Flora and fauna

Our continent supports nearly 600,000 native species, and a very high proportion of these are found nowhere else in the world (Cassis et al. 2017). For example, about 85% of Australia’s plant species are endemic, and Australia is home to half of the world’s marsupial species.

Taxonomists are continually discovering and describing new Australian species. In 2020, 763 new species were named, including 297 insects, 166 fungi, 77 plants, 57 spiders and 21 new vertebrates (Taxonomy Australia 2020). In some groups, there are many more species that are unknown than are known.

In 2010, the Bush Blitz program was established to investigate and document Australian species. Bush Blitz has discovered more than 1,735 new species; extended the known range of 250 species; and generated more than 500 records of species listed as Threatened, Vulnerable or Endangered, and more than 1,200 records of pest species. The program has also recorded more than 25,000 occurrences of plants and animals, which can be accessed by land managers, scientists and the general public using online tools such as the Atlas of Living Australia (ALA). ALA is a collaborative, digital, open infrastructure that is mobilising biodiversity data for use by research, industry and government. Its growing database holds 85 million records of more than 111,000 species from across Australia (Figures 2 and 3).

Indigenous culturally significant species

Indigenous Australians attribute tremendous spiritual, cultural and symbolic value to many animals, plants and ecological communities. Species can be spiritually or culturally important; they may be totems, provide a source of food or medicine, be used as materials for tools or implements to undertake customary activities, be indicators of health of Country, or be used in ceremonial activities. Culturally significant species feature prominently in Indigenous knowledge, including language, ceremonies, lore, identity and narratives, and are considered cultural icons (Gore-Birch et al. 2020).

Examples of culturally significant species are highlighted throughout this chapter. The Indigenous chapter also describes Indigenous people’s connection to Country through plant and animal totems, traditional food sources, use and knowledge of native plants, and through knowledge, languages and practices (see the Indigenous chapter).

Threatened species

Under the Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act), Australia identifies and lists threatened species. States and territories also maintain listings of threatened species.

The number and trend of these lists can be used as a simple indication of the health of Australia’s biodiversity.

In June 2021, 533 animal and 1,385 plant species were listed under the EPBC Act; 53% of the listed species are Endangered or Critically Endangered (Table 1). The number of threatened species listed under the EPBC Act has risen for almost all taxa over the past 5 years (Figures 4–6). The list includes 105 species that are Extinct or Extinct in the Wild (June 2021).

An April 2019 collation of global, national, and state and territory threatened species lists 100 Australian endemic species (38 vascular plants, 34 mammals, 10 invertebrates, 9 birds, 4 frogs, 3 reptiles, 1 fish and 1 protist) that are validly listed as Extinct or Extinct in the Wild since European settlement in 1788 (Woinarski et al. 2019), representing about 6–10% of the world’s extinctions (post-1500s). This compilation highlighted deficiencies in listings for some taxa, especially invertebrates. It also showed that the number of formally listed extinct species is likely to be a substantial underestimate of actual extinctions, partly because many likely extinctions are not recognised in formal lists and others are likely to have occurred without being noticed.

Increases and decreases in threatened species listing categories sometimes reflect uplistings (where species are transferred to a higher threat category within the list) and downlistings (where species are transferred to a lower threat category). These mainly occur because more information has become available to support assessment about a species’ vulnerability to extinction, or the application of the listing criteria has been refined, rather than true changes in status, so caution should be used in interpreting trends. A large number of plants were delisted in 2013, mainly because of changes in taxonomic understanding (Figures 4–6). The rate of change in the threatened species list is also a function of collaborations between jurisdictions on the listing process (see IUCN Red List categories).

IUCN Red List categories

The global standard for assessing extinction risk is the International Union for the Conservation of Nature (IUCN) Red List criteria. Under this system, species are assigned a ranked threat category (Figure 7). Australian species have been assessed against IUCN Red List criteria several times in the past 5 years.

Since 2015, the Australian, state and territory governments have collaborated through an intergovernmental memorandum of understanding to assess and list threatened species using a listing process known as the Common Assessment Method, which is based on the IUCN Red List of Threatened Species. Species are assessed at a national level by one jurisdiction and the assessment is shared with other jurisdictions where the species occurs, and the Australian Government, and used to make consistent listing decisions. To December 2020, assessments for 125 species have been prepared by the states and territories and provided to the Australian Government to make listing decisions under the EPBC Act.

As each jurisdiction makes administrative and legislative changes to adopt the method, threatened species lists are becoming more aligned. This alignment enables IUCN assessments to guide the prioritisation of species for statutory assessment and listing. Some amendments have been made to suit the Australian context. The method does not recognise the Least Concern or Near Threatened IUCN categories. The method also includes a Conservation Dependent category for fish species that are the focus of a plan of management in force under law. This provides for management actions to halt decline and support recovery so that the chances of long-term survival in nature are maximised.

Collaboration through the method has resulted in improved efficiency and consistency in the listing process nationally. It has also initiated an increase in the rate of change in the threatened species list.

Plants

Approximately 10% of the world’s plants occur in Australia, equating to approximately 21,000 species. Many of these are endemic (Table 2). Two areas in particular, south-western Australia and the forests of eastern Australia, are considered global biodiversity hotspots due to their large concentration of endemic plant species, including many of Australia’s threatened species, combined with an exceptional loss of habitat (CEPF 2021).

Across Australia, about 4,000 plant species were, and many still are, used by Indigenous people as food and medicine, equating to about 20% of named Australian vascular plants (Isaacs 1987 in Ens et al. 2017) (see the Indigenous chapter). Evidence from Madjedbebe rock-shelter in northern Australia, in the form of charred plant food remains dated to between 65,000 and 53,000 years ago, indicates that Australia’s earliest known human population exploited a range of plant foods, including those requiring processing (Florin et al. 2020). Many more plant species were used as materials for tools, shelter and ceremonial items.

A wide diversity of plants are sources of edible seeds for Indigenous Australians; the seeds of more than 220 native plant species were traditionally ground for food (Mildwaters & Clarkson 2020). The effects that Indigenous peoples had on the distribution of species by transporting plants from their native habitats, and propagating seeds and other vegetative material is becoming increasingly apparent to the scientific community (Silcock 2018, Lullfitz et al. 2020). Recent genetic studies of some Indigenous food plants have continued to reveal distribution patterns best explained by seed being moved by humans, including boab (Adansonia gregorii) in the Kimberley (Rangan et al. 2015) and black bean (Castanospermum australe) in northern New South Wales (Rossetto et al. 2017).

Plants comprise 73% of Australia’s national threatened species list, with 1,385 listed species, including 37 extinct species (Table 1). A large number of plant species are listed as Extinct, Extinct in the Wild, Critically Endangered, Endangered or Vulnerable under state and territory legislation, and many are not listed nationally. For example, in Western Australia, 9 species are listed as Extinct nationally, while the state recognises 15 species as being Extinct under the Biodiversity Conservation Act 2016. Similar disparities occur for Critically Endangered, Endangered and Vulnerable species, with 61, 225 and 105 species listed nationally and 160, 140 and 129 listed by Western Australia, respectively. Such discrepancies will be tempered with use of the Common Assessment Method (see IUCN Red List categories).

Overall, the major pressure causing population declines for threatened plant species is habitat destruction. This can leave fragmented populations in small remnants that then become vulnerable to other pressures (e.g. invasive weeds) and degradation. Thus, declining species and those at most risk of extinction are concentrated in highly modified agricultural and urban landscapes. Changes in fire regimes, either too frequent or too infrequent, are also a significant pressure for many species (see Changing fire regimes).

Trends and distribution of threatened plants

The overall Threatened Plant Index in 2017 was 0.28, indicating that, on average, the size of threatened plant populations has decreased by 72% between 1995 and 2017 (Figure 8). The index shows that management actions, such as weed or pest control, result in lower rates of decline. Populations of species that have been translocated have the slowest rates of decline.

 

Recently, 1,135 plant species in Australia were assessed to determine those most at risk of extinction (Silcock & Fensham 2018):

• 418 taxa were assessed as having a continuing decline and 296 species were determined to be at risk of extinction under current management regimes, including 55 at high risk of extinction.
• 12 of the 55 species determined to be at high risk of extinction are listed as Critically Endangered under the EPBC Act and 13 are not listed at all.
• 56 taxa were assessed as having no documented declines, or even as being stable or increasing, but are currently listed as Critically Endangered nationally; these are mostly narrow-ranged endemics that meet criteria for listing because of small population size, extent of occurrence or area of occupancy.
• Species predicted to be at most risk of extinction are concentrated where high areas of endemism co-occur with highly modified agricultural and urban landscapes. Very few listed or declining species are in arid and semi-arid Australia, which have been far less modified by humans (Figure 9).

Some plants listed as threatened may be considered ‘functionally extinct’, having fallen below the critical number to sustain their populations in the long term. Of the 660 species listed as Critically Endangered or Endangered at a national level, 62 are known from fewer than 50 individuals, and 300 from fewer than 250 individuals. Many of these are now restricted to tiny remnants that are vulnerable to further degradation, and where maintenance of population size and growth is unlikely (Silcock et al. 2020).

Recently, the 822 eucalypt species within Australia were assessed using IUCN criteria (see IUCN Red List categories) (Fensham et al. 2020b). Overall, 193 eucalypts qualified as threatened, most (70%) because of irreversible population declines of more than 30% (Figure 10). Habitat loss due to expanding agriculture and urbanisation was identified as the most important threat to eucalypts. The most threatened species were concentrated in south-western Australia and in other areas of Australia where intensive land use has resulted in deforestation. The remaining species qualified as threatened because they had small geographic ranges with ongoing threats, mostly mining or urbanisation.

Orchids are the most threatened group of flowering plants globally. Australia is no exception, with 10% (184 species of a total of around 1,794) of Australian orchid species listed as threatened under the EPBC Act (Wraith & Pickering 2019). The major threats to orchids are similar to those for all other species: invasive species, inappropriate fire regimes, grazing, and habitat modification, including land clearing.

Orchids in the wild have added pressures of high levels of illegal collecting, and increasingly are the focus of specialist nature-based tourism, particularly in some protected areas. Illegal collecting, especially of epiphytes, affects around 46% of threatened species, particularly in Queensland, New South Wales and Victoria, while tourism and recreation impacts, mostly associated with trampling, affect 47% of threatened orchids (Wraith & Pickering 2019).

Plant extinctions

Plant extinctions in Australia can be difficult to verify, in part due to taxonomic uncertainty and because threatened species lists change regularly as a result of new evaluations and rediscoveries. For example, since 1984, more than 120 presumed extinct plant taxa have been rediscovered, mostly through additional field surveys; 23 taxa have been rediscovered since 2000, with 8 rediscoveries since 2010 (Silcock et al. 2020).

Fifty-one Australian plant species with sound taxonomy and unambiguous occurrence records in Australia are currently presumed extinct. Eighteen of the species are listed as Extinct under the EPBC Act and a further 14 are listed as Extinct under state legislation. However, experts consider that only 12 are probably extinct and a further 21 are possibly extinct, with the remaining 18 species possibly still occurring in Australia and requiring field surveys to assess their status (Silcock et al. 2020). Western Australia has the highest number of presumed extinct taxa (15), along with New South Wales (15) and Queensland (13). All taxa presumed extinct seem to have been rare or restricted in their historical range.

Animals

Threatened animal species are widely distributed across Australia. Most taxonomic groups are represented in threatened species lists in all states, and there is considerable regional variation in the relative proportion of different taxonomic groups (Figure 11) (Allek et al. 2018). For example, threatened amphibians occur mostly in Queensland, New South Wales and Victoria. Amphibians are extremely sensitive to changes in temperature, and climate change and extreme weather are a larger threat to them in these states than elsewhere. Birds constitute the single largest proportion of threatened animal species in all areas except the Northern Territory, where mammals make up the largest proportion.

Mammals

Terrestrial mammals across Australia have experienced high rates of extinction, with 10% of endemic species becoming extinct over the past 200 years. Approximately 21% are now assessed as threatened (Woinarski et al. 2015, Woinarski et al. 2019). Most mammal extinctions in Australia have been driven by predation from introduced species, especially the feral cat and European red fox; extinctions have been particularly high in arid and semi-arid regions.

Since 2016, 2 species have been transferred from Critically Endangered to Extinct. The Christmas Island pipistrelle (Pipistrellus murrayi) was listed as Extinct in 2021 but experts considered it to be extinct much earlier. The last echolocation call of the species was detected in August 2009. The Bramble Cay melomys (Melomys rubicola) was transferred from Endangered to Extinct under the EPBC Act in 2019 but experts considered it to be extinct by 2014. Both species were reported as Extinct in the 2016 state of the environment report. Another 10 mammals were recognised as Extinct under the EPBC Act in March 2021, although all were considered to have become extinct sometime between European settlement and the 1950s.

The National Environmental Science Program’s Threatened Mammal Index indicates that the abundance of many mammal species for which monitoring data are available has declined; between 1995 and 2016, the abundance of threatened mammals that have been monitored decreased by an average of 38% (Figures 12 and 13). Where no management occurs, threatened mammals have declined by an average of 60% since 2000 (Figure 13a).

For the smaller number of species monitored at sites where activities such as baiting of predators or ecological fire management has occurred, the index shows that populations have increased by 46% on average since 2000 (Figure 13b). For sites where predators have been excluded, all species have increased in abundance since 2000 (Figure 13c).

The 20 mammal species most at risk from extinction over the next 20 years mostly occur in northern Australia and south-west Western Australia (Figure 14) (Geyle et al. 2018). Five of the 20 most at-risk mammals occur only on islands.

The mammals considered most at risk from extinction in the next 20 years are the central rock-rat (Zyzomys pedunculatus), the northern hopping-mouse (Notomys aquilo), the Carpentarian rock-rat (Z. palatalis), the Christmas Island flying fox (Pteropus natalis) and the black-footed tree-rat (Mesembriomys gouldii gouldii) (Geyle et al. 2018). Ten of the top 20 mammals judged most at risk from extinction are included under the 2015–20 Threatened Species Strategy.

The Antarctic chapter describes the state and trend of mammals, including ice-breeding seals (4 species), fur seals (3 species), sea lions (1 species) and elephant seals (1 species), that are part of the Antarctic fauna (see the Antarctica chapter). The Marine chapter describes the state and trend of the 48 species of cetaceans (whales and dolphins), 3 species of pinnipeds (seals) and the dugong that make up Australia’s marine mammal fauna. Populations of marine mammals are generally in good condition, except for the Australian sea lion (Neophoca cinerea; very poor condition) and fur seals (poor condition) (see the Marine chapter).

Birds

The state and trend of many birds is relatively well studied compared with other native species. This is partly because citizens have ready access to high-quality field guides, and BirdLife Australia has been compiling and collating data collected by the public for many years (see Citizen science).

The Antarctic chapter describes the state and trend of seabirds (7 species on the Antarctic continent and 13 on subantarctic islands) and penguins (2 species on the continent and 5 on subantarctic islands) (see the Antarctica chapter). The Marine chapter discusses the overall state and trend of the approximately 60 species of seabirds that are known to breed in and around Australia and its external territories, including albatrosses, boobies, cormorants, frigatebirds, gulls, noddies, pelicans, penguins, petrels, prions, shearwaters, storm petrels, terns and tropicbirds (see the Marine chapter).

Since October 2016, 3 new bird species have been listed under the threatened species provisions of the EPBC Act. The grey falcon (Falco hypoleucos) and the white-throated needle-tail (Hirundapus caudacutus) were listed as Vulnerable, and the shy albatross (Thalassarche cauta) was listed as Endangered. Seven species were uplisted (were recognised as more threatened): 6 from Vulnerable to Endangered, and 1, the Tiwi Islands hooded robin (Melanodryas cucullata melvillensis), from Endangered to Critically Endangered.

The National Environmental Science Program Threatened Bird Index indicates significant declines in abundance of threatened birds for which monitoring data are available (Figure 15). Between 1985 and 2017, the relative abundance of threatened birds decreased by an average of more than 60%.

Researchers have integrated multiple approaches to assessing extinction risk, to identify the 20 Australian birds most at risk from extinction and forecast likely extinction timeframes under current management approaches. They found that many of the most at-risk bird species are found only on islands or occur in southern Australia (Figure 16) (Geyle et al. 2018).

The 5 species considered most at risk from extinction were the King Island brown thornbill (Acanthiza pusilla archibaldi), the orange-bellied parrot (Neophema chrysogaster), the King Island scrubtit (Acanthornis magna greeniana), the western ground parrot (Pezoporus wallicus flaviventris) and the Houtman Abrolhos painted button quail (Turnix varius scintillans). Ten of the 20 bird species judged at most risk of extinction are included in the 2015–20 Threatened Species Strategy (Geyle et al. 2018).

Waterbirds and shorebirds

At least 161 Australia birds depend on wetlands, waterways or shorelines for feeding or breeding habitats. Many more species also rely on these habitats for some of their needs throughout their lifecycle. Many waterbirds have been systematically surveyed across one-third of the Australian continent for more than 3 decades as part of the Eastern Australian Waterbird Survey. These data, along with numerous other datasets, give a good picture of the long-term changes in state and trend of Australian waterbirds (Clemens et al. 2019).

Consistent with reporting in previous state of the environment reports, waterbirds continue to show declines in abundance (Figure 17). While waterbird numbers increased after the 2011 flood in eastern Australia, they have decreased dramatically since then. At least 27 species (for which there is long-term data) show widespread long-term population declines. A further 17 species show no long-term trend but a significant decline in the past 5 years.

Millions of migratory shorebirds fly from breeding grounds in northern China, Mongolia and Russia to East Asia and Australia each year, traversing more than 20 countries while migrating. During their nonbreeding season, from spring to autumn, 37 species regularly and predictably visit Australia.

Understanding the state and trend of migratory species and the pressures affecting them is complex and requires collation of data from hundreds of different sites across multiple countries. However, it is clear that many species are in decline, and several migratory shorebird species are globally threatened (Fuller et al. 2020) (Figure 17). The Coasts chapter contains a comprehensive account of shorebird state and trends, and the escalating pressures on shorebirds (see the Coasts chapter).

Twelve of 19 migratory shorebird species with long-term data show population decline (Clemens et al. 2019). Loss and degradation of stopover habitat is the main cause of declines of migratory shorebirds. In particular, the birds congregate at high densities on tidal mudflats in the Yellow Sea region of East Asia. This region is increasingly degraded by coastal development and has shrunk by more than 65% in recent decades. As a consequence, the populations of migratory species that rely heavily on this region to rest and refuel show significant declines. For example, populations of the great knot (Calidris tenuirostris) and far eastern curlew (Numenius madagascariensis), both of which are listed as globally threatened, have declined more than 5% per year on average since 1993 (see the Coastal species section in the Coasts chapter). The far eastern curlew is one of the 20 target bird species in the 2015–20 Threatened Species Strategy.

Australia has entered into 3 bilateral migratory bird agreements – with Japan (Japan–Australia Migratory Bird Agreement – JAMBA), China (China–Australia Migratory Bird Agreement – CAMBA) and the Republic of Korea (Republic of Korea – Australia Migratory Bird Agreement – ROKAMBA). These agreements provide an important mechanism for pursuing conservation outcomes for migratory birds.

The Australian Government’s Wildlife Conservation Plan for Migratory Shorebirds covers 35 species that regularly visit Australia. The plan outlines a national framework identifying research and management actions to protect migratory shorebirds in Australia. All 35 species covered by the plan are listed migratory species under the EPBC Act.

Many Indigenous Protected Areas (IPAs) include migratory bird habitat. At least 20 IPA management plans address threats to migratory birds and the protection of migratory bird habitats.

Reptiles

Australia is home to about 10% of the world’s known reptile species, and about 90% of species are endemic. Understanding of the conservation status of reptiles has increased significantly since 2016. Key new sources of knowledge include a comprehensive assessment of the conservation status of snakes and lizards (Tingley et al. 2019, Geyle et al. 2020) and an action plan for them (Chapple et al. 2019), and specific assessments for Australian freshwater turtles (Van Dyke et al. 2018), crocodiles (Somaweera et al. 2019) and earless dragons (Melville et al. 2019). The Marine chapter describes the state and trend of the 6 species of marine turtles and 33 species of seas snakes that occur in Australian waters (see the Marine chapter).

Many of Australia’s reptiles are declining, and the past decade saw the first Australian reptile extinctions in the wild. The proportion of species assessed under the EPBC Act as Critically Endangered is increasing (Figure 5). Two endemic Christmas Island species currently listed as Critically Endangered – blue-tailed skink (Cryptoblepharus egeriae) and Lister’s gecko (Lepidodactylus listeri) – are only known to exist in captivity. The Christmas Island forest skink (Emoia nativitatis) was transferred to Extinct in March 2021. It was last seen in the wild in 2010, and the last known individual died in captivity in 2014.

A recent assessment of 948 species of Australian lizards and snakes against IUCN criteria confirmed and expanded the EPBC Act listings (Tingley et al. 2019):

• 67 species were assessed as threatened
  • 28 as Vulnerable
  • 26 as Endangered
  • 10 as Critically Endangered
  • 1 as recently Extinct (E. nativitatis)
  • 2 as Extinct in the Wild (C. egeriae and L. listeri)
• 19 species were classified as Near Threatened
• 819 species were classified as Least Concern
• 43 species were classified as Data Deficient.

Most species were classified in the threatened categories largely because of having a small geographic range and an ongoing threat that is likely to reduce their distribution further. The assessment found that the number of threatened species was highest in the Alps of south-eastern Australia, and in northern Australia in the vicinity of Kakadu National Park and across the Kimberley region.

Reptile experts suggest that, by 2040, up to 11 snakes and lizards, all with restricted ranges and threatened by invasive plants and animals, could become extinct (Geyle et al. 2020). Three of the reptiles with the highest extinction risk over the next 20 years occur only on islands, and more than half occur only in Queensland (Figure 18).

Australian reptile species are poorly taxonomically described, partly because several species are sometimes erroneously classified (and hidden) under 1 species name. For example, taxonomic uncertainties in the characterisation of grassland earless dragon lizards of southern Australia were clarified recently, resulting in the naming of 2 new species, while restricting the distribution of 1 existing species (Tympanocryptis pinguicolla) (Melville et al. 2019). This taxonomic revision has significant conservation implications because the last confident sighting of T. pinguicolla was in 1969, raising the possibility of the first extinction of a reptile on mainland Australia. The species is currently listed as Endangered under the EPBC Act.

Freshwater turtles

About half of the 25 species of Australian freshwater turtles are currently listed as Vulnerable, Endangered or Critically Endangered, and ongoing declines are being recorded in many parts of Australia. Sea turtles are discussed in the Marine chapter (see the Marine chapter).

Invasive predators have been highlighted as a primary threat, but drought, habitat modification and disease events are also contributing to declines (Van Dyke et al. 2018). Nest predation by invasive foxes has driven declines in freshwater turtles in the Murray–Darling Basin (Van Dyke et al. 2019). Turtle declines of up to 91% have also been observed in sections of the Murray River because of drying caused by climate change, which may be compounded by nest predation.

A new disease caused the near-extinction of an Australian freshwater turtle – the Bellinger River snapping turtle (Myuchelys georgesi) – and may be a symptom of deteriorating water quality and climate change (Spencer et al. 2018).

Amphibians

The publication of the Status of conservation and decline of amphibians in Australia, New Zealand and Pacific Islands (Heatwole & Rowley 2018) consolidates much knowledge about the state and trend of amphibians, greatly improving our understanding of them compared with reporting in 2016.

Currently, 243 native species of frogs are known in Australia (Gillespie et al. 2020) and most of these (around 93%) are endemic (Heatwole & Rowley 2018). More species are being discovered; 21 new species, representing 9% of Australia’s known frog fauna, have been discovered in the past decade alone. Most of these species were hidden within known ‘species’ that were found to be complexes of several, morphologically similar species (Heatwole & Rowley 2018).

The number of EPBC Act–listed species has increased since 2016 (Figure 4). Most of these additions have been to the Critically Endangered category (Figure 5).

All 243 species of Australian frogs have been recently assessed against the IUCN Red List criteria (Gillespie et al. 2020). Forty-five species (18.5%) were assessed as either extinct or threatened: 5 Extinct, 13 Critically Endangered, 11 Endangered and 16 Vulnerable. A further 4 species were considered Near Threatened, and 7 species were considered Data Deficient. Most of the threatened frog species occur along the eastern coast of Australia and the Great Dividing Range; 23 occur in Queensland and 17 occur in New South Wales.

The high number of Critically Endangered and Endangered amphibian species in eastern Australia reflects the devastating impact of chytridiomycosis, which is caused by the invasive fungus Batrachochytrium dendrobatidis (chytrid fungus), on many frog species (see Animal diseases) (Allek et al. 2018). The regions affected by chytrid fungus are also among the most urbanised in Australia, and widespread loss and degradation of habitats has contributed to broadscale decline of amphibians in these areas (Heatwole & Rowley 2018).

Processes that modify the distribution, frequency and extent of available surface water in the landscape are a significant threat to amphibians across Australia. Even in arid and central Australia, where amphibians are adapted to highly variable water availability, long-term changes in patterns of rainfall as a result of climate change can be expected to be a significant ongoing pressure (Ocock & Wassens 2018).

Fish

Australia is home to almost 300 bony freshwater fish species, most of which are small-bodied (less than 20 cm total length), with only 19 reaching a total length of more than 1 m (Humphries & Walker 2013).

Freshwater fishes are culturally significant to Indigenous Australians, whether for spiritual or ceremonial reasons, or simply as a stable food source (Toussaint 2014, Pyke et al. 2018, Milgin et al. 2020). Notable examples of fish with multiple societal values include the freshwater sawfish (Pristis microdon), which provides material for use as a weapon, is a totem, and is also believed to be a creator of rivers in northern Australia (McDavitt 2005). The iconic barramundi (Lates calcarifer) is another species of great cultural significance, both as a staple food source and as an ancestral being; according to Dambimangari Traditional Owners of the north-west Kimberley, ‘Barramundi was splashing around and made Walcott Inlet’ (D Woolagoodja, quoted in Allbrook et al. 2017).

Currently, 62 Australian fish species are listed under the EPBC Act; of these, 38 are freshwater fish (Lintermans et al. 2020). The Pedder galaxias (Galaxias pedderensis) is known to be extinct in the wild (Chilcott et al. 2013).

A recent analysis of 22 Australian freshwater fish species considered by experts to be most at risk of imminent extinction found that 20 have more than a 50% risk of extinction in the next 20 years (Lintermans et al. 2020) (Figure 20). But of the 22 species assessed, only 3 are listed under the EPBC Act and 7 are undescribed species, which makes them ineligible for listing.

Galaxiids (small, scaleless fish) dominate the list of Australia’s most threatened freshwater fishes (14 of 22 species). Trout invasion is the main threat to these species because small-bodied species are most at risk of predation. This threat is compounded by inappropriate fire regimes and climate-related threats (Lintermans et al. 2020).

The 2015–20 Threatened Species Strategy did not contain any identified priority fishes for recovery actions, although the new 2021–31 strategy will include priority fish.

Prolonged drought conditions between 2017 and 2019 resulted in lower than average streamflows in rivers across much of Australia, with significant impacts on aquatic biodiversity. The interacting effects of water regulation (see Aquatic ecosystems and habitats) (see the Inland water chapter) and drought conditions, combined with bushfires in the summer of 2019–20, culminated in major fish kills across the Murray–Darling Basin (Vertessy et al. 2019) (see Bushfires – summer 2019–20). The main native fish species involved included Murray cod (Maccullochella peelii), silver perch (Bidyanus bidyanus), golden perch (Macquaria ambigua) and bony herring (Nematalosa erebi), with mortality estimates in the range of hundreds of thousands to more than a million fish. Overall, deaths were reported in around 27 species of freshwater and estuarine fish, and in 4 species of crustaceans, some of which are endemic, from 15 waterways and 17 locations across New South Wales and Victoria (Silva et al. 2020). Climate change predictions indicate that such extremes will occur more frequently and become more intense, affecting already stressed river systems.

The Marine chapter describes the state and trend of marine sharks, rays, chimaeras, tuna, billfish, reef fishes and other fish (see the Marine chapter).

Invertebrates

Australia has approximately 320,465 invertebrate species, of which about 35% have been described. More than 80% of all invertebrates are grouped into the phylum Arthropoda, which includes arachnids (spiders, ticks, mites and scorpions), crustaceans (e.g. crabs, shrimps, barnacles), centipedes, millipedes and insects. Insects are the largest class of invertebrates, accounting for more than 75% of all animal species, and include beetles, butterflies and moths, ants, bees, wasps, flies, mosquitos, bugs and grasshoppers. Australia has a rich insect biodiversity, and taxonomists estimate that there may be more than 200,000 species in Australia, although only around 62,000 have been described.

Many invertebrates are of significant cultural importance to Indigenous Australians, particularly those valued as a nutritional food source or used for medicinal purposes. Species of freshwater crayfish (marron), beetle larvae (witchetty or bardi grubs), native bees (sweat bees), sap-sucking insects (lerps), irruptive insects (swarming locusts) and mass migratory species (bogong moths) are all examples of invertebrates that are highly prized by Traditional Owners as sources of food. Many of these invertebrates and a plethora of others, such as termites, ants and processionary caterpillars, were also medicinally useful to treat various ailments and conditions (Faast & Weinstein 2020). In some instances, invertebrates were central to the ceremonies, mythology and cosmology reinforcing the connection people had to Country, and facilitated the congregation of people at feasts such as those documented for the bogong moth on Ngarigu Country in the Australia Alps, which are estimated to have been practised for more than 2,000 years (Stephenson et al. 2020).

A recent review of the conservation status of all insects and allied invertebrates in terrestrial and freshwater environments in Australia (excluding molluscs, annelids (segmented worms) and nematodes) has greatly improved knowledge about these taxa since 2016 state of the environment reporting (Taylor et al. 2018a).

A total of 285 invertebrate species are listed as threatened under various state and territory conservation Acts, the EPBC Act and the IUCN Red List (Taylor et al. 2018a), and 10 species are listed as Extinct. These known invertebrate extinctions have occurred in both terrestrial and aquatic environments, and include 2 insects, 1 isopod, 1 spider, 1 worm, 4 land snails and 1 freshwater snail (Braby 2019).

Most threatened species have been listed from the wetter areas of Australia, with particularly high concentrations of species in coastal regions of eastern Australia. There are no listed species in 40% of the bioregions in the Interim Biogeographic Regionalisation for Australia (see Ecosystems and habitats) that are mostly in semi-arid or arid areas of the continent.

Major threats to insect biodiversity come from habitat loss through broadscale clearing of native vegetation, invasion by weeds, habitat fragmentation, loss of natural corridors and inappropriate fire regimes (Braby 2019). Other threats include disturbance of plant communities on hilltops, creek embankments and in water courses; pesticides; trampling and grazing by stock and feral animals; and non-native predators (Sands 2018). Climate change affects insects that have limited thermal and moisture tolerances (climate envelopes), with changes in temperature and rainfall potentially affecting their distribution, development and reproduction (Sands 2018).

The vast number of insect species in Australia means that most are poorly described and their ecology and distribution little understood, which has led to difficulties in distinguishing their threats. This is coupled with a gradual loss of taxonomic expertise needed for identifications and descriptions (Braby & Williams 2016). As a consequence, the conservation status and management needs of most threatened insect species are poorly understood and documented (Sands 2018). For example, despite being one of the better studied and more charismatic invertebrate groups, only 10 butterflies are currently recognised as threatened under the EPBC Act, equating to around 1.6% of the recognised 614 Australian butterfly taxa (Taylor et al. 2018a).

In addition, invertebrate species are generally not considered to be particularly charismatic, and for most species there is little public concern for their potential demise. Some are even considered largely expendable. For example, parasites of mammals and insect herbivores are rarely considered in the context of conservation, and their decline and extinction are often overlooked (Moir 2020). An Australian mealybug species (Pseudococcus markharveyi) was discovered and described less than 15 years ago, and was highlighted recently as one of 5 most threatened invertebrates in Australia, requiring urgent management intervention to avoid extinction (Moir 2020). Unfortunately, it may be too late. All individual plants of the Critically Endangered Stirling Range dryandra (Banksia montana) that were known to host the species have died as a result of the 2018 bushfires in Western Australia, and the mealybug is now likely to be extinct.

Declines in other invertebrate taxa have been documented or suggested recently, with poorly known invertebrate species disappearing ‘silently’. For example, the likely decline of members of the trapdoor spiders (Mygalomorphae: Idiopidae) of southern Australia has been noted due to intensive land clearing and stocking (Rix et al. 2017). Knowledge about the distributions of this poorly taxonomically documented yet diverse assemblage of long-lived fossorial spiders is very limited, making conservation assessment impossible. Only 1 species, the shield-backed trapdoor spider (Idiosoma nigrum), is listed under the EPBC Act as Vulnerable.

Conversely, invertebrate species are sometimes rediscovered. The second known specimen of the bee Hesperocolletes douglasi was recently reported as a serendipitous find among a collection of insect pollinators from an isolated woodland remnant in the Southwest Floristic Region of Western Australia. The only other collection of this species was 80 years ago, and it was officially gazetted as presumed extinct in 1994; however, it now appears that H. douglasi may persist as a localised population (Arnold et al. 2019).

The Coasts chapter describes invertebrates of Australian bays and estuaries and the impacts of coastal development, catchment development, invasive species and climate change on these species (see the Coasts chapter). The Antarctica chapter describes threats to Antarctic terrestrial and Southern Ocean invertebrates (see the Antarctica chapter). The Marine chapter describes the wide range of mobile marine invertebrates, as well as habitat-forming invertebrates such as corals, sponges and bryozoans (see the Marine chapter).

The extent and rate of extinction of Australian insects and other invertebrates are poorly know.

Subterranean fauna

Across large parts of Australia, it has become apparent that underground aquifers and underground caves support a diverse array of subterranean invertebrates. Troglofauna is the name given to species that live in air-filled cavities, voids or pores in rocks, typically in the unsaturated zone above the watertable; while stygofauna are aquatic species that live in the groundwater, often tens of metres below the surface.

The diversity of Australian subterranean fauna is extremely high. More than 4,100 species are estimated to occur in Western Australia alone based on the rate of species discovery in the early part of last decade (Guzik et al. 2010), in part thanks to new molecular and genomic techniques. For example, 24 new species of microcrustacean (Parabathynellidae) have been recently identified in the Pilbara, representing 22% of the world’s diversity (Matthews et al. 2020). At least 3 fish species also occur in groundwater systems. The blind cave gudgeon (Milyeringa veritas) and the blind cave eel (Ophisternon candidum) are both listed as Vulnerable freshwater fish species under the EPBC Act.

However, as elsewhere, Australia’s subterranean fauna is poorly known, although its role in ecosystem services is thought to be substantial (Hose & Stumpp 2019). Knowledge gained in the past decade shows that much of the Australian subterranean fauna occurs nowhere else (Mokany et al. 2019) and has highly restricted ranges (Hyde et al. 2017). For example, in south-west Western Australia, unique stygofaunal communities are associated with mats of submerged rootlets of trees in limestone caves underneath the Leeuwin–Naturaliste Ridge. Several of these communities have been listed as Endangered under the EPBC Act. Major threats to these communities include declining water levels, mainly due to groundwater abstraction for urban, rural and industry needs, and destruction or accidental damage of the tree roots. Other threats include the pollution of groundwater, cave collapse and possible introduction of species such as yabbies, which are thought to have had a serious impact on other root mat communities.

Very little is known about the basic biology and ecology of subterranean fauna (Humphreys 2018). This is a key issue for assessing and remediating impacts as part of the environmental impact assessment process, especially as poor knowledge suggests that caution should be taken with any management (the precautionary principle).

Mining activities, such as mineral exploration, resource excavation, and groundwater drawdown and reinjection, can threaten the persistence of entire populations and even entire species of subterranean fauna (Halse 2018). Injection of treated greywater or sewage water into aquifers (called managed aquifer reinjection) is also a potential threat in urban areas. Changes to microclimate, contamination from pollutants and hydrocarbons, and increased nutrient loads are added threats to subterranean fauna, especially stygofauna and other entities in groundwater-dependent ecosystems (Hose et al. 2015, Hose & Stumpp 2019, Castaño-Sánchez et al. 2020).

Fungi and other microorganisms

Australia is home to more than 15,000 known species of fungi, 8,000 of which are visible to the naked eye, with the remainder being microscopic. The Antarctica chapter has more information about Antarctic fungi and soil microorganisms (see the Terrestrial species section in the Antarctica chapter). Many more species, possibly tens of thousands, are undescribed. Fungi provide critical ecosystem services by decomposing the complex cellulose and lignin molecules in wood. They also provide food to a wide range of vertebrates and invertebrates. At least 30 species of Australian mammals have been found to eat fungal fruiting bodies in habitats ranging from rainforest to deserts.

Despite the very important roles that fungi and other microorganisms play in ecosystems and ecological processes, the overall level of knowledge about their taxonomy, biology and ecology is very limited. However, some regional programs are making progress in more comprehensively documenting these components of biodiversity. For example, FORESTCHECK is one of only a few programs in the world collecting regional-scale information on mosses, lichens, fungi and invertebrates, as well as the better-known components of forest biodiversity.

The IUCN Red List has 408 fungi species listed. However, with an estimated 5 million fungal species globally, there is still a very long way to go in assessing the conservation status of these critically important species. Thirty-six Australian species are listed, including 1 Critically Endangered and 4 Endangered species, which is a considerable improvement on the 1 species reported as listed in 2016. Twenty-seven of the listed species occur in temperate forest habitats. No fungi are currently listed under the EPBC Act, and only a few are listed under state conservation Acts.

Tea-tree fingers (Hypocreopsis amplectens) is the only species listed as Critically Endangered on the IUCN Red List. It is endemic to south-eastern Australia and the South Island of New Zealand. Despite intense survey effort for this readily recognisable and persistent fungus for more than 30 years, it has only ever been recorded at 7 sites, and it can no longer be found at some. Although the known sites are all in areas managed for nature conservation, there is continuing significant disturbance, including motorbike riding and horse riding. Fire is also considered a significant threat, especially repeated fires at short intervals.

Of the species listed on the IUCN Red List, the most frequently cited threats are housing and urban area expansion, increases in fire frequency or intensity, and tourism and recreational activities.

Aquatic microorganisms

The Marine chapter describes changes in the microbial communities of ocean waters, with significant geographic shifts in distribution of marine algae, including pathogenic and harmful algal bloom species, as ocean waters warm (see the Marine chapter).

Diatoms (Bacillariophyta) are the most species-rich group of algae on Earth, with global estimates varying between 30,000 and 200,000 taxa. The freshwater diatom flora of Australia is estimated to be about 1,400 species, of which about 200 species are endemic. The highest species richness appears to be in temperate Australia, where about 650 taxa are recorded (around 90 new taxa described in 2018); however, this may be a conservative estimate, because 609 taxa have been recorded from Tasmania alone, and 80 of these were new to science and 100 new to Australia (John 2018). Tropical Australia supports about 500 taxa, while 400 taxa are known from arid Australia; 50 and 60 taxa, respectively, are considered new to science (John 2020, John in press).

Diatoms and other freshwater microorganisms are highly sensitive to water quality and are often used as bioindicators of change in water-quality parameters. For example, in Moreton Bay in Queensland, the composition of the diatom community has shown distinct changes in relation to floods, increasing urbanisation and agriculture in the large catchment. Since the mid-20th century, the growth of bloom-forming marine planktonic diatoms has increased compared with the dominant benthic diatom. This transition is most likely due to a shift in the quality of run-off entering the bay, with run-off events in the latter half of the century characterised by increased fine sediment, nitrogen and pollutant loads (Coates-Marnane et al. 2021).