Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera 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 pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.

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In this study, the effects of a syntrophic methanogen on the growth of Pecoramyces sp. F1 was investigated by characterizing fermentation profiles, as well as functional genomic, transcriptomic, and proteomic analysis. The estimated genome size, GC content, and protein coding regions of strain F1 are 106.83 Mb, 16.07%, and 23.54%, respectively. Comparison of the fungal monoculture with the methanogen co-culture demonstrated that during the fermentation of glucose, the co-culture initially expressed and then down-regulated a large number of genes encoding both enzymes involved in intermediate metabolism and plant cell wall degradation. However, the number of up-regulated proteins doubled at the late-growth stage in the co-culture. In addition, we provide a mechanistic understanding of the metabolism of this fungus in co-culture with a syntrophic methanogen. Further experiments are needed to explore this interaction during degradation of more complex plant cell wall substrates.

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This study investigated the effect of saponins gypenoside (gynosaponins) on methane production and microbe numbers in a co-culture of a fungus, Piromyces sp. F1, and a methanogen, Methanobrevibacter sp.. Two co-culture systems were used: with methanogen (co-culture I) and without methanogen (co-culture II; methanogen growth inhibited by chloramphenicol). Each co-culture system was treated with 0, 50, 100 or 200 mg gynosaponins/l culture medium. Gas production, methane concentration and volatile fatty acid concentration (VFA) were measured for each treatment group. The numbers of anaerobic fungi and methanogen were quantified by real time PCR. The results showed that, compared with the control, gynosaponin significantly reduced the gas production, methane concentration, methane to TVFA ratio (total volatile fatty acid), TVFA concentration, number of fungi (except for 50 mg dose of gynosaponin in co-culture I) and number of methanogens. Methane was not detected in co-culture II. The individual VFAs proportion of TVFA were not affected by gynosaponins in either of the co-cultures. The pH was higher in both co-cultures than that of the control (P<0.01). These data suggest that gynosaponins has the potential for being used as feed additive to modulate the ruminal fermentation, inhibit the methanogen growth and reduce methane production.