Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees.

tvBOT is a user-friendly and efficient web application for visualizing, modifying, and annotating phylogenetic trees. It is highly efficient in data preparation without requiring redundant style and syntax data. Tree annotations are powered by a data-driven engine that only requires practical data organized in uniform formats and saved as one table file. A layer manager is developed to manage annotation dataset layers, allowing the addition of a specific layer by selecting the columns of a corresponding annotation data file. Furthermore, tvBOT renders style adjustments in real-time and diversified ways. All style adjustments can be made on a highly interactive user interface and are available for mobile devices. The display engine allows the changes to be updated and rendered in real-time. In addition, tvBOT supports the combination display of 26 annotation dataset types to achieve multiple formats for tree annotations with reusable phylogenetic data. Besides several publication-ready graphics formats, JSON format can be exported to save the final drawing state and all related data, which can be shared with other users, uploaded to restore the final drawing state for re-editing or used as a style template for quickly retouching a new tree file. tvBOT is freely available at: https://www.chiplot.online/tvbot.html.

Opacimonas viscosa gen. nov., sp. nov., a novel bacterium isolated from phycosphere.

A novel strain of a member of the family Alteromonadaceae was isolated from the phycosphere of a diatom and designated as LMIT007T. LMIT007T could form milk-white, opaque, circular and smooth colonies on 2216E marine agar. LMIT007T cells were around 1.0-1.8 µm long, 0.8-1.8 µm wide, round or oval shaped and had polar flagella but were non-motile. Optimum conditions for growth were 25 °C, pH 7.0 and 6 % (w/v) NaCl. The results of 16S rRNA gene-based analysis indicated that LMIT007T had the highest similarity with the type strains Aestuaribacter halophilus JC2043T (95.95 %), Alteromonas lipolytica JW12T (95.60 %) and Alteromonas halophila KCTC 22164T (94.21 %). Furthermore, the results of phylogenetic analysis based on 16S rRNA gene sequences and of phylogenomic analysis indicated that LMIT007T could be clustered into the family Alteromonadaceae but formed a separate branch. The genome size of the strain was 2.95 Mbp and the DNA G+C content was 41.6 %. The average nucleotide identity (ANI) values of orthologous genes between LMIT007T and species of other closely related genera within the family Alteromonadaceae ranged from 66.9 to 69.2 %, and the average amino acid identity (AAI) values ranged from 60.0 to 65.7 %. The main respiratory quinone was ubiquinone-8. The major fatty acids were summed feature 3 (C16 : 1ω7c / C16 : 1ω6c) and C16 : 0. The polar lipid profile contain phosphatidylethanolamine, phosphatidylglycerol, aminolipid, two phospholipid and an unknown polar lipid. On the basis of the results of the polyphasic analysis, strain LMIT007T is suggested to represent a novel genus and species within the family Alteromonadaceae, for which the name Opacimonas viscosa gen. nov., sp. nov. is proposed. The type strain is LMIT007T (=MCCC 1K08161T=KCTC 92597T).

Hydroxylation with Unusual Stereoinversion Catalyzed by an FeII /2-OG Dependent Oxidase and 3,6-Diene-2,5-diketopiperazine Formation in the Biosynthesis of Brevianamide†K.

Natural products with the 3,6-diene-2,5-diketopiperazine core are widely distributed in nature; however, the biosynthetic mechanism of 3,6-diene-2,5-diketopiperazine in fungi remains to be further elucidated. Through heterologous expression and biochemical investigation of an FeII /2-oxoglutarate-dependent oxidase (AspE) and a heme-dependent P450 enzyme (AspF), we report that AspE, AspF and subsequent dehydration account for the formation of the 3,6-diene-2,5-diketopiperazine substructure of brevianamide K from Aspergillus sp. SK-28, a symbiotic fungus of mangrove plant Kandelia candel. More interestingly, in-depth investigation of the enzymatic mechanism showed that AspE promotes hydroxylation of brevianamide Q with unprecedented stereoinversion through hydrogen atom abstraction and water nucleophilic attack from the opposite face of the resultant iminium cation intermediate.

Secondary metabolites from mangrove-associated fungi: source, chemistry and bioactivities.

Covering 1989 to 2020The mangrove forests are a complex ecosystem occurring at tropical and subtropical intertidal estuarine zones and nourish a diverse group of microorganisms including fungi, actinomycetes, bacteria, cyanobacteria, algae, and protozoa. Among the mangrove microbial community, mangrove associated fungi, as the second-largest ecological group of the marine fungi, not only play an essential role in creating and maintaining this biosphere but also represent a rich source of structurally unique and diverse bioactive secondary metabolites, attracting significant attention of organic chemists and pharmacologists. This review summarizes the discovery relating to the source and characteristics of metabolic products isolated from mangrove-associated fungi over the past thirty years (1989-2020). Its emphasis included 1387 new metabolites from 451 papers, focusing on bioactivity and the unique chemical diversity of these natural products.

Cave Microbes as a Potential Source of Drugs Development in the Modern Era.

The world is constantly facing threats, including the emergence of new pathogens and antibiotic resistance among extant pathogens, which is a matter of concern. Therefore, the need for natural and effective sources of drugs is inevitable. The ancient and pristine ecosystems of caves contain a unique microbial world and could provide a possible source of antimicrobial metabolites. The association between humans and caves is as old as human history itself. Historically, cave environments have been used to treat patients with respiratory tract infections, which is referred to as speleotherapy. Today, the pristine environment of caves that comprise a poorly explored microbial world is a potential source of antimicrobial and anticancer drugs. Oligotrophic conditions in caves enhance the competition among microbial communities, and unique antimicrobial agents may be used in this competition. This review suggests that the world needs a novel and effective source of drug discovery. Therefore, being the emerging spot of modern human civilization, caves could play a crucial role in the current medical crisis, and cave microorganisms may have the potential to produce novel antimicrobial and anticancer drugs.

Identification of antibacterial metabolites produced by a marine bacterium Halobacillus marinus HMALI004.

AIMS: This study examined and characterized the extract for metabolites of Halobacillus marinus HMALI004 to understand their antibacterial activities against opportunistic marine pathogens, that is, Vibrio parahaemolyticus and Vibrio cholerae. METHODS AND RESULTS: The bacterial strain HMALI004 was characterized as H. marinus, and an antibacterial spectral test revealed its inhibition against two opportunistic marine pathogens (V. parahaemolyticus and V. cholera). Fermentation broth of strain HMALI004 was subjected to column chromatography and high-performance liquid chromatography to separate antibacterial substances. Two compounds were successfully isolated and identified as 1H-pyrrole-2-carboxylic acid and 4-chloro-1H-pyrrole-2-carboxylic acid by mass spectrometry (MS) and nuclear magnetic resonance. The minimal inhibition concentration (MIC) values of 1H-pyrrole-2-carboxylic acid and 4-chloro-1H-pyrrole-2-carboxylic acid for V. parahaemolyticus were 25 µg/ml, while their MIC values for V. cholerae were 50 and 100 µg/ml, respectively. The reactive oxygen species (ROS) production of two pathogen strains treated with 1H-pyrrole-2-carboxylic acid and 4-chloro-1H-pyrrole-2-carboxylic acid were detected to investigate the antimicrobial mechanism. The results suggested that 4-chloro-1H-pyrrole-2-carboxylic acid exerted enhanced ROS production in V. parahaemolyticus, whereas 1H-pyrrole-2-carboxylic acid had a weaker effect. Both compounds caused a significant rise in ROS production in V. cholerae, causing severe damage to the cell wall and cytoplasm, leading to cell death. CONCLUSIONS: The bacterium H. marinus HMALI004 was isolated from a shrimp pond and was found to produce antimicrobial compounds, which could inhibit the growth of opportunistic marine pathogens V. parahaemolyticus and V. cholerae by increasing ROS. SIGNIFICANCE AND IMPACT OF THE STUDY: Successfully isolated antibacterial-producing strain, H. marinus HMALI004, and its antimicrobial compounds could be used as biological control agents for marine pathogens.

Azaphilone derivatives with anti-inflammatory activity from the mangrove endophytic fungus Penicillium sclerotiorum ZJHJJ-18.

Nine undescribed azaphilone derivatives, sclerazaphilones A-H (1-9), and three known analogues (10-12), were obtained and identified from the fermented rice cultures of a mangrove endophytic fungus Penicillium sclerotiorum ZJHJJ-18. 1D and 2D NMR, HRESIMS and spectral data indicated the chemical structures of 1-9, and their absolute configurations were assigned by experimental and computational analyses of electronic circular dichroism (ECD) spectra, and application of the chemical transformations. Compounds 1-4 were the first reported N-containing azaphilone derivatives with 5/6 dicyclic core. The bioassay results showed that compounds 3-5 exhibited effective inhibitory effects on the nitric oxide (NO) production in lipopolysaccharide (LPS)-induced RAW264.7 macrophage cells with IC50 values in the range of 6.30-9.45 µM. Moreover, a molecular docking study was conducted to investigate the probable binding interaction of 3-5 with inducible nitric oxide synthase (iNOS).

Metagenomic assemblage genomes analyses reveal the polysaccharides hydrolyzing potential of marine group II euryarchaea.

Marine group II euryarchaea (MGII) dominates the planktonic archaeal community in global surface seawater and is associated to particulate organic matters mainly composed of polysaccharides. However, the polysaccharides metabolism of MGII euryarchaea is unclear. In this study, the distribution and polysaccharides metabolism potential of MGII euryarchaea in the estuary were investigated. High-throughput sequencing of 16S rRNA genes showed that MGII euryarchaea was the predominant archaeal group in the Pearl River Estuary (PRE), and the relative abundance of MGII euryarchaea in particle-attached fraction was higher than that in free-living fractions. A total of 19 metagenome-assembled genomes (MAGs) were successfully reconstructed from metagenomic data, of which 10 MAGs were grouped as MGII euryarchaea according to phylogenomic analysis. Genes encoding a variety of carbohydrate-active enzymes (CAZymes) were found in MAGs/genomes of MGII euryarchaea. These CAZymes annotated in MAGs were capable of hydrolyzing many polysaccharides, including α-glucans, ß-glucans, xylans, nitrogen-containing polysaccharides, and some insoluble galactans. The results also indicated that MGII euryarchaea has some unique enzymes that can hydrolyze starch, ß-1,3-glucans, complex xylans, carrageenan, and agarose. Collectively, our results demonstrated that MGII euryarchaea has great polysaccharides hydrolysis potential and could play an important role in the carbon cycle of marine ecosystem.

Two Antimicrobial Heterodimeric Tetrahydroxanthones with a 7,7'-Linkage from Mangrove Endophytic Fungus Aspergillus flavus QQYZ.

Mangrove endophytic fungi represent significant and sustainable sources of novel metabolites with unique structures and excellent biological activities, attracting extensive chemical investigations. In this research, two novel heterodimeric tetrahydroxanthones, aflaxanthones A (1) and B (2), dimerized via an unprecedented 7,7'-linkage, a sp3-sp3 dimeric manner, were isolated from the mangrove endophytic fungus Aspergillus flavus QQYZ. Their structures were elucidated through high resolution electrospray ionization mass spectroscopy (HRESIMS) and nuclear magnetic resonance (NMR) spectroscopy, the absolute configurations of them were determined by a single-crystal X-ray diffraction combined with calculated electronic circular dichroism (ECD) spectra and a 1D potential energy scan. These compounds were evaluated for antifungal activities in vitro and exhibited broad-spectrum and potential antifungal activities against several pathogenic fungi with minimum inhibitory concentration (MIC) values in the range of 3.13-50 µM. They also performed moderate antibacterial activities against several bacteria with MIC values in the range of 12.5-25 µM. This research enriched the resources of lead compounds and templates for marine-derived antimicrobial drugs.

Penaeicolahalotolerans gen. nov., sp. nov., a novel bacterium of the family Cyclobacteriaceae isolated from a shrimp pond.

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterium (designated as LMIT005T) was isolated from shrimp ponds in Shantou, China. The new isolate was characterized taxonomically using a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain LMIT005T was found to be affiliated with the family Cyclobacteriaceae of the order Cytophagales while appearing as a distinct lineage. The 16S rRNA gene sequence similarity between strain LMIT005T and Algoriphagus yeomjeoni KCTC 12309T, the closest type strain in the family, was 91.3 %. Strain LMIT005T grew optimally at 25 °C, pH 7 and in the presence of 2.0 % (w/v) NaCl. The DNA G+C content (data from genome sequence) was 40.5 mol%. Compared with reference strain A. yeomjeoni KCTC 12309T, the average nucleotide identity (ANI) of LMIT005T was 70 %. The sole respiratory quinone of LMIT005T was menaquinone (MK-7), and the major fatty acids were summed feature 3 (C16 : 1 ω6c / C16 : 1 ω7c). The polar lipids of strain LMIT005T were mainly composed of phosphatidylethanolamine, phosphatidylcholine, two unidentified amino lipids, two unidentified lipids, one unidentified glycolipid and one unidentified phospholipid. The draft genome of strain LMIT005T comprised 3 089 781 bp (3.09 Mb) nucleotides and 2773 genes. Antimicrobial resistant-related genes (blal, mexA, and mexb) were annotated in the genome of strain LMIT005T, which indicated that it might be able to resist ß-lactam antibiotics. This was further verified by antimicrobial resistant test. Given its distinct genomic, morphological, and physiological differences from previously described type strains, strain LMIT005T is proposed as a representative of a novel genus of the family Cyclobacteriaceae, with the name Penaeicola halotolerans gen. nov., sp. nov. The type strain is LMIT005T (=KCTC 82616T=CICC 25047T).

Benzopyran Derivatives and an Aliphatic Compound from a Mangrove Endophytic Fungus Penicillium citrinum QJF-22.

Two new benzopyran derivatives, (2R,4S)-5-methoxy-2-methyl-3,4-dihydro-2H-1-benzopyran-4-ol and (2S,4R,2'S,4'R)-4,4'-oxybis(5-methoxy-2-methyl-3,4-dihydro-2H-1-benzopyran), and a new aliphatic compound, (3E,5Z,8S,10E)-8-hydroxytrideca-3,5,10,12-tetraen-2-one, together with three known benzopyran derivatives, were obtained from a mangrove endophytic fungus Penicillium citrinum QJF-22 collected in Hainan island. Their structures were determined by analysis of spectroscopic data and the relative configuration of (2R,4S)-5-methoxy-2-methyl-3,4-dihydro-2H-1-benzopyran-4-ol was also confirmed by single-crystal X-ray diffraction. The absolute configurations of four compounds were established by comparison of ECD spectra to calculations. The configuration of (3E,5Z,8S,10E)-8-hydroxytrideca-3,5,10,12-tetraen-2-one was confirmed by comparison of optical value to the similar compound. The configurations of the compounds (2S,4S)-5-methoxy-2-methyl-3,4-dihydro-2H-1-benzopyran-4-ol and (2R,4R)-5-methoxy-2-methyl-3,4-dihydro-2H-1-benzopyran-4-ol were first determined. (3R,4S)-3,4,8-Trihydroxy-3,4-dihydronaphthalen-1(2H)-one exhibited moderate inhibitory effects on LPS-induced NO production in RAW264.7 cells with IC50 of 44.7 µM, and without cytotoxicity to RAW264.7 cells within 50 µM.

Ophiobolin-Type Sesterterpenoids from the Mangrove Endophytic Fungus Aspergillus sp. ZJ-68.

Eleven new ophiobolin-type sesterterpenoids, asperophiobolins A-K (1-11), along with 12 known analogues (12-23) were isolated from the cultures of the mangrove endophytic fungus Aspergillus sp. ZJ-68. The structures of the new compounds were elucidated through spectroscopic analyses, and their absolute configurations were assigned by a combination of Mo2(AcO)4-induced electronic circular dichroism spectra and quantum chemical calculations. Asperophiobolins A-D (1-4) represent the first examples possessing a five-membered lactam unit between C-5 and C-21 in ophiobolin derivatives. In the bioactivity assays, compounds 8-10 and 14-17 exhibited inhibitory effects on lipopolysaccharide-induced nitric oxide production in RAW 264.7 macrophage cells with IC50 values ranging from 9.6 to 25 µM, and compound 8 was found to show comparable inhibition of Mycobacterium tuberculosis protein tyrosine phosphatase B with an IC50 value of 19 µM.

New Benzofuranoids and Phenylpropanoids from the Mangrove Endophytic Fungus, Aspergillus sp. ZJ-68.

Three new benzofuranoids, asperfuranoids A-C (1-3), two new phenylpropanoid derivatives (6 and 7), and nine known analogues (4, 5, and 8-14) were isolated from the liquid substrate fermentation cultures of the mangrove endopytic fungus Aspergillus sp. ZJ-68. The structures of the new compounds were determined by extensive spectroscopic data interpretation. The absolute configurations of 1-3 were assigned via the combination of Mosher's method, and experimental and calculated electronic circular dichroism (ECD) data. Compounds 4 and 5 were a pair of enantiomers and their absolute configurations were established for the first time on the basis of their ECD spectra aided with ECD calculations. All isolated compounds (1-14) were evaluated for their enzyme inhibitory activity against α-glucosidase and antibacterial activities against four pathogenic bacteria (Staphylococcus aureus, Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa). Among them, compound 6 exhibited potent inhibitory activity against α-glucosidase in a standard in vitro assay, with an IC50 value of 12.4 µM, while compounds 8 and 11 showed activities against S. aureus, E. coli, and B. subtilis, with MIC values in the range of 4.15 to 12.5 µg/mL.

Secondary Metabolites with α-Glucosidase Inhibitory Activity from the Mangrove Fungus Mycosphaerella sp. SYSU-DZG01.

Four new metabolites, asperchalasine I (1), dibefurin B (2) and two epicoccine derivatives (3 and 4), together with seven known compounds (5-11) were isolated from a mangrove fungus Mycosphaerella sp. SYSU-DZG01. The structures of compounds 1-4 were established from extensive spectroscopic data and HRESIMS analysis. The absolute configuration of 1 was deduced by comparison of ECD data with that of a known structure. The stereostructures of 2-4 were further confirmed by single-crystal X-ray diffraction. Compounds 1, 8 and 9 exhibited significant α-glucosidase inhibitory activity with IC50 values of 17.1, 26.7 and 15.7 µM, respectively. Compounds 1, 4, 6 and 8 showed antioxidant activity by scavenging DPPH· with EC50 values ranging from 16.3 to 85.8 µM.

Peniisocoumarins A-J: Isocoumarins from Penicillium commune QQF-3, an Endophytic Fungus of the Mangrove Plant Kandelia candel.

Ten new isocoumarins, named peniisocoumarins A-J (1-9 and 11), along with three known analogues (10, 12, and 13) were obtained from the fermentation of an endophytic fungus, Penicillium commune QQF-3, which was isolated from a fresh fruit of the mangrove plant Kandelia candel. Their structures were elucidated through extensive spectroscopic analysis. The absolute configurations of 1-7 were determined by single-crystal X-ray diffraction and modified Mosher's method, and those of 8, 9, and 11 were assigned on the basis of experimental and calculated electronic circular dichroism data. Compounds 1 and 2 were unusual dimeric isocoumarins with a symmetric four-membered core. These isolated compounds (1-13) were evaluated for their cytotoxicity and enzyme inhibitory activities against α-glucosidase and Mycobacterium tuberculosis protein tyrosine phosphatase B (MptpB). Among them, compounds 3, 7, 9, and 11 exhibited potent inhibitory effects against α-glucosidase with IC50 values ranging from 38.1 to 78.1 µM, and compound 7 was found to inhibit MptpB with an IC50 value of 20.7 µM.

Cytotoxic and Antibacterial Preussomerins from the Mangrove Endophytic Fungus Lasiodiplodia theobromae ZJ-HQ1.

Two new chlorinated preussomerins, chloropreussomerins A and B (1 and 2), together with nine known preussomerin analogues, 3-11, were obtained from the endophytic fungus Lasiodiplodia theobromae ZJ-HQ1. Their structures were elucidated by a combination of spectroscopic analyses. The absolute configurations of 1 and 2 were both determined by single-crystal X-ray diffraction using Cu Kα radiation. Chloropreussomerins A and B (1 and 2) are the first chlorinated compounds in the preussomerin family, and preussomerin M (3) is reported for the first time as a natural product. Compounds 1 and 2 showed potent in vitro cytotoxicity against A549 and MCF-7 human cancer cell lines, with IC50 values ranging from 5.9 to 8.9 µM, and compounds 4-7 exhibited significant bioactivity against A549, HepG2, and MCF-7 human cancer cell lines, with IC50 values of 2.5-9.4 µM. In the antibacterial assay, compounds 1, 2, 5-7, and 11 exhibited significant activities against Staphylococcus aureus, with MIC values between 1.6 and 13 µg/mL.

New furoisocoumarins and isocoumarins from the mangrove endophytic fungus Aspergillus sp. 085242.

The chemical investigation of the mangrove endophytic fungus Aspergillus sp. 085242 afforded eight isocoumarin derivatives 1-8 and one isoquinoline 9. Asperisocoumarins A and B (1 and 2) were new furoisocoumarins, and asperisocoumarins E and F (5 and 6) were new isocoumarins. Their structures were established by analysis of their spectroscopic data and the absolute configuration of compound 2 was unambiguously determined by X-ray structure analysis and ECD calculation. Moreover, the absolute configurations of compounds 3-5 were assigned by comparison of their ECD spectra with isocoumarins described in the literature. Asperisocoumarins C and D (3 and 4) were fully characterized spectroscopically and isolated from a natural source for the first time. Asperisocoumarins A-D (1-4) related to the class of furo[3,2-h]isocoumarins are rarely occurring in natural sources. Compounds 2, 5, and 6 showed moderate α-glucosidase inhibitory activity with IC50 of 87.8, 52.3, and 95.6 µM, respectively. In addition, compounds 1 and 3 exhibited weak radical scavenging activity with EC50 values of 125 and 138 µM, respectively.

The novel application of violacein produced by a marine Duganella strain as a promising agent for controlling Heterosigma akashiwo bloom: Algicidal mechanism, fermentation optimization and agent formulation.

Controlling harmful algal blooms with algicidal bacteria is thought to be an efficient and eco-friendly way but lack of comprehensive studies from theory to practice limited the field application. Here we presented a purple bacterial strain Duganella sp. A3 capable of killing several harmful algae, including Heterosigma akashiwo, a world-wide fish-killing microalga. A bioactivity-guided purification and identification approach revealed the major algicidal compound of A3 as the pigment violacein, which was never reported for its algicidal potential before. Violacein rapidly disrupted cell permeability, caused long-term oxidative stress, but mildly affected algal photosystem, which might explain its highly species-specific activity against unarmored H. akashiwo. To explore the application potential of violacein, a fermentation optimization approach combing single-factor and multi-factor experiments was conducted to increase the violacein yield, which finally reached 0.4199 g/L just using a simple medium formula beneficial for compound purification. Finally, taking advantages of the physical and chemical stabilities, we successfully developed the novel application of violacein as a sustained-releasing and easy-to-preserve algicidal agent using alginate-acacia-gum-chitosan encapsulation, which paved the path for its future application in controlling H. akashiwo bloom.

A sonication-filtration method for acquisition of integrated bacterial communities from phycosphere.

Bacteria in phycosphere engage in intricate interactions with microalgae by exchanging organic and inorganic matter. However, elucidating the primary roles of bacteria in phycosphere has been a big challenge, due to the lack of adequate methods for separating tightly associated bacteria from microalgal cells. In this study we evaluated several isolation methods including centrifugation, filtration, sonication combined with filtration, and tween lysis followed by sonication and filtration, aiming to efficiently acquire complete bacterial communities from phycosphere. The results demonstrated that the sonication-filtration approach maximally preserves the original characteristics of the bacterial communities. This method will facilitate the acquisition and further analysis of future experimental data.