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.

Food resources contaminated with spoilage or pathogenic microorganisms pose severe problems to all higher organisms. Here, we describe a food-hygienic strategy of the emerald cockroach wasp Ampulex compressa . The wasp larvae develop on and inside the American cockroach Periplaneta americana , a host that can harbor various putrefactive microbes, as well as human and insect pathogens. From P. americana , we isolated the Gram-negative bacterium Serratia marcescens , which is a potent entomopathogen that can rapidly kill insect larvae. It is also known as a food contaminant and as an opportunistic human pathogen. Using behavioral observations and chemical analyses, we demonstrated that A. compressa larvae impregnate their cockroach hosts from inside with large amounts of an oral secretion containing a blend of γ-lactones and isocoumarins with ( R )-(-)-mellein [( R )-(-)-3,4-diydro-8-hydroxy-3-methylisocoumarin] and micromolide [(4 R ,9 Z )-octadec-9-en-4-olide] as dominant components. We fractionated hexane extracts of the secretion and investigated the antimicrobial properties of the fraction containing the lactones and isocoumarins, as well as of synthetic ( R )-(-)-mellein and micromolide, against S. marcescens and a Gram-positive bacterium, Staphylococcus hyicus , in broth microdilution assays. The test fraction inhibited growth of both tested bacteria. The activity of the fraction against S. marcescens was explained by ( R )-(-)-mellein alone, and the activity against S. hyicus was explained by the combined action of ( R )-(-)-mellein and micromolide. Our data suggest that the specific combination of antimicrobials in the larval secretion provides an effective frontline defense against the unpredictable spectrum of microbes that A. compressa larvae may encounter during their development inside their cockroach hosts.

Plant biomass is the largest reservoir of environmentally friendly renewable energy on earth. However, the complex and recalcitrant structure of these lignocellulose-rich substrates is a severe limitation for biogas production. Microbial pro-ventricular anaerobic digestion of ruminants can serve as a model for improvement of converting lignocellulosic biomass into energy. Anaerobic fungi are key players in the digestive system of various animals, they produce a plethora of plant carbohydrate hydrolysing enzymes. Combined with the invasive growth of their rhizoid system their contribution to cell wall polysaccharide decomposition may greatly exceed that of bacteria. The cellulolytic arsenal of anaerobic fungi consists of both secreted enzymes, as well as extracellular multi-enzyme complexes called cellulosomes. These complexes are extremely active, can degrade both amorphous and crystalline cellulose and are probably the main reason of cellulolytic efficiency of anaerobic fungi. The synergistic use of mechanical and enzymatic degradation makes anaerobic fungi promising candidates to improve biogas production from recalcitrant biomass. This chapter presents an overview about their biology and their potential for implementation in the biogas process.

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Bioaugmentation with anaerobic fungi (AF) is promising for improved biogas generation from lignocelluloses-rich substrates. However, before implementing AF into biogas processes it is necessary to investigate their natural occurrence, community structure and transcriptional activity in agricultural biogas plants. Thus, AF were detected with three specific PCR based methods: (i) Copies of their 18S genes were found in 7 of 10 biogas plants. (ii) Transcripts of a GH5 endoglucanase gene were present at low level in two digesters, indicating transcriptional cellulolytic activity of AF. (iii) Phylogeny of the AF-community was inferred with the 28S gene. A new Piromyces species was isolated from a PCR-positive digester. Evidence for AF was only found in biogas plants operated with high proportions of animal feces. Thus, AF were most likely transferred into digesters with animal derived substrates. Additionally, high process temperatures in combination with long retention times seemed to impede AF survival and activity.