DSN Report 3.1.2: Sediment transport processes within coral reef and vegetated coastal ecosystems: a review

As part of one of Australia’s biggest scientific efforts towards minimising the impact of dredging related operations Dredging Science Node researchers have, for the first time, reviewed the current state of knowledge and gaps required to predict sediment transport within coral reef and vegetated coastal ecosystems.

Coral reefs, seagrass meadows and mangrove forests are ecologically-important and prominent features along Australia’s coastline, and considered to be particularly sensitive to dredging-related pressures. The potential for adverse impacts from exposure to suspended sediment plumes is well known; in turbid waters, a higher concentration of suspended sediment reduces light availability for photosynthesis and can clog feeding mechanisms. Indeed, the ecological function of marine biological communities exposed to sediment plumes from dredging or other activity (e.g. river inputs, cyclones, shipping and trawling) can be greatly compromised. As a result, these ecosystems are often prioritised in dredging monitoring and management programs.

These coastal ecosystems contain large and complex bottom roughness (or canopies) on the seafloor that can dramatically influence both near-bed water movement, and in turn, how sediment is transported.  However, modern sediment transport theory and models, including those used to predict the impact of dredging plumes, are still based entirely on the mechanics of how sediment is transported over open (bare) sediment beds.

(Source: Lowe R, Ghisalberti M: Sediment transport processes within coral reef and vegetated coastal ecosystems: a review)

Although many knowledge gaps still remain, the review looked at the existing framework for predicting flows within the canopies present in coastal ecosystems and how this can serve as a foundation for developing new sediment transport models that are applicable to these environments. Specifically it reviewed:

• The traditional approaches and models used to predict near-bed sediment transport in the coastal ocean;
• The unique hydrodynamic interactions of currents and waves with submerged canopies, and why traditional engineering approaches fail
• Existing observations of sediment transport within aquatic vegetation and over coral reefs;
• Measurement techniques for quantifying and monitoring near-bed sediment changes in coastal canopies; and
• Prospects for improving predictions for the fate and transport of natural and dredging-derived sediments in these environments.

(Source: Lowe R, Ghisalberti M: Sediment transport processes within coral reef and vegetated coastal ecosystems: a review)

Based on this review, the following issues were considered important when making predictions of dredging impacts in these environments:

• Detailed habitat maps prior to dredging projects should be used to assess potential biological impacts and the role that habitat type may have on sediment transport and where it deposits.
• Within benthic ecosystems such as coral reefs and seagrasses, sediments are usually biogenic-derived (comprised of calcium carbonate) with physical characteristics that differ substantially from traditional siliciclastic sediments in coastal systems. Suspended sediment monitoring instrumentation may show very different responses to carbonate sediments and instrument calibration should be conducted with in situ water samples obtained on a site-by-site basis.
• At present there are still major knowledge gaps in how the varied bottom roughness of natural coastal ecosystems controls sediment transport rates.
• Due to this large uncertainty in sediment transport rates over benthic (seabed) canopies, model predictions over areas that include coral reefs and aquatic vegetation should be treated with extreme caution.

The report concludes, it is clear that new observations of sediment transport within environments such as coral reefs and seagrass meadows are needed to:

1. provide the missing quantitative insight needed to better understand these processes;
2. incorporate these dynamics into new predictive sediment transport formulations applicable to these environments; and
3. finally embed these dynamics in process-based numerical models that can eventually be applied within predictive models.

Links:

• DSN Report 3.1.2: Lowe R, Ghisalberti M: Sediment transport processes within coral reef and vegetated coastal ecosystems: a review
• All Dredging Science Node Reports can be found at: www.wamsi.org.au/dredging-science-node/dsn-reports

Background:

The Western Australian Marine Science Institution is delivering one of the largest single-issue marine research programs in Australia. It will vastly improve the planning and regulation of major dredging operations in our precious marine environment.

This world-class marine research is enhancing capacity within government and the private sector to predict and manage the environmental impacts of dredging in Western Australia. The outcomes will increase the confidence, timeliness and efficiency of the assessment, approval and regulatory processes associated with dredging projects.

The WAMSI Dredging Science Node is made possible through $9.5 million invested by Woodside, Chevron and BHP as environmental offsets. A further $9.5 million has been co-invested by the WAMSI Joint Venture partners, adding significantly more value to this initial industry investment. The node is also supported through critical data provided by Chevron, Woodside and Rio Tinto Iron Ore.

Dredging Science

Sediment researchers may have cracked a key to early recognition of coral stress by observing mucous build-up in response to dredge related sediment.

The research undertaken as part of the Western Australian Marine Science Institution’s Dredging Science Node found that colonies of the massive stony coral Porites, located off Barrow Island, produced mucous sheets that encompassed the entire colony in response to settling and suspended sediment.

Lead researcher PhD candidate Pia Bessell-Browne from The UWA Oceans Institute and AIMS says it’s the first time scientists have been able to view sediment related stress on coral from a dive in situ.

“This study has examined the production of mucous sheets through time on tagged colonies that were monitored during a large scale dredging project,” Pia explained. We looked at the coral health monitoring photos and noticed the phenomenon of increased mucus production near dredging activity. We also ran experiments with the same species to confirm results at the AIMS Sea Simulator aquarium facility.”

Experimental work undertaken in the National Sea Simulator observed similar patterns of mucus production in Porites fragments after exposure to elevated sediment deposition

A number of hypotheses have been proposed to explain why and how this sheet production occurs, yet at this stage there isn’t enough quantitative data on mucus production and associated potential triggers to confirm whether it is a result of suspended or deposited sediment.

The results suggest that the production of mucus is closely linked with the presence of sediment stressors, where the quantity and characteristics of sediments can affect the physical, chemical, and biological stability of marine ecosystems. A strong relationship between mucus production and distance from dredging was also observed.

“It’s a stress a response,” Pia said. “We still don’t know what the long-term impact is but it is apparent that these corals can produce mucous sheets up to seven times in an 18 month period without suffering substantial mortality.”

The findings suggest that mucous sheet production by massive Porites colonies is an effective indicator of sediment related stress to be considered when monitoring the impacts of suspended sediment on coral populations.

The WAMSI Dredging Science Node is made possible through $9.5 million invested by Woodside, Chevron and BHP as environmental offsets. A further $9.5 million has been co-invested by the WAMSI Joint Venture partners, adding significantly more value to this initial industry investment. The node is also supported through critical data provided by Chevron, Woodside and Rio Tinto Iron Ore.

Dredging Science

The release of data records within confidential reports has given researchers rare access to information that is providing a new insight into the unique reproductive cycles for the remote coral reefs along Western Australia’s (WA’s) coastline.

While the rapid industrial expansion through regions of WA in the last decade has seen an increase in the number of studies of coral reproduction, access to data within confidential reports to industry and government has only now unlocked information relating to tens of thousands of corals and hundreds of species, from over a dozen reefs spanning 20 degrees of latitude.

Project leader Dr James Gilmour from the Australian Institute of Marine Science, along with CSIRO Marine and Atmospheric Researchers found that the results from the Western Australian Marine Science Institution (WAMSI) Dredging Science Node published this month in the journal Peer J carry important management implications.

“Environmental managers aim to minimise human impacts during significant periods of larval production and recruitment on reefs, but doing so requires knowledge of the modes and timing of coral reproduction,” Dr Gilmour said. “From these data we were able to identify broad latitudinal patterns, but many gaps in knowledge remain due to paucity of data, biased sampling, issues with methodology and the profound difficulty in distinguishing coral species.”

Because of WA’s phenomenal diversity of habitats and coral communities, and wide range in reef-level patterns of coral reproduction, the examination of patterns of reproduction has been divided among six regions:

1. Kimberley Oceanic;
2. Kimberley;
3. Pilbara;
4. Ningaloo;
5. Abrolhos and Shark Bay; and
6. Rottnest and southwest WA

Source: Gilmour J, Speed CW, Babcock R. (2016) Coral reproduction in Western Australia. PeerJ 4:e2010 doi.org/10.7717/peerj.2010

Among these regions, the diversity of coral was found to decrease with increasing latitude, with the Houtman Abrolhos Islands having the highest latitude coral reefs in Western Australia.

The study found that mass spawning during autumn occurred on all tropical and sub-tropical reefs. A smaller, multi-specific spawning during spring decreased from approximately one quarter of corals on the Kimberley Oceanic reefs to little participation at Ningaloo.

Within these seasons, spawning was concentrated in March and/or April, and October and/or November, depending on the timing of the full moon. The timing of the full moon was critical to determining the month of spawning within these seasons, and whether spawning was ‘split’ over two consecutive months.

Mixed coral assemblage of spawning and brooding corals (Image: James Gilmour)

Most studies were found to have focused on species of Acropora, which include some of the major corals responsible for building the complexity that supports reef diversity. However, other reefs are dominated by non-Acropora corals, for which far less is known about their reproduction.

Studies conducted by industry and consultants in the Dampier Archipelago highlight the different patterns of reproduction among reefs in WA, according to their contrasting species abundances. For example, functionally important species of massive Porites seemed to spawn through spring to autumn on Kimberley Oceanic reefs and during summer in the Pilbara region.

“Most studies of coral reproduction in WA have been conducted over a few months at several reefs, of which there are few published accounts, leaving large gaps in knowledge,” Dr Gilmour said. “The gaps are significant because the existing data illustrate just how unique the patterns of reproduction displayed by WA coral communities are and the extent to which they vary among habitats and regions.

“Even for reefs and species that are relatively well-studied, the patterns of reproduction are complex,” Dr Gilmour said. “Recent work suggests that within a single site on some northern reefs, colonies within the same species may consistently spawn during different seasons (Gilmour et al. 2016, Rosser 2015), leading to massive genetic differentiation and questions of whether, in a reproductive sense, they are considered the same species. Addressing these issues is again confounded by the morphological and reproductive plasticity for which corals are infamous.”

Related links

Gilmour J, Speed CW, Babcock R. (2016) Coral reproduction in Western Australia. PeerJ 4:e2010 doi.org/10.7717/peerj.2010

Gilmour JP, Underwood JN, Howells EJ, Gates E, Heyward AJ (2016) Biannual Spawning and Temporal Reproductive Isolation in Acropora Corals. PLoS ONE 11(3): e0150916. doi:10.1371/journal.pone.0150916

Rosser, N. L. (2015), Asynchronous spawning in sympatric populations of a hard coral reveals cryptic species and ancient genetic lineages. Mol Ecol, 24: 5006–5019. doi:10.1111/mec.13372

The WAMSI Dredging Science Node is made possible through $9.5 million invested by Woodside, Chevron and BHP as environmental offsets. A further $9.5 million has been co-invested by the WAMSI Joint Venture partners, adding significantly more value to this initial industry investment. The node is also supported through critical data provided by Chevron, Woodside and Rio Tinto Iron Ore.

Dredging Science

Research from the WAMSI Dredging Science Node has provided new insight into how seagrasses in the Pilbara may recover from disturbance events such as dredging.

While some seagrasses can potentially recover from dredging related pressures over a 200 kilometre radius, others require another meadow within five kilometres to survive, or need to be regenerated from a seed bank.

The research, which is important to the ongoing management of the region’s coastal biodiversity, has produced the first real insight into the genetic variability of the area’s seagrass and the level of connectivity among different seagrass populations.

Pilbara seagrass meadows are an important source of food and habitat for the endangered dugong, sea turtles and prawns, the latter of which makes up part of the region’s multi-million dollar commercial fishing industry.

Lead researcher, Edith Cowan University’s Kathryn McMahon, described how several WA Marine Science Institution (WAMSI) projects are revealing more about the genetic diversity and connectivity of Pilbara seagrasses and how this is revealing the possible ways seagrasses may resist or recover from disturbance, insights which are critical to better management of seagrass meadows.

“In one WAMSI project we determined where the seagrass meadows are, how much there is and how it varies seasonally throughout the year” Dr McMahon said. “In a complementary genetics project we examined which species had the higher genetic diversity and therefore a better chance to resist change and recover from dredging pressures.”

Of the 15 species of seagrass found in the Pilbara, the WAMSI team, including researchers from CSIRO, the University of Adelaide and Department of Parks and Wildlife, looked specifically at three of the most common; Halophila ovalis (6 populations), Halodule uninervis (8 populations) and Thalassia hemprichii (3 populations).

“What we found is that Halophila ovalis and Thalassia hemprichii have high genetic diversity in most meadows that we sampled,” Dr McMahon said. “Thalassia showed a high connectivity over distance; the fruit from one meadow can potentially float to a meadow up to 200km away and successfully recruit into that meadow.

“Whereas with Halophila ovalis and Halodule uninervis gene flow is over a much smaller scale. So a meadow which is completely lost could only recover if there was another meadow within about 5kms.

“So from a dredging perspective, if we lose a seagrass meadow, we can give an indication of when or if they are likely to recover within five years based on the WA EPA’s Dredging Guidelines of irreversible loss,” Dr McMahon said.

Seagrasses tend to be found in the coastal zone and grow in soft sand and muddy sediment but some species can also grow on reefs. They are found in more shallow water to a depth of 10 metres, but can be found in clear water down to 50-60 metres. In the Pilbara, seagrass meadows are mostly found in shallower water.

Based on genetic differentiation, two to three management areas were identified. Exmouth Gulf was distinct from Thevenard Island, Rosemary Island and Balla Balla, and Balla Balla was distinct from the island sites.

“Long distance migration was detected but this is likely to be rare based on the genetic differentiation among sites,” Dr McMahon said. “This long distance dispersal was occurring both in a northward direction, against the direction of the dominant oceanographic current, and southwards, with the direction of the dominant current. There was no association of genotypes with habitat. Some meadows appear to be resilient from a genetic perspective, but others not.”

Halophila ovalis genetic connectivity among sites over a local scale in the Exmouth region. This network analysis is stylised on the site map to show the major migration pathways (relative migration rates >0.8). 1=Exmouth Gulf 1, 2=Exmouth Gulf 2, 3=Mangrove Bay, 4=Muiron Is. North, 5=Muiron Is. South.

“As a result, we feel that incorporating analysis of genetic diversity of seagrass meadows (clonal richness, allelic diversity, heterozygosity) into pre-dredging surveys would allow dredging proponents to identify sites, which are more resilient and hence better able to cope with or recover from dredging related pressures, or conversely, less resistant and in need of more stringent management measures,” Dr McMahon said.

A summary of the genetic resilience of seagrass meadows in the Pilbara based on clonal richness, allelic diversity and heterozygosity. The potential to adapt to pressures over generations was based on allelic richness, to recover from declines in a generation was based on heterozygosity and to recover from complete loss using seed banks was based on clonal richness.

The WAMSI research has also found that the diversity of Thalassia hemprichii is higher in the Pilbara than in the Kimberley, which was unexpected.

“The hotspot for seagrass in this region is in the Coral Triangle of Indonesia and since the Kimberley is closer to this hotspot, we expected to find higher diversity there than in the Pilbara.  However, it may be that the massive tides in the Kimberly result in it being more isolated from the rest of the coast.” Dr McMahon said.

FACT FILE:

Seagrasses are clonal, marine flowering plants that form critical habitat in coastal waters. They are found in coastal waters of all continents except Antarctica, where they provide significant ecosystem services including: primary productivity; a food source for critically endangered fauna; habitat for many marine flora and fauna; sediment stabilisation; and carbon storage.

Globally, seagrasses are threatened with 29 per cent of the known areal extent estimated to be lost.  Since 1990 the loss rate is reported to have increased from 0.9% per year to 7% per year, comparable to loss rates reported for mangroves, coral reefs and tropical rainforests.

The WAMSI Dredging Science Node is made possible through $9.5 million invested by Woodside, Chevron and BHP as environmental offsets. A further $9.5 million has been co-invested by the WAMSI Joint Venture partners, adding significantly more value to this initial industry investment. The node is also supported through critical data provided by Chevron, Woodside and Rio Tinto Iron Ore.

Dredging Science

Researchers in the WAMSI Dredging Science Node are developing new automated scientific instruments to measure sediment deposition in the field with prototypes deployed and tested.

Sediment deposition and subsequent smothering of marine habitats such as corals and seagrasses is one of the mechanisms by which dredging can impact on the environment.

This pressure parameter is incorporated into sediment transport models by proponents during the Environmental Impact Assessment (EIA) process to make predictions of the likely extent, severity and duration of their impacts on the environment.

However, according to Dr James Whinney from James Cook University there are no scientific instruments that can actually measure net deposition in the field.

“Measuring net sediment deposition is quite challenging” Dr Whinney said. “When sediment falls out of the water column and deposits on the seafloor, not all of it will stay there with the energy from waves and currents causing some of those sediments to resuspend and be transported elsewhere. This is what we mean by net deposition and is the actual pressure that will be exerted on an organism.

Deposition sensor deployed in laboratory experiments alongside traditional sediment traps and sedpods.

“The most common technique currently used to measure deposition is to use a sediment trap which typically comprise of vertical PVC tubes that are closed at the bottom and open at the top and mounted on a frame on the seafloor. These are generally deployed for months at a time before they are retrieved and the amount and characteristics of the sediment in the tube can be measured.” Dr Whinney said.

“The problem with this is that once sediments have settled in the tube, they get trapped there and can’t be resuspended by wave energy. So while they can accurately tell you the total amount of sediment that settles, they can’t tell you what the net deposition would be after some of this has been resuspended and transported elsewhere. “Another problem is that they can’t tell you how much settles each day. Just averaging the total amount of sediment by the number of days it was deployed is not accurate as on calm days more sediment would settle out of the water column whereas on rough and windy days less would settle.

This is important to know for organisms like corals as they can actively remove sediment that has deposited on them but only up to a point. If the rate of deposition becomes too great, they will not be able to keep up and begin to get buried by that sediment.

To address this problem Dr Whinney and his colleagues have been developing an automated deposition sensor that can measure net deposition as well as provide accurate information of the amount settling each day.

“The deposition sensor we are developing uses optical back scatter allowing readings to be taken every few minutes and uses a perforated plate on top of the sensors to mimic the surface of a coral so that deposition occurring on the instrument is similar to that on a coral.”

“During the development of this sensor it has been tested at AIMS, used in experiments at SEASIM and also deployed off Townsville and on the site of the Wheatstone Project, off Onslow. The data from the sensor is promising, measuring expected levels of sedimentation in the laboratory and gathering interesting data from the field which compares well with wave and turbidity data.”

Calibrating deposition sensor in laboratory by adding known quantity of sediment.

Dr Ray Masini from the Office of the Environmental Protection Authority and the Node Leader – Policy, said developing an instrument that can accurately measure net sediment deposition will be a major step forward and improve confidence during the EIA process.

“While proponents use sediment transport models to make predictions of the amount of sediment deposition that will occur, because we can’t actually measure net sediment deposition in the field, there is no way to verify and refine the sediment deposition rates that were predicted by those models” Dr Masini said. “This reduces confidence for both the Environmental Protection Authority and project proponents in the prediction of impacts during the EIA process.”

“It is also important for scientists conducting experiments to establish thresholds of response to dredging-related pressures.  To accurately define the sediment deposition rates that led to mortality, sub-lethal impact and first observable effect, you have to be able to accurately measure this in the first place.”

“Therefore the development of this deposition sensor will be an important step forward and provide both the Environmental Protection Authority and project proponents a greater level of confidence in the prediction of impacts during the EIA process,” Dr Masini said. “Which is what the Dredging Science Node is designed to do – to increase the confidence, timeliness and efficiency of the assessment, approval and regulatory processes associated with dredging projects.”

The WAMSI Dredging Science Node is made possible through $9.5 million invested by Woodside, Chevron and BHP as environmental offsets. A further $9.5 million has been co-invested by the WAMSI Joint Venture partners, adding significantly more value to this initial industry investment. The node is also supported through critical data provided by Chevron, Woodside and Rio Tinto Iron Ore.

Dredging Science