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) |
1 | 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. DOI |
2 | 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. |
3 | Huson DH, Auch AF, Qi J, Schuster SC. 2007. MEGAN analysis of metagenomic data. Genome Res. 17: 377-386. DOI |
4 | 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. DOI |
5 | 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. DOI |
6 | 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. DOI |
7 | 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. DOI |
8 | 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. DOI |
9 | 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. DOI |
10 | 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. DOI |
11 | 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. DOI |
12 | 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. DOI |
13 | 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. DOI |
14 | 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. DOI |
15 | 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. DOI |
16 | 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. DOI |
17 | 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. DOI |
18 | Morozova O, Marra MA. 2008. Applications of nextgeneration sequencing technologies in functional genomics. Genomics 92: 255-264. DOI |
19 | 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. DOI |
20 | 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. |
21 | 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. DOI |
22 | 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. DOI |
23 | 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. DOI |
24 | Metzker ML. 2010. Sequencing technologies - the next generation. Nat. Rev. Genet. 11: 31-46. DOI |
25 | 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. DOI |
26 | Deutschbauer AM, Chivian D, Arkin AP. 2006. Genomics for environmental microbiology. Curr. Opin. Biotechnol. 17: 229-235. DOI |
27 | 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. DOI |
28 | Balat M. 2011. Production of bioethanol from lignocellulosic materials via the biochemical pathway: a review. Energy Convers. Manage. 52: 858-875. DOI |
29 | 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. DOI |
30 | Williams MA, Taylor EB, Mula HP. 2010. Metaproteomic characterization of a soil microbial community following carbon amendment. Soil Biol. Biochem. 42: 1148-1156. DOI |
31 | 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. DOI |
32 | 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. |
33 | She R, Chu JS, Wang K, Pei J, Chen N. 2009. GenBlastA: enabling BLAST to identify homologous gene sequences. Genome Res. 19: 143-149. |
34 | 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. DOI |
35 | Wilmes P, Wexler M, Bond PL. 2008. Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS One 3: e1778. DOI |
36 |
Shin KC, Oh DK. 2014. Characterization of a novel recombinant |
37 | Chynoweth DP, Owens JM, Legrand R. 2001. Renewable methane from anaerobic digestion of biomass. Renew. Energy 22: 1-8. DOI |
38 | 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. DOI |
39 | 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. DOI |
40 | 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. DOI |
41 | 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. |
42 | Barnard D, Casanueva A, Tuffin M, Cowan D. 2010. Extremophiles in biofuel synthesis. Environ. Technol. 31: 871-888. DOI |
43 | 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). |
44 | 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. DOI |
45 | Zhao C, Ruan LW. 2011. Biodegradation of Enteromorpha prolifera by mangrove degrading micro-community with physical-chemical pretreatment. Appl. Microbiol. Biotechnol. 92: 709-716. DOI |
46 | Zhou J, Liu L, Shi Z, Du G, Chen J. 2009. ATP in current biotechnology: regulation, applications and perspectives. Biotechnol. Adv. 27: 94-101. DOI |
47 | 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. DOI |
48 | 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. DOI |
49 | 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. DOI |
50 | 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. DOI |
51 | Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Wheeler D. 2006. GenBank. Nucleic Acids Res. 34: D16-D20. DOI |
52 | 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. DOI |
53 | 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. DOI |
54 | 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. DOI |
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