Biology subjects

Nagasaki, K.

Publications and source records attributed to Nagasaki, K..

5 recordsLinked to original sources

bioRxiv2026

Rapid diversification of a natural Heterosigma akashiwo virus population during a host bloom

Despite the ecological importance of viruses, our understanding of their evolutionary dynamics in natural environments remains limited. This gap is particularly pronounced for giant dsDNA viruses of the phyla Nucleocytoviricota and Mirusviricota. Most knowledge on their population genetic dynamics is derived from a small number of laboratory-based experiments, whereas patterns in nature are rarely observed. To overcome this limitation, we traced genetic structure and transcription status of Heterosigma akashiwo virus (HaV) using high-frequency, time-resolved sampling during a host bloom in a coastal area of Japan, by integrating cell counting, metabarcoding, metagenomic and metatranscriptomic sequencing. Our study revealed that HaV dominated the giant virus community in most samples, with the relative abundances of up to 56%. Despite the high abundances, the HaV population exhibited a relatively low level of microdiversity but with a high pN/pS ratio compared to other giant viruses in the study site. Microdiversity increased during the early sampling period, reached a maximum at mid-sampling, and decreased during the later period, consistent with rapid diversification during viral expansion, possibly driven by both in situ mutations and the succession of pre-existing minor variants. Several accessory genes, including a glycosyltransferase and an endonuclease, were highly expressed, providing functional evidence consistent with host interaction-driven selective pressure during the bloom. Together, these results indicate that HaV population dynamics during algal blooms are shaped by host-driven selection acting on standing genetic variation.

ecology↗

bioRxiv2024

Viral infection to the raphidophycean alga Heterosigma akashiwo affects both intracellular organic matter composition and dynamics of a coastal prokaryotic community

Marine microalgae play a crucial role in marine ecosystem by supplying dissolved organic matter to heterotrophic prokaryotes, which mediate the microbial loop. Microalgae are often infected by viruses, and in infected cells (virocells), the viruses modulate and often change the host metabolism for propagation and thereby endo-metabolites. However, the impact of algal virocells on prokaryotic communities is not fully been understood. In this study, we investigated whether lysates from virocell of Heterosigma akashiwo, a globally prevalent bloom-forming raphidophycean alga, causes shifts inn prokaryotic community structure, and which metabolic compounds in the viral lysate might affect the surrounding prokaryotic populations. Using microcosm experiments, we cultured prokaryotic communities with a dissolved fraction derived from the viral lysate (VDF) of H. akashiwo. Results revealed that certain prokaryotic populations assigned as the Vibrio spp. pathogenic against fish and crustaceans grew specifically responding to the VDF. These Vibrio species possessed a gene module for branched-chain amino acids transporters, which were revealed to be enriched in VDF by gas chromatography-mass spectrometry analysis. Altogether, our findings suggest that viral infection-induced changes in biochemical properties of H. akashiwo cells can promote the growth of taxonomically and metabolically different prokaryotic populations, potentially impacting higher trophic-level consumers in marine ecosystems. HighlightsO_LIThe effect of viral infection to microalgae on marine prokaryotes was investigated. C_LIO_LIViral lysate of Heterosigma akashiwo promoted growth of certain Vibrio population. C_LIO_LIThose Vibrio likely have ability to utilize the compounds enriched in the lysate. C_LIO_LIThose Vibrio have been known as pathogen of fish or crustacean. C_LIO_LIViral infection to H. akashiwo can indirectly affect higher trophic-level consumers. C_LI

microbiology↗

bioRxiv2024

Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity

Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic community structure, accelerate carbon and nutrient cycles, and drive the evolution of their hosts through co-evolutionary processes. Previously reported long-term observations revealed that these viruses display fluctuations in abundance. However, the underlying genetic mechanisms driving such dynamics in these viruses remain largely unknown. In this study, we investigated population and intra-population dynamics of giant viruses using time-series metagenomes from eutrophic coastal seawater samples collected over 20 months. A newly developed near-automatic computational pipeline generated 1,065 high-quality metagenome-assembled genomes covering six major giant virus lineages. These genomic data revealed year-round recovery of the viral community at the study site and distinct dynamics of different viral populations classified as persistent (n = 9), seasonal (n = 389), sporadic (n = 318), or others. Notably, year-round recovery patterns were observed at the intra-population genetic diversity level for viruses classified as persistent or seasonal. Our results further indicated that the viral genome dynamics were associated with intra-population diversity; specifically, giant viruses with broader niche breadth tended to exhibit greater levels of microdiversity. We argue that greater microdiversity in viruses likely enhances adaptability and thus survival under the virus-host arms race during prolonged interactions with their hosts.

microbiology↗

bioRxiv2024

Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages

Restriction modification (RM) systems are ubiquitous bacterial defense systems; however, some phages evade RM system and adapt to their bacterial hosts. In such cases, phages are thought to stochastically acquire DNA methylation from host-encoded DNA methyltransferases (MTases), facilitating host adaptation. However, no studies have directly compared the methylomes of host bacteria and their infecting phages. Here, we demonstrate the epigenetic landscape of adapted phages with diverse infection histories, focusing on the broad host-range phage KHP30T as its adapts to three Helicobacter pylori strains. Using a multistage infection system, we observed that the adapted phages displayed significantly high titers against the last infected H. pylori strain, suggesting an attendant change in host tropism. Single-molecule real-time sequencing revealed that methylated motifs were predominantly shared between the adapted phages and their most recent host. Our findings enhance our understanding of epigenetic phage-host interactions, which have significant implications for microbial ecology.

microbiology↗

bioRxiv2021

Year-round dynamics of amplicon sequence variant communities differ among eukaryotes, Mimiviridae, and prokaryotes in a coastal ecosystem

Coastal seawater is the habitat of different microbial communities. These communities are affected by seasonal environmental changes and fluctuating nutrient availability, as well as competitive and cooperative interspecific interactions. In this work, we investigated the seasonal dynamics of communities of eukaryotes, a major group of double-stranded DNA viruses infecting eukaryotes (i.e. Mimiviridae), as well as prokaryotes in the Uranouchi Inlet, Kochi, Japan. We performed metabarcoding using ribosomal RNA genes and the Mimiviridae polB gene as marker genes in 43 seawater samples collected during 20 months. Communities characterized by the compositions of amplicon sequence variants (ASVs) showed synchronic seasonal cycles for eukaryotes, Mimiviridae, and prokaryotes. However, the community dynamics showed intriguing differences in several aspects such as the recovery rate after a year. We further show that the differences in the community dynamics can be explained by differences in the recurrence/persistence levels of individual ASVs among eukaryotes, Mimiviridae, and prokaryotes. Mimiviridae ASVs were less persistent than eukaryotic ASVs, and prokaryotic ASVs were the most persistent. We argue that the differences in the specificity of interactions (i.e. virus-eukaryote vs prokaryote-eukaryote) as well as the survival strategies are at the origin of the distinct community dynamics among eukaryotes, Mimiviridae, and prokaryotes. One sentence summaryA one year observation of coastal microbial communities revealed similar but different community dynamics for eukaryotes, a group of large viruses, and prokaryotes.

microbiology↗