Multi-omics analysis reveals the roles of purple acid phosphatases in organic phosphorus utilization by the tropical legume Stylosanthes guianensis.

Stylo (Stylosanthes guianensis) is a tropical legume known for its exceptional tolerance to low phosphate (Pi), a trait believed to be linked to its high acid phosphatase (APase) activity. Previous studies have observed genotypic variations in APase activity in stylo; however, the gene encoding the crucial APase responsible for this variation remains unidentified. In this study, transcriptomic and proteomic analyses were employed to identify eight Pi starvation-inducible (PSI) APases belonging to the purple APase (PAP) family in the roots of stylo and seven in the leaves. Among these PSI-PAPs, SgPAP7 exhibited a significantly positive correlation in its expression levels with the activities of both internal APase and root-associated APase across 20 stylo genotypes under low-Pi conditions. Furthermore, the recombinant SgPAP7 displayed high catalytic activity toward adenosine 5'-diphosphate (ADP) and phosphoenolpyruvate (PEP) in vitro. Overexpression (OE) of SgPAP7 in Arabidopsis facilitated exogenous organic phosphorus utilization. Moreover, SgPAP7 OE lines showed lower shoot ADP and PEP levels than the wild type, implying that SgPAP7 is involved in the catabolism and recycling of endogenous ADP and PEP, which could be beneficial for plant growth in low-Pi soils. In conclusion, SgPAP7 is a key gene with a major role in stylo adaptation to low-Pi conditions by facilitating the utilization of both exogenous and endogenous organic phosphorus sources. It may also function as a PEP phosphatase involved in a glycolytic bypass pathway that minimizes the need for adenylates and Pi. Thus, SgPAP7 could be a promising target for improving tolerance of crops to low-Pi availability.

Greenhouse gas emissions from cattle dung depositions in two Urochloa forage fields with contrasting biological nitrification inhibition (BNI) capacity.

Grazing-based production systems are a source of soil greenhouse gas (GHG) emissions triggered by excreta depositions. The adoption of Urochloa forages (formerly known as Brachiaria) with biological nitrification inhibition (BNI) capacity is a promising alternative to reduce nitrous oxide (N2O) emissions from excreta patches. However, how this forage affects methane (CH4) or carbon dioxide (CO2) emissions from excreta patches remains unclear. This study investigated the potential effect of soils under two Urochloa forages with contrasting BNI capacity on GHG emissions from cattle dung deposits. Additionally, the N2O and CH4 emission factors (EF) for cattle dung under tropical conditions were determined. Dung from cattle grazing star grass (without BNI) was deposited on both forage plots: Urochloa hybrid cv. Mulato and Urochloa humidicola cv. Tully, with a respectively low and high BNI capacity. Two trials were conducted for GHG monitoring using the static chamber technique. Soil and dung properties and GHG emissions were monitored in trial 1. In trial 2, water was added to simulate rainfall and evaluate GHG emissions under wetter conditions. Our results showed that beneath dung patches, the forage genotype influenced daily CO2 and cumulative CH4 emissions during the driest conditions. However, no significant effect of the forage genotype was found on mitigating N2O emissions from dung. We attribute the absence of a significant BNI effect on N2O emissions to the limited incorporation of dung-N into the soil and rhizosphere where the BNI effect occurs. The average N2O EFs was 0.14%, close to the IPCC 2019 uncertainty range (0.01-0.13% at 95% confidence level). Moreover, CH4 EFs per unit of volatile solid (VS) averaged 0.31 g CH4 kgVS-1, slightly lower than the 0.6 g CH4 kgVS-1 developed by the IPCC. This implies the need to invest in studies to develop more region-specific Tier 2 EFs, including farm-level studies with animals consuming Urochloa forages to consider the complete implications of forage selection on animal excreta based GHG emissions.

Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency.

BACKGROUND: Phosphorus (P) is an essential macronutrient for plant growth that participates in a series of biological processes. Thus, P deficiency limits crop growth and yield. Although Stylosanthes guianensis (stylo) is an important tropical legume that displays adaptation to low phosphate (Pi) availability, its adaptive mechanisms remain largely unknown. RESULTS: In this study, differences in low-P stress tolerance were investigated using two stylo cultivars ('RY2' and 'RY5') that were grown in hydroponics. Results showed that cultivar RY2 was better adapted to Pi starvation than RY5, as reflected by lower values of relative decrease rates of growth parameters than RY5 at low-P stress, especially for the reduction of shoot and root dry weight. Furthermore, RY2 exhibited higher P acquisition efficiency than RY5 under the same P treatment, although P utilization efficiency was similar between the two cultivars. In addition, better root growth performance and higher leaf and root APase activities were observed with RY2 compared to RY5. Subsequent RNA-seq analysis revealed 8,348 genes that were differentially expressed under P deficient and sufficient conditions in RY2 roots, with many Pi starvation regulated genes associated with P metabolic process, protein modification process, transport and other metabolic processes. A group of differentially expressed genes (DEGs) involved in Pi uptake and Pi homeostasis were identified, such as genes encoding Pi transporter (PT), purple acid phosphatase (PAP), and multidrug and toxin extrusion (MATE). Furthermore, a variety of genes related to transcription factors and regulators involved in Pi signaling, including genes belonging to the PHOSPHATE STARVATION RESPONSE 1-like (PHR1), WRKY and the SYG1/PHO81/XPR1 (SPX) domain, were also regulated by P deficiency in stylo roots. CONCLUSIONS: This study reveals the possible mechanisms underlying the adaptation of stylo to P deficiency. The low-P tolerance in stylo is probably manifested through regulation of root growth, Pi acquisition and cellular Pi homeostasis as well as Pi signaling pathway. The identified genes involved in low-P tolerance can be potentially used to design the breeding strategy for developing P-efficient stylo cultivars to grow on acid soils in the tropics.

A new genome allows the identification of genes associated with natural variation in aluminium tolerance in Brachiaria grasses.

Toxic concentrations of aluminium cations and low phosphorus availability are the main yield-limiting factors in acidic soils, which represent half of the potentially available arable land. Brachiaria grasses, which are commonly sown as forage in the tropics because of their resilience and low demand for nutrients, show greater tolerance to high concentrations of aluminium cations (Al3+) than most other grass crops. In this work, we explored the natural variation in tolerance to Al3+ between high and low tolerant Brachiaria species and characterized their transcriptional differences during stress. We identified three QTLs (quantitative trait loci) associated with root vigour during Al3+ stress in their hybrid progeny. By integrating these results with a new Brachiaria reference genome, we identified 30 genes putatively responsible for Al3+ tolerance in Brachiaria. We observed differential expression during stress of genes involved in RNA translation, response signalling, cell wall composition, and vesicle location homologous to aluminium-induced proteins involved in limiting uptake or localizing the toxin. However, there was limited regulation of malate transporters in Brachiaria, which suggests that exudation of organic acids and other external tolerance mechanisms, common in other grasses, might not be relevant in Brachiaria. The contrasting regulation of RNA translation and response signalling suggests that response timing is critical in high Al3+-tolerant Brachiaria.

Allele mining in diverse accessions of tropical grasses to improve forage quality and reduce environmental impact.

BACKGROUND AND AIMS: The C4Urochloa species (syn. Brachiaria) and Megathyrsus maximus (syn. Panicum maximum) are used as pasture for cattle across vast areas in tropical agriculture systems in Africa and South America. A key target for variety improvement is forage quality: enhanced digestibility could decrease the amount of land required per unit production, and enhanced lipid content could decrease methane emissions from cattle. For these traits, loss-of-function (LOF) alleles in known gene targets are predicted to improve them, making a reverse genetics approach of allele mining feasible. We therefore set out to look for such alleles in diverse accessions of Urochloa species and Megathyrsus maximus from the genebank collection held at the CIAT. METHODS: We studied allelic diversity of 20 target genes (11 for digestibility, nine for lipid content) in 104 accessions selected to represent genetic diversity and ploidy levels of U. brizantha, U. decumbens, U. humidicola, U. ruziziensis and M. maximum. We used RNA sequencing and then bait capture DNA sequencing to improve gene models in a U. ruziziensis reference genome to assign polymorphisms with high confidence. KEY RESULTS: We found 953 non-synonymous polymorphisms across all genes and accessions; within these, we identified seven putative LOF alleles with high confidence, including those in the non-redundant SDP1 and BAHD01 genes present in diploid and tetraploid accessions. These LOF alleles could respectively confer increased lipid content and digestibility if incorporated into a breeding programme. CONCLUSIONS: We demonstrated a novel, effective approach to allele discovery in diverse accessions using a draft reference genome from a single species. We used this to find gene variants in a collection of tropical grasses that could help reduce the environmental impact of cattle production.

Rhizosphere pH and cation-anion balance determine the exudation of nitrification inhibitor 3-epi-brachialactone suggesting release via secondary transport.

Biological nitrification inhibition (BNI) of Brachiaria humidicola has been attributed to nitrification-inhibiting fusicoccanes, most prominently 3-epi-brachialactone. However, its release mechanism from B. humidicola roots remains elusive. Two hydroponic experiments were performed to investigate the role of rhizosphere pH and nutritional N form in regulating 3-epi-brachialactone release by B. humidicola and verify the underlying release pathway. Low rhizosphere pH and NH4 + nutrition promoted 3-epi-brachialactone exudation. However, the substitution of NH4 + by K+ revealed that the NH4 + effect was not founded in a direct physiological response to the N form but was related to the cation-anion balance during nutrient uptake. Release of 3-epi-brachialactone correlated with the transmembrane proton gradient ΔpH and NH4 + uptake (R2 = 0.92 for high ~6.8 and R2 = 0.84 for low ~4.2 trap solution pH). This corroborated the release of 3-epi-brachialactone through secondary transport, with the proton motive force (ΔP) defining transport rates across the plasma membrane. It was concluded that 3-epi-brachialactone release cannot be conceptualized as a regulated response to soil pH or NH4 + availability, but merely as the result of associated changes in ΔP.

Maize-Brachiaria intercropping: A strategy to supply recycled N to maize and reduce soil N2O emissions?

Nitrogen use in agriculture directly impacts food security, global warming, and environmental degradation. Forage grasses intercropped with maize produce feed for animals and or mulch for no-till systems. Forage grasses may exude nitrification inhibitors. It was hypothesized that brachiaria intercropping increases N recycling and maize grain yield and reduces nitrous oxide (N2O) emissions from soil under maize cropping. A field experiment was set up in December 2016 to test three cropping system (maize monocropped, maize intercropped with Brachiaria brizantha or with B. humidicola) and two N rates (0 or 150 kg ha-1). The grasses were sown with maize, but B. humidicola did not germinate well in the first year. B. brizantha developed slowly during the maize cycle because of shading but expanded after maize was harvested. The experiment was repeated in 2017/2018 when B. humidicola was replanted. N2O and carbon dioxide (CO2) emissions, maize grain yield and N content were measured during the two seasons. After the first maize harvest, the above- and below-ground biomass, C and N content of B. brizantha grown during fall-winter, and the biological nitrification inhibition potential of B. brizantha were evaluated. Maize yield responded to N fertilization (5.1 vs. 9.8 t ha-1) but not to brachiaria intercropping. B. brizantha recycled approximately 140 kg N ha-1 and left 12 t dry matter ha-1 for the second maize crop. However, the 2017/18 maize yields were not affected by the N recycled by B. brizantha, whereas N2O emissions were higher in the plots with brachiaria, suggesting that part of the recycled N was released too early after desiccation. Brachiarias showed no evidence of causing nitrification inhibition. The strategy of intercropping brachiarias did not increase maize yield, although it added C and recycled N in the system.

Effect of the addition of Enterolobium cyclocarpum pods and Gliricidia sepium forage to Brachiaria brizantha on dry matter degradation, volatile fatty acid concentration, and in vitro methane production.

The purpose of this study was to determine the in vitro fermentation and methane (CH4) production in the grass Brachiaria brizantha (B) alone or when mixed with Gliricidia sepium forage (G) and/or Enterolobium cyclocarpum pods (E). Theses substrates were incubated in the following proportions: B100 (B100%), B85E15 (B85% + E15%), B85G15 (B85% + G15%), B85GE15 (B85% + G7.5% + E7.5%), and B70GE30 (B70% + G15% + E15%). Dry matter degradation (DMD), volatile fatty acid (VFA) concentration, and CH4 production were measured at 12, 24, and 48 h of incubation. Experimental design was a randomized complete block. At 48-h incubation, DMD ranged between 46.5 and 51.2% (P = 0.0015). The lowest cumulative gas production (CGP) was observed in B85E15 and B85G15 (160 mL CGP/g organic matter, on average). At 48 h, B85G15 and B100 produced 28.8 and 30.2 mg CH4/g DMD, respectively, while B85E15 or the mixtures, 33.5 mg CH4/g DMD, on average (P ≤ 0.05). B85E15 and B70G30 had the highest concentration of total VFA (P ≤ 0.05). Results showed that B85E15 and B70GE30 favor DMD and increased total production of VFA and CH4 at 48 h. Supplementing livestock feed with legume forages and pods allows improves the nutritional quality of the diet and the fermentation patterns.

Translocation of a parthenogenesis gene candidate to an alternate carrier chromosome in apomictic Brachiaria humidicola.

BACKGROUND: The apomictic reproductive mode of Brachiaria (syn. Urochloa) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In Brachiaria, reproductive mode segregates as single dominant locus, the apospory-specific genomic region (ASGR). The AGSR has been mapped to an area of reduced recombination on Brachiaria decumbens chromosome 5. A primer pair designed within ASGR-BABY BOOM-like (BBML), the candidate gene for the parthenogenesis component of apomixis in Pennisetum squamulatum, was diagnostic for reproductive mode in the closely related species B. ruziziensis, B. brizantha, and B. decumbens. In this study, we used a mapping population of the distantly related commercial species B. humidicola to map the ASGR and test for conservation of ASGR-BBML sequences across Brachiaria species. RESULTS: Dense genetic maps were constructed for the maternal and paternal genomes of a hexaploid (2n = 6x = 36) B. humidicola F1 mapping population (n = 102) using genotyping-by-sequencing, simple sequence repeat, amplified fragment length polymorphism, and transcriptome derived single nucleotide polymorphism markers. Comparative genomics with Setaria italica provided confirmation for x = 6 as the base chromosome number of B. humidicola. High resolution molecular karyotyping indicated that the six homologous chromosomes of the sexual female parent paired at random, whereas preferential pairing of subgenomes was observed in the apomictic male parent. Furthermore, evidence for compensated aneuploidy was found in the apomictic parent, with only five homologous linkage groups identified for chromosome 5 and seven homologous linkage groups of chromosome 6. The ASGR mapped to B. humidicola chromosome 1, a region syntenic with chromosomes 1 and 7 of S. italica. The ASGR-BBML specific PCR product cosegregated with the ASGR in the F1 mapping population, despite its location on a different carrier chromosome than B. decumbens. CONCLUSIONS: The first dense molecular maps of B. humidicola provide strong support for cytogenetic evidence indicating a base chromosome number of six in this species. Furthermore, these results show conservation of the ASGR across the Paniceae in different chromosomal backgrounds and support postulation of the ASGR-BBML as candidate genes for the parthenogenesis component of apomixis.

Carotene Hydroxylase Activity Determines the Levels of Both α-Carotene and Total Carotenoids in Orange Carrots.

The typically intense carotenoid accumulation in cultivated orange-rooted carrots (Daucus carota) is determined by a high protein abundance of the rate-limiting enzyme for carotenoid biosynthesis, phytoene synthase (PSY), as compared with white-rooted cultivars. However, in contrast to other carotenoid accumulating systems, orange carrots are characterized by unusually high levels of α-carotene in addition to ß-carotene. We found similarly increased α-carotene levels in leaves of orange carrots compared with white-rooted cultivars. This has also been observed in the Arabidopsis thaliana lut5 mutant carrying a defective carotene hydroxylase CYP97A3 gene. In fact, overexpression of CYP97A3 in orange carrots restored leaf carotenoid patterns almost to those found in white-rooted cultivars and strongly reduced α-carotene levels in the roots. Unexpectedly, this was accompanied by a 30 to 50% reduction in total root carotenoids and correlated with reduced PSY protein levels while PSY expression was unchanged. This suggests a negative feedback emerging from carotenoid metabolites determining PSY protein levels and, thus, total carotenoid flux. Furthermore, we identified a deficient CYP97A3 allele containing a frame-shift insertion in orange carrots. Association mapping analysis using a large carrot population revealed a significant association of this polymorphism with both α-carotene content and the α-/ß-carotene ratio and explained a large proportion of the observed variation in carrots.

Evidence of Epigenetic Mechanisms Affecting Carotenoids.

Epigenetic mechanisms are able to regulate plant development by generating non-Mendelian allelic interactions. An example of these are the responses to environmenal stimuli that result in phenotypic variability and transgression amongst important crop traits. The need to predict phenotypes from genotypes to understand the molecular basis of the genotype-by-environment interaction is a research priority. Today, with the recent discoveries in the field of epigenetics, this challenge goes beyond analyzing how DNA sequences change. Here we review examples of epigenetic regulation of genes involved in carotenoid synthesis and degradation, cases in which histone- and/or DNA-methylation, and RNA silencing at the posttranscriptional level affect carotenoids in plants.

Provitamin A accumulation in cassava (Manihot esculenta) roots driven by a single nucleotide polymorphism in a phytoene synthase gene.

Cassava (Manihot esculenta) is an important staple crop, especially in the arid tropics. Because roots of commercial cassava cultivars contain a limited amount of provitamin A carotenoids, both conventional breeding and genetic modification are being applied to increase their production and accumulation to fight vitamin A deficiency disorders. We show here that an allelic polymorphism in one of the two expressed phytoene synthase (PSY) genes is capable of enhancing the flux of carbon through carotenogenesis, thus leading to the accumulation of colored provitamin A carotenoids in storage roots. A single nucleotide polymorphism present only in yellow-rooted cultivars cosegregates with colored roots in a breeding pedigree. The resulting amino acid exchange in a highly conserved region of PSY provides increased catalytic activity in vitro and is able to increase carotenoid production in recombinant yeast and Escherichia coli cells. Consequently, cassava plants overexpressing a PSY transgene produce yellow-fleshed, high-carotenoid roots. This newly characterized PSY allele provides means to improve cassava provitamin A content in cassava roots through both breeding and genetic modification.

Evaluation of a Model (RUMINANT) for Prediction of DMI and CH4 from Tropical Beef Cattle.

Simulation models represent a low-cost approach to evaluating agricultural systems. In the current study, the precision and accuracy of the RUMINANT model to predict dry matter intake (DMI) and methane emissions from beef cattle fed tropical diets (characteristic of Colombia) was assessed. Feed intake (DMI) and methane emissions were measured in Brahman steers housed in polytunnels and fed six forage diets. In addition, DMI and methane emissions were predicted by the RUMINANT model. The model's predictive capability was measured on the basis of precision: coefficients of variation (CV%) and determination (R2, percentage of variance accounted for by the model), and model efficiency (ME) and accuracy: the simulated/observed ratio (S/O ratio) and slope and mean bias (MB%). In addition, combined measurements of accuracy and precision were carried out by means of mean square prediction error (MSPE) and correlation correspondence coefficient (CCC) and their components. The predictive capability of the RUMINANT model to simulate DMI resulted as valuable for mean S/O ratio (1.07), MB% (2.23%), CV% (17%), R2 (0.886), ME (0.809), CCC (0.869). However, for methane emission simulations, the model substantially underestimated methane emissions (mean S/O ratio = 0.697, MB% = -30.5%), and ME and CCC were -0.431 and 0.485, respectively. In addition, a subset of data corresponding to diets with Leucaena was not observed to have a linear relationship between the observed and simulated values. It is suggested that this may be related to anti-methanogenic factors characteristic of Leucaena, which were not accounted for by the model. This study contributes to improving national inventories of greenhouse gases from the livestock of tropical countries.

Root exudate fingerprint of Brachiaria humidicola reveals vanillin as a novel and effective nitrification inhibitor.

Introduction: Biological Nitrification Inhibition (BNI) is defined as the plant-mediated control of soil nitrification via the release of nitrification inhibitors. BNI of Brachiaria humidicola (syn. Urochloa humidicola) has been mainly attributed to root-exuded fusicoccane-type diterpenes, e.g., 3-epi-brachialactone. We hypothesized, however, that BNI of B. humidicola is caused by an assemblage of bioactive secondary metabolites. Methods: B. humidicola root exudates were collected hydroponically, and metabolites were isolated by semi-preparative HPLC. Chemical structures were elucidated by HRMS as well as 1D and 2D NMR spectroscopy. Nitrification inhibiting potential of isolated metabolites was evaluated by a Nitrosomonas europaea based bioassay. Results and discussion: Besides previously described brachialactone isomers and derivatives, five phenol and cinnamic acid derivatives were identified in the root exudates of B. humidicola: 2-hydroxy-3-(hydroxymethyl)benzaldehyde, vanillin, umbelliferone and both trans- and cis-2,6-dimethoxycinnamic acid. Notably, vanillin revealed a substantially higher nitrification inhibiting activity than 3-epi-brachialactone (ED50 ∼ 12.5 µg·ml-1, ED80 ∼ 20 µg·ml-1), identifying this phenolic aldehyde as novel nitrification inhibitor (NI). Furthermore, vanillin exudation rates were in the same range as 3-epi-brachialactone (1-4 µg·h-1·g-1 root DM), suggesting a substantial contribution to the overall inhibitory activity of B. humidicola root exudates. In relation to the verification of the encountered effects within soils and considering the exclusion of any detrimental impact on the soil microbiome, the biosynthetic pathway of vanillin via the precursor phenylalanine and the intermediates p-coumaric acid/ferulic acid (precursors of further phenolic NI) might constitute a promising BNI breeding target. This applies not only to Brachiaria spp., but also to crops in general, owing to the highly conserved nature of these metabolites.

Methane Emission, Carbon Footprint and Productivity of Specialized Dairy Cows Supplemented with Bitter Cassava (Manihot esculenta Crantz).

The objective of this research was to determine the effect of cassava (Manihot esculenta Crantz) supplementation on enteric methane (CH4) emissions, carbon footprint, and production parameters in dairy cows. Daily concentrate supply for Jersey and Jersey * Holstein breeds was evaluated in four treatments (T): T1: 100% commercial concentrate; T2: 70% concentrate + 30% cassava leaves; T3: 70% concentrate + 30% cassava roots; and T4: 70% concentrate + 15% cassava leaves + 15% cassava root chips. Measurements of CH4 emissions were performed using the polytunnel technique. Average daily dry matter intake ranged from 7.8 to 8.5 kg dry matter (DM). Cassava leaves were characterized by a high crude protein (CP) content (171 g CP/kg DM), with 5 times more neutral detergent fiber (NDF) content than cassava root (587 vs. 108 g NDF/kg DM). Average enteric CH4 emissions per animal ranged from 194 to 234 g/d (p > 0.05). The carbon footprint was reduced by replacing 30% of the concentrate with cassava leaves and/or roots. Energy-corrected milk production was 1.15 times higher in Jersey * Holstein animals than Jersey cows (47 vs. 55 kg). Therefore, supplementation with cassava leaves and/or roots is a nutritionally and environmentally sustainable strategy.

Effect of Pelagic Sargassum on In Vitro Dry Matter and Organic Matter Degradation, Gas Production, and Protozoa Population.

This study determined the effect of pelagic Sargassum on in vitro dry matter and organic matter degradation, total gas production (TGP), and protozoa population. The treatments were different levels of Sargassum inclusion on a basal substrate (Stargrass hay; Cynodon nlemfuensis) as follows: T0 (control treatment based on Stargrass hay), T10 (90% Stargrass hay + 10% Sargassum), T20 (80% Stargrass hay + 20% Sargassum), and T30 (70% Stargrass hay + 30% Sargassum). Ruminal fermentation kinetics and protozoa population were determined during 72 h of in vitro incubations. Compared to control, dry matter degradability at 48 and 72 h and organic matter degradability at 24 and 48 h were higher in Sargassum treatments. TGP was lower with T20 at 48 h. The total population of protozoa and the concentration of Entodinium spp. were lower at T20 at 48 h and T30 at 72 h. Cl, S, Ca, K, and Zn (103, 5.97, 88.73, 285.70 g/kg, and 15,900 mg/kg) were high in Sargassum, reaching twice or even nine times higher than the contents in Stargrass (11.37, 1.60, 43.53, 87.73 g/kg, and 866.67 mg/kg). Overall, up to 30% pelagic Sargassum could be included in hay-based substrates from tropical grasses without negative effects on in vitro dry matter and organic matter degradability.

Improving the accuracy of beef cattle methane inventories in Latin America and Caribbean countries.

On-farm methane (CH4) emissions need to be estimated accurately so that the mitigation effect of recommended practices can be accounted for. In the present study prediction equations for enteric CH4 have been developed in lieu of expensive animal measurement approaches. Our objectives were to: (1) compile a dataset from individual beef cattle data for the Latin America and Caribbean (LAC) region; (2) determine main predictors of CH4 emission variables; (3) develop and cross-validate prediction models according to dietary forage content (DFC); and (4) compare the predictive ability of these newly-developed models with extant equations reported in literature, including those currently used for CH4 inventories in LAC countries. After outlier's screening, 1100 beef cattle observations from 55 studies were kept in the final dataset (∼ 50 % of the original dataset). Mixed-effects models were fitted with a random effect of study. The whole dataset was split according to DFC into a subset for all-forage (DFC = 100 %), high-forage (94 % ≥ DFC ≥ 54 %), and low-forage (50 % ≥ DFC) diets. Feed intake and average daily gain (ADG) were the main predictors of CH4 emission (g d-1), whereas this was feeding level [dry matter intake (DMI) as % of body weight] for CH4 yield (g kg-1 DMI). The newly-developed models were more accurate than IPCC Tier 2 equations for all subsets. Simple and multiple regression models including ADG were accurate and a feasible option to predict CH4 emission when data on feed intake are not available. Methane yield was not well predicted by any extant equation in contrast to the newly-developed models. The present study delivered new models that may be alternatives for the IPCC Tier 2 equations to improve CH4 prediction for beef cattle in inventories of LAC countries based either on more or less readily available data.

Impact of orange essential oil on enteric methane emissions of heifers fed bermudagrass hay.

In this study, the effects of orange essential oil (OEO) on the rumen fermentation, nutrient utilization, and methane (CH4) emissions of beef heifers fed a diet of bermudagrass (Cynodon dactylon) were examined. In addition, in vitro and in situ experiments were conducted. The in vitro experiment consisted of three treatments: control (CTL, no OEO), OEO1 (0.25% OEO), and OEO2 (0.5% OEO). The forage to concentrate ratio was 70:30 (dry matter [DM] basis) in all treatments. No changes in pH, proportions of volatile fatty acids, and the acetate:propionate ratio were observed (P > 0.05). The addition of 0.25% OEO resulted in a reduction in CH4 production (mL/g) relative to the control (P < 0.05). In the in situ experiment, 5 g of total mixed ration (CTL, OEO1, and OEO2) were incubated for 6, 12, 24, 48, and 72 h. Potential and effective degradability were not affected by OEO supplementation (P > 0.05). In the in vivo study, six crossbred beef heifers (Bos indicus × Bos taurus), fitted with rumen cannulas, were assigned to three different treatments: no additive (CTL), 0.25% OEO (OEO1), and 0.5% OEO (OEO2) in a replicated 3 × 3 Latin square (21-day periods). Heifers were fed at 2.8% body weight. In vivo CH4 production was measured in open-circuit respiration chambers. Reductions in gross energy consumption, apparent total tract digestibility, and rumen valerate concentration were observed for OEO2 compared to the control (P < 0.05). Additionally, decreases in CH4 emissions (g/day; P < 0.05) and CH4 (MJ gross energy intake/day; P < 0.05) were observed in response to supplementation of 0.5% OEO as compared to the CTL treatment. Thus, supplementation of 0.5% OEO reduced CH4 emissions (g/day) by 12% without impacting the DM intake of heifers fed bermudagrass hay as a basal ration.

Quantification of methane emitted by ruminants: a review of methods.

The contribution of greenhouse gas (GHG) emissions from ruminant production systems varies between countries and between regions within individual countries. The appropriate quantification of GHG emissions, specifically methane (CH4), has raised questions about the correct reporting of GHG inventories and, perhaps more importantly, how best to mitigate CH4 emissions. This review documents existing methods and methodologies to measure and estimate CH4 emissions from ruminant animals and the manure produced therein over various scales and conditions. Measurements of CH4 have frequently been conducted in research settings using classical methodologies developed for bioenergetic purposes, such as gas exchange techniques (respiration chambers, headboxes). While very precise, these techniques are limited to research settings as they are expensive, labor-intensive, and applicable only to a few animals. Head-stalls, such as the GreenFeed system, have been used to measure expired CH4 for individual animals housed alone or in groups in confinement or grazing. This technique requires frequent animal visitation over the diurnal measurement period and an adequate number of collection days. The tracer gas technique can be used to measure CH4 from individual animals housed outdoors, as there is a need to ensure low background concentrations. Micrometeorological techniques (e.g., open-path lasers) can measure CH4 emissions over larger areas and many animals, but limitations exist, including the need to measure over more extended periods. Measurement of CH4 emissions from manure depends on the type of storage, animal housing, CH4 concentration inside and outside the boundaries of the area of interest, and ventilation rate, which is likely the variable that contributes the greatest to measurement uncertainty. For large-scale areas, aircraft, drones, and satellites have been used in association with the tracer flux method, inverse modeling, imagery, and LiDAR (Light Detection and Ranging), but research is lagging in validating these methods. Bottom-up approaches to estimating CH4 emissions rely on empirical or mechanistic modeling to quantify the contribution of individual sources (enteric and manure). In contrast, top-down approaches estimate the amount of CH4 in the atmosphere using spatial and temporal models to account for transportation from an emitter to an observation point. While these two estimation approaches rarely agree, they help identify knowledge gaps and research requirements in practice.

There is a need to accurately and precisely quantify greenhouse gas (GHG) emissions, specifically methane (CH4), to ensure correct reporting of GHG inventories and, perhaps more importantly, determine how to best mitigate CH4 emissions. The objective of this study was to review existing methods and methodologies to quantify and estimate CH4 emissions from ruminants. Historically, most techniques were developed for specific purposes that may limit their widespread use on commercial farms and for inventory purposes and typically required frequent calibration and equipment maintenance. Whole animal and head respiration chambers, spot sampling techniques, and tracer gas methods can be used to measure enteric CH4 from individual animals, but each technique has its own inherent limitations. The measurement of CH4 emissions from manure depends on the type of storage, animal housing, CH4 concentration inside and outside the boundaries of the area of interest, and ventilation rate, which is likely the most complex variable creating many uncertainties. For large-scale areas, aircraft, drones, and satellites have been used in association with the tracer flux method, inverse modeling, imagery, and LiDAR (Light Detection and Ranging), but research is lagging in validating these methods. Bottom-up approaches to estimating CH4 emissions rely on empirical or mechanistic modeling to quantify the contribution of individual sources. Top-down approaches estimate the amount of CH4 in the atmosphere using spatial and temporal models to account for transportation from an emitter to an observation point.

Environmental impact of primary beef production chain in Colombia: Carbon footprint, non-renewable energy and land use using Life Cycle Assessment.

In Colombia, the beef production chain accounts for approximately 11.6 million cattle heads and annually produces 933 million kg of the beef carcass. There are no life cycle assessment (LCA) studies that have evaluated the environmental performance of Colombian beef systems. The present study aimed to estimate the carbon footprint (CF), non-renewable energy use, and land use of 251 cow-calf and 275 fattening farms in Colombia. The study also aimed to identify the main hotspots of adverse environmental impacts and propose possible mitigation options and their cost-effectiveness. The impact categories were estimated using the 2006 IPCC and the 2019 Refinement to 2006 IPCC guidelines, databases, and locally estimated emission factors. The functional units used were 1 kg fat and protein corrected milk (FPCM) and 1 kg live weight gain (LWG), leaving the farm gate. Three methods of allocating environmental burdens to meat and milk products were applied: economic, energy, and mass allocation. The adoption of improved pastures was considered a mitigation measure, and an economic assessment was performed to estimate the relative cost-effectiveness of its establishment. A principal component multivariate analysis and a Hierarchical Clustering on Principal Components were performed. The economic allocation method assigned a greater environmental burden to meat (83%), followed by energy content (80%) and mass production (73%). The largest sources of GHG emissions were enteric fermentation and manure deposited on pasture. Both cow-calf and fattening systems had a cluster of farms with better productivity, pasture and cattle management practices, and environmental performance. The CF for meat could be reduced by 33 to 56% for cow-calf and 21 to 25% for fattening farms, by adopting improved pastures. Therefore, our results suggest that GHG emissions can be reduced by adopting improved pastures, better agricultural management practices, efficient fertilizer usage, using the optimal stocking rate, and increasing productivity.