A reduced model of the fluorescence from the cyanobacterial photosynthetic apparatus designed for the in situ detection of cyanobacteria

Fluorometric determination of the chlorophyll (Chl) content of cyanobacteria is impeded by the unique structure of their photosynthetic apparatus, i.e., the phycobilisomes (PBSs) in the light-harvesting antennae. The problems are caused by the variations in the ratio of the pigment PC to Chl a resulting from adaptation to varying environmental conditions. In order to include cyanobacteria in fluorometric analysis of algae, a simplified energy distribution model describing energy pathways in the cyanobacterial photosynthetic apparatus was conceptualized. Two sets of mathematical equations were derived from this model and tested. Fluorescence of cyanobacteria was measured with a new fluorometer at seven excitation wavelength ranges and at three detection channels (650, 685 and 720 nm) in vivo. By employing a new fit procedure, we were able to correct for variations in the cyanobacterial fluorescence excitation spectra and to account for other phytoplankton signals. The effect of energy-state transitions on the PC fluorescence emission of PBSs was documented. The additional use of the PC fluorescence signal in combination with our recently developed mathematical approach for phytoplankton analysis based on Chl fluorescence spectroscopy allows a more detailed study of cyanobacteria and other phytoplankton in vivo and in situ.     

Analysis of cylindrospermopsin- and microcystin-producing genotypes and cyanotoxin concentrations in the Macau storage reservoir

The Macau storage reservoir (MSR) has experienced algal blooms in recent years, with high levels of Cylindrospermopsis and Microcystis and detectable concentrations of cyanotoxins. To analyze the cyanotoxin-producing genotypes and relate the corresponding cyanotoxins to the water quality parameters, a quantitative real-time polymerase chain reaction was developed and applied to the water samples in three locations of MSR. Cylindrospermopsin polyketide synthetase (pks) gene and a series of microcystin synthetase (mcy) genes were used for identifying and quantifying cylindrospermopsin- and microcystin-producing genes, and the corresponding water parameters were measured accordingly. Our results showed that high concentrations of cylindrospermopsin and low concentrations of microcystin were measured during the study period. There was a strong correlation between the pks gene numbers and cylindrospermopsin concentrations (R ² = 0.95), while weak correlations were obtained between the mcy genes numbers and microcystin concentrations. Furthermore, the pks gene numbers were strongly related to Cylindrospermopsis (R ² = 0.88), cyanobacterial cell numbers (R ² = 0.96), total algae numbers (R ² = 0.95), and chlorophyll-a concentrations (R ² = 0.83), consistent with the dominant species of Cylindrospermopsis among the cyanobacteria existing in MSR. NH₄–N (R ² = 0.68) and pH (R ² = 0.89) were the water quality parameters most highly correlated with the pks gene numbers. These results contribute to monitoring for potential cyanotoxins in raw water.     

Incidence of microcystin‐producing cyanobacteria in Lake Tana,the largest waterbody in Ethiopia

The occurrence of toxic cyanobacterial blooms is a serious problem for fast‐developing countries in Africa, such as Ethiopia, that are struggling with significant degradation of the natural environment and limited access to water of good quality. Research undertaken on Lake Tana in Ethiopia between 2009 and 2011 was intended to assess the seasonal threat from cyanobacteria and to select methods for tracking of this threat in the future. The cyanobacterial genus Microcystis was found to be present throughout the monitoring period, and M. aeruginosa was determined as the dominant species. Moreover, in all samples, toxigenic cyanobacteria with the potential to produce microcystins were detected. High levels of microcystins, ranging from 0.58 to 2.65 μg L^?1, were detected each November, which indicates that in the postrainy season, water usage should be limited. The correlation between concentrations of chlorophyll‐a and microcystins suggested that chlorophyll‐a could be used as an indicator of the potential presence of cyanobacterial‐derived hepatotoxins in Lake Tana in the future. Furthermore, for quick quantitative confirmation of the presence of microcystins, a simple and rapid ELISA test was recommended.     

Using Landsat and in situ data to map turbidity as a proxy of cyanobacteria in a hypereutrophic Mediterranean reservoir

Satellite remote estimates of phycocyanin (PC) have become valuable for monitoring the quality of inland waters affected by harmful cyanobacterial blooms. In this study, we developed an algorithm for mapping turbidity as a proxy of PC content through Landsat 8 Operational Land Imager (OLI) data and in situ measurements. The chosen study site is Karaoun Reservoir, in Lebanon, a hypereutrophic freshwater body where turbidity is mostly driven by cyanobacteria. Satellite images were corrected for atmospheric effects with the 6S (Second Simulation of the Satellite Signal in the Solar Spectrum) code which proved to be more accurate than the DOS (Dark Object Subtraction) approach with R = 0.98 and R = 0.5, respectively. A strong relationship was found between turbidity and PC measurements (R = 0.92, R² = 0.86), as well as between turbidity and the ratio of band 5 to band 4 of the OLI (R = 0.88, R² = 0.77). Results reveal a promising performance of the algorithm for predicting PC concentrations with high correlations determined through simple linear regression analysis for both the calibration (R = 0.92, R² = 0.85) and validation (R = 0.88, R² = 0.78) periods. An application of the approach to a set of historical Landsat images revealed a time series of cyanobacterial bloom occurrence with high variation in surface area at the study site. The algorithm is considered to be suitable for retrieving cyanobacteria in highly eutrophic waters dominated by cyanobacteria where turbidity is mostly a function of the latter. This approach will improve monitoring cyanobacterial blooms on a spatial and timely basis.     

Controlling Harmful Cyanobacteria: Taxa-Specific Responses of Cyanobacteria to Grazing by Large-Bodied Daphnia in a Biomanipulation Scenario

Lake restoration practices based on reducing fish predation and promoting the dominance of large-bodied Daphnia grazers (i.e., biomanipulation) have been the focus of much debate due to inconsistent success in suppressing harmful cyanobacterial blooms. While most studies have explored effects of large-bodied Daphnia on cyanobacterial growth at the community level and/or on few dominant species, predictions of such restoration practices demand further understanding on taxa-specific responses in diverse cyanobacterial communities. In order to address these questions, we conducted three grazing experiments during summer in a eutrophic lake where the natural phytoplankton community was exposed to an increasing gradient in biomass of the large-bodied Daphnia magna. This allowed evaluating taxa-specific responses of cyanobacteria to Daphnia grazing throughout the growing season in a desired biomanipulation scenario with limited fish predation. Total cyanobacterial and phytoplankton biomasses responded negatively to Daphnia grazing both in early and late summer, regardless of different cyanobacterial densities. Large-bodied Daphnia were capable of suppressing the abundance of Aphanizomenon, Dolichospermum, Microcystis and Planktothrix bloom-forming cyanobacteria. However, the growth of the filamentous Dolichospermum crassum was positively affected by grazing during a period when this cyanobacterium dominated the community. The eutrophic lake was subjected to biomanipulation since 2005 and nineteen years of lake monitoring data (1996–2014) revealed that reducing fish predation increased the mean abundance (50%) and body-size (20%) of Daphnia, as well as suppressed the total amount of nutrients and the growth of the dominant cyanobacterial taxa, Microcystis and Planktothrix. Altogether our results suggest that lake restoration practices solely based on grazer control by large-bodied Daphnia can be effective, but may not be sufficient to control the overgrowth of all cyanobacterial diversity. Although controlling harmful cyanobacterial blooms should preferably include other measures, such as nutrient reductions, our experimental assessment of taxa-specific cyanobacterial responses to large-bodied Daphnia and long-term monitoring data highlights the potential of such biomanipulations to enhance the ecological and societal value of eutrophic water bodies.     

Charismatic microfauna alter cyanobacterial production through a trophic cascade

The trophic ecology of cyanobacterial blooms is poorly understood on coral reefs. Blooms of toxic cyanobacteria, Lyngbya majuscula, can quickly form large mats. The herbivorous sea hare, Stylocheilus striatus, and the predatory nudibranch, Gymnodoris ceylonica, often associate with these blooms, forming a linear food chain: nudibranch—sea hare—cyanobacteria. Using laboratory studies, this study quantified (1) the functional response of nudibranchs, (2) the effect of sea hare size on predation rates, and (3) the strength of the indirect effect of sea hare predation on cyanobacteria (i.e., a trophic cascade). Nudibranchs consumed on average 2.4 sea hares d^?1, with the consumption of small sea hares 22 times greater than the consumption of large sea hares. Predation of sea hares reduced herbivory. Cyanobacterial biomass was 1.5 times greater when nudibranchs were present relative to when nudibranchs were absent. Although sea hare grazing can substantially reduce cyanobacterial biomass, predation of sea hares may mitigate grazing pressure, and therefore increase the abundance of cyanobacteria.     

Fluorescent Fingerprints of Endolithic Phototrophic Cyanobacteria Living within Halite Rocks in the Atacama Desert

Halite deposits from the hyperarid zone of the Atacama Desert reveal the presence of endolithic microbial colonization dominated by cyanobacteria associated with heterotrophic bacteria and archaea. Using the λ-scan confocal laser scanning microscopy (CLSM) option, this study examines the autofluorescence emission spectra produced by single cyanobacterial cells found inside halite rocks and by their photosynthetic pigments. Photosynthetic pigments could be identified according to the shapes of the emission spectra and wavelengths of fluorescence peaks. According to their fluorescence fingerprints, three groups of cyanobacterial cells were identified within this natural extreme microhabitat: (i) cells producing a single fluorescence peak corresponding to the emission range of phycobiliproteins and chlorophyll a, (ii) cells producing two fluorescence peaks within the red and green signal ranges, and (iii) cells emitting only low-intensity fluorescence within the nonspecific green fluorescence signal range. Photosynthetic pigment fingerprints emerged as indicators of the preservation state or viability of the cells. These observations were supported by a cell plasma membrane integrity test based on Sytox Green DNA staining and by transmission electron microscopy ultrastructural observations of cyanobacterial cells.     

Late-summer phytoplankton in western Lake Erie (Laurentian Great Lakes): bloom distributions,toxicity, and environmental influences

Phytoplankton abundance and composition and the cyanotoxin, microcystin, were examined relative to environmental parameters in western Lake Erie during late-summer (2003–2005). Spatially explicit distributions of phytoplankton occurred on an annual basis, with the greatest chlorophyll (Chl) a concentrations occurring in waters impacted by Maumee River inflows and in Sandusky Bay. Chlorophytes, bacillariophytes, and cyanobacteria contributed the majority of phylogenetic-group Chl a basin-wide in 2003, 2004, and 2005, respectively. Water clarity, pH, and specific conductance delineated patterns of group Chl a, signifying that water mass movements and mixing were primary determinants of phytoplankton accumulations and distributions. Water temperature, irradiance, and phosphorus availability delineated patterns of cyanobacterial biovolumes, suggesting that biotic processes (most likely, resource-based competition) controlled cyanobacterial abundance and composition. Intracellular microcystin concentrations corresponded to Microcystis abundance and environmental parameters indicative of conditions coincident with biomass accumulations. It appears that environmental parameters regulate microcystin indirectly, via control of cyanobacterial abundance and distribution.     

On-line monitoring of marine cyanobacterial cultivation based on phycocyanin fluorescence.

A novel on-line fluorescence monitoring system for marine cyanobacterial cultivation was developed. This method is based on the measurement of intracellular phycocyanin content, which is the major light harvesting protein. A fluorescence spectrophotometer, equipped with a flow cell connected with a culture liquid recycling tube was used. Experiments were carried out using a marine unicellular cyanobacteria Synechococcus sp. NKBG 042902 isolated from Japanese coastal sea water. We have optimized excitation wavelength to avoid the light scattering, using non-pigmented old cells which no longer contained phycocyanin. At an excitation wavelength of 590 nm, light scattering was minimized. Viable cell concentration could be measured in the range of 2 x 10(6) to 2 x 10(8) cells per ml, without pronounced light scattering. Continuous monitoring of marine cyanobacteria cultivation was performed. Cell concentrations were determined by both culture fluorescence and by using a hemacytometer. A good linear correlation was obtained. We conclude that on-line monitoring of cyanobacterial culture fluorescence based on phycocyanin is a rapid, efficient and also versatile method for determining viable cell concentration.     

Fluorometric estimation of surface associated microbial abundance

Surface associated microbes have historically been difficult to accurately and effectively enumerate. In the current study, we propose a rapid and simple method for estimating abundance of surface associated microbial cells by fluorescence of SYBRGreen stained bacteria and in vivo chlorophyll a fluorescence of benthic diatoms in 24 and 48-well microtiter plates. The effectiveness of this high-throughput technique is demonstrated by assessing sensitivity of a clinical strain of Vibrio cholerae, a benthic bacterial isolate and the benthic microalgae Cylindrotheca closterium to three antibiotics — tylosin, lincomycin and ciproflaxacin. We report on the significant linear relationships between spectral chl a fluorescence and cell abundance and between microalgal growth rates derived from cell counts and fluorescence. Additionally, we provide a simplified and improved method for preparation of a silica gel matrix (SGM), which is an ideal plating media for fluorescence applications. These findings indicate that spectrofluorometry is an inexpensive tool for rapidly estimating abundance of surface associated microbiota and can be employed for assessing antibiotic sensitivity.     

Using absorbance and fluorescence spectra to discriminate microalgae

The utility of absorbance and fluorescence-emission spectra for discriminating among microalgal phylogenetic groups, selected species, and phycobilin- and non-phycobilin-containing algae was examined using laboratory cultures. A similarity index algorithm, in conjunction with fourth-derivative transformation of absorbance spectra, provided discrimination among the chlorophyll [Chl] a/phycobilin (cyanobacteria), Chl a/Chl c/phycobilin (cryptophytes), Chl a/Chl b (chlorophytes, euglenophytes, prasinophytes), Chl a/Chl c/fucoxanthin (diatoms, chrysophytes, raphidophytes) and Chl a/Chl c/peridinin (dinoflagellates) spectral classes, and often between}among closely related phylogenetic groups within a class. Spectra for phylogenetic groups within the Chl a/Chl c/fucoxanthin, Chl a/Chl c/peridinin, Chl a/phycobilins and Chl a/Chl c/phycobilin classes were most distinguishable from spectra for groups within the Chl a/Chl b spectral class. Chrysophytes/diatoms/raphidophytes and dinoflagellates (groups within the comparable spectral classes, Chl a/Chl c/fucoxanthin and Chl a/Chl c/peridinin, respectively) displayed the greatest similarity between/among groups. Spectra for phylogenetic groups within the Chl a/Chl c classes displayed limited similarity with spectra for groups within the Chl/phycobilin classes. Among the cyanobacteria and chlorophytes surveyed, absorbance spectra of species possessing dissimilar cell morphologies were discriminated, with the greatest range of differentiation occurring among cyanobacteria. Among the cyanobacteria, spectra for selected problematic species were easily discriminated from spectra from each other and from other cyanobacteria. Fluorescence-emission spectra were distinct among spectral classes and the similarity comparisons involving fourth-derivative transformation of spectra discriminated the increasing contribution of distinct cyanobacterial species and between phycobilin- and non-phycobilin-containing species within a hypothetical mixed assemblage. These results were used to elucidate the application for in situ moored instrumentation incorporating such approaches in water quality monitoring programmes, particularly those targeting problematic cyanobacterial blooms.     

Development of a Universal Microarray Based on the Ligation Detection Reaction and 16S rRNA Gene Polymorphism To Target Diversity of Cyanobacteria

The cyanobacteria are photosynthetic prokaryotes of significant ecological and biotechnological interest, since they strongly contribute to primary production and are a rich source of bioactive compounds. In eutrophic fresh and brackish waters, their mass occurrences (water blooms) are often toxic and constitute a high potential risk for human health. Therefore, rapid and reliable identification of cyanobacterial species in complex environmental samples is important. Here we describe the development and validation of a microarray for the identification of cyanobacteria in aquatic environments. Our approach is based on the use of a ligation detection reaction coupled to a universal array. Probes were designed for detecting 19 cyanobacterial groups including Anabaena/Aphanizomenon, Calothrix, Cylindrospermopsis, Cylindrospermum, Gloeothece, halotolerants, Leptolyngbya, Palau Lyngbya, Microcystis, Nodularia, Nostoc, Planktothrix, Antarctic Phormidium, Prochlorococcus, Spirulina, Synechococcus, Synechocystis, Trichodesmium, and Woronichinia. These groups were identified based on an alignment of over 300 cyanobacterial 16S rRNA sequences. For validation of the microarrays, 95 samples (24 axenic strains from culture collections, 27 isolated strains, and 44 cloned fragments recovered from environmental samples) were tested. The results demonstrated a high discriminative power and sensitivity to 1 fmol of the PCR-amplified 16S rRNA gene. Accurate identification of target strains was also achieved with unbalanced mixes of PCR amplicons from different cyanobacteria and an environmental sample. Our universal array method shows great potential for rapid and reliable identification of cyanobacteria. It can be easily adapted to future development and could thus be applied both in research and environmental monitoring.     

Field and laboratory methods to monitor lake aerosols for cyanobacteria and microcystins

This study tested field and laboratory methods for the collection of cyanobacteria and microcystins emitted from lake water. These methods feature a highly portable, on-lake system for collecting aerosols directly from the lake, as well as a laboratory system for measurement of aerosols from freshly collected water samples under controlled conditions. Membrane air filters (0.45 μm) collected small particles such as picoplankton (0.2–2.0 μm) from aerosolized lake water. Picocyanobacteria were distinguished from other photosynthetic cells with epifluorescence microscopy using excitation filters for chlorophyll a (435 nm) and for phycobilin pigments (572 nm), characteristic of cyanobacteria. Aerosolization of picocyanobacteria ranged from 8872 to 167,297 cells m ^?3 in the field and 23,764 to 365,011 cells m ^?3 in the laboratory. Microcystin levels from field air filters ranged (below detectable limits) <13–384 pg MC m ^?3 of air. The described methods could be used for monitoring aerosolized cyanobacteria for public health purposes.     

Hyperspectral remote sensing of cyanobacterial pigments as indicators of the iron nutritional status of cyanobacteria-dominant algal blooms in eutrophic lakes

Iron can stimulate cyanobacterial growth. Determining iron availability to cyanobacteria is therefore essential for timely warnings of bloom development. The objectives of this study were to determine the key spectral parameters indicating cellular iron status in cyanobacteria and to establish reliable equations for estimating iron nutrition in cyanobacterial cells. Cells, pigments, cellular iron, and spectra of cyanobacteria were measured monthly at 17 sites in Meiliang Bay of Taihu Lake during the summer period of cyanobacterial blooms from 2010 to 2013. Pronounced spatial and temporal variability of cellular iron of cyanobacteria was observed. The previously developed structure-insensitive pigment index (SIPI) and plant senescence reflectance index (PSRI) and the newly proposed chlorophyll a/phycocyanin index (R_Chl/PC) exhibited strong relationships with cyanobacterial cellular iron content. The relationships between the cellular iron concentration and SIPI, PSRI and R_Chl/PC could be expressed as linear, quadratic and cubic functions, respectively. The equations derived herein were tested using independent data from 2008 to 2009, obtained from 31 sites within Taihu Lake. For the three models that included SIPI, PSRI and R_Chl/PC as predictors, the coefficients of determination (R²) between the measured and estimated cellular iron concentration were 0.549, 0.584 and 0.909, and the mean relative errors (RE) were 17.1%, 18.1% and 8.0%, respectively. The overall results indicated that use of the three key hyperspectral parameters, SIPI, PSRI and R_Chl/PC, could be used for non-destructive and real-time monitoring of the iron nutritional status of cyanobacteria-dominant algal blooms in eutrophic lakes.     

Chlorophyll a Fluorescence Yield as a Monitor of Both Active CO(2) and HCO(3) Transport by the Cyanobacterium Synechococcus UTEX 625

Simultaneous measurements have been made of inorganic carbon accumulation (by mass spectrometry) and chlorophyll a fluorescence yield of the cyanobacterium Synechococcus UTEX 625. The accumulation of inorganic carbon by the cells was accompanied by a substantial quenching of chlorophyll a fluorescence. The quenching occurred even when CO₂ fixation was inhibited by iodoacetamide and whether the accumulation of inorganic carbon resulted from either active CO₂ or HCO₃⁻ transport. Measurement of chlorophyll a fluorescence yield of cyanobacteria may prove to be a rapid and convenient means of screening for mutants of inorganic carbon accumulation.     

Relationship between abundance of N2-fixing cyanobacteria and environmental features of Spanish rice fields

In order to estimate the potential utilization of N₂-fixing (heterocystous) cyanobacteria as natural biofertilizers in the Valencian rice fields (Spain), the distribution and seasonal variation of these microorganisms in water and sediment samples were evaluated, and the relationships among cyanobacterial abundance and physical and chemical characteristics of soil and water were investigated. N₂-fixing cyanobacteria were present in all the samples analyzed (25 sampling points sampled three times per year during two years). The relative cyanobacterial abundance in soil and water followed contrasting patterns, maximum presence in soil coincided with minimum abundance in water. Correlation analysis showed that cyanobacterial abundance in the two phases (water and sediment) was influenced more by water than by soil properties. Salinity, mineralization variables, and soluble reactive phosphate (SRP) correlated positively with heterocystous cyanobacteria presence. Furthermore, dissolved inorganic nitrogen (DIN) and the ratio DIN: SRP correlated negatively with cyanobacterial abundance. However DIN: SRP ratio better described the cyanobacterial distribution, with a threshold effect: below the Redfield ratio value (7.2 in mass units) cyanobacterial abundance was clearly higher. Correspondence to: A. Quesada.     

Co-regulation of photosynthetic processes under potassium deficiency across CO<Subscript>2</Subscript> levels in soybean: mechanisms of limitations and adaptations

The slow kinetic phases of the chlorophyll a fluorescence transient (induction) are valuable tools in studying dynamic regulation of light harvesting, light energy distribution between photosystems, and heat dissipation in photosynthetic organisms. However, the origin of these phases are not yet fully understood. This is especially true in the case of prokaryotic oxygenic photoautotrophs, the cyanobacteria. To understand the origin of the slowest (tens of minutes) kinetic phase, the M–T fluorescence decline, in the context of light acclimation of these globally important microorganisms, we have compared spectrally resolved fluorescence induction data from the wild type Synechocystis sp. PCC 6803 cells, using orange (λ?=?593 nm) actinic light, with those of mutants, ΔapcD and ΔOCP, that are unable to perform either state transition or fluorescence quenching by orange carotenoid protein (OCP), respectively. Our results suggest a multiple origin of the M–T decline and reveal a complex interplay of various known regulatory processes in maintaining the redox homeostasis of a cyanobacterial cell. In addition, they lead us to suggest that a new type of regulatory process, operating on the timescale of minutes to hours, is involved in dissipating excess light energy in cyanobacteria.     

Molecular (PCR-DGGE) versus morphological approach: analysis of taxonomic composition of potentially toxic cyanobacteria in freshwater lakes

Background

The microscopic Utermöhl method is commonly used for the recognition of the presence and taxonomic composition of potentially toxic cyanobacteria and is especially useful for monitoring reservoirs used as drinking water, recreation and fishery resources. However, this method is time-consuming and does not allow potentially toxic and nontoxic cyanobacterial strains to be distinguished. We have developed a method based on denaturing gradient gel electrophoresis (DGGE) of the marker gene ITS and the mcy-gene cluster, and DNA sequencing. We have attempted to calibrate the DGGE-method with a microscopic procedure, using water samples taken in 2011 from four lakes of the Great Mazurian Lakes system.

Results

Results showed that the classic microscopic method was much more precise and allowed the classification of the majority of cyanobacterial taxa to the species or genus. Using the molecular approach, most of the sequences could only be assigned to a genus or family. The results of DGGE and microscopic analyses overlapped in the detection of the filamentous cyanobacteria. For coccoid cyanobacteria, we only found two taxa using the molecular method, which represented 17% of the total taxa identified using microscopic observations. The DGGE method allowed the identification of two genera of cyanobacteria (Planktothrix and Microcystis) in the studied samples, which have the potential ability to produce toxins from the microcystins group.

Conclusions

The results confirmed that the molecular approach is useful for the rapid detection and taxonomic distinction of potentially toxic cyanobacteria in lake-water samples, also in very diverse cyanobacterial communities. Such rapid detection is unattainable by other methods. However, with still limited nucleotide sequences deposited in the public databases, this method is currently not sufficient to evaluate the entire taxonomic composition of cyanobacteria in lakes.     

Chlorophyll Fluorescence Analysis of Cyanobacterial Photosynthesis and Acclimation

Cyanobacteria are ecologically important photosynthetic prokaryotes that also serve as popular model organisms for studies of photosynthesis and gene regulation. Both molecular and ecological studies of cyanobacteria benefit from real-time information on photosynthesis and acclimation. Monitoring in vivo chlorophyll fluorescence can provide noninvasive measures of photosynthetic physiology in a wide range of cyanobacteria and cyanolichens and requires only small samples. Cyanobacterial fluorescence patterns are distinct from those of plants, because of key structural and functional properties of cyanobacteria. These include significant fluorescence emission from the light-harvesting phycobiliproteins; large and rapid changes in fluorescence yield (state transitions) which depend on metabolic and environmental conditions; and flexible, overlapping respiratory and photosynthetic electron transport chains. The fluorescence parameters F_V/F_M, F_V′/F_M′,q_p,q_N, NPQ, and PS II were originally developed to extract information from the fluorescence signals of higher plants. In this review, we consider how the special properties of cyanobacteria can be accommodated and used to extract biologically useful information from cyanobacterial in vivo chlorophyll fluorescence signals. We describe how the pattern of fluorescence yield versus light intensity can be used to predict the acclimated light level for a cyanobacterial population, giving information valuable for both laboratory and field studies of acclimation processes. The size of the change in fluorescence yield during dark-to-light transitions can provide information on respiration and the iron status of the cyanobacteria. Finally, fluorescence parameters can be used to estimate the electron transport rate at the acclimated growth light intensity.