The AFBI Repository
Not a member yet
442 research outputs found
Sort by
Effects of grassland management on plant C:N:P stoichiometry: implications for soil element cycling and storage
Get PDFPublication history: Accepted - 30 August 2017; Published online - 5 October 2017.The functioning of human-managed grassland ecosystems strongly depends on how common
management practices (e.g., animal grazing and the chronic addition of fertilizing materials to soils) interact to influence plant and soil element stoichiometry. Here we use data from a 22-yr-long grassland experiment to address whether and how plant element stoichiometry (i.e., carbon [C], nitrogen [N], phosphorus
[P] ratios) might respond to (1) animal grazing, (2) agricultural liming (i.e., CaCO3) applications, and (3)
nutrient fertilization. We also ask whether plant C:N:P stoichiometry could predict changes in soil N and P
availability and in soil C, N, and P stocks. We found that grassland management significantly affected
plant C:N:P ratios as predicted by ecological stoichiometry theory. For example, plant aboveground and
belowground C:N and C:P ratios decreased under chronic N and P fertilization, respectively. Plant C:N
and C:P ratios were significantly greater in unfertilized (control) soils. Also plant C:N ratios were highest
under P-only additions, whereas plant C:P ratios were highest under N-only additions. However, unpredictable changes in C:N:P ratios also occurred, suggesting that plant tissue chemistry may not be a simple
reflection of soil nutrient availability. Changes in plant C:nutrient ratios well predicted variation in soil
nutrient availability, but not in soil C, N, and P stocks. Contrary to expectations, soil C stocks significantly
increased with decreasing plant C:N ratios in the nutrient-fertilized grasslands and not with increasing
plant C:N ratios in the unfertilized grasslands. We suggest that a better mechanistic understanding of the
negative relationship between plant C:N stoichiometry and soil C accrual will greatly help in improving
the sustainability of human-managed grasslands.This study was funded by a DELNI (Northern Ireland) postgraduate studentship
Methane Emissions from Grazing Holstein-Friesian Heifers at Different Ages Estimated Using the Sulfur Hexafluoride Tracer Technique
Get PDFPublication history: Accepted - 9 May 2017; Published online - 17 May 2017Although the effect of animal and diet factors on enteric methane (CH4) emissions from confined cattle has
been extensively examined, less data is available regarding CH4 emissions from grazing young cattle. A study
was undertaken to evaluate the effect of the physiological state of Holstein-Friesian heifers on their enteric
CH4 emissions while grazing a perennial ryegrass sward. Two experiments were conducted: Experiment 1
ran from May 2011 for 11 weeks and Experiment 2 ran from August 2011 for 10 weeks. In each experiment,
Holstein-Friesian heifers were divided into three treatment groups (12 animals/group) consisting of calves,
yearling heifers, and in-calf heifers (average ages: 8.5, 14.5, and 20.5 months, respectively). Methane emissions were estimated for each animal in the final week of each experiment using the sulfur hexafluoride
tracer technique. Dry matter (DM) intake was estimated using the calculated metabolizable energy (ME)
requirement divided by the ME concentration in the grazed grass. As expected, live weight increased with
increasing animal age (P < 0.001); however, there was no difference in live weight gain among the three
groups in Experiment 1, although in Experiment 2, this variable decreased with increasing animal age
(P < 0.001). In Experiment 1, yearling heifers had the highest CH4 emissions (g·d–1) and in-calf heifers produced more than calves (P < 0.001). When expressed as CH4 emissions per unit of live weight, DM intake,
and gross energy (GE) intake, yearling heifers had higher emission rates than calves and in-calf heifers
(P < 0.001). However, the effects on CH4 emissions were different in Experiment 2, in which CH4 emissions
(g·d–1) increased linearly with increasing animal age (P < 0.001), although the difference between yearling
and in-calf heifers was not significant. The CH4/live weight ratio was lower in in-calf heifers than in the other two groups (P < 0.001), while CH4 energy output as a proportion of GE intake was lower in calves than in
yearling and in-calf heifers (P < 0.05). All data were then pooled and used to develop prediction equations for
CH4 emissions. All relationships are significant (P < 0.001), with R2
values ranging from 0.630 to 0.682. These
models indicate that CH4 emissions could be increased by 0.252 g·d–1 with an increase of 1 kg live weight
or by 14.9 g·d–1 with an increase of 1 kg·d–1 of DM intake; or, the CH4 energy output could be increased by
0.046 MJ·d–1 with an increase of 1 MJ·d–1 of GE intake. These results provide an alternative approach for estimating CH4 emissions from grazing dairy heifers when actual CH4 emission data are not availableThe study was funded by the Department for Environment Food
& Rural Affairs, the Scottish Government, the Department of Agriculture and Rural Development for Northern Ireland, and the Welsh
Government, as part of the UK’s Agricultural GHG Research Platform
initiativ
The effect of floor type on the performance, cleanliness, carcass characteristics and meat quality of dairy origin bulls
Get PDFPublication history: Accepted - 8 August 2017; Published online - 2 October 2017The aim of this study was to evaluate the effect of using different floor types to accommodate growing and finishing beef cattle on their performance, cleanliness, carcass characteristics and meat quality. In total, 80 dairy origin young bulls (mean initial live weight 224 kg (SD=28.4 kg)) were divided into 20 blocks with four animals each according to live weight. The total duration of the experimental period was 204 days. The first 101 days was defined as the growing period, with the remainder of the study defined as the finishing period. Cattle were randomly assigned within blocks to one of four floor type treatments, which included fully slatted flooring throughout the entire experimental period (CS); fully slatted flooring covered with rubber strips throughout the entire experimental period (RS); fully slatted flooring during the growing period and moved to a solid floor covered with straw bedding during the finishing period (CS-S) and fully slatted flooring during the growing period and moved to fully slatted flooring covered with rubber strips during the finishing period (CS-RS). Bulls were offered ad libitum grass silage supplemented with concentrates during the growing period. During the finishing period, bulls were offered concentrates supplemented with chopped barley straw. There was no significant effect of floor type on total dry matter intake (DMI), feed conversion ratio, daily live weight gain or back fat depth during the growing and finishing periods. Compared with bulls accommodated on CS, RS and CS-RS, bulls accommodated on CS-S had a significantly lower straw DMI (P<0.01). Although bulls accommodated on CS and CS-S were significantly dirtier compared with those accommodated on RS and CS-RS on days 50 (P<0.05) and 151 (P<0.01), there was no effect of floor type on the cleanliness of bulls at the end of the growing and finishing periods. There was also no significant effect of floor type on carcass characteristics or meat quality. However, bulls accommodated on CS-S had a tendency for less channel, cod and kidney fat (P=0.084) compared with those accommodated on CS, RS and CS-RS. Overall, floor type had no effect on the performance, cleanliness, carcass characteristics or meat quality of growing or finishing beef cattle.This research project was funded by the Department of Agriculture, Environment and Rural Affairs in Northern Irelan
The effect of foraging and ontogeny on the prevalence and intensity of the invasive parasite Anguillicola crassus in the European eel Anguilla anguilla
Get PDFPublication history: Accepted - 10 November 2016; Published online - 13 January 2017.Infection patterns of the invasive Anguillicola crassus
nematode were investigated in a population of
the European eel Anguilla anguilla where parasite
invasion is very recent, Loch Lomond, Scotland.
Intensity levels of the parasite were associated with
differences in fish ontogeny and trophic ecology.
Although eels foraged on both fish and invertebrates,
individuals which were smaller and fed on
invertebrates (>70% contribution to diet) were
found to contain a greater number of swim bladder
parasites compared to larger eel with a predominance
of fish (>60% contribution) in their
diet. Within affected fish, a significant negative
relationship was found between fish length and
parasite intensity, with smaller individuals having
higher parasite intensity than larger individuals.
This study indicates that food intake and infection
risk are linked in this recently infected host–parasite
system. From a management perspective
increasing our understanding of how infection
intensity and repeated exposure is linked to
resource use in an ecosystem is important for the
future management of this endangered species in
Europe.This work was supported by funding from the
European Union’s INTERREG IVA Programme
(project 2859 ‘IBIS’) managed by the Special EU
Programmes Body.
Stable isotope
analysis was undertaken at the NERC Life
Sciences Mass Spectrometry Facility SUERC East
Kilbride Glasgow G750QF UK :award code
EK212-06/13
RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity
Get PDFPublication history: Accepted - 4 January 2017; Published online - 1 February 2017.The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops (Pecten maximus) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher Fst values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying population structure and phenotypic plasticity in natural populations
Nematode neuropeptides as transgenic nematicides
Get PDFNDW was supported by a Bill and Melinda Gates Foundation grand challenge exploration grant. LW was supported by a PhD studentship from the EUPHRESCO Plant Health Fellowship Scheme, and an Eaton Visitorship Award. JJD was supported by a Leverhulme Trust early career fellowship and a Bill and Melinda Gates Foundation grand challenge exploration grant.Plant parasitic nematodes (PPNs) seriously threaten global food security. Conventionally an
integrated approach to PPN management has relied heavily on carbamate, organophosphate and fumigant nematicides which are now being withdrawn over environmental health
and safety concerns. This progressive withdrawal has left a significant shortcoming in our
ability to manage these economically important parasites, and highlights the need for novel
and robust control methods. Nematodes can assimilate exogenous peptides through retrograde transport along the chemosensory amphid neurons. Peptides can accumulate within
cells of the central nerve ring and can elicit physiological effects when released to interact
with receptors on adjoining cells. We have profiled bioactive neuropeptides from the neuropeptide-like protein (NLP) family of PPNs as novel nematicides, and have identified numerous discrete NLPs that negatively impact chemosensation, host invasion and stylet thrusting
of the root knot nematode Meloidogyne incognita and the potato cyst nematode Globodera
pallida. Transgenic secretion of these peptides from the rhizobacterium, Bacillus subtilis, and
the terrestrial microalgae Chlamydomonas reinhardtii reduce tomato infection levels by up to
90% when compared with controls. These data pave the way for the exploitation of nematode
neuropeptides as a novel class of plant protective nematicide, using novel non-food transgenic delivery systems which could be deployed on farmer-preferred cultivars
Nitrogen dynamics and phytoplankton community structure: the role of organic nutrients
Get PDFPublication history: Accepted - 7 June 2017; Published online - 15 June 2017.Dissolved organic nitrogen (DON) is
recognised as an important N source for phytoplankton. However, its relative importance for phytoplankton nutrition and community composition has not
been studied comprehensively. This study, conducted
in a typical Scottish fjord, representative of nearpristine coastal environments, evaluates the utilisation
of DON and dissolved inorganic nitrogen (DIN) by
different microbial size fractions and the relationship
of phytoplankton community composition with DON
and other parameters. The study demonstrated that
DON was important in supporting phytoplankton
throughout the yearly production cycle. The higherthan-expected urea uptake rates and large fraction of
the spring bloom production supported by DON
suggested that organic N not only contributes to
regenerated production and to the nutrition of the
small phytoplankton fraction, but can also contribute
substantially to new production of the larger phytoplankton in coastal waters. Multivariate statistical
techniques revealed two phytoplankton assemblages
with peaks in abundance at different times of the year:
a spring group dominated by Skeletonema spp.,
Thalassiosira spp., and Pseudo-nitzschia spp. group
delicatissima; and a summer/autumn group dominated
by Chaetoceros spp., Scrippsiella spp., and Pseudonitzschia spp. group seriata. The multivariate pattern
in community composition and abundance of these
taxa was significantly correlated with the multivariate
pattern of DON, urea, dissolved free amino acids,
DIN, temperature, salinity, and daylength, with daylength and urea being particularly important, suggesting both physical and chemical controls on community
composition.The authors wish to acknowledge the National Environment Research Council (NERC) for funding and the officers and crew of RV Seòl Mara for assisting with sample collection. This is contribution number 5318 from the University of Maryland Center for Environmental Science
Fine-mapping host genetic variation underlying outcomes to Mycobacterium bovis infection in dairy cows
Get PDFPublication history: Accepted - 31 May 2017; Published online - 24 June 2017.Background: Susceptibility to Mycobacterium bovis infection in cattle is governed in part by host genetics.
However, cattle diagnosed as infected with M. bovis display varying signs of pathology. The variation in host
response to infection could represent a continuum since time of exposure or distinct outcomes due to differing
pathogen handling. The relationships between host genetics and variation in host response and pathological
sequelae following M. bovis infection were explored by genotyping 1966 Holstein-Friesian dairy cows at 538,231
SNPs with three distinct phenotypes. These were: single intradermal cervical comparative tuberculin (SICCT) test
positives with visible lesions (VLs), SICCT-positives with undetected visible lesions (NVLs) and matched controls
SICCT-negative on multiple occasions.
Results: Regional heritability mapping identified three loci associated with the NVL phenotype on chromosomes
17, 22 and 23, distinct to the region on chromosome 13 associated with the VL phenotype. The region on
chromosome 23 was at genome-wide significance and candidate genes overlapping the mapped window included
members of the bovine leukocyte antigen class IIb region, a complex known for its role in immunity and disease
resistance. Chromosome heritability analysis attributed variance to six and thirteen chromosomes for the VL and
NVL phenotypes, respectively, and four of these chromosomes were found to explain a proportion of the
phenotypic variation for both the VL and NVL phenotype. By grouping the M. bovis outcomes (VLs and NVLs)
variance was attributed to nine chromosomes. When contrasting the two M. bovis infection outcomes (VLs vs NVLs)
nine chromosomes were found to harbour heritable variation. Regardless of the case phenotype under
investigation, chromosome heritability did not exceed 8% indicating that the genetic control of bTB resistance
consists of variants of small to moderate effect situated across many chromosomes of the bovine genome.
Conclusions: These findings suggest the host genetics of M. bovis infection outcomes is governed by distinct and
overlapping genetic variants. Thus, variation in the pathology of M. bovis infected cattle may be partly genetically
determined and indicative of different host responses or pathogen handling. There may be at least three distinct
outcomes following M. bovis exposure in dairy cattle: resistance to infection, infection resulting in pathology or no
detectable pathologyWe acknowledge financial support from the Biotechnology and
Biological Sciences Research Council through CEDFAS initiative grants
BB/E018386/1 and BB/E018335/1 and 2 and Animal Health Research Club
grant BB/L004054/1; EJ Glass, JA Woolliams and SC Bishop were also
supported by the Biotechnology and Biological Sciences Research
Council (BBSRC) Institute Strategic Programme Grants (ISP3 Innate
Immunity & Endemic Disease) [BB/J004227/1], (ISP1 Analysis and
Prediction in Complex Animal Systems) [BB/J004235/1] and (ISP2 Control
of Infectious Diseases) [BB/P013740/1]
Evidence of non-extractable florfenicol residues: The development and validation of a confirmatory method for total florfenicol content in kidney by UPLC-MS/MS
Get PDFPublication history: Accepted - 27 March 2016; Published online - 20 May 2016.The parent compound florfenicol (FF) is a broad-spectrum antibacterial compound licensed in the UK for use in cattle, pigs and the aquaculture industry. The analysis of porcine tissues in this study demonstrates that significant amounts of solvent non-extractable FF-related residues are present in incurred tissues (kidney and muscle) from treated animals. The results indicate that methods based on solvent extraction alone may carry a significant risk of reporting false-negative results. The use of a strong acid hydrolysis step prior to solvent extraction of tissue samples is necessary for an accurate estimate of the total tissue FF content. A robust and sensitive method for the determination of total FF residue content in kidney samples by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) has been developed and validated. This method covers the synthetic amphenicol drug FF and its metabolites, measured as the marker residue florfenicol amine (FFA) as per Commission Regulation (EU) No. 37/2010. Non-extractable and intermediate metabolites are converted to the hydrolysis product FFA, and then partitioned into ethyl acetate. Extracts are solvent exchanged prior to a dispersive solid-phase extraction step, then analysed using an alkaline reverse-phase gradient separation by UPLC-MS/MS. The method was validated around the maximum residue levels (MRLs) set out in Regulation (EU) No. 37/2010 for bovine kidney in accordance with Commission Decision No. 2002/657/EC. The following method performance characteristics were assessed during a single laboratory validation study: selectivity, specificity, sensitivity, linearity, matrix effects, accuracy and precision (decision limit (CCα) and detection capability (CCβ) were determined)
Genetic diversity of ruminant Pestivirus strains collected in Northern Ireland between 1999 and 2011 and the role of live ruminant imports
Get PDFBackground: The genus pestivirus within the family Flaviviridae includes bovine viral diarrhoea virus (BVDV) types 1
and 2, border disease virus (BDV) and classical swine fever virus. The two recognised genotypes of BVDV are divided
into subtypes based on phylogenetic analysis, namely a-p for BVDV-1 and a-c for BVDV-2.
Methods: Three studies were conducted to investigate the phylogenetic diversity of pestiviruses present in
Northern Ireland. Firstly, pestiviruses in 152 serum samples that had previously tested positive for BVDV between
1999 and 2008 were genotyped with a RT-PCR assay. Secondly, the genetic heterogeneity of pestiviruses from
91 serum samples collected between 2008 and 2011 was investigated by phylogenetic analysis of a 288 base
pair portion of the 5’ untranslated region (UTR). Finally, blood samples from 839 bovine and 4,437 ovine animals
imported in 2010 and 2011 were tested for pestiviral RNA. Analysis of animal movement data alongside the
phylogenetic analysis of the strains was carried out to identify any links between isolates and animal movement.
Results: No BVDV-2 strains were detected. All of the 152 samples in the first study were genotyped as BVDV-1.
Phylogenetic analysis indicated that the predominant subtype circulating was BVDV-1a (86 samples out of 91).
The remaining five samples clustered close to reference strains in subtype BVDV-1b. Out of the imported animals,
18 bovine samples tested positive and 8 inconclusive (Ct ≥36), while all ovine samples were negative. Eight
sequences were obtained and were defined as BVDV-1b. Analysis of movement data between herds failed to find
links between herds where BVDV-1b was detected.
Conclusion: Given that only BVDV-1a was detected in samples collected between 1968 and 1999, this study
suggests that at least one new subtype has been introduced to Northern Ireland between 1999 and 2011 and
highlights the potential for importation of cattle to introduce new strains.
Keywords: Bovine viral diarrhoea virus, Phylogenetic analysis, 5’untranslated region, Importatio