Katarapko : Talking fish - making connections with the rivers of the Murray-Darling Basin

Once known as Crabb’s Creek, Katarapko Creek is a small anabranch of the Murray River, located between the towns of Berri and Loxton in the Riverland region of South Australia. Its 9 000 hectare grey clay floodplain is covered with blackbox, saltbush and lignum. The creek’s horseshoe lagoons, marshes and islands are the traditional lands of the Meru peoples. They fished the creek and surrounding waterways and hunted the wetlands. The ebb and flow of water guided their travels and featured in their stories. The Meru have seen their land and the river change...

Murray : Talking fish - making connections with the rivers of the Murray-Darling Basin

The Murray River is the boundary between NSW and Victoria. The river both defines boundaries and unites them with the waters that sustain townships, irrigation and the floodplain forests, including the 70 000ha of the iconic Barmah and Millewa Forest. The river and its floodplain are the traditional lands of the Yorta Yorta and Bangerang people. The Murray is a very different river to the one the Yorta Yorta and Bangerang peoples once knew and fished...

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.

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.

The Coorong and Lower Lakes : Talking fish - making connections with the rivers of the Murray-Darling Basin

After gathering water from 23 river valleys, the Murray empties into Lakes Alexandrina and Albert before making its way to the Coorong and out the Murray Mouth to Encounter Bay in South Australia. The entire Murray‐Darling Basin is upstream. Everything that happens there affects what goes on here...

Namoi : Talking fish - making connections with the rivers of the Murray-Darling Basin

The Namoi River winds its way through 42 000 square kilometres of blacksoil plain in the north east of New South Wales. Fed by the rivers of the western slopes of the Great Dividing Range, it contributes about one quarter of the Darling River’s flow. The river, its floodplain, wetlands, swamps and waterholes, are the traditional lands of the Gamilaraay* people. The Namoi is a very different river to the one the Gamilaraay people once knew and fished...

Goulburn : Talking fish - making connections with the rivers of the Murray-Darling Basin

The Goulburn River’s cold, clear waters rush westward down from the steep hills and mountains of the Great Dividing Range toward Seymour. The river then turns northward and meanders through hills and plains until the river meets the Murray upstream of Echuca. These are the traditional lands of the Taungurung, Bangerang and Yorta Yorta peoples. However, the Goulburn River today is not the river the Taungurung, Bangerang and Yorta Yorta once knew and fished...

Upper Murrumbidgee : Talking fish - making connections with the rivers of the Murray-Darling Basin

The Upper Murrumbidgee cuts its way through the Snowy Mountains in south‐eastern New South Wales, snaking its way south, then turning north before dropping into the lowland and heading west to join the Murray downstream of Swan Hill. The Upper ‘Bidgee floodplain is only a couple of hundred metres wide, a stark contrast to the kilometres‐wide floodplains in other parts of the Murray‐ Darling Basin. When the floods come, they come up quickly and roar through the narrow valleys. These are the traditional lands of the Ngunnawal and Ngarigo peoples. They fished the river and surrounding waterways and hunted the wetlands. The seasonal rise and fall of the water guided their travels and featured in their stories. The Ngunnawal and Ngarigo people have seen their land and the river change...

Darling and the Great Anabranch : Talking fish - making connections with the rivers of the Murray-Darling Basin

The Lower Darling River and Great Darling Anabranch are located in south west New South Wales. Muddy waters meander over the grey soil floodplains past red dunes, spiky saltbush and gnarled red gums. These are the traditional lands of the Paakintji people. But the land and the river are no longer what the Paakintji once knew and fished...

Upper Darling: Brewarrina to Bourke : Talking fish - making connections with the rivers of the Murray-Darling Basin

To say ‘Back o’ Bourke’ means ‘miles from anywhere’ to most Australians, however the Barwon and Darling Rivers that pass by the townships of Brewarrina and Bourke, respectively, are at the heart of the Murray‐Darling Basin. These are the traditional lands of the Ngiyampaa, Murawari and Yuwalaraay peoples (refer Aboriginal language groups in the Bringing back the fish section at the back of this booklet). They fished the river and surrounding waterways and hunted the wetlands. The Ngiyampaa, Murawari and Yuwalaraay people have seen their land and the rivers change...

Ovens : Talking fish - making connections with the rivers of the Murray-Darling Basin

The Ovens River rises in the Victorian Alps where it is linked to significant freshwater meadows and marshes. It flows past Harrietville, Bright, Myrtleford and Wangaratta where it is joined by the King River on its way to meet the Murray near the top of Lake Mulwala. These the traditional lands of the Bangerang people and their neighbours the Taungurung and Yorta Yorta peoples. They have fished the river and surrounding waterways and hunted the wetlands. The ebb and flow of water guided their travels and featured in their stories. The Bangerang, Taungurung and Yorta Yorta have seen their land and the river change...

Taxonomic resolution and quantification of freshwater macroinvertebrate samples from an Australian dryland river : The benefits and costs of using species abundance data

In studies using macroinvertebrates as indicators for monitoring rivers and streams, species level identifications in comparison with lower resolution identifications can have greater information content and result in more reliable site classifications and better capacity to discriminate between sites, yet many such programmes identify specimens to the resolution of family rather than species. This is often because it is cheaper to obtain family level data than species level data. Choice of appropriate taxonomic resolution is a compromise between the cost of obtaining data at high taxonomic resolutions and the loss of information at lower resolutions. Optimum taxonomic resolution should be determined by the information required to address programme objectives. Costs saved in identifying macroinvertebrates to family level may not be justified if family level data can not give the answers required and expending the extra cost to obtain species level data may not be warranted if cheaper family level data retains sufficient information to meet objectives. We investigated the influence of taxonomic resolution and sample quantification (abundance vs. presence/absence) on the representation of aquatic macroinvertebrate species assemblage patterns and species richness estimates. The study was conducted in a physically harsh dryland river system (Condamine-Balonne River system, located in south-western Queensland, Australia), characterised by low macroinvertebrate diversity. Our 29 study sites covered a wide geographic range and a diversity of lotic conditions and this was reflected by differences between sites in macroinvertebrate assemblage composition and richness. The usefulness of expending the extra cost necessary to identify macroinvertebrates to species was quantified via the benefits this higher resolution data offered in its capacity to discriminate between sites and give accurate estimates of site species richness. We found that very little information (<6%) was lost by identifying taxa to family (or genus), as opposed to species, and that quantifying the abundance of taxa provided greater resolution for pattern interpretation than simply noting their presence/absence. Species richness was very well represented by genus, family and order richness, so that each of these could be used as surrogates of species richness if, for example, surveying to identify diversity hot-spots. It is suggested that sharing of common ecological responses among species within higher taxonomic units is the most plausible mechanism for the results. Based on a cost/benefit analysis, family level abundance data is recommended as the best resolution for resolving patterns in macroinvertebrate assemblages in this system. The relevance of these findings are discussed in the context of other low diversity, harsh, dryland river systems.