A novel freshwater cyanophage vB_MelS-Me-ZS1 infecting bloom-forming cyanobacterium Microcystis elabens.

Blooms of cyanobacteria cause enormous losses in both the economy and environment. Cyanophages are of great potential for fighting blooming cyanobacteria. Research report on cyanophage of bloom-forming cyanobacterium, Microcystis elabens is deficient. vB_MelS-Me-ZS1 (abbreviated as Me-ZS1) was isolated from fresh water by double-layer agar plate method using M. elabens. TEM exhibited that cyanosiphovirus Me-ZS1 has an icosahedral head about 60 nm in diameter, and a noncontractile tail approximately 260 nm. Experimental infection against 15 cyanobacterial strains showed that Me-ZS1 can infect 12 strains across taxonomic orders (Chroococcales, Nostocales and Oscillatoriales). High-throughput sequencing and bioinformatics analysis revealed that Me-ZS1 has a double-stranded DNA genome of 49,665 bp, with a G + C content of 58.22%, and 73 predicted open reading frames (ORFs). BLASTn and ORF comparisons showed that Me-ZS1 shares very low homology with the public sequences, and the phylogenetic tree based on TerL indicated that Me-ZS1 may delegate a novel and genetically distinct clade of Siphoviridae phages. In microcosm experiment, Me-ZS1 represented apparent effect on reducing relative abundance of cyanobacteria, increasing relative abundance of Saprospiraceae and protecting brocade carp (Carassius auratus) in cyanobacterial bloom water. This study isolated and characterized a novel broad-host-range Microcystis phage Me-ZS1 presenting a genetically distinct clade of freshwater cyanophage. The features of cyanophage Me-ZS1 provide a potential solution to the loss caused by cyanobacterial bloom.

Cooccurrence of Broad- and Narrow-Host-Range Viruses Infecting the Bloom-Forming Toxic Cyanobacterium Microcystis aeruginosa.

Viruses play important roles in regulating the abundance and composition of bacterial populations in aquatic ecosystems. The bloom-forming toxic cyanobacterium Microcystis aeruginosa is predicted to interact with diverse cyanoviruses, resulting in Microcystis population diversification. However, current knowledge of the genomes from these viruses and their infection programs is limited to those of Microcystis virus Ma-LMM01. Here, we performed a time series sampling at a small pond in Japan during a Microcystis bloom and then investigated the genomic information and transcriptional dynamics of Microcystis-interacting viruses using metagenomic and metatranscriptomic approaches. We identified 15 viral genomic fragments classified into three groups, groups I (including Ma-LMM01), II (high abundance and transcriptional activity), and III (new lineages). According to the phylogenetic distribution of Microcystis strains possessing spacers against each viral group, the group II-original viruses interacted with all three phylogenetically distinct Microcystis population types (phylotypes), whereas the groups I and III-original viruses interacted with only one or two phylotypes, indicating the cooccurrence of broad- (group II) and narrow (groups I and III)-host-range viruses in the bloom. These viral fragments showed the highest transcriptional levels during daytime regardless of their genomic differences. Interestingly, M. aeruginosa expressed antiviral defense genes in the environment, unlike what was seen with an Ma-LMM01 infection in a previous culture experiment. Given that broad-host-range viruses often induce antiviral responses within alternative hosts, our findings suggest that such antiviral responses might inhibit viral multiplication, mainly that of broad-host-range viruses like those in group II.IMPORTANCE The bloom-forming toxic cyanobacterium Microcystis aeruginosa is thought to have diversified its population through the interactions between host and viruses in antiviral defense systems. However, current knowledge of viral genomes and infection programs is limited to those of Microcystis virus Ma-LMM01, which was a narrow host range in which it can escape from the highly abundant host defense systems. Our metagenomic approaches unveiled the cooccurrence of narrow- and broad-host-range Microcystis viruses, which included fifteen viral genomic fragments from Microcystis blooms that were classified into three groups. Interestingly, Microcystis antiviral defense genes were expressed against viral infection in the environment, unlike what was seen in a culture experiment with Ma-LMM01. Given that viruses with a broad host range often induce antiviral responses within alternative hosts, our findings suggest that antiviral responses inhibit viral reproduction, especially that of broad-range viruses like those in group II. This paper augments our understanding of the interactions between M. aeruginosa and its viruses and fills an important knowledge gap.

The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary.

Harmful blooms of the cyanobacterium Microcystis sp. have become increasingly pervasive in the San Francisco Estuary Delta (USA) since the early 2000s and their rise has coincided with substantial decreases in several important fish species. Direct and indirect effects Microcystis blooms may have on the Delta food web were investigated. The Microcystis population was tracked for 2 years at six sites throughout the Delta using quantitative PCR. High-throughput amplicon sequencing and colony PCR sequencing revealed the presence of 10 different strains of Microcystis, including 6 different microcystin-producing strains. Shotgun metagenomic analysis identified a variety of Microcystis secondary metabolite pathways, including those for the biosynthesis of: aeruginosin, cyanopeptolin, microginin, microviridin and piricyclamide. A sizable reduction was observed in microbial community diversity during a large Microcystis bloom (H' = 0.61) relative to periods preceding (H' = 2.32) or following (H' = 3.71) the bloom. Physicochemical conditions of the water column were stable throughout the bloom period. The elevated abundance of a cyanomyophage with high similarity to previously sequenced isolates known to infect Microcystis sp. was implicated in the bloom's collapse. Network analysis was employed to elucidate synergistic and antagonistic relationships between Microcystis and other bacteria and indicated that only very few taxa were positively correlated with Microcystis.

Cyanophages Infection of Microcystis Bloom in Lowland Dam Reservoir of Sulejów, Poland.

An increased incidence of cyanobacterial blooms, which are largely composed of toxigenic cyanobacteria from the Microcystis genus, leads to a disruption of aquatic ecosystems worldwide. Therefore, a better understanding of the impact of environmental parameters on the development and collapse of blooms is important. The objectives of the present study were as follows: (1) to investigate the presence and identity of Microcystis-specific cyanophages capable of cyanobacterial cell lysis in a lowland dam reservoir in Central Europe; (2) to investigate Microcystis sensitivity to phage infections with regard to toxic genotypes; and (3) to identify key abiotic parameters influencing phage infections during the summer seasons between 2009 and 2013. Sequencing analysis of selected g91 gene amplification products confirmed that the identified cyanophages belonged to the family Myoviridae (95 % homology). Cyanophages and Microcystis hosts, including toxic genotypes, were positively correlated in 4 of the 5 years analyzed (r = 0.67-0.82). The average percentage of infected Microcystis cells varied between 0.1 and 32 %, and no particular sensitivity of the phages to toxigenic genotypes was recorded. The highest number of cyanophages (>10(4) gene copy number per microliter) was observed in the period preceded by the following: an increase of the water retention time, growth of the water temperature, optimum nutrient concentrations, and the predomination of Microcystis bloom.

Genome analysis and gene nblA identification of Microcystis aeruginosa myovirus (MaMV-DC) reveal the evidence for horizontal gene transfer events between cyanomyovirus and host.

The genome sequence, genetic characterization and nblA gene function of Microcystis aeruginosa myovirus isolated from Lake Dianchi in China (MaMV-DC) have been analysed. The genome DNA is 169 223 bp long, with 170 predicted protein-coding genes (001L­170L) and a tRNA gene. About one-sixth of these genes have homologues in the host cyanobacteria M. aeruginosa. The genome carries a gene homologous to host nblA, which encodes a protein involved in the degradation of cyanobacterial phycobilisome. Its expression during MaMV-DC infection was confirmed by reverse transcriptase PCR and Western blot detection and abundant expression was companied by the significant decline of phycocyanin content and massive release of progeny MaMV-DC. In addition, expressing MaMV-DC nblA reduced the phycocyanin peak and the phycocyanin to chlorophyll ratio in model cyanobacteria. These results confirm that horizontal gene transfer events have occurred between cyanobacterial host and cyanomyovirus and suggest that MaMV-DC carrying host-derived genes (such as 005L, that codes for NblA) is responsible for more efficient expression of cyanophage genes and release of progeny cyanophage. This study provides novel insight into the horizontal gene transfer in cyanophage and the interactions between cyanophage and their host.

Development of a real-time PCR assay for the quantification of Ma-LMM01-type Microcystis cyanophages in a natural pond.

UNLABELLED: Microcystis aeruginosa forms toxic cyanobacterial blooms throughout the world where its infectious phages are thought to influence host population dynamics. To assess the cyanophage impact on the host dynamics, we previously monitored Ma-LMM01-type phage abundance using a real-time PCR with a primer set designed based on the sequence of Microcystis phage Ma-LMM01; and we estimated the phage-infected host cell abundance. However, a recent study shows the Ma-LMM01 g91 gene sequence belongs to the smallest group, group III, of the three genotype groups, suggesting Ma-LMM01-type phage abundance was underestimated. Therefore, to re-evaluate the effect of Ma-LMM01-type phages on their hosts, we monitored the abundance of Ma-LMM01-type phages using real-time PCR with a new primer set designed based on the sequences of genotype groups I-III. We found phage abundance between 10(3) and 10(4) ml(-1) using the new primer set in samples where previously these phages were not detected using the old primer set. The frequency of Ma-LMM01-type phage-infected cells to Ma-LMM01-type phage-susceptible host cells may be as high as 30%, suggesting the phages may occasionally affect not only shifts in the genetic composition but also the dynamics of Ma-LMM01-type phage-susceptible host populations. SIGNIFICANCE AND IMPACT OF THE STUDY: Phages are one of the factors that may control the ecology of their host blooms. Therefore, it is essential to estimate phage abundance to understand phage impact on host populations. A real-time PCR assay was improved to detect a larger range of Microcystis cyanophages in natural surroundings where no phages were detected using a previous method by re-designing a new primer set based on sequences from three Ma-LMM01-type phage genetic groups. The new method allows us to determine the distribution, dynamics and infection cycle of the phage to help understand the interaction between the phages and the hosts.

Genetic diversity of Microcystis cyanophages in two different freshwater environments.

Bacteriophages rapidly diversify their genes through co-evolution with their hosts. We hypothesize that gene diversification of phages leads to locality in phages genome. To test this hypothesis, we investigated the genetic diversity and composition of Microcystis cyanophages using 104 sequences of Ma-LMM01-type cyanophages from two geographically distant sampling sites. The intergenetic region between the ribonucleotide reductase genes nrdA and nrdB was used as the genetic marker. This region contains the host-derived auxiliary metabolic genes nblA, an unknown function gene g04, and RNA ligase gene g03. The sequences obtained were conserved in the Ma-LMM01 gene order and contents. Although the genetic diversity of the sequences was high, it varied by gene. The genetic diversity of nblA was the lowest, suggesting that nblA is a highly significant gene that does not allow mutation. In contrast, g03 sequences had many point mutations. RNA ligase is involved in the counter-host's phage defense mechanism, suggesting that phage defense also plays an important role for rapid gene diversification. The maximum parsimony network and phylogenic analysis showed the sequences from the two sampling sites were distinct. These findings suggest Ma-LMM01-type phages rapidly diversify their genomes through co-evolution with hosts in each location and eventually provided locality of their genomes.

Profiling the interplay and coevolution of Microcystis aeruginosa and cyanosiphophage Mic1.

The cyanosiphophage Mic1 specifically infects the bloom-forming Microcystis aeruginosa FACHB 1339 from Lake Chaohu, China. Previous genomic analysis showed that its 92,627 bp double-stranded DNA genome consists of 98 putative open reading frames, 63% of which are of unknown function. Here, we investigated the transcriptome dynamics of Mic1 and its host using RNA sequencing. In the early, middle, and late phases of the 10 h lytic cycle, the Mic1 genes are sequentially expressed and could be further temporally grouped into two distinct clusters in each phase. Notably, six early genes, including gp49 that encodes a TnpB-like transposase, immediately reach the highest transcriptional level in half an hour, representing a pioneer cluster that rapidly regulates and redirects host metabolism toward the phage. An in-depth analysis of the host transcriptomic profile in response to Mic1 infection revealed significant upregulation of a polyketide synthase pathway and a type III-B CRISPR system, accompanied by moderate downregulation of the photosynthesis and key metabolism pathways. The constant increase of phage transcripts and relatively low replacement rate over the host transcripts indicated that Mic1 utilizes a unique strategy to gradually take over a small portion of host metabolism pathways after infection. In addition, genomic analysis of a less-infective Mic1 and a Mic1-resistant host strain further confirmed their dynamic interplay and coevolution via the frequent horizontal gene transfer. These findings provide insights into the mutual benefit and symbiosis of the highly polymorphic cyanobacteria M. aeruginosa and cyanophages. IMPORTANCE: The highly polymorphic Microcystis aeruginosa is one of the predominant bloom-forming cyanobacteria in eutrophic freshwater bodies and is infected by diverse and abundant cyanophages. The presence of a large number of defense systems in M. aeruginosa genome suggests a dynamic interplay and coevolution with the cyanophages. In this study, we investigated the temporal gene expression pattern of Mic1 after infection and the corresponding transcriptional responses of its host. Moreover, the identification of a less-infective Mic1 and a Mic1-resistant host strain provided the evolved genes in the phage-host coevolution during the multiple-generation cultivation in the laboratory. Our findings enrich the knowledge on the interplay and coevolution of M. aeruginosa and its cyanophages and lay the foundation for the future application of cyanophage as a potential eco-friendly and bio-safe agent in controlling the succession of harmful cyanobacterial blooms.

Rapid microcystis cyanophage gene diversification revealed by long- and short-term genetic analyses of the tail sheath gene in a natural pond.

Viruses influence the abundance of host populations through virus-mediated host cell lysis. Viruses contribute to the generation and maintenance of host diversity, which also results in viral diversity throughout their coevolution. Here, to determine the phage gene diversification throughout the coevolution of host and phage in a natural environment, we investigated the genetic diversity and temporal changes in Microcystis cyanophage populations using a total of 810 sequences of the Ma-LMM01-type cyanophage tail sheath gene (g91) from 2006 to 2011 in a natural pond. The sequences obtained were highly diverse and assigned to 419 different genotypes (GT1 to GT419) clustered at 100% nucleotide sequence similarity. A maximum-parsimony network showed that the genotypes were largely divided into three sequence groups, which were dominated by major genotypes (more than 24 sequences: GT2, GT53, and GT163 in group I; GT25 in group II; and GT1 in group III). These major genotypes coexisted and oscillated throughout the sampling periods, suggesting that the Microcystis-cyanophage coevolution was partly driven by a negative frequency-dependent selection. Meanwhile, the high viral genetic diversity observed was derived from a large number of the variants of each major and moderately frequent genotype (including 7 to 18 sequences: GT7, GT26, GT56, GT149, and GT182 in group I; GT152 in group II) (1 or 2 nucleotide substitutions). The variants almost always co-occurred with their origin genotypes. This manner of variant emergence suggests that increased contact frequency within a host-phage population promotes rapid coevolution in a form of "arms race."

Diurnal infection patterns and impact of Microcystis cyanophages in a Japanese pond.

Viruses play important roles in regulating the abundance, clonal diversity, and composition of their host populations. To assess their impact on the host populations, it is essential to understand the dynamics of virus infections in the natural environment. Cyanophages often carry host-like genes, including photosynthesis genes, which maintain host photosynthesis. This implies a diurnal pattern of cyanophage infection depending on photosynthesis. Here we investigated the infection pattern of Microcystis cyanophage by following the abundances of the Ma-LMM01-type phage tail sheath gene g91 and its transcript in a natural population. The relative g91 mRNA abundance within host cells showed a peak during the daylight hours and was lowest around midnight. The phage g91 DNA copy numbers in host cell fractions, which are predicted to indicate phage replication, increased in the afternoon, followed by an increase in the free-phage fractions. In all fractions, at least 1 of 71 g91 genotypes was observed (in tested host cell, free-phage, and RNA fractions), indicating that the replication cycle of the cyanophage (i.e., injection, transcription, replication, and release of progeny phages) was occurring. Thus, Microcystis cyanophage infection occurs in a diel cycle, which may depend on the light cycle. Additionally, our data show that the abundance of mature cyanophage produced within host cells was 1 to 2 orders of magnitude greater than that of released phages, suggesting that phage production may be higher than previously reported.

Intricate interactions between the bloom-forming cyanobacterium Microcystis aeruginosa and foreign genetic elements, revealed by diversified clustered regularly interspaced short palindromic repeat (CRISPR) signatures.

Clustered regularly interspaced short palindromic repeats (CRISPR) confer sequence-dependent, adaptive resistance in prokaryotes against viruses and plasmids via incorporation of short sequences, called spacers, derived from foreign genetic elements. CRISPR loci are thus considered to provide records of past infections. To describe the host-parasite (i.e., cyanophages and plasmids) interactions involving the bloom-forming freshwater cyanobacterium Microcystis aeruginosa, we investigated CRISPR in four M. aeruginosa strains and in two previously sequenced genomes. The number of spacers in each locus was larger than the average among prokaryotes. All spacers were strain specific, except for a string of 11 spacers shared in two closely related strains, suggesting diversification of the loci. Using CRISPR repeat-based PCR, 24 CRISPR genotypes were identified in a natural cyanobacterial community. Among 995 unique spacers obtained, only 10 sequences showed similarity to M. aeruginosa phage Ma-LMM01. Of these, six spacers showed only silent or conservative nucleotide mutations compared to Ma-LMM01 sequences, suggesting a strategy by the cyanophage to avert CRISPR immunity dependent on nucleotide identity. These results imply that host-phage interactions can be divided into M. aeruginosa-cyanophage combinations rather than pandemics of population-wide infectious cyanophages. Spacer similarity also showed frequent exposure of M. aeruginosa to small cryptic plasmids that were observed only in a few strains. Thus, the diversification of CRISPR implies that M. aeruginosa has been challenged by diverse communities (almost entirely uncharacterized) of cyanophages and plasmids.

A Review of Cyanophage-Host Relationships: Highlighting Cyanophages as a Potential Cyanobacteria Control Strategy.

Harmful algal blooms (HABs) are naturally occurring phenomena, and cyanobacteria are the most commonly occurring HABs in freshwater systems. Cyanobacteria HABs (cyanoHABs) negatively affect ecosystems and drinking water resources through the production of potent toxins. Furthermore, the frequency, duration, and distribution of cyanoHABs are increasing, and conditions that favor cyanobacteria growth are predicted to increase in the coming years. Current methods for mitigating cyanoHABs are generally short-lived and resource-intensive, and have negative impacts on non-target species. Cyanophages (viruses that specifically target cyanobacteria) have the potential to provide a highly specific control strategy with minimal impacts on non-target species and propagation in the environment. A detailed review (primarily up to 2020) of cyanophage lifecycle, diversity, and factors influencing infectivity is provided in this paper, along with a discussion of cyanophage and host cyanobacteria relationships for seven prominent cyanoHAB-forming genera in North America, including: Synechococcus, Microcystis, Dolichospermum, Aphanizomenon, Cylindrospermopsis, Planktothrix, and Lyngbya. Lastly, factors affecting the potential application of cyanophages as a cyanoHAB control strategy are discussed, including efficacy considerations, optimization, and scalability for large-scale applications.

A Novel Freshwater Cyanophage, Mae-Yong924-1, Reveals a New Family.

Cyanobacterial blooms are a worldwide ecological issue. Cyanophages are aquatic viruses specifically infecting cyanobacteria. Little is known about freshwater cyanophages. In this study, a freshwater cyanophage, Mae-Yong924-1, was isolated by the double-layer agar plate method using Microcystis aeruginosa FACHB-924 as an indicator host. Mae-Yong924-1 has several unusual characteristics: a unique shape, cross-taxonomic order infectivity and a very unique genome sequence. Mae-Yong924-1 contains a nearly spherical head of about 100 nm in diameter. The tail or tail-like structure (approximately 40 nm in length) is like the tassel of a round Chinese lantern. It could lyse six diverse cyanobacteria strains across three orders including Chroococcales, Nostocales and Oscillatoriales. The genome of the cyanophage is 40,325 bp in length, with a G + C content of 48.32%, and 59 predicted open reading frames (ORFs), only 12 (20%) of which were functionally annotated. Both BLASTn and BLASTx scanning resulted in "No significant similarity found", i.e., the Mae-Yong924-1 genome shared extremely low homology with sequences in NCBI databases. Mae-Yong924-1 formed a root node alone and monopolized a root branch in the proteomic tree based on genome-wide sequence similarities. The results suggest that Mae-Yong924-1 may reveal a new unknown family apparently distinct from other viruses.

A Novel Wide-Range Freshwater Cyanophage MinS1 Infecting the Harmful Cyanobacterium Microcystis aeruginosa.

Microcystis aeruginosa, as one of the major players in algal bloom, produces microcystins, which are strongly hepatotoxic, endangering human health and damaging the ecological environment. Biological control of the overgrowth of Microcystis with cyanophage has been proposed to be a promising solution for algal bloom. In this study, a novel strain of Microcystis cyanophage, MinS1, was isolated. MinS1 contains an icosahedral head approximately 54 nm in diameter and a 260 nm-long non-contractile tail. The phage genome consists of a linear, double-stranded 49,966 bp DNA molecule, which shares very low homology with known phages in the NCBI database (only 1% of the genome showed weak homology with known phages when analyzed by megablast). The phage contains 75 ORFs, of which 23 ORFs were predicted to code for proteins of known function, 39 ORFs were predicted to code for proteins of unknown function, and 13 ORFs showed no similarity to any protein sequences. Transmission electron microscopy and phylogenetic analysis showed that MinS1 belongs to the family Siphoviridae. Various experiments confirmed that the phage could infect several different orders of cyanobacteria, including Chroococcales, Nostocales, Oscillatoriales, Hormogonales, and Synechococcales, indicating that it has a very broad host range. In addition, MinS1 has no known antibiotic tolerance genes, virulence genes, and tRNAs, and it is tolerant to temperature, pH, UV, and salinity, suggesting that MinS1 has good potential for application as a biological control agent against cyanobacterial blooms. This study expands the diversity and knowledge of cyanophages, and it provides useful information for the development of novel prevention and control measures against cyanobacterial blooms.

Occurrence and diversity of viruses associated with cyanobacterial communities in a Brazilian freshwater reservoir.

As part of the phytoplankton of marine and freshwater environments around the world, cyanobacteria interact with viruses (cyanophages) that affect their abundance and diversity. Investigations focusing on cyanophages co-occurring with freshwater cyanobacteria are scarce, particularly in Brazil. The aim of this study was to assess the diversity of cyanophages associated with a Microcystis-dominated cyanobacterial bloom in a tropical reservoir. Samples were processed as viral fractions of water and cellular fractions, and temporal fluctuations in the abundance of Ma-LMM01-type cyanophages and their Microcystis hosts were determined by qPCR. We applied shotgun metagenomics to obtain a wider characterization of the cyanophage community. During the study period, Microcystis gene copies were quantified in all cellular fractions, and the copy number of the Ma-LMM01 phage gene tended to increase with host abundance. Metagenomic analysis demonstrated that Caudovirales was the major viral order associated with the cyanophage families Myoviridae (34-88%), Podoviridae (3-42%), and Siphoviridae (6-23%). The metagenomic analysis results confirmed the presence of Microcystis cyanophages in both viral and cellular fractions and demonstrated a high relative abundance of picocyanobacteria-related viruses and Prochlorococcus (36-52%) and Synechococcus (37-50%) phages. For other main cyanobacterial genera, no related cyanophages were identified, which was probably due to the scarce representation of cyanophage sequences in databanks. Thus, the studied reservoir hosted a diverse cyanophage community with a remarkable contribution of phages related to picoplanktonic cyanobacteria. These results provide insights that motivate future sequencing efforts to assess cyanophage diversity and recover complete genomes.

Tracing the active genetic diversity of Microcystis and Microcystis phage through a temporal survey of Taihu.

Harmful algal blooms are commonly thought to be dominated by a single genus, but they are not homogenous communities. Current approaches, both molecular and culture-based, often overlook fine-scale variations in community composition that can influence bloom dynamics. We combined homology-based searches (BLASTX) and phylogenetics to distinguish and quantify Microcystis host and phage members across a summer season during a 2014 Microcystis- dominated bloom that occurred in Lake Tai (Taihu), China. We found 47 different genotypes of the Microcystis-specific DNA-dependent RNA polymerase (rpoB), which included several morphospecies. Microcystis flos-aquae and Microcystis wesenbergii accounted for ~86% of total Microcystis transcripts, while the more commonly studied Microcystis aeruginosa only accounted for ~7%. Microcystis genotypes were classified into three temporal groups according to their expression patterns across the course of the bloom: early, constant and late. All Microcystis morphospecies were present in each group, indicating that expression patterns were likely dictated by competition driven by environmental factors, not phylogeny. We identified three primary Microcystis-infecting phages based on the viral terminase, including a novel Siphoviridae phage that may be capable of lysogeny. Within our dataset, Myoviridae phages consistent with those infecting Microcystis in a lytic manner were positively correlated to the early host genotypes, while the Siphoviridae phages were positively correlated to the late host genotypes, when the Myoviridae phages express putative genetic markers for lysogeny. The expression of genes in the microcystin-encoding mcy cassette was estimated using mcyA, which revealed 24 Microcystis-specific genotypes that were negatively correlated to the early host genotypes. Of all environmental factors measured, pH best described the temporal shift in the Microcystis community genotypic composition, promoting hypotheses regarding carbon concentration mechanisms and oxidative stress. Our work expounds on the complexity of HAB events, using a well-studied dataset to highlight the need for increased resolution of community dynamics.

Capsid Structure of a Freshwater Cyanophage Siphoviridae Mic1.

Cyanobacteria are the most abundant photosynthetic microorganisms, the global distribution of which is mainly regulated by the corresponding cyanophages. A systematic screening of water samples in the Lake Chaohu enabled us to isolate a freshwater siphocyanophage that infects Microcystis wesenbergii, thus termed Mic1. Using cryoelectron microscopy, we solved the 3.5-Å structure of Mic1 capsid. The major capsid protein gp40 of an HK97-like fold forms two types of capsomers, hexons and pentons. The capsomers interact with each other via the interweaved N-terminal arms of gp40 in addition to a tail-in-mouth joint along the three-fold symmetric axis, resulting in the assembly of capsid in a mortise-and-tenon pattern. The novel-fold cement protein gp47 sticks at the two-fold symmetric axis and further fixes the capsid. These findings provide structural insights into the assembly of cyanophages, and set up a platform to explore the mechanism of specific interactions and co-evolution with cyanobacteria.

Characterization of Cyanophages in Lake Erie: Interaction Mechanisms and Structural Damage of Toxic Cyanobacteria.

Cyanophages are abundant in aquatic environments and play a critical role in bloom dynamics, including regulation of cyanobacteria growth and photosynthesis. In this study, cyanophages from western Lake Erie water samples were screened for lytic activities against the host cell (Microcystis aeruginosa), which was also originated from Lake Erie and identified with real-time sequencing (Nanopore sequencing). M. aeruginosa was mixed with the cyanophages and their dynamic interactions were examined over two weeks using atomic force microscopy (AFM) as well as transmission electron microscopy (TEM), qPCR, phycocyanin and chlorophyll-a production, and optical absorbance measurements. The TEM images revealed a short-tailed virus (Podoviridae) in 300 nm size with unique capsid, knob-like proteins. The psbA gene and one knob-like protein gene, gp58, were identified by PCR. The AFM showed a reduction of mechanical stiffness in the host cell membranes over time after infection, before structural damage became visible. Significant inhibition of the host growth and photosynthesis was observed from the measurements of phycocyanin and chlorophyll-a concentrations. The results provide an insight into cyanobacteria-cyanophage interactions in bloom dynamics and a potential application of cyanophages for bloom control in specific situations.

Ma-LMM01 infecting toxic Microcystis aeruginosa illuminates diverse cyanophage genome strategies.

Cyanobacteria and their phages are significant microbial components of the freshwater and marine environments. We identified a lytic phage, Ma-LMM01, infecting Microcystis aeruginosa, a cyanobacterium that forms toxic blooms on the surfaces of freshwater lakes. Here, we describe the first sequenced freshwater cyanomyovirus genome of Ma-LMM01. The linear, circularly permuted, and terminally redundant genome has 162,109 bp and contains 184 predicted protein-coding genes and two tRNA genes. The genome exhibits no colinearity with previously sequenced genomes of cyanomyoviruses or other Myoviridae. The majority of the predicted genes have no detectable homologues in the databases. These findings indicate that Ma-LMM01 is a member of a new lineage of the Myoviridae family. The genome lacks homologues for the photosynthetic genes that are prevalent in marine cyanophages. However, it has a homologue of nblA, which is essential for the degradation of the major cyanobacteria light-harvesting complex, the phycobilisomes. The genome codes for a site-specific recombinase and two prophage antirepressors, suggesting that it has the capacity to integrate into the host genome. Ma-LMM01 possesses six genes, including three coding for transposases, that are highly similar to homologues found in cyanobacteria, suggesting that recent gene transfers have occurred between Ma-LMM01 and its host. We propose that the Ma-LMM01 NblA homologue possibly reduces the absorption of excess light energy and confers benefits to the phage living in surface waters. This phage genome study suggests that light is central in the phage-cyanobacterium relationships where the viruses use diverse genetic strategies to control their host's photosynthesis.

Ecological dynamics of the toxic bloom-forming cyanobacterium Microcystis aeruginosa and its cyanophages in freshwater.

The abundance of potentially Microcystis aeruginosa-infectious cyanophages in freshwater was studied using g91 real-time PCR. A clear increase in cyanophage abundance was observed when M. aeruginosa numbers declined, showing that these factors were significantly negatively correlated. Furthermore, our data suggested that cyanophage dynamics may also affect shifts in microcystin-producing and non-microcystin-producing populations.