Tim A. McAllister

Greenhouse gas mitigation in agriculture

Agricultural lands occupy 37% of the earths land surface. Agriculture accounts for 52 and 84% of global anthropogenic methane and nitrous oxide emissions. Agricultural soils may also act as a sink or source for CO2, but the net flux is small. Many agricultural practices can potentially mitigate greenhouse gas (GHG) emissions, the most prominent of which are improved cropland and grazing land management and restoration of degraded lands and cultivated organic soils. Lower, but still significant mitigation potential is provided by water and rice management, set-aside, land use change and agroforestry, livestock management and manure management. The global technical mitigation potential from agriculture (excluding fossil fuel offsets from biomass) by 2030, considering all gases, is estimated to be approximately 5500–6000 Mt CO2-eq. yr−1, with economic potentials of approximately 1500–1600, 2500–2700 and 4000–4300 Mt CO2-eq. yr−1 at carbon prices of up to 20, up to 50 and up to 100 US

Nutritional management for enteric methane abatement: a review

t CO2-eq.−1, respectively. In addition, GHG emissions could be reduced by substitution of fossil fuels for energy production by agricultural feedstocks (e.g. crop residues, dung and dedicated energy crops). The economic mitigation potential of biomass energy from agriculture is estimated to be 640, 2240 and 16 000 Mt CO2-eq. yr−1 at 0–20, 0–50 and 0–100 US

Giardia and Cryptosporidium in Canadian farm animals

t CO2-eq.−1, respectively.

Distribution of sulfamethazine, chlortetracycline and tylosin in manure and soil of Canadian feedlots after subtherapeutic use in cattle

A variety of nutritional management strategies that reduce enteric methane (CH4) production are discussed. Strategies such as increasing the level of grain in the diet, inclusion of lipids and supplementation with ionophores (>24 ppm) are most likely to be implemented by farmers because there is a high probability that they reduce CH4 emissions in addition to improving production efficiency. Improved pasture management, replacing grass silage with maize silage and using legumes hold some promise for CH4 mitigation but as yet their impact is not sufficiently documented. Several new strategies including dietary supplementation with saponins and tannins, selection of yeast cultures and use of fibre-digesting enzymes may mitigate CH4, but these still require extensive research. Most of the studies on reductions in CH4 from ruminants due to diet management are short-term and focussed only on changes in enteric emissions. Future research must examine long-term sustainability of reductions in CH4 production and impacts on the entire farm greenhouse gas budget.

Characterization of the Core Rumen Microbiome in Cattle during Transition from Forage to Concentrate as Well as during and after an Acidotic Challenge

Giardia intestinalis and Cryptosporidium spp. are commonly identified intestinal pathogens in humans and animals. In light of the clinical disease, production losses and zoonotic potential of both Giardia and Cryptosporidium infections, a study was undertaken to investigate the prevalence of these parasites in cattle, sheep, pigs and horses in Canadian farms at different geographical locations. A total of 104 cattle, 89 sheep, 236 pigs and 35 horses were sampled from 15 different Canadian geographical locations. Fecal samples were examined after concentration and immunofluorescent staining. Giardia and Cryptosporidium were present in cattle and sheep in six out of six sites sampled. In cattle the overall prevalence was 29% for Giardia and 20% for Cryptosporidium. Giardia was identified in 38% of sheep while 23% of sheep were positive for Cryptosporidium. Giardia and Cryptosporidium were identified in four out of six hog operations with an overall prevalence of 9% for Giardia and 11% for Cryptosporidium. All horse sampling locations (4/4) were positive for Giardia with 20% of animals infected. Cryptosporidium was identified in three out of four sampling sites with a prevalence of 17%. The prevalence of Giardia and Cryptosporidium was greater in calves and lambs compared to adults. This study demonstrates that both Giardia and Cryptosporidium appear to be prevalent in farm livestock.

Lipid-induced depression of methane production and digestibility in the artificial rumen system (RUSITEC)

Feedlots are potential point sources for the flow of antibiotics into the environment due to common use of antibiotics such as sulfamethazine, chlortetracycline and tylosin. Hence soils and manures originating from a grassland control, an experimental and a commercial feedlot were analyzed and mass balances were calculated for these antibiotics. Up to 9990 microg kg(-1) sulfamethazine and 401microg kg(-1) chlortetracycline on a dry matter basis were determined in feedlot manure. Soil concentrations were two orders of magnitude smaller. This corresponds to 7-40% of the calculated residual amount. In the commercial feedlot chlortetracycline was found down to soil depths of -40 cm; sulfamethazine was still detectable 1 year after medication. Sulfamethazine and chlortetracycline were additionally determined in manure of a control treatment in the experimental feedlot where cattle never received antibiotics. This was attributed to runoff from upslope pens. Consequently, antibiotics partially persist within feedlots and may be dislocated into the surrounding environment by vertical transport and runoff.

Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach

This study investigated the effect of diet and host on the rumen bacterial microbiome and the impact of an acidotic challenge on its composition. Using parallel pyrosequencing of the V3 hypervariable region of 16S rRNA gene, solid and liquid associated bacterial communities of 8 heifers were profiled. Heifers were exclusively fed forage, before being transitioned to a concentrate diet, subjected to an acidotic challenge and allowed to recover. Samples of rumen digesta were collected when heifers were fed forage, mixed forage, high grain, during challenge (4 h and 12 h) and recovery. A total of 560,994 high-quality bacterial sequences were obtained from the solid and liquid digesta. Using cluster analysis, prominent bacterial populations differed (P≤0.10) in solid and liquid fractions between forage and grain diets. Differences among hosts and diets were not revealed by DGGE, but real time qPCR showed that several bacteria taxon were impacted by changes in diet, with the exception of Streptococcus bovis. Analysis of the core rumen microbiome identified 32 OTUs representing 10 distinct bacterial taxa including Bacteroidetes (32.8%), Firmicutes (43.2%) and Proteobacteria (14.3%). Diversity of OTUs was highest with forage with 38 unique OTUs identified as compared to only 11 with the high grain diet. Comparison of the microbial profiles of clincial vs. subclinical acidotic heifers found a increases in the relative abundances of Acetitomaculum, Lactobacillus, Prevotella, and Streptococcus. Increases in Streptococcus and Lactobacillus likely reflect the tolerance of these species to low pH and their ability to proliferate on surplus fermentable carbohydrate. The acetogen, Acetitomaculum may thereforeplay a role in the conversion of lactate to acetate in acidotic animals. Further profiling of the bacterial populations associated with subclinical and clinical acidosis could establish a microbial fingerprint for these disorders and provide insight into whether there are causative microbial populations that could potentially be therapeutically manipulated.

Escherichia coli O157:H7 excretion by commercial feedlot cattle fed either barley- or corn-based finishing diets.

An artificial rumen (RUSITEC) equipped with eight fermenters was used to examine the effects of canola oil (CA), cod liver oil (CD) and coconut oil (CO) on methane production, dietary digestibility and rumen microbial populations. The experiment, repeated three times, involved two diets (100% grass hay or a 90%:10% wheat:hay mixture) either untreated (controls) or sprayed with CA, CD or CO (10%, wt/wt) in a 2 × 4 factorial arrangement. Dry matter disappearance and CH4 production were greater (P < 0.05) from untreated concentrate diet than from untreated hay. There were significant interactions (P < 0.05) between diet and lipid type for DM digestion and several of the fermentation parameters. Coconut oil decreased (P < 0.05) DM and neutral detergent fibre disappearance of hay but did not affect digestion of concentrate. All oils, especially CO, depressed (P < 0.05) CH4 production (mmol g−1 digestible DM) and methanogenic populations regardless of diet. Methanogens on CO-treated diets numbered less than 1% ...

Oral and rectal administration of bacteriophages for control of Escherichia coli O157:H7 in feedlot cattle.

Background Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches. Methodology/Principal Findings In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus), with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies. Conclusions/Significance The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.

A biosecure composting system for disposal of cattle carcasses and manure following infectious disease outbreak.

Effective preharvest control measures for Escherichia coli O157:H7 in cattle may significantly reduce the incidence of human disease caused by this organism. The prevalence and magnitude of fecal E. coli O157:H7 excretion was evaluated in 15 pens (300 to 500 cattle per pen) of commercial feedlot cattle fed a barley-based finishing ration and compared with that in 15 pens of cattle fed a corn-based ration. Average E. coli O157:H7 prevalence was 2.4% in barley-fed cattle and 1.3% in the corn-fed cattle (P < 0.05), and average magnitude of fecal E. coli O157:H7 excretion was 3.3 log CFU/g in the barley-fed cattle and 3.0 log CFU/g in the corn-fed cattle (P < 0.01). Corn-fed cattle had lower average fecal pH values (5.85) than did barley-fed cattle (6.51) (P < 0.01), and the average total generic fecal E. coli concentration in this group of animals (6.24 log CFU/g) was greater than that in the barley-fed cattle (5.55 log CFU/g) (P < 0.01). Specific feed ingredients may impact the frequency and magnitude of fecal excretion of E. coli O157:H7 by cattle.