Molecular evolutionary dynamics of Ross River virus and implications for vaccine efficacy

Ross River virus (RRV) is a mosquito-borne member of the genus Alphavirus that causes epidemic polyarthritis in humans, costing the Australian health system at least US$10 million annually. Recent progress in RRV vaccine development requires accurate assessment of RRV genetic diversity and evolution, particularly as they may affect the utility of future vaccination. In this study, we provide novel RRV genome sequences and investigate the evolutionary dynamics of RRV from time-structured E2 gene datasets. Our analysis indicates that, although RRV evolves at a similar rate to other alphaviruses (mean evolutionary rate of approx. 8x10(-4) nucleotide substitutions per site year(-1)), the relative genetic diversity of RRV has been continuously low through time, possibly as a result of purifying selection imposed by replication in a wide range of natural host and vector species. Together, these findings suggest that vaccination against RRV is unlikely to result in the rapid antigenic evolution that could compromise the future efficacy of current RRV vaccines.

Turbulence and suspended sediment measurements in an urban environment during the Brisbane River flood of January 2011

In urbanised areas, the flood flows constitute a hazard to populations and infrastructure as illustrated during major floods in 2011. During the 2011 Brisbane River flood, some turbulent velocity data were collected using acoustic Doppler velocimetry in an inundated street. The field deployment showed some unusual features of flood flow in the urban environment. That is, the water elevations and velocities fluctuated with distinctive periods between 50 and 100 s linked with some local topographic effects. The instantaneous velocity data were analysed using a triple decomposition. The velocity fluctuations included a large energy component in the slow fluctuation range, while the turbulent motion components were much smaller. The suspended sediment data showed some significant longitudinal flux. Altogether the results highlighted that the triple decomposition approach originally developed for period flows is well suited to complicated flows in an inundated urban environment.

Characterisation and source apportionment of polycyclic aromatic hydrocarbons in the sediments of Brisbane River

The thesis was a step forward in predicting the levels and sources of polycyclic aromatic hydrocarbons (PAHs) in sediments of Brisbane river, especially after the Brisbane floods in 2011. It employed different statistical techniques to provide valuable information that may assist source control and formulation of pollution mitigation measures for the river.

Influence of historical landscapes, drainage evolution and ecological traits on patterns of genetic diversity in Southeast Asian freshwater snakehead fishes

Snakehead fishes in the family Channidae are obligate freshwater fishes represented by two extant genera, the African Parachannna and the Asian Channa. These species prefer still or slow flowing water bodies, where they are top predators that exercise high levels of parental care, have the ability to breathe air, can tolerate poor water quality, and interestingly, can aestivate or traverse terrestrial habitat in response to seasonal changes in freshwater habitat availability. These attributes suggest that snakehead fishes may possess high dispersal potential, irrespective of the terrestrial barriers that would otherwise constrain the distribution of most freshwater fishes. A number of biogeographical hypotheses have been developed to account for the modern distributions of snakehead fishes across two continents, including ancient vicariance during Gondwanan break-up, or recent colonisation tracking the formation of suitable climatic conditions. Taxonomic uncertainty also surrounds some members of the Channa genus, as geographical distributions for some taxa across southern and Southeast (SE) Asia are very large, and in one case is highly disjunct. The current study adopted a molecular genetics approach to gain an understanding of the evolution of this group of fishes, and in particular how the phylogeography of two Asian species may have been influenced by contemporary versus historical levels of dispersal and vicariance. First, a molecular phylogeny was constructed based on multiple DNA loci and calibrated with fossil evidence to provide a dated chronology of divergence events among extant species, and also within species with widespread geographical distributions. The data provide strong evidence that trans-continental distribution of the Channidae arose as a result of dispersal out of Asia and into Africa in the mid–Eocene. Among Asian Channa, deep divergence among lineages indicates that the Oligocene-Miocene boundary was a time of significant species radiation, potentially associated with historical changes in climate and drainage geomorphology. Mid-Miocene divergence among lineages suggests that a taxonomic revision is warranted for two taxa. Deep intra-specific divergence (~8Mya) was also detected between C. striata lineages that occur sympatrically in the Mekong River Basin. The study then examined the phylogeography and population structure of two major taxa, Channa striata (the chevron snakehead) and the C. micropeltes (the giant snakehead), across SE Asia. Species specific microsatellite loci were developed and used in addition to a mitochondrial DNA marker (Cyt b) to screen neutral genetic variation within and among wild populations. C. striata individuals were sampled across SE Asia (n=988), with the major focus being the Mekong Basin, which is the largest drainage basin in the region. The distributions of two divergent lineages were identified and admixture analysis showed that where they co-occur they are interbreeding, indicating that after long periods of evolution in isolation, divergence has not resulted in reproductive isolation. One lineage is predominantly confined to upland areas of northern Lao PDR to the north of the Khorat Plateau, while the other, which is more closely related to individuals from southern India, has a widespread distribution across mainland SE Asian and Sumatra. The phylogeographical pattern recovered is associated with past river networks, and high diversity and divergence among all populations sampled reveal that contemporary dispersal is very low for this taxon, even where populations occur in contiguous freshwater habitats. C. micropeltes (n=280) were also sampled from across the Mekong River Basin, focusing on the lower basin where it constitutes an important wild fishery resource. In comparison with C. striata, allelic diversity and genetic divergence among populations were extremely low, suggesting very recent colonisation of the greater Mekong region. Populations were significantly structured into at least three discrete populations in the lower Mekong. Results of this study have implications for establishing effective conservation plans for managing both species, that represent economically important wild fishery resources for the region. For C. micropeltes, it is likely that a single fisheries stock in the Tonle Sap Great Lake is being exploited by multiple fisheries operations, and future management initiatives for this species in this region will need to account for this. For C. striata, conservation of natural levels of genetic variation will require management initiatives designed to promote population persistence at very localised spatial scales, as the high level of population structuring uncovered for this species indicates that significant unique diversity is present at this fine spatial scale.

Development and validation of novel methods for microbial source tracking based on Escherichia coli as an indicator of water quality

Microbial pollution in water periodically affects human health in Australia, particularly in times of drought and flood. There is an increasing need for the control of waterborn microbial pathogens. Methods, allowing the determination of the origin of faecal contamination in water, are generally referred to as Microbial Source Tracking (MST). Various approaches have been evaluated as indicatorsof microbial pathogens in water samples, including detection of different microorganisms and various host-specific markers. However, until today there have been no universal MST methods that could reliably determine the source (human or animal) of faecal contamination. Therefore, the use of multiple approaches is frequently advised. MST is currently recognised as a research tool, rather than something to be included in routine practices. The main focus of this research was to develop novel and universally applicable methods to meet the demands for MST methods in routine testing of water samples. Escherichia coli was chosen initially as the object organism for our studies as, historically and globally, it is the standard indicator of microbial contamination in water. In this thesis, three approaches are described: single nucleotide polymorphism (SNP) genotyping, clustered regularly interspaced short palindromic repeats (CRISPR) screening using high resolution melt analysis (HRMA) methods and phage detection development based on CRISPR types. The advantage of the combination SNP genotyping and CRISPR genes has been discussed in this study. For the first time, a highly discriminatory single nucleotide polymorphism interrogation of E. coli population was applied to identify the host-specific cluster. Six human and one animal-specific SNP profile were revealed. SNP genotyping was successfully applied in the field investigations of the Coomera watershed, South-East Queensland, Australia. Four human profiles [11], [29], [32] and [45] and animal specific SNP profile [7] were detected in water. Two human-specific profiles [29] and [11] were found to be prevalent in the samples over a time period of years. The rainfall (24 and 72 hours), tide height and time, general land use (rural, suburban), seasons, distance from the river mouth and salinity show a lack of relashionship with the diversity of SNP profiles present in the Coomera watershed (p values > 0.05). Nevertheless, SNP genotyping method is able to identify and distinquish between human- and non-human specific E. coli isolates in water sources within one day. In some samples, only mixed profiles were detected. To further investigate host-specificity in these mixed profiles CRISPR screening protocol was developed, to be used on the set of E. coli, previously analysed for SNP profiles. CRISPR loci, which are the pattern of previous DNA coliphages attacks, were considered to be a promising tool for detecting host-specific markers in E. coli. Spacers in CRISPR loci could also reveal the dynamics of virulence in E. coli as well in other pathogens in water. Despite the fact that host-specificity was not observed in the set of E. coli analysed, CRISPR alleles were shown to be useful in detection of the geographical site of sources. HRMA allows determination of ‘different’ and ‘same’ CRISPR alleles and can be introduced in water monitoring as a cost-effective and rapid method. Overall, we show that the identified human specific SNP profiles [11], [29], [32] and [45] can be useful as marker genotypes globally for identification of human faecal contamination in water. Developed in the current study, the SNP typing approach can be used in water monitoring laboratories as an inexpensive, high-throughput and easy adapted protocol. The unique approach based on E. coli spacers for the search for unknown phage was developed to examine the host-specifity in phage sequences. Preliminary experiments on the recombinant plasmids showed the possibility of using this method for recovering phage sequences. Future studies will determine the host-specificity of DNA phage genotyping as soon as first reliable sequences can be acquired. No doubt, only implication of multiple approaches in MST will allow identification of the character of microbial contamination with higher confidence and readability.

Assessing the suitability of existing spatial data for disaster planning and mitigation in Queensland

The Council of Australian Governments (COAG) in 2003 gave in-principle approval to a best-practice report recommending a holistic approach to managing natural disasters in Australia incorporating a move from a traditional response-centric approach to a greater focus on mitigation, recovery and resilience with community well-being at the core. Since that time, there have been a range of complementary developments that have supported the COAG recommended approach. Developments have been administrative, legislative and technological, both, in reaction to the COAG initiative and resulting from regular natural disasters. This paper reviews the characteristics of the spatial data that is becoming increasingly available at Federal, state and regional jurisdictions with respect to their being fit for the purpose for disaster planning and mitigation and strengthening community resilience. In particular, Queensland foundation spatial data, which is increasingly accessible by the public under the provisions of the Right to Information Act 2009, Information Privacy Act 2009, and recent open data reform initiatives are evaluated. The Fitzroy River catchment and floodplain is used as a case study for the review undertaken. The catchment covers an area of 142,545 km2, the largest river catchment flowing to the eastern coast of Australia. The Fitzroy River basin experienced extensive flooding during the 2010–2011 Queensland floods. The basin is an area of important economic, environmental and heritage values and contains significant infrastructure critical for the mining and agricultural sectors, the two most important economic sectors for Queensland State. Consequently, the spatial datasets for this area play a critical role in disaster management and for protecting critical infrastructure essential for economic and community well-being. The foundation spatial datasets are assessed for disaster planning and mitigation purposes using data quality indicators such as resolution, accuracy, integrity, validity and audit trail.

Impact of recent coastal development and human activities on Nha Trang Bay, Vietnam : evidence from a Porites lutea geochemical record

Nha Trang Bay (NTB) is located on the Central Vietnam coast, western South China Sea. Recent coastal development of Nha Trang City has raised public concern over an increasing level of pollution within the bay and degradation of nearby coral reefs. In this study, multiple proxies (e.g., trace metals, rare earth elements (REEs), and Y/Ho) recorded in a massive Porites lutea coral colony were used to reconstruct changes in seawater conditions in the NTB from 1995 to 2009. A 14-year record of REEs and other trace metals revealed that the concentrations of terrestrial trace metals have increased dramatically in response to an increase in coastal development projects such as road, port, and resort constructions, port and river dredging, and dumping activities since 2000. The effects of such developmental processes are also evident in changes in REE patterns and Y/Ho ratios through time, suggesting that both parameters are critical proxies for marine pollution.

Terrestrial invertebrates of dry river beds are not simply subsets of riparian assemblages

Dry river beds are common worldwide and are rapidly increasing in extent due to the effects of water management and prolonged drought periods due to climate change. While attention has been given to the responses of aquatic invertebrates to drying rivers, few studies exist on the terrestrial invertebrates colonizing dry river beds. Dry river beds are physically harsh and they often differ substantially in substrate, topography, microclimate and inundation frequency from adjacent riparian zones. Given these differences, we predicted that dry river beds provide a unique habitat for terrestrial invertebrates, and that their assemblage composition differs from that in adjacent riparian zones. Dry river beds and riparian zones in Australia and Italy were sampled for terrestrial invertebrates with pitfall traps. Sites differed in substrate type, climate and flow regime. Dry river beds contained diverse invertebrate assemblages and their composition was consistently different from adjacent riparian zones, irrespective of substrate, climate or hydrology. Although some taxa were shared between dry river beds and riparian zones, 66 of 320 taxa occurred only in dry river beds. Differences were due to species turnover, rather than shifts in abundance, indicating that dry river bed assemblages are not simply subsets of riparian assemblages. Some spatial patterns in invertebrate assemblages were associated with environmental variables (irrespective of habitat type), but these associations were statistically weak. We suggest that dry river beds are unique habitats in their own right. We discuss potential human stressors and management issues regarding dry river beds and provide recommendations for future research.

Are alien fish a reliable indicator of river health?

1. The ability of many introduced fish species to thrive in degraded aquatic habitats and their potential to impact on aquatic ecosystem structure and function suggest that introduced fish may represent both a symptom and a cause of decline in river health and the integrity of native aquatic communities. 2. The varying sensitivities of many commonly introduced fish species to degraded stream conditions, the mechanism and reason for their introduction and the differential susceptibility of local stream habitats to invasion because of the environmental and biological characteristics of the receiving water body, are all confounding factors that may obscure the interpretation of patterns of introduced fish species distribution and abundance and therefore their reliability as indicators of river health. 3. In the present study, we address the question of whether alien fish (i.e. those species introduced from other countries) are a reliable indicator of the health of streams and rivers in south-eastern Queensland, Australia. We examine the relationships of alien fish species distributions and indices of abundance and biomass with the natural environmental features, the biotic characteristics of the local native fish assemblages and indicators of anthropogenic disturbance at a large number of sites subject to varying sources and intensities of human impact. 4. Alien fish species were found to be widespread and often abundant in south-eastern Queensland rivers and streams, and the five species collected were considered to be relatively tolerant to river degradation, making them good candidate indicators of river health. Variation in alien species indices was unrelated to the size of the study sites, the sampling effort expended or natural environmental gradients. The biological resistance of the native fish fauna was not concluded to be an important factor mediating invasion success by alien species. Variation in alien fish indices was, however, strongly related to indicators of disturbance intensity describing local in-stream habitat and riparian degradation, water quality and surrounding land use, particularly the amount of urban development in the catchment. 5. Potential confounding factors that may influence the likelihood of introduction and successful establishment of an alien species and the implications of these factors for river bioassessment are discussed. We conclude that the potentially strong impact that many alien fish species can have on the biological integrity of natural aquatic ecosystems, together with their potential to be used as an initial basis to find out other forms of human disturbance impacts, suggest that some alien species (particularly species from the family Poeciliidae) can represent a reliable 'first cut' indicator of river health.

Ross River virus disease activity associated with naturally occurring non-tidal flood events in Australia : A systematic review

Ross River virus (RRV) disease is the most common and widespread mosquito-borne disease in Australia, resulting in considerable health and economic cost to communities. While naturally occurring non-tidal flood events may enhance mosquito abundance, little is known about the impact of such events on RRV transmission. This paper critically reviews the existing evidence for an association between naturally occurring non-tidal flood events and RRV transmission. A systematic literature search was conducted on RRV transmission related to flooding and inundation from rain and riverine overflow. Overall, the evidence to support a positive association between flooding and RRV outbreaks is largely circumstantial, with the literature mostly reporting only coincidental occurrence between the two. However, for the Murray River, river flow and height (surrogates of flooding) were positively and significantly associated with RRV transmission. The association between non-tidal flooding and RRV transmission has not been studied comprehensively. More frequent flood events arising from climate change may result in increased outbreaks of RRV disease. Understanding the link between flood events and RRV transmission is necessary if resources for mosquito spraying and public health warnings are to be utilized more effectively and efficiently.

Ecosystem management along ephemeral rivers: Trading off socio-economic water supply and vegetation conservation under flood regime uncertainty

In ecosystems driven by water availability, plant community dynamics depend on complex interactions between vegetation, hydrology, and human water resources use. Along ephemeral rivers—where water availability is erratic—vegetation and people are particularly vulnerable to changes in each other's water use. Sensible management requires that water supply be maintained for people, while preserving ecosystem health. Meeting such requirements is challenging because of the unpredictable water availability. We applied information gap decision theory to an ecohydrological system model of the Kuiseb River environment in Namibia. Our aim was to identify the robustness of ecosystem and water management strategies to uncertainties in future flood regimes along ephemeral rivers. We evaluated the trade-offs between alternative performance criteria and their robustness to uncertainty to account for both (i) human demands for water supply and (ii) reducing the risk of species extinction caused by water mining. Increasing uncertainty of flood regime parameters reduced the performance under both objectives. Remarkably, the ecological objective (species coexistence) was more sensitive to uncertainty than the water supply objective. However, within each objective, the relative performance of different management strategies was insensitive to uncertainty. The ‘best’ management strategy was one that is tuned to the competitive species interactions in the Kuiseb environment. It regulates the biomass of the strongest competitor and, thus, at the same time decreases transpiration, thereby increasing groundwater storage and reducing pressure on less dominant species. This robust mutually acceptable strategy enables species persistence without markedly reducing the water supply for humans. This study emphasises the utility of ecohydrological models for resource management of water-controlled ecosystems. Although trade-offs were identified between alternative performance criteria and their robustness to uncertain future flood regimes, management strategies were identified that help to secure an ecologically sustainable water supply.

Raman and infrared spectroscopic study of turquoise minerals

Raman and infrared spectra of three well-defined turquoise samples, CuAl6(PO4)4(OH)8·4H2O, from Lavender Pit, Bisbee, Cochise county, Arizona; Kouroudaiko mine, Faleme river, Senegal and Lynch Station, Virginia were studied, interpreted and compared. Observed Raman and infrared bands were assigned to the stretching and bending vibrations of phosphate tetrahedra, water molecules and hydroxyl ions. Approximate O–H⋯O hydrogen bond lengths were inferred from the Raman and infrared spectra. No Raman and infrared bands attributable to the stretching and bending vibrations of (PO3OH)2− units were observed.

Characterization of alluvial formation by stochastic modelling of paleo-fluvial processes: The concept and method

Modelling fluvial processes is an effective way to reproduce basin evolution and to recreate riverbed morphology. However, due to the complexity of alluvial environments, deterministic modelling of fluvial processes is often impossible. To address the related uncertainties, we derive a stochastic fluvial process model on the basis of the convective Exner equation that uses the statistics (mean and variance) of river velocity as input parameters. These statistics allow for quantifying the uncertainty in riverbed topography, river discharge and position of the river channel. In order to couple the velocity statistics and the fluvial process model, the perturbation method is employed with a non-stationary spectral approach to develop the Exner equation as two separate equations: the first one is the mean equation, which yields the mean sediment thickness, and the second one is the perturbation equation, which yields the variance of sediment thickness. The resulting solutions offer an effective tool to characterize alluvial aquifers resulting from fluvial processes, which allows incorporating the stochasticity of the paleoflow velocity.

Probabilistic assessment of herbicide runoff from Japanese rice paddies: The effects of local meteorological conditions and site-specific water management

Uncertainty assessments of herbicide losses from rice paddies in Japan associated with local meteorological conditions and water management practices were performed using a pesticide fate and transport model, PCPF-1, under the Monte Carlo (MC) simulation scheme. First, MC simulations were conducted for five different cities with a prescribed water management scenario and a 10-year meteorological dataset of each city. The effectiveness of water management was observed regarding the reduction of pesticide runoff. However, a greater potential of pesticide runoff remained in Western Japan. Secondly, an extended analysis was attempted to evaluate the effects of local water management and meteorological conditions between the Chikugo River basin and the Sakura River basin using uncertainty inputs processed from observed water management data. The results showed that because of more severe rainfall events, significant pesticide runoff occurred in the Chikugo River basin even when appropriate irrigation practices were implemented. © Pesticide Science Society of Japan.