Absolute Quantification of Individual Biomass Concentrations in a Methanogenic Coculture

AMB Express

Volumn 4, Issue 1, 2014, Pages 1-8

  Junicke, Helena ^a   Abbas, Ben ^a   Oentoro, Joanna ^a   van Loosdrecht, Mark ^a   Kleerebezem, Robbert ^a  

^a DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

Author keywords

Anaerobic digestion; Biomass specific conversion rates; Individual biomass concentration; qPCR

Indexed keywords

DNA 16S;

ARTICLE; BIOMASS CONCENTRATION; BIOTECHNOLOGICAL PROCEDURES; CENTRIFUGATION; COCULTURE; CONCENTRATION (PARAMETERS); CULTURE MEDIUM; DESULFOVIBRIO; DNA EXTRACTION; DRY WEIGHT; MEASUREMENT ACCURACY; METHANOGENIC BACTERIUM; METHANOSPIRILLUM HUNGATEI; NONHUMAN; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SUSPENDED PARTICULATE MATTER;

EID: 84947045526     PISSN: None     EISSN: 21910855     Source Type: Journal    
DOI: 10.1186/s13568-014-0035-x     Document Type: Article

References (58)

1. Ahn JH, Yu R, Chandran K (2008) Distinctive microbial ecology and biokinetics of autotrophic ammonia and nitrite oxidation in a partial nitrification Bioreactor. Biotechnol Bioeng 100(6):1078–1087. doi:10.1002/Bit.21863
2. Albertsen M, Hansen LBS, Saunders AM, Nielsen PH, Nielsen KL (2012) A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal. Isme J 6(6):1094–1106. doi:10.1038/ismej.2011.176
3. Altmann D, Stief P, Amann R, de Beer D, Schramm A (2003) In situ distribution and activity of nitrifying bacteria in freshwater sediment. Environ Microbiol 5(9):798–803. doi:10.1046/j.1469-2920.2003.00469.x
4. Amend AS, Seifert KA, Bruns TD (2010) Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Mol Ecol 19(24):5555–5565. doi:10.1111/j.1365-294X.2010.04898.x
5. Batstone DJ, Keller J, Angelidaki I, Kalyuzhnyi SV, Pavlostathis SG, Rozzi A, Sanders WTM, Siegrist H, Vavilin VA (2002) The IWA Anaerobic Digestion Model No 1 (ADM1). Water Sci Technol 45(10):65–73
6. Chen Y, Cheng JJ, Creamer KS (2008) Inhibition of anaerobic digestion process: A review. Bioresource Technol 99(10):4044–4064. doi:10.1016/j.biortech.2007.01.057
7. Cheng CH, Hsu SC, Wu CH, Chang PW, Lin CY, Hung CH (2011) Quantitative analysis of microorganism composition in a pilot-scale fermentative biohydrogen production system. Int J Hydrogen Energ 36(21):14153–14161. doi:10.1016/j.ijhydene.2011.05.023
8. Cho K, Nguyen DX, Lee S, Hwang S (2013) Use of real-time QPCR in biokinetics and modeling of two different ammonia-oxidizing bacteria growing simultaneously. J Ind Microbiol Biot 40(9):1015–1022. doi:10.1007/s10295-013-1297-z
9. Chon K, Chang JS, Lee E, Lee J, Ryu J, Cho J (2011) Abundance of denitrifying genes coding for nitrate (narG), nitrite (nirS), and nitrous oxide (nosZ) reductases in estuarine versus wastewater effluent-fed constructed wetlands. Ecol Eng 37(1):64–69. doi:10.1016/j.ecoleng.2009.04.005
10. Coskuner G, Ballinger SJ, Davenport RJ, Pickering RL, Solera R, Head IM, Curtis TP (2005) Agreement between theory and measurement in quantification of ammonia-oxidizing bacteria. Appl Environ Microb 71(10):6325–6334. doi:10.1128/Aem.71.10.6325-6334.2005
11. Daims H, Ramsing NB, Schleifer KH, Wagner M (2001) Cultivation-independent, semiautomatic determination of absolute bacterial cell numbers in environmental samples by fluorescence in situ hybridization. Appl Environ Microb 67(12):5810–5818. doi:10.1128/Aem.67.12.5810-5818.2001
12. Egli K, Langer C, Siegrist HR, Zehnder AJB, Wagner M, van der Meer JR (2003) Community analysis of ammonia and nitrite oxidizers during start-up of nitritation reactors. Appl Environ Microb 69(6):3213–3222. doi:10.1128/Aem.69.6.3213-3222.2003
13. Gavala HN, Angelidaki I, Ahring BK (2003) Kinetics and modeling of anaerobic digestion process. In: Ahring BK (ed) Biomethanation I. Springer, Berlin/Heidelberg
14. Gieseke A, Nielsen JL, Amann R, Nielsen PH, de Beer D (2005) In situ substrate conversion and assimilation by nitrifying bacteria in a model biofilm. Environ Microbiol 7(9):1392–1404. doi:10.1111/j.1462-2920.2005.00826.x
15. Griffin ME, McMahon KD, Mackie RI, Raskin L (1998) Methanogenic population dynamics during start-up of anaerobic digesters treating municipal solid waste and biosolids. Biotechnol Bioeng 57(3):342–355. doi:10.1002/(Sici)1097-0290(19980205)57:3<342::Aid-Bit11>3.0.Co;2-I
16. Gujer W, Zehnder AJB (1983) Conversion Processes in Anaerobic-Digestion. Water Sci Technol 15(8–9):127–167
17. Hall SJ, Hugenholtz P, Siyambalapitiya N, Keller J, Blackall LL (2002) The development and use of real-time PCR for the quantification of nitrifiers in activated sludge. Water Sci Technol 46(1–2):267–272
18. Harms G, Layton AC, Dionisi HM, Gregory IR, Garrett VM, Hawkins SA, Robinson KG, Sayler GS (2003) Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant. Environ Sci Technol 37(2):343–351, doi:10.1021/Es0257164
19. Heijnen JJ (2010) Mass Balances, Rates, and Experiments. In: Smolke CD (ed) The metabolic pathway engineering handbook: Fundamentals. CRC Press/Taylor & Francis, Boca Raton
20. Jaenicke S, Ander C, Bekel T, Bisdorf R, Droge M, Gartemann KH, Junemann S, Kaiser O, Krause L, Tille F, Zakrzewski M, Puhler A, Schluter A, Goesmann A (2011) Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing. Plos One 6(1).ᅟ doi:ARTN e14519 doi:10.1371/journal.pone.00145190
21. Jiang Y, Marang L, Kleerebezem R, Muyzer G, van Loosdrecht MCM (2011) Polyhydroxybutyrate Production From Lactate Using a Mixed Microbial Culture. Biotechnol Bioeng 108(9):2022–2035. doi:10.1002/Bit.23148
22. Juretschko S, Loy A, Lehner A, Wagner M (2002) The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Syst Appl Microbiol 25(1):84–99. doi:10.1078/0723-2020-00093
23. Kim YM, Lee DS, Park C, Park D, Park JM (2011) Effects of free cyanide on microbial communities and biological carbon and nitrogen removal performance in the industrial activated sludge process. Water Res 45(3):1267–1279. doi:10.1016/j.watres.2010.10.003
24. Kim J, Lim J, Lee C (2013) Quantitative real-time PCR approaches for microbial community studies in wastewater treatment systems: Applications and considerations. Biotechnology advances 31(8):1358–1373. doi:10.1016/j.biotechadv.2013.05.010
25. Kindaichi T, Kawano Y, Ito T, Satoh H, Okabe S (2006) Population dynamics and in situ kinetics of nitrifying bacteria in autotrophic nitrifying biofilms as determined by real-time quantitative PCR. Biotechnol Bioeng 94(6):1111–1121. doi:10.1002/Bit.20926
26. Kindaichi T, Tsushima I, Ogasawara Y, Shimokawa M, Ozaki N, Satoh H, Okabe S (2007) In situ activity and spatial organization of anaerobic ammonium-oxidizing (anammox) bacteria in biofilms. Appl Environ Microb 73(15):4931–4939. doi:10.1128/Aem.00156-07
27. Kleerebezem R, van Loosdrecht MCM (2007) Mixed culture biotechnology for bioenergy production. Curr Opin Biotech 18(3):207–212. doi:10.1016/j.copbio.2007.05.001
28. Konuma S, Satoh H, Mino T, Matsuo T (2000) Comparison of enumeration methods for ammonia-oxidizing bacteria. Water Science & Technology 43(1):107–114
29. Kragelund C, Thomsen TR, Mielczarek AT, Nielsen PH (2011) Eikelboom's morphotype 0803 in activated sludge belongs to the genus Caldilinea in the phylum Chloroflexi. Fems Microbiol Ecol 76(3):451–462. doi:10.1111/j.1574-6941.2011.01065.x
30. Kröber M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehover P, Puhler A, Schluter A (2009) Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. J Biotechnol 142(1):38–49. doi:10.1016/j.jbiotec.2009.02.010
31. Kwon S, Kim TS, Yu GH, Jung JH, Park HD (2010) Bacterial Community Composition and Diversity of a Full-Scale Integrated Fixed-Film Activated Sludge System as Investigated by Pyrosequencing. J Microbiol Biotechn 20(12):1717–1723. doi:10.4014/jmb.1007.07012
32. Lopez-Vazquez CM, Hooijmans CM, Brdjanovic D, Gijzen HJ, van Loosdrecht MCM (2007) A practical method for quantification of phosphorus- and glycogen-accumulating organism populations in activated sludge systems. Water Environ Res 79(13):2487–2498. doi:10.2175/106143007x220798
33. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar A, Yadhukumar A, Buchner A, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32(4):1363–1371. doi:10.1093/Nar/Gkh293
34. Lyberatos G, Skiadas IV (1999) Modelling of anaerobic digestion–a review. Global Nest Int J 1:63–76
35. Malandrin L, Huber H, Bernander R (1999) Nucleoid structure and partition in Methanococcus jannaschii: An Archaeon with multiple copies of the chromosome. Genetics 152(4):1315–1323
36. Manz W, Wagner M, Amann R, Schleifer K-H (1994) In situ characterization of the microbial consortia active in two wastewater treatment plants. Water Res 28(8):1715–1723
37. Mariakakis I, Bischoff P, Krampe J, Meyer C, Steinmetz H (2011) Effect of organic loading rate and solids retention time on microbial population during bio-hydrogen production by dark fermentation in large lab-scale. Int J Hydrogen Energ 36(17):10690–10700. doi:10.1016/j.ijhydene.2011.06.008
38. Mileyko Y, Joh RI, Weitz JS (2008) Small-scale copy number variation and large-scale changes in gene expression. P Natl Acad Sci USA 105(43):16659–16664. doi:10.1073/pnas.0806239105
39. Okabe S, Itoh T, Satoh H, Watanabe Y (1999) Analyses of spatial distributions of sulfate-reducing bacteria and their activity in aerobic wastewater biofilms. Appl Environ Microb 65(11):5107–5116
40. Plugge CM (2005) Anoxic media design, preparation, and considerations. Environ Microbiol 397:3–16. doi:10.1016/S0076-6879(05)97001-8
41. Rittmann BE, McCarty PL (2001) Environmental biotechnology. McGraw-Hill, New York
42. Rittmann BE, Laspidou CS, Flax J, Stahl DA, Urbain V, Harduin H, van der Waarde JJ, Geurkink B, Henssen MJC, Brouwer H, Klapwijk A, Wetterauw M (1999) Molecular and modeling analyses of the structure and function of nitrifying activated sludge. Water Sci Technol 39(1):51–59. doi:10.1016/S0273-1223(98)00775-6
43. Ronaghi M, Elahi E (2002) Pyrosequencing for microbial typing. J Chromatogr B 782(1–2):67–72. doi:10.1016/S1570-0232(02)00693-1
44. Schippers A, Neretin LN (2006) Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR. Environ Microbiol 8(7):1251–1260. doi:10.1111/j.1462-2920.2006.01019.x
45. Schlüter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Kromeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Puhler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehover P, Goesmann A (2008) The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. J Biotechnol 136(1–2):77–90. doi:10.1016/j.jbiotec.2008.05.008
46. Seitz HJ, Schink B, Pfennig N, Conrad R (1990) Energetics of Syntrophic Ethanol Oxidation in Defined Chemostat Cocultures.2. Energy Sharing in Biomass Production. Arch Microbiol 155(1):89–93. doi:10.1007/Bf00291280
47. Shin SG, Zhou BW, Lee S, Kim W, Hwang S (2011) Variations in methanogenic population structure under overloading of pre-acidified high-strength organic wastewaters. Process Biochem 46(4):1035–1038. doi:10.1016/j.procbio.2011.01.009
48. Stams AJM, Plugge CM (2009) Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol 7(8):568–577. doi:10.1038/Nrmicro2166
49. Taras MJ, Greenberg AE, Hoak RD, Rand MC (1971) Standard methods for the examination of water and waste water. American Public Health Association, New York
50. Wagner M, Rath G, Amann R, Koops HP, Schleifer KH (1995) In-Situ Identification of Ammonia-Oxidizing Bacteria. Syst Appl Microbiol 18(2):251–264
51. Wagner M, Horn M, Daims H (2003) Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr Opin Microbiol 6(3):302–309. doi:10.1016/S1369-5274(03)00054-7
52. Winkler MKH, Bassin JP, Kleerebezem R, Sorokin DY, van Loosdrecht MCM (2012) Unravelling the reasons for disproportion in the ratio of AOB and NOB in aerobic granular sludge. Appl Microbiol Biot 94(6):1657–1666. doi:10.1007/s00253-012-4126-9
53. Worm P, Stams AJM, Cheng X, Plugge CM (2011) Growth- and substrate-dependent transcription of formate dehydrogenase and hydrogenase coding genes in Syntrophobacter fumaroxidans and Methanospirillum hungatei. Microbiol-Sgm 157:280–289. doi:10.1099/Mic.0.043927-0
54. WSLH (1993) Total suspended solids, mass balance, volatile suspended solids. Wisconsin State Laboratory of Hygiene, Environmental Sciences Section Inorganic Chemistry Unitᅟ
55. Yu Y, Lee C, Kim J, Hwang S (2005) Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol Bioeng 89(6):670–679. doi:10.1002/Bit.20347
56. Yu Y, Kim J, Hwang S (2006) Use of real-time PCR for group-specific quantification of aceticlastic methanogens in anaerobic processes: Population dynamics and community structures. Biotechnol Bioeng 93(3):424–433. doi:10.1002/Bit.20724
57. Zhang T, Fang HHP (2006) Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples. Appl Microbiol Biot 70(3):281–289. doi:10.1007/s00253-006-0333-6
58. Zhang T, Shao MF, Ye L (2012) 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. Isme J 6(6):1137–1147. doi:10.1038/ismej.2011.188