Stories in the sediment : an analysis of phytoplankton pigments within lake sediment to predict and retrodict water quality in New Zealand lakes : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Ecology at Massey University, Manawatū, New Zealand

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When lakes experience an increase in nutrient availability, the phytoplankton and the primary productivity of the lake will also increase. This increase provides a robust means of signifying lake trophic fluctuations. The phytoplankton from the surface of the lake (photic zone) will sediment out, leading to the accumulation of both planktonic and benthic phytoplankton remains at the bottom of the water column. It is these past fluctuations in phytoplankton biomass, which accumulate in the lake sediments, provide indications of past environmental conditions and lake health. This research aimed to assess the potential of phytoplankton pigments preserved/captured within sediments as indicators of lake water quality in both neoliminological and paleolimnological lake sediments from a dataset of 223 New Zealand Lakes (≈ 6% of the lakes in New Zealand) was used for the analysis of surface sediments. These lakes ranged from low elevation lakes (<10 m) to high elevation lakes (up to 1,839 m) and included a range of geomorphic classifications. The catchments ranged from 35,288 m² to 704,470,618 m² and included shallow lakes (<10 m) to deep lakes (up to 445 m). In addition to accessing the use of hyperspectral imaging (HSI) techniques as a method for detecting phytoplankton pigments within sediments. The assessment of calibrating chlorophyll-a (chl-a) detected by HSI in lake core sediment samples to chl-a quantified by analytical chemistry methods (High performance liquid chromatography and spectrophotometry analyses), found that the use of spectrophotometry without acidification provided more consistent results (with an error rate of less than 7.5%) when compared to spectrophotometry analysis with acidification. Additionally, the use of spectrophotometry without acidification for chl-a calibration revealed the potential for a universal equation to be researched. Within lakes, high trophic levels are positively correlated with cyanobacterial dominance. One of the complications of high trophic levels is cyanobacterial blooms, which can be toxic. A reliable pigment indicator for the presence of cyanobacteria is phycocyanin. Therefore, the use of HSI was assessed as an analytical technique utilised for detecting and quantifying the concentration of phycocyanin within lake core sediment samples. This study revealed that phycocyanin could not be detected within the lake sediments within this research. Suggesting that phycocyanin was not incorporated into the lake sediment within the lakes assessed. Additionally, the HSI signal thought to be detecting phycocyanin is potentially measuring chlorophyll-a within the lake core rather than phycocyanin. To predict lake water quality through the lake trophic level index (TLI) several machine learning models were created (regression trees, random forest models, and boosted regression trees) The random forest model was created using the quantification of key phytoplankton pigments within surface sediments plus five static lake physical characteristics this model was the most accurate (within 10% of the TLI). This model provides a predictive tool to access lake TLI using a single sample of surface sediment. This model was then applied to lake core sediment samples to retrodict lake water quality. The assumption of many degraded lakes throughout New Zealand, is that this is of anthropogenic origin. The retrodicted TLI’s suggests, that while anthropogenic influence is exacerbating the degradation of the lakes, prior to this the trophic levels of these lakes did not fluctuate beyond one trophic level (i.e., moving from oligotrophic to mesotrophic). Additionally, apparent in the retrodiction of the lakes is the integration of cyanobacteria indicator pigments into the sediments relatively recently. The integration of these pigments coincides with the arrival of Europeans to the respective areas.