a single group, even though microbiologists have been accumulating for several years information about the taxonomic and phylogenetic make up (‘community structure’) of heterotrophic bacterial communities. Only recently, however, have microbial ecologists been able to link community structure with specific biogeochemical processes (‘function’) 3. Here I summarize briefly our progress in these areas while discussing what we know about Cytophaga–Flavobacteria in aquatic habitats. This microbial group is a natural starting point because of its high abundance in many freshwater and marine systems. The Cytophaga–Flavobacteria cluster belongs to a diverse bacterial division that has been labeled differently over …