Biology subjects

Mitarai, S.

Publications and source records attributed to Mitarai, S..

17 recordsLinked to original sources

bioRxiv2026

Transposon insertion sequencing identifies genetic determinants of intrinsic rifamycin resistance in Mycobacterium abscessus

Mycobacterium abscessus exhibits intrinsic resistance to many antimicrobial agents, including rifampicin, a frontline anti-tuberculosis drug, severely limiting treatment options. Here, we used transposon insertion sequencing (Tn-Seq) to perform a genomewide screen to identify genes required for intrinsic rifampicin resistance in M. abscessus. We uncovered candidate genes that confer intrinsic resistance to the rifamycin-class antibiotics, rifampicin and rifabutin. The genes we identified included previously reported genes such as arr, helR, and MAB_2807. By comparing our results with the rifampicin intrinsic resistance gene in Mycobacterium tuberculosis, we found that the mechanisms underlying rifampicin intrinsic resistance were distinct between the two species. The contribution of seven representative candidate genes to rifampicin resistance was confirmed by characterizing targeted gene deletion or transposon insertion mutants. Among these determinants, MAB_2807 was identified as a major efflux-based contributor to rifamycin resistance, and its disruption increased intracellular rifampicin accumulation. In addition to known resistance determinants, Tn-Seq revealed contributions from many genes involved in cell envelope processes to rifamycin resistance. Guided by this genetic signature, we evaluated the combined effects of cell wall-targeting antimicrobial agents with rifamycins. We found that rifamycins displayed selective synergistic interactions with specific {beta}-lactam antibiotics. Interestingly, we found that rifamycin exposure altered cell envelope ultrastructure and increased the accumulation of the peptidoglycan precursor UDP-N-acetylglucosamine, suggesting that rifampicin perturbs envelope-associated metabolic homeostasis. These findings highlight rifamycin-induced vulnerable cellular processes that may inform rational combination strategies. ImportanceRifamycins are cornerstone antibiotics for the treatment of mycobacterial infections, yet they are ineffective against Mycobacterium abscessus. Although several key resistance mechanisms have been described, the full genetic basis of intrinsic rifamycin resistance remains to be elucidated. Here, we used transposon insertion sequencing to systematically identify genes that contribute to intrinsic rifamycin resistance in M. abscessus. Because recent studies have shown that chemical modification of rifamycins can overcome specific intrinsic resistance mechanisms, a comprehensive understanding of these determinants could facilitate the development of next-generation rifamycins with improved activity against M. abscessus. In addition, we unexpectedly found that rifamycin exposure alters cell envelope structure, the intracellular levels of a key metabolic intermediate in peptidoglycan biosynthesis, and susceptibility to certain {beta}-lactams in M. abscessus. These findings may help guide the rational development of combination therapeutic strategies with next-generation rifamycins.

microbiology↗

bioRxiv2026

Analysis of publicly available genomic data

Ethambutol (EMB) is a vital drug for treating Mycobacterium avium-intracellulare (MAI) infections; however, the genomic mutations underlying EMB resistance in MAI remain unclear. Herein, we evaluated eight sets of MAI clinical isolates, each containing at least two serial isolates collected from the same patient who received EMB in Japan. In four sets, the isolates independently increased EMB MIC by 4-fold, coinciding with mutations in the upstream region of embA or those corresponding to Mycobacterium tuberculosis (Mtb) embB Met306Val and Gln497Arg. Based on the increased EMB MIC values, we defined normal and elevated EMB MICs as [≤]8 {micro}g/mL and [≥]16 {micro}g/mL, respectively. In the other four sets, all of the isolates had elevated EMB MICs. In silico promoter prediction and expression analysis indicated that the upstream region of embA corresponds to the embA-embB promoter region, and mutations in this region increased the transcription of embA and embB, increasing EMB MICs. Furthermore, the analysis of 60 epidemiologically unrelated strains revealed that isolates with mutations in the embA-embB promoter and at embB codons 306/497 exhibited significantly higher EMB MICs compared with those without mutations. Publicly available genomic data demonstrate the worldwide occurrence of these mutations in clinical isolates. These results establish an association between elevated EMB MICs and mutations at embB codons 306/497 and the embA-embB promoter and are expected to predict EMB resistance.

microbiology↗

bioRxiv2025

Concentration-dependent suppression of macrolide resistance in Mycobacterium avium by combination therapy: an improved in vitro time-kill assay and PK/PD modelling study

ObjectivesMacrolides are key drugs in the treatment for Mycobacterium avium pulmonary disease, and combination chemotherapy is essential to preventing macrolide resistance. However, the concentrations of concomitant agents required to suppress resistance emergence remain undefined. This study aimed to quantify the concentration-dependent effects of companion drugs on macrolide resistance using an improved time-kill assay and pharmacokinetic/pharmacodynamic (PK/PD) modelling approach. MethodsTime-kill assays were performed on M. avium ATCC 700898 using azithromycin alone or in combination with ethambutol, rifampicin, amikacin, or clofazimine. Total and resistant bacterial populations were quantified over 28 days. A pharmacodynamic (PD) model describing the dynamics of susceptible and resistant subpopulations was linked to a pharmacokinetic (PK) model incorporating alveolar macrophage concentrations to simulate resistance and bactericidal rates under various dosing regimens. ResultsMacrolide resistance most frequently emerged at 2-4x the minimum inhibitory concentration (MIC) of azithromycin, whereas resistance was less frequent at 8-16x MIC or sub-MIC levels. The addition of companion drugs suppressed resistance emergence even at sub-MIC levels. PK/PD simulations demonstrated that standard-dose ethambutol effectively prevented macrolide resistance, whereas rifampicin provided minimal protection. More frequent dosing schedules enhanced resistance suppression compared with once-daily regimens. ConclusionThis study defines the concentration-dependent contributions of concomitant agents to macrolide resistance suppression in M. avium and establishes a quantitative PK/PD framework for evaluating resistance emergence. These findings provide mechanistic insights to support the optimization of combination dosing strategies for M. avium pulmonary disease.

pharmacology and toxicology↗

bioRxiv2024

Urbanization of a subtropical island (Okinawa, Japan) alters physicochemical characteristics and disrupts microbial community dynamics in nearshore ecosystems

Subtropical and tropical islands are undergoing rapid urbanization as human populations and tourism expand worldwide. Urbanization disrupts coastal ecosystems by replacing forests and other natural habitats with roads, parking lots, and buildings. These impervious surfaces increase the amount of runoff and pollution that reaches coastal ecosystems. Urbanization also comes with increased industry, waste treatment needs, fishing and aquaculture pressure, and coastline engineering. Despite the major changes to coasts that accompany urbanization, specific impacts on marine ecosystems can be difficult to measure due to missing baselines. Here, we take advantage of a large gradient in urbanization on the subtropical island of Okinawa, Japan, to evaluate the impact of urbanization on nearshore ecosystems. We measured physicochemical parameters and assessed bacterial community composition every two weeks for one year at two nearshore sites adjacent to watersheds with >70% urban land use and two nearshore sites adjacent to watersheds with >70% rural land use. Our results show that urbanization increases freshwater input and nutrient loading to nearshore ecosystems and profoundly alters the microbial community, overriding the natural seasonal succession observed at rural sites. At urban sites, we detected multiple bacterial species that are fecal indicators and human or marine organism pathogens. The altered physicochemical conditions and microbial communities at urban sites can contribute to the degradation of nearby coral reefs. Results highlight the importance of a "ridge-to-reef" management mindset, as restoring natural coastlines could buffer the impact of urbanization on the marine environment.

ecology↗

bioRxiv2023

The Role of Reproductive Periodicity in Dispersal Among Hydrothermal Vents and its Implications for Regional Connectivity and Conservation

Connectivity among isolated habitat patches via planktonic larval dispersal is crucial for maintaining the regional diversity of hydrothermal vents. Despite, increasing sophistication of techniques for simulating dispersal, limited information on biological and behavioural traits of vent-associated species has unknown affects on the applicability of these methods for conservation. Here we focus on the role of periodic reproduction on dispersal among hydrothermal vents, as periodic spawning has increasingly been observed in a variety of taxa. For generalizeability, we simulate the dispersal of larvae under treatments of periodic and aperiodic release timing at various depths, with a consistant but variable planktonic larval duration. Our results show a highly variable effect of periodicity on the characteristics and distribution of dispersal, which are heavily modified by the dispersal depth and source location. The capacity for reproductive periodicity to impact the among-site dispersal warrents further investigation into its prevelance and timing among vent-associated fauna.

biophysics↗

bioRxiv2022

Hydrothermal Vent Species Assemblage Networks Identify Regional Connectivity Patterns in the Northwest Pacific

The distribution of species among spatially isolated habitat patches supports regional biodiversity and stability, so understanding the underlying processes and structure is a key target of conservation. Although multivariate statistics can infer the connectivity processes driving species distribution, such as dispersal and habitat suitability, they rarely explore structure. Methods from graph theory, applied to distribution data, give insights into both connectivity pathways and processes by intuitively formatting the data as a network of habitat patches. We apply these methods to empirical data from the hydrothermal vent habitats of the Northwest Pacific. Hydrothermal vents are oases of biological productivity and endemicity on the seafloor that are imminently threatened by anthropogenic disturbances with unknown consequences to biodiversity. Here, we describe the structure of hydrothermal vent species assemblage networks, how local and regional parameters affect their structure, and the implications this has for conservation. Two complementary networks were formed from an extensive species assemblage dataset: a bipartite network of species nodes linked to vent site nodes at which they are present, and a similarity network of vent site nodes linked by weighted edges based on their pairwise assemblage similarity. Using these networks, we assessed the role of individual vent sites in linking their network and identified biogeographic sub-regions. The three sub-regions and two outlying sites are separated by their spatial arrangement and local environmental filters. Both networks detected vent sites that play a disproportionately important role in regional pathways, while the bipartite network also identified key vent sites maintaining the distinct species assemblages of their sub-regions. These regional connectivity pathways provide insights into historical colonisation routes, while sub-regional connectivity pathways are of value when selecting sites for conservation and/or estimating the multi-vent impacts from proposed deep-sea mining.

ecology↗

bioRxiv2022

Microbiomes of the bloom-forming alga, Phaeocystis globosa, are stable, consistently recruited communities with symbiotic and opportunistic modes

Phaeocystis is a cosmopolitan, bloom-forming phytoplankton genus that contributes significantly to global carbon and sulfur cycles. During blooms, Phaeocystis species produce large carbon-rich colonies, thus creating a unique interface for bacterial interactions. While bacteria are known to interact with phytoplankton--e.g., they promote growth by producing phytohormones and vitamins--such interactions have not been shown for Phaeocystis. Therefore, we investigated the composition and function of P. globosa microbiomes. Specifically, we tested whether microbiome compositions are consistent across individual colonies from four P. globosa strains, whether similar microbiomes are re-recruited after antibiotic treatment, and how microbiomes affect P. globosa growth under limiting conditions. Results illuminated a core colonial P. globosa microbiome--including bacteria from the orders Alteromonadales, Burkholderiales, and Rhizobiales--that was re-recruited after microbiome disruption. Consistent microbiome composition and recruitment is indicative that P. globosa microbiomes are stable-state systems undergoing deterministic community assembly and suggests there are specific, beneficial interactions between Phaeocystis and bacteria. Growth experiments with axenic and nonaxenic cultures demonstrated that microbiomes allowed continued growth when B-vitamins were withheld, but that microbiomes accelerated culture collapse when nitrogen was withheld. In sum, this study reveals interactions between Phaeocystis colonies and microbiome bacteria that could influence large-scale phytoplankton bloom dynamics and biogeochemical cycles.

microbiology↗

bioRxiv2021

Bovine serum albumin as a resuscitation promoting factor for viable but non-culturable Mycobacterium tuberculosis via the activation of protein kinase A-dependent cellular processes

We investigated the mechanisms underlying the fetal bovine serum (FBS)-induced reactivation of the viable but non-culturable (VBNC) state of Mycobacterium tuberculosis (Mtb) using the H37Rv strain. We found that bovine serum albumin (BSA), a major component of FBS, could reactivate the VBNC state of Mtb cells without other reactivation-promoting agents. Human serum albumin also had a restorative effect similar to BSA, but mouse serum albumin and egg-white albumin (ovalbumin) did not, suggesting that a common protein structure between bovine and human serum albumin is essential for reactivation. In addition, antioxidative agents, such as N-acetyl-L-cysteine, showed no restorative effect, suggesting that the restoration of culturability might not be due to the antioxidative property of BSA. BSA-mediated reactivation is inhibited by H89 and staurosporine. These inhibitors are known to inhibit multiple protein kinases, including serine/threonine protein kinases, in Mtb, suggesting the involvement of mycobacterial protein kinases in cell division during reactivation. These findings provide new insights into the mechanisms of Mtb reactivation, and may contribute to the development of novel strategies for the treatment of latent tuberculosis. ImportanceReactivation of dormant, including viable but non-culturable (VBNC) Mycobacterium tuberculosis (Mtb) cells, represents a critical step in the progression from latent infection to active tuberculosis. However, the molecular mechanisms that trigger this transition are not yet fully understood. We herein report that bovine serum albumin (BSA), a major component of fetal bovine serum, can restore the culturability of VBNC Mtb cells. Human serum albumin showed a similar effect, whereas mouse and egg-white albumins did not, suggesting that the specific structural features shared between bovine and human albumins are essential for reactivation. The lack of reactivation by the antioxidant N-acetyl-L-cysteine indicates that the mechanism is not related to redox balance. Inhibition of BSA-induced reactivation by H89 and staurosporine implicates mycobacterial serine/threonine protein kinases in this process. These findings highlight the previously unrecognized role of albumin-kinase signaling in Mtb reactivation and suggest new molecular targets for preventing tuberculosis relapse.

microbiology↗

bioRxiv2021

Sequestration and efflux largely account for Cd and Cu resistance in the deep sea Epsilonproteobacterium Nitratiruptor sp. SB155 2

In deep sea hydrothermal vent environments, metal- and metalloid-enriched fluids and sediments abound, making these habitats ideal to study metal resistance in prokaryotes. In this investigation, the architecture of the epsilonproteobacterium, Nitratiruptor sp. SB155-2 transcriptome in combination with sub-cellular analysis using scanning transmission electron microscopy and energy-dispersive X-ray spectroscopy (STEM-EDX) was examined to better understand mechanisms of tolerance for cadmium (Cd) and copper (Cu) at stress-inducing concentrations. Transcriptomic expression profiles were remarkably different in the presence of these two metals, displaying 385 (19%) and 629 (31%) genes differentially expressed (DE) in the presence of Cd and Cu, respectively, while only 7% of DE genes were shared, with genes for non-specific metal transporters and genes involved in oxidative stress-response predominating. The principal metal-specific DE pathways under Cu stress, including those involving sulfur, cysteine, and methionine, are likely required for high-affinity efflux systems, while flagella formation and chemotaxis were over-represented under Cd stress. Consistent with these differences, STEM-EDX analysis revealed that polyphosphate-like granules (pPLG), the formation of CdS particles, and the periplasmic space may be crucial for Cd sequestration. Overall, this study provides new insights regarding metal-specific adaptations of Epsilonproteobacteria to deep sea hydrothermal vent environments. Significance originality statementDeep sea hydrothermal vents are unique environments in which metals and metalloids abound. Despite being a dominant phylum in these environments, adaptations enabling Epsilonproteobacteria to thrive in metal-rich environments remain poorly understood. In this study, a combination of high-throughput, whole-transcriptome RNA-seq analysis, scanning transmission electron microscopy, and energy-dispersive X-ray spectroscopy provide a comprehensive picture of molecular and morphological adaptations controlling metal efflux and sequestration systems of this bacterium in response to cadmium and copper. Many of these responses are metal-specific.

microbiology↗

bioRxiv2020

Cytoklepty in the plankton: a host strategy to optimize the bioenergetic machinery of endosymbiotic algae

Endosymbioses have shaped the evolutionary trajectory of life and remain widespread and ecologically important. Investigating modern oceanic photosymbioses can illuminate how algal endosymbionts are energetically exploited by their heterotrophic hosts, and inform on putative initial steps of plastid acquisition in eukaryotes. By combining 3D subcellular imaging with photophysiology, carbon flux imaging and transcriptomics, we show that cell division of algal endosymbionts (Phaeocystis) is blocked within hosts (Acantharia), and that their cellular architecture and bioenergetic machinery are radically altered. Transcriptional evidence indicates that a nutrient-independent mechanism prevents symbiont cell division and decouples nuclear and plastid division. As endosymbiont plastids proliferate, the volume of the photosynthetic machinery volume increases 100-fold in correlation with expansion of a reticular mitochondrial network in close proximity to plastids. Photosynthetic efficiency tends to increase with cell size and photon propagation modeling indicates that the networked mitochondrial architecture enhances light capture. This is accompanied by 150-fold higher carbon uptake and upregulation of genes involved in photosynthesis and carbon fixation, which, in conjunction with a ca.15-fold size increase of pyrenoids demonstrates enhanced primary production in symbiosis. NanoSIMS analysis revealed major carbon allocation to plastids and transfer to the host cell. Invagination of the symbiosome into endosymbionts to optimize metabolic exchanges is strong evidence that the algal metamorphosis is irreversible. Hosts therefore trigger and unambiguously benefit from major bioenergetic remodeling of symbiotic microalgae with important consequences for the oceanic carbon cycle. Unlike other photosymbioses, this interaction represents a so-called cytoklepty, which is a putative initial step towards plastid acquisition.

physiology↗

bioRxiv2020

A Novel DNA Chromatography Method to Distinguish M. abscessus Subspecies and Macrolide Susceptibility

RationaleThe clinical impact of infection with Mycobacterium abscessus complex (MABC), a group of emerging non-tuberculosis mycobacteria (NTM), is increasing. Mycobacterium abscessus subsp. abscessus/bolletii frequently shows natural resistance to macrolide antibiotics, whereas Mycobacterium abscessus subsp. massiliense is generally susceptible. Therefore, rapid and accurate discrimination of macrolide-susceptible MABC subgroups is required for effective clinical decisions about macrolide treatments for MABC infection. ObjectivesTo develop a simple and rapid diagnostic that can identify MABC isolates showing macrolide susceptibility. MethodsWhole genome sequencing (WGS) was performed for 148 clinical or environmental MABC isolates from Japan to identify genetic markers that can discriminate three MABC subspecies and the macrolide-susceptible erm(41) T28C sequevar. Using the identified genetic markers, we established PCR based- or DNA chromatography-based assays. Validation testing was performed using MABC isolates from Taiwan. Measurements and Main ResultsWe identified unique sequence regions that could be used to differentiate the three subspecies. Our WGS-based phylogenetic analysis indicated that M. abscessus carrying the macrolide-susceptible erm(41) T28C sequevar were tightly clustered, and identified 11 genes that were significantly associated with the lineage for use as genetic markers. To detect these genetic markers and the erm(41) locus, we developed a DNA chromatography method that identified three subspecies, the erm(41) T28C sequevar and intact erm(41) for MABC in a single assay within one hour. The agreement rate between the DNA chromatography-based and WGS-based identification was 99.7%. ConclusionsWe developed a novel, rapid and simple DNA chromatography method for identification of MABC macrolide susceptibility with high accuracy.

microbiology↗

bioRxiv2020

Paired high-throughput, in-situ imaging and high-throughput sequencing illuminate acantharian abundance and vertical distribution

Acantharians are important contributors to surface primary production and to carbon flux to the deep sea, but are often underestimated because their delicate structures are destroyed by plankton nets or dissolved by preservatives. As a result, relatively little is known about acantharian biology, especially regarding their life cycles. Here, we take a paired approach, bringing together high-throughput, in-situ imaging and high-throughput sequencing, to investigate acantharian abundance, vertical distribution, and life-history in the western North Pacific. Observed concentrations of acantharian cells correlated well with sequence abundances from acantharians with known, recognizable morphologies, but not to sequences from those without known morphology (basal environmental clades). These results suggest basal clades may lack characteristic star-shaped skeletons or are much smaller than known acantharians. The decreased size-range of acantharians imaged at depth supports current hypotheses regarding asymbiotic acantharian life cycles: cysts or vegetative cells release reproductive swarmer cells at depth and juvenile cells grow as they ascend towards the surface. Moreover, sequencing data present the possibility that photosymbiotic acantharians also reproduce at depth, like their asymbiotic, encysting relatives, which is counter to previous hypotheses. Finally, in-situ imaging captured a new acantharian behavior that may be a previously undescribed predation strategy.

microbiology↗

bioRxiv2019

Extreme storm-induced run-off causes rapid, context-dependent shifts in nearshore subtropical bacterial communities

Climate change scenarios predict tropical cyclones will increase in both frequency and intensity, which will escalate the amount of terrestrial run-off and mechanical disruption affecting coastal ecosystems. Bacteria are key contributors to ecosystem functioning, but relatively little is known about how they respond to extreme storm events, particularly in nearshore subtropical regions. In this study, we combine field observations and mesocosm experiments to assess bacterial community dynamics and changes in physicochemical properties during early- and late-season tropical cyclones affecting Okinawa, Japan. Storms caused large and fast influxes of freshwater and terrestrial sediment--locally known as red soil pollution--and caused moderate increases of macronutrients--especially SiO2 and PO43-. We detected shifts in relative abundances of marine bacteria and the introduction of terrestrially-derived bacteria, including putative coral and human pathogens, during storm events. Soil input alone did not substantially affect marine bacterial communities in mesocosms, indicating that other components of run-off or other storm effects likely exert a larger influence on bacterial communities. The storm effects were short-lived and bacterial communities quickly recovered following both storm events. The early- and late-season storms caused different physicochemical and bacterial community changes, demonstrating the context-dependency of extreme storm responses in a subtropical coastal ecosystem.

microbiology↗

bioRxiv2019

Hydrothermal activity and water mass composition shape microbial eukaryote diversity and biogeography in the Okinawa Trough

Microbial eukaryotes (protists) contribute substantially to ecological functioning in marine ecosystems, but factors shaping protist diversity, such as dispersal barriers and environmental selection, remain difficult to parse. Deep-sea water masses, which form geographic barriers, and hydrothermal vents, which represent isolated productivity hotspots, are ideal opportunities for studying the effects of dispersal barriers and environmental selection on protist communities. The Okinawa Trough, a deep, back-arc spreading basin, contains distinct water masses in the bottom waters of northern and southern regions and at least twenty-five active hydrothermal vents. In this study, we used metabarcoding to characterize protist communities from fourteen stations spanning the length of the Okinawa Trough, including three hydrothermal vent sites. Significant differences in community structure reflecting regional oceanography and water mass composition were present, indicating the importance of geographic factors in shaping protist communities. Protist communities in bottom waters affected by hydrothermal activity were significantly different from communities in other bottom waters, suggesting that environmental factors can be especially important in shaping community composition under specific conditions. Amplicon sequence variants that were enriched in hydrothermally influenced bottom waters largely derived from cosmopolitan protists that were present, but rare, in other near-bottom samples, thus highlighting the importance of the rare biosphere.

ecology↗

bioRxiv2018

Differential gene expression supports a resource-intensive, defensive role for colony production in the bloom-forming haptophyte, Phaeocystis globosa

Phaeocystis globosa forms dense, monospecific blooms in temperate, northern waters. Blooms are usually dominated by the colonial morphotype--non-flagellated cells embedded in a secreted mucilaginous mass. Colonial Phaeocystis blooms significantly affect food-web structure and function and negatively impact fisheries and aquaculture, but factors initiating colony production remain enigmatic. Destructive P. globosa blooms have been reported in tropical and subtropical regions more recently and warm-water blooms could become more common with continued climate change and coastal eutrophication. We therefore assessed genetic pathways associated with colony production by investigating differential gene expression between colonial and solitary cells in a warm-water Phaeocystis globosa strain. Our results illustrate a transcriptional shift in colonial cells with most of the differentially expressed genes downregulated, supporting a reallocation of resources associated with colony production. Dimethylsulfide and acrylate production and pathogen interaction pathways were upregulated in colonial cells, suggesting a defensive role for colony production. We identify several protein kinase signaling pathways that may influence the transition between morphotypes, providing targets for future research into factors triggering colony production. This study provides novel insights into genetic mechanisms involved in Phaeocystis colony formation and provides new evidence supporting a defensive role for Phaeocystis colonies.

ecology↗

bioRxiv2018

Six species of non-tuberculosis mycobacteria carry non-identical 16S rRNA gene copies

Non-tuberculosis mycobacteria (NTM) can carry two or more 16S rRNA gene copies that are, in some instances, non-identical. In this study, we used a combined cloning and sequencing approach to analyze the 16S rRNA gene sequences of six NTM species, Mycobacterium cosmeticum, M. pallens, M. hodleri, M. crocinum, M. flavescens, and M. xenopi. The approach facilitated the identification of two distinct gene copies in each species. The two M. cosmeticum genes had a single nucleotide difference, whereas two nucleotide polymorphisms were identified in M. hodleri, M. flavescens, and M. xenopi. M. pallens had a difference in four nucleotides and M. crocinum in 23. Hence, we showed that the six NTM species possess at least two non-identical 16S rRNA gene copies.\n\nImportanceThe presence of multiple 16S rRNA gene copies with nucleotide polymorphisms represents a challenge for species identification using 16S rRNA as the target sequence. Our analysis was focused on six NTM species, M. cosmeticum, M. pallens, M. hodleri, M. crocinum, M. flavescens, and M. xenopi. As a result, we generated the full-length sequences of two non-identical 16S rRNA copies for each NTM species. The data will be helpful for the sequence analysis of specimens or other samples.

bioinformatics↗

bioRxiv2018

Intra-host symbiont diversity and extended symbiont maintenance in photosymbiotic Acantharea (clade F)

Photosymbiotic protists contribute to surface primary production in low-nutrient, open-ocean ecosystems and constitute model systems for studying plastid acquisition via endosymbiosis. Little is known, however, about host-symbiont dynamics in these important relationships, and whether these symbioses constitute mutualisms is debated. In this study, we applied single-cell sequencing methods and advanced fluorescent microscopy to investigate host-symbiont dynamics in clade F acantharians, a major group of photosymbiotic protists in oligotrophic subtropical gyres. We amplified the 18S rRNA gene from single acantharian hosts and environmental samples to assess intra-host symbiont diversity and to determine whether intra-host symbiont community composition directly reflects the available symbiont community in the surrounding environment. Our results demonstrate that clade F acantharians simultaneously host multiple species from the haptophyte genera Phaeocystis and Chrysochromulina. The intra-host symbiont community composition was distinct from the external free-living symbiont community, suggesting that these acantharians maintain symbionts for extended periods of time. After selective staining of digestive organelles, fluorescent confocal microscopy showed that symbionts were not being systematically digested, which is consistent with extended symbiont maintenance within hosts. Extended maintenance within hosts may benefit symbionts through protection from grazing or viral lysis, and therefore dispersal, provided that symbionts retain reproductive capacity.

ecology↗