Evaluation of culture-based techniques and 454 pyrosequencing for the analysis of fungal diversity in potting media and organic fertilizers

Journal of Applied Microbiology

Volumn 119, Issue 2, 2015, Pages 500-509

  Al Sadi, Abdullah M ^a   Al Mazroui, S S ^b   Phillips, A J L ^c  

^a SULTAN QABOOS UNIVERSITY   (Oman)

^b THE RESEARCH COUNCIL   (Oman)

^c UNIVERSIDADE NOVA DE LISBOA   (Portugal)

Author keywords

Ascomycota; Baiting; Basidiomycota; Chytridiomycetes; Next generation sequencing; Plating; Sordariomycetes

Indexed keywords

EFFICIENCY; FERTILIZERS; PLATING; POPULATION STATISTICS; RNA;

ASCOMYCOTA; BAITING; BASIDIOMYCOTA; CHYTRIDIOMYCETE; FUNGAL DIVERSITY; NEXT-GENERATION SEQUENCING; ORGANIC FERTILIZERS; POTTING MEDIA; PYROSEQUENCING; SORDARIOMYCETE;

FUNGI;

INTERNAL TRANSCRIBED SPACER; ORGANIC FERTILIZER; RIBOSOME RNA; FERTILIZER;

BIOFERTILIZER; BIOTECHNOLOGY; DETECTION METHOD; DICOTYLEDON; EFFICIENCY MEASUREMENT; FUNGUS; LABORATORY METHOD; MICROBIOLOGY; MOLECULAR ANALYSIS; POPULATION DENSITY; POTATO; RNA; ROOT VEGETABLE; SEED; SPECIES DIVERSITY;

ALTERNARIA; ARTICLE; ASPERGILLUS; CHAETOMIUM; CHYTRIDIOMYCETES; CLADOSPORIUM; CUNNINGHAMELLA; DILUTION; FUNGUS CULTURE; FUSARIUM; LECANICILLIUM; MICROBIAL DIVERSITY; MORTIERELLA; NONHUMAN; PENICILLIUM; PYROSEQUENCING; RNA SEQUENCE; TRICHODERMA; ZYGOMYCETES; BIODIVERSITY; CELL CULTURE TECHNIQUE; CLASSIFICATION; EVALUATION STUDY; FUNGUS; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; MICROBIOLOGY; PROCEDURES;

ASCOMYCOTA; BASIDIOMYCOTA; CHYTRIDIOMYCOTA; CUCUMIS SATIVUS; DAUCUS CAROTA; FUNGI; RAPHANUS SATIVUS; SOLANUM TUBEROSUM; SORDARIOMYCETES; ZYGOMYCOTA;

BIODIVERSITY; CULTURE TECHNIQUES; FERTILIZERS; FUNGI; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SOIL MICROBIOLOGY;

EID: 84937635417     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/jam.12854     Document Type: Article

References (43)

1. Abed, R.M.M., Al-Sadi, A.M., Al-Shihi, M.A., Al-Hinai, S. and Robinson, M.D. (2013) Diversity of free-living and lichenized fungal communities in biological desert crusts of the Sultanate of Oman and their role in improving soil properties. Soil Biol Biochem 57, 695-705.
2. Al-Sa'di, A.M., Drenth, A., Deadman, M., de Cock, A.W.A.M. and Aitken, E.A.B. (2007) Molecular characterization and pathogenicity of Pythium species associated with damping-off in greenhouse cucumber (Cucumis sativus L.) in Oman. Plant Pathol 56, 140-149.
3. Al-Sa'di, A.M., Drenth, A., Deadman, M.L., Al-Said, F.A., Khan, I. and Aitken, E.A.B. (2008) Potential sources of Pythium inoculum into greenhouse soils with no previous history of cultivation. J Phytopathol 156, 502-505.
4. Al-Sadi, A.M., Al-Said, F.A., Al-Jabri, A.H., Al-Mahmooli, I.H., Al-Hinai, A.H. and de Cock, A.W.A.M. (2011) Occurrence and characterization of fungi and oomycetes transmitted via potting mixtures and organic manures. Crop Prot 30, 38-44.
5. Al-Sadi, A.M., Al-Ghaithi, A.G., Al-Balushi, Z.M. and Al-Jabri, A.H. (2012) Analysis of diversity in Pythium aphanidermatum populations from a single greenhouse reveals phenotypic and genotypic changes over 2006 to 2011. Plant Dis 96, 852-858.
6. Al-Sadi, A.M., AL-Wehaibi, A.N., Al-Shariqi, R.M., Al-Hammadi, M.S., Al-Hosni, I.A., Al-Mahmooli, I.H. and Al-Ghaithi, A.G. (2013) Population genetic analysis reveals diversity in Lasiodiplodia species infecting date palm, Citrus, and mango in Oman and the UAE. Plant Dis 97, 1363-1369.
7. Al-Sadi, A.M. and Deadman, M.L. (2010) Influence of seedborne Cochliobolus sativus (anamorph: Bipolaris sorokiniana) on crown rot and root rot of barley and wheat. J Phytopathol 158, 683-690.
8. Andersen, R., Francez, A.J. and Rochefort, L. (2006) The physicochemical and microbiological status of a restored bog in Québec: identification of relevant criteria to monitor success. Soil Biol Biochem 38, 1375-1387.
9. Blaya, J., López-Mondéjar, R., Lloret, E., Pascual, J.A. and Ros, M. (2013) Changes induced by Trichoderma harzianum in suppressive compost controlling Fusarium wilt. Pesticide Biochem Physiol 107, 112-119.
10. Bridge, P. and Spooner, B. (2003) Soil fungi: diversity and detection. Plant Soil 232, 147-154.
11. Brown, S.P. and Jumpponen, A. (2014) Contrasting primary successional trajectories of fungi and bacteria in retreating glacier soils. Mol Ecol 23, 481-497.
12. Cavagnaro, T.R. (2014) Impacts of compost application on the formation and functioning of arbuscular mycorrhizas. Soil Biol Biochem 78, 38-44.
13. Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., Kulam-Syed-Mohideen, A.S., McGarrell, D.M. et al. (2009) The ribosomal database project: improved alignment and new tools for rRNA analysis. Nucleic Acids Res 37, D141-D145.
14. Davison, E.M., Drenth, A., Kumar, S., Mack, S., Mackie, A.E. and McKirdy, S. (2006) Pathogens associated with nursery plants imported into Western Australia. Australas Plant Pathol 35, 473-475.
15. De Gannes, V., Eudoxie, G. and Hickey, W.J. (2013) Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety. Front Microbiol 4, 164.
16. Dowd, S.E., Zaragoza, J., Rodriguez, J.R., Oliver, M.J. and Payton, P.R. (2005) Windows.NET network distributed basic local alignment search toolkit (W.ND-BLAST). BMC Bioinform 6, 93.
17. Dowd, S.E., Callaway, T.R., Wolcott, R.D., Sun, Y., McKeehan, T., Hagevoort, R.G. and Edrington, T.S. (2008a) Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol 8, 125.
18. Dowd, S.E., Sun, Y., Wolcott, R.D., Domingo, A. and Carroll, J.A. (2008b) Bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies:bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog Dis 5, 459-472.
19. Edel-Hermann, V., Gautheron, N., Mounier, A. and Steinberg, C. (2015) Fusarium diversity in soil using a specific molecular approach and a cultural approach. J Microbiol Methods 111, 64-71.
20. Gleason, F.H., Letcher, P.M. and McGee, P.A. (2007) Some aerobic Blastocladiomycota and Chytridiomycota can survive but cannot grow under anaerobic conditions. Australas Mycol 26, 57-64.
21. Grishkan, I., Tsatskin, A. and Nevo, E. (2005) Diversity of cultured microfungal communities in surface horizons of soils on different lithologies in upper Galilee, Israel. Eur J Soil Biol 44, 180-190.
22. Harper, D.A.T. (1999) Numerical Palaeobiology. New York: John Wiley & Sons.
23. Hernández, T., Chocano, C., Moreno, J.-L. and García, C. (2014) Towards a more sustainable fertilization: combined use of compost and inorganic fertilization for tomato cultivation. Agric Ecosys Environ 196, 178-184.
24. Jeewon, R. and Hyde, K.D. (2007) Detection and diversity of fungi from environmental samples: traditional versus molecular approaches. Soil Biol 11, 1-15.
25. Jumpponen, A. and Jones, K.L. (2009) Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol 184, 438-448.
26. Jumpponen, A. and Jones, K.L. (2010) Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments. New Phytol 186, 496-513.
27. Lee, S.B. and Taylor, J.W. (1990) Isolation of DNA from fungal mycelia and single spores. In PCR Protocols: A Guide to Methods and Applications ed. Innis, M.A., Gelfand, D.H., Sninsky, J.J. and White, T.J. pp. 282-287. New York, NY, USA: Academic Press.
28. Lin, Y., Du, D., Si, C., Zhao, Q., Li, Z. and Li, P. (2014) Potential biocontrol Bacillus sp. strains isolated by an improved method from vinegar waste compost exhibit antibiosis against fungal pathogens and promote growth of cucumbers. Biol Control 71, 7-15.
29. Lozupone, C.A. and Klein, D.A. (2002) Molecular and cultural assessment of chytrid and Spizellomyces populations in grassland soils. Mycologia 94, 411-420.
30. Nannipieri, P., Ascher, J., Ceccherini, M.T., Landi, L., Pietra-mellara, G. and Renella, G. (2003) Microbial diversity and soil functions. Europ J Soil Sci 54, 65-70.
31. Neher, D.A., Weicht, T.R., Bates, S.T., Leff, J.W. and Fierer, N. (2013) Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times. PLoS ONE 8, e79512.
32. Ranganayaki, M., Tilak, K.V.B.R., Manoharachary, C. and Mukerji, K.G. (2006) Methods and techniques for isolation, enumeration and characterization of rhizosphere microorganisms. Soil Biol 7, 17-38.
33. Sapkota, R. and Nicolaisen, M. (2015) An improved high throughput sequencing method for studying oomycete communities. J Microbiol Methods 110, 33-39.
34. Saravanakumar, K. and Kaviyarasan, V. (2010) Seasonal distribution of soil fungi and chemical properties of montane wet temperate forest types of Tamil Nadu. Afric J Plant Sci 4, 190-196.
35. Shen, Z., Wang, D., Ruan, Y., Xue, C., Zhang, J., Li, R. and Shen, Q. (2014) Deep 16S rRNA pyrosequencing reveals a bacterial community associated with banana Fusarium wilt disease suppression induced by bio-organic fertilizer application. PLoS ONE 9, e98420.
36. Shi, L.-L., Mortimer, P.E., Ferry Slik, J.W., Zou, X.-M., Xu, J., Feng, W.-T. and Qiao, L. (2014) Variation in forest soil fungal diversity along a latitudinal gradient. Fungal Div 64, 305-315.
37. Smith, G.W. and Skipper, H.D. (1979) Comparison of methods to extract spores of vesicular-arbuscular mycorrhizal fungi. Soil Sci Soc Am J 43, 722-725.
38. Thormann, M.N. and Rice, A.V. (2007) Fungi from peatlands. Fungal Div 24, 241-299.
39. Tian, Y. and Gao, L. (2014) Bacterial diversity in the rhizosphere of cucumbers grown in soils covering a wide range of cucumber cropping histories and environmental conditions. Microb Ecol 68, 794-806.
40. Vieira, F.C.S. and Nahas, E. (2005) Comparison of microbial numbers in soils by using various culture media and temperatures. Microbiol Res 160, 197-202.
41. Volossiouk, T., Robb, E.J. and Nazar, R.N. (1995) Direct DNA extraction for PCR-mediated assays of soil organisms. Appl Environ Microbiol 61, 3972-3976.
42. White, T.J., Bruns, T., Lee, S. and Taylor, J. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR protocols: A Guide to Methods and Applications eds. Innis, M.A., Gelfand, D.H., Sninsky, J.J. and White, T.J., pp. 315-322. New York, USA: Academic Press.
43. Williams, R.T. and Crawford, R.L. (1983) Microbial diversity of Minnesota peatlands. Microbial Ecol 9, 201-214.