Taxonomy of the anaerobic gut fungi (Neocallimastigomycota): a review of classification criteria and description of current taxa

INTERNATIONAL SYMPOSIUM ON RUMINANT PHYSIOLOGY: Rumen fungi, archaea and their interactions

Anaerobic gut fungi (AGF) were the last phylum to be identified within the rumen microbiome and account for 7-9% of microbial biomass. They produce potent lignocellulases that degrade recalcitrant plant cell walls, and rhizoids that can penetrate the cuticle of plant cells, exposing internal components to other microbiota. Interspecies H2 transfer between AGF and rumen methanogenic archaea is an essential metabolic process in the rumen that occurs during the reduction of CO2 to CH4 by methanogens. This symbiotic relationship is bolstered by hydrogensomes, fungal organelles that generate H2 and formate. Interspecies H2 transfer prevents the accumulation of reducing equivalents that would otherwise impede fermentation. The extent to which hydrogenosomes serve as a conduit for H2 flow to methanogens is unknown, but it is likely greater with low quality forages. Strategies that alter the production of CH4 could also have implications for H2 transfer by anaerobic fungi. Understanding the factors that drive these interactions and H2 flow could provide insight into the effect of reducing CH4 production on the activity of ruminal fungi and the digestion of low-quality feeds.

Evaluating the impact of redox potential on the growth capacity of anaerobic gut fungi

Anaerobic gut fungi (AGF, Neocallimastigomycota) inhabit the alimentary tract of herbivores. Although strict anaerobes, studies have suggested their capacity to retain viability after various durations of air exposure. It is currently unclear whether AGF can actively grow, and not merely survive, in redox potentials (Eh) higher than those encountered in the herbivorous gut. We evaluated the growth of two AGF strains (Orpinomyces joyonii and Testudinimyces gracilis) at various Eh levels, achieved by manipulating the concentrations of reductant (cysteine hydrochloride) in culture media. Both strains exhibited robust and sustainable growth at negative Eh (-50 mV or below). However, growth in the absence of cysteine hydrochloride (Eh value around +50 mV) was possible only for O. joyonii and only for one subcultivation. The capacity to grow at +50 mV was further confirmed in four additional taxa (Pecoramyces ruminatium, Anaeromyces mucronatus, Aklioshbmyces papillarum, and Piromyces communis), while two (Aestipascuomyces dupliciliberans and Capellomyces foraminis) failed to grow under these conditions. Our results establish the ability of AGF to grow at redox potential values higher than those encountered in their natural habitats. Such capability could contribute to efficient AGF dispersal and horizontal transmission between hosts, and could have important implications for industrial applications of AGF.

Santiago ALCM, Saxena RK, Schoutteten N, Wimalasena MK, Aleoshin VV, Al-Hatmi AMS, Ariyawansa KGSU, Assunção AR, Bamunuarachchige TC, Baral HO, Bhat DJ, Błaszkowski J, Boekhout T, Boonyuen N, Brysch-Herzberg M, Cao B, Cazabonne J, Chen XM, Coleine C, Dai DQ, Daniel HM, da Silva SBG, de Souza FA, Dolatabadi S, Dubey MK, Dutta AK, Ediriweera A, Egidi E, Elshahed MS, Fan X, Felix JRB, Galappaththi MCA, Groenewald M, Han LS, Huang B, Hurdeal VG, Ignatieva AN, Jerônimo GH, de Jesus AL, Kondratyuk S, Kumla J, Kukwa M, Li Q, Lima JLR, Liu XY, Lu W, Lumbsch HT, Madrid H, Magurno F, Marson G, McKenzie EHC, Menkis A, Mešić A, Nascimento ECR, Nassonova ES, Nie Y, Oliveira NVL, Ossowska EA, Pawłowska J, Peintner U, Pozdnyakov IR, Premarathne BM, Priyashantha AKH, Quandt CA, Queiroz MB, Rajeshkumar KC, Raza M, Roy N, Samarakoon MC, Santos AA, Santos LA, Schumm F, Selbmann L, Selçuk F, Simmons DR, Simakova AV, Smith MT, Sruthi OP, Suwannarach N, Tanaka K, Tibpromma S, Tomás EO, Ulukapı M, Van Vooren N, Wanasinghe DN, Weber E, Wu Q, Yang EF, Yoshioka R, Youssef NH, Zandijk A, Zhang GQ, Zhang JY, Zhao H, Zhao R, Zverkov OA, Thines M, Karpov SA. Classes and phyla of the kingdom Fungi

Fungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2–3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the ‘true fungi’ have been revised in several subsequent publications. Rapid accumulation of novel genomic data and the advancements in phylogenetics now facilitate a robust and precise foundation for the higher-level classification within the kingdom. This study provides an updated classification of the kingdom Fungi, drawing upon a comprehensive phylogenomic analysis of Holomycota, with which we outline well-supported nodes of the fungal tree and explore more contentious groupings. We accept 19 phyla of Fungi, viz. Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota, Sanchytriomycota, and Zoopagomycota. In the phylogenies, Caulochytriomycota resides in Chytridiomycota; thus, the former is regarded as a synonym of the latter, while Caulochytriomycetes is viewed as a class in Chytridiomycota. We provide a description of each phylum followed by its classes. A new subphylum, Sanchytriomycotina Karpov is introduced as the only subphylum in Sanchytriomycota. The subclass Pneumocystomycetidae Kirk et al. in Pneumocystomycetes, Ascomycota is invalid and thus validated. Placements of fossil fungi in phyla and classes are also discussed, providing examples.

Exploring near-infrared spectroscopy and hyperspectral imaging as novel characterization methods for anaerobic gut fungi

Neocallimastigomycota are a phylum of anaerobic gut fungi (AGF) that inhabit the gastrointestinal tract of herbivores and play a pivotal role in plant matter degradation. Their identification and characterization with marker gene regions has long been hampered due to the high inter- and intraspecies length variability in the commonly used fungal marker gene region internal transcribed spacer (ITS). While recent research has improved methodology (i.e. switch to LSU D2 as marker region), molecular methods will always introduce bias through nucleic acid extraction or PCR amplification. Here, near-infrared spectroscopy (NIRS) and hyperspectral imaging (HSI) are introduced as two nucleic acid sequence-independent tools for the characterization and identification of AGF strains. We present a proof-of-concept for both, achieving an independent prediction accuracy of above 95% for models based on discriminant analysis trained with samples of three different genera. We further demonstrated the robustness of the NIRS model by testing it on cultures of different growth times. Overall, NIRS provides a simple, reliable, and nondestructive approach for AGF classification, independent of molecular approaches. The HSI method provides further advantages by requiring less biomass and adding spatial information, a valuable feature if this method is extended to mixed cultures or environmental samples in the future.

Efficient methane production from agro-industrial residues using anaerobic fungal-rich consortia

Anaerobic digestion (AD) emerges as a pivotal technique in climate change mitigation, transforming organic materials into biogas, a renewable energy form. This process significantly impacts energy production and waste management, influencing greenhouse gas emissions. Traditional research has largely focused on anaerobic bacteria and methanogens for methane production. However, the potential of anaerobic lignocellulolytic fungi for degrading lignocellulosic biomass remains less explored. In this study, buffalo rumen inocula were enriched and acclimatized to improve lignocellulolytic hydrolysis activity. Two consortia were established: the anaerobic fungi consortium (AFC), selectively enriched for fungi, and the anaerobic lignocellulolytic microbial consortium (ALMC). The consortia were utilized to create five distinct microbial cocktails-AF0, AF20, AF50, AF80, and AF100. These cocktails were formulated based on varying of AFC and ALMC by weights (w/w). Methane production from each cocktail of lignocellulosic biomasses (cassava pulp and oil palm residues) was evaluated. The highest methane yields of CP, EFB, and MFB were obtained at 337, 215, and 54 mL/g VS, respectively. Cocktails containing a mix of anaerobic fungi, hydrolytic bacteria (Sphingobacterium sp.), syntrophic bacteria (Sphaerochaeta sp.), and hydrogenotrophic methanogens produced 2.1-2.6 times higher methane in cassava pulp and 1.1-1.2 times in oil palm empty fruit bunch compared to AF0. All cocktails effectively produced methane from oil palm empty fruit bunch due to its lipid content. However, methane production ceased after 3 days when oil palm mesocarp fiber was used, due to long-chain fatty acid accumulation. Anaerobic fungi consortia showed effective lignocellulosic and starchy biomass degradation without inhibition due to organic acid accumulation. These findings underscore the potential of tailored microbial cocktails for enhancing methane production from diverse lignocellulosic substrates.

Anaerobic gut fungal communities in marsupial hosts

The anaerobic gut fungi (AGF) inhabit the alimentary tracts of herbivores. In contrast to placental mammals, information regarding the identity, diversity, and community structure of AGF in marsupials is extremely sparse. Here, we characterized AGF communities in 61 fecal samples from 10 marsupial species belonging to four families in the order Diprotodontia: Vombatidae (wombats), Phascolarctidae (koalas), Phalangeridae (possums), and Macropodidae (kangaroos, wallabies, and pademelons). An amplicon-based diversity survey using the D2 region of the large ribosomal subunit as a phylogenetic marker indicated that marsupial AGF communities were dominated by eight genera commonly encountered in placental herbivores (Neocallimastix, Caecomyces, Cyllamyces, Anaeromyces, Orpinomyces, Piromyces, Pecoramyces, and Khoyollomyces). Community structure analysis revealed a high level of stochasticity, and ordination approaches did not reveal a significant role for the animal host, gut type, dietary preferences, or lifestyle in structuring marsupial AGF communities. Marsupial foregut and hindgut communities displayed diversity and community structure patterns comparable to AGF communities typically encountered in placental foregut hosts while exhibiting a higher level of diversity and a distinct community structure compared to placental hindgut communities. Quantification of AGF load using quantitative PCR indicated a significantly smaller load in marsupial hosts compared to their placental counterparts. Isolation efforts were only successful from a single red kangaroo fecal sample and yielded a Khoyollomyces ramosus isolate closely related to strains previously isolated from placental hosts. Our results suggest that AGF communities in marsupials are in low abundance and show little signs of selection based on ecological and evolutionary factors.IMPORTANCEThe AGF are integral part of the microbiome of herbivores. They play a crucial role in breaking down plant biomass in hindgut and foregut fermenters. The majority of research has been conducted on the AGF community in placental mammalian hosts. However, it is important to note that many marsupial mammals are also herbivores and employ a hindgut or foregut fermentation strategy for breaking down plant biomass. So far, very little is known regarding the AGF diversity and community structure in marsupial mammals. To fill this knowledge gap, we conducted an amplicon-based diversity survey targeting AGF in 61 fecal samples from 10 marsupial species. We hypothesize that, given the distinct evolutionary history and alimentary tract architecture, novel and unique AGF communities would be encountered in marsupials. Our results indicate that marsupial AGF communities are highly stochastic, present in relatively low loads, and display community structure patterns comparable to AGF communities typically encountered in placental foregut hosts. Our results indicate that marsupial hosts harbor AGF communities; however, in contrast to the strong pattern of phylosymbiosis typically observed between AGF and placental herbivores, the identity and gut architecture appear to play a minor role in structuring AGF communities in marsupials.

A Deep Insight into the Diversity of Microfungal Communities in Arctic and Antarctic Lakes

We assessed fungal diversity in water and sediment samples obtained from five Arctic lakes in Ny-Ålesund (Svalbard Islands, High Arctic) and five Antarctic lakes on Livingston and Deception Islands (South Shetland Islands), using DNA metabarcoding. A total of 1,639,074 fungal DNA reads were detected and assigned to 5980 ASVs amplicon sequence variants (ASVs), with only 102 (1.7%) that were shared between the two Polar regions. For Arctic lakes, unknown fungal taxa dominated the sequence assemblages, suggesting the dominance of possibly undescribed fungi. The phylum Chytridiomycota was the most represented in the majority of Arctic and Antarctic samples, followed by Rozellomycota, Ascomycota, Basidiomycota, and the less frequent Monoblepharomycota, Aphelidiomycota, Mortierellomycota, Mucoromycota, and Neocallimastigomycota. At the genus level, the most abundant genera included psychrotolerant and cosmopolitan cold-adapted fungi including Alternaria, Cladosporium, Cadophora, Ulvella (Ascomycota), Leucosporidium, Vishniacozyma (Basidiomycota), and Betamyces (Chytridiomycota). The assemblages displayed high diversity and richness. The assigned diversity was composed mainly of taxa recognized as saprophytic fungi, followed by pathogenic and symbiotic fungi.

Forage lignocellulose is an important factor in driving the seasonal dynamics of rumen anaerobic fungi in grazing yak and cattle

Anaerobic fungi (AF) inhabit the gastrointestinal tract of ruminants and play an important role in the degradation of fiber feed. However, limited knowledge is available on seasonal dynamics and inter-species differences in rumen AF community in yak and cattle under natural grazing systems. Using the random forests model, the null model, and structural equation model, we investigated the seasonal dynamics and key driving factors of fiber-associated rumen AF in grazing yak and cattle throughout the year on the Qinghai-Tibet Plateau (QTP). We found that the richness and diversity of rumen AF of grazing yak and cattle in cold season were significantly higher than those in warm season (P < 0.05). We identified 12 rumen AF genera, among which , Cyllamyces, and Orpinomyces were predominant in the rumen of both grazing yak and cattle. LEfSe and random forest analysis showed that Feramyces, Tahromyces, and Buwchfawromyces were important seasonal indicator of rumen AF in grazing yak (P < 0.05), and Caecomyces, Cyllamyces, and Piromyces in grazing cattle (P < 0.05). Null model analysis revealed that the dynamic changes of rumen AF community structure were mainly affected by deterministic factors. Notably, mantel test and structural equation model revealed that forage physical-chemical properties, including dry matter (DM), neutral detergent fiber (NDF), and hemicellulose contents (HC) were the key factors driving the seasonal variations of the rumen AF community (P < 0.05). The results revealed that forage lignocellulose was probably an important factor affecting the seasonal dynamics and inter-species differences of the rumen AF community under natural grazing conditions. IMPORTANCE The seasonal dynamics of rumen anaerobic fungi in nature grazing yak and cattle were determined during cold and warm seasons based on pasture nutritional quality and environmental data sets. The main driving factors of anaerobic fungi in yak and cattle rumen were explored by combining random forest and structural equation models. In addition, the dynamic differences in the composition of the anaerobic fungi community in the yak and cattle in different seasons were characterized. It was found that some rumen anaerobic fungi have contributed to high fiber degradation rate in yak. These novel findings improve our understanding of the association of environmental and dietary seasonal variations with anaerobic fungal community, facilitating yak adaptation to high altitude.

Fungal taxonomy: A puzzle with many missing pieces

Fungi are multifaceted organisms found in almost all ecosystems on Earth, where they establish various types of symbiosis with other living beings. Despite being recognized by humans since ancient times, and the high number of works delving into their biology and ecology, much is still unknown about these organisms. Some criteria classically used for their study are nowadays limited, generating confusion in categorizing them, and even more, when trying to understand their genealogical relationships. To identify species within Fungi, phenotypic characters to date are not sufficient, and to construct a broad phylogeny or a phylogeny of a particular group, there are still gaps affecting the generated trees, making them unstable and easily debated. For health professionals, fungal identification at lower levels such as genus and species, is enough to select the most appropriate therapy for their control, understand the epidemiology of clinical pictures associated, and recognize outbreaks and antimicrobial resistance. However, the taxonomic location within the kingdom, information with apparently little relevance, can allow phylogenetic relationships to be established between fungal taxa, facilitating the understanding of their biology, distribution in nature, and pathogenic potential evolution. Advances in molecular biology and computer science techniques from the last 30 years have led to crucial changes aiming to establish the criteria to define a fungal species, allowing us to reach a kind of stable phylogenetic construction. However, there is still a long way to go, and it requires the joint work of the scientific community at a global level and support for basic research.

Phylogenomic analysis of the Neocallimastigomycota: proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae

The anaerobic gut fungi (AGF) represent a coherent phylogenetic clade within the Mycota. Twenty genera have been described so far. Currently, the phylogenetic and evolutionary relationships between AGF genera remain poorly understood. Here, we utilized 52 transcriptomic datasets from 14 genera to resolve AGF inter-genus relationships using phylogenomics, and to provide a quantitative estimate (amino acid identity, AAI) for intermediate rank assignments. We identify four distinct supra-genus clades, encompassing all genera producing polyflagellated zoospores, bulbous rhizoids, the broadly circumscribed genus Piromyces, and the Anaeromyces and affiliated genera. We also identify the genus Khoyollomyces as the earliest evolving AGF genus. Concordance between phylogenomic outputs and RPB1 and D1/D2 LSU, but not RPB2, MCM7, EF1α or ITS1, phylogenies was observed. We combine phylogenomic analysis and AAI outputs with informative phenotypic traits to propose accommodating 14/20 AGF genera into four families: Caecomycetaceae fam. nov. (encompassing the genera Caecomyces and Cyllamyces), Piromycetaceae fam. nov. (encompassing the genus Piromyces), emend the description of the family Neocallimastigaceae to encompass the genera Neocallimastix, Orpinomyces, Pecoramyces, Feramyces, Ghazallomyces, Aestipascuomyces and Paucimyces, as well as the family Anaeromycetaceae to include the genera Oontomyces, Liebetanzomyces and Capellomyces in addition to Anaeromyces. We refrain from proposing families for the deeply branching genus Khoyollomyces and for genera with uncertain position (Buwchfawromyces, Joblinomyces, Tahromyces, Agriosomyces and Aklioshbomyces) pending availability of additional isolates and sequence data; and these genera are designated as 'genera incertae sedis' in the order Neocallimastigales. Our results establish an evolutionary-grounded Linnaean taxonomic framework for the AGF, provide quantitative estimates for rank assignments, and demonstrate the utility of RPB1 as an additional informative marker in Neocallimastigomycota taxonomy.

Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats

Anaerobic fungi (AF), belonging to the phylum Neocallimastigomycota, are a pivotal component of the digestive tract microbiome of various herbivorous animals. In the last decade, the diversity of AF has rapidly expanded due to the exploration of numerous (novel) habitats. Studies aiming at understanding the role of AF require robust and reliable isolation and cultivation techniques, many of which remained unchanged for decades. Using amplicon sequencing, we compared three different media: medium with rumen fluid (RF), depleted rumen fluid (DRF), and no rumen fluid (NRF) to enrich the AF from the feces of yak, as a rumen control; and Przewalski's horse, llama, guanaco, and elephant, as a non-rumen habitats. The results revealed the selective enrichment of Piromyces and Neocallimastix from the feces of elephant and llama, respectively, in the RF medium. Similarly, the enrichment culture in DRF medium explicitly manifested Piromyces-related sequences from elephant feces. Five new clades (MM1-5) were defined from llama, guanaco, yak, and elephant feces that could as well be enriched from llama and elephant samples using non-conventional DRF and NRF media. This study presents evidence for the selective enrichment of certain genera in medium with RF and DRF from rumen as well as from non-rumen samples. NRF medium is suggested for the isolation of AF from non-rumen environments.

No time to die: Comparative study on preservation protocols for anaerobic fungi

Anaerobic fungi (AF, phylum Neocallimastigomycota) are best known for their ability to anaerobically degrade recalcitrant lignocellulosic biomass through mechanic and enzymatic means. While their biotechnological potential is well-recognized, applied research on AF is still hampered by the time-consuming and cost-intensive laboratory routines required to isolate, maintain, and preserve AF cultures. Reliable long-term preservation of specific AF strains would aid basic as well as applied research, but commonly used laboratory protocols for AF preservation can show erratic survival rates and usually exhibit only moderate resuscitation success for up to one or two years after preservation. To address both, the variability, and the preservation issues, we have set up a cross-laboratory, year-long study. We tested five different protocols for the preservation of AF. The experiments were performed at three different laboratories (Austria, Germany, Switzerland) with the same three morphologically distinct AF isolates (Anaeromyces mucronatus, Caeocmyces sp., and Neocallimastix cameroonii) living in stable co-culture with their naturally occurring, syntrophic methanogens. We could show that handling greatly contributes to the variability of results, especially in Anaeromyces mucronatus. Cryopreservation of (mature) biomass in liquid nitrogen had the highest overall survival rates (85-100%, depending on the strain and laboratory). Additionally, preservation on agar at 39°C had surprisingly high survival rates for up to 9 months, if pieces of agar containing mature AF thalli were resuscitated. This low-cost, low-effort method could replace consecutive batch cultivation for periods of up to 6 months, while long-term preservation is best done by cryopreservation in liquid nitrogen. Regardless of the method, however, preserving several replicates (>three) of the same strain is highly advisable.

Characterization and rank assignment criteria for the anaerobic fungi (Neocallimastigomycota)

Establishing a solid taxonomic framework is crucial for enabling discovery and documentation efforts. This ensures effective communication between scientists as well as reproducibility of results between laboratories, and facilitates the exchange and preservation of biological material. Such framework can only be achieved by establishing clear criteria for taxa characterization and rank assignment. Within the anaerobic fungi (phylum Neocallimastigomycota), the need for such criteria is especially vital. Difficulties associated with their isolation, maintenance and long-term storage often result in limited availability and loss of previously described taxa. To this end, we provide here a list of morphological, microscopic, phylogenetic and phenotypic criteria for assessment and documentation when characterizing newly obtained Neocallimastigomycota isolates. We also recommend a polyphasic rank-assignment scheme for novel genus-, species- and strain-level designations for newly obtained Neocallimastigomycota isolates.