To address the long-standing need for more precise descriptions of natural microbial ecosystems, 16S rRNAs were used to track certain species and phylogenetically coherent groups of microorganisms in their natural setting without culturing. Speciesand group-specific 16S rRNA-targeted oligonucleotide hybridization probes were developed to enumerate various strains of Bacteroides succinogenes and Lachnospira multiparus-like organisms in the bovine rumen before, during, and after perturbation of that ecosystem by the addition of the ionophore antibiotic monensin. Based on probe hybridization, relative numbers of L. multiparus-like organisms were depressed about 2-fold during monensin addition and demonstrated a transient 5to 10-fold increase immediately after removal of the antibiotic from the diet. The most pronounced population changes were observed among different strains of B. succinogenes, as evaluated by three hybridization probes. One probe hybridized to all strains, whereas the other two identified genetically distinct groups represented by strains isolated from the rumen and from the ceca of nonruminants. The rumen-type strains predominated on most days (ca. 0.2 to 0.8% of total ribosome numbers). Their proportion transiently increased about fivefold immediately after the addition of monensin to the feed and then transiently fell below the average premonensin level. During this time (ca. 2 weeks after monensin addition) the cecal type predominated (ca. 0.1 to 0.2%). Cultural enumeration of B. succinogenes on nonselective agar and by observing clearings in cellulose agar media were largely unsuccessful due to the low number of organisms present and the predominance of other cellulolytic species. The results demonstrate the utility of rRNA-targeted hybridization to monitor complex microbial communities and are most consistent with the hypothesis that altered microbial metabolism, rather than altered population composition, is primarily responsible for changes in ruminal fermentation patterns resulting from the feeding of monensin.

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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...

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