Novel paramyxoviruses in Australian flying-fox populations support host–virus co-evolution

Understanding the diversity of henipaviruses and related viruses is important in determining the viral ecology within flying-fox populations and assessing the potential threat posed by these agents. This study sought to identify the abundance and diversity of previously unknown paramyxoviruses (UPVs) in Australian flying-fox species (Pteropus alecto, Pteropus scapulatus, Pteropus poliocephalus and Pteropus conspicillatus) and in the Christmas Island species Pteropus melanotus natalis. Using a degenerative reverse transcription-PCR specific for the L gene of known species of the genus Henipavirus and two closely related paramyxovirus genera Respirovirus and Morbillivirus, we identified an abundance and diversity of previously UPVs, with a representative 31 UPVs clustering in eight distinct groups (100 UPVs/495 samples). No new henipaviruses were identified. The findings were consistent with a hypothesis of co-evolution of paramyxoviruses and their flying-fox hosts. Quantification of the degree of co-speciation between host and virus (beyond the scope of this study) would strengthen this hypothesis.

Variability in the growth, feeding and condition of barramundi (Lates calcarifer Bloch) in a northern Australian coastal river and impoundment

Lates calcarifer supports important fisheries throughout tropical Australia. Community-driven fish stocking has resulted in the creation of impoundment fisheries and supplemental stocking of selected wild riverine populations. Using predominantly tag-recapture methods, condition assessment and stomach flushing techniques, this study compared the growth of stocked and wild L. calcarifer in a tropical Australian river (Johnstone River) and stocked fish in a nearby impoundment (Lake Tinaroo). Growth of L. calcarifer in the Johnstone River appeared resource-limited, with juvenile fish in its lower freshwater reaches feeding mainly on small aytid shrimp and limited quantities of fish. Growth was probably greatest in estuarine and coastal areas than in the lower freshwater river. Fish in Lake Tinaroo, where prey availability was greater, grew faster than either wild or stocked fish in the lower freshwater areas of the Johnstone River. Growth of L. calcarifer was highly seasonal with marked declines in the cooler months. This was reflected in both stomach fullness and the percentage of fish with empty stomachs but the condition of L. calcarifer was similar across most sites. In areas where food resources appear stretched, adverse effects on resident L. calcarifer populations and their attendant prey species should be minimised through cessation of, or more conservative, stocking practices.

Strangers in a strange land: do life history traits differ for alien and native colonisers of novel environments?

Do alien invasive species exhibit life history characteristics that are similar to those of native species that have become pests in their continent of origin? We compared eucalypt specialists that have become pests in Australian plantations (natives) to those that have established overseas (aliens) using 13 life history traits and found that although traits that support rapid population build-up were shared, overall, aliens and native colonisers differed significantly. Distance from source (New Zealand vs. other) had no significant effect, but species that established more than 50 years ago exhibited different life history traits from those that established within the last 50 years, possibly because of more effective quarantine. Native and alien eucalypt insect invaders differed predominantly in traits that facilitate long-distance movement (pathway traits), compared to traits that facilitate establishment and spread. Aliens had longer adult flight seasons, were smaller and more closely host-associated (cryptic eggs and larvae), had lower incidence of diapause (i.e. were more seasonally plastic) and more generations per year than natives. Thus, studies of species invasive within their country of origin can shed light on alien invasions.

Plasmopara sphagneticolae sp. nov. (Peronosporales) on Sphagneticola (Asteraceae) in Australia

A specimen of downy mildew on leaves of Sphagneticola trilobata found in northern Queensland was identified by a systematic approach as a novel species of Plasmopara. A new species, Plasmopara sphagneticolae, is proposed for this specimen, which differs from other species of Plasmopara by morphology, host range, and sequence data from nuclear-ribosomal DNA and mitochondrial DNA. Plasmopara sphagneticolae, together with P. halstedii, are downy mildews found on host species in the tribe Heliantheae (Asteraceae). Plasmopara halstedii causes downy mildew on Helianthus annuus, and is not present on sunflower in Australia. Phylogenetic analysis of the large subunit region of ribosomal DNA showed that P. sphagneticolae was sister to P. halstedii on sunflower.

Markers for seedling and adult plant crown rot resistance in four partially resistant bread wheat sources

QTL identified for seedling and adult plant crown rot resistance in four partially resistant hexaploid wheat sources. PCR-based markers identified for use in marker-assisted selection. Crown rot, caused by Fusarium pseudograminearum, is an important disease of wheat in many wheat-growing regions globally. Complete resistance to infection by F. pseudograminearum has not been observed in a wheat host, but germplasm with partial resistance to this pathogen has been identified. The partially resistant wheat hexaploid germplasm sources 2-49, Sunco, IRN497 and CPI133817 were investigated in both seedling and adult plant field trials to identify markers associated with the resistance which could be used in marker-assisted selection programs. Thirteen different quantitative trait loci (QTL) conditioning crown rot resistance were identified in the four different sources. Some QTL were only observed in seedling trials whereas others appeared to be adult plant specific. For example while the QTL on chromosomes 1AS, 1BS, and 4BS contributed by 2-49 and on 2BS contributed by Sunco were detected in both seedling and field trials, the QTL on 1DL present in 2-49 and the QTL on 3BL in IRN497 were only detected in seedling trials. Genetic correlations between field trials of the same population were strong, as were correlations between seedling trials of the same population. Low to moderate correlations were observed between seedling and field trials. Flanking markers, most of which are less than 10 cM apart, have now been identified for each of the regions associated with crown rot resistance.

Reply to Bonten and Mevius : Less Evidence for an Important Role of Food-Producing Animals as Source of Antibiotic Resistance in Humans

To the Editor—We thank Bonten and Mevius for their interest in our systematic review [1]. In their letter, they disagree with our finding that whole-bacterium transmission (WBT) of expanded-spectrum cephalosporin-resistant (ESCR) Escherichia coli between food-producing animals and humans likely contributes to the burden of human extraintestinal infections. We respectfully argue against 2 assumptions that underlie their assertion.

Eco-Taxonomic Insights into Actinomycete Symbionts of Termites for Discovery of Novel Bioactive Compounds

Termites play a major role in foraging and degradation of plant biomass as well as cultivating bioactive microorganisms for their defense. Current advances in "omics'' sciences are revealing insights into function-related presence of these symbionts, and their related biosynthetic activities and genes identified in gut symbiotic bacteria might offer a significant potential for biotechnology and biodiscovery. Actinomycetes have been the major producers of bioactive compounds with an extraordinary range of biological activities. These metabolites have been in use as anticancer agents, immune suppressants, and most notably, as antibiotics. Insect-associated actinomycetes have also been reported to produce a range of antibiotics such as dentigerumycin and mycangimycin. Advances in genomics targeting a single species of the unculturable microbial members are currently aiding an improved understanding of the symbiotic interrelationships among the gut microorganisms as well as revealing the taxonomical identity and functions of the complex multilayered symbiotic actinofloral layers. If combined with target-directed approaches, these molecular advances can provide guidance towards the design of highly selective culturing methods to generate further information related to the physiology and growth requirements of these bioactive actinomycetes associated with the termite guts. This chapter provides an overview on the termite gut symbiotic actinoflora in the light of current advances in the "omics'' science, with examples of their detection and selective isolation from the guts of the Sunshine Coast regional termite Coptotermes lacteus in Queensland, Australia.

A new species of gall midge (Diptera: Cecidomyiidae) feeding on ornamental Cordyline fruticosa(Asparagaceae) in Australia

Larvae of an undescribed gall midge were found feeding on leaves and stems within leaf sheaths and between leaf blades of potted plants of Cordyline fruticosa (Asparagaceae) in a production nursery in Queensland. The following varieties of the host plant were infested: Apple Blossom', Glauca', Kilauea', Negra', Pink Diamond, 'Purple Prince' and Willy's Gold'. The new species, Dasineura cordylineaeKolesik sp. nov., is described and its cytochrome oxidase unit I mitochondrial gene segment is sequenced. The new species is the first known gall midge feeding on a plant species of the genus Cordyline. Orange larvae induce oval shallow swellings on the leaf and stem tissue, which becomes necrotised during the later stage of larval feeding. Necrotic areas remain visible to the end of leaves' lives and decrease the market value of the plants. In the production nursery investigated, the lesions caused by the gall midge provided an entry for a fungal infection by Fusarium sp. inflicting further injury to plants. Larvae of the new species were preyed on by larvae of Gaurax sp. (Diptera: Chloropidae). This is the first worldwide record of Chloropidae preying on Cecidomyiidae.

Estimates of genetic parameters for growth and wood properties in Eucalyptus pellita F. Muell. to support tree breeding in Vietnam

Eucalyptus pellita demonstrated good growth and wood quality traits in this study, with young plantation grown timber being suitable for both solid and pulp wood products. All traits examined were under moderate levels of genetic control with little genotype by environment interaction when grown on two contrasting sites in Vietnam. Eucalyptus pellita currently has a significant role in reforestation in the tropics. Research to support expanded of use of this species is needed: particularly, research to better understand the genetic control of key traits will facilitate the development of genetically improved planting stock. This study aimed to provide estimates of the heritability of diameter at breast height over bark, wood basic density, Kraft pulp yield, modulus of elasticity and microfibril angle, and the genetic correlations among these traits, and understand the importance of genotype by environment interactions in Vietnam. Data for diameter and wood properties were collected from two 10-year-old, open-pollinated progeny trials of E. pellita in Vietnam that evaluated 104 families from six native range and three orchard sources. Wood properties were estimated from wood samples using near-infrared (NIR) spectroscopy. Data were analysed using mixed linear models to estimate genetic parameters (heritability, proportion of variance between seed sources and genetic correlations). Variation among the nine sources was small compared to additive variance. Narrow-sense heritability and genetic correlation estimates indicated that simultaneous improvements in most traits could be achieved from selection among and within families as the genetic correlations among traits were either favourable or close to zero. Type B genetic correlations approached one for all traits suggesting that genotype by environment interactions were of little importance. These results support a breeding strategy utilizing a single breeding population advanced by selecting the best individuals across all seed sources. Both growth and wood properties have been evaluated. Multi-trait selection for growth and wood property traits will lead to more productive populations of E. pellita both with improved productivity and improved timber and pulp properties.

Parental contribution to progeny during experimental spawning of jungle perch, Kuhlia rupestris

When releasing captive-bred animals into wild populations, it is essential to maintain the capacity for adaptation and resilience by minimising the effect on population genetic diversity. Populations of the jungle perch (Kuhlia rupestris) have become reduced or locally extinct along the Queensland coast; thus, captive breeding of K. rupestris for restocking is presently underway. Currently, multiple individuals are placed in a tank to produce larvae, yet the number of adults contributing to larval production is unknown. We performed a power analysis on pre-existing microsatellite loci to determine the minimum number of loci and larvae required to achieve accurate assignment of parentage. These loci were then used to determine the number of contributing participants during a series of four spawning events through the summer breeding season in 2012-2013. Not all fish contributed to larval production and no relationship was found between male body size and parentage success. In most cases, there was a high skew of offspring to one mating pair (62% was the average contribution of the most successful pair per tank). This has significant implications for the aquaculture, restocking and conservation of K. rupestris.

First complete genome sequence of a capsicum chlorosis tospovirus isolate from Australia with an unusually large S RNA intergenic region

The first complete genome sequence of capsicum chlorosis virus (CaCV) from Australia was determined using a combination of Illumina HiSeq RNA and Sanger sequencing technologies. Australian CaCV had a tripartite genome structure like other CaCV isolates. The large (L) RNA was 8913 nucleotides (nt) in length and contained a single open reading frame (ORF) of 8634 nt encoding a predicted RNA-dependent RNA polymerase (RdRp) in the viral-complementary (vc) sense. The medium (M) and small (S) RNA segments were 4846 and 3944 nt in length, respectively, each containing two non-overlapping ORFs in ambisense orientation, separated by intergenic regions (IGR). The M segment contained ORFs encoding the predicted non-structural movement protein (NSm; 927 nt) and precursor of glycoproteins (GP; 3366 nt) in the viral sense (v) and vc strand, respectively, separated by a 449-nt IGR. The S segment coded for the predicted nucleocapsid (N) protein (828 nt) and non-structural suppressor of silencing protein (NSs; 1320 nt) in the vc and v strand, respectively. The S RNA contained an IGR of 1663 nt, being the largest IGR of all CaCV isolates sequenced so far. Comparison of the Australian CaCV genome with complete CaCV genome sequences from other geographic regions showed highest sequence identity with a Taiwanese isolate. Genome sequence comparisons and phylogeny of all available CaCV isolates provided evidence for at least two highly diverged groups of CaCV isolates that may warrant re-classification of AIT-Thailand and CP-China isolates as unique tospoviruses, separate from CaCV.

Effect of citrus peel chemicals on Bactrocera tryonilarval survival

Queensland fruit fly, Bactrocera tryoni (Froggatt) (Diptera: Tephritidae) is a major horticultural insect pest in Australia which significantly limits domestic and international market access for Australian horticultural produce. Citrus is one of the industries seriously affected by the fruit fly problem in Australia. This research investigated the effect of citrus peel essential oil chemicals on B. tryoni larval survival in five different commercially important Citrus species and cultivars as a way of better understanding fruit susceptibility. The fruits used were Murcott Mandarin, Navel orange, Eureka lemon, Valencia orange and yellow grapefruit. The essential oils of each citrus type were extracted using hydrodistillation and then mixed, at different concentrations, with artificial larval diets to which B. tryoni eggs were added. Surviving larvae were counted after five trial days. The same process was repeated for six essential oil components. Regression analysis of increasing oil concentration against larval survival showed that the crude oil blends of Navel orange, Eureka lemon and yellow grapefruit had significant negative effects on B. tryoni larval survival, but no such effects were seen for Murcott Mandarin and Valencia orange. Of the individual essential oil fractions, only D-limonene had a significant effect on B. tryoni larval survival, with this chemical being highly toxic at very low concentrations. The results of this study open up opportunities for incorporating B. tryoni resistance mechanisms into citrus through minor peel property changes which would not impact on the eating attributes of the fruit.

Review of greenhouse gas emissions from the storage and land application of farm dairy effluent

The amounts of farm dairy effluent stored in ponds and irrigated to land have steadily increased with the steady growth of New Zealand's dairy industry. About 80% of dairy farms now operate with effluent storage ponds allowing deferred irrigation. These storage and irrigation practices cause emissions of greenhouse gases (GHG) and ammonia. The current knowledge of the processes causing these emissions and the amounts emitted is reviewed here. Methane emissions from ponds are the largest contributor to the total GHG emissions from effluent in managed manure systems in New Zealand. Nitrous oxide emissions from anaerobic ponds are negligible, while ammonia emissions vary widely between different studies, probably because they depend strongly on pH and manure composition. The second-largest contribution to GHG emissions from farm dairy effluent comes from nitrous oxide emissions from land application. Ammonia emissions from land application of effluent in New Zealand were found to be less than those reported elsewhere from the application of slurries. Recent studies have suggested that New Zealand's current GHG inventory method to estimate methane emissions from effluent ponds should be revised. The increasing importance of emissions from ponds, while being a challenge for the inventory, also provides an opportunity to achieve mitigation of emissions due to the confined location of where these emissions occur. © 2015 © 2015 The Royal Society of New Zealand.

Improved models for estimating temporal changes in carbon sequestration in above-ground biomass of mixed-species environmental plantings

Plantings of mixed native species (termed 'environmental plantings') are increasingly being established for carbon sequestration whilst providing additional environmental benefits such as biodiversity and water quality. In Australia, they are currently one of the most common forms of reforestation. Investment in establishing and maintaining such plantings relies on having a cost-effective modelling approach to providing unbiased estimates of biomass production and carbon sequestration rates. In Australia, the Full Carbon Accounting Model (FullCAM) is used for both national greenhouse gas accounting and project-scale sequestration activities. Prior to undertaking the work presented here, the FullCAM tree growth curve was not calibrated specifically for environmental plantings and generally under-estimated their biomass. Here we collected and analysed above-ground biomass data from 605 mixed-species environmental plantings, and tested the effects of several planting characteristics on growth rates. Plantings were then categorised based on significant differences in growth rates. Growth of plantings differed between temperate and tropical regions. Tropical plantings were relatively uniform in terms of planting methods and their growth was largely related to stand age, consistent with the un-calibrated growth curve. However, in temperate regions where plantings were more variable, key factors influencing growth were planting width, stand density and species-mix (proportion of individuals that were trees). These categories provided the basis for FullCAM calibration. Although the overall model efficiency was only 39-46%, there was nonetheless no significant bias when the model was applied to the various planting categories. Thus, modelled estimates of biomass accumulation will be reliable on average, but estimates at any particular location will be uncertain, with either under- or over-prediction possible. When compared with the un-calibrated yield curves, predictions using the new calibrations show that early growth is likely to be more rapid and total above-ground biomass may be higher for many plantings at maturity. This study has considerably improved understanding of the patterns of growth in different types of environmental plantings, and in modelling biomass accumulation in young (<25. years old) plantings. However, significant challenges remain to understand longer-term stand dynamics, particularly with temporal changes in stand density and species composition. © 2014.