English Channel towed sledge seabed images. Phase 2: Analysis of selected tow images

During the 1970s and 1980s, the late Dr Norman Holme undertook extensive towed sledge surveys in the English Channel and some in the Irish Sea. Only a minority of the resulting images were analysed and reported before his death in 1989 but logbooks, video and film material has been archived in the National Marine Biological Library (NMBL) in Plymouth. A study was therefore commissioned by the Joint Nature Conservation Committee and as a part of the Mapping European Seabed Habitats (MESH) project to identify the value of the material archived and the procedure and cost to undertake further work (Phase 1 of the study reported here: Oakley & Hiscock, 2005). Some image analysis was undertaken as a part of Phase 1. Phase 2 (this report) was to further analyse selected images. Having determined in Phase 1 that only the 35 mm photographic transparencies provided sufficient clarity to identify species and biotopes, the tows selected for analysis were ones where 35mm images had been taken. The tows selected for analysis of images were mainly in the vicinity of Plymouth and especially along the area between Rame Head and the region of the Eddystone. The 35 mm films were viewed under a binocular microscope and the taxa that could be recognised recorded in note form. Twenty-five images were selected for inclusion in the report. Almost all of the images were of level sediment seabed. Where rocks were included, it was usually unplanned and the sled was hauled before being caught or damaged. The main biotopes or biotope complexes identified were: SS.SMU.CSaMu. Circalittoral sandy mud. Extensively present between the shore and the Eddystone Reef complex and at depths of about 48 to 52 m. At one site offshore of Plymouth Sound, the turret shell Turritella communis was abundant. In some areas, this biotope had dense anemones, Mesacmaea mitchelli and (more rarely) Cerianthus lloydii. Queen scallops, Aequipecten opercularis and king scallops, Pecten maximus, were sometimes present in small numbers. Hard substratum species such as hydroids, dead mens fingers Alcyonium digitatum and the cup coral Caryophyllia smithii occurred in a few places, probably attached to shells or stones beneath the surface. South of the spoil ground off Hilsea Point at 57m depth, the sediment was muddier but is still assigned to this biotope complex. It is notable that three small sea pens, most likely Virgularia mirabilis, were seen here. SS.SMx.CMx. Circalittoral mixed sediment. Further offshore but at about the same depth as SS.SMU.CSaMu occurred, coarse gravel with some silt was present. The sediment was characterised must conspicuously by small queen scallops, Aequipecten opercularis. Peculiarly, there were ‘bundles’ of the branching bryozoan Cellaria sp. – a species normally found attached to rock. It could not be seen whether these bundles of Cellaria had been brought-together by terebellid worms but it is notable that Cellaria is recorded in historical surveys. As with many other sediments, there were occasional brittle stars, Ophiocomina nigra and Ophiura ophiura. Where sediments were muddy, the burrowing anemone Mesacmaea mitchelli was common. Where pebbles or cobbles occurred, there were attached species such as Alcyonium digitatum, Caryophyllia smithii and the fleshy bryozoan Alcyonidium diaphanum. Undescribed biotope. Although most likely a part of SS.SMx.CMx, the biotope visually dominated by a terebellid worm believed to be Thelepus cincinnatua, is worth special attention as it may be an undescribed biotope. The biotope occurred about 22 nautical miles south of the latitude of the Eddystone and in depths in excess of 70 m. SS.SCS.CCS.Blan. Branchiostoma lanceolatum in circalittoral coarse sand with shell gravel at about 48m depth and less. This habitat was the ‘classic’ ‘Eddystone Shell Gravel’ which is sampled for Branchiostoma lanceolatum. However, no Branchiostoma lanceolatum could be seen. The gravel was almost entirely bare of epibiota. There were occasional rock outcrops or cobbles which had epibiota including encrusting calcareous algae, the sea fan Eunicella verrucosa, cup corals, Caryophyllia smithii, hydroids and a sea urchin Echinus esculentus. The variety of species visible on the surface is small and therefore identification to biotope not usually possible. Historical records from sampling surveys that used grabs and dredges at the end of the 19th century and early 20th century suggest similar species present then. Illustrations of some of the infaunal communities from work in the 1920’s is included in this report to provide a context to the epifaunal photographs.

Spatio-temporal variability in ammonia oxidation and ammonia oxidising bacteria and archaea in coastal sediments of the Western English Channel

The abundance of ammonia-oxidising bacterial (AOB) and ammonia-oxidising archaeal (AOA) (amoA) genes and ammonia oxidation rates were compared bimonthly from July 2008 to May 2011 in 4 contrasting coastal sediments in the western English Channel. Despite a higher abundance of AOA amoA genes within all sediments and at all time-points, rates of ammonia oxidation correlated with AOB and not AOA amoA gene abundance. Sediment type was a major factor in determining both AOB amoA gene abundance and AOB community structure, possibly due to deeper oxygen penetration into the sandier sediments, increasing the area available for ammonia oxidation. Decreases in AOB amoA gene abundance were evident during summer and autumn, with maximum abundance and ammonia oxidation rates occurring in winter and early spring. PCR-DGGE of AOB amoA genes indicated that no seasonal changes to community composition occurred; however, a gradual movement in community composition occurred at 3 of the sites studied. The lack of correlation between AOA amoA gene abundance and ammonium oxidation rates, or any other environmental variable measured, may be related to the higher spatial variation amongst measurements, obscuring temporal trends, or the bimonthly sampling, which may have been too infrequent to capture temporal variability in the deposition of fresh organic matter. Alternatively, AOA may respond to changing substrate concentrations by an increase or decrease in transcript rather than gene abundance.

Recovery from TBT pollution in English Channel environments: A problem solved?

Following recognition of effects in the 1980s, tributyltin (TBT) has been monitored at sites in the English Channel to evaluate the prognosis for biota – spanning the introduction of restrictions on TBT use on small boats and the recent phase-out on the global fleet. We describe how persistence and impact of TBT in clams Scrobicularia plana has changed during this period in Southampton Water and Poole Harbour. TBT contamination (and loss) in water, sediment and clams reflects the abundance and type of vessel activity: half-times in sediment (up to 8y in Poole, 33y in Southampton) are longest near commercial shipping. Recovery of clam populations – slowest in TBT-contaminated deposits – provides a useful biological measure of legislative efficacy in estuaries. On rocky shores, recovery from imposex in Nucella lapillus is evident at many sites but, near ports, is prolonged by shipping impacts, including sediment legacy, for example, in the Fal.

Abundance of a chlorophyll a precursor and the oxidation product hydroxychlorophyll a during seasonal phytoplankton community progression in the Western English Channel

This study presents the first in-situ measurements of the chlorophyll a oxidation product, hydroxychlorophyll a as well as the chlorophyll a precursor, chlorophyll aP276 conducted over an annual cycle. Chlorophyll a oxidation products, such as hydroxychlorophyll a may be associated with the decline of algal populations and can act as an initial step in the degradation of chlorophyll a into products which can be found in the geochemical record, important for studying past climate change events. Here, hydroxychlorophyll a and chlorophyll aP276 were measured at the long-term monitoring station L4, Western Channel Observatory (UK, www.westernchannelobservatory.org) over an annual cycle (2012). Weekly measurements of phytoplankton species composition and abundance enabled detailed analysis of possible sources of hydroxychlorophyll a. Dinoflagellates, 2 diatom species, the prymnesiophyte Phaeocystis spp. and the coccolithophorid Emiliania huxleyi were all associated with hydroxychlorophyll a occurrence. However, during alternate peaks in abundance of the diatoms, no association with hydroxychlorophyll a occurred, indicating that the oxidation of chlorophyll a was dependant not only on species but also on additional factors such as the mode of mortality, growth limiting factor (i.e. nutrient concentration) or phenotypic plasticity. Surface sediment samples contained 10 times more hydroxychlorophyll a (relative to chlorophyll a) than pelagic particulate samples, indicating that more chlorophyll a oxidation occurred during sedimentation or at the sediment���water interface, than in the pelagic environment. In addition, chlorophyll aP276 correlated with chl-a concentration, thus supporting its assignment as a chl-a precursor.

Dynamic responses of the benthic bacterial community at the Western English Channel observatory site L4 are driven by deposition of fresh phytodetritus

The impact of the seasonal deposition of phytoplankton and phytodetritus on surface sediment bacterial abundance and community composition was investigated at the Western English Channel site L4. Sediment and water samples were collected from January to September in 2012, increasing in frequency during periods of high water column phytoplankton abundance. Compared to the past two decades, the spring bloom in 2012 was both unusually long in duration and contained higher than average biomass. Within spring months, the phytoplankton bloom was well mixed through the water column and showed accumulations near the sea bed, as evidenced by flow cytometry measurements of nanoeukaryotes, water column chlorophyll a and the appearance of pelagic phytoplankton at the sediment. Measurements of chlorophyll and chlorophyll degradation products indicated phytoplankton material was heavily degraded after it reached the sediment surface: the nature of the chlorophyll degradation products (predominantly pheophorbide, pyropheophorbide and hydroxychlorophyllone) was indicative of grazing activity. The abundance of bacterial 16S rRNA genes g−1 sediment (used as a proxy for bacterial biomass) increased markedly with the onset of the phytoplankton bloom, and correlated with measurements of chlorophyll at the surface sediment. Together, this suggests that bacteria may have responded to nutrients released via grazing activity. In depth sequencing of the 16S rRNA genes indicated that the composition of the bacterial community shifted rapidly through-out the prolonged spring bloom period. This was primarily due to an increase in the relative sequence abundance of Flavobacteria.

On the function of the internal cavity of histone deacetylase protein 8: R37 is a crucial residue for catalysis

Biochemical studies reveal that a conserved arginine residue (R37) at the centre of the 14 angstrom internal cavity of histone deacetylase (HDAC) 8 is important for catalysis and acetate affinity. Computational studies indicate that R37 forms multiple hydrogen bonding interactions with the backbone carbonyl oxygen atoms of two conserved glycine residues, G303 and G305, resulting in a 'closed' form of the channel. One possible rationale for these data is that water or product (acetate) transit through the catalytically crucial internal channel of HDAC8 is regulated by a gating interaction between G139 and G303 tethered in position by the conserved R37. (C) 2011 Elsevier Ltd. All rights reserved.

Downstream changes in the transport and storage of sediment-associated contaminants (P, Cr and PCBs) in agricultural and industrialized drainage basins

Samples of suspended, floodplain and channel bed sediment have been used to examine downstream changes in ediment-associated contaminant transport and storage in contrasting rivers in Yorkshire, UK. The concentrations of hosphorus, chromium and selected PCBs associated with sediment in the River Aire and its main tributary, the River Calder, which drain an urbanized and industrialized catchment, are considerably higher than those in the relatively unpolluted River Swale, which drains an agricultural catchment. Concentrations of sediment-associated contaminants in the Aire/Calder system increase downstream, reflecting the location of urban and industrial areas in the middle and lower reaches, and the location of point source inputs, such as sewage treatment works. The ontaminant concentrations associated with floodplain and channel bed sediment in the Rivers Aire and Calder are high, particularly in the lower reaches. This, combined with measurements of sediment storage on the floodplain and channel bed, indicate that significant storage of sediment-associated contaminants occurs in the Rivers Aire and Calder.

Source as a controlling factor on the quality and interpretation of sediment magnetic records from the northern North Atlantic

Magnetic properties of eight particle size ranges from nine locations in Iceland and 26 locations in southern Greenland reveal the importance of source variation for our understanding of paleomagnetic and environmental magnetic records in the marine environment. These terrestrial samples show varying degrees of particle size dependence with all samples showing that the silt fraction possesses greater concentrations of ferrimagnetic minerals than either clay or sand. Fine pseudo-single domain (PSD) size magnetic grains dominate the magnetic assemblage of all Icelandic fractions. In contrast, Greenlandic samples possess greater variation in magnetic grain size; only fine silt and clay are as magnetically fine as the Icelandic PSD grains, while Greenlandic silts and sands are dominated by coarser PSD and multi-domain grains. These observations from potential marine sediment sources suggest that the silt size fraction is a likely driver for much of the concentration-dependent parameters derived from bulk magnetic records and that the magnetic grain size of the silt fraction can be used to discriminate between Icelandic and Greenlandic sources. Using these results to examine magnetic grain size records from marine sediment cores collected across the northern North Atlantic suggests that source, not just transport-controlled physical grain-size, has a significant impact on determining the magnetic grain size at a particular location. Homogeneity of magnetic grain size in Icelandic sediments at least partially explains the consistent quality of paleomagnetic records derived from cores surrounding Iceland and their ability to buffer large environmental changes. © 2013 Elsevier B.V.

Predicting critical source areas of sediment in headwater catchments

Mitigation of diffuse nutrient and sediment delivery to streams requires successful identification andmanagement of critical source areas within catchments. Approaches to predicting high risk areas forsediment loss have typically relied on structural drivers of connectivity and risk, with little considera-tion given to process driven water quality responses. To assess the applicability of structural metrics topredict critical source areas, geochemical tracing of land use sources was conducted in three headwateragricultural catchments in Co. Down and Co. Louth, Ireland, within a Monte Carlo framework. Outputswere applied to the inverse optimisation of a connectivity model, based on LiDAR DEM data, to assess theefficacy of land use risk weightings to predict sediment source contributions over the 18 month studyperiod in the Louth Upper, Louth Lower and Down catchments. Results of the study indicated sedimentproportions over the study period varied from 6 to 10%, 84 to 87%, 4%, and 2 to 3% for the Down Catch-ment, 79 to 85%, 9 to 17%, 1 to 3% and 2 to 3% in the Louth Upper and 2 to 3%, 79 to 85%, 10 to 17%and 2 to 3% in the Louth Lower for arable, channel bank, grassland, and woodland sources, respectively.Optimised land use risk weightings for each sampling period showed that at the larger catchment scale,no variation in median land use weightings were required to predict land use contributions. However,for the two smaller study catchments, variation in median risk weightings was considerable, which mayindicate the importance of functional connectivity processes at this spatial scale. In all instances, arableland consistently generated the highest risk of sediment loss across all catchments and sampling times.This study documents some of the first data on sediment provenance in Ireland and indicates the needfor cautious consideration of land use as a tool to predict critical source areas at the headwater scale

Challenges in mercury speciation and fractionation in soil and sediment

This investigation focused on the development, test and validation of methodologies for mercury fractionation and speciation in soil and sediment. After an exhaustive review of the literature, several methods were chosen and tested in well characterised soil and sediment samples. Sequential extraction procedures that divide mercury fractions according to their mobility and potential availability in the environment were investigated. The efficiency of different solvents for fractionation of mercury was evaluated, as well as the adequacy of different analytical instruments for quantification of mercury in the extracts. Kinetic experiments to establish the equilibrium time for mercury release from soil or sediment were also performed. It was found that in the studied areas, only a very small percentage of mercury is present as mobile species and that mobility is associated to higher aluminium and manganese contents, and that high contents of organic matter and sulfur result in mercury tightly bound to the matrix. Sandy soils tend to release mercury faster that clayey soils, and therefore, texture of soil or sediment has a strong influence on the mobility of mercury. It was also understood that analytical techniques for quantification of mercury need to be further developed, with lower quantification limits, particularly for mercury quantification of less concentrated fractions: water-soluble e exchangeable. Although the results provided a better understanding of the distribution of mercury in the sample, the complexity of the procedure limits its applicability and robustness. A proficiency-testing scheme targeting total mercury determination in soil, sediment, fish and human hair was organised in order to evaluate the consistency of results obtained by different laboratories, applying their routine methods to the same test samples. Additionally, single extractions by 1 mol L-1 ammonium acetate solution, 0.1 mol L-1 HCl and 0.1 mol L-1 CaCl2, as well as extraction of the organometallic fraction were proposed for soil; the last was also suggested for sediment and fish. This study was important to update the knowledge on analytical techniques that are being used for mercury quantification, the associated problems and sources of error, and to improve and standardize mercury extraction techniques, as well as to implement effective strategies for quality control in mercury determination. A different, “non chemical-like” method for mercury species identification was developed, optimised and validated, based on the thermo-desorption of the different mercury species. Compared to conventional extraction procedures, this method has advantages: it requires little to no sample treatment; a complete identification of species present is obtained in less than two hours; mercury losses are almost neglectable; can be considered “clean”, as no residues are produced; the worldwide comparison of results obtained is easier and reliable, an important step towards the validation of the method. Therefore, the main deliverables of this PhD thesis are an improved knowledge on analytical procedures for identification and quantification of mercury species in soils and sediments, as well as a better understanding of the factors controlling the behaviour of mercury in these matrices.

Bauxite residue (Red mud) as a pulverised fuel ash substitute in the manufacture of lightweight aggregate

This study looked at the potential of bauxite residue or red mud to be used in the manufacture of lightweight aggregate in replacement of pulverised fuel ash (PFA), commonly used as a way of recycling problematic wastes. The percentage replacements of red mud with PFA were as follows: 25, 31, 38, 44 and 50%. These were blended in a mix with waste excavated clay and sewage sludge – all from the Chongqing municipality in China. Lightweight pellets were produced using a Trefoil rotary kiln and were sintered to 1200 °C. Results showed that 44 % bauxite residue replacement produced lightweight pellets with the highest compressive strength, highest density and largest water holding capacity. This would be expected in materials with a low level of silicates, which causes insufficient glass phase viscosity and therefore poor bloating during firing; producing an aggregate with a higher density but with open pores that allowed for larger water absorption. All ratios of red mud aggregates were significantly reduced in pH after firing to around pH 8, and this reduced the leachability of the aggregates to levels below those set by the European landfill directive (2003/33/EC).

Hydrodynamic and sediment fluxes through the inlets of the Ria Formosa

Tese de dout., Ciências do Mar, da Terra e do Ambiente (Ciências do Mar-Oceanografia Física), Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2011

Sediment dynamics and tidal inlet relocation in mixed-energy settings: the case of Ancão inlet (Algarve - Portugal)

Tese de dout., Ciências do Mar, Faculdade de Ciências do Mar e do Ambiente, Univ. do Algarve, 2003

Sources and transport of surface sediment and metals in B.C. fjord, Tahsis Inlet

Senior thesis written for Oceanography 445

Abrasion, transport and distribution of sediment in selected streams of Southern Ontario and Western New York /

The rate of decrease in mean sediment size and weight per square metre along a 54 km reach of the Credit River was found to depend on variations in the channel geometry. The distribution of a specific sediment size consist of: (1) a transport zone; (2) an accumulation zone; and (3) a depletion zone. These zones shift downstream in response to downcurrent decreases in stream competence. Along a .285 km man-made pond, within the Credit River study area, the sediment is also characterized by downstream shifting accumulation zones for each finer clast size. The discharge required to initiate movement of 8 cm and 6 cm blocks in Cazenovia Creek is closely approximated by Baker and Ritter's equation. Incipient motion of blocks in Twenty Mile Creek is best predicted by Yalin's relation which is more efficient in deeper flows. The transport distance of blocks in both streams depends on channel roughness and geometry. Natural abrasion and distribution of clasts may depend on the size of the surrounding sediment and variations in flow competence. The cumulative percent weight loss with distance of laboratory abraded dolostone is defined by a power function. The decrease in weight of dolostone follows a negative exponential. In the abrasion mill, chipping causes the high initial weight loss of dolostone; crushing and grinding produce most of the subsequent weight loss. Clast size was found to have little effect on the abrasion of dolostone within the diameter range considered. Increasing the speed of the mill increased the initial amount of weight loss but decreased the rate of abrasion. The abrasion mill was found to produce more weight loss than stream action. The maximum percent weight loss determined from laboratory and field abrasion data is approximately 40 percent of the weight loss observed along the Credit River. Selective sorting of sediment explains the remaining percentage, not accounted for by abrasion.