Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge

Environmental Microbiology

Volumn 12, Issue 5, 2010, Pages 1205-1217

  He, Shaomei ^a   Kunin, Victor ^b   Haynes, Matthew ^c   Martin, Hector Garcia ^b   Ivanova, Natalia ^b   Rohwer, Forest ^c   Hugenholtz, Philip ^b   McMahon, Katherine D ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b DOE JOINT GENOME INSTITUTE   (United States)

^c SAN DIEGO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; BACTERIAL RNA; PHOSPHORUS; SEWAGE;

AEROBIC METABOLISM; ANAEROBIC GROWTH; ARTICLE; BETAPROTEOBACTERIA; BIOREMEDIATION; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METABOLISM; METAGENOMICS; METHODOLOGY; MICROBIOLOGY; SEWAGE; PROCEDURES;

AEROBIOSIS; ANAEROBIOSIS; BACTERIAL PROTEINS; BETAPROTEOBACTERIA; BIODEGRADATION, ENVIRONMENTAL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; METAGENOMICS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHOSPHORUS; RNA, BACTERIAL; SEWAGE;

ACCUMULIBACTER PHOSPHATIS;

EID: 77953124142     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2010.02163.x     Document Type: Article

References (38)

1. Ahn KH, Kornberg A. Polyphosphate kinase from Escherichia coli - purification and demonstration of a phosphoenzyme intermediate. J Biol Chem 1990, 265:11734-11739.
2. Arai H, Mizutani M, Igarashi Y. Transcriptional regulation of the nos genes for nitrous oxide reductase in Pseudomonas aeruginosa. Microbiology 2003, 149:29-36.
3. Baek JH, Lee SY. Transcriptome analysis of phosphate starvation response in Escherichia coli. J Microbiol Biotechnol 2007, 17:244-252.
4. Burow LC, Mabbett AN, Blackall LL. Anaerobic glyoxylate cycle activity during simultaneous utilization of glycogen and acetate in uncultured Accumulibacter enriched in enhanced biological phosphorus removal communities. ISME J 2008a, 2:1040-1051.
5. Burow LC, Mabbett AN, McEwan AG, Bond PL, Blackall LL. Bioenergetic models for acetate and phosphate transport in bacteria important in enhanced biological phosphorus removal. Environ Microbiol 2008b, 10:87-98.
6. Comeau Y, Hall KJ, Hancock REW, Oldham WK. Biochemical model for enhanced biological phosphorus removal. Water Res 1986, 20:1511-1521.
7. Crocetti GR, Hugenholtz P, Bond PL, Schuler A, Keller J, Jenkins D, Blackall LL. Identification of polyphosphate accumulating organisms and the design of 16S rRNA-directed probes for their detection and quantitation. Appl Environ Microbiol 2000, 66:1175-1182.
8. Garcia Martin H, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol 2006, 24:1263-1269.
9. Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. Plos ONE 2008, 3:e3042.
10. He S, Gall DL, McMahon KD. 'Candidatus Accumulibacter' population structure in enhanced biological phosphorus removal sludges as revealed by polyphosphate kinase genes. Appl Environ Microbiol 2007, 73:5865-5874.
11. He S, Gu AZ, McMahon KD. Progress towards understanding the distribution of Accumulibacter among full-scale enhanced biological phosphorus removal systems. Microb Ecol 2008, 55:229-236.
12. Hesselmann RPX, Werlen C, Hahn D, van der Meer JR, Zehnder AJB. Enrichment, phylogenetic analysis and detection of a bacterium that performs enhanced biological phosphate removal in activated sludge. Syst Appl Microbiol 1999, 22:454-465.
13. Hesselmann RPX, von Rummell R, Resnick SM, Hany R, Zehnder AJB. Anaerobic metabolism of bacteria performing enhanced biological phosphate removal. Water Res 2000, 34:3487-3494.
14. Kong YH, Nielsen JL, Nielsen PH. Microautoradiographic study of Rhodocyclus-related polyphosphate accumulating bacteria in full-scale enhanced biological phosphorus removal plants. Appl Environ Microbiol 2004, 70:5383-5390.
15. Kornberg A. Inorganic polyphosphate: a molecule of many functions. Prog Mol Subcell Biol 1999, 23:1-18.
16. Korner H, Zumft WG. Expression of denitrification enzymes in response to the dissolved-oxygen level and respiratory substrate in continuous culture of Pseudomonas-stutzeri. Appl Environ Microbiol 1989, 55:1670-1676.
17. Kunin V, He S, Warnecke F, Peterson SB, Garcia Martin H, Haynes M. A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Res 2008, 18:293-297.
18. Lynch AS, Lin ECC. Response to molecular oxygen. Escherichia coli and Salmonella: Cellular and Molecular Biology 1996, 1526-1538. Neidhardt FC, Curtis RIngraham JLLin ECCLow KBMagasanik B. In, eds, Washington DC, USA, American Society for Microbiology, pp.
19. Mino T, Arun V, Yoshiaki T, Matsuo T. Effect of phosphorus accumulation on acetate metabolism in the biological phosphorus removal process. Advances in Water Pollution Control - Biological Phosphate Removal from Wastewaters 1987, 27. Ramadori R, In, ed., Oxford, UK, Pergamon Press, p
20. Mino T, Van Loosdrecht MCM, Heijnen JJ. Microbiology and biochemistry of the enhanced biological phosphate removal process. Water Res 1998, 32:3193-3207.
21. Neethling J, Bakke B, Benisch M, Gu A, Stephens H. Factors Influencing the Reliability of Enhanced Biological Phosphorus Removal 2005, Alexandria, VA, USA, Water Environment Research Foundation, Report OICTS3
22. Oehmen A, Lemos PC, Carvalho G, Yuan ZG, Keller J, Blackall LL, Reis MAM. Advances in enhanced biological phosphorus removal: from micro to macro scale. Water Res 2007, 41:2271-2300.
23. Parro V, Moreno-Paz M, Gonzalez-Toril E. Analysis of environmental transcriptomes by DNA microarrays. Environ Microbiol 2007, 9:453-464.
24. Pereira H, Lemos PC, Reis MAM, Crespo JPSG, Carrondo MJT, Santos H. Model for carbon metabolism in biological phosphorus removal process based on in vivo 13C-NMR labelling experiments. Water Res 1996, 30:2128-2138.
25. Poretsky RS, Bano N, Buchan A, LeCleir G, Kleikemper J, Pickering M. Analysis of microbial gene transcripts in environmental samples. Appl Environ Microbiol 2005, 71:4121-4126.
26. Pramanik J, Trelstad PL, Schuler AJ, Jenkins D, Keasling JD. Development and validation of a flux-based stoichiometric model for enhanced biological phosphorus removal metabolism. Water Res 1999, 33:462-476.
27. Ren DC, Bedzyk LA, Setlow P, England DF, Kjelleberg S, Thomas SM. Differential gene expression to investigate the effect of (5Z)-4-bromo-5-(bromomethylene)-3-butyl-2(5H)-furanone on Bacillus subtilis. Appl Environ Microbiol 2004, 70:4941-4949.
28. Resch A, Rosenstein R, Nerz C, Gotz F. Differential gene expression profiling of Staphylococcus aureus cultivated under biofilm and planktonic conditions. Appl Environ Microbiol 2005, 71:2663-2676.
29. Richardson DJ. Bacterial respiration: a flexible process for a changing environment. Microbiology 2000, 146:551-571.
30. Saleh-Lakha S, Miller M, Campbell RG, Schneider K, Elahimanesh P, Hart MM, Trevors JT. Microbial gene expression in soil: methods, applications and challenges. J Microbiol Methods 2005, 63:1.
31. Tao H, Bausch C, Richmond C, Blattner FR, Conway T. Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J Bacteriol 1999, 181:6425-6440.
32. Veit K, Ehlers C, Ehrenreich A, Salmon K, Hovey R, Gunsalus RP. Global transcriptional analysis of Methanosarcina mazei strain Go1 under different nitrogen availabilities. Mol Genet Genomics 2006, 276:41-55.
33. Wexler M, Richardson DJ, Bond PL. Radiolabelled proteomics to determine differential functioning of Accumulibacter during the anaerobic and aerobic phases of a bioreactor operating for enhanced biological phosphorus removal. Environ Microbiol 2009, 11:3029-3044.
34. Wilmes P, Bond PL. Towards exposure of elusive metabolic mixed-culture processes: the application of metaproteomic analyses to activated sludge. Water Sci Technol 2006, 54:217-226.
35. Wilmes P, Andersson AF, Lefsrud MG, Wexler M, Shah M, Zhang B. Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J 2008, 2:853-864.
36. Yuste L, Hervas AB, Canosa I, Tobes R, Jimenez JI, Nogales J. Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray. Environ Microbiol 2006, 8:165-177.
37. Zhou JZ, Thompson DK. Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol 2002, 13:204-207.
38. Zilles JL, Hung CH, Noguera DR. Presence of Rhodocyclus in a full-scale wastewater treatment plant and their participation in enhanced biological phosphorus removal. Water Sci Technol 2002, 46:123-128.