South Australian Research and Development Institute

Transgenic plants expressing insecticidal proteins from the bacterium, Bacillus thuringiensis (Bt), are revolutionizing agriculture. Bt, which had limited use as a foliar insecticide, has become a major insecticide because genes that produce Bt toxins have been engineered into major crops grown on 11.4 million ha worldwide in 2000. Based on the data collected to date, generally these crops have shown positive economic benefits to growers and reduced the use of other insecticides. The potential ecological and human health consequences of Bt plants, including effects on nontarget organisms, food safety, and the development of resistant insect populations, are being compared for Bt plants and alternative insect management strategies. Scientists do not have full knowledge of the risks and benefits of any insect management strategies. Bt plants were deployed with the expectation that the risks would be lower than current or alternative technologies and that the benefits would be greater. Based on the data to date, these expectations seem valid.

SUMMARY In designed experiments and in particular longitudinal studies, the aim may be to assess the effect of a quantitative variable such as time on treatment effects. Modelling treatment effects can be complex in the presence of other sources of variation. Three examples are presented to illustrate an approach to analysis in such cases. The first example is a longitudinal experiment on the growth of cows under a factorial treatment structure where serial correlation and variance heterogeneity complicate the analysis. The second example involves the calibration of optical density and the concentration of a protein DNase in the presence of sampling variation and variance heterogeneity. The final example is a multienvironment agricultural field experiment in which a yield–seeding rate relationship is required for several varieties of lupins. Spatial variation within environments, heterogeneity between environments and variation between varieties all need to be incorporated in the analysis. In this paper, the cubic smoothing spline is used in conjunction with fixed and random effects, random coefficients and variance modelling to provide simultaneous modelling of trends and covariance structure. The key result that allows coherent and flexible empirical model building in complex situations is the linear mixed model representation of the cubic smoothing spline. An extension is proposed in which trend is partitioned into smooth and non-smooth components. Estimation and inference, the analysis of the three examples and a discussion of extensions and unresolved issues are also presented.

Contrasting regional changes in Southern Ocean sea ice have occurred over the last 30 years with distinct regional effects on ecosystem structure and function. Quantifying how Antarctic predators respond to such changes provides the context for predicting how climate variability/change will affect these assemblages into the future. Over an 11-year time-series, we examine how inter-annual variability in sea ice concentration and advance affect the foraging behaviour of a top Antarctic predator, the southern elephant seal. Females foraged longer in pack ice in years with greatest sea ice concentration and earliest sea ice advance, while males foraged longer in polynyas in years of lowest sea ice concentration. There was a positive relationship between near-surface meridional wind anomalies and female foraging effort, but not for males. This study reveals the complexities of foraging responses to climate forcing by a poleward migratory predator through varying sea ice property and dynamic anomalies.

All is not well for biodiversity in the tropics. Despite recent debate over the extent of future tropical extinctions and the effectiveness of reserve systems, the continued disappearance of habitat, soaring human population, and loss of vital ecosystem services demand immediate action. This crisis is worrying, given that tropical regions support over two‐thirds of all known species and are populated by some of the world's poorest people, who have little recourse to lower environmental‐impact lifestyles. Recent evidence has shown that – in addition to unabated rates of forest loss – coastal development, overexploitation of wildlife, catchment modification, and habitat conversion are threatening human well‐being. We argue that the recent technical debate about likely extinctions masks the real issue – that, to prevent further loss of irreplaceable tropical biodiversity, we must err on the side of caution. We need to avoid inadvertently supporting political agendas that assume low future extinction rates, because this will result in further destruction of tropical biodiversity.

Fungal trunk diseases are some of the most destructive diseases of grapevine in all grape growing areas of the world. Management of GTDs has been intensively studied for decades with some great advances made in our understanding of the causal pathogens, their epidemiology, impact, and control. However, due to the breadth and complexity of the problem, no single effective control measure has been developed. Management of GTD must be holistic and integrated, with an interdisciplinary approach conducted in both nurseries and vineyards that integrates plant pathology, agronomy, viticulture, microbiology, epidemiology, biochemistry, physiology, and genetics. In this review, we identify a number of areas of future prospect for effective management of GTDs worldwide, which, if addressed, will provide a positive outlook on the longevity of vineyards in the future.

Abstract The burgeoning global market for soil microbial inoculants for use in agriculture is being driven by pressure to increase sustainable crop production by managing pests and diseases without environmental impacts. Microbial inoculants, based predominantly on bacteria and fungi, are applied to soil as alternatives to conventional inorganic fertilizers (biofertilizers) or to carry out specific functions including biocontrol of pests and diseases (biopesticides), or for bioremediation and enhancement of soil characteristics. While some soil inoculants such as rhizobia have a long and successful history of use, others have performed inconsistently in the field and failed to live up to their promise suggested by laboratory testing. A more precise understanding of the ecology and modes of action of inoculant strains is key to optimizing their efficacy and guiding their targeted use to situations where they address key limitations to crop production. This will require greater collaboration between science disciplines, including microbiology, plant and soil science, molecular biology and agronomy. Inoculants must be produced and formulated to ensure their effective establishment in the soil and practicality of implementation alongside existing cropping practices. New approaches to strain selection and construction of beneficial microbial consortia should lead to more efficacious inoculant products. Extensive and rigorous field evaluation of inoculants under a range of soil and environmental conditions has rarely been undertaken and is urgently needed to validate emerging inoculant products and underpin successful implementation by growers, especially in a market that is largely unregulated at present.

Key points Three weeks of intensified training and mild energy deficit in elite race walkers increases peak aerobic capacity independent of dietary support. Adaptation to a ketogenic low carbohydrate, high fat (LCHF) diet markedly increases rates of whole‐body fat oxidation during exercise in race walkers over a range of exercise intensities. The increased rates of fat oxidation result in reduced economy (increased oxygen demand for a given speed) at velocities that translate to real‐life race performance in elite race walkers. In contrast to training with diets providing chronic or periodised high carbohydrate availability, adaptation to an LCHF diet impairs performance in elite endurance athletes despite a significant improvement in peak aerobic capacity. Abstract We investigated the effects of adaptation to a ketogenic low carbohydrate (CHO), high fat diet (LCHF) during 3 weeks of intensified training on metabolism and performance of world‐class endurance athletes. We controlled three isoenergetic diets in elite race walkers: high CHO availability (g kg −1 day −1 : 8.6 CHO, 2.1 protein, 1.2 fat) consumed before, during and after training (HCHO, n = 9); identical macronutrient intake, periodised within or between days to alternate between low and high CHO availability (PCHO, n = 10); LCHF (< 50 g day −1 CHO; 78% energy as fat; 2.1 g kg −1 day −1 protein; LCHF, n = 10). Post‐intervention, during race walking increased in all groups ( P < 0.001, 90% CI: 2.55, 5.20%). LCHF was associated with markedly increased rates of whole‐body fat oxidation, attaining peak rates of 1.57 ± 0.32 g min −1 during 2 h of walking at ∼80% . However, LCHF also increased the oxygen (O 2 ) cost of race walking at velocities relevant to real‐life race performance: O 2 uptake (expressed as a percentage of new ) at a speed approximating 20 km race pace was reduced in HCHO and PCHO (90% CI: −7.047, −2.55 and −5.18, −0.86, respectively), but was maintained at pre‐intervention levels in LCHF. HCHO and PCHO groups improved times for 10 km race walk: 6.6% (90% CI: 4.1, 9.1%) and 5.3% (3.4, 7.2%), with no improvement (−1.6% (−8.5, 5.3%)) for the LCHF group. In contrast to training with diets providing chronic or periodised high‐CHO availability, and despite a significant improvement in , adaptation to the topical LCHF diet negated performance benefits in elite endurance athletes, in part due to reduced exercise economy.

Three broiler feeding trials were investigated in order to identify gut bacteria consistently linked with improvements in bird performance as measured by feed efficiency. Trials were done in various geographic locations and varied in diet composition, broiler breed, and bird age. Gut microbial communities were investigated using microbial profiling. Eight common performance-linked operational taxonomic units (OTUs) were identified within both the ilea (180, 492, and 564-566) and ceca (140-142, 218-220, 284-286, 312, and 482) across trials. OTU 564-566 was associated with lower performance, while OTUs 140-142, 482, and 492 were associated with improved performance. Targeted cloning and sequencing of these eight OTUs revealed that they represented 26 bacterial species or phylotypes which clustered phylogenetically into seven groups related to Lactobacillus spp., Ruminococcaceae, Clostridiales, Gammaproteobacteria, Bacteroidales, Clostridiales/Lachnospiraceae, and unclassified bacteria/clostridia. Where bacteria were identifiable to the phylum level, they belonged predominantly to the Firmicutes, with Bacteroidetes and Proteobacteria also identified. Some of the potential performance-related phylotypes showed high sequence identity with classified bacteria (Lactobacillus salivarius, Lactobacillus aviarius, Lactobacillus crispatus, Faecalibacterium prausnitzii, Escherichia coli, Gallibacterium anatis, Clostridium lactatifermentans, Ruminococcus torques, Bacteroides vulgatus, and Alistipes finegoldii). The 16S rRNA gene sequence information generated will allow quantitative assays to be developed which will enable elucidations of which of these phylotypes are truly performance related. This information could be used to monitor strategies to improve feed efficiency and feed formulation for optimal gut health.

Aims Australia is among one of the world’s wealthiest nations; yet, its relatively small human population (22.5 million) has been responsible for extensive deforestation and forest degradation since European settlement in the late 18th century. Despite most (∼75%) of Australia's 7.6 million-km2 area being covered in inhospitable deserts or arid lands generally unsuitable to forest growth, the coastal periphery has witnessed a rapid decline in forest cover and quality, especially over the last 60 years. Here I document the rates of forest loss and degradation in Australia based on a thorough review of existing literature and unpublished data. Important Findings Overall, Australia has lost nearly 40% of its forests, but much of the remaining native vegetation is highly fragmented. As European colonists expanded in the late 18th and the early 19th centuries, deforestation occurred mainly on the most fertile soils nearest to the coast. In the 1950s, southwestern Western Australia was largely cleared for wheat production, subsequently leading to its designation as a Global Biodiversity Hotspot given its high number of endemic plant species and rapid clearing rates. Since the 1970s, the greatest rates of forest clearance have been in southeastern Queensland and northern New South Wales, although Victoria is the most cleared state. Today, degradation is occurring in the largely forested tropical north due to rapidly expanding invasive weed species and altered fire regimes. Without clear policies to regenerate degraded forests and protect existing tracts at a massive scale, Australia stands to lose a large proportion of its remaining endemic biodiversity. The most important implications of the degree to which Australian forests have disappeared or been degraded are that management must emphasize the maintenance of existing primary forest patches, as well as focus on the regeneration of matrix areas between fragments to increase native habitat area, connectivity and ecosystem functions.

There is concern about historical and continuing loss of canopy-forming algae across the world's temperate coastline. In South Australia, the sparse cover of canopy-forming algae on the Adelaide metropolitan coast has been of public concern with continuous years of anecdotal evidence culminating in 2 competing views. One view considers that current patterns existed before the onset of urbanisation, whereas the alternate view is that they developed after urbanisation. We tested hypotheses to distinguish between these 2 models, each centred on the reconstruction of historical covers of canopies on the metropolitan coast. Historically, the metropolitan sites were indistinguishable from contemporary populations of reference sites across 70 km (i.e. Gulf St. Vincent), and could also represent a random subset of exposed coastal sites across 2100 km of the greater biogeographic province. Thus there was nothing 'special' about the metropolitan sites historically, but today they stand out because they have sparser covers of canopies compared to equivalent locations and times in the gulf and the greater province. This is evidence of wholesale loss of canopy-forming algae (up to 70%) on parts of the Adelaide metropolitan coast since major urbanisation. These findings not only set a research agenda based on the magnitude of loss, but they also bring into question the logic that smaller metropolitan populations of humans create impacts that are trivial relative to that of larger metropolitan centres. Instead, we highlight a need to recognise the ecological context that makes some coastal systems more vulnerable or resistant to increasing human-domination of the world's coastlines. We discuss challenges to this kind of research that receive little ecological discussion, particularly better leadership and administration, recognising that the systems we study out-live the life spans of individual research groups and operate on spatial scales that exceed the capacity of single research providers.

study area was trawled, and 86% was not trawled. Trawling activity was aggregated; the most intensively trawled areas accounting for 90% of activity comprised 77% of footprint on average. Regional swept area ratio (SAR; ratio of total swept area trawled annually to total area of region, a metric of trawling intensity) and footprint area were related, providing an approach to estimate regional trawling footprints when high-resolution spatial data are unavailable. If SAR was ≤0.1, as in 8 of 24 regions, there was >95% probability that >90% of seabed was not trawled. If SAR was 7.9, equal to the highest SAR recorded, there was >95% probability that >70% of seabed was trawled. Footprints were smaller and SAR was ≤0.25 in regions where fishing rates consistently met international sustainability benchmarks for fish stocks, implying collateral environmental benefits from sustainable fishing.

Some 290 species of squids comprise the order Teuthida that belongs to the molluscan Class Cephalopoda. Of these, about 30-40 squid species have substantial commercial importance around the world. Squid fisheries make a rather small contribution to world landings from capture fisheries relative to that of fish, but the proportion has increased steadily over the last decade, with some signs of recent leveling off. The present overview describes all substantial squid fisheries around the globe. The main ecological and biological features of exploited stocks,

Global declines of shark populations are of concern because of their largely assumed role as moderators of ecosystem function. Without long-term data on movement patterns for many species, it is impossible to infer relative extinction risk, which varies as a function of range, dispersal and habitat specificity and use. The past 50 yr of research on coastal sharks has revealed common movement patterns among species. In the horizontal plane, measured home range size generally increases with body size. We demonstrate meta-analytically the effects of increasing body size and monitoring time on home range size. Changes in the extent of horizontal movement might arise from ontogeny, predator avoidance or environmental tolerances. In the vertical plane, movement patterns include oscillatory vertical displacement, surface swimming, diel vertical migration and swimming at depth. These vertical movements are often attributed to foraging or navigation, but have been quantified less than horizontal patterns. Habitat specificity is often correlated with environmental conditions such as depth, salinity, substratum, and in some cases, prey availability. Site fidelity is common in species that use nursery areas. However, fidelity to mating, pupping, feeding and natal sites has only been observed in a few species. To date, few studies have examined habitat partitioning, although some general patterns have emerged: habitats appear to be subdivided by benthos type, prey availability and depth. The conservation of coastal sharks can be facilitated in some cases by the use of marine protected areas, especially for coastal resident species using specific nursery, reproduction or feeding areas. Partial protected-area closures might be effective during aggregation or migration periods to protect older size classes, but these must be applied with other management strategies such as reduced fishing and size or bag limits to protect individuals throughout different life history phases. More long-term research on habitat use, migration patterns and habitat partitioning is essential for developing successful management initiatives for coastal shark populations.

Background and Aim: We tested the hypothesis that elevated temperature decouples anthocyanins and total soluble solids (TSS) in developing berries and explored the effects of fruit load and water supply on the putative decoupling. Methods and Results: We established three 22 factorial experiments where two thermal regimes (elevated temperature, control) where combined with varieties (Shiraz, Cabernet Franc), fruit loads (bunch removal, control) or water regimes (irrigated, water deficit). The relationship between anthocyanins and TSS had a lag phase where TSS increased with no change in anthocyanins and an approximately linear phase where both traits increased in parallel for TSS > 11.4°Brix. Mean residuals in the linear phase were 0.065 mg/g in controls compared with −0.064 mg/g in the heated treatment, hence demonstrating the thermal decoupling of anthocyanins and TSS across varieties fruit loads and water regimes (P < 0.0001). Delayed onset of anthocyanin accumulation at elevated temperature explained the decoupling. Water deficit increased the anthocyanin : TSS ratio. Conclusion: Elevated temperature decoupled anthocyanins and sugars in berries by a relative shift in onset rather than rate of accumulation of these berry components. Significance of the Study: Warming trends are likely to disrupt the anthocyanin : sugar ratio in berries with consequences for colour : alcohol balance in red wines. Water deficit established shortly before veraison could partially restore these ratios.

Studies investigating the role that complex microbiotas associated with animals and humans play in health and wellbeing have been greatly facilitated by advances in DNA sequencing technology. Due to the still relatively high sequencing costs and the expense of establishing and running animal trials and collecting clinical samples, most of the studies reported in the literature are limited to a single trial and relatively small numbers of samples. Results from different laboratories, investigating similar trials and samples, have often produced quite different pictures of microbiota composition. This study investigated batch to batch variations in chicken cecal microbiota across three similar trials, represented by individually analysed samples from 207 birds. Very different microbiota profiles were found across the three flocks. The flocks also differed in the efficiency of nutrient use as indicated by feed conversion ratios. In addition, large variations in the microbiota of birds within a single trial were noted. It is postulated that the large variability in microbiota composition is due, at least in part, to the lack of colonisation of the chicks by maternally derived bacteria. The high hygiene levels maintained in modern commercial hatcheries, although effective in reducing the burden of specific diseases, may have the undesirable effect of causing highly variable bacterial colonization of the gut. Studies in humans and other animals have previously demonstrated large variations in microbiota composition when comparing individuals from different populations and from different environments but this study shows that even under carefully controlled conditions large variations in microbiota composition still occur.

Identification of bacteria associated with desirable productivity outcomes in animals may offer a direct approach to the identification of probiotic bacteria for use in animal production. We performed three controlled chicken trials (n = 96) to investigate caecal microbiota differences between the best and poorest performing birds using four performance measures; feed conversion ratio (FCR), utilization of energy from the feed measured as apparent metabolisable energy, gain rate (GR), and amount of feed eaten (FE). The shifts in microbiota composition associated with the performance measures were very different between the three trials. Analysis of the caecal microbiota revealed that the high and low FCR birds had significant differences in the abundance of some bacteria as demonstrated by shifts in microbiota alpha and beta diversity. Trials 1 and 2 showed significant overall community shifts, however, the microbial changes driving the difference between good and poor performers were very different. Lachnospiraceae, Ruminococcaceae, and Erysipelotrichaceae families and genera Ruminococcus, Faecalibacterium and multiple lineages of genus Clostridium (from families Lachnospiraceae, Ruminococcaceae, and Erysipelotrichaceae) were highly abundant in good FCR birds in Trial 1. Different microbiota was associated with FCR in Trial 2; Catabacteriaceae and unknown Clostridiales family members were increased in good FCR and genera Clostridium (from family Clostridiaceae) and Lactobacillus were associated with poor FCR. Trial 3 had only mild microbiota differences associated with all four performance measures. Overall, the genus Lactobacillus was correlated with feed intake which resulted in poor FCR performance. The genus Faecalibacterium correlated with improved FCR, increased GR and reduced FE. There was overlap in phylotypes correlated with improved FCR and GR, while different microbial cohorts appeared to be correlated with FE. Even under controlled conditions different cohorts of birds developed distinctly different microbiotas. Within the different trial groups the abundance of certain bacterial groups correlated with productivity outcomes. However, with different underlying microbiotas there were different bacteria correlated with performance. The challenge will be to identify probiotic bacteria that can reliably deliver favorable outcomes from diverse microbiotas.

Attainable water-use efficiency relates attainable yield, i.e. the best yield achieved through skilful use of available technology, and seasonal evapotranspiration (ET). For wheat crops in south-eastern Australia, there is a common, often large gap between actual and attainable water-use efficiency. To evaluate whether this gap is only an Australian problem or a general feature of dry environments, we compared water-use efficiency of rainfed wheat in south-eastern Australia, the North American Great Plains, China Loess Plateau, and the Mediterranean Basin. A dataset of published data was compiled (n = 691); water-use efficiency (WUEY/ET) was calculated as the ratio between actual grain yield and seasonal ET. Maximum WUEY/ET was 22 kg grain/ha.mm. Average WUEY/ET (kg grain/ha.mm) was 9.9 for south-eastern Australia, 9.8 for the China Loess Plateau, 8.9 for the northern Great Plains of North America, 7.6 for the Mediterranean Basin, and 5.3 for the southern-central Great Plains; the variation in average WUEY/ET was largely accounted for by reference evapotranspiration around flowering. Despite substantial differences in important factors including soils, precipitation patterns, and management practices, crops in all these environments had similarly low average WUEY/ET, between 32 and 44% of attainable efficiency. We conclude that low water-use efficiency of Australian crops is not a local problem, but a widespread feature of dry environments. Yield gap analysis for crops in the Mallee region of Australia revealed low availability of phosphorus, late sowing, and subsoil chemical constraints as key factors reducing water-use efficiency, largely through their effects on soil evaporation.

SUMMARY The paper is in two parts. Part I presents results of a Monte Carlo randomization study of Papadakis's covariance method of NN analysis which show that (i) a non-iterated Papadakis analysis tends to be conservatively biassed; (ii) iteration of the analysis as suggested by Bartlett (1978) leads to substantial positive bias in the treatment F ratio; (iii) the method is very inefficient when there are substantial trend effects in the data. A theoretical explanation of these results is given. Part II describes a new method of NN analysis discovered by the first author and developed in collaboration with the co-authors. The method is essentially a “moving-block” analogue of classical forms of analysis for “fixed” blocks (or rows, columns). It avoids the defects of Papadakis's method and leads to approximately unbiassed analyses. It is nearly always and often substantially more efficient on average than classical analyses of complete or incomplete block experiments, and also more efficient than standard analyses of Latin or lattice square designs if there are appreciable row x column interactions in the data. New criteria of design for NN balance are described. Validity of the new method under randomization is demonstrated empirically with Monte Carlo studies.

Abstract The mucosal surfaces of fish represent an important barrier that supports and regulates a diverse array of microbial assemblages and contributes to the overall health and fitness of the host. For farmed species, knowledge of how these host–microbial systems adapt and respond to various stressors is pivotal for managing health, nutrition and optimizing productivity in aquaculture. While our understanding of these communities and the factors that shape them now suggest that a diverse balanced microbiota is critical for healthy functioning in fish, the mechanisms behind these interactions are still poorly understood. Much of the existing research has focused on characterizing the taxonomic diversity of these assemblages in different fish species, across body surfaces (e.g. skin, gills and gastrointestinal tract), and in response to changing nutrition, health and environmental conditions. However, the specific functional contributions of these communities (or specific members) remain elusive, especially in farmed or diseased fish. Here, we review our current understanding of the microbiota in fish, their interplay and the likely functional involvement with the host. We also seek to address and identify gaps in knowledge and explore the future prospects for improving our understanding of these communities in aquaculture.

1. We review the mechanisms behind ecosystem functions, the processes that facilitate energy transfer along food webs, and the major processes that allow the cycling of carbon, oxygen and nitrogen, and use case studies to show how these have already been, and will continue to be, altered by global warming. 2. Increased temperatures will affect the interactions between heterotrophs and autotrophs (e.g. pollination and seed dispersal), and between heterotrophs (e.g. predators-prey, parasites/pathogens-hosts), with generally negative ramifications for important ecosystem services (functions that provide direct benefit to human society such as pollination) and potential for heightened species co-extinction rates. 3. Mitigation of likely impacts of warming will require, in particular, the maintenance of species diversity as insurance for the provision of basic ecosystem services. Key to this will be long-term monitoring and focused research that seek to maintain ecosystem resilience in the face of global warming. 4. We provide guidelines for pursuing research that quantifies the nexus between ecosystem function and global warming. These include documentation of key functional species groups within systems, and understanding the principal outcomes arising from direct and indirect effects of a rapidly warming environment. Localized and targeted research and monitoring, complemented with laboratory work, will determine outcomes for resilience and guide adaptive conservation responses and long-term planning.