Causes of reduced leaf‐level photosynthesis during strong El Niño drought in a Central Amazon forest

Sustained drought and concomitant high temperature may reduce photosynthesis and cause tree mortality. Possible causes of reduced photosynthesis include stomatal closure and biochemical inhibition, but their relative roles are unknown in Amazon trees during strong drought events. We assessed the effects of the recent (2015) strong El Niño drought on leaf‐level photosynthesis of Central Amazon trees via these two mechanisms. Through four seasons of 2015, we measured leaf gas exchange, chlorophyll a fluorescence parameters, chlorophyll concentration, and nutrient content in leaves of 57 upper canopy and understory trees of a lowland terra firme forest on well‐drained infertile oxisol. Photosynthesis decreased 28% in the upper canopy and 17% in understory trees during the extreme dry season of 2015, relative to other 2015 seasons and was also lower than the climatically normal dry season of the following non‐El Niño year. Photosynthesis reduction under extreme drought and high temperature in the 2015 dry season was related only to stomatal closure in both upper canopy and understory trees, and not to chlorophyll a fluorescence parameters, chlorophyll, or leaf nutrient concentration. The distinction is important because stomatal closure is a transient regulatory response that can reverse when water becomes available, whereas the other responses reflect more permanent changes or damage to the photosynthetic apparatus. Photosynthesis decrease due to stomatal closure during the 2015 extreme dry season was followed 2 months later by an increase in photosynthesis as rains returned, indicating a margin of resilience to one‐off extreme climatic events in Amazonian forests.     

Photosynthetic acclimation of Chlorella saccharophila to heat stress

Photosynthesis is one of the most important metabolic processes of algae; which is altered as a stress response. During mass cultivation of algae, temperature rise and high light are major factors that affect biomass productivity. High temperature affects photosystem II (PSII) complex irreversibly, damaging intermolecular interactions in it. However, the impact of high temperature on photosynthesis is highly variable among different algal species, depending on the prior acclimation to environmental conditions they were exposed to. The acclimation plays an important role in combating high temperature stress via regulation of photosynthetic responses. Chlorophyll a fluorescence is a highly sensitive, non‐destructive and reliable tool for such measurements of photosynthetic parameters, which provides information about algal photosynthetic performance under given conditions. To understand the effect of heat stress on the responses of high light acclimated alga Chlorella saccharophila, chlorophyll a fluorescence transients were measured after heat exposure at 40°C. Our study demonstrates that rise in temperature for short duration; during open field cultivation reversibly affects the efficiency of PSII in light acclimated alga C. saccharophila. The effects of heat stress on chlorophyll a fluorescence in this alga, grown under high light (max‐1600 μmol photons m^?2 s^?1) are presented here; they are used to infer changes in photosynthetic process during its exposure to heat, as well as their recovery after 72 h. We speculate that heat resistance may have been acquired due to prior exposures to high light.     

The usefulness of the chlorophyll fluorescence parameters in harvest prediction in 10 genotypes of winter triticale under optimal growth conditions

The aim of the experiment was to detect differences in the activity of the photosynthetic apparatus in 10 genotypes of winter triticale. Measurements of gas exchange and chlorophyll fluorescence were performed. Among the tested genotypes, the photosynthetic apparatus of Timbo and Piano was the most active, while the photosynthesis of both Babor and Boreas was highly reduced. Additionally, we have found significant correlations between the yield and some parameters of chlorophyll fluorescence and leaf gas exchange. Parameters of chlorophyll fluorescence are useful for estimation of the functional state of the photosynthetic apparatus and could become selection criteria in plant breeding. Moreover, such parameters permit definition of the effectiveness of the utilization of chlorophyll a excitation energy and co‐operation of the light phase reactions, with reactions occurring during the dark phase of photosynthesis.     

The Adaptation of Plankton Algae

The variation in Skeletonema cells grown at 3 klux continuous illumination and 20°C is reported. Four different types of lamps gave no difference in the photosynthetic characteristics. The average diameter of the cells decreased from 8–3.5 μ during their six months vegetative period. The ratio between the pigment content in the largest and the smallest cells was about 2:1. A good correlation between cell volume and chlorophyll a content was found for this species. The content of chlorophyll c generally varied between 4 and 17 per cent of the chlorophyll a content. — A distinct correlation between the chlorophyll a content and the rate of photosynthesis per unit of cells at low light intensity was found. The rate of photosynthesis, in mg C per mg chlorophyll a and hour at 1 klux, varied between 0.40 and 0.70 for all 60 experiments with an average value of 0.56. The corresponding value for cells deficient in phosophorus was 0.19 and for cells deficient in nitrogen 0.09. — The material also showed a good correlation between the rate of photosynthesis per cell at 1 klux and the light-saturated rate of photosynthesis. I_k varied between 7 and 13 klux.     

In vivo temperature response functions of parameters required to model RuBP-limited photosynthesis

The leaf model of C₃ photosynthesis of Farquhar, von Caemmerer & Berry (Planta 149, 78–90, 1980) provides the basis for scaling carbon exchange from leaf to canopy and Earth‐System models, and is widely used to project biosphere responses to global change. This scaling requires using the leaf model over a wider temperature range than that for which the model was originally parameterized. The leaf model assumes that photosynthetic CO₂ uptake within a leaf is either limited by the rate of ribulose‐1,5‐bisphosphate (RuBP) regeneration or the activity of RuBP carboxylase‐oxygenase (Rubisco). Previously we reported a re‐parameterization of the temperature responses of Rubisco activity that proved robust when applied to a range of species. Herein this is extended to re‐parameterizing the response of RuBP‐limited photosynthesis to temperature. RuBP‐limited photosynthesis is assumed to depend on the whole chain electron transport rate, which is described as a three‐parameter non‐rectangular hyperbolic function of photon flux. Herein these three parameters are determined from simultaneous measurement of chlorophyll fluorescence and CO₂ exchange of tobacco leaves, at temperatures from 10 to 40 °C. All varied significantly with temperature and were modified further with variation in growth temperature from 15 to 35 °C. These parameters closely predicted the response of RuBP‐limited photosynthesis to temperature measured in both lemon and poplar and showed a significant improvement over predictions based on earlier parameterizations. We provide the necessary equations for use of the model of Farquhar et al. (1980) with our newly derived temperature functions for predicting both Rubisco‐ and RuBP‐limited photosynthesis.     

Contrasting effects of high‐intensity photosynthetically active radiation on two bloom‐forming dinoflagellates

While light limitation can inhibit bloom formation in dinoflagellates, the potential for high‐intensity photosynthetically active radiation (PAR) to inhibit blooms by causing stress or damage has not been well‐studied. We measured the effects of high‐intensity PAR on the bloom‐forming dinoflagellates Alexandrium fundyense and Heterocapsa rotundata. Various physiological parameters (photosynthetic efficiency F_v/F_m, cell permeability, dimethylsulfoniopropionate [DMSP], cell volume, and chlorophyll‐a content) were measured before and after exposure to high‐intensity natural sunlight in short‐term light stress experiments. In addition, photosynthesis‐irradiance (P‐E) responses were compared for cells grown at different light levels to assess the capacity for photophysiological acclimation in each species. Experiments revealed distinct species‐specific responses to high PAR. While high light decreased F_v/F_m in both species, A. fundyense showed little additional evidence of light stress in short‐term experiments, although increased membrane permeability and intracellular DMSP indicated a response to handling. P‐E responses further indicated a high light‐adapted species with Chl‐a inversely proportional to growth irradiance and no evidence of photoinhibition; reduced maximum per‐cell photosynthesis rates suggest a trade‐off between photoprotection and C fixation in high light‐acclimated cells. Heterocapsa rotundata cells, in contrast, swelled in response to high light and sometimes lysed in short‐term experiments, releasing DMSP. P‐E responses confirmed a low light‐adapted species with high photosynthetic efficiencies associated with trade‐offs in the form of substantial photoinhibition and a lack of plasticity in Chl‐a content. These contrasting responses illustrate that high light constrains dinoflagellate community composition through species‐specific stress effects, with consequences for bloom formation and ecological interactions within the plankton.     

Recurrent seascape units identify key ecological processes along the western Antarctic Peninsula

The western Antarctic Peninsula (WAP) is a bellwether of global climate change and natural laboratory for identifying interactions between climate and ecosystems. The Palmer Long‐Term Ecological Research (LTER) project has collected data on key ecological and environmental processes along the WAP since 1993. To better understand how key ecological parameters are changing across space and time, we developed a novel seascape classification approach based on in situ temperature, salinity, chlorophyll a, nitrate + nitrite, phosphate, and silicate. We anticipate that this approach will be broadly applicable to other geographical areas. Through the application of self‐organizing maps (SOMs), we identified eight recurrent seascape units (SUs) in these data. These SUs have strong fidelity to known regional water masses but with an additional layer of biogeochemical detail, allowing us to identify multiple distinct nutrient profiles in several water masses. To identify the temporal and spatial distribution of these SUs, we mapped them across the Palmer LTER sampling grid via objective mapping of the original parameters. Analysis of the abundance and distribution of SUs since 1993 suggests two year types characterized by the partitioning of chlorophyll a into SUs with different spatial characteristics. By developing generalized linear models for correlated, time‐lagged external drivers, we conclude that early spring sea ice conditions exert a strong influence on the distribution of chlorophyll a and nutrients along the WAP, but not necessarily the total chlorophyll a inventory. Because the distribution and density of phytoplankton biomass can have an impact on biomass transfer to the upper trophic levels, these results highlight anticipated links between the WAP marine ecosystem and climate.     

INFLUENCE OF ULTRAVIOLET RADIATION ON GROWTH AND PHOTOSYNTHESIS OF TWO COLD OCEAN DIATOMS1

The influence of chronic exposure to UV-B and UV-A radiation on growth and photosynthesis of two polar marine diatoms (Pseudonitzschia seriata and Nitzschia sp.) was investigated in cultures exposed to moderate photon fluences for 3–7 days. Population growth rates were diminished 50% by UV-B. Fluorescence induction kinetics of photo-system II (PSII) revealed that UV-B caused lower F_v/F_m ratios and half-rise times, indicating damage to the reaction center of PSII and to related elements of the photosynthetic electron transport chain. Carbon assimilation rates per cell and per chlorophyll a were nonetheless highest for UV-B—exposed populations, which also had the highest chlorophyll a content per cell. The UV-B—exposed cells were, however, more vulnerable to visible light-induced photoinhibition. Exposure to UV-A in the absence of UV-B had little effect on growth, fluorescence induction of PSII, or chlorophyll a contents but did have some inhibitory effects on carbon assimilation per chlorophyll a and per cell. The increased photosynthetic capacity of UV-B-exposed cells suggested some ability to compensate for damage to the photosynthetic apparatus.     

Spectral analysis on origination of the bands at 437 nm and 475.5 nm of chlorophyll fluorescence excitation spectrum in Arabidopsis chloroplasts

Chlorophyll fluorescence has been often used as an intrinsic optical molecular probe to study photosynthesis. In this study, the origin of bands at 437 and 475.5 nm in the chlorophyll fluorescence excitation spectrum for emission at 685 nm in Arabidopsis chloroplasts was investigated using various optical analysis methods. The results revealed that this fluorescence excitation spectrum was related to the absorption characteristics of pigment molecules in PSII complexes. Moreover, the excitation band centred at 475.5 nm had a blue shift, but the excitation band at 437 nm changed relatively less due to induction of non‐photochemical quenching (NPQ). Furthermore, fluorescence emission spectra showed that this blue shift occurred when excitation energy transfer from both chlorophyll b (Chl b) and carotenoids (Cars) to chlorophyll a (Chl a) was blocked. These results demonstrate that the excitation band at 437 nm was mainly contributed by Chl a, while the excitation band at 475.5 nm was mainly contributed by Chl b and Cars. The chlorophyll fluorescence excitation spectrum, therefore, could serve as a useful tool to describe specific characteristics of light absorption and energy transfer between light‐harvesting pigments. Copyright © 2015 John Wiley & Sons, Ltd.     

Recurrent microbial community types driven by nearshore and seasonal processes in coastal Southern California

A multitude of concurrent biological and physical processes contribute to microbial community turnover, especially in highly dynamic coastal environments. Characterizing what factors contribute most to shifts in microbial community structure and the specific organisms that correlate with changes in the products of photosynthesis improves our understanding of nearshore microbial ecosystem functions. We conducted high frequency sampling in nearshore Southern California in order to capture sub-weekly microbial community dynamics. Microbial communities were characterized by flow cytometry and 16S rRNA gene sequencing, and placed in the context of physicochemical parameters. Within our time-series, season and nutrient availability corresponded to changes in dominant microbial community members. Concurrent aseasonal drivers with overlapping scales of variability were also apparent when we used network analysis to assess the microbial community as subsets of the whole. Our analyses revealed the microbial community as a mosaic, with overlapping groups of taxa that varied on different timescales and correlated with unique abiotic and biotic factors. Specifically, a subnetwork associated with chlorophyll a exhibited rapid turnover, indicating that ecologically important subsets of the microbial community can change on timescales different than and in response to factors other than those that govern turnover of most members of the assemblage.     

Environmental parasitology: stressor effects on aquatic parasites

Anthropogenic stressors are causing fundamental changes in aquatic habitats and to the organisms inhabiting these ecosystems. Yet, we are still far from understanding the diverse responses of parasites and their hosts to these environmental stressors and predicting how these stressors will affect host–parasite communities. Here, we provide an overview of the impacts of major stressors affecting aquatic ecosystems in the Anthropocene (habitat alteration, global warming, and pollution) and highlight their consequences for aquatic parasites at multiple levels of organisation, from the individual to the community level. We provide directions and ideas for future research to better understand responses to stressors in aquatic host–parasite systems.     

Imaging chlorophyll a fluorescence reveals specific spatial distributions under different stress conditions

Chlorophyll a fluorescence has been adopted as a fast, non-invasive, and cheap method to detect stress effects in plants. The majority of these chl-fluorescence measurements have been carried out with ‘clamping’ fluorometers recording punctual chlorophyll a fluorescence at isolated parts of the leaf. However, this method is inherently limited in providing information on the homogeneity of responses to stresses at the leaf or whole plant level. Therefore the purpose of this study was to measure imaging chlorophyll a fluorescence and to compare the temporal and spatial distribution of this emission under allelochemical (2-3H-benzoxazolinone and 3,4-dihydroxybenzaldehyde), thermal and salt, and heavy metal (cadmium, copper and zinc) treatment in the model plant Arabidopsis thaliana (L.) Heynh. The results suggested different spatial distributions for each condition: the two allelochemicals showed inhibition spots at the edges of the oldest leaves and both did not affect the photosynthetic activity of young leaves; treatment with the three heavy metals revealed highly homogenous effects over the whole plant with a quite uniform decrease of maximum PSII efficiency (also in youngest leaves). On the contrary, temperature (heat and cold) and salt stress showed an initial decrease of fluorescence in the tissues around the vascular bundles that lasted between 2 and 3 h depending on the treatment. These irregularities in chlorophyll fluorescence make it difficult to correlate punctual measures (typical for clamping fluorometers) with the effect on the whole plant, ignoring effects that are evident when imaging is used. Therefore these results show that monitoring chlorophyll a fluorescence by imaging improves the measurement of stress effects on treated plants, suggesting that punctual fluorescence measurements do not always reveal the heterogeneity of the stress-related effects in treated plants.     

Herbivory facilitates growth of a key reef‐building Caribbean coral

The decline of reef‐building corals in conjunction with shifts to short‐lived opportunistic species has prompted concerns that Caribbean reef framework‐building capacity has substantially diminished. Restoring herbivore populations may be a potential driver of coral recovery; however, the impact of herbivores on coral calcification has been little studied. We performed an exclusion experiment to evaluate the impact of herbivory on Orbicella faveolata coral growth over 14 months. The experiment consisted of three treatments: full exclusion cages; half cage procedural controls; and uncaged control plates, each with small O. faveolata colonies. We found that herbivorous fish exclusion had a substantial impact on both macroalgal cover and coral growth. Fleshy macroalgae reached 50% cover within some exclusion cages, but were almost absent from uncaged control plates. Critically, O. faveolata calcification rates were suppressed by almost half within exclusion cages, with monthly coral growth negatively related to overgrowth by fleshy macroalgae. These findings highlight the importance of herbivorous fishes for coral growth and the detrimental impact of macroalgal proliferation in the Caribbean. Policy makers and local managers should consider measures to protect herbivorous fishes and reduce macroalgal proliferation to enable coral communities to continue to grow and function.     

Influence of low temperatures on the growth and photosynthetic activity of industrial chicory, <Emphasis Type="Italic">Cichorium intybus</Emphasis> L. partim

The cold stress effect on early vigour and photosynthesis efficiency was evaluated for five industrial chicory varieties with contrasting early vigour. The relationships between the growth and physiological parameters were assessed. The varieties were examined at three growth temperatures: 16 (reference), 8 (intermediate) and 4 °C (stress). The effect was measured using physiological processes (growth, photosynthesis, chlorophyll a fluorescence), and pigment content. The analysis of the measured growth parameters (dry leaf and root mass, and leaf area) indicated that temperature had a significant effect on the varieties, but the overall reaction of the varieties was similar with lowering temperatures. The photosynthesis and chlorophyll a fluorescence measurements revealed significant changes for the photosynthesis (maximum net photosynthesis, quantum efficiency, light compensation point and dark respiration) and chlorophyll a fluorescence parameters (photochemical and non-photochemical quenching) with lowering temperatures for Hera and Eva, two extremes in youth growth. No significant differences could be found between the extremes for the different temperatures. The pigment content analysis revealed significant differences at 4 °C in contrast to 16 and 8 °C, especially for the xanthophyll/carotenoid pool, suggesting a protective role. Subsequently, the relationship between the physiological processes was evaluated using principal component analysis. At 4 °C, 2 principal components were detected with high discriminating power for the varieties and similar classification of the varieties as determined in the growth analysis. This provides a preview on the possible relationships between photosynthesis and growth for industrial chicory at low temperatures.     

Local human impacts decouple natural biophysical relationships on Pacific coral reefs

Human impacts can homogenize and simplify ecosystems, favoring communities that are no longer naturally coupled with (or reflective of) the background environmental regimes in which they are found. Such a process of biophysical decoupling has been explored little in the marine environment due to a lack of replication across the intact‐to‐degraded ecosystem spectrum. Coral reefs lacking local human impacts provide critical baseline scenarios in which to explore natural biophysical relationships, and provide a template against which to test for their human‐induced decoupling. Using 39 Pacific islands, 24 unpopulated (relatively free from local human impacts) and 15 populated (with local human impacts present), spanning 45° of latitude and 65° of longitude, we ask, what are ‘natural’ biophysical relationships on coral reefs and do we see evidence for their human‐induced decoupling? Estimates of the percent cover of benthic groups were related to multiple physical environmental drivers (sea surface temperature, irradiance, chlorophyll‐a, and wave energy) using mixed‐effects models and island mean condition as the unit of replication. Models across unpopulated islands had high explanatory power, identifying key physical environmental drivers of variations in benthic cover in the absence of local human impacts. These same models performed poorly and lost explanatory power when fitted anew to populated (human impacted) islands; biophysical decoupling was clearly evident. Furthermore, key biophysical relationships at populated islands (i.e. those relationships driving benthic variation across space in conjunction with chronic human impact) bore little resemblance to the baseline scenarios identified from unpopulated islands. Our results highlight the ability of local human impacts to decouple biophysical relationships in the marine environment and fundamentally restructure the natural rules of nature.     

Salinization and sedimentation drive contrasting assembly mechanisms of planktonic and sediment-bound bacterial communities in agricultural streams

Agriculture is the most dominant land use globally and is projected to increase in the future to support a growing human population but also threatens ecosystem structure and services. Bacteria mediate numerous biogeochemical pathways within ecosystems. Therefore, identifying linkages between stressors associated with agricultural land use and responses of bacterial diversity is an important step in understanding and improving resource management. Here, we use the Mississippi Alluvial Plain (MAP) ecoregion, a highly modified agroecosystem, as a case study to better understand agriculturally associated drivers of stream bacterial diversity and assembly mechanisms. In the MAP, we found that planktonic bacterial communities were strongly influenced by salinity. Tolerant taxa increased with increasing ion concentrations, likely driving homogenous selection which accounted for ~90% of assembly processes. Sediment bacterial phylogenetic diversity increased with increasing agricultural land use and was influenced by sediment particle size, with assembly mechanisms shifting from homogenous to variable selection as differences in median particle size increased. Within individual streams, sediment heterogeneity was correlated with bacterial diversity and a subsidy-stress relationship along the particle size gradient was observed. Planktonic and sediment communities within the same stream also diverged as sediment particle size decreased. Nutrients including carbon, nitrogen, and phosphorus, which tend to be elevated in agroecosystems, were also associated with detectable shifts in bacterial community structure. Collectively, our results establish that two understudied variables, salinity and sediment texture, are the primary drivers of bacterial diversity within the studied agroecosystem, whereas nutrients are secondary drivers. Although numerous macrobiological communities respond negatively, we observed increasing bacterial diversity in response to agricultural stressors including salinization and sedimentation. Elevated taxonomic and phylogenetic bacterial diversity likely increases the probability of detecting community responses to stressors. Thus, bacteria community responses may be more reliable for establishing water quality goals within highly modified agroecosystems that have experienced shifting baselines.     

Recovery in Diversity of Fish and Invertebrate Communities Following Remediation of a Polluted Stream: Investigating Causal Relationships

Spatial and temporal responses of biota to anthropogenic disturbance were measured over a 15 year period in a contaminated stream undergoing remediation and recovery. Along the spatial gradient of the stream, levels of contaminants decreased downstream along with improved responses of instream biota at several levels of biological organization. Recovery of the biota in this stream over the 15 year study period is demonstrated by the temporal relationships between levels of decreasing contaminants and the concomitant responses of the periphyton, macroinvertebrate, and fish communities and changes in the various bioindicators of individual fish health. Decreases in contaminants over a temporal scale were followed closely by an improvement in physiological and organismal-level indicators, increases in the diversity of macroinvertebrate and fish communities, and rapid increases in the chlorophyll a biomass and photosynthesis rate of the periphyton community. These results emphasize that field studies designed to assess and evaluate the effectiveness of restoration activities on stream recovery should incorporate a variety of response endpoints ranging from sensitive and short-term responses to long-term but ecological relevant indicators of change. The close spatial and temporal relationships observed between changes in physicochemical factors and positive responses in various components of the stream biota over the 15-year study period suggest a strong cause and effect relationship between remediation activities and stream recovery. Understanding causal relationships and the mechanistic processes between environmental stressors, stress responses of biota, and the recovery process is important in the effective management and restoration of aquatic ecosystems. An erratum to this article is available at .     

Multiple stressor effects on coral reef ecosystems

Global climate change has profound implications on species distributions and ecosystem functioning. In the coastal zone, ecological responses may be driven by various biogeochemical and physical environmental factors. Synergistic interactions can occur when the combined effects of stressors exceed their individual effects. The Red Sea, characterized by strong gradients in temperature, salinity, and nutrients along the latitudinal axis provides a unique opportunity to study ecological responses over a range of these environmental variables. Using multiple linear regression models integrating in situ, satellite and oceanographic data, we investigated the response of coral reef taxa to local stressors and recent climate variability. Taxa and functional groups responded to a combination of climate (temperature, salinity, air‐sea heat fluxes, irradiance, wind speed), fishing pressure and biogeochemical (chlorophyll a and nutrients ‐ phosphate, nitrate, nitrite) factors. The regression model for each species showed interactive effects of climate, fishing pressure and nutrient variables. The nature of the effects (antagonistic or synergistic) was dependent on the species and stressor pair. Variables consistently associated with the highest number of synergistic interactions included heat flux terms, temperature, and wind speed followed by fishing pressure. Hard corals and coralline algae abundance were sensitive to changing environmental conditions where synergistic interactions decreased their percentage cover. These synergistic interactions suggest that the negative effects of fishing pressure and eutrophication may exacerbate the impact of climate change on corals. A high number of interactions were also recorded for algae, however for this group, synergistic interactions increased algal abundance. This study is unique in applying regression analysis to multiple environmental variables simultaneously to understand stressor interactions in the field. The observed responses have important implications for understanding climate change impacts on marine ecosystems and whether managing local stressors, such as nutrient enrichment and fishing activities, may help mitigate global drivers of change.     

Photochemical and Thermal Phases of Chlorophyll a Fluorescence

The measurement of variable chlorophyll (Chl) a fluorescence is widely used as a convenient and versatile tool in photosynthesis research. In many applications empirical correlations and simplified models of Chl a fluorescence are used with success. Nevertheless, variable Chl a fluorescence provides only indirect and complex image of processes occurring within photosynthetic membranes and such simplifications have only limited validity. In this review we elucidate some controversial and still unresolved questions about the origin and interpretation of the variable Chl a fluorescence induction and the proper use of variable Chl a fluorescence for studies of photochemical events in photosystem 2 (PS2). Although the major part of variable Chl a fluorescence reflects the photochemical closure of the PS2 reaction centers (RCs) and can be considered as a function of the redox state of the primary acceptor Q_A, up to 50 % of the change in the Chl a fluorescence yield can be of secondary, nonphotochemical origin. We review the possible sources of the inherent heterogeneity in the origin of variable Chl a fluorescence. We also comment on the practical implications this bears for the use of variable Chl a fluorescence. This revised version was published online in August 2006 with corrections to the Cover Date.