eDNA survey of the Painkalac Valley

The DNA of a living, connected valley

When you are monitoring the health of a waterway, how do you know what’s living in the water and its surrounds? Terrestrial surveys can use traps and cameras but that’s a bit harder in the water. Environmental DNA (eDNA) surveys can help solve the problem. These surveys work by collecting tiny traces of genetic material – such as cells, scales, or waste – that organisms leave behind in water, soil, or air. Analysing that DNA can then identify which species are, or were recently, present in the environment.

The Painkalac Valley Network undertook a ‘Tree of Life’ eDNA survey in June 2025 to increase the network’s understanding of the health of the Painkalac Creek and its surrounds by providing a non-invasive, high-resolution snapshot of the total biodiversity including aquatic, rare, microscopic and invasive species. The survey results serve as a baseline and indicator of the ecosystem’s ecological status and reveals the diversity and balance of life of the Painkalac wetlands, river, and estuary.

The survey covered five sites: the Reservoir in the freshwater reaches of the Painkalac Creek; Bimbadeen in the upper estuary; the Bend in mid-estuary; the lower estuary at the creek mouth and the freshwater wetland of the Allen Noble Sanctuary.

Two samples of water were collected at each of these sites, filtered and the filters sent to the EnviroDNA laboratory for analysis of DNA in the water samples.

A ‘Tree of Life’ survey investigates all the functional elements of an ecosystem:

• Producers: Plants, moss, algae and phytoplankton convert sunlight into energy and form the base of the food web
• Consumers (herbivores and carnivores) – zooplankton, mussels, insects, snails, crustaceans, fish and birds
• Decomposers – bacteria, fungi and animals that feed on dead plants and animals including worms, crabs and insect larvae transform dead matter into the building blocks that fuel new life.
• Pollinators – insects and birds that transfer pollen from one flower to another
• Habitat formers – seagrass, seaweeds and oysters shape the ecosystem

Examples of producers:

 

Examples of Consumers:

 

Examples of Decomposers:

Results

The Painkalac samples found 499 taxa, or groups of organisms, of which 65 per cent were identified as specific species. All six animal Kingdoms were represented.

It is worth noting that the number of bacterial taxa is almost identical to the number of animal and plant taxa combined!

Detailed results can be found in the appendices below.

The absence of a species in an eDNA survey doesn’t necessarily mean that it wasn’t there; it was just not detected in this sample at this time. For example, DNA only persists in an aquatic environment for a week or two and kangaroos and horses possibly didn’t have enough contact with water to register in this survey despite them being in abundance on the paddocks adjoining the creek. Other datasets (e.g .iNaturalist, EstuaryWatch) should always be used to complement eDNA results to provide a more complete picture of biodiversity and the health of an ecosystem, especially as eDNA results cannot be used to make an estimate of abundance or density.

Survey highlights

Vertebrates (animals with a backbone or spine)

The following vertebrates were identified in the survey: 26 taxa of fish (including two introduced species – European Carp and Mosquitofish); 24 taxa of birds; 17 taxa of mammals including nine introduced species (cow, dog, deer, cat, house mouse, rabbit, rat, pig, fox) and four taxa of frogs.

Differences between the sites:

Vertebrate taxa by site	Allen Noble Sanctuary	Bimbadeen	Reservoir	Creek mouth	The Bend
Fish	4	18	9	19	15
Bird	9	11	9	12	11
Mammal	11	5	7	8	8
Frog	3	0	1	2	0
Total vertebrates	27	34	26	41	34

 

Fish

The survey identified 24 native fish species. (This can be compared with results from 15 estuaries in Corangamite, as detailed in the Index of Estuarine Condition 2021, which recorded between 1 and 19 species of native fish species per estuary (average ~10 species)).

 

There were 18 native species in the Painkalac estuary, four in the Allen Noble Sanctuary and seven native species in the Reservoir.

The differences can be attributed to the creek mouth being an ecological junction, where the freshwater system meets the ocean. This creates many more kinds of habitats and feeding conditions than exist in stable freshwater systems. By contrast, the Reservoir and Allen Noble Sanctuary are more isolated, stable freshwater habitats that support fewer specialist species that are adapted to freshwater only.

Rich fish biodiversity in the estuary implies a good food web because it shows that many species at different levels — predators, prey, and microbial and animal decomposers (e.g. worms, insect larvae) — can find enough food, oxygen, and habitat that confirms a balanced, functional ecosystem with plentiful resources.

Arthropods (invertebrates) and bacteria

By contrast a higher number of arthropod detections (insects, crustaceans, mites, etc.) and bacteria at the Allen Noble Sanctuary and the Reservoir compared to those at the creek mouth reflects the fact that arthropods and bacteria generally prefer stable environments rich in organic debris with low flow and consistent salinity. At the creek mouth there are more changes in flow, salinity and sediment with fluctuating water levels. Here are only those arthropods and bacteria that can cope with frequent changes and physiologically stressful conditions.

Mammals

The endangered Broad-toothed Rat was found at the Creek Mouth and the Bend and the vulnerable Swamp Antechinus was identified at the Allen Noble Sanctuary – both listed under the Environment Protection and Biodiversity Conservation Act. These findings show that the Painkalac Valley is an important wildlife sanctuary which must be protected.

It was concerning but not surprising to detect feral cats, foxes, deer and rabbits emphasising the need to continue control measures. On a lighter note, it is believed that the detection of ‘pig’ in the Creek Mouth and ‘cow’ in Allen Noble Sanctuary is likely to be due to food scraps (e.g. ham sandwich, beef sausage) finding their way into the waterway rather than DNA from live/recently dead animals. The ‘cow’ in the upper estuary may well have come from the farm below the Reservoir.

Ecological analysis of the five sites

Allen Noble Sanctuary – Stable Freshwater Wetland: A well-established microbial base with a good number of bacterial decomposers implies steady nutrient cycling while rich arthropod diversity shows good oxygenation and habitat complexity supported by submerged vegetation and organic sediments.

Reservoir – Controlled Freshwater System: Moderate biodiversity richness with bacterial decomposer dominance typical of recycling organic matter in slower, controlled waters. Abundant arthropods reflect detritus-based food hubs. The Reservoir functions as a nutrient-processing hub — a stable microbial engine dominated by decomposers and detritus-feeders rather than photosynthetic groups.

Bimbadeen (upper estuary) and the Bend (mid-estuary) – Mixed Habitat and Ecologic Resilience: Bimbadeen and the Bend show broad functional diversity (multi-phyla representation), suggesting mosaic habitat structure — alternating pools, vegetated edges, riffles and open patches – supporting a mixed, dynamic ecosystem.

These two sites appear ecologically resilient – diverse, resilient, and functionally rich, combining features of wetland and flow-through systems – able to maintain diversity across changing water levels and seasonal variation.

The Creek Mouth – Dynamic Estuarine Transition: Transitional estuarine zone with a richness of bird, fish and green plants adapted to fluctuating salinity and turbidity indicating resilience to mixing of river and ocean waters. The Creek Mouth has the lowest bacterial richness but the broadest functional overlap, linking marine and freshwater systems. The presence of marine protists and fish taxa confirms tidal connectivity and planktonic exchange. The creek mouth has the highest proportion of Streptophyta (land plants and some green algae), possibly due to the fringing vegetation.

 

A Living, Connected Valley

The patterns observed at each site highlight how connected the Painkalac Valley system is – each site contributing to overall ecosystem health through its unique role.

From a management perspective, maintaining a balance between stability (as seen at Allen Noble Sanctuary) and diversity (as seen at The Bend and Bimbadeen) is essential.

Ongoing monitoring through eDNA surveys can track how changes in land use, flows, disturbances (fire, flood, drought) and climate affect the valley’s living systems.

 

Acknowledgements

This survey was made possible by a generous grant from the Victorian Field Naturalists Club of Victoria plus donations by Angair and two community members.

 

Appendix 1 Taxa by Kingdom

Protista – single cell organisms that bridge the gap between plants, animals and fungi

Bacteria – single-celled organisms that recycle nutrients and break down waste – the world’s invisible recyclers

Chromista – microscopic algae and plankton in water that produce oxygen and support food webs

Fungi – mushroom, moulds and yeast that act as the ecosystem’s decomposers helping plants grow

Animals – insects, worms, fish, birds, humans

Green plants – plants and algae that make food through photosynthesis

 

Appendix 2 Distribution of Taxa Across Major Phyla by Site

The distribution of taxa across major phyla at each site (see chart below) shows how many different kinds of organisms — from microbes and algae to invertebrates and vertebrates — coexist and depend on one another.

This diversity and balance across sites reflect the complex, interconnected web of life in which each group plays a role in nutrient cycling, energy flow, and overall ecosystem health.

 

Appendix 3: Identified animals (metazoa) by phyla

Phylum	Total taxa in phylum	Description
Annelida	5	Segmented worms
Arthropoda	40	Insects, spider, crustaceans, centipedes
Chordata	71	Vertebrates
Cnidaria	1	Jellyfish, sea anemones
Gastrotricha	4	Microscopic, cylindrical animals
Mollusca	4	Snails, mussels, octopuses, squids
Platyhelminthes	3	Flatworms
Porifera	1	Sponges
Rotifera	2	Microscopic, wheel animals
Not classified	1	DNA at kingdom level only
	Total: 132

 

Appendix 4: Identified Vertebrate Species

Group	Species		Common name
Birds	Accipitridae		Hawks, eagles, kites, harriers
	Anatidae		Ducks, geese and swans
	Aves
	Cacatuidae
	Chenonetta jubata		Australian wood duck
	Corvus		Ravens and crows
	Cygnus atratus		Black swan
	Eolophus roseicapilla		Galah
	Fulica atra		Eurasian coot
	Gallinula tenebrosa		Dusky moorhen
	Hirundinidae		Swallows, martins, saw-wings
	Hypotaenidia		Rails
	Microcarbo melanoleucos		Little pied cormorant
	Pelecaniformes
	Phalacrocorax		Old World cormorants
	Phalacrocorax carbo		Great cormorant
	Phasianidae		Chickens, turkeys, pheasants, quail
	Poliocephalus poliocephalus		Hoary-headed grebe
	Porphyrio		Purple swamphen
	Procellariidae		Atlantic petrel
	Rallidae		Common moorhen
	Tachybaptus novaehollandiae		Australasian grebe
	Threskiornithidae		Spoonbills
	Trichoglossus moluccanus		Rainbow lorikeet
Fishes	Acanthopagrus		Seabreams, porgies
	Acanthopagrus butcheri		Black bream
	Afurcagobius		Gobies
	Afurcagobius tamarensis		Tamar goby
	Aldrichetta forsteri		Yelloweye mullet
	Ammotretis rostratus		Longsnout flounder
	Anguilla australis		Short-finned eel
	Arenigobius bifrenatus		Bridled goby
	Arenigobius frenatus		Halfbridled goby
	Atherinosoma microstoma		Smallmouth hardyhead
	Cyprinodontiformes
	Cyprinus carpio		European carp
		Galaxias
		Galaxias brevipinnis		Climbing galaxias
		Galaxias maculatus		Common galaxias
		Galaxias truttaceus		Spotted galaxias
		Galaxiidae
		Gambusia holbrooki		Mosquitofish
		Liza argentea		Goldspot mullet
		Macquaria colonorum		Estuary perch
		Mugil cephalus		Sea mullet
		Notolabrus gymnogenis		Crimsonband wrasse
		Philypnodon grandiceps		Flathead gudgeon
		Pseudaphritis urvillii		Tupong
		Pseudogobius		Gobies
		Pseudogobius olorum		Bluespot goby
Frogs		Crinia signifera		Common Eastern froglet
		Limnodynastes		Australian ground-dwelling frogs
		Litoria		Australasian tree frogs
		Litoria ewingii		Brown tree frog
Mammals		Antechinus
		Antechinus minimus		Swamp antechinus
		Bos taurus		Cow
		Canis lupus		Dog or dingo
		Cervus		Unidentified deer
		Felis catus		Cat
		Macropus giganteus		Eastern grey kangaroo
		Mastacomys fuscus		Broad-toothed rat
		Mus musculus		House mouse
		Oryctolagus cuniculus		Rabbit
		Pseudocheirus peregrinus		Common ringtail possum
		Rattus		Rats
		Rattus lutreolus		Swamp rat
		Sus scrofa		Pig
		Trichosurus vulpecula		Common brushtail possum
		Vespadelus darlingtoni		Large forest bat
		Vulpes vulpes		Fox

 

Appendix 5: Identified green plants by phyla

Phylum	Total taxa in phylum	Description
Chlorophyta	26	Aquatic green algae
Streptophyta	58	Land plants and some green algae
Not classified	2
	Total: 86

Painkalac Valley Network home page

Painkalac Resource Repository
Explore the links below to learn about the importance, complexity and wonder of the Painkalac Valley – from the source to the sea:

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Topics

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