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ABSTRACT Although evidence indicates that viruses are important in the ecology ofMicrocystisspp., many questions remain. For example, how doesMicrocystisexist at high, bloom-associated cell concentrations in the presence of viruses that infect it? The phenomenon of lysogeny and associated homoimmunity offer possible explanations for this question. Virtually nothing is known about lysogeny inMicrocystis, but a metatranscriptomic study suggests that widespread, transient lysogeny is active during blooms. These observations lead us to posit that lysogeny is important in modulatingMicrocystisblooms. Using a classic mitomycin C-based induction study, we tested for lysogeny in aMicrocystis-dominated community in Lake Erie in 2019. Treated communities were incubated with 1 mg L⁻¹mitomycin C for 48 h alongside unamended controls. We compared direct counts of virus-like particles (VLPs) and examined community transcription for active infection by cyanophage. Mitomycin C treatment did not increase VLP count. Mitomycin C effectively eliminated transcription in the cyanobacterial community, while we detected no evidence of induction. Metatranscriptomic analysis demonstrated that the standard protocol of 1 mg L⁻¹was highly toxic to the cyanobacterial population, which likely inhibited induction of any prophage present. Follow-up lab studies indicated that 0.1 mg L⁻¹may be more appropriate for use in freshwater cyanobacterial studies. These findings will guide future efforts to detect lysogeny inMicrocystisblooms.IMPORTANCEHarmful algal blooms dominated byMicrocystisspp. occur throughout the world’s freshwater ecosystems, leading to detrimental effects on ecosystem services that are well documented. After decades of research, the scientific community continues to struggle to understand the ecology ofMicrocystisblooms. The phenomenon of lysogeny offers an attractive potential explanation for several ecological questions surrounding blooms. However, almost nothing is known about lysogeny inMicrocystis. We attempted to investigate lysogeny in aMicrocystisbloom in Lake Erie and found that the standard protocols used to study lysogeny in aquatic communities are inappropriate for use inMicrocystisstudies, and perhaps freshwater cyanobacterial studies more broadly. This work can be used to design better methods to study the viral ecology ofMicrocystisblooms. 

Abstract Cyanobacterial blooms dominated by Microcystis spp. pose significant ecological challenges, including the release of toxins and disruption of aquatic food webs. Although Microcystis can exist as free-living single cells or within dense mucilaginous colonies, the drivers and consequences of colony formation remain unclear. Here, we integrated metatranscriptomic datasets from two Microcystis bloom events in Lake Taihu, China, to analyze and to support findings on the functional differences between colonial and single-cell Microcystis. Our results confirmed colony expression profiles were disproportionately enriched in Microcystis transcripts compared to other prokaryotic taxa. This pattern exhibits Black Queen-like dynamics, where Microcystis assumes greater metabolic and defensive roles while associated bacteria reduce their transcriptional activity. Concomitantly, viral infection strategies diverged by Microcystis community morphology: colony-associated cells expressed lysogeny-associated genes, whereas single cells exhibited increased signatures of lytic infection. These data are consistent with the hypothesis that Microcystis colonies foster conditions favorable to lysogen formation—likely due to local high cell densities and the resulting advantage of superinfection immunity—whereas solitary cells experience stronger lytic pressure. On a broader scale, our findings refine the understanding of bloom dynamics by identifying how community morphological states coincide with distinct host–virus interactions. Cumulatively, this work underscores the importance of colony formation in shaping Microcystis ecology and highlights the need for further mechanistic studies to disentangle the complex interplay between phage infection modes, colony formation, and microbial community structure. 

Abstract While resequencing Microcystis aeruginosa (PCC7806) and its nontoxigenic mutant (PCC7806 ΔmcyB), we discovered identical unreported plasmids in both strains. These strains were separated in culture over 25 years ago, resulting in sequence divergence among their chromosomes. RNA-seq data demonstrated these plasmids were transcriptionally active during chemostat growth. Moreover, in situ metatranscriptomes from Lake Erie revealed genes like those on the PCC7806 plasmid were expressed in the environment. As we investigated plasmids in Microcystis, we found that M. aeruginosa NIES-298 also had a putatively conserved plasmid, but with phage-like features. To gain an understanding of the ecological relevance of these plasmids, we examined Lake Erie metatranscriptomes and found that transcript abundance for predicted plasmid-like contigs was significantly higher than predicted virus-like contigs across the microbial community: this trend was also present when metatranscriptomic reads were mapped to Microcystis-infecting phage and Microcystis-specific plasmid genomes. Our observations demonstrate a potential ecological importance and stability of these extrachromosomal elements in Microcystis. Additionally, this work draws attention to the potential overlap between Microcystis plasmid and phage genomes, and how this may complicate molecular investigations. 

ABSTRACT Here, we report on the raw and coassembled metatranscriptomes of 39 Lake Erie surface (1.0 m) water samples collected over a 2-day diel period encompassing episodic weather and bloom events. Preliminary taxonomic annotations and read mappings revealed thatMicrocystisspp. accounted for up to ~47% of the transcriptionally active community. 

Abstract The rediscovery of diatom blooms embedded within and beneath the Lake Erie ice cover (2007–2012) ignited interest in psychrophilic adaptations and winter limnology. Subsequent studies determined the vital role ice plays in winter diatom ecophysiology as diatoms partition to the underside of ice, thereby fixing their location within the photic zone. Yet, climate change has led to widespread ice decline across the Great Lakes, with Lake Erie presenting a nearly “ice-free” state in several recent winters. It has been hypothesized that the resultant turbid, isothermal water column induces light limitation amongst winter diatoms and thus serves as a competitive disadvantage. To investigate this hypothesis, we conducted a physiochemical and metatranscriptomic survey that spanned spatial, temporal, and climatic gradients of the winter Lake Erie water column (2019–2020). Our results suggest that ice-free conditions decreased planktonic diatom bloom magnitude and altered diatom community composition. Diatoms increased their expression of various photosynthetic genes and iron transporters, which suggests that the diatoms are attempting to increase their quantity of photosystems and light-harvesting components (a well-defined indicator of light limitation). We identified two gene families which serve to increase diatom fitness in the turbid ice-free water column: proton-pumping rhodopsins (a potential second means of light-driven energy acquisition) and fasciclins (a means to “raft” together to increase buoyancy and co-locate to the surface to optimize light acquisition). With large-scale climatic changes already underway, our observations provide insight into how diatoms respond to the dynamic ice conditions of today and shed light on how they will fare in a climatically altered tomorrow. 

Huisman et al . claim that our model is poorly supported or contradicted by other studies and the predictions are “seriously flawed.” We show their criticism is based on an incomplete selection of evidence, misinterpretation of data, or does not actually refute the model. Like all ecosystem models, our model has simplifications and uncertainties, but it is better than existing approaches hat ignore biology and do not predict toxin concentration.