High and stable substrate specificities of microorganisms in enhanced biological phosphorus removal plants

Environmental Microbiology

Volumn 15, Issue 6, 2013, Pages 1821-1831

  Kindaichi, Tomonori ^a,b   Nierychlo, Marta ^b   Kragelund, Caroline ^b   Nielsen, Jeppe Lund ^b   Nielsen, Per Halkjær ^b  

^a HIROSHIMA UNIVERSITY   (Japan)

^b AALBORG UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHORUS; POLYPHOSPHATE;

ARTICLE; BACTERIUM; DENITRIFICATION; ENZYME SPECIFICITY; FLUORESCENCE IN SITU HYBRIDIZATION; METABOLISM; MICROBIOLOGY; WASTE WATER; WATER MANAGEMENT;

BACTERIA; DENITRIFICATION; IN SITU HYBRIDIZATION, FLUORESCENCE; PHOSPHORUS; POLYPHOSPHATES; SUBSTRATE SPECIFICITY; WASTE WATER; WATER PURIFICATION;

AZOARCUS; CALDILINEA; CANDIDATUS MICROTHRIX;

EID: 84878658247     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12074     Document Type: Article

References (50)

1. Albertsen, M., Hansen, L.B., Saunders, A.M., Nielsen, P.H., and Nielsen, K.L. (2012) A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal. ISME J 6: 1094-1106.
2. Alonso-Sáez, L., Galand, P.E., Casamayor, E.O., and Pedrós-Alió, C. (2010) High bicarbonate assimilation in the dark by Arctic bacteria. ISME J 4: 1581-1590.
3. Amann, R.I. (1995) In situ identification of micro-organisms by whole cell hybridization with rRNA-targeted nucleic acid probes. In Molecular Microbial Ecology Manual. Akkermans, A.D.L., Van Elsas, J.D., and De Bruijn, F.J. (eds). London, UK: Kluwer Academic Publications, pp. MMEM-3.3.6/1-MMEM-3.3.6/15.
4. Amann, R.I., Binder, B.J., Olson, R.J., Chisholm, S.W., Devereux, R., and Stahl, D.A. (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56: 1919-1925.
5. Andreasen, K., and Nielsen, P.H. (1997) Application of microautoradiography to the study of substrate uptake by filamentous microorganisms in activated sludge. Appl Environ Microbiol 63: 3662-3668.
6. Andreasen, K., and Nielsen, P.H. (2000) Growth of Microthrix parvicella in nutrient removal activated sludge plants, studies of in situ physiology. Water Res 34: 1559-1569.
7. Blount, Z.D., Borland, C.Z., and Lenski, R.E. (2008) Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci USA 105: 7899-7906.
8. Cohan, F.M. (2006) Towards a conceptual and operational union of bacterial systematics, ecology and evolution. Philos Trans R Soc Lond B Biol Sci 361: 1985-1996.
9. Cohan, F.M. (2011) Are species cohesive - a view from bacteriology. In Population Genetics of Bacteria: A Tribute to Thomas S. Whittam. Walk, S., and Feng, P. (eds). Washington, USA: American Society for Microbiology Press, pp. 43-65.
10. Cohan, F.M., and Koeppel, A.F. (2008) The origins of ecological diversity in prokaryotes. Curr Biol 18: R1024-R1034.
11. Daims, H., Bruhl, A., Amann, R., Schleifer, K.H., and Wagner, M. (1999) The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22: 434-444.
12. Egli, T. (1995) The ecological and physiological significance of the growth of heterotrophic microorganisms with mixtures of substrates. Adv Microb Ecol 14: 305-386.
13. Egli, T. (2010) How to live at very low substrate concentration. Water Res 44: 4826-4837.
14. Elowitz, M.B., Leine, A.J., Siggia, E.D., and Swain, P.S. (2002) Stochastic gene expression in a single cell. Science 297: 1183-1186.
15. Erhart, R., Bradford, D., Seviour, R.J., Amann, R., and Blackall, L.L. (1997) Development and use of fluorescent in situ hybridization probes for the detection and identification of 'Microthrix parvicella' in activated sludge. Syst Appl Microbiol 20: 310-318.
16. Flowers, J.J., He, S., Yilmaz, S., Noguera, D.R., and McMahon, K.D. (2009) Denitrification capabilities of two biological phosphorus removal sludges dominated by different 'Candidatus Accumulibacter' clades. Environ Microbiol Rep 6: 583-588.
17. Fraser, C., Alm, E.J., Polz, M.F., Spratt, B.G., and Hanage, W.P. (2009) The bacterial species challenge: making sense of genetic and ecological diversity. Science 323: 741-746.
18. Freese, H.M., Karsten, U., and Schumann, R. (2010) Bacterial abundance, activity, and viability in the eutrophic river Warnow, Northeast Germany. Microb Ecol 51: 117-127.
19. García Martín, H., Ivanova, N., Kunin, V., Warnecke, F., Barry, K.W., McHardy, A.C., etal. (2006) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol 24: 1263-1269.
20. Hagman, H., Nielsen, J.L., Nielsen, P.H., and Jansen, J.C. (2008) Mixed carbon sources for nitrate reduction in activated sludge - identification of bacteria and process activity studies. Water Res 42: 1539-1546.
21. Hess, A., Zarda, B., Hahn, D., Häner, A., Stax, D., Höhener, P., and Zeyer, J. (1997) In situ analysis of denitrifying toluene- and m-xylene-degrading bacteria in a diesel fuel-contaminated laboratory aquifer column. Appl Environ Microbiol 63: 2136-2141.
22. Ihssen, J., and Egli, T. (2004) Specific growth rate and not cell density controls the general stress response in Escherichia coli. Microbiology 150: 1637-1648.
23. Ihssen, J., and Egli, T. (2005) Global physiological analysis of carbon- and energy-limited growing Escherichia coli confirms a high degree of catabolic flexibility and preparedness for mixed substrate utilization. Environ Microbiol 7: 1568-1581.
24. Jasmin, J.N., and Kassen, R. (2007) On the experimental evolution of specialization and diversity in heterogeneous environments. Ecol Lett 10: 272-281.
25. Kirchman, D., K'nees, E., and Hodson, R. (1985) Leucine incorporation and its potential as a measure of protein synthesis by bacteria in natural aquatic systems. Appl Environ Microbiol 49: 599-607.
26. Kong, Y., Nielsen, J.L., and Nielsen, P.H. (2004) Microautoradiographic study of Rhodocyclus-related poly-P accumulating bacteria in full-scale enhanced biological phosphorus removal plants. Appl Environ Microbiol 70: 5383-5390.
27. Kragelund, C., Thomsen, T.R., Mielczarek, A.T., and Nielsen, P.H. (2011) Eikelboom's morphotype 0803 in activated sludge belongs to the genus Caldilinea in the phylum Chloroflexi. FEMS Microbiol Ecol 76: 451-462.
28. Lee, M.C., Chou, H.H., and Marx, C.J. (2009) Asymmetric, bimodal trade-offs during adaptation of Methylobacterium to distinct growth substrates. Evolution Int J Org Evolution 63: 2816-2830.
29. Liu, M., Durfee, T., Cabrera, J.E., Zhao, K., Jin, D.J., and Blattner, F.R. (2005) Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J Biol Chem 280: 15921-15927.
30. McIlroy, S.J., Kristiansen, R., Albertsen, M., Karst, S.K., Rossetti, S., Nielsen, J.L., etal. (2013) Metabolic model for filamentous 'Candidatus Microthrix parvicella' based on genomic and metagenomic analyses. ISME J (in press).
31. Mayali, X., Weber, P.K., Brodie, E.L., Mabery, S., Hoeprich, P.D., and Pett-Ridge, J. (2011) High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use. ISME J 6: 1210-1221.
32. Misko, A.L., and Germida, J.L. (2002) Taxonomic and functional diversity of pseudomonads isolated from the roots of field-grown canola. FEMS Microbiol Ecol 42: 399-407.
33. Morgan-Sagastume, F., Nielsen, J.L., and Nielsen, P.H. (2008) Substrate-dependent denitrification of abundant probe-defined denitrifying bacteria in activated sludge. FEMS Microbiol Ecol 66: 447-461.
34. Nielsen, J.L., and Nielsen, P.H. (2005) Advances in microscopy: microautoradiography of single cells. Methods Enzymol 397: 237-256.
35. Nielsen, J.L., Christensen, D., Kloppenborg, M., and Nielsen, P.H. (2003) Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization. Environ Microbiol 5: 202-211.
36. Nielsen, P.H., Roslev, P., Dueholm, T., and Nielsen, J.L. (2002) Microthrix parvicella, a specialized lipid consumer in anaerobic-aerobic activated sludge plants. Water Sci Technol 46: 73-80.
37. Nielsen, P.H., Kragelund, C., Seviour, R.J., and Nielsen, J.L. (2009) Identity and ecophysiology of filamentous bacteria in activated sludge. FEMS Microbiol Rev 33: 969-998.
38. Nielsen, P.H., Mielczarek, A.T., Kragelund, C., Nielsen, J.L., Saunders, A.M., and Kong, Y. (2010) A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants. Water Res 44: 5070-5088.
39. Nielsen, P.H., Saunders, A.M., Hansen, A.A., Larsen, P., and Nielsen, J.L. (2012) Microbial communities involved in enhanced biological phosphorus removal from wastewater - a model system in environmental biotechnology. Curr Opin Biotechnol 23: 452-459.
40. Ofiteru, I.D., Lunn, M., Curtis, T.P., Wells, G.F., Criddle, C.S., Francis, C.A., and Sloan, W.T. (2010) Combined niche and neutral effects in a microbial wastewater treatment community. Proc Natl Acad Sci USA 107: 15345-15350.
41. Philippot, L., Andersson, S.G., Battin, T.J., Prosser, J.I., Schimel, J.P., Whitman, W.B., and Hallin, S. (2010) The ecological coherence of high bacterial taxonomic ranks. Nat Rev Microbiol 8: 523-529.
42. Porter, K.G., and Feig, Y.S. (1980) The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr 25: 943-948.
43. Rossetti, S., Tomei, M.C., Nielsen, P.H., and Tandoi, V. (2005) 'Microthrix parvicella', a filamentous bacterium causing bulking and foaming in activated sludge systems: a review of current knowledge. FEMS Microbiol Rev 29: 49-64.
44. Seviour, R.J., Lindrea, K.C., and Oehmen, A. (2010) The activated sludge process. In Microbial Ecology of Activated Sludge. Seviour, R.J., and Nielsen, P.H. (eds). London, UK: IWA publishing, pp. 57-94.
45. Shapiro, B.J., David, L.A., Friedman, J., and Alm, E.J. (2009) Looking for Darwin's footprints in the microbial world. Trends Microbiol 17: 196-204.
46. Šimek, K., Kasalický, V., Hornák, K., Hahn, M.W., and Weinbauer, M.G. (2010) Assessing niche separation among coexisting Limnohabitans strains through interactions with a competitor, viruses, and a bacterivore. Appl Environ Microbiol 76: 1406-1416.
47. Thomsen, T.R., Kong, Y., and Nielsen, P.H. (2007) Ecophysiology of dominant denitrifying bacteria in activated sludge. FEMS Microbiol Ecol 60: 370-382.
48. Ward, N. (2006) New directions and interactions in metagenomics research. FEMS Microbiol Ecol 55: 331-338.
49. Yoon, D.N., Park, S.J., Kim, S.J., Jeon, C.O., Chae, J.C., and Rhee, S.K. (2010) Isolation, characterization, and abundance of filamentous members of Caldilineae in activated sludge. J Microbiol 48: 275-283.
50. Zhou, J., Fries, M.R., Chee-Sanford, J.C., and Tiedje, J.M. (1995) Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth on toluene and description of Azoarcus tolulyticus sp. nov. Int J Syst Bacteriol 45: 500-506.