Aestipascuomyces dupliciliberans gen. nov, sp. nov., the First Cultured Representative of the Uncultured SK4 Clade from Aoudad Sheep and Alpaca

Metabolic influence of core ciliates within the rumen microbiome

Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the entodiniomorphs (order: Entodiniomorphida) and holotrichs (order: Vestibuliferida) are consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that protozoal species exert, their major biological and metabolic contributions to rumen function remain largely undescribed in vivo. Here, we have leveraged (meta)genome-centric metaproteomes from rumen fluid samples originating from both cattle and goats fed diets with varying inclusion levels of lipids and starch, to detail the specific metabolic niches that protozoa occupy in the context of their microbial co-habitants. Initial proteome estimations via total protein counts and label-free quantification highlight that entodiniomorph species Entodinium and Epidinium as well as the holotrichs Dasytricha and Isotricha comprise an extensive fraction of the total rumen metaproteome. Proteomic detection of protozoal metabolism such as hydrogenases (Dasytricha, Isotricha, Epidinium, Enoploplastron), carbohydrate-active enzymes (Epidinium, Diplodinium, Enoploplastron, Polyplastron), microbial predation (Entodinium) and volatile fatty acid production (Entodinium and Epidinium) was observed at increased levels in high methane-emitting animals. Despite certain protozoal species having well-established reputations for digesting starch, they were unexpectedly less detectable in low methane emitting-animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation irrespective of host. Finally, we reaffirmed our abovementioned observations in geographically independent datasets, thus illuminating the substantial metabolic influence that under-explored eukaryotic populations have in the rumen, with greater implications for both digestion and methane metabolism.

Isolation, morphological identification, and xylanase characteristics of anaerobic gut fungi Neocallimastix from Anatolian wild goat

This study shows the morphological identification of anaerobic fungal strains isolated from fecal samples of goats inhabiting Turkey and the effects of various metal ions and chemicals on extracellular xylanase production. Three different anaerobic gut fungi isolated from wild goats in Turkey were identified as Neocallimastix spp. xylanase, cellulase, and lichenase production were tested in culture supernatants, and the maximum-specific activities were found as 560.42 ± 9.39, 159.70 ± 3.88, and 157.36 ± 3.83 (μmol/min/mg protein), respectively. While the optimum temperature range of exo-xylanases was found as 40-50°C, their optimum pH range was determined as 6.0-6.5. Xylanase activity decreased in metal ions and other chemical reactants based on dose. The metal ion that significantly inhibited xylanase activity was Fe⁺³ . It was found that the ferric ions inhibited xylanase activity in all three anaerobic gut fungi by 30%-90% depending on molarity. On the contrary, the 1 mM concentrations of the Mn⁺² , Ba⁺² , Co⁺² , Cu⁺² , Sn⁺² , and Mg⁺² metal ions and the ethylenediaminetetraacetic acid and β-mercaptoethanol reagents had a positive effect at rates in the range of 3%-92%. In conclusion, these findings demonstrate that anaerobic gut fungus has very stable fibrolytic enzymes that need to be separated, as well and the existence of a unique resource for industrial applications.

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.

Understanding the microbial fibre degrading communities & processes in the equine gut

The equine gastrointestinal tract is a self-sufficient fermentation system, housing a complex microbial consortium that acts synergistically and independently to break down complex lignocellulolytic material that enters the equine gut. Despite being strict herbivores, equids such as horses and zebras lack the diversity of enzymes needed to completely break down plant tissue, instead relying on their resident microbes to carry out fibrolysis to yield vital energy sources such as short chain fatty acids. The bulk of equine digestion occurs in the large intestine, where digesta is fermented for 36-48 h through the synergistic activities of bacteria, fungi, and methanogenic archaea. Anaerobic gut dwelling bacteria and fungi break down complex plant polysaccharides through combined mechanical and enzymatic strategies, and notably possess some of the greatest diversity and repertoire of carbohydrate active enzymes among characterized microbes. In addition to the production of enzymes, some equid-isolated anaerobic fungi and bacteria have been shown to possess cellulosomes, powerful multi-enzyme complexes that further enhance break down. The activities of both anaerobic fungi and bacteria are further facilitated by facultatively aerobic yeasts and methanogenic archaea, who maintain an optimal environment for fibrolytic organisms, ultimately leading to increased fibrolytic microbial counts and heightened enzymatic activity. The unique interactions within the equine gut as well as the novel species and powerful mechanisms employed by these microbes makes the equine gut a valuable ecosystem to study fibrolytic functions within complex communities. This review outlines the primary taxa involved in fibre break down within the equine gut and further illuminates the enzymatic strategies and metabolic pathways used by these microbes. We discuss current methods used in analysing fibrolytic functions in complex microbial communities and propose a shift towards the development of functional assays to deepen our understanding of this unique ecosystem.

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.

Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages

Anaerobic fungi from the herbivore digestive tract (Neocallimastigomycetes) are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. We developed and validated a Neocallimastigomycetes-specific PCR primer pair targeting the D2 region of the ribosomal large subunit suitable for screening, quantifying, and sequencing. We evaluated this primer pair in silico on sequences from all known genera, in vitro with pure cultures covering 16 of the 20 known genera, and on environmental samples with highly diverse microbiomes. The amplified region allowed phylogenetic differentiation of all known genera and most species. The amplicon is about 350 bp long, suitable for short-read high-throughput sequencing as well as qPCR assays. Sequencing of herbivore fecal samples verified the specificity of the primer pair and recovered highly diverse and so far unknown anaerobic gut fungal taxa. As the chosen barcoding region can be easily aligned and is taxonomically informative, the sequences can be used for classification and phylogenetic inferences. Several new Neocallimastigomycetes clades were obtained, some of which represent putative novel lineages such as a clade from feces of the rodent Dolichotis patagonum (mara).

Anaerobic Fungi Isolated From Bactrian Camel Rumen Contents Have Strong Lignocellulosic Bioconversion Potential

This study aims to obtain anaerobic fungi from the rumen and fecal samples and investigates their potential for lignocellulosic bioconversion. Multiple anaerobic strains were isolated from rumen contents (CR1–CR21) and fecal samples (CF1–CF10) of Bactrian camel using the Hungate roll tube technique. After screening for fiber degradability, strains from rumen contents (Oontomyces sp. CR2) and feces (Piromyces sp. CF9) were compared with Pecoramyces sp. F1 (earlier isolated from goat rumen, having high CAZymes of GHs) for various fermentation and digestion parameters. The cultures were fermented with different substrates (reed, alfalfa stalk, Broussonetia papyrifera leaves, and Melilotus officinalis) at 39°C for 96 h. The Oontomyces sp. CR2 had the highest total gas and hydrogen production from most substrates in the in vitro rumen fermentation system and also had the highest digestion of dry matter, neutral detergent fiber, acid detergent fiber, and cellulose present in most substrates used. The isolated strains provided higher amounts of metabolites such as lactate, formate, acetate, and ethanol in the in vitro rumen fermentation system for use in various industrial applications. The results illustrated that anaerobic fungi isolated from Bactrian camel rumen contents (Oontomyces sp. CR2) have the highest lignocellulosic bioconversion potential, suggesting that the Bactrian camel rumen could be a good source for the isolation of anaerobic fungi for industrial applications.

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

Members of the anaerobic gut fungi (Neocallimastigomycota) reside in the rumen and alimentary tract of larger mammalian and some reptilian, marsupial and avian herbivores. The recent decade has witnessed a significant expansion in the number of described Neocallimastigomycota genera and species. However, the difficulties associated with the isolation and maintenance of Neocallimastigomycota strains has greatly complicated comparative studies to resolve inter- and intra-genus relationships. Here, we provide an updated outline of Neocallimastigomycota taxonomy. We critically evaluate various morphological, microscopic and phylogenetic traits previously and currently utilized in Neocallimastigomycota taxonomy, and provide an updated key for quick characterization of all genera. We then synthesize data from taxa description manuscripts, prior comparative efforts and molecular sequence data to present an updated list of Neocallimastigomycota genera and species, with an emphasis on resolving relationships and identifying synonymy between recent and historic strains. We supplement data from published manuscripts with information and illustrations from strains in the authors' collections. Twenty genera and 36 species are recognized, but the status of 10 species in the genera Caecomyces, Piromyces, Anaeromyces and Cyllamyces remains uncertain due to the unavailability of culture and conferre (cf.) strains, lack of sequence data, and/or inadequacy of available microscopic and phenotypic data. Six cases of synonymy are identified in the genera Neocallimastix and Caecomyces, and two names in the genus Piromyces are rejected based on apparent misclassification.

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.

Hydrogenosome, Pairing Anaerobic Fungi and H2-Utilizing Microorganisms Based on Metabolic Ties to Facilitate Biomass Utilization

Anaerobic fungi, though low in abundance in rumen, play an important role in the degradation of forage for herbivores. When only anaerobic fungi exist in the fermentation system, the continuous accumulation of metabolites (e.g., hydrogen (H₂) and formate) generated from their special metabolic organelles—the hydrogenosome—inhibits the enzymatic reactions in the hydrogenosome and reduces the activity of the anaerobic fungi. However, due to interspecific H₂ transfer, H₂ produced by the hydrogenosome can be used by other microorganisms to form valued bioproducts. This symbiotic interaction between anaerobic fungi and other microorganisms can be used to improve the nutritional value of animal feeds and produce value-added products that are normally in low concentrations in the fermentation system. Because of the important role in the generation and further utilization of H₂, the study of the hydrogensome is increasingly becoming an important part of the development of anaerobic fungi as model organisms that can effectively improve the utilization value of roughage. Here, we summarize and discuss the classification and the process of biomass degradation of anaerobic fungi and the metabolism and function of anaerobic fungal hydrogensome, with a focus on the potential role of the hydrogensome in the efficient utilization of biomass.

Early-diverging fungal phyla: taxonomy, species concept, ecology, distribution, anthropogenic impact, and novel phylogenetic proposals

The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa, has dramatically changed the classification system of early-diverging fungi over the past several decades. The number of phyla established for non-Dikarya fungi has increased from 2 to 17. However, to date, both the classification and phylogeny of the basal fungi are still unresolved. In this article, we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal phyla. We also provide information on the ecology and distribution in Mucoromycota and highlight the impact of chytrids on amphibian populations. Species concepts in Chytridiomycota, Aphelidiomycota, Rozellomycota, Neocallimastigomycota are discussed in this paper. To preserve the current application of the genus Nephridiophaga (Chytridiomycota: Nephridiophagales), a new type species, Nephridiophaga blattellae, is proposed.

Isolation and Biochemical Characterization of Six Anaerobic Fungal Strains from Zoo Animal Feces

Anaerobic fungi are prime candidates for the conversion of agricultural waste products to biofuels. Despite the increasing interest in these organisms, their growth requirements and metabolism remain largely unknown. The isolation of five strains of anaerobic fungi and their identification as Neocallimastix cameroonii, Caecomyces spec., Orpinomyces joyonii, Pecoramyces ruminantium, and Khoyollomyces ramosus, is described. The phylogeny supports the reassignment of Neocallimastix californiae and Neocallimastix lanati to Neocallimastix cameroonii and points towards the redesignation of Cyllamyces as a species of Caecomyces. All isolated strains including strain A252, which was described previously as Aestipascuomyces dubliciliberans, were further grown on different carbon sources and the produced metabolites were analyzed; hydrogen, acetate, formate, lactate, and succinate were the main products. Orpinomyces joyonii was lacking succinate production and Khoyollomyces ramosus was not able to produce lactate under the studied conditions. The results further suggested a sequential production of metabolites with a preference for hydrogen, acetate, and formate. By comparing fungal growth on monosaccharides or on the straw, a higher hydrogen production was noticed on the latter. Possible reactions to elevated sugar concentrations by anaerobic fungi are discussed.

Paucimyces polynucleatus gen. nov, sp. nov., a novel polycentric genus of anaerobic gut fungi from the faeces of a wild blackbuck antelope

The anaerobic gut fungi (AGF; phylum Neocallimastigomycota) reside in the alimentary tracts of herbivores. Multiple novel, yet-uncultured AGF taxa have recently been identified in culture-independent diversity surveys. Here, we report on the isolation and characterization of the first representative of the RH5 lineage from faecal samples of a wild blackbuck (Indian Antelope, Antilope cervicapra) from Sutton County, Texas, USA. The isolates displayed medium sized (2-4 mm) compact circular colonies on agar roll tubes and thin loose biofilm-like growth in liquid medium. Microscopic examination revealed monoflagellated zoospores and polycentric thalli with highly branched nucleated filamentous rhizomycelium, a growth pattern encountered in a minority of described AGF genera so far. The obtained isolates are characterized by formation of spherical vesicles at the hyphal tips from which multiple sporangia formed either directly on the spherical vesicles or at the end of sporangiophores. Phylogenetic analysis using the D1/D2 regions of the large ribosomal subunit (D1/D2 LSU) and the ribosomal internal transcribed spacer 1 (ITS1) revealed sequence similarities of 93.5 and 81.3%, respectively, to the closest cultured relatives (Orpinomyces joyonii strain D3A (D1/D2 LSU) and Joblinomyces apicalis strain GFH681 (ITS1). Substrate utilization experiments using the type strain (BB-3^T) demonstrated growth capabilities on a wide range of mono-, oligo- and polysaccharides, including glucose, xylose, mannose, fructose, cellobiose, sucrose, maltose, trehalose, lactose, cellulose, xylan, starch and raffinose. We propose accommodating these novel isolates in a new genus and species, for which the name Paucimyces polynucleatus gen. nov., sp. nov. is proposed.

The Anaerobic Fungi: Challenges and Opportunities for Industrial Lignocellulosic Biofuel Production

Lignocellulose is a promising feedstock for biofuel production as a renewable, carbohydrate-rich and globally abundant source of biomass. However, challenges faced include environmental and/or financial costs associated with typical lignocellulose pretreatments needed to overcome the natural recalcitrance of the material before conversion to biofuel. Anaerobic fungi are a group of underexplored microorganisms belonging to the early diverging phylum Neocallimastigomycota and are native to the intricately evolved digestive system of mammalian herbivores. Anaerobic fungi have promising potential for application in biofuel production processes due to the combination of their highly effective ability to hydrolyse lignocellulose and capability to convert this substrate to H2 and ethanol. Furthermore, they can produce volatile fatty acid precursors for subsequent biological conversion to H2 or CH4 by other microorganisms. The complex biological characteristics of their natural habitat are described, and these features are contextualised towards the development of suitable industrial systems for in vitro growth. Moreover, progress towards achieving that goal is reviewed in terms of process and genetic engineering. In addition, emerging opportunities are presented for the use of anaerobic fungi for lignocellulose pretreatment; dark fermentation; bioethanol production; and the potential for integration with methanogenesis, microbial electrolysis cells and photofermentation.

The Present Role and New Potentials of Anaerobic Fungi in Ruminant Nutrition

The ruminal microbiota allows ruminants to utilize fibrous feeds and is in the limelight of ruminant nutrition research for many years. However, the overwhelming majority of investigations have focused on bacteria, whereas anaerobic fungi (AF) have been widely neglected by ruminant nutritionists. Anaerobic fungi are not only crucial fiber degraders but also important nutrient sources for the host. This review summarizes the current findings on AF and, most importantly, discusses their new application potentials in modern ruminant nutrition. Available data suggest AF can be applied as direct-fed microbials to enhance ruminal fiber degradation, which is indeed of interest for high-yielding dairy cows that often show depressed ruminal fibrolysis in response to high-grain feeding. Moreover, these microorganisms have relevance for the nutrient supply and reduction of methane emissions. However, to reach AF-related improvements in ruminal fiber breakdown and animal performance, obstacles in large-scale AF cultivation and applicable administration options need to be overcome. At feedstuff level, silage production may benefit from the application of fungal enzymes that cleave lignocellulosic structures and consequently enable higher energy exploitation from forages in the rumen. Concluding, AF hold several potentials in improving ruminant feeding and future research efforts are called for to harness these potentials.

The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi

This work investigated the changes of the rumen microbiome of goats switched from a forage to a concentrate diet with special attention to anaerobic fungi (AF). Female goats were fed an alfalfa hay (AH) diet (0% grain; n = 4) for 20 days and were then abruptly shifted to a high-grain (HG) diet (40% corn grain, 60% AH; n = 4) and treated for another 10 days. Rumen content samples were collected from the cannulated animals at the end of each diet period (day 20 and 30). The microbiome structure was studied using high-throughput sequencing for bacteria, archaea (16S rRNA gene) and fungi (ITS2), accompanied by qPCR for each group. To further elucidate unclassified AF, clone library analyses were performed on the ITS1 spacer region. Rumen pH was significantly lower in HG diet fed goats, but did not induce subacute ruminal acidosis. HG diet altered prokaryotic communities, with a significant increase of Bacteroidetes and a decrease of Firmicutes. On the genus level Prevotella 1 was significantly boosted. Methanobrevibacter and Methanosphaera were the most abundant archaea regardless of the diet and HG induced a significant augmentation of unclassified Thermoplasmatales. For anaerobic fungi, HG triggered a considerable rise in Feramyces observed with both ITS markers, while a decline of Tahromyces was detected by ITS2 and decrease of Joblinomyces by ITS1 only. The uncultured BlackRhino group revealed by ITS1 and further elucidated in one sample by LSU analysis, formed a considerable part of the AF community of goats fed both diets. Results strongly indicate that the rumen ecosystem still acts as a source for novel microorganisms and unexplored microbial interactions and that initial rumen microbiota of the host animal considerably influences the reaction pattern upon diet change.