Contribution of rumen protozoa to fibre degradation and cellulase activity in vitro

Feeding an unsalable carrot total-mixed ration altered bacterial amino acid degradation in the rumen of lambs

The objective of this study was to determine the influence of a total-mixed ration including unsalable carrots at 45% DM on the rumen microbiome; and the plasma, rumen and liver metabolomes. Carrots discarded at processing were investigated as an energy-dense substitute for barley grain in a conventional feedlot diet, and improved feed conversion efficiency by 25%. Here, rumen fluid was collected from 34 Merino lambs at slaughter (n = 16 control; n = 18 carrot) after a feeding period of 11-weeks. The V4 region of the 16S rRNA gene was sequenced to profile archaeal and bacterial microbe communities. Further, a comprehensive, targeted profile of known metabolites was constructed for blood plasma, rumen fluid and biopsied liver metabolites using a gas chromatography mass spectrometry (GC-MS) metabolomics approach. An in vitro batch culture was used to characterise ruminal fermentation including gas and methane (CH₄) production. In vivo rumen microbial community structure of carrot fed lambs was dissimilar (P < 0.01; PERMANOVA), and all measures of alpha diversity were greater (P < 0.01), compared to those fed the control diet. Unclassified genera in Bacteroidales (15.9 ± 6.74% relative abundance; RA) were more abundant (P < 0.01) in the rumen fluid of carrot-fed lambs, while unclassified taxa in the Succinivibrionaceae family (11.1 ± 3.85% RA) were greater (P < 0.01) in the control. The carrot diet improved in vitro ruminal fermentation evidenced as an 8% increase (P < 0.01) in DM digestibility and a 13.8% reduction (P = 0.01) in CH₄ on a mg/ g DM basis, while the control diet increased (P = 0.04) percentage of propionate within total VFA by 20%. Fourteen rumen fluid metabolites and 27 liver metabolites were influenced (P ≤ 0.05) by diet, while no effect (P ≥ 0.05) was observed in plasma metabolites. The carrot diet enriched (impact value = 0.13; P = 0.01) the tyrosine metabolism pathway (acetoacetic acid, dopamine and pyruvate), while the control diet enriched (impact value = 0.42; P ≤ 0.02) starch and sucrose metabolism (trehalose and glucose) in rumen fluid. This study demonstrated that feeding 45% DM unsalable carrots diversified bacterial communities in the rumen. These dietary changes influenced pathways of tyrosine degradation, such that previous improvements in feed conversion efficiency in lambs could be explained.

Design and validation of four new primers for next-generation sequencing to target the 18S rRNA genes of gastrointestinal ciliate protozoa

Four new primers and one published primer were used to PCR amplify hypervariable regions within the protozoal 18S rRNA gene to determine which primer pair provided the best identification and statistical analysis. PCR amplicons of 394 to 498 bases were generated from three primer sets, sequenced using Roche 454 pyrosequencing with Titanium, and analyzed using the BLAST database (NCBI) and MOTHUR version 1.29. The protozoal diversity of rumen contents from moose in Alaska was assessed. In the present study, primer set 1, P-SSU-316F and GIC758R (amplicon of 482 bases), gave the best representation of diversity using BLAST classification, and the set amplified Entodinium simplex and Ostracodinium spp., which were not amplified by the other two primer sets. Primer set 2, GIC1080F and GIC1578R (amplicon of 498 bases), had similar BLAST results and a slightly higher percentage of sequences that were identified with a higher sequence identity. Primer sets 1 and 2 are recommended for use in ruminants. However, primer set 1 may be inadequate to determine protozoal diversity in nonruminants. The amplicons created by primer set 1 were indistinguishable for certain species within the genera Bandia, Blepharocorys, Polycosta, and Tetratoxum and between Hemiprorodon gymnoprosthium and Prorodonopsis coli, none of which are normally found in the rumen.

Microbial ecology of anaerobic digesters: the key players of anaerobiosis

Anaerobic digestion is the method of wastes treatment aimed at a reduction of their hazardous effects on the biosphere. The mutualistic behavior of various anaerobic microorganisms results in the decomposition of complex organic substances into simple, chemically stabilized compounds, mainly methane and CO₂. The conversions of complex organic compounds to CH₄ and CO₂ are possible due to the cooperation of four different groups of microorganisms, that is, fermentative, syntrophic, acetogenic, and methanogenic bacteria. Microbes adopt various pathways to evade from the unfavorable conditions in the anaerobic digester like competition between sulfate reducing bacteria (SRB) and methane forming bacteria for the same substrate. Methanosarcina are able to use both acetoclastic and hydrogenotrophic pathways for methane production. This review highlights the cellulosic microorganisms, structure of cellulose, inoculum to substrate ratio, and source of inoculum and its effect on methanogenesis. The molecular techniques such as DGGE (denaturing gradient gel electrophoresis) utilized for dynamic changes in microbial communities and FISH (fluorescent in situ hybridization) that deal with taxonomy and interaction and distribution of tropic groups used are also discussed.

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.

Effect of biomass concentration and inoculum source on the rate of anaerobic cellulose solubilization

This study determines cellulose solubilization kinetics from controlled batch digestions and shows the effect of inoculum biomass concentrations. Separate measurements and analyzes were performed for sessile biomass (biofilms) and planktonic biomass (free suspensions). Experiments were conducted using either leachate enriched on cellulose or rumen fluid as inoculum to assess if the effect of biomass concentration was consistent for microbial populations from different source environments. All batch digestions were fitted to a first-order kinetic model (R(2) ranging from 0.94 to 0.99). Regression analysis used to compare the first-order hydrolysis rate showed that the first-order hydrolysis rate was most strongly correlated with the concentration of sessile biomass rather than with the concentration of total or planktonic biomass. The correlation between solubilization rate and sessile biomass was statistically the same for the rumen and leachate inoculated reactors indicating that at low concentration ratios of inoculum to cellulose, the rate of cellulose solubilization is dependant primarily on sessile biomass concentration rather than the species profile of the cellulolytic community.

The effect of biomass density on cellulose solubilisation rates

The aim of this work was to compare the impact of inoculation density on the rate of cellulose hydrolysis by a rumen derived culture with that of a microbial enrichment from an organic waste anaerobic digester. The results showed a linear relationship between the mass of biomass at the start of the first order degradation phase (Xo) and the first order hydrolysis rate (r) for both rumen inoculated and leachate inoculated cellulose digestions and that the slopes of these relationships were not distinguishable. This suggested that differences in the microbial community, media and other environmental factors had a lesser impact on the hydrolysis rate compared to the effect of the number of cells in the system. This could be of great importance to industrial applications of anaerobic digestion technologies as it suggested that if cells densities in the waste treatment digesters could be boosted to match those seen in the rumen, then the rates of the cellulose hydrolysis would rise.

Simulation of the effects of diet on the contribution of rumen protozoa to degradation of fibre in the rumen

A previously described mathematical model, that stimulates the metabolic activities of rumen bacteria and protozoa, was used to examine the contribution of protozoa to neutral-detergent fibre (NDF) degradation in the rumen of cattle. Comparisons between predicted and experimentally observed NDF degradation showed general agreement. Further simulations were performed with diets containing variable proportions of concentrate (between 0 and 1 kg/kg diet DM) and at intake levels ranging between 5.3 and 21.0 kg DM/d. The simulated protozoal contribution to NDF degradation was 17-21% at the lowest intake level. Except for the all-concentrate diets, raising the feed intake level reduced this contribution to 5-13% at the highest intake level. The changes in contribution of protozoa to NDF degradation were related to variations in the fibrolytic bacteria: protozoa value and the NDF-degrading activities of protozoa predicted by the model. In simulations where dietary NDF levels were reduced and starch and sugar levels were increased independently, protozoal contribution to NDF degradation generally increased. These differences were reflected also in the generally increased protozoal contribution to NDF degradation predicted in response to a decreased roughage:concentrate value. The contribution of protozoa also generally declined in response to added N. These changes in predicted protozoal contribution to NDF degradation resulting from dietary variations provided possible explanations for the differences in rumen NDF degradation observed when animals are defaunated.

Effect of ciliate protozoa on the activity of polysaccharide-degrading enzymes and fibre breakdown in the rumen ecosystem

The effect of ciliate protozoa on the activity of polysaccharide-degrading enzymes in microbial populations from the digesta solids and liquor fractions of rumen contents was examined after the refaunation of ciliate-free sheep with an A-type rumen protozoal population. Although the culturable rumen bacterial population was reduced after refaunation the number of fibrolytic micro-organisms detected was higher; the xylanolytic bacterial population and numbers of fungal zoospores were increased after refaunation. The proportion of propionic acid was lower in the refaunated animals, whereas the concentration of ammonia and the acidic metabolites acetate, butyrate and valerate were all increased. The range of enzyme activities present in the digesta subpopulations were the same in defaunated and refaunated animals. The activities of the polysaccharide-degrading enzymes, however, were increased in the microbial populations associated with the digesta solids after refaunation, and at 16 h after feeding the activities were 4-8 times (beta-D-xylosidase 20 times) higher than the levels detected in the adherent population from defaunated sheep. The protozoa, either directly through their own enzymes or indirectly as a consequence of their effects on the population size and activity of the other fibrolytic micro-organisms present, have an important role in determining the level of activity of polysaccharide-degrading enzymes in the rumen ecosystem. Although the extent of ryegrass (Lolium perenne) hay digestion was similar after 24 h in the absence or presence of protozoa, the initial ruminal degradation was higher in refaunated sheep.