Partial characterization of Agrobacterium vitis strains

Seventeen strains of Agrobacterium vitis (formerly classified A. tumefaciens biovar 3) were characterized using part of the T-DNA and virA regions of the Ti plasmid as probes. All strains except one were of the wide host range (WHR) strains and were classified into two groups depending on their ability to utilize octopine or nopaline. These WHR type oncogenic strains had homology with the limited host range type (LHR) virA gen of A. vitis but not with the WHR virA gene of A. tumefaciens. The frequency of T-DNA excision in some Agrobacterium strains was estimated with the plasmid pTMA which mimics T-DNA excision from Ti plasmid DNA. In an A. vitis strain isolated from grapevine, T-DNA excision occurred after co-cultivation with grapevine tissues, but not with acetosyringone. In contrast, in A. tumefaciens, T-DNA excision occurred after co-cultivation with acetosyringone, but not with grapevine tissue

A TaqMan real-time PCR assay for Rhizoctonia cerealis and its use in wheat and soil

Rhizoctonia cerealis causes sharp eyespot in cereals and the pathogen survives as mycelia or sclerotia in soil. Real-time Polymerase Chain Reaction (qPCR) assays based on TaqMan chemistry are highly suitable for use on DNA extracted from soil. We report here the first qPCR assay for R. cerealis using TaqMan primers and a probe based on a unique Sequence Characterised Amplified Region (SCAR). The assay is highly specific and did not amplify DNA from a range of other binucleate Rhizoctonia species or isolates of anastomosis groups of Rhizoctonia solani. The high sensitivity of the assay was demonstrated in soils using a bulk DNA extraction method where 200 μg sclerotia in 50 g of soil were detected. DNA of the pathogen could also be amplified from asymptomatic wheat plants. Using the assay on soil samples from fields under different crop rotations, R. cerealis was most frequently detected in soils where wheat was grown or soil under pasture. It was detected least frequently in fields where potatoes were grown. This study demonstrates that assays derived from SCAR sequences can produce specific and sensitive qPCR assays

Molecular techniques for pathogen identification and fungus detection in the environment

Many species of fungi can cause disease in plants, animals and humans. Accurate and robust detection and quantification of fungi is essential for diagnosis, modeling and surveillance. Also direct detection of fungi enables a deeper understanding of natural microbial communities, particularly as a great many fungi are difficult or impossible to cultivate. In the last decade, effective amplification platforms, probe development and various quantitative PCR technologies have revolutionized research on fungal detection and identification. Examples of the latest technology in fungal detection and differentiation are discussed here

The cost-effectiveness of providing antenatal lifestyle advice for women who are overweight or obese: the LIMIT randomised trial

Background: Overweight and obesity during pregnancy is common, although robust evidence about the economic implications of providing an antenatal dietary and lifestyle intervention for women who are overweight or obese is lacking. We conducted a health economic evaluation in parallel with the LIMIT randomised trial. Women with a singleton pregnancy, between 10+0-20+0weeks, and BMI ≥ 25 kg/m2were randomised to Lifestyle Advice (a comprehensive antenatal dietary and lifestyle intervention) or Standard Care. The economic evaluation took the perspective of the health care system and its patients, and compared costs encountered from the additional use of resources from time of randomisation until six weeks postpartum. Increments in health outcomes for both the woman and infant were considered in the cost-effectiveness analysis. Mean costs and effects in the treatment groups allocated at randomisation were compared, and incremental cost effectiveness ratios (ICERs) and confidence intervals (95%) calculated. Bootstrapping was used to confirm the estimated confidence intervals, and to generate acceptability curves representing the probability of the intervention being cost-effective at alternative monetary equivalent values for the outcomes avoiding high infant birth weight, and respiratory distress syndrome. Analyses utilised intention to treat principles. Results: Overall, the increase in mean costs associated with providing the intervention was offset by savings associated with improved immediate neonatal outcomes, rendering the intervention cost neutral (Lifestyle Advice Group 11261.19±14573.97 versus Standard Care Group 11306.70±14562.02; p=0.094). Using a monetary value of $20,000 as a threshold value for avoiding an additional infant with birth weight above 4 kg, the probability that the antenatal intervention is cost-effective is 0.85, which increases to 0.95 when the threshold monetary value increases to$45,000. Conclusions: Providing an antenatal dietary and lifestyle intervention for pregnant women who are overweight or obese is not associated with increased costs or cost savings, but is associated with a high probability of cost effectiveness. Ongoing participant follow-up into childhood is required to determine the medium to long-term impact of the observed, short-term endpoints, to more accurately estimate the value of the intervention on risk of obesity, and associated costs and health outcomes

The use of ARMS PCR in detection and identification of xanthomonads associated with pistachio dieback in Australia

The original publication can be found at www.springerlink.comPistachio dieback occurs in the main pistachio growing areas of Australia. Xanthomonas strains belonging to the translucens group have been identified as the causal agent of the disease and two distinct groups, A and B, have been recognised within the pathogen population. In this study, specific primers for amplification of DNA of the pathogen were developed by sequencing the Internal Transcribed Spacer (ITS) region of rDNA from strains representing groups A and B, as well as from X. translucens isolated from wheat in Australia and one Xanthomonas translucens strain from orchard floor grasses. Primers were designed for amplification of DNA sequences specific to each group and a multiplex PCR test was developed that identified and differentiated strains of each group in a single PCR assay. To determine the specificity of the primers, PCR was carried out with DNA from 65 strains of the pistachio pathogen, 31 type and reference strains of Xanthomonas, and from 191 phytobacteria commonly found in and around pistachio orchards. In the multiplex PCR, a 331 bp fragment was amplified from all strains belonging to group A and a 120 bp fragment from all strains in group B. No PCR products were obtained from the other bacteria tested except for the type strain of X. translucens pv. cerealis, which has not been found in Australia. The assay was used to detect strains from both groups of the pathogen in pistachio plant material

Management of soilborne Rhizoctonia disease risk in cropping systems

Rhizoctonia continues to be an important (average annual cost $59 million with potential costs$165 million, Brennan and Murray, 2009) but complex disease in the southern agricultural region, especially lower rainfall region. The fungus Rhizoctonia solani AG8 is present in Australian soils as part of the microbial community. This pathogenic fungus is a good saprophyte (grows on crop residues and soil organic matter), adapted to dry conditions and lower fertility soils. The aim of this research was to improve our understanding of the interactions between pathogen inoculum levels and natural soil biological activity for long term control of Rhizoctonia and to improve the prediction and management of the disease. A series of multi-year field trials were conducted at sites in SA, Victoria and NSW to determine key soil, environment and management factors influencing the pathogen dynamics and disease impact in cereal crops. These trials were complemented with annual field experiments to investigate the effect of specific management practices including fungicide evaluation

Suppression of Rhizoctonia solani anastomosis group 8 in Australia and its biological nature

The nature of suppression in a field soil showing a decline in the Rhizoctonia barepatch disease of wheat (causal agent Rhizoctonia solani AG-8), in a minimum tillage system in southern Australia was investigated. The suppressive characteristics of the soil could be transferred to an autoclaved or pasteurized soil by adding 10% (w/w) of the unsterilised soil. This resulted in less disease following inoculation with R. solani AG-8. No transfer of suppression was observed when non-suppressive soil from an adjacent trial was added to the autoclaved or pasteurised soil. Gamma irradiation or pasteurisation at 60, 70 or 80 degrees C for 30 min eliminated both the ability of the soil to suppress disease and also differences in the soil microflora of suppressive soil and non-suppressive soil observed in untreated or 50 degrees C steam pasteurised soils. This is the first report of biologically-based suppression of this root rotting disease of wheat caused by R. solani AG-8

The post-hatch gut microbiota development in broiler chickens

V.A. Torok, G.E. Allison, K. Ophel-Keller and R.J. Hughe

Variation in rDNA ITS sequences in Glomus mosseae and Gigaspora margarita spores from a permanent pasture

To study the genetic variability in Glomus mosseae and Gigaspora margarita sequence similarities of ITS regions of rDNA were analysed from spores collected from a permanent pasture and from pot cultures. PCR amplification with the primers ITS1 and ITS4 was performed and products were cloned and sequenced. The sequences from single spores of G. mosseae and Gi. margarita confirmed that there is variation in the ITS region in a single spore. Phenetic analysis of sequences from both species supported the morphological identification which placed the species into two separate groups. Through the analysis of these sequences an estimate of genetic diversity was derived which clearly showed that the three field spores of G. mosseae were at least 2-5 times more genetically diverse than one single spore (field) and a pool of spores (pot culture) of Gigaspora margarita. This demonstrates that a high degree of variation exists in this natural population of G. mosseae.Z.I. Antoniolli, D.P. Schachtman, K. Ophel-Keller and S.E. Smit