RESUMO
The marine dinoflagellate Alexandrium is known to form harmful algal blooms, and at least 14 species within the genus can produce saxitoxins (STXs). STX biosynthesis genes (sxt) are individually revealed in toxic dinoflagellates; however, the evolutionary history remains controversial. Herein, we determined the transcriptome sequences of toxic Alexandrium (A. catenella and A. pacificum) and non-toxic Alexandrium (A. fraterculus and A. fragae) and characterized their sxt by focusing on evolutionary events and STX production. Comparative transcriptome analysis revealed higher homology of the sxt in toxic Alexandrium than in non-toxic species. Notably, non-toxic Alexandrium spp. were found to have lost two sxt core genes, namely sxtA4 and sxtG. Expression levels of 28 transcripts related to eight sxt core genes showed that sxtA, sxtG, and sxtI were relatively high (>1.5) in the toxic group compared to the non-toxic group. In contrast, the non-toxic group showed high expression levels in sxtU (1.9) and sxtD (1.7). Phylogenetic tree comparisons revealed distinct evolutionary patterns between 28S rDNA and sxtA, sxtB, sxtI, sxtD, and sxtU. However, similar topology was observed between 28S rDNA, sxtS, and sxtH/T. In the sxtB and sxtI phylogeny trees, toxic Alexandrium and cyanobacteria were clustered together, separating from non-toxic species. These suggest that Alexandrium may acquire sxt genes independently via horizontal gene transfer from toxic cyanobacteria and other multiple sources, demonstrating monocistronic transcripts of sxt in dinoflagellates.
Assuntos
Dinoflagellida , Filogenia , Saxitoxina , Transcriptoma , Dinoflagellida/genética , Dinoflagellida/metabolismo , Saxitoxina/genética , Saxitoxina/biossíntese , Perfilação da Expressão Gênica , Evolução MolecularRESUMO
Toxic dinoflagellate Alexandrium can produce saxitoxins (STXs) and cause paralytic shellfish poisoning (PSP), and thus they are monitored for environmental safety management. Microscopic discrimination of dinoflagellates is difficult to distinguish between toxic and non-toxic species due to their similar morphology. Meanwhile, an alternative quantitative PCR (qPCR) assay is sensitive, rapid, and cost-effective for harmful species monitoring. Herein, we developed a novel qPCR assay to detect the STXs biosynthesis gene sxtB of Alexandrium catenella and A. pacificum, the leading cause of PSP outbreaks in Asian coasts and worldwide. The newly designed sxtB TaqMan probes target the species without any positive signal in other relative dinoflagellates. Deming regression analysis revealed that the sxtB copy number of A. catenella and A. pacificum was 3.6 and 4.1 copies per cell, respectively. During the blooming periods (April 13th-14th, 2020), only A. catenella cells were detected through the qPCR assay, ranging from 5.0 × 10 to 2.5 × 104 eq cells L-1. In addition, sxtB qPCR quantified more accurately compared to large subunit (LSU) rRNA targeting qPCR assay that overestimate cell density. Besides, the sensitivity of sxtB was higher compared to the microscope when the species were rarely present (5.0 × 102 cells L-1). These suggest that the sxtB qPCR assay can be applied to toxic Alexandrium monitoring in the Korean coast, even in the early stage of bloomings.
Assuntos
Dinoflagellida , Reação em Cadeia da Polimerase em Tempo Real , Saxitoxina , Dinoflagellida/genética , Saxitoxina/genética , Saxitoxina/biossíntese , República da Coreia , Reação em Cadeia da Polimerase em Tempo Real/métodos , Proliferação Nociva de AlgasRESUMO
A novel strictly anaerobic bacterium, strain JBNU-10 T, was isolated from BALB/c mouse feces. Cells of the strain JBNU-10 T were Gram-stain positive, non-motile and rod-shaped. Optimum growth occurred at 37â, with 1% (w/v) NaCl and at pH 7. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain JBNU-10 T belonged to the genus Adlercreutzia and were closely related to Adlercreutzia muris WCA-131-CoC-2 T (95.90%). The genome sequencing of strain JBNU-10 T revealed a genome size of 2,790,983 bp, a DNA G + C content of 69.4 mol%. It contains a total of 2,266 CDSs, 5 rRNA genes and 49 tRNA genes. According to the data obtained strain JBNU-10 T shared ANI value below 77.6- 67.7%, dDDH value below 23.8% with the closely type species. Strain JBNU-10 T possessed iso-C16:0 DMA, C18:1 CIS 9 FAME, and C18:0 DMA as the major fatty acids and had DMMK-6. The major end products of fermentation is propionate and acetate. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain JBNU-10 T represent a novel species of the genus Adlercreutzia. The type strain is JBNU-10 T (= KCTC 25028 T = CCUG 75610 T).
Assuntos
Acetatos , Composição de Bases , Fezes , Camundongos Endogâmicos BALB C , Filogenia , Propionatos , RNA Ribossômico 16S , Animais , Fezes/microbiologia , Camundongos , RNA Ribossômico 16S/genética , Acetatos/metabolismo , Propionatos/metabolismo , DNA Bacteriano/genética , Ácidos Graxos/metabolismo , Ácidos Graxos/análise , Técnicas de Tipagem Bacteriana , Análise de Sequência de DNA , Genoma BacterianoRESUMO
The marine dinoflagellate Alexandrium is known to form harmful algal blooms (HABs) and produces saxitoxin (STX) and its derivatives (STXs) that cause paralytic shellfish poisoning (PSP) in humans. Cell growth and cellular metabolism are affected by environmental conditions, including nutrients, temperature, light, and the salinity of aquatic systems. Abiotic factors not only engage in photosynthesis, but also modulate the production of toxic secondary metabolites, such as STXs, in dinoflagellates. STXs production is influenced by a variety of abiotic factors; however, the relationship between the regulation of these abiotic variables and STXs accumulation seems not to be consistent, and sometimes it is controversial. Few studies have suggested that abiotic factors may influence toxicity and STXs-biosynthesis gene (sxt) regulation in toxic Alexandrium, particularly in A. catenella, A. minutum, and A. pacificum. Hence, in this review, we focused on STXs production in toxic Alexandrium with respect to the major abiotic factors, such as temperature, salinity, nutrients, and light intensity. This review informs future research on more sxt genes involved in STXs production in relation to the abiotic factors in toxic dinoflagellates.
Assuntos
Dinoflagellida , Saxitoxina , Dinoflagellida/genética , Dinoflagellida/metabolismo , Saxitoxina/genética , Saxitoxina/biossíntese , Saxitoxina/metabolismo , Saxitoxina/toxicidade , Proliferação Nociva de Algas , Salinidade , Intoxicação por Frutos do MarRESUMO
The field of hybrid engineered living materials seeks to pair living organisms with synthetic materials to generate biocomposite materials with augmented function since living systems can provide highly-programmable and complex behavior. Engineered living materials have typically been fabricated using techniques in benign aqueous environments, limiting their application. In this work, biocomposite fabrication is demonstrated in which spores from polymer-degrading bacteria are incorporated into a thermoplastic polyurethane using high-temperature melt extrusion. Bacteria are engineered using adaptive laboratory evolution to improve their heat tolerance to ensure nearly complete cell survivability during manufacturing at 135 °C. Furthermore, the overall tensile properties of spore-filled thermoplastic polyurethanes are substantially improved, resulting in a significant improvement in toughness. The biocomposites facilitate disintegration in compost in the absence of a microbe-rich environment. Finally, embedded spores demonstrate a rationally programmed function, expressing green fluorescent protein. This research provides a scalable method to fabricate advanced biocomposite materials in industrially-compatible processes.
Assuntos
Materiais Biocompatíveis , Poliuretanos , Esporos Bacterianos , Poliuretanos/química , Materiais Biocompatíveis/química , Resistência à Tração , Temperatura Alta , Proteínas de Fluorescência Verde/metabolismo , Proteínas de Fluorescência Verde/genéticaRESUMO
Recent progress in high-throughput sequencing technologies has dramatically increased availability of genome data for prokaryotes and eukaryotes. Dinoflagellates have distinct chromosomes and a huge genome size, which make their genomic analysis complicated. Here, we reviewed the nuclear genomes of core dinoflagellates, focusing on the genome and cell size. Till now, the genome sizes of several dinoflagellates (more than 25) have been measured by certain methods (e.g., flow cytometry), showing a range of 3-250 pg of genomic DNA per cell. In contrast to their relatively small cell size, their genomes are huge (about 1-80 times the human haploid genome). In the present study, we collected the genome and cell size data of dinoflagellates and compared their relationships. We found that dinoflagellate genome size exhibits a positive correlation with cell size. On the other hand, we recognized that the genome size is not correlated with phylogenetic relatedness. These may be caused by genome duplication, increased gene copy number, repetitive non-coding DNA, transposon expansion, horizontal gene transfer, organelle-to-nucleus gene transfer, and/or mRNA reintegration into the genome. Ultimate verification of these factors as potential causative mechanisms would require sequencing of more dinoflagellate genomes in the future.
Assuntos
Dinoflagellida , Humanos , Filogenia , Dinoflagellida/genética , Genoma/genética , Evolução Biológica , DNARESUMO
A Gram-stain-positive, anaerobic, motile, and short rod-shaped bacterium, designated KGMB12511T, was isolated from the feces of healthy Koreansubjects. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain KGMB12511T was closely related to Gordonibacter pamelaeae 7-10-1-bT (95.2%). The draft genome of KGMB12511T comprised 33 contigs and 2,744 protein-coding genes. The DNA G + C content was 59.9% based on whole-genome sequences. The major cellular fatty acids (>10%) of strain KGMB12511T were C18:1 cis9, C18:1 cis9 DMA (dimethylacetal), and C16:0 DMA. The predominant polar lipids included a diphosphatydilglycerol, four glycolipids, and an unidentified phospholipid. The major respiratory quinones were menaquinone 6 (MK-6) and monomethylmenaquinone 6 (MMK-6). Furthermore, HPLC analysis demonstrated the ability of strain KGMB12511T to convert ellagic acid into urolithin. Based on a comprehensive analysis of phenotypic, chemotaxonomic, and phylogenetic data, strain KGMB12511T represents a novel species in the genus Gordonibacter. The type strain is KGMB12511T (= KCTC 25343T = NBRC 116190T).
Assuntos
Ácido Elágico , Taninos Hidrolisáveis , Humanos , Filogenia , RNA Ribossômico 16S/genética , Fezes , República da CoreiaRESUMO
An obligately anaerobic, non-motile, Gram-stain-negative, and rod-shaped strain KGMB11183T was isolated from the feces of healthy Koreans. The growth of strain KGMB11183T occurred at 30-45 °C (optimum 37 °C), at pH 6-9 (optimum pH 7), and in the presence of 0-0.5% NaCl (optimum 0%). Strain KGMB11183T showed 16S rRNA gene sequence similarities of 95.4% and 94.2% to the closest recognized species, Phocaeicola plebeius M12T, and Phocaeicola faecicola AGMB03916T. Phylogenetic analysis showed that strain KGMB11183T is a member of the genus Phocaeiocla. The major end products of fermentation are acetic acid and isobutyric acid. The major cellular fatty acids (> 10%) of this isolate were C18:1 cis 9, anteiso-C15:0, and summed feature 11 (iso-C17:0 3-OH and/or C18:2 DMA). The assembled draft genome sequences of strain KGMB11183T consisted of 3,215,271 bp with a DNA G + C content of 41.4%. According to genomic analysis, strain KGMB11183T has a number of genes that produce acetic acid. The genome of strain KGMB11183T encoded the starch utilization system (Sus) operon, SusCDEF suggesting that strain uses many complex polysaccharides that cannot be digested by humans. Based on the physiological, chemotaxonomic, phenotypic, and phylogenetic data, strain KGMB11183T is regarded a novel species of the genus Phocaeicola. The type strain is KGMB11183T (= KCTC 25284T = JCM 35696T).
Assuntos
Ácido Acético , Ácidos Graxos , Humanos , Ácido Butírico , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Técnicas de Tipagem Bacteriana , DNA Bacteriano/genética , Ácidos Graxos/química , Bacteroidetes/genética , FezesRESUMO
A novel actinobacterial strain, SB3-54T was isolated from rhizosphere soil of Cynanchum wilfodill, Jaecheon, Chungcheongbuk-do, Republic of Korea. Cells of strain SB3-54T were Gram-stain-positive, aerobic, rod-shaped, and flagellated which formed pale yellow colonies on Reasoner's 2A (R2A) agar. Growth occurred at 15-30 °C (optimum 25 °C), pH 5-8 (optimum pH 7), and 0-2.5% NaCl (optimum 0%). Phylogenetic and phylogenomic analyses showed that strain SB3-54T formed a separate lineage in the genus Jatrophihabitans with Jatrophihabitans telluris N237T. Strain SB3-54T was positive for catalase activity. Genomic analysis showed that SB3-54T has plant-beneficial function contributing (referred to as PBFC) genes such as root colonization and plant protection from oxidative stress. Furthermore, genome of SB3-54T contained gene clusters related to cytokinin biosynthesis, auxin response, tryptophan biosynthesis, siderophore biosynthesis and bacterial toxin-antitoxin systems. Strain SB3-54T contained iso-C16:0 as the major fatty acid and MK-9(H4) and MK-9(H6) as the predominant quinones. The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylinositol polymannosides, two unidentified aminoglycophospholipids and three unidentified phospholipids. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain SB3-54T represents a novel species of the genus Jatrophihabitans. The type strain is SB3-54T (= KCTC 49134T = NBRC 114108T).
Assuntos
Actinomycetales , Cynanchum , Filogenia , Rizosfera , ÁgarRESUMO
The rhizosphere microbial community is closely associated with plant disease by regulating plant growth, agricultural production, nutrient availability, plant hormone and adaptation to environmental changes. Therefore, it is very important to identify the rhizosphere microbes around plant roots and understand their functions. While studying the differences between the rhizosphere microbiota of healthy and diseased apple trees to find the cause of apple tree disease, we isolated a novel strain, designated as B3-10T, from the rhizosphere soil of a healthy apple tree. The genome relatedness indices between strain B3-10T and other type species of family Chitinophagaceae were in the ranges of 62.4-67.0% for ANI, 18.6-32.1% for dDDH, and 39.0-56.6% for AAI, which were significantly below the cutoff values for the species delineation, indicating that strain B3-10T could be considered to represent a novel genus in family Chitinophagaceae. Interestingly, the complete genome of strain B3-10T contained a number of genes encoding ACC-deaminase, siderophore production, and acetoin production contributing to plant-beneficial functions. Furthermore, strain B3-10T was found to significantly promote the growth of shoots and roots of the Nicotiana benthamiana, which is widely used as a good model for plant biology, demonstrating that strain B3-10T, a rhizosphere microbe of healthy apple trees, has the potential to promote growth and reduce disease. The phenotypic, chemotaxonomic, phylogenetic, genomic, and physiological properties of this plant growth-promoting (rhizo)bacterium, strain B3-10T supported the proposal of a novel genus in the family Chitinophagaceae, for which the name Rhizosphaericola mali gen. nov., sp. nov. (= KCTC 72123T = NBRC 114178T).
Assuntos
Malus , Solo , Mali , Filogenia , Desenvolvimento Vegetal , BacteroidetesRESUMO
The present study identified two novel glutathione S-transferase (GST) genes from the toxic dinoflagellate Alexandrium pacificum and examined their molecular characteristics and transcriptional responses to algicides and environmental contaminants. Bioinformatic analysis revealed that both ApGSTs are cytosolic, belonging to the chi-like class (ApGST1) and an undefined class (ApGST2). The overall expression of ApGSTs showed similar patterns depending on the exposed contaminants, while they were differently regulated by polychlorinated biphenyl (PCB). Copper treatments (CuCl2 and CuSO4) did not significantly induce the expression of ApGSTs. The highest up-regulations of ApGST1 and ApGST2 were under 6-h treatments of 0.10 and 0.50 mg L-1 NaOCl. Interestingly, only ApGST1 increased significantly after 0.10, 0.50, and 1.00 mg L-1 of PCB exposure (6 h). Intracellular reactive oxygen species (ROS) increased considerably under NaOCl; however, it was not significantly higher in the PCB-treated cells. GST activity was increased by NaOCl and PCB treatments, but only PCB caused apoptosis. These results suggest that GSTs are involved in the first line of phase II detoxification, protecting dinoflagellate cells against oxidative damage.
Assuntos
Dinoflagellida , Bifenilos Policlorados , Glutationa Transferase/metabolismo , Dinoflagellida/fisiologia , Estresse Oxidativo , Espécies Reativas de Oxigênio/metabolismo , Cobre/toxicidade , Bifenilos Policlorados/metabolismoRESUMO
Ultraviolet (UV) photodetectors are key devices required in the industrial, military, space, environmental, and biological fields. The Schottky barrier (SB)-MOSFET, with its high hole and electron barrier, and given its extremely low dark current, has broad development prospects in the optoelectronics field. We analyze the effects of trap states on the output characteristics of an inversion mode n-channel GaN SB-MOSFET using TCAD simulations. At the oxide/GaN interface below the gate, it was demonstrated that shallow donor-like traps were responsible for degrading the subthreshold swing (SS) and off-state current density (Ioff), while deep donor-like traps below the Fermi energy level were insignificant. In addition, shallow acceptor-like traps shifted the threshold voltage (Vt) positively and deteriorated the SS and on-state current density (Ion), while deep acceptor-like traps acted on a fixed charge. The output characteristics of the GaN SB-MOSFET were related to the resistive GaN path and the tunneling rate due to the traps at the metal (source, drain)/GaN interface. For the UV responses, the main mechanism for the negative Vt shift and the increases in the Ion and spectral responsivity was related to the photo-gating effect caused by light-generated holes trapped in the shallow trap states. These results will provide insights for UV detection technology and for a high-performance monolithic integration of the GaN SB-MOSFET.