Degree Name

Doctor of Philosophy


School of Earth and Environmental Sciences / School of Biological Sciences - Faculty of Sciences


Seagrass meadows are of economic importance and high conservation significance; they may also offer a sensitive bioindicator of the condition of the whole estuarine ecosystem. Successful management depends on appropriate monitoring of the health and extent of the seagrass meadows. This field-based spectral reflectance study generated baseline data that optimises the mapping of seagrass meadows, and has laid the groundwork for the monitoring of the physiological condition of meadows by hyperspectral remote sensing. A comprehensive spectral library of the three common seagrass species nominating meadows in south eastern Australia (Zostera capricorni, Posidonia australis and Halophila ovalis) was produced by field spectrometry in order to characterise the spectral response and the variability inherent in the reflectance of these seagrasses growing in their natural environment across different estuaries, habitats, seasons and years. There was small but significant spatial and temporal variability in the spectral reflectance recorded for each seagrass species, and in addition, the level of epibiont fouling of the seagrass leaves also induced significant intraspecific spectral differences. Despite this within-species variability, the seagrasses Z. capricorni, P. australis and H. ovalis were shown to be spectrally distinct across wide regions of the visible wavelengths, notably in those wavelength regions least affected by attenuation in an estuarine water column. Differences in the spectral signatures of the three seagrass species could mainly be attributed to differences in leaf morphology, although photosynthetic and accessory pigment concentrations, determined using high performance liquid chromatography (HPLC) and spectrophotometry, did play an important role in determining reflectance. Within-species differences in seagrass leaf reflectance were linked to differences in leaf pigment composition, predominantly chlorophyll content, but structural changes in the internal anatomy of the leaves and differences in epibiont fouling were also implicated. Piece-wise multiplicative scatter correction (PMSC) was found to be a useful tool for the compilation of spectral libraries since it removes external spectral variation associated with sample illumination and viewing geometry from the reflectance signatures, while highlighting the spectral reflectance variability inherent in the plants themselves. Laboratory spectrometry was used to characterise the spectral changes that occurred in Z. capricorni leaves as the health of this seagrass declined in response to conditions of low and high light stress in laboratory experiments. Zostera capricorni was able to photoacclimate and chromatically acclimate to changes in irradiance over the short term (within days). Low light treated Z. capricorni were subjected to irradiance levels below their compensation point and within one to three months these samples were dead or had lost most of their biomass. Photosynthetic rate, measured by pulse amplitude modulated (PAM) fluoro metry, was reduced and the efficiency of light use maximised in light-deprived Z. capricorni compared with control plants. Low light stress ed leaves displayed lower chlorophyll a:b, zeaxanthin and antheraxanthin concentrations (measured by HPLC) than control plants within two weeks of exposure, but over the longer term showed a general increase in photosynthetic pigment concentration to maximise light harvesting. Orange shoulder (far-green to near–red) reflectance decreased significantly in response to shade treatment in concert with these pigment changes, however, significant increases in the green peak and NIR reflectance of low light stressed Z. capricorni were considered to represent changes in leaf internal structure rather than pigment content. Exposure to high irradiance decreased the efficiency of photosynthetic energy conversion in Z. capricorni leaves compared to samples grown at moderate light levels but increased photosynthetic rate. High light treatment significantly increased the concentration of xanthophyll cycle carotenoids (VAZ, i.e. violaxanthin + antheraxanthin + zeoxanthin) relative to other Z. capricorni leaf pigments and increased the proportion of VAZ pool occurring in the de-epoxidised state compared to controls. Hence, Z. capricorni displayed light-dependent downregulation of photosynthesis in response to high light stress and did not suffer photooxidative damage or reductions in growth or biomass during high light experiments. High light treated seagrass leaves displayed significantly lower green and far-red reflectance and significantly higher orange shoulder reflectance concurrent with these pigment changes and probable changes in leaf structure. In addition, a blue shift of the red edge and a red shift of the green edge were detected in the spectral reflectance of high light stressed seagrass leaves. The anthocyanin content of Z. capricorni leaves was not affected by ambient irradiance levels in these laboratory experiments. Significant linear relationships were observed for Z. capricorni in the concentration of chlorophyll a:b, VAZ:total carotenoids, VAZ:total chlorophyll, and A+Z:VAZ concentrations, and in spectral reflectance at wavelengths 550, 630 and 685 nm, as a function of average daily irradiance measured in the laboratory and in the field. These pigment-based indicators of light stress in Z. capricorni were significantly correlated with a number of hyperspectral reflectance indices and derivative indices, however correlation coefficients were typically low (r < 0.66). The blue-green, blue-orange index [BGBO = (R495/R550) - (R495/R635)] developed in this thesis displayed significant linear relationships with chlorophyll a:b, VAZ:total carotenoids and VAZ:total chlorophyll content and showed the best potential as a remote sensing index for monitoring light stress in seagrass meadows. For an independent data set consisting of field-measured spectral reflectance for three seagrass species, measured chlorophyll a:b content explained 48% of the variation in chlorophyll a:b predicted by the bluegreen, blue-orange index. Estuary managers should look toward the future by establishing high spectral and spatial resolution seagrass mapping and monitoring campaigns. This study has produced the first spectral library of aquatic plant species to take into account the range of spectral variability expected for the species under natural conditions. In addition, the research comprehensively combined ecophysiology and biochemical analysis with hyperspectral data to establish the characteristic spectral reflectance changes occurring in Z. capricorni in response to light stress. The results provide a sound basis for future mapping and monitoring of seagrass species in Australia. Furthermore, this research has laid the groundwork for the early detection of physiological stress in seagrass meadows, including development of a new plant stress index applicable to vegetation in general.