Biology subjects

Wagatsuma, R.

Publications and source records attributed to Wagatsuma, R..

5 recordsLinked to original sources

bioRxiv2024

Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria

The ecological importance of virus-host interactions is unclear due to the limited ability of metagenomics to resolve virus-host pairs and the infection state of individual cells. We addressed these problems using single-cell genomics combined with published metagenomic data on lake bacterioplankton. We obtained 862 medium- to high-quality single-cell amplified genomes (SAGs) from two water layers and two seasons in Lake Biwa, Japan. We assembled 176 viral (dsDNA phage) contigs in the SAGs, and identified novel virus-host pairs including the discovery of viruses infecting CL500-11, the dominant bacterioplankton lineage in deep freshwater lakes worldwide. A virus was detected in 133 (15.4%) SAGs through read mapping analysis. The viral detection rate showed little variation among samples (12.1-18.1%) but significant variation in host taxonomy (4.2-65.3%), with copiotrophs showing higher values than oligotrophs. The high infection rates of copiotrophs were achieved by collective infection by diverse viruses, suggesting weak density-dependent virus-host selections, presumably because of their non-persistent interactions with viruses due to their fluctuating abundance. In contrast, the low infection rates of oligotrophs supported the idea that their co-dominance with viruses is achieved by genomic microdiversification that diversifies the virus-host specificity, sustained by their large population size and persistent density-dependent fluctuating selection. Overall, we demonstrated that virus-host interactions are highly diverse within and between host lineages, which was overlooked by metagenomics analysis, as exemplified by the CL500-11 virus, which showed extremely high read coverages in cellular and virion metagenomes, but infected < 1% of host cells. Significance statementVirus-host interactions are among the most significant driving forces of microbial biogeochemical cycles and genomic diversification. Unlike experimental conditions, bacterial cells in the natural environment are not uniformly infected by a single virus, but interact with diverse viruses under heterogeneous eco-physiological and genetic conditions. The specificity and heterogeneity of infection are the keys to understanding complex virus-host interactions and the mechanisms behind their co-existence. However, these interactions remain unclear due to the limitations of conventional metagenomic approaches. We addressed this issue by detecting viral signals from single-cell-amplified genomes of lake bacterial communities. The results revealed novel virus-host pairs and their infection rates, suggesting that viral defense strategies differ among host lineages, reflecting their ecological characteristics.

ecology↗

bioRxiv2024

Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles

Environmental viruses (primarily bacteriophages) are widely recognized as playing an important role in ecosystem homeostasis through the infection of host cells. However, the majority of environmental viruses are still unknown as their mosaic structure and frequent mutations in their sequences hinder genome construction in current metagenomics. To enable the large-scale acquisition of environmental viral genomes, we developed a new single-viral genome sequencing platform with microfluidic-generated gel beads. Amplification of individual DNA viral genomes in mass-produced gel beads allows high-throughput genome sequencing compared to conventional single-virus genomics. The sequencing analysis of river water samples yielded 1431 diverse viral single-amplified genomes, while viral metagenomics recovered 100 viral metagenome-assembled genomes at the comparable sequence depth. The 99.5% of viral single-amplified genomes were determined novel at the species level, most of which could not be recovered by a metagenomic assembly. The large-scale acquisition of diverse viral genomes identified protein clusters commonly detected in different viral strains, allowing the gene transfer to be tracked. Moreover, comparative genomics within the same viral species revealed that the profiles of various methyltransferase subtypes were diverse, suggesting an enhanced escape from host bacterial internal defense mechanisms. Our use of gel bead-based single-virus genomics will contribute to exploring the nature of viruses by accelerating the accumulation of draft genomes of environmental DNA viruses.

genomics↗

bioRxiv2022

Variation of length and sequence of the nuclear ribosomal DNA internal transcribed spacer 1 supports hermit-to-king crab hypothesis

Lithodoid and paguroid crabs are morphologically assigned to the superfamilies Lithodoidea and Paguroidea, respectively. Molecular analyses, however, have revealed closer genetic proximity of the lithodoid crabs to the family Paguridae than to other families of Paguroidea, provoking a long debate. We investigated the length and nucleotide sequence variation of the nuclear ribosomal DNA internal transcribed spacer 1 (ITS1) in lithodoid and paguroid species. Uniquely short ITS1s (215-253 bp) were observed in seven lithodoid species belonging to the families Lithodidae and Hapalogastridae. In contrast, ITS1 length varied considerably in 13 paguroid species belonging to the families Coenobitidae, Diogenidae, and Paguridae. Short-to-long ITS1s (238-1090 bp) were observed in five species of the family Paguridae, and medium to long ITS1s (573-1166 bp) were observed in eight species of the families Coenobitidae and Diogenidae. Interestingly, ITS1s of considerably different sizes coexist in individual paguroid species. Nucleotide sequence analysis indicated that the short ITS1s observed in the family Paguridae were descendants of longer ITS1s and were homologous to the short ITS1 of lithodoid species. ITS1 sequences of the families Coenobitidae and Diogenidae shared no nucleotide elements similar to those of lithodoid and pagurid species. These molecular signals indicate that the short ITS1 in pagurid lineage was passed on to lithodoid lineage, strongly supporting the "hermit-to-king" crab hypothesis.

evolutionary biology↗

bioRxiv2022

Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral

Endozoicomonas bacteria symbiose with various marine organisms and are known to be beneficial for coral health. However, genome analysis of coral-associated Endozoicomonas has been limited owing to the difficulty in cultivation and metagenomic approach by contamination of host-derived sequences. In this study, we applied a novel single-cell genomics technique using droplet microfluidics to obtain single-cell amplified genome (SAGs) for coral-associated Endozoicomonas spp. genome. We obtained seven novel Endozoicomonas genomes from Acropora tenuis coral. These genomes revealed that Endozoicomonas bacteria played host-associated functions in host corals and had undergone independent host-adaptive evolution in different clades. These adaptive evolutions were mediated by host-derived eukaryotic-like genes, some of which were speculated to influence host immune mechanisms. These genes are speculated to enhance coral tolerance to environmental stresses. This study suggests the possibility of host adaptation of Endozoicomonas spp. in symbiosis with corals and their contribution to coral bleaching tolerance.

microbiology↗

bioRxiv2022

Reproducible and sensitive micro-tissue RNA-sequencing from formalin-fixed paraffin-embedded tissue for spatial gene expression analysis

Spatial transcriptome analysis of formalin-fixed paraffin-embedded (FFPE) tissues using RNA-sequencing (RNA-seq) provides interactive information on morphology and gene expression, which is useful for clinical applications. However, despite the advantages of long-term storage at room temperature, FFPE tissues may be severely damaged by methylene crosslinking and provide less gene information than fresh-frozen tissues. In this study, we proposed a sensitive FFPE micro-tissue RNA-seq method that combines the punching of tissue sections (diameter: 100 m) and the direct construction of RNA-seq libraries. We evaluated a method using mouse liver tissues at 2 years after fixation and embedding and detected approximately 7,000 genes in micro-punched tissue-spots (thickness: 10 m), similar to that detected with purified total RNA (2.5 ng) equivalent to the several dozen cells in the spot. We applied this method to clinical FFPE specimens of lung cancer that had been fixed and embedded 6 years prior, and found that it was possible to determine characteristic gene expression in the microenvironment containing tumor and non-tumor cells of different morphologies. This result indicates that spatial gene expression analysis of the tumor microenvironment is feasible using FFPE tissue sections stored for extensive periods in medical facilities.

molecular biology↗