16S rRNA GENE HETEROGENEITY IN THE FILAMENTOUS MARINE CYANOBACTERIAL GENUSLYNGBYA¹

Abstract

The SSU (16S) rRNA gene was used to investigate the phylogeny of the cyanobacterial genus Lyngbya as well as examined for its capacity to discriminate between different marine species of Lyngbya. We show that Lyngbya forms a polyphyletic genus composed of a marine lineage and a halophilic/brackish/freshwater lineage. In addition, we found morphological and genetic evidence that Lyngbya spp. often grow in association with other microorganisms, in particular smaller filamentous cyanobacteria such as Oscillatoria, and propose that these associated microorganisms have led to extensive phylogenetic confusion in identification of Lyngbya spp. At the species level, the phylogenetic diversity obtained from the comparison of 16S rRNA genes exceeded morphological diversity in Lyngbya. However, the expectation that this improved phylogeny would be useful to species and subspecies identification was eliminated by the fact that phylogenetic species did not correlate in any respect with the species obtained from current taxonomic systems. In addition, phylogenetic identification was adversely affected by the presence of multiple gene copies within individual Lyngbya colonies. Analysis of clonal Lyngbya cultures and multiple displacement amplified (MDA) single‐cell genomes revealed that Lyngbya genomes contain two 16S rRNA gene copies, and that these typically are of variable sequence. Furthermore, intragenomic and interspecies 16S rRNA gene heterogeneity was approximately of the same magnitude. Hence, the intragenomic heterogeneity of the 16S rRNA gene overestimates the microdiversity of different strains and does not accurately reflect speciation within cyanobacteria, including the genus Lyngbya.

Comparison of Quantitative PCR and Droplet Digital PCR Multiplex Assays for Two Genera of Bloom-Forming Cyanobacteria, Cylindrospermopsis and Microcystis

“…Multiple gene copy numbers found in human eukaryotic organisms and bacteria have been shown to be associated with human diseases, a faster cellular response to resource availability, and a higher cell growth rate (39). Variation in 16S rRNA gene copy numbers for cyanobacterial genera has been described previously (40,41). It is believed that gene copy number variation at a specific gene is a result of positive selection, contributing to phenotypic differences in adaptive traits, and it could be phylogenetically informative (39,42).…”

Identificación y caracterización molecular de cianobacterias tropicales de los géneros Nostoc, Calothrix, Tolypothrix y Scytonema (Nostocales: Nostocaceae), con posible potencial biotecnológico

“…Existen amplios reportes sobre el empleo del gen 16S ribosomal como herramienta para desarrollar aproximaciones filogenéticas en cianobacterias (Wilmotte & Herdman, 2001;Svenning, Eriksson, & Rasmussen, 2005;Engene, Cameron & Gerwick, 2010;Bohunická et al, 2015). Estos estudios resaltan la importancia del uso de métodos moleculares asociados a aproximaciones fenotípicas para la correcta identificación taxonómica de las cianobacterias.…”

Intra-genomic 16S rRNA gene heterogeneity in cyanobacterial genomes.

“…Furthermore, the average cyanobacterial intra-genomic 16S rRNA gene heterogeneity (mean = 0.2%) is of an order less than the 3% gene sequence divergence typically used to delineate microbial species (tindall et al 2010). It is, however, important to note that much higher degrees of intra-genomic gene heterogeneity (>1%) have been reported in filamentous marine cyanobacteria (EngEnE et al 2010). Moreover, single nucleotide substitutions can, in principal, have large impacts on the Fig.…”

“…Recent studies have detected intra-genomic gene heterogeneity of the 16S rRNA gene in cyanobacteria of the genus Lyngbya (EngEnE et al 2010). In this cyanobacterial genus the genetic variation between the paralogous 16S rRNA gene copies was of equivalent magnitude to sequence variation between different morphological species.…”