The targeting of mcrA or 16S rRNA genes by quantitative PCR (qPCR) has become the dominant method for quantifying methanogens in rumen. There are considerable discrepancies between estimates based on different primer sets, and the literature is equivocal about the relationship with methane production. There are a number of problems with qPCR, including low primer specificity, multiple copies of genes and multiple genomes per cell. Accordingly, we have investigated alternative markers for methanogens, on the basis of the distinctive ether lipids of archaeal cell membranes. The membranes of Archaea contain dialkyl glycerol ethers such as 2,3-diphytanayl-O-sn-glycerol (archaeol), and glycerol dialkyl glycerol tetraethers (GDGTs) such as caldarchaeol (GDGT-0) in different proportions. The relationships between estimates of methanogen abundance using qPCR and archaeol measurements varied across primers. Studies in other ecosystems have identified environmental effects on the profile of ether lipids in Archaea. There is a long history of analysing easily accessible samples, such as faeces, urine and milk, to provide information about digestion and metabolism in livestock without the need for intrusive procedures. Purine derivatives in urine and odd-chain fatty acids in milk have been used to study rumen function. The association between volatile fatty acid proportions and methane production is probably the basis for empirical relationships between milk fatty acid profiles and methane production. However, these studies have not yet identified consistent predictors. We have evaluated the relationship between faecal archaeol concentration and methane production across a range of diets in studies on beef and dairy cattle. Faecal archaeol is diagnostic for ruminant faeces being below the limit of detection in faeces from non-ruminant herbivores. The relationship between faecal archaeol and methane production was significant when comparing treatment means across diets, but appears to be subject to considerable between-animal variation. This variation was also evident in the weak relationship between archaeol concentrations in rumen digesta and faeces. We speculate that variation in the distribution and kinetics of methanogens in the rumen may affect the survival and functioning of Archaea in the rumen and therefore contribute to genetic variation in methane production. Indeed, variation in the relationship between the numbers of micro-organisms present in the rumen and those leaving the rumen may explain variation in relationships between methane production and both milk fatty acid profiles and faecal archaeol. As a result, microbial markers in the faeces and milk are unlikely to relate well back to methanogenesis in the rumen. This work has also highlighted the need to describe methanogen abundance in all rumen fractions and this may explain the difficulty interpreting results on the basis of samples taken using stomach tubes or rumenocentesis.

Nitrous oxide (N2O) is a potent greenhouse gas and the dominant anthropogenic stratospheric ozone-depleting emission. The tropospheric concentration of N2O continues to increase, with animal production systems constituting the largest anthropogenic source. Stable isotopes of nitrogen (N) provide tools for constraining emission sources and, following the temporal dynamics of N2O, providing additional insight and unequivocal proof of N2O source, production pathways and consumption. The potential for using stable isotopes of N is underutilised. The intent of this article is to provide an overview of what these tools are and demonstrate where and how these tools could be applied to advance the mitigation of N2O emissions from animal production systems. Nitrogen inputs and outputs are dominated by fertiliser and excreta, respectively, both of which are substrates for N2O production. These substrates can be labelled with 15N to enable the substrate-N to be traced and linked to N2O emissions. Thus, the effects of changes to animal production systems to reduce feed-N wastage by animals and fertiliser wastage, aimed at N2O mitigation and/or improved animal or economic performance, can be traced. Further 15N-tracer studies are required to fully understand the dynamics and N2O fluxes associated with excreta, and the biological contribution to these fluxes. These data are also essential for the new generation of 15N models. Recent technique developments in isotopomer science along with stable isotope probing using multiple isotopes also offer exciting capability for addressing the N2O mitigation quest.

The Carbon Navigator has been developed to support the objective of reducing the carbon intensity of the dairy and beef sectors of Irish agriculture. The system is designed as a knowledge transfer (KT) tool aimed at supporting the realisation at farm level of the mitigation potential. The objective of this paper is to outline the potential role of KT in reducing greenhouse gas emissions in the context of a growing body of science, which identifies potential mitigation. The EU policy framework for agriculture and the environment is examined in terms of its effectiveness in supporting the reduction in emission intensity of agriculture. The important role for KT in reducing agricultural emissions is highlighted. The Carbon Navigator is introduced as a potential aid to achieving improved adoption of emission-reducing technologies and practices at farm level. The paper outlines the criteria guiding the selection of mitigation technologies in Irish ruminant agriculture, describes the technologies and practices included in the system and outlines the basis for their inclusion. The approach of developing the Carbon Navigator to integrate into existing infrastructure and data systems as well as into the existing KT systems is outlined.

The user inputs to OVERSEER® Nutrient Budgets (Overseer) allow farm-specific greenhouse gas (GHG) emissions to be estimated. Since the development of the original model, life cycle assessment standards (e.g. PAS 2050) have been proposed and adopted for determining GHG or carbon footprints, which are usually reported as emissions per unit of product, for example, per kg milk, meat or wool. New Zealand pastoral farms frequently generate a range of products with different management practices. A robust system is required to allocate the individual sources of GHGs (e.g. methane, nitrous oxide, direct carbon dioxide and embodied carbon dioxide emissions for inputs used on the farm) to each product from a farm. This paper describes a method for allocating emissions to co-products from New Zealand farms. The method requires allocating the emissions, first, to an animal enterprise, separating the emissions between breeding and trading animals, and then allocating to a specific product to give product (e.g. milk, meat, wool, velvet) footprints from the ‘cradle-to-farm-gate’. The meat product was based on live-weight gain. Procedures were adopted so that emissions associated with rearing of young stock used in live-weight gain systems, both as a by-product or a primary product could be estimated. This allows the possibility of total emissions for a meat product to be built up from contributing farms along the production chain.