Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation.

Consortium-based approaches are a promising avenue toward efficient bioprocessing. However, many complex microbial interactions dictate community dynamics and stability that must be replicated in synthetic systems. The rumen and/or hindguts of large mammalian herbivores harbor complex communities of biomass-degrading fungi and bacteria, as well as archaea and protozoa that work collectively to degrade lignocellulose, yet the microbial interactions responsible for stability, resilience, and activity of the community remain largely uncharacterized. In this work, we demonstrate a "top-down" enrichment-based methodology for selecting a minimal but effective lignocellulose-degrading community that produces methane-rich fermentation gas (biogas). The resulting enrichment consortium produced 0.75-1.9-fold more fermentation gas at 1.4-2.1 times the rate compared to a monoculture of fungi from the enrichment. Metagenomic sequencing of the top-down enriched consortium revealed genomes encoding for functional compartmentalization of the community, spread across an anaerobic fungus (Piromyces), a bacterium (Sphaerochaeta), and two methanogenic archaea (Methanosphaera and Methanocorpusculum). Guided by the composition of the top-down enrichment, several synthetic cocultures were formed from the "bottom-up" using previously isolated fungi, Neocallimastix californiae and Anaeromyces robustus paired with the methanogen Methanobacterium bryantii. While cross-feeding occurred in synthetic co-cultures, removal of fungal metabolites by methanogens did not increase the rate of gas production or the rate of substrate deconstruction by the synthetic community relative to fungal monocultures. Metabolomic characterization verified that syntrophy was established within synthetic co-cultures, which generated methane at similar concentrations compared to the enriched consortium but lacked the temporal stability (resilience) seen in the native system. Taken together, deciphering the membership and metabolic potential of an enriched gut consortium enables the design of methanogenic synthetic co-cultures. However, differences in the growth rate and stability of enriched versus synthetic consortia underscore the difficulties in mimicking naturally occurring syntrophy in synthetic systems.

Effect of the Associated Methanogen Methanobrevibacter thaueri on the Dynamic Profile of End and Intermediate Metabolites of Anaerobic Fungus Piromyces sp. F1.

Although the scheme of metabolic pathways involved in the production of the major end products has been described, the dynamic profile of metabolites of anaerobic fungi co-cultured with methanogens is limited, especially for the intermediate metabolites. In the present study, the fermentation of the co-culture of Piromyces sp. F1 and Methanobrevibacter thaueri on glucose was investigated. The presence of methanogens shortened the growth lag time of anaerobic fungi and enhanced the total gas production. The occurrence of the maximum cell dry weight and the disappearance of most of the substrate were observed at 24 h for the co-culture and 48 h for the fungal mono-culture. In the co-culture, hydrogen was detected at a very low level during fermentation, and formate transitorily accumulated at 24 h and disappeared at 48 h, resulting in an increase of pH. Acetate was higher during the fermentation in the co-culture (P < 0.05), while lactate and ethanol were higher only in the initial stage of fermentation (P < 0.05). After 48 h, lactate in the mono-culture became much higher than that in the co-culture (P < 0.05), and ethanol tended to remain the same in both cultures. Moreover, malate tended to be exhausted in the co-culture, while it accumulated in the mono-culture. Citrate was also detected in both co-culture and mono-culture. Collectively, these results suggest that methanogen enhanced the malate pathway and weakened the lactate pathway of anaerobic fungus.

Effect of administration of rumen fungi on production performance of lactating buffaloes.

Anaerobic fungi were orally dosed to lactating buffaloes to study their effect on the digestibility of a diet (composed of 50% wheat straw and 50% concentrate along with six kg maize green/animal/day), rumen fermentation patterns and milk production. Group I (control) was administered with fungus-free anaerobic broth, while group II and III were administered with Orpinomyces sp. C-14 or Piromyces sp. WNG-12 (250 ml; 3-5 days of growth/animal/ week), respectively. Milk production was higher in group II and III (8.42 and 8.48 kg/d) than in the control (8.03 kg/d) with virtually the same feed intake (i.e. 11.50 and 10.62 and 11.79 kg, respectively). There was an increase of 6% fat-corrected milk yield/animal/day in group II and III, respectively compared to the control. The milk fat was higher in the fungal culture administered groups than in the control group. The digestibility of dry matter, crude protein, neutral detergent fibre, acid detergent fibre, cellulose and digestible energy also increased significantly in group II and III. The pH and ammonia nitrogen were lower, whereas total volatile fatty acids, total nitrogen, trichloroacid precipitable nitrogen and number of zoospores/ml of rumen liquor were higher in group II and III when compared to the control. Hence, it can be stated that rumen fungi can be used as a direct-fed microbial in lactating buffaloes, to enhance the digestibility of wheat straw based diets leading to higher production.

Effects of emulsified octadecanic acids on gas production and cellulolysis by the rumen anaerobic fungus, Piromyces communis M014.

Responses of the rumen anaerobic fungus, Piromyces communis M014, to octadecanic long-chain fatty acids (LCFAs) were evaluated by measuring total and hydrogen gas productions, filter paper (FP) cellulose degradation and polysaccharidase enzyme activities. Octadecanic acids (stearic acid, C(18:0); oleic acid, C(18:1); linoleic acid, C(18:2) and linolenic acid, C(18:3)) were emulsified by ultrasonication under anaerobic conditions, and added to the medium at the level of 0.001%. When P. communis M014 was grown in culture with stearic and oleic acids, the cumulative gas production, FP cellulose digestion and enzyme activities were significantly (p<0.05) increased in the early incubation times relative to those for the control. However, the addition of linolenic acid inhibited all of the investigated parameters, including cellulose degradation, enzyme activities and gas production, up to 168h incubation. These results indicated that stearic and oleic acids tended to have stimulatory effects on fungal cellulolysis, whereas linolenic acid caused a significant (p<0.05) inhibitory effect on cellulolysis by the rumen fungus. The fungus, P. communis M014, can biohydrogenate C(18) unsaturated fatty acids to escape from their toxic effects. Therefore, in this study, the results indicated that the more highly the added C(18) LCFA to the fungal culture was unsaturated, the higher the inhibition of gas production and cellulase enzyme activity was.

Characterization of a double dockerin from the cellulosome of the anaerobic fungus Piromyces equi.

The assembly into supramolecular complexes of proteins having complementary activities is central to cellular function. One such complex of considerable biological and industrial significance is the plant cell wall-degrading apparatus of anaerobic microorganisms, termed the cellulosome. A central feature of bacterial cellulosomes is a large non-catalytic protein, the scaffoldin, which contains multiple cohesin domains. An array of digestive enzymes is incorporated into the cellulosome through the interaction of the dockerin domains, present in the catalytic subunits, with the cohesin domains that are present in the scaffoldin. By contrast, in anaerobic fungi, such as Piromyces equi, the dockerins of cellulosomal enzymes are often present in tandem copies; however, the identity of the cognate cohesin domains in these organisms is unclear, hindering further biotechnological development of the fungal cellulosome. Here, we characterise the solution structure and function of a double-dockerin construct from the P. equi endoglucanase Cel45A. We show that the two domains are connected by a flexible linker that is short enough to keep the binding sites of the two domains on adjacent surfaces, and allows the double-dockerin construct to bind more tightly to cellulosomes than a single domain and with greater coverage. The double dockerin binds to the GH3 beta-glucosidase component of the fungal cellulosome, which is thereby identified as a potential scaffoldin.

Effects of aromatic amino acids, phenylacetate and phenylpropionate on fermentation of xylan by the rumen anaerobic fungi, Neocallimastix frontalis and Piromyces communis.

AIMS: Anaerobic fungi are important members of the fibrolytic community of the rumen. The aim of this study was to study their requirement for aromatic amino acids (AA) and related phenyl acids (phenylpropionic and phenylacetic acids) for optimal xylan fermentation. METHODS AND RESULTS: Neocallimastix frontalis RE1 and Piromyces communis P were grown in a defined medium containing oat spelts xylan as the sole energy source, plus one of the following N sources: ammonia; ammonia plus a complete mixture of 20 AA commonly found in protein; ammonia plus complete AA mixture minus aromatic AA; ammonia plus phenyl acids; ammonia plus complete AA mixture without aromatic AA plus phenyl acids. Both species grew in all the media, indicating no absolute requirement for AA. The complete AA mixture increased (P<0.05) acetate concentration by 18% and 15%, sugar utilization by 33% and 22% and microbial yield by about 22% and 15% in N. frontalis and P. communis, respectively, in comparison with the treatments that had ammonia as the only N source. Neither the supply of aromatic AA or phenol acids, nor their deletion from the complete AA mixture, affected the fermentation rate, products or yield of either species. CONCLUSIONS: AA were not essential for N. frontalis and P. communis, but their growth on xylan was stimulated. The effects could not be explained in terms of aromatic AA alone. SIGNIFICANCE AND IMPACT OF THE STUDY: Ruminant diets should contain sufficient protein to sustain optimal fibre digestion by ruminal fungi. Aromatic AA or phenyl acids alone cannot replace the complete AA mixture.

Effect of phenolic monomers on biomass and hydrolytic enzyme activities of an anaerobic fungus isolated from wild nil gai (Baselophus tragocamelus).

AIMS: To test the anaerobic fungus, Piromyces sp. FNG5, for its tolerance to phenolic monomers released in the rumen by degradation of lignocellulosic poor-quality feeds. METHODS AND RESULTS: Effects of phenolic monomers on biomass and fibrolytic enzyme activities of a pure culture of lignocellulolytic anaerobic fungus (Piromyces sp. FNG5) isolated from faeces of wild nil gai (blue bull, Baselophus tragocamelus) were evaluated. There was a reduction in fungal biomass at 1 mm concentration of catechol with complete inhibition at 10 mm. p-Coumaric acid caused a reduction in biomass at 10 mm and no growth was observed above 20 mm concentration. The fungal isolate could tolerate up to 5 mm of ferulic acid without any reduction in biomass level, and was able to grow to some extent up to the highest level of ferulic acid tested (20 mm). Vanillic acid had no effect on biomass of the fungus even up to 50 mm level. The phenolic monomers varied in their potential to inhibit the secretion of carboxymethyl cellulase, xylanase, beta-glucosidase and acetyl esterase activities with catechol being the most inhibitory and vanillic acid being the least inhibitory. After 14 days of incubation, 38.49-65.14%p-Coumaric acid, 65.22-74.10% ferulic acid and 34.13-66.78% vanillic acid disappeared from the medium under anaerobic conditions. CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY: It is concluded that the anaerobic fungus Piromyces sp. FNG5 is tolerant to phenolic monomers and has ability to degrade them. Therefore, such anaerobic fungi may play an important role in fibre degradation in the rumen.