Fungal communities in composting systems revealed by DNA-based molecular methods

  • Adrian Langarica Fuentes

    Student thesis: Unknown


    Despite being the central aspect of the composting process, the microbial communities carrying out the degradation of organic matter in these environments have not been characterised in detail due to their complexity and the limitations of the previously available tools. This study aimed to i) investigate the fungal communities of composting environments using culture-based methods, denaturing gradient gel electrophoresis (DGGE) and tag-encoded pyrosequencing, ii) to identify the most abundant groups of fungi found in these environments and iii) to identify thermophilous fungi and evaluate their abundance. The fungal community diversity was studied in two different commercial composts produced in large-scale facilities. 454 pyrosequencing recovered a total of 175 OTUs between the two composts and revealed that the fungal community in these systems is composed of species belonging to the phylum Ascomycota, Basidiomycota and subphylum Mucoromycotina. At the order level, the Sordariales, Eurotiales, Orbiliales, Microascales and Hypocreales were the most abundant taxa. Incubation at 50°C was used to identify the main thermophilous organisms in the composts, which included Scytalidium thermophilum, Thermomyces lanuginosus, Coprinopsis sp., Myriococcum thermophilum, Pseudallescheria boydii, Pseudallescheria fimeti and several uncultured fungi. The succession of fungal species in a large-scale, industrial composting process was studied in collaboration with a private composting company (TEG Group PLC). Composting materials were sampled at different times of the process and in different sections of the composting pile in order to reveal the species that are abundant at the different stages of composting. A complex succession of fungi was revealed in this system, with 251 different fungal OTUs identified throughout the process. The Ascomycota were the dominant phylum, followed by the Basidiomycota and the subphylum Mucoromycotina. Examination at the order level revealed that in the starting materials and early stages of the process, yeast species from the Saccharomycetales and Tremellales orders were abundant, while in latter stages and in the high temperature sections of the composting pile, fungi from the orders Eurotiales, Sordariales, Mucorales, Agaricales and Microascales were the dominant members of the community.The fungal community diversity of domestic composts from the Greater Manchester area was studied. 478 different OTUs were recovered from 10 composts. Phylum-level distribution of OTUs in home composts was similar to commercial composts, with most OTUs recovered belonging to the Ascomycota, the subphylum Mucoromycotina and the Basidiomycota. However, at the order and genus level the fungal communities were different with species from the Microascales and Hypocreales being highly abundant. The most abundant genera were Pseudallescheria, Penicillium, Mortierella and Fusarium. Thermophilic and thermotolerant fungi were present in much lower numbers in the home compost samples than in industrial composts.
    Date of Award1 Aug 2014
    Original languageEnglish
    Awarding Institution
    • The University of Manchester
    SupervisorGeoffrey Robson (Supervisor) & Anil Day (Supervisor)


    • metabarcoding
    • next generation sequencing
    • microbial ecology
    • diversity
    • fungi
    • compost
    • DGGE

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