Metagenomic analysis of fungal communities inhabiting the fairy ring zone of Tricholoma matsutake

Journal of Microbiology and Biotechnology

Volumn 23, Issue 10, 2013, Pages 1347-1356

  Kim, Miae ^a   Yoon, Hyeokjun ^a   You, Young Hyun ^a   Kim, Ye Eun ^a   Woo, Ju Ri ^a   Seo, Yeonggyo ^a   Lee, Gyeong Min ^a   Kim, Young Ja ^b   Kong, Won Sik ^c   Kim, Jong Guk ^a  

^a Kyungpook National University   (South Korea)

^b Korea Environmental Industry and Technology Institute (KEITI)   (South Korea)

^c Rural Development Administration   (South Korea)

Author keywords

Fungal communities; Metagenomic analysis; Pyrosequencing; Tricholoma matsutake

Indexed keywords

ARTICLE; BOLETOPSIS; COMMUNITY STRUCTURE; CONTROLLED STUDY; FUNGAL COMMUNITY; FUNGUS; HEMIMYCENA; METAGENOMICS; MICROBIAL DIVERSITY; MYCENA; NONHUMAN; PYROSEQUENCING; REPETOPHRAGMA; SAMPLING; SOIL ANALYSIS; SOUTH KOREA; TAXONOMY; TRICHOLOMA MATSUTAKE;

BOLETOPSIS; FUNGI; HEMIMYCENA; MYCENA; OTUS; TRICHOLOMA MATSUTAKE;

ASIA; BIOTA; DNA, FUNGAL; METAGENOMICS; MOLECULAR SEQUENCE DATA; MYCORRHIZAE; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; TRICHOLOMA;

EID: 84885943832     PISSN: 10177825     EISSN: 17388872     Source Type: Journal    
DOI: 10.4014/jmb1306.06068     Document Type: Article

References (54)

1. Agerer R. 2006. Fungal relationships and structural identity of their ectomycorrhizae. Mycol. Prog. 5: 67-107.
2. Ahn JS, Lee KH. 1986. Studies on the volatile aroma components of edible mushroom (Tricholoma matsutake) of Korea. J. Kor. Soc. Food Nutr. 15: 253-257.
3. Amann RI, Ludwig W, Schleifer K-H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143-169.
4. Amend AS, Keeley S, Garbelotto M. 2009. Forest age correlates with fine-scale spatial structure of Matsutake mycorrhizas. Mycol. Res. 113: 541-550.
5. Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, et al. 2009. 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol. 184: 449-456.
6. Danielsen L, Thürmer A, Meinicke P, Buée M, Morin E, Martin F, et al. 2012. Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities. Ecol. Evol. 2: 1935-1948.
7. Deacon JW, Fleming LV. 1992. Interactions of ectomycorrhizal fungi, pp. 249-300. In M. F. Allen (ed.). Mycorrhizal Functioning: An Integrative Plant-fungal Process. Chapman and Hall, New York.
8. Ding X, Tang J, Cao M, Guo CX, Zhang X, Zhong J, et al. 2010. Structure elucidation and antioxidant activity of a novel polysaccharide isolated from Tricholoma matsutake. Int. J. Biol. Macromol. 47: 271-275.
9. Gottel NR, Castro HF, Kerley M, Yang Z, Pelletier DA, Podar M, et al. 2011. Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl. Environ. Microbiol. 77: 5934-5944.
10. Guerin-Laguette A, Shindo K, Matsushita N, Suzuki K, Lapeyrie F. 2004. The mycorrhizal fungus Tricholoma matsutake stimulates Pinus densiflora seedling growth in vitro. Mycorrhiza 14: 397-400.
11. Handelsman J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68: 669-685.
12. Harley JL, Smith SE. 1983. Mycorrhizal Symbiosis. Academic Press, Toronto.
13. Harley JL. 1989. The significance of mycorrhiza. Mycol. Res. 92: 129-139.
14. Hebert PD, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proc. Biol. Sci. 270: 313-321.
15. Heck KL, van Belle G, Simberloff D. 1975. Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology 56: 1459-1461.
16. Hosford D, Pliz D, Molina R, Amaranthus M. 1997. Ecology and Management of the Commercially Harvested American Matsutake. General Technical Report PNW-GTR-412. USDA Forest Service, Pacific Northwest Research Station, Portland, OR.
17. Hoshi H, Yagi Y, Iijima H, Matsunaga K, Ishihara Y, Yasuhara T. 2005. Isolation and characterization of a novel immunomodulatory alpha-glucan-protein complex from the mycelium of Tricholoma matsutake in basidiomycetes. J. Agric. Food Chem. 53: 8948-8956.
18. Kataoka R, Siddiqui ZA, Kikuchi J, Ando M, Sriwati R, Nozaki A, et al. 2012. Detecting nonculturable bacteria in the active mycorrhizal zone of the pine mushroom Tricholoma matsutake. J. Microbiol. 50: 199-206.
19. Kawagishi H, Hamajima K, Takanami R, Nakamura T, Sato Y, Akiyama Y, et al. 2004. Growth promotion of mycelia of the Matsutake mushroom Tricholoma matsutake by D-isoleucine. Biosci. Biotechnol. Biochem. 68: 2405-2407.
20. Kawai M, Terada O. 1976. Artificial reproduction of Tricholoma matsutake (S. Ito et Imai) Sing. II. Effects of vitamins, nucleic acid-related substances, phytohormones and metal ions in the media on the vegetative growth of T. Matsutake. Trans. Mycol. Soc. Japan 17: 168-174
21. Kim JY, Byeon SE, Lee YG, Lee JY, Park J, Hong EK, et al. 2008. Immunostimulatory activities of polysaccharides from liquid culture of pine-mushroom Tricholoma matsutake. J. Microbiol. Biotechnol. 18: 95-103.
22. Kolbert CP, Persing DH. 1999. Ribosomal DNA sequencing as a tool for identification of bacterial pathogens. Curr. Opin. Microbiol. 2: 299-305.
23. Lang C, Seven J, Polle A. 2011. Host preferences and differential contributions of deciduous tree species shape mycorrhizal species richness in a mixed Central European forest. Mycorrhiza 21: 297-308.
24. Li W, Godzik A. 2006. Cd -hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
25. Lian C, Narimatsu M, Nara K, Hogetsu T. 2006. Tricholoma matsutake in a natural Pinus densiflora forest: correspondence between above- and below-ground genets, association with multiple host trees and alteration of existing ectomycorrhizal communities. New Phytol. 171: 825-836.
26. Liu K-L, Porras-Alfaro A, Kuske CR, Eichorst SA, Xie G. 2012. Accurate, rapid taxonomic classification of fungal large-subunit rRNA genes. Appl. Environ. Microbiol. 78: 1523-1533.
27. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
28. Ogawa M. 1975. Microbial ecology of mycorrhizal fungus Tricholoma matsutake Ito et Imai (Sing.) in pine forests. I. Fungal colony ('shiro') of Tricholoma matsutake. Bull. Gov. For. Exp. Stat. 272: 79-121.
29. Ogawa M. 1975. Microbial ecology of mycorrhizal fungus Tricholoma matsutake Ito et Imai (Sing.) in pine forest. II. Mycorrhiza formed by Tricholoma matsutake. Bull. Gov. For. Exp. Stat. 278: 21-49.
30. Ogawa M. 1978. Biology of Matsutake Mushroom, pp. 168-175. Tsukiji Shokan, Tokyo.
31. Ogawa M. 1991. Biology of Matsutake Mushroom 2nd Ed. Tsukiji Shokan, Tokyo.
32. Ogawa M, Umehara T, Kontani S, Yamaji K. 1978. Cultivating method of the mycorrhizal fungus, Tricholoma matsutake (Ito et Imai) Sing. (1) Growing method of pine saplings infected with T. matsutake in the field. J. Jpn. For. Soc. 60: 119-128.
33. Ohnuma N, Amemiya K, Kakuda R, Yaoita Y, Machida K, Kikuchi M. 2000. Sterol constituents from the edible mushrooms, Lentinula edodes and Tricholoma matsutake. Chem. Pharm. Bull. 48: 749-751.
34. Ohta A. 1986. Basidiospore germination of Tricholoma matsutake. (I) Effects of organic acids on swelling and germination of basidiospores. Trans. Mycol. Soc. Jpn. 27: 167-173.
35. Olsen GJ, Woese CR. 1993. Ribosomal RNA: a key to phylogeny. FASEB J. 7: 113-123.
36. Panaro NJ, Yuen PK, Sakazume T, Fortina P, Kricka LJ, Wilding P. 2000. Evaluation of DNA fragment sizing and quantification by the Agilent 2100 bioanalyzer. Clin. Chem. 46: 1851-1853.
37. Porter TM, Golding GB. 2012. Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error. PLoS One 7: e35749.
38. Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, et al. 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4: 1340-1351.
39. Rousk J, Brookes PC, Bååth E. 2009. Contrasting soil pH effects on fungal and bacterial growth suggests functional redundancy in carbon mineralization. Appl. Environ. Microbiol. 75: 1589-1596.
40. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. 2009. Introducing Mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75: 7537-7541.
41. Shokralla S, Spall J, Gibson J, Hajibabaei M. 2012. Next-generation sequencing technologies for environmental DNA research. Mol. Ecol. 21: 1794-1805.
42. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, et al. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc. Natl. Acad. Sci. USA 103: 12115-12120.
43. Streit WR, Schmitz RA. 2004. Metagenomics - the key to the uncultured microbes. Curr. Opin. Microbiol. 7: 492-498.
44. Taminaga Y, Komeyama S. 1987. Practice of Matsutake Cultivation. Youken Press, Tokyo.
45. Vaario LM, Guerin-Laguette A, Matsushita N, Suzuki K, Lapeyrie F. 2002. Saprobic potential of Tricholoma matsutake: growth over pine bark treated with surfactants. Mycorrhiza 12: 1-5.
46. Vaario LM, Fritze H, Spetz P, Heinonsalo J, Hanajík P, Pennanen T. 2011. Tricholoma matsutake dominates diverse microbial communities in different forest soils. Appl. Environ. Microbiol. 77: 8523-8531.
47. Vaario LM, Pennanen T, Sarjala T, Savonen EM, Heinonsalo J. 2010. Ectomycorrhization of Tricholoma matsutake and two main forest tree species in Finland - an assessment of in vitro mycorrhiza formation. Mycorrhiza 20: 511-518.
48. Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J, Young JP. 2002. Extensive fungal diversity in plant roots. Science 295: 2051.
49. Vilgalys R, Hester M. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J. Bacteriol. 172: 4238-4246.
50. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73: 5261-5267.
51. Yamada A, Maeda K, Kobayashi H, Murata H. 2005. Ectomycorrhizal symbiosis in vitro between Tricholoma matsutake and Pinus densiflora seedlings that resembles naturally occurring 'shiro'. Mycorrhiza 16: 111-116.
52. Yamada A, Maeda K, Ohmasa M. 1999. Ectomycorrhiza formation of Tricholoma matsutake isolates on seedlings of Pinus densiflora in vitro. Mycoscience 40: 455-463.
53. Yamada A, Kanekawa S, Ohmasa M. 1999. Ectomycorrhiza formation of Tricholoma matsutake on Pinus densiflora. Mycoscience 40: 193-198.
54. Zinger L, Coissac E, Choler P, Geremia RA. 2009. Assessment of microbial communities by graph partitioning in a study of soil fungi in two alpine meadows. Appl. Environ. Microbiol. 75: 5863-5870.