Molecular prediction of lytic vs lysogenic states for Microcystis phage: Metatranscriptomic evidence of lysogeny during large bloom events

Abstract

Microcystis aeruginosa is a freshwater bloom-forming cyanobacterium capable of producing the potent hepatotoxin, microcystin. Despite increased interest in this organism, little is known about the viruses that infect it and drive nutrient mobilization and transfer of genetic material between organisms. The genomic complement of sequenced phage suggests these viruses are capable of integrating into the host genome, though this activity has not been observed in the laboratory. While analyzing RNA-sequence data obtained from Microcystis blooms in Lake Tai (Taihu, China), we observed that a series of lysogeny-associated genes were highly expressed when genes involved in lytic infection were down-regulated. This pattern was consistent, though not always statistically significant, across multiple spatial and temporally distinct samples. For example, samples from Lake Tai (2014) showed a predominance of lytic virus activity from late July through October, while genes associated with lysogeny were strongly expressed in the early months (June–July) and toward the end of bloom season (October). Analyses of whole phage genome expression shows that transcription patterns are shared across sampling locations and that genes consistently clustered by co-expression into lytic and lysogenic groups. Expression of lytic-cycle associated genes was positively correlated to total dissolved nitrogen, ammonium concentration, and salinity. Lysogeny-associated gene expression was positively correlated with pH and total dissolved phosphorous. Our results suggest that lysogeny may be prevalent in Microcystis blooms and support the hypothesis that environmental conditions drive switching between temperate and lytic life cycles during bloom proliferation.

Cylindrospermopsis raciborskii Virus and host: genomic characterization and ecological relevance

“…In contrast, supported by observations that virus to microbe ratios frequently decrease at high cell concentrations, Knowles and colleagues () proposed the alternative ‘Piggyback‐the‐Winner’ model in which the lysogenic cycle of temperate phages is favoured at high cell abundance. With evidence of cycles in lytic versus lysogenic viral gene expression during a Microcystis bloom and by application of the ‘Piggyback‐the‐Winner’ model, Stough and colleagues () postulated a link between lysogeny and Microcystis success, positing that shifts to lysogenic infection might offer resistance against superinfection or infection by related lytic phages. In this scenario, blooms could temporarily escape density dependent lysis, allowing prolonged periods of high cell concentration.…”

“…We found no evidence of CrV‐like viruses in metagenomes targeting the viral fraction in freshwater lakes in France (Roux et al ., ) or Taiwan (Tseng et al ., ). Likewise, metatranscriptomes targeting the cell‐fraction of Microcystis ‐dominated blooms in Lake Tai (China) (Stough et al ., ) and in Lake Erie (Davenport, ; Steffen et al ., ) provided no evidence of CrV‐like viruses. We assumed the probability of finding CrV‐like viruses would be greatest in environments with a significant presence of Cylindrospermopsis or closely related species, but were able to identify only one dataset meeting this profile, that of a metagenome collected from Lake Samsonvale (Australia) during a C. raciborskii bloom (Woodhouse and Willis et al ., in preparation).…”

“…Datasets examined include metagenomes targeting viral fractions in Lakes Pavin and Bourget (France) (Roux et al ., ) (Sequence Read Archive (SRA) accession number PRJEB2280) and in Feitsui Reservoir (Taiwan) (Tseng et al ., ) (SRA accession SRP009395). Metatranscriptomes examined include those targeting the cell fractions of: Lake Erie 2014 (Davenport, ) (SRA accession numbers PRJNA405733, 405772, 405774, 405775, 429068, 429071, 429072); Lake Erie 2014 (Steffen et al ., ) (SRA accession PRJNA354726); Lake Tai (China) 2013 (Krausfeldt et al ., in preparation) (MG‐RAST project number mgp82644); and Lake Tai 2014 (Stough et al ., ) (MG‐RAST project number mgp14658). Details of library preparation for the above datasets are provided in the respective publications.…”

“…Details of library preparation for the above datasets are provided in the respective publications. Libraries for Lake Tai 2013 were prepared following the method of Stough et al (2017).…”

“…Genome sequences can also be used to leverage metagenomic datasets to provide valuable ecological insight on abundance, distribution or activity (from metatranscriptomes) of viruses. For example, using metatranscriptomic data, Stough and colleagues () were able to demonstrate oscillating cycles of putative lytic and lysogenic gene expression in Ma‐LMM01‐like phages during a Microcystis bloom in Lake Tai (China). Yet, despite availability of a few isolates, we have no sequences of cyanophages infecting C. raciborskii .…”