Quantifying primary production of microphytobenthos: application of optical methods

Edward Morris

    Research output: PhD ThesisPhD thesis


    Intertidal mudflats are an important component of estuaries. Benthic microalgae, also called microphytobenthos (MPB) are the main primary producers on these mudflats, and they can contribute up to 50% of total primary production of the estuary. Quantifying MPB biomass and primary production is, however, difficult because of their patchy occurrence and rapid population dynamics. To solve these problems, new approaches are necessary. The potential of virtually instantaneous measurements of photosynthesis, biomass and absorption properties of MPB biofilms carried out in a truly non-invasive way at a range of scales using PAM fluorescence and reflectance methodologies is particularly attractive for estuarine primary production studies.
    Quantitative investigations of the relationship between PB (µmol O2 (mg chl a)-1 h-1 or µmol C (mg chl a)-1 h-1), and electron transport rate (ETR, µmol e- mg chl a-1 s-1) derived using pulse amplitude modulated (PAM) fluorometry, were carried out over a range of temperatures and growth rates using suspensions of MPB. Extreme temperatures and very low growth rates were shown to affect the functional relationship between PB and ETR, but in general the relationship between ETR and PB was quite robust, as shown in Chapter 2 and 3. When the PAM methodology was used to measure the photosynthetic parameters of a biofilm grown on undisturbed sediments over 21 days (chapter 3), deviations between in-situ and slurry methods were largest at very low biomass and very high biomass, and were most likely caused by optical artefacts in the in-situ methodology e.g. interference from background fluorescence and the contribution of ‘deep layer fluorescence’. Net primary production of the biofilm was calculated using a vertically resolved primary production model, and was closely coupled to observed changes in biomass, which suggested that both Carbon to chl a ratios and respiration rates of the biofilm showed little variability over time. With incorporation of the derived temperature relationship, this approach has strong potential for estimating primary carbon production at very high temporal resolution.
    Although minimum fluorescence and hyperspectral reflectance spectra could be adequately used to follow the development of the mesocosm biofilm described in chapter 3, the minimum fluorescence yield was influenced by the photophysiological state of the MPB, and fluorescence quenching caused by photoprotective mechanisms could be mistaken for downward migration. This was further investigated in chapter 4. Fluorescence quenching was observed during daytime emersion in the mesocosm biofilm as well as in other experimentally manipulated biofilms. In these cases the fluorescence decreased, whereas the normalized difference vegetation index (NDVI), derived from the reflectance spectra, remained constant. Interestingly, the changes in fluorescence yield could be derived from the hyperspectral reflectance spectra, and a new index, the normalized difference fluorescence index (NDFI) was developed. Using this NDFI it may be possible to derive the quantum efficiency for photosynthesis, although this needs further investigation.
    At the scale of estuaries estimates of primary production are dominated by the distribution of biomass. We show for a number of estuaries bordering the North Sea that although the average values for [chl a] in surface sediments varies by only a factor of 2, the distribution of [chl a] is highly structured and not very predictable between estuaries, meaning that high spatial coverage and replication is required (chapter 5). Remote sensing is probably the best way to achieve this, and we present a practical algorithm for predicting [chl a + phaeo] of fine grained sediments using the normalised difference vegetation index (NDVI) (which is applicable to many remote sensing platforms). We investigate the effectiveness of minimum fluorescence as a biomass predictor and discuss the use of both techniques for the investigation of MPB vertical migration. Possible further applications of hyper spectral reflectance to the study of intertidal MPB assemblages are also discussed.
    Overall, PAM fluorescence and reflectance methodologies are highly complimentary and together can provide many of the parameters required for quantifying primary production of MPB, yet like all primary production methods, they require careful attention to the assumptions used when applied to field situations.
    Original languageEnglish
    QualificationDoctor (dr.)
    Awarding Institution
    • University of Groningen
    • Heip, C.H.R., Promotor
    Award date20 May 2005
    Place of PublicationGroningen
    Publication statusPublished - 20 May 2005


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