Dynamics of Mycobiota during Composting of Cow Manure and Straw

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Abstract

The study of the dynamics of mycobiota during composting of cow manure and wheat straw using DNA barcoding and culture method was carried out. Using DNA barcoding, fungi of phylla Ascomycota, Basidiomycota, Mortierellomycota, Chytridiomycota, Rozellomycota, Aphelidiomycota were found. Cultural method (plating) identified Ascomycota, Basidiomycota, Mucoromycota. All the orders of fungi established by the plating method, with the exception of Saccharomycetales in Ascomycota and Mucorales in Mucoromycota, were also discovered using DNA barcoding, but many others were the latter. The coincidence of the species detected by both methods was very rare. Changes in the number of colony-forming and operational-taxonomic units of taxa of different levels during the transformation of manure with straw into compost were traced. DNA barcoding made more fully identify changes in the taxonomic and ecological-trophic structure of the fungal community during composting of manure and straw. They are expressed in a significant increase in the representation of basidiomycetes, especially Coprinus spp., Coprinellus spp., in compost, capable of transformation of lignin, complex organic substances of manure, and a decrease in the proportion of abundantly spore-bearing, “sugar” and cellulolytic ascomycetes dominating in the initial substrates: Sordariomycetes in manure and Dothideomycetes in straw. During composting, significant rearrangements occurred in the composition of coprophilic, epiphytic and phytopathogenic fungi. The importance of toxin-forming, allergenic and thermophilic species of fungi that pose a danger to human health, and the possibility of assessing the readiness of compost for application to the soil as a biofertilizer, taking into account data on mycobiota, are discussed.

About the authors

A. V. Kurakov

Moscow State University, Faculty of Biology

Author for correspondence.
Email: kurakov57@mail.ru
Russia, 119991, Moscow, Leninskie Gory, 1

E. N. Bilanenko

Moscow State University, Faculty of Biology

Email: kurakov57@mail.ru
Russia, 119991, Moscow, Leninskie Gory, 1

References

  1. Кононенко Г.П. Токсигенные микромицеты-космополиты рода Aspergillus: новые факты последних десятилетий // Иммунопатология, аллергология, инфектология. 2021. № 4. С. 77–82.
  2. М-МВИ-80-2008. Методика выполнения измерений массовой доли элементов в пробах почв, грунтов и донных отложений методами атомно-эмиссионной и атомно-абсорбционной спектрометрии. 000 Мониторинг. СПб., 2008. 27 с.
  3. Ножевникова А.Н., Миронов В.В., Бочкова Е.А., Литти Ю.В., Русскова Ю.И. Состав микробного сообщества на разных стадиях компостирования, перспектива получения компоста из муниципальных органических отходов (обзор) // Прикладная биохимия и микробиология. 2019. Т. 55. № 3. С. 211–221.
  4. Antunes L.P., Martins L.F., Pereira R.V., Thomas A.M., Barbosa D., Lemos L.N., Machado Silva G.M. et al. Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics // Sci. Rep. 2016. V. 6. № 38915. https://doi.org/10.1038/srep38915
  5. Arx von J.A. The Genera of fungi sporulating in pure culture. Vaduz, 1981. 424 p.
  6. Bertoldi de M., Vallini G., Pera A. The biology of composting: a review // Waste Management Research. 1983. № 133. P. 157–176.
  7. Booth C. Fusarium. Laboratory guide to the identification of the major species. C.M.I., 1977. 57 p.
  8. Crous P.W., Braun U., Schubert K., Groenewald J.Z. The genus Cladosporium and similar dematiaceous hyphomycetes // Stud Mycol. 2007. V. 58. P. 1–253.
  9. De Hoog G.S., Guarro J., Gené J., Figueras M.J. Atlas of Clinical Fungi. Utrecht: CBS-KNAW. Fungal Biodiversity Centre, 2011. 1126 p.
  10. De Gannes V., Eudoxie G., Hickey W.J. Prokaryotic successions and diversity in composts as revealed by 454-pyrosequencing // Bioresour. Technol. 2013a. № 133. P. 573–580. https://doi.org/10.1016/j.biortech.2013.01.138
  11. De Gannes V., Eudoxie G., Hickey W.J. Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety // Frontiers Microbiology. 2013. V. 4. № 164. P. 1–9.
  12. Domsch K.H., Gams W., Anderson T.-H. Compendium of Soil Fungi. IHW-Verlag et Verlagsbuchhandlung, Eching, 2007. 672 p.
  13. Ellis M.B. Dematiaceous Hyphomycetes. Commonwealth Mycological Institute, Kew, 390 Surrey. England. 1971. 608 p.
  14. Glushakova A.M., Kachalkin A.V. Yeasts of Nikitsky Botanical Garden Plants // Microbiology. 2017. V. 86. № 5. P. 647–652.
  15. Green S.J., Michel F.C., Yadar Y., Minz D. Similarity of bacterial community in sawdust – and straw-amended cow manure compost // FEMS Microbiol. Lett. 2004. V. 233. P. 115–123. https://doi.org/10.1016/j.femsle.2004.01.049
  16. Hansgate A.M., Schloss P.D., Anthony G.H., Walker L.P. Molecular characterization of fungal community dynamics in the initial stages of composting // FEMS Microbiol. Ecol. 2005. № 51. P. 209–214. https://doi.org/10.1016/j.femsec.2004.08.009
  17. Keirle M.R, Hemmes D.E., Desjardin D.E. Agaricales of the Hawaiian Islands. 8. Agaricaceae: Coprinus and Podaxis; Psathyrellaceae: Coprinopsis, Coprinellus and Parasola. Fungal Diversity. 2004. № 15. P. 33–124.
  18. Kirk P.M., Cannon P.F., Minter D.W., Stalpers J.A. Dictionary of the Fungi. Wallingford: CAB Int., 2008. 2600 p.
  19. Klich M.A. Identification of Common Aspergillus Species. Utrecht: Centraalbureau voor Schimmelcultures, 2002. 528 p.
  20. Latgé J.-P., Chamilos G. Aspergillus fumigatus and Aspergillosis in 2019 // Am. Soc. Microbiol. 2019. V. 33. № 1. https://doi.org/10.1128/CMR.00140-18
  21. Lopez–Gonzalez J.A., Suarez–Estrella F., Vargas–García M.C., Lopez M.J., Jurado M.M., Moreno J. Dynamics of bacterial microbiota during lignocellulosic waste composting: Studies upon its structure, functionality and biodiversity // Bioresour. Technol. 2015. № 175. P. 406–416.
  22. Melo R.F.R., Maia L.C., Miller A.N. Coprophilous ascomycetes with passive ascospore liberation from Brazil // Phytotaxa. 2017. V. 295. № 2. P. 159–172. https://doi.org/10.11646/phytotaxa.295.2.4
  23. Mohammadipour Z., Enayatizamir N., Ghezelbash G., Moezzi A. Bacterial Diversity and Chemical Properties of Wheat Straw-Based Compost Leachate and Screening of Cellulase Producing Bacteria // Waste and Biomass Valorization. 2021. V. 12. № 6. https://doi.org/10.1007/s12649-020-01119-w
  24. Neher D.A., Weicht T.R., Bates S.T., Leff J.W., Fierer N. Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting Times // PLoS One. 2013. V. 8. № 11. https://doi.org/10.1371/journal.pone.0079512
  25. Oliver J.P., Perkins J., Jellison J. Effect of fungal pretreatment of wood on successional decay by several inky cap mushroom species // Int. Biodeterioration Biodegradation. 2010. V. 64. № 7. P. 646–651.
  26. Partanen P., Hultman J., Paulin L., Auvinen P., Romantschuk M. Bacterial diversity at different stages of the composting process // BMC Microbiol. 2010. № 10. P. 94. https://doi.org/10.1186/1471-2180-10-94
  27. Paulussen C., Hallsworth J.E., Alvarez-Perez S., Nierman W.C., Hamill P.G., Blain D., Rediers H., Lievens B. Ecology of aspergillosis: insights into the pathogenic potency of Aspergillus fumigatus and some other Aspergillus species // Microbial Biotechnology. 2017. V. 10. № 2. P. 296–322. https://doi.org/10.1111/1751-7915.12367
  28. Peters S., Koschinsky S., Schwieger, Tebbe C.C. 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. 2000. V. 66. P. 930–936.
  29. Raper K.B., Fennell D.I. The Genus Aspergillus. The Williams and Wilkins Company, Baltimore. 1965. 686 p.
  30. Raper K.B., Thom C., Fennell D.I. A Manual of the Penicillia. N.Y.: Hafner Publishing Company, 1968. 875 p.
  31. Rifai M.A. A revision on the genus Trichoderma // Mycol Pap. 1969. V. 116. P. 1–56.
  32. Ryckeboer J., Mergaert J., Vaes K., Klammer S., De Clerco D., Coosemans J., Insam H., Swings J. A survey of bacteria and fungi occurring during composting and self-heating processes // Annals Microbiol. 2003. V. 53. № 4. P. 349–410.
  33. Samson R.A, Houbraken J. Phylogenetic and taxonomic studies on the genera Penicillium and Talaromyces // Stud Mycol. 2011. V. 70. P. 1–183.
  34. Schipper M.A. On certain species of Mucor with a key to all accepted species: 2. On the genera Rhizomucor and Parasitella // Stud. Mycol. 1978. V. 17. P. 1–71.
  35. Schloss P.D., Hay A.G., Wilson D.B., Walker L.P. Tracking temporal changes of bacterial community fingerprints during the initial stages of composting // FEMS Microbiol. Ecol. 2003. V. 46. P. 1–9.
  36. Seifert K., Morgan–Jones G., Gams W., Kendrick B. The Genera of Hyphomycetes. Utrecht: CBS-KNAW Fungal Biodiversity Centre, 2011. 997 p. https://doi.org/10.3767/003158511X617435
  37. Takaku H., Kodaira S., Kimoto A., Nashimoto M., Takagi M. Microbial communities in the garbage composting with rice hull as an amendment revealed by culture-dependent and independent approaches // J. Biosci. Bioeng. 2006. V. 101. P. 42–50.
  38. Tuomela M., Vikman M., Hatakka A., Itavaara M. Biodegradation of lignin in a compost environment: a review // Bioresource Technology. 2000. V. 72. P. 169–183.
  39. Wang C., Guo X., Deng H., Dong D., Tu Q., Wu W. New insights into the structure and dynamics of actinomycetal community during manure composting // Appl. Microbiol. Biotechnol. 2014. V. 98. № 7. P. 3327–3337.
  40. Yi X.W., He J., Sun L.T., Liu J.K., Wang G.K., Feng T. 3-Decalinoyltetramic acids from kiwi-associated fungus Zopfiella sp. and their antibacterial activity against Pseudomonas syringae // RSC advances. 2021. V. 11. № 31. P. 18827–18831. https://doi.org/10.1039/d1ra02120f
  41. Zhang L.L., Zhang H.Q., Wang Z.H., Chen G.J., Wang L.S. Dynamic changes of the dominant functioning microbial community in the compost of a 90-m(3) aerobic solid state fermentor revealed by integrated meta-omics // Bioresource Technol. 2016. V. 203. P. 1–10. https://doi.org/10.1016/j.biortech.2015.12.040

Copyright (c) 2023 А.В. Кураков, Е.Н. Биланенко

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies