Abstract
To investigate the changes in the microbial community structure during composting and to compare the differences in the structures between different composting processes, amplified ribosomal DNA restriction analysis (ARDRA) patterns of entire microbial communities were developed. Rapid degradation of polyhydroxyalkanoates (PHAs) in a model composting process was studied by changing the operation conditions and initial conditions as well as by addition of PHA-degrading microorganisms. Azotobacter sp. AZ34, which was isolated from our compost and could degrade PHA, was added at high concentrations at the beginning of composting. The differences in ARDRA patterns between composting with and without addition of the bacteria were investigated. There was a significant difference in microbial community structures between the two cases at the early stage, but ARDRA patterns at the middle and final stages appeared to be almost the same. No effect was observed at least in terms of PHA degradation rate compared, between AZ34 and the control, which was primed with the seed compost without addition of PHA-degrading bacteria. After autoclaving the raw materials of the compost, AZ34 was initially added and the seed compost was added at 72 hours and composting process continued. The effect of the PHA-degrading bacteria was observed, in this case. This experiment demonstrated that if the initial microbial population in the raw materials of the compost is significantly reduced, AZ34 can grow preferentially and promotes PHA degradation during the composting process. The same effect as that observed in this experiment was found by recycling fairly large amounts of the compost. This finding of the preferential growth of microorganisms in a microbial community will be utilized for the production of functional composts.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Berthelet M, Whyte LG, Greer CH (1996) Rapid, direct extraction of DNA from soils for PCR analysis using polyvinylpolypyrrolidone spin columns. FEMS Microbiol Lett 138: 17–22
Blanc M, Marilley L, Beffa T, Aragno M (1997) Rapid identification of heterotrophic, thermophilic, spore-forming bacteria isolated from hot composts. Int J Syst Bacteriol 47: 1246–1248
Chelly J, Montarras D, Pinset C, Berwald-Netter Y, Kaplan A (1990) Quantitative estimation of minor mRNAs by cDNA-polymerase chain reaction: application to dystrophin mRBA in cultured myogenic and brain cells. Eur J Biochem 187: 691–698
Duineveld B M, Rosado AS, Van Elsas JD, Van Veen JA (1998) Analysis of the dynamics of bacterial communities in the rhizosphere of the chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns. Appl Environ Microbiol 64: 4950–4957
Felske A, Akkermans ADL, De Vos WM (1998) Quantification of 16S rRNA in complex bacterial communities by multiple competitive reverse transcriptional-PCR in temperature gradient gel electrophoresis fingerprints. Appl Environ Microbiol 64: 4581–4587
Ferris MJ, Muyzer G, Ward DM (1996) Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial community. Appl Environ Microbiol 62: 340–346
Fischer SG, Lerman LS (1979) Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. Cell 16: 191–200
Garland JL (1997) Analysis and interpretation of community-level physiological profiles in microbial ecology. FEMS Microbiol Ecol 24: 289–300
Ibelwe AM, Kennedy AC (1998) Phospholipid fatty acid profiles and carbon utilization patterns for analysis of microbial community structure under field and greenhouse conditions. FEMS Microbiol Ecol 26: 151–163
Kandeler E (1996) Total Nitrogen. In: Schinner F, Öhlinger R, Kandeler E, Margesin R (eds.) Methods in soil biology, Springer, Berlin, Heidelberg, New York, pp. 403–406
Konopka A, Oliver L, Turco R F Jr (1998) The use of carbon substrate utilization patterns in environmental and ecological microbiology. Microb Ecol 35: 103–1 15
Lee DH, Zo YG, Kim SJ (1996) Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Appl Environ Microbiol 62: 3112–3120
Massol-Dcya AA, Odelson DA, Hickey RF, Tiedje JM (1995) Bacterial community fingerprinting of amplified 16S and 16–23S ribosomal DNA gene sequences and restriction endonuclease analysis (ARDRA). In: Akkermans ADL, Van Elsas JD, de Bruijn FJ (eds) Molecular microbial ecology manual, Kluwer, Dordrecht, 3.3. 2
Matavulj M, Molitoris H P (1992) FEMS Microbiol Rev 103: 323–332
Muyzer G, De Waal EC, Uitterlinden AG (1993) Profiling of complexed microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695–700
Myers R M, Fischer S G, Lerman L S, Maniatis T (1985) Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acid Research 13: 3131–3144
Peters S, Koschinsky S, Schwieger F, Tebbe CC (2000) Succession of microbial communities during hot composting as detected by PCR-single-strand-conformation polymorphism-based genetic profiles of small-subunit rRNA genes. Appl Environ. Microbiol 66: 930–936
Poulsen LK, Dalton HM, Angles ML, Marshall KC, Mohn S, Goodman AE (1997) Simultaneous determination of gene expression and bacterial identity in single cells in defined mixtures of pure cultures. Appl Environ Microbiol 63: 3698–3702
Purdy K J, Embley TM, Takii S, Nedwell DB (1996) Rapid extraction of DNA and rRNA from sediments by a novel hydroxyapatite spin-column method. Appl Environ Microbiol 62: 3905–3907
Riesner D, Steger G, Zimmat R, Owens RA, Wagenhofer M, Hillen W, Vollbach S, Henco K (1989) Temperature-gradient gel electrophoresis of nucleic acid: analysis of conformational transitions, sequence variations, and protein-nucleic acid interactions. Electrophoresis 10: 377–389
Schmit E, Leeflang P, Wernars K (1997) Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis. FEMS Microbiol Ecol 23: 249–261
Schwieger F, Tebbe CC (1998) A new approach to utilize PCR—single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol 64: 4870–4876
Steffan RJ, Goksoyr J, Bej AK, Atlas RM (1988) Recovery of DNA from soils and sediments. Appl Environ Microbiol 54: 2908–2915
Tsai YL, Olson BH. (1991) Rapid method for direct extraction of DNA from soils and sediments. Appl Environ Microbiol 57: 1070–1074
Tyurin IV (1931) A modification of a volumetric method of humus determination with chromic acid. Pochvovedenie 5–6: 36
Vaneechoutte M, Rossau R, De Vos P, Gillis M, Janssens D, Paepc N, De Rouck A, Fiers T, Claeys G, Kersters K (1992) Rapid identification of bacteria of Comamonadaceac with amplified ribosomal DNA-restriction analysis ( ARDRA ). FEMS Microbiol Lett 93: 227–234
Wang AM, Doyle MV, Mark DF (1989) Quantitation of mRNA by the polymerase chain reaction. Proc Natl Acad Sci USA 86: 9717–9721
Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316–323
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Uchiyama, K., Suzuki, T., Tatsumi, H., Kanetake, H., Shioya, S. (2002). Amplified 16S Ribosomal DNA Restriction Analysis of Microbial Community Structure During Rapid Degradation of a Biopolymer, PHA, by Composting. In: Insam, H., Riddech, N., Klammer, S. (eds) Microbiology of Composting. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-08724-4_7
Download citation
DOI: https://doi.org/10.1007/978-3-662-08724-4_7
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-08705-9
Online ISBN: 978-3-662-08724-4
eBook Packages: Springer Book Archive