Periodic Reporting for period 3 - GEOSTICK (Morphodynamic Stickiness: the influence of physical and biological cohesion in sedimentary systems)
Reporting period: 2020-05-01 to 2021-10-31
Riverine and coastal environments are some of the most sensitive systems to sea-level rise & environmental change. In order to manage these systems, & adapt to future changes, we desperately need to be able to predict how they will alter under various future climate change scenarios. This has direct societal relevance as flood risk is set to double by 2050. GEOSTICK is addressing this need because our predictive models for these environments are not yet robust enough to predict, with confidence, very far into the future. Moreover, we also need to improve how we use our understanding of modern environments in reconstructing paleo-environments, where significant assumptions have been made in the way in which relationships derived from the modern have been applied to the interpretation of ancient rocks. GEOSTICK is addressing the primary shortfall in these predictive models, namely that our present predictions are based on assumptions that these systems are composed of only non-cohesive sands. However, mud is the most common sediment on Earth & many of these systems are actually dominated by biologically-active muds & complex sediment mixtures. We need to therefore find ways to incorporate the effect of sticky mud & sticky biological components into our predictions. Abiotic-biotic interactions \re now known to impact these relationships and GEOSTICK is addressing questions of how much: inclusion of only relatively small (<0.1% by mass) quantities of biological material into sediment mixtures can reduce alluvial bedform size by an order of magnitude.
The overarching aim of this work is to therefore develop and apply new predictive tools for modelling large-scale bio-morphodynamics of coasts, estuaries and riverine systems and directly addresses a set of three critical knowledge gaps:
a) The influence of biotic components in mediating morphodynamics across a range of scales and environments - GEOSTICK is conducting state-of-the-art laboratory flume experiments that have teased out the self-organising balance and interplay between bio-morphodynamic stabilisation (i.e. complexity of substrate) and the erosive hydrodynamic forces (e.g. waves, flows and tides) and test how sensitive and resilient this balance is to changes in boundary conditions.
b) The relative timescales and efficiencies of biotic and abiotic processes within system function-ing and system linkage tipping-points: GEOSTICK is significantly advancing the understanding of the interactive timescales of these processes through a set of ground-breaking laboratory and numerical experiments and we are using this information to identify and test thresholds, and critically any tipping points, in behaviour of the abiotic and biotic component interactions under different change vectors.
c) The geological expression of biologically-mediated morphodynamics: GEOSTICK has explored the scales of preserved sedimentary structures within deposits formed in substrates containing sand, mud and microbiota through a specific set of experiments and has begun to determine, across a range of conditions, how the structures diverge from those established for substrates devoid of such cohesion. This framework is being used to revaluate and examination of classic ancient sequences in Newfoundland and also Mars.
The overarching aim of this work is to therefore develop and apply new predictive tools for modelling large-scale bio-morphodynamics of coasts, estuaries and riverine systems and directly addresses a set of three critical knowledge gaps:
a) The influence of biotic components in mediating morphodynamics across a range of scales and environments - GEOSTICK is conducting state-of-the-art laboratory flume experiments that have teased out the self-organising balance and interplay between bio-morphodynamic stabilisation (i.e. complexity of substrate) and the erosive hydrodynamic forces (e.g. waves, flows and tides) and test how sensitive and resilient this balance is to changes in boundary conditions.
b) The relative timescales and efficiencies of biotic and abiotic processes within system function-ing and system linkage tipping-points: GEOSTICK is significantly advancing the understanding of the interactive timescales of these processes through a set of ground-breaking laboratory and numerical experiments and we are using this information to identify and test thresholds, and critically any tipping points, in behaviour of the abiotic and biotic component interactions under different change vectors.
c) The geological expression of biologically-mediated morphodynamics: GEOSTICK has explored the scales of preserved sedimentary structures within deposits formed in substrates containing sand, mud and microbiota through a specific set of experiments and has begun to determine, across a range of conditions, how the structures diverge from those established for substrates devoid of such cohesion. This framework is being used to revaluate and examination of classic ancient sequences in Newfoundland and also Mars.
Over 650 hours of experimental measurements and observations have been conducted in the Total Environmental Simulator to investigate the formation and evolution of combined-flow (wave + current) bedforms in substrates with varying degrees of cohesion (different clay/sand ratios) addressing WP1 and WP2. Eight different substrates were used under two different flow conditions (wave-dominated, current-dominated) to investigate ripple dynamics and evolution. The preliminary results from data derived from the ultra-sonic range system show a clear reverse relation between the initial clay content and ripple dimension. Figure 1A displays ripple planform geometry at the end of each run of wave-dominated Experiment A. Two-dimensional mature ripples characterised by a continuous and straight ripple crestline were developed in the control experiment with pure sand and in the beds with the initial clay content <12%. Relatively smaller ripples evolved from substrates with higher clay fraction. As shown in Figure 1B, there was an inverse relation between the initial clay fraction and ripple length (λ) and height (η). Moreover, bed roughness (Ks=27.7η2/ λ) decreased with the initial clay fraction increasing. Experiments to study the initiation motion of substrates with varying degrees of cohesion (different cohesive to non-cohesive particle ratios) are in progress. Currently, motion detection algorithms are being developed to determine: 1) incipient motion thresholds, 2) characteristics of the winnowing processes, and 3) threshold for bed collapse (plucking as opposed to single particle erosion). Preliminary investigations into the crucial process of flocculation of complex kaolin clay flocs/aggregates revealed that increased ambient water acidity leads to higher settling velocities but smaller aggregate sizes, suggesting an effect on aggregate density. By testing acidity levels predicted for past and future estuarine conditions, this aspect addresses climate change-associated effects on sediment transport.
The field campaigns have been progressing well. The Humber field work is underway with the aim to address all relevant factors required for experimental, analytical and theoretical aspects and link the laboratory to the modelling. The actual field campaign has been slightly delayed due to COVID19 over the past few months. However, fieldwork in the Amazon, Tocantins, and Parnaiba Rivers and Estuaries in Brazil, Yangstze in China, and the Mekong River in Vietnam have been conducted with samples collected from the different sites to determine the predominant clay minerals in each area and compare to large-scale coastal morphodynamics.
In terms of the numerical modelling components, for the detailed, small scale processes two bio-functions have been considered: 1) the bio-stabilization model considering the effect of the surface biofilm in increasing the bed resistance and 2) the bio-mediated sediment model to compute transport of biofilm-coated sediments, which considers the enhanced bed resistance and changes of bio-flocs dimensions on the sediment transport mechanism. A one-dimensional morphodynamic model for tide-dominated channels transporting non-uniform sand and interacting with the ocean has been implemented with both the bio-models. The model stores the information of the stratigraphy of the deposit and simulations were performed on a scaled real case (Rotterdam Estuary) to (i) validate the model, (ii) analyse the sensitivity of model parameters, (iii) investigate the effect of hydroclimate changes on bio-stabilized sediment for 5 different cases (clean sediment/ logarithmic growth of surface biofilm/ logarithmic growth regulated by seasonality/ logarithmic growth regulated by catastrophic removal of biofilm/ logarithmic growth regulated by seasonality and catastrophic removal due to hydrodynamic forces (tides)), and (iv) investigate the impact of anthropogenic and land use changes mediated by biofilm with respect to grain size distribution for fine and coarse sediment mixtures. The surface biofilm growth model is implemented in Delft3D-FM. Future simulations will involve an initial test on a simplified channel geometry and estuary model, and field scale application to the Wadden Sea.
The work addressing WP6 and the geological record has been particulary fruitful. noxic conditions were characteristic of marine sediments throughout the Precambrian, with infauna evolving during the mid to late Cambrian. How early infauna colonised such hostile sediments is controversial. Thin section analysis and CT scans of samples taken from Bell Island, Newfoundland, were examined to study the distribution of and changes in the preserved species of trace fossils (fossil burrows) in response to the presence of Precambrian-like conditions and matgrounds preserved in the lithology. Bell Island’s trace fossils imply that opportunistic animals with simple, near surface but densely packed burrows were much more successful in Precambrian conditions (Fig. 6). Experimental work (see WP2) indicates that opportunistic, deposit feeding animals, are less impacted by anoxia, producing extensive burrows under both oxygenated and anoxic conditions. Unlike the Bell Island trace makers, these animals produce relatively deep burrows. However, more specialised animals do alter their burrow morphologies in response to anoxia producing simple near-surface structures. These results indicate that early infauna used a mixture of the densely packed opportunistic feeding behaviours and more specialised, near-surface burrow structures.
The field campaigns have been progressing well. The Humber field work is underway with the aim to address all relevant factors required for experimental, analytical and theoretical aspects and link the laboratory to the modelling. The actual field campaign has been slightly delayed due to COVID19 over the past few months. However, fieldwork in the Amazon, Tocantins, and Parnaiba Rivers and Estuaries in Brazil, Yangstze in China, and the Mekong River in Vietnam have been conducted with samples collected from the different sites to determine the predominant clay minerals in each area and compare to large-scale coastal morphodynamics.
In terms of the numerical modelling components, for the detailed, small scale processes two bio-functions have been considered: 1) the bio-stabilization model considering the effect of the surface biofilm in increasing the bed resistance and 2) the bio-mediated sediment model to compute transport of biofilm-coated sediments, which considers the enhanced bed resistance and changes of bio-flocs dimensions on the sediment transport mechanism. A one-dimensional morphodynamic model for tide-dominated channels transporting non-uniform sand and interacting with the ocean has been implemented with both the bio-models. The model stores the information of the stratigraphy of the deposit and simulations were performed on a scaled real case (Rotterdam Estuary) to (i) validate the model, (ii) analyse the sensitivity of model parameters, (iii) investigate the effect of hydroclimate changes on bio-stabilized sediment for 5 different cases (clean sediment/ logarithmic growth of surface biofilm/ logarithmic growth regulated by seasonality/ logarithmic growth regulated by catastrophic removal of biofilm/ logarithmic growth regulated by seasonality and catastrophic removal due to hydrodynamic forces (tides)), and (iv) investigate the impact of anthropogenic and land use changes mediated by biofilm with respect to grain size distribution for fine and coarse sediment mixtures. The surface biofilm growth model is implemented in Delft3D-FM. Future simulations will involve an initial test on a simplified channel geometry and estuary model, and field scale application to the Wadden Sea.
The work addressing WP6 and the geological record has been particulary fruitful. noxic conditions were characteristic of marine sediments throughout the Precambrian, with infauna evolving during the mid to late Cambrian. How early infauna colonised such hostile sediments is controversial. Thin section analysis and CT scans of samples taken from Bell Island, Newfoundland, were examined to study the distribution of and changes in the preserved species of trace fossils (fossil burrows) in response to the presence of Precambrian-like conditions and matgrounds preserved in the lithology. Bell Island’s trace fossils imply that opportunistic animals with simple, near surface but densely packed burrows were much more successful in Precambrian conditions (Fig. 6). Experimental work (see WP2) indicates that opportunistic, deposit feeding animals, are less impacted by anoxia, producing extensive burrows under both oxygenated and anoxic conditions. Unlike the Bell Island trace makers, these animals produce relatively deep burrows. However, more specialised animals do alter their burrow morphologies in response to anoxia producing simple near-surface structures. These results indicate that early infauna used a mixture of the densely packed opportunistic feeding behaviours and more specialised, near-surface burrow structures.
Progress across the 6 work packages has been to plan with little variation or delays. The field campaigns have recently been impacted by COVID19, but the period prior to this have gone to plan. Other delays have centred on the WP2 experiments and the tempreture control installation, but a plan is now in place for this and results are expected from these experiments by the end of 2020. It is thus anticipated that all the planned work will be completed as per the original proposals.
Opportunities have also been exploited through the programme that go beyond some of the plans in the original proposals, following avenues of interesting research. Research has been conducted that addresses the knowledge gap on relative timescales and efficiencies of biotic and abiotic processes within system functioning and system linkage tipping-points with a specific focus on climate change (past and future). It adds a chemical dimension, which goes beyond the initial proposal. It covers (1) the link between sediment biochemical profiles (EPS chemistry) and sediment stickiness, and (2) how changes to the chemically-mediated interactions within biofilms and between biofilms & grazers affect sediment stability today and under climate change scenarios. For (1), initial test samples of Humber sediment revealed a promising diversity of fatty acids and enabled the development of an extraction & analytical protocol (similar protocol for amino acids in progress) for samples collected during future field campaigns, where sediment cohesion will also be determined in situ. For the most common biomolecules an investigation of the physical-chemical basis of biomolecules sticking to sediment particles by means of computational models and experiments on chemical binding will be the focus of future work. For aspect (2), available literature on autoinducers, chemicals that mediate environmental biofilm bacteria-bacteria/ bacteria-microalgae interactions, was reviewed and synthesised with related physico-chemical data, which revealed that these chemicals are highly pH dependent and likely affected by temperature changes, hence potentially affected by climate change. N-Acetyl homoserine lactones, known to be required for growth, EPS production and reproduction in sediment-associated biofilms, are more stable in lower pH conditions. Laboratory experiments are planned to assess whether future/past climate conditions have a de-/stabilising effect on the functionality of biofilms to stabilise sediments. These aspects will add significantly to WP2 - WP4 by addressing the underlying mechanism how biotic-abiotic interactions cause stickiness and assesses potential impacts of climate change, an important component to include for the investigation across timescales and modelling future developments. Finally, a new and topical angle will be provided by linking plastic pollution and sediment stickiness. A new set of experiments will investigate the interactions between microplastics, sediment and biota and assess how biostabilisation of sediment surfaces influences the transport and fate of microplastic particles.
Opportunities have also been exploited through the programme that go beyond some of the plans in the original proposals, following avenues of interesting research. Research has been conducted that addresses the knowledge gap on relative timescales and efficiencies of biotic and abiotic processes within system functioning and system linkage tipping-points with a specific focus on climate change (past and future). It adds a chemical dimension, which goes beyond the initial proposal. It covers (1) the link between sediment biochemical profiles (EPS chemistry) and sediment stickiness, and (2) how changes to the chemically-mediated interactions within biofilms and between biofilms & grazers affect sediment stability today and under climate change scenarios. For (1), initial test samples of Humber sediment revealed a promising diversity of fatty acids and enabled the development of an extraction & analytical protocol (similar protocol for amino acids in progress) for samples collected during future field campaigns, where sediment cohesion will also be determined in situ. For the most common biomolecules an investigation of the physical-chemical basis of biomolecules sticking to sediment particles by means of computational models and experiments on chemical binding will be the focus of future work. For aspect (2), available literature on autoinducers, chemicals that mediate environmental biofilm bacteria-bacteria/ bacteria-microalgae interactions, was reviewed and synthesised with related physico-chemical data, which revealed that these chemicals are highly pH dependent and likely affected by temperature changes, hence potentially affected by climate change. N-Acetyl homoserine lactones, known to be required for growth, EPS production and reproduction in sediment-associated biofilms, are more stable in lower pH conditions. Laboratory experiments are planned to assess whether future/past climate conditions have a de-/stabilising effect on the functionality of biofilms to stabilise sediments. These aspects will add significantly to WP2 - WP4 by addressing the underlying mechanism how biotic-abiotic interactions cause stickiness and assesses potential impacts of climate change, an important component to include for the investigation across timescales and modelling future developments. Finally, a new and topical angle will be provided by linking plastic pollution and sediment stickiness. A new set of experiments will investigate the interactions between microplastics, sediment and biota and assess how biostabilisation of sediment surfaces influences the transport and fate of microplastic particles.