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A R T IC L E Anaerobic Fungi: Neocallimastigomycota

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A R T IC L E Anaerobic Fungi: Neocallimastigomycota View metadata, citation and similar papers at core.ac.uk brought to you by CORE IMA FuNgus · voluMe 1 · No 2: 181–185provided by PubMed Central Anaerobic fungi: Neocallimastigomycota ARTICLE Gareth W Griffith1, Scott Baker2, Kate Fliegerova3, Audra Liggenstoffer4, Mark van der Giezen5, Kerstin Voigt6 and Gordon Beakes7 1IBERS, Aberystwyth University, Aberystwyth SY23 3DD, Wales; corresponding author e-mail: [email protected] 2Chemical and Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN P8-60 Richland, WA 99352 USA 3Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, Videnska 1083, Prague 4 - Krc, 142 20 Czech Republic 4Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA 5Centre for Eukaryotic Evolutionary Microbiology, Biosciences, College of Life & Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK 6Friedrich Schiller University Jena, Institute of Microbiology, Department of Microbiology and Molecular Biology, Jena Microbial Research Collection, Neugasse 25, 07743 Jena, Germany 7School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK Abstract: This contribution is based on the six oral presentations given at the Special Interest Group Key words: session on anaerobic fungi held during IMC9. These fungi, recently elevated to the status of a separate chytrid phylum (Neocallimastigomycota), distinct from the chytrid fungi, possess several unique traits that make basal fungi their study both fascinating yet challenging to mycologists. There are several genome sequencing programs genome sequencing underway in the US but these are hampered by the highly AT-rich genomes. Next-generation sequencing phylogenetics has also allowed more detailed investigation of the ecology and diversity of these fungi, and it is apparent next-generation sequencing that several new taxa beyond the six genera already named exist within the digestive tracts of mammalian hydrogenosome herbivores, with others potentially inhabiting other anaerobic niches. By increased collaboration between the various labs studying these fungi, it is hoped to develop a stable taxonomic backbone for these fungi and to facilitate exchange of both cultures and genetic data. Article info: Submitted: 27 October 2010; Accepted: 20 November 2010; Published: 23 November 2010. INtroductIoN coNtrIbutIoNs Since their discovery by Colin Orpin in the 1970s, the The session began with a presentation from Scott Baker on anaerobic fungi, now members of the recently erected the status of two genome sequencing projects (Piromyces E2 phylum Neocallimastigomycota, have aroused the curiosity and Orpinomyces SR2). The AT richness of these genomes of mycologists, not only due to their distinctive physiology (approaching 80 % in non-coding regions) has caused but also because of their biotechnological potential, for more significant technical problems for genomic sequencing and efficient animal nutrition and also biomass conversion/biofuel assembly. The Joint Genome Initiative (JGI) is working through production. This contribution, based on a Special Interest technical issues with assembling the genome, but does plan Group session held during IMC9, brought together mycologists to release the sequence in the near future. In contrast, the interested in anaerobic fungi to share recent discoveries and Expressed Sequence Tag (EST) library sequencing project to discuss how best to move forward research in this area. Six did not encounter any technical issues and will be made speakers kindly agreed to speak at the session, with a further available concurrent with the eventual release of the genome seven non-speakers in attendance. Given the small numbers sequence. Until then, contact Scott for information on of mycologists now engaged in research on anaerobic fungi, accessing ESTs ([email protected]). Much of the interest this was a pleasing quorum, with expertise in genomic, in these fungi relates to the genes/enzymes important for phylogenetic, morphological, physiological and ecological biorefining and biofuel production, notably xylose isomerases aspects of the biology of these fungi being represented. and glycosyl hydrolases (xylanases, cellulases). This synopsis of the session amounts to a mini-review of the Kate Fliegerova, who also presented a poster (4.015) at current state of research on these fascinating fungi. the main IMC9 congress, further explored the biotechnological © 2010 International Mycological Association You are free to share - to copy, distribute and transmit the work, under the following conditions: Attribution: You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Non-commercial: You may not use this work for commercial purposes. No derivative works: You may not alter, transform, or build upon this work. For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights. volume 1 · no. 2 181 griffith et al. potential of these fungi. Some of the cellulases of anaerobic The application of culture-independent approaches to fungi originated via horizontal gene transfer from bacteria, assessing the diversity of anaerobic fungi was the subject of so these are the only fungi known to possess cellulosomes, Audra Liggenstoffer’s presentation. Her PhD project at the cell-wall associated multienzyme complexes (Garcia-Vallve Oklahoma State University used barcoded 454 sequencing et al. 2000, Steenbakkers et al. 2001). Combined with to determine the fungal symbionts present in the faeces of 30 ARTICLE their anaerobic metabolism and ability grow at elevated species of larger herbivores, many from Oklahoma City Zoo. temperatures (39 ºC), they have great biotechnological Her findings have recently been published (Liggenstoffer potential. In Prague, Kate and her colleagues have explored et al. 2010) and demonstrated not only confirmation of the the use of anaerobic fungi to improve the hydrolytic phase of occurrence of anaerobic fungi in a non-mammal host (green biogas production. They have also investigated which fungi iguana) but also the existence of eight novel groups of are present in the cow manure used to prime the biogas fungi, with these new taxa (likely to represent new genera) fermentations (Fliegerova et al. 2010), finding members of comprising almost 40 % of the >250,000 ITS sequences the genus Cyllamyces, the sixth and most recently discovered obtained. Whilst it can be difficult to be certain that zoo animals group of anaerobic fungi (Ozkose et al. 2001) to be dominant, have not acquired new symbionts whilst in captivity, some of with the ‘most famous’ (and type) genus Neocallimastix these novel groups (NG) did show some host specificity, for comprising only a small proportion of the population. This example with NG6 comprising nearly all the fungi in kudu and imbalance is also reflected in the literature, possibly a result NG8 being found only in Somali wild ass (Fig. 1). of the widespread use of wheat straw for the culture-based With such a high rate of taxon discovery, the isolation of these organisms (Griffith et al. 2009). Neocallimastigomycota, the newest of the fungal phyla Fig. 1. Network graph highlighting shared OTUs between different anaerobic fungal communities in different animal hosts. The graph is colour- coded by animal host phylogeny (family). Circular nodes indicate animal data sets, whereas smaller square, grey nodes represent individual OTUs. Data sets with a higher proportion of shared OTUs are pulled to the middle, whereas data sets with a high proportion of unique OTUs remain on the periphery. The distance between any two data sets is a function of the number of shared OTUs between the two. Figure supplied by Audra Liggenstoffer. 182 i m a f u n G u S Anaerobic fungi: Neocallimastigomycota (Hibbett et al. 2007) clearly has more taxonomic gems more robust phylogenies. A key element of this approach is ARTICLE awaiting discovery, notably in habitats beyond the digestive the use of orthologous genes for comparisons, requiring first tracts of vertebrates. Anaerobic fungal sequences do appear the identification of the original member of any gene family in environmental clone libraries (Lockhart et al. 2006) but this within an organism, prior to any interspecific comparisons. attests more to the resilience of their resting spores (Ozkose Application of this more robust approach for the anaerobic 2001) than to their active metabolism in these habitats. fungi requires sequence data from genes other than the However, it is already clear that a robust taxonomic scheme rRNA locus, however, Kerstin’s initial analyses, like Audra’s based on gene sequence data rather than the meagre 454 data, revealed the presence of four novel genera (Fig. morphological traits is needed. Kerstin Voigt specialises in the 2). It was also clear that some GenBank accessions are phylogenetics of the lower fungi and questions the acceptability mis-labelled, highlighting the difficulty in morphological of the phylum Neocallimastigomycota (Ebersberger et classification of these fungi. al. 2010).
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