Short sequences of the 16S rRNA gene misidentify and underestimate the diversity of Aeromonas associated to cyanobacterial water blooms. Identification of Aeromonas species associated to cyanobacterial water blooms

Cyanobacterial water blooms can cause adverse health effects in humans and animals. However, recent studies in Finland have demonstrated, using short partial 16S rRNA gene sequences, that bacteria belonging to the genus Aeromonas are associated with cyanobacterial blooms and that these bacteria were responsible of the symptoms manifested by the population exposed to these waters. Considering that many other metagenomic studies and the Ribosomal Database Project II (RDPII) classifier for the identification of the species use short partial sequences of the 16S rRNA gene, the aim of the present study is to determine the accuracy of this identification approach comparing the results with the ones obtained after sequencing the rpoD gene. Only 55.2% (64/116) of the strains showed concordance between the rpoD and 16S rRNA gene approaches (sequence similarities and phylogenetic analysis) indicating that the 16S rRNA gene clearly misidentifies some strains and underestimates the real species diversity. Furthermore, the RDPII classifier tool based on sequence similarity was unable to detect new species that could be recognized using a 16S rRNA phylogenetic analysis. The species diversity after the rpoD identification was: 25 A. veronii (21.6%), 25 A. popoffii (21.6%), 17 A. salmonicida (14.7%), 14 A. piscicola (12.1%), 7 A. bestiarum (6.0%), 7 A. hydrophila (6.0%), 4 A. sobria (3.4%), 3 A. jandaei (3.4%), 1 A. allosaccharophila (0.9%) and 1 A. encheleia (0.9%). Additionally, 12 strains (10.3%) formed 4 independent clusters and they have recently been identified as the new species A. finlandiensis (n=7), A. lacus (n=2), A. aquatica (n=2) and A. aquatilis (n=1). The abundance of potential pathogenic Aeromonas species like A. veronii and A. hydrophila associated to diarrhoea and gastroenteritis in humans should be taken into consideration when assessing the risks caused by cyanobacterial blooms.