Structure of Vibrio Phage XM1, a Simple Contractile DNA Injection Machine.

Antibiotic resistance poses a growing risk to public health, requiring new tools to combat pathogenic bacteria. Contractile injection systems, including bacteriophage tails, pyocins, and bacterial type VI secretion systems, can efficiently penetrate cell envelopes and become potential antibacterial agents. Bacteriophage XM1 is a dsDNA virus belonging to the Myoviridae family and infecting Vibrio bacteria. The XM1 virion, made of 18 different proteins, consists of an icosahedral head and a contractile tail, terminated with a baseplate. Here, we report cryo-EM reconstructions of all components of the XM1 virion and describe the atomic structures of 14 XM1 proteins. The XM1 baseplate is composed of a central hub surrounded by six wedge modules to which twelve spikes are attached. The XM1 tail contains a fewer number of smaller proteins compared to other reported phage baseplates, depicting the minimum requirements for building an effective cell-envelope-penetrating machine. We describe the tail sheath structure in the pre-infection and post-infection states and its conformational changes during infection. In addition, we report, for the first time, the in situ structure of the phage neck region to near-atomic resolution. Based on these structures, we propose mechanisms of virus assembly and infection.

Three new phomalone derivatives from a deep-sea-derived fungus Alternaria sp. MCCC 3A00467.

Three new phomalone derivatives, phomalichenones E-G (1-3), and seven known analogues (4-10) were isolated from the cultures of a deep-sea-derived fungus Alternaria sp. MCCC 3A00467. Their structures were elucidated by spectroscopic methods, including the 1D and 2D NMR, and ECD spectrum. Among the compounds isolated, phomalichenone F (2) presented cytotoxic activity against human myeloma cancer U266 cells with IC50 value of 24.99 µg/mL. The most active compound, 10, showed cytotoxicity against U266, HepG2 and A549 cells with IC50 values of 13.26, 14.69 and 24.39 µg/mL, respectively.

Fungal diversity in deep-sea sediments from the Magellan seamounts as revealed by a metabarcoding approach targeting the ITS2 regions.

Recent reports have revealed diverse and abundant fungal communities in the deep-sea biosphere, while their composition, distribution, and variations in seamount zones are poorly understood. Using a metabarcoding approach targeting the ITS2 regions, we present the structure of the fungal community in 18 sediment samples from the Magellan seamount area of the northwest Pacific. A total of 1,979 fungal OTUs was obtained, which were taxonomically assigned to seven phyla, 17 classes, 43 orders, 7 families, and 98 genera. The majority of these OTUs were affiliated to Basidiomycota (873 OTUs, 44.11% of total OTUs) and Ascomycota (486 OTUs, 24.56% of total OTUs), followed by other five minor phyla (Mortierellomycota, Chytridiomycota, Mucoromycota, Glomeromycota, and Monoblepharidomycota). Sordriomycetes is the most abundant class, followed by Eurotiomycetes, and Dothideomycetes. Five genera were common in most of the samples, including worldwide reported genera Aspergillus, Cladosporium, Fusarium, Chaetomium, and Penicillium. The environmental data we collected (sampling depth, sampling location latitude and longitude, organic carbon content, and organic nitrogen content in the sediment) had no significant influence on the composition and distribution of fungal communities. Our findings provide valuable information for understanding the distribution and potential ecological functions of fungi in the deep-sea sediments of the Magellan seamounts.

Asperochratides A-J, Ten new polyketides from the deep-sea-derived Aspergillus ochraceus.

Ten new C9 polyketides (asperochratides A-J, 1-10) and 14 known miscellaneous compounds (11-24) were isolated from the deep-sea-derived fungus Aspergillus ochraceus. Structures of the new compounds were elucidated by extensive spectroscopic analyses, modified Mosher's method, Mo2(OAc)4 induced circular dichroism (ICD) experiments, and ECD calculations. Structurally, compounds 1-11 and 16-18 share the same polyketide origin of the skeleton and belong to aspyrone co-metabolites. All isolates were tested for cytotoxic, anti-food allergic, anti-H1N1 virus, anti-microbe, and anti-inflammatory activities in vitro. Results showed that compounds 5-8 and 13-17 exerted significant cytotoxic effects on BV-2 cell line, and compound 16 showed the potential of anti-inflammatory activities.

Fungal diversity in deep-sea sediments from Magellan seamounts environment of the western Pacific revealed by high-throughput Illumina sequencing.

There are lots of seamounts globally whose primary production is disproportionally greater than the surrounding areas. Compared to other deep-sea environments, however, the seamounts environment is relatively less explored for fungal diversity. In the present study, we explored the fungal community structure in deep-sea sediments from four different stations of the Magellan seamounts environment by using high-throughput sequencing of the ITS1 region. A total of 1,897,618 ITS1 sequences were obtained. Among these sequences, fungal ITS1 sequences could be clustered into 1,662 OTUs. The majority of these sequences belonged to Ascomycota. In the genera level, the most abundant genus was Mortierella (4.79%), which was reported as a common fungal genus in soil and marine sediments, followed by Umbelopsis (3.80%), Cladosporium (2.98%), Saccharomycopsis (2.53%), Aspergillus (2.42%), Hortaea (2.36%), Saitozyma (2.20%), Trichoderma (2.12%), Penicillium (2.11%), Russula (1.86%), and Verticillium (1.40%). Most of these recovered genera belong to Ascomycota. The Bray-Curtis analysis showed that there was 37 to 85% dissimilarity of fungal communities between each two sediment samples. The Principal coordinates analysis clearly showed variations in the fungal community among different sediment samples. These results suggested that there was a difference in fungal community structures not only among four different sampling stations but also for different layers at the same station. The depth and geographical distance significantly affect the fungal community, and the effect of depth and geographical distance on the structure of the fungal community in the Magellan seamounts is basically same. Most of the fungi were more or less related to plants, these plant parasitic/symbiotic/endophytic fungi constitute a unique type of seamounts environmental fungal ecology, different from other marine ecosystems.

Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment.

Hydrothermal vents release reduced compounds and small organic carbon compounds into the surrounding seawater, providing essential substrates for microbial growth and bioenergy transformations. Despite the wide distribution of the marine benthic group E archaea (referred to as Hydrothermarchaeota) in the hydrothermal environment, little is known about their genomic repertoires and biogeochemical significance. Here, we studied four highly complete (>80%) metagenome-assembled genomes (MAGs) from a black smoker chimney and the surrounding sulfur-rich sediments on the South Atlantic Mid-Ocean Ridge and publicly available data sets (the Integrated Microbial Genomes system of the U.S. Department of Energy-Joint Genome Institute and NCBI SRA data sets). Genomic analysis suggested a wide carbon metabolic diversity of Hydrothermarchaeota members, including the utilization of proteins, lactate, and acetate; the anaerobic degradation of aromatics; the oxidation of C1 compounds (CO, formate, and formaldehyde); the utilization of methyl compounds; CO2 incorporation by the tetrahydromethanopterin-based Wood-Ljungdahl pathway; and participation in the type III ribulose-1,5-bisphosphate carboxylase/oxygenase-based Calvin-Benson-Bassham cycle. These microbes also potentially oxidize sulfur, arsenic, and hydrogen and engage in anaerobic respiration based on sulfate reduction and denitrification. Among the 140 MAGs reconstructed from the black smoker chimney microbial community (including Hydrothermarchaeota MAGs), community-level metabolic predictions suggested a redundancy of carbon utilization and element cycling functions and interactive syntrophic and sequential utilization of substrates. These processes might make various carbon and energy sources widely accessible to the microorganisms. Further, the analysis suggested that Hydrothermarchaeota members contained important functional components obtained from the community via lateral gene transfer, becoming a distinctive clade. This might serve as a niche-adaptive strategy for metabolizing heavy metals, C1 compounds, and reduced sulfur compounds. Collectively, the analysis provides comprehensive metabolic insights into the Hydrothermarchaeota IMPORTANCE This study provides comprehensive metabolic insights into the Hydrothermarchaeota from comparative genomics, evolution, and community-level perspectives. Members of the Hydrothermarchaeota synergistically participate in a wide range of carbon-utilizing and element cycling processes with other microorganisms in the community. We expand the current understanding of community interactions within the hydrothermal sediment and chimney, suggesting that microbial interactions based on sequential substrate metabolism are essential to nutrient and element cycling.

Insights into fungal diversity of a shallow-water hydrothermal vent field at Kueishan Island, Taiwan by culture-based and metabarcoding analyses.

This paper reports the diversity of fungi associated with substrates collected at a shallow hydrothermal vent field at Kueishan Island, Taiwan, using both culture-based and metabarcoding methods. Culture of fungi from yellow sediment (with visible sulfur granules), black sediment (no visible sulfur granules), the vent crab Xenograpsus testudinatus, seawater and, animal egg samples resulted in a total of 94 isolates. Species identification based on the internal transcribed spacer regions of the rDNA revealed that the yellow sediment samples had the highest species richness with 25 species, followed by the black sediment (23) and the crab (13). The Ascomycota was dominant over the Basidiomycota; the dominant orders were Agaricales, Capnodiales, Eurotiales, Hypocreales, Pleosporales, Polyporales and Xylariales. Hortaea werneckii was the only common fungus isolated from the crab, seawater, yellow and black sediment samples. The metabarcoding analysis amplifying a small fragment of the rDNA (from 18S to 5.8S) recovered 7-27 species from the black sediment and 12-27 species from the yellow sediment samples and all species belonged to the Ascomycota and the Basidiomycota. In the yellow sediments, the dominant order was Pleosporales and this order was also dominant in the black sediment together with Sporidiobolales. Based on the results from both methods, 54 and 49 species were found in the black and yellow sediments, respectively. Overall, a higher proportion of Ascomycota (~70%) over Basidiomycota was recovered in the yellow sediment and the two phyla were equally abundant in the black sediment. The top five dominant fungal orders in descending order based on species richness were Pleosporales>Eurotiales>Polyporales>Hypocreales>Capnodiales in the black sediment samples, and Polyporales>Pleosporales>Eurotiales>Capnodiales>Hypocreales in the yellow sediment samples. This study is the first to observe a high diversity of fungi associated with various substrates at a marine shallow water hydrothermal vent ecosystem. While some fungi found in this study were terrestrial species and their airborne spores might have been deposited into the marine sediment, several pathogenic fungi of animals, including Acremonium spp., Aspergillus spp., Fusarium spp., Malassezia spp., Hortaea werneckii, Parengyodontium album, and Westerdykella dispersa, were recovered suggesting that these fungi may be able to cause diseases of marine animals.

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.

Aphidicolin Chemistry of the Deep-Sea-Derived Fungus Botryotinia fuckeliana MCCC 3A00494.

Aphidicolin, a potent DNA polymerase α inhibitor, has been explored in clinical trials for the treatment of cancer. So far, about 300 modified aphidicolins have been discovered. However, none have shown a stronger effect. Herein, we report 71 new (aphidicolins A1-A71, 1-71) and eight known (72-79) aphidicolin congeners from Botryotinia fuckeliana MCCC 3A00494, a fungus isolated from the western Pacific Ocean (-5572 m). The structures of 1-71 were determined through extensive spectroscopic analysis, X-ray crystallography, chemical derivatization, modified Mosher's method, and the ECD exciton chirality method. Compounds 54-57 and 58-64 are novel 6/6/5/6/5 pentacyclic aphidicolins featuring tetrahydrofuran and dihydrofuran rings, respectively, while compounds 65-71 are rare noraphidicolins. Aphidicolin A8 (8) significantly induced apoptosis in T24 (IC50 = 2.5 µM) and HL-60 (IC50 = 6.1 µM) cancer cells by causing DNA damage. By docking its structure to the human DNA polymerase α binding pocket, 8 was found to form tight intermolecular contacts, elaborating aphidicolin A8 as a potently cytotoxic lead compound.

Sarocladione, a unique 5,10:8,9-diseco-steroid from the deep-sea-derived fungus Sarocladium kiliense.

A novel ergostane, sarocladione (1), was isolated from the deep-sea-derived fungus Sarocladium kiliense, along with 20 known compounds. The structure of 1 was determined mainly by a detailed analysis of its experimental and calculated NMR spectroscopic data. It is worth noting that 1 was the first steroid bearing a 5,10:8,9-diseco moiety. All 21 compounds were tested for in vitro antitumor activities against five cancer cell lines. ß-Sitostenone (7) and 4,6-dihydroxyeudesmane (20) showed significant effects on HeLa-S3 cells with the IC50 values of 9.2 µM and 9.3 µM, respectively.

Discovery, gene modification, and optimization of fermentation of an enduracidin-producing strain.

Enduracidin significantly inhibits Gram-positive bacteria and had been widely used in many fields. However, as the poor technology for production of enduracidin and its scarcity, identification of novel strategies for production of enduracidin is important. Our group developed two methods to improve the yield of the production of enduracidin. The yield of enduracidin was increased by three- to fivefold. The highest yields of enduracidin A and enduracidin B achieved were 63.7 and 82.13 mg/ml. Thus, our results might provide a new reference method for the industrial production of enduracidin.

New anti-inflammatory guaianes from the Atlantic hydrotherm-derived fungus Graphostroma sp. MCCC 3A00421.

Nine new guaianes (graphostromanes A-I, 1-9) were isolated from the deep-sea-derived fungus Graphostroma sp. MCCC 3A00421, along with four known ones (10-13). The relative configurations were established mainly by detailed analysis of the NMR and HRESIMS data, while the absolute configurations were assigned using the X-ray crystallography and modified Mosher's method. All isolates were evaluated for their inhibitory effects against lipopolysaccharide (LPS)-induced nitric oxide (NO) production in RAW264.7 macrophages. Graphostromanes F (6) showed remarkable inhibitory effect with an IC50 value of 14.2 µM, which was even stronger than that of aminoguanidine, a positive control with an IC50 value of 23.4 µM.

Polyketides from the Deep-Sea-Derived Fungus Graphostroma sp. MCCC 3A00421 Showed Potent Antifood Allergic Activities.

To discover antifood allergic components from deep-sea-derived microorganisms, we performed a systematic chemical investigation of the Atlantic hydrothermal fungus Graphostroma sp. MCCC 3A00421. Consequently, nine new (1-9) and 19 known (10-28) polyketides were isolated. The planar structures of the new compounds were elucidated mainly by detailed analysis of their nuclear magnetic resonance and high-resolution electrospray ionization mass spectrometry data, while the absolute configurations were established using the modified Mosher's method in association with electronic circular dichroism spectra. Graphostrin A (1) is a novel chlorinated polyketide derivate bearing an oxazole moiety. All isolates were tested for antifood allergic bioactivities in immunoglobulin E-mediated rat basophilic leukemia-2H3 cells. Reticulol (10) significantly decreased the rates of degranulation and histamine release with IC50 values of 13.5 and 13.7 µM, respectively, suggesting reticulol could be a potential antifood allergic medicine.

Spirograterpene A, a Tetracyclic Spiro-Diterpene with a Fused 5/5/5/5 Ring System from the Deep-Sea-Derived Fungus Penicillium granulatum MCCC 3A00475.

A novel spiro-tetracyclic diterpene, spirograterpene A (1), was isolated from the deep-sea-derived fungus Penicillium granulatum MCCC 3A00475, together with two biosynthetically related cyclopianes, conidiogenone I (2) and conidiogenone C (3). The relative configuration of 1 was elucidated by extensive spectroscopic analyses, and the absolute structure was established by the modified Mosher's method. Compound 1 is the second example of a diterpene featuring a 5/5/5/5 spirocyclic carbon skeleton. It showed modest antiallergic activity.

Complete genome sequence of a giant Vibrio bacteriophage VH7D.

A Vibrio sp. lytic phage VH7D was isolated from seawater of an abalone farm in Xiamen, China. The phage was capable of lysing Vibrio rotiferianus DSM 17186(T) and Vibrio harveyi DSM 19623(T). The complete genome of this phage consists of 246,964 nucleotides with a GC content of 41.31%, which characterized it as a giant vibriophage. Here we report the complete genome sequence and major findings from the genomic annotation.

Spatial distribution and abundance of ammonia-oxidizing microorganisms in deep-sea sediments of the Pacific Ocean.

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is performed by nitrifying microbes including ammonia-oxidizing bacteria (AOB) and archaea (AOA). In the current study, the phylogenetic diversity and abundance of AOB and AOA in deep-sea sediments of the Pacific Ocean were investigated using ammonia monooxygenase subunit A (amoA) coding genes as molecular markers. The study uncovered 3 AOB unique operational taxonomic units (OTUs, defined at sequence groups that differ by ≤5 %), which indicates lower diversity than AOA (13 OTUs obtained). All AOB amoA gene sequences were phylogenetically related to amoA sequences similar to those found in marine Nitrosospira species, and all AOA amoA gene sequences were affiliated with the marine sediment clade. Quantitative PCR revealed similar archaeal amoA gene abundances [1.68 × 10(5)-1.89 × 10(6) copies/g sediment (wet weight)] among different sites. Bacterial amoA gene abundances ranged from 5.28 × 10(3) to 2.29 × 10(6) copies/g sediment (wet weight). The AOA/AOB amoA gene abundance ratios ranged from 0.012 to 162 and were negatively correlated with total C and C/N ratio. These results suggest that organic loading may be a key factor regulating the relative abundance of AOA and AOB in deep-sea environments of the Pacific Ocean.

High fungal diversity and abundance recovered in the deep-sea sediments of the Pacific Ocean.

Knowledge about the presence and ecological significance of bacteria and archaea in the deep-sea environments has been well recognized, but the eukaryotic microorganisms, such as fungi, have rarely been reported. The present study investigated the composition and abundance of fungal community in the deep-sea sediments of the Pacific Ocean. In this study, a total of 1,947 internal transcribed spacer (ITS) regions of fungal rRNA gene clones were recovered from five sediment samples at the Pacific Ocean (water depths ranging from 5,017 to 6,986 m) using three different PCR primer sets. There were 16, 17, and 15 different operational taxonomic units (OTUs) identified from fungal-universal, Ascomycota-, and Basidiomycota-specific clone libraries, respectively. Majority of the recovered sequences belonged to diverse phylotypes of Ascomycota (25 phylotypes) and Basidiomycota (18 phylotypes). The multiple primer approach totally recovered 27 phylotypes which showed low similarities (≤97 %) with available fungal sequences in the GenBank, suggesting possible new fungal taxa occurring in the deep-sea environments or belonging to taxa not represented in the GenBank. Our results also recovered high fungal LSU rRNA gene copy numbers (3.52 × 10(6) to 5.23 × 10(7)copies/g wet sediment) from the Pacific Ocean sediment samples, suggesting that the fungi might be involved in important ecological functions in the deep-sea environments.

Bacteria dominate the ammonia-oxidizing community in a hydrothermal vent site at the Mid-Atlantic Ridge of the South Atlantic Ocean.

Ammonia oxidation is the first and rate-limiting step of nitrification, which is carried out by two groups of microorganisms: ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). In this study, diversity and abundance of AOB and AOA were investigated in five rock samples from a deep-sea hydrothermal vent site at the Mid-Atlantic Ridge (MAR) of the South Atlantic Ocean. Both bacterial and archaeal ammonia monooxygenase subunit A (amoA) gene sequences obtained in this study were closely related to the sequences retrieved from deep-sea environments, indicating that AOB and AOA in this hydrothermal vent site showed typical deep ocean features. AOA were more diverse but less abundant than AOB. The ratios of AOA/AOB amoA gene abundance ranged from 1/3893 to 1/242 in all investigate samples, indicating that bacteria may be the major members responding to the aerobic ammonia oxidation in this hydrothermal vent site. Furthermore, diversity and abundance of AOA and AOB were significantly correlated with the contents of total nitrogen and total sulfur in investigated samples, suggesting that these two environmental factors exert strong influences on distribution of ammonia oxidizers in deep-sea hydrothermal vent environment.

Pseudoalteromonas xiamenensis sp. nov., a marine bacterium isolated from coastal surface seawater.

A Gram-negative, oxidase- and catalase-positive, rod-shaped, non-spore-forming, motile, aerobic bacterium, designated Y2(T), was isolated from surface seawater of Yundang Lake, Xiamen, China. The strain was able to grow in the presence of 0.5-6.0% NaCl (optimum 1.0-1.5%), at pH 5-10 (optimum pH 8) and at 10-40 °C (optimum 25 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Y2(T) belongs to the genus Pseudoalteromonas, with the highest sequence similarity of 94.9% to Pseudoalteromonas tunicata D2(T); within the genus Pseudoalteromonas, it showed the lowest similarity of 92.8% to Pseudoalteromonas denitrificans ATCC 43337(T). The G+C content of the chromosomal DNA of strain Y2(T) was 45.1 mol%. The predominant fatty acids were summed feature 3 (C(16 : 1)ω6c and/or C(16 : 1)ω7c), C(16 : 0), C(12 : 0) 3-OH and summed feature 8 (C(18 : 1)ω6c and/or C(18 : 1)ω7c). The only respiratory quinone detected was Q-8. Based on the phylogenetic and phenotypic characteristics, strain Y2(T) represents a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas xiamenensis sp. nov. is proposed; the type strain is Y2(T) ( = CGMCC 1.12157(T) = JCM 18779(T)).