The diversity of fungi in aerobic sewage granules assessed by 18S rRNA gene and ITS sequence analyses

FEMS Microbiology Ecology

Volumn 68, Issue 2, 2009, Pages 246-254

  Weber, Silvia D ^b   Hofmann, Andreas ^c   Pilhofer, Martin ^b   Wanner, Gerhard ^d   Agerer, Reinhard ^d   Ludwig, Wolfgang ^b   Schleifer, Karl Heinz ^b   Fried, Johannes ^a  

^a UNIVERSITY OF INNSBRUCK   (Austria)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c INSTITUTE OF EPIDEMIOLOGY   (Germany)

^d UNIVERSITY OF MUNICH   (Germany)

Author keywords

18S rRNA gene; Aerobic granule; Fungal ITS; Fungi; Wastewater biofilm

Indexed keywords

INTERNAL TRANSCRIBED SPACER; RNA 18S;

BIOFILM; COMMUNITY COMPOSITION; FUNGUS; ISOLATED POPULATION; OXIC CONDITIONS; POLYMERASE CHAIN REACTION; RNA; SEWAGE; SPECIES DIVERSITY; TAXONOMY; WASTE TREATMENT;

ARTICLE; ASCOMYCETES; AUREOBASIDIUM; BIODIVERSITY; CANDIDA; CANDIDA BOLETICOLA; CLAVICEPS; CONTROLLED STUDY; DNA EXTRACTION; DNA ISOLATION; FUNGAL COMMUNITY; FUNGUS ISOLATION; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLEOSPORACEAE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SCANNING ELECTRON MICROSCOPY; SEQUENCE ANALYSIS; SEWAGE; TAXONOMY; THELEOBOLACEAE; TREMELLOMYCETES; UNINDEXED SEQUENCE; WASTE WATER; XYLARIALES;

BIOFILMS; DNA PRIMERS; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; FUNGI; PHYLOGENY; RNA, FUNGAL; RNA, RIBOSOMAL, 18S; RNA, RIBOSOMAL, 5.8S; SEQUENCE ANALYSIS, DNA; SEWAGE;

AUREOBASIDIUM; CANDIDA BOLETICOLA; CLAVICEPS; FUNGI; PLEOSPORACEAE; XYLARIALES;

EID: 64149121478     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2009.00660.x     Document Type: Article

References (39)

1. Alam MZ, Fakhru'l-Razia A Molla AH (2003) Biosolids accumulation and biodegradation of domestic wastewater treatment plant sludge by developed liquid state bioconversion process using a batch fermenter. Water Res 37 : 3569 3578.
2. Aleshin VV, Milyutina IA, Kedrova OS, Vladychenskaya NS Petrov NB (1998) Phylogeny of Nematoda and Cephalorhyncha derived from 18S rDNA. J Mol Evol 47 : 597 605.
3. Beun JJ, Hendriks A, van Loosdrecht MCM, Morgenroth E, Wilderer PA Heijnen JJ (1999) Aerobic granulation in a sequencing batch reactor. Water Res 33 : 2283 2290.
4. Borneman J Hartin RJ (2000) PCR primers that amplify fungal rRNA genes from environmental samples. Appl Environ Microb 66 : 4356 4360.
5. Chen SC, Halliday CL Meyer W (2002) A review of nucleic acid-based diagnostic tests for systemic mycoses with an emphasis on polymerase chain reaction-based assays. Med Mycol 40 : 333 357.
6. Chen YC, Eisner JD, Kattar MM, Rassoulian-Barrett SL, Lafe K, Bui U, Limaye AP Cookson BT (2001) Polymorphic internal transcribed spacer region 1 DNA sequences identify medically important yeasts. J Clin Microbiol 39 : 4042 4051.
7. Chou Q, Russell M, Birch DE, Raymond J Bloch W (1992) Prevention of pre-PCR mis-priming and primer dimerization improves low-copy-number amplifications. Nucleic Acids Res 20 : 1717 1723.
8. Etterer T Wilderer PA (2001) Generation and properties of aerobic granular sludge. Water Sci Technol 43 : 19 26.
9. Fakhru'l-Razi A, Alam MZ, Idris A, Abd-Aziz S Molla AH (2002) Filamentous fungi in Indah Water Konsortium (IWK) sewage treatment plant for biological treatment of domestic wastewater sludge. J Environ Sci Healt 37 : 309 320.
10. Fried J (2002) Isolation and identification of protozoa from biological wastewater treatment plants. Dissertation, University of Innsbruck, Austria.
11. Guest RK Smith DW (2002) A potential new role for fungi in a wastewater MBR biological nitrogen reduction system. J Environ Eng Sci 1 : 433 437.
12. Hughes AL Piontkivska H (2003) Phylogeny of Trypanosomatidae and Bodonidae (Kinetoplastida) based on 18S rRNA: evidence for paraphyly of Trypanosoma and six other genera. Mol Biol Evol 20 : 644 652.
13. Karakousis A, Tan L, Ellis D, Alexiou H Wormald PJ (2005) An assessment of the efficiency of fungal DNA extraction methods for maximizing the detection of medically important fungi using PCR. J Microbiol Meth 65 : 38 48.
14. Kendall JM Rygiewicz PT (2005) Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiol 5 : 28.
15. Kowalchuk GA (1999) New perspectives towards analysing fungal communities in terrestrial environments. Curr Opin Biotech 10 : 247 251.
16. Kowalchuk GA Smit E (2004) Fungal community analysis using PCR Denaturing Gradient Gel Electrophoresis (DGGE). Molecular Microbial Ecology Manual, 2nd edn (Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans ADL van Elsas JD, eds), pp. 771 788. Kluwer Academic Publishers, Dordrecht, the Netherlands.
17. Lüders T, Manefield M Friedrich MW (2004) Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ Microbiol 6 : 73 78.
18. Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J, Bachleitner M Schleifer KH (1998) Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19 : 554 568.
19. Ludwig W, Strunk O, Westram R et al 2004) ARB: a software environment for sequence data. Nucleic Acids Res 32 : 1363 1371.
20. Mannan S, Fakhru'l-Razi A Alam MZ (2005) Use of fungi to improve bioconversion of activated sludge. Water Res 39 : 2935 2943.
21. Manter DK Vivanco JM (2007) Use of the ITS primers, ITS1F and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis. J Microbiol Meth 71 : 7 14.
22. Molla AH, Fakhru'l-Razi A, Abd-Aziz S, Hanafi MM, Roychoudhury PK Alam MZ (2002) A potential resource for bioconversion of domestic wastewater sludge. Bioresource Technol 85 : 263 272.
23. Morgenroth E, Sherden T, van Loosdrecht MCM, Heijnen JJ Wilderer PA (1997) Aerobic granular sludge in a sequencing batch reactor. Water Res 31 : 3191 3194.
24. Moy BYP, Tay J-H, Toh S-K, Liu Y Tay STL (2002) High organic loading influences the physical characteristics of aerobic sludge granules. Lett Appl Microbiol 34 : 407 412.
25. Mudrack K Kunst S (1988) Biologie der Abwasserreinigung. 2. Auflage. Gustav Fischer Verlag, Stuttgart, Germany.
26. Ranjard L, Poly F, Lata J-C, Mougel C, Thioulouse J Nazaret S (2001) Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl Environ Microb 67 : 4479 4487.
27. Schaap P, Winckler T, Nelson M et al 2006) Molecular phylogeny and evolution of morphology in the social amoebas. Science 314 : 661 663.
28. Selitrennikoff CP (2001) Antifungal proteins. Appl Environ Microb 67 : 2883 2894.
29. Smit E, Leeflang P, Glandorf B, van Elsas JD Wernars K (1999) Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microb 65 : 2614 2621.
30. Subramanian CV (1983) Hyphomycetes, Taxonomy and Biology. Academic Press, New York.
31. Vainio EJ Hantula J (2000) Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol Res 104 : 927 936.
32. van Elsas JD, Duarte GF, Keijzer-Wolters A Smit E (2000) Analysis of the dynamics of fungal communities in soil via fungal-specific PCR of soil DNA followed by denaturing gradient gel electrophoresis. J Microbiol Meth 43 : 133 151.
33. Vilgalys R Hester M (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 172 : 4238 4246.
34. Wang Q, Du G Chen J (2004) Aerobic granular sludge cultivated under the selective pressure as a driving force. Process Biochem 39 : 557 563.
35. Wargo MJ Hogan DA (2006) Fungal-bacterial interactions: a mixed bag of mingling microbes. Curr Opin Microbiol 9 : 1 6.
36. Weber SD, Wanner G, Ludwig W, Schleifer KH Fried J (2007) Microbial composition and structure of aerobic granular sewage biofilms. Appl Environ Microb 73 : 6233 6240.
37. White TJ, Bruns T, Lee S Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Applications (Innis MA, Gelfand DH, Sninsky JJ White TJ, eds), pp. 315 322. Academic Press Inc., New York.
38. Wilderer PA McSwain BS (2004) The SBR and its biofilm application potentials. Water Sci Technol 50 : 1 10.
39. Yeo SF Wong B (2002) Current status of nonculture methods for diagnosis of invasive fungal infections. Clin Microbiol Rev 15 : 465 484.