Rumen protozoa are a hub for diverse hydrogenotrophic functions

Ciliate protozoa are an integral part of the rumen microbial community involved in a variety of metabolic processes. These processes are thought to be in part the outcome of interactions with their associated prokaryotic community. For example, methane production is enhanced through interspecies hydrogen transfer between protozoa and archaea. We hypothesize that ciliate protozoa are host to a stable prokaryotic community dictated by specific functions they carry. Here, we modify the microbial community by varying the forage-to-concentrate ratios and show that, despite major changes in the prokaryotic community, several taxa remain stably associated with ciliate protozoa. By quantifying genes belonging to various known reduction pathways in the rumen, we find that the bacterial community associated with protozoa is enriched in genes belonging to hydrogen utilization pathways and that these genes correspond to the same taxonomic affiliations seen enriched in protozoa. Our results show that ciliate protozoa in the rumen may serve as a hub for various hydrogenotrophic functions and a better understanding of the processes driven by different protozoa may unveil the potential role of ciliates in shaping rumen metabolism.

Dynamics of the ruminal microbial ecosystem, and inhibition of methanogenesis and propiogenesis in response to nitrate feeding to Holstein calves

It is known that nitrate inhibits ruminal methanogenesis, mainly through competition with hydrogenotrophic methanogens for available hydrogen (H₂) and also through toxic effects on the methanogens. However, there is limited knowledge about its effects on the others members of ruminal microbiota and their metabolites. In this study, we investigated the effects of dietary nitrate inclusion on enteric methane (CH₄) emission, temporal changes in ruminal microbiota, and fermentation in Holstein calves. Eighteen animals were maintained in individual pens for 45 d. Animals were randomly allocated to either a control (CTR) or nitrate (NIT, containing 15 g of calcium nitrate/kg dry matter) diets. Methane emissions were estimated using the sulfur hexafluoride (SF₆) tracer method. Ruminal microbiota changes and ruminal fermentation were evaluated at 0, 4, and 8 h post-feeding. In this study, feed dry matter intake (DMI) did not differ between dietary treatments (P > 0.05). Diets containing NIT reduced CH₄ emissions by 27% (g/d) and yield by 21% (g/kg DMI) compared to the CTR (P < 0.05). The pH values and total volatile fatty acids (VFA) concentration did not differ between dietary treatments (P > 0.05) but differed with time, and post-feeding (P < 0.05). Increases in the concentrations of ruminal ammonia nitrogen (NH₃–N) and acetate were observed, whereas propionate decreased at 4 h post-feeding with the NIT diet (P < 0.05). Feeding the NIT diet reduced the populations of total bacteria, total methanogens, Ruminococcus albus and Ruminococcus flavefaciens, and the abundance of Succiniclasticum, Coprococcus, Treponema, Shuttlewortia, Succinivibrio, Sharpea, Pseudobutyrivibrio, and Selenomona (P < 0.05); whereas, the population of total fungi, protozoa, Fibrobacter succinogenes, Atopobium and Erysipelotrichaceae L7A_E11 increased (P < 0.05). In conclusion, feeding nitrate reduces enteric CH₄ emissions and the methanogens population, whereas it decreases the propionate concentration and the abundance of bacteria involved in the succinate and acrylate pathways. Despite the altered fermentation profile and ruminal microbiota, DMI was not influenced by dietary nitrate. These findings suggest that nitrate has a predominantly direct effect on the reduction of methanogenesis and propionate synthesis.

Inhibition of methanogenesis by nitrate, with or without defaunation, in continuous culture

Within the rumen, nitrate can serve as an alternative sink for aqueous hydrogen [H₂(aq)] accumulating during fermentation, producing nitrite, which ideally is further reduced to ammonium but can accumulate under conditions not yet explained. Defaunation has also been associated with decreased methanogenesis in meta-analyses because protozoa contribute significantly to H₂ production. In the present study, we applied a 2 × 2 factorial treatment arrangement in a 4 × 4 Latin square design to dual-flow continuous culture fermentors (n = 4). Treatments were control without nitrate (-NO₃^-) versus with nitrate (+NO₃^-; 1.5% of diet dry matter), factorialized with normal protozoa (faunated, FAUN) versus defaunation (DEF) by decreasing the temperature moderately and changing filters over the first 4 d of incubation. We detected no main effects of DEF or interaction of faunation status with +NO₃^-. The main effect of +NO₃^- increased H₂(aq) by 11.0 µM (+117%) compared with -NO₃^-. The main effect of +NO₃^- also decreased daily CH₄ production by 8.17 mmol CH₄/d (31%) compared with -NO₃^-. Because there were no treatment effects on neutral detergent fiber digestibility, the main effect of +NO₃^- also decreased CH₄ production by 1.43 mmol of CH₄/g of neutral detergent fiber degraded compared with -NO₃^-. There were no effects of treatment on other nutrient digestibilities, N flow, or microbial N flow per gram of nutrient digested. The spike in H₂(aq) after feeding NO₃^- provides evidence that methanogenesis is inhibited by substrate access rather than concentration, regardless of defaunation, or by direct inhibition of NO₂^-. Methanogens were not decreased by defaunation, suggesting a compensatory increase in non-protozoa-associated methanogens or an insignificant contribution of protozoa-associated methanogens. Despite adaptive reduction of NO₃^- to NH₄⁺ and methane inhibition in continuous culture, practical considerations such as potential to depress dry matter intake and on-farm ration variability should be addressed before considering NO₃^- as an avenue for greater sustainability of greenhouse gas emissions in US dairy production.

Dietary nitrate and presence of protozoa increase nitrate and nitrite reduction in the rumen of sheep

Nitrate ( NO 3 - ) supplementation is an effective methane (CH₄ ) mitigation strategy for ruminants but may produce nitrite ( NO 2 - ) toxicity. It has been reported that rumen protozoa have greater ability for NO 3 - and NO 2 - reduction than bacteria. It was hypothesised that the absence of ruminal protozoa in sheep may lead to higher NO 2 - accumulation in the rumen and a higher blood methaemoglobin (MetHb) concentration. An in vivo experiment was conducted with defaunated (DEF) and faunated (FAU) sheep supplemented with 1.8% NO 3 - in DM. The effects of rumen protozoa on concentrations of plasma and ruminal NO 3 - and NO 2 - , blood MetHb, ruminal volatile fatty acid (VFA) and ruminal ammonia (NH₃ ) were investigated. Subsequently, two in vitro experiments were conducted to determine the contribution of protozoa to NO 3 - and NO 2 - reduction rates in DEF and FAU whole rumen digesta (WRD) and its liquid (LIQ) and solid (SOL) fractions, incubated alone (CON), with the addition of NO 3 - or with the addition of NO 2 - . The results from the in vivo experiment showed no differences in total VFA concentrations, although ruminal NH₃ was greater (p < .01) in FAU sheep. Ruminal NO 3 - , NO 2 - and plasma NO 2 - concentrations tended to increase (p < .10) 1.5 hr after feeding in FAU relative to DEF sheep. In vitro results showed that NO 3 - reduction to NH₃ was stimulated (p < .01) by incoming NO 3 - in both DEF and FAU relative to CON digesta. However, adding NO 3 - increased (p < .05) the rate of NO 2 - accumulation in the SOL fraction of DEF relative to both fractions of FAU digesta. Results observed in vivo and in vitro suggest that NO 3 - and NO 2 - are more rapidly metabolised in the presence of rumen protozoa. Defaunated sheep may have an increased risk of NO 2 - poisoning due to NO 2 - accumulation in the rumen.

Extending Burk Dehority's Perspectives on the Role of Ciliate Protozoa in the Rumen

Dr. Burk Dehority was an international expert on the classification and monoculture of ruminal ciliated protozoa. We have summarized many of the advancements in knowledge from his work but also in his scientific way of thinking about interactions of ruminal ciliates with the entire rumen microbial community and animal host. As a dedication to his legacy, an electronic library of high-resolution images and video footage catalogs numerous species and techniques involved in taxonomy, isolation, culture, and ecological assessment of ruminal ciliate species and communities. Considerable promise remains to adapt these landmark approaches to harness eukaryotic cell signaling technology with genomics and transcriptomics to assess cellular mechanisms regulating growth and responsiveness to ruminal environmental conditions. These technologies can be adapted to study how protozoa interact (both antagonism and mutualism) within the entire ruminal microbiota. Thus, advancements and limitations in approaches used are highlighted such that future research questions can be posed to study rumen protozoal contribution to ruminant nutrition and productivity.

Potential roles of nitrate and live yeast culture in suppressing methane emission and influencing ruminal fermentation, digestibility, and milk production in lactating Jersey cows

Concern over the carbon footprint of the dairy industry has led to various dietary approaches to mitigate enteric CH₄ production. One approach is feeding the electron acceptor NO₃^-, thus outcompeting methanogens for aqueous H₂. We hypothesized that a live yeast culture (LYC; Saccharomyces cerevisiae from Yea-Sacc 1026, Alltech Inc., Nicholasville, KY) would stimulate the complete reduction of NO₃^- to NH₃ by selenomonads, thus decreasing the quantity of CH₄ emissions per unit of energy-corrected milk production while decreasing blood methemoglobin concentration resulting from the absorbed intermediate, NO₂^-. Twelve lactating Jersey cows (8 multiparous and noncannulated; 4 primiparous and ruminally cannulated) were used in a replicated 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments. Cattle were fed diets containing 1.5% NO₃^- (from calcium ammonium nitrate) or an isonitrogenous control diet (containing additional urea) and given a top-dress of ground corn without or with LYC, with the fourth week used for data collection. Noncannulated cows were spot measured for CH₄ emission by mouth using GreenFeed (C-Lock Inc., Rapid City, SD). The main effect of NO₃^- decreased CH₄ by 17% but decreased dry matter intake by 10% (from 19.8 to 17.8 kg/d) such that CH₄:dry matter intake numerically decreased by 8% and CH₄:milk net energy for lactation production was unaffected by treatment. Milk and milk fat production were not affected, but NO₃^- decreased milk protein from 758 to 689 g/d. Ruminal pH decreased more sharply after feeding for cows fed diets without NO₃^-. Acetate:propionate was greater for cows fed NO₃^-, particularly when combined with LYC (interaction effect). Blood methemoglobin was higher for cattle fed NO₃^- than for those fed the control diet but was low for both treatments (1.5 vs. 0.5%, respectively; only one measurement exceeded 5%), indicating minimal risk for NO₂^- accumulation at our feeding level of NO₃^-. Although neither apparent organic matter nor neutral detergent fiber digestibilities were affected, apparent N digestibility had an interaction for NO₃^- × LYC such that apparent N digestibility was numerically lowest for diets containing both NO₃^- and LYC compared with the other 3 diets. Under the conditions of this study, NO₃^- mitigated ruminal methanogenesis but also depressed dry matter intake and milk protein yield. Based on the fact that few interactions were detected, LYC had a minimal role in attenuating negative cow responses to NO₃^- supplementation.

Rumen microbial responses to supplemental nitrate. II. Potential interactions with live yeast culture on the prokaryotic community and methanogenesis in continuous culture

Nitrates have been fed to ruminants, including dairy cows, as an electron sink to mitigate CH₄ emissions. In the NO₃^- reduction process, NO₂^- can accumulate, which could directly inhibit methanogens and possibly other microbes in the rumen. Saccharomyces cerevisiae yeast was hypothesized to decrease NO₂^- through direct reduction or indirectly by stimulating the bacterium Selenomonas ruminantium, which is among the ruminal bacteria most well characterized to reduce both NO₃^- and NO₂^-. Ruminal fluid was incubated in continuous cultures fed diets without or with NaNO₃ (1.5% of diet dry matter; i.e., 1.09% NO₃^-) and without or with live yeast culture (LYC) fed at a recommended 0.010 g/d (scaled from cattle to fermentor intakes) in a 2 × 2 factorial arrangement of treatments. Treatments with LYC had increased NDF digestibility and acetate:propionate by increasing acetate molar proportion but tended to decrease total VFA production. The main effect of NO₃^- increased acetate:propionate by increasing acetate molar proportion; NO₃^- also decreased molar proportions of isobutyrate and butyrate. Both NO₃^- and LYC shifted bacterial community composition (based on relative sequence abundance of 16S rRNA genes). An interaction occurred such that NO₃^- decreased valerate molar proportion only when no LYC was added. Nitrate decreased daily CH₄ emissions by 29%. However, treatment × time interactions were present for both CH₄ and H₂ emission from the headspace; CH₄ was decreased by the main effect of NO₃^- until 6 h postfeeding, but NO₃^- and LYC decreased H₂ emission up to 4 h postfeeding. As expected, NO₃^- decreased methane emissions in continuous cultures; however, contrary to expectations, LYC did not attenuate NO₂^- accumulation.