Dehydration can be extremely damaging to the performance and welfare of indigenous chickens. The effect of water restriction on haematological and biochemical parameters was compared in Naked Neck (NNK) and Ovambo (OVB) chickens. A total of 54 8-week-old pullets each of NNK and OVB chickens with an initial average weight of 641 ± 10 g/bird were randomly assigned to three water intake treatments with three replications, each having six birds. The water restriction treatments were ad libitum, 70% and 40% of ad libitum intake. Nine experimental pens with a floor space of 3.3 m2 per strain were used. Feed was provided ad libitum. Packed cell volume (PCV), erythrocyte count (RBC), mean corpuscular volume (MCV) and total leucocyte count (WBC), and biochemical parameters (uric acid (UA)), creatinine (CREAT), total protein (TP), albumin (ALB), globulin (GLOB), triglyceride (TGA), total cholesterol (TC), high- (HDLC) and low- (LDLC) density lipoprotein cholesterol and activity of alanine transaminase (ALT), alkaline phosphatase (ALP) and aspartate transaminase (AST) were determined from blood collected after 60 days of water restriction. PCV was higher (P < 0.05) in NNK than OVB chickens offered water ad libitum, but similar in birds offered 70% and 40% of ad libitum. There were no differences in RBC and MCV values between strains, but MCV was higher in birds on 40% than 70% of ad libitum water intake, irrespective of strain. Naked neck chickens had higher (P < 0.05) WBC values than OVB at 40% restriction level, but lower WBC than OVB at 70% water restriction level. UA, CREAT, TGA, TC, LDLC, TP and GLOB increased (P < 0.05) with each increment in water restriction, but the increase in CREAT and TC was more pronounced in OVB than NNK chickens. The opposite was observed for UA. ALT activity indicated that liver function was not affected by water restriction. It was concluded that the two strains can withstand up to 40% of ad libitum water restriction, but NNK tolerated water stress better than OVB chickens.

The mapping of complete sets of genes, transcripts and proteins from many organisms has prompted the development of new ‘-omic’ technologies for collecting and analysing very large amounts of data. Now that the tools to generate and interrogate such complete data sets are widely used, much of the focus of biological research has begun to turn towards understanding systems as a whole, rather than studying their components in isolation. This very broadly defined systems approach is being deployed across a range of problems and scales of organisation, including many aspects of the animal sciences. Here I review selected examples of this systems approach as applied to poultry and livestock production, product quality and welfare.

Dietary melatonin supplementation during mid- to late-gestation increased umbilical artery blood flow and caused disproportionate fetal growth. This melatonin-induced increase in umbilical artery blood flow may alter nutrient availability to the fetus, which may lead to alterations in fetal size. The objectives of the current experiment were to determine amino acid (AA) and glucose concentrations as well as AA and glucose flux across the uteroplacenta using a mid- to late-gestation model of intrauterine growth restriction supplemented with dietary melatonin as a 2 × 2 factorial design. At day 50 of gestation, 32 ewes were supplemented with 5 mg of melatonin (MEL) or no melatonin (CON) and were allocated to receive 100% (adequate; ADQ) or 60% (restricted; RES) of nutrient requirements. On day 130 of gestation, uterine and umbilical blood flows were determined via Doppler ultrasonography during a non-survival surgery. Blood samples were collected under general anesthesia from the maternal saphenous artery, gravid uterine vein, umbilical artery, and umbilical vein for AA analysis and glucose. Total α-AA concentrations in maternal artery and gravid uterine vein were decreased (P < 0.05) in RES v. ADQ fed ewes. Maternal arterial − venous difference in total α-AA was increased (P ⩽ 0.01) in RES v. ADQ fed ewes, while total uterine α-AA flux was not different (P > 0.40) across all treatment groups. Fetal venous − arterial difference in total α-AA as well as uteroplacental flux of total α-AA were decreased (P < 0.05) in CON-RES v. CON-ADQ, and similar (P > 0.20) in MEL-RES v. CON-ADQ. Maternal concentrations and uterine flux of branched-chain AA (BCAA) were not different across all treatment groups; however, fetal uptake of BCAA was decreased (P < 0.05) in CON-RES v. CON-ADQ, and similar (P > 0.20) in MEL-RES v. CON-ADQ. Uterine uptake of glucose was not different (P ⩾ 0.08) across all treatment groups, while uteroplacental uptake of glucose was increased (P ⩽ 0.05) in RES v. ADQ ewes. In conclusion, maternal nutrient restriction increased maternal arterial − venous difference in total α-AA, while total uterine α-AA flux was unaffected by maternal nutrient restriction. Melatonin supplementation did not impact maternal serum concentrations or uterine flux of glucose or AA; however, melatonin did improve fetal BCAA uptake during maternal nutrient restriction.

The greenhouse gas (GHG) emissions, expressed in carbon dioxide equivalents (CO2-eq), of different Austrian biogas systems were analyzed and evaluated using life-cycle assessment (LCA) as part of a national project. Six commercial biogas plants were investigated and the analysis included the complete process chain: viz., the production and collection of substrates, the fermentation of the substrates in the biogas plant, the upgrading of biogas to biomethane (if applicable) and the use of the biogas or biomethane for heat and electricity or as transportation fuel. Furthermore, the LCA included the GHG emissions of construction, operation and dismantling of the major components involved in the process chain, as well as the use of by-products (e.g. fermentation residues used as fertilizers). All of the biogas systems reduced GHG emissions (in CO2-eq) compared with fossil reference systems. The potential for GHG reduction of the individual biogas systems varied between 60% and 100%. Type of feedstock and its reference use, agricultural practices, coverage of storage tanks for fermentation residues, methane leakage at the combined heat and power plant unit and the proportion of energy used as heat were identified as key factors influencing the GHG emissions of anaerobic digestion processes.

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 growing global demand for food of animal origin will be the incentive for countries such as Australia and Brazil to increase their beef production and international exports. This increased supply of beef is expected to occur primarily through on-farm productivity increases. The strategies for reducing resultant greenhouse gas (GHG) emissions should be evaluated in the context of the production system and should encompass a broader analysis, which would include the emissions of methane (CH4) and nitrous oxide (N2O) and carbon sequestration. This paper provides an insight into CH4 measurement techniques applicable to grazing environments and proposed mitigation strategies, with relevance to the production systems that are predominant in grazing systems of Australia and Brazil. Research and technology investment in both Australia and Brazil is aimed at developing measurement techniques and increasing the efficiency of cattle production by improving herd genetics, utilization of the seasonal feed-base and reducing the proportion of metabolizable energy lost as CH4. Concerted efforts in these areas can be expected to reduce the number of unproductive animals, reduce age at slaughter and inevitably reduce emission intensity (EI) from beef production systems. Improving efficiency of livestock production systems in tropical grazing systems for Australia and Brazil will be based on cultivated and existing native pastures and the use of additives and by-products from other agricultural sectors. This approach spares grain-based feed reserves typically used for human consumption, but potentially incurs a heavier EI than current intensive feeding systems. The determination of GHG emissions and the value of mitigation outcomes for entire beef production systems in the extensive grazing systems is complex and require a multidisciplinary approach. It is fortunate that governments in both Australia and Brazil are supporting ongoing research activities. Nevertheless, to achieve an outcome that feeds a growing population while reducing emissions on a global scale continues to be a monumental challenge for ruminant nutritionists.

Ruminant-derived methane (CH4), a potent greenhouse gas, is a consequence of microbial fermentation in the digestive tract of livestock. Development of mitigation strategies to reduce CH4 emissions from farmed animals is currently the subject of both scientific and environmental interest. Methanogens are the sole producers of ruminant CH4, and therefore CH4 abatement strategies can either target the methanogens themselves or target the other members of the rumen microbial community that produce substrates necessary for methanogenesis. Understanding the relationship that methanogens have with other rumen microbes is crucial when considering CH4 mitigation strategies for ruminant livestock. Genome sequencing of rumen microbes is an important tool to improve our knowledge of the processes that underpin those relationships. Currently, several rumen bacterial and archaeal genome projects are either complete or underway. Genome sequencing is providing information directly applicable to CH4 mitigation strategies based on vaccine and small molecule inhibitor approaches. In addition, genome sequencing is contributing information relevant to other CH4 mitigation strategies. These include the selection and breeding of low CH4-emitting animals through the interpretation of large-scale DNA and RNA sequencing studies and the modification of other microbial groups within the rumen, thereby changing the dynamics of microbial fermentation.

Ongoing intensification and specialisation of livestock production lead to increasing volumes of manure to be managed, which are a source of the greenhouse gases (GHGs) methane (CH4) and nitrous oxide (N2O). Net emissions of CH4 and N2O result from a multitude of microbial activities in the manure environment. Their relative importance depends not only on manure composition and local management practices with respect to treatment, storage and field application, but also on ambient climatic conditions. The diversity of livestock production systems, and their associated manure management, is discussed on the basis of four regional cases (Sub-Saharan Africa, Southeast Asia, China and Europe) with increasing levels of intensification and priorities with respect to nutrient management and environmental regulation. GHG mitigation options for production systems based on solid and liquid manure management are then presented, and potentials for positive and negative interactions between pollutants, and between management practices, are discussed. The diversity of manure properties and environmental conditions necessitate a modelling approach for improving estimates of GHG emissions, and for predicting effects of management changes for GHG mitigation, and requirements for such a model are discussed. Finally, we briefly discuss drivers for, and barriers against, introduction of GHG mitigation measures for livestock production. There is no conflict between efforts to improve food and feed production, and efforts to reduce GHG emissions from manure management. Growth in livestock populations are projected to occur mainly in intensive production systems where, for this and other reasons, the largest potentials for GHG mitigation may be found.

Ruminant production contributes to emissions of nitrogen (N) to the environment, principally ammonia (NH3), nitrous oxide (N2O) and di-nitrogen (N2) to air, nitrate (NO3−) to groundwater and particulate N to surface waters. Variation in dietary N intake will particularly affect excretion of urinary N, which is much more vulnerable to losses than is faecal N. Our objective is to review dietary effects on the level and form of N excreted in cattle urine, as well as its consequences for emissions of N2O. The quantity of N excreted in urine varies widely. Urinary N excretion, in particular that of urea N, is decreased upon reduction of dietary N intake or an increase in the supply of energy to the rumen microorganisms and to the host animal itself. Most of the N in urine (from 50% to well over 90%) is present in the form of urea. Other nitrogenous components include purine derivatives (PD), hippuric acid, creatine and creatinine. Excretion of PD is related to rumen microbial protein synthesis, and that of hippuric acid to dietary concentration of degradable phenolic acids. The N concentration of cattle urine ranges from 3 to 20 g/l. High-dietary mineral levels increase urine volume and lead to reduced urinary N concentration as well as reduced urea concentration in plasma and milk. In lactating dairy cattle, variation in urine volume affects the relationship between milk urea and urinary N excretion, which hampers the use of milk urea as an accurate indicator of urinary N excretion. Following its deposition in pastures or in animal houses, ubiquitous microorganisms in soil and waters transform urinary N components into ammonium (NH4+), and thereafter into NO3− and ultimately in N2 accompanied with the release of N2O. Urinary hippuric acid, creatine and creatinine decompose more slowly than urea. Hippuric acid may act as a natural inhibitor of N2O emissions, but inhibition conditions have not been defined properly yet. Environmental and soil conditions at the site of urine deposition or manure application strongly influence N2O release. Major dietary strategies to mitigating N2O emission from cattle operations include reducing dietary N content or increasing energy content, and increasing dietary mineral content to increase urine volume. For further reduction of N2O emission, an integrated animal nutrition and excreta management approach is required.

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.

Vaccination against rumen methanogens offers a practical approach to reduce methane emissions in livestock, particularly ruminants grazing on pasture. Although successful vaccination strategies have been reported for reducing the activity of the rumen-dwelling organism Streptococcus bovis in sheep and S. bovis and Lactobacillus spp. in cattle, earlier approaches using vaccines based on whole methanogen cells to reduce methane production in sheep have produced less promising results. An anti-methanogen vaccine will need to have broad specificity against methanogens commonly found in the rumen and induce antibody in saliva resulting in delivery of sufficiently high levels of antibodies to the rumen to reduce methanogen activity. Our approach has focussed on identifying surface and membrane-associated proteins that are conserved across a range of rumen methanogens. The identification of potential vaccine antigens has been assisted by recent advances in the knowledge of rumen methanogen genomes. Methanogen surface proteins have been shown to be immunogenic in ruminants and vaccination of sheep with these proteins induced specific antibody responses in saliva and rumen contents. Current studies are directed towards identifying key candidate antigens and investigating the level and types of salivary antibodies produced in sheep and cattle vaccinated with methanogen proteins, stability of antibodies in the rumen and their impact on rumen microbial populations. In addition, there is a need to identify adjuvants that stimulate high levels of salivary antibody and are suitable for formulating with protein antigens to produce a low-cost and effective vaccine.

With the human population predicted to reach nine billion by 2050, demand for food is predicted to more than double over this time period, a trend which will lead to increased greenhouse gas (GHG) emissions from agriculture. Furthermore, expansion in food production is predicted to occur primarily in the developing world, where adaptation to climate change may be more difficult and opportunities to mitigate emissions limited. In the establishment of the United Nations Framework Convention on Climate Change (UNFCCC), ‘ensuring that food production is not threatened’ is explicitly mentioned in the objective of the Convention. However, the focus of negotiations under the Convention has largely been on reducing GHG emissions from energy, and industrial activities and realizing the potential of forestry as a carbon sink. There has been little attention by the UNFCCC to address the challenges and opportunities for the agriculture sector. Since 2006, concerted efforts have been made to raise the prominence of agriculture within the negotiations. The most recent The Intergovernmental Panel on Climate Change report and ‘The Emissions Gap Report’ by the UNEP highlighted the significant mitigation potential of agriculture, which can help contribute towards keeping global temperature rises below the 2°C limit agreed in Cancun. Agriculture has to be a part of the solution to address climate change, but this will also require a focus on how agriculture systems can adapt to climate change in order to continue to increase food output. However, to effectively realize this potential, systematic and dedicated discussion and decisions within the UNFCCC are needed. UNFCCC discussions on a specific agriculture agenda item started in 2012, but are currently inconclusive. However, Parties are generally in agreement on the importance of agriculture in contributing to food security and employment as well as the need to improve understanding of agriculture and how it can contribute to realizing climate objectives. Discussions on agriculture are continuing with a view to finding an acceptable approach to address the climate change related challenges faced by agriculture worldwide and to ensure that ‘food production is not threatened’.

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.

Agriculture and livestock production systems are two major emitters of greenhouse gases. Methane with a GWP (global warming potential) of 21, and nitrous oxide (N2O) with a GWP of 300, are largely emitted from animal production agriculture, where livestock production is based on pasture and feed grains. The principal biological processes involved in N2O emissions are nitrification and denitrification. Biological nitrification inhibition (BNI) is the natural ability of certain plant species to release nitrification inhibitors from their roots that suppress nitrifier activity, thus reducing soil nitrification and N2O emission. Recent methodological developments (e.g. bioluminescence assay to detect BNIs in plant root systems) have led to significant advances in our ability to quantify and characterize the BNI function. Synthesis and release of BNIs from plants is a highly regulated process triggered by the presence of NH4+ in the rhizosphere, which results in the inhibitor being released precisely where the majority of the soil-nitrifier population resides. Among the tropical pasture grasses, the BNI function is strongest (i.e. BNI capacity) in Brachiaria sp. Some feed-grain crops such as sorghum also have significant BNI capacity present in their root systems. The chemical identity of some of these BNIs has now been established, and their mode of inhibitory action on Nitrosomonas has been characterized. The ability of the BNI function in Brachiaria pastures to suppress N2O emissions and soil nitrification potential has been demonstrated; however, its potential role in controlling N2O emissions in agro-pastoral systems is under investigation. Here we present the current status of our understanding on how the BNI functions in Brachiaria pastures and feed-grain crops such as sorghum can be exploited both genetically and, from a production system's perspective, to develop low-nitrifying and low N2O-emitting production systems that would be economically profitable and ecologically sustainable.

Micrometeorological techniques can be applied to estimate methane (CH4) emissions from ruminants and livestock manure using CH4 concentration measured within the internal surface boundary layer. The main advantage of these techniques is that they are non-intrusive, thereby eliminating the impact of the measurement set-up on the calculated CH4 emission. This review focuses on four micrometeorological techniques, namely, the integrated horizontal flux (IHF), flux gradient (FG), eddy covariance (EC) and the dispersion modelling using the backward Lagrangian stochastic method (BLS). Each technique has unique advantages and limitations when used for estimating enteric (ruminant) and manure CH4 emissions. The IHF technique may be theoretically simpler then the FG, EC or BLS techniques, but all require high-resolution instruments to measure concentration. The EC and BLS techniques also require a measurement of the wind statistics. This review discusses the appropriate use of these four micrometeorological techniques for estimating CH4 emissions in animal agriculture and the recent advances in measurement technology.

The last decade has seen an increase in environmental systems analysis of livestock production, resulting in a significant number of studies with a holistic approach often based on life-cycle assessment (LCA) methodology. The growing public interest in global warming has added to this development; guidelines for carbon footprint (CF) accounting have been developed, including for greenhouse gas (GHG) accounting of animal products.

Here we give an overview of methods for estimating GHG emissions, with emphasis on nitrous oxide, methane and carbon from land use change, presently used in LCA/CF studies of animal products. We discuss where methods and data availability for GHGs and nitrogen (N) compounds most urgently need to be improved in order to produce more accurate environmental assessments of livestock production. We conclude that the top priority is to improve models for N fluxes and emissions from soils and to implement soil carbon change models in LCA/CF studies of animal products. We also point at the need for more farm data and studies measuring emissions from soils, manure and livestock in developing countries.

The livestock sector and agriculture as a whole face unprecedented challenges to increase production while improving the environment. On the basis of a literature review, the paper first discusses challenges related to climate change, food security and other drivers of change in livestock production. On the basis of a recent discourse in ecology, a framework for assessing livestock species’ and breeds’ vulnerability to climate change is presented. The second part of the paper draws on an analysis of data on breed qualities obtained from the Food and Agriculture Organization's Domestic Animal Diversity Information System (DAD-IS) to explore the range of adaptation traits present in today's breed diversity. The analysis produced a first mapping of a range of ascribed adaptation traits of national breed populations. It allowed to explore what National Coordinators understand by ‘locally adapted’ and other terms that describe general adaptation, to better understand the habitat, fodder and temperature range of each species and to shed light on the environments in which targeted search for adaptation traits could focus.

A short term enteric methane emission measurement is not identical to a measure of daily methane production (DMP) made in a respiration chamber (RC). While RC curtail most variation except that from quantity and composition of feed supplied, all short-term measurements contain additional sources of variation. The points of difference can include measurement time(s) relative to feeding, feed intake before measurement, animal behaviour in selection of diet and level of activity before measurement. For systems where a short-term emission measurement is made at the same time in the daily feeding cycle (e.g. during twice-daily milking) scaling up of short-term emission rates to estimate DMP is feasible but the scaling coefficient(s) will be diet dependent. For systems such as GreenFeed where direct emission rates are measured on occasion throughout day and night, no scaling up may be required to estimate DMP. For systems where small numbers of emission measures are made, and there is no knowledge of prior feed intake, such as for portable accumulation chambers, scaling to DMP is not currently possible. Even without scaling up to DMP, short-term measured emission rates are adequate for identifying relative emission changes induced by mitigation strategies and could provide the data to support genetic selection of ruminants for reduced enteric emissions.