João Serôdio

Frequently asked questions about in vivo chlorophyll fluorescence: practical issues

The aim of this educational review is to provide practical information on the hardware, methodology, and the hands on application of chlorophyll (Chl) a fluorescence technology. We present the paper in a question and answer format like frequently asked questions. Although nearly all information on the application of Chl a fluorescence can be found in the literature, it is not always easily accessible. This paper is primarily aimed at scientists who have some experience with the application of Chl a fluorescence but are still in the process of discovering what it all means and how it can be used. Topics discussed are (among other things) the kind of information that can be obtained using different fluorescence techniques, the interpretation of Chl a fluorescence signals, specific applications of these techniques, and practical advice on different subjects, such as on the length of dark adaptation before measurement of the Chl a fluorescence transient. The paper also provides the physiological background for some of the applied procedures. It also serves as a source of reference for experienced scientists.

NONDESTRUCTIVE TRACING OF MIGRATORY RHYTHMS OF INTERTIDAL BENTHIC MICROALGAE USING IN VIVO CHLOROPHYLL A FLUORESCENCE1,2

In vivo chlorophyll (Chl) a fluorescence was measured in undisturbed intertidal sediments with the purpose of tracing the vertical migratory rhythms of benthic microalgae. A pulse amplitude fluorometer, an instrument which does not require physical contact with the sample, was used, thus allowing successive measurements to be taken on the same sample without causing any type of disturbance to the sediment structure. The basis of the method is the possibility to detect changes in the Chl a concentration near the sediment surface caused by the vertical movement of the microalgae. This requires the verification of two conditions: the possibility to follow changes in the sediment Chl a content from fluorescence intensity, and a sediment photic depth smaller than the vertical distances covered by the moving microalgae. Both conditions were experimentally verified in intertidal muddy sediments of the Tagus estuary, Portugal. In vivo fluorescence was shown to vary linearly with the sediment Chl a content, and the sediment photic depth was estimated to reach 0.27 mm, a value clearly smaller than the reported depths for microalgal migrations. Sediment samples kept under in situ conditions exhibited large hourly Variations (over 400%) in the Chl a fluorescence intensity, which were closely synchronized with the daytime periods of emersion. The rhythmic fluctuations in Chl a fluorescence were confirmed further to represent microalgal migration by (1) its endogenous nature (fluorescence continued to follow diurnal and tidal cycles after removal of environmental stimuli), (2) its dependence on the vertical distribution of the microalgal population within the sediment (vertically homogenized samples failed to display fluorescence variations), and (3) the lack of significant temperature and light effects on the fluorescence emission under in situ conditions (tested in three species representative of the main groups found in the studied microphytobenthic communities—the diatom Phaeodactylum tricornutum (Böhlin), the cyanobacterium Spirulina maxima (Setch. et Gard.), and the euglenophyte Euglena granulata (Klebs) Lemm.). The results obtained indicate that, in spite of the potential concurrent effects of factors other than the Chl a concentration on the fluorescence intensity, in vivo Chl a fluorescence can be used to trace nondestructively the migratory behavior of benthic microalgae.

Trends in the Discovery of New Marine Natural Products from Invertebrates over the Last Two Decades – Where and What Are We Bioprospecting?

It is acknowledged that marine invertebrates produce bioactive natural products that may be useful for developing new drugs. By exploring untapped geographical sources and/or novel groups of organisms one can maximize the search for new marine drugs to treat human diseases. The goal of this paper is to analyse the trends associated with the discovery of new marine natural products from invertebrates (NMNPI) over the last two decades. The analysis considers different taxonomical levels and geographical approaches of bioprospected species. Additionally, this research is also directed to provide new insights into less bioprospected taxa and world regions. In order to gather the information available on NMNPI, the yearly-published reviews of Marine Natural Products covering 1990–2009 were surveyed. Information on source organisms, specifically taxonomical information and collection sites, was assembled together with additional geographical information collected from the articles originally describing the new natural product. Almost 10000 NMNPI were discovered since 1990, with a pronounced increase between decades. Porifera and Cnidaria were the two dominant sources of NMNPI worldwide. The exception was polar regions where Echinodermata dominated. The majority of species that yielded the new natural products belong to only one class of each Porifera and Cnidaria phyla (Demospongiae and Anthozoa, respectively). Increased bioprospecting efforts were observed in the Pacific Ocean, particularly in Asian countries that are associated with the Japan Biodiversity Hotspot and the Kuroshio Current. Although results show comparably less NMNPI from polar regions, the number of new natural products per species is similar to that recorded for other regions. The present study provides information to future bioprospecting efforts addressing previously unexplored taxonomic groups and/or regions. We also highlight how marine invertebrates, which in some cases have no commercial value, may become highly valuable in the ongoing search for new drugs from the sea.

A model for describing the light response of the nonphotochemical quenching of chlorophyll fluorescence.

The operation of photosynthetic energy-dissipating processes is commonly characterized by measuring the light response of the nonphotochemical quenching (NPQ) of chlorophyll fluorescence, or NPQ versus E curves. This study proposes a mathematical model for the quantitative description of the generic NPQ versus E curve. The model is an adaptation of the Hill equation and is based on the close dependence of NPQ on the xanthophyll cycle (XC). The model was tested on NPQ versus E curves measured in the plant Arabidopsis thaliana and the diatom Nitzschia palea, representing the two main types of XC, the violaxanthin–antheraxanthin–zeaxanthin (VAZ) type and the diadinoxanthin–diatoxanthin (DD–DT) type, respectively. The model was also fitted to a large number of published light curves, covering the widest possible range of XC types, taxa, growth conditions, and experimental protocol of curve generation. The model provided a very good fit to experimental and published data, coping with the large variability in curve characteristics. The model was further used to quantitatively compare the light responses of NPQ and of PSII electron transport rate, ETR, through the use of indices combining parameters of the models describing the two types of light–response curves. Their application to experimental and published data showed a systematic large delay of the buildup of NPQ relatively to the saturation of photochemistry. It was found that when ETR reaches saturation, NPQ is on average still below one fifth of its maximum attainable level, which is only reached at irradiances about three times higher. It was also found that organisms having the DD–DT type of XC appeared to be able to start operating the XC at lower irradiances than those of the VAZ type.

A CHLOROPHYLL FLUORESCENCE INDEX TO ESTIMATE SHORT‐TERM RATES OF PHOTOSYNTHESIS BY INTERTIDAL MICROPHYTOBENTHOS1

An index based on chl a fluorescence quenching analysis was tested as a predictor of photosynthetic rates of undisturbed intertidal microphytobenthic assemblages. The fluorescence index, Pfluo, was derived from the combination of different chl a fluorescence parameters chosen to represent the two main sources of short‐term variability in the community‐level microphytobenthic photosynthesis: 1) the quantum yield of photosynthesis of the microalgae present in the photic zone of the sediment, φP, and 2) the community‐level efficiency of photosynthetic light absorption, ɛ, determined by the microalgal concentration in the photic zone. Variations in φP were traced by the fluorescence index ΔF/Fm′ (the effective quantum yield of charge separation at PSII), whereas changes in ɛ were followed by the fluorescence parameter Fo (dark or minimum fluorescence level). Gross photosynthetic rate, P, and fluorescence parameters were measured nondestructively and simultaneously under in situ conditions, on the same samples, using oxygen microelectrodes and pulse amplitude modulation fluorometry, respectively. Despite the large and uncorrelated hourly variability in irradiance, photosynthetic rate, and fluorescence parameters included in Pfluo, highly significant correlations between Pfluo and P were found for all the sampling periods, encompassing hourly, biweekly, and seasonal time scales. The variability in P explained by Pfluo ranged from 84.3% to 91.4% when sampling periods were considered separately and reached 81.1% when all data were pooled. The results of the study show that despite its simplicity, the index Pfluo can be used to trace short‐term variations in the photosynthetic rate of undisturbed microphytobenthic assemblages undergoing rhythmic vertical migration.

The application of variable chlorophyll fluorescence to microphytobenthic biofilms

Community assemblages of diatoms, green algae and cyanobacteria comprise the microphytobenthos (MPB), which inhabit benthic sediment ecosystems (Admiraal 1984; Underwood and Kromkamp 1999; Consalvey et al. 2004). Particular attention has been paid to the analysis of intertidal soft sediment systems, e.g. cohesive mudflat and sandy substrata typical of estuarine habitats. Variable chlorophyll fluorescence has been applied to these systems since the 1990s, in an attempt to investigate the primary productivity and photophysiology of the integrated biofilms, when viewed as a “black box system”, and also at the species level (Sections 5, 6 and 7). These transient (i.e. temporary) biofilms are not confined to such soft sediment habitats however, and more recently application of fluorescence methodologies has been applied to biofilms inhabiting rocky shores and stromatolite systems (Kromkamp et al. 2007; Perkins et al. 2007). However the large majority of published work has centred upon benthic soft-sediment biofilms, due to their important ecosystem functions of carbon flow and sediment stability (Underwood and Kromkamp 1999). In the former their high magnitude of productivity fuels carbon flow through invertebrate and bacterial food webs to support important trophic levels of anthropogenically exploited taxa, including coastal fish and shell fisheries and coastal avifauna. In the case of sediment stability, biogenic exopolymers, usually referred to as extracellular polymeric substances (EPS), produced by the MPB in part to facilitate mobility, may contribute significantly to sediment stability, hence increasing the sediment resistance to hydrodynamic stresses and thus resistance to coastal erosion (e.g. Underwood and Kromkamp 1999 and citations there-in). Finally, the photosynthetic production of oxygen can be regarded as an important ecosystem function.

Light response curves for Gelidium sesquipedale from different depths, determined by two methods: O2 evolution and chlorophyll fluorescence

Photosynthesis-light response curves of Gelidium sesquipedale from the west coast of Portugal (Cape Espichel) were determined at four different depths, 3, 10, 15 and 22 m. Data acquisition using chlorophyll a fluorescence methodology and oxygen electrode measurements were compared. Response curves were determined over an increasing range of irradiance values (I), from darkness to 900 μmol photon m-2 s-1 PAR. In general, light response curves obtained for G. sesquipedale showed a similar pattern whether determined by the chlorophyll fluorescence method or by oxygen evolution. The photosynthetic capacity of G. sesquipedale decreased with depth, as expected, revealing a ‘sun’ and ‘shade’ acclimation pattern, between shallow and deeper waters.

In situ measurements of photosynthetic activity and respiration of intertidal benthic microalgal communities undergoing vertical migration

Abstract This paper presents the results of a field study on the short-term variability in photosynthetic activity of inter-tidal microphytobenthos using non-destructive techniques in situ. Photosynthetic rate (measured using oxygen microelectrodes), productive biomass and photosynthetic efficiency (dark-fluorescence and effective quantum efficiency of PSII, respectively, measured by PAM fluorometry) were measured in situ during a low-tide exposure period on an intertidal mudflat in the Tagus Estuary, Portugal. Community photosynthesis displayed large temporal variation. Maximum activity (24.3 mmol O2 m-2 h-1) was found at noon while minimum activity (8.7 mmol O2 m-2 h-1) was found at the end of the exposure period. Productive biomass followed a similar pattern. During the course of the exposure period, productive biomass peaked halfway through, and decreased by 80% towards the end of the exposure period. These changes in productive biomass were followed by significant changes in the species composition/cell size as well as changes in photosynthetic efficiency of the microphytobenthic community in the surface sediment. The obtained results therefore suggest that microphytobenthic community-level photosynthesis is controlled by migratory movements of microalgae and by variations in photosynthetic efficiency. The latter could be induced by changes in the species composition/cell size in the photic zone due to microalgal migrations. It is suggested that the migration pattern and, hence, photosynthesis is linked to changes in salinity, temperature and light, changes that are difficult to simulate accurately in the laboratory. Respiration rates obtained during the day were much higher than those obtained at night, and also displayed a marked hour-to-hour variation. Depth integrated respiration within the photosynthesis zone (0.33 mm) represented 80 to 90% of the respiration in the entire oxic zone, suggesting a tight coupling between photosynthesis and respiration.

Photophysiology of kleptoplasts: photosynthetic use of light by chloroplasts living in animal cells

Kleptoplasty is a remarkable type of photosynthetic association, resulting from the maintenance of functional chloroplasts—the ‘kleptoplasts’—in the tissues of a non-photosynthetic host. It represents a biologically unique condition for chloroplast and photosynthesis functioning, occurring in different phylogenetic lineages, namely dinoflagellates, ciliates, foraminiferans and, most interestingly, a single taxon of metazoans, the sacoglossan sea slugs. In the case of sea slugs, chloroplasts from macroalgae are often maintained as intracellular organelles in cells of these marine gastropods, structurally intact and photosynthetically competent for extended periods of time. Kleptoplasty has long attracted interest owing to the longevity of functional kleptoplasts in the absence of the original algal nucleus and the limited number of proteins encoded by the chloroplast genome. This review updates the state-of-the-art on kleptoplast photophysiology, focusing on the comparative analysis of the responses to light of the chloroplasts when in their original, macroalgal cells, and when sequestered in animal cells and functioning as kleptoplasts. It covers fundamental but ecologically relevant aspects of kleptoplast light responses, such as the occurrence of photoacclimation in hospite, operation of photoprotective processes and susceptibility to photoinhibition. Emphasis is given to host-mediated processes unique to kleptoplastic associations, reviewing current hypotheses on behavioural photoprotection and host-mediated enhancement of photosynthetic performance, and identifying current gaps in sacoglossan kleptoplast photophysiology research.

Endogenous versus environmental control of vertical migration by intertidal benthic microalgae

The vertical migratory behaviour of estuarine microphytobenthos, i.e. the biofilm-forming microalgae inhabiting intertidal sediments, is probably a significant factor for their success in this extreme and unstable environment. The present work aimed to assess the relative role of endogenous versus environmental control of benthic microalgal vertical migratory behaviour. This was done by comparing the patterns of vertical migration in undisturbed sediment samples kept under constant conditions of darkness and low light with those in ambient light conditions, by measuring the changes in the surface microalgal biomass during daytime low-tide periods. The results showed that the formation of a biofilm was a two-phase process. It began with a relatively small accumulation of cells at the surface, starting hours before the beginning of the light period and endogenously driven. However, the full formation of the biofilm required exposure to light by the expected beginning of the photoperiod, which further promoted upward migration and accelerated the cell accumulation at the surface. In the absence of light, upward migration was interrupted and the incipient biofilm began to disaggregate. The relative importance of the endogenously controlled behaviour varied during the spring–neap tidal cycle, reaching a maximum on those days when low tide occurred in the middle of the day, suggesting its entrainment by the duration of light exposure on previous days. The regulation of the surface cell concentration during daytime low tides was found to be strongly dependent on exogenous factors, particularly irradiance. The spontaneous disaggregation of the biofilm shortly before the end of the low-tide period (due to tidal flood or sunset), both under constant as well as ambient light conditions, suggested the presence of an endogenously controlled positive geotaxis.