Complete Genome Sequence of Microcystis aeruginosa NIES-2549, a Bloom-Forming Cyanobacterium from Lake Kasumigaura, Japan

Amplicon-based and metagenomic approaches provide insights into toxigenic potential in understudied Atlantic Canadian lakes

Cyanobacterial blooms and their toxigenic potential threaten freshwater resources worldwide. In Atlantic Canada, despite an increase of cyanobacterial blooms in the last decade, little is known about the toxigenic potential and the taxonomic affiliation of bloom-forming cyanobacteria. In this study, we employed polymerase chain reaction (PCR) and metagenomic approaches to assess the potential for cyanotoxin and other bioactive metabolite production in Harvey Lake (oligotrophic) and Washademoak Lake (mesotrophic) in New Brunswick, Canada, during summer and early fall months. The PCR survey detected the potential for microcystin (hepatotoxin) and anatoxin-a (neurotoxin) production in both lakes, despite a cyanobacterial bloom only being visible in Washademoak. Genus-specific PCR associated microcystin production potential with the presence of Microcystis in both lakes. The metagenomic strategy provided insight into temporal variations in the microbial communities of both lakes. It also permitted the recovery of a near-complete Microcystis aeruginosa genome with the genetic complement to produce microcystin and other bioactive metabolites such as piricyclamide, micropeptin/cyanopeptolin, and aeruginosin. Our approaches demonstrate the potential for production of a diverse complement of bioactive compounds and establish important baseline data for future studies of understudied lakes, which are frequently affected by cyanobacterial blooms.

Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade

Cyanobacteria are a diverse group of Gram-negative prokaryotes that perform oxygenic photosynthesis. Cyanobacteria have been used for research on photosynthesis and have attracted attention as a platform for biomaterial/biofuel production. Cyanobacteria are also present in almost all habitats on Earth and have extensive impacts on global ecosystems. Given their biological, economical, and ecological importance, the number of high-quality genome sequences for Cyanobacteria strains is limited. Here, we performed genome sequencing of Cyanobacteria strains in the National Institute for Environmental Studies microbial culture collection in Japan. We sequenced 28 strains that can form a heterocyst, a morphologically distinct cell that is specialized for fixing nitrogen, and 3 non-heterocystous strains. Using Illumina sequencing of paired-end and mate-pair libraries with in silico finishing, we constructed highly contiguous assemblies. We determined the phylogenetic relationship of the sequenced genome assemblies and found potential difficulties in the classification of certain heterocystous clades based on morphological observation. We also revealed a bias on the sequenced strains by the phylogenetic analysis of the 16S rRNA gene including unsequenced strains. Genome sequencing of Cyanobacteria strains deposited in worldwide culture collections will contribute to understanding the enormous genetic and phenotypic diversity within the phylum Cyanobacteria.

Comparative genomics analysis of c-di-GMP metabolism and regulation in Microcystis aeruginosa

BACKGROUND

Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically diverse habitats because of their capacity to rapidly respond to environmental changes through a web of complex signaling networks, including using second messengers to regulate physiology or metabolism. A ubiquitous second messenger, bis-(3',5')-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has been found to regulate essential behaviors in a few cyanobacteria but not Microcystis, which are the most dominant species in cyanobacterial blooms. In this study, comparative genomics analysis was performed to explore the genomic basis of c-di-GMP signaling in Microcystis aeruginosa.

RESULTS

Proteins involved in c-di-GMP metabolism and regulation, such as diguanylate cyclases, phosphodiesterases, and PilZ-containing proteins, were encoded in M. aeruginosa genomes. However, the number of identified protein domains involved in c-di-GMP signaling was not proportional to the size of M. aeruginosa genomes (4.97 Mb in average). Pan-genome analysis showed that genes involved in c-di-GMP metabolism and regulation are conservative in M. aeruginosa strains. Phylogenetic analysis showed good congruence between the two types of phylogenetic trees based on 31 highly conserved protein-coding genes and sensor domain-coding genes. Propensity for gene loss analysis revealed that most of genes involved in c-di-GMP signaling are stable in M. aeruginosa strains. Moreover, bioinformatics and structure analysis of c-di-GMP signal-related GGDEF and EAL domains revealed that they all possess essential conserved amino acid residues that bind the substrate. In addition, it was also found that all selected M. aeruginosa genomes encode PilZ domain containing proteins.

CONCLUSIONS

Comparative genomics analysis of c-di-GMP metabolism and regulation in M. aeruginosa strains helped elucidating the genetic basis of c-di-GMP signaling pathways in M. aeruginosa. Knowledge of c-di-GMP metabolism and relevant signal regulatory processes in cyanobacteria can enhance our understanding of their adaptability to various environments and bloom-forming mechanism.

Genomic Characteristics of the Toxic Bloom-Forming Cyanobacterium Microcystis aeruginosa NIES-102

Microcystis aeruginosa, a bloom-forming cyanobacterium distributed mainly in freshwater environments, can be divided into at least 12 groups (A-K and X) based on multi-locus phylogenetic analyses. In this study, we characterized the genome of microcystin-producing M. aeruginosa NIES-102, assigned to group A, isolated from Lake Kasumigaura, Japan. The complete genome sequence of M. aeruginosa NIES-102 comprised a 5.87-Mbp circular chromosome containing 5,330 coding sequences. The genome was the largest among all sequenced genomes for the species. In a comparison with the genome of M. aeruginosa NIES-843, which belongs to the same group, the microcystin biosynthetic gene cluster and CRISPR-Cas locus were highly similar. A synteny analysis revealed small-scale rearrangements between the two genomes. Genes encoding transposases were more abundant in these two genomes than in other Microcystis genomes. Our results improve our understanding of structural genomic changes and adaptation to a changing environment in the species.

A novel salt-tolerant genotype illuminates the sucrose gene evolution in freshwater bloom-forming cyanobacterium Microcystis aeruginosa

Microcystis aeruginosa is a water bloom-forming cyanobacterium found in fresh and brackish water ecosystems worldwide. Previously, we showed that several instances of M. aeruginosa bloom in brackish water can be explained by the proliferation of salt-tolerant M. aeruginosa strains harboring genes for a compatible solute sucrose. However, evolutionary history of sucrose genes in M. aeruginosa remains unclear because salt-tolerant strains have been poorly described. Here, we characterized a novel salt-tolerant strain of M. aeruginosa (NIES-4325) isolated from the brackish water of Lake Abashiri, Japan. A whole-genome analysis of M. aeruginosa NIES-4325 identified genes for sucrose synthesis (sppA, spsA and susA). Quantitative sucrose and gene expression analyses suggested that sucrose is implicated in acclimation to high salt in NIES-4325. Notably, the sucrose genes of M. aeruginosa are monophyletic, yet sucrose genes of NIES-4325 are highly divergent from those of other salt-tolerant M. aeruginosa strains. This suggests an early sucrose gene import into M. aeruginosa from other cyanobacteria, followed by multiple losses during intraspecific diversification. One of a few survivors of salt-tolerant strains is a likely donor of recent horizontal spreads of sucrose genes across M. aeruginosa lineages.

Allelopathic effects of harmful algal extracts and exudates on biofilms on leaves of Vallisneria natans

This study investigated the allelopathic effects of Microcystis aeruginosa (M. aeruginosa) extracts and exudates on the physiological responses, photosynthetic activity, and microbial structure of biofilms on leaves of Vallisneria natans (V. natans). By measuring physiological and photosynthetic indices, the results showed that M. aeruginosa allelochemicals inhibited photosynthesis, oxidative stress and antioxidant system stress response in the biofilms of V. natans leaves. Multifractal analysis found that the surface topography of V. natans leaves was altered due to the allelochemicals found in M. aeruginosa. Microbial diversity on the leaves was analyzed using high-throughput sequencing, and the results showed that M. aeruginosa exudates had a stronger effects on the microbial community structure of biofilms compared to extracts. These findings highlight how cyanobacterial allelochemicals induce negative effects on submerged macrophytes.

Responses of leaf-associated biofilms on the submerged macrophyte Vallisneria natans during harmful algal blooms

The present study investigated the physiological responses, photosynthetic activity, and microbial community structure of leaf-associated biofilms on the microphyte Vallisneria natans during a harmful algal bloom. Results of the physiological and photosynthetic indices (F_v/F_m ratios [maximum quantum yield of photosystem II (PSII)]; malondialdehyde content; total chlorophyll; and activities of superoxide dismutase, catalase and peroxidase) indicated that algal blooms could cause inhibition of photosynthesis, oxidative stress and an antioxidant system stress response in Vallisneria natans leaf-associated biofilms. Multifractal analysis suggested that allelochemicals or algal organic matter released by cyanobacteria could reduce the surface roughness of the leaf. Microbial diversity analysis of the biofilms showed that algal blooms slightly altered the microbial community structure while the richness and evenness of the microbial composition remained stable. This study provided useful information to better understand the adverse effects of algal blooms on submerged macrophytes.

Inhibitory effect and mechanism of linoleic acid sustained-release microspheres on Microcystis aeruginosa at different growth phases

Environment-friendly algaecides based on allelopathy have been extensively studied to control harmful algal blooms (HABs). The inhibitory effects of linoleic acid (LA) sustained-release microspheres on different cell densities of Microcystis aeruginosa (M. aeruginosa) at different growth phases were studied. The results showed that the growth of M. aeruginosa could be inhibited within 4 days and the constant inhibitory rate with initial algal density of 8 × 10⁵ cells∙mL^-1 (exponential phase) was up to 96% compared with control. The chlorophyll-a content in the treatment group had the same change trend with the algal density and declined significantly at day 20th, which suggested that the microspheres could promote the degradation of chlorophyll-a. The activities of superoxide dismutase (SOD) and catalase (CAT) increased gradually within 5 days but then declined sharply, which indicated that LA microspheres could cause oxidative damage to M. aeruginosa during the process of inhibition and reduce the activities of antioxidant enzymes. In addition, the concentration of oxygen free radical (O₂^-) increased at day 10th and rose constantly, and the content of malodialdehyde (MDA) increased to 2.7 times as much as control at day 20th. Furthermore, the content of protein, nucleic acid and the conductivity in culture solution showed a significant rise. These results showed that algal cell membrane lipid peroxidation occurred and the membrane permeability increased, accompanied by the damage of cell membrane. To sum up, the destruction of algal cell membrane is the main mechanism of LA microspheres inhibiting algal growth.

The highly heterogeneous methylated genomes and diverse restriction-modification systems of bloom-forming Microcystis

The occurrence of harmful Microcystis blooms is increasing in frequency in a myriad of freshwater ecosystems. Despite considerable research pertaining to the cause and nature of these blooms, the molecular mechanisms behind the cosmopolitan distribution and phenotypic diversity in Microcystis are still unclear. We compared the patterns and extent of DNA methylation in three strains of Microcystis, PCC 7806SL, NIES-2549 and FACHB-1757, using Single Molecule Real-Time (SMRT) sequencing technology. Intact restriction-modification (R-M) systems were identified from the genomes of these strains, and from two previously sequenced strains of Microcystis, NIES-843 and TAIHU98. A large number of methylation motifs and R-M genes were identified in these strains, which differ substantially among different strains. Of the 35 motifs identified, eighteen had not previously been reported. Strain NIES-843 contains a larger number of total putative methyltransferase genes than have been reported previously from any bacterial genome. Genomic comparisons reveal that methyltransferases (some partial) may have been acquired from the environment through horizontal gene transfer.

Complete Genome Sequence of Microcystis aeruginosa NIES-2481 and Common Genomic Features of Group G M. aeruginosa

Microcystis aeruginosa is a freshwater bloom-forming cyanobacterium that is distributed worldwide. M. aeruginosa can be divided into at least 8 phylogenetic groups (A-G and X) at the intraspecific level. Here, we report the complete genome sequence of M. aeruginosa NIES-2481, which was isolated from Lake Kasumigaura, Japan, and is assigned to group G. The complete genome sequence of M. aeruginosa NIES-2481 comprises a 4.29-Mbp circular chromosome and a 147,539-bp plasmid; the circular chromosome and the plasmid contain 4,332 and 167 protein-coding genes, respectively. Comparative analysis with the complete genome of M. aeruginosa NIES-2549, which belongs to the same group with NIES-2481, showed that the genome size is the smallest level in previously sequenced M. aeruginosa strains, and the genomes do not contain a microcystin biosynthetic gene cluster in common. Synteny analysis revealed only small-scale rearrangements between the two genomes.

Structural and functional diversity of caspase homologues in non-metazoan organisms

Caspases, the proteases involved in initiation and execution of metazoan programmed cell death, are only present in animals, while their structural homologues can be found in all domains of life, spanning from simple prokaryotes (orthocaspases) to yeast and plants (metacaspases). All members of this wide protease family contain the p20 domain, which harbours the catalytic dyad formed by the two amino acid residues, histidine and cysteine. Despite the high structural similarity of the p20 domain, metacaspases and orthocaspases were found to exhibit different substrate specificities than caspases. While the former cleave their substrates after basic amino acid residues, the latter accommodate substrates with negative charge. This observation is crucial for the re-evaluation of non-metazoan caspase homologues being involved in processes of programmed cell death. In this review, we analyse the structural diversity of enzymes containing the p20 domain, with focus on the orthocaspases, and summarise recent advances in research of orthocaspases and metacaspases of cyanobacteria, algae and higher plants. Although caspase homologues were initially proposed to be involved in execution of cell death, accumulating evidence supports the role of metacaspases and orthocaspases as important contributors to cell homeostasis during normal physiological conditions or cell differentiation and ageing.

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

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.

Draft Genome Sequence of Microcystis aeruginosa NIES-98, a Non-Microcystin-Producing Cyanobacterium from Lake Kasumigaura, Japan

Microcystis aeruginosa is a well-known bloom-forming cyanobacterium. We newly sequenced the whole genome of M. aeruginosa NIES-98, which is a non-microcystin-producing strain isolated from Lake Kasumigaura, Japan. The genome contains approximately 5.0 Mbp, with an average G+C content of 42.41% and 5,140 predicted protein-coding genes.

Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102

Background

Very few closed genomes of the cyanobacteria that commonly produce toxic blooms in lakes and reservoirs are available, limiting our understanding of the properties of these organisms. A new anatoxin-a-producing member of the Nostocaceae, Anabaena sp. WA102, was isolated from a freshwater lake in Washington State, USA, in 2013 and maintained in non-axenic culture.

Results

The Anabaena sp. WA102 5.7 Mbp genome assembly has been closed with long-read, single-molecule sequencing and separately a draft genome assembly has been produced with short-read sequencing technology. The closed and draft genome assemblies are compared, showing a correlation between long repeats in the genome and the many gaps in the short-read assembly. Anabaena sp. WA102 encodes anatoxin-a biosynthetic genes, as does its close relative Anabaena sp. AL93 (also introduced in this study). These strains are distinguished by differences in the genes for light-harvesting phycobilins, with Anabaena sp. AL93 possessing a phycoerythrocyanin operon. Biologically relevant structural variants in the Anabaena sp. WA102 genome were detected only by long-read sequencing: a tandem triplication of the anaBCD promoter region in the anatoxin-a synthase gene cluster (not triplicated in Anabaena sp. AL93) and a 5-kbp deletion variant present in two-thirds of the population. The genome has a large number of mobile elements (160). Strikingly, there was no synteny with the genome of its nearest fully assembled relative, Anabaena sp. 90.

Conclusion

Structural and functional genome analyses indicate that Anabaena sp. WA102 has a flexible genome. Genome closure, which can be readily achieved with long-read sequencing, reveals large scale (e.g., gene order) and local structural features that should be considered in understanding genome evolution and function.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2738-7) contains supplementary material, which is available to authorized users.

A review of the global ecology, genomics, and biogeography of the toxic cyanobacterium, Microcystis spp

This review summarizes the present state of knowledge regarding the toxic, bloom-forming cyanobacterium, Microcystis, with a specific focus on its geographic distribution, toxins, genomics, phylogeny, and ecology. A global analysis found documentation suggesting geographic expansion of Microcystis, with recorded blooms in at least 108 countries, 79 of which have also reported the hepatatoxin microcystin. The production of microcystins (originally "Fast-Death Factor") by Microcystis and factors that control synthesis of this toxin are reviewed, as well as the putative ecophysiological roles of this metabolite. Molecular biological analyses have provided significant insight into the ecology and physiology of Microcystis, as well as revealed the highly dynamic, and potentially unstable, nature of its genome. A genetic sequence analysis of 27 Microcystis species, including 15 complete/draft genomes are presented. Using the strictest biological definition of what constitutes a bacterial species, these analyses indicate that all Microcystis species warrant placement into the same species complex since the average nucleotide identity values were above 95%, 16S rRNA nucleotide identity scores exceeded 99%, and DNA-DNA hybridization was consistently greater than 70%. The review further provides evidence from around the globe for the key role that both nitrogen and phosphorus play in controlling Microcystis bloom dynamics, and the effect of elevated temperature on bloom intensification. Finally, highlighted is the ability of Microcystis assemblages to minimize their mortality losses by resisting grazing by zooplankton and bivalves, as well as viral lysis, and discuss factors facilitating assemblage resilience.