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Metagenomic and Proteomic Analyses of a Mangrove Microbial Community Following Green Macroalgae Enteromorpha prolifera Degradation

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초록

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. Twodimensional 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.

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. Twodimensional 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.

참고문헌 (54)

  1. Adenle AA, "Global assessment of research and development for algae biofuel production and its potential role for sustainable development in developing countries", Energ. Policy, 61, pp.182~195 (2013)
  2. Balat M, "Production of bioethanol from lignocellulosic materials via the biochemical pathway: a review", Energy Convers. Manage, 52, pp.858~875 (2011)
  3. Barnard D, "Extremophiles in biofuel synthesis", Environ. Technol, 31, pp.871~888 (2010)
  4. Benson D, "GenBank", Nucleic Acids Res, 34, pp.D16~D20 (2006)
  5. Bradford MM, "A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding", Anal. Biochem, 72, pp.248~254 (1976)
  6. Chen Y, "Kraft lignin biodegradation by Novosphingobium sp. B-7 and analysis of the degradation process", Bioresour. Technol, 123, pp.682~685 (2012)
  7. Chynoweth DP, "Renewable methane from anaerobic digestion of biomass", Renew. Energy, 22, pp.1~8 (2001)
  8. Deswal D, "Optimization of cellulase production by a brown rot fungus Fomitopsis sp. RCK2010 under solid state fermentation", Bioresour. Technol, 102, pp.6065~6072 (2011)
  9. Deutschbauer AM, "Genomics for environmental microbiology", Curr. Opin. Biotechnol, 17, pp.229~235 (2006)
  10. Eargle J, "Dynamics of recognition between tRNA and elongation factor Tu", J. Mol. Biol, 377, pp.1382~1405 (2008)
  11. Hanreich A, "Metagenome and metaproteome analyses of microbial communities in mesophilic biogasproducing anaerobic batch fermentations indicate concerted plant carbohydrate degradation", Syst. Appl. Microbiol, 36, pp.330~338 (2013)
  12. Heyer R, "Metaproteome analysis of the microbial communities in agricultural biogas plants", Nat. Biotechnol, 30, pp.614~622 (2013)
  13. Huson DH, "MEGAN analysis of metagenomic data", Genome Res, 17, pp.377~386 (2007)
  14. Izzo V, "a-Rhamnosidase activity in the marine isolate Novosphingobium sp. PP1Y and its use in thebioconversion of flavonoids", J. Mol. Catal. B Enzym, 105, pp.95~103 (2014)
  15. Jehmlich N, "Phylogenetic and proteomic analysis of an anaerobic toluene-degrading community", J. Appl. Microbiol, 109, pp.1937~1945 (2010)
  16. Jia B, "NeSSM: a next-generation sequencing simulator for metagenomics", PLoS One, 8, pp.e75448~ (2013)
  17. Kato S, "Effective cellulose degradation by a mixed-culture system composed of a cellulolytic Clostridium and aerobic non-cellulolytic bacteria", FEMS Microbiol. Ecol, 51, pp.133~142 (2004)
  18. Kato S, "Stable coexistence of five bacterial strains as a cellulose-degrading community", Appl. Environ. Microbiol, 71, pp.7099~7106 (2005)
  19. Kohrs F, "Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants", Anaerobe, 29, pp.59~67 (2014)
  20. Kumar A, "Exploration of bacterial laccase in Pseudomonas stutzeri and its application in bleaching the wood pulp", FEBS J, 272(s1) (2005)
  21. Li A, "A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor", Biotechnol. Biofuels, 6, pp.3~ (2013)
  22. Li DM, "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, pp.647~652 (2010)
  23. Li R, "SOAP2 : an improved ultrafast tool for short read alignment", Bioinformatics, 25, pp.1966~1967 (2009)
  24. Li X, "Transcriptome analysis and discovery of genes involved in immune pathways from hepatopancreas of microbial challenged mitten crab Eriocheir sinensis", PLoS One, 8, pp.e68233~ (2013)
  25. Liao QY, "An ecological analysis of soil sarcodina at Dongzhaigang mangrove in Hainan Island", China. Eur. J. Soil Biol, 45, pp.214~219 (2009)
  26. Liu DY, "World’s largest macroalgal bloom caused by expansion of seaweed aquaculture in China", Mar. Pollut. Bull, 58, pp.888~895 (2009)
  27. Luo C, "Direct comparisons of Illumina vs. Roche 454sequencing technologies on the same microbial community DNA sample", PLoS One, 7, pp.e30087~ (2012)
  28. Maalej H, "Production and biochemical characterization of a high maltotetraose (G4) producing amylase from Pseudomonas stutzeri AS22", Biomed. Res. Int, 2014, pp.156438~ (2014)
  29. Sam Mathew, "High Throughput Screening Methods for ω-Transaminases", Biotechnology and Bioprocess Engineering, 18(1), pp.1~7 (2013), 한국생물공학회
  30. Margulies M, "Genome sequencing in microfabricated high-density picolitre reactors", Nature, 437, pp.376~380 (2005)
  31. Metzker ML, "Sequencing technologies - the next generation", Nat. Rev. Genet, 11, pp.31~46 (2010)
  32. Morozova O, "Applications of nextgeneration sequencing technologies in functional genomics", Genomics, 92, pp.255~264 (2008)
  33. Nkemka VN, "Evaluation of biogas production from seaweed in batch tests and in UASB reactors combined with the removal of heavy metals", J. Environ. Manage, 91, pp.1573~1579 (2010)
  34. Oda K, "Proteomic analysis of extracellular proteins from Aspergillus oryzae grown under submerged and solid-state culture conditions", Appl. Environ. Microbiol, 72, pp.3448~3457 (2006)
  35. Perkins DN, "Probability-based protein identification by searching sequence databases using mass spectrometry data", Electrophoresis, 20, pp.3551~3567 (1999)
  36. Quail MA, "A large genome center’s improvements to the Illumina sequencing system", Nat. Methods, 5, pp.1005~1010 (2008)
  37. Quince C, "Accurate determination of microbial diversity from 454 pyrosequencing data", Nat. Methods, 6, pp.639~641 (2009)
  38. Sharafi-Yazdi MK, "Isolation and identification of bacteria present in the activated sludge unit, in the treatment of industrial waste water", Iranian J. Publ. Health, 30, pp.91~94 (2001)
  39. She R, "GenBlastA:enabling BLAST to identify homologous gene sequences", Genome Res, 19, pp.143~149 (2009)
  40. Shin KC, "Characterization of a novel recombinant β-glucosidase from Sphingopyxis alaskensis that specifically hydrolyzes the outer glucose at the C-3 position in protopanaxadiol-type ginsenosides", J. Biotechnol, 172, pp.30~37 (2014)
  41. Simmons CW, "Metatranscriptomic analysis of lignocellulolytic microbial communities involved in highsolids decomposition of rice straw", Biotechnol. Biofuels, 7, pp.495~ (2014)
  42. Syn CK, "A scalable protocol for the isolation of large-sized genomic DNA within an hour from several bacteria", Anal. Biochem, 278, pp.86~90 (2000)
  43. Tatusov RL, "The COG database: a tool for genome-scale analysis of protein functions and evolution", Nucleic Acids Res, 28, pp.33~36 (2000)
  44. Taylor CR, "Isolation of bacterial strains able to metabolize lignin from screening of environmental samples", J. Appl. Microbiol, 113, pp.521~530 (2012)
  45. Toyoda A, "Isolation and identification of cellulose-binding proteins from sheep rumen contents", 75, pp.1667~1673 (2009)
  46. Wargacki AJ, "An engineered microbial platform for direct biofuel production from brown macroalgae", Science, 335, pp.308~313 (2012)
  47. Wenzel M, "Aerobic and facultatively anaerobic cellulolytic bacteria from the gut of the termite Zootermopsis angusticollis", J. Appl. Microbiol, 92, pp.32~40 (2002)
  48. Williams MA, "Metaproteomic characterization of a soil microbial community following carbon amendment", Soil Biol. Biochem, 42, pp.1148~1156 (2010)
  49. Wilmes P, "The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms", Environ. Microbiol, 6, pp.911~920 (2004)
  50. Wilmes P, "Metaproteomics provides functional insight into activated sludge wastewater treatment", PLoS One, 3, pp.e1778~ (2008)
  51. Yu H, "The identification of the determinants of the cyclic, sequential binding of elongation factors Tu and G to the ribosome", J. Mol. Biol, 386, pp.802~813 (2009)
  52. Zhao C, "Purification and composition analysis of polysaccharide from edible seaweed Enteromorpha prolifera and polysaccharides depolymerized enzymes from microorganisms", Res. J. Biotechnol, 9, pp.30~36 (2014)
  53. Zhao C, "Biodegradation of Enteromorpha prolifera by mangrove degrading micro-community with physical-chemical pretreatment", Appl. Microbiol. Biotechnol, 92, pp.709~716 (2011)
  54. Zhou J, "ATP in current biotechnology: regulation, applications and perspectives", Biotechnol. Adv, 27, pp.94~101 (2009)

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