Campylobacter jejuni and Campylobacter coli Genotyping by High-Resolution Melting Analysis of a flaA Fragment.

The highly variable flagellin-encoding flaA gene has long been used for genotyping Campylobacter jejuni and Campylobacter coli. High-resolution melting (HRM) analysis is emerging as an efficient and robust method for discriminating DNA sequence variants. The objective of this study was to apply HRM analysis to flaA-based genotyping. The initial aim was to identify a suitable flaA fragment. It was found that the PCR primers commonly used to amplify the flaA short variable repeat (SVR) yielded a mixed PCR product unsuitable for HRM analysis. However, a PCR primer set composed of the upstream primer used to amplify the fragment used for flaA restriction fragment length polymorphism (RFLP) analysis and the downstream primer used for flaA SVR amplification generated a very pure PCR product, and this primer set was used for the remainder of the study. Eighty-seven C. jejuni and 15 C. coli isolates were analyzed by flaA HRM and also partial flaA sequencing. There were 47 flaA sequence variants, and all were resolved by HRM analysis. The isolates used had previously also been genotyped using single-nucleotide polymorphisms (SNPs), binary markers, CRISPR HRM, and flaA RFLP.flaA HRM analysis provided resolving power multiplicative to the SNPs, binary markers, and CRISPR HRM and largely concordant with the flaA RFLP. It was concluded that HRM analysis is a promising approach to genotyping based on highly variable genes.

Bromus catharticus striate mosaic virus: a new mastrevirus infecting Bromus catharticus from Australia.

Although monocotyledonous-plant-infecting mastreviruses (in the family Geminiviridae) are known to cause economically significant crop losses in certain areas of the world, in Australia, they pose no obvious threat to agriculture. Consequently, only a few Australian monocot-infecting mastreviruses have been described, and only two have had their genomes fully sequenced. Here, we present the third full-genome sequence of an Australian monocot-infecting mastrevirus from Bromus catharticus belonging to a distinct species, which we have tentatively named Bromus catharticus striate mosaic virus (BCSMV). Although the genome of this new virus shares only 57.7% sequence similarity with that of its nearest known relative, Digitaria didactyla striate mosaic virus (DDSMV; also from Australia), it has features typical of all other known mastrevirus genomes. Phylogenetic analysis showed that both the full genome and each of its probable expressed proteins group with the two other characterised Australian monocot-infecting mastreviruses. Besides the BCSMV genome sequence revealing that Australian monocot-infecting mastrevirus diversity rivals that seen in Africa, it has enabled us, for the first, to time detect evidence of recombination amongst the Australian viruses. Specifically, it appears that DDSMV possesses a short intergenic region sequence that has been recombinationally derived from either BCSMV or a close relative that has not yet been identified.

Variable-number tandem repeats genotyping used to aid and inform management strategies for a bovine Johne's disease incursion in tropical and subtropical Australia

The application of variable-number tandem repeats (VNTR) genotyping of Mycobacterium avium subsp. paratuberculosis isolates to assist in investigating incidents of bovine Johne’s disease in a low-prevalence region of Australia is described in the current study. Isolates from a response to detection of bovine Johne’s disease in Queensland were compared with strains from national and international sources. The tandem application of mycobacterial interspersed repetitive unit (MIRU) and multilocus short sequence repeats (MLSSR) genotyping identified 2 strains, 1 that infected cattle on multiple properties with trace-forward histories from a common infected property, and 1 genotypically different strain recovered from a single property. The former strain showed an identical genotype to an isolate from India. Neither strain showed a genotypic link to regions of Australia with a higher prevalence of the disease. Genotyping has indicated incursions from 2 independent sources. This intelligence has informed investigations into potential routes of entry and the soundness of ongoing control measures, and supported strategy and policy decisions regarding management of Mycobacterium avium subsp. paratuberculosis incursions for Queensland.

The microbiological status of prawns from retail and wholesale outlets in the Brisbane region

Cooked prawns from retail and wholesale outlets in the Brisbane region included a large proportion with high bacterial counts (10(6)-10(8)/g) indicating a short remaining shelflife. Microbially inferior product entering the wholesale and retail trade indicated poor handling and storage practices from point of capture all along the distribution chain to the retail outlets. Current handling practices need to be upgraded and HACCP principles adopted.

New annual and short-lived perennial pasture legumes for Australian agriculture--15 years of revolution

Fifteen years ago subterranean clover (Trifolium subterraneum) and annual medics (Medicago spp.) dominated annual pasture legume sowings in southern Australia, while limited pasture legume options existed for cropping areas of subtropical Australia. Since then a number of sustainability and economic challenges to existing farming systems have emerged, exposing shortcomings in these species and the lack of legume biodiversity. Public breeding institutions have responded to these challenges by developing 58 new annual and short-lived perennial pasture legumes with adaptation to both existing and new farming systems. This has involved commercialisation of new species and overcoming deficiencies in traditional species. Traits incorporated in legumes of Mediterranean Basin origin for the Mediterranean, temperate and southern subtropical climates of Australia include deeper root systems, protection from false breaks (germination-inducing rainfall events followed by death from drought), a range of hardseed levels, acid-soil tolerant root nodule symbioses, tolerance to pests and diseases and provision of lower cost seed through ease of seed harvesting and processing. Ten new species, French serradella (Ornithopus sativus), biserrula (Biserrula pelecinus), sulla (Hedysarum coronarium), gland (Trifolium glanduliferum), arrowleaf (Trifolium vesiculosum), eastern star (Trifolium dasyurum) and crimson (Trifolium incarnatum) clovers and sphere (Medicago sphaerocarpos), button (Medicago orbicularis) and hybrid disc (Medicago tornata x Medicago littoralis) medics have been commercialised. Improved cultivars have also been developed of subterranean (T. subterraneum), balansa (Trifolium michelianum), rose (Trifolium hirtum), Persian (Trifolium resupinatum) and purple (Trifolium purpureum) clovers, burr (Medicago polymorpha), strand (M. littoralis), snail (Medicago scutellata) and barrel (Medicago truncatula) medics and yellow serradella (Ornithopus compressus). New tropical legumes for pasture phases in subtropical cropping areas include butterfly pea (Clitoria ternatea), burgundy bean (Macroptilium bracteatum) and perennial lablab (Lablab purpureus). Other species and cultivars of Mediterranean species are likely to be released soon. The contributions of genetic resources, rhizobiology, pasture ecology and agronomy, plant pathology, entomology, plant chemistry and animal science have been paramount to this success. A farmer survey in Western Australia has shown widespread adoption of the new pasture legumes, while adoption of new tropical legumes has also been high in cropping areas of the subtropics. This trend is likely to increase due to the increasing cost of inorganic nitrogen, the need to combat herbicide-resistant crop weeds and improved livestock prices. Mixtures of these legumes allows for more robust pastures buffered against variable seasons, soils, pests, diseases and management decisions. This paper discusses development of the new pasture legumes, their potential use and deficiencies in the current suite. 'Ground–breaking Stuff’- Proceedings of the 13th Australian Society of Agronomy Conference, 10-14 September 2006, Perth, Western Australia.

Validating economic and environmental sustainability of a short-term summer forage legume in dryland wheat cropping systems in south-west Queensland.

The present study set out to test the hypothesis through field and simulation studies that the incorporation of short-term summer legumes, particularly annual legume lablab (Lablab purpureus cv. Highworth), in a fallow-wheat cropping system will improve the overall economic and environmental benefits in south-west Queensland. Replicated, large plot experiments were established at five commercial properties by using their machineries, and two smaller plot experiments were established at two intensively researched sites (Roma and St George). A detailed study on various other biennial and perennial summer forage legumes in rotation with wheat and influenced by phosphorus (P) supply (10 and 40 kg P/ha) was also carried out at the two research sites. The other legumes were lucerne (Medicago sativa), butterfly pea (Clitoria ternatea) and burgundy bean (Macroptilium bracteatum). After legumes, spring wheat (Triticum aestivum) was sown into the legume stubble. The annual lablab produced the highest forage yield, whereas germination, establishment and production of other biennial and perennial legumes were poor, particularly in the red soil at St George. At the commercial sites, only lablab-wheat rotations were experimented, with an increased supply of P in subsurface soil (20 kg P/ha). The lablab grown at the commercial sites yielded between 3 and 6 t/ha forage yield over 2-3 month periods, whereas the following wheat crop with no applied fertiliser yielded between 0.5 to 2.5 t/ha. The wheat following lablab yielded 30% less, on average, than the wheat in a fallow plot, and the profitability of wheat following lablab was slightly higher than that of the wheat following fallow because of greater costs associated with fallow management. The profitability of the lablab-wheat phase was determined after accounting for the input costs and additional costs associated with the management of fallow and in-crop herbicide applications for a fallow-wheat system. The economic and environmental benefits of forage lablab and wheat cropping were also assessed through simulations over a long-term climatic pattern by using economic (PreCAPS) and biophysical (Agricultural Production Systems Simulation, APSIM) decision support models. Analysis of the long-term rainfall pattern (70% in summer and 30% in winter) and simulation studies indicated that ~50% time a wheat crop would not be planted or would fail to produce a profitable crop (grain yield less than 1 t/ha) because of less and unreliable rainfall in winter. Whereas forage lablab in summer would produce a profitable crop, with a forage yield of more than 3 t/ha, ~90% times. Only 14 wheat crops (of 26 growing seasons, i.e. 54%) were profitable, compared with 22 forage lablab (of 25 seasons, i.e. 90%). An opportunistic double-cropping of lablab in summer and wheat in winter is also viable and profitable in 50% of the years. Simulation studies also indicated that an opportunistic lablab-wheat cropping can reduce the potential runoff+drainage by more than 40% in the Roma region, leading to improved economic and environmental benefits.

Performance of Pinus elliottii, Pinus caribaea, their F-1, F-2 and backcross hybrids and Pinus taeda to 10 years in the Mesopotamia region, Argentina

Performances of Pinus taxa were studied to 10 years of age in two trials in each of Misiones and Entre Rios provinces across the Mesopotamia region of Argentina. Taxa comprised 22 populations from sources in Argentina, Australia, Brazil and Zimbabwe including Pinus elliottii var. elliottii (Pee), Pinus caribaea var. hondurensis (Pch), their four, inter-specific hybrids (F-1, F-2 and backcrosses from F-1 to Pch and to Pee-all as broadly based bulks); other Pee and Pinus taeda (Pt) comprised narrower or unspecified bulks. Variable numbers of taxa were missing at each site. Mean survival across sites at age 10 years ranged 53.2-91.3% averaging 74.2%. Analysis of variance of plot means indicated population effect was statistically significant (p < 0.05) for all or most growth and quality traits at all sites. However, significant differences from the nominated check seedlot at the Entre Rios sites (Pee, Australia) were extremely rare, while quite common at the northern, Misiones sites (check seedlot a Pt population). In the Misiones trials, F-1, F-2 and both backcross hybrids showed better stem straightness than Pee and Pt from Argentina, generally with statistically significant differences (p < 0.05). Pt showed lowest forking scores (desirable). Taxon x environment interaction was statistically significant (p < 0.01) for growth traits only (p > 0.05). However, this interaction contributed an average of only 34.1% of the taxon variance suggesting a lack of practical importance. Taxa most suitable for deployment in the Mesopotamia region, Argentina are suggested.

Optimizing sowing management for short duration dry seeded aman rice on the High Ganges River Floodplain of Bangladesh

Dry seeding of aman rice can facilitate timely crop establishment and early harvest and thus help to alleviate the monga (hunger) period in the High Ganges Flood Plain of Bangladesh. Dry seeding also offers many other potential benefits, including reduced cost of crop establishment and improved soil structure for crops grown in rotation with rice. However, the optimum time for seeding in areas where farmers have access to water for supplementary irrigation has not been determined. We hypothesized that earlier sowing is safer, and that increasing seed rate mitigates the adverse effects of significant rain after sowing on establishment and crop performance. To test these hypotheses, we analyzed long term rainfall data, and conducted field experiments on the effects of sowing date (target dates of 25 May, 10 June, 25 June, and 10 July) and seed rate (20, 40, and 60 kg ha−1) on crop establishment, growth, and yield of dry seeded Binadhan-7 (short duration, 110–120 d) during the 2012 and 2013 rainy seasons. Wet soil as a result of untimely rainfall usually prevented sowing on the last two target dates in both years, but not on the first two dates. Rainfall analysis also suggested a high probability of being able to dry seed in late May/early June, and a low probability of being able to dry seed in late June/early July. Delaying sowing from 25 May/10 June to late June/early July usually resulted in 20–25% lower plant density and lower uniformity of the plant stand as a result of rain shortly after sowing. Delaying sowing also reduced crop duration, and tillering or biomass production when using a low seed rate. For the late June/early July sowings, there was a strong positive relationship between plant density and yield, but this was not the case for earlier sowings. Thus, increasing seed rate compensated for the adverse effect of untimely rains after sowing on plant density and the shorter growth duration of the late sown crops. The results indicate that in this region, the optimum date for sowing dry seeded rice is late May to early June with a seed rate of 40 kg ha−1. Planting can be delayed to late June/early July with no yield loss using a seed rate of 60 kg ha−1, but in many years, the soil is simply too wet to be able to dry seed at this time due to rainfall.

Crop design for specific adaptation in variable dryland production environments

Climatic variability in dryland production environments (E) generates variable yield and crop production risks. Optimal combinations of genotype (G) and management (M) depend strongly on E and thus vary among sites and seasons. Traditional crop improvement seeks broadly adapted genotypes to give best average performance under a standard management regime across the entire production region, with some subsequent manipulation of management regionally in response to average local environmental conditions. This process does not search the full spectrum of potential G × M × E combinations forming the adaptation landscape. Here we examine the potential value (relative to the conventional, broad adaptation approach) of exploiting specific adaptation arising from G × M × E. We present an in-silico analysis for sorghum production in Australia using the APSIM sorghum model. Crop design (G × M) is optimised for subsets of locations within the production region (specific adaptation) and is compared with the optimum G across all environments with locally modified M (broad adaptation). We find that geographic subregions that have frequencies of major environment types substantially different from that for the entire production region show greatest advantage for specific adaptation. Although the specific adaptation approach confers yield and production risk advantages at industry scale, even greater benefits should be achievable with better predictors of environment-type likelihood than that conferred by location alone.

Understanding the barriers to the implementation of precision agriculture in the central region

There is an increasing requirement for more astute land resource management through efficiencies in agricultural inputs in a sugar cane production system. A precision agriculture (PA) approach can provide a pathway for a sustainable sugarcane production system. One of the impediments to the adoption of PA practices is access to paddock-scale mapping layers displaying variability in soil properties, crop growth and surface drainage. Variable rate application (VRA) of nutrients is an important component of PA. However, agronomic expertise within PA systems has fallen well behind significant advances in PA technologies. Generally, advisers in the sugar industry have a poor comprehension of the complex interaction of variables that contribute to within-paddock variations in crop growth. This is regarded as a significant impediment to the progression of PA in sugarcane and is one of the reasons for the poor adoption of VRA of nutrients in a PA approach to improved sugar cane production. This project therefore has established a number of key objectives which will contribute to the adoption of PA and the staged progression of VRA supported by relevant and practical agronomic expertise. These objectives include provision of base soils attribute mapping that can be determined using Veris 3100 Electrical Conductivity (EC) and digital elevation datasets using GPS mapping technology for a large sector of the central cane growing region using analysis of archived satellite imagery to determine the location and stability of yield patterns over time and in varying seasonal conditions on selected project study sites. They also include the stablishment of experiments to determine appropriate VRA nitrogen rates on various soil types subjected to extended anaerobic conditions, and the establishment of trials to determine nitrogen rates applicable to a declining yield potential associated with the aging of ratoons in the crop cycle. Preliminary analysis of archived yield estimation data indicates that yield patterns remain relatively stable overtime. Results also indicate the where there is considerable variability in EC values there is also significant variation in yield.

Strategic tillage in no-till farming systems in Australia’s northern grains-growing regions: II. Implications for agronomy, soil and environment

In semi-arid sub-tropical areas, a number of studies concerning no-till (NT) farming systems have demonstrated advantages in economic, environmental and soil quality aspects over conventional tillage (CT). However, adoption of continuous NT has contributed to the build-up of herbicide resistant weed populations, increased incidence of soil- and stubble-borne diseases, and stratification of nutrients and organic carbon near the soil surface. Some farmers often resort to an occasional strategic tillage (ST) to manage these problems of NT systems. However, farmers who practice strict NT systems are concerned that even one-time tillage may undo positive soil condition benefits of NT farming systems. We reviewed the pros and cons of the use of occasional ST in NT farming systems. Impacts of occasional ST on agronomy, soil and environment are site-specific and depend on many interacting soil, climatic and management conditions. Most studies conducted in North America and Europe suggest that introducing occasional ST in continuous NT farming systems could improve productivity and profitability in the short term; however in the long-term, the impact is negligible or may be negative. The short term impacts immediately following occasional ST on soil and environment include reduced protective cover, soil loss by erosion, increased runoff, loss of C and water, and reduced microbial activity with little or no detrimental impact in the long-term. A potential negative effect immediately following ST would be reduced plant available water which may result in unreliability of crop sowing in variable seasons. The occurrence of rainfall between the ST and sowing or immediately after the sowing is necessary to replenish soil water lost from the seed zone. Timing of ST is likely to be critical and must be balanced with optimising soil water prior to seeding. The impact of occasional ST varies with the tillage implement used; for example, inversion tillage using mouldboard tillage results in greater impacts as compared to chisel or disc. Opportunities for future research on occasional ST with the most commonly used implements such as tine and/or disc in Australia’s northern grains-growing region are presented in the context of agronomy, soil and the environment.

Climate savvy grazing (Developing improved grazing and related practices to assist beef production enterprises across northern Australia to adapt to a changing and more variable climate)

There is uncertainty over the potential changes to rainfall across northern Australia under climate change. Since rainfall is a key driver of pasture growth, cattle numbers and the resulting animal productivity and beef business profitability, the ability to anticipate possible management strategies within such uncertainty is crucial. The Climate Savvy Grazing project used existing research, expert knowledge and computer modelling to explore the best-bet management strategies within best, median and worse-case future climate scenarios. All three scenarios indicated changes to the environment and resources upon which the grazing industry of northern Australia depends. Well-adapted management strategies under a changing climate are very similar to best practice within current climatic conditions. Maintaining good land condition builds resource resilience, maximises opportunities under higher rainfall years and reduces the risk of degradation during drought and failed wet seasons. Matching stocking rate to the safe long-term carrying capacity of the land is essential; reducing stock numbers in response to poor seasons and conservatively increasing stock numbers in response to better seasons generally improves profitability and maintains land in good condition. Spelling over the summer growing season will improve land condition under a changing climate as it does under current conditions. Six regions were included within the project. Of these, the Victoria River District in the Northern Territory, Gulf country of Queensland and the Kimberley region of Western Australia had projections of similar or higher than current rainfall and the potential for carrying capacity to increase. The Alice Springs, Maranoa-Balonne and Fitzroy regions had projections of generally drying conditions and the greatest risk of reduced pasture growth and carrying capacity. Encouraging producers to consider and act on the risks, opportunities and management options inherent in climate change was a key goal of the project. More than 60,000 beef producers, advisors and stakeholders are now more aware of the management strategies which build resource resilience, and that resilience helps buffer against the effects of variable and changing climatic conditions. Over 700 producers have stated they have improved confidence, skills and knowledge to attempt new practices to build resilience. During the course of the project, more than 165 beef producers reported they have implemented changes to build resource and business resilience.

Application of commercially available, low-cost, miniaturised NIR spectrometers to the assessment of the sugar content of intact fruit

Recent decreases in costs, and improvements in performance, of silicon array detectors open a range of potential applications of relevance to plant physiologists, associated with spectral analysis in the visible and short-wave near infra-red (far-red) spectrum. The performance characteristics of three commercially available ‘miniature’ spectrometers based on silicon array detectors operating in the 650–1050-nm spectral region (MMS1 from Zeiss, S2000 from Ocean Optics, and FICS from Oriel, operated with a Larry detector) were compared with respect to the application of non-invasive prediction of sugar content of fruit using near infra-red spectroscopy (NIRS). The FICS–Larry gave the best wavelength resolution; however, the narrow slit and small pixel size of the charge-coupled device detector resulted in a very low sensitivity, and this instrumentation was not considered further. Wavelength resolution was poor with the MMS1 relative to the S2000 (e.g. full width at half maximum of the 912 nm Hg peak, 13 and 2 nm for the MMS1 and S2000, respectively), but the large pixel height of the array used in the MMS1 gave it sensitivity comparable to the S2000. The signal-to-signal standard error ratio of spectra was greater by an order of magnitude with the MMS1, relative to the S2000, at both near saturation and low light levels. Calibrations were developed using reflectance spectra of filter paper soaked in range of concentrations (0–20% w/v) of sucrose, using a modified partial least squares procedure. Calibrations developed with the MMS1 were superior to those developed using the S2000 (e.g. coefficient of correlation of 0.90 and 0.62, and standard error of cross-validation of 1.9 and 5.4%, respectively), indicating the importance of high signal to noise ratio over wavelength resolution to calibration accuracy. The design of a bench top assembly using the MMS1 for the non-invasive assessment of mesocarp sugar content of (intact) melon fruit is reported in terms of light source and angle between detector and light source, and optimisation of math treatment (derivative condition and smoothing function).

Distribution of barnacle epizoites of the crab Portunus pelagicus in the Moreton Bay region, eastern Australia

The parasites of some decapod crustaceans are known to cause sterilisation of their hosts, and can thus have an important impact on the population dynamics of infested species. Blue swimmer crabs (Portunus pelagicus) collected in three areas around Moreton Bay, Australia were examined for the presence of epizoic barnacles in their branchial chambers and on their carapace. Of the 952 crabs inspected 92% were infested with Octolasmis spp. The mean number of barnacles (predominantly Octolasmis warwickii) per carapace and gill chamber (mainly O. angulata) were 2.35 and 71.1, respectively. Barnacle infestation of gills was found to differ significantly by area, season and sex with the deeper offshore areas exhibiting the highest number of barnacles. The distribution within the hosts showed barnacles were more likely to be distributed in areas closer to the inhalant aperture. Highest abundances were found on the proximal surface of the hypobranchial side of gills 3, 4 and 5. Host moult stage and parasitism by Sacculina granifera were also found to affect the abundance of epizoic barnacles in some areas.