Comparative evaluation of analytical pipelines for illumina short- and nanopore long-read 16S rRNA gene amplicon sequencing with mock microbial communities.

Utility of a recently developed long-read pipeline, Emu, was assessed using an expectation-maximization algorithm for accurate read classification. We compared it to conventional short- and long-read pipelines, using well-characterized mock bacterial samples. Our findings highlight the necessity of appropriate data-processing for taxonomic descriptions, expanding our understanding of the precise microbiome.

Isotope Distribution Analysis in H218O Pulse-Labeled Trees Frozen with Liquid Nitrogen.

Tracer injection has long been recognized as a valuable tool for delineating tree hydraulics and assessing water transport pathways. Recently, isotope tracers have emerged as innovative instruments for investigating tree hydraulics, providing new insights into tree water dynamics. Nevertheless, there is a critical need for further research to comprehensively grasp water movement and distribution within trees. A previously introduced technique for analyzing the isotopic ratio of water in wet tissues, offering millimeter-scale resolution for visualizing tracer movement, faces challenges due to its underdeveloped sample preparation techniques. In this study, we introduced an H2 18O tracer into S. gracilistyla samples, exclusively comprising indeterminate roots, stems, and leaves, cultivated through hydroponics and grown within the current year. Our objective was to assess the axial distribution of the tracer in the xylem. Additionally, we devised a novel method for preparing frozen wet tissue samples, enhancing the repeatability and success rate of experiments. The results demonstrated that all frozen wet tissue samples exhibited an average water loss rate of less than 0.6%. Isotopic analysis of these samples unveiled a consistent decline in tracer concentration with increasing height in all Salix specimens, with three out of five samples revealing a significant isotope gradient. Our findings affirm the efficacy and practicality of combining isotopic labeling with freezing, stabilization, and preparation techniques. Looking ahead, our isotopic labeling and analysis methods are poised to transcend woody plants, finding extensive applications in plant physiology and ecohydrology.

Effects of esaxerenone on blood pressure, urinary albumin excretion, serum levels of NT-proBNP, and quality of life in patients with primary aldosteronism.

Primary aldosteronism (PA) is typically managed with mineralocorticoid receptor antagonists (MRAs) barring adrenalectomy. The efficacy of esaxerenone, a nonsteroidal MRA, were explored in patients with PA. Various parameters such as the urinary albumin to creatinine ratio (UACR) and serum levels of N-terminal prohormone of brain natriuretic peptide (NT-proBNP) were evaluated in 25 PA patients before and 3 and 6 months after esaxerenone treatment. Systolic and diastolic blood pressure (BP), and the estimated glomerular filtration rate decreased after treatment, while serum levels of potassium and active renin increased. Significant reductions were observed in UACR 3 and 6 months after treatment. A significant decrease in NT-proBNP was evident at 6 months but not 3 months after treatment. Correlation analysis indicated that the reductions in BP and UACR at 3 months were independent of estimated daily salt intake. Furthermore, the effect of esaxerenone treatment on lowering UACR and NT-proBNP levels was independent of BP reduction. Responders whose systolic BP decreased 6 months after esaxerenone treatment by more than 10 mmHg compared to pretreatment had higher pretreatment NT-proBNP and similar UACR before and after treatment when compared with nonresponders. Esaxerenone improved mental, physical, and social quality of life (QOL) 6 months after treatment compared to healthy controls and increased over time. No patients discontinued treatment due to severe hyperkalemia or renal dysfunction. In conclusion, esaxerenone is a safe and effective MRA for PA treatment, offering significant benefits in terms of hypertension, albuminuria, NT-proBNP levels, and QOL improvement. Esaxerenone effectively lowers BP, UACR, and serum levels of NT-proBNP independent of dietary salt intake in mild PA patients. ARC active renin concentration, DBP diastolic blood pressure, MR mineralocorticoid receptor, MRA mineralocorticoid receptor antagonist, NT-proBNP N-terminal pro-brain natriuretic peptide, PA primary aldosteronism, QOL quality of life, SBP systolic blood pressure, SF-36 Medical Outcomes Study 36-Item Short-Form Health Survey, UACR urinary albumin to creatinine ratio.

Thecal plate morphology, molecular phylogeny, and toxin analyses reveal two novel species of Alexandrium (Dinophyceae) and their potential for toxin production.

This study describes two novel species of marine dinophytes in the genus Alexandrium. Morphological characteristics and phylogenetic analyses support the placement of the new taxa, herein designated as Alexandrium limii sp. nov. and A. ogatae sp. nov. Alexandrium limii, a species closely related to A. taylorii, is distinguished by having a shorter 2'/4' suture length, narrower plates 1' and 6'', with larger length: width ratios, and by the position of the ventral pore (Vp). Alexandrium ogatae is distinguishable with its metasert plate 1' having almost parallel lateral margins, and by lacking a Vp. Production of paralytic shellfish toxins (PSTs), cycloimines, and goniodomins (GDs) in clonal cultures of A. ogatae, A. limii, and A. taylorii were examined analytically and the results showed that all strains contained GDs, with GDA as major variants (6-14 pg cell-1) for all strains except the Japanese strain of A. limii, which exclusively had a desmethyl variant of GDA (1.4-7.3 pg cell-1). None of the strains contained detectable levels of PSTs and cycloimines.

Injury Prevalence among Young Elite Baseball Players.

This study aimed to describe the injury profiles of young Korean baseball players according to position and age as the proportion and distribution of injuries based on playing position and age remains unclear. A total of 271 elite youth baseball players aged 8 to 16 years were divided into two groups: elementary school (ES) (n = 135) and middle school (MS) (n = 136). The participants' basic, baseball practice, and injury information were collected. Injuries in the MS group were not limited to the elbow and shoulder, and injury prevalence varied by age group and baseball position. The most injured body region in the ES group was the elbow joint, regardless of the position. In contrast, the most injured body region in the MS group was the lower back, except for infielders whose elbows were the most injured. Additionally, the MS group was more likely to experience injuries to the lower back (OR = 4.27, 95% CI = 2.47-7.40), shoulder (OR = 1.93, 95% CI = 1.08-3.43; p = 0.024), and knee (OR = 2.15, 95% CI = 1.17-3.94; p = 0.012). Our findings indicate that excessive practice and a lack of rest during MS (growth spurt period) can significantly increase the risk of lower back problems in young baseball players.

Improving taxonomic classification of marine zooplankton by molecular approach: registration of taxonomically verified 18S and 28S rRNA gene sequences.

Background: Zooplankton plays an important role in the marine ecosystem. A high level of taxonomic expertise is necessary for accurate species identification based on morphological characteristics. As an alternative method to morphological classification, we focused on a molecular approach using 18S and 28S ribosomal RNA (rRNA) gene sequences. This study investigates how the accuracy of species identification by metabarcoding improves when taxonomically verified sequences of dominant zooplankton species are added to the public database. The improvement was tested by using natural zooplankton samples. Methods: rRNA gene sequences were obtained from dominant zooplankton species from six sea areas around Japan and registered in the public database for improving the accuracy of taxonomic classifications. Two reference databases with and without newly registered sequences were created. Comparison of detected OTUs associated with single species between the two references was done using field-collected zooplankton samples from the Sea of Okhotsk for metabarcoding analysis to verify whether or not the newly registered sequences improved the accuracy of taxonomic classifications. Results: A total of 166 sequences in 96 species based on the 18S marker and 165 sequences in 95 species based on the 28S marker belonging to Arthropoda (mostly Copepoda) and Chaetognatha were registered in the public database. The newly registered sequences were mainly composed of small non-calanoid copepods, such as species belonging to Oithona and Oncaea. Based on the metabarcoding analysis of field samples, a total of 18 out of 92 OTUs were identified at the species level based on newly registered sequences in the data obtained by the 18S marker. Based on the 28S marker, 42 out of 89 OTUs were classified at the species level based on taxonomically verified sequences. Thanks to the newly registered sequences, the number of OTUs associated with a single species based on the 18S marker increased by 16% in total and by 10% per sample. Based on the 28S marker, the number of OTUs associated with a single species increased by 39% in total and by 15% per sample. The improved accuracy of species identification was confirmed by comparing different sequences obtained from the same species. The newly registered sequences had higher similarity values (mean >0.003) than the pre-existing sequences based on both rRNA genes. These OTUs were identified at the species level based on sequences not only present in the Sea of Okhotsk but also in other areas. Discussion: The results of the registration of new taxonomically verified sequences and the subsequent comparison of databases based on metabarcoding data of natural zooplankton samples clearly showed an increase in accuracy in species identification. Continuous registration of sequence data covering various environmental conditions is necessary for further improvement of metabarcoding analysis of zooplankton for monitoring marine ecosystems.

Growth, Toxin Content and Production of Dinophysis Norvegica in Cultured Strains Isolated from Funka Bay (Japan).

The successful cultivation of Dinophysis norvegica Claparède & Lachmann, 1859, isolated from Japanese coastal waters, is presented in this study, which also includes an examination of its toxin content and production for the first time. Maintaining the strains at a high abundance (>2000 cells per mL-1) for more than 20 months was achieved by feeding them with the ciliate Mesodinium rubrum Lohmann, 1908, along with the addition of the cryptophyte Teleaulax amphioxeia (W.Conrad) D.R.A.Hill, 1992. Toxin production was examined using seven established strains. At the end of the one-month incubation period, the total amounts of pectenotoxin-2 (PTX2) and dinophysistoxin-1 (DTX1) ranged between 132.0 and 375.0 ng per mL-1 (n = 7), and 0.7 and 3.6 ng per mL-1 (n = 3), respectively. Furthermore, only one strain was found to contain a trace level of okadaic acid (OA). Similarly, the cell quota of pectenotoxin-2 (PTX2) and dinophysistoxin-1 (DTX1) ranged from 60.6 to 152.4 pg per cell-1 (n = 7) and 0.5 to 1.2 pg per cell-1 (n = 3), respectively. The results of this study indicate that toxin production in this species is subject to variation depending on the strain. According to the growth experiment, D. norvegica exhibited a long lag phase, as suggested by the slow growth observed during the first 12 days. In the growth experiment, D. norvegica grew very slowly for the first 12 days, suggesting they had a long lag phase. However, after that, they grew exponentially, with a maximum growth rate of 0.56 divisions per day (during Days 24-27), reaching a maximum concentration of 3000 cells per mL-1 at the end of the incubation (Day 36). In the toxin production study, the concentration of DTX1 and PTX2 increased following their vegetative growth, but the toxin production still increased exponentially on Day 36 (1.3 ng per mL-1 and 154.7 ng per mL-1 of DTX1 and PTX2, respectively). The concentration of OA remained below detectable levels (≤0.010 ng per mL-1) during the 36-day incubation period, with the exception of Day 6. This study presents new information on the toxin production and content of D. norvegica, as well as insights into the maintenance and culturing of this species.

The difference in the functional water flow network between the stem and current-year root cross-sectional surfaces in Salix gracilistyla stem xylem.

The dye injection method has been applied to many species to analyze the xylem water transport pathway in trees. However, traditional dye injection methods introduced dye tracers from the surface of cut stems, including several annual rings. Furthermore, the traditional dye injection method did not evaluate radial water movement from the outermost annual rings to the inner annual rings. In this study, we assessed the difference in radial water movement visualized by an injected dye, between stem base cut and current-year root cut samples of Salix gracilistyla Miq., with current-year roots grown hydroponically. The results showed that the number of stained annual rings in the root cut samples was smaller than that in the stem cut samples, and the percentage of stained vessels in the root cut samples was significantly smaller than that in the stem base cut samples in the second and third annual rings. In the current-year root cut samples, water transport mainly occurred in the outermost rings from the current-year roots to leaves. In addition, the theoretical hydraulic conductivity of stained vessels in the stem cut samples was higher in the current-year root cut samples in the second and third annual rings. These findings indicate that the previously reported dye injection method using stem cut samples overestimated the water transport pathway in the inner part of the stems. Moreover, previous hydraulic conductivity measurement methods might not have considered the effects of radial resistance through the annual ring boundary, and they might have overestimated the hydraulic conductivity in the inner annual rings.

Construction and Validation of an Image Discrimination Algorithm to Discriminate Necrosis from Wounds in Pressure Ulcers.

Artificial intelligence (AI) in medical care can raise diagnosis accuracy and improve its uniformity. This study developed a diagnostic imaging system for chronic wounds that can be used in medically underpopulated areas. The image identification algorithm searches for patterns and makes decisions based on information obtained from pixels rather than images. Images of 50 patients with pressure sores treated at Kobe University Hospital were examined. The algorithm determined the presence of necrosis with a significant difference (p = 3.39 × 10-5). A threshold value was created with a luminance difference of 50 for the group with necrosis of 5% or more black pixels. In the no-necrosis group with less than 5% black pixels, the threshold value was created with a brightness difference of 100. The "shallow wounds" were distributed below 100, whereas the "deep wounds" were distributed above 100. When the algorithm was applied to 24 images of 23 new cases, there was 100% agreement between the specialist and the algorithm regarding the presence of necrotic tissue and wound depth evaluation. The algorithm identifies the necrotic tissue and wound depth without requiring a large amount of data, making it suitable for application to future AI diagnosis systems for chronic wounds.

A survey of Dinophysis spp. and their potential to cause diarrhetic shellfish poisoning in coastal waters of the United States.

Multiple species of the genus Dinophysis produce diarrhetic shellfish toxins (okadaic acid and Dinophysis toxins, OA/DTXs analogs) and/or pectenotoxins (PTXs). Only since 2008 have DSP events (illnesses and/or shellfish harvesting closures) become recognized as a threat to human health in the United States. This study characterized 20 strains representing five species of Dinophysis spp. isolated from three US coastal regions that have experienced DSP events: the Northeast/Mid-Atlantic, the Gulf of Mexico, and the Pacific Northwest. Using a combination of morphometric and DNA-based evidence, seven Northeast/Mid-Atlantic isolates and four Pacific Northwest isolates were classified as D. acuminata, a total of four isolates from two coasts were classified as D. norvegica, two isolates from the Pacific Northwest coast were identified as D. fortii, and three isolates from the Gulf of Mexico were identified as D. ovum and D. caudata. Toxin profiles of D. acuminata and D. norvegica varied by their geographical origin within the United States. Cross-regional comparison of toxin profiles was not possible with the other three species; however, within each region, distinct species-conserved profiles for isolates of D. fortii, D. ovum, and D. caudata were observed. Historical and recent data from various State and Tribal monitoring programs were compiled and compared, including maximum recorded cell abundances of Dinophysis spp., maximum concentrations of OA/DTXs recorded in commercial shellfish species, and durations of harvesting closures, to provide perspective regarding potential for DSP impacts to regional public health and shellfish industry.

Phytoplankton and Microzooplankton Community Structure and Assembly Mechanisms in Northwestern Pacific Ocean Estuaries with Environmental Heterogeneity and Geographic Segregation.

Phytoplankton and microzooplankton are crucial players in marine ecosystems and first responders to environmental changes, but their community structures and how they are shaped by environmental conditions have rarely been studied simultaneously. In this study, we conducted an eDNA metabarcoding sequencing combined with multiple statistical methods to simultaneously analyze the phytoplankton and microzooplankton in Liaohe (LH) and Yalujiang (YLJ) estuaries. The major objective was to examine how plankton community structure and assembly mechanism may differ between two estuaries with similar latitudinal position and climate but geographical segregation and differential level of urbanization (more in LH). Clear differences in diversity and composition of phytoplankton and microzooplankton communities between LH and YLJ estuaries were observed. Richness of phytoplankton was significantly higher in LH than YLJ, while richness of microzooplankton was higher in YLJ. The magnitude of intrahabitat variations in phytoplankton communities was significantly stronger than that of microzooplankton. Some phytoplankton and microzooplankton taxa also showed interhabitat differences in their relative abundances. Phytoplankton showed a stronger geographic distance-decay of similarity than microzooplankton, while significant environmental distance-decay of similarity in microzooplankton was found in the less urbanized YLJ estuary. Community assembly of phytoplankton was, based on the neutral community models, driven primarily by stochastic processes, while deterministic processes contributed more for microzooplankton. Furthermore, we detected wider habitat niche breadths and stronger dispersal abilities in phytoplankton than in microzooplankton. These results suggest that passive dispersal shapes the phytoplankton community whereas environmental selection shapes the microzooplankton community. IMPORTANCE Understanding the underlying mechanisms shaping a metacommunity is useful to management for improving the ecosystem function. The research presented in the manuscript mainly tried to address the effects of habitat geography and environmental conditions on the phytoplankton and microzooplankton communities, and the underlying mechanisms of community assembly in temperate estuaries. In order to achieve this purpose, we developed a metabarcoding sequencing method based on 18S rRNA gene. The phytoplankton and microzooplankton communities from two estuaries with similar latitude and climatic conditions but obvious geographical segregation and significant environmental heterogeneity were investigated. The results of our study could lay a solid foundation for ascertaining phytoplankton and microzooplankton communities in estuaries with obvious environmental heterogeneity and geographic segregation and mechanisms underlying community assembly.

Reasons for the Reporting Behavior of Japanese Collegiate Rugby Union Players Regarding Suspected Concussion Symptoms: A Propensity Analysis.

While previous research has identified the reasons for the concussion-reporting behavior of rugby union players, the influence of confounding factors such as concussion experience, education, and knowledge of concussion symptoms, any of which may have influenced the results, has not been considered. This study aimed to clarify the reasons for the reporting behavior of college rugby union players regarding suspected concussion symptoms by adjusting for confounding factors using the propensity score. A questionnaire about both concussion knowledge and concussion-reporting behavior was administered to 240 collegiate rugby union players. Of the 208 (86.7%) valid respondents to the questionnaire, 196 (94.2%) had experienced any one symptom of a suspected concussion, such as headache, at least once, and 137 (65.9%) reported symptoms to someone else. This study's results revealed two important reasons for reporting symptoms: (1) the willingness of players to report experienced symptoms to someone else, along with realizing a concussion, and (2) the willingness of players to report suspected concussion symptoms, despite the absence of a doctor or trainer. These results suggest that providing educational opportunities to recognize suspected concussion symptoms and establishing a team culture of reporting physical problems to someone else is important for improving concussion-reporting behavior.

New Knowledge on Distribution and Abundance of Toxic Microalgal Species and Related Toxins in the Northwestern Black Sea.

Numerous potentially toxic plankton species commonly occur in the Black Sea, and phycotoxins have been reported. However, the taxonomy, phycotoxin profiles, and distribution of harmful microalgae in the basin are still understudied. An integrated microscopic (light microscopy) and molecular (18S rRNA gene metabarcoding and qPCR) approach complemented with toxin analysis was applied at 41 stations in the northwestern part of the Black Sea for better taxonomic coverage and toxin profiling in natural populations. The combined dataset included 20 potentially toxic species, some of which (Dinophysis acuminata, Dinophysis acuta, Gonyaulax spinifera, and Karlodinium veneficum) were detected in over 95% of the stations. In parallel, pectenotoxins (PTX-2 as a major toxin) were registered in all samples, and yessotoxins were present at most of the sampling points. PTX-1 and PTX-13, as well as some YTX variants, were recorded for the first time in the basin. A positive correlation was found between the cell abundance of Dinophysis acuta and pectenotoxins, and between Lingulodinium polyedra and Protoceratium reticulatum and yessotoxins. Toxic microalgae and toxin variant abundance and spatial distribution was associated with environmental parameters. Despite the low levels of the identified phycotoxins and their low oral toxicity, chronic toxic exposure could represent an ecosystem and human health hazard.

Mapping the development of a Dinophysis bloom in a shellfish aquaculture area using a novel molecular qPCR assay.

Diarrhetic shellfish toxins produced by certain species of the marine dinoflagellate Dinophysis can accumulate in shellfish in high concentrations, representing a significant food safety issue worldwide. This risk is routinely managed by monitoring programs in shellfish producing areas, however the methods used to detect these harmful marine microbes are not usually automated nor conducted onsite, and are often expensive and require specialized expertise. Here we designed a quantitative real-time polymerase chain reaction (qPCR) assay based on the ITS-5.8S ribosomal region of Dinophysis spp. and evaluated its specificity, efficiency, and sensitivity to detect species belonging to this genus. We designed and tested twenty sets of primers pairs using three species of Dinophysis - D. caudata, D. fortii and D. acuminata. We optimized a qPCR assay using the primer pair that sufficiently amplified each of the target species (Dacu_11F/Dacu_11R), and tested this assay for cross-reactivity with other dinoflagellates and diatoms in the laboratory (11 species) and in silico 8 species (15 strains) of Dinophysis, 3 species of Ornithocercus and 2 species of Phalacroma. The qPCR assay returned efficiencies of 92.4% for D. caudata, 91.3% for D fortii, and 91.5% for D. acuminata, while showing no cross-reactivity with other phytoplankton taxa. Finally, we applied this assay to a D. acuminata bloom which occurred in an oyster producing estuary in south eastern Australia, and compared cell numbers inferred by qPCR to those determined by microscopy counts (max abund. ∼6.3 × 103 and 5.3 × 103 cells L-1 respectively). Novel molecular tools such as qPCR have the potential to be used on-farm, be automated, and provide an early warning for the management of harmful algal blooms.

Knowledge of, and Attitudes Toward, Concussion in Japanese Male Collegiate Athletes.

Japan has no streamlined concussion education for collegiate athletes, and guidelines vary by sport. In particular, research on knowledge of, and attitudes toward, concussion is necessary for the establishment of concussion education for Japanese collegiate athletes. The aim of the present study was to assess the knowledge of, and attitudes toward, concussion in Japanese male collegiate athletes and to investigate their experiences with suspected concussion symptoms. An online questionnaire was administered to 390 collegiate athletes participating in the following five sports with a high incidence of concussion: rugby union, soccer, basketball, American football, and judo. Of the 121 valid responses, 91 (77.1%) indicated that they had experienced suspected concussion symptoms at least once and 46 of these 91 respondents had not reported their symptoms of suspected concussion at least once. Athletes who had never experienced concussion symptoms were significantly less likely to recognize the symptoms of concussion (p < 0.001). Most athletes recognized headache and dizziness as suspected concussion symptoms. However, the recognition rate for several symptoms was lower than the prevalence of these symptoms as shown in previous studies. This suggests that educational initiatives might be important to bridge the gap between athletes' knowledge and understanding of frequently occurring concussion symptoms and to improve reporting behavior.

Adrenal Vein Sampling With Gadolinium Contrast Medium in a Patient With Florid Primary Aldosteronism and Iodine Allergy.

We describe a 35-year-old woman who was allergic to iodine contrast medium and was diagnosed with primary aldosteronism (PA) based on functional confirmatory tests. She was suspected to have unilateral PA because of marked hypertension, spontaneous hypokalemia, high plasma aldosterone, reduced plasma renin activity, and a right hypodense adrenal tumor. She wanted to become pregnant and requested adrenalectomy instead of medical treatment with mineralocorticoid receptor antagonists. Localization of PA by adrenal vein sampling (AVS) was necessary, but angiography with iodine contrast medium was not possible because of her allergy. AVS was performed using gadolinium contrast agent (gadoterate meglumine) instead of iodine, in combination with computed tomography angiography (CTA). In AVS, before and after adrenocorticotropin (ACTH) loading, 12 blood samples were drawn from the right adrenal vein, left adrenal central vein, left adrenal common duct, left and right renal veins, and the lower inferior vena cava with only 5 mL of gadolinium medium. There were no complications during AVS. Examination revealed an elevated aldosterone/cortisol ratio on the right side, lateralized ratio of 7.4, and contralateral ratio of 0.76; the patient was diagnosed with right unilateral PA. She underwent right adrenalectomy and showed improvements in aldosterone level from 312.4 pg/mL to 83.0 pg/mL, potassium from 3.0 mEq/L to 3.9 mEq/L, and systolic blood pressure from 138 mm Hg to 117 mm Hg. In PA patients with iodine allergy, AVS can be performed safely and precisely using gadolinium contrast combined with CTA.

Seasonal genotype dynamics of a marine dinoflagellate: Pelagic populations are homogeneous and as diverse as benthic seed banks.

Genetic diversity is the basis for evolutionary adaptation and selection under changing environmental conditions. Phytoplankton populations are genotypically diverse, can become genetically differentiated within small spatiotemporal scales and many species form resting stages. Resting stage accumulations in sediments (seed banks) are expected to serve as reservoirs for genetic information, but so far their role in maintaining phytoplankton diversity and in evolution has remained unclear. In this study we used the toxic dinoflagellate Alexandrium ostenfeldii (Dinophyceae) as a model organism to investigate if (i) the benthic seed bank is more diverse than the pelagic population and (ii) the pelagic population is seasonally differentiated. Resting stages (benthic) and plankton (pelagic) samples were collected at a coastal bloom site in the Baltic Sea, followed by cell isolation and genotyping using microsatellite markers (MS) and restriction site associated DNA sequencing (RAD). High clonal diversity (98%-100%) combined with intermediate to low gene diversity (0.58-0.03, depending on the marker) was found. Surprisingly, the benthic and pelagic fractions of the population were equally diverse, and the pelagic fraction was temporally homogeneous, despite seasonal fluctuation of environmental selection pressures. The results of this study suggest that continuous benthic-pelagic coupling, combined with frequent sexual reproduction, as indicated by persistent linkage equilibrium, prevent the dominance of single clonal lineages in a dynamic environment. Both processes harmonize the pelagic with the benthic population and thus prevent seasonal population differentiation. At the same time, frequent sexual reproduction and benthic-pelagic coupling maintain high clonal diversity in both habitats.

Isolation and Characterization of the Polyhexamethylene Biguanide Hydrochloride-Resistant Fungus, Purpureocillium lilacinum.

We isolated a fungus from a 20% (= 200,000 µg/mL) aqueous solution of polyhexamethylene biguanide hydrochloride (PHMB), a widely used antimicrobial and examined its morphology and drug resistance profile. Based on the sequence of the internal transcribed spacer region of ribosomal DNA, the fungus was identified as Purpureocillium lilacinum. Although the P. lilacinum type and resistant strains showed similar morphology, the latter had extremely low PHMB susceptibility and was able to grow in 20% aqueous solution of PHMB, which eliminated the type strain. The minimum inhibitory concentration (MIC) of PHMB for the resistant strain was significantly higher than that of the type strain and other pathogenic filamentous fungi and yeasts. The susceptibility to antimicrobial agents and antifungal agents other than PHMB was similar to that of the type strain, therefore the drug resistance of the isolate was specific to PHMB. Furthermore, we sequenced the genome of the isolate to predict PHMB resistance-related genes. Despite its high resistance to PHMB, no well-known genes homologous to fungal PHMB-resistant genes were detected in the genome of the resistant strain. In summary, P. lilacinum was found to be significantly more resistant to PHMB than previously reported, via an unidentified mechanism of drug resistance.

A Standardized Procedure for Monitoring Harmful Algal Blooms in Chile by Metabarcoding Analysis.

Harmful algae blooms (HABs) monitoring has been implemented worldwide, and Chile, a country famous for its fisheries and aquaculture, has intensively used microscopic and toxin analyses for decades for this purpose. Molecular biological methods, such as high-throughput DNA sequencing and bacterial assemblage-based approaches, are just beginning to be introduced in Chilean HAB monitoring, and the procedures have not yet been standardized. Here, 16S rRNA and 18S rRNA metabarcoding analyses for monitoring Chilean HABs are introduced stepwise. According to a recent hypothesis, algal-bacterial mutualistic association plays a critical synergetic or antagonistic relationship accounting for bloom initiation, maintenance, and regression. Thus, monitoring HAB from algal-bacterial perspectives may provide a broader understanding of HAB mechanisms and the basis for early warning. Metabarcoding analysis is one of the best suited molecular-based tools for this purpose because it can detect massive algal-bacterial taxonomic information in a sample. The visual procedures of sampling to metabarcoding analysis herein provide specific instructions, aiming to reduce errors and collection of reliable data.

Development of an absolute quantification method for ribosomal RNA gene copy numbers per eukaryotic single cell by digital PCR.

Recent increase of Harmful Algal Blooms (HAB) causes world-wide ecological, economical, and health issues, and more attention is paid to frequent coastal monitoring for the early detection of HAB species to prevent or reduce such impacts. Use of molecular tools in addition to traditional microscopy-based observation has become one of the promising methodologies for coastal monitoring. However, as ribosomal RNA (rRNA) genes are commonly targeted in molecular studies, variability in the rRNA gene copy number within and between species must be considered to provide quantitative information in quantitative PCR (qPCR), digital PCR (dPCR), and metabarcoding analyses. Currently, this information is only available for a limited number of species. The present study utilized a dPCR technology to quantify copy numbers of rRNA genes per single cell in 16 phytoplankton species, the majority of which are toxin-producers, using a newly developed universal primer set accompanied by a labeled probe with a fluorophore and a double-quencher. In silico PCR using the newly developed primers allowed the detection of taxa from 8 supergroups, demonstrating universality and broad coverage of the primer set. Chelex buffer was found to be suitable for DNA extraction to obtain DNA fragments with suitable size to avoid underestimation of the copy numbers. The study successfully demonstrated the first comparison of absolute quantification of 18S rRNA copy numbers per cell from 16 phytoplankton species by the dPCR technology.