Fishery independent survey datasets of abalone populations on subtidal coastal reefs in southeastern Australia.

Assessing the status or exploited marine fish populations often relies on fishery dependent catch and effort data reported by licensed commercial fishers in compliance with regulations and by recreational anglers voluntarily. This invariably leads to bias towards the fraction of a fish population or community that can be legally fished i.e., the stock as defined by legal minimum lengths and spatial boundaries. Data are restricted to populations which continue to be exploited at the expense of obtaining data on previously exploited and unexploited populations [1,2], so if a fishery is contracting spatially over time, then successively less of the overall fish community is monitored with bias towards where biomass is highest or most accessible [3]. A viable alternative is to conduct population monitoring surveys independently of a fishery to obtain information that is more broadly representative of the abundance, composition and size structure of fish communities and their supporting habitats [4-6]. Whereas catch and effort data often must be de-identified and aggregated to protect the confidentiality of fishers' commercial and personal interests, this constraint does not exist for independently acquired monitoring data, collected at public expense and hence publicly available at high levels of spatial and temporal resolution. Time series underpins the utility of fishery independent survey (FIS) datasets in terms of the life histories of exploited fish species and the time frames of their responses to various combinations of fishing mortality and environmental fluctuations and trends [7]. One-off surveys can establish a baseline and spatial distribution pattern, but regular surveys conducted consistently over time are necessary to detect trends from which population status can be inferred. We present several unique datasets focused on the commercially valuable blacklip abalone (Haliotis rubra), spanning three decades of annually collected data from up to 204 locations on subtidal rocky reefs along a coastline of almost 2500 km, the State of Victoria, Australia. It is rare for data to be collected consistently at this intensity over such a long period of monitoring [2], especially with surveys conducted by small teams of highly skilled research divers, some of whom up until recently had participated in every year. The data comprises ∼28,000 records from ∼4500 site surveys conducted during 1992 to 2021 [2]. Although the fixed site design remained unchanged, the number of sites surveyed varied over time, mostly increasing in number periodically, and the survey method was refined on several occasions. We defined three different variants in the survey method due to technological advancement for both enumerating abalone abundance and measuring shell size structure [7]. The relative abundance counts were standardized using a Bayesian generalized linear mixed model (GLMM) to test for interannual trends whilst allowing for inherent differences among sites, research divers, and their interactions [8].

Preweaning Nutrition and Its Effects on the Growth, Immune Competence and Metabolic Characteristics of the Dairy Calf.

Feeding increased volumes of milk in the preweaning phase has been shown to improve growth, morbidity and mortality rates in calves (Bos Taurus). This experiment enlisted 20 Holstein-Friesian dairy replacement calves from birth until weaning (at 10 weeks of age) and assessed the effect of feeding either 4 L (Low) or 8 L (High) of milk per calf per day on their growth, immune competence and metabolic characteristics. The responsiveness of these systems was compared through a vaccination immune challenge. Calves in the High treatment group were significantly heavier from two weeks of age and were 19 kg heavier than calves in the Low treatment group at weaning. Calves in the High treatment group also exhibited greater immune responses, with significantly higher white cell counts and neutrophil counts than calves in the Low treatment group post-vaccination. Calves in the High treatment group also had lower beta-hydroxybutyrate both pre- and post-vaccination, and higher glucose and insulin levels post-vaccination, indicating superior metabolic characteristics. Calves had ad libitum access to lucerne hay (Medicago sativa) and a commercial concentrate. Solid feed intakes were mostly the same between treatments, with differences in hay intake only detected at 7 and 8 weeks of age. Results from this experiment are indicative of a positive influence of accelerated preweaning nutrition on growth, immune response and metabolic characteristics.

The Preservation of the Effects of Preweaning Nutrition on Growth, Immune Competence and Metabolic Characteristics of the Developing Heifer.

This experiment investigated the preservation effects of two preweaning milk feeding nutritional treatments (High: 8 L and Low: 4 L milk per day) on 20, 12-month-old Holstein-Friesian dairy heifers (Bos taurus). A vaccination immune challenge was initially implemented on these 20 heifers at 6 weeks of age and the findings indicated superior growth, immune competence and favorable metabolic characteristics from the calves that had been fed 8 L milk per day. Postweaning, all heifers were treated the same under non-experimental conditions, and the immune challenge was repeated at 12 months of age for the current experiment. Consistent with the first immune challenge, heifers from the High preweaning treatment group still had higher white cell count and neutrophil count, indicating superior immune competence. The differences found in metabolic biomarkers, including beta-hydroxybutyrate, glucose and insulin, in the preweaning phase had disappeared, suggesting these biomarkers were influenced directly by the nutritional input at the time. There were no differences in NEFA levels between treatments at either stage of development. Postweaning, the heifers from the Low preweaning treatment group experienced accelerated growth with slightly numerically higher ADG (0.83 kg/day vs. 0.89 kg/day), resulting in the initial differences in bodyweight recorded at weaning being eliminated by 13 months of age. These results are evidence of a form of immunological developmental programming as a result of accelerated preweaning nutrition and therefore, are not supportive of restricted milk feeding of calves.

Dairy Cows Offered Fresh Chicory Instead of Ensiled Pasture during an Acute Heat Challenge Produced More Milk and Had Lower Body Temperatures.

The frequency, duration, and intensity of heat waves in Australia are increasing. To reduce the impact of heat waves on milk production, novel management strategies are required. Altering the forage type and amount offered affect the heat load on dairy cows and offer potential strategies to ameliorate the effects of hot weather. Thirty-two multiparous, lactating Holstein-Friesian cows were assigned one of four dietary treatments: chicory high amount, chicory low amount, pasture silage high amount, or pasture silage low amount. These cows were exposed to a heat wave in controlled-environment chambers. Cows that were offered fresh chicory had similar feed intake to cows that were offered pasture silage (15.3 kg DM/d). However, cows that were offered chicory produced greater energy-corrected milk (21.9 vs. 17.2 kg/d) and had a lower maximum body temperature (39.4 vs. 39.6 °C) than cows that were offered pasture silage overall. Cows that were offered the high amount of forage had greater feed intake (16.5 vs. 14.1 kg DM/d) and energy corrected milk yield (20.0 vs. 17.9 kg/d) than cows that were offered the low amount, as intended, but with no difference in maximum body temperature (39.5 °C). We conclude that feeding chicory instead of pasture silage to dairy cows shows promise as a dietary strategy to ameliorate the effect of heat exposure, and there was no advantage in restricting feed amount.

An Improved Approach to Automated Measurement of Body Condition Score in Dairy Cows Using a Three-Dimensional Camera System.

Body condition scoring is a valuable tool used to assess the changes in subcutaneous tissue reserves of dairy cows throughout the lactation resulting from changes to management or nutritional interventions. A subjective visual method is typically used to assign a body condition score (BCS) to a cow following a standardized scale, but this method is subject to operator bias and is labor intensive, limiting the number of animals that can be scored and frequency of measurement. An automated three-dimensional body condition scoring camera system is commercially available (DeLaval Body Condition Scoring, BCS DeLaval International AB, Tumba, Sweden), but the reliability of the BCS data for research applications is still unknown, as the system's sensitivity to change in BCS over time within cows has yet to be investigated. The objective of this study was to evaluate the suitability of an automated body condition scoring system for dairy cows for research applications as an alternative to visual body condition scoring. Thirty-two multiparous Holstein-Friesian cows (9 ± 6.8 days in milk) were body condition scored visually by three trained staff weekly and automatically twice each day by the camera for at least 7 consecutive weeks. Measurements were performed in early lactation, when the greatest differences in BCS of a cow over the lactation are normally present, and changes in BCS occur rapidly compared with later stages, allowing for detectable changes in a short timeframe by each method. Two data sets were obtained from the automatic body condition scoring camera: (1) raw daily BCS camera values and (2) a refined data set obtained from the raw daily BCS camera data by fitting a robust smooth loess function to identify and remove outliers. Agreement, precision, and sensitivity properties of the three data sets (visual, raw, and refined camera BCS) were compared in terms of the weekly average for each cow. Sensitivity was estimated as the ratio of response to precision, providing an objective performance criterion for independent comparison of methods. The camera body condition scoring method, using raw or refined camera data, performed better on this criterion compared with the visual method. Sensitivities of the raw BCS camera method, the refined BCS camera method, and the visual BCS method for changes in weekly mean score were 3.6, 6.2, and 1.7, respectively. To detect a change in BCS of an animal, assuming a decline of about 0.2 BCS (1-8 scale) per month, as was observed on average in this experiment, it would take around 44 days with the visual method, 21 days with the raw camera method, or 12 days with the refined camera method. This represents an increased capacity of both camera methods to detect changes in BCS over time compared with the visual method, which improved further when raw camera data were refined as per our proposed method. We recommend the use of the proposed refinement of the camera's daily BCS data for research applications.

Novel bioassay to assess antibiotic effects of fungal endophytes on aphids.

Perennial ryegrass is an important feed base for the dairy and livestock industries around the world. It is often infected with mutualistic fungal endophytes that confer protection to the plant against biotic and abiotic stresses. Bioassays that test their antibiotic effect on invertebrates are varied and range from excised leaves to whole plants. The aim of this study was to design and validate a "high-throughput" in-planta bioassay using 7-day-old seedlings confined in small cups, allowing for rapid assessments of aphid life history to be made while maintaining high replication and treatment numbers. Antibiosis was evaluated on the foliar and the root aphid species; Diuraphis noxia (Mordvilko) and Aploneura lentisci (Passerini) feeding on a range of perennial ryegrass-Epichloë festucae var. Lolii endophyte symbiota. As expected, both D. noxia and A. lentisci reared on endophyte-infected plants showed negatively affected life history traits by comparison to non-infected plants. Both species exhibited the highest mortality at the nymphal stage with an average total mortality across all endophyte treatments of 91% and 89% for D. noxia and A. lentisci respectively. Fecundity decreased significantly on all endophyte treatments with an average total reduction of 18% and 16% for D. noxia and A. lentisci respectively by comparison to non-infected plants. Overall, the bioassay proved to be a rapid method of evaluating the insecticidal activity of perennial ryegrass-endophyte symbiota on aphids (nymph mortality could be assessed in as little as 24 and 48 hours for D. noxia and A. lentisci respectively). This rapid and simple approach can be used to benchmark novel grass-endophyte symbiota on a range of aphid species that feed on leaves of plants, however we would caution that it may not be suitable for the assessment of root-feeding aphids, as this species exhibited relatively high mortality on the control as well.

Controls on species distribution and biogeochemical cycling in nitrate-contaminated groundwater and surface water, southeastern Australia.

A detailed study of groundwater and surface water nitrate over four seasons across an area of varied landuse provided insights into the mechanisms that underlie accumulation and transport of nitrate. High nitrate concentrations found in a significant percentage of surface water and shallow groundwater samples are due to anthropogenic contamination. Statistics (PCA, ANOVA, parsimonious model and general linear regression) were used to explore the relationship between NO3- and land use, and confirmed that areas of high NO3- concentration are associated with dairy pasture and horticulture. Seasonally, NO3- levels are greater during winter, the wettest part of the year. Values of δ15N showed that most nitrate is sourced from livestock waste, with a smaller contribution from synthetic fertilizer. Direct wash-off of animal waste from dairy farms results in higher NO3- concentrations in surface water than in groundwater. Denitrification is an important NO3- attenuation mechanism which reduces NO3- to NH4, as demonstrated by the PCA analysis, which showed positive correlation of NO3- concentrations with dissolved oxygen and negative correlations with NH4+, Fe2+and Mn2+; the latter two species may act as the electron donors necessary for reduction of NO3-. The often high NO3- concentrations in shallow groundwater are decreased by denitrification, which can occur at relatively shallow depths (<3 m). The relatively small NO3- concentrations in deeper groundwater are due partly to denitrification, but more to originally lower NO3- concentrations, as the age of deeper groundwater shows that it was recharged before agriculture was established in the study area. Overall, the study demonstrates the usefulness of hydrogeochemical characterisation and multivariate statistics in the evaluation of impacts of agricultural land-use on regional N cycling. In particular, the results show that efforts to mitigate NO3- pollution from farms should concentrate more on wash-off of animal waste than the contribution of nitrogenous synthetic fertilizer.

Development and Validation of a Phenotyping Computational Workflow to Predict the Biomass Yield of a Large Perennial Ryegrass Breeding Field Trial.

Increasing dry matter yield (DMY) is the most important objective in perennial ryegrass breeding programs. Current yield assessment methods like cutting are time-consuming and destructive, non-destructive measures such as scoring yield on single plants by visual inspection may be subjective. These assessments involve multiple measurements and selection procedures across seasons and years to evaluate biomass yield repeatedly. This contributes to the slow process of new cultivar development and commercialisation. This study developed and validated a computational phenotyping workflow for image acquisition, processing and analysis of spaced planted ryegrass and investigated sensor-based DMY yield estimation of individual plants through normalized difference vegetative index (NDVI) and ultrasonic plant height data extraction. The DMY of 48,000 individual plants representing 50 advanced breeding lines and commercial cultivars was accurately estimated at multiple harvests across the growing season. NDVI, plant height and predicted DMY obtained from aerial and ground-based sensors illustrated the variation within and between cultivars across different seasons. Combining NDVI and plant height of individual plants was a robust method to enable high-throughput phenotyping of biomass yield in ryegrass breeding. Similarly, the plot-level model indicated good to high-coefficients of determination (R 2) between the predicted and measured DMY across three seasons with R 2 between 0.19 and 0.81 and root mean square errors (RMSE) values ranging from 0.09 to 0.21 kg/plot. The model was further validated using a combined regression of the three seasons harvests. This study further sets a foundation for the application of sensor technologies combined with genomic studies that lead to greater rates of genetic gain in perennial ryegrass biomass yield.

Muscle Antioxidant Enzymes Activity and Gene Expression Are Altered by Diet-Induced Increase in Muscle Essential Fatty Acid (α-linolenic acid) Concentration in Sheep Used as a Model.

This study investigated the effect of dietary manipulations on muscle fatty acid composition, the activities and relative mRNA expressions of antioxidant enzymes and the relationship between muscle enzyme activity or mRNA expression and alpha linolenic acid (ALA) concentration in sheep. Eighty-four lambs blocked on liveweight were randomly allocated to four dietary treatments, lucerne pasture (Lucerne), annual ryegrass pasture (Ryegrass), feedlot pellets (Feedlot) or annual ryegrass plus feedlot pellets (RyeFeedlot). After six weeks of feeding, lambs were slaughtered and within 30 min post-mortem, samples collected from the longissimus lumborum (LL) muscle for RNA isolation and measurement of antioxidant enzyme activities. At 24 h post-mortem, LL samples were collected for determination of fatty acid concentrations. Feedlot treatment decreased ALA, eicosapentaenoic (EPA), docosapentaenoic (DPA) and docosahexaenoic (DHA) concentrations compared with other treatments and increased linoleic acid (LA) and arachidonic acid (AA) compared with Lucerne and Ryegrass (p < 0.001). The activity of Glutathione peroxidase (GPX1, p < 0.001) and Superoxide dismutase (SOD2, p < 0.001) enzymes in the muscle increased with Lucerne compared to other treatments. Lucerne increased muscle gpx1 mRNA expression by 1.74-fold (p = 0.01) and 1.68-fold (p = 0.05) compared with Feedlot and other diets, respectively. The GPX1 (r² = 0.319, p = 0.002) and SOD2 (r² = 0.244, p = 0.009) enzyme activities were positively related to ALA. There was a positive linear relationship between muscle gpx1 (r² = 0.102, p = 0.017) or sod2 (r² = 0.049, p = 0.09) mRNA expressions and ALA concentration. This study demonstrates that diet can affect concentrations of ALA and other fatty acids as well as change activities and gene expression of antioxidant enzymes in muscle. Increased antioxidant activity may, in turn, have beneficial effects on the performance, health and wellbeing of animals and humans.