Hemicellulose-degrading enzymes in rumen ciliate protozoa

Plant cell wall chemistry: implications for ruminant utilisation

Ruminants have adapted to cope with bulky, fibrous forage diets by accommodating a large, diverse microbial population in the reticulo-rumen. Ruminants are dependent on forages as their main sources of energy and other nutrients. Forages are comprised of a complex matrix of cellulose, hemicellulose, protein, minerals and phenolic compounds (including lignin and tannins) with various linkages; many of which are poorly defined. The composition and characteristics of polysaccharides vary greatly among forages and plant cell walls. Plant cell walls are linked and packed together in tight configurations to resist degradation, and hence their nutritional value to animals varies considerably, depending on composition, structure and degradability. An understanding of the inter-relationship between the chemical composition and the degradation of plant cell walls by rumen microorganisms is of major economic importance to ruminant production. Increasing the efficiency of fibre degradation in the rumen has been the subject of extensive research for many decades. This review summarises current knowledge of forage chemistry in order to develop strategies to increase efficiency of forage utilisation by ruminants.

Moderate Coconut Oil Supplement Ameliorates Growth Performance and Ruminal Fermentation in Hainan Black Goat Kids

The study investigated amelioration effects of coconut oil (CO) on growth performance, nutrient digestibility, ruminal fermentation, and blood metabolites in Hainan Black goat kids. Twenty-four Hainan Black goat kids (10 days of age) were assigned randomly to four treatments for 90 days, including pre-weaning (10-70 d of age) and post-weaning (70-100 d of age) days. The treatment regimens were control (CON), low CO (LCO), medium CO (MCO), and high CO (HCO) with 0, 4, 6, 8 g CO per goat per day, respectively. During the pre-weaning period, the average daily gain (ADG) linearly and quadratically increased (P < 0.05), whereas the average daily feed intake (ADFI) linearly decreased, and the feed conversion ratio (FCR) also decreased linearly and quadratically by increasing CO supplementation (P < 0.05). During the post-weaning period, increasing CO supplementation linearly and quadratically increased the BW at 100 days and ADG (P < 0.05), but quadratically decreased the ADFI and FCR (P < 0.05). The digestibility of ether extract (EE) linearly and quadratically increased with increasing CO supplementation (P < 0.05). Supplementation of CO linearly increased ruminal pH (P < 0.05), but linearly decreased (P < 0.05) ammonia-N, total VFAs, molar proportions of acetate, ruminal microbial enzyme activity of carboxymethyl-cellulase, cellobiase, xylanase, pectinase and α-amylase, and number of total protozoa, the abundance of Ruminococcus albus, Ruminococcus flavefaciens, Fibrobacter succinogenes, Butyrivibrio fibrisolvens, Prevotella ruminicola, and Ruminobacter amylophilus. The estimated methane emission decreased linearly and quadratically with increasing CO addition (P < 0.05). The serum concentration of triglycerides (TG), non-esterified fatty acids (NEFA) and growth hormone (GH) linearly (P < 0.05) increased by raising the CO supplementation. The present results indicate that CO supplementation at 6 g/day per goats is optimum due to improved growth performance and decreased estimated methane emission. Supplementation CO up to 8 g/day depressed growth and feed conversion due to its suppression of growth performance, rumen protozoa, cellulolytic bacteria and microbial enzyme activity, and reduced ADF and ADF digestibility.

Rumen Protozoa Play a Significant Role in Fungal Predation and Plant Carbohydrate Breakdown

The rumen protozoa, alongside fungi, comprise the eukaryotic portion of the rumen microbiome. Rumen protozoa may account for up to 50% of biomass, yet their role in this ecosystem remains unclear. Early experiments inferred a role in carbohydrate and protein metabolism, but due to their close association with bacteria, definitively attributing these functions to the protozoa was challenging. The advent of ‘omic technologies has created opportunities to broaden our understanding of the rumen protozoa. This study aimed to utilize these methods to further our understanding of the role that protozoa play in the rumen in terms of their metabolic capacities, and in doing so, contribute valuable sequence data to reduce the chance of mis or under-representation of the rumen protozoa in meta’omic datasets. Rumen protozoa were isolated and purified using glucose-based sedimentation and differential centrifugation, extracted RNA was Poly(A) fraction enriched and DNase treated before use in a phage-based, cDNA metatranscriptomic library. Biochemical activity testing of the phage library showed 6 putatively positive plaques in response to carboxymethyl cellulose agar (indicative of cellulose activity), and no positive results for tributyrin (indicative of esterase/lipase activity) or egg yolk agar (indicative of proteolysis). Direct sequencing of the cDNA was also conducted using the Illumina HiSeq 2500. The metatranscriptome identified a wealth of carbohydrate-active enzymes which accounted for 8% of total reads. The most highly expressed carbohydrate-active enzymes were glycosyl hydrolases 5 and 11, polysaccharide lyases and deacetylases, xylanases and enzymes active against pectin, mannan and chitin; the latter likely used to digest rumen fungi which contain a chitin-rich cell membrane. Codon usage analysis of expressed genes also showed evidence of horizontal gene transfer, suggesting that many of these enzymes were acquired from the rumen bacteria in an evolutionary response to the carbohydrate-rich environment of the rumen. This study provides evidence of the significant contribution that the protozoa make to carbohydrate breakdown in the rumen, potentially using horizontally acquired genes, and highlights their predatory capacity.

Differently Pre-treated Alfalfa Silages Affect the in vitro Ruminal Microbiota Composition

Alfalfa (Medicago sativa L.) silage (AS) is an important feedstuff in ruminant nutrition. However, its high non-protein nitrogen content often leads to poor ruminal nitrogen retention. Various pre-ensiling treatments differing with respect to dry matter concentrations, wilting intensities and sucrose addition have been previously shown to improve the quality and true protein preservation of AS, and have substantial effects on in vitro ruminal fermentation of the resulting silages. However, it is unknown how these pre-ensiling treatments affect the ruminal microbiota composition, and whether alterations in the microbiota explain previously observed differences in ruminal fermentation. Therefore, during AS incubation in a rumen simulation system, liquid and solid phases were sampled 2 and 7 days after first incubating AS, representing an early (ET) and late (LT) time point, respectively. Subsequently, DNA was extracted and qPCR (bacteria, archaea, and anaerobic fungi) and prokaryotic 16S rRNA gene amplicon sequence analyses were performed. At the ET, high dry matter concentration and sucrose addition increased concentrations of archaea in the liquid phase (P = 0.001) and anaerobic fungi in the solid phase (P < 0.001). At the LT, only sucrose addition increased archaeal concentration in the liquid phase (P = 0.014) and anaerobic fungal concentration in the solid phase (P < 0.001). Bacterial concentrations were not affected by pre-ensiling treatments. The prokaryotic phylogenetic diversity index decreased in the liquid phase from ET to LT (P = 0.034), whereas the solid phase was not affected (P = 0.060). This is suggestive of a general adaption of the microbiota to the soluble metabolites released from the incubated AS, particularly regarding the sucrose-treated AS. Redundancy analysis of the sequence data at the genus level indicated that sucrose addition (P = 0.001), time point (P = 0.001), and their interaction (P = 0.001) affected microbial community composition in both phases. In summary, of the pre-ensiling treatments tested sucrose addition had the largest effect on the microbiota, and together with sampling time point affected microbiota composition in both phases of the rumen simulation system. Thus, microbiota composition analysis helped to understand the ruminal fermentation patterns, but could not fully explain them.

Single-cell transcriptome sequencing of rumen ciliates provides insight into their molecular adaptations to the anaerobic and carbohydrate-rich rumen microenvironment

Rumen ciliates are a specialized group of ciliates exclusively found in the anaerobic, carbohydrate-rich rumen microenvironment. However, the molecular and mechanistic basis of the physiological and behavioral adaptation of ciliates to the rumen microenvironment is undefined. We used single-cell transcriptome sequencing to explore the adaptive evolution of three rumen ciliates: two entodiniomorphids, Entodinium furca and Diplodinium dentatum; and one vestibuliferid, Isotricha intestinalis. We found that all three species are members of monophyletic orders within the class Litostomatea, with E. furca and D. dentatum in Entodiniomorphida and I. intestinalis in Vestibuliferida. The two entodiniomorphids might use H₂-producing mitochondria and the vestibuliferid might use anaerobic mitochondria to survive under strictly anaerobic conditions. Moreover, carbohydrate-active enzyme (CAZyme) genes were identified in all three species, including cellulases, hemicellulases, and pectinases. The evidence that all three species have acquired prokaryote-derived genes by horizontal gene transfer (HGT) to digest plant biomass includes a significant enrichment of gene ontology categories such as cell wall macromolecule catabolic process and carbohydrate catabolic process and the identification of genes in common between CAZyme and HGT groups. These findings suggest that HGT might be an important mechanism in the adaptive evolution of ciliates to the rumen microenvironment.

Efeito da inclusão da torta de macaúba na população de protozoários do rúmen de vacas leiteiras

Avaliaram-se os efeitos da inclusão da torta de macaúba (TM) na dieta sobre a concentração e o perfil da população de protozoários ciliados do rúmen. Foram utilizadas oito vacas Holandesas, dispostas em dois quadrados latinos 4x4 e alimentadas com diferentes níveis de inclusão da TM (0, 100, 200 e 300g kg-1 de matéria seca na dieta total). Para quantificação e identificação dos protozoários, amostras de 1mL do líquido ruminal de cada animal foram diluídas em 9mL de solução de formaldeído a 10%. Após diluições decimais sucessivas em solução salina, os protozoários foram quantificados em câmara de Sedgewick. A identificação foi realizada sob a luz da microscopia óptica, utilizando-se a objetiva de 40x para caracterizar o mínimo de 100 indivíduos por amostra. As concentrações de protozoários pequenos (P<0,01), médios (P=0,05), grandes (P=0,01) e o número total (P<0,01) apresentaram comportamento linear decrescente com o aumento dos níveis de inclusão da TM nas dietas. Foram encontradas características morfológicas típicas de 16 gêneros de protozoários ciliados, sendo os gêneros Entodinium e Eodinium os mais frequentes no líquido ruminal dos animais avaliados. O perfil da população de protozoários ciliados sofreu pequenas alterações com a inclusão da TM, sendo observada alteração na participação percentual dos gêneros Charonina (P = 0,03) e Polyplastron (P<0,01). A utilização da TM na dieta de bovinos promove redução na concentração e modificação no perfil da população de protozoários ciliados do rúmen.

Isolation and in vitro cultivation of the fibrolytic rumen ciliate Eremoplastron (Eudiplodinium) dilobum

The rumen ciliate Eremoplastron dilobum was isolated from sheep rumen fluid and cultivated in vitro as a species population. Four different salt solutions were used to prepare the culture media. However, only the "Artificial rumen fluid" composed of (g/L): K2HPO4-3.48, NaHCO3-2.1, NaCl-0.76, CaCl2×6H2O-0.33, CH3COONa-6.12, MgCl2×6H2O-0.3, Na2HPO4-1.71, NaHPO4×H2O-1.01 and distilled water enabled cultivation of this species for over 56 weeks. The protozoa were able to grow in a medium consisting of culture salt solution and powdered meadow hay (0.6mg/ml per d). The addition of wheat gluten did not increase the population density of E. dilobum whereas the supplemented crystalline cellulose and/or barley flour improved the growth of ciliates (P<0.05). The influence of xylan depended on its dose. The enzymatic studies confirmed the fibrolytic and amylolytic abilities of ciliates. Neither the solubility nor the increase of the supplemented dose of purified protein influenced the density of the ciliate population. The recommended food consisted of meadow hay, wheat gluten, crystalline cellulose and barley flour when supplied in the proportions of 0.6, 0.16, 0.12 and 0.12mg/mL per day. We observed morphological variation of the ciliates, involving partial or complete reduction of the caudal lobes.

Activity-based metagenomic screening and biochemical characterization of bovine ruminal protozoan glycoside hydrolases

The rumen, the foregut of herbivorous ruminant animals such as cattle, functions as a bioreactor to process complex plant material. Among the numerous and diverse microbes involved in ruminal digestion are the ruminal protozoans, which are single-celled, ciliated eukaryotic organisms. An activity-based screen was executed to identify genes encoding fibrolytic enzymes present in the metatranscriptome of a bovine ruminal protozoan-enriched cDNA expression library. Of the four novel genes identified, two were characterized in biochemical assays. Our results provide evidence for the effective use of functional metagenomics to retrieve novel enzymes from microbial populations that cannot be maintained in axenic cultures.

The ciliate, Troglodytella abrassarti, contributes to polysaccharide hydrolytic activities in the chimpanzee colon

Entodiniomorphid ciliates are intestinal protists inhabiting the colons of African great apes. The participation of intestinal entodiniomorphid ciliates in ape hindgut digestion has been proposed, but little data have been available to support the hypothesis. We measured the specific activities of carboxymethyl cellulase, xylanase, inulinase, and α-amylase against different polysaccharides in the feces of captive chimpanzees and evaluated the participation of the entodiniomorphid ciliate, Troglodytella abrassarti, in these activities. T. abrassarti contributed to the total fecal hydrolytic activities of CM-cellulase by 16.2%, α-amylase by 5.95%, and xylanase by 0.66%. Inulinase activity in T. abrassarti samples was not measurable at reaction conditions used. The ciliates, T. abrassarti, actively participate in the chimpanzee hindgut fermentation of fiber and starch.

Ruminal methane inhibition potential of various pure compounds in comparison with garlic oil as determined with a rumen simulation technique (Rusitec)

Ruminants represent an important source of methane (CH(4)) emissions; therefore, CH(4) mitigation by diet supplementation is a major goal in the current ruminant research. The objective of the present study was to use a rumen simulation technique to evaluate the CH(4)-mitigating potential of pure compounds in comparison with that achieved with garlic oil, a known anti-methanogenic supplement. A basal diet (15 g DM/d) consisting of ryegrass hay, barley and soyabean meal (1:0·7:0·3) was incubated with the following additives: none (negative control); garlic oil (300 mg/l incubation liquid; positive control); allyl isothiocyanate (75 mg/l); lovastatin (150 mg/l); chenodeoxycholic acid (150 mg/l); 3-azido-propionic acid ethyl ester (APEE, 150 mg/l); levulinic acid (300 mg/l); 4-[(pyridin-2-ylmethyl)-amino]-benzoic acid (PABA, 300 mg/l). Fermentation profiles (SCFA, microbial counts and N turnover) and H(2) and CH(4) formation were determined. Garlic oil, allyl isothiocyanate, lovastatin and the synthetic compound APEE decreased the absolute daily CH(4) formation by 91, 59, 42 and 98 %, respectively. The corresponding declines in CH(4) emitted per mmol of SCFA were 87, 32, 40 and 99 %, respectively, compared with the negative control; the total SCFA concentration was unaffected. Garlic oil decreased protozoal numbers and increased bacterial counts, while chenodeoxycholic acid completely defaunated the incubation liquid. In vitro, neutral-detergent fibre disappearance was lower following chenodeoxycholic acid and PABA treatments (- 26 and - 18 %, respectively). In conclusion, garlic oil and APEE were extremely efficient at mitigating CH(4) without noticeably impairing microbial nutrient fermentation. Other promising substances were allyl isothiocyanate and lovastatin.

Xylanases and carboxymethylcellulases of the rumen protozoaPolyplastron multivesiculatum,Eudiplodinium maggiiandEntodiniumsp

Endoglucanase and xylanase activities of three rumen protozoa, Polyplastron multivesiculatum, Eudiplodinium maggii, and Entodinium sp. were compared qualitatively by zymograms and quantitatively by measuring specific activities against different polysaccharides. A set of carboxymethylcellulases and xylanases was produced by the large ciliates whereas no band of activity was observed for Entodinium sp. in zymograms. Specific activity of endoglucanases from P. multivesiculatum (1.3 micromol mg prot(-1) min(-1)) was twice that of E. maggii, whereas xylanase specific activity (4.5 micromol mg prot(-1) min(-1)) was only half. Very weak activities were observed for Entodinium sp. A new xylanase gene, xyn11D, from P. multivesiculatum was reported and its gene product compared to 33 other family 11 xylanases. Phylogenetic analysis showed that xylanase sequences from rumen protozoa are closely related to those of bacteria.

A xylanase produced by the rumen anaerobic protozoan Polyplastron multivesiculatum shows close sequence similarity to family 11 xylanases from gram-positive bacteria

We report for the first time the cloning and characterisation of a protozoal enzyme involved in plant cell wall polysaccharide degradation. A cDNA library was constructed from the ruminal protozoan Polyplastron multivesiculatum and a stable clone expressing xylanase activity was isolated. The encoded enzyme belongs to the glycoside hydrolase family 11, and phylogenetic analysis indicates a closer relationship with catalytic domains from Gram-positive bacteria than the other fibrolytic eukaryotes from the rumen, the anaerobic fungi.

Molecular cloning, expression, and characterization of an endo-beta-1,4-glucanase cDNA from Epidinium caudatum1

An endo-beta-1,4-glucanase gene (epi3) from the rumen ciliated protozoan Epidinium caudatum was cloned from a cDNA library constructed by using the lambda ZAP II vector. The enzymatic activity of the gene product was detected by the Congo red assay, using carboxymethyl cellulose (CMC) as substrate. The nucleotide sequence of epi3 revealed 1,253 nucleotides with an open reading frame for a protein (Epi3) of 356 amino acids (Mr -41,014). Epi3 shows high homology with family 5 endoglucanase genes and with genes from protozoa isolated from sources other than the rumen. The specific activity of Epi3 produced in Escherichia coli was 5.544, 2.754, and 0.295 mmol of glucose min(-1) mg(-1) protein when the substrates used were CMC, beta-glucan, and xylan, respectively. A beta-1,4-linked trisaccharide of glucose was the preferred substrate of Epi3, as determined by analysis with the p-nitrophenyl form of the substrate. To our knowledge, this is the first report of the isolation of an endoglucanase gene from a rumen protozoan.

Balancing carbohydrates and proteins for optimum rumen microbial yield

Establishing conditions under which rumen fermentation will be optimized requires an understanding of the nutrient requirements of the mixed microbial population. The major nutrients required by rumen microbes are carbohydrates and proteins, but the most suitable sources and quantities needed to support maximum growth have not been determined. Digestion of proteins results in the production of peptides, which can accumulate in the rumen. Peptides are further hydrolyzed to amino acids, some of which are deaminated, producing ammonia. Although peptides, amino acids, and ammonia all may individually serve as sources of N for various microbes, the total population achieves the highest growth rate on mixtures of all three sources. In a somewhat analogous manner, carbohydrates are digested by exoenzymes to oligosaccharides that are available for crossfeeding by the mixed microbial population. Based on data from both in vitro and in vivo studies, there is general agreement that rate of digestion of carbohydrates is the major factor controlling the energy available for microbial growth; in addition, rate of digestion of total carbohydrate is directly related to proportion of starches, pectins, and sugars. Proteins affect both total fermentation and production of microbial DM per unit of carbohydrate fermented. It appears that the quantity of ruminally available protein needed to optimize microbial growth may, under some conditions, be as high as 14 to 15% of diet DM.

Effect of defaunation on protein and fibre digestion in sheep fed on ammonia-treated straw-based diets with or without maize

Using a defaunating method which preserved bacteria and fungi in the rumen, the effect of protozoa on protein and fibre digestion was studied in six adult wethers in relation to the nature of the diet. Sheep were given daily, 42 g dry matter (DM)/kg metabolic body-weight (W0.75), one of two isonitrogenous diets: one contained ammonia-treated wheat straw as the only energy source (diet S) and the other was supplemented with maize grain pellets (diet SM). Mean daily intakes (g/d) of nitrogen, neutral-detergent fibre and acid-detergent fibre were respectively 22, 573 and 373 for diet S and 23, 450 and 334 for diet SM. Elimination of protozoa increased duodenal non-ammonia-nitrogen flow. This result was mainly due to an increase in microbial protein flow and, to a lesser extent, to a higher dietary protein flow. Defaunation markedly increased the efficiency of microbial protein synthesis. Maize-grain supplementation had a net positive effect on this variable in defaunated sheep, but not in faunated sheep. Cell-wall carbohydrates were less well digested in the defaunated rumen, and the negative effect of defaunation was greatest with the diet SM. Intestinal fibre digestion increased in the defaunated sheep especially in those fed on diet SM, but not enough to compensate for the decrease in rumen digestion.