The effect of anaerobic fungal inoculation on the fermentation characteristics of rice straw silages

Effects of rehydrated corn silage inoculated with Rhodotorula mucilaginosa + Trichoderma longibrachiatum on finisher lambs fed a tropical hay-based diet

It is well established in the scientific literature that tropical forages are characterized by low soluble carbohydrates and a high proportion of cell walls containing lignin, negatively impacting animal productivity. Using live microorganisms in diets, such as fungi and yeasts, can benefit animal nutrition and health. This study assessed the effects of using rehydrated ground corn silage as a vehicle for providing an inoculant composed of fungus and yeast (Rhodotorula mucilaginosa + Trichoderma longibrachiatum) isolated from the gastrointestinal contents of sheep on the productive performance of confined lambs. Twenty-two entire male lambs of the Dorper × Santa Inês breed (14.20 ± 1.74 kg body weight) were randomly assigned to two treatments: 1) control diet containing rehydrated corn silage without inoculant (CTL); 2) diet containing rehydrated ground corn silage with inoculant of indigenous microorganisms (INO). Rhodotorula mucilaginosa and Trichoderma longibrachiatum were observed only in samples of rehydrated corn with inoculant (P<0.0001). The inoculated silage had lower neutral detergent fiber (NDF) content (89.9g/kg dry matter - DM) than the control silage (134.8g/kg DM). CTL treatment showed higher other mycelial fungi count than treatment INO (P=0.04). However, the total count of mycelial fungi did not differ between treatments. Treatments did not affect silage pH; however, pH was reduced in samples taken 56 days after ensiling (P<0.001). No differences were observed between treatments for DM digestibility and nutrient and nitrogen balance (P<0.05). Although the combination of microorganisms reduced dry matter intake (DMI) (P<0.05), no treatment effect was observed on growth performance over the 63-day experimental period. These results indicate that Rhodotorula mucilaginosa and Trichoderma longibrachiatum inoculated in rehydrated corn silage can improve feed quality by lowering fiber content without compromising animal growth. In conclusion, feeding lamb with rehydrated corn silage inoculated with Rhodotorula mucilaginosa and Trichoderma longibrachiatum reduces dry matter intake of tropical hay-based diets without affecting body weight gain.

Anaerobic microbial cocktail of lignocellulolytic fungi and bacteria with methanogens for boosting methane production from unpretreated rice straw

Rice straw (RS) has been recognized as a sustainable renewable energy resource for converting into sugars and volatile fatty acids (acetate, propionate, and butyrate) and subsequently to produce biogas. Enhanced production of these intermediates from RS by the different combinations of two consortia was investigated. Anaerobic microbial cocktails of fungi, bacteria, and methanogens were evaluated for performance and stability in the anaerobic digestion of untreated RS. The best-defined anaerobic microbial cocktail for high RS degradation and methane production, consisting of anaerobic bacteria (mainly Proteiniphilum acetatigenes, Pyramidobacter piscolens, and Mesotoga prima) and anaerobic lignocellulolytic/fermentative fungi (uncultured Neocallimastigales, Orpinomyces, Anaeromyces, and Feramyces sp.) at a copy number ratio of 10³-10⁵ copies/mL, including hydrogenotrophic and acetoclastic methanogens (Methanosarcina mazei, Methanoculleus marisnigri, Methanofollis liminatans, Methanoculleus bourgensis, and Methanosaeta harundinacea) concentration of 10⁶ copies/mL, was successfully constructed. The system performance was 80% VS (volatile solids) RS degradation, 34 mL/day methane production rate, 318 mL/g VS_added methane yield, and a pH range of 6.90-7.70 within a short time of 14 days. A defined microbial cocktail has been proven as a potential alternative process for lignocellulose hydrolysis and methane production.

Isolation and identification of ligninolytic bacterium (Bacillus cereus) from buffalo (Bubalus bubalis) rumen and its effects on the fermentation quality, nutrient composition, and bacterial community of rape silage

This study aimed to isolate and identify a ligninolytic bacterium from the rumen of buffalo (Bubalus bubalis) and investigate its effects as a silage additive for whole-plant rape. Three lignin-degradation strains were isolated from the buffalo rumen, with AH7-7 being chosen for further experiments. Strain AH7-7, with acid tolerance and a 51.4% survival rate at pH 4, was identified as Bacillus cereus. It exhibited a lignin-degradation rate of 20.5% after being inoculated in a lignin-degrading medium for 8 days. We divided the rape into four groups according to the various additive compositions to examine the fermentation quality, nutritional value, and bacterial community after ensiling: Bc group (inoculated with B. cereus AH7-7 3.0 × 10⁶ CFU g FW^-1), Blac group (inoculated with B. cereus AH7-7 1.0 × 10⁶ CFU g FW^-1, L. plantarum 1.0 × 10⁶ CFU g FW^-1, and L. buchneri 1.0 × 10⁶ CFU g FW^-1), Lac group (inoculated with L. plantarum 1.5 × 10⁶ CFU g FW^-1 and L. buchneri 1.5 × 10⁶ CFU g FW^-1), and Ctrl group (no additives). After 60 days of fermentation, the application of B. cereus AH7-7 was potent in modulating the fermentation quality of silage, especially when combined with L. plantarum and L. buchneri, as indicated by lower dry matter loss and higher contents of crude protein, water-soluble carbohydrate, and lactic acid. Furthermore, treatments with the B. cereus AH7-7 additive decreased the contents of acid detergent lignin, cellulose, and hemicellulose. The B. cereus AH7-7 additive treatments reduced the bacterial diversity and optimized the bacterial community compositions of silage, with an increase in the relative abundance of beneficial Lactobacillus and a decrease in the relative abundance of undesirable Pantoea and Erwinia. Functional prediction revealed that inoculation with B. cereus AH7-7 could increase the cofactors and vitamins metabolism, amino acid metabolism, translation, replication and repair, and nucleotide metabolism, while decreasing the carbohydrate metabolism, membrane transport, and energy metabolism. In brief, B. cereus AH7-7 improved the microbial community, fermentation activity, and ultimately the quality of silage. The ensiling with B. cereus AH7-7, L. plantarum, and L. buchneri combination is an effective and practical strategy to improve the fermentation and nutrition preservation of rape silage.

Effect of Fibrolytic Enzymes, Cellulolytic Fungi and Lactic Acid Bacteria on Fermentation Characteristics, Structural Carbohydrate Composition and In Vitro Digestibility of Rice Straw Silage

This study aimed to investigate the effect of fibrolytic enzymes, cellulolytic fungi and lactic acid bacteria on the fermentation quality, structural carbohydrate composition and in vitro digestibility of rice straw silage. This experiment followed a completely randomised block design; four treatments were designed: (1) distilled water (control, CON); (2) fibrolytic enzymes (2.0 g/kg fresh weight (FW), E); (3) Trichoderma reesei (4400 U/kg FW, F); (4) Enterococcus faecium Y83 (1 × 106 cfu/g FW, Y83). All additives were diluted with distilled water and sprayed onto the rice straw (20 mL/kg FW). The rice straw was placed into a laboratory silo (10 L) after uniformly mixing and stored at ambient temperature (17–22 °C) ensiling for 3, 7, 14, 30 and 60 days. The fermentation quality in treated silages was improved compared to the CON, as indicated by lower pH, propionic acid, acetic acid and ammonia nitrogen (NH3-N) contents. Furthermore, Y83 had the lowest (p < 0.05) pH and highest (p < 0.05) lactic acid content after 60 days of ensiling. Y83 significantly (p < 0.05) decreased the neutral detergent fibre content compared with CON, E and F. In addition, E and Y83 had significantly (p < 0.05) higher in vitro dry matter digestibility and in vitro neutral detergent fibre digestibility than CON and F. Overall, Y83 can be used as a promising inoculant for improving the fermentation quality of rice straw silage.

Microbial Community, Co-Occurrence Network Relationship and Fermentation Lignocellulose Characteristics of Broussonetia papyrifera Ensiled with Wheat Bran

Broussonetia papyrifera has a high lignocellulose content leading to poor palatability and low digestion rate of ruminants. Thus, dynamic profiles of fermentation lignocellulose characteristics, microbial community structure, potential function, and interspecific relationships of B. papyrifera mixing with wheat bran in different ratios: 100:0 (BP100), 90:10 (BP90), 80:20 (BP80), and 65:35 (BP65) were investigated on ensiling days 5, 15, 30, and 50. The results showed that adding bran increased the degradation rate of hemicellulose, neutral detergent fiber, and the activities of filter paper cellulase, endoglucanase, acid protease, and neutral protease, especially in the ratio of 65:35. Lactobacillus, Pediococcus, and Weissella genus bacteria were the dominant genera in silage fermentation, and Pediococcus and Weissella genus bacteria regulated the process of silage fermentation. Compared with monospecific B. papyrifera silage, adding bran significantly increased the abundance of Weissella sp., and improved bacterial fermentation potential in BP65 (p < 0.05). Distance-based redundancy analysis showed that lactic acid bacteria (LAB) were significantly positive correlated with most lignocellulose content and degrading enzymes activities, while Monascus sp. and Syncephalastrum sp. were opposite (p < 0.05). Co-occurrence network analysis indicated that there were significant differences in microbial networks among different mixing ratios of B. papyrifera silage prepared with bran. There was a more complex, highly diverse and less competitive co-occurrence network in BP65, which was helpful to silage fermentation. In conclusion, B. papyrifera ensiled with bran improved the microbial community structure and the interspecific relationship and reduced the content of lignocellulose.

Suitability of anaerobic fungi culture supernatant or mixed ruminal fluid as novel silage additives

Abstract

This study investigated silage quality characteristics and ruminal fiber degradability of grass and straw ensiled with either anaerobic fungi (AF) supernatant with active fungal enzymes or mixed ruminal fluid as novel silage additives. Compared to control silages, AF supernatant improved the quality of grass and straw silages as evidenced by decreased pH, acetic acid concentration, and dry matter losses. Likewise, mixed ruminal fluid enhanced lactic acid fermentation, which further resulted in lower pH of the treated grass silage. The ruminal fiber degradability was determined using in situ incubations and, compared to controls, the cellulose degradability was higher for grass silage with AF supernatant, whereas ruminal degradability of straw silage was reduced by this treatment. In contrast, mixed ruminal fluid did not influence fiber degradability of silages in the rumen. Concluding, both novel additives improved silage quality, whereas only AF supernatant enhanced ruminal fiber degradability of grass silage and therefore may represent an approach for improving forage utilization by ruminants.

Key points

• Enzymes of anaerobic fungi supernatant improve quality of grass and straw silages.

• Mixed ruminal fluid enhances lactic acid fermentation when ensiling grass and straw.

• Enzymes of anaerobic fungi supernatant increase ruminal grass silage degradability.

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.

The Fibrolytic Enzyme Profiles and the Composition of Fungal Communities in Donkey Cecum-Colon Ecosystem

Simple Summary

The donkey hindgut is a microbial-rich ecosystem in which caecum and colon fungi play an important role in dietary fiber degradation. In addition, the fibrolytic enzymes produced by hindgut microorganisms are key to the ability of equines to hydrolysis plant fiber. In the present study, the fibrolytic enzyme activities within donkey caecum and colon were firstly measured by spectrophotometry. The dorsal colon presented a higher fibrolytic enzyme activity in comparison with caecum. The fungal community composition along donkey caecum and colon was determined by sequencing an internal transcribed spacer region (ITS) using Illumina MiSeq. The predominant fungi at phylum level were Ascomycota, Basidiomycota, and Neocallimastigomycota. The Aspergillus, Wallemia, Phanerochaete, Fusarium, and Penicillium were detected as the dominant genera, but their metabolic and functional significance in donkey cecum-colon ecosystem need further investigation. In terms of the anaerobic fungi Neocallimastigomycota, its abundance was greater in donkey colon than in caecum. The relative abundance of enzymes related to plant cell wall breakdown were also predicted by PICRUSt, and they were also greater in donkey colon than in caecum. The present study provided new information about fibrolytic enzyme profiles and fungal communities in donkey hindgut. The findings could therefore contribute to the further understanding of the fungal taxa and their dietary fiber degradation mechanisms in donkey hindgut ecosystem.

Abstract

The fibrolytic enzymes and the hindgut fungi in donkey cecum-colon ecosystem play an important role in dietary fiber digestion. A better understanding of the fibrolytic enzyme profiles and the fungal community along donkey caecum and colon is key for optimizing hindgut function. In the present study, the fibrolytic enzyme activities within donkey caecum and colon were firstly measured by spectrophotometry. Activities of carboxymethyl cellulase, avicelase, xylanase, and acetyl esterase were greater in donkey dorsal colon than in caecum, indicating that the colon microorganisms may be more efficient in producing fibrolytic enzymes compared to caecum microbes. The fungal community composition along donkey hindgut was determined by sequencing ITS region using Illumina MiSeq. Three fungal phyla were identified by sequence comparison: Ascomycota (66.8%–74.4%), Basidiomycota (21.6%–30.9%), and Neocallimastigomycota (0.9%–3.3%). The Aspergillus, Wallemia, Phanerochaete, Fusarium, and Penicillium were detected as the dominant genera, but their metabolic and functional significance in donkey cecum-colon ecosystem need further investigation. In terms of the anaerobic fungi Neocallimastigomycota, its abundance was greater in donkey colon than in caecum (p < 0.05), indicating that the donkey hindgut region was associated with differences in fungal community composition. Moreover, the relative abundance of enzymes related to plant cell wall degradation were predicted by PICRUSt, and they were also lower in caecum than in colon. The present study provided new information about fibrolytic enzyme profiles and fungal composition in donkey hindgut ecosystem.

Decoding the roles of extremophilic microbes in the anaerobic environments: Past, Present, and Future

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The inaccessible extreme environments harbor a large majority of anaerobic microbes which remain unknown.

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Anaerobic microbes are used in a variety of industrial applications.

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In the future, metagenomic-assisted techniques can be used to identify novel anaerobic microbes from the unexplored extreme environments.

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Genetic engineering can be used to enhance the efficiency of anaerobic microbes for various processes.

The genome of an organism is directly or indirectly correlated with its environment. Consequently, different microbes have evolved to survive and sustain themselves in a variety of environments, including unusual anaerobic environments. It is believed that their genetic material could have played an important role in the early evolution of their existence in the past. Presently, out of the uncountable number of microbes found in different ecosystems we have been able to discover only one percent of the total communities. A large majority of the microbial populations exists in the most unusual and extreme environments. For instance, many anaerobic bacteria are found in the gastrointestinal tract of humans, soil, and hydrothermal vents. The recent advancements in Metagenomics and Next Generation Sequencing technologies have improved the understanding of their roles in these environments. Presently, anaerobic bacteria are used in various industries associated with biofuels, fermentation, production of enzymes, vaccines, vitamins, and dairy products. This broad applicability brings focus to the significant contribution of their genomes in these functions. Although the anaerobic microbes have become an irreplaceable component of our lives, a major and important section of such anaerobic microbes still remain unexplored. Therefore, it can be said that unlocking the role of the microbial genomes of the anaerobes can be a noteworthy discovery not just for mankind but for the entire biosystem as well.

Complementary Contribution of Fungi and Bacteria to Lignocellulose Digestion in the Food Stored by a Neotropical Higher Termite

Lignocellulose digestion in termites is achieved through the functional synergy between gut symbionts and host enzymes. However, some species have evolved additional associations with nest microorganisms that collaborate in the decomposition of plant biomass. In a previous study, we determined that plant material packed with feces inside the nests of Cornitermes cumulans (Syntermitinae) harbors a distinct microbial assemblage. These food nodules also showed a high hemicellulolytic activity, possibly acting as an external place for complementary lignocellulose digestion. In this study, we used a combination of ITS sequence analysis, metagenomics, and metatranscriptomics to investigate the presence and differential expression of genes coding for carbohydrate-active enzymes (CAZy) in the food nodules and the gut of workers and soldiers. Our results confirm that food nodules express a distinct set of CAZy genes suggesting that stored plant material is initially decomposed by enzymes that target the lignin and complex polysaccharides from fungi and bacteria before the passage through the gut, where it is further targeted by a complementary set of cellulases, xylanases, and esterases produced by the gut microbiota and the termite host. We also showed that the expression of CAZy transcripts associated to endoglucanases and xylanases was higher in the gut of termites than in the food nodules. An additional finding in this study was the presence of fungi in the termite gut that expressed CAZy genes. This study highlights the importance of externalization of digestion by nest microbes and provides new evidence of complementary digestion in the context of higher termite evolution.

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 Composition of Fungal Communities in the Rumen of Gayals (Bos frontalis), Yaks (Bos grunniens), and Yunnan and Tibetan Yellow Cattle (Bos taurs)

The rumen is a microbial-rich ecosystem in which rumen fungi play an important role in the feed digestion of ruminants. The composition of rumen fungi in free-range ruminants such as gayals, yaks, Tibetan yellow cattle, and the domesticated Yunnan yellow cattle was investigated by sequencing an internal transcribed spacer region 1 (ITS1) using Illumina MiSeq. A total of 285 092 optimized sequences and 904 operational taxonomic units (OTUs) were obtained from the four cattle breeds. The rumen fungi abundance and Chao and Simpson indexes were all higher in free-range ruminants than in domesticated ruminants. Three fungal phyla were identified by sequence comparison: Neocallimastigomycota, Basidiomycota, and Ascomycota. Basidiomycota and Ascomycota have very low abundance in the rumen of four breeds cattle but anaerobic fungi (AF) Neocallimastigomycota occurred in a high abundance. In Neocallimastigomycota, the dominant genera were Piromyces, Anaeromyces, Cyllamyces, Neocallimastix, and Orpionmyces in four cattle breeds. The composition of the major genera of Neocallimastigaceae varied greatly among the four cattle breeds. The unclassified genera were unequally distributed in gayals, yaks, Tibetan and Yunnan yellow cattle, accounting for 90.63%, 98.52%, 97.79%, and 27.01% respectively. It appears that free-range ruminants have more unknown rumen fungi than domesticated ruminants and the cattle breeds and animal diets had an impact on the diversity of rumen fungi.

Enzymatic reactions in the production of biomethane from organic waste

Enzymatic reactions refer to organic reactions catalyzed by enzymes. This review aims to enrich the documentation relative to enzymatic reactions occurring during the anaerobic degradation of residual organic substances with emphasis on the structures of organic compounds and reaction mechanisms. This allows to understand the displacement of electrons between electron-rich and electron-poor entities to form new bonds in products. The detailed mechanisms of enzymatic reactions relative to the production of biomethane have not yet been reviewed in the scientific literature. Hence, this review is novel and timely since it discusses the chemical behavior or reactivity of different functional groups, thereby allowing to better understand the enzymatic catalysis in the transformations of residual proteins, carbohydrates, and lipids into biomethane and fertilizers. Such understanding allows to improve the overall biomethanation efficiency in industrial applications.

Effects of Piromyces sp. CN6 CGMCC 14449 on fermentation quality, nutrient composition and the in vitro degradation rate of whole crop maize silage

This study investigated the effects of the rumen fungus Piromyces sp. CN6 CGMCC 14449 as a silage additive on the fermentation quality, nutrient composition and in vitro digestibility of whole crop maize silage. Whole crop maize served as the silage material and was vacuum packed in polyethylene bags. Three ensiling treatments were applied: a control (CK), addition of a fungus (FU) at 10⁵ thallus-forming units per gram, and addition of compound enzyme (EN) at 0.033 mg/g (containing cellulase and xylanase at activities of 90 filter paper units and 6000 IU per gram, respectively). Compared with the CK, the FU and EN treatments decreased the pH after 30 days fermentation (P <0.05). Both FU and EN treatments increased the lactate, crude protein, and water-soluble carbohydrate contents (P <0.05), whereas reduced the acetate, ADF and NDF contents as well as the ammonia nitrogen to total nitrogen ratio in silage after 30 days of ensilaging (P <0.05), compared with those for the CK, while no changes were found in the dry matter and dry matter recovery (P > 0.05). The fungal inoculant increased the in vitro digestibility of dry matter, NDF and ADF in silage after 30 days fermentation (P <0.05). In conclusion, the rumen fungus Piromyces sp. CN6 CGMCC 14449 can improve the quality and nutrient composition of whole crop maize silage and increase the crude fibre digestibility.

The effects of fibrolytic enzymes, cellulolytic fungi and bacteria on the fermentation characteristics, structural carbohydrates degradation, and enzymatic conversion yields of Pennisetum sinese silage

Biological inoculants were tested on Pennisetum sinese for their effects on fermentation characteristics, structural carbohydrates degradation, and enzymatic conversion yields. Pennisetum sinese was ensiled without additive, Lactobacillus plantarum (Lp), Trichoderma reesei (Tr), fibrolytic enzymes (E), and Enterococcus faecium (Y83) for 90 days. Y83 silages had higher LA and lower AA, ammonia-N and DM loss as compared to E and Tr silages. Tr and E had superior effects for degrading lignocellulose while Y83 had intermediate effects. The first-order exponential decay models (R² = 0.928-0.998) predicted nonstructural carbohydrates kinetics and demonstrated high water soluble carbohydrate (g/kg DM) preservation potential in Y83 (21.40), followed by Tr (18.94) and E (16.74). Addition of Y83 improved the conversion efficiency of P. sinese silage than Tr and E, indicated by higher glucose and total reducing sugars yield (22.49 and 36.89 w/w % DM, respectively). In conclusion, Y83 can be exploited for the ensiling lignocellulosic biomass before grass processing.

Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A

Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute, Neurospora crassa QDE-3 homolog DNA helicase, Argonaute-interacting protein, and Neurospora crassa QIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lower ldhD transcriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade.

PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities

Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.

Anaerobic Fungi and Their Potential for Biogas Production

Plant biomass is the largest reservoir of environmentally friendly renewable energy on earth. However, the complex and recalcitrant structure of these lignocellulose-rich substrates is a severe limitation for biogas production. Microbial pro-ventricular anaerobic digestion of ruminants can serve as a model for improvement of converting lignocellulosic biomass into energy. Anaerobic fungi are key players in the digestive system of various animals, they produce a plethora of plant carbohydrate hydrolysing enzymes. Combined with the invasive growth of their rhizoid system their contribution to cell wall polysaccharide decomposition may greatly exceed that of bacteria. The cellulolytic arsenal of anaerobic fungi consists of both secreted enzymes, as well as extracellular multi-enzyme complexes called cellulosomes. These complexes are extremely active, can degrade both amorphous and crystalline cellulose and are probably the main reason of cellulolytic efficiency of anaerobic fungi. The synergistic use of mechanical and enzymatic degradation makes anaerobic fungi promising candidates to improve biogas production from recalcitrant biomass. This chapter presents an overview about their biology and their potential for implementation in the biogas process.