Sample collection

To examine the temporal variations in benthic foraminiferal assemblage structure, bottom water and surface sediment samples were collected on a monthly basis by SCUBA divers at the NERC National Facility for Scientific Diving facility (NFSD) from September 2008 to August 2009. During each dive, two replicate samples of the surface sediment and bottom water were collected. The top 1 cm of the soft sediment was collected into plastic bags at the seabed. Following sample collection, the two replicate sediment samples were preserved and stored in 95% ethanol made up as 1 g L−1 _{Rose Bengal solution. The bottom water samples and the}

The samples analysed within this study were obtained from a longer-term time series sediment archive held at the University of St Andrews, which collates the sediment samples collected by the NFSD at the site locality (Dunstaffnage) from 2007 up to the present day. The period of investigation from August 2008 to September 2009 was chosen for analysis because the samples comprised of a series of previously undisturbed and unprocessed sediment samples. In total 24 sediment samples were analysed (two replicate samples for each month). For a detailed account of the sampling employed and the general site conditions, refer to the Appendix.

4.2.3 Foraminiferal analysis

The sediment volume of each replicate was calculated; following methods set out in Chapter 2.3.2. The sediment samples were then wet sieved at 63 µm using a fine water spray. The sieved samples were left to oven dry at 40o_{C. The total weight of the dry residues was then calculated.}

From each of the samples, a target of 300 Rose Bengal stained specimens were picked using a 0000 paintbrush. In samples with low foraminiferal density, at least 100 Rose Bengal stained specimens were picked where possible. A minimum number of 100 specimens have been deemed sufficient for detecting up to 99% of species that make up ≥ 5 % of an assemblage (Fatela and Taborda, 2002) and 95% species making up to 3% of an assemblage (Dennison and Hay, 1967). In order to minimise the over-estimation of ‘live’ specimens by Rose Bengal staining (Bernhard 1988, 2000), a strict staining protocol was adopted. Specimens were considered ‘live’ when individuals were stained bright pink or red. In situations where the degree of staining of a specimen is unclear, the specimen was directly compared to examples of perfectly stained specimens within each individual sample. Special attention was given to assessing the degree of staining of agglutinates and miliolids, as it was difficult to recognise colouration within these taxa. Consequently, specimens within these taxonomic groups were evaluated following protocols set out in Schönfeld et al. (2012); whereby dry specimens were wetted to assess the degree of staining.

4.2.3.1 Foraminiferal species identification

Specimens were then classified into species based on their morphological characteristics primarily using taxonomy descriptions from Loeblich and Tappan (1987, 1992), Haynes (1973), Austin (1991) and Murray (2003a). This study also utilises the new integrated taxonomic framework of Ammonia presented in Chapter 3, to re-evaluate the diversity of Ammonia species found at the sampling location. This taxonomic framework revealed the presence of three genetically distinct sympatric species of Ammonia in the Scottish shelf seas (Chapter 3, Table

3.10). As previously discussed in Chapter 3 (Table 3.7), these sympatric genotypes can be clearly delineated based on key diagnostic morphological test characteristics, which are visible under a light microscope. Specimens of Ammonia identified in this study are provisionally ascribed to a genotype based upon their morphological features.

4.2.3.2 Foraminiferal community structure

The foraminiferal community structure was derived from counting live (stained) specimens from each month. Initially the assemblage structure for each of the replicate samples was individually analysed. However, this yielded insufficient numbers for the robust determination of the foraminiferal community structure. As a consequence, in order to obtain statistically significant census counts, the counts from the two replicates were pooled together and then analysed. The absolute abundance of stained individuals (total standing stock) calculated for each month was standardised to a sediment volume of 100 ml. To provide an assessment of the degree of spatial heterogeneity at this site, the standard error of the standing stock of the two replicate samples was calculated. In addition, the percentage relative abundance of each species was calculated for each month (the two replicate samples were aggregated).

For each month diversity indices including: species richness (the total number of species), Pileou species evenness index, Shannon Weiner diversity index (H’), and Fisher Alpha diversity index were calculated. The foraminiferal diversity measures were calculated using PAST statistics v.2.17.

4.2.3.3 Population dynamics of Ammonia species

To evaluate the population dynamics of Ammonia species identified at this site locality, the maximum test diameter of each Ammonia specimen was measured under a binocular microscope using a calibrated eyepiece graticule. The Ammonia specimens were then grouped into size classes based upon the range of maximum test diameters identified. The population dynamics of each Ammonia species were calculated as a percentage of the relative abundance of each size fraction. This allows for the identification of periods of peak reproduction, which is commonly expressed by a shift towards a dominance of smaller test sizes in the population structure (Murray, 1982).

4.2.4 Environmental variables