Overview of the Marine Roseobacter Lineage

Abstract

3Despite the overwhelming bacterial diversity present in the world's oceans, the majority of recognized marine bacteria fall into as few as nine major clades (36), many of which have yet to be cultivated in the laboratory. Molecular-based approaches targeting 16S rRNA genes demonstrate that the Roseobacter clade is one of these major marine groups, typically comprising upwards of 20% of coastal and 15% of mixed-layer ocean bacterioplankton communities (see, e.g., references 36, 37, 42, 98, and 109). Roseobacters are well represented across diverse marine habitats, from coastal to open oceans and from sea ice to sea floor (see, e.g., references 16, 28, 37, 42, 52, and 98). Members have been found to be free living, particle associated, or in commensal relationships with marine phytoplankton, invertebrates, and vertebrates (see, e.g., references 4, 6, 7, 44, 49, 115, and 119). Furthermore, representatives of the clade stand out as representing one of the most readily cultivated of the major marine lineages (36). These isolated representatives are serving as the foundation for an improved understanding of marine bacterial ecology and physiology. DESCRIPTION OF THE GROUPThe Roseobacter clade falls within the ␣-3 subclass of the class Proteobacteria, with members sharing Ͼ89% identity of the 16S rRNA gene. The first strain descriptions appeared in 1991, about the time that 16S rRNA-based approaches for cataloging microbial diversity were revealing the immensity of prokaryotic diversity in the world's oceans. Interest in the clade has risen steadily since the initial discovery of these strains; at present the clade contains 36 described species, representing 17 genera, and literally hundreds of uncharacterized isolates and clone sequences. The first described members were Roseobacter litoralis and Roseobacter denitrificans, both pinkpigmented bacteriochlorophyll a-producing strains isolated from marine algae (99). Subsequent cultivation of clade members, however, revealed that many strains are neither pink nor bacteriochlorophyll a producers (see, e.g., references 20, 41, 43, and 61). With the exceptions of the described strains of the genus Ketogulonicigenium (113) and several clones from a South African gold mine (GenBank accession numbers AF546906, -13, -17, -22 to -24, and -26), the Roseobacter clade is exclusively marine or hypersaline, with characterized isolates demonstrating either a salt requirement or tolerance (see, e.g., references 60 and 62 ABUNDANCE AND DISTRIBUTION IN MARINE ENVIRONMENTSBased on culture collections, 16S rRNA clone libraries, and single-cell analyses, roseobacters have been identified in most marine environments sampled. The group is prevalent in 16S rRNA gene inventories of seawater (Table 1) and marine sediments (Table 2) and is noticeably absent from analogous inventories of freshwater and terrestrial soil environments. Fluorescent in situ hybridization (FISH) studies quantifying Roseobacter populations in coastal waters of the southeastern United States and the North Sea indicate ...

Grazing rates and functional diversity of uncultured heterotrophic flagellates

“…Finally, besides differences related to cell viability, no other differences in measured grazing rates were seen when using the two bacterial strains, even though they belong to distant phylogenetic groups with different life strategies. Members of the Roseobacter lineage tend to be free-living bacteria and typical of somewhat rich conditions (Buchan et al, 2005), whereas flavobacteria tend to be particle-associated bacteria with high exoenzymatic activity (Kirchman, 2002). In our study, Roseobacter and flavobacteria cells were ingested equally by MAST-4, so these important differences in phylogeny and life strategy did not determine prey preference.…”

“…In addition to the in situ sample we analyzed a sample from an unamended incubation (Massana et al, 2006b), which promote the growth of uncultured HF and therefore increase the chances of finding specific predators. For the second objective, besides the standard FLB, we used live bacteria that affiliate to the well-represented marine groups Roseobacter and Flavobacteriaceae (Kirchman, 2002; Buchan et al, 2005;Alonso-Sáez et al, 2007). The strains we used as tracers were isolated from the sampling point (Blanes Bay) and were too scarce in the original sample to interfere with the grazing experiments.…”

Gene transfer agents: phage-like elements of genetic exchange

“…The possibility of widespread conservation of GTA production in this particular group of bacteria is especially interesting because roseobacters (within the order Rhodobacterales) appear to account for >25% of the total bacterial and archaeal community in some marine environments 47 . Therefore, GTAs could make up a sizable portion of the viral community in places where the abundance of Rhodobacterales members is high.…”

Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing

“…However, several studies have indicated that fosmid clone DNA libraries are not fully consistent with other assessments of natural microbial communities, with a poor representation of key members such as SAR11 (Suzuki et al, 2004;DeLong et al, 2006;Gilbert et al, 2008) and a high dominance of Roseobacter spp. (Suzuki et al, 1997;Buchan et al, 2005). In contrast to an estimated 25% abundance of SAR11 in marine microbial communities from plasmid libraries (Giovannoni et al, 2005) and 12-37% abundance from direct counting of SAR11 using fluorescent in situ hybridization (Mary et al, 2006), Gilbert et al (2008) isolated only a single clone containing a 16S rRNA gene with homology to the SAR11 clade from a marine surface water fosmid library of 10 000 clones.…”