Monitoring functions in managed microbial systems by cytometric bar coding

Environmental Science and Technology

Volumn 47, Issue 3, 2013, Pages 1753-1760

  Koch, Christin ^a   Fetzer, Ingo ^a   Schmidt, Thomas ^b   Harms, Hauke ^a   Müller, Susann ^a  

^a HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH UFZ   (Germany)

^b DBFZ DEUTSCHES BIOMASSEFORSCHUNGSZENTRUM GEMEINNÜTZIGE GMBH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACIDOGENIC; BAR CODING; BIOGAS PRODUCTION; CELL ABUNDANCE; CELL NUMBER; CORRELATION COEFFICIENT; DIAGNOSTIC VALUE; DNA FINGERPRINTING; MICROBIAL COMMUNITIES; MICROBIAL PROCESS; MICROBIAL SYSTEM; MONITORING FUNCTIONS; ON-SITE MONITORING; REACTOR PARAMETERS; STRUCTURE VARIATION;

BIOGAS; CYTOLOGY; DATA HANDLING; GENETIC ENGINEERING; MICROORGANISMS;

CELLS;

BIOACCUMULATION; BIOGAS; BIOREACTOR; CELL ORGANELLE; COMMUNITY COMPOSITION; COMMUNITY DYNAMICS; DIVERGENCE; ENVIRONMENTAL MONITORING; GAS PRODUCTION; IDENTIFICATION METHOD; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; PHYLOGENETICS;

ARTICLE; BACTEROIDETES; CELL COUNT; CELL FUNCTION; CELL SELECTION; CELLULAR DISTRIBUTION; CHROMOSOME NUMBER; COMMUNITY STRUCTURE; CONTINUOUS STIRRED TANK REACTOR; CYTOMETRY; DNA FINGERPRINTING; DNA PROBE; DNA SEQUENCE; FIRMICUTES; FLOW CYTOMETRY; METABOLIC CAPACITY; METHANOGEN; MICROBIAL COMMUNITY; MOLECULAR CLONING; NONHUMAN; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

BACTERIA; CYTOLOGICAL TECHNIQUES; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH;

EID: 84873425622     PISSN: 0013936X     EISSN: 15205851     Source Type: Journal    
DOI: 10.1021/es3041048     Document Type: Article

References (40)

1. Turnbaugh, P. J.; Ley, R. E.; Hamady, M.; Fraser-Liggett, C. M.; Knight, R.; Gordon, J. I. The human microbiome project Nature 2007, 449, 804-810
2. Talbot, G.; Topp, E.; Palin, M. F.; Massé, D. I. Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors Water Res. 2008, 42, 513-537
3. Morales, S. E.; Holben, W. E. Linking bacterial identities and ecosystem processes: can 'omic' analyses be more than the sum of their parts? FEMS Microbiol. Ecol. 2011, 75, 2-16
4. Günther, S.; Trutnau, M.; Kleinsteuber, S.; Hause, G.; Bley, T.; Röske, I.; Harms, H.; Müller, S. Dynamics of polyphosphate- accumulating bacteria in wastewater treatment plant microbial communities detected via DAPI (4′,6′-diamidino-2-phenylindole) and tetracycline labeling Appl. Environ. Microbiol. 2009, 75, 2111-2121
5. Amann, R.; Fuchs, B. M. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques Nat. Rev. Microbiol. 2008, 6, 339-348
6. Müller, S.; Nebe-von-Caron, G. Functional single-cell analyses: flow cytometry and cell sorting of microbial populations and communities FEMS Microbiol. Rev. 2010, 34, 554-587
7. Lebaron, P.; Servais, P.; Agogué, H.; Courties, C.; Joux, F. Does the high nucleic acid content of individual bacterial cells allow us to discriminate between active cells and inactive cells in aquatic systems? Appl. Environ. Microbiol. 2001, 67, 1775-1782
8. Wang, Y.; Hammes, F.; De Roy, K.; Verstraete, W.; Boon, N. Past, present and future applications of flow cytometry in aquatic microbiology Trends Biotechnol. 2010, 28, 416-424
9. Kuczynski, J.; Lauber, C. L.; Walters, W. A.; Wegener Parfrey, L.; Clemente, J. C.; Gevers, D.; Knight, R. Experimental and analytical tools for studying the human microbiome Nat. Rev. Genet. 2012, 13, 47-58
10. Hamady, M.; Knight, R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges Genome Res. 2009, 19, 1141-1152
11. Werner, J. J.; Knights, D.; Garcia, M. L.; Scalfone, N. B.; Smith, S.; Yarasheski, K.; Cummings, T. A.; Beers, A. R.; Knight, R.; Angenent, L. T. Bacterial community structures are unique and resilient in full-scale bioenergy systems Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 4158-4163
12. Günther, S.; Koch, C.; Hübschmann, T.; Röske, I.; Müller, R. A.; Bley, T.; Harms, H.; Müller, S. Correlation of community dynamics and process parameters as a tool for the prediction of the stability of wastewater treatment Environ. Sci. Technol. 2012, 46, 84-92
13. R Development Core Team R: a language and environment for statistical computing. R Foundation for Statistical Computing; Vienna, Austria, 2011. http://www.R-project.org/.
14. Gregory, R. W.; Bolker, B.; Bonebakker, L.; Gentleman, R.; Huber, W.; Liaw, A.; Lumley, T.; Maechler, M.; Magnusson, A.; Moeller, S.; Schwartz, M.; Venables, B. Gplots: various R programming tools for plotting data. R package version 2.10.1; 2011. http://CRAN.R-project.org/package=gplots.
15. Gentleman, R. C.; Carey, V. J.; Bates, D. M.; Bolstad, B.; Dettling, M.; Dudoit, S.; Ellis, B.; Gautier, L.; Ge, Y.; Gentry, J.; Hornik, K.; Hothorn, T.; Huber, W.; Iacus, S.; Irizarry, R.; Leisch, F.; Li, C.; Maechler, M.; Rossini, A. J.; Sawitzki, G.; Smith, C.; Smyth, G.; Tierney, L.; Yang, J. Y. H.; Zhang, Z. Bioconductor: open software development for computational biology and bioinformatics Genome Biol. 2004, 5, R80
16. Demirel, B.; Scherer, P. The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review Rev. Environ. Sci. Biotechnol. 2008, 7, 173-190
17. Fernandez, A. S.; Hashsham, S. A.; Dollhopf, S. L.; Raskin, L.; Glagoleva, O.; Dazzo, F. B.; Hickey, R. F.; Criddle, C. S.; Tiedje, J. M. Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose Appl. Environ. Microbiol. 2000, 66, 4058-4067
18. Ziganshin, A.; Schmidt, T.; Scholwin, F.; Il'inskaya, O. N.; Harms, H.; Kleinsteuber, S. Bacteria and archaea involved in anaerobic digestion of distillers grains with solubles Appl. Microbiol. Biotechnol. 2011, 89, 2039-2052
19. Schlüter, A.; Bekel, T.; Diaz, N. N.; Dondrup, M.; Eichenlaub, R.; Gartemann, K. H.; Krahn, I.; Krause, L.; Krömeke, H.; Kruse, O.; Mussgnug, J. H.; Neuweger, H.; Niehaus, K.; Pühler, A.; Runte, K. J.; Szczepanowski, R.; Tauch, A.; Tilker, A.; Viehöver, P.; Goesmann, A. The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology J. Biotechnol. 2008, 136, 77-90
20. Koch, C.; Günther, S.; Desta, A. F.; Hübschmann, T.; Müller, S. Cytometric fingerprinting for analysing microbial intra-community structure variation and identifying sub-community function. Nat. Protoc. In press.
21. Kleinsteuber, S.; Riis, V.; Fetzer, I.; Harms, H.; Müller, S. Population dynamics within a microbial consortium during growth on diesel fuel in saline environments Appl. Environ. Microbiol. 2006, 72, 3531-3542
22. Müller, S.; Harms, H.; Bley, T. Origin and analysis of microbial population heterogeneity in bioprocesses Curr. Opin. Biotechnol. 2010, 21, 100-113
23. Müller, S. Modes of cytometric bacterial DNA pattern: a tool for pursuing growth Cell Prolif. 2007, 40, 621-639
24. Bombach, P.; Resolution of natural microbial community dynamics by community fingerprinting, flow cytometry, and trend interpretation analysis. In High Resolution Microbial Single Cell Analytics. Advances in Biochemical Engineering and Biotechnology 124; Müller, S.; Bley, T., Eds.; Springer: Berlin, Heidelberg, 2011; p 151.
25. Karhadkar, P. P.; Audic, J.-M.; Faup, G. M.; Khanna, P. Sulfide and sulphate inhibition of methanogenesis Water Res. 1987, 21, 1061-1066
26. Pobeheim, H.; Munk, B.; Lindorfer, H.; Guebitz, G. M. Impact of nickel and cobalt on biogas production and process stability during semi-continuous anaerobic fermentation of a model substrate for maize silage Water Res. 2011, 45, 781-787
27. Demirel, B.; Scherer, P. Trace element requirements of agricultural biogas digesters during biological conversion of renewable biomass to methane Biomass Bioenergy 2001, 35, 992-998
28. Sundh, I.; Carlsson, H.; Nordberg, Å.; Hansson, M.; Mathisen, B. Effects of glucose overloading on microbial community structure and biogas production in a laboratory-scale anaerobic digester Bioresour. Technol. 2003, 89, 237-243
29. Girvan, M. S.; Campbell, C. D.; Killham, K.; Prosser, J. I.; Glover, L. A. Bacterial diversity promotes community stability and functional resilience after perturbation Environ. Microbiol. 2005, 7, 301-313
30. Gunderson, L. H. Ecological resilience-in theory and application Annu. Rev. Ecol. Syst. 2000, 31, 425-439
31. Scheffer, M.; Carpenter, S. R. Catastrophic regime shifts in ecosystems: linking theory to observation Trends Ecol. Evol. 2003, 18, 648-656
32. Schröder, A.; Persson, L.; De Roos, A. M. Direct experimental evidence for alternative stable states: a review Oikos 2005, 110, 3-19
33. Schnürer, A.; Zellner, G.; Svensson, B. H. Mesophilic syntrophic acetate oxidation during methane formation in biogas reactors FEMS Microbiol. Ecol. 1999, 29, 249-261
34. Xing, J.; Criddle, C.; Hickey, R. Long-term adaptive shifts in anaerobic community structure in response to a sustained cyclic substrate perturbation Microb. Ecol. 1997, 33, 58-58
35. Hattori, S. Syntrophic acetate-oxidizing microbes in methanogenic environments Microbes Environ. 2008, 23, 118-127
36. Fernández, A.; Huang, S.; Seston, S.; Xing, J.; Hickey, R.; Criddle, C.; Tiedje, J. How stable is stable? Function versus community composition Appl. Environ. Microbiol. 1999, 65, 3697-3704
37. Martinez-Garcia, M.; Swan, B. K.; Poulton, N. J.; Gomez, M. L.; Masland, D.; Sieracki, M. E.; Stepanauskas, R. High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton ISME J. 2012, 6, 113-123
38. Fuhrmann, J. A. Microbial community structure and its functional implications Nature 2009, 459, 193-199
39. Pedros-Alio, C. Marine microbial diversity: can it be determined? Trends Microbiol. 2006, 14, 257-263
40. Koch, C.; Fetzer, I.; Harms, H.; Müller, S. CHIC-an automated approach for the detection of dynamic variations in complex microbial communities. Manuscript in revision.