Physical, biogeochemical, biological and ecological processes are an important component of marine ecosystem function. Together with the status 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). Ecosystem health affects the services provided by the environment, and the industries and societies that use the marine environment, either directly (e.g. fishing) or indirectly (e.g. carbon sequestration and climate).

Several initiatives at local, regional and international levels recognise that monitoring key processes as indicators of marine ecosystem health is required to assess, adapt and revise management actions. As a result, there has been considerable discussion in the scientific and management community about the appropriate variables to measure and monitor. They include identifying the processes and components of the marine environment that managers and society value, such as those that support ecosystem services. Examples include ‘key biological areas’ (Eken et al. 2004), ‘key ecological features’ (Dambacher et al. 2012), ‘ecologically or biologically significant marine areas’ (Dunn et al. 2014, Bax et al. 2015) and the ‘key environmental variables of the Global Ocean Observing System’ (see Sustained ocean monitoring). Processes for identifying measurable variables also vary; they include simple selection criteria–based and more complex model-based frameworks (e.g. Hayes et al. 2015).

Within the Australian marine environment, the identification of key ecological features has been central to the marine bioregional planning process (see Box MAR10). Considerable effort has gone into identifying important ecosystem components and processes associated with each key ecological feature, and the biological variables that have high commonality across the features, which could therefore comprise essential variables for measurement and monitoring (Hayes et al. 2015). To date, this process has been completed for 32 of the 53 key ecological features. For pelagic key ecological features, identified indicators include biogeochemical (nutrients) and biological (phytoplankton) indicators at the bottom of the food web, and predators (large pelagic predatory fish and seabirds) at the top of the food web. In shelf systems, identified indicators include those that are habitat forming (macroalgae and coral; see Hayes et al. 2015). Further detail on Australian and global efforts to identify key indicators for measurement and monitoring is provided in Sustained ocean monitoring.

The biophysical and ecological indicators of marine health discussed here were identified in SoE 2011, and, for comparative purposes, we update them here. These include indicators of physically driven processes (water column turbidity and connectivity), productivity (microbes, phytoplankton and zooplankton), food webs (trophic processes), disease and outbreaks, and invasive species.

Overall, biophysical and ecological indicators of marine health within the Australian marine environment are in good condition, although several indicators are highly spatially and temporally variable. The methods used to measure each indicator are also variable. Current monitoring of many indicators is not spatially and temporally comprehensive enough to capture such dynamics in a robust manner. Therefore, assessment at a national scale and determination of trends for these indicators are difficult. Where indicators are highly dynamic (i.e. there is high variability), it is often difficult to distinguish trends from variability (i.e. the signal from the noise). Care must be taken in deriving trends across short timeseries, because these may capture only a portion of a highly variable signal and may not be indicative of longer-term trends (Hobday & Evans 2013, Harrison & Chiodi 2015). In addition, interpreting any observed trends requires identifying and understanding the relevant components of ecosystem structure, which can vary depending on interpretation, and between different areas or systems. Given the limited spatial and temporal extent of most information and data available, state and trends of these processes will be provided more generally for the Australian region rather than for each marine region.

Physical, biogeochemical and biological processes

Water column turbidity and transparency

Australian marine waters are generally low in turbidity and colour, and high in transparency (Shi & Wang 2010). In oceanic and outer continental-shelf waters, the major determinant of turbidity, transparency and colour is the biomass of phytoplankton, whereas, in inshore regions, sediment flows from river systems or land run-off and high tidal flows have the most influence. Observations from the network of IMOS National Reference Stations show low suspended solids across all stations except Darwin (Figure MAR31).

Although spatially and temporally variable overall, the transparency of the water column in open-water environments has significantly increased since 1997, largely associated with improved wastewater treatment, reduced nutrient inputs, and improved management of agricultural practices and associated run-off (see the Coasts report for further detail on inshore, embayment and estuarine regions, and see GBRMPA [2014a] for an assessment of waters associated with the Great Barrier Reef). In regions not greatly affected by these processes, transparency has remained stable (Figure MAR31), with this stability reflected in the generally comparable grade and trend of SoE 2016 to SoE 2011.

Microbial processes and ocean productivity

Marine waters typically contain 10,000–1000,000 microbial (bacteria, archaea and unicellular algae) cells per millilitre, belonging to hundreds to thousands of different species (Fuhrman et al. 1989, Morris et al. 2002). This highly diverse and abundant community has an intimate connection with its environment. Marine microbial assemblages are the first to respond to changes in the chemical and physical properties of the surrounding water. Microbes also shape the marine environment by:

• driving most of the biogeochemical cycles
• supporting phytoplankton and primary productivity
• contributing to the ocean carbon pump (the uptake of carbon by phytoplankton through photosynthesis in the upper ocean and transfer of this carbon to the ocean’s interior)
• sequestering carbon in ‘recalcitrant’ forms (i.e. resistant to decomposition)
• removing a wide range of organics and pollutants (e.g. Follows & Dutkiewicz 2011, Kujawinski 2011).

Understanding of marine microbial communities in Australia’s waters is an emerging field. The high throughput genomics methods that allow assessment of communities at relevant spatial and temporal scales have only been available for the past 4–5 years. Because of the emerging nature of this field, generation of baseline databases of microbial community compositions linked to physical, chemical and higher-level biological parameters in the Australian environment has only just started. Therefore, an assessment of microbial communities is not possible at this time, and it is not clear how the assessment in 2011 was achieved. Once generated, these baselines will provide an in-depth understanding of how the state of the marine environment is reflected in the microbial community structure and allow more definitive assessments in future SoE reports.

Within Australian waters, trends of primary production are variable. As warm waters extend further south, tropical phytoplankton species that are lower in productivity are also moving south (Thompson et al. 2015a). Regions of declining primary productivity include most oceanic waters north of 35°S, especially the North West Shelf (Figure MAR32) and the Great Australian Bight (Thompson et al. 2015a). Conversely, areas of increasing primary productivity have been observed, including the continental shelf off the east coast of Australia, the Coral Sea and the southern Tasman Sea, potentially because of increased eddy activity and southwards extension of EAC eddies in the region (Kelly et al. 2015). Above average rainfall across various parts of northern and north-eastern regions in 2010–15 contributed to localised increases in nutrients, phytoplankton biomass and primary productivity across the region (Figure MAR32). Globally, ocean warming is expected to result in overall decreases in primary production and phytoplankton biomass in pelagic waters, largely because of increasing stratification of oceanic waters and an associated reduction in the supply of nutrients from deep water to surface light-filled waters (Chavez et al. 2011).

Zooplankton biomass (an indicator of secondary productivity), similarly to phytoplankton biomass, is highly dynamic through space and time. No general trends of zooplankton biomass have been recorded from the IMOS National Reference Stations or the Australian Continuous Plankton Recorder Survey (Richardson et al. 2015). It must be noted, however, that observations are from a limited number of coastal stations, with the majority from the south and east of Australia, where primary production was observed to increase in the past 5 years.