Structural Alteration of Humic Acids by Pseudomonas spp. from Deep Terrestrial Subsurface Diatomite Formations in Northernmost Japan

References

• Alex S, Savoie R, Corbeil M-C, Beauchamp AL. 1986. Complexation of glycylglycine by the methylmercury cation: a vibrational spectroscopy and X-ray diffraction study. Can J Chem 64:148–157.
   Web of Science ®Google Scholar
• Asakawa D, Kiyota T, Yanagi Y, Fujitake N. 2008. Optimization of conditions for high-performance size-exclusion chromatography of different soil humic acids. Anal Sci 24:607–613.
   PubMed Web of Science ®Google Scholar
• Chen M, Yan Y, Zhang W, Lu W, Wang J, Ping S, Lin M. 2011. Complete genome sequence of the type strain Pseudomonas stutzeri CGMCC 1.1803. J Bacteriol 193:6095.
   PubMed Web of Science ®Google Scholar
• Dari K, Béchet M, Blondeau R. 1995. Isolation of soil Streptomyces strains capable of degrading humic acids and analysis of their peroxidase activity. FEMS Microbiol Ecol 16:115–122.
   Web of Science ®Google Scholar
• De Haan H. 1974. Effect of a fulvic acid fraction on the growth of a Pseudomonas from Tjeukemeer (the Netherlands). Freshwat Biol 4:301–310.
   Web of Science ®Google Scholar
• Esham EC, Ye W, Moran MA. 2000. Identification and characterization of humic substances-degrading bacterial isolates from an estuarine environment. FEMS Micriobiol Ecol 34:103–111.
   PubMed Web of Science ®Google Scholar
• Filip Z, Berthelin J. 2001. Analytical determination of the microbial utilization and transformation of humic acids extracted from municipal refuse. Fresenius J Anal Chem 371:675–681.
   PubMedGoogle Scholar
• Filip Z, Tesařová M. 2004. Microbial degradation and transformation of humic acids from permanent meadow and forest soils. Inter Biodeterior Biodeg 54:225–231.
   Web of Science ®Google Scholar
• Grinhut T, Hertkorn N, Schmitt-Kopplin P, Hadar Y, 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.
   PubMed Web of Science ®Google Scholar
• Hatakka A. 2001. Biodegradation of lignin, In: Hofrichter M, Steinbüchel A, editors. Biopolymers (Volume 1) Lignin, Humic Substances and Coal. Weinheim: Wiley-VCH. P 129–180.
   Google Scholar
• Hertkorn N, Claus H, Schmitt-Kopplin P, Perdue EM, Filip Z. 2002. Utilization and transformation of aquatic humic substances by autochthonous microorganisms. Environ Sci Technol 36:4334–4345.
   PubMed Web of Science ®Google Scholar
• Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Microbiol 62:716–721.
   PubMed Web of Science ®Google Scholar
• Kontchou CY, Blondeau R. 1992. Biodegradation of soil humic acids by Streptomyces viridosporus. Can J Microbiol 38:203–208.
   PubMed Web of Science ®Google Scholar
• Köberl M, Muller H, Ramadan EM, Berg G. 2011. Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health. PLoS One 6:e24452.
   PubMed Web of Science ®Google Scholar
• Kronvall G, Myhre E. 1977. Differential staining of bacteria in clinical specimens using acridine orange buffered at low pH. Acta Pathol Microbiol Scand Sect B 85:249–254.
   PubMedGoogle Scholar
• Kuwatsuka S, Watanabe A, Itoh K, Arai S. 1992. Comparison of two methods of preparation of humic and fulvic acids, IHSS method and NAGOYA method. Soil Sci Plant Nutr 38:23–30.
   Web of Science ®Google Scholar
• Lalucat J, Bennasar A, Bosch R, García-Valdés E, Palleroni NJ. 2006. Biology of Pseudomonas stutzeri. Microbiol Mol Biol Rev 70:510–547.
   PubMed Web of Science ®Google Scholar
• Lane DJ. 1991. 16S/23S rRNA sequencing. In: Stackebrandt E, and Goodfellow M, editors. Nucleic Acid Techniques in Bacterial Systematics. New York: John Wiley and Sons. p115–175.
   Google Scholar
• Li D, Yan Y, Ping S, Chen M, Zhang W, Li L, Lin W, Geng L, Liu W, Lu W, Lin M. 2010. Genome-wide investigation and functional characterization of the beta-ketoadipate pathway in the nitrogen-fixing and root-associated bacterium Pseudomonas stutzeri A1501. BMC Microbiol 10:36.
   PubMed Web of Science ®Google Scholar
• MacCarthy P. 2001. The principles of humic substances. Soil Sci 166:738–751.
   Web of Science ®Google Scholar
• McKnight D, Thurman EM, Wershaw RL. 1985. Biogeochemistry of aquatic humic substances in Thoreau's Bog, Concord, Massachusetts. Ecology 6:1339–1352.
   Web of Science ®Google Scholar
• Michel FC, Reddy CA, Forney LJ. 1995. Microbial degradation and humification of the lawn care pesticide 2,4-dichlorophenoxyacetic acid during the composting of yard trimmings. Appl Environ Microbiol 61:2566–2571.
   PubMed Web of Science ®Google Scholar
• Romanenko LA, Uchino M, Falsen E, Lysenko AM, Zhukova NV, Mikhailov VV. 2005. Pseudomonas xanthomarina sp. nov., a novel bacterium isolated from marine ascidian. J Gen Appl Microbiol 51:65–71.
   PubMed Web of Science ®Google Scholar
• Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425.
   PubMed Web of Science ®Google Scholar
• Sakellariadou F. 2006. Spectroscopic studies of humic acids from subsurface sediment samples collected across the Aegean Sea. Medit Mar Sci 7/2:11–17.
   Web of Science ®Google Scholar
• Senesi N, Loffredo E. 2001. Soil humic substances. In: Hofrichter M, Steinbüchel A, editors. Biopolymers (Volume 1) Lignin, Humic Substances and Coal. Weinheim: Wiley-VCH. P 247–299.
   Google Scholar
• Shimizu S, Akiyama M, Ishijima Y, Hama K, Kunimaru T, Naganuma T. 2006. Molecular characterization of microbial communities in fault-bordered aquifers in the Miocene formation of northernmost Japan. Geobiology 4:203–213.
   Web of Science ®Google Scholar
• Sidorenko OD, Aristarkhova VI, Chernikov VA. 1979. Changes in the composition and properties of humic acids about by the action of microorganisms of the genus Nocardia. Biol Bull Acad Sci USSR 5:150–155.
   Google Scholar
• Steffen KT, Hatakka A, Hofrichter M. 2002. Degradation of humic acids by the litter-decomposing basidiomycete Collybia dryophila. Appl Environ Microbiol 68: 3442–3448.
   PubMed Web of Science ®Google Scholar
• Stevenson FJ. 1994. Humus chemistry. Genesis, composition, reactions, 2nd ed. New York, NY: John Wiley & Sons, p1–21.
   Google Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetic analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739.
   PubMed Web of Science ®Google Scholar
• Thurman EM. 1985. Organic Geochemistry of Natural Waters. Dordrecht: Nijhoff/Junk, p113–150.
   Google Scholar
• Wang Y, Qian PY. 2009. Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PLoS One 4:e7401.
   PubMed Web of Science ®Google Scholar
• Willmann G, Fakoussa RM. 1997. Biological bleaching of water-soluble coal macromolecules by a basidiomycete strain. Appl Microbiol Biotechnol 47:95–101.
   Web of Science ®Google Scholar
• Wolkers WF, Bochicchio A, Selvaggi G, Hoekstra FA. 1998. Fourier transform infrared microspectroscopy detects changes in protein secondary structure associated with desiccation tolerance in developing maize embryos. Plant Physiol 116:1169–1177.
   PubMed Web of Science ®Google Scholar
• Wolkers WF, Hoekstra FA. 1995. Aging of dry desiccation-tolerant pollen does not affect protein secondary structure. Plant Physiol 109:907–915.
   PubMed Web of Science ®Google Scholar
• Yanagi Y, Hamaguchi S, Tamaki H, Suzuki T, Otsuka H, Fujitake N. 2003. Relation of chemical properties of soil humic acids to decolorization by white rot fungus–Coriolus consors. Soil Sci Plant Nutr 49:201–206.
   Web of Science ®Google Scholar
• Yanagi Y, Yoda K, Ogura K, Fujitake N. 2008. Population of humic acid degrading microorganisms in andosols under different vegetation types and grassland management regimens. Microbes Environ 23:44–48.
   PubMed Web of Science ®Google Scholar
• Yonebayashi K, Hattori T. 1989. Chemical and biological studies on environmental humic acids. Soil Sci Plant Nutr 35:383–392.
   Web of Science ®Google Scholar
• Yumoto I, Yamazaki K, Hishinuma M, Nodasaka Y, Suemori A, Nakajima K, Inoue N, Kawasaki K. 2001. Pseudomonas alcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile isolated from seawater. Inter J Syst Evol Microbiol 51:349–355.
   PubMed Web of Science ®Google Scholar