The structure and function of marine ecosystems are underpinned by key physical, biogeochemical, biological and ecological processes. These affect all the services provided by the marine environment, including supporting (e.g. production of atmospheric oxygen), provisioning (e.g. fisheries) and regulating (e.g. carbon sequestration and climate) services. Together with the state and trends of marine habitats, communities and species groups, they provide an indication of the health of the marine ecosystem (e.g. Rombouts et al. 2013). The health of the marine ecosystem in turn underpins human health and wellbeing – both for Australians and worldwide. Indigenous knowledge systems are based on understandings of complex environmental processes and interactions. Traditional Custodians have lived alongside changing ecosystems, with a deep connectedness and lore for looking after land and sea Country. The turning of the seasons and cycle of changes in animals and plants influence when to protect, when to hunt and when to hold ceremonies. To many Aboriginal and Torres Strait Islander people, these changes are known contemporarily as seasonal indicators, captured visually through seasonal calendars (Prober et al. 2011, Woodward & Marrfurra McTaggart 2019). This knowledge is enhanced by continued presence and continuation of culture. Assessment State of marine ecosystem processes 2021 Limited confidence Indigenous assessment Marine ecosystem processes are generally in a good and stable condition, but almost as many processes assessed were found to be deteriorating. Some deteriorating processes play a key role in ecosystem structure and functioning: connectivity and species redistribution are in poor condition and deteriorating, and microbial communities and processes are also deteriorating. Traditional Owners assessed algal blooms and trophic (food web) structures and relationships to be in worse condition than reflected by the ‘western science’ assessments. Note that the spatial scale of Indigenous and western science assessments may be different. Related to United Nations Sustainable Development Goal targets 14.C, 14.2 Legend How was this assessment made Share on Twitter Share on Facebook Share on Linkedin Share this link Assessment Water clarity (turbidity, transparency and colour) 2021 Somewhat adequate confidence 2016 2011 Water transparency is relatively good and stable across most of Australia’s marine estate. However, water transparency is decreasing in southern regions as a result of increasing chlorophyll-a. Climate change is expected to cause continuing increases in chlorophyll-a in southern Australia and decreases in northern Australia (Doblin et al. 2021). The Indigenous assessment regionally was poor, with a stable trend. Assessment Connectivity 2021 Adequate confidence Both physical and biological connectivity have changed around Australia as a result of human activities (Condie et al. 2021a). The Indigenous assessment regionally was poor, with a stable trend. Assessment Food webs (trophic structures and relationships) 2021 Limited confidence 2016 2011 Highly variable. Locations under heavy climate or cumulative pressure are poor; other locations are stable and in good condition (Fulton et al. 2021a). The national Indigenous assessment was very poor, with a deteriorating trend. Assessment Marine microbial communities and processes 2021 Limited confidence 2011 Australian waters support generally healthy microbial assemblages. Regional oceanographic changes lead to organismal shifts, with consequences for entire ecosystems (Brown & Bodrossy 2021). The Indigenous assessment locally was poor, with a deteriorating trend. Assessment Primary productivity 2021 Limited confidence 2016 Primary production has decreased in the north-west and north-east shelf, and offshore in the Indian Ocean, whereas increases have been evident in all waters south of about 25°S (van Ruth & Matear 2021). The Indigenous assessment locally was poor, with a deteriorating trend. Assessment Secondary productivity 2021 Somewhat adequate confidence 2016 Zooplankton abundance has increased in most regions, whereas trends are unclear for copepod diversity (Richardson et al. 2021b). Assessment Viral diseases, parasitic infestations and mass die-offs 2021 Limited confidence 2016 2011 Major disease outbreaks, such as white spot disease (Queensland) and Pacific oyster mortality syndrome (New South Wales, Tasmania and South Australia), have occurred. Overall national conditions are unclear (Nowak & Hood 2021). The Indigenous assessment regionally was good, with a stable trend. Assessment Algal blooms 2021 Limited confidence 2016 2011 Different harmful algal blooms occur in different regions and show different trends; there has been no strong overall trend in frequency of blooms (Hallegraeff et al. 2021). The national Indigenous assessment was poor, with an unclear trend. Assessment Species redistribution 2021 Adequate confidence An increasing number of species are shifting their distributions poleward; however, most observations are in temperate regions (Gervais & Pecl 2021). The Indigenous assessment regionally was poor, with a deteriorating trend. Water clarity (turbidity, transparency and colour) Water clarity (determined by turbidity, transparency and colour) is a key aspect of water quality. It is determined by the concentration and nature of the dissolved and particulate materials in sea water. Water clarity determines how deep light can penetrate from the surface, and therefore affects the distribution and growth of light-dependent marine plants and corals (Doblin et al. 2021). Australia’s marine ecosystems are adapted to clear conditions, and any deterioration in water quality (i.e. increased turbidity or decreased transparency) threatens pelagic primary producers (phytoplankton), and key habitat-forming benthic primary producers such as kelps and corals. The Coasts chapter includes seagrasses in coastal environments (see the Coasts chapter). In oceanic and outer continental shelf waters, the major determinant of turbidity, transparency and colour is the biomass of phytoplankton (Yentsch 1960). Phytoplankton growth is largely driven by the availability of dissolved nutrients, and so water transparency declines strongly towards shore as a result of increased sources of sediment and nutrients, and greater phytoplankton biomass. The northern waters of Australia (Timor and Arafura seas) have higher suspended sediment (lowest transparency) than southern waters, and waters in the Coral Sea have greater transparency (Secchi disk depth; Doblin et al. 2021; Figure 12). Water transparency is strongly seasonal, reaching a minimum in spring in the Temperate East and South-east marine regions, and in winter in the North, North-west, South-west and Coral Sea marine regions, due to growth of phytoplankton (as indicated by peaks in chlorophyll-a concentration; Thompson et al. 2020; Figure 12). Tidal flows and waves contribute to turbidity, and extreme events such as tropical cyclones and storms can increase the level of suspended sediment by up to 3 orders of magnitude (×1,000) due to both run-off and bottom disturbance by waves. In addition, tropical rivers in areas of high rainfall can deliver large amounts of sediment to the coastal zone, with plumes sometimes being quite extensive. Water transparency in marine waters is declining across subtropical and temperate Australia but remains stable in tropical marine waters in the north and the north-east (Coral Sea). In the South-east and South-west marine regions, decreasing transparency in marine waters is linked to significant increases in chlorophyll-a with no significant change in suspended matter (Figure 12). Sedimentation is expected to become an increasingly important issue under climate change, with evidence suggesting that increased water temperature and acidification make juvenile corals more sensitive to smothering (Brunner et al. 2021). Sediment and nutrient input have much greater impacts on water quality (and resulting ecosystem impacts) in inshore waters, as described in the Coasts chapter (see the Coasts chapter) (see also Bartley et al. 2017, Schaffelke et al. 2017, DES 2019, GBRMPA 2019). Figure 12 Interannual variability and long-term trend in water quality parameters as estimated from satellites for North-west, North, Coral Sea, Temperate East, South-east and South-west marine regions Expand View Figure 12 Interannual variability and long-term trend in water quality parameters as estimated from satellites for North-west, North, Coral Sea, Temperate East, South-east and South-west marine regions m =metre; mg/m3 =milligram per cubic metre; TSS = total suspended solids Notes: Secchi disk depth is an indicator of water transparency that is a function of dissolved and particulate material in the water column. TSS comprise both pigmented and nonpigmented particles, and chlorophyll-a concentration represents pigmented particles. Black line indicates no significant trend; blue line indicates significant negative trend; red line indicates significant positive trend (P < 0.05). Points represent individual measurements. Units for y axes are given in column headings. See details for the assessment in Doblin et al. (2021). Share on Twitter Share on Facebook Share on Linkedin Share this link Microbial processes Australian marine waters typically contain between 100,000 and 10 million microbial (bacteria, archaea and unicellular algae) cells per millilitre, belonging to tens of thousands of different species (Brown et al. 2018). This highly diverse and abundant community responds sensitively and rapidly to changes in environmental conditions, and is hence a valuable indicator of ecosystem status and health. For example, changes already happening in the microbial assemblage of temperate waters have been clearly associated with ocean warming and the increasing impact of warm currents (Leeuwin Current and East Australian Current) flowing towards the poles (Seymour et al. 2012, Phelps et al. 2018, Messer et al. 2020). Microbes also shape the marine environment through biogeochemical cycles, supporting phytoplankton primary productivity, contributing to the ocean carbon pump, and removing a wide range of chemical pollutants. Microbial communities are highly diverse and adaptable to a range of environmental conditions; however, it is not yet clear how much of a buffer this flexibility might provide against environmental changes before major ecosystem shifts occur. Microbial abundance and community composition vary between regions and seasons (Seymour et al. 2012, Bibiloni-Isaksson et al. 2016, Jeffries et al. 2016, Brown et al. 2018, Raes et al. 2018, Frade et al. 2020, Messer et al. 2020), and finer-scale patterns (e.g. daily) are also likely to exist (Carney et al. 2020). Ocean warming is changing the microbial community composition of temperate waters (Seymour et al. 2012, Phelps et al. 2018, Messer et al. 2020). Small phytoplankton, including important cyanobacterial groups, are becoming the main primary producers in temperate waters (PG Thomson, University of Western Australia, pers. comm., March 2018; Ajani et al. 2020, Messer et al. 2020, Ostrowski et al. 2020, Brown & Bodrossy 2021). This shift from large to small species will reduce the phytoplankton biomass and thus may reduce available food and carbon transfer to higher levels of the food chain (higher trophic levels). As with more abundant species, the geographic distribution of pathogenic and harmful algal bloom species is shifting poleward with warming waters (see Introduced species, diseases, pests and algal blooms). Increasing frequency of marine heatwaves (Roberts et al. 2019) and excess nutrients (eutrophication) may also affect regional microbial communities (Carney et al. 2020). Although seasonal and annual patterns and regional biogeography can be determined, increased high-resolution monitoring will be required to assess the influence of these pressures on microbial assemblages and the outlook for different microbial communities. Primary production (phytoplankton) Primary production is the process by which phytoplankton convert dissolved inorganic carbon into the organic compounds that underpin the marine food web (see Food webs and connectivity) through photosynthesis. Rates of primary production and concentrations of phytoplankton biomass depend on the available light (irradiance), and the magnitude and timing of nutrient supply. Trends in primary production and primary product over time around Australia are seasonally and regionally variable (Antoine et al. 2020, Thompson & McDonald 2020, van Ruth et al. 2020, van Ruth & Matear 2021). Overall, the average trend is weakly increasing, with regional increases evident in all waters south of about 25°S, particularly throughout the South-east Marine Region, and in offshore waters in the Great Australian Bight (van Ruth & Matear 2021; Figure 13). Regions of decreasing primary production and phytoplankton biomass include the north-west and north-east shelf, and offshore in the Indian Ocean. The overall small increasing trend in primary production and phytoplankton biomass may have a positive benefit on ecosystem production, but potential ecosystem effects remain poorly understood. Marine heatwaves, which are expected to increase in frequency and intensity in Australian waters (see case study: Marine heatwaves), can significantly impact primary producers by changing phytoplankton biomass and community composition (Roberts et al. 2019, Hayashida et al. 2020) (see Microbial processes). This can have both beneficial and detrimental effects on the ecosystem (Chiswell & Sutton 2020). Dust and particulates carried by the wind from the land to the ocean (including smoke from bushfires) can stimulate phytoplankton blooms under some conditions, so changes in land management practices and fire frequency are likely to have implications for primary production. However, the nature and magnitude of these changes are currently unclear (Cropp et al. 2013, Gabric et al. 2016, Perron et al. 2020, Li et al. 2021). Figure 13 (a) Annual mean net primary productivity and (b) annual mean phytoplankton biomass, with (c) the trend in net primary productivity and (d) phytoplankton biomass, 1997–2020 Expand View Figure 13 (a) Annual mean net primary productivity and (b) annual mean phytoplankton biomass, with (c) the trend in net primary productivity and (d) phytoplankton biomass, 1997–2020 C = carbon; chl-a = chlorophyll-a; g/m2/d = gram per square metre per day; g/m2/yr = gram per square metre per year; mg/m3 = milligram per cubic metre; mg/m3/yr = milligram per cubic metre per year; NPP = net primary productivity Source: van Ruth & Matear (2021) Share on Twitter Share on Facebook Share on Linkedin Share this link Secondary production (zooplankton) Secondary production in the ocean is the generation of biomass when zooplankton (herbivores) eat phytoplankton (plants; see Primary production (phytoplankton)), and grow and reproduce. The most common zooplankton, the copepods, are arguably the most abundant animals on Earth, even potentially outnumbering insects (Schminke 2007). Secondary production is essential to healthy fisheries and ecosystems, because animals higher in the food web (e.g. fish, squid, shellfish, marine mammals, seabirds, sea turtles; see Food webs and connectivity) depend on secondary production (Bakun 2006). Productivity hotspots, such as the Eden and Bonney upwelling zones, have high densities of zooplankton, sustaining invertebrates, fish and whales (Gill 2002). Zooplankton are also important components of the biological pump, shunting carbon from surface to deeper waters through sinking of faeces, moulted exoskeletons (exuviae) and carcasses (Turner 2015). Measurements of zooplankton biomass and abundance from the Integrated Marine Observing System National Reference Stations and the Australian Continuous Plankton Recorder Survey indicate that zooplankton have increased in Australian waters over the past decade (Everett et al. 2020, Richardson et al. 2021b; Figure 3). The causes of this likely increase are unknown. At the same time, there has been no detectable change in the diversity of zooplankton species. In coastal areas, zooplankton can be influenced by excess nutrients (eutrophication; Uye 1994). However, over large areas, climate change is likely to be the major pressure (Richardson & Schoeman 2004). Fishing and its influence on higher levels of the food web can change the top-down control of zooplankton, resulting in changes in biomass (Cury et al. 2000), but this is probably rare over large areas (Richardson & Schoeman 2004). Zooplankton are generally more resilient to human pressures than species higher in the food web (higher trophic levels). However, the impact of global warming on thermal niches of zooplankton could lead to rapid regime shifts, with impacts on higher trophic levels (Beaugrand 2015), and changes in the abundance and diversity of zooplankton could be the first indication of mass extinction events (Sheets et al. 2016). Local management interventions to decrease pressures associated with eutrophication may be possible in coastal bays; however, reducing the impacts associated with climate change will only be possible by reducing greenhouse gas emissions. Food webs and connectivity Ocean connectivity refers to a range of processes that govern the movement of physical, chemical and biological material within the ocean (Condie et al. 2021a). Ocean currents transport heat, salt, nutrients and planktonic organisms, whereas many larger organisms can control their connectivity through active swimming between habitat patches (e.g. reefs) or over longer migratory pathways (e.g. seasonal migrations of marine mammals and birds). Changes in connectivity may result from seasonal, interannual or long-term changes in patterns of ocean currents (see Changes to ocean circulation); changes in habitat distributions; species changes; barriers to movement, including structures in the ocean (which may present barriers in some cases, but act as stepping stones for dispersal in others); and noise and light pollution (see Anthropogenic marine noise). Healthy ecosystems are characterised by structural and functional connectivity, where species interact and rely on other species for food and lifecycle processes (Fulton et al. 2021a). The food web – a system of interlocking food chains – is the most obvious ecosystem structure. Modelling studies (e.g. Fulton et al. 2005, Klaer 2006), reconstructions (e.g. Carnell & Keough 2019) and comparative studies (e.g. Harasti et al. 2018) indicate that many food webs have been highly modified around Australia. This is particularly the case for food webs containing species that have previously been, or are currently, exploited by fisheries or disturbed by other human activities (GBRMPA 2014) and climate change (Holland et al. 2020). Human populations are growing, marine industries are expanding, and the magnitude of effects from climate change is increasing (NMSC 2015, IPCC 2018, Jouffray et al. 2020). These stresses are likely to keep food webs in an altered state or reshape them further. This may reduce energy flow to higher food-web levels, affecting larger species (Hempson et al. 2017, Ullah et al. 2018, Nagelkerken et al. 2020) (see also Secondary production (zooplankton)). As diversity is reduced in a region or population sizes are reduced, food webs can become shorter. Reduced resilience of species is a common feature of shortened or otherwise modified food webs (Nyström et al. 2012, O’Gorman et al. 2012). Changes to Australian marine food webs and connectivity Ocean currents and the distribution of habitats and communities are all changing in response to climate change (Condie et al. 2021a) (see Species redistribution). Trends in migratory connectivity are not available, although baseline estimates of connectivity for individual populations and species have been published (e.g. Sequeira et al. 2013), and new tools to house information on connectivity are being developed (see the eAtlas and MiCO websites), along with system-level indicators to track changes in connectivity (e.g. Condie et al. 2018). Changes in food webs and connectivity can have wide-ranging impacts and can be due to several pressures: Habitat degradation can reshape food-web connections, either through the loss of feeding areas and refuges or by altering the mix of species present, favouring more generalist and often fast-turnover species (i.e. species that reproduce rapidly and have short lifespans; Sainsbury 1991, Darling et al. 2017). Historical declines in the numbers of large predatory species, such as sharks and marine mammals, have had pervasive effects on marine ecosystem structure worldwide (Estes et al. 2011, McCauley et al. 2015): large predatory species are in notably lower abundance than in the pre-European period, and declines in some species in Australia have continued in recent decades (Roff et al. 2018, Gibbs et al. 2020). Effects include cascading changes in biomass and abundance at lower levels in the food web, as well as weakened connections between spatially dispersed food webs (e.g. coastal, pelagic and benthic food webs; Johnson et al. 2011, McCauley et al. 2012, Brown & Trebilco 2014). Where recovery of predatory species is well underway (e.g. some seal and whale populations), the ecosystem is likely to restructure around the new predation pressure. Artificial structures in the ocean can change food-web structures. Offshore structures can support large filter-feeding populations (Malerba et al. 2019), which can influence the productivity of surrounding waters and support diverse fish communities. At the coast, breakwaters attract fish of many sizes and feeding types, rivalling nearby natural systems (Pereira et al. 2016), although, at larger geographic scales, they are more homogeneous than natural habitats (Porter et al. 2018). Changing connectivity patterns can undermine the resilience of marine communities by obstructing links with spawning grounds and thereby reducing recruitment rates to nursery areas (Condie et al. 2018). There is also potential for increased recruitment of invasive species, leading to ecological regime shifts (Ling et al. 2019) (see Introduced species, diseases, pests and algal blooms). It is unclear how climate change–associated shifts in environmental conditions and acute events, such as marine heatwaves, are affecting deeper and more remote marine ecosystems that have previously been less exposed to stressors that might result in changes to ecosystem structure (Ruthrof et al. 2018, Roberts et al. 2019). As climate-driven shifts in species ranges become more pronounced (see Species redistribution), it is likely that there will be poleward shifts in food-web structure, such as increased mass of herbivores at mid-latitudes and increased mass of planktivores at higher latitudes (e.g. Bennett et al. 2015, Holland et al. 2020, Zarco-Perello et al. 2020). Tropicalised reefs (Figure 14) may start to resemble coral‐dominated systems, with a higher proportion of primary production being consumed and recycled locally. This may result in increased flow of energy to higher trophic levels, potentially leading to increases in the biomass of benthic (ocean floor) species (Vergés et al. 2016). Figure 14 Conceptual model of how fish control macroalgal biomass on coral reefs, unimpacted and tropicalised temperate reefs Expand View Figure 14 Conceptual model of how fish control macroalgal biomass on coral reefs, unimpacted and tropicalised temperate reefs Share on Twitter Share on Facebook Share on Linkedin Share this link Restoration (Layton et al. 2020, Loch et al. 2020) and spatial management (Cheng et al. 2019) have the potential to rebuild trophic relationships (Sih et al. 2019), but only if these efforts are not undermined by climate-driven species shifts (Sunday et al. 2015, Marzloff et al. 2016), depressed prey fields (Kelly et al. 2016), pollution or other chronic pressures, such as local urbanisation (Malerba et al. 2019). Traditional ecological knowledge can inform our understanding of migratory connectivity, and thus Indigenous communities should be included in assessments of state and trends (Vierros et al. 2020). Species redistribution Since 2003, at least 198 Australian marine species have undergone long-term shifts in their geographic distributions, and range shifts are becoming more frequent (Gervais & Pecl 2021, Gervais et al. 2021). Extensive species redistributions are projected to occur around the Australian coastline for the foreseeable future (see Figure 15). These redistributions are strongly associated with ocean warming: 87.3% of shifts (173 species) are towards cooler waters (Gervais et al. 2021). Extreme climate events such as the El Niño–Southern Oscillation and marine heatwaves have also facilitated the contraction of warmer (northern) range limits and the extension of cooler (poleward) range limits of species in Australia (Sunday et al. 2015, Pecl et al. 2017, Day et al. 2018). Species redistributions will be an important consideration in the management of all activities in the marine environment in the face of climate change, both in Australia and worldwide (Melbourne-Thomas et al. 2021). Impacts of shifting species In some cases, redistribution of species may act similarly to invasive or pest species, altering native ecosystems and processes, with economic and sociological ramifications. For example, within the past 40 years, long-spined sea urchins (Centrostephanus rodgersii) have shifted poleward from New South Wales to Tasmania. This has resulted in macroalgal loss due to overgrazing, causing an estimated minimum net loss of around 150 macroalgae-associated species. Reported range shifts are likely a considerable underestimate, given that research and observations are spatially biased towards human population centres, under-represented in tropical systems and commonly focused on only 1 range edge (i.e. the extending range edge). Globally, where many species are analysed, 25–85% of species have been documented to be shifting, but little is known about the cumulative ecosystem-level impacts of multiple shifts. In addition to latitudinal shifts in species distributions, some species are thought to be retreating to deeper (cooler) waters; however, these trends are largely unknown for Australian waters. Similarly, with increasing tidal height, intertidal species and ecosystems may also be shifting, but again there is very little focus on these systems. Figure 15 Species representation and spatial distribution of observed range-shifting species across Australia Expand View Figure 15 Species representation and spatial distribution of observed range-shifting species across Australia Share on Twitter Share on Facebook Share on Linkedin Share this link Range shift research Observations of species outside their known range are increasing, although structured scientific surveys are urgently required to document these properly. Citizen science programs have underpinned one-fifth of range shift reports and are able to cover large spatial scales, although these programs need funding to operate. There is less evidence of range contractions, apart from some macroalgae species (see Wernberg et al. 2011) and local extinction events. However, these trends are difficult to observe and thus are unclear. Little is known about species that are not shifting to keep pace with climate or are unable to do so. This is especially relevant to species that may lack suitable habitat necessary to shift (e.g. obligate coral reef fish, coastal species along Tasmania’s southern edge). Predictive modelling and exploration of the mechanisms that drive or limit species distributions are needed, along with an understanding of the ecosystem-level implications of multiple losses and gains of species. Understanding implications of range shifts for the Australian marine park network will also be an important future research need.