Assessment of carbon footprint of milk production and identification of its major determinants in smallholder dairy farms in Karnataka, India

Indian dairy enterprise is dominated by smallholder dairy farms that contribute 72% of the country's total milk production. These smallholder dairy farms are often considered to emit substantial greenhouse gases (GHG) but are poor in productive performances. Therefore, it is crucial to estimate the carbon footprint (CF) of milk production of the smallholder Indian dairy farms. The primary objectives of the study were (1) Assessing the CF of milk production of smallholder dairy farms through life cycle analysis in south-interior Karnataka, India; (2) Identifying the hotspots of GHG emissions and significant factors influencing the CF of milk production in smallholder dairy production system. The study accounted GHG emissions from different sources and considered multiple functions of the smallholder production system. Estimations were made based on primary data collected from 47 farms and associated secondary data. For estimating the CF of milk production, the emissions of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) on a CO2-equivalent (CO2-eq) basis from feed production, enteric fermentation, manure management, transport and energy usage were allocated to fat- and protein-corrected milk (FPCM) based on mass balance, price (crop byproducts and residues) and feed digestibility. Principal component analysis and stepwise linear regression analysis were performed to identify the major factors influencing the CF. The average total GHG emissions (kg CO2-eq yr-1 farm-1) attributable to milk production based on mass, economic, and digestibility allocations were 8,936, 8,641, and 8,759, respectively. The contributions of CH4, N2O, and CO2 to the total farm GHG emission were 70.6%, 20.5%, and 7.69%, respectively. The major emission hotspots were CH4 emission from enteric fermentation (66.8%) and GHG emission from feed production (23.0%). The average CF of cradle-to-dairy cooperative milk production varied from 1.45 to 1.81 kg CO2-eq kg FPCM-1. The CF of milk production was more than 2-fold greater, when milk yield was below 3,500 kg lactating cow-1 yr-1. The FPCM yield 100 kg body weight-1, dry matter intake, and CH4 emission from manure management were the strongest determinants of the CF and explained 83.4% of the observed variation. The study emphasized the importance of considering multiple functions of a mixed crop-livestock-based dairy production system for estimating CF per unit of product. The results suggest that maintaining high-yielding dairy animals and adopting appropriate feeding strategies for better feed utilization are the possible effective interventions for reducing the CF of milk production.

Comparison of enteric methane yield and diversity of ruminal methanogens in cattle and buffaloes fed on the same diet

An in vivo study was conducted to compare the enteric methane emissions and diversity of ruminal methanogens in cattle and buffaloes kept in the same environment and fed on the same diet. Six cattle and six buffaloes were fed on a similar diet comprising Napier (Pennisetum purpureum) green grass and concentrate in 70:30. After 90 days of feeding, the daily enteric methane emissions were quantified by using the SF6 technique and ruminal fluid samples from animals were collected for the diversity analysis. The daily enteric methane emissions were significantly greater in cattle as compared to buffaloes; however, methane yields were not different between the two species. Methanogens were ranked at different taxonomic levels against the Rumen and Intestinal Methanogen-Database. The archaeal communities in both host species were dominated by the phylum Euryarchaeota; however, Crenarchaeota represented <1% of the total archaea. Methanogens affiliated with Methanobacteriales were most prominent and their proportion did not differ between the two hosts. Methanomicrobiales and Methanomassillicoccales constituted the second largest group of methanogens in cattle and buffaloes, respectively. Methanocellales (Methanocella arvoryza) were exclusively detected in the buffaloes. At the species level, Methanobrevibacter gottschalkii had the highest abundance (55-57%) in both the host species. The relative abundance of Methanobrevibacter wolinii between the two hosts differed significantly. Methanosarcinales, the acetoclastic methanogens were significantly greater in cattle than the buffaloes. It is concluded that the ruminal methane yield in cattle and buffaloes fed on the same diet did not differ. With the diet used in this study, there was a limited influence (<3.5%) of the host on the structure of the ruminal archaea community at the species level. Therefore, the methane mitigation strategies developed in either of the hosts should be effective in the other. Further studies are warranted to reveal the conjunctive effect of diet and geographical locations with the host on ruminal archaea community composition.

EXPLORING THE METABOLICALLY ACTIVE RUMEN MICROBIOTA AND ITS FIBROLYTIC POTENTIAL IN CROSSBRED CATTLE FED ON FIBROUS DIET THROUGH METATRANSCRIPTOMICS

The rumen wharves conglomerate of symbiotic fibrolytic microflora with the potential to produce repertoire of carbohydrate-active enzymes to elicit the degradation of recalcitrant plant lignocellulosic complex into simpler forms that can be utilized by the host. A metatranscriptomics approach was adopted to explore the metabolically active microbiota and the transcripts involved in the deconstruction of lignocellulose in Indian crossbred cattle rumen. The experimental animals were fed with mixed diet for a period of twenty-one days and the total RNA was isolated from the rumen digesta using a modified total RNA extraction protocol. After mRNA enrichment, the cDNA libraries were subjected to sequencing under Illumina HiSeq platform and generated about 2.89 GB of raw sequences. The contig assembly was accomplished using two different tools and the redundant sequences were removed before further processing. A total of 133,930 orfs were predicted from the assembled contigs using MetaGeneMark tool and the taxonomic affiliation of orfs were achieved using MEGAN 6.0 Community Edition. A total of 17 bacterial, 5 eukaryotic and 1 archaeal phylum were identified from rumen metatranscriptomic dataset. Phylum Bacteroidetes were acknowledged as the most abundant and metabolically active rumen bacterial populations in cattle rumen with 36,414 orfs corresponding to it, followed by Firmicutes with 6,349 orfs. Further, MEGAN annotation of metatranscriptomic data at species level revealed that Prevotella brevis and Prevotella ruminicola as the most metabolically active bacterial populations representing 4,022 and 2,725 orfs each. The functional annotation of metatranscriptomic data using COG database revealed that a large number of transcripts (~16%) were corresponding to translation, ribosomal structure and biogenesis and carbohydrate transport and metabolism (15%). dbCAN annotation of rumen metatranscriptomic data identified and classified 5,267 transcripts belonging to 168 CAZyme families (GH-52%, GT-26%, CBM-14%, CE-6%, PL-2% and AA-0%). The microbial community analysis of the CAZyme encoding transcripts using M5NR database revealed that a significant proportion of CAZymes were contributed by genera Prevotella (37%) and Bacteroides (21%). The cattle rumen microbiome metatranscriptome analysis presented in this study facilitated the detection of large number of transcripts encoding diverse CAZymes that actively take part in the hydrolysis of plant lignocellulose complex that may be useful for improving livestock and biofuel generation.

Effect of silkworm (Bombyx mori) pupae oil supplementation on enteric methane emission and methanogens diversity in sheep

In vitro and in vivo studies were conducted to examine the effect of silkworm pupae oil on methane (CH₄) emission and methanogens diversity. Five graded levels (2, 4, 6, 8 and 10%) of silkworm pupae oil were tested in vitro. Eighteen Mandya adult sheep were divided into three groups. All the animals were fed on similar basal diet except the oil supplementation in test groups. Oil level for supplementation was decided on the basis of in vitro study. In vitro study indicated a reduction of 22% in CH₄ production with 2% oil supplementation. Animals in test groups were supplemented with oil (2%) either daily (CON) or intermittently (INT) on every alternate week for all the seven days. A significant reduction of 17-20% in enteric CH₄ emission (g/d) was achieved due to oil supplementation in sheep. However, No variation was established between test groups CON and INT. In present study, Methanobrevibacter was major genus contributed ∼90% of the total rumen methanogens; whilst Methanobrevibacter gottschalkii was the most abundant methanogens species. Abundance of Methanobrevibacter ruminantium was affected with the oil supplementation. It can be concluded that the silkworm pupae oil at 2% can decrease CH₄ emission by 15-20%.

Assessment of Fecal Microflora Changes in Pigs Supplemented with Herbal Residue and Prebiotic

Antibiotic usage in animals as a growth promoter is considered as public health issue due to its negative impact on consumer health and environment. The present study aimed to evaluate effectiveness of herbal residue (ginger, Zingiber officinale, dried rhizome powder) and prebiotic (inulin) as an alternative to antibiotics by comparing fecal microflora composition using terminal restriction fragment length polymorphism. The grower pigs were offered feed containing antibiotic (tetracycline), ginger and inulin separately and un-supplemented group served as control. The study revealed significant changes in the microbial abundance based on operational taxonomic units (OTUs) among the groups. Presumptive identification of organisms was established based on the fragment length of OTUs generated with three restriction enzymes (MspI, Sau3AI and BsuRI). The abundance of OTUs representing Bacteroides intestinalis, Eubacterium oxidoreducens, Selonomonas sp., Methylobacterium sp. and Denitrobacter sp. was found significantly greater in inulin supplemented pigs. Similarly, the abundance of OTUs representing Bacteroides intestinalis, Selonomonas sp., and Phascolarcobacterium faecium was found significantly greater in ginger supplemented pigs. In contrast, the abundance of OTUs representing pathogenic microorganisms Atopostipes suicloacalis and Bartonella quintana str. Toulouse was significantly reduced in ginger and inulin supplemented pigs. The OTUs were found to be clustered under two major phylotypes; ginger-inulin and control-tetracycline. Additionally, the abundance of OTUs was similar in ginger and inulin supplemented pigs. The results suggest the potential of ginger and prebioticsto replace antibiotics in the diet of grower pig.

Enzymatic production of xylooligosaccharides from alkali solubilized xylan of natural grass (Sehima nervosum)

In this study, a process for producing XOS from Sehima nervosum grass was developed. The grass contains 28.1% hemicellulose. NaOH and steam application yielded 98% of original xylan in contrast to 85% by KOH application. Hydrolysis of xylan with commercial xylanase caused breakdown into XOS comprising of xylobiose, xylotriose along with xylose. Response surface model (RSM) revealed highest xylobiose yield (11 g/100g xylan) at pH 5.03, temperature 45.19°C, reaction time 10.11h with enzyme dose 17.41 U. Similarly for maximizing xylotriose yield, ideal hydrolysis conditions were pH 5.11, temperature 40.33°C, reaction time 16.55 h with enzyme dose 13.20 U. A two step process encompassing xylan fractionation and enzymatic hydrolysis enabled XOS production from the S. nervosum grass.

Effects of the Booroola (FecB) genotypes on growth performance, ewe's productivity efficiency and litter size in Garole x Malpura sheep

The present study was conducted to evaluate the effects of FecB genotypes on body weight, average daily gain (ADG), ewe's productivity efficiency (EPE) and litter size in FecB introgressed GarolexMalpura (GM) crossbred sheep. A total of 235 GM lambs were selected randomly and screened for FecB mutation using forced RFLP-PCR. The majority (69.8%) of GM individuals were carriers (BB and B+) for the FecB mutation and frequency of the FecB allele was about 0.40. The FecB genotypes were significantly (P<0.01) associated with the lamb's body weights from birth to 12 months of age. The generation wise (F(1), F(2) and F(3)), lamb's body weight did not differ significantly at birth, 6 and 12 months of the age, while it differed significantly (P<0.05) at 3 and 9 months of age. The ADG1 (0-3 months) was significantly associated (P<0.05), but not the ADG2 (3-6 months) and ADG3 (6-12 months) between genotypes. Type of birth and sex significantly (P<0.01) affected the body weight from birth to 12 months of age; and body weight of single born lambs was significantly higher (P<0.01) than that of twins and triplets from birth to 12 months of age. Type of birth significantly (P<0.01) affected the ADG1, but had no significant effect on ADG2 and ADG3. Year of birth did not affect the birth and weaning weights, but it significantly affected (P<0.01) the body weight and ADG's after weaning ages. The EPE was affected significantly (P<0.01) by the FecB genotypes at birth, 3 and 12 months of age. The EPE of B+ and BB ewes were 7.86 kg (36.9%) and 2.32 kg (10.9%) higher as compared to ++ ewes at 12 months of age, respectively. The mean litter size of BB ewes (2.17+/-0.24) was significantly higher (P<0.01) than that of B+ ewes (1.73+/-0.04) and ++ ewes (1.03+/-0.23). The present study indicated that the body weight and ADG of carrier lambs (BB and B+) was comparatively lower than that of non-carriers (++), while EPE of B+ ewes was comparatively higher than that of BB and ++ ewes. Further, it is interesting to note that heterozygous and homozygous state of individuals increased 0.70 and 1.14 extra lambs as compared to non-carriers (++), respectively.

Production of prolific microsheep by embryo transfer into large non-prolific sheep

The Garole is a prolific breed of microsheep that possesses the FecB gene, which increases ovulation rate. The purpose of this study was to compare embryo production by multiple ovulation in seven Garole ewes with that in seven normal size, non-prolific Malpura ewes, and assess the influence of the large body size of Awassi crossbred recipient ewes on the birth-weight of Garole lambs. Oestrus was synchronised with two intramuscular injections of 7.5 mg prostaglandin F(2alpha) administered 10 days apart. The donor ewes were superovulated by the use of pregnant mare serum gonadotrophin and follicle-stimulating hormone. The onset and duration of oestrus were similar in both breeds. The Garole donors had higher total mean (se) ovarian responses (15.6 [3.6] v 9.1 [2.3]), ovulation rate (13.6 [3.1] v 8.4 [2.2]) and produced more transferable embryos (6.0 [3.5] v 4.0 [0.9]) than the Malpura donors, but the differences were not statistically significant. The Garole lambs produced by embryo transfer were on average 57.8 per cent heavier at birth than contemporary Garole lambs produced by natural mating.

Detection of benzimidazole resistance in Haemonchus contortus using RFLP-PCR technique

Benzimidazole (BZ) resistance in Haemonchus contortus is linked primarily with the mutation in the beta-tubulin isotype 1 gene that substitute phenylalanine (Phe) to tyrosine (Tyr) at 200 codon of the gene. In the present study, a new restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) technique has been developed for detection of BZ resistance in the beta-tubulin isotype 1 gene of H. contortus. The technique utilizes two primers viz. AvikaF and AvikaR to amplify the region containing mutation in the beta-tubulin gene followed by restriction digestion. After digestion, the 'rr' individuals (homozygous resistant) revealed 257 and 48 bp bands, the 'rS' individuals (heterozygous) showed 305, 257 and 48 bp bands, while 'SS' individuals (homozygous susceptible) revealed uncut 305 bp band. A total of 162 adult male H. contortus collected from Avikanagar, Jaipur and Bikaner regions (54 from each region) were genotyped for analyzing BZ resistance in the beta-tubulin gene. Out of which, 130 adults were 'rr' types, 20 'rS' types and 12 'SS' types. The results showed that genotypic frequencies of different genotypes (rr, rS and SS) were highly significant difference among the three regions (P<0.001). The 'rr' individuals were higher (98%) in Jaipur followed by Avikanagar (93%) and Bikaner (50%) regions. Overall, the prevalence of BZ resistant allele (r) was higher (86%) as compared to BZ susceptible allele (S) (14%). The technique was also found suitable for genotyping of larvae of H. contortus and yielded reproducible results. The study indicated that RFLP-PCR is an easy, reproducible and less expensive than allele specific PCR. This technique will be helpful in establishing the prevalence rate of BZ resistance in H. contortus and can also be utilized for existing worm control programme.