Exophilone, a Tetrahydrocarbazol-1-one Analogue with Anti-Pulmonary Fibrosis Activity from the Deep-Sea Fungus Exophiala oligosperma MCCC 3A01264.

A new compound, exophilone (1), together with nine known compounds (2-10), were isolated from a deep-sea-derived fungus, Exophiala oligosperma. Their chemical structures, including the absolute configuration of 1, were elucidated using nuclear magnetic resonance (NMR) spectroscopy, high-resolution electrospray ionization mass spectroscopy (HRESIMS), and electronic circular dichroism (ECD) calculation. Compounds were preliminarily screened for their ability to inhibit collagen accumulation. Compounds 1, 4, and 7 showed weaker inhibition of TGF-ß1-induced total collagen accumulation in compared with pirfenidone (73.14% inhibition rate). However, pirfenidone exhibited cytotoxicity (77.57% survival rate), while compounds 1, 4, and 7 showed low cytotoxicity against the HFL1 cell line. Particularly, exophilone (1) showed moderate collagen deposition inhibition effect (60.44% inhibition rate) and low toxicity in HFL1 cells (98.14% survival rate) at a concentration of 10 µM. A molecular docking study suggests that exophilone (1) binds to both TGF-ß1 and its receptor through hydrogen bonding interactions. Thus, exophilone (1) was identified as a promising anti-pulmonary fibrosis agent. It has the potential to be developed as a drug candidate for pulmonary fibrosis.

Discovery of andrastones from the deep-sea-derived Penicillium allii-sativi MCCC 3A00580 by OSMAC strategy.

Andrastones are unusual 6,6,6,5-tetracyclic meroterpenoids that are rarely found in nature. Previously, three andrastones were obtained from the rice static fermentation extract of the deep-sea-derived fungus Penicillium allii-sativi MCCC 3A00580. Inspired by one strain many compounds (OSMAC) approach, the oat static fermentation on P. allii-sativi was conducted. As a result, 14 andrastones were isolated by UV-guided isolation. The chemical structures of the nine new compounds (1-9) was established by comprehensive analysis of the NMR, MS, ECD, and X-ray crystallography and the five known ones (10-14) were assigned by comparing their NMR, MS, and OR data with those reported in literature. Compound 1 bears a novel hemiketal moiety while 2 is the first example to possess a novel tetrahydrofuran moiety via C-7 and C-15. All isolates were tested for anti-allergic bioactivity. Compound 10, 3-deacetylcitreohybridonol, significantly decreased degranulation with the IC50 value of 14.8 µM, compared to that of 92.5 µM for the positive control, loratadine. Mechanism study indicated 10 could decrease the generation of histamine and TNF-α by reducing the accumulation of Ca2+ in RBL-2H3 cells. These findings indicate andrastones could be potential to discover new anti-allergic candidate drugs.

Chemical Constituents of the Deep-Sea-Derived Penicillium solitum.

A systematic chemical investigation of the deep-sea-derived fungus Penicillium solitum MCCC 3A00215 resulted in the isolation of one novel polyketide (1), two new alkaloids (2 and 3), and 22 known (4-25) compounds. The structures of the new compounds were established mainly on the basis of exhaustive analysis of 1D and 2D NMR data. Viridicatol (13) displayed moderate anti-tumor activities against PANC-1, Hela, and A549 cells with IC50 values of around 20 µM. Moreover, 13 displayed potent in vitro anti-food allergic activity with an IC50 value of 13 µM, compared to that of 92 µM for the positive control, loratadine, while indole-3-acetic acid methyl ester (9) and penicopeptide A (10) showed moderate effects (IC50 = 50 and 58 µM, respectively).

Pseudooceanicola lipolyticus sp. nov., a marine alphaproteobacterium, reclassification of Oceanicola flagellatus as Pseudooceanicola flagellatus comb. nov. and emended description of the genus Pseudooceanicola.

A Gram-stain-negative, rod-shaped bacterium, designated 157T, was isolated from seawater collected from the Philippine Sea. Cells of strain 157T grew in medium containing 0.5-10.0 % NaCl (w/v, optimum 3 %), at pH 6.0-8.5 (optimum 7.0) and at 15-40 °C (optimum 30 °C). Tweens 20, 40 and 80 as well as urea were hydrolysed. The 16S rRNA gene sequence of strain 157T had a high sequence similarity with respect to Pseudooceanicola marinus AZO-CT (97.2 %), and exhibited less than 97.0 % sequence similarity to other type strains of the species with validly published names. Phylogenetic analyses revealed that strain 157T fell within a cluster comprising the Pseudooceanicola species and formed a coherent clade with P. marinus AZO-CT and Pseudooceanicola antarcticus Ar-45T. Strain 157T exhibited average nucleotide identity values of 74.5 and 74.9 % to P. marinus LMG 23705T and P. antarcticus Ar-45T, respectively. In silico DNA-DNA hybridization analysis revealed that strain 157T shared 20.2 % DNA relatedness with P. marinus LMG 23705T and 20.6 % with P. antarcticus Ar-45T, respectively. The sole isoprenoid quinone was ubiquinone 10. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C19 : 0 cyclo ω8c, C16 : 0 2-OH and C16 : 0. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid and one unidentified glycolipid. The DNA G+C content was 64.6 mol%. According to the phylogenetic, chemotaxonomic and phenotypic data, it represents a novel species of the genus Pseudooceanicola, for which the name Pseudooceanicolalipolyticus is proposed. The type strain is 157T (=KCTC 52654T=MCCC 1K03317T). In addition, the description of the genus Pseudooceanicola is emended and Oceanicola flagellatus is reclassified as Pseudooceanicola flagellatus comb. nov., with the type strain DY470T (=CGMCC 1.12664T=LMG 27871T) proposed.

Identification, Characteristics and Mechanism of 1-Deoxy-N-acetylglucosamine from Deep-Sea Virgibacillus dokdonensis MCCC 1A00493.

Xanthomonas oryzae pv. oryzae, which causes rice bacterial blight, is one of the most destructive pathogenic bacteria. Biological control against plant pathogens has recently received increasing interest. 1-Deoxy-N-acetylglucosamine (1-DGlcNAc) was extracted from the supernatant of Virgibacillus dokdonensis MCCC 1A00493 fermentation through antibacterial bioassay-guided isolation. Its structure was elucidated by LC/MS, NMR, chemical synthesis and time-dependent density functional theory (TD-DFT) calculations. 1-DGlcNAc specifically suppressed X. oryzae pv. oryzae PXO99A (MIC was 23.90 µg/mL), but not other common pathogens including Xanthomonas campestris pv. campestris str.8004 and Xanthomonas oryzae pv. oryzicola RS105. However, its diastereomer (2-acetamido-1,5-anhydro-2-deoxy-d-mannitol) also has no activity to X. oryzae pv. oryzae. This result suggested that activity of 1-DGlcNAc was related to the difference in the spatial conformation of the 2-acetamido moiety, which might be attributed to their different interactions with a receptor. Eighty-four unique proteins were found in X. oryzae pv. oryzae PXO99A compared with the genome of strains8004 and RS105 by blastp. There may be unique interactions between 1-DGlcNAc and one or more of these unique proteins in X. oryzae pv. oryzae. Quantitative real-time PCR and the pharmMapper server indicated that proteins involved in cell division could be the targets in PXO99A. This research suggested that specificity of active substance was based on the active group and spatial conformation selection, and these unique proteins could help to reveal the specific mechanism of action of 1-DGlcNAc against PXO99A.

Anti-Allergic Compounds from the Deep-Sea-Derived Actinomycete Nesterenkonia flava MCCC 1K00610.

A novel cyclic ether, nesterenkoniane (1), was isolated from the deep-sea-derived actinomycete Nesterenkonia flava MCCC 1K00610, together with 12 known compounds, including two macrolides (2, 3), two diketopiperazines (4, 5), two nucleosides (6, 7), two indoles (8, 9), three phenolics (10-12), and one butanol derivate (13). Their structures were established mainly on detailed analysis of the NMR and MS spectroscopic data. All 13 compounds were tested for anti-allergic activities using immunoglobulin E (IgE) mediated rat mast RBL-2H3 cell model. Under the concentration of 20 µg/mL, 1 exhibited moderate anti-allergic activity with inhibition rate of 9.86%, compared to that of 37.41% of the positive control, loratadine. While cyclo(d)-Pro-(d)-Leu (4) and indol-3-carbaldehyde (8) showed the most potent effects with the IC50 values of 69.95 and 57.12 µg/mL, respectively, which was comparable to that of loratadine (IC50 = 35.01 µg/mL). To the best of our knowledge, it is the first report on secondary metabolites from the genus of Nesterenkonia.

Croceicoccus pelagius sp. nov. and Croceicoccus mobilis sp. nov., isolated from marine environments.

Strain Ery9T, isolated from surface seawater of the Atlantic Ocean, and strain Ery22T, isolated from deep-sea sediment of the Indian Ocean, were subjected to a taxonomic study using a polyphasic approach. Cells of the two strains were Gram-stain-negative, aerobic and rod-shaped. They produced yellow pigments and lacked bacteriochlorophyll a. On the basis of 16S rRNA gene sequence analysis, strain Ery9T was closely related to Croceicoccus naphthovorans PQ-2T (with 16S rRNA gene sequence similarity of 97.7 %), and strain Ery22T was closely related to Croceicoccusmarinus E4A9T (98.3 %). The 16S rRNA gene sequence similarity between strain Ery9T and strain Ery22T was 96.6 %. Phylogenetic analyses revealed that strains Ery9T and Ery22T fell within the cluster of the genus Croceicoccus and represented two independent lineages. The average nucleotide identity (ANI) values and the genome-to-genome distances between strains Ery9T and Ery22T and the type strains of species of the genus Croceicoccus with validly published names were 73.7-78.4 % and 20.1-22.3 %, respectively. The major respiratory quinone of the two isolates was ubiquinone-10 (Q-10). The DNA G+C contents of strains Ery9T and Ery22T were 62.8 and 62.5 mol%, respectively. Differential phylogenetic distinctiveness and chemotaxonomic differences, together with phenotypic properties, revealed that strains Ery9T and Ery22T could be differentiated from their closely related species. Therefore, it is concluded that strains Ery9T and Ery22T represent two novel species of the genus Croceicoccus, for which the names Croceicoccus pelagius sp. nov. (type strain Ery9T=CGMCC 1.15358T=DSM 101479T) and Croceicoccus mobilis sp. nov. (type strain Ery22T=CGMCC 1.15360T=DSM 101481T), are proposed.

ß-Carboline Alkaloids From the Deep-Sea Fungus Trichoderma sp. MCCC 3A01244 as a New Type of Anti-pulmonary Fibrosis Agent That Inhibits TGF-ß/Smad Signaling Pathway.

Pulmonary fibrosis is a scarring disease of lung tissue, which seriously threatens human health. Treatment options are currently limited, and effective strategies are still lacking. In the present study, 25 compounds were isolated from the deep-sea fungus Trichoderma sp. MCCC 3A01244. Among them, two ß-carboline alkaloids, trichocarbolines A (1) and C (4) are new compounds. The chemical structures of these compounds were elucidated based on their HRESIMS, 1D and 2D NMR spectra, optical rotation calculation, and comparisons with data reported in the literature. Trichocarboline B [(+)- and (-)-enantiomers] had previously been synthesized, and this is its first report as a natural product. Their anti-pulmonary fibrosis (PF) activity and cytotoxicity were investigated. Compounds 1, 11, and 13 strongly inhibited TGF-ß1-induced total collagen accumulation and showed low cytotoxicity against the HFL1 cell line. Further studies revealed compound 1 inhibited extracellular matrix (ECM) deposition by downregulating the expression of protein fibronectin (FN), proliferating cell nuclear antigen (PCNA), and α-smooth muscle actin (α-SMA). Mechanistic study revealed that compound 1 decreased pulmonary fibrosis by inhibiting the TGF-ß/Smad signaling pathway. As a newly identified ß-carboline alkaloid, compound 1 may be used as a lead compound for developing more efficient anti-pulmonary fibrosis agents.

Metabolic tuning of a stable microbial community in the surface oligotrophic Indian Ocean revealed by integrated meta-omics.

Understanding the mechanisms, structuring microbial communities in oligotrophic ocean surface waters remains a major ecological endeavor. Functional redundancy and metabolic tuning are two mechanisms that have been proposed to shape microbial response to environmental forcing. However, little is known about their roles in the oligotrophic surface ocean due to less integrative characterization of community taxonomy and function. Here, we applied an integrated meta-omics-based approach, from genes to proteins, to investigate the microbial community of the oligotrophic northern Indian Ocean. Insignificant spatial variabilities of both genomic and proteomic compositions indicated a stable microbial community that was dominated by Prochlorococcus, Synechococcus, and SAR11. However, fine tuning of some metabolic functions that are mainly driven by salinity and temperature was observed. Intriguingly, a tuning divergence occurred between metabolic potential and activity in response to different environmental perturbations. Our results indicate that metabolic tuning is an important mechanism for sustaining the stability of microbial communities in oligotrophic oceans. In addition, integrated meta-omics provides a powerful tool to comprehensively understand microbial behavior and function in the ocean. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-021-00119-6.

Andrastone A From the Deep-Sea-Derived Fungus Penicillium allii-sativi Acts as an Inducer of Caspase and RXRα-Dependent Apoptosis.

Two new (1, 2) and one known (3) meroterpenoids were isolated from the deep-sea-derived fungus Penicillium allii-sativi. The relative structures of new compounds were determined on the basis of an extensive analysis of the NMR and MS data, and the absolute configurations were established by ECD calculations. Andrastone A (1) is a rare andrastin bearing an unusual cyclopentan-1,3-dione. It shows a selectively antiproliferative effect against HepG2 tumor cells with an IC50 value of 7.8 µM. Mechanism study showed that apoptosis via Caspase and RXRα pathways are responsible for the inhibitory effect.

Two new phenylspirodrimanes from the deep-sea derived fungus Stachybotrys sp. MCCC 3A00409.

Two new phenylspirodrimanes, stachybotrin H (1) and stachybotrysin H (9) together with eleven known analogues (2-8, 10-13) were isolated from deep-sea derived Stachybotrys sp. MCCC 3A00409. Their structures were determined by extensive NMR data and mass spectroscopic analysis. Compounds 9-12 showed weak cytotoxicity against three human cancer cell lines K562, Hela and HL60 with IC50 in the range of 18.5-52.8 µM.

[Screening and function analysis of a cyclohexanone-degrading bacterium CN1 from deep sea sediment].

Micrococcu luteus CN1 was found to be able to utilize cyclohexanone well from the strains originally isolated from Pacific Ocean sediment. The optimum conditions for its growth were determined as 25 degrees C -37 degrees C, pH 8, salinity 6%. It could survive in the medium with high concentration of cyclohexanone ( > 44% V/V), and grew most vigorously in medium with 16.7% (V/V) cyclohexanone. CN1 could transform cyclohexanol to cyclohexanone which could be further degraded and mineralized quickly. This indicated the presence of cyclohexanol dehydrogenase and probable presence of cyclohexanone monooxygenase. With degenerate PCR for cloning part of cyclohexanone monooxygenase gene, the DNA fragment of 450bp was gotten. Amino acid sequence analysis showed that it owned the conserved sequence of the Baeyer-Villiger monooxygenase family and had the highest homology of 80% with cyclohexanone monooxygenase from Arthrobacter sp. BP2, only 53% with that from Acinetobacter sp. NCIMB 9871 which had been the most deeply investigated. So far as we know, both cyclohexanol and cyclohexanone degradation resorted to cyclohexanone monooxygenase. So this gene should be responsible for cyclohexanone degradation in CN1. All the cyclohexanone-degraders previously reported could degrade cyclopentanone, but, CN1 did not degrade cyclopentanone. This indicated that cyclohexanone monooxygenase in CN1 was special. Additionally, it was found for the first time that cyclohexanol could inhibit cyclohexanone degradation to certain degree in CN1.

[The diversity of alkane degrading bacteria in the enrichments with deep sea sediment of the South China Sea].

Deep sea sediment samples of the South Sea of China were used for isolation and biodiversity examination of hydrocarbon degrading bacterium. 48 isolates were obtained from the enrichments with hexadecane as the sole carbon sources. Among them, 27 isolates were capable of degrading alkane; and 4 could produce biosurfactant significantly as determined by the surface tension measurement. 2 isolates belonging to Dietzia maris lowered water surface tension to 33 mN/m. This is the first report about D. maris in biosurfactant production. The results of polymerase chain reaction (PCR) followed by Denaturing Gradient Gel Electrophoresis (DGGE) and DNA sequencing suggested that Bacillus was the dominant member in the hexadecane enriched communities. Isolates of Bacillus aquimaris were demonstrated to be the most predominant degraders in all 7 samples at 2 sampling sites. In addition, Sporosarcina, Halomonas and Brevibacterium were also found as one of the dominant members in some samples. Therefore, species of Bacillus might play an important role in alkane degradation in the sediments of the sampling sites.

[Isolation and characterization of 4 benzene/toluene-degrading bacterial strains and detection of related degradation genes].

Four bacteria with the ability of benzene or toluene degradation were isolated from the active sludge of a life sewage treatment farm, two of which degraded benzene, and named B1 and B2; and other two degraded toluene, and named J2 and J6, respectively. Sequence analysis of 16S rDNA showed that strain B1 and J2 belonged to Pseudomonas, and B2, J6 belonged to Acinetobacter. They all well adapted to the circumstances from 18 degrees C to 37 degrees C, 0% to 3% NaCl, and pH 7-10. The isolate J2 showed a high tolerance to organic solvent as it could grow well in the medium containing 70% (V/V) toluene, and degraded 92.4% of 0.1% (V/V) toluene within 72 hrs in a medium with toluene as the sole carbon source; while J6 presented 84.8% degradation under the same conditions to toluene. In the case of B1 and B2, they degraded 67.7% and 94.2% of 0.1% (V/V) benzene within 72 hours, respectively. Moreover, all strains were detected harboring the same benzene dioxygenase gene. In addition, J2 and J6 also had toluene dioxygenase genes which share 86.5% homology from each other. These bacteria are of potential in bio-treatment of benzene and toluene pollutants.

[Isolation of phenol-degrading bacteria from coking wastewater and their degradation gene].

Phenol and phenolic compounds are main pollutants in wastewater of coking factories. To identify the bacteria responsible for phenol removal in the activated sludge of a coking factory, we isolated bacteria from the sludge directly or after enrichment. From two samples from the aerobic and anaerobic pools, 28 strains belonging to 28 species of 20 genera were obtained after identification with BOX-PCR and further 16S rDNA sequence analyses. Most of them belonged to beta- and gamma-Proteobacteria, four of which are potential novel species of low 16S rDNA sequence similarity to corresponding type strains. From the m-cresol enrichment community, two strains identified and named as Pseudomonas monteilii GCS-AE-J-1 and Pseudomonas plecoglossicida GCS-AN-J-3 were obtained as the efficient degraders; The former can remove 94.6% m-cresol (791 mg/L) in just 48 h; while the latter metabolized 92.2% m-cresol (763 mg/L). Furthermore, the phenol hydroxylase gene was surveyed by PCR from the phenol-degrading strains,and 4 were positively detected. Summarily, quite diverse bacteria were proved of high capability to degrade phenol and phenolic compounds in this report, which play important role in biotreatment of phenol compounds.

[Marine SRB community reducing sulfate wastewater in flue gas desulfurization].

An SRB community (SRB-2) was enriched from marine sediment for the treatment of sulfate-rich wastewater of high salinity, and the effect of salinity, temperature, pH value, carbon source, concentration of sulfate and the form of Fe on the activity of SRB-2 was studied. The results show that SRB-2 is a halophilous and moderately mesophilous SRB community. The optimal conditions for its growth are as follows: temperature of 30-40 degrees C and pH value of 7.4-8.3; it can endure 5,200 mg/L SO4(2-) and 60g/L NaCl. Zero-valent Fe can promote the reductive activity of SRB-2, while Fe2+ inhibits that. SEM and optical microscopic measurements indicate many rod-shaped and spiral bacteria on the surface of padding in reactor and black sticky substance composed of rod-shaped bacteria on the bottom of reactor. This sticky substance might be cumulus of culture SRB-2-64 (GenBank accession number: EU167911).

[Isolation and identification of two marine bacteria with hydrocarbon-biodegradation activity].

Two bacterial strains, able to degrade both diesel fuel and PAHs, were isolated from the oil sewage of oil storage dock in Xiamen. Analysis of 16S rDNA sequences showed that both strains had high homology (99%) with Pseudomonas stutzeri and should be classified to this species. But Biolog analysis showed they were quite different strains. Tests of temperature, salinity, pH on cell growth suggested that they were from marine environment. Both showed high degradation activity to naphthalene, 87.53% and 84.01% within 3 days; and slight activity to pyrene, 8.35% and 5.37% within 7 days. And both harbored naphthalene dioxygenase genes of 98% identity with other those from Pseudomonas strains.