PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities
Journal Article - Open Access
Wageningen University and Research Wageningen Netherlands
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Anaerobic fungi phylum Neocallimastigomycota are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20 percent of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenicarchaea, which increases their fiber degradation activity. To date, nine anaerobic fungalgenera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region ITS1 has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA LSU is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in puremixed cultures and environmental samples will be invaluable in this process.