Nipah Virus in the Fruit Bat Pteropus vampyrus in Sumatera, Indonesia

Nipah virus causes periodic livestock and human disease with high case fatality rate, and consequent major economic, social and psychological impacts. Fruit bats of the genus Pteropus are the natural reservoir. In this study, we used real time PCR to screen the saliva and urine of P. vampyrus from North Sumatera for Nipah virus genome. A conventional reverse transcriptase (RT-PCR) assay was used on provisionally positive samples to corroborate findings. This is the first report of Nipah virus detection in P. vampyrus in Sumatera, Indonesia.

Field inoculation with arbuscular-mycorrhizal fungi overcomes phosphorus and zinc deficiencies of linseed (Linum usitatissimum) in a vertisol subject to long-fallow disorder

Long-fallow disorder is expressed as exacerbated deficiencies of phosphorus (P) and/or zinc (Zn) in field crops growing after long periods of weed-free fallow. The hypothesis that arbuscular-mycorrhizal fungi (AMF) improve the P and Zn nutrition, and thereby biomass production and seed yield of linseed (Linum usitatissimum) was tested in a field experiment. A factorial combination of treatments consisting of +/- fumigation, +/- AMF inoculation with Glomus spp., +/- P and +/- Zn fertilisers was used on a long-fallowed vertisol. The use of such methods allowed an absolute comparison of plants growing with and without AMF in the field for the first time in a soil disposed to long-fallow disorder. Plant biomass, height, P and Zn concentrations and contents, boll number and final seed yield were (a) least in fumigated soil with negligible AMF colonisation of the roots, (b) low initially in long-fallow soil but increased with time as AMF colonisation of the roots developed, and (c) greatest in soil inoculated with AMF cultures. The results showed for the first time in the field that inflows of both P and Zn into linseed roots were highly dependent on %AMF-colonisation (R-2 = 0.95 for P and 0.85 for Zn, P < 0.001) in a soil disposed to long-fallow disorder. Relative field mycorrhizal dependencies without and with P+Zn fertiliser were 85 % and 86 % for biomass and 68 % and 52 % for seed yield respectively. This research showed in the field that AMF greatly improved the P and Zn nutrition, biomass production and seed yield of linseed growing in a soil disposed to long-fallow disorder. The level of mycorrhizal colonisation of plants suffering from long-fallow disorder can increase during the growing season resulting in improved plant growth and residual AMF inoculum in the soil, and thus it is important for growers to recognise the cause and not terminate a poor crop prematurely in order to sow another. Other positive management options to reduce long fallows and foster AMF include adoption of conservation tillage and opportunity cropping.

Managing glyphosate resistance in Australian cotton farming: modelling shows how to delay evolution and maintain long-term population control

Glyphosate resistance is a rapidly developing threat to profitability in Australian cotton farming. Resistance causes an immediate reduction in the effectiveness of in-crop weed control in glyphosate-resistant transgenic cotton and summer fallows. Although strategies for delaying glyphosate resistance and those for managing resistant populations are qualitatively similar, the longer resistance can be delayed, the longer cotton growers will have choice over which tactics to apply and when to apply them. Effective strategies to avoid, delay, and manage resistance are thus of substantial value. We used a model of glyphosate resistance dynamics to perform simulations of resistance evolution in Sonchus oleraceus (common sowthistle) and Echinochloa colona (awnless barnyard grass) under a range of resistance prevention, delaying, and management strategies. From these simulations, we identified several elements that could contribute to effective glyphosate resistance prevention and management strategies. (i) Controlling glyphosate survivors is the most robust approach to delaying or preventing resistance. High-efficacy, high-frequency survivor control almost doubled the useful lifespan of glyphosate from 13 to 25 years even with glyphosate alone used in summer fallows. (ii) Two non-glyphosate tactics in-crop plus two in-summer fallows is the minimum intervention required for long-term delays in resistance evolution. (iii) Pre-emergence herbicides are important, but should be backed up with non-glyphosate knockdowns and strategic tillage; replacing a late-season, pre-emergence herbicide with inter-row tillage was predicted to delay glyphosate resistance by 4 years in awnless barnyard grass. (iv) Weed species' ecological characteristics, particularly seed bank dynamics, have an impact on the effectiveness of resistance strategies; S. oleraceus, because of its propensity to emerge year-round, was less exposed to selection with glyphosate than E. colona, resulting in an extra 5 years of glyphosate usefulness (18 v. 13 years) even in the most rapid cases of resistance evolution. Delaying tactics are thus available that can provide some or many years of continued glyphosate efficacy. If glyphosate-resistant cotton cropping is to remain profitable in Australian farming systems in the long-term, however, growers must adapt to the probability that they will have to deal with summer weeds that are no longer susceptible to glyphosate. Robust resistance management systems will need to include a diversity of weed control options, used appropriately.

Effect of Broadcast Baiting on Abundance Patterns of Red Imported Fire Ants (Hymenoptera: Formicidae) and Key Local Ant Genera at Long-Term Monitoring Sites in Brisbane, Australia

In 2001, the red imported fire ant (Solenopsis invicta Buren) was identified in Brisbane, Australia. An eradication program involving broadcast bait treatment with two insect growth regulators and a metabolic inhibitor began in September of that year and is currently ongoing. To gauge the impacts of these treatments on local ant populations, we examined long-term monitoring data and quantified abundance patterns of S. invicta and common local ant genera using a linear mixed-effects model. For S. invicta, presence in pitfalls reduced over time to zero on every site. Significantly higher numbers of S. invicta workers were collected on high-density polygyne sites, which took longer to disinfest compared with monogyne and low-density polygyne sites. For local ants, nine genus groups of the 10 most common genera analyzed either increased in abundance or showed no significant trend. Five of these genus groups were significantly less abundant at the start of monitoring on high-density polygyne sites compared with monogyne and low-density polygyne sites. The genus Pheidole significantly reduced in abundance over time, suggesting that it was affected by treatment efforts. These results demonstrate that the treatment regime used at the time successfully removed S. invicta from these sites in Brisbane, and that most local ant genera were not seriously impacted by the treatment. These results have important implications for current and future prophylactic treatment efforts, and suggest that native ants remain in treated areas to provide some biological resistance to S. invicta.

Isolation of multiple novel paramyxoviruses from pteropid bat urine

Bats have been found to harbor a number of new emerging viruses with zoonotic potential and there has been a great deal of interest in identifying novel bat pathogens to determine risk to human and animal health. Many groups have identified novel viruses in bats by detection of viral nucleic acid, however virus isolation is still a challenge and there are few reports of viral isolates from bats. In recent years, our group has developed optimized procedures for virus isolation from bat urine, including the use of primary bat cells. In previous reports we have described the isolation of Hendra virus, Menangle virus and Cedar virus, in Queensland, Australia. Here, we report the isolation of four additional novel bat paramyxoviruses from urine collected from beneath pteropid bat (flying fox) colonies in Queensland and New South Wales during 2009-2011.

Ecological dynamics of emerging bat virus spillover

Viruses that originate in bats may be the most notorious emerging zoonoses that spill over from wildlife into domestic animals and humans. Understanding how these infections filter through ecological systems to cause disease in humans is of profound importance to public health. Transmission of viruses from bats to humans requires a hierarchy of enabling conditions that connect the distribution of reservoir hosts, viral infection within these hosts, and exposure and susceptibility of recipient hosts. For many emerging bat viruses, spillover also requires viral shedding from bats, and survival of the virus in the environment. Focusing on Hendra virus, but also addressing Nipah virus, Ebola virus, Marburg virus and coronaviruses, we delineate this cross-species spillover dynamic from the within-host processes that drive virus excretion to land-use changes that increase interaction among species. We describe how land-use changes may affect co-occurrence and contact between bats and recipient hosts. Two hypotheses may explain temporal and spatial pulses of virus shedding in bat populations: episodic shedding from persistently infected bats or transient epidemics that occur as virus is transmitted among bat populations. Management of livestock also may affect the probability of exposure and disease. Interventions to decrease the probability of virus spillover can be implemented at multiple levels from targeting the reservoir host to managing recipient host exposure and susceptibility.

Immediate, cumulative and residual effects of short- and long-term low plane of nutrition on milk protein and casein composition

Immediate and residual effects of two lengths of low plane of nutrition (PON) on the synthesis of milk protein and protein fractions were studied at the Mutdapilly Research Station, in south-east Queensland. Thirty-six multiparous Holstein-Friesian cows, between 46 and 102 days in milk (DIM) initially, were used in a completely randomised design experiment with three treatments. All cows were fed on a basal diet of ryegrass pasture (7.0 kg DM/cow.day), barley-sorghum concentrate mix (2.7 kg DM/cow.day) and a canola meal-mineral mix (1.3 kg DM/cow.day). To increase PON, 5.0 kg DM/cow.day supplemental maize and forage sorghum silage was added to the basal diet. The three treatments were (C) high PON (basal diet + supplemental silage); (L9) low PON (basal diet only) for a period of 9 weeks; and (L3) low PON (basal diet only) for a period of 3 weeks. The experiment comprised three periods (1) covariate – high PON, all groups (5 weeks), (2) period of low PON for either 3 weeks (L3) or 9 weeks (L9), and (3) period of high PON (all groups) to assess ability of cows to recover any production lost as a result of treatments (5 weeks). The low PON treatment periods for L3 and L9 were end-aligned so that all treatment groups began Period 3 together. Although there was a significant effect of L9 on yields of milk, protein, fat and lactose, and concentrations of true protein, whey protein and urea, these were not significantly different from L3. There were no residual effects of L3 or L9 on protein concentration or nitrogen distribution after 5 weeks of realimentation. There was no significant effect of low PON for 3 or 9 weeks on casein concentration or composition.

Australian bat lyssavirus infection in two horses

In May 2013, the first cases of Australian bat lyssavirus infections in domestic animals were identified in Australia. Two horses (filly-H1 and gelding-H2) were infected with the Yellow-bellied sheathtail bat (YBST) variant of Australian bat lyssavirus (ABLV). The horses presented with neurological signs, pyrexia and progressing ataxia. Intra-cytoplasmic inclusion bodies (Negri bodies) were detected in some Purkinje neurons in haematoxylin and eosin (H&E) stained sections from the brain of one of the two infected horses (H2) by histological examination. A morphological diagnosis of sub-acute moderate non-suppurative, predominantly angiocentric, meningo-encephalomyelitis of viral aetiology was made. The presumptive diagnosis of ABLV infection was confirmed by the positive testing of the affected brain tissue from (H2) in a range of laboratory tests including fluorescent antibody test (FAT) and real-time PCR targeting the nucleocapsid (N) gene. Retrospective testing of the oral swab from (H1) in the real-time PCR also returned a positive result. The FAT and immunohistochemistry (IHC) revealed an abundance of ABLV antigen throughout the examined brain sections. ABLV was isolated from the brain (H2) and oral swab/saliva (H1) in the neuroblastoma cell line (MNA). Alignment of the genome sequence revealed a 97.7% identity with the YBST ABLV strain.

Ecological dynamics of emerging bat virus spillover

Viruses that originate in bats may be the most notorious emerging zoonoses that spill over from wildlife into domestic animals and humans. Understanding how these infections filter through ecological systems to cause disease in humans is of profound importance to public health. Transmission of viruses from bats to humans requires a hierarchy of enabling conditions that connect the distribution of reservoir hosts, viral infection within these hosts, and exposure and susceptibility of recipient hosts. For many emerging bat viruses, spillover also requires viral shedding from bats, and survival of the virus in the environment. Focusing on Hendra virus, but also addressing Nipah virus, Ebola virus, Marburg virus and coronaviruses, we delineate this cross-species spillover dynamic from the within-host processes that drive virus excretion to land-use changes that increase interaction among species. We describe how land-use changes may affect co-occurrence and contact between bats and recipient hosts. Two hypotheses may explain temporal and spatial pulses of virus shedding in bat populations: episodic shedding from persistently infected bats or transient epidemics that occur as virus is transmitted among bat populations. Management of livestock also may affect the probability of exposure and disease. Interventions to decrease the probability of virus spillover can be implemented at multiple levels from targeting the reservoir host to managing recipient host exposure and susceptibility.

Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning

Soil biogeochemical cycles are largely mediated by microorganisms, while fire significantly modifies biogeochemical cycles mainly via altering microbial community and substrate availability. Majority of studies on fire effects have focused on the surface soil; therefore, our understanding of the vertical distribution of microbial communities and the impacts of fire on nitrogen (N) dynamics in the soil profile is limited. Here, we examined the changes of soil denitrification capacity (DNC) and denitrifying communities with depth under different burning regimes, and their interaction with environmental gradients along the soil profile. Results showed that soil depth had a more pronounced impact than the burning treatment on the bacterial community size. The abundance of 16S rRNA and denitrification genes (narG, nirK, and nirS) declined exponentially with soil depth. Surprisingly, the nosZ-harboring denitrifiers were enriched in the deeper soil layers, which was likely to indicate that the nosZ-harboring denitrifiers could better adapt to the stress conditions (i.e., oxygen deficiency, nutrient limitation, etc.) than other denitrifiers. Soil nutrients, including dissolved organic carbon (DOC), total soluble N (TSN), ammonium (NH4 +), and nitrate (NO3 −), declined significantly with soil depth, which probably contributed to the vertical distribution of denitrifying communities. Soil DNC decreased significantly with soil depth, which was negligible in the depths below 20 cm. These findings have provided new insights into niche separation of the N-cycling functional guilds along the soil profile, under a varied fire disturbance regime.

Extremely Low Microsatellite Diversity but Distinct Population Structure in a Long-Lived Threatened Species, the Australian Lungfish Neoceratodus forsteri (Dipnoi)

The Australian lungfish is a unique living representative of an ancient dipnoan lineage, listed as ‘vulnerable’ to extinction under Australia’s Environment Protection and Biodiversity Conservation Act 1999. Historical accounts indicate this species occurred naturally in two adjacent river systems in Australia, the Burnett and Mary. Current day populations in other rivers are thought to have arisen by translocation from these source populations. Early genetic work detected very little variation and so had limited power to answer questions relevant for management including how genetic variation is partitioned within and among sub-populations. In this study, we use newly developed microsatellite markers to examine samples from the Burnett and Mary Rivers, as well as from two populations thought to be of translocated origin, Brisbane and North Pine. We test whether there is significant genetic structure among and within river drainages; assign putatively translocated populations to potential source populations; and estimate effective population sizes. Eleven polymorphic microsatellite loci genotyped in 218 individuals gave an average within-population heterozygosity of 0.39 which is low relative to other threatened taxa and for freshwater fishes in general. Based on F_ST values (average over loci = 0.11) and STRUCTURE analyses, we identify three distinct populations in the natural range, one in the Burnett and two distinct populations in the Mary. These analyses also support the hypothesis that the Mary River is the likely source of translocated populations in the Brisbane and North Pine rivers, which agrees with historical published records of a translocation event giving rise to these populations. We were unable to obtain bounded estimates of effective population size, as we have too few genotype combinations, although point estimates were low, ranging from 29 - 129. We recommend that, in order to preserve any local adaptation in the three distinct populations that they be managed separately.

The global distribution of Banana bunchy top virus reveals little evidence for frequent recent, human-mediated long distance dispersal events

Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component single-stranded DNA virus, which infects banana plants in many regions of the world, often resulting in large-scale crop losses. Weanalyzed 171 banana leaf samples from fourteen countries and recovered, cloned, and sequenced 855 complete BBTV components including ninety-four full genomes. Importantly, full genomes were determined from eight countries, where previously no full genomes were available (Samoa, Burundi, Republic of Congo, Democratic Republic of Congo, Egypt, Indonesia, the Philippines, and the USA [HI]). Accounting for recombination and genome component reassortment, we examined the geographic structuring of global BBTV populations to reveal that BBTV likely originated in Southeast Asia, that the current global hotspots of BBTV diversity are Southeast Asia/Far East and India, and that BBTV populations circulating elsewhere in the world have all potentially originated from infrequent introductions. Most importantly, we find that rather than the current global BBTV distribution being due to increases in human-mediated movements of bananas over the past few decades, it is more consistent with a pattern of infrequent introductions of the virus to different parts of the world over the past 1,000 years.

Long-term frequent prescribed fire decreases surface soil carbon and nitrogen pools in a wet sclerophyll forest of Southeast Queensland, Australia

Prescribed fire is one of the most widely-used management tools for reducing fuel loads in managed forests. However the long-term effects of repeated prescribed fires on soil carbon (C) and nitrogen (N) pools are poorly understood. This study aimed to investigate how different fire frequency regimes influence C and N pools in the surface soils (0–10 cm). A prescribed fire field experiment in a wet sclerophyll forest established in 1972 in southeast Queensland was used in this study. The fire frequency regimes included long unburnt (NB), burnt every 2 years (2yrB) and burnt every 4 years (4yrB), with four replications. Compared with the NB treatment, the 2yrB treatment lowered soil total C by 44%, total N by 54%, HCl hydrolysable C and N by 48% and 59%, KMnO4 oxidizable C by 81%, microbial biomass C and N by 42% and 33%, cumulative CO2–C by 28%, NaOCl-non-oxidizable C and N by 41% and 51%, and charcoal-C by 17%, respectively. The 4yrB and NB treatments showed no significant differences for these soil C and N pools. All soil labile, biologically active and recalcitrant and total C and N pools were correlated positively with each other and with soil moisture content, but negatively correlated with soil pH. The C:N ratios of different C and N pools were greater in the burned treatments than in the NB treatments. This study has highlighted that the prescribed burning at four year interval is a more sustainable management practice for this subtropical forest ecosystem.

Silica Vesicle Nanovaccine Formulations Stimulate Long-Term Immune Responses to the Bovine Viral Diarrhoea Virus E2 Protein

Bovine Viral Diarrhoea Virus (BVDV) is one of the most serious pathogen, which causes tremendous economic loss to the cattle industry worldwide, meriting the development of improved subunit vaccines. Structural glycoprotein E2 is reported to be a major immunogenic determinant of BVDV virion. We have developed a novel hollow silica vesicles (SV) based platform to administer BVDV-1 Escherichia coli-expressed optimised E2 (oE2) antigen as a nanovaccine formulation. The SV-140 vesicles (diameter 50 nm, wall thickness 6 nm, perforated by pores of entrance size 16 nm and total pore volume of 0.934 cm(3)g(-1)) have proven to be ideal candidates to load oE2 antigen and generate immune response. The current study for the first time demonstrates the ability of freeze-dried (FD) as well as non-FD oE2/SV140 nanovaccine formulation to induce long-term balanced antibody and cell mediated memory responses for at least 6 months with a shortened dosing regimen of two doses in small animal model. The in vivo ability of oE2 (100 mu g)/SV-140 (500 mu g) and FD oE2 (100 mu g)/SV-140 (500 mu g) to induce long-term immunity was compared to immunisation with oE2 (100 mu g) together with the conventional adjuvant Quil-A from the Quillaja saponira (10 mu g) in mice. The oE2/SV-140 as well as the FD oE2/SV-140 nanovaccine generated oE2-specific antibody and cell mediated responses for up to six months post the final second immunisation. Significantly, the cell-mediated responses were consistently high in mice immunised with oE2/SV-140 (1,500 SFU/million cells) at the six-month time point. Histopathology studies showed no morphological changes at the site of injection or in the different organs harvested from the mice immunised with 500 mu g SV-140 nanovaccine compared to the unimmunised control. The platform has the potential for developing single dose vaccines without the requirement of cold chain storage for veterinary and human applications.

A crop productivity research protocol for long wall mining

Springsure Creek Coal (SCC) intends to develop a coal mine using the long wall mining process under grain farming land near Emerald in Central Queensland (CQ). While this technology will result in some subsidence of the land surface, SCC wishes to maintain productivity of the grain cropping land in the precinct after coal mining. However, the impact of the surface subsidence resulting from that mining process on productivity of cropping land in any Australian landscape is currently unclear. A research protocol to investigate the impacts of subsidence on grain productivity for when the SCC project becomes operational is proposed. The protocol has wider application for other similar mining projects throughout the country. A copy of the full report is accessible on www.aginstitute.com.au.