Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Metagenomic and Proteomic Analyses of a Mangrove Microbial Community Following Green Macroalgae Enteromorpha prolifera Degradation

  • Wu, Yijing (College of Food Science, Fujian Agriculture and Forestry University) ;
  • Zhao, Chao (College of Food Science, Fujian Agriculture and Forestry University) ;
  • Xiao, Zheng (College of Food Science, Fujian Agriculture and Forestry University) ;
  • Lin, Hetong (College of Food Science, Fujian Agriculture and Forestry University) ;
  • Ruan, Lingwei (Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration) ;
  • Liu, Bin (College of Food Science, Fujian Agriculture and Forestry University)
  • Received : 2016.07.11
  • Accepted : 2016.08.10
  • Published : 2016.12.28
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Abstract

A mangrove microbial community was analyzed at the gene and protein levels using metagenomic and proteomic methods with the green macroalgae Enteromorpha prolifera as the substrate. Total DNA was sequenced on the Illumina HiSeq 2000 PE-100 platform. Two-dimensional gel electrophoresis in combination with liquid chromatography tandem mass spectrometry was used for proteomic analysis. The metagenomic data revealed that the orders Pseudomonadales, Rhizobiales, and Sphingomonadales were the most prevalent in the mangrove microbial community. By monitoring changes at the functional level, proteomic analyses detected ATP synthase and transporter proteins, which were expressed mainly by members of the phyla Proteobacteria and Bacteroidetes. Members of the phylum Proteobacteria expressed a high number of sugar transporters and demonstrated specialized and efficient digestion of various glycans. A few glycoside hydrolases were detected in members of the phylum Firmicutes, which appeared to be the main cellulose-degrading bacteria. This is the first report of multiple "omics" analysis of E. prolifera degradation. These results support the fact that key enzymes of glycoside hydrolase family were expressed in large quantities, indicating the high metabolic activity of the community.

Keywords

References

  1. Adenle AA, Haslam GE, Lee L. 2013. Global assessment of research and development for algae biofuel production and its potential role for sustainable development in developing countries. Energ. Policy 61: 182-195. https://doi.org/10.1016/j.enpol.2013.05.088
  2. Balat M. 2011. Production of bioethanol from lignocellulosic materials via the biochemical pathway: a review. Energy Convers. Manage. 52: 858-875. https://doi.org/10.1016/j.enconman.2010.08.013
  3. Barnard D, Casanueva A, Tuffin M, Cowan D. 2010. Extremophiles in biofuel synthesis. Environ. Technol. 31: 871-888. https://doi.org/10.1080/09593331003710236
  4. Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Wheeler D. 2006. GenBank. Nucleic Acids Res. 34: D16-D20. https://doi.org/10.1093/nar/gkj157
  5. Bradford MM. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72: 248-254. https://doi.org/10.1016/0003-2697(76)90527-3
  6. Chen Y, Chai L, Tang C, Yang Z, Zheng Y, Shi Y, Zhang H. 2012. Kraft lignin biodegradation by Novosphingobium sp. B-7 and analysis of the degradation process. Bioresour. Technol. 123: 682-685. https://doi.org/10.1016/j.biortech.2012.07.028
  7. Chynoweth DP, Owens JM, Legrand R. 2001. Renewable methane from anaerobic digestion of biomass. Renew. Energy 22: 1-8. https://doi.org/10.1016/S0960-1481(00)00019-7
  8. Deswal D, Khasa YP, Kuhad RC. 2011. Optimization of cellulase production by a brown rot fungus Fomitopsis sp. RCK2010 under solid state fermentation. Bioresour. Technol. 102: 6065-6072. https://doi.org/10.1016/j.biortech.2011.03.032
  9. Deutschbauer AM, Chivian D, Arkin AP. 2006. Genomics for environmental microbiology. Curr. Opin. Biotechnol. 17: 229-235. https://doi.org/10.1016/j.copbio.2006.04.003
  10. Eargle J, Black AA, Sethi A, Trabuco LG, Luthey-Schulten Z. 2008. Dynamics of recognition between tRNA and elongation factor Tu. J. Mol. Biol. 377: 1382-1405. https://doi.org/10.1016/j.jmb.2008.01.073
  11. Hanreich A, Schimpf U, Zakrzewski M, Schlüter A, Benndorf D, Heyer R, et al. 2013. Metagenome and metaproteome analyses of microbial communities in mesophilic biogasproducing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. Syst. Appl. Microbiol. 36: 330-338. https://doi.org/10.1016/j.syapm.2013.03.006
  12. Heyer R, Kohrs F, Benndorf D, Rapp E, Kausmann R, Heiermann M, et al. 2013. Metaproteome analysis of the microbial communities in agricultural biogas plants. Nat. Biotechnol. 30: 614-622.
  13. Huson DH, Auch AF, Qi J, Schuster SC. 2007. MEGAN analysis of metagenomic data. Genome Res. 17: 377-386. https://doi.org/10.1101/gr.5969107
  14. Izzo V, Tedesco P, Notomista E, Pagnotta E, Donato AD, Trincone A, Tramice A. 2014. a-Rhamnosidase activity in the marine isolate Novosphingobium sp. PP1Y and its use in the bioconversion of flavonoids. J. Mol. Catal. B Enzym. 105: 95-103. https://doi.org/10.1016/j.molcatb.2014.04.002
  15. Jehmlich N, Kleinsteuber S, Vogt C, Benndorf D, Harms H, Schmidt F, et al. 2010. Phylogenetic and proteomic analysis of an anaerobic toluene-degrading community. J. Appl. Microbiol. 109: 1937-1945. https://doi.org/10.1111/j.1365-2672.2010.04823.x
  16. Jia B, Xuan L, Cai K, Hu Z, Ma L, Wei C. 2013. NeSSM: a next-generation sequencing simulator for metagenomics. PLoS One 8: e75448. https://doi.org/10.1371/journal.pone.0075448
  17. Kato S, Haruta S, Cui ZJ, Ishii M, Igarashi Y. 2004. Effective cellulose degradation by a mixed-culture system composed of a cellulolytic Clostridium and aerobic non-cellulolytic bacteria. FEMS Microbiol. Ecol. 51: 133-142. https://doi.org/10.1016/j.femsec.2004.07.015
  18. Kato S, Haruta S, Cui ZJ, Ishii M, Igarashi Y. 2005. Stable coexistence of five bacterial strains as a cellulose-degrading community. Appl. Environ. Microbiol. 71: 7099-7106. https://doi.org/10.1128/AEM.71.11.7099-7106.2005
  19. Kohrs F, Heyer R, Magnussen A, Benndorf D, Muth T, Behne A, et al. 2014. Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants. Anaerobe 29: 59-67. https://doi.org/10.1016/j.anaerobe.2013.11.009
  20. Kumar A, Vanamala A, Kumar R. 2005. Exploration of bacterial laccase in Pseudomonas stutzeri and its application in bleaching the wood pulp. FEBS J. 272(s1)(N6-008P).
  21. Li A, Chu Y, Wang X, Ren L, Yu J, Liu X, et al. 2013. A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor. Biotechnol. Biofuels 6: 3. https://doi.org/10.1186/1754-6834-6-3
  22. Li DM, Chen LM, Zhao JS, Zhang XW, Wang QY, Wang HX, Ye NH. 2010. Evaluation of the pyrolytic and kinetic characteristics of Enteromorpha prolifera as a source of renewable bio-fuel from the Yellow Sea of China. Chem. Eng. Res. Des. 88: 647-652. https://doi.org/10.1016/j.cherd.2009.10.011
  23. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. 2009. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967. https://doi.org/10.1093/bioinformatics/btp336
  24. Li X, Cui Z, Liu Y, Song C, Shi G. 2013. Transcriptome analysis and discovery of genes involved in immune pathways from hepatopancreas of microbial challenged mitten crab Eriocheir sinensis. PLoS One 8: e68233. https://doi.org/10.1371/journal.pone.0068233
  25. Liao QY, Li J, Zhang JH, Li M, Lu Y, Xu RL. 2009. An ecological analysis of soil sarcodina at Dongzhaigang mangrove in Hainan Island, China. Eur. J. Soil Biol. 45: 214-219. https://doi.org/10.1016/j.ejsobi.2008.12.003
  26. Liu DY, Keesing JK, Xing QG, Shi P. 2009 World's largest macroalgal bloom caused by expansion of seaweed aquaculture in China. Mar. Pollut. Bull. 58: 888-895. https://doi.org/10.1016/j.marpolbul.2009.01.013
  27. Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT. 2012. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One 7: e30087. https://doi.org/10.1371/journal.pone.0030087
  28. Maalej H, Ben Ayed H, Ghorbel-Bellaaj O, Nasri M, Hmidet N. 2014. Production and biochemical characterization of a high maltotetraose (G4) producing amylase from Pseudomonas stutzeri AS22. Biomed. Res. Int. 2014: 156438.
  29. Maalej H, Hmidet N, Ghorbel-Bellaaj O, Nasri M. 2013. Purification and biochemical characterization of a detergent stable a-amylase from Pseudomonas stutzeri AS22. Biotechnol. Bioprocess Eng. 18: 1-10. https://doi.org/10.1007/s12257-012-0544-x
  30. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380. https://doi.org/10.1038/nature03959
  31. Metzker ML. 2010. Sequencing technologies - the next generation. Nat. Rev. Genet. 11: 31-46. https://doi.org/10.1038/nrg2626
  32. Morozova O, Marra MA. 2008. Applications of nextgeneration sequencing technologies in functional genomics. Genomics 92: 255-264. https://doi.org/10.1016/j.ygeno.2008.07.001
  33. Nkemka VN, Murto M. 2010. Evaluation of biogas production from seaweed in batch tests and in UASB reactors combined with the removal of heavy metals. J. Environ. Manage. 91: 1573-1579. https://doi.org/10.1016/j.jenvman.2010.03.004
  34. Oda K, Kakizono D, Yamada O, Iefuji H, Akita O, Iwashita K. 2006. Proteomic analysis of extracellular proteins from Aspergillus oryzae grown under submerged and solid-state culture conditions. Appl. Environ. Microbiol. 72: 3448-3457. https://doi.org/10.1128/AEM.72.5.3448-3457.2006
  35. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. 1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551-3567. https://doi.org/10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2
  36. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, et al. 2008. A large genome center's improvements to the Illumina sequencing system. Nat. Methods 5: 1005-1010. https://doi.org/10.1038/nmeth.1270
  37. Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, et al. 2009. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 6: 639-641. https://doi.org/10.1038/nmeth.1361
  38. Sharafi-Yazdi MK, Azimi C, Khalili MB. 2001. Isolation and identification of bacteria present in the activated sludge unit, in the treatment of industrial waste water. Iranian J. Publ. Health 30: 91-94.
  39. She R, Chu JS, Wang K, Pei J, Chen N. 2009. GenBlastA: enabling BLAST to identify homologous gene sequences. Genome Res. 19: 143-149.
  40. Shin KC, Oh DK. 2014. Characterization of a novel recombinant ${\beta}$-glucosidase from Sphingopyxis alaskensis that specifically hydrolyzes the outer glucose at the C-3 position in protopanaxadiol-type ginsenosides. J. Biotechnol. 172: 30-37. https://doi.org/10.1016/j.jbiotec.2013.11.026
  41. Simmons CW, Reddy AP, D'Haeseleer P, Khudyakov J, Billis K, Pati A, et al. 2014. Metatranscriptomic analysis of lignocellulolytic microbial communities involved in highsolids decomposition of rice straw. Biotechnol. Biofuels 7: 495. https://doi.org/10.1186/s13068-014-0180-0
  42. Syn CK, Swarup S. 2000. A scalable protocol for the isolation of large-sized genomic DNA within an hour from several bacteria. Anal. Biochem. 278: 86-90. https://doi.org/10.1006/abio.1999.4410
  43. Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28: 33-36. https://doi.org/10.1093/nar/28.1.33
  44. Taylor CR, Hardiman EM, Ahmad M, Sainsbury PD, Norris PR, Bugg TD. 2012. Isolation of bacterial strains able to metabolize lignin from screening of environmental samples. J. Appl. Microbiol. 113: 521-530. https://doi.org/10.1111/j.1365-2672.2012.05352.x
  45. Toyoda A, Iio W, Mitsumori M, Minato H. 2009. Isolation and identification of cellulose-binding proteins from sheep rumen contents. Appl. Environ. Microbiol. 75: 1667-1673. https://doi.org/10.1128/AEM.01838-08
  46. Wargacki AJ, Leonard E, Win MN, Regitsky DD, Santos CN, Kim PB, et al. 2012. An engineered microbial platform for direct biofuel production from brown macroalgae. Science 335: 308-313. https://doi.org/10.1126/science.1214547
  47. Wenzel M, Schönig I, Berchtold M, Kämpfer P, König H. 2002. Aerobic and facultatively anaerobic cellulolytic bacteria from the gut of the termite Zootermopsis angusticollis. J. Appl. Microbiol. 92: 32-40. https://doi.org/10.1046/j.1365-2672.2002.01502.x
  48. Williams MA, Taylor EB, Mula HP. 2010. Metaproteomic characterization of a soil microbial community following carbon amendment. Soil Biol. Biochem. 42: 1148-1156. https://doi.org/10.1016/j.soilbio.2010.03.021
  49. Wilmes P, Bond PL. 2004. The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ. Microbiol. 6: 911-920. https://doi.org/10.1111/j.1462-2920.2004.00687.x
  50. Wilmes P, Wexler M, Bond PL. 2008. Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS One 3: e1778. https://doi.org/10.1371/journal.pone.0001778
  51. Yu H, Chan YL, Wool IG. 2009. The identification of the determinants of the cyclic, sequential binding of elongation factors Tu and G to the ribosome. J. Mol. Biol. 386: 802-813. https://doi.org/10.1016/j.jmb.2008.12.071
  52. Zhao C. 2014. Purification and composition analysis of polysaccharide from edible seaweed Enteromorpha prolifera and polysaccharides depolymerized enzymes from microorganisms. Res. J. Biotechnol. 9: 30-36.
  53. Zhao C, Ruan LW. 2011. Biodegradation of Enteromorpha prolifera by mangrove degrading micro-community with physical-chemical pretreatment. Appl. Microbiol. Biotechnol. 92: 709-716. https://doi.org/10.1007/s00253-011-3384-2
  54. Zhou J, Liu L, Shi Z, Du G, Chen J. 2009. ATP in current biotechnology: regulation, applications and perspectives. Biotechnol. Adv. 27: 94-101. https://doi.org/10.1016/j.biotechadv.2008.10.005

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