Publications

4619

Summary Candidatus Chloracidobacterium thermophilum, which naturally inhabits microbial mats of alkaline siliceous hot springs in Yellowstone National Park, is the only known chlorophototroph in the phylum Acidobacteria . The Ca . C .  thermophilum genome was composed of two chromosomes (2 683 362 bp and 1 012 010 bp), and both encoded essential genes. The genome included genes to produce chlorosomes, the Fenna‐Matthews‐Olson protein, bacteriochlorophylls a and c as principal pigments, and type‐1, homodimeric reaction centres. Ca . C. thermophilum is an aerobic photoheterotroph that lacks the ability to synthesize several essential nutrients. Key genes of all known carbon fixation pathways were absent, as were genes for assimilatory nitrate and sulfate reduction and vitamin B 12 synthesis. Genes for the synthesis of branched‐chain amino acids (valine, isoleucine and leucine) were also absent, but genes for catabolism of these compounds were present. This observation suggested that Ca . C. thermophilum may synthesize branched‐chain amino acids from an intermediate(s) of the catabolic pathway by reversing these reactions. The genome encoded an aerobic respiratory electron transport chain that included NADH dehydrogenase, alternative complex III and cytochrome oxidase. The chromosomes of the laboratory isolate were compared with assembled, metagenomic scaffolds from the major Ca . C. thermophilum population in hot‐spring mats. The larger chromosomes of the two populations were highly syntenous but significantly divergent (∼13%) in sequence. In contrast, the smaller chromosomes have undergone numerous rearrangements, contained many transposases, and might be less constrained by purifying selection than the large chromosomes. Some transposases were homologous to those of mat community members from other phyla.

ABSTRACT Members of the noncultured clade of Frankia enter into root nodule symbioses with actinorhizal species from the orders Cucurbitales and Rosales. We report the genome sequence of a member of this clade originally from Pakistan but obtained from root nodules of the American plant Datisca glomerata without isolation in culture.

Summary In this study, members of a specific group of thin (6–14 µm filament diameter), vacuolated Beggiatoa‐ like filaments from six different hypersaline microbial mats were morphologically and phylogenetically characterized. Therefore, enrichment cultures were established, filaments were stained with fluorochromes to show intracellular structures and 16S rRNA genes were sequenced. Morphological characteristics of Beggiatoa‐ like filaments, in particular the presence of intracellular vacuoles, and the distribution of nucleic acids were visualized. In the intracellular vacuole nitrate reached concentrations of up to 650 mM. Fifteen of the retrieved 16S rRNA gene sequences formed a monophyletic cluster and were phylogenetically closely related (≥ 94.4% sequence identity). Sequences of known filamentous sulfide‐oxidizing genera Beggiatoa and Thioploca that comprise non‐vacuolated and vacuolated filaments from diverse habitats clearly delineated from this cluster. The novel monophyletic cluster was furthermore divided into two sub‐clusters: one contained sequences originating from Guerrero Negro (Mexico) microbial mats and the other comprised sequences from five distinct Spanish hypersaline microbial mats from Ibiza, Formentera and Lake Chiprana. Our data suggest that Beggiatoa ‐like filaments from hypersaline environments displaying a thin filament diameter contain nitrate‐storing vacuoles and are phylogenetically separate from known Beggiatoa . Therefore, we propose a novel genus for these organisms, which we suggest to name ‘ Candidatus Allobeggiatoa’.