The Swale Estuary Marine Conservation Zone (MCZ) Monitoring Report 2016

MPA Monitoring Programme Contract Reference: MB0129 Report Number: 8 Version 2 July 2018

Project Title: Marine Protected Areas (MPA) Monitoring Programme

Report No 8. Title: The Swale Estuary MCZ Characterisation Report 2016

Defra Project Code: MB0129

Defra Contract Manager: Carole Kelly

Funded by:

Department for Environment, Food and Rural Affairs (Defra)

Marine Science and Evidence Unit

Marine Directorate

Nobel House

17 Smith Square

London SW1P 3JR

Authorship

Clare Miller

Estuarine and Coastal Monitoring & Assessment Service, Environment Agency [email protected]

Ben Green

Estuarine and Coastal Monitoring & Assessment Service, Environment Agency [email protected]

Acknowledgements

We thank the Chris Cesar from the Environment Agency and Marine Protected Areas Group (MPAG) representatives for reviewing earlier drafts of this report.

Disclaimer: The content of this report does not necessarily reflect the views of Defra, nor is Defra liable for the accuracy of information provided, or responsible for any use of the reports content. Although the data provided in this report have been quality assured, the final products - e.g. habitat maps – may be subject to revision following any further data provision or once they have been used in Statutory Nature Conservation Body (SNCB) advice or assessments.

Environment Agency Document Control Title: The Swale Estuary MCZ Characterisation Report 2016

Submitted to: Marine Protected Areas Group (MPAG) Date submitted: July 2018 Portfolio Lead: Clare Leech Project Manager: Mark Etherton Principal Investigator: Sue Ware MPA Programme Science Lead: Tammy Noble-James and Ross Bullimore Report compiled by: Clare Miller and Ben Green Quality control by: Sue Ware and Silke Kröger Approved by & date: Ross Bullimore 10/08/2018 Version: V2

Version Control History Author Date Comment Version Miller, C & Green, 12/12/2017 Draft submitted for MPAG and external review V1 B. Miller, C & Green, 16/07/2018 Comments from MPAG and external reviewers V2 B. addressed.

Contents Tables ...... iii Figures ...... iv Executive Summary ...... 1 1 Introduction ...... 2 1.1 Site overview ...... 2 1.2 Aims and objectives ...... 3 1.2.1 High-level conservation objectives ...... 3 1.2.2 Definition of favourable condition ...... 6 1.2.3 Report aims and objectives ...... 7 1.2.4 Feature attributes and supporting processes ...... 8 2 Methods ...... 9 2.1 Data sources ...... 9 2.2 Survey design ...... 9 2.3 Data acquisition and processing ...... 11 2.3.1 Seabed sediments ...... 11 2.4 Data preparation and analysis...... 11 2.4.1 Sediment particle size distribution ...... 11 2.4.2 Biological community data preparation ...... 12 2.4.3 Statistical analyses ...... 12 2.4.4 Contaminants sampling ...... 13 3 Results and Interpretation ...... 14 3.1 Site overview ...... 14 3.2 Subtidal sediment BSH: Sediment composition and biological communities .. …………………………………………………………………………………………..15 3.2.1 Subtidal mud ...... 20 3.2.2 Subtidal mixed sediments ...... 21 3.2.3 Subtidal coarse sediment and Subtidal sand ...... 24 3.3 Habitat and Species Features of Conservation Importance (FOCI) ...... 25 3.4 Non-indigenous species (NNS) ...... 25 3.5 Supporting processes ...... 26 3.5.1 Water quality parameters ...... 26 3.5.2 Sediment quality parameters ...... 26

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3.6 Additional monitoring ...... 28 3.6.1 Marine litter ...... 28 4 Discussion ...... 29 4.1 Subtidal sediment BSH: Sediment composition and biological communities ……………………………………………………………………………………...29 4.1.1 Extent and distribution of features ...... 29 4.1.2 Distribution: presence and spatial distribution of biological communites .. …………………………………………………………………………………………..29 4.1.3 Structure: species composition of component communities ...... 30 4.1.4 Structure: presence and abundance of key structural and influential species …………………………………………………………………………………31 4.2 Non-indigenous species (NIS) ...... 31 4.3 Supporting processes ...... 32 4.3.1 Supporting processes: Sediment contaminants ...... 32 5 Recommendations for future monitoring ...... 33 6 References ...... 35 Annex 1. Infauna data truncation protocol...... 38 Annex 2. Seafloor litter monitoring...... 39 Annex 3. Non-indigenous species (NIS)...... 40

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Tables Table 1. The Swale Estuary MCZ site overview, including General Management Approach (GMA) for designated features...... 5 Table 2. Survey elements and outputs aligned with the feature attributes and supporting processes identified at The Swale Estuary MCZ...... 9 Table 3. Number of samples collected in each BSH...... 14 Table 4. Subtidal sediment Broadscale Habitat (BSH) features designated in The Swale Estuary MCZ. Summary of presence recorded by the Selection Assessment Document (SAD) and subsequent surveys (PSA = particle size analysis sample)…15 Table 5. Mean (± standard error) infaunal species abundance, richness, total biomass, infaunal quality index (IQI) and other univariate indices ...... 17 Table 6. A posteriori power analysis of the 2016 MCZ baseline survey data (at 0.5 mm mesh size), identifying the level of statistical power used to detect a 10% or 20% change in selected diversity metrics...... 31

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Figures Figure 1. Location of The Swale Estuary Marine Conservation Zone in the context of Marine Protected Areas and management jurisdictions proximal to the site...... 4 Figure 2. Location of ground truth samples collected at The Swale Estuary MCZ in 2016...... 10 Figure 3. Classification of sediment Broadscale Habitats sampled in the 2016 survey of The Swale Estuary MCZ ...... 14 Figure 4. Broadscale Habitat classifications of PSA samples collected during the 2016 baseline survey, 2012 verification survey and 2015 and 2012 Water Framework Directive surveys of The Swale Estuary MCZ ...... 16 Figure 5. Distribution of sediment fractions at PSA sample locations. Inset box shows sample distribution around Queenborough Harbour in the western Swale...... 18 Figure 6. Example images of biotopes of the ‘A5.3 Subtidal mud’ feature from The Swale Estuary MCZ 2016 survey ...... 19 Figure 7. Example images of the ‘A5.4 Subtidal mixed sediments’ feature from The Swale Estuary MCZ 2016 survey ...... 19 Figure 8. Infaunal Quality Index status of infaunal samples collected during The Swale Estuary MCZ 2016 baseline survey. Inset shows sample distribution around Queenborough Harbour in the western Swale...... 21 Figure 9. Boxplots of Infaunal quality index (IQI) Ecological Quality Ratios (EQR) of BSHs in different areas of The Swale Estuary MCZ in the 2016 Baseline survey. ... 22 Figure 10. Multidimensional scaling (MDS) plot of infaunal communities sampled in the 2016 Swale Estuary MCZ baseline survey, split across sediment Broadscale Habitats and location...... 23 Figure 11. Multidimensional scaling (MDS) plot of infaunal communities (sieved to 1.0 mm and analysed to genus level) sampled in Whitstable Bay during the 2016 Swale Estuary MCZ baseline survey and the 2012 and 2015 WFD grab surveys...... 24 Figure 12. Changes in particle size distribution between 2012 and 2016 of seven stations sampled as ‘A5.1 Subtidal coarse sediment’ or ‘A5.2 Subtidal sand’ in 2012...... 25 Figure 13. Distribution of surficial sediment contaminant samples across The Swale Estuary MCZ, sampled in 2016...... 27 Figure 14. Distribution of plastic fragments greater than 1 mm present in Day Grab samples across the Swale Estuary MCZ in 2016...... 28

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Executive Summary This report is one of a series of Marine Protected Area (MPA) characterisation and monitoring reports delivered to Defra by the Marine Protected Areas Group (MPAG). The purpose of the report series is to provide the necessary information to allow Defra to fulfil its obligations in relation to MPA assessment and reporting, currently in relation to OSPAR, the UK Marine & Coastal Act (2009) and other relevant Directives (e.g., Marine Strategy Framework Directive). This monitoring report is informed by data acquired during a number of dedicated surveys carried out at The Swale Estuary Marine Conservation Zone (MCZ) (between 2012 and 2016) and will form part of the ongoing time series data and evidence for this MPA. The Swale Estuary MCZ is an inshore site located on the North coast of Kent within the ‘Southern North Sea’ Charting Progress 2 (CP2) sea area. The Swale Estuary MCZ comprises of the Swale channel, from the point where it meets the Medway, South of the Isle of Sheppey to Whitstable, and Whitstable Bay, extending off the coast at Whitstable for 4 km. The area of the MCZ is 51 km2. This report provides information on the two Broadscale Habitats (BSHs) observed in this survey; ‘A5.3 Subtidal mud’ and ‘A5.4 Subtidal mixed sediments’. Sediments in the subtidal areas of the site were sampled using a Day grab to provide information on the structure and diversity of the infaunal communities and the particle size distribution (PSA) and contaminant loading of the sediments. The sediment in Whitstable Bay sampled in 2016 was predominantly ‘A5.4 Subtidal mixed sediments’, and in the Swale, ‘A5.3 Subtidal mud’. Although ‘A5.1 Subtidal coarse sediment’ and ‘A5.2 Subtidal sand’ had been identified in previous MCZ verification and Water Framework Directive (WFD) surveys, neither Broadscale Habitat were observed in the 2016 baseline survey. There was a significant spatial difference in ‘A5.4 Subtidal mixed sediment’ communities between the Swale channel and Whitstable Bay, although no temporal change was observed in the community structure of both Broadscale Habitats ‘A5.3 Subtidal mud’ and ‘A5.4 Subtidal mixed sediments’ between 2012 and 2016. Three biotopes characteristic of transitional mud and mixed sediment environments were identified from the infauna data. Both Broadscale Habitats were assessed by the WFD Infaunal Quality Index as being at ‘Good ecological status’. Seven non- indigenous species were present in the site, including Pacific oyster Crassostrea gigas, slipper limpet Crepidula fornicata and American jackknife clam Ensis directus. Future monitoring should consider focusing on areas that could be subject to elevated sediment contaminant concentrations. This would identify temporal and spatial trends in contaminant concentrations and consequential effects on the sediment fauna. A number of recommendations for future assessment and monitoring of designated features within The Swale Estuary MCZ (and other comparable sites) are provided.

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1 Introduction The Swale Estuary Marine Conservation Zone (MCZ) is included in a network of sites, designed to meet conservation objectives under the Marine and Coastal Access Act 2009 and to complete a ‘Blue Belt’ of Marine Protected Areas (MPAs) around the UK coast. These sites will also contribute to an Ecologically Coherent Network of MPAs in the North-East Atlantic agreed under the Oslo Paris (OSPAR) Convention and other international commitments. Under the UK Marine & Coastal Access Act (2009), Defra is required to provide a report to Parliament every six years that includes an assessment of the degree to which the conservation objectives set for MCZs are being achieved. In order to fulfil its obligations, Defra has directed the Statutory Nature Conservation Bodies (SNCBs) to carry out a programme of MPA monitoring. The SNCB responsible for nature conservation inshore (between 0 nm and 12 nm from the coast) is Natural England (NE) and the SNCB responsible for nature conservation offshore (between 12 nm and 200 nm from the coast) is the Joint Nature Conservation Committee (JNCC). Where possible, this monitoring will also inform assessment of the status of the wider UK marine environment; for example, assessment of whether Good Environmental Status (GES) has been achieved, as required under Article 11 of the Marine Strategy Framework Directive (MSFD). This report primarily explores data acquired from the first dedicated monitoring survey of The Swale Estuary MCZ, which will form the initial point in a monitoring time series against which feature (and site) condition can be assessed in the future. The specific aims of the report are discussed in more detail in section 1.2. 1.1 Site overview The Swale Estuary MCZ is an inshore site on the northern coast of Kent (Figure 1). The Swale Estuary MCZ was recommended as a MCZ by the ‘Balanced Seas’ regional stakeholder group project. It is located in the jurisdictional area of the ‘Kent and Essex Inshore Fisheries Conservation Authority’ (IFCA) and falls within the wider ‘Charting Progress 2’ (CP2) area ‘Southern North Sea’. The site is neighboured by ‘The Swale Site of Special Scientific Interest’ (SSSI) and ‘Special Protection Area’ (SPA), ‘Medway Estuary and Marshes’ SSSI and SPA and the wetlands throughout the estuary are also designated under the International Ramsar Convention. The ‘Swale’ Water Framework Directive (WFD) transitional water body and ‘Whitstable Bay’ and ‘Thames Coastal South’ coastal water bodies overlap the Swale Estuary MCZ (Figure 1). Monthly water quality surveys for WFD, Environmental Quality Standards Directive (EQSD) and Urban Waste Water Treatment Directive (UWWTD) are undertaken by the EA in the Whitstable Bay and Swale water bodies as part of both surveillance and operational monitoring programmes. The EQSD surveillance programme operates according to a three-year cycle, with Whitstable Bay monitored for aqueous

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contaminants between April 2016 and March 2017. The Whitstable Bay water body is also monitored monthly at three locations for dissolved inorganic nutrients, chlorophyll concentrations and phytoplankton species composition under WFD and UWWTD programmes. The Swale water body is monitored quarterly for aqueous contaminants under the EQSD operation programme. The MCZ extends from the confluence of the Swale with the Medway estuary towards the end of a shingle spit known as ‘The Street’ in Whitstable Bay, ranging from the intertidal to ~9.4 metres below sea level (chart datum). The site was designated due to the wide range of intertidal and subtidal sediment seabed habitats present. These sediment habitats support a range of species including bristleworms, sand mason worms, amphipods, burrowing anemones and cockles (Balanced Seas, 2011; Defra, 2016). The area is also an important spawning and nursery ground for species such as sea bass (Dicentrarchus labrax) (Colclough et al., 2002) The Swale and Whitstable Bay are important shellfish grounds. Pacific oysters (Crassostrea gigas) are trestle cultured off Seasalter in the eastern Swale, whilst native oysters (Ostrea edulis) are seasonally dredged in Whitstable Bay. There is a small fishery for Manila clam (Ruditapes philippinarum) east of Leysdown, off the Isle of Sheppey (Cefas, 2011). Table 1 lists the BSHs and Features of Conservation Importance (FOCI) that have been reported to be present at the site by previous dedicated site surveys. The features afforded protection in the site designation order are identified and their General Management Approach (GMA) listed.

1.2 Aims and objectives

1.2.1 High-level conservation objectives High-level site-specific conservation objectives serve as benchmarks against which the efficacy of the GMA in achieving the conservation objectives (i.e., maintaining designated features at, or recovering them to, ‘favourable condition’) can be assessed and monitored. As detailed in The Swale Estuary MCZ designation order1, the conservation objectives for the site are that the designated features: a) So far as already in favourable condition, remain in such condition; and b) So far as not already in favourable condition, be brought into such condition, and remain in such condition.

1 http://www.legislation.gov.uk/ukmo/2016/20/contents/created [accessed 19/12/2017]

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It should be noted that the ‘maintain’ GMAs have been applied based on a proxy assessment, as opposed to being based on empirical monitoring evidence (i.e., direct observations). As such, the vulnerability assessment took into account the level of exposure of the features to those pressures to which they are perceived to be sensitive.

Figure 1. Location of The Swale Estuary Marine Conservation Zone in the context of Marine Protected Areas and management jurisdictions proximal to the site.

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Table 1. The Swale Estuary MCZ site overview, including General Management Approach (GMA) for designated features.

Site Details Charting Progress 2 Region2 ‘Southern North Sea’ Spatial Area (km2) 51 km2 Water Depth Range (m) Intertidal to ~9.4 metres below sea level (chart datum) Existing Data & Information Miller, C. and Easter, J. (2016). The Swale Estuary MCZ 2016 Baseline Survey Report. Environment Agency, Bristol, UK. Godsell, N., Fraser, M. and Jones, N. (2013). The Swale MCZ 2012 Habitat Verification Survey Report. Environment Agency, Bristol, UK. 53 pp. Current & Proposed Management Kent & Essex IFCA Cockle fishery flexible permit byelaw3. Measures Features Present (BSH) Designated GMA A1.3 Low energy intertidal rock*  Maintain A2.1 Intertidal coarse sediment*  Maintain A2.2 Intertidal sand and muddy sand*  Maintain A2.4 Intertidal mixed sediments*  Maintain A3.3 Low energy infralittoral rock  N/A A5.1 Subtidal coarse sediment  Maintain A5.2 Subtidal sand  Maintain A5.3 Subtidal mud  Maintain A5.4 Subtidal mixed sediments  Maintain Features Present (Habitat FOCI) Blue mussel beds  N/A Estuarine rocky habitats* ✓ Maintain Peat and clay exposures  N/A Ross Worm (Sabellaria spinlosa) reefs  N/A Sheltered muddy gravels  N/A Subtidal sands and gravels  N/A Features Present (Species FOCI) Native Oyster (Ostrea edulis)**  N/A European Eel (Anguilla anguilla)***  N/A

* The characterisation survey reported here did not extend into the intertidal. ** The characterisation survey was not specifically designed to target species FOCI. *** MCZs are no longer considered to be an appropriate tool for the protection of European eels. They have been identified as habitat generalists for which it is particularly difficult to identify unique nursery or foraging grounds due to their wide distribution across coastal and freshwater zones. Conservation and management of European eels is considered to be more effectively achieved through the Eel Regulations and Eel Management Plans.

2 http://webarchive.nationalarchives.gov.uk/20141203170558tf_/http://chartingprogress.defra.gov.uk/ [accessed 19/12/2017] 3 https://www.kentandessex-ifca.gov.uk/i-want-to-find-out-about/regulations/keifca-byelaws/keifca- district-byelaws/ [accessed 19/12/2017]

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1.2.2 Definition of favourable condition For habitat features, a number of attributes4 (shown below in bold) are assessed and monitored to determine whether or not features are in favourable condition. Favourable condition, with respect to a habitat feature, means that: a) Its extent and distribution is stable or increasing; b) Its structures and functions, including its quality, and the composition of its characteristic biological communities, are such as to ensure that it remains in a condition which is healthy and not deteriorating; and c) Its natural supporting processes are unimpeded. The extent of a habitat feature refers to the total area in the site occupied by the qualifying feature and must also include consideration of its distribution. A reduction in feature extent has the potential to alter the physical and biological functioning of sediment habitat types (Elliott et al., 1998). The distribution of a habitat feature influences the component communities present and can contribute to the condition and resilience of the feature (JNCC, 2004). The assessment and monitoring of extent is only appropriate for those features with a discrete boundary, which are likely to be affected by pressures that can be regulated as part of the management approach. Examples of such features are, among others, biogenic reefs and maerl beds. The spatial extent of most Broadscale Habitats is not likely to change in response to most pressures. Exceptions to this include activities such as dredging and disposal of dredged materials, which will directly impact the type of seabed habitat present. The other components (i.e., feature structure and function) are more appropriate measures of favourable condition for most habitat features. Feature and sub-feature specific targets (and details of their supporting processes) are provided in the supplementary advice4 for designated sites. Structure encompasses the physical components of a habitat type and the key and influential species present. Physical structure refers to topography, sediment composition and distribution. Physical structure can have a significant influence on the hydrodynamic regime, operating at varying spatial scales in the marine environment, as well as influencing the presence and distribution of associated biological communities (Elliott et al., 1998). The function of habitat features includes processes such as: sediment reworking (e.g., through bioturbation) and habitat modification, primary and secondary production and recruitment dynamics. Habitat features rely on a range of supporting processes (e.g., hydrodynamic regime, water

4 https://designatedsites.naturalengland.org.uk/Marine/SupAdvice.aspx?SiteCode=UKMCZ0041&SiteN ame=swale&SiteNameDisplay=The+Swale+Estuary+MCZ&countyCode=&responsiblePerson=&SeaA rea=&IFCAArea= [accessed 19/12/2017]

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quality and sediment quality), which act to support their functioning as well as their resilience (e.g., ability to recover following impact). For species features, favourable condition means that: a) The quality and quantity of its habitat are such as to ensure that the population is maintained in numbers which enable it to thrive; b) The composition of its population in terms of number, age and sex ratio are such as to ensure that the population is maintained in numbers which enable it to thrive; and c) Its natural supporting processes are unimpeded.

1.2.3 Report aims and objectives The primary aim of this characterisation report is to explore and describe the attributes of the designated features within The Swale Estuary MCZ (details of the specific attributes and supporting processes for designated features within The Swale Estuary MCZ are provided in Appendix 1), to enable future assessment and monitoring of feature condition. The results presented will be used to develop recommendations for future monitoring, including the operational testing of specific metrics, which may indicate whether the condition of the feature has been maintained, is improving or is in decline. The broad objectives of this monitoring report are provided below: 1) Provide a description of the extent5, distribution, structural and (where possible) functional attributes, and the supporting processes, of the designated features within the site (see Table 2 for more detail), to enable subsequent condition assessment and monitoring; 2) Present evidence relating to indicators under the Marine Strategy Framework Directive; 3) Note records of any Habitat or Species FOCI not covered by Designation Order; 4) Provide practical recommendations for appropriate future monitoring approaches for both the designated features and their natural supporting processes (e.g., metric selection, survey design, data collection approaches) with a discussion of their requirements.

5 Note that where updated habitat maps are not available, extent will be described within the limits of available data.

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To achieve these aims, the report investigates the biological characteristics of the conservation features designated for protection within The Swale Estuary MCZ through analysis of grab sample data collected at the site in targeted surveys conducted between 2012 and 2016. Taxa observed in grab samples have been examined in order to describe the biological communities present in association with the designated BSHs. The current condition of the site has been investigated using several diversity metrics, including the number of taxa (S), total abundance of enumerable individuals (N), Infaunal Quality Index (IQI), Simpson’s (1-λ’) and Shannon (Loge) and Hill’s (N1) diversity metrics. Consideration has also been given to the distribution of non-indigenous species, marine litter, sediment contaminants and biotopes. As the site is mostly an estuary, with an adjacent estuarine marine conservation zone along its western border, it was considered that there was no comparable area within a reasonable distance of the site to allow a ‘before-after, control-impact’ (BACI) survey approach to be adopted. Instead, a densely-sampled grab survey inside the MCZ was considered a suitable survey methodology, providing sufficient information on the distribution of BSH across the site.

1.2.4 Feature attributes and supporting processes The features and sub-features designated at The Swale Estuary MCZ, along with their attributes and supporting processes, are detailed in the supplementary advice on designated features4. To achieve objective 1, as set out above, this report provides data and evidence of the status of designated features in alignment with the conservation advice available for this MCZ (Table 2). It should be noted, that not all feature attributes could be addressed due to the comprehensive nature of the attribute lists for each feature. The feature attributes were therefore rationalised and prioritised, resulting in a smaller sub-set of attributes. The list of selected feature attributes and supporting processes considered in this report is presented in Table 2, alongside the generated outputs for each.

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Table 2. Survey elements and outputs aligned with the feature attributes and supporting processes identified at The Swale Estuary MCZ. Attribute/Supporting Process Features Surveyed Outputs Attributes: Distribution, structure and function Extent and distribution A5.3 Subtidal mud Results of high-density A5.4 Subtidal mixed sediments grab sampling survey

Distribution: presence and A5.3 Subtidal mud Biological communities spatial distribution of biological A5.4 Subtidal mixed sediments (and derived biotopes) communities derived from high- density grab sampling survey Structure: species composition A5.3 Subtidal mud Biological communities, of component communities A5.4 Subtidal mixed sediments multi-variate community analysis results and Infaunal Quality Index (IQI), derived from high- density grab sampling survey Structure: presence and A5.3 Subtidal mud Species abundance abundance of key structural and A5.4 Subtidal mixed sediments results derived from influential species high-density grab sampling survey Non-indigenous species (NIS) A5.3 Subtidal mud Species recorded and A5.4 Subtidal mixed sediments general location derived from high-density grab sampling survey Supporting process: Supporting processes: Physio- A5.3 Subtidal mud Results of near seabed chemical properties A5.4 Subtidal mixed sediments water column salinity recorded from grab sample stations Supporting processes: Sediment A5.3 Subtidal mud Locations and results of contaminants A5.4 Subtidal mixed sediments sediment contaminant analysis

2 Methods 2.1 Data sources

Data used to inform this report has been compiled from surveys carried out in the Swale Estuary MCZ between 2012 and 2016 by the Environment Agency (EA) (Godsell et al., 2013; Miller and Easter, 2016). Locations of grab samples collected during these surveys are shown in Figure 2. No bathymetric or backscatter data was available for most of the site; the only acoustic coverage was from 2013 in the area of the Swale Channel and Whitstable Bay, covering the underwater cables for the London Array offshore wind farm. For the baseline survey, a 500 m ‘no sampling’ buffer was placed around the cable route, so the 2013 acoustic data was not able to assist in planning the survey.

2.2 Survey design

Nineteen stations located within the Swale Estuary part of the MCZ were surveyed in March 2012 by the EA as part of the Swale Estuary MCZ verification survey. The stations were selected using a minimum grid spacing of 300 m, in the absence of a

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habitat layer covering the site, and were distributed from the confluence with the Medway west to Conyer Creek (SWLE 19, Figure 4). No acoustic data were available for 75% of the site; therefore, no habitat map was generated as a result of the 2012 verification survey (Godsell et al., 2013). The April 2016 baseline survey resurveyed the nineteen stations that were sampled in 2012, and an additional 36 stations covering areas not sampled previously (Figure 2). Changes to the MCZ boundary following designation resulted in one station (SWLE01) sampled in both 2012 and 2016 being outside the MCZ boundary. Water Framework Directive (WFD) grab surveys at 10 stations within the Whitstable Bay coastal water body were also undertaken by the EA in 2012 and 2015 as part of a surveillance monitoring programme (Figure 4). Data collected during the 2016 baseline survey aimed to provide as much information as possible on the distribution of BSH across the site. For vessel safety reasons, an area in the east of the estuary, with underwater obstructions linked to cables for the London Array wind farm, was avoided.

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2.3 Data acquisition and processing 2.3.1 Seabed sediments Sediment samples for particle size analysis and benthic infauna analyses were collected using a 0.1 m2 Day Grab as described in the Environment Agency WFD operational instructions 104_10 (Environment Agency, 2012) and 009_07 (Environment Agency, 2014). The Environment Agency WFD sampling methodology required two similar samples; the first was used to obtain a faunal sample (to a minimum depth of 5 cm in sand habitat and 7 cm in mud habitat); and the second to obtain a sub-sample for Particle Size Analysis (PSA). Full depth-integrated cores of sediment (approx. volume of 500 ml) were taken for Particle Size Analysis. Sediment samples for PSA were processed by The National Laboratory Service following the recommended methodology of the North East Atlantic Marine Biological Analytical Quality Control (NMBAQC) scheme (Mason, 2011). The less than 1 mm sediment fraction was analysed using laser diffraction and the greater than 1 mm fraction was dried, sieved and weighed at 0.5 phi (ϕ) intervals. Sediment distribution data were merged and used to classify samples into sediment Broadscale Habitats. The faunal sample was then processed by washing over a sieve (0.5 mm and 1.0 mm meshes). Samples collected by the EA in 2012 and 2015 for the Whitstable Bay WFD survey were sieved over a 1.0 mm mesh (standard protocol for a survey in a coastal waterbody), so the 2016 samples were sieved using both 1.0 mm and 0.5 mm mesh sizes to allow intercomparison with both datasets (Environment Agency, 2012). The retained material was photographed on the sieve and preserved in a buffered 6% formaldehyde solution. Faunal samples were processed by Thompson Ecology to extract all fauna present in each sample. Fauna were identified to the lowest taxonomic level possible, enumerated and weighed (blotted wet weight) to the nearest 0.0001 g following the recommendations of the NMBAQC scheme (Worsfold et al., 2010). 2.4 Data preparation and analysis 2.4.1 Sediment particle size distribution Sediment particle size data (half phi classes) were grouped into the percentage contribution of gravel, sand and mud derived from the classification proposed by Folk (1954). In addition, each sample was assigned to one of four sediment Broadscale Habitats using a modified version of the classification model produced during the Mapping European Seabed Habitats (MESH) project (Long, 2006).

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2.4.2 Biological community data preparation Benthic infauna data sets were checked to ensure consistent nomenclature and identification policies. Discrepancies were resolved using expert judgement following the truncation protocol presented in Annex 1. Invalid taxa and fragments of countable taxa were removed from the data set and the presence of colonial taxa was changed to a numeric value of one. Records were combined where a species was identified correctly both by using its binomial name and by using its binomial name with a qualifier e.g. Lumbrinereis cingulata ‘aggregate’. Records labelled as ‘juvenile’ were combined with ‘adults’ of the same genus/species/family. Temporal community analysis was undertaken at the genus level (in order to remove any species identification errors) as the infauna samples from the four different surveys (MCZ verification, baseline and two WFD surveys) were analysed by two different contractors (APEM and Thomson Unicomarine). The four surveys are: • 2016 Swale Estuary MCZ baseline survey (this survey, sieved to 0.5 and 1.0 mm) • 2015 Environment Agency WFD grab survey of Whitstable Bay (sieved to 1.0 mm only) • 2012 Environment Agency WFD grab survey of Whitstable Bay (sieved to 1.0 mm only) • 2012 Swale Estuary MCZ verification survey (covering western Swale, sieved to 0.5 mm only).

The distribution of the samples collected in these surveys is shown in Figure 4.

2.4.3 Statistical analyses The truncated infauna abundance and biomass data were imported into PRIMER v6 (Clarke and Gorley, 2006) to enable multivariate analysis and the derivation of various metrics for univariate analysis. Species classification information and a number of relevant factors/indicators were also assigned to the data at this stage. The number of taxa (S), total abundance of enumerable individuals (N), Shannon (H’ loge), species evenness (1-λ’) and Hills (N1) diversity metrics were derived for each sample using the DIVERSE function within PRIMER v6. The Infaunal Quality Index (IQI) was calculated using the Environment Agency database modules (Phillips et al., 2014). Non-metric multidimensional scaling (MDS) ordination plots, analysis of similarity between (ANOSIM) and within (SIMPER) groups were produced in PRIMER v6 to explore any temporal and spatial differences in the benthic communities. Spatial differences were examined on a finer scale by undertaking analyses separately on samples collected in the Swale (SWLE 2 – 36) and Whitstable Bay (SWLE 37 – 55).

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Summary statistics, data interpretation/manipulation and non-parametric Mann- Whitney tests were performed on the sample level metrics to test for, and explain, any significant differences between spatial or temporal groups (Minitab 17 Statistical Software, 2010). A posteriori power analysis of the 2016 data (at 0.5 mm mesh size) using two diversity metrics (species richness and Shannon index) was undertaken, to identify the level of statistical power available to detect a 10% or 20% change in selected diversity metrics.

2.4.4 Contaminants sampling At six evenly distributed stations, additional grabs were collected for sediment contaminant analysis, providing a record of the most recent contaminant levels deposited in the sediment. Surface sediment scrapes were sampled to a maximum depth of 1 cm (or to the depth of the apparent Redox Potential Depth if shallower), following the methodology described in Environment Agency (2016). Sediment dry weight contaminant concentrations were normalised to 5% aluminium (for heavy metals) and 2.5% total organic carbon content (for organics) to take account of the variation between sediment types (OSPAR Commission, 2014) for comparison. Results were compared against OSPAR background assessment criteria (BAC) considered to be background level thresholds and Environmental Assessment Criteria / Effects Range Low (EAC/ERL), thresholds for heavy metals, polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs above which concentrations may chronically impact marine fauna).

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3 Results and Interpretation

3.1 Site overview

The Swale Estuary MCZ 2016 subtidal baseline survey was completed in April 2016, and was characterised by two BSHs: ‘A5.3 Subtidal mud’; and ‘A5.4 Subtidal mixed sediments’. Results are presented for the 2016 sediment samples, within the MCZ boundary, where both particle size and infauna community analyses were conducted (n = 52). Table 3 shows the number of samples collected from the sediment BSHs that they were assigned. No samples were acquired from the BSH ‘A5.1 Subtidal coarse sediment’ and ‘A5.2 Subtidal sand’ features in 2016, preventing comparisons with these features observed in the 2012 survey data (Figure 3). A summary of the designated subtidal sediment BSH features identified during this 2016, and previous surveys is given in Table 4.

Table 3. Number of samples collected in each BSH. Broadscale Habitat (BSH) Grab – PSA & Infauna Grab – PSA only A5.3 Subtidal mud 30 0 A5.4 Subtidal mixed sediments 22 2

Figure 3. Classification of sediment Broadscale Habitats sampled in the 2016 survey of The Swale Estuary MCZ based on the simplified subdivision of the Folk triangle for UKSeaMap (Long, 2006; Folk, 1954).

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3.2 Subtidal sediment BSH: Sediment composition and biological communities

The distribution of sediment samples and assigned BSHs collected during The Swale Estuary MCZ 2016 baseline survey and the 2015 and 2012 surveys are illustrated in Figure 4. The percentage contribution of gravel, sand and mud to the 2016 samples is illustrated in Figure 5. Spatially, ‘A5.4 Subtidal mixed sediments’ were dominant in Whitstable Bay (16 out of the 19 samples collected), whilst ‘A5.3 Subtidal mud’ was more frequently encountered in the Swale (27 out of the 36 samples collected).

In total, 273 taxa were identified from sediment samples collected in 2016 (195 from ‘A5.3 Subtidal mud’ and 235 ‘A5.4 Subtidal mixed sediments’ samples). Table 5 shows the mean (± standard error) infaunal species abundance, richness, infaunal quality index (IQI) and other univariate indices calculated for the infaunal samples collected using a Day Grab within the two BSHs sampled within The Swale Estuary MCZ. Overall, 29 % of the IQI samples collected were at ‘High’

Table 4. Subtidal sediment Broadscale Habitat (BSH) features designated in The Swale Estuary MCZ. Summary of presence recorded by the Selection Assessment Document (SAD) and subsequent surveys (PSA = particle size analysis sample).

Presence Presence Presence Presence Extent following following following following Feature Name according 2012 2016 2012 WFD 2015 WFD to SAD verification baseline survey2 survey2 survey¹ survey

A5.1 Subtidal coarse Not N/A 4 PSA 5 PSA Not recorded sediment recorded

Not Not A5.2 Subtidal sand 9.23 km2 1 PSA Not recorded recorded recorded

A5.3 Subtidal mud 6.84 km2 7 PSA 1 PSA 1 PSA 30 PSA

A5.4 Subtidal mixed 13.53 km2 14 PSA 2 PSA 9 PSA 24 PSA sediments

1Only 19 stations were surveyed in the western Swale in 2012 due to underwater obstructions (London Array submarine cables), commercial shellfisheries, and samples were not collected from the seabed within the Lees Court estate. 2 The WFD surveys only surveyed within the Whitstable Bay coastal waterbody boundary.

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© Crown copyright 2017 Figure 4. Broadscale Habitat classifications of PSA samples collected during the 2016 baseline survey, 2012 verification survey and 2015 and 2012 Water Framework Directive surveys of The Swale Estuary MCZ (only subtidal areas included).

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Table 5. Mean (± standard error) infaunal species abundance, richness, total biomass, infaunal quality index (IQI) and other univariate indices of the Day Grab samples for the two Broadscale Habitats collected within The Swale Estuary MCZ in 2016 (sieved to 0.5

samples

N Total Biomass Total Total Abundance Taxa Richness Shannon Simpsons Hill’s taxa IQI o. o. -1 -1 (g) Broadscale Habitat (n sample ) (S sample ) H’(loge) (1-λ’) N1

(BSH) Mea

±S.E. Mean ±S.E. Mean ±S.E. Mean ±S.E. ±S.E. Mean ±S.E. Mean ±S.E. Mean n Whole MCZ 30 195 814.5 269.0 35.63 2.71 60.06 48.08 2.19 0.12 0.77 0.03 10.86 1.23 0.680 0.02 A5.3 Whitstable 3 94 626.3 354.8 41.70 10.50 479.59 478.68 2.29 0.07 0.83 0.02 9.95 0.70 0.714 0.04 Subtidal Bay mud Swale 27 177 835.4 297.4 34.96 2.83 13.44 8.39 2.18 0.13 0.76 0.03 10.96 1.37 0.676 0.02 Estuary Whole MCZ 22 235 1081.6 245.7 58.23 4.50 29.19 12.99 2.66 0.18 0.83 0.03 18.43 2.39 0.668 0.02 A5.4 Whitstable Subtidal 14 212 740.2 105.6 65.64 4.71 36.92 19.40 2.95 0.34 0.88 0.02 12.75 4.17 0.677 0.03 Bay mixed Swale sediments 8 127 1679.1 618.0 45.25 7.58 15.68 11.28 2.15 0.16 0.73 0.06 21.67 2.63 0.652 0.05 Estuary

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Two variable salinity mud community biotopes (Aphelochaeta marioni and Tubificoides spp. in variable salinity infralittoral mud (SS.SMu.SMuVS.AphTubi, EUNIS A5.322) and Nephtys hombergii and Tubificoides spp. in variable salinity infralittoral soft mud (SS.SMu.SMuVS.NhomTubi, A5.323); Figure 6) and a variable salinity mixed sediment community biotope (Crepidula fornicata and Mediomastus fragilis in variable salinity infralittoral mixed sediment (SS.SMx.SMxVS.CreMed, A5.422); Figure 7) were identified within the MCZ boundary, indicating the estuarine nature of the site. All three biotopes were distributed across the site. The C. fornicata biotope, SS.SMx.SMxVS.CreMed had a clustered distribution; notably around the confluence of the Medway and the Swale (SWLE 1, 2 and 7), the mouth of Faversham Creek (SWLE 31 and 33), and in southwest Whitstable Bay (SWLE 47, 51, 52 and 55).

For 20 out of the 52 samples collected inside the MCZ, there was a discrepancy between the BSH of the biotope derived from the community data and the BSH derived from the associated PSA sample (e.g. ‘A5.4 Subtidal mud’ biotope present in ‘A5.4 Subtidal mixed sediments’).

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Subtidal Mud (SS.SMu.SMuVS.AphTubi) Aphelochaeta marioni and Tubificoides spp. in variable salinity infralittoral mud

Subtidal Mud (SS.SMu.SMuVS.NhomTubi) Nephtys hombergii and Tubificoides spp. in variable salinity infralittoral soft mud

Figure 6. Example images of biotopes of the ‘A5.3 Subtidal mud’ feature from The Swale Estuary MCZ 2016 survey (left) in the Day Grab and (right) material retained after sieving.

Subtidal Mixed Sediments (SS.SMx.SMxVS.CreMed) Crepidula fornicata and Mediomastus fragilis in variable salinity infralittoral mixed sediment

Figure 7. Example images of the ‘A5.4 Subtidal mixed sediments’ feature from The Swale Estuary MCZ 2016 survey (left) in the Day Grab and (right) material retained after sieving.

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3.2.1 Subtidal mud 71 % of the taxa encountered in the 2016 survey were present in the samples collected from the ‘A5.3 Subtidal mud’ BSH within the MCZ (samples were pooled into BSHs based on their associated PSA sample, rather than by biotope).

There was low (28.5 %) mean similarity among the infaunal assemblages in samples assigned to this BSH. The status of the ‘A5.3 Subtidal mud’ samples collected across the site were classified as ‘Good’ according to the IQI with a mean EQR score of 0.68 (Good status range is 0.64 – 0.75) (Figure 8). However, there was significant variability in the EQR scores, ranging from High to Moderate status (EQRs ranged from 0.45 to 0.84). Stations SWLE 17 and SWLE 19 near Conyer Creek had EQR scores at the low end of the Moderate status category (0.45 and 0.48 respectively, Figure 9). The mean total biomass of ‘A5.3 Subtidal mud’ samples was higher in Whitstable Bay than in the Swale area of the MCZ due to high biomass of Crepidula fornicata (with shells) present in three mud samples, notably 1.32 kg in SWLE 47.

There were too few grab samples assigned to ‘A5.3 Subtidal mud’ to allow spatial comparison of benthic infauna metrics (i.e. three samples in Whitstable Bay, 27 samples in the Swale estuary), although SIMPER analysis showed that the mud samples collected in Whitstable Bay were characterised by higher abundances of the polychaete Nephtys sp., oligochaete Tubificoides benedii, the horseshoe worm Phoronis sp. and the cumacean Pseudocuma longicornis. Samples from the Swale were characterised by higher abundances of the polychaetes Tharyx maryae and Streblospio sp., and nematode worms.

There was no significant difference in > 0.5 mm infaunal community structure between the subtidal mud samples collected between 2016 and the 2012 verification survey (comparing only between samples collected in the same extent of the western Swale across both years, Figure 4) (ANOSIM global R = 0.20, p = 0.09). However, the sample size was small and imbalanced between years (2016 = 10 samples, 2012 = 4 samples) which limited the application of statistical testing to explore temporal differences in the assemblages.

Only one ‘A5.3 Subtidal mud’ sample was collected in the 2015 and 2012 WFD surveys of Whitstable Bay, so a temporal comparison was not possible for this area.

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© Crown copyright 2017 Figure 8. Infaunal Quality Index status of infaunal samples collected during The Swale Estuary MCZ 2016 baseline survey. Inset shows sample distribution around Queenborough Harbour in the western Swale.

3.2.2 Subtidal mixed sediments 86 % of benthic infaunal taxa encountered in the grab samples collected in 2016 were represented in samples from BSH ‘A5.4 Subtidal mixed sediments’ (samples were pooled into the BSH based on their associated PSA sample, rather than by biotope). There was low (33.7 %) average similarity among the infaunal assemblages in samples assigned to ‘A5.4 Subtidal mixed sediments’. The mean dissimilarity between ‘A5.4 Subtidal mixed sediments and ‘A5.3 Subtidal mud’ was 75.4%, predominately due to the higher abundances of Tharyx sp. and Tubificoides sp.in subtidal mixed sediments samples. Across the MCZ, the status of the 2016 ‘A5.4 Subtidal mixed sediments’ samples were classified as ‘Good’ using the IQI, with a mean EQR score of 0.68 (Figure 7), although there was significant variability in the station EQRs, ranging from High to Moderate status boundaries (EQR range from 0.44 (SWLE 55 in central Whitstable Bay) to 0.82 (SWLE 33 in the eastern Swale)). Species richness was higher in High IQI status stations, and lower in Moderate IQI status stations (Figure 9).

Species richness was significantly higher in ‘A5.4 Subtidal mixed sediments’ samples from Whitstable Bay than the Swale (W = 60.0, p = 0.032). No significant differences (at p < 0.05) were identified for any of the other infaunal metrics.

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There was a significant difference between 2016 ‘A5.4 Subtidal mixed sediments’ communities in the Swale estuary and Whitstable Bay (ANOSIM global R = 0.41, p < 0.001), due to the higher abundances of Tharyx maryae (and other Tharyx species) and Tubificoides sp. in samples from the Swale, and myodocopid ostracods and Mediomastus fragilis from samples in Whitstable Bay (Figure 10).

Figure 9. Boxplots of (a) Infaunal quality index (IQI) Ecological Quality Ratios (EQR) of BSHs in different areas of The Swale Estuary MCZ in the 2016 Baseline survey. The crosshair symbol indicates the mean; the grey diamonds are EQRs of individual grab samples. Reference lines indicate the High/Good/ Moderate/Poor Ecological Status Water Framework Directive status thresholds; and (b) Species richness of the 2016 samples classified using IQI EQRs into in each WFD status, split by BSH and MCZ area.

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Figure 10. Multidimensional scaling (MDS) plot of infaunal communities (sieved to 0.5 mm) sampled in the 2016 Swale Estuary MCZ baseline survey, split across sediment Broadscale Habitats and location. The point label indicates the station number.

There was no significant difference in any infaunal metrics or community structure (>1.0 mm infauna fraction; analysed at the genus level) between sampling years for the nine ‘A5.4 Subtidal mixed sediments’ samples collected within the Whitstable Bay WFD water body in 2015 and the eight samples collected within the same boundary in 2016 (ANOSIM global R = 0.07, p = 0.17). The mean IQI scores in 2015 and 2016 were within the ‘Good ecological status’ boundary. Only two samples from the 2012 WFD Whitstable survey were mixed sediments, so a comparison was not possible.

When samples from all BSHs are pooled together, there was no significant difference in >1.0 mm fraction of infaunal community structure between sampling years (2016, 2015 and 2012) for samples collected in Whitstable Bay (Global R = 0.04, p = 0.19, Figure 11).

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Figure 11. Multidimensional scaling (MDS) plot of infaunal communities (sieved to 1.0 mm and analysed to genus level) sampled in Whitstable Bay during the 2016 Swale Estuary MCZ baseline survey and the 2012 and 2015 WFD grab surveys, across all sediment Broadscale Habitats.

3.2.3 Subtidal coarse sediment and Subtidal sand ‘A5.1 Subtidal coarse sediment’ was recorded in the western Swale and in the main channel near Milton Creek at four stations (SWLE 5, 9, 15, and 17) during the 2012 verification survey and at five stations in the 2012 Whitstable Bay WFD survey. ‘A5.2 Subtidal sand’ was recorded from a single station (SWLE 14) near to the mouth of Milton Creek in the 2012 verification survey (. All Swale ‘A5.1 Subtidal coarse sediment’ / ‘A5.2 Subtidal sand’ stations and two Whitstable Bay ‘A5.1 Subtidal coarse sediment’ stations were resampled in 2016, but neither features were recorded at the stations or at other locations in the MCZ. In the Swale, stations SWLE 5, 9, 15 and 17 were recorded in the 2016 survey as ‘A5.3 Subtidal mud’, and station SWLE 14 was recorded as ‘A5.4 Subtidal mixed sediments’. There were large temporal changes in sediment composition (reduction in gravel content and increase in mud content) for every station, rather than minor changes that nudge a sample across a BSH boundary (Figure 12). Whilst repeat samples were planned for collection at the same station location during different years, there was up to 42 m variation in the spatial location of the seabed sampled between the 2012 and 2016 surveys. Consequentially, fine-scale spatial variability (notably the cross-section across the estuary channel) may be the cause of observed differences in sediment type at a repeat station.

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Figure 12. Changes in particle size distribution between 2012 and 2016 of seven stations sampled as ‘A5.1 Subtidal coarse sediment’ or ‘A5.2 Subtidal sand’ in 2012. Symbol shapes indicate the same station (up to 42 m between sample locations) sampled in both 2012 and 2016.

3.3 Habitat and Species Features of Conservation Importance (FOCI)

No habitat FOCI proposed in the SAD and able to be sampled with a Day Grab (e.g. Ross worm (Sabellaria spinulosa) reef, Blue mussel beds or Peat and clay exposures) were recorded in either the 2012 and 2016 MCZ surveys or the 2015 WFD survey. The survey did not target the ‘Estuarine rocky habitats’ FOCI. All taxa identified in grab samples collected in 2016 were searched against a list of rare species and scarce species identified by Sanderson (1996). No rare and scare species were present. The native oyster (Ostrea edulis) was not recorded.

3.4 Non-indigenous species (NNS)

All taxa identified in grab samples collected in 2016 were cross referenced with the list of non-indigenous species compiled in Eno et al. (1997), and the 49 non- indigenous target species which have been selected for assessment of Good Environmental Status (GES) in UK waters under MSFD D2 (Stebbing et al., 2014; Annex 3). Seven non-indigenous species, and one additional potential non- indigenous species were identified from infaunal samples and a sample retained for cobble analysis. A total of 779 individuals of the ostracod Eusarsiella zostericola associated with imported oysters (Crassostrea virginica), were present in 83% (43/52) of infaunal samples. The Bamboo worm (Clymenella torquata), also associated with imported

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oysters, was found at three stations in Whitstable Bay. There were 16 individuals of the Pacific oyster (Crassostrea gigas) present at four stations in both the Swale estuary and Whitstable Bay. Other non-indigenous species observed in the survey data included the slipper limpet Crepidula fornicata, the razor clam Ensis directus, the barnacle Austrominius modestus and the amphipod Monocorophium sextonae. C. gigas, C. fornicata and E. directus are all species selected for assessment of GES for MSFD D2 (Annex 3). Colonial tunicates from the family Didemnidae were found at eight stations in Whitstable Bay, but could not be identified to species level. Further investigation should be undertaken to confirm whether non-indigenous species of this tunicate are present. The tunicate Styela clava was present at a single station in the 2012 verification survey of the Swale Estuary MCZ, but was not found in the 2016 baseline survey (resampled as station SWLE 19 in the 2016 survey).

3.5 Supporting processes

3.5.1 Water quality parameters Near seabed water column salinity was recorded using a conductivity probe at all stations and ranged from 27.8 to 31.3, with a mean (± S.E.) of 28.3 ± 0.1 in the Swale and 30.9 ± 0.1 in Whitstable Bay. 3.5.2 Sediment quality parameters Surface sediment scrapes were taken at six grab stations across the length of the Swale, providing a record of the most recent contaminant levels deposited in the sediment (Figure 13). Chromium levels exceeded the OSPAR Effects Range Low (ERL) threshold at all six stations. Mercury levels were also elevated above background level thresholds (OSPAR Background Assessment Criteria (BAC)) at five out of the six stations, but below the ERL threshold at which they would be considered to have a chronic impact on infauna. Station 12 in the central Swale estuary had 8 Polycyclic Aromatic Hydrocarbons (PAHs) and one Polychlorinated Biphenyl (PCB) congener elevated above the OSPAR BAC threshold. Four stations (3, 12, 26 and 31) had concentrations of the PAH pyrene above the BAC threshold.

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© Crown copyright 2017 Figure 13. Distribution of surficial sediment contaminant samples across The Swale Estuary MCZ, sampled in 2016. The bubbles illustrate the concentration (normalised to the total organic carbon content of each sample) of the PAH pyrene at each site.

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3.6 Additional monitoring

3.6.1 Marine litter Plastic fragments larger than 1 mm found in infauna samples were counted and categorised by type. Plastic fragments were present in 34 samples, with a median of two fragments per sample. Fragments were categorised by colour and material when possible, with ‘unidentified flat white plastic’ being the most frequently encountered category. Fragments fell under four MSFD seafloor litter categories: A5 (monofilament line, recorded at 15 stations), A7 (synthetic rope, recorded at 3 stations), A14 (other plastic, recorded at 32 stations) and C5 (other rubber, recorded at 1 station) (Annex 2). The largest number of fragments (252) was recorded at station SWLE 14, at the mouth of Milton Creek, which flows out of Sittingbourne (Figure 14).

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4 Discussion This baseline monitoring report provides the initial temporal characterisation of designated features within The Swale Estuary MCZ from a grab sampling survey conducted within the site. Any statements or interim conclusions on feature condition or ecological status provided in this report are underpinned by the evidence collected, collated and analysed herein. Formal assessment of the condition status of designated features is carried out for this MCZ by Natural England using all available data, including the information presented in this report. This discussion now presents evidence in relation to the sub-set of feature attributes set out in table 2 from the list of attributes described in the supplementary advice on designated features4.

4.1 Subtidal sediment BSH: Sediment composition and biological communities The infaunal communities of the designated sediment Broadscale Habitats sampled in this survey are considered to be representative of transitional sediment communities located along the eastern English Channel. The structural composition of the biological communities characterising the sediment features in The Swale Estuary MCZ, and their current status/condition, suggests they remain in a condition which is healthy. Further detailed surveys are required to understand whether the site is deteriorating. 4.1.1 Extent and distribution of features Two of the four designated subtidal sediment BSHs were observed in the 2016 baseline survey. No ‘A5.1 Subtidal coarse sediment’ or ‘A5.2 Subtidal sand’ were observed, as stations recorded as such in 2012 had sufficiently different particle size when resampled in 2016 to be classified as a different BSH. However, as only single grab samples were collected at each station, it is not possible to rule out the locally heterogeneous nature of the seabed as a potential cause of this, particularly as replicate grabs at some stations were up to 42 m apart between surveys, due to the difficulty in sampling in shallow tidal conditions. 4.1.2 Distribution: presence and spatial distribution of biological communites Three biotopes (SS.SMx.SMxVS.CreMed, SS.SMu.SMuVS.NhomTubi and SS.SMu.SMuVS.AphTubi) were observed during the 2016 survey and all three were present across the MCZ. Biotopes had not been characterised for the WFD surveys or the 2012 verification survey, so it was not possible to assess if there was a temporal change in biotope presence/distribution over time. The presence of the SS.SMx.SMxVS.CreMed biotope in Whitstable Bay indicates that Crepidula fornicata

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is established at high densities. The mismatch between the biotope and BSH classifications indicates that the biotope definitions cross 5% gravel content boundary that defines the two BSHs ‘A5.3 Subtidal mud’ and ‘A5.4 Subtidal mixed sediments’. 4.1.3 Structure: species composition of component communities Samples classified as BSH ‘A5.4 Subtidal mixed sediments’ typically had higher taxa richness than the BSH ‘A5.3 Subtidal mud’ samples. Taxa richness was higher in Whitstable Bay, but faunal abundance was higher in the Swale across both BSHs. There was high within BSH variability, which reflects the extent of the site, the variation between transitional and coastal environments and the variety of natural (e.g. low-water environments) and anthropogenic pressures. Temporally, there had been no significant change in the > 1.0 mm infaunal community structure (analysed to genus level) over a four-year period in Whitstable Bay. This suggests there is limited variability in infaunal communities in the sediments, although the 0.5 – 1.0 mm infaunal fraction was not analysed for change over time, and may not show a similar response. Future surveys should incorporate analysis of infauna > 0.5 mm. The mean Infaunal Quality Index across the site indicated that both subfeatures, ‘A5.3 Subtidal mud’ and ‘A5.4 Subtidal mixed sediments’, were at ‘good’ ecological status for equivalent Water Framework Directive classifications. It should be noted, that the IQI has not been shown to consistently respond to the presence of non- indigenous species (notably Crepidula fornicata) or abrasion pressure from fishing activities on faunal communities (Phillips and Green, in prep). Impacts of non- indigenous species could be monitored by assessing the pre- and post-colonisation change in community structure of fixed sample areas. Spatially, there were areas of the Swale (notably stations 16 to 19, between Sittingbourne and Conyer) that were indicated to be in moderate ecological status, and could be considered to be in unfavourable condition. The assignment of unfavourable status to these samples was due to the relatively high abundance of Tharyx spp. and Tubificoides spp. These genera are classified as category IV and V in the AMBI index respectively, indicating they are tolerant of moderately-heavily polluted conditions. No contaminant samples were collected in this area, although infauna samples collected at stations with elevated levels of contaminants (e.g. SWLE 3, 12 and 31) had EQRs at ‘Moderate’ ecological status. Whilst the IQI EQRs should not be interpolated, due to the level of natural variability in the samples, such areas of the site could be flagged up for future operational surveys in order to determine if there are significant localised contaminant impacts in the MCZ. A posteriori power analysis of the 2016 data (at 0.5 mm mesh size) using two diversity metrics (species richness and Shannon index) showed that, across the site, the samples collected in the ‘A5.3 Subtidal mud’ feature could detect a 20% change in the Shannon Index at 73.3% statistical power (assuming α = 0.05), or at 55.6% power for ‘A5.4 Subtidal mixed sediments’ (although this increased to 73.2% when selecting for samples collected in Whitstable Bay only) (Table 6). Therefore, future

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surveys, aiming to compare temporal changes in diversity metrics, should aim to collect enough samples to achieve a 20% change at 80% power (e.g. 40 samples using Shannon Index for ‘A5.4 Subtidal mixed sediments’ in Whitstable Bay), as recommended by Marubini (2014), or consider lowering α to 0.10.

Table 6. A posteriori power analysis of the 2016 MCZ baseline survey data (at 0.5 mm mesh size), identifying the level of statistical power used to detect a 10% or 20% change in selected diversity metrics. Species Richness (S) Shannon Index (H’loge) Broadscale Habitat (BSH) N 10% change 20 % change 10% change 20 % change Whole MCZ 30 15.0% 44.7 % 25.3 % 73.3 % A5.3 Subtidal mud Swale Estuary 27 13.8 % 40.3 % 21.1 % 63.6 %

Whole MCZ 22 14.5% 43.1 % 18.3 % 55.6 % A5.4 Subtidal mixed sediments Whitstable 14 15.8 % 47.6 % 25.2 % 73.2 % Bay

4.1.4 Structure: presence and abundance of key structural and influential species Guidance is still being developed by Natural England on the selection of species that fall under this category. Species present in this study that could be considered under this attribute (based on their abundances, biomass and ecology), include: o The cirratulid polychaete Tharyx maryae was present in 71% of the samples collected (predominately from the Swale) with abundances up to 3316 individuals per grab sample, and was a key indicator of the lower salinity environment. o The predatory polychaete Nephtys hombergii was present in 63% of samples collected, with abundances of up to 33 per grab sample, and can be considered a key structural species as it creates networks of temporary mucus-lined burrows in the seabed sediments in order to hunt for food (Holme, 1949). o The bivalve Abra alba was present in 46% of the samples, predominately in mixed sediments, and is a rapid-recruiting species that can quickly colonise after disturbances.

4.2 Non-indigenous species (NIS)

Seven non-indigenous species, and one potential non-indigenous species (Didemnidae sea squirts), were found in the 2016 survey. Only Pacific oyster Crassostrea gigas, slipper limpet Crepidula fornicata and American jackknife clam Ensis directus are among the taxa selected for assessment of Good Environmental Status in GB waters under MSFD Descriptor 2 (Stebbing et al., 2014; Annex 3), whilst the bamboo worm Clymenella torquata, ostracod Eusarsiella zostericola (originally from North America) and amphipod Morocorophium sextonae (from New Zealand) have been known to exist in the area for decades and are not considered to have significant impacts on the environment (Eno et al., 1997).

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4.3 Supporting processes

4.3.1 Supporting processes: Sediment contaminants Whilst many contaminants were above the background levels, only chromium exceeded the OSPAR ERL threshold, which is the same as the BAC threshold of 81 mg kg-1. Chromium is not one of the substances identified by OSPAR for ‘priority action’ but its concentrations should continue to be monitored to observe future trends, and establish is still being accumulated in the site (OSPAR, 2014). It is not possible to determine the cause of multiple contaminants to be above background levels at station SWLE 12 without further sample collection. It should be noted that an industrialised part of the Swale estuary lies ~1 km to the north of the station and sewage works ~1 km to the south. This area of the MCZ should be examined more closely in future monitoring surveys, with replicate infauna samples and sediment/ biota contaminant analyses spaced at regular intervals along the estuary in order to identify the extent of any impact and the potential source of the elevated concentrations.

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5 Recommendations for future monitoring

• Surveys to date have only partially covered the full extent of The Swale Estuary MCZ, resulting in imbalanced survey designs and preventing robust spatial and temporal comparisons. A BACI design was not appropriate for this site, as most of the MCZ is a sheltered heterogeneous estuarine environment, which is unique for the Kent coast. Other nearby estuaries were all protected areas (e.g. Medway Estuary MCZ, Essex Estuaries SAC), therefore it was not considered suitable to use a BACI approach to compare the impact of potential future management measures to an ‘unprotected’ comparable area of seabed. Therefore, future surveys (in coordination with WFD monitoring, where possible) should repeat the survey design, in order to improve our understanding of the observed spatial and temporal variability, with additional detailed sampling of contaminants and the effects on infauna. • Based on the a posteriori power analysis undertaken on the data collected in 2016, future monitoring surveys aiming to compare temporal changes in diversity metrics should aim to collect enough samples to achieve a 20% change at 80% power (e.g. 40 samples using Shannon Index for ‘A5.4 Subtidal mixed sediments’ in Whitstable Bay), as recommended by Marubini (2014), or consider lowering α to 0.10. • Existing habitat maps of The Swale Estuary MCZ are of low resolution and need to be improved to support modifications to the survey design, such that sampling can be properly targeted at the features of interest.. Other approaches could be considered for mapping of the site, including interpolating between existing data points, and considering depth and cross- sections across the estuary channel, when mapping BSHs. • Future studies should consider increased localised sampling in areas where ‘A5.1 subtidal coarse sediment’ or ‘A5.2 Subtidal sand’ are visually assessed as being present during the survey. This would allow further understanding of the distribution and extent of BSHs with low spatial extent within the site. • The Swale Estuary MCZ contains a large number of non-indigenous species, particularly in Whitstable Bay. Future sampling designs should consider resampling previous stations to explore the species spread, frequency of occurrence and impact on native species across the site. • The non-indigenous ascidian Didemnum vexillum was not identified within the site, but individuals of its parent family Didemidae were confirmed at eight stations. D. vexillum has a range of morphotypes and was not able to be positively identified from grab samples fixed in 6% formaldehyde (Thomson Unicomarine, pers. comm.). It has been previously recorded from the Kent coast using mitochondrial DNA analysis (Graham et al., 2015), so future grab surveys in north Kent should collect samples for suspected D. vexillum

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presence separately from grab samples fixed for infauna analysis, in order to confirm identification using molecular approaches. • Contaminant and litter samples should be resampled at the same stations in future monitoring surveys to identify trends in densities / concentrations, and potentially the source of the input. This could be undertaken by finer scale sampling (e.g. every 500 m) along the estuary channel to narrow down the potential source. Consideration should also be given to whether the contaminants are being taken up by the associated biota; therefore, further sampling could be undertaken on polychaete or mussel specimens (following EQSD monitoring protocols, European Union (2010).

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6 References Balanced Seas (2011). Balanced Seas Final Recommendations Report Sept 2011. http://webarchive.nationalarchives.gov.uk/20120502155440/http:/www.balancedseas .org/ [Accessed 02/11/2017]. Cefas (2011). Sanitary survey of North Kent. Cefas report on behalf of the Food Standards Agency, to demonstrate compliance with the requirements for classification of bivalve mollusc production areas in England And Wales under EC Regulation No. 854/2004. Lowestoft, UK, 133 pp.

Clarke, K.R. and Gorley, R.N. (2006). PRIMER v6: User Manual/Tutorial. PRIMER- E, Plymouth, 192pp.

Colclough, S.R., Gray, G., Bark, A., Knights, B., (2002). Fish and fisheries of the tidal Thames: management of the modern resource, research aims and future pressures. Journal of Fish Biology 61 (sA): 64-73. Defra (2016). Marine Conservation Zone: The Swale Estuary. https://www.gov.uk/government/publications/marine-conservation-zones-the-swale- estuary [Accessed 02/11/2017].

Elliott, M., Nedwell, S., Jones, N., Read, S.J., Cutts, N.D. and Hemingway, K.L., (1998). Volume II: Intertidal sand and mudflats and subtidal mobile sandbanks. An overview of dynamic and sensitivity characteristics for conservation management of marine SACs. UK Marine SACs project, Oban, Scotland. English Nature.

Eno., N.C., Clark, R.A. and Sanderson, W.G. (1997). Non-native marine species in British waters: a review and directory. http://jncc.defra.gov.uk/page-2597 [Accessed 02/11/2017]. Environment Agency (2012). Water Framework Directive (WFD) sampling of macrobenthic invertebrates in Transitional and Coastal Waters. Operational Instruction 104_10. Bristol, UK (internal document Environment Agency (2014). Sampling and processing marine benthic invertebrates. Operational Instruction 009_07. Bristol, UK (internal document). Environment Agency (2016). Sediment sampling in water for chemical and particle size analysis. Operational Instruction 10_07. Bristol, UK internal document). European Union (2010). Guidance on chemical monitoring of sediment and biota under the Water Framework Directive. Common Implementation Strategy for the Water Framework Directive (2000/60/EC) Guidance Document 25, Technical Report 2010.3991. Office for Official Publications of the European Communities, Luxembourg.

Folk, R.L. (1954). The distinction between grain size and mineral composition in sedimentary rock nomenclature. Journal of Geology 62, 344-359.

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Godsell, N., Fraser, M. and Jones, N (2013). The Swale MCZ 2012 Habitat Verification Survey Report. Environment Agency, Bristol, UK. 53 pp. Graham, J., Collins, C., Lacaze, J-P., Brown, L. and McCollin, T. (2015). Molecular identification of Didemnum vexillum Kott, 1982 from sites around the UK coastline. BioInvasions Records 4, 171-177. Holme, N.A. (1949). The fauna of sand and mud banks near the mouth of the Exe Estuary. Journal of the Marine Biological Association of the United Kingdom, 28, 189-237.

JNCC (2004). Common standards monitoring guidance for littoral sediment habitats. Peterborough, JNCC.

Long, D. (2006). BGS detailed explanation of seabed sediment modified folk classification.

Marubini, F. (2014). Levels of statistical significance and power in marine biodiversity monitoring. HBDSEG paper 29.1.2, presented to HBDSEG 29, London, 5-6 Feb 2014.

Mason, C. (2011). NMBAQC’s Best Practice Guidance Particle Size Analysis (PSA) for Supporting Biological Analysis.

Miller, C. and Easter, J. (2016). The Swale Estuary MCZ 2016 Baseline Survey Report. Environment Agency, Bristol, UK. Minitab 17 Statistical Software (2010). [Computer software]. State College, PA: Minitab, Inc. (www.minitab.com) MSFD GES Technical Subgroup on Marine Litter. (2013). Guidance on Monitoring of Marine Litter in European Seas. Publications Office of the European Union. EUR 26113. http://publications.jrc.ec.europa.eu/repository/handle/JRC83985 [accessed 19/2/2017] OSPAR Commission (2014). Levels and trends in marine contaminants and their biological effects. CEMP Assessment Report 2013, Monitoring and Assessment Series. Phillips, G.R. and Green, B.C. (in prep.). Marine Strategy Framework Directive multi- metric index: applying Water Framework Directive methods to the MSFD – validation of the Infaunal Quality Index (IQI) and AZTI Marine Biotic Index (AMBI). Environment Agency, Bristol, UK. Phillips, G.R., Anwar, A., Brooks, L., Martina, L.J., Prior, A. and Miles, A.C. (2014). Infaunal Quality Index: WFD Classification Scheme for marine benthic invertebrates. Environment Agency, Bristol, UK. 193 pp. Sanderson, W.G. (1996). Rare benthic marine flora and fauna in Great Britain: the development of criteria for assessment. Joint Nature Conservation Committee Report 240. JNCC, Peterborough, UK.

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Stebbing, P., Murray, J., Whomersley, P. and Tidbury, H. (2014). Monitoring and surveillance for non-indigenous species in UK marine waters. www.nonnativespecies.org/downloadDocument.cfm?id=1232 [Accessed 02/11/2017/].

Worsfold, T.M., Hall., D.J. and O’Reilly, M. (2010). Guidelines for processing marine macrobenthic invertebrate samples: a processing requirements protocol version 1 (June 2010). Unicomarine Report NMBAQCMbPRP to the NMBAQC Committee. 33 pp. [Accessed 24/10/2016].

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Annex 1. Infauna data truncation protocol. A number of decisions applied during the data truncation process are described here, in the hope that by following such decisions, a greater degree of consistency in truncation exercises across different studies may be achieved. Raw taxon-by-sample matrices can often contain entries that include the same taxa recorded differently, erroneously or differentiated according to unorthodox, subjective criteria, for example: Each row should represent a legitimate taxon to be used in analytical software packages as a unit for the calculation of diversity indices and of similarity amongst groups of samples. An artificially inflated taxon list (i.e., one that has not had spurious entries removed) risks distorting the interpretation of pattern contained within the sampled assemblage. The truncation exercise aims to identify and neutralise such entries to reduce the risk of them supporting an artificial pattern in the assemblage. It is often the case that to overcome uncertainty and to avoid the introduction of unsupported certainty, some taxa have to be merged to a level in the taxonomic hierarchy that is higher than the level at which they were identified. In such situations, a compromise must be reached between the level of information lost by discarding recorded detail on a taxon’s identity, and the potential for error in analyses, results and interpretation if that detail is retained. Where there are records of one named species together with records of members of the same genus but the latter not identified to species level, the entries are merged and the resulting entry retains only the name of the genus (i.e., species level information is forfeited). In this way, the entries identified only to genus are not assigned to a level that is unsupported by the evidence, and the resulting single entry is representative of both original entries, albeit with a little less information, but a loss that will not affect the pattern in the assemblage as a whole. Additionally, taxa are often assigned as ‘juveniles’ during the identification stage with little evidence for their actual reproductive natural history (with the exception of some well-studied molluscs and commercial species). Many truncation methods involve the removal of all ‘juveniles’. However, a decision must be made on how to avoid the issues discussed above while retaining valuable information within the multivariate data set. The term ‘juvenile’ is often used to refer to individuals which do not exhibit the morphological features to resolve them to species level. In this case, these records were removed from the analysis rather than lowering the taxonomic resolution of other species level identifications. When a species level identification was labelled ‘juvenile’, the record was combined with the associated species level identification, when present, or the ‘juvenile’ label removed.

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Annex 2. Seafloor litter monitoring. Categories and sub-categories of litter items for Sea-Floor from the OSPAR/ICES/IBTS for North East Atlantic and Baltic. Guidance on Monitoring of Marine Litter in European Seas, MSFD GES Technical Subgroup on Marine Litter, 2013.

A: Plastic B: Metals C: Rubber D: Glass/ E: Natural F: Miscellaneous Ceramics products/ Clothes A1. Bottle B1. Cans C1. Boots D1. Jar E1. Clothing/ F1. Wood (food) rags (processed) A2. Sheet B2. Cans C2. D2. Bottle E2. Shoes F2. Rope (beverage) Balloons A3. Bag B3. Fishing C3. Bobbins D3. Piece E3. Other F3. Paper/ related (fishing) cardboard A4. Caps/ lids B4. Drums C4. Tyre D4. Other F4. Pallets A5. Fishing line B5. C5. Other F5. Other (monofilament) Appliances A6. Fishing line B6. Car (entangled) parts A7. Synthetic B7. Cables Related size categories rope A: ≤ 5*5 cm = 25 cm2 A8. Fishing net B8. Other B: ≤ 10*10 cm = 100 cm2 A9. Cable ties C: ≤ 20*20 cm = 400 cm2 A10. Strapping D: ≤ 50*50 cm = 2500 cm2 band E: ≤ 100*100 cm = 10000 cm2 A11. Crates and containers F: ≥ 100*100 cm = 10000 cm2 A12. Plastic diapers A13. Sanitary towels/ tampons A14. Other

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Annex 3. Non-indigenous species (NIS). Taxa listed as non-indigenous species (present and horizon) which have been selected for assessment of Good Environmental Status in GB waters under MSFD Descriptor 2 (Stebbing et al., 2014).

Species name List Species name List Acartia (Acanthacartia) tonsa Present Alexandrium catenella Horizon Amphibalanus amphitrite Present Amphibalanus reticulatus Horizon

Asterocarpa humilis Present Asterias amurensis Horizon Bonnemaisonia hamifera Present Caulerpa racemosa Horizon

Caprella mutica Present Caulerpa taxifolia Horizon

Crassostrea angulata Present Celtodoryx ciocalyptoides Horizon

Crassostrea gigas Present Chama sp. Horizon

Crepidula fornicata Present Dendostrea frons Horizon

Diadumene lineata Present Gracilaria vermiculophylla Horizon

Didemnum vexillum Present Hemigrapsus penicillatus Horizon

Dyspanopeus sayi Present Hemigrapsus sanguineus Horizon

Ensis directus Present Hemigrapsus takanoi Horizon

Eriocheir sinensis Present Megabalanus coccopoma Horizon

Ficopomatus enigmaticus Present Megabalanus zebra Horizon

Grateloupia doryphora Present Mizuhopecten yessoensis Horizon

Grateloupia turuturu Present Mnemiopsis leidyi Horizon

Hesperibalanus fallax Present Ocenebra inornata Horizon

Heterosigma akashiwo Present Paralithodes camtschaticus Horizon

Homarus americanus Present Polysiphonia subtilissima Horizon

Rapana venosa Present Pseudochattonella verruculosa Horizon

Sargassum muticum Present Rhopilema nomadica Horizon

Schizoporella japonica Present Telmatogeton japonicus Horizon

Spartina townsendii var. anglica Present

Styela clava Present

Undaria pinnatifida Present

Urosalpinx cinerea Present

Watersipora subatra Present

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Additional taxa listed as non-indigenous species in the JNCC ‘Non-native marine species in British waters: a review and directory’ report by Eno et al. (1997) which have not been selected for assessment of Good Environmental Status in GB waters under MSFD Descriptor 2.

Species name (1997) Updated name (2017) Thalassiosira punctigera

Thalassiosira tealata

Coscinodiscus wailesii Odontella sinensis Pleurosigma simonsenii

Grateloupia doryphora

Grateloupia filicina var. luxurians Grateloupia subpectinata

Pikea californica

Agardhiella subulata

Solieria chordalis

Antithamnionella spirographidis

Antithamnionella ternifolia

Polysiphonia harveyi Neosiphonia harveyi

Colpomenia peregrine

Codium fragile subsp. atlanticum

Codium fragile subsp. tomentosoides Codium fragile subsp. atlanticum

Gonionemus vertens

Clavopsella navis Pachycordyle navis

Anguillicoloides crassus

Goniadella gracilis Marenzelleria viridis

Clymenella torquata Hydroides dianthus

Hydroides ezoensis

Janua brasiliensis

Pileolaria berkeleyana

Ammothea hilgendorfi Elminius modestus Austrominius modestus

Eusarsiella zostericola

Corophium sextonae Rhithropanopeus harrissii

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Potamopyrgus antipodarum Tiostrea lutaria Tiostrea chilensis

Mercenaria mercenaria

Petricola pholadiformis

Mya arenaria

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