Halotolerant aerobic heterotrophic bacteria from the Great Salt Plains of Oklahoma.

The Salt Plains National Wildlife Refuge (SPNWR) near Cherokee, Oklahoma, contains a barren salt flat where Permian brine rises to the surface and evaporates under dry conditions to leave a crust of white salt. Rainfall events dissolve the salt crust and create ephemeral streams and ponds. The rapidly changing salinity and high surface temperatures, salinity, and UV exposure make this an extreme environment. The Salt Plains Microbial Observatory (SPMO) examined the soil microbial community of this habitat using classic enrichment and isolation techniques and phylogenetic rDNA studies. Rich growth media have been emphasized that differ in total salt concentration and composition. Aerobic heterotrophic enrichments were performed under a variety of conditions. Heterotrophic enrichments and dilution plates have generated 105 bacterial isolates, representing 46 phylotypes. The bacterial isolates have been characterized phenotypically and subjected to rDNA sequencing and phylogenetic analyses. Fast-growing isolates obtained from enrichments with 10% salt are predominantly from the gamma subgroup of the Proteobacteria and from the low GC Gram-positive cluster. Several different areas on the salt flats have yielded a variety of isolates from the Gram-negative genera Halomonas, Idiomarina, Salinivibrio, and Bacteroidetes. Gram-positive bacteria are well represented in the culture collection including members of the Bacillus, Salibacillus, Oceanobacillus, and Halobacillus.

Molecular diversity among communities of freshwater microchlorophytes.

Current hypotheses on the distribution of freshwater microchlorophytes lead to predictions of low diversity and wide environmental tolerances. Thus, the same few species should be found worldwide in many different habitats. However, these hypotheses are based on a morphospecies concept, which precludes the possibility of numerous cryptic species among these organisms. In this study, we examined the diversity of coccoid green microalgae and chlamydomonads (Chlorophyta) isolated from sites in Minnesota and North Dakota (USA) using techniques of 18S rDNA sequence analysis. Of 93 distinct 18S rDNA sequences identified from among 273 isolates examined by molecular techniques, all but four are new to science. The spatial distribution of organisms represented by these 18S rDNA sequences was not uniform, because some lakes and ponds yielded distinct 18S rDNA types not found at other sites. In addition, organisms generally considered to be cosmopolitan, such as Chlamydomonas reinhardtii and Chlorella vulgaris, were not found. These results challenge predictions of low species number and wide environmental tolerances among these eukaryotic microorganisms.

DNA-repair potential of Halomonas spp. from the Salt Plains Microbial Observatory of Oklahoma.

The Great Salt Plains (GSP), an unvegetated, barren salt flat that is part of the Salt Plains National Wildlife Refuge near Cherokee, Oklahoma, is the site of the Salt Plains Microbial Observatory. At the GSP the briny remains of an ancient sea rise to the surface, evaporate under dry conditions, and leave crusts of white salt. Adaptation to this environment requires development of coping mechanisms providing tolerance to desiccating conditions due to the high salinity, extreme temperatures, alkaline pH, unrelenting exposure to solar UV radiation, and prevailing winds. Several lines of evidence suggest that the same DNA repair mechanisms that are usually associated with UV light or chemically induced DNA damage are also important in protecting microbes from desiccation. Because little is known about the DNA repair capacity of microorganisms from hypersaline terrestrial environments, we explored the DNA repair capacity of microbial isolates from the GSP. We used survival following exposure to UV light as a convenient tool to assess DNA repair capacity. Two species of Halomonas (H. salina and H. venusta) that have been isolated repeatedly from the GSP were chosen for analysis. The survival profiles were compared to those of Escherichia coli, Pseudomonas aeruginosa, and Halomonas spp. from aquatic saline environments. Survival of GSP organisms exceeded that of the freshwater organism P. aeruginosa, although they survived no better than E. coli. The GSP isolates were much more resistance to killing by UV than were the aquatic species of Halomonas reported in the literature [Martin et al. (2000) Can J Microbiol 46:180-187]. Unlike E. coli, the GSP isolates did not appear to have an inducible, error-prone repair mechanism. However, they demonstrated high levels of spontaneous mutation.

Phylogeny of the Chlamydomonadales (Chlorophyceae): a comparison of ribosomal RNA gene sequences from the nucleus and the chloroplast.

Phylogenetic analyses of nuclear-encoded small-subunit rRNA sequences and chloroplast-encoded large-subunit rRNA sequences from flagellate green algae representing the order Chlamydomonadales were found to show considerable congruence. In general, the chloroplast data set exhibited more robust support for comparable lineages than the nuclear data set. The phylogenetic inferences derived from the independent data sets support some, but also challenge many, traditional taxonomic and phylogenetic concepts regarding the green flagellates. Results from phylogenetic analyses of both molecular data sets support six distinct lineages that include taxa from the biflagellate genus, Chlamydomonas, and a basal lineage that comprises taxa from the quadriflagellate genus, Carteria. Both data sets support the conclusion that Chlamydomonas is not monophyletic. Although the chloroplast data are ambiguous regarding the question of Carteria monophyly, the nuclear data fail to support Carteria monophyly. The chlorococcalean genus Chlorococcum was found to have affinities with the Chlamydomonadales, indicating that the traditional concepts of both Chlorococcales and Chlamydomonadales may need revision. The genus Dunaliella is allied within the Chlamydomonadales, supporting the contention that it has lost a typical glycoprotein cell wall.

Multiple origins of colonial green flagellates from unicells: evidence from molecular and organismal characters.

Phylogenetic hypotheses generated from cladistic analysis of organismal and molecular data are shown to be generally congruent and/or complementary for comparisons of unicellular and colonial green algae in the Chlorophyceae. Cladistic analysis of organismal character data corroborates the alliance of colonial Stephanosphaera with unicellular Haematococcus (Haematococcaceae sensu Smith), inferred from previous studies of nuclear-encoded rRNA sequence data. The organismal data also support monophyly of the colonial Volvocaceae (sensu Smith). Alliances of other unicellular taxa, including those ascribed to the "Euchlamydomonas" Hauptgruppe (sensu Ettl), are not resolved by organismal characters principally because the structure of the data is skewed to shared ancestral characters (symplesiomorphies) and unique characters (autapomorphies) which define individual taxa only. Reanalysis of rRNA sequence data, with additional sequence data for critical taxa, does not support monophyly of the colonial Volvocaceae (sensu Smith). However, these data are weak in the support of the alternate hypothesis of nonmonophyly. In contrast, relationships among most unicellular flagellates are unambiguously resolved by the molecular data. Although the failure of the sequence data to resolve relationships among colonial flagellates appears to be due to a sampling of conservative sequences, an ancient, rapid radiation event or taxon sampling bias may also be contributing to the ambiguity problem. Results from analysis of a combined data set (organismal and molecular) are generally consistent with the inferences of the organismal character data regarding the colonial flagellates and are also consistent with the inferences of the sequence data regarding the unicellular taxa.

Green algae and the evolution of land plants: inferences from nuclear-encoded rRNA gene sequences.

Phylogenetic analysis of 381 informative sites in partial sequences of nuclear-encoded large and small subunit ribosomal RNAs from 38 chlorophyll a- and b-containing plants (Chlorobionta sensu Bremer) including tracheophytes, bryophytes, charophytes and chlorophytes, supports the hypotheses of: (1) monophyly of the green plants (excluding Euglenophyta); (2) monophyly of the embryophytes; (3) non-monophyly of the bryophytes; (4) monophyly of the tracheophytes; and (5) a single origin of embryophytes from charophycean green algae. The Charales and Klebsormidium appear to be the green algae most closely related to the land plants. The unexpected basal divergence of Coleochaete and the apparent non-monophyly of the Zygnematales are not robustly supported and, thus, are interpreted to be sources of new questions, rather than new phylogenetic hypotheses.

Phylogeny of the colonial green flagellates: a study of 18S and 26S rRNA sequence data.

A study of phylogenetic relationships of the colonial green algal flagellates based on nuclear 18S and 26S rRNA sequence data suggests that the colonial habit has had at least two independent origins. All colonial taxa included in the analysis, except Stephanosphaera, are allied in a clade with Chlamydomonas reinhardtii and other Chlamydomonas taxa ascribed to the Euchlamydomonas group by Ettl. In contrast, Stephanosphaera is allied with other unicellular flagellates including Haematococcus. Comparison of the 18S and 26S data shows that the two sets of data yield different results following cladistic analysis. The 18S data provide the principal signal that supports the more basal divergences, but the data do not unambiguously address relationships among taxa in the clade that includes most colonial flagellates and Chlamydomonas taxa representative of the Euchlamydomonas group (sensu Ettl). In contrast, the 26S data have fewer informative sites that support basal divergences than the 18S data, but provide much of the signal that supports resolution of taxa in the colonial flagellate clade in an analysis of the combined 18S and 26S rRNA sequence data. Additional sequence data from the 26S molecule and additional taxa may reduce the topological ambiguity inferred from the sequence data for the colonial flagellates. Alternatively, an ancient and rapid radiation of taxa in the colonial lineage could account for the topological ambiguity. Despite some unresolved questions of relationships, cladistic analysis of the combined data sets provides some robustly supported concepts of evolution in these flagellates.