Tracking a novel cyanobacterium bloom in the Indian River Lagoon, Florida, U.S.A., during the summer and fall of 2020

A bloom of an unidentified nano-sized cyanobacterium (~3-4 μm x 5 μm) was observed in the
Indian River Lagoon (IRL) system, Florida, U.S.A. from August through December 2020, causing
greenish water discoloration. Enumeration by light microscopy revealed concentrations of > 106
cells mL-1 in the northern and central IRL proper, Banana River Lagoon, and Mosquito Lagoon
(maximum of 3 x 106 cells mL-1). Bloom concentrations (2 x 105 cells mL-1) were first observed
in the northern IRL and Banana River where it persisted longer than in other basins, but cell
abundance rapidly declined throughout the system as water temperatures decreased in December.
Inspection of archived samples suggested this taxon had been in the system since at least late
June. Bloom development and decline was readily observed by satellite imagery (Sentinel-2,
Landsat-8). Cells were round to oblong, often with two or more cells aligned in a chain. Live
cells had an elongated aerotope that became inconspicuous upon preservation. Flow cytometry
indicated that this cyanobacterium had low chlorophyll a and high phycocyanin-like fluorescence.
Toxin analysis at five time points between 9/24 and 12/03 returned non-detected concentrations
of anatoxin-a and cylindrospermopsin, trace levels of total microcystin-LR in four samples, and
saxitoxin in three samples; these positive results are likely unrelated to the cyanobacterium bloom.
Direct sequencing followed by PacBio 16S amplicon sequencing revealed a novel cyanobacterial
ribotype in bloom samples (i.e., >75% of 16S amplicons). A complete metagenome assembled
genome was retrieved and phylogenetic analysis placed this organism adjacent to Prochlorothrix
hollandica, although within a clade and tree that encompasses large genetic distances between
taxa indicating that specific evolutionary and ecological affinities must be interpreted with caution.