High pathogenicity avian influenza: targeted active surveillance of wild birds to enable early detection of emerging disease threats.

Avian influenza (AI) is an important disease that has significant implications for animal and human health. High pathogenicity AI (HPAI) has emerged in consecutive seasons within the UK to cause the largest outbreaks recorded. Statutory measures to control outbreaks of AI virus (AIV) at poultry farms involve disposal of all birds on infected premises. Understanding of the timing of incursions into the UK could facilitate decisions on improved responses. During the autumnal migration and wintering period (autumn 2019- spring 2020), three active sampling approaches were trialled for wild bird species considered likely to be involved in captive AI outbreaks with retrospective laboratory testing undertaken to define the presence of AIV.Faecal sampling of birds (n = 594) caught during routine and responsive mist net sampling failed to detect AIV. Cloacal sampling of hunter-harvested waterfowl (n = 146) detected seven positive samples from three species with the earliest detection on the 17 October 2020. Statutory sampling first detected AIV in wild and captive birds on 3 November 2020. We conclude that hunter sourced sampling of waterfowl presents an opportunity to detect AI within the UK in advance of outbreaks on poultry farms and allow for early intervention measures to protect the national poultry flock.

Impacts of COVID-19 on agriculture and food systems in Pacific Island countries (PICs): Evidence from communities in Fiji and Solomon Islands.

CONTEXT: COVID-19 mitigation measures including border lockdowns, social distancing, de-urbanization and restricted movements have been enforced to reduce the risks of COVID-19 arriving and spreading across PICs. To reduce the negative impacts of COVID-19 mitigation measures, governments have put in place a number of interventions to sustain food and income security. Both mitigation measures and interventions have had a number of impacts on agricultural production, food systems and dietary diversity at the national and household levels. OBJECTIVE: Our paper conducted an exploratory analysis of immediate impacts of both COVID-19 mitigation measures and interventions on households and communities in PICs. Our aim is to better understand the implications of COVID-19 for PICs and identify knowledge gaps requiring further research and policy attention. METHODS: To understand the impacts of COVID-19 mitigation measures and interventions on food systems and diets in PICs, 13 communities were studied in Fiji and Solomon Islands in July-August 2020. In these communities, 46 focus group discussions were carried out and 425 households were interviewed. Insights were also derived from a series of online discussion sessions with local experts of Pacific Island food and agricultural systems in August and September 2020. To complement these discussions, an online search was conducted for available literature. RESULTS AND CONCLUSIONS: Identified impacts include: 1) Reduced agricultural production, food availability and incomes due to a decline in local markets and loss of access to international markets; 2) Increased social conflict such as land disputes, theft of high-value crops and livestock, and environmental degradation resulting from urban-rural migration; 3) Reduced availability of seedlings, planting materials, equipment and labour in urban areas; 4) Reinvigoration of traditional food systems and local food production; and 5) Re-emergence of cultural safety networks and values, such as barter systems. Households in rural and urban communities appear to have responded positively to COVID-19 by increasing food production from home gardens, particularly root crops, vegetables and fruits. However, the limited diversity of agricultural production and decreased household incomes are reducing the already low dietary diversity score that existed pre-COVID-19 for households. SIGNIFICANCE: These findings have a number of implications for future policy and practice. Future interventions would benefit from being more inclusive of diverse partners, focusing on strengthening cultural and communal values, and taking a systemic and long-term perspective. COVID-19 has provided an opportunity to strengthen traditional food systems and re-evaluate, re-imagine and re-localize agricultural production strategies and approaches in PICs.

Methane emission during on-site pre-storage of animal manure prior to anaerobic digestion at biogas plant: Effect of storage temperature and addition of food waste.

This study investigated the temperature dependency of CH4 emission from pre-storage of animal manure prior to anaerobic digestion at 15, 20, 25 and 30 °C using lab-scale anaerobic digesters. The manure was added and removed daily to simulate the pre-storage process at biogas plants. CH4 emission accounted for 1-46% of total CH4 potential from pig manure (PM) and 1-2% of that from cattle manure (CM) at the investigated temperatures, with significant increases above 25 °C. Addition of food waste (FW) reduced the CH4 emission when storage temperature was 20 °C or lower for PM and 25 °C or lower for CM due to volatile fatty acid accumulation and lower pH (<5.5) but emissions increased with higher storage temperatures.

Quantifying contribution of synthrophic acetate oxidation to methane production in thermophilic anaerobic reactors by membrane inlet mass spectrometry.

A unique method was developed and applied for monitoring methanogenesis pathways based on isotope labeled substrates combined with online membrane inlet quadrupole mass spectrometry (MIMS). In our study, a fermentation sample from a full-scale biogas plant fed with pig and cattle manure, maize silage, and deep litter was incubated with 100 mM of [2-(13)C] sodium acetate under thermophilic anaerobic conditions. MIMS was used to measure the isotopic distribution of dissolved CO2 and CH4 during the degradation of acetate, while excluding interference from water by applying a cold trap. After 6 days of incubation, the proportion of methane derived from reduction of CO2 had increased significantly and reached up to 87% of total methane, suggesting that synthrophic acetate oxidation coupled to hydrogenotrophic methanogenesis (SAO-HM) played an important role in the degradation of acetate. This study provided a new approach for online quantification of the relative contribution of methanogenesis pathways to methane production with a time resolution shorter than one minute. The observed contribution of SAO-HM to methane production under the tested conditions challenges the current widely accepted anaerobic digestion model (ADM1), which strongly emphasizes the importance of the acetoclastic methanogenesis.

The effect of mixed-enzyme addition in anaerobic digestion on methane yield of dairy cattle manure.

This study investigates the effect of applying a mixture of enzymes (ME) to dairy cattle manure (DCM) as substrate in anaerobic digestion (AD). The aims of this study were to evaluate different methods of ME application to DCM at different temperatures and to investigate the effect of adding ME during the pre-treatment of the solid fractions of dairy cattle manure (SFDCM). The results showed that there was no positive effect of direct ME addition to substrate at either mesophilic (35 degrees C) or thermophilic (50 degrees C) process temperatures, but there was a significant 4.44% increase in methane yield when DCM, which had been incubated with ME addition at 50 degrees C for three days, was fed to a digester when compared to a control digester operating at the same retention time. Methane production was detected during the pre-treatment incubation, and the total sum methane yield during pre-treatment and digestion was found to be 8.33% higher than in the control. The addition of ME to the SFDCM in a pre-incubation stage of 20 h at 35 degrees C gave a significant increase in methane yield by 4.15% in a digester treating a mixed substrate (30% liquid fractions DCM and 70% enzyme-treated SFDCM) when compared with the control digester treating a similar mixed substrate with inactivated enzyme addition. The results indicate that direct physical contact of enzyme molecules and organic material in DCM prior to AD, without the intervention of extracellular enzymes from the indigenous microorganism population, was needed in order to increase methane yields.

Repeatability and reproducibility of hunter-harvest sampling for avian influenza virus surveillance in Great Britain.

Emerging pathogens can threaten human and animal health, necessitating reliable surveillance schemes to enable preparedness. We evaluated the repeatability and reproducibility of a method developed previously during a single year at one study site. Hunter-harvested ducks and geese were sampled for avian influenza virus at three discrete locations in the UK. H5N1 highly pathogenic avian influenza (HPAIV) was detected in four species (mallard [Anas platyrhynchos], Eurasian teal [Anas crecca], Eurasian wigeon [Mareca penelope] and pink-footed goose [Anser brachyrhynchus]) across all three locations and two non-HPAIV H5N1, influenza A positive detections were made from a mallard and Eurasian wigeon at two locations. Virus was detected within 1-to-4 days of sampling at every location. Application of rapid diagnostic methods to samples collected from hunter-harvested waterfowl offers potential as an early warning system for the surveillance and monitoring of emerging and existing strains of avian influenza A viruses in key avian species.

Effects of high-temperature isochoric pre-treatment on the methane yields of cattle, pig and chicken manure.

Cattle manure, dewatered pig manure and chicken manure were pre-treated in a high-temperature reactor under isochoric conditions for 15 min at temperatures between 100 and 225 degrees C with 25 degrees C intervals to study the effect on their methane yield. After 27 days of batch incubation, cattle manure showed a significant improvement in its biochemical methane potential (BMP) of 13% at 175 degrees C and 21% at 200 degrees C. Pig manure showed improvements at temperatures of 125 degrees C and above, with a maximum 29% increase in yield at 200 degrees C. The BMP of chicken manure was reduced by 18% at 225 degrees C, but at lower temperatures there were no significant changes. It was found that this method of pre-treatment could be feasible if sufficient surplus energy was available or if the energy used in the pre-treatment could be recovered.

Developing a biogas centralised circular bioeconomy using agricultural residues - Challenges and opportunities.

Anaerobic digestion (AD) can be used as a stand-alone process or integrated as part of a larger biorefining process to produce biofuels, biochemicals and fertiliser, and has the potential to play a central role in the emerging circular bioeconomy (CBE). Agricultural residues, such as animal slurry, straw, and grass silage, represent an important resource and have a huge potential to boost biogas and methane yields. Under the CBE concept, there is a need to assess the long-term impact and investigate the potential accumulation of specific unwanted substances. Thus, a comprehensive literature review to summarise the benefits and environmental impacts of using agricultural residues for AD is needed. This review analyses the benefits and potential adverse effects related to developing biogas-centred CBE. The identified potential risks/challenges for developing biogas CBE include GHG emission, nutrient management, pollutants, etc. In general, the environmental risks are highly dependent on the input feedstocks and resulting digestate. Integrated treatment processes should be developed as these could both minimise risks and improve the economic perspective.

NIR monitoring of ammonia in anaerobic digesters using a diffuse reflectance probe.

The feasibility of using a diffuse reflectance probe attached to a near infrared spectrometer to monitor the total ammonia nitrogen (TAN) content in an anaerobic digester run on cattle manure was investigated; as a previous study has indicated that this probe can be easily attached to an anaerobic digester. Multivariate modelling techniques such as partial least squares regression and interval partial least squares methods were used to build models. Various data pre-treatments were applied to improve the models. The TAN concentrations measured were in the range of 1.5 to 5.5 g/L. An R(2) of 0.91 with an RMSEP of 0.32 was obtained implying that the probe could be used for monitoring and screening purposes.

Rapid assessment of mineral concentration in meadow grasses by near infrared reflectance spectroscopy.

A near infrared reflectance spectroscopy (NIRS) method for rapid determination of nitrogen, phosphorous and potassium in diverse meadow grasses was developed with a view towards utilizing this material for biogas production and organic fertilizer. NIRS spectra between 12,000 cm(-1) and 4,000 cm(-1) were used. When validated on samples from different years to those used for the calibration set, the NIRS prediction of nitrogen was considered moderately useful with R(2) = 0.77, ratio of standard error of prediction to reference data range (RER) of 9.32 and ratio of standard error of prediction to standard deviation of reference data (RPD) of 2.33. Prediction of potassium was less accurate, with R(2) = 0.77, RER of 6.56 and RPD of 1.45, whilst prediction of phosphorous was not considered accurate enough to be of any practical use. This work is of interest from the point of view of both the removal of excess nutrients from formerly intensively farmed areas and also for assessing the plant biomass suitability for conversion into carbon neutral energy through biogas production.

A novel acoustic sensor approach to classify seeds based on sound absorption spectra.

A non-destructive and novel in situ acoustic sensor approach based on the sound absorption spectra was developed for identifying and classifying different seed types. The absorption coefficient spectra were determined by using the impedance tube measurement method. Subsequently, a multivariate statistical analysis, i.e., principal component analysis (PCA), was performed as a way to generate a classification of the seeds based on the soft independent modelling of class analogy (SIMCA) method. The results show that the sound absorption coefficient spectra of different seed types present characteristic patterns which are highly dependent on seed size and shape. In general, seed particle size and sphericity were inversely related with the absorption coefficient. PCA presented reliable grouping capabilities within the diverse seed types, since the 95% of the total spectral variance was described by the first two principal components. Furthermore, the SIMCA classification model based on the absorption spectra achieved optimal results as 100% of the evaluation samples were correctly classified. This study contains the initial structuring of an innovative method that will present new possibilities in agriculture and industry for classifying and determining physical properties of seeds and other materials.

Modeling current and potential distributions of mammal species using presence-only data: A case study on British deer.

AIM: Decisions on wildlife conservation, management, and epidemiological risk are best based on robust evidence. The continual improvement of species distributions, such that they can be relied upon in decision-making, is important. Here we seek to refine aspects of a generic modelling approach and improve the utility of species distribution maps. LOCATION: Great Britain (GB). METHODS: We applied a modeling framework based on hierarchical Bayesian species distribution models exploiting opportunistic occurrence records from citizen science datasets to predict both current and potential distributions for each of the six deer species known to be present in GB. Using the resulting maps, we performed a simple analysis of the overlap between species to illustrate possible contact, which we interpret as the relative risk of potential disease spread given an introduction. RESULTS: Predicted distribution maps showed good agreement with the broader scale occurrence reported by a recent national deer survey with an average True Skill Statistics and AUC of 0.69 and 0.89, respectively. Aggregation of the maps for all species highlighted regions of central and eastern England as well as parts of Scotland where extensive areas of range overlap could result in interspecific contact with consequences for risk assessments for diseases of deer. However, if populations are allowed to expand to their predicted potential, then areas of overlap, and therefore disease interspecific transmission risk, will become extensive and widespread across all of mainland Britain. MAIN CONCLUSIONS: The generic modeling approach outlined performed well across all of the deer species tested, offering a robust and reliable tool through which current and potential animal distributions can be estimated and presented. Our application, intended to inform quantitative risk assessments, demonstrates the practical use of such outputs to generate the valuable evidence required to inform policy decisions on issues such as management strategy.

Effect of different feeding management on the respiratory methane emission and feces-derived methane yield of goat.

OBJECTIVE: This study aimed to evaluate the respiratory methane emission and ultimate methane yield (B 0) of goat feces that fed roughage consisted of Pennisetum purpureum and Gliricidia) and fed roughage and concentrate with different protein source in the ration (fish meal and soybean meal). MATERIALS AND METHODS: Fifteen Kacang bucks were allocated to the control group (T0): goats were fed roughage only, T1: goats were fed roughage and concentrate with fish meal as protein sources, and T2: goats were fed roughage and concentrate and the protein source in the ration was soybean meal. RESULTS: The protein content of feces from T0 was significantly lower (p < 0.05) than that from the other treatments. The same phenomenon was also found in the respiratory methane emission in terms of l/head/d, l/kg digestible dry matter, and l/kg body weight. However, there was no significant effect (p > 0.05) of different ration composition on the ultimate methane yield (B0 ) of goat feces. This study found that B0 of goat feces from treatment T0, T1, and T2 was 17.40%, 25.78%, and 61.29%, respectively, higher than that from the international default value for developing countries. CONCLUSION: Feeding grass and legume can reduce methane respiration emission in goat. B0 of feces in the present study was higher than that in the international default value; therefore, the potential emission of goat manure in tropical developing countries could be higher than that in the present estimation.

Optimisation of the anaerobic digestion of agricultural resources.

It is in the interest of operators of anaerobic digestion plants to maximise methane production whilst concomitantly reducing the chemical oxygen demand of the digested material. Although the production of biogas through anaerobic digestion is not a new idea, commercial anaerobic digestion processes are often operated at well below their optimal performance due to a variety of factors. This paper reviews current optimisation techniques associated with anaerobic digestion and suggests possible areas where improvements could be made, including the basic design considerations of a single or multi-stage reactor configuration, the type, power and duration of the mixing regime and the retention of active microbial biomass within the reactor. Optimisation of environmental conditions within the digester such as temperature, pH, buffering capacity and fatty acid concentrations is also discussed. The methane-producing potential of various agriculturally sourced feedstocks has been examined, as has the advantages of co-digestion to improve carbon-to-nitrogen ratios and the use of pre-treatments and additives to improve hydrolysis rates or supplement essential nutrients which may be limiting. However, perhaps the greatest shortfall in biogas production is the lack of reliable sensory equipment to monitor key parameters and suitable, parallelised control systems to ensure that the process continually operates at optimal performance. Modern techniques such as software sensors and powerful, flexible controllers are capable of solving these problems. A direct comparison can be made here with, for instance, oil refineries where a more mature technology uses continuous in situ monitoring and associated feedback procedures to routinely deliver continuous, optimal performance.

Influence on anaerobic digestion by intermediate thermal hydrolysis of waste activated sludge and co-digested wheat straw.

This paper analyses time (30 and 60 min) and temperature (120-190 °C) effects of intermediate thermal hydrolysis (ITHP) in a two-step anaerobic digestion of waste activated sludge (WAS) with and without wheat straw as a co-substrate. Effects were analyzed by measuring biochemical methane potential for 60 days and assessing associated kinetic and chemical data. Compared to non-treatment, ITHP increased the secondary step methane yield from 52 to 222 L CH4 kg VS-1 and from 147 to 224 L CH4 kg VS-1 for pre-digested WAS and pre-co-digested WAS respectively at an optimum of 170 °C and 30 min. The hydrolysis coefficients (khyd) increased by up to 127% following treatment. Increasing ITHP time from 30 to 60 min showed ambiguous results regarding methane yields, whilst temperature had a clear and proportional effect on the concentrations of acetic acid. The energy balances were found to be poor and dewatering to increase total solids above the values tested here is necessary for this process to be energetically feasible.

Facilitating permeability of landscapes impacted by roads for protected amphibians: patterns of movement for the great crested newt.

Amphibian populations are highly vulnerable to road mortality and habitat fragmentation caused by road networks. Wildlife road tunnels are considered the most promising road mitigation measure for amphibians yet generally remain inadequately monitored, resulting in mixed success rates in the short-term and uncertain conservation benefits in the long-term. We monitored a complex multi-tunnel and fence system over five years and investigated the impact of the scheme on movement patterns of two newt species, including the largest known UK population of the great crested newt (Triturus cristatus), a European Protected Species. We used a stage descriptive approach based on capture positions to quantify newt movement patterns. Newt species successfully used the mitigation but the system constituted a bottleneck to movements from the fences to the tunnels. Crossing rates varied widely among years and were skewed towards autumn dispersal rather than spring breeding migration. There was a substantial negative bias against adult male great crested newts using the system. This study indicates that road tunnels could partially mitigate wider connectivity loss and fragmentation at the landscape scale for newt species. However, the observed bottleneck effects and seasonal bias could have population-level effects which must be better understood, especially for small populations, so that improvements can be made. Current requirements for monitoring mitigation schemes post-implementation are probably too short to assess their effectiveness in maintaining connectivity and to adequately understand their population-level impacts.

Exogenous addition of H2 for an in situ biogas upgrading through biological reduction of carbon dioxide into methane.

Biological reduction of CO2 into CH4 by exogenous addition of H2 is a promising technology for upgrading biogas into higher CH4 content. The aim of this work was to study the feasibility of exogenous H2 addition for an in situ biogas upgrading through biological conversion of the biogas CO2 into CH4. Moreover, this study employed systematic study with isotope analysis for providing comprehensive evidence on the underlying pathways of CH4 production and upstream processes. Batch reactors were inoculated with digestate originating from a full-scale biogas plant and fed once with maize leaf substrate. Periodic addition of H2 into the headspace resulted in a completely consumption of CO2 and a concomitant increase in CH4 content up to 89%. The microbial community and isotope analysis shows an enrichment of hydrogenotrophic Methanobacterium and the key role of hydrogenotrophic methanogenesis for biogas upgrading to higher CH4 content. Excess H2 was also supplied to evaluate its effect on overall process performance. The results show that excess H2 addition resulted in accumulation of H2, depletion of CO2 and inhibition of the degradation of acetate and other volatile fatty acids (VFA). A systematic isotope analysis revealed that excess H2 supply led to an increase in dissolved H2 to the level that thermodynamically inhibit the degradation of VFA and stimulate homo-acetogens for production of acetate from CO2 and H2. The inhibition was a temporary effect and acetate degradation resumed when the excess H2 was removed as well as in the presence of stoichiometric amount of H2 and CO2. This inhibition mechanism underlines the importance of carefully regulating the H2 addition rate and gas retention time to the CO2 production rate, H2-uptake rate and growth of hydrogenotrophic methanogens in order to achieve higher CH4 content without the accumulation of acetate and other VFA.

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics.

Inhibition of anaerobic digestion through accumulation of volatile fatty acids occasionally occurs as the result of unbalanced growth between acidogenic bacteria and methanogens. A fast recovery is a prerequisite for establishing an economical production of biogas. However, very little is known about the microorganisms facilitating this recovery. In this study, we investigated the organisms involved by a novel approach of mapping protein-stable isotope probing (protein-SIP) onto a binned metagenome. Under simulation of acetate accumulation conditions, formations of (13)C-labeled CO2 and CH4 were detected immediately following incubation with [U-(13)C]acetate, indicating high turnover rate of acetate. The identified (13)C-labeled peptides were mapped onto a binned metagenome for improved identification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia. The acetate-consuming organisms affiliating with Clostridia all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis, indicating that these organisms are possible syntrophic acetate-oxidizing (SAO) bacteria that can facilitate acetate consumption via SAO, coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms utilizing specific pathways.

Exclusions for resolving urban badger damage problems: outcomes and consequences.

Increasing urbanisation and growth of many wild animal populations can result in a greater frequency of human-wildlife conflicts. However, traditional lethal methods of wildlife control are becoming less favoured than non-lethal approaches, particularly when problems involve charismatic species in urban areas. Eurasian badgers (Meles meles) excavate subterranean burrow systems (setts), which can become large and complex. Larger setts within which breeding takes place and that are in constant use are known as main setts. Smaller, less frequently occupied setts may also exist within the social group's range. When setts are excavated in urban environments they can undermine built structures and can limit or prevent safe use of the area by people. The most common approach to resolving these problems in the UK is to exclude badgers from the problem sett, but exclusions suffer a variable success rate. We studied 32 lawful cases of badger exclusions using one-way gates throughout England to evaluate conditions under which attempts to exclude badgers from their setts in urban environments were successful. We aimed to identify ways of modifying practices to improve the chances of success. Twenty of the 32 exclusion attempts were successful, but success was significantly less likely if a main sett was to be excluded in comparison with another type of sett and if vegetation was not completely removed from the sett surface prior to exclusion attempts. We recommend that during exclusions all vegetation is removed from the site, regardless of what type of sett is involved, and that successful exclusion of badgers from a main sett might require substantially more effort than other types of sett.