水圏ウイルスおよび原生生物の分子生物学的研究

概要

令和 4 年度

京都大学化学研究所 スーパーコンピュータシステム 利用報告書
水圏ウイルスおよび原生生物の分子生物学的研究
Molecular biology of aquatic viruses, and protists

Kyoto University, Graduate School of Agriculture, Division of Applied Biosciences,
Laboratory of Marine Microbiology, Takashi Yoshida
研究成果概要
Viruses infecting marine prokaryotes have a large impact on the diversity and dynamics of
their hosts. Model systems suggest that viral infection is frequency dependent and constrained
by the virus-host encounter rate. However, it is unclear whether frequency-dependent infection
is pervasive among the abundant prokaryotic populations with different temporal dynamics. To
address this question, we performed a comparison of prokaryotic and viral communities using
16S rRNA amplicon and virome sequencing based on samples collected monthly for 2 years at a
Japanese coastal site, Osaka Bay. Concurrent seasonal shifts observed in prokaryotic and viral
community dynamics indicated that the abundance of viruses correlated with that of their
predicted host phyla (or classes). Cooccurrence network analysis between prokaryotes and
viruses revealed 6,423 cooccurring pairs, suggesting a tight coupling of host and viral
abundances and their “one-to-many” correspondence. Although stable dominant species showed
few cooccurring viruses, a fast succession of their viruses suggests that viruses infecting these
populations changed continuously. Our results suggest that frequency-dependent viral infection
prevails in coastal marine prokaryotes regardless of host taxa and temporal dynamics.
Viral infection of marine microalgae alters organic matter composition of the algae, which
should affect prokaryotic dynamics. We investigated the effects of viral infection of the red tide
alga Heterosigma akashiwo on prokaryotic communities. Cell lysate of H. akashiwo infected by
a virus was abundant in branched-chain amino acids, and enhanced growth of different
prokaryotes including Vibrio compared to cell extracts from non-infected H. akashiwo. It
suggested that Vibrio, which utilize branched-chain amino acids, respond to the lysate of
virus-infected cells.
Microcystis aeruginosa is predicted to interact and coexist with broad- and
narrow-host-range viruses within a bloom; however, little is known about their effects on
Microcystis population dynamics. Here, we developed a real-time PCR assay to quantify these
viruses with broad- and narrow-host-range and monitored these viruses in a environment with
host Microcystis population dynamics. In the sampling period, total Microcystis abundance
showed two peaks in May and August with a temporary decrease in June. The abundances of the
broad-host-range virus increased from April to May and from July to October with a temporary

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decrease in June, in which its dynamics were in proportion to the increase of total Microcystis
abundances regardless of changes in host population composition. The narrow-host-range
viruses were considerably less abundant than the broad-host-range virus and generally did not
fluctuate in the environment. Considering that M. aeruginosa increased the abundance and
sustain the bloom under the prevalence of the broad-host-range virus, host abundant and diverse
antiviral mechanisms might contribute to coexistence with its viruses.
Viral infection dynamics of marine cyanobacteria affects nutrient cycles, however, the
number of infection pairs of cyanobacteria and viruses, and the daily dynamics of each pair
remain unsolved. Therefore, we performed time-course metagenomic and metatranscriptomic
analyses of seawater of Osaka Bay. We found 169 viruses closely related to viruses which infect
Synechococcus. The transcript abundance of these viruses and Synechococcus peaked at the
same time, suggesting that different viruses infect simultaneously.
The growth of marine microalgae is influenced by coexisting prokaryotes. The haptophyte
Pavlomulina ranunculiformis is globally distributed, but ecological knowledge is scarce.
Therefore, we investigated the effect of coexisting prokaryotic communities on the growth of P.
ranunculiformis. In the absence of prokaryotes, the loss of the cells of P. ranunculiformis was
faster after the late log phase than in the presence of prokaryotes, suggesting that prokaryotes
affect the survival of this alga. Prokaryotic community structure analysis suggested that bacteria
of the families Rhodobacteraceae and Flavobacteriaceae were dominant during the logarithmic
and stationary phases, respectively, and that they affected the survival of this alga.

発表論文（謝辞あり）
・Prevalence of Viral Frequency-Dependent Infection in Coastal Marine Prokaryotes Revealed
Using Monthly Time Series Virome Analysis (2023). mSystems, e00931-22
・ Ecological Dynamics of Broad- and Narrow-Host-Range Viruses Infecting the
Bloom-Forming Toxic Cyanobacterium Microcystis aeruginosa (2023) Appl. Environ.
Microbiol., e02111-22
・Taxonomic difference in marine bloom-forming phytoplanktonic species affects dynamics of
both

bloom-responding

prokaryotes

and

prokaryotic

viruses.

(2023).

biorxiv. ...