Feeding to increase productivity and reduce greenhouse gas emissions

Methane is a by-product in the digestion of plant material by all cattle and sheep. Effectively it is wasted feed material and energy that could otherwise be available for animal production. It is also a major greenhouse gas (14% of Australia’s emissions). Beef cattle contribute 50% of these emissions. Feed materials containing lipid can reduce methane and increase productivity. We evaluated coconut and cottonseed oil containing feed supplements both in the laboratory and as feed supplements for beef cattle. Both supplements increased liveweight gain (up to 20-30 kg) over a 7 week period. There was no overall increase in methane emissions per head but a substantial decrease in methane emitted per unit of production. We recommended the use of coconut and cottonseed additives, with oil content up to 6%, to increase liveweight gain in cattle and decrease methane per kilogram of average daily gain

Enhancing digestibility of native pastures by cattle using kangaroo fibrolytic bacteria

This project investigated whether plant fibrolytic bacteria from the kangaroo gut could establish stable populations in cattle and improve digestion of native pastures. Four fibrolytic bacterial isolates were evaluated. All except one species failed to persist when introduced to a rumen-based fermentation in vitro and unfortunately all rapidly disappeared when inoculated into the rumen of rumen cannulated cattle. Analysis of kangaroo forestomach contents from 42 kangaroos indicated that the fibrolytic bacteria that had been evaluated were unlikely to be the dominant fibrolytic species in vivo, suggesting a culture-based bias towards these fibrolytic species. Culture-independent, DNA-based techniques have now provided a more accurate picture of the dominant fibrolytic community in the kangaroo gut. However, additional research would be required to isolate, characterise and assess the ability of these fibrolytic bacteria to colonise the rumen and improve the digestion of native pastures

Using kangaroo bacteria to reduce emissions of methane and increase productivity

This project investigated the roles of reductive acetogenesis and methanogenesis in the foregut of kangaroos to determine whether, in the future, reductive acetogenesis could be used to reduce methane emissions from sheep and cattle and increase productivity. It was reaffirmed that most kangaroos don’t generate methane and shown that when methanogenesis is inhibited reductive acetogens can survive in a rumen-like environment. The reductive acetogens in culture represent a fraction of the diversity present and there are unusual archaea, whose role is still to be defined, associated with kangaroos. Further research is recommended, if the pivotal mechanisms and the microbes involved in reductive acetogenesis in kangaroos could be determined and understood, it is possible that methane emissions from cattle and sheep could be markedly reduced and productivity and profitability increased

Methanotrophs from natural ecosystems as biocontrol agents for ruminant methane emissions

In ruminant cattle, the anaerobic fermentation of ingested plant biomass results in the production of methane (CH4). This CH4 is subsequently eructated to the environment, where it acts as a potent greenhouse gas and is one of the leading sources of anthropogenic CH4 in Australia. Methane oxidising microorganisms are an important environmental sink for CH4; however the possibility that methanotrophs are native to the rumen has received little attention. This project aimed to characterise methanotrophs from a range of environments, and to subsequently determine the metabolic activity of these microorganisms under in vitro rumen-like conditions. This study is the first to characterise rumen methanotrophs using molecular methodology. Using a combination of denaturing gradient gel electrophoresis and phylogenetic analysis, it was found that simple communities of Proteobacterial methanotrophs can be native residents of the rumen microbial community in grain-fed Bos indicus steers. A putative methanotrophic Gamma-proteobacterial Methylobacter species was also enriched from grain-fed whole rumen contents using novel techniques. However, the activity of these organisms in situ remains to be fully understood. Furthermore, the possibility that a grain-based dietary affect influences the diversity and activity of methanotrophs in situ is intriguing. Future work to address these questions is necessary to evaluate the potential for methanotrophs to act as biocontrol agents for ruminant CH4 emissions.

Rumen bacterial diversity with and without mulga (Acacia aneura) tannins

Feral goats are able to survive in many semi-arid areas of Australia. Under drought conditions, the only form of available feed is often mulga, which has a very high content of condensed tannins (5-24% dry weight). While feral goats apparently thrive on this diet, sheep do very poorly and lose liveweight rapidly. It has been shown that the transfer of rumen contents from feral goats to sheep can significantly improve mulga digestion, suggesting that the ruminal microflora of feral goats may contain tannin tolerant or degrading bacteria. To identify likely communities or associations of bacteria that may undertake this task, a comparative study of the bacterial ecology of the rumens of feral goats fed mulga and sheep fed either mulga or grass was undertaken. This study used the culture independent techniques of generation of 16S rDNA clone libraries and fluorescence in situ hybridisation (FISH) probing. From the clone libraries, bacteria were mainly (>90%) within the divisions Cytophaga-Flexibacter-Bacteroides (CFB) and low mol% G+C Gram positive bacteria (LGCGPB). In animals fed mulga, the CFB predominated (goat - 82% CFB and 11% LGCGPB; sheep - 78% CFB and 21% LGCGPB) whereas in sheep fed grass, the LGCGPB predominated (25% CFB vs 74% LGCGPB). In all clone libraries, few bacterial species were closely related to previously cultured bacteria, making it difficult to assign phenotypic traits. FISH probing of mulga fed -rumen (feral goats and sheep) or -fermentor samples demonstrated a predominance of CFB and gamma proteobacteria. This first molecular ecological study of tannin associated microbial communities suggested that bacteria from these two groups may be either more tolerant to tannins or able to degrade tannins. Further work will be required to elucidate the important members of these groups and to obtain them in culture

Archaeaphage therapy to control rumen methanogens

Phage therapy is becoming increasingly important as a means of eradicating or controlling microbial populations and has been raised as a potential strategy to reduce methane emissions from ruminants. To date, very little is currently known about phages which may infect the methane-producing archaeal strains (methanogens) dominant within the rumen of Australian cattle, such as the Methanobrevibacter ruminantium. This project aimed to assemble a collection of phages to be employed in phage therapy. A range of animal-derived and environmental source samples were tested using culture-based methodology, however no lytic phages of methanogens were isolated. Given the dearth of knowledge regarding phages of rumen methanogens, this project established that these naturally-occurring phages may be present in very low concentrations within the rumen and this will need to be considered in future methanogen-phage isolation investigations. The project has begun the process of developing and adapting new methodologies for detecting and examining these phages

Increasing productivity and reducing methane emissions by supplementing feed with dietary lipids

Methane (CH4) is a by-product in the digestion of plant material by all cattle and sheep. Effectively it is wasted feed material and energy that could otherwise be available for animal production. It is also a major greenhouse gas (14% of Australia’s emissions). Beef cattle contribute 50% of these emissions. Many lipid containing feed materials are known to reduce methane emissions, as well as increasing productivity when used as supplementary feeds. The purpose of this project is to investigate the impact of lipid containing feed additives on the suppression of methane emissions and improvements in the growth rate of steers fed a basal diet of tropical pastures

Bacteriophages in the rumen: types present, population size and implications for the efficiency of feed utilisation

One cause of a reduction in the efficiency of feed utilisation in the rumen is the non-specific lysis of bacteria within the rumen and subsequent fermentation of the bacterial protoplasm. Bacteriophages are implicated in this lysis, are obligate pathogens of bacteria and occur in dense populations in the rumen. Large numbers are present (up to lo*’ per millilitre of fluid) in the rumen. These viruses are morphologically diverse with 26 distinct types from three viral families (Myoviridae, Siphoviridae and Podoviridae) being represented. The use of the DNA-based methodology, Pulsed Field Gel Electrophoresis, has allowed an estimate of phage numbers in the rumen at a point in time. This procedure will enable investigations of changes in the phage population in relation to changing dietary regimes. Preliminary evidence suggests that diet may influence viral activity and therefore dietary manipulation could, in the future, be used to reduce viral activity and improve the flow of microbial protein to the intestines

Ammonia-hyperproducing bacteria from New Zealand ruminants

Pasture-grazed dairy cows, deer, and sheep were tested for the presence of ammonia-hyperproducing (HAP) bacteria in roll tubes containing a medium in which tryptone and Casamino Acids were the sole nitrogen and energy sources. Colonies able to grow on this medium represented 5.2, 1.3, and 11.6% of the total bacterial counts of dairy cows, deer, and sheep, respectively. A total of 14 morphologically distinct colonies were purified and studied further. Restriction fragment length polymorphisms of 16S rRNA genes indicated that all isolates differed from the previously described HAP bacteria,Clostridium aminophilum, Clostridium sticklandii, and Peptostreptococcus anaerobius. Carbon source utilization experiments showed that five isolates (C2, D1, D4, D5, and S1) were unable to use any, or very few, of the carbon sources tested. Biochemical tests and phylogenetic analyses of 16S ribosomal DNA sequences indicated that all isolates were monensin sensitive; that D1 and S1 belonged to the genusPeptostreptococcus, that D4 and D5 belonged to the familyBacteroidaceae, where D4 was similar to Fusobacterium necrophorum; and that C2 was most similar to an unidentified species from the genus Eubacterium. Growth on liquid medium containing tryptone and Casamino Acids as the sole nitrogen and energy source showed that D1, D4, and S1 grew rapidly (specific growth rates of 0.40, 0.35, and 0.29 h−1, respectively), while C2 and D5 were slow growers (0.25 and 0.10 h−1, respectively). Ammonia production rates were highest in D1 and D4, which produced 945.5 and 748.3 nmol/min per mg of protein, respectively. Tests of individual nitrogen sources indicated that D1 and D4 grew best on tryptone, S1 grew equally well on Casamino Acids or tryptone, and C2 and D5 grew poorly on all nitrogen sources. The intact proteins casein and gelatin did not support significant growth of any of the isolates. These isolates extend the diversity of known HAP rumen bacteria and indicate the presence of significant HAP bacterial populations in pasture-grazed New Zealand ruminants

Effects of adsorbents and probiotics in mitigating simplexin poisoning effects in cattle fed Pimelea

Pimelea poisoning of cattle occurs only in arid inland Australia and is caused by the toxin, simplexin found in some native Pimelea plant species. Pimelea-affected cattle show distinctive physical symptoms including subcutaneous oedema under the jaw and brisket, diarrhoea and anaemia. Simplexin was thought to be circulated in the bloodstream to exert its toxic effect, but due to its hydrophobic nature the extent of its blood carriage is unknown. Fletcher et al. (2014) postulated a possible role of rumen microorganisms adapting to detoxify simplexin in cattle fed Pimelea over a prolonged period of time. Anecdotal reports have suggested cattle supplemented with biochar and bentonite showed resistance towards Pimelea poisoning. In this project, a pen trial (QAFFI/QASP/337/20/DAF) was conducted to determine the efficacy of adsorbents (biochar and bentonite) and a bacterial inoculum for reducing the effects of Pimelea poisoning in steers