Distribution of anaerobic fungi in the digestive tract of cattle and their survival in faeces

The role of anaerobic gut fungi in ruminants

Anaerobic chytridiomycete fungi are found in the gastrointestinal tracts of sheep, cattle and goats, as well as in many other domesticated ruminant and nonruminant herbivores and a wide variety of wild herbivorous mammals. They are principally found associated with the fibrous plant particles of digesta and as free swimming zoospores in the fluid phase. The presence of large fungal populations in animals consuming mature pasture or diets largely composed of hay or straw together with the production of highly active fibre degrading enzymes lead to' the belief that anaerobic fungi may have a significant role to play in the assimilation of fibrous feeds by ruminants. While many early studies focused on anaerobic fungi because of their unusual biology and metabolism, the large part of subsequent research has emphasized the biotechnological potential of their cellulases, xylanases and phenolic esterases. In recent years, the extent of the contribution of anaerobic fungi to the nutrition of ruminants has also been established through studies of fungal populations in the rumen and the dietary factors which influence them, as presented in this review. Further, we discuss the evidence supporting an important contribution of anaerobic fungal populations in the rumen to feed intake and digestion of poor quality feed by domesticated ruminants. In conclusion, the review explores some different methods for manipulating fungi in the rumen for increased feed intake and digestion.

Diversity and activity of enriched ruminal cultures of anaerobic fungi and methanogens grown together on lignocellulose in consecutive batch culture

Consecutive batch cultures (CBC), involving nine serial transfers at 3, 5 and 7d intervals (21, 45 and 63d, respectively) were established to enrich for plant fibre degrading co-cultures of anaerobic fungi and methanogens from rumen digesta. Microbial diversity and fermentation end-products were measured at appropriate intervals over each CBC time-course. While methanogenic populations remained diverse, anaerobic fungal diversity was related to transfer interval and appeared to decrease with increasing transfer number. Acetate was the principal aqueous fermentation end-product with minimal quantities of lactate and formate detected. Methane and carbon dioxide were detected in the gaseous head-space of all co-cultures and the total amounts of gas generated per transfer was greater with transfer intervals of 5 and 7d compared with a 3d interval, although the 3d interval tended to be more efficient per unit time. In conclusion, rapidly growing, methane producing co-cultures of anaerobic fungi and methanogens from rumen digesta were easy to establish on lignocellulose (barley straw) and maintain over considerable time periods. These results suggest such co-cultures have potential in industrial scale anaerobic digestion (AD) of highly fibrous substrates, which are resistant to degradation in conventional AD plants.

Diversity of anaerobic gut fungal populations analysed using ribosomal ITS1 sequences in faeces of wild and domesticated herbivores

Gut fungal-specific PCR primers have been used to selectively amplify the ITS1 region of gut fungal rDNA recovered from faeces of domestic and wild animals to investigate population diversity. Two different gel-based methods are described for separating populations of gut fungal rDNA amplicons, namely (1) denaturing gradient gel electrophoresis (DGGE) and (2) separation according to small size differences using Spreadex, a proprietary matrix for electrophoresis. Gut fungal populations were characterised by analysis of rDNA in faeces of seventeen domesticated and ten wild herbivores. Sequences derived from these gel-based characterisations were analysed and classified using a hidden Markov model-based fingerprint matching algorithm. Faecal samples contained a broad spectrum of fungi and sequences from five of the six recognised genera were identified, including Cyllamyces, the most recently described gut fungal genus, which was found to be widely distributed in the samples. Furthermore, four other novel groupings of gut fungal sequences were identified that did not cluster with sequences from any of the previously described genera. Both gel- and sequence- based profiles for gut fungal populations suggested a lack of geographical restriction on occurrence of any individual fungal type.

Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen

Traditional methods for enumerating and identifying microbial populations within the rumen can be time consuming and cumbersome. Methods that involve culturing and microscopy can also be inconclusive, particularly when studying anaerobic rumen fungi. A real-time PCR SYBR Green assay, using PCR primers to target total rumen fungi and the cellulolytic bacteria Ruminococcus flavefaciens and Fibrobacter succinogenes, is described, including design and validation. The DNA and crude protein contents with respect to the fungal biomass of both polycentric and monocentric fungal isolates were investigated across the fungal growth stages to aid in standard curve generation. The primer sets used were found to be target specific with no detectable cross-reactivity. Subsequently, the real-time PCR assay was employed in a study to detect these populations within cattle rumen. The anaerobic fungal target was observed to increase 3.6-fold from 0 to 12 h after feeding. The results also indicated a 5.4-fold increase in F. succinogenes target between 0 and 12 h after feeding, whereas R. flavefaciens was observed to maintain more or less consistent levels. This is the first report of a real-time PCR assay to estimate the rumen anaerobic fungal population.

Dilution rate increases production of plant cell-wall degrading enzymes by anaerobic fungi in continuous-flow culture

The gut anaerobic fungi,Neocallimastix hurleyensis and aOrpinomyces sp., were grown in 100 mL batch and continuous-flow cultures on wheat straw at a concentration of 80 g dry matter/L of culture liquid. In batch cultures,N. hurleyensis and Orpinomyces sp. degraded only ca. 9% and 5% of the wheat straw, respectively. In continuous-flow cultures, however, the two fungi degraded 52-56% of the apparent dry matter of wheat straw. Both fungi were able to produce greater quantities (up to x 30) of cell-wall degrading enzymes (CMCase, xylanase, beta-glucosidase and beta-xylosidase) in continuous-flow cultures than in the corresponding batch cultures. Increasing the dilution rate in continuous-flow culture resulted in the production of increased enzyme activity for all the measured cell-wall degrading enzymes, with proportional relationships between dilution rate and the cumulative activities of beta-glucosidase and beta-xylosidase. Dilution rates, however, had no consistent effect on the cumulative production of the fermentation end-products, acetate, formate, D- and L-lactate from both fungi. In addition to acetate and formate,N. hurleyens is produced D- and L-lactate in both batch and continuous-flow cultures, whereas only trace amounts of L-lactate were detected in the Orpinomyces sp. cultures.

In vitro degradation of wheat straw by anaerobic fungi from small ruminants

Anaerobic ruminal fungi may play an active role in fibre degradation as evidenced by the production of different fibrolytic enzymes in culture filtrate. In the present study, 16 anaerobic fungal strains were isolated from ruminal and faecal samples of sheep and goats. Based on their morphological characteristics they were identified as species of Anaeromyces, Orpinomyces, Piromyces and Neocallimastix. Isolated Neocallimastix sp. from goat rumen showed a maximum activity of CMCase (47.9 mIU ml(-1)) and filter paper cellulase (48.3 mIU ml(-1)), while Anaeromyces sp. from sheep rumen showed a maximum xylanolytic activity (48.3 mIU ml(-1)). The cellobiase activity for all the isolates ranged from 178.0-182.7 mIU ml(-1). Based on the enzymatic activities, isolated Anaeromyces sp. from sheep rumen and Neocallimastix sp. from goat rumen were selected for their potential of in vitro fibre degradation. The highest in vitro digestibility of NDF (23.2%) and DM (34.4%) was shown for Neocallimastix sp. from goat rumen, as compared to the digestibility of NDF and DM in the control group of 17.5 and 25.0%, respectively.

Relative fibrolytic activities of anaerobic rumen fungi on untreated and sodium hydroxide treated barley straw in in vitro culture

The fibrolytic activities of rumen fungi were studied in terms of dry matter loss, plant cell wall degradation and enzyme (cellulase and xylanase) activities, when grown in vitro on either untreated or sodium hydroxide treated stems of barley straw over a 12 day period. Changes in fungal growth, development and overall biomass were followed using chitin assay and scanning electron microscopy. Treatment with sodium hydroxide resulted in a decrease in the NDF content together with the disruption of cuticle and the loosening and separation of the plant cells within the straw fragments. The enzyme activities of the anaerobic fungi have a high positive correlation (R(2)=0.99) with their biomass concentration assessed by chitin assay indicating that chitin is a valuable index for the estimation of the fungal biomass in vitro. The anaerobic fungi produced very extensive rhizoidal systems in these in vitro cultures. After incubation with rumen fungi, dry matter losses were, respectively, 35% and 38% for the untreated and treated straw samples and the overall fungal biomass, determined by chitin assay, was significantly higher in the treated samples. In vitro degradation of cellulose and hemicellulose was also higher in the treated than that of untreated cultures. Although, comparatively, xylanase activity was higher than that of cellulase, the cellulose fraction of the straw was degraded more than hemicellulose in both treated and untreated straw.

Distribution and estimation of anaerobic zoosporic fungi along the digestive tracts of sheep

The status of anaerobic zoosporic (Chytridiomycota) fungi along the entire digestive tract of sheep was assessed both analytically and microscopically. Digest samples were taken from different segments of the digestive tracts of three newly killed sheep that previously had been used in experimental dietary studies. These digest samples were tested for the presence of rumen fungi by assessing the recovery of live fungi from the samples, direct observation of digested plant remains under the scanning electron microscope (SEM), and using a chitin assay as an estimation of fungal biomass. Live anaerobic fungi were recovered from the abomasum, small and large intestine, caecum and faeces of sheep, but not from the digest samples of rumen and omasum. However, SEM examination of the samples confirmed the presence of fungal structures from all of these organs. In the large intestine and caecum samples the observed sporangial structures were rounded and showed conspicuous surface pitting. Results of the chitin assay indicated that the anaerobic fungi might account for up to 20% of the total microbial biomass in the rumen of sheep. The results of this study support the view that anaerobic fungi may be present as a resistant stage in the lower reaches of the digestive tract.

Methods for the isolation, culture and assessment of the status of anaerobic rumen chytrids in both in vitro and in vivo systems

Anaerobic fungi were isolated from both the rumen and faeces of nine sheep and a cow. A reliable and simple method for the isolation of anaerobic fungi using 24 h rumen incubated milled straw as the inoculum source was developed. We also evaluate the use of chitin measurements as an assay of rumen fungal biomass. Chitin levels were determined from various sample sources (milled barley straw used as the fungal culture substrate in vitro; plant particulate digests from the rumen (PLP) and centrifuged strained rumen fluid (CSRF) using both HPLC and colorimetric methods. Both methods were highly correlated and consequently the simpler colorimetric method was adopted for subsequent studies. There was also a high degree of correlation between anaerobic fungal cellulase activities with the assayed chitin content of milled barley straw cultures over 12 d of an in vitro experiment. The colorimetric chitin assay protocol was then used to assess the diurnal variation and abundance of rumen fungi in in vivo assays. We assessed the distribution of chitin (mg g(-1) dry matter) in various fractions of the strained rumen fluid (SRF) and PLP samples from the rumen of sheep. Chitin was detected in all fractions of strained rumen fluid but the main source of chitin in the samples may be attributed to the fungal biomass. We did not detect any significant differences in chitin levels over a 24 h sampling period. Finally, an SEM study on subsamples of milled straw and plant particulate matter used in the chitin assays, revealed that the pattern of the fungal development on substrate material differs from the culture medium to the rumen.

Some Chytridiomycota in soil recover from drying and high temperatures

Rhizophlyctis rosea was found in 44% of 59 soil samples from national parks, urban reserves and gardens, and agricultural lands of eastern New South Wales, Australia. As some of the soils are periodically dry and hot, we examined possible mechanisms that enable survival in stressful environments such as agricultural lands. Air-dried thalli of R. rosea in soil and pure cultures of R. rosea, two isolates of Allomyces anomalus, one isolate of Catenaria sp., one of Catenophlyctis sp. and one of Spizellomyces sp. recovered following incubation at 90 degrees C for two days. Powellomyces sp. recovered following incubation at 80 degrees. Sporangia of all seven fungi shrank during air-drying, and immediately returned to turgidity when rehydrated. Some sporangia of R. rosea released zoospores immediately upon rehydration. These data indicate that some Chytridiomycota have resistant structures that enable survival through periodic drying and high summer temperatures typical of soils used for cropping. Eleven Chytridiomycota isolated from soil did not survive either drying or heat. Neither habitat of the fungus nor morphological type correlated with the capacity to tolerate drying and heat.

Technical note: A proposed method to determine the extent of degradation of a feed in the rumen from the degradation profile obtained with the in vitro gas production technique using feces as the inoculum1

A method is proposed to determine the extent of degradation in the rumen involving a two-stage mathematical modeling process. In the first stage, a statistical model shifts (or maps) the gas accumulation profile obtained using a fecal inoculum to a ruminal gas profile. Then, a kinetic model determines the extent of degradation in the rumen from the shifted profile. The kinetic model is presented as a generalized mathematical function, allowing any one of a number of alternative equation forms to be selected. This method might allow the gas production technique to become an approach for determining extent of degradation in the rumen, decreasing the need for surgically modified animals while still maintaining the link with the animal. Further research is needed before the proposed methodology can be used as a standard method across a range of feeds.

Cyllamyces aberensis gen.nov. sp.nov., a new anaerobic gut fungus with branched sporangiophores isolated from cattle

A new genus of the anaerobic gut fungi (Neocallimastigales), Cyllamyces aberensis gen.nov. sp.nov., with bulbous holdfast, branched sporangiophores and limited polycentric thallus development is described. The fungus was isolated from fresh cattle faeces. Free-swimming zoospores were spherical, uninucleate, and uniflagellate. After encystment, zoospores germinated and gave rise to a single, bulbous holdfast. One or several branched sporangiophores were produced from different locations on the holdfast, each bearing several spherical sporangia. DAPI staining of thalli indicated that nuclei were present in the holdfast, sporangiophores, and sporangia. As many as 12 sporangia were observed per thallus on up to 5 sporangiophores, with zoosporogenesis beginning 16–18 h after encystment. Zoospore ultrastructure was examined by transmission electron microscopy and found to be similar to that reported for other anaerobic chytrid fungi. Organelles were evenly distributed throughout the cell, except for the posteriorly attached flagellum and associated attachment apparatus, the hydrogenosomes, which were mainly situated in the posterior parts of the cell and a posteriorly directed, beak-shaped nucleus. Limited polycentric thallus development (including branched sporangiophores), the possession of a single bulbous holdfast and the absence of rhizoids were stable features of this fungus that distinguished it from the other five genera of gut fungi. Therefore, we have used these characteristics to assign the fungus to a new genus, Cyllamyces, with the specific name C. aberensis.Key words: rumen, fungal taxonomy, Neocallimastigales, chytrid, zoospore ultrastructure.

Evidence of a role for plant proteases in the degradation of herbage proteins in the rumen of grazing cattle

Protein breakdown in the rumen is generally regarded as a two-stage process in which proteases produced by rumen microorganisms cleave plant protein into peptides and amino acids. However, many of the fiber-degrading cellulolytic species in the rumen are not in fact proteolytic, and the proteolytic activity of the entire rumen microbial population is only moderate when compared to the gastric and pancreatic secretions in the abomasum. Moreover, plant cell walls remain largely intact after initial chewing (particularly in cattle), presenting a physical barrier that must be breached prior to their effective colonization. The present study considers the hypothesis that the plant enzymes are at least partly responsible for herbage protein degradation in grazing ruminants. Ryegrass, red clover, white clover, and bird's-foot trefoil were incubated in the presence and absence of rumen microorganisms. The production of volatile fatty acids indicated the level of microbial activity, whereas the relative disappearance of the large subunit of ribulose 1,5 bisphosphate carboxylase/oxygenase (Rubisco LSU) indicated proteolytic activity. In all incubations, the relative abundance of the Rubisco LSU decreased as the incubation progressed. When rumen microorganisms were absent, low molecular weight peptides (below 20 kDa) accumulated as the incubation progressed. This accumulation was not observed in the presence of rumen microorganisms. Therefore we suggest that the intrinsic plant proteases contribute to the initial stages of proteolysis of grazed herbage.

Isozyme and morphological characteristics of the anaerobic fungus Piromyces mae isolated from the duodenum, rumen and faeces of sheep

Isolates of anaerobic fungi obtained from the rumen, duodenum and faeces of sheep were identified as Piromyces mae based on their morphological characteristics observed using light microscopy. There was no significant morphological variation among the isolates of P. mae from the rumen, duodenum and faeces. Isozymes of 12 isolates of P. mae (one each from the rumen, duodenum and faeces from 4 different sheep) were analysed by PAGE. A total of 12 isozymes were studied and 5 isozyme loci were successfully typed. They were malic enzyme, malate dehydrogenase, shikimate dehydrogenase, alpha-esterase and beta-esterase. All the isolates of P. mae regardless of whether they were from the rumen, duodenum or faeces or from different animals produced very similar isozyme banding patterns for each of the enzyme systems. The similar isozyme profiles of the isolates indicate that they are of the same species although they exist in different regions of the alimentary tract.