Large-chamber methane and nitrous oxide measurements are comparable to the backward Lagrangian stochastic method

Measurement of individual emission sources (e.g., animals or pen manure) within intensive livestock enterprises is necessary to test emission calculation protocols and to identify targets for decreased emissions. In this study, a vented, fabric-covered large chamber (4.5 × 4.5 m, 1.5 m high; encompassing greater spatial variability than a smaller chamber) in combination with on-line analysis (nitrous oxide [N2O] and methane [CH4] via Fourier Transform Infrared Spectroscopy; 1 analysis min-1) was tested as a means to isolate and measure emissions from beef feedlot pen manure sources. An exponential model relating chamber concentrations to ambient gas concentrations, air exchange (e.g., due to poor sealing with the surface; model linear when ≈ 0 m3 s-1), and chamber dimensions allowed data to be fitted with high confidence. Alternating manure source emission measurements using the large-chamber and the backward Lagrangian stochastic (bLS) technique (5-mo period; bLS validated via tracer gas release, recovery 94-104%) produced comparable N2O and CH4 emission values (no significant difference at P < 0.05). Greater precision of individual measurements was achieved via the large chamber than for the bLS (mean ± standard error of variance components: bLS half-hour measurements, 99.5 ± 325 mg CH4 s-1 and 9.26 ± 20.6 mg N2O s-1; large-chamber measurements, 99.6 ± 64.2 mg CH4 s-1 and 8.18 ± 0.3 mg N2O s-1). The large-chamber design is suitable for measurement of emissions from manure on pen surfaces, isolating these emissions from surrounding emission sources, including enteric emissions. © © American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.

Nipah Virus in the Fruit Bat Pteropus vampyrus in Sumatera, Indonesia

Nipah virus causes periodic livestock and human disease with high case fatality rate, and consequent major economic, social and psychological impacts. Fruit bats of the genus Pteropus are the natural reservoir. In this study, we used real time PCR to screen the saliva and urine of P. vampyrus from North Sumatera for Nipah virus genome. A conventional reverse transcriptase (RT-PCR) assay was used on provisionally positive samples to corroborate findings. This is the first report of Nipah virus detection in P. vampyrus in Sumatera, Indonesia.

An improved real-time PCR assay for the detection of Old World screwworm flies

The Old World screwworm (OWS) fly, Chrysomya bezziana, is a serious pest of livestock, wildlife and humans in tropical Africa, parts of the Middle East, the Indian subcontinent, south-east Asia and Papua New Guinea. Although to date Australia remains free of OWS flies, an incursion would have serious economic and animal welfare implications. For these reasons Australia has an OWS fly preparedness plan including OWS fly surveillance with fly traps. The recent development of an improved OWS fly trap and synthetic attractant and a specific and sensitive real-time PCR molecular assay for the detection of OWS flies in trap catches has improved Australia's OWS fly surveillance capabilities. Because all Australian trap samples gave negative results in the PCR assay, it was deemed necessary to include a positive control mechanism to ensure that fly DNA was being successfully extracted and amplified and to guard against false negative results. A new non-competitive internal amplification control (IAC) has been developed that can be used in conjunction with the OWS fly PCR assay in a multiplexed single-tube reaction. The multiplexed assay provides an indicator of the performance of DNA extraction and amplification without greatly increasing labour or reagent costs. The fly IAC targets a region of the ribosomal 16S mitochondrial DNA which is conserved across at least six genera of commonly trapped flies. Compared to the OWS fly assay alone, the multiplexed OWS fly and fly IAC assay displayed no loss in sensitivity or specificity for OWS fly detection. The multiplexed OWS fly and fly IAC assay provides greater confidence for trap catch samples returning negative OWS fly results. © 2014 International Atomic Energy Agency.

Good science for improving policy: greenhouse gas emissions from agricultural manures

Australia’s and New Zealand’s major agricultural manure management emission sources are reported to be, in descending order of magnitude: (1) methane (CH4) from dairy farms in both countries; (2) CH4 from pig farms in Australia; and nitrous oxide (N2O) from (3) beef feedlots and (4) poultry sheds in Australia. We used literature to critically review these inventory estimates. Alarmingly for dairy farm CH4 (1), our review revealed assumptions and omissions that when addressed could dramatically increase this emission estimate. The estimate of CH4 from Australian pig farms (2) appears to be accurate, according to industry data and field measurements. The N2O emission estimates for beef feedlots (3) and poultry sheds (4) are based on northern hemisphere default factors whose appropriateness for Australia is questionable and unverified. Therefore, most of Australasia’s key livestock manure management greenhouse gas (GHG) emission profiles are either questionable or are unsubstantiated by region-specific research. Encouragingly, GHG from dairy shed manure are relatively easy to mitigate because they are a point source which can be managed by several ‘close-to-market’ abatement solutions. Reducing these manure emissions therefore constitutes an opportunity for meaningful action sooner compared with the more difficult-to-implement and long-term strategies that currently dominate agricultural GHG mitigation research. At an international level, our review highlights the critical need to carefully reassess GHG emission profiles, particularly if such assessments have not been made since the compilation of original inventories. Failure to act in this regard presents the very real risk of missing the ‘low hanging fruit’ in the rush towards a meaningful response to climate change

Sympatric prey responses to lethal top-predator control: predator manipulation experiments

Introduction Many prey species around the world are suffering declines due to a variety of interacting causes such as land use change, climate change, invasive species and novel disease. Recent studies on the ecological roles of top-predators have suggested that lethal top-predator control by humans (typically undertaken to protect livestock or managed game from predation) is an indirect additional cause of prey declines through trophic cascade effects. Such studies have prompted calls to prohibit lethal top-predator control with the expectation that doing so will result in widespread benefits for biodiversity at all trophic levels. However, applied experiments investigating in situ responses of prey populations to contemporary top-predator management practices are few and none have previously been conducted on the eclectic suite of native and exotic mammalian, reptilian, avian and amphibian predator and prey taxa we simultaneously assess. We conducted a series of landscape-scale, multi-year, manipulative experiments at nine sites spanning five ecosystem types across the Australian continental rangelands to investigate the responses of sympatric prey populations to contemporary poison-baiting programs intended to control top-predators (dingoes) for livestock protection. Results Prey populations were almost always in similar or greater abundances in baited areas. Short-term prey responses to baiting were seldom apparent. Longer-term prey population trends fluctuated independently of baiting for every prey species at all sites, and divergence or convergence of prey population trends occurred rarely. Top-predator population trends fluctuated independently of baiting in all cases, and never did diverge or converge. Mesopredator population trends likewise fluctuated independently of baiting in almost all cases, but did diverge or converge in a few instances. Conclusions These results demonstrate that Australian populations of prey fauna at lower trophic levels are typically unaffected by top-predator control because top-predator populations are not substantially affected by contemporary control practices, thus averting a trophic cascade. We conclude that alteration of current top-predator management practices is probably unnecessary for enhancing fauna recovery in the Australian rangelands. More generally, our results suggest that theoretical and observational studies advancing the idea that lethal control of top-predators induces trophic cascades may not be as universal as previously supposed.

The (Non)Effects of Lethal Population Control on the Diet of Australian Dingoes

Top-predators contribute to ecosystem resilience, yet individuals or populations are often subject to lethal control to protect livestock, managed game or humans from predation. Such management actions sometimes attract concern that lethal control might affect top-predator function in ways ultimately detrimental to biodiversity conservation. The primary function of a predator is predation, which is often investigated by assessing their diet. We therefore use data on prey remains found in 4,298 Australian dingo scats systematically collected from three arid sites over a four year period to experimentally assess the effects of repeated broad-scale poison-baiting programs on dingo diet. Indices of dingo dietary diversity and similarity were either identical or near-identical in baited and adjacent unbaited treatment areas in each case, demonstrating no control-induced change to dingo diets. Associated studies on dingoes' movement behaviour and interactions with sympatric mesopredators were similarly unaffected by poison-baiting. These results indicate that mid-sized top-predators with flexible and generalist diets (such as dingoes) may be resilient to ongoing and moderate levels of population control without substantial alteration of their diets and other related aspects of their ecological function.

The Genetic Architecture of Climatic Adaptation of Tropical Cattle

Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation. One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity.

Ecological dynamics of emerging bat virus spillover

Viruses that originate in bats may be the most notorious emerging zoonoses that spill over from wildlife into domestic animals and humans. Understanding how these infections filter through ecological systems to cause disease in humans is of profound importance to public health. Transmission of viruses from bats to humans requires a hierarchy of enabling conditions that connect the distribution of reservoir hosts, viral infection within these hosts, and exposure and susceptibility of recipient hosts. For many emerging bat viruses, spillover also requires viral shedding from bats, and survival of the virus in the environment. Focusing on Hendra virus, but also addressing Nipah virus, Ebola virus, Marburg virus and coronaviruses, we delineate this cross-species spillover dynamic from the within-host processes that drive virus excretion to land-use changes that increase interaction among species. We describe how land-use changes may affect co-occurrence and contact between bats and recipient hosts. Two hypotheses may explain temporal and spatial pulses of virus shedding in bat populations: episodic shedding from persistently infected bats or transient epidemics that occur as virus is transmitted among bat populations. Management of livestock also may affect the probability of exposure and disease. Interventions to decrease the probability of virus spillover can be implemented at multiple levels from targeting the reservoir host to managing recipient host exposure and susceptibility.

Using UHF proximity loggers to quantify male–female interactions: A scoping study of estrous activity in cattle

Reproductive efficiency is an important determinant of profitable cattle breeding systems and the success of assisted reproductive techniques (ART) in wildlife conservation programs. Methods of estrous detection used in intensive beef and dairy cattle systems lack accuracy and remain the single biggest issue for improvement of reproductive rates and such methods are not practical for either large-scale extensive beef cattle enterprises or free-living mammalian species. Recent developments in UHF (ultra high frequency) proximity logger telemetry devices have been used to provide a continuous pair-wise measure of associations between individual animals for both livestock and wildlife. The objective of this study was to explore the potential of using UHF telemetry to identify the reproductive cycle phenotype in terms of intensity and duration of estrus. The study was conducted using Belmont Red (interbred Africander Brahman Hereford–Shorthorn) cattle grazing irrigated pasture on Belmont Research Station, northeastern Australia. The cow-bull associations from three groups of cows each with one bull were recorded over a 7-week breeding season and the stage of estrus was identified using ultrasonography. Telemetry data from bull and cows, collected over 4 8-day logger deployments, were log transformed and analyzed by ANOVA. Both the number and duration of bull-cow affiliations were significantly (P < 0.001) greater in estrous cows compared to anestrus cows. These results support the development of the UHF technology as a hands-off and noninvasive means of gathering socio-sexual information on both wildlife and livestock for reproductive management.

The need for speed: Timely prevention of the dispersal of noxious weeds in relief fodder using efficient sampling procedures

Invasive and noxious weeds are well known as a pervasive problem, imposing significant economic burdens on all areas of agriculture. Whilst there are multiple possible pathways of weed dispersal in this industry, of particular interest to this discussion is the unintended dispersal of weed seeds within fodder. During periods of drought or following natural disasters such as wild fire or flood, there arises the urgent need for 'relief' fodder to ensure survival and recovery of livestock. In emergency situations, relief fodder may be sourced from widely dispersed geographic regions, and some of these regions may be invaded by an extensive variety of weeds that are both exotic and detrimental to the intended destination for the fodder. Pasture hay is a common source of relief fodder and it typically consists of a mixture of grassy and broadleaf species that may include noxious weeds. When required urgently, pasture hay for relief fodder can be cut, baled, and transported over long distances in a short period of time, with little opportunity for prebaling inspection. It appears that, at the present time, there has been little effort towards rapid testing of bales, post-baling, for the presence of noxious weeds, as a measure to prevent dispersal of seeds. Published studies have relied on the analysis of relatively small numbers of bales, tested to destruction, in order to reveal seed species for identification and enumeration. The development of faster, more reliable, and non-destructive sampling methods is essential to increase the fodder industry's capacity to prevent the dispersal of noxious weeds to previously unaffected locales.

Methane in Australian agriculture: current emissions, sources and sinks, and potential mitigation strategies

Methane is a potent greenhouse gas with a global warming potential ∼28 times that of carbon dioxide. Consequently, sources and sinks that influence the concentration of methane in the atmosphere are of great interest. In Australia, agriculture is the primary source of anthropogenic methane emissions (60.4% of national emissions, or 3260kt-1methaneyear-1, between 1990 and 2011), and cropping and grazing soils represent Australia's largest potential terrestrial methane sink. As of 2011, the expansion of agricultural soils, which are ∼70% less efficient at consuming methane than undisturbed soils, to 59% of Australia's land mass (456Mha) and increasing livestock densities in northern Australia suggest negative implications for national methane flux. Plant biomass burning does not appear to have long-term negative effects on methane flux unless soils are converted for agricultural purposes. Rice cultivation contributes marginally to national methane emissions and this fluctuates depending on water availability. Significant available research into biological, geochemical and agronomic factors has been pertinent for developing effective methane mitigation strategies. We discuss methane-flux feedback mechanisms in relation to climate change drivers such as temperature, atmospheric carbon dioxide and methane concentrations, precipitation and extreme weather events. Future research should focus on quantifying the role of Australian cropping and grazing soils as methane sinks in the national methane budget, linking biodiversity and activity of methane-cycling microbes to environmental factors, and quantifying how a combination of climate change drivers will affect total methane flux in these systems.

Demographic and functional responses of wild dogs to poison baiting

Lethal control of wild dogs - that is Dingo (Canis lupus dingo) and Dingo/Dog (Canis lupus familiaris) hybrids - to reduce livestock predation in Australian rangelands is claimed to cause continental-scale impacts on biodiversity. Although top predator populations may recover numerically after baiting, they are predicted to be functionally different and incapable of fulfilling critical ecological roles. This study reports the impact of baiting programmes on wild dog abundance, age structures and the prey of wild dogs during large-scale manipulative experiments. Wild dog relative abundance almost always decreased after baiting, but reductions were variable and short-lived unless the prior baiting programme was particularly effective or there were follow-up baiting programmes within a few months. However, age structures of wild dogs in baited and nil-treatment areas were demonstrably different, and prey populations did diverge relative to nil-treatment areas. Re-analysed observations of wild dogs preying on kangaroos from a separate study show that successful chases that result in attacks of kangaroos by wild dogs occurred when mean wild dog ages were higher and mean group size was larger. It is likely that the impact of lethal control on wild dog numbers, group sizes and age structures compromise their ability to handle large difficult-to-catch prey. Under certain circumstances, these changes sometimes lead to increased calf loss (Bos indicus/B. taurus genotypes) and kangaroo numbers. Rangeland beef producers could consider controlling wild dogs in high-risk periods when predation is more likely and avoid baiting at other times.

Ecological dynamics of emerging bat virus spillover

Viruses that originate in bats may be the most notorious emerging zoonoses that spill over from wildlife into domestic animals and humans. Understanding how these infections filter through ecological systems to cause disease in humans is of profound importance to public health. Transmission of viruses from bats to humans requires a hierarchy of enabling conditions that connect the distribution of reservoir hosts, viral infection within these hosts, and exposure and susceptibility of recipient hosts. For many emerging bat viruses, spillover also requires viral shedding from bats, and survival of the virus in the environment. Focusing on Hendra virus, but also addressing Nipah virus, Ebola virus, Marburg virus and coronaviruses, we delineate this cross-species spillover dynamic from the within-host processes that drive virus excretion to land-use changes that increase interaction among species. We describe how land-use changes may affect co-occurrence and contact between bats and recipient hosts. Two hypotheses may explain temporal and spatial pulses of virus shedding in bat populations: episodic shedding from persistently infected bats or transient epidemics that occur as virus is transmitted among bat populations. Management of livestock also may affect the probability of exposure and disease. Interventions to decrease the probability of virus spillover can be implemented at multiple levels from targeting the reservoir host to managing recipient host exposure and susceptibility.

Floristic composition and pasture condition of Aristida/Bothriochloa pastures in central Queensland. I. Pasture floristics

A survey was conducted in central inland Queensland, Australia of 108 sites that were deemed to contain Aristida/Bothriochloa native pastures to quantitatively describe the pastures and attempt to delineate possible sub-types. The pastures were described in terms of their floristic composition, plant density and crown cover. There were generally ~20 (range 5–33) main pasture species at a site. A single dominant perennial grass was rare with three to six prominent species the norm. Chrysopogon fallax (golden-beard grass) was the perennial grass most consistently found in all pastures whereas Aristida calycina (dark wiregrass), Enneapogon spp. (bottlewasher grasses), Brunoniella australis (blue trumpet) and Panicum effusum (hairy panic) were all regularly present. The pastures did not readily separate into broad floristic sub-groups, but three groups that landholders could recognise from a combination of the dominant tree and soil type were identified. The three groups were Eucalyptus crebra (narrow-leaved ironbark), E. melanophloia (silver-leaved ironbark) and E. populnea (poplar box). The pastures of the three main sub-groups were then characterised by the prominent presence, singly or in combination, of Bothriochloa ewartiana (desert bluegrass), Eremochloa bimaculata (poverty grass), Bothriochloa decipiens (pitted bluegrass) or Heteropogon contortus (black speargrass). The poplar box group had the greatest diversity of prominent grasses whereas the narrow-leaved ironbark group had the least. Non-native Cenchrus ciliaris (buffel grass) and Melinis repens (red Natal grass) were generally present at low densities. Describing pastures in terms of frequency of a few species or species groups sometimes failed to capture the true nature of the pasture but plant abundance for most species, as density, herbage mass of dry matter or plant crown cover, was correlated with its recorded frequency. A quantitative description of an average pasture in fair condition is provided but it was not possible to explain why some species often occur together or fail to co-exist in Aristida/Bothriochloa pastures, for example C. ciliaris and E. bimaculata rarely co-exist whereas Tragus australianus (small burrgrass) and Enneapogon spp. are frequently recorded together. Most crown cover was provided by perennial grasses but many of these are Aristida spp. (wiregrasses) and not regarded as useful forage for livestock. No new or improved categorisation of the great variation evident in the Aristida/Bothriochloa native pasture type can be given despite the much improved detail provided of the floristic composition by this survey.

Boosting the productivity and profitability of northern Australian beef enterprises: Exploring innovation options using simulation modelling and systems analysis

The financial health of beef cattle enterprises in northern Australia has declined markedly over the last decade due to an escalation in production and marketing costs and a real decline in beef prices. Historically, gains in animal productivity have offset the effect of declining terms of trade on farm incomes. This raises the question of whether future productivity improvements can remain a key path for lifting enterprise profitability sufficient to ensure that the industry remains economically viable over the longer term. The key objective of this study was to assess the production and financial implications for north Australian beef enterprises of a range of technology interventions (development scenarios), including genetic gain in cattle, nutrient supplementation, and alteration of the feed base through introduced pastures and forage crops, across a variety of natural environments. To achieve this objective a beef systems model was developed that is capable of simulating livestock production at the enterprise level, including reproduction, growth and mortality, based on energy and protein supply from natural C4 pastures that are subject to high inter-annual climate variability. Comparisons between simulation outputs and enterprise performance data in three case study regions suggested that the simulation model (the Northern Australia Beef Systems Analyser) can adequately represent the performance beef cattle enterprises in northern Australia. Testing of a range of development scenarios suggested that the application of individual technologies can substantially lift productivity and profitability, especially where the entire feedbase was altered through legume augmentation. The simultaneous implementation of multiple technologies that provide benefits to different aspects of animal productivity resulted in the greatest increases in cattle productivity and enterprise profitability, with projected weaning rates increasing by 25%, liveweight gain by 40% and net profit by 150% above current baseline levels, although gains of this magnitude might not necessarily be realised in practice. While there were slight increases in total methane output from these development scenarios, the methane emissions per kg of beef produced were reduced by 20% in scenarios with higher productivity gain. Combinations of technologies or innovative practices applied in a systematic and integrated fashion thus offer scope for providing the productivity and profitability gains necessary to maintain viable beef enterprises in northern Australia into the future.