海洋優占原核生物へのウイルス感染の影響に関する分子生態学的研究

京都大学新制・課程博士博士(農学)甲第23236号農博第2443号新制||農||1083(附属図書館)学位論文||R3||N5326京都大学大学院農学研究科応用生物科学専攻(主査)教授 吉田 天士, 教授 澤山 茂樹, 准教授 神川 龍馬学位規則第4条第1項該当Doctor of Agricultural ScienceKyoto UniversityDGA

Prevalence of Viral Frequency-Dependent Infection in Coastal Marine Prokaryotes Revealed Using Monthly Time Series Virome Analysis

海洋微生物も”密”ならウイルスに感染する --頻度依存的なウイルス感染を大阪湾で実証--. 京都大学プレスリリース. 2023-02-24.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 abundant 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, such as SAR11, 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

Diel cycling of the cosmopolitan abundant Pelagibacter virus 37‐F6: one of the most abundant viruses on earth

The spatiotemporal dynamics for marine viral populations has only recently been explored. However, nothing is known about temporal activities of the uncultured Pelagibacter virus vSAG 37‐F6, which was discovered by single‐virus genomics as potentially the most abundant marine virus. Here, we investigate the diel cycling of 37‐F6 virus and the putative SAR11 host using coastal and oceanic transcriptomic and viromic time‐series data from Osaka Bay and North Pacific Subtropical Gyre. Virus 37‐F6 and relatives displayed diel cycling of transcriptional activities synchronized with its putative host. In both virus and host, the lowest transcription rates were observed at 14:00–15:00, coinciding roughly with maximum solar irradiance, while higher transcriptional rates were detected during the night/early morning and afternoon. Diel abundance of free viruses of 37‐F6 in seawater roughly mirrored the transcriptional activities of both virus and host. In Osaka Bay, among viral relatives (genus level), virus 37‐F6 specifically showed the highest ratio of transcriptional activity to virome abundance, a proxy for viral transcriptional activity relative to free viral particle abundance. This high ratio suggests high infection rate efficiencies in vSAG 37‐F6 virus compared to viral relatives. Thus, time‐series data revealed temporal transcript activities in one of the most abundant viruses in Earth.This work has been supported by Spanish Ministry of Economy and Competitiveness to MMG (Ref. RTI2018-094248-B-100), Generalitat Valenciana to FMH (ACIF/2015/332), and Gordon and Betty Moore Foundation to MMG (grant 5334). Gordon and Betty Moore Foundation to EFD (3777) and Simons Foundation Grant #329108 (to EFD)

Population-level prokaryotic community structures associated with ferromanganese nodules in the Clarion-Clipperton Zone (Pacific Ocean) revealed by 16S rRNA gene amplicon sequencing

Although deep-sea ferromanganese nodules are a potential resource for exploitation, their formation mechanisms remain unclear. Several nodule-associated prokaryotic species have been identified by amplicon sequencing of 16S rRNA genes and are assumed to contribute to nodule formation. However, the recent development of amplicon sequence variant (ASV)-level monitoring revealed that closely related prokaryotic populations within an operational taxonomic unit often exhibit distinct ecological properties. Thus, conventional species-level monitoring might have overlooked nodule-specific populations when distinct populations of the same species were present in surrounding environments. Herein, we examined the prokaryotic community diversity of nodules and surrounding environments at the Clarion-Clipperton Zone in Japanese licensed areas by 16S rRNA gene amplicon sequencing with ASV-level resolution for three cruises from 2017 to 2019. Prokaryotic community composition and diversity were distinct by habitat type: nodule, nodule-surface mud, sediment, bottom water and water column. Most ASVs (~80%) were habitat-specific. We identified 178 nodule-associated ASVs and 41 ASVs associated with nodule-surface mud via linear discriminant effect size analysis. Moreover, several ASVs, such as members of SAR324 and Woeseia, were highly specific to nodules. These nodule-specific ASVs are promising targets for future investigation of the nodule formation process

Viral Nature of the Aquatic Ecosystems

Part of the Advances in Environmental Microbiology book series (AEM, volume 9)Viruses infecting microorganisms are ubiquitous and highly abundant in aquatic environments. They considerably affect the dynamics, diversity, and evolution of their host microorganisms. In this review, we discuss the ecological implications of viruses from the perspectives of the biogeochemical cycles, microbial diversity, and virus–host coevolutionary dynamics in aquatic environments. Generally, viruses redirect host metabolism toward reproduction through molecular host–virus interactions characterized by the compositional and stoichiometric changes in intracellular metabolites, which are eventually released into the environment when the infected host cells are lysed, thus also changing the chemical composition of the water. Therefore, the modulation of metabolite biosynthesis and promotion of their recycling are major viral functions. Viruses also maintain microbial community diversity via increased infection and lysis rates of the dominant taxa and genotypes in a frequency-dependent manner, thereby allowing the co-existence of members with various competitive abilities. Finally, viruses can expand their own genotypic diversity and that of the host through complex defense and counter-defense interactions, including loss of host fitness due to the cost of resistance and the possible need for antiviral defense-specific (e.g., intra- vs. extracellular) changes in the hosts genome diversification. Continuous interactions drive the coevolution of hosts and viruses, thereby increasing both the host and viral micro-diversity. Hence, these fundamental functions are viral “raison d’etre” and are essential for the functioning of aquatic ecosystems and its components

Correlation between Solvation Structure and Ion-Conductive Behavior of Concentrated Poly(ethylene carbonate)-Based Electrolytes

Solid polymer electrolytes are important materials in realizing safe and flexible energy storage devices. The present study looks at correlation between solvation structure and the ion-conductive behavior of poly­(ethylene carbonate) (PEC)/lithium bis­(fluorosulfonyl)­imide (LiFSI) electrolytes which have high Li transference number (<i>t</i>₊) and show unusual salt-concentration dependence of conductivity. From FT-IR and Raman spectroscopy, we determined that Li ions interact with carbonyl (CO) groups and also with FSI ions, which can be referred to as contact ion pair or aggregate. ⁷Li magic-angle-spinning NMR spectroscopy and density functional theory calculations for model species suggest that a loose coordination structure, in which Li ions interact with CO groups and FSI ions with appropriate strength, allows the electrolytes to have both reasonable conductivity and high <i>t</i>₊ with a flexible and transparent character. A high salt dissociation rate is generally considered essential in SPEs, but the presence of aggregated ions having the loose coordination structure gives rise to favorable performance in highly concentrated PEC-based solid polymer electrolytes

A QuaternaryPoly(ethylene carbonate)-Lithium Bis(trifluoromethanesulfonyl)imide-Ionic Liquid-Silica Fiber Composite Polymer Electrolyte for Lithium Batteries

Poly(ethylene carbonate) (PEC) is known as an alternating copolymer derived from carbon dioxide (CO2) and an epoxide as monomers. Here, we describe a new quaternary PEC-based composite electrolyte containing lithium bis(trifluoromethanesulfonyl) imide (LiTFSI) salt, N-n-butyl-N-methylpyrrolidinium bis(trifluoromethanesulfonyl) imide (Pyr14TFSI) ionic liquid, and an electrospun silica (SiO2) fiber (SiF) with a submicron diameter in view of its possible applications in solid-state Li polymer batteries. A free-standing electrolyte membrane is prepared by a solvent casting method. The Pyr14TFSI ionic liquid enhances the ionic conductivity of the electrolyte as a result of its plasticizing effect. The electrochemical properties, such as ionic conductivity and Li transference number (tLi+), as well as mechanical strength of the electrolyte, are further improved by the SiF. We show that the quaternary electrolyte has a conductivity of the order of 10-7 S cm-1 at ambient temperature and a high tLi+ value of 0.36 with an excellent flexibility. A prototype Li polymer cell using LiFePO4 as a cathode material is assembled and tested. We demonstrate that this battery delivers a reversible charge-discharge capacity close to 100 mAh g-1 at 75 oC and C/15 rate. We believe that this work may pave the road to utilize CO2 as a carbon source for highly-demanded, functional battery materials in future

Taxonomic difference in marine bloom-forming phytoplanktonic species affects the dynamics of both bloom-responding prokaryotes and prokaryotic viruses

ABSTRACTThe production of dissolved organic matter during phytoplankton blooms and consumption by heterotrophic prokaryotes promote marine carbon biogeochemical cycling. Although prokaryotic viruses presumably affect this process, their dynamics during blooms are not fully understood. Here, we investigated the effects of taxonomic difference in bloom-forming phytoplankton on prokaryotes and their viruses. We analyzed the dynamics of coastal prokaryotic communities and viruses under the addition of dissolved intracellular fractions from taxonomically distinct phytoplankton, the diatom Chaetoceros sp. (CIF) and the raphidophycean alga Heterosigma akashiwo (HIF), using microcosm experiments. Ribosomal RNA gene amplicon and viral metagenomic analyses revealed that particular prokaryotes and prokaryotic viruses specifically increased in either CIF or HIF, indicating that taxonomic difference in bloom-forming phytoplankton promotes distinct dynamics of not only the prokaryotic community but also prokaryotic viruses. Furthermore, combining our microcosm experiments with publicly available environmental data mining, we identified both known and novel possible host-virus pairs. In particular, the growth of prokaryotes associating with phytoplanktonic organic matter, such as Bacteroidetes (Polaribacter and NS9 marine group), Vibrio spp., and Rhodobacteriales (Nereida and Planktomarina), was accompanied by an increase in viruses predicted to infect Bacteroidetes, Vibrio, and Rhodobacteriales, respectively. Collectively, our findings suggest that changes in bloom-forming species can be followed by an increase in a specific group of prokaryotes and their viruses and that elucidating these tripartite relationships among specific phytoplankton, prokaryotes, and prokaryotic viruses improves our understanding of coastal biogeochemical cycling in blooms.IMPORTANCEThe primary production during marine phytoplankton bloom and the consumption of the produced organic matter by heterotrophic prokaryotes significantly contribute to coastal biogeochemical cycles. While the activities of those heterotrophic prokaryotes are presumably affected by viral infection, the dynamics of their viruses during blooms are not fully understood. In this study, we experimentally demonstrated that intracellular fractions of taxonomically distinct bloom-forming phytoplankton species, the diatom Chaetoceros sp. and the raphidophycean alga Heterosigma akashiwo, promoted the growth of taxonomically different prokaryotes and prokaryotic viruses. Based on their dynamics and predicted hosts of those viruses, we succeeded in detecting already-known and novel possible host-virus pairs associating with either phytoplankton species. Altogether, we propose that the succession of bloom-forming phytoplankton would change the composition of the abundant prokaryotes, resulting in an increase in their viruses. These changes in viral composition, depending on bloom-forming species, would alter the dynamics and metabolism of prokaryotes, affecting biogeochemical cycling in blooms