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The successful application of variable chlorophyll fluorescence methodology to higher plants and other phototrophs inspired workers in the 1990s to apply the methods to microalgal communities inhabiting benthic soft sediments, the microphytobenthos (MPB) of estuarine and other coastal habitats. It was quickly identified that particular aspects of the physiology (cellular vertical migration within the sediment matrix), photophysiology (high capacity for down regulation, e.g. NPQ, and chlororespiration in the dark) and the effects of the physical structure of the sediment/biofilm matrix (light attenuation by the matrix itself) confounded the interpretation of fluorescence information obtained. In this chapter, the authors attempt to explain these and other issues pertinent to MPB biofilms and to summarise how methods have been developed to alleviate the problems encountered. Although much work is still needed to fully understand fluorescence data for the MPB, studies to date have been highly illuminating with regard to rhythms of productivity, photoacclimatory mechanisms and the behavioural ecology and physiology of MPB at an integrated biofilm level and at a cellular level. This chapter therefore introduces benthic biofilms and relevant specific fluorescence methodological issues, expands on subsurface fluorescence signal and migration, discusses down regulatory nonphotochemical quenching (NPQ) resulting from xanthophylls cycle induction, compares measurement of electron transport rate proxies, examines light curve methodology, and concludes by comparing fluorescence productivity measurements with those of other methodologies such as oxygen evolution and carbon uptake. Contents 1. Introduction to benthic biofilms 2. The effects of subsurface signal 2.1 Microphytobenthic biofilms on soft sediments 2.2 Stromatolites -the effect of "layered" biofilms 2.3 Deconvolution of depth integrated signals 3. Down regulation through Non Photochemical Quenching 3.1 NPQ and the Xanthophyll cycle in diatoms 3.2 NPQ in the dark 4. The quantification of the microalgal biomass using fluorescence 5. Calculation of electron transport rate: ETR v rETR 5.1 Multiple and single turnover methods 5.2 The MT-method. 5.3 The ST-method 5.4 Assumptions and uncertainties.

Intertidal soft sediment microphytobenthic biofilms are often dominated by diatoms, which are able to regulate their photosynthesis by physiological processes (e.g. down-regulation through the xanthophyll cycle, referred to as non-photochemical quenching, NPQ) and behavioural processes (e.g. vertical cell movement in the sediment -biofilm matrix). This study investigated these 2 processes over a 6 h emersion period using chemical inhibitors under 2 light treatments (ambient and constant light at 300 µmol m -2 s -1). Latrunculin A (Lat A) was used to inhibit cell movement and dithiothreitol (DTT) to inhibit NPQ. HPLC analysis for chlorophyll a and spectral analysis (Normalised Difference Vegetation Index) indicated that Lat A significantly inhibited cell movement. Photosynthetic activity was measured using variable chlorophyll fluorescence and radiolabelled carbon uptake and showed that the non-migratory, Lat A-treated biofilms were severely inhibited as a result of the high accumulated light dose (significantly reduced maximum relative electron transport rate, rETR max , and light utilisation coefficient, α, compared to the migratory DTT and control-treated biofilms). No significant patterns were observed for 14 C data, although a decrease in uptake rate was observed over the measurement period. NPQ was investigated using HPLC analysis of xanthophyll pigments (diatoxanthin and the percentage de-epoxidation of diadinoxanthin), chlorophyll fluorescence (change in maximum fluorescence yield) and the 2nd order spectral derivative index (diatoxanthin index). Patterns between methods varied, but overall data indicated greater NPQ induction in the non-migratory Lat A treatment and little or no NPQ induction in the DTT and control treatments. Overall, the data resulted in 2 main conclusions: (1) the primary response to accumulated light dose was vertical movement, which when inhibited resulted in severe down-regulation/photoinhibition; (2) diatoms down-regulated their photosynthetic activity in response to accumulated light dose (e.g. over an emersion period) using a combination of vertical migration and physiological mechanisms that may contribute to diel and/or tidal patterns in productivity.KEY WORDS: Benthic · Diatom · Down-regulation · Migration · Photophysiology · ProductivityResale or republication not permitted without written consent of the publisher

The structure of intertidal benthic diatoms assemblages in the Tagus estuary was investigated during a 2-year survey, carried out in six stations with different sediment texture. Nonparametric multivariate analyses were used to characterize spatial and temporal patterns of the assemblages and to link them to the measured environmental variables. In addition, diversity and other features related to community physiognomy, such as size-class or life-form distributions, were used to describe the diatom assemblages. A total of 183 diatom taxa were identified during cell counts and their biovolume was determined. Differences between stations (analysis of similarity (ANOSIM), R = 0.932) were more evident than temporal patterns (R = 0.308) and mud content alone was the environmental variable most correlated to the biotic data (BEST, ρ = 0.863). Mudflat stations were typically colonized by low diversity diatom assemblages (H' ~ 1.9), mainly composed of medium-sized motile epipelic species (250-1,000 μm(3) ), that showed species-specific seasonal blooms (e.g., Navicula gregaria Donkin). Sandy stations had more complex and diverse diatom assemblages (H' ~ 3.2). They were mostly composed by a large set of minute epipsammic species (<250 μm(3) ) that, generally, did not show temporal patterns. The structure of intertidal diatom assemblages was largely defined by the interplay between epipelon and epipsammon, and its diversity was explained within the framework of the Intermediate Disturbance Hypothesis. However, the spatial distribution of epipelic and epipsammic life-forms showed that the definition of both functional groups should not be over-simplified.

Abstract. Some benthic foraminifera have the ability to incorporate functional chloroplasts from diatoms (kleptoplasty). Our objective was to investigate chloroplast functionality of two benthic foraminifera (Haynesina germanica and Ammonia tepida) exposed to different irradiance levels (0, 25, 70 µmol photon m −2 s −1 ) using spectral reflectance, epifluorescence observations, oxygen evolution and pulse amplitude modulated (PAM) fluorometry (maximum photosystem II quantum efficiency (Fv/Fm) and rapid light curves (RLC)). Our results clearly showed that H. germanica was capable of using its kleptoplasts for more than 1 week while A. tepida showed very limited kleptoplastic ability with maximum photosystem II quantum efficiency (Fv/Fm = 0.4), much lower than H. germanica and decreasing to zero in only 1 day. Only H. germanica showed net oxygen production with a compensation point at 24 µmol photon m −2 s −1 and a production up to 1000 pmol O 2 cell −1 day −1 at 300 µmol photon m −2 s −1 . Haynesina germanica Fv/Fm slowly decreased from 0.65 to 0.55 in 7 days when kept in darkness; however, it quickly decreased to 0.2 under high light. Kleptoplast functional time was thus estimated between 11 and 21 days in darkness and between 7 and 8 days at high light. These results emphasize that studies about foraminifera kleptoplasty must take into account light history. Additionally, this study showed that the kleptoplasts are unlikely to be completely functional, thus requiring continuous chloroplast resupply from foraminifera food source. The advantages of keeping functional chloroplasts are discussed but more information is needed to better understand foraminifera feeding strategies.

This review covers the literature published for marine natural products isolated from macroalgae and addresses the taxonomic details of source organisms, the chemical types of isolated compounds and the location of sampling sites. The emphasis of this review is on the identification of the most bioprospected taxa and regions, as well as on how these trends have shifted over time.