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http://dx.doi.org/10.7845/kjm.2019.9037

Draft genome sequence of humic substances-degrading Pseudomonas kribbensis CHA-19 from temperate forest soil  

Kim, Dockyu (Division of Polar Life Sciences, Korea Polar Research Institute)
Lee, Hyoungseok (Unit of Polar Genomics, Korea Polar Research Institute)
Publication Information
Korean Journal of Microbiology / v.55, no.2, 2019 , pp. 177-179 More about this Journal
Abstract
Pseudomonas kribbensis CHA-19 was isolated from a temperate forest soil (mid latitude) in New Jersey, USA, for its ability to degrade humic acids, a main component of humic substances (HS), and subsequently confirmed to be able to decolorize lignin (a surrogate for HS) and catabolize lignin-derived ferulic and vanillic acids. The draft genome sequence of CHA-19 was analyzed to discover the putative genes for depolymerization of polymeric HS (e.g., dye-decolorizing peroxidases and laccase-like multicopper oxidases) and catabolic degradation of HS-derived small aromatics (e.g., vanillate O-demethylase and biphenyl 2,3-dioxygenase). The genes for degradative activity were used to propose a HS degradation pathway of soil bacteria.
Keywords
catabolic pathway; degradative enzyme; humic acids; soil bacteria;
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1 Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov AS, Lesin V, Nikolenko S, Pham S, Prjibelski A, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477.   DOI
2 Bugg TD, Ahmad M, Hardiman EM, and Rahmanpour R. 2011. Pathways for degradation of lignin in bacteria and fungi. Nat. Prod. Rep. 28, 1883-1896.   DOI
3 Grinhut T, Hertkorn N, Schmitt-Kopplin P, Hadar Y, and Chen Y. 2011. Mechanisms of humic acids degradation by white rot fungi explored using $^1H$ NMR spectroscopy and FTICR mass spectrometry. Environ. Sci. Technol. 45, 2748-2754.   DOI
4 Kamimura N, Takahashi K, Mori K, Araki T, Fujita M, Higuchi Y, and Masai E. 2017. Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism. Environ. Microbiol. Rep. 9, 679-705.   DOI
5 Kim D, Park HJ, Sul WJ, and Park H. 2018. Transcriptome analysis of Pseudomonas sp. from subarctic tundra soil: pathway description and gene discovery for humic acids degradation. Folia Microbiol. (Praha) 63, 315-323.   DOI
6 Lipczynska-Kochany E. 2018. Humic substances, their microbial interactions and effects on biological transformations of organic pollutants in water and soil: A review. Chemosphere 202, 420-437.   DOI
7 Lomsadze A, Gemayel K, Tang S, and Borodovsky M. 2018. Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes. Genome Res. 28, 1079-1089.   DOI