Open access peer-reviewed chapter

The Physics-Biology Links in Suspended and Settled Estuarine Mud Dynamics: A Review

Written By

Eric Wolanski and Michael Elliott

Submitted: 29 December 2023 Reviewed: 01 March 2024 Published: 04 July 2024

DOI: 10.5772/intechopen.1005423

From the Edited Volume

Sediment Transport Research - Further Recent Advances

Andrew J. Manning

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Abstract

In marine, coastal and estuarine environments, it is not possible to understand the ecological processes unless there is a very good understanding of the physical forcing factors. In turn, once the physics of an area creates the conditions for colonisation by the biota, then, very often, the biota modifies the physical and biogeochemical processes. This review details the physical processes involved both in the substratum and the water column, especially in muddy sedimentary systems typical of estuaries and coastal areas. Using recent studies to show that the physical and biological structure and processes work in tandem to create the water column and sedimentary features, the analysis shows that the physics creates the conditions both for chemical mediation and for biological colonisation. The responses on and by the biota include both the micro- and macroorganisms that influence flocculation, floc creation and disintegration, especially through the production of extracellular mucous substances, bioerosion and biostabilisation. Colonisation is firstly by microorganisms and then by macroorganisms. These organisms then create feedback loops where they modify the structure of both the flocs and the bed sediment. It is emphasised that these aspects need to be incorporated into the engineering models of fine sediment dynamics of estuarine and coastal waters, in order to increase their reliability.

Keywords

  • erosion
  • settling
  • flocculation
  • bioconsolidation
  • bioerosion
  • feedback loops
  • modelling

1. Introduction

Much of the scientific and engineering literature about the physical aspects of cohesive sediment (mud) dynamics comes from laboratory experiments, whereas the biological information comes from laboratory, field and field mescosm studies (e.g., [1]). Clay particles have a diameter <4 μm, whereas silt particles are 4–63 μm, and silt and clay together are usually termed ‘mud’ [2]. The silt particles have microbial coatings, whereas clay particles have electrostatic charged surfaces, and both types adhere to each other to form flocs in the presence of salt in the water. Such flocs have a diameter of typically 50–1000 μm, and they contain thousands of mud particles. The clay crystallite has positive ions on the face surfaces and negative charges in the interior, but a broken bond at the edges. The formation of the flocs created by clays, in the absence of biology, is due to electric attraction between the dissolved salt ions Na+ in salt water and the negative charges of the clay particles at the edges [3]. The microbial coating on the silt particles, and to a lesser extent sand grains (>63 μm), creates adhesion between particles which varies with salinity and pH of the water column [4].

Although originally based on the physics indicated by Stoke’s Law, more accurately based on laboratory studies of the erosion and settling of mud, engineers have derived formulae for the erosion rate E and the settling rate D [5].

E={0, ifu<ucA(u/uc1)n, ifu>uc}E1
D={SSCwf(1u/ud)2, ifu<ud;0, ifu>ud}E2

In these equations, SSC is the suspended solids concentration, wf is the settling velocity of the suspended sediment, u is the water speed, uc and ud are threshold velocities for respectively entrainment and deposition, A is an erosion parameter (that is generally assumed to have a fixed value for a given mud at a given site) and n is a constant (2 < n < 4).

However, when the various parameters and constants in the above equations are derived from laboratory experiments, these equations are inaccurate for field applications [6]. The reason for that is that biological materials and processes and organisms play a dominant role in fine sediment dynamics. This is described and explained here for (a) settling, (b) consolidation, and (c) erosion.

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2. The influence of the biological materials in mud dynamics

2.1 Settling

The pioneer laboratory studies [7, 8, 9] showed that wf varies with SSC and that there are two different ranges: firstly, an enhanced settling range whereby for SSC values typically <1 g L−1, where wf increases with increasing SSC values. Secondly, there is a hindered settling range whereby for larger values of SSC (typically >5 g L−1), wf decreases with increasing SSC values. The common assumption was that, in the enhanced settling range, the floc size (and hence also the settling velocity if the floc density remains constant) increases with increasing SSC values and that in the longer settling range, the flocs hinder their descent by interfering with each other.

The commercialization of optical backscatter instruments to measure SSC greatly advanced the knowledge of suspended mud particle dynamics in the field as it enabled wf to be measured from the sequential vertical profile of the suspended particle concentration around slack tide (when the turbulence is the weakest in the tidal cycle); this is derived using a string of optical backscatter profiles or frequent measurements of the vertical profile using a CTD equipped with an optical backscatter. These field studies indicated that the settling velocity derived from laboratory studies differs by up to an order of magnitude from that measured in the field. The enhanced settling range is shown in Figure 1.

Figure 1.

Dependence of the settling velocity wf of the suspended sediment on the suspended sediment concentration (SSC) in the enhanced settling range from (1) laboratory experiments with mud from the Elbe, Weser and Severn estuaries and (+) from Hinchinbrook Channel and (2) in the field in Hinchinbrook Channel and Muddy Creek, tropical Australia. The value of wf in the laboratory is comparable for all the sampled estuaries, and it is about an order of magnitude smaller than that in the field. Modified from [10].

The difference by an order of magnitude of the floc settling velocity in nature and in laboratory experiments is the result of the influence of biological interactions. Firstly, biology-generated flocculation is very rapid (Figure 2). Secondly, biology-derived flocculation increases the size of the flocs by orders of magnitude from that due to salt-induced flocculation and is determined not by fractal properties (such as prevails for snowflakes) but instead by the biological materials on the surface and inside the flocs (Figure 3). As shown in Figure 3, the mucus has produced a complex shape and size of the flocs.

Figure 2.

Microphotographs of suspended fine sediment in the muddy La Sa Fua River in (a) freshwater about to enter Fouha Bay in Guam, (b) mixed with 17 ppt salinity Fouha Bay water after (b) 5 min, (c) 10 min and (d) 30 min. The width of the microphotographs is 1000 μm.

Figure 3.

Microphotographs of typical flocs in muddy estuaries and coastal waters in Papua New Guinea and tropical Australia. The width of the microphotographs varies between 500 and 1000 μm.

Each floc is a matrix (mesh-like structure) of inorganic and organic matter, forming a maze of low-density zones and impervious zones. The settling floc displaces water, some of which flows around the floc and some through the floc [1]. The extreme situation of biological control of the settling occurs for large sticky mucus sheets with a few attached particles of mud that act as a ballast. This makes the mucus sheet form an inverse parachute dragged downward by the settling floc [11].

In nature, as opposed to laboratory experiments, the estuarine flocs appear as marine snow flocs of fine (silt and clay) particles. The particles are bound together with a sticky mucus membrane called EPS and TEP (extra-cellular polymeric substances and transparent exopolymer particles from bacteria and diatoms). Hence, the floc becomes a complex mixture of microbial coatings, absorbed and adsorbed organic matter, silt and clay particles, dead and live plankton and macroscopic aggregates of biological origin [1, 12]. The floc structure is fundamentally controlled by the mucus (mucopolysaccharides/glycosaminoglycans) [13].

The formation of larger and faster sinking flocs is facilitated by the fresh TEP, which is highly sticky and traps small flocs that small-scale turbulence brings in contact. In a temperate climate, the smallest amount of fresh TEP and the smallest floc size occur in winter when the biological activity is the smallest [14]. Small mud flocs grow into large muddy marine snow flocs by using the mucus to stick on the clay and silt particles and the dead organic matter [15, 16, 17, 18, 19, 20, 21]. In some cases, clay and silt particles are segregated in small sub-units held together by mucus. Fine sediment flocs can reach as large as 2 cm in length when they aggregate over dead chain-forming diatoms [22]. The porosity of such flocs is high. In turbid waters (SSC > 500 mg l−1), the flocs are smaller, because of the lack of light for photosynthesis.

As the small flocs cluster together with increasing turbulence, the growing aggregate is more porous and its strength reduced. Consequently, these large but weak aggregates are broken by a high shear rate once the turbulent kinetic energy dissipation rate exceeds a threshold value of the order of 10−6 W kg−1 [23, 24]. Thus, the floc size varies within a tidal cycle because the turbulence also varies within that cycle [25]. At the same time, the biological processes, materials and organisms constantly change the flocs in time [1]. The influence of organisms is dictated by their biological traits (their mobility, mode of feeding and position in the water column). For example, the zooplankton feed on the flocs and on the mucus (Figure 4a and b); also, they move through the floc while the mud sticks on their bodies, thus changing the shape of the flocs (Figure 4c); also, faecal pellets produced by the zooplankton are created by aggregating small flocs (Figure 4d); the plankton live in the high-mucus, low-density/porous area of the muddy marine snow floc that it disturbs (Figure 4e), and the plankton change the shape and density of the floc by being ‘glued’ to it (Figure 4f). The biological materials are a fundamental building block of muddy marine snow. These biological processes then influence the size and shape of the flocs, thereby affecting the way in which the flocs are influenced by the physical processes, a de facto feedback loop. In essence, the physical and microbiological processes create the flocs and then the macrobiology (the organism behaviour) modifies the flocs which in turn creates a further change by physical processes. This gives a physical-biological-physical loop. Secondly, as indicated above, are the interactions with the physical processes – the turbulence affects the floc size because, at small turbulence intensity, it helps small flocs collide with each other and aggregate to form larger flocs, and, at high levels of turbulence (e.g., during peak tidal currents or under wave action), it breaks up the larger flocs into smaller flocs [25].

Figure 4.

Video clips available at https://intech-files.s3.amazonaws.com/a043Y00000yGSwYQAW/a093Y00001h6OeqQAE/Videos%20%28Full%20Chapter%29-The%20physics-biology%20links%20in%20fine%20sediment%20dynamic%20%282024-04-23%2015%3A48%3A53%29.zip. (a) The mucus enveloping small sediment particles attracts a copepod that feeds on it. (b) A copepod feeding on a muddy marine snow floc. (c) A plankton moving through a mud floc with mud sticking on its body and preventing it from escaping. (d) The process of pelletisation. (e) A plankton immersed in a highly porous, muddy marine snow floc comprising clay, silt particles and TEP. (f) A plankton stuck in a sticky floc and making it in increase in size by more mud sticking on it. (g) Consolidation processes of the highly organic Lake Apopka mud, Florida. The view shows the sediment both above and below the bed. Flocs above the bed are settling down. The left arrow points to a growing micro-channel. Water moves upwards in the micro-channel and rolls flocs upwards along the walls of the micro-channel to keep it open. The right arrow points to a channel that is getting blocked by flocs settling in its opening and plugging it. (h–j) settling muddy marine snow flocs stick to the tentacle-like cirri of a Pyrgomatid barnacle and smother it as the barnacle is unable to dislodge the sticky flocs and sedimentation continues. (a) and (b) are adapted from [26].

The microbial loop is a central process in using and recycling nutrients in the water column [27], and its efficiency relies on the amount of surface available over which it occurs; this is particularly important in the turbidity maximum areas of estuaries [28]. The flocs may be formed from organic detritus as predominantly carbon, but with increasing bacterial colonisation, the nitrogen component increases, that is, with age, there is often a decrease in the C/N ratio. In turn, this increases the nutritional value of the flocs for planktonic and macrobenthic suspension feeding organisms. Given the increasing surface area:volume ratio with decreasing size of particle, smaller particles have a large surface area on which the bacterial film can form.

The density of the organic-rich flocs varies from floc to floc [21, 29, 30]. For instance, faecal pellets are formed by suspension-feeding benthic bivalves and are much denser and have a faster settling velocity than other biology-rich flocs, whereas the looser pseudo-faeces produced are mucus-rich and they add to the floc material. Further, their rate of production is not constant; for SPM < 300 mg l−1, the filtration rate by bivalves increases with increasing SPM, but it decreases for SPM > 300 mg l−1. Also, macro-flocs aggregated by the mucus (EPS and TEP) appear to have the lowest density, then likely the smallest settling velocity. Further, zooplankton break up flocs by feeding on them and thus decrease the floc settling velocity, while other plankton break flocs by moving through them while being glued to them by the mucus (Figure 4af).

While physical and physico-chemical processes can create the sedimentary systems, both on the bed and in the water column, it is then that biological processes modify those physical processes with feedback loops [1]. Previously, engineers neglected these interactions—for example, they applied the fractal theory to mud particle flocs to parameterise their shape and size, assuming thus that mud flocs are similar to snowflakes and that the biology can be ignored (e.g., [31]). However, from Figures 2, 3 and 4af, it is clear that there is little in natural estuaries and coastal waters that visually resembles the ‘fractal flocs’ derived from theoretical or laboratory models with no biology. That the biology has a dominant effect on the settling velocity wf is evidenced by the failure of models to predict wf from flocculation models and fractal theory that ignore the biology. The common observation from field studies is that the floc size varies during the tidal cycle [9, 32].

Clearly, wf cannot be measured in the laboratory and from models where the biology is neglected. There is a difference by a factor of 5–10 between the observed settling velocity of mud flocs with and without the biology (Figure 1). For all these biological and physical reasons, as indicated above, the settling velocity of individual mud flocs at a given site also varies greatly during a tidal cycle [33]. In the hindered settling range, the settling of flocs strongly depends on the density, hence on the biology as biological-rich flocs have a much lower density than inorganic flocs. At SSC > 5 g L−1, the settling flocs align themselves one behind the other, each floc settling in the lee of the preceding floc (Figure 5; [34]). Water moves upwards in micro-channels. In the presence of turbulence, settling is locally stopped by the turbulence moving a floc sideways in the micro-channel and blocking it.

Figure 5.

Settling of high-density mud flocs for SSC > 5 g L−1. Adapted from [1].

2.2 Consolidation

The settled mud is initially water-rich as the flocs are very porous. It is thus readily erodible. It slowly consolidates by expelling water through micro-channels. This process is very slow; typically, it takes 3 weeks to 3 months per m for organic-poor mud. For organic-rich mud, it can take up to 20 years [35] because inorganic mud, i.e., the mineral particles, is heavier and therefore it expels water faster sideway towards the micro-channels than organic mud does. Dewatering occurs when the water moves upwards through micro-channels (Figure 6). While doing so, it rolls mud flocs upwards along the walls of the micro-channel to finally expel them, thus widening the micro-channels and accelerating the dewatering (Figure 4g). Occasionally, a micro-channel can get plugged on top by mud flocs in the overlying water column settling in the opening of the micro-channel (Figure 4g).

Figure 6.

Photograph of a dewatering micro-channel in Lake Apopka mud. The mud is consolidating by expelling water sideway from the flocs, and this water flows upwards in the micro-channel.

Mud deposition at tidal frequencies commonly forms laminae several cm thick, therefore creating strata (laminae) (Figure 7). Each lamina was deposited in a discrete hydrodynamic event. Each lamina has a different density varying between 1.4 and 2.1 g cm−3 [36]. Older (deeper) laminae can have a smaller density than overlying laminae, because a new lamina settled on top of another one can block its dewatering micro-channels and hence prevent consolidation.

Figure 7.

(a) Photograph of muddy laminae on the banks of the Ord estuary, Australia. (b) Vertical profile of density as a function of depth through a sequence of muddy laminae in the Scheldt estuary, Belgium-the Netherlands, adapted from [36].

2.3 Erosion

Once the particles have settled, the sediment created is subject to physical, chemical and biological forces and interactions (Figure 8). Microorganisms continue to coat the particles and lead to biogeochemical processes, while macroorganisms will colonise the sediments according to the environmental tolerances and biological traits of the organisms [37, 38]. Biological processes by those macroorganisms such as bioturbation, biodeposition and bioerosion will dictate the nature of the sediments; bioturbation (the process of burrowing and sediment turnover by organisms) will aerate cohesive sediments and therefore change the chemical regime. Cohesive sediments with a low porosity and poor permeability will become anoxic, as shown by the position of the redox potential discontinuity [1, 12]. The erosion rate is greatly affected by the biological activity in the bottom mud. The bed can be destabilised or stabilised, according to the specific biological activity although wider climatic and ambient conditions will also influence these characteristics [12, 39, 40].

Figure 8.

Physical, chemical and biological processes in cohesive sediments. Adapted from [12].

2.3.1 Destabilisation by bioturbation

At a microorganism level, diatoms produce oxygen that can form an air bubble in the sediment. The bubble loosens and even dislodge the sediment. This increases the erosion rate [41]. At a microorganism level, burrowing animals disturb the sediment to a depth of typically ~1 m for mangrove crabs, down to ~ a few mm for meiofauna; erosion is increased by the feeding behaviours of large bivalves (Figure 9; [39, 40, 43, 44, 45]). The sediment is deposited at the surface from where it is easily eroded [21]. The small bioturbating macrofauna are apparently the most efficient organisms to erode a highly muddy substratum [46]. Biological processes may initiate the formation of tidal creeks in the case of the crab Chasmagnathus granulatus digging burrows. A depression ring results, which grows and links with other rings; in turn, this directs the tidal flows that excavate a tidal creek [47, 48].

Figure 9.

(a) A 10 cm deep burrow structure produced by H. diversicolor as revealed by computer-aided tomography, adapted from [42] (b) A 1.2 m deep mangrove mud crab burrow. Adapted from [1].

2.3.2 Stabilisation by filtering the mud and armouring the bed

Conversely, the biological processes and organisms can stabilise the mud [21]. Algae mats and biofilms armour the surface of mud banks and protect the sediment from erosion (Figure 10a; [30, 49, 50]). Benthic diatoms biostabilise the mud surface [51, 52].

Figure 10.

(a) A biofilm on a tropical mud flat armouring the underlying mud flat. Source: Norman Duke. Adapted from [1]. (b) A mussel bed armouring the mud. Source: Wadden Sea National Park of Lower Saxony. (c) The leather mudweed Avrainvillea amadelpha trapping mud in Maunalua Bay, Hawaii. (d) The dense vegetation of a Rhizophora mangrove forest. (e) The dense salt marsh vegetation along a tidal creek. Source: Steve Hillebrand.

Especially as the result of mucopolysaccharide production. However, this process is reversed when the amphipod Corophium volutar feeds on the benthic diatoms that bind the sediment particles; in turn, this process can be controlled by birds feeding on this amphipod. Tube worms such as Terebellids or Sabellids whose tube protrude above the sediment surface also affect the boundary layer currents and may reduce erosion [12]. Fauna living on the bottom also trap the mud flocs because they are sticky. For instance, barnacles trap the mud flocs as they stick on their tentacle-like cirri that they try to dislodge, a process that is increasingly less successful with increased sedimentation rate (Figure 4hj; [19]). In addition to producing faecal pellets and pseudofaeces, oyster and mussel beds armour the bed, thus preventing erosion (Figure 10b; [53, 54, 55]). The leather mudweed Avrainvillea amadelpha, a marine invader in Maunalua Bay, Hawaii, traps 0.2 kg of mud /m2 below the canopy for years and another 0.2 kg of mud/m2 in the canopy (Figure 10c; [56]).

The mangrove or saltmarsh vegetation fringing the open water of an estuary is a mud trap due to the small-scale recirculating flows behind the vegetation that create flow stagnation, which in turn promotes the settling of mud (Figure 10d-ed-e; [157, 58, 59, 60, 61, 62, 63]). The trapping of mud in this dense vegetation is most efficient; for instance, a mangrove forest that covers only 3.8% of the river drainage area traps 40% of the riverine mud inflow [63, 64]. Mangroves can trap up to 1000 tonnes of mud km−2 yr−1 [63, 64]. Similar processes occur in saltmarsh-fringed estuaries, and especially so when the saltmarsh vegetation is taller than 8 cm [65, 66, 67, 68, 69]. The rates of sedimentation in U.K. saltmarshes average 4.3 mm yr−1 over two years of observation, with large local spatial and temporal fluctuations [70, 71]. A similar high sedimentation rate is found in U.S. saltmarshes [72].

Also, at the macro-scale, biology also helps mitigate bank erosion, for which no reliable engineering formulae are available. Mass slippage often occurs at low water after a river flood when the soil is saturated and its weight is increased by the groundwater [73]. In macro- and hyper-tidal estuaries, the banks experience a frequent transition between stability at high tide and instability at low tide, and this also leads to bank slippage [74]. Nevertheless, some estuaries with steep banks remain stable against bank slippage because slippage is hindered by the roots of the trees and plants on the shores that increase the cohesiveness of the soils, by the vegetation covering the banks and protecting them from the swift currents, and by the organics from decaying roots making the soil more cohesive [1, 75, 76, 77, 78, 79]. When the freshwater region of an estuary transitions permanently from fresh to saline, such as in the Mary River, Northern Territory, Australia, its freshwater vegetation is killed, thus removing the protection that the freshwater vegetation provided. This results in swift bank erosion, in the lengthening of the tidal creek in the formerly freshwater floodplains and in the formation of new, bare mud flats that erode and provide new mud to the estuary (Figure 11; [80]). However, in many estuaries, the freshwater vegetation will give way to reedbeds, such as Phragmites australis, and then saltmarsh and seagrass beds with a progression down the estuary and increasing salinity. While reedbeds may create 1.5 high reeds during the growing season, at the end of the growing season, the reeds collapse and are added to the detrital pool of the estuary. The stubble (broken straws) left behind then traps sediment, reduces bed erosion and stabilises the reed-bed area [81].

Figure 11.

An aerial photograph of the dying freshwater vegetation and the resulting bare mud areas following the permanent intrusion of a tidal creek in the formerly freshwater floodplains of the Mary River, Northern Territory, Australia.

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3. Some engineering implications

The long-term sequestration in the mud of persistent organic pollutants, radionuclides and heavy metals on the fine sediment is a serious problem for industrialised countries attempting to clean up their estuaries from legacy pollution that started with industrialisation 100–200 years ago [82, 83]. Those contaminants may be stored in the sediments through diagenetic processes, especially if these sediments are anoxic and consolidated, thereby creating biogeochemical conditions leading to insoluble stored products [27]. Aeration by bioturbation will then change the oxygenated regime and so liberate newly soluble products. Hence, bioturbation is important in slowly cleaning up this polluted mud by allowing ventilation of the mud through animal burrows and increasing the depth of oxidation of the mud [84]. The flushing out of these pollutants depends on the biology through the occurrence of anoxia generated by plankton or algae blooms, the role of bacteria, DOM and the presence of macroalgae and macrophyte roots, all of which generally decrease metal mobility [85, 86, 87, 88]. However, not all these natural processes are beneficial; for instance, the bacterial communities convert mercury to its more toxic methylmercury form [89] and methanogenic and reducing bacteria will produce methane CH4 and the more toxic hydrogen sulphide H2S. Also, some of these processes will prevent permeability and hence oxygenation of the sediments, and so the sediments remain anoxic.

Cholera is still causing morbidity and mortality in many developing countries. Its causative agents are Vibrio cholerae O1 and O139. It is transmitted mainly through water and by eating shrimps and fish that host the bacteria. The zooplankton responding to anthropogenic inputs controls cholera incidence [90]. In addition, the resuspension of fine sediments from polluted tidal flats raises Vibrio cholera concentration in the water, which suggests a Vibrio cholera-coupled mud-pelagic dynamics [91].

Fluid mud impacts the propagation of tides in an estuary by diminishing bottom friction [92, 93, 94]. Its removal by dredging can make the estuary self-deepening, which in turn generates severe environmental and socio-economic problems [95].

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4. Concluding remarks

It is emphasised here that in all estuarine and coastal sedimentary systems, the physical and biological structure and processes work in tandem to create the resulting water column and sedimentary features. The physics then creates the conditions both for chemical mediation and for biological colonisation that occurs in all estuarine and coastal environments worldwide and is dependent on the prevailing temperature, salinity and pH conditions. That colonisation will be firstly by microorganisms and then by macroorganisms. These organisms then always create feedback loops where they modify the structure of both the flocs and the bed sediment. This changes the behaviour of the flocs and the bed sediment features. This should always be incorporated into the engineering models of fine sediment dynamics of estuarine and coastal waters, for those models to become reliable.

Land use in the catchment upstream of estuaries and along the shores of estuaries, land claim in coastal wetlands, pollution, dams/barriers and dredging, among many other causes, have profoundly degraded many estuaries worldwide [96]. There are attempts worldwide in many, if not all, maritime states to restore the ecosystem health of the degraded estuaries [97, 98]. The degradation of estuaries in the developed world started in the 1700s with land claim for agriculture and then continued through the Industrial Revolution of the 1800s with the addition of contaminants from industries. Many of the underlying causes for degradation are due to mishandling the mud either at the source (e.g., erosion) or at the sink (deposition). Most commonly, the experience suggests that the solution involves combining the use of plants and animals and acknowledging the role of the microbial populations and the materials that they exude, together with wise engineering, eco-engineering (i.e. nature-based solutions) and geo-engineering measures [1, 99, 100, 101, 102, 103].

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Written By

Eric Wolanski and Michael Elliott

Submitted: 29 December 2023 Reviewed: 01 March 2024 Published: 04 July 2024