Abstract
Catalase plays an important role in the metabolism of marine bacteria and has potential impact on the marine environment. Four PCR primers were designed to amplify the catalase gene fragments in marine bacteria by applying metagenomic DNA from Yellow Sea surface water as the template. Of the four reproducible target PCR products, the longest one with 900 bp were chosen for catalase gene library construction by the T-vector and the white Escherichia coli colonies in the library was screened through restriction-digesting the reamplified insert fragments by the selected restriction endonuclease MboI, and then the bands of the resulting products were displayed in the agarose gel by electrophoresis. The unique restriction fragment length polymorphism (RFLP) pattern was selected and the corresponding catalase gene fragments were sequenced, which verified that every unique RFLP pattern represented one type of catalase. This PCR–RFLP method above was established to investigate the bacterial catalase diversity in seawater.
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Zamocky M, Furtmüller PG, Obinger C (2008) Evolution of catalases from bacteria to humans. Antioxid Redox Sign 10:1527–1547. doi:10.1089/ars.2008.2046
Margesin R, Neuner G, Storey KB (2007) Cold-loving microbes, plants, and animals—fundamental and applied aspects. Naturwissenschaften 94:77–99. doi:10.1007/s00114-006-0162-6
Abele D, Ferreyra GA, Schloss I (1999) H2O2 accumulation from photochemical production and atmospheric wet deposition in Antarctic coastal and off-shore waters of Potter Cove, King George Island, South Shetland Islands. Antarct Sci 11:131–139. doi:10.1017/S095410209900019X
Morris JJ, Johnson ZI, Szul MJ, Keller M, Zinser ER (2011) Dependence of the cyanobacterium Prochlorococcus on hydrogen peroxide scavenging microbes for growth at the ocean’s surface. PLoS ONE 6:e16805. doi:10.1371/journal.pone.0016805
Moreno CM (2012) Hydrogen peroxide production driven by UV-B in planktonic microorganisms: a photocatalytic factor in sea warming and ice melting in regions with ozone depletion? Biogeochemistry 107:1–8. doi:10.1007/s10533-010-9566-7
den Besten HMW, Effraimidou S, Abee T (2013) Catalase activity as a biomarker for mild-stress-induced robustness in Bacillus weihenstephanensis. Appl Environ Microbiol 79:57–62. doi:10.1128/AEM.02282-12
Klotz MG, Loewen PC (2003) The molecular evolution of catalatic hydroperoxidases: evidence for multiple lateral transfer of genes between prokaryota and from bacteria into eukaryota. Mol Biol Evol 20:1098–1112. doi:10.1093/molbev/msg129
Lal S, Cheema S, Kalia VC (2008) Phylogeny vs genome reshuffling: horizontal gene transfer. Ind J Microbiol 48:228–242. doi:10.1007/s12088-008-0034-1
Kobayashi T, Koide O, Mori K, Shimamura S, Matsuura T, Miura T, Takaki Y, Morono Y, Nunoura T, Imachi H, Inagaki F, Takai K, Horikoshi K (2008) Phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula. Extremophiles 12:519–527. doi:10.1007/s00792-008-0157-7
Sharma N, Tanksale H, Kapley A, Purohit HJ (2012) Mining the metagenome of activated biomass of an industrial wastewater treatment plant by a novel method. Ind J Microbiol 52:538–543. doi:10.1007/s12088-012-0263-1
Kalia VC, Mukherjee T, Bhushan A, Joshi J, Shankar P, Huma N (2011) Analysis of the unexplored features of rrs (16S rDNA) of the genus Clostridium. BMC Genomics 12:18. doi:10.1186/1471-2164-12-18
Porwal S, Lal S, Cheema S, Kalia VC (2009) Phylogeny in aid of the present and novel microbial lineages: diversity in Bacillus. PLoS ONE 4:e4438. doi:10.1371/journal.pone.0004438
Rose TM, Schultz ER, Henikoff JG, Pietrokovski S, McCallum CM, Henikoff S (1998) Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly-related sequences. Nucleic Acids Res 26:1628–1635. doi:10.1093/nar/26.7.1628
Pei J, Tang M, Grishin NV (2008) PROMALS3D web server for accurate multiple protein sequence and structure alignments. Nucleic Acids Res 36:W30–W34. doi:10.1093/nar/gkn322
Barengo NG, Benito JM, Abate CM (2004) Molecular characterization of microbial communities from marine environments. In: Spencer JFT, Ragout de Spencer AL (eds) Environmental microbiology: methods and protocols (Methods in biotechnology 16). Humana, Totowa, pp 75–82
Cai H, Jiao N (2008) Diversity and abundance of nitrate assimilation genes in the Northern South China Sea. Microb Ecol 56:751–764. doi:10.1007/s00248-008-9394-7
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98
Vincze T, Posfai J, Roberts RJ (2003) NEBcutter: a program to cleave DNA with restriction enzymes. Nucleic Acids Res 31:3688–3691. doi:10.1093/nar/gkg526
Singhal H, Ren YR, Kern SE (2010) Improved DNA electrophoresis in conditions favoring polyborates and lewis acid complexation. PLoS ONE 5:e11318. doi:10.1371/journal.pone.0011318
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi:10.1093/molbev/msr121
Wang W, Wang F, Ji X, Liu S, Yuan C, Sun M (2011) Cloning and characterization of a psychrophilic catalase gene from an Antarctic bacterium. Afr J Microbiol Res 5:3195–3199. doi:10.5897/AJMR11.166
Phucharoen K, Hoshino K, Takenaka Y, Shinozawa T (2002) Purification, characterization, and gene sequencing of a catalase from an alkali- and halo-tolerant bacterium, Halomonas sp. SK1. Biosci Biotechnol Biochem 66:955–962. doi:10.1271/bbb.68.814
Pommier T, Canbäck B, Riemann L, Boström KH, Simu K, Lundberg P, Tunlid A, Hagström Å (2007) Global patterns of diversity and community structure in marine bacterioplankton. Mol Ecol 16:867–880. doi:10.1111/j.1365-294X.2006.03189.x
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This work was supported by the National Natural Science Foundation of China (41006119) and the National High Technology Research and Development Program of China (2011AA090703).
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Wang, W., Ji, X., Yuan, C. et al. A Method for Molecular Analysis of Catalase Gene Diversity in Seawater. Indian J Microbiol 53, 477–481 (2013). https://doi.org/10.1007/s12088-013-0404-1
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DOI: https://doi.org/10.1007/s12088-013-0404-1