Simon P. Neill

Second-generation environmental sequencing unmasks marine metazoan biodiversity

Biodiversity is of crucial importance for ecosystem functioning, sustainability and resilience, but the magnitude and organization of marine diversity at a range of spatial and taxonomic scales are undefined. In this paper, we use second-generation sequencing to unmask putatively diverse marine metazoan biodiversity in a Scottish temperate benthic ecosystem. We show that remarkable differences in diversity occurred at microgeographical scales and refute currently accepted ecological and taxonomic paradigms of meiofaunal identity, rank abundance and concomitant understanding of trophic dynamics. Richness estimates from the current benchmarked Operational Clustering of Taxonomic Units from Parallel UltraSequencing analyses are broadly aligned with those derived from morphological assessments. However, the slope of taxon rarefaction curves for many phyla remains incomplete, suggesting that the true alpha diversity is likely to exceed current perceptions. The approaches provide a rapid, objective and cost-effective taxonomic framework for exploring links between ecosystem structure and function of all hitherto intractable, but ecologically important, communities.

Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems

Assessing how natural environmental drivers affect biodiversity underpins our understanding of the relationships between complex biotic and ecological factors in natural ecosystems. Of all ecosystems, anthropogenically important estuaries represent a ‘melting pot’ of environmental stressors, typified by extreme salinity variations and associated biological complexity. Although existing models attempt to predict macroorganismal diversity over estuarine salinity gradients, attempts to model microbial biodiversity are limited for eukaryotes. Although diatoms commonly feature as bioindicator species, additional microbial eukaryotes represent a huge resource for assessing ecosystem health. Of these, meiofaunal communities may represent the optimal compromise between functional diversity that can be assessed using morphology and phenotype–environment interactions as compared with smaller life fractions. Here, using 454 Roche sequencing of the 18S nSSU barcode we investigate which of the local natural drivers are most strongly associated with microbial metazoan and sampled protist diversity across the full salinity gradient of the estuarine ecosystem. In order to investigate potential variation at the ecosystem scale, we compare two geographically proximate estuaries (Thames and Mersey, UK) with contrasting histories of anthropogenic stress. The data show that although community turnover is likely to be predictable, taxa are likely to respond to different environmental drivers and, in particular, hydrodynamics, salinity range and granulometry, according to varied life-history characteristics. At the ecosystem level, communities exhibited patterns of estuary-specific similarity within different salinity range habitats, highlighting the environmental sequencing biomonitoring potential of meiofauna, dispersal effects or both.

Identification of genetically and oceanographically distinct blooms of jellyfish

Reports of nuisance jellyfish blooms have increased worldwide during the last half-century, but the possible causes remain unclear. A persistent difficulty lies in identifying whether blooms occur owing to local or regional processes. This issue can be resolved, in part, by establishing the geographical scales of connectivity among locations, which may be addressed using genetic analyses and oceanographic modelling. We used landscape genetics and Lagrangian modelling of oceanographic dispersal to explore patterns of connectivity in the scyphozoan jellyfish Rhizostoma octopus, which occurs en masse at locations in the Irish Sea and northeastern Atlantic. We found significant genetic structure distinguishing three populations, with both consistencies and inconsistencies with prevailing physical oceanographic patterns. Our analyses identify locations where blooms occur in apparently geographically isolated populations, locations where blooms may be the source or result of migrants, and a location where blooms do not occur consistently and jellyfish are mostly immigrant. Our interdisciplinary approach thus provides a means to ascertain the geographical origins of jellyfish in outbreaks, which may have wide utility as increased international efforts investigate jellyfish blooms.

A coupled tide-wave model for the NW European shelf seas

Understanding the interaction of tides and waves is essential in many studies, including marine renewable energy, sediment transport, long-term seabed morphodynamics, storm surges and the impacts of climate change. In the present research, a COAWST model of the NW European shelf seas has been developed and applied to a number of physical processes. Although many aspects of wave–current interaction can be investigated by this model, our focus is on the interaction of barotropic tides and waves at shelf scale. While the COWAST model was about five times more computationally expensive than running decoupled ROMS (ocean model) and SWAN (wave model), it provided an integrated modelling system which could incorporate many wave–tide interaction processes, and produce the tide and wave parameters in a unified file system with a convenient post-processing capacity. Some applications of the model such as the effect of tides on quantifying the wave energy resource, which exceeded 10% in parts of the region, and the effect of waves on the calculation of the bottom stress, which was dominant in parts of the North Sea and Scotland, during an energetic wave period are presented, and some challenges are discussed. It was also shown that the model performance in the prediction of the wave parameters can improve by 25% in some places where the wave-tide interaction is significant.

Some numerical aspects of modelling flow around hydraulic structures using incompressible SPH

Here, we apply incompressible smoothed particle hydrodynamics (ISPH) to simulate free-surface flow around hydraulic structures using several classical case studies including dambreak, flow under a submerged gate, and simultaneous operation of a weir and gate. Due to many complexities such as unknown free-surface, rapidly varied flow, trans-critical flow, complicated geometry, and non-hydrostatic pressures, flow fields have traditionally been investigated by experimental methods, while powerful computational techniques such as ISPH are gradually being adopted for such studies. This research provides further details about the application of ISPH in this area. Two projection methods to enforce incompressibility of SPH were compared from mathematical and numerical view points. Further, two pressure formulations for approximating the left-hand-side of the Poisson equation resulted in a similar trend.

Cover: Observing estuarine currents and fronts in the Tay Estuary, Scotland, using an airborne SAR with along track interferonmetry (ATI)

Estuaries are extremely dynamic environments where large and frequent changes in bathymetry and channel locations can occur. Because estuaries are major centres of population and industry, there is an ongoing requirement to monitor and predict changes in the current fields. The tidal range, surface wind speed, atmospheric pressure, fresh water inflow and most importantly the stage of the tidal cycle affect the flow vectors. Existing boat‐based methods are unable to provide measurements of current fields with sufficient spatial and depth coverage for accurate modelling of hydrodynamic processes in estuaries. Remotely sensed data offer more extensive, synoptic, spatial coverage. However, previous studies to map the full details of the current field based on conventional optical and thermal imaging have been limited by insufficient temporal coverage and the lack of identifiable features that can be tracked. Synthetic aperture radar (SAR) imaging with along‐track interferometry (ATI) has the potential to overcome both of these limitations because it can retrieve quantitative measurements of sea surface state parameters and instantaneous surface flow from a single pass over a whole estuary. The preliminary results of ATI observations over the Tay Estuary, Scotland, validated with coincident in situ boat based observations, are presented here.

The Impact of Marine Renewable Energy Extraction on Sediment Dynamics

The extraction of marine energy , through either tidal or wave array operation, will clearly influence the hydrodynamics of a region. Although the influence on tidal currents and wave properties is likely to be very small for most extraction scenarios, the influence on bed shear stress is likely to be greater, because bed shear stress is quadratically related to tidal currents and wave orbital velocities. Further, the transport of sediments is a function of tidal current and wave orbital velocity cubed. Therefore, even small modifications to the flow field through tidal or wave array operation could lead to significant impacts on regional sediment dynamics. In this chapter, after providing an introduction to sediment dynamics in the marine environment, we explore the impact of tidal energy devices/arrays on regional sediment dynamics, with a particular emphasis on offshore sand banks —important sedimentary systems that protect our coastlines from the full impact of storm waves. Next, we discuss how generating electricity from waves could influence nearshore sediment processes, such as beach erosion or replenishment, over a range of timescales. To assess the magnitude of impacts on sedimentary systems, it is essential to consider the scale of the impact in relation to the range of natural variability. We suggest ways in which impacts can be assessed using numerical models, tuned by in situ measurements, that quantify variability over a range of timescales from individual storm events and lunar cycles to seasonal and interannual periods. We also discuss the sedimentary processes associated with tidal lagoons , such as scour and sediment drift outside a lagoon and sediment accretion inside a lagoon.

In Situ and Remote Methods for Resource Characterization

Although wave and tidal energy resources can be either simulated or estimated from various products (e.g. tidal atlases), the resource can only truly be characterized by direct observation. Whilst observational campaigns are costly and logistically challenging, such direct measurements can accurately quantify the resource at high spatial and temporal resolution, and without the assumptions that are necessary when parameterizing numerical simulations. In addition, observations are essential for validating numerical simulations ( Chapter 8 ), which can then be applied to understand processes over longer timescales or hypothetical scenarios such as sea-level rise or assessing impacts (preconstruction) of large engineering projects, in addition to investigating neighbouring regions of interest that have not been directly observed. In this chapter, we introduce various methods of measuring wave and tidal resources both in situ and remotely. We describe the principal of some of the main instruments used to quantify waves and tides, particularly acoustic Doppler current profilers and directional wave buoys. We also discuss ship-based sampling techniques (e.g. sea bed sediment grabs and water column profiling), and remote-sensing technologies, including X-band and high-frequency radar.

A Progress Report on the Control of the Free Surface in a 3D Navier Stokes Solver for Coastal Applications

This paper reports work in progress on the development of a data assimilation capacity for an existing 3D Navier Stokes solver with application as an ocean model. The project is a collaboration between University of Strathclyde and Imperial College, London with the assistance of Dr. Neill from the University of Wales, Bangor. This paper reports work carried out at Strathclyde University. The 3D NS solver developed by the Imperial team uses finite element methods and adaptive meshing, is non-hydrostatic and includes the free surface. However, proper treatment of the free surface in the adjoint problem is not straightforward. This paper describes a method of controlling the forward solution using either surface elevation or current data by solving an appropriate adjoint problem. This is formulated in a new way using a co-ordinate transformation such that the control problem appears in a fixed domain even though the forward problem has a variable domain due to the presence of the free surface.