Efficient means for measuring the abundance and species composition of phytoplankton in situ continue to pose a big challenge to scientists. Hitherto, analyses and interpretations have been based mainly on small numbers of data acquired from microscopic examinations of water samples. Hence, information on devices facilitating such measurements is highly desirable. This paper examines the opportunities offered by the LISST-100X instrument for measuring in situ the concentrations and spatially variable biovolumes of a species dominant in the southern Baltic during the autumnal bloom. Microscopic analysis of phytoplankton in water sampled from different locations in the southern Baltic confirmed earlier results, indicating that this bloom was due to the overriding prevalence of one microplankton diatom species—Coscinodiscus granii. Combining the microscopic measurements of C. granii cell sizes with the size distribution ranges employed by the LISST-100X yielded equivalent spherical diameters (EDSs) ranging from 47.4 to 188.0 µm, with maxima in the 78.4–92.6 and 92.6–109 ranges. Comparative analysis of the particle size distribution (PSD) spectra was used to separate the abundance of C. granii from the total suspended particulate matter (SPM). Spatial in situ measurements in 2012 and 2014 of C. granii concentrations in surface waters showed that both its abundance and its percentage contribution to the total SPM were highly variable. Over a distance of several km, these concentrations varied from values close to zero to 0.2 µL L−1 in 2012 and from 0.3 to 0.9 µL L−1 in 2014, whereas the percentage in the total SPM was found to vary locally from a few to c. 50%. The proposed method and results demonstrate the success of the LISST-100X instrument in detecting size and volume concentrations of phytoplankton in size classes ranging from 1.25 to 250 μm. However, the correct interpretation of LISST data requires that the dominant phytoplankton species concentration in the suspensions be large enough for the signal (peak) to be readily visible against the background PSD of other SPM.
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