Single-colony sequencing reveals phylosymbiosis, co-phylogeny, and horizontal gene transfer between the cyanobacteriumMicrocystisand its microbiome

Abstract

Cyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria – their microbiome. However, the nature of the relationship between Microcystis and its microbiome remains unclear. Is it a long-term, evolutionarily stable association? Which partners benefit? Here we report the genomic diversity of 109 individual Microcystis colonies – including cyanobacteria and associated bacterial genomes – isolated in situ and without culture from Lake Champlain, Canada and Pampulha Reservoir, Brazil. We found 14 distinct Microcystis genotypes from Canada, of which only two have been previously reported, and four genotypes specific to Brazil. Microcystis genetic diversity was much greater between than within colonies, consistent with colony growth by clonal expansion rather than aggregation of Microcystis cells. We also identified 72 bacterial species in the microbiome. Each Microcystis genotype had a distinct microbiome composition, and more closely-related genotypes had more similar microbiomes. This pattern of phylosymbiosis could be explained by co-phylogeny in two out of the nine most prevalent associated bacterial genera, Roseomonas and Rhodobacter, suggesting long-term evolutionary associations. Roseomonas and Rhodobacter genomes encode functions which could complement the metabolic repertoire of Microcystis, such as cobalamin and carotenoid biosynthesis, and nitrogen fixation. In contrast, other colony-associated bacteria showed weaker signals of co-phylogeny, but stronger evidence of horizontal gene transfer with Microcystis. These observations suggest that acquired genes are more likely to be retained in both partners (Microcystis and members of its microbiome) when they are loosely associated, whereas one gene copy is sufficient when the association is physically tight and evolutionarily long-lasting.

The genetic and ecophysiological diversity of Microcystis

“…This is in line with species-specific microbiome assembly experimentally observed for other phytoplankton (Jackrel, Yang, et al, 2020). Sequence data from single colonies of Microcystis show that several taxa are prevalent but none universally present across colonies, and more closely related genotypes, either based on Microcystis oligotypes or whole genomes, harbored more similar microbiomes (Smith et al submitted;Pérez-Carrascal et al, 2020).…”

“…Microcystis cells clump together within an exopolysaccharide‐rich mucilage matrix to form colonies of various sizes and shapes. Recent evidence from metagenomic sequencing of single colonies or cultures suggests that colonies initiated from clonal expansion from single cells are more prevalent than clumping of distinct genotypes (Jackrel et al ., 2019; Pérez‐Carrascal et al ., 2020). Although colony morphology was once used for species identification (Otsuka et al ., 2000), this trait is now known to change with environmental conditions and season, and genetic data support the unification of morphospecies into a single species (Harke et al ., 2016a; Xiao et al ., 2018; Pérez‐Carrascal et al ., 2019).…”

“…This is in line with species‐specific microbiome assembly experimentally observed for other phytoplankton (Jackrel et al ., 2020b). Sequence data from single colonies of Microcystis show that several taxa are prevalent but none universally present across colonies, and more closely related genotypes, either based on Microcystis oligotypes or whole genomes, harboured more similar microbiomes (Smith et al ., 2021; Pérez‐Carrascal et al ., 2020). Despite this taxonomic correlation, the relationship between host functions and microbiome functions is weak, and microbiomes broadly converge at a functional level (Jackrel et al ., 2019; Cook et al ., 2020).…”

“…Some of the same taxa are regularly observed during Microcystis blooms (Cook et al ., 2020), but its microbial community composition varies considerably as a function of time (Parveen et al ., 2013; Berry et al ., 2017; Chun et al ., 2020; Jankowiak and Gobler, 2020), location (Jankowiak and Gobler, 2020), or the dominating genotype of Microcystis (Chun et al ., 2020). Analysis of communities associated with Microcystis , either via culturing or direct sequencing of single colonies, shows that different Microcystis strains have distinct microbiomes at a taxonomic level (Smith et al ., 2021; Jackrel et al ., 2019; Pérez‐Carrascal et al ., 2020). This is in line with species‐specific microbiome assembly experimentally observed for other phytoplankton (Jackrel et al ., 2020b).…”

The microbiome impacts host hybridization and speciation

“…Without knowing the transmission routes of all members of the microbiome across closely related species, it is notable that the pattern of phylosymbiosis has emerged as a widespread, though not universal, trend in the microbiome sciences. Phylosymbiosis occurs when hosts harbor less microbiome variation within species than between species, and microbiome compositional relationships (i.e., beta diversity) mirror the evolutionary relationships of the host species [ 61 , 62 , 71 – 74 ]. As such, more closely related host species harbor more similar microbiomes in parasitoid wasps [ 75 ], termites [ 76 ], deer [ 77 ], mice [ 73 , 78 ], primates [ 79 ], and others.…”