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Micro-algae play important roles in primary production, nutrient cycling, and applied biotechnology. Mico-algae are phylogenetically, morphologically and physiologically diverse and often easy to grow in cultures. Growth is the key parameter of viability and crucial for survival insitu and efficiency invitro. Therefore, growth is often used in eco-physiological experiments to describe the fundamental niche and optimum conditions. Invivo chlorophyll-a fluorescence (IVCF) is a well-established proxy for the growth of micro-algae and is based on constant cell properties during exponential growth. High-throughput IVCF measurements have been applied for about 20 years for few, mostly green algal strains. Here, we tested the IVCF using microtiter plates on strains of four different algal phyla (Chlorophyceae, Cyanobacteria, Bacillariophyceae, Rhodophyceae) and compared the data with cell counts and chlorophyll contents. The microtiter plate reader based IVCF (MPR-IVCF) approach worked best for the diatom Cylindrothecaclosterium and the cyanobacterium Synechococcuselongatus. Differences between IVCF and cell count-based growth rates were found for Chlorellavulgaris and Rhodella sp. The IVCF growth rates were lower than the growth rates based on cell counts in both cases, thus underestimating absolute growth rates. The MPR-IVCF method is robust in terms of light scattering and non-photosynthetic contamination but prone to changes in light regimes and also to aggregating algal cells. Thus, we recommend using the MPR-IVCF approach (1) for diatoms and cyanobacteria as an absolute growth rate measure, (2) for relative measures of growth rates, intra and interspecific during the same experiment, also for all algal phyla except Rhodophyta. [ABSTRACT FROM AUTHOR]