Genome sequence analyses of cyanobacteria, green sulfur bacteria, and filamentous anoxygenic phototrophs, and the discovery of novel phototrophs from the mat ecosystems of Octopus and Mushroom Springs.
Donald A. Bryant1, John F. Heidelberg2, and David M. Ward3
1Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA 16802; 2The Institute for Genomic Research, Rockville, MD, USA 20850; 3Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA 59717-3120. email@example.com; firstname.lastname@example.org; email@example.com
The Bryant laboratory studies phototrophic bacteria through biochemical, physiological, genetic, genomic, and bioinformatic approaches. We have sequenced the genome of the marine unicellular cyanobacterium Synechococcus sp. PCC 7002, and the genomes of 12 green sulfur bacteria (GSB) and 7 filamentous anoxygenic phototrophs (FAPs) have been sequenced (or sequencing will be completed in 2006). In addition to characterizing the genomes of phototrophs, we study the photosynthetic apparatus in GSB (see Fig. 1) as well as the biochemical pathways for bacteriochlorophyll and carotenoid biosynthesis in these bacteria.
Roseiflexus sp. strain RS-1 is an axenic isolate of the major FAP of the Octopus and Mushroom Springs mat ecosystems. The draft genome of this bacterium is now >99% complete. The present dataset includes 5.8 Mb of DNA sequence with a G+C content of 60.3% that has been assembled into 73 contigs of >20 reads. Finishing, annotation and analyses of the data are in progress. The genome contains 46 tRNA genes, none of which are pseudogenes, and more than 4700 protein encoding gene models have been identified and annotated by computer. Comparisons of the sequence data for Roseiflexus sp. RS-1 with sequence reads derived from the metagenomic analysis of the Octopus and Mushroom Springs mat ecosystems indicate that strain RS-1 is very closely related, and thus representative, of the predominant FAP from these mats.
By analyzing the mat metagenomic sequence data for Octopus and Mushroom Springs, the existence of a GSB population in these mats has been demonstrated. Sequences of diagnostic genes, such as fmoA, pscA, pscB, bchQ and bchR, among others, were found in the metagenome. The Ward laboratory had previously shown the presence of 16S rRNA sequences similar to those of GSB in DNA isolated from the phototrophic portion of the mat. Phylogenetic analyses of the sequences indicate that this GSB may be the most divergent member of this phylum.
By searching the mat metagenomic data for sequences with similarity to pscA/psaA/B and fmoA, evidence for an even more divergent phototroph was also discovered. A pscA-pscB-fmoA operon was identified, and four independent clones from total mat DNA of Octopus Springs were completely sequenced. The resulting sequences are similar but unique, suggesting they derive from a population of closely related organisms within the mat. The PscA product is much larger than other Type-1 reaction center polypeptides, and it includes an insertion between transmembrane alpha-helices VIII and IX. By subtracting Type A and Type B Synechococcus sp. reads and Roseiflexus sp. RS-1 reads from the mat metagenome, and by binning and assembling the remaining sequences into contigs and scaffolds, this novel, highly divergent phototroph has tentatively been identified as belonging to a poorly characterized phylum previously unknown to contain phototrophic members. This organism has been grown in primary enrichment cultures and using PCR analyses for the novel pscA gene and 16S rRNA primers specific for this bacterium, conditions under which the organism can grow have tentatively been identified. Efforts to isolate and characterize this novel phototrophic microbe are in progress.