Detection of Chlamydiaceae DNA in veterinary specimens using a family-specific PCR

Aims: The aim of this work was to develop a rapid molecular test for the detection of the Chlamydiaceae family, irrespective of the species or animal host. Methods and Results: The method described herein is a polymerase chain reaction targeting the 16S rRNA gene of the Chlamydiaceae family, and the results demonstrate that the test reacts with five reference Chlamydiaceae but none of the 19 other bacterial species or five uninfected animal tissues tested. The results also indicate the enhanced sensitivity of this test when compared with conventional culture or serology techniques. This is demonstrated through parallel testing of six real clinical veterinary cases and confirmatory DNA sequence analysis. Conclusions, Significance and Impact of the Study: This test can be used by veterinary diagnostic laboratories for rapid detection of Chlamydiaceae in veterinary specimens, with no restriction of chlamydial species or animal host. The test does not differentiate chlamydial species, and if required, speciation must be carried out retrospectively using alternate methods. However, for the purpose of prescribing therapy for chlamydiosis, this test would be an invaluable laboratory tool.

Abaca bunchy top virus, a new member of the genus Babuvirus (family Nanoviridae)

Two isolates of a novel babuvirus causing "bunchy top" symptoms were characterised, one from abaca (Musa textilis) from the Philippines and one from banana (Musa sp.) from Sarawak (Malaysia). The name abacá bunchy top virus (ABTV) is proposed. Both isolates have a genome of six circular DNA components, each ca. 1.0-1.1 kb, analogous to those of isolates of Banana bunchy top virus (BBTV). However, unlike BBTV, both ABTV isolates lack an internal ORF in DNA-R, and the ORF in DNA-U3 found in some BBTV isolates is also absent. In all phylogenetic analyses of nanovirid isolates, ABTV and BBTV fall in the same clade, but on separate branches. However, ABTV and BBTV isolates shared only 79-81% amino acid sequence identity for the putative coat protein and 54-76% overall nucleotide sequence identity across all components. Stem-loop and major common regions were present in ABTV, but there was less than 60% identity with the major common region of BBTV. ABTV and BBTV were also shown to be serologically distinct, with only two out of ten BBTV-specific monoclonal antibodies reacting with ABTV. The two ABTV isolates may represent distinct strains of the species as they are less closely related to each other than are isolates of the two geographic subgroups (Asian and South Pacific) of BBTV.

Phosphorus nutrition and tolerance of cotton to water stress: II. Water relations, free and bound water and leaf expansion rate

In previous experiments, increased leaf-Phosphorus (P) content with increasing P supply enhanced the individual leaf expansion and water content of fresh cotton leaves in a severely drying soil. In this paper, we report on the bulk water content of leaves and its components, free and bound water, along with other measures of plant water status, in expanding cotton leaves of various ages in a drying soil with different P concentrations. The bound water in living tissue is more likely to play a major role in tolerance to abiotic stresses by maintaining the structural integrity and/or cell wall extensibility of the leaves, whilst an increased amount of free water might be able to enhance solute accumulation, leading to better osmotic adjustment and tolerance to water stress, and maintenance of the volumes of sub-cellular compartments for expansive leaf growth. There were strong correlations between leaf-P%, leaf water (total, free and bound water) and leaf expansion rate (LER) under water stress conditions in a severely drying soil. Increased soil-P enhanced the uptake of P from a drying soil, leading to increased supply of osmotically active inorganic solutes to the cells in growing leaves. This appears to have led to the accumulation of free water and more bound water, ultimately leading to increased leaf expansion rates as compared to plants in low P soil under similar water stress conditions. The greater amount of bound and free water in the high-P plants was not necessarily associated with changes in cell turgor, and appears to have maintained the cell-wall properties and extensibility under water stressed conditions in soils that are nutritionally P-deficient.

Phosphorus nutrition and tolerance of cotton to water stress I. Seed cotton yield and leaf morphology

Seed cotton yield and morphological changes in leaf growth were examined under drying soil with different phosphorus (P) concentrations in a tropical climate. Frequent soil drying is likely to induce a decrease in nutrients particularly P due to reduced diffusion and poor uptake, in addition to restrictions in available water, with strong interactive effects on plant growth and functioning. Increased soil P in field and in-ground soil core studies increased the seed cotton yield and related morphological growth parameters in a drying soil, with hot (daily maximum temperature >33°C) and dry conditions (relative humidity, 25% to 35%), particularly during peak boll formation and filling stage. The soil water content in the effective rooting zone (top 0.4 m) decreased to -1.5 MPa by day 5 of the soil drying cycle. However, the increased seed cotton yield for the high-P plants was closely related to increasing leaf area with increased P supply. Plant height, leaf fresh mass and leaf area per plant were positively related to the leaf P%, which increased with increasing P supply. Low P plants were lower in plant height, leaf area, and leaf tissue water in the drying soil. Individual leaf area and the water content of the fresh leaf (ratio of dry mass to fresh mass) were significantly dependent on leaf P%.

Genetic control of propagation traits in a single Corymbia torelliana x Corymbia variegata family

Genetic control of vegetative propagation traits was described for a second-generation, outbred, intersectional hybrid family (N = 208) derived from two species, Corymbia torelliana (F. Muell.) K.D. Hill & L.A.S. Johnson and Corymbia variegata (F. Muell.) K.D. Hill & L.A.S. Johnson, which contrast for propagation characteristics and in their capacity to develop lignotubers. Large phenotypic variances were evident for rooting and most other propagation traits, with significant proportions attributable to differences between clones (broad-sense heritabilities 0.2-0.5). Bare root assessment of rooting rate and root quality parameters tended to have the highest heritabilities, whereas rooting percentage based on root emergence from pots and shoot production were intermediate. Root biomass and root initiation had the lowest heritabilities. Strong favourable genetic correlations were found between rooting percentage and root quality traits such as root biomass, volume, and length. Lignotuber development on a seedling was associated with low rooting and a tendency to poor root quality in cuttings and was in accord with the persistence of species parent types due to gametic phase disequilibrium. On average, nodal cuttings rooted more frequently and with higher quality root systems, but significant cutting type x genotype interaction indicated that for some clones, higher rooting rates were obtained from tips. Low germination, survival of seedlings, and rooting rates suggested strong hybrid breakdown in this family.

Remote sensing of nitrogen and water stress in wheat

Nitrogen (N) is the largest agricultural input in many Australian cropping systems and applying the right amount of N in the right place at the right physiological stage is a significant challenge for wheat growers. Optimizing N uptake could reduce input costs and minimize potential off-site movement. Since N uptake is dependent on soil and plant water status, ideally, N should be applied only to areas within paddocks with sufficient plant available water. To quantify N and water stress, spectral and thermal crop stress detection methods were explored using hyperspectral, multispectral and thermal remote sensing data collected at a research field site in Victoria, Australia. Wheat was grown over two seasons with two levels of water inputs (rainfall/irrigation) and either four levels (in 2004; 0, 17, 39 and 163 kg/ha) or two levels (in 2005; 0 and 39 kg/ha N) of nitrogen. The Canopy Chlorophyll Content Index (CCCI) and modified Spectral Ratio planar index (mSRpi), two indices designed to measure canopy-level N, were calculated from canopy-level hyperspectral data in 2005. They accounted for 76% and 74% of the variability of crop N status, respectively, just prior to stem elongation (Zadoks 24). The Normalised Difference Red Edge (NDRE) index and CCCI, calculated from airborne multispectral imagery, accounted for 41% and 37% of variability in crop N status, respectively. Greater scatter in the airborne data was attributable to the difference in scale of the ground and aerial measurements (i.e., small area plant samples against whole-plot means from imagery). Nevertheless, the analysis demonstrated that canopy-level theory can be transferred to airborne data, which could ultimately be of more use to growers. Thermal imagery showed that mean plot temperatures of rainfed treatments were 2.7 °C warmer than irrigated treatments (P < 0.001) at full cover. For partially vegetated fields, the two-Dimensional Crop Water Stress Index (2D CWSI) was calculated using the Vegetation Index-Temperature (VIT) trapezoid method to reduce the contribution of soil background to image temperature. Results showed rainfed plots were consistently more stressed than irrigated plots. Future work is needed to improve the ability of the CCCI and VIT methods to detect N and water stress and apply both indices simultaneously at the paddock scale to test whether N can be targeted based on water status. Use of these technologies has significant potential for maximising the spatial and temporal efficiency of N applications for wheat growers. ‘Ground–breaking Stuff’- Proceedings of the 13th Australian Society of Agronomy Conference, 10-14 September 2006, Perth, Western Australia.

Architectural modelling of maize under water stress

Two field experiments using maize (Pioneer 31H50) and three watering regimes [(i) irrigated for the whole crop cycle, until anthesis, (ii) not at all (experiment 1) and (iii) fully irrigated and rain grown for the whole crop cycle (experiment 2)] were conducted at Gatton, Australia, during the 2003-04 season. Data on crop ontogeny, leaf, sheath and internode lengths and leaf width, and senescence were collected at 1- to 3-day intervals. A glasshouse experiment during 2003 quantified the responses of leaf shape and leaf presentation to various levels of water stress. Data from experiment 1 were used to modify and parameterise an architectural model of maize (ADEL-Maize) to incorporate the impact of water stress on maize canopy characteristics. The modified model produced accurate fitted values for experiment 1 for final leaf area and plant height, but values during development for leaf area were lower than observed data. Crop duration was reasonably well fitted and differences between the fully irrigated and rain-grown crops were accurately predicted. Final representations of maize crop canopies were realistic. Possible explanations for low values of leaf area are provided. The model requires further development using data from the glasshouse study and before being validated using data from experiment 2 and other independent data. It will then be used to extend functionality in architectural models of maize. With further research and development, the model should be particularly useful in examining the response of maize production to water stress including improved prediction of total biomass and grain yield. This will facilitate improved simulation of plant growth and development processes allowing investigation of genotype by environment interactions under conditions of suboptimal water supply.

Sulfur-associated polioencephalomalacia in cattle grazing plants in the Family Brassicaceae

Polioencephalomalacia was diagnosed histologically in cattle from two herds on the Darling Downs, Queensland, during July-August 2007. In the first incident, 8 of 20 18-month-old Aberdeen Angus steers died while grazing pastures comprising 60% Sisymbrium irio (London rocket) and 40% Capsella bursapastoris (shepherd's purse). In the second incident, 2 of 150 mixed-breed adult cattle died, and another was successfully treated with thiamine, while grazing a pasture comprising almost 100% Raphanus raphanistrum (wild radish). Affected cattle were either found dead or comatose or were seen apparently blind and head-pressing in some cases. For both incidents, plant and water assays were used to calculate the total dietary sulfur content in dry matter as 0.62% and 1.01% respectively, both exceeding the recommended 0.5% for cattle eating more than 40% forage. Blood and tissue assays for lead were negative in both cases. No access to thiaminase, concentrated sodium ion or extrinsic hydrogen sulfide sources were identified in either incident. Below-median late summer and autumn rainfall followed by above-median unseasonal winter rainfall promoted weed growth at the expense of wholesome pasture species before these incidents.

Analysis and Modelling of the Effects of Water Stress on Maize Growth and Yield in Dryland Conditions.

It is essential to provide experimental evidence and reliable predictions of the effects of water stress on crop production in the drier, less predictable environments. A field experiment undertaken in southeast Queensland, Australia with three water regimes (fully irrigated, rainfed and irrigated until late canopy expansion followed by rainfed) was used to compare effects of water stress on crop production in two maize (Zea mays L.) cultivars (Pioneer 34N43 and Pioneer 31H50). Water stress affected growth and yield more in Pioneer 34N43 than in Pioneer 31H50. A crop model APSIM-Maize, after having been calibrated for the two cultivars, was used to simulate maize growth and development under water stress. The predictions on leaf area index (LAI) dynamics, biomass growth and grain yield under rain fed and irrigated followed by rain fed treatments was reasonable, indicating that stress indices used by APSIM-Maize produced appropriate adjustments to crop growth and development in response to water stress. This study shows that Pioneer 31H50 is less sensitive to water stress and thus a preferred cultivar in dryland conditions, and that it is feasible to provide sound predictions and risk assessment for crop production in drier, more variable conditions using the APSIM-Maize model.

Optimising between and within family selection for harvest weight in prawns with restricted harvest size.

Manual grading of prawns restricts the number that can be harvested. A restricted harvest size places a limit on the opposing within family and between family sources of selection pressure. A simulation study with inbreeding constrained at 0.5% per generation, a harvest size of 2000, heritability of 0.3, common family environmental effect of 0.1, indicates that maximum response to selection could be achieved with as few as 40 families. Increasing the number of families above 80 may reduce total selection response. It is important to be aware that increasing the number of families may not always yield a greater genetic response.

A novel species of mastrevirus (family Geminiviridae) isolated from Digitaria didactyla grass from Australia.

Mastreviruses (family Geminiviridae) that infect monocotyledonous plants occur throughout the temperate and tropical regions of Asia, Africa, Europe and Australia. Despite the identification of a very diverse array of mastrevirus species whose members infect African monocots, few such species have been discovered in other parts of the world. For example, the sequence of only a single monocot-infecting mastrevirus, Chloris striate mosaic virus (CSMV), has been reported so far from Australia, even though earlier biological and serological studies suggested that other distinct mastreviruses were present. Here, we have obtained the complete nucleotide sequence of a virus from the grass Digitaria didactyla originating from Australia. Analysis of the sequence shows the virus to be a typical mastrevirus, with four open reading frames, two in each orientation, separated by two non-coding intergenic regions. Although it showed the highest levels of sequence identity to CSMV (68.7%), their sequences are sufficiently diverse for the virus to be considered a member of a new species in the genus Mastrevirus, based on the present species demarcation criteria. We propose that the name first used during the 1980s be used for this species, Digitaria didactyla striate mosaic virus (DDSMV).

Isohydric and anisohydric characterisation of vegetable crops. The classification of vegetables by their physiological responses to water stress

Research on the physiological response of crop plants to drying soils and subsequent water stress has grouped plant behaviours as isohydric and anisohydric. Drying soil conditions, and hence declining soil and root water potentials, cause chemical signals—the most studied being abscisic acid (ABA)—and hydraulic signals to be transmitted to the leaf via xylem pathways. Researchers have attempted to allocate crops as isohydric or anisohydric. However, different cultivars within crops, and even the same cultivars grown in different environments/climates, can exhibit both response types. Nevertheless, understanding which behaviours predominate in which crops and circumstances may be beneficial. This paper describes different physiological water stress responses, attempts to classify vegetable crops according to reported water stress responses, and also discusses implications for irrigation decision-making.

Damage and physiological stress to juvenile eastern rock lobster (Sagmariasus verreauxi) discarded after trapping and hand collection

Large numbers of Sagmariasus verreauxi are trapped and hand collected in Australia, but discarded due to size and quota restrictions, and under the unevaluated assumption of few impacts. To test the validity of enforced discarding, trapped and hand-collected S. verreauxi (49-143. mm carapace length - CL) were examined for external damage, placed into cages, transferred to aquaria and monitored (with controls) over three months. Haemolymph was non-repetitively sampled immediately and at one, three, and seven days to quantify stress. Most trapped (64%) and hand-collected (79%) specimens were undersized (<104. mm CL), with the latter method yielding broader ranges of sizes and moult stages. Within-trap Octopus tetricus predation caused the only mortalities (3.3%). Hand collection resulted in much greater antennae and pereopod loss than trapping (53 vs. 4%) but, compared to controls, both methods evoked benign physiological responses that resolved within a week. While most wounded S. verreauxi regenerated all or some missing appendages post-moult, their mean CLs were less than those from intact conspecifics. Simple strategies, including larger mesh sizes, and/or installing modifications to reduce bycatch in traps, careful hand collection, and appropriate release techniques might minimise impacts (including predation) to unwanted S. verreauxi, and help to control stock exploitation. © 2012 Elsevier B.V.

Identification of a new Polerovirus (family Luteoviridae) associated with cotton bunchy top disease in Australia

Cotton bunchy top (CBT) disease has caused significant yield losses in Australia and is now managed by control of its vector, the cotton aphid (Aphis gossypii). Its mode of transmission and similarities in symptoms to cotton Blue Disease suggested it may also be caused by a luteovirus or related virus. Degenerate primers to conserved regions of the genomes of the family Luteoviridae were used to amplify viral cDNAs from CBT-affected cotton leaf tissue that were not present in healthy plants. Partial genome sequence of a new virus (Cotton bunchy top virus, CBTV) was obtained spanning part of the RNA-dependent-RNA-polymerase (RdRP), all of the coat protein and part of the aphid-transmission protein. CBTV sequences could be detected in viruliferous aphids able to transmit CBT, but not aphids from non-symptomatic plants, indicating that it is associated with the disease and may be the causal agent. All CBTV open-reading frames had their closest similarity to viruses of the genus Polerovirus. The partial RdRP had 90 % amino acid identity to the RdRP of Cotton leafroll dwarf virus (CLRDV) that causes cotton blue disease, while other parts of the genome were more similar to other poleroviruses. The sequence similarity and genome organization of CBTV suggest that it should be considered a new member of the genus Polerovirus. This partial genome sequence of CBTV opens up the possibility for developing diagnostic tests for detection of the virus in cotton plants, aphids and weeds as well as alternative strategies for engineering CBT resistance in cotton plants through biotechnology. © 2012 Australasian Plant Pathology Society Inc.

Drought stress characterization of post-rainy season (rabi) sorghum in India

During the post-rainy (rabi) season in India around 3 million tonnes of sorghum grain is produced from 5.7 million ha of cropping. This underpins the livelihood of about 5 million households. Severe drought is common as the crop grown in these areas relies largely on soil moisture stored during the preceding rainy season. Improvement of rabi sorghum cultivars through breeding has been slow but could be accelerated if drought scenarios in the production regions were better understood. The sorghum crop model within the APSIM (Agricultural Production Systems sIMulator) platform was used to simulate crop growth and yield and the pattern of crop water status through each season using available historical weather data. The current model reproduced credibly the observed yield variation across the production region (R2=0.73). The simulated trajectories of drought stress through each crop season were clustered into five different drought stress patterns. A majority of trajectories indicated terminal drought (43%) with various timings of onset during the crop cycle. The most severe droughts (25% of seasons) were when stress began before flowering and resulted in failure of grain production in most cases, although biomass production was not affected so severely. The frequencies of drought stress types were analyzed for selected locations throughout the rabi tract and showed different zones had different predominating stress patterns. This knowledge can help better focus the search for adaptive traits and management practices to specific stress situations and thus accelerate improvement of rabi sorghum via targeted specific adaptation. The case study presented here is applicable to other sorghum growing environments. © 2012 Elsevier B.V.