Biology subjects

Tominaga, K.

Publications and source records attributed to Tominaga, K..

At least 19 recordsLinked to original sources

bioRxiv2026

NLGN3-tagging system for Evaluating Membrane Localization Applied to Drug Screening

Aberrant membrane localization of proteins often results in functional impairment, contributing to the development of pathological conditions. Neuroligin-3 (NLGN3) is a rare but recurrent genetic risk factor for autism spectrum disorder (ASD). Comparing surface localization across NLGN3 variants requires that surface signal be referenced to expression level in the same cell. Using NLGN3 as a model, we developed I-CLiQ, a live-cell method in which the target coding sequence is introduced at a single site of a fixed vector backbone and DsRed is co-encoded as an internal expression reference, based on a 2A peptide of Perina nuda virus modified to abolish ribosomal skipping. Combining I-CLiQ with AlphaFold/AlphaMissense analysis, we evaluated ASD-associated NLGN3 variants. Structural modeling predicted steric clashes for p.R451C, p.P514S, and p.R597W. I-CLiQ-based flow cytometry confirmed that these variants significantly decrease surface expression. Furthermore, as a proof-of-concept application, we used I-CLiQ to evaluate two compounds, 4-phenylbutyrate (4-PBA) and 3-amino-1-propanesulfonic acid (3-APS); 4-PBA partially restored the surface expression of p.R451C and p.R597W. These findings establish I-CLiQ as a quantitative tool for analyzing membrane trafficking defects and demonstrate its applicability to compound screening for variants associated with conformational diseases.

cell biology↗

bioRxiv2026

Dietary phosphorus restriction enables multigenerational breeding of α-Klotho-deficient rats

Severe -Klotho deficiency causes early mortality and reproductive impairment, limiting the maintenance and physiological analysis of rat models. We generated rats carrying a CRISPR/Cas9-mediated -Klotho deletion spanning exons 1-5 and evaluated dietary phosphorus restriction primarily in the Wistar-Imamichi background. Maternal low-phosphorus (LP) feeding from mating through lactation was associated with higher overall survival to weaning (92.6% versus 85.8% under normal-phosphorus conditions) and a higher proportion of KO animals among weaned survivors (34/113 versus 23/145). Maternal LP feeding also reduced plasma phosphorus in KO pups. Continued LP feeding after weaning supported growth, gonadal development, and natural KO x KO breeding. Across 15 litters, 74 of 85 offspring survived to weaning, and KO colonies were maintained to at least the fifth generation. We additionally characterized 24-h metabolic rhythms in LP-maintained KO animals using indirect calorimetry. These profiles remained heterogeneous under a light-dark cycle. In conclusion, dietary phosphorus restriction provides a reliable strategy for the multigenerational maintenance of severe -Klotho-deficient rats, establishing a maintainable model to investigate residual metabolic and physiological phenotypes.

physiology↗

bioRxiv2026

SAR11 Genome Atlas: a genome and gene catalog for functional profiling of the most abundant bacterial clade in the ocean

The SAR11 clade, also known as the order Candidatus Pelagibacterales, is among the most abundant bacterial lineages in the ocean and plays central roles in marine biogeochemical cycles. However, many SAR11 genes remain functionally uncharacterized, highlighting the need for a comprehensive, integrated catalog that supports genomic, functional, and ecological analyses across the clade. Here, we present the SAR11 Genome Atlas, an interactive ortholog group (OG)-centered web resource that integrates 542 SAR11 genomes, including all 132 cultured strain genomes, with functional annotations, synteny, phylogenetic distribution, metatranscriptomic expression, and predicted protein structure information. To demonstrate its utility, we used environmental expression profiles to identify OGs associated with high-latitude environments, recovering OGs known to be involved in cold adaptation and proposing a hypothesis for the function of uncharacterized protein. We further analyzed phylogenetic distribution patterns to identify mutually exclusive functional modules, including candidate alternative systems for Mn/Zn homeostasis and phosphate acquisition, and to associate these modules with distinct oceanographic environments. Together, these case studies demonstrate that the SAR11 Genome Atlas supports complementary analyses that connect environmental signals to genes of interest and use phylogenetic or functional distributions to generate hypotheses about ecological specialization. Through a user-friendly web interface, the SAR11 Genome Atlas enables researchers to explore genomic, environmental, and structural information without specialized computational expertise. All data and analysis outputs are freely accessible online at [https://stsnsn.github.io/SAR11_Atlas/]. The SAR11 Genome Atlas thus provides a scalable framework for generating and testing hypotheses that connect SAR11 genomic variation to protein function and oceanographic context, supporting advances in marine microbial ecology and biogeochemistry.

microbiology↗

bioRxiv2026

Regucalcin-containing extracellular vesicles suppress M2 macrophage polarization and attenuate tumor progression in vivo

Regucalcin (RGN) plays diverse roles in cell biology, highlighting its importance in both physiological and pathological conditions. Prostate cancer patients with higher RGN expression exhibited significantly longer disease-free survival. Although RGN is a cell signaling suppressor, the molecular mechanisms underlying tumor suppression by RGN in the tumor microenvironment through cell-cell communication remain unclear. PC3 prostate cancer cell lines stably expressing RGN or a control vector were generated for this study. Extracellular vesicles (EVs) were isolated from these cell lines using differential ultracentrifugation. The murine macrophage cell line J7441 was treated with isolated EVs, and effects on M2 polarization were evaluated using qRT-PCR and western blot analysis. To assess the potential anti-tumor effects of EVs, PC3 parental cells were subcutaneously implanted at two sites per mouse, followed by intratumoral injection of the respective EVs. Tumor volume was monitored. Harvested fresh frozen tumor tissues underwent immunofluorescence staining for CD206, an M2 macrophage marker. RGN was detected in EVs from RGN-expressing cells, and treatment with these RGN-containing EVs was associated with reduced tumor growth and reduced M2 macrophage polarization in vitro and in vivo. Furthermore, recombinant RGN protein reduced the levels of p-AKT1 and p-ERK1/2. Moreover, the suppression of M2 macrophage polarization by RGN-containing EVs was accompanied by decreased p-AKT1 and p-ERK1/2 in vitro. This study describes an EV-associated mechanism that may contribute to the regulation of macrophage polarization and indicates that RGN-containing EVs merit further evaluation as a candidate approach for cancer treatment. Causal validation, such as macrophage depletion or CD206 knockdown, and evaluation in additional models remain to be addressed in future studies.

cancer biology↗

bioRxiv2026

Genomic, spatial, and evolutionary insights into a dominant Mycoplasmatota symbiont colonizing the body wall of deep-sea holothurians

Subcuticular bacteria (SCB) are widespread symbionts of echinoderms and often dominate the body-wall microbiome, suggesting important roles in host physiology. However, their diversity, metabolic properties, and host associations remain poorly characterized. Here, we report a novel dominant SCB lineage associated with deep-sea holothurians, Scotoplanes spp. collected from the Northwest Pacific. We recovered two high-quality genomes, including a 649-kb complete circular genome, and propose a new genus and species, "Candidatus Abyssoplasma scotoplanesicola", within Mycoplasmatota. The two genomes showed a highly reduced metabolic repertoire, lacking central pathways including glycolysis. In contrast, acidic cell-surface-associated proteins, including large proteins exceeding 5,000 amino acids, accounted for 27.6% of the complete genome and clustered near defense islands. Localized genome plasticity in these regions, revealed by comparison between the two closely related genomes, suggests a possible mechanism for diversification of cell-surface proteins at the host-symbiont interface. "Candidatus Abyssoplasma scotoplanesicola" occupied 76.4-98.9% of the body-wall microbiome of the Scotoplanes specimens. Fluorescence in situ hybridization analysis confirmed that these bacteria formed aggregates on the epidermal side of the body wall. Overall, this study provides genome-and spatially resolved views of dominant SCB in holothurians and offers evolutionary insights into host-interface diversification in the deep-sea holothurian body wall.

microbiology↗

bioRxiv2026

4-Phenylbutyric Acid Activates an NF-κB - Egr-1 Axis to Control Myoblast Proliferation and ECM Gene Expression Profiles

Myoblast proliferation and differentiation are tightly controlled by epigenetic mechanisms, yet how clinically used epigenetic modulators influence myogenic cell fate remains incompletely understood. Here, we demonstrate that the histone deacetylase inhibitor and chemical chaperone 4-phenylbutyric acid (4-PBA) selectively promotes myoblast proliferation without inducing differentiation in C2C12 cells. Mechanistically, 4-PBA increases histone H3 acetylation at lysines 18 and 27 via downregulation of HDAC5, resulting in activation of NF-{kappa}B p65. Chromatin immunoprecipitation identifies early growth response 1 (Egr-1) as a direct transcriptional target of NF-{kappa}B p65. Transcriptomic analyses reveal that Egr-1 regulates extracellular matrix- and myogenesis-associated gene programs, including multiple collagen genes. Consistently, 4-PBA induces a transcriptional signature that significantly overlaps with Egr-1-dependent gene expression. Functional studies further establish that the NF-{kappa}B p65 - Egr-1 axis is required for 4-PBA-mediated transcriptional remodeling in proliferating myoblasts. Together, these findings uncover an epigenetic mechanism by which 4-PBA modulates myoblast proliferation through HDAC5-dependent histone acetylation and NF-{kappa}B p65 - Egr-1 driven transcriptional programs, providing insight into how epigenetic therapeutics influence skeletal muscle cell behavior. HighlightO_LI4-PBA enhances murine myoblast proliferation independently of differentiation induction. C_LIO_LI4-PBA enhances H3K18 and H3K27 acetylation through downregulation of HDAC5. C_LIO_LINF-{kappa}B p65 activates Egr-1 by directly binding to the Egr-1 promoter region. C_LIO_LI4-PBA stimulates the HDAC5 - NF-{kappa}B p65 - Egr-1 axis drives extracellular matrix-related gene profiles. C_LI

molecular biology↗

bioRxiv2025

Functional Unknomics of the SAR11 clade using bioinformatics approaches

A substantial fraction of the genes in marine bacteria lack detectable sequence similarity to genes with known functions. These functionally uncharacterized genes--collectively referred to as the "unknome"--represent a largely unexplored genetic repertoire harboring insights into marine bacterial ecology. In this study, we explored the function of the unknome of SAR11 clade, the most abundant bacterial lineage in the ocean, with a particular focus on genes that provide insight into their ecology. Based on the COG classification, approximately 58% of SAR11 ortholog groups were classified as unknome. Among the SAR11 unknome, we successfully inferred the functions of 69 ortholog groups that are conserved in SAR11 clade by protein structure similarity searches and genomic context analyses. These ortholog groups include putative transporter components, supporting the current ecological understanding that SAR11 clade is specialized in substrate uptake to adapt to oligotrophic marine environments. Furthermore, structural analysis indicated that the DUF2237-containing protein, enriched in marine environments, has potential interactions with purine nucleotide-containing compounds. This may suggest the existence of unique nucleotide utilization mechanisms in marine bacteria. In addition, we found candidates of virus defense systems within the unknome, which demonstrates that diverse defense systems are present at least in one-third of the cultured SAR11 strains. The conservation of these viral defense systems, even within streamlined SAR11 genomes, suggests that they confer significant ecological advantages. Our exploration provided insights into the genetic basis of bottom-up processes (adaptation to oligotrophic environments) and top-down processes (antiviral defense strategy) contributing to ecological success of SAR11.

microbiology↗

bioRxiv2025

Age-dependent Dysferlin Accumulation in Macrophages Promotes STAT1 Activation via Calcium Influx, Impairing Myogenesis

DYSF functions as a regulator of Ca{superscript 2} in the skeletal muscle and facilitates muscle repair following injury. It is also highly expressed in monocytes and macrophages and related to inflammation, immune regulation, and the mononuclear phagocyte system. Macrophages are pivotal in driving myogenesis, and specific cytokine-induced macrophage differentiation plays a role in maintaining skeletal muscle during disease and aging. Thus, a comprehensive understanding of the mechanisms by which DYSF operates in macrophages may inform the development of novel treatments for muscle atrophy. In this study, we demonstrated that DYSF expression is associated with monocyte differentiation and increases with age. Our findings indicate that DYSF overexpression induces the generation of M1-type macrophages, which subsequently secrete inflammatory cytokines and promote cell invasion. Furthermore, we observed that DYSF regulates Ca{superscript 2} influx into the cell and activates the STAT1 signaling pathway, whereas DYSF deficiency suppresses these processes. Macrophages overexpressing DYSF are associated with the inhibition of myoblast differentiation during myogenesis in a co-culture system involving macrophages and myoblasts. Therefore, the balance between the STAT1 signaling pathway and Ca{superscript 2}, which are regulated by DYSF abundance, may play a crucial role in myogenesis.

immunology↗

bioRxiv2025

Genomic and evolutionary factors influencing the prediction accuracy of optimal growth temperature in prokaryotes

Bacteria and archaea have evolved diverse genomic adaptations to thrive across various temperatures. These adaptations include genome sequence optimizations, such as increased GC content in rRNA and tRNA, shifts in codon and amino acids usage, and the acquisition of functional genes conferring adaptation for specific temperatures. Since the experimental determination of optimal growth temperatures (OGT) is only possible for cultured species, predicting OGT from genomic information has become increasingly important given the exponential increase in genomic data. Although previous studies developed prediction models integrating multiple features based on genome composition using machine learning, the accuracy was variable depending on the target species, with models performing well for thermophiles but less accurately for psychrophiles. In this study, we curated the OGT and genomic data of 2,869 bacterial species to develop a novel prediction model incorporating features reflecting genomic adaptation toward lower temperatures. We found that species with rapid OGT shifts from their ancestors, including psychrophiles, showed less accuracy in genome composition-based models. Incorporating the gene presence/absence information associated with the rapid changes in OGT improved the prediction accuracy for psychrophiles. We also observed that OGT in archaea is phylogenetically more conserved than in bacteria, which may lead to the long-term optimization of the genome composition and explain high predictability of OGT in archaea. These findings highlight the importance of integrating long- and short-term evolutionary adaptations for phenotype prediction models.

genomics↗

bioRxiv2025

CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset

The recent expansion of prokaryotic genomes reveals many ortholog groups (OGs) whose function cannot be inferred from conventional, sequence similarity-based annotation methods, especially in metagenome-assembled genomes. Phylogenetic profiling is one of the promising methods to annotate these OGs, by identifying functional relationships of OGs using co- or anti-occurrence of OGs distributions, not sequence similarity. Here, we proposed two new phylogenetic methods for large-scale data, Ancestral State Adjustment (ASA) and Simultaneous EVolution test (SEV), which consider the ancestral state of gene presence/absence. In evaluations using three distinct prokaryotic datasets, ASA and SEV showed better or comparable performance to both established and recently proposed methods for large-scale data. We compared the functionally related genes detected by each method and found that SEV and its predecessor can identify slowly evolving genes, such as housekeeping genes. In contrast, ASA and its predecessors can detect functionally related genes that tend to be gained or lost in a fixed-order, indicating a strong evolutionary constraint that provides clues for functional prediction. Using matrix multiplication, we showed that SEV is scalable in the latest genome databases.

bioinformatics↗

bioRxiv2025

Endothelial Sphingosine-1-Phosphate Receptor (S1PR) 1, a Functional S1PR in the Human Cerebrovascular Endothelium, Limits Blood Brain Barrier Permeability and Neuronal Injury following Subarachnoid Hemorrhage in Mice.

Hypoxia-induced blood-brain barrier (BBB) permeability has been identified as a key contributor to the progression of ischemic-hypoxic brain injury and neuronal dysfunction in stroke and other cerebrovascular diseases. Emerging clinical evidence highlights that the vasoprotective signaling properties of high-density lipoprotein (HDL), mediated through its bioactive lipid component sphingosine-1-phosphate (S1P), may be impaired in cardiovascular and inflammatory conditions. Nonetheless, the precise contributions and mechanistic roles of S1P signaling within the cerebral microvasculature remain insufficiently characterized. In this study, we aimed to elucidate the role of S1P signaling via its endothelial receptor S1PR1 in the pathophysiology of early brain injury following subarachnoid hemorrhage (SAH), a particularly severe form of stroke. Additionally, we sought to evaluate the relevance of the endothelial S1PR1 pathway in the human cerebrovascular endothelium, its functional role in hypoxia-induced cerebral endothelial barrier dysfunction, and its underlying molecular mechanisms. To address these objectives, we utilized endothelial-specific S1PR1 knockout mice subjected to the endovascular rupture model of aneurysmal SAH, performed mechanistic studies in primary human cerebral microvascular endothelial cells, and characterized S1PR1 expression in human brain tissue using validated protocols. Our findings reveal robust expression of S1PR1 in the cerebrovascular endothelium of both mice and humans. Functional analyses demonstrated that S1PR1 is critical for maintaining BBB integrity and mitigating neuronal injury in the context of SAH. Mechanistic in vitro studies indicated that S1PR1 exerts a vasoprotective effect by limiting hypoxia-induced BBB dysfunction in human primary brain microvascular endothelial cells through inhibition of Rho-associated kinase (ROCK)-mediated phosphorylation of myosin light chain (MLC), suppression of stress fiber formation and caveolin-1-dependent endosomal trafficking. These results highlight the pivotal role of endothelial S1PR1 signaling in preserving cerebral vascular integrity and provide a strong scientific foundation for developing novel therapeutic approaches targeting the S1P pathway in the endothelium to enhance neurovascular protection.

neuroscience↗

bioRxiv2024

Carotenoid pigments enhance rhodopsin-mediated phototrophy by light-harvesting and photocycle-accelerating

Microbial rhodopsins, photoreceptor proteins widely distributed in marine microorganisms, receive large amount of light energy that sustains marine ecosystems. Although rhodopsins generally harbor retinal as their only chromophore, a recent study reported that carotenoid antennae transfer light energy to the retinal in proteorhodopsins, proton pump rhodopsins abundant in marine environments. Here, using marine bacterial isolates, we detected energy transfer from a carotenoid (myxol) to retinal not only in proteorhodopsin but also in the chloride ion-pumping rhodopsin. Carotenoid binding improved the light utilization efficiency of the proteorhodopsin by accelerating the photocycle, together with facilitating light-harvesting. The carotenoid-binding ability is conserved in rhodopsins of the phylum Bacteroidota, which are widely transcribed in the photic zone. These findings suggest that the distribution of carotenoid-binding rhodopsins is more taxon-specific than previously thought, thus underscoring the importance of carotenoid-binding rhodopsins that provide an extended light utilization strategy in the environmental adaptation of marine bacteria.

microbiology↗

bioRxiv2024

Angiogenin regulates mitochondrial stress and function via tRNA-derived fragments generation and impacting tRNA modifications.

Mitochondrial stress and dysfunction play an important role in many diseases, such as cancer, diabetes, and neurodegenerative diseases. We previously observed that mitochondrial electron transport chain (ETC) inhibition can induce tRNA cleavage and tsRNAs (tRNA-derived small non-coding RNAs) generation. However, whether this process is mediated via Angiogenin (ANG), the canonical enzyme responsible for tRNA cleavage, and whether it has a role in regulating the mitochondrial stress response remains to be understood. ANG is linked to Amyotrophic Lateral Sclerosis (ALS) and other conditions where mitochondrial stress plays a role in pathophysiology. Here, we aimed to examine the role of ANG in regulating the translational response to mitochondrial stress. We observed that ANG protected the cells from respiratory complex III and V inhibition specifically. Furthermore, we validated that the tsRNAs generated during mitochondrial and oxidative stress are mediated by ANG, given that their production is abrogated after ANG knock-out (KO). In addition, we observed that ANG-KO altered the tRNA modification status. Namely, we observed that ANG-KO led to the downregulation of queuosine tRNA modifications (tRNA-Q). tRNA-Q itself is related to mitochondrial translation and function. Indeed, we observed that ANG-KO led to reduced mitochondrial respiration and function. ANG altered how the cells respond to mitochondrial stress by altering the dynamic tRNA modification changes occurring during the stress response. We further examined the impact of ANG-KO on stress granules (SG) assembly as well as the knockdown of G3BP1 (core protein of SGs) on tsRNAs generation. Our results indicate that ANG regulates mitochondrial function and stress via tsRNAs generation as well as altering tRNA modifications levels. Our data also indicate that there are no direct links between tRNA cleavage and SG assembly, and both could be parallel systems for translation repression during stress.

molecular biology↗

bioRxiv2024

Eicosatetraynoic Acid Regulates Pro-Fibrotic Pathways in an Induced Pluripotent Stem Cell Derived Macrophage:Human Intestinal Organoid Model of Crohns Disease

Background and AimsWe previously identified small molecules predicted to reverse an ileal gene signature for future Crohns Disease (CD) strictures. Here we used a new human intestinal organoid (HIO) model system containing macrophages to test a lead candidate, eicosatetraynoic acid (ETYA). MethodsInduced pluripotent stem cell lines (iPSC) were derived from CD patients and differentiated into macrophages and HIOs. Macrophages and macrophage:HIO co-cultures were exposed to lipopolysaccharide (LPS) with and without ETYA pre-treatment. Cytospin and flow cytometry characterized macrophage morphology and activation markers, and RNA sequencing defined the global pattern of macrophage gene expression. TaqMan Low Density Array, Luminex multiplex assay, immunohistologic staining, and sirius red polarized light microscopy were performed to measure macrophage cytokine production and HIO pro-fibrotic gene expression and collagen content. ResultsiPSC-derived macrophages exhibited morphology similar to primary macrophages and expressed inflammatory macrophage cell surface markers including CD64 and CD68. LPS-stimulated macrophages expressed a global pattern of gene expression enriched in CD ileal inflammatory macrophages and matrisome secreted products, and produced cytokines and chemokines including CCL2, IL1B, and OSM implicated in refractory disease. ETYA suppressed CD64 abundance and pro-fibrotic gene expression pathways in LPS stimulated macrophages. Co-culture of LPS-primed macrophages with HIO led to up-regulation of fibroblast activation genes including ACTA2 and COL1A1, and an increase in HIO collagen content. ETYA pre-treatment prevented pro-fibrotic effects of LPS-primed macrophages. ConclusionsETYA inhibits pro-fibrotic effects of LPS-primed macrophages upon co-cultured HIO. This model may be used in future untargeted screens for small molecules to treat refractory CD.

molecular biology↗

bioRxiv2023

Characteristics of the rumen virome in Japanese cattle

The rumen microbiome is a highly complex ecosystem that includes bacteria, archaea, protozoa, fungi, and viruses. Viruses have a high potential to modify the rumen digestion of feeds via infection and cell lysis of prokaryotes in the rumen; however, understanding of the rumen virome is substantially less advanced due to limitations of the reference genome database. In this study, we conducted metagenomic sequencing of virus-like particles (VLPs) in the rumens of 22 Japanese cattle to construct a reference viral genome catalog of the rumen and uncover the rumen virome characteristics. We succeeded in construction of 8 232 nonredundant viral genomes ([≥]5 kb length and [≥]50% completeness). Among them, putative hosts of 1 223 virus genomes were predicted, and 1 053 virus genomes were taxonomically classified, mainly Siphoviridae, Myoviridae, and Podoviridae. Additionally, 2 764 putative auxiliary metabolic genes (AMGs) were identified in the viral genomes. Importantly, 22 viral genomes associated with archaea in the rumen were identified. Some archaeal viruses have AMGs related to DNA synthesis, suggesting that archaeal viruses control archaeal populations in the rumen and affect methane production from the rumen. Furthermore, we revealed that most rumen viruses were highly rumen-and individual-specific and related to rumen-specific prokaryotes. Overall, the rumen viral catalog and findings of this study will help future analyses to uncover the roles of rumen viruses in feed digestion, productivity, and methane production.

microbiology↗

bioRxiv2023

Identification of key virus--prokaryote infection pairs that contribute to viral shunt in a freshwater lake

Viruses infect and kill productive prokaryotes in a density-or frequency-dependent manner and affect carbon cycling. However, the effects of the stratification transition, including the stratified and destratified periods, on the changes in prokaryotic/viral communities and the interactions among them remain unclear. We conducted a monthly survey of the surface and deep layers of a large and deep freshwater lake (Lake Biwa, Japan) for a year and analyzed the prokaryotic production and prokaryotic/viral metagenome. Our analysis (including 1 608 prokaryotes and 13 761 viruses) revealed that 19 prokaryotic species, accounting for [~]40% of total abundance, might be suppressed by viruses when prokaryotic production is higher. This suggests that a small proportion of prokaryotes contribute to a large amount of prokaryotic abundance, and these prokaryotes are infected and lysed by viruses, driving the viral shunt in the freshwater lake. Furthermore, we found that annual vertical mixing might yield a similar rate of community change between the surface and deep layers. This finding might be valuable in understanding how the communities change when the stratification of freshwater lakes is affected by global warming in the future.

microbiology↗

bioRxiv2023

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

The production of dissolved organic matter during phytoplankton blooms and consumption by heterotrophic prokaryotes promotes marine carbon biogeochemical cycling. Although prokaryotic viruses are crucial biological entities, their dynamics during such blooms are not fully understood. Here, we investigated the dynamics of coastal prokaryotic communities and viruses during blooms in a microcosm experiment using dissolved intracellular fractions of taxonomically distinct phytoplankton, the diatom Chaetoceros sp. (CIF) and the raphidophycean alga Heterosigma akashiwo (HIF). Ribosomal RNA gene amplicon and viral metagenomic analyses revealed that particular prokaryotes and prokaryotic viruses specifically increased in either CIF and HIF, indicating that different phytoplankton intracellular fractions promote distinct dynamics of not only prokaryotic community but also prokaryotic viruses. Our microcosm experiments and environmental data mining identified both known and novel possible host-virus pairs. In particular, a growth of phytoplanktonic organic matter-associated prokaryotes, 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 elucidating tripartite relationships among phytoplankton, prokaryotes, and prokaryotic viruses would further our understanding of coastal microbial ecosystems. We state that -All the data underlying the study are available at the DNA Data Bank of Japan (DDBJ) under project number PRJDB14359 and accession number DRA014887. -This study was supported by Grants-in-Aid for Scientific Research (No. 16H06429, No. 17H03850, No. 21H05057, and No. 21J14854) from the Japan Society for the Promotion of Science (JSPS). -We have no potential conflicts of interest to declare. -We have read and understood your journals policies, and we believe that neither the manuscript nor the study violates any of these. -We do not use any clinical data, human subjects, or laboratory animals. -None of the materials have been published or are under consideration for publication elsewhere. CRediTHiroaki Takebe: Funding acquisition, conceptualization, investigation, formal analysis, visualization, and writing (original draft). Kento Tominaga: Conceptualization, investigation, and writing (review and editing). Tatsuhiro Isozaki: investigation. Tetsuhiro Watanabe: Resources. Keigo Yamamoto: Resources. Ryoma Kamikawa: Conceptualization, supervision, and writing (review and editing). Takashi Yoshida: Funding acquisition, project administration, conceptualization, supervision, and writing (review and editing).

microbiology↗

bioRxiv2021

Prevalence of viral frequency-dependent infection in coastal marine prokaryotes revealed using monthly time series virome analysis

Viruses infecting marine prokaryotes have large impacts on the diversity and dynamics of their hosts. Model systems suggest viral infection is frequency-dependent and constrained by the virus-host encounter rate. However, it is unclear whether the frequency-dependent infection is pervasive among the abundant prokaryotic populations with different growth strategies (i.e. r-strategy and K-strategy). 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 two years at a Japanese coastal site, Osaka Bay. Concurrent seasonal shifts observed in prokaryotic and viral community dynamics indicated that abundances of viruses correlated with that of their predicted host phyla (or classes). Co-occurrence network analysis between abundant prokaryotes and viruses revealed 6 423 co-occurring pairs, suggesting a tight coupling of host and viral abundances and their "one to many" correspondence. Although dominant K-strategist like species, such as SAR11, showed few co-occurring viruses, a fast succession of their viruses suggests viruses infecting these populations changed continuously. Our results suggest the frequency-dependent viral infection prevailed in coastal marine prokaryotes regardless of host taxa and growth strategy.

microbiology↗