Australia’s marine ecosystems span from nearshore reefs to the soft-sediment communities of the abyssal plains at more than 5,000 metres (m) depth, including the vast volumes of open ocean that lie between the surface and the sea floor (Figure 1). The ecosystems can be characterised by groupings of types of habitats and communities based on where they are found and the dominant species (Figure 2). These habitats and communities support a great diversity of species, many of which are of substantial economic and cultural importance.
Marine habitats are of varied significance to the diverse range of Traditional Owners around Australia’s coastline. Many of these habitats have provided protection, food and cultural resources for more than 60,000 years and continue to be closely tied to the wellbeing of Indigenous Australians.
Because of the long occupation by Aboriginal and Torres Strait Islander peoples of what is now known as Australia, there are many ancestral connections to seabeds that were previously above sea level; it is estimated that an extra 2 million hectares in landmass would have been exposed and been included in Country for Aboriginal people before the area was inundated during the Meltwater Pulse 1a between 35,000 and 8,000 years ago (Williams et al. 2018c, Benjamin et al. 2020). Coastal communities still have connections to the inundated sites, with sacred stories attached to these spaces (Przeslawski et al. 2020). For many communities, the connection continues, as is the case with kelp forests around Tasmania, and the close cultural, spiritual and ancestral connections women have to these habitats.
For this report, we consider the state and trends of 16 habitats and communities that together broadly encompass the diversity of Australia’s marine ecosystems. In addition to the habitats and communities described here, other habitats that are often considered ‘marine’ but are primarily restricted to coastal environments (such as mangroves and seagrasses) are considered in the Coasts chapter (see the Coastal ecosystems and habitats section in the Coasts chapter).
Most marine habitats and communities are in a good and stable condition. However, reef ecosystems are in poor condition and are declining, and seamounts remain in poor condition because they are recovering extremely slowly from the historical impacts of bottom fishing. It is notable that Traditional Owners assessed habitats and communities as in worse condition than reflected by the ‘western science’ assessments – poor and deteriorating were the most common grades provided by Traditional Owners. Note that the spatial scale of Indigenous and western science assessments may be different. Related to United Nations Sustainable Development Goal targets 14.1, 14.2, 14.4, 14.5
Inshore non-reef habitats at 0–30 m are in good condition, except for the south-east and east, based on expert knowledge. The south-east and east are likely in locally poor condition as a result of historical trawling and nutrient inputs (Barrett et al. 2021b). The Indigenous assessment locally was poor, with an unclear trend.
Good condition generally, with poorer condition in areas subject to frequent (current or historical) bottom fishing (Barrett et al. 2021c).
Spatially restricted habitat is impacted by concentrated commercial bottom fishing in some areas; biota is slow to recover. Available information is generally poor. State is poorest in the South-east and Temperate East marine regions (Althaus et al. 2021a).
State is highly variable for 700–1,500 m, dependent on historical fishing impacts; fishing footprint has decreased since 2016. Habitats beyond 1,500 m are overall in a very good, stable condition in all regions, due to minimal human interactions at these depths to date (O’Hara et al. 2021).
No consistent trend among locations based on an assessment of phytoplankton, zooplankton and fish larvae (Richardson et al. 2021a). The Indigenous assessment locally was poor, with a deteriorating trend.
No consistent trend among locations based on an assessment of phytoplankton and zooplankton (Richardson et al. 2021c).
State and trends of biological components of the deep parts of the water column are largely unknown, but available evidence suggests a good status with likely improvements in some areas, but potential declines elsewhere (Trebilco 2021b).
Bottom-fishing impacts determine the condition of individual submarine canyons; variation is from highly impacted to largely pristine and functionally intact. State is poorest in the south-east region (Nichol et al. 2021). The Indigenous assessment locally was good, with an unclear trend.
Habitats range from very good to very poor, with trends stable to improving. Recovery from historical fishing pressure is expected to be extremely slow and potentially impeded by ocean acidification (Althaus & Williams 2021). The Indigenous assessment locally was good, with an unclear trend.
Warmer seas and associated coral bleaching may be starting to erode what has been a very good state, but not at all reefs (Stuart-Smith & Edgar 2021b).
Trend data are lacking for large parts of the coast. Warm-water events and overgrazing by sea urchins negatively affect some temperate reef habitat, particularly in the east and south-east (Stuart-Smith et al. 2021b). The Indigenous assessment regionally was poor, with an unclear trend.
Algal beds are in good condition nationally, but poorer and continuing to decline in the east and south-east as a result of warming and cascading effects of fishing. Stable elsewhere but vulnerable to heatwaves (Barrett et al. 2021e).
Overall, Australian coral reefs are in a poor state and declining. However, their condition varies considerably within and among regions (Richards et al. 2021) The Indigenous assessment regionally was poor, with a deteriorating trend.
Good condition nationally, but with south-east and east under some ongoing trawl pressure on low vertical relief systems. Ocean warming is an increasing threat (Barrett et al. 2021a).
Slow-growing fauna are exposed to direct fishing impacts, resulting in highly variable condition across depths and between regions. The south-east and east regions have the highest historical impacts from bottom fishing, especially trawling (Althaus et al. 2021b).
Nationally, the overall grade for bryozoan reefs is good condition, with stable to slightly improving trend, and poor for the south-east and east (Barrett et al. 2021d).
Water column
The water column (pelagic environment) provides habitat for microbes, phytoplankton, zooplankton, fish and animals at higher levels in the food web (higher trophic levels), including seabirds, marine reptiles and marine mammals. Many of the species found in water column habitats have substantial economic and social value (see Marine species).
Overall, water column habitats can be considered to be in a good state with a stable trend, based on chlorophyll-a (representing an index of phytoplankton biomass), zooplankton biomass and fish larval abundance (Richardson et al. 2021a, Richardson et al. 2021c, Trebilco 2021b; Figure 3).
The main pressures on all water column habitats are climate change, causing acidification and declines in dissolved oxygen, fishing and pollution (Richardson & Schoeman 2004, Burgess et al. 2018).
Condition of depth zones
The water column of the ocean is often subdivided into depth zones (Figure 2):
- neritic zone – waters over the continental shelf in depths of 0–200 m
- epipelagic zone – waters offshore in depths of 0–200 m
- mesopelagic zone – waters offshore in depths of 200–1,000 m
- bathypelagic zone – waters offshore in depths of 1,000–4,000 m
- abyssal zone waters offshore in depths more than 4,000 m.
In neritic waters, phytoplankton biomass, zooplankton biomass and larval fish abundance appear to be stable. Excess nutrients (eutrophication), sedimentation and run-off are important pressures in some regions (Uye 1994, Lin et al. 2020).
In epipelagic waters, phytoplankton and zooplankton biomass are increasing in the South-east and South-west marine regions (see Marine ecosystem processes), but trends in all other regions are less clear. Pelagic fisheries within Australian waters are generally in good state and well managed (Molony et al. 2021) (see Other fishes and Commercial fishing). Offshore oil and gas exploration can act as a pressure on these habitats and communities (see Marine petrochemical and mineral industries), with several impacts, including from noise (see Anthropogenic marine noise).
The habitats and communities in waters below 200 m are currently thought to be relatively pristine (Kloser & Kunnath 2020, Martin et al. 2020, Kloser & Kunnath 2021, Trebilco 2021b), although large-scale oceanographic changes are likely to be changing the distribution and characteristics of these habitats and communities in some areas (see Climate and climate change). Measurements of mesopelagic communities in the south-east over recent decades may indicate an increase in overall biomass, but could also indicate changes in the mix of species (community composition). Trends in other regions are unclear.
Close to the sea floor, bottom fishing is an important additional pressure (Hidalgo & Browman 2019, Drazen et al. 2020, Martin et al. 2020); however, impacts on deepwater habitats and communities are poorly understood. Deepwater species may be less resilient to changes than those from shallower waters, because these species are relatively long-lived and slow to reproduce.
The Integrated Marine Observing System (IMOS) measures various aspects of the water column, with some measurements (e.g. chlorophyll) taken over the long term (approaching 20 years). Continued monitoring will enable future identification of both abrupt and long-term changes. It will also provide the ability to distinguish long-term trends from short-term variability (Poloczanska et al. 2013, Hoegh-Guldberg et al. 2014).
Coral reefs
Coral reefs provide immense value to oceanic ecosystems, and the Australian community and economy. They act as spawning and nursery grounds for many fish species; as tourism and recreation areas; and as buffer zones against high tides, rising sea levels and storms for coastal areas and communities.
Overall, Australian coral reefs are in a poor and declining condition (Richards et al. 2021, Stuart-Smith & Edgar 2021b). Climate change is the most significant pressure on Australian coral reefs, and the outlook for our coral reefs is poor.
High water temperatures result in coral bleaching, which occurs when corals expel the algae (zooxanthellae) living in their tissues, often causing the coral to turn completely white. If high temperatures persist, or if other pressures further stress already bleached corals, the coral dies.
Coral die-off affects other species that depend on coral reefs for food and habitat (GBRMPA 2019) (see case study: Australia’s changing reefs). For example, the impacts of mass coral bleaching events in 2016 and 2017 extended to other reef-dwelling animals in the North-east, North-west and Temperate East marine regions (Stuart-Smith et al. 2018, Stuart-Smith et al. 2019, Edgar et al. 2020).
Regional reef condition
Although overall assessments are poor, reef condition varies within and among regions, with reefs in some localities in good condition (Richards et al. 2021, Stuart-Smith & Edgar 2021b):
- Most offshore (oceanic) reef systems are in good condition, with fewer signs of human impacts than inshore reef systems. Elizabeth and Middleton reefs remain in a very good state by global standards (Edgar et al. 2014, Edgar et al. 2018b, Hoey et al. 2018) but are increasingly subject to marine heatwaves (Carroll et al. 2021).
- Some inshore reefs in the North-west Marine Region are in good condition (Figure 4; (Richards et al. 2019)). Coral cover at Cocos (Keeling) Islands, at Rowley Shoals and in the Northern Territory are considered in good condition overall (Ferns 2016, Edgar et al. 2017, Gilmour et al. 2019), although localised bleaching events have occurred at Rowley Shoals.
- Coral reefs in the north-east (including the Coral Sea) are generally in poor condition and declining (AIMS 2020, Hoey et al. 2020, Thompson et al. 2021), as are many offshore reef systems in the North-west Marine Region (Moore et al. 2012, Holmes et al. 2017, Evans et al. 2020a, Schoepf et al. 2020). There has been some short-term recovery of coral cover on the Great Barrier Reef with a low-disturbance year in 2021, but the long term-decline is expected to continue given the future prognosis for increased and longer lasting marine heatwaves and a greater proportion of severe tropical cyclones (AIMS 2021b). Reefs in the Pilbara region have experienced repeated heatwaves, resulting in extensive coral mortality (Babcock et al. 2020, Evans et al. 2020b).
- Changes in overall finfish and invertebrate communities following bleaching events in 2016 and 2017 appeared more related to warmer temperatures than to coral mortality, although some coral-dependent species were affected in some reefs in the north-east (Richardson et al. 2018, Stuart-Smith et al. 2018, GBRMPA 2019) and in the North-west Marine Region (Edgar et al. 2020).
- Bleaching events occurred in the Temperate East Marine Region in 2010–11 and 2016, with reefs having generally since recovered to a good state (Stuart-Smith et al. 2019, Dalton et al. 2020). However, there have also been localised bleaching events in other parts of the region in recent years (Harrison et al. 2011, Goyen et al. 2019, Kim et al. 2019).
- Reefs at Lord Howe Island remain in very good condition, although the biomass of large fish appears to have been affected by a combination of fishing pressure and warmer waters, which have become less suitable for the main local species (Stuart-Smith et al. 2019).
There continues to be a lack of systematic monitoring in some marine regions (e.g. the North-west), for reefs below the safe working depths for scuba diving (generally more than 15 m) and for offshore reefs. Also lacking is the collection of metrics other than coral cover, which prevents assessment of the state and trends of overall biodiversity (Richards & Day 2018) and important ecosystem change (e.g. flow-on effects of fishing; (Nash & Graham 2016)). A coordinated approach is needed to integrate monitoring data across studies.
Reef recovery and management
Many Australian reefs appear able to recover from individual disturbance events, given enough time. However, the complex, global and pervasive nature of climate change makes the outlook for coral reefs very poor. The frequency, severity and spatial extent of disturbances to reefs are expected to continue to increase with climate change, reducing the opportunity for recovery. In addition, recovery can be slowed by local pressures, such as poor water quality (Osborne et al. 2017, Ortiz et al. 2018, Evans et al. 2020b, Thompson et al. 2021).
Management interventions and restoration strategies are increasingly being investigated to mitigate declines (National Academies of Sciences 2019) (see also case study: Marine restoration in a changing climate). Some of these initiatives have had positive outcomes on small scales, such as through implementation and enforcement of protected areas, and management of land-based and coastal activities that affect reefs (GBRMPA 2019). For example, long-term enforcement of Ashmore Reef Marine Park has resulted in apparent increases in the biomass of large fish populations from previously depressed levels. Oceanic reefs may be more resilient than coastal reefs; fish, in particular, seem to be less affected by habitat change and recover when there is adequate protection from fishing.
Upscaled application of safe and effective interventions may provide opportunities for building reef resilience. However, unless climate change is addressed, no intervention strategy will slow the deterioration of coral reefs (Condie et al. 2021b).
Rocky reefs and kelp beds
Rocky reefs and kelp (algal) beds are iconic of Australia’s temperate waters, and have immense economic and cultural importance to Australians (see the Coasts chapter).
Overall, the condition of Australian rocky reefs is poor, particularly in the east and around major cities, but is still generally good in southern regions (Stuart-Smith et al. 2021b). Whereas algal beds are currently in good condition overall nationally, and large canopy-forming seaweeds are still dominant in many locations in south-western Australia, western Victoria and Tasmania, they are deteriorating in the east and south-east (Butler et al. 2020, Glasby & Gibson 2020, Barrett et al. 2021e). The health of rocky reef and algal beds nationally is being affected by:
- climate change, through rising temperatures and heatwaves, and nutrient and pH variation associated with changing current systems
- overgrazing by sea urchins and other species, resulting from range extensions and removal of top predators by fishing
- decreasing water quality from coastal run-off.
Managing pressures on rocky reefs and kelp beds
Since ocean warming and heatwaves cannot be locally controlled, it is important to manage fishing pressure and coastal inputs of nutrients to build the resilience of rocky reefs and algal beds to future warming stresses and reduce degradation related to excess nutrients.
Implementing marine reserves to aid the recovery of sea urchin predators, such as lobsters and large fishes, will be important to reduce the risk of overgrazing by urchins and increase the chances of improvement in this habitat in the longer term (Johnson et al. 2013). Restoration efforts are emerging as a possible way of reducing the risk of kelp loss (see case study: Marine restoration in a changing climate), including rebuilding predator populations through directed strategies.
Management may also need to consider emerging pressures:
- At present, introduced species do not seem to have had large effects; however, the invasive algae species Undaria pinnatifida (wakame) and Caulerpa taxifolia remain problematic in some areas. As well, the red alga Grateloupia turutura is increasing in range, cover and seasonal extent in Tasmania and may extend to other states in the future.
- An emerging pressure also associated with climate change is increasing tropicalisation (change in fish community composition with greater representation of tropical species), which may increase the extent of grazing on algal beds by herbivorous fish species.
In recent years, new monitoring initiatives have narrowed gaps in the understanding of endemic seaweed and invertebrate species, and significantly improved the ability to detect and track changes in rocky reefs and algal beds around temperate Australia. These include the IMOS autonomous underwater vehicle program, ecological monitoring programs associated with the establishment of coastal marine parks, and the Reef Life Survey, a citizen science program that monitors reef systems around Australia. However, data are still very limited for large parts of the coastline, and for most endemic and rare species.
Canyons and seamounts
Marine canyons and seamounts are defined as marine key ecological features because of their influence and value for marine biodiversity (Harris et al. 2008, DAWE 2015):
- Canyons provide a pathway for the transport of sediments and nutrients (and pollutants), laterally from the shelf to the deep sea, and also vertically via upwelling of cold, nutrient-rich waters from the deep ocean towards the shelf (Kämpf 2010, Currie et al. 2012).
- Seamounts provide ‘oasis’ habitats in the deep sea that often support increased biomass and productivity, including dense aggregations of corals with high associated biodiversity (Clark et al. 2010, Rowden et al. 2010). These may represent Vulnerable Marine Ecosystems, as defined by the United Nations (Clark et al. 2011, Williams et al. 2020b).
Submarine canyons are located around the Australian continental margin, but are most common in the South-east and South-west marine regions (Figure 9). Australia also has many seamounts (undersea mountains, often with volcanic origin); the best known are the Tasmanian seamounts in the South-East Marine Region and the Tasmantid seamount chain in the Temperate East Marine Region.
Canyon and seamount condition
The condition of Australian marine canyons and seamounts ranges from very good to very poor, depending largely on the level of historical and current bottom fishing (Althaus & Williams 2021, Nichol et al. 2021).
Bottom fishing has had the largest impact on biodiversity in Australian marine canyons and seamounts (Althaus et al. 2009, Clark et al. 2016, Williams et al. 2020a). Canyons and seamounts that are in reserves or areas where bottom fishing is excluded are stable or improving, although baseline and timeseries data are very limited (Althaus & Williams 2021, Nichol et al. 2021).
Climate change is a major emerging pressure; acidification associated with climate change presents an important threat, particularly for corals and other calcifying organisms (Thresher et al. 2015, Trotter et al. 2019) (see Ocean acidification). Shelf-incising canyons are potentially vulnerable to marine heatwave events.
Pollution is another emerging pressure. Significant volumes of microplastics have recently been found to be accumulating in deep-sea sediments in the Great Australian Bight (Barrett et al. 2020), and may be even more concentrated in submarine canyons (e.g. Mordecai et al. 2011, Pham et al. 2014).
Resilience of the biological communities in canyon and seamount habitats is likely to be very low, with recovery from physical disturbance requiring timescales of decades to centuries (Harris 2014, Goode et al. 2020, Williams et al. 2020a).
There is no ongoing monitoring of canyon benthic communities in Australian marine parks to determine their effectiveness in protecting or promoting recovery of regions affected by bottom fishing. Recent surveys in the North-west (Post et al. 2020), South-west (Trotter & Montagna 2020) and Coral Sea (Brooke & Nichol 2020) marine regions have sought to gather baseline information to assess future trends in canyon benthic communities, although within a limited number of canyons.
Other seabed habitats
Other seabed habitats and communities include those found on soft bottoms (i.e. silt, sand and gravel) at all depths, as well as reef habitats and communities found in waters deeper than 30 m in both temperate and tropical waters (Figure 2). These include both ‘twilight’ (‘mesophotic’) reefs (those in waters of approximately 30–150 m, where a small amount of light from the surface is still present) and ‘dark’ reefs (those below approximately 150 m, where no light from the surface reaches). Seabed habitats include reefs formed by deepwater corals (both hard and soft corals), sponges and bryozoans (e.g. Figure 10). Coral species are found throughout Australia’s shelf waters and can make up a significant component of the cold-water assemblage. Both sponges and corals are frequently used as indicators of benthic Vulnerable Marine Ecosystems in conservation planning because they are vulnerable to demersal fishing (Tracey et al. 2008, FAO 2009, Williams et al. 2015a) and climate impacts (ocean warming and acidification; Thresher et al. 2015, Stevenson et al. 2020). They may also be vulnerable to emerging offshore activities that include bottom contact.
Australia’s seabed habitats harbour a highly diverse benthic fauna (Schlacher et al. 2007, Williams et al. 2010a, McEnnulty et al. 2011, Dunstan et al. 2012, McCallum et al. 2013), including commercially targeted fish species. Many valuable and highly regarded fish species occur in these habitats – for example, blue-eye trevalla (Hyperoglyphe antarctica, Schedophilus labyrinthica), pink ling (Genypterus blacodes) and blue grenadier (Macruronus novaezelandiae). Also occurring in these habitats are threatened or management-dependent species, such as many deepwater sharks, including gulper sharks (Centrophorus spp.) (Williams et al. 2012).
Condition of seabed habitats
The state of Australia’s seabed habitats is highly variable among and within regions (Althaus et al. 2021b, Althaus et al. 2021a, Barrett et al. 2021c, Barrett et al. 2021d, Barrett et al. 2021a, Barrett et al. 2021b), and largely linked to historical and current levels and distributions of commercial bottom fishing (e.g. Pitcher 2016, Pitcher et al. 2016, Pitcher et al. 2018). A lack of data on pre-impact conditions has made assessment of the current state difficult (Foster et al. 2015). However, knowledge of very deep-sea habitats around Australia has increased substantially since the 2016 assessment due to recent survey effort in the Great Australian Bight, off the eastern Australian margin and in the Coral Sea (MacIntosh et al. 2018, Williams et al. 2018a, Williams et al. 2018b, O’Hara et al. 2020, Schmidt Ocean Institute 2020).
Deepwater corals and sponges have low resilience to impact. Individuals of many of these species are centuries old, and recovery would not be expected within management timeframes (Williams et al. 2010b, Fallon et al. 2014). Australia’s longest deepwater biological timeseries shows little recovery 20 years after the cessation of fishing (Williams et al. 2020a). Many species have a small range of tolerance to changes in temperature or water chemistry, reducing their resilience to effects of climate change (Stevenson et al. 2020).
Even for habitats where recovery from historical impacts of fishing has been more evident, this improvement is increasingly being offset by impacts from climate change and pollution (Althaus & Williams 2021, Althaus et al. 2021a, Barrett et al. 2021a, O’Hara et al. 2021). The longer-term outlook for Australia’s seabed habitats is therefore for declining condition, or at least significant species turnover, as temperate regions undergo tropicalisation, and the warmest tropical regions warm beyond the tolerance of species, with no possibility of replacement with other species (Marzloff et al. 2016, Marzloff et al. 2018).
There is no ongoing monitoring of deep seafloor habitats in Australia, so biodiversity or oceanographic trends are unknown. The impact of plastics, dissolved pollutants or electric cables on the deep ocean is unknown.
The IMOS autonomous underwater vehicle program, in conjunction with Australian marine park and marine protected area monitoring programs, is likely to be a key source of information for understanding the state and trends of seabed habitats in the future.
Managing pressures on seabed habitats
Deepwater bottom fisheries are considered to be sustainably managed in Australia, so damage to further areas is not anticipated, but caution will be needed as other offshore industries develop. Recovery of habitat-forming biota, as well as of some of the most impacted species such as gulper sharks, is predicted to be very slow (Williams et al. 2012). Thus, long-term commitments to management – through both reserves and fishery closures, and effort management – are necessary to achieve improvements in condition.