Complete genome sequence of Tolumonas auensis type strain (TA 4T)
Olga Chertkov,Olga Chertkov,Alex Copeland,Susan Lucas,Alla Lapidus,Kerrie W. Berry,John C. Detter,John C. Detter,Tijana Glavina del Rio,Nancy Hammon,Eileen Dalin,Hope Tice,Sam Pitluck,Paul G. Richardson,David Bruce,David Bruce,Lynne Goodwin,Lynne Goodwin,Cliff Han,Cliff Han,Roxanne Tapia,Roxanne Tapia,Elizabeth Saunders,Elizabeth Saunders,Jeremy Schmutz,Thomas Brettin,Thomas Brettin,Frank W. Larimer,Frank W. Larimer,Miriam Land,Miriam Land,Loren Hauser,Loren Hauser,Stefan Spring,Manfred Rohde,Nikos C. Kyrpides,Natalia Ivanova,Markus Göker,Harry R. Beller,Hans-Peter Klenk,Tanja Woyke +40 more
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TLDR
The Tolumonas auensis strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine.Abstract:
Tolumonas auensis Fischer-Romero et al. 1996 is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine. This is of interest because toluene is normally considered to be a tracer of anthropogenic pollution in lakes, but T. auensis represents a biogenic source of toluene. Other than Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4T is the only other member in the family Aeromonadaceae with a completely sequenced type-strain genome. The 3,471,292 bp chromosome with a total of 3,288 protein-coding and 116 RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI 2008.read more
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In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community
Kamrun Zargar,R. Saville,Ryan M. Phelan,Susannah G. Tringe,Christopher J. Petzold,Jay D. Keasling,Harry R. Beller +6 more
TL;DR: This first-time study of the phenylacetate decarboxylase reaction constitutes an important step in understanding and ultimately harnessing it for making bio-based toluene.
Journal ArticleDOI
In silico prospection of microorganisms to produce polyhydroxyalkanoate from whey: Caulobacter segnis DSM 29236 as a suitable industrial strain.
Daniel Bustamante,Silvia Segarra,Marta Tortajada,Daniel Ramón,Carlos del Cerro,María Auxiliadora Prieto,José Ramón Iglesias,Antonia Rojas +7 more
TL;DR: This study reveals Caulobacter segnis DSM 29236 as a PHA producer and experimentally validates the in silico bioprospecting strategy for selecting microorganisms for waste re‐valorization for whey surplus valorization.
Journal ArticleDOI
Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens.
Briallen Lobb,Rhiannon Hodgson,Michael D. Lynch,Michael J. Mansfield,Jiujun Cheng,Trevor C. Charles,Josh D. Neufeld,Paul M. Craig,Andrew C. Doxey +8 more
TL;DR: The results demonstrate that wild-caught fish have a reproducible decomposer succession and that the fish necrobiome serves as a potential source of putative pathogens and toxigenic bacteria.
GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes - eScholarship
TL;DR: It is found that manual curation of gene models using the anomaly reports generated by GenePRIMP improved their quality, and the applicability of GenePRP in improving finishing quality and comparing different genome-sequencing and annotation technologies is demonstrated.
Journal ArticleDOI
Organic carbon and eukaryotic predation synergistically change resistance and resilience of aquatic microbial communities.
Wenwen Fang,M.J.Y. Lin,Jiang Tian Shi,Zhiwei Liang,Xiang Tu,Zhili He,Rongliang Qiu,Shanquan Wang +7 more
TL;DR: In this paper , the impact of dissolved organic carbon (DOC) and nutrients on aquatic microbial communities in urban rivers was investigated, and the results showed that low DOC enriched K-selection microorganisms (e.g., C39, Tolumonas and CR08G) had low biomass and low resilience, as well as high resistance to perturbations in changing microbial community assemblies.
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
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TL;DR: BCL3 and Sheehy cite Bergey's manual of determinative bacteriology of which systematic bacteriology, first edition, is an expansion.
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