Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. Export

@article{citeulike:2393552, abstract = {Marine sediments are frequently covered by mats of the filamentous Beggiatoa and other large nitrate-storing bacteria that oxidize hydrogen sulfide using either oxygen or nitrate, which they store in intracellular vacuoles. Despite their conspicuous metabolic properties and their biogeochemical importance, little is known about their genetic repertoire because of the lack of pure cultures. Here, we present a unique approach to access the genome of single filaments of Beggiatoa by combining whole genome amplification, pyrosequencing, and optical genome mapping. Sequence assemblies were incomplete and yielded average contig sizes of approximately 1 kb. Pathways for sulfur oxidation, nitrate and oxygen respiration, and CO2 fixation confirm the chemolithoautotrophic physiology of Beggiatoa. In addition, Beggiatoa potentially utilize inorganic sulfur compounds and dimethyl sulfoxide as electron acceptors. We propose a mechanism of vacuolar nitrate accumulation that is linked to proton translocation by vacuolar-type ATPases. Comparative genomics indicates substantial horizontal gene transfer of storage, metabolic, and gliding capabilities between Beggiatoa and cyanobacteria. These capabilities enable Beggiatoa to overcome non-overlapping availabilities of electron donors and acceptors while gliding between oxic and sulfidic zones. The first look into the genome of these filamentous sulfur-oxidizing bacteria substantially deepens the understanding of their evolution and their contribution to sulfur and nitrogen cycling in marine sediments.}, address = {Max Planck Institute for Marine Microbiology, Bremen, Germany. mussmann@mpi-bremen.de}, author = {Mussmann, M. and Hu, F. Z. and Richter, M. and de Beer, D. and Preisler, A. and J{\o}rgensen, B. B. and Huntemann, M. and Gl\"{o}ckner, F. O. and Amann, R. and Koopman, W. J. and Lasken, R. S. and Janto, B. and Hogg, J. and Stoodley, P. and Boissy, R. and Ehrlich, G. D.}, citeulike-article-id = {2393552}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pbio.0050230}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17760503}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17760503}, day = {28}, doi = {10.1371/journal.pbio.0050230}, issn = {1545-7885}, journal = {PLoS biology}, keywords = {beggiatoa, filament, genome, mda, metagenomics}, month = {September}, number = {9}, pages = {e230+}, posted-at = {2009-01-09 13:19:04}, priority = {2}, publisher = {Public Library of Science}, title = {Insights into the genome of large sulfur bacteria revealed by analysis of single filaments.}, url = {http://dx.doi.org/10.1371/journal.pbio.0050230}, volume = {5}, year = {2007} }

TY - JOUR ID - citeulike:2393552 L3 - citeulike-article-id:2393552 N2 - Marine sediments are frequently covered by mats of the filamentous Beggiatoa and other large nitrate-storing bacteria that oxidize hydrogen sulfide using either oxygen or nitrate, which they store in intracellular vacuoles. Despite their conspicuous metabolic properties and their biogeochemical importance, little is known about their genetic repertoire because of the lack of pure cultures. Here, we present a unique approach to access the genome of single filaments of Beggiatoa by combining whole genome amplification, pyrosequencing, and optical genome mapping. Sequence assemblies were incomplete and yielded average contig sizes of approximately 1 kb. Pathways for sulfur oxidation, nitrate and oxygen respiration, and CO2 fixation confirm the chemolithoautotrophic physiology of Beggiatoa. In addition, Beggiatoa potentially utilize inorganic sulfur compounds and dimethyl sulfoxide as electron acceptors. We propose a mechanism of vacuolar nitrate accumulation that is linked to proton translocation by vacuolar-type ATPases. Comparative genomics indicates substantial horizontal gene transfer of storage, metabolic, and gliding capabilities between Beggiatoa and cyanobacteria. These capabilities enable Beggiatoa to overcome non-overlapping availabilities of electron donors and acceptors while gliding between oxic and sulfidic zones. The first look into the genome of these filamentous sulfur-oxidizing bacteria substantially deepens the understanding of their evolution and their contribution to sulfur and nitrogen cycling in marine sediments. IS - 9 JF - PLoS biology SN - 1545-7885 AD - Max Planck Institute for Marine Microbiology, Bremen, Germany. mussmann@mpi-bremen.de TI - Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PB - Public Library of Science VL - 5 SP - e230 KW - beggiatoa KW - filament KW - genome KW - mda KW - metagenomics AU - Mussmann, M AU - Hu, FZ AU - Richter, M AU - de Beer, D AU - Preisler, A AU - Jørgensen, BB AU - Huntemann, M AU - Glöckner, FO AU - Amann, R AU - Koopman, WJ AU - Lasken, RS AU - Janto, B AU - Hogg, J AU - Stoodley, P AU - Boissy, R AU - Ehrlich, GD PY - 2007/09/28/ UR - http://dx.doi.org/10.1371/journal.pbio.0050230 ER -