The phylogeny of marine and freshwater caulobacters reflects their habitat

Abstract

Caulobacter is a distinctive genus of prosthecate bacteria. Because caulobacters adhere to surfaces and are found in diverse locales, their role in oligotrophic environments and bacterial biofilm communities is of interest. The phylogenetic relationships of a group of marine and freshwater caulobacters were examined in part to address whether the taxonomic grouping of these bacteria (based primarily on morphological characters) was consistent with 16S rRNA sequence divergence. The caulobacters examined (9 marine and 11 freshwater species or strains) were affiliated with the alpha proteobacteria. They made up a diverse yet, with the possible exception of a strain of Caulobacter subvibrioides, coherent assemblage. The diversity was most apparent in a comparison of freshwater and marine isolates; an early divergence within the main caulobacter lineage generally corresponded to strains isolated from freshwater and marine habitats. The marine caulobacter assemblage was not exclusive; it also embraced strains of marine hyphomonads and Rhodobacter capsulatus. We hypothesize that these genera are derived from more ancestral caulobacters. Overall, the data are consistent with the interpretation that all of the caulobacters examined, with the possible exception of C.subvibrioides, are ancestrally related, albeit anciently, and that most often division by terrestrial and marine habitats corresponds to an early evolutionary divergence within the genus.Given the simple shapes of most bacteria, morphologically conspicuous groups have long been a source of interest to general microbiologists. Among the better characterized of such bacteria are budding and/or prosthecate nonphototrophic bacteria. These include the genera Hyphomicrobium, Hyphomonas, Pedomicrobium, Filomicrobium, Stella, and Caulobacter. The taxonomy of these groups has relied primarily upon morphological criteria and required growth factors (27)(28)(29). In the case of caulobacters, beyond some consideration of the environment in which they are found, what visually appears to be a caulobacter is generally sufficient to be called one without challenge. This is due mainly to a lack of other defining physiological or metabolic traits, a recognized problem in the taxonomy of all of the prosthecate bacteria (27) and, indeed, other groups of environmentally relevant bacteria.Such a paucity of factors upon which to base affiliations, aside from taxonomy issues, leads to a variety of questions concerning origins and coherence. Are the caulobacters derived from common ancestry (monophyletic), reflecting a single origin of their distinctive morphological and developmental characteristics? Or, do the structural components, notably the long stalk, represent the convergent discovery of a useful structural adaptation? For example, the stalk might be a means of increasing the surface area of the bacterium to enhance nutrient uptake that has been adopted by many species. Alternatively, the stalk with attendant adhesive at the tip (15) might reflect a common strategy to secure a...

Phylogenetic Evidence for Sphingomonas and Rhizomonas as Nonphotosynthetic Members of the Alpha-4 Subclass of the Proteobacteria

“…To clarify the phylogenetic relationships of the species belonging to the genera Sphingomonas and Rhizomonas and Erythrobacter longus, we determined the 16s rRNA sequence of Rhizomonas suberifaciens I F 0 1521 lT (Fig. 1) and compared it with the sequences of eight species belonging to the genus Sphingomonas (29), the sequences of the bacteriochlorophyll-containing bacteria Porphyrobacter neustonensis (4) and Roseobacter denitriJicans (22), and the sequences of 30 other species belonging to the alpha subclass (30,40), Magnetospirillum magnetotacticum (2), and Rhodospirillum rubrum (30,40); alpha-2 group species Hyphomicrobium vulgare (25), Rhodomicrobium vanniefii (40), Ancyfobacter aquaticus (39), Afipia felis (37), Blastobacter denitrificans (37), Bradyrhizobium japonicum (37), Methylosinus trichosporium (30), Methylobacterium organophilum (30), Agrobacterium tumefaciens (30,40), Bartonella bacilliformis (18), Rochalimaea quintana (36), Caulobacter bacteroides (27), and Pseudomonas diminuta (30); alpha-3 group species Hyphomonas jannaschiana (25), Hirschia baltica (21), Paracoccus denitr$cans (15,40), Rhodobacter capsufatus (30,40), and Roseobacter denitrificans (4); alpha4 group species Erythrobacter longus (40) and Porphyrobacter neustonensis (4); alpha group species Cowdria ruminantium (3), Ehrlichia risticii (34,35), Rickettsia prowazekii (35), and Wolbachia pipientis (16); delta-3 group species Escherichia coli (30). Bar = 0.01 K,,, unit.…”

Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages

“…The most striking enrichment was an OTU belonging to the Hyphomonadaceae family of Alphaproteobacteria ( Figures 2 and 3), with close similarity to isolates of Hyphomonas and Caulobacter (Table 5; Supplementary Figure S6), which came to compose nearly 3.5% of the total 16S sequences. These OTUs belong to a group of widespread oligotrophic budding organisms found in many aquatic environments but with no evidence for pathogenicity (Stahl et al, 1992;Weiner et al, 2000;Badger et al, 2005). Other taxa enriched in the Porites exudate amendments included OTUs closely related to the Alphaproteobacteria Sneathiella and Erythrobacter and to the Gammaproteobacteria Haliea and Thalassobius, all associated with free-living oligotrophic to mesotrophic coastal marine environments and with no known pathogenic lifestyles (Koblížek et al, 2003;Jordan et al, 2007;Urios et al, 2008;Park et al, 2012).…”

Classification of Pseudomonas diminuta Leifson and Hugh 1954 and Pseudomonas vesicularis Busing, Doll, and Freytag 1953 in Brevundimonas gen. nov. as Brevundimonas diminuta comb. nov. and Brevundimonas vesicularis comb. nov., Respectively

“…Both of these species can be distinguished from most gram-negative bacteria by a combination of characteristics, including flagellar morphology, nutritional properties, acid tolerance, type of pigmentation, nature of carbon reserve materials, and DNA base composition (1, 16,24). The results of DNA-rRNA hybridization experiments (12), 16s rRNA cataloging (42), and 16s rRNA sequencing (30) and a cluster analysis was performed by using the unweighted average linkage algorithm (36). Gas chromatographic analysis of methylated fatty acids.…”