Chemolithoautotrophic diazotrophs dominate dark nitrogen fixation in mangrove sediments.

Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. So far chemolithoautotrophic bacteria are widely recognized as the principal diazotrophs in oligotrophic marine and terrestrial ecosystems. However, the contribution of chemolithoautotrophs to nitrogen fixation in organic-rich habitats remains unclear. Here, we utilized metagenomic and metatranscriptomic approaches integrated with cultivation assays to investigate the diversity, distribution, and activity of diazotrophs residing in Zhangzhou mangrove sediments. Physicochemical assays show that the studied mangrove sediments are typical carbon-rich, sulfur-rich, nitrogen-limited, and low-redox marine ecosystems. These sediments host a wide phylogenetic variety of nitrogenase genes, including groups I-III and VII-VIII. Unexpectedly diverse chemolithoautotrophic taxa including Campylobacteria, Gammaproteobacteria, Zetaproteobacteria, and Thermodesulfovibrionia are the predominant and active nitrogen fixers in the 0-18 cm sediment layer. In contrast, the 18-20 cm layer is dominated by active diazotrophs from the chemolithoautotrophic taxa Desulfobacterota and Halobacteriota. Further analysis of MAGs show that the main chemolithoautotrophs can fix nitrogen by coupling the oxidation of hydrogen, reduced sulfur, and iron, with the reduction of oxygen, nitrate, and sulfur. Culture experiments further demonstrate that members of chemolithoautotrophic Campylobacteria have the nitrogen-fixing capacity driven by hydrogen and sulfur oxidation. Activity measurements confirm that the diazotrophs inhabiting mangrove sediments preferentially drain energy from diverse reduced inorganic compounds other than from organics. Overall, our results suggest that chemolithoautotrophs rather than heterotrophs are dominant nitrogen fixers in mangrove sediments. This study underscores the significance of chemolithoautotrophs in carbon-dominant ecosystems.

Arcobacteraceae are ubiquitous mixotrophic bacteria playing important roles in carbon, nitrogen, and sulfur cycling in global oceans.

Mixotrophy is an important trophic strategy for bacterial survival in the ocean. However, the global relevance and identity of the major mixotrophic taxa remain largely elusive. Here, we combined phylogenetic, metagenomic, and metatranscriptomic analyses to characterize ubiquitous Arcobacteraceae based on our deep-sea in situ incubations and the global data. The phylogenomic tree of Arcobacteraceae is divided into three large clades, among which members of clades A and B are almost all from terrestrial environments, while those of clade C are widely distributed in various marine habitats in addition to some terrestrial origins. All clades harbor genes putatively involved in chitin degradation, sulfide oxidation, hydrogen oxidation, thiosulfate oxidation, denitrification, dissimilatory nitrate reduction to ammonium, microaerophilic respiration, and metal (iron/manganese) reduction. Additionally, in clade C, more unique pathways were retrieved, including thiosulfate disproportionation, ethanol fermentation, methane oxidation, fatty acid oxidation, cobalamin synthesis, and dissimilatory reductions of sulfate, perchlorate, and arsenate. Within this clade, two mixotrophic Candidatus genera represented by UBA6211 and CAIJNA01 harbor genes putatively involved in the reverse tricarboxylic acid pathway for carbon fixation. Moreover, the metatranscriptomic data in deep-sea in situ incubations indicated that the latter genus is a mixotroph that conducts carbon fixation by coupling sulfur oxidation and denitrification and metabolizing organic matter. Furthermore, global metatranscriptomic data confirmed the ubiquitous distribution and global relevance of Arcobacteraceae in the expression of those corresponding genes across all oceanic regions and depths. Overall, these results highlight the contribution of previously unrecognized Arcobacteraceae to carbon, nitrogen, and sulfur cycling in global oceans.IMPORTANCEMarine microorganisms exert a profound influence on global carbon cycling and ecological relationships. Mixotrophy, characterized by the simultaneous utilization of both autotrophic and heterotrophic nutrition, has a significant impact on the global carbon cycling. This report characterizes a group of uncultivated bacteria Arcobacteraceae that thrived on the "hot time" of bulky particulate organic matter and exhibited mixotrophic strategy during the in situ organic mineralization. Compared with clades A and B, more unique metabolic pathways were retrieved in clade C, including the reverse tricarboxylic acid pathway for carbon fixation, thiosulfate disproportionation, methane oxidation, and fatty acid oxidation. Global metatranscriptomic data from the Tara Oceans expeditions confirmed the ubiquitous distribution and extensive transcriptional activity of Arcobacteraceae with the expression of genes putatively involved in carbon fixation, methane oxidation, multiple sulfur compound oxidation, and denitrification across all oceanic regions and depths.

Cytotoxic Pentaketide-Sesquiterpenes from the Marine-Derived Fungus Talaromyces variabilis M22734.

Talaromyces, a filamentous fungus widely distributed across terrestrial and marine environments, can produce a diverse array of natural products, including alkaloids, polyketones, and polyketide-terpenoids. Among these, chrodrimanins represented a typical class of natural products. In this study, we isolated three previously undescribed pentaketide-sesquiterpenes, 8,9-epi-chrodrimanins (1-3), along with eight known compounds (4-11). The structures of compounds 1-3 were elucidated using nuclear magnetic resonance (NMR) and mass spectrometry (MS), while their absolute configurations were determined through X-ray crystallography and electronic circular dichroism (ECD) computations. The biosynthetic pathways of compounds 1-3 initiate with 6-hydroxymellein and involve multiple stages of isoprenylation, cyclization, oxidation, and acetylation. We selected four strains of gastrointestinal cancer cells for activity evaluation. We found that compound 3 selectively inhibited MKN-45, whereas compounds 1 and 2 exhibited no significant inhibitory activity against the four cell lines. These findings suggested that 8,9-epi-chrodrimanins could serve as scaffold compounds for further structural modifications, potentially leading to the development of targeted therapies for gastric cancer.

Evolution and adaptation of terrestrial plant-associated Plantibacter species into remote marine environments.

Microbes are thought to be distributed and circulated around the world, but the connection between marine and terrestrial microbiomes remains largely unknown. We use Plantibacter, a representative genus associated with plants, as our research model to investigate the global distribution and adaptation of plant-related bacteria in plant-free environments, particularly in the remote Southern Ocean and the deep Atlantic Ocean. The marine isolates and their plant-associated relatives shared over 98% whole-genome average nucleotide identity (ANI), indicating recent divergence and ongoing speciation from plant-related niches to marine environments. Comparative genomics revealed that the marine strains acquired new genes via horizontal gene transfer from non-Plantibacter species and refined existing genes through positive selection to improve adaptation to new habitats. Meanwhile, marine strains retained the ability to interact with plants, such as modifying root system architecture and promoting germination. Furthermore, Plantibacter species were found to be widely distributed in marine environments, revealing an unrecognized phenomenon that plant-associated microbiomes have colonized the ocean, which could serve as a reservoir for plant growth-promoting microbes. This study demonstrates the presence of an active reservoir of terrestrial plant growth-promoting bacteria in remote marine systems and advances our understanding of the microbial connections between plant-associated and plant-free environments at the genome level.

Genome-based analysis of the family Paracoccaceae and description of Ostreiculturibacter nitratireducens gen. nov., sp. nov., isolated from an oyster farm on a tidal flat.

Two bacterial strains, designated FR2A1T and MT2-5-38, were isolated from the surface sediments of an oyster farm on a tidal flat in Quanzhou Bay, China. Both strains were Gram-stain-negative, rod-shaped, aerobic, catalase-positive, and oxidase-positive. The 16S rRNA gene sequences of the two strains were 100% identical and had the highest similarity (97.1%) with Phaeovulum vinaykumarii JA123T. The average nucleotide identity (ANI) value and digital DNA-DNA hybridization (DDH) value indicated that the two strains belonged to a single species. Gene annotation revealed that the two strains contained a gene cluster for nitrate reduction and a gene cluster for sulfur oxidation, indicating a possible role in N and S cycling in the tidal flat sediment. The phylogeny inferred from the 16S rRNA gene and 120 conserved proteins indicated that the two strains formed a distinct monophyletic clade within the family Paracoccaceae. The respiratory quinone was Q-10. The major fatty acids consisted of summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C18:0. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, and several unidentified phospholipids. Based on the above characteristics, strains FR2A1T and MT2-5-38 represent a novel genus and a novel species, for which we propose the name Ostreiculturibacter nitratireducens gen. nov., sp. nov. The type strain is FR2A1T (=MCCC 1K08809T = KCTC 8317T). Phylogenomic analysis of 1,606 high-quality genomes of the family Paracoccaceae, including type strains, non-type strains, and uncultivated bacteria, was performed using the Genome Taxonomic Database Toolkit (GTDB-Tk), and the average amino acid identity (AAI) value of the phylogenetic clade was estimated. We found that 35 species of the family Paracoccaceae needed re-classification, and an AAI value of 70% was chosen as the genus boundary within the family Paracoccaceae.

Disentangling associations between complex traits and cell types with seismic.

Integrating single-cell RNA sequencing (scRNA-seq) with Genome-Wide Association Studies (GWAS) can help reveal GWAS-associated cell types, furthering our understanding of the cell-type-specific biological processes underlying complex traits and disease. However, current methods have technical limitations that hinder them from making systematic, scalable, interpretable disease-cell-type associations. In order to rapidly and accurately pinpoint associations, we develop a novel framework, seismic, which characterizes cell types using a new specificity score. We compare seismic with alternative methods across over 1,000 cell type characterizations at different granularities and 28 traits, demonstrating that seismic both corroborates findings and identifies trait-relevant cell groups which are not apparent through other methodologies. Furthermore, as part of the seismic framework, the specific genes driving cell type-trait associations can easily be accessed and analyzed, enabling further biological insights. The advantages of seismic are particularly salient in neurodegenerative diseases such as Parkinson's and Alzheimer's, where disease pathology has not only cell-specific manifestations, but also brain region-specific differences. Interestingly, a case study of Alzheimer's disease reveals the importance of considering GWAS endpoints, as studies relying on clinical diagnoses consistently identify microglial associations, while GWAS with a tau biomarker endpoint reveals neuronal associations. In general, seismic is a computationally efficient, powerful, and interpretable approach for identifying associations between complex traits and cell type-specific expression.

Isolation and Characterization of Paracoccus maritimus sp. nov., from Intertidal Sediment.

A novel Paracoccus-related strain, designated YLB-12T, was isolated from a sediment sample from the tidal zone of Shapowei Port, Xiamen, Fujian Province, PR China. The novel strain is a Gram-stain-negative, short, rod-shaped, nonmotile, catalase- and oxidase-positive strain that grows at 10-37 °C and pH 5.0-9.0 in the presence of 0-12.0% (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain belongs to the genus Paracoccus and that its highest sequence similarity was to Paracoccus homiensis DD-R11T (98.5%), followed by Paracoccus zeaxanthinifaciens ATCC 21588T (97.4%), Paracoccus rhizosphaerae LMG 26205T (97.2%), Paracoccus beibuensis CGMCC 1.7295T (97.1%) and Paracoccus halotolerans CFH 90064T (97.0%). The DNA‒DNA hybridization values between strain YLB-12T and the five closely related type strains ranged from 20.4 to 22.4%. The genomic G+C content of strain YLB-12T was 63.7%. In addition to diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol, the polar lipids of the strain YLB-12T also consisted of an unidentified glycolipid and four unidentified polar lipids. The cells contained summed feature 8 (C18: 1ω6c /C18: 1ω7c, 62.7%) as the major cellular fatty acid and ubiquinone-10 as the predominant menaquinone. On the basis of its phenotypic and genotypic characteristics, strain YLB-12T represents a novel species within the genus Paracoccus, for which the name Paracoccus maritimus sp. nov. is proposed. The type strain was YLB-12T (= MCCC 1A17213T = KCTC 82197T).

Metabolomics and Molecular Networking-Guided Screening of Bacillus-Derived Bioactive Compounds Against a Highly Lethal Vibrio Species.

Microorganisms are important sources of bioactive natural products. However, the complexity of microbial metabolites and the low abundance of active compounds render the isolation and purification process laborious and inefficient. During our search for active substances capable of inhibiting the newly discovered highly lethal Vibrio strain vp-HL, we found that the fermentation broth of multiple Bacillus strains exhibited antibacterial activity. However, the substances responsible for the activity remained unclear. Metabolomics, molecular networking (MN), and the Structural similarity Network Annotation Platform for Mass Spectrometry (SNAP-MS) were employed in conjunction with bioactivity screening to predict the antibacterial compounds from Bacillus strains. The analysis of fractions, and their isolation, NMR-based annotation, and bioactivity evaluation of an amicoumacin compound partially confirmed the prediction from these statistical analyses. This work presents the potential of marine Bacillus in producing active substances against Vibrio species. Additionally, it highlighted the significance and feasibility of metabolomics and MN in the dereplication of compounds and the determination of isolation targets.

A Semisynthesis Platform for the Efficient Production and Exploration of Didemnin-Based Drugs.

Plitidepsin (or dehydrodidemnin B), an approved anticancer drug, belongs to the didemnin family of cyclic depsipeptides, which are found in limited quantities in marine tunicate extracts. Herein, we introduce a new approach that integrates microbial and chemical synthesis to generate plitidepsin and its analogues. We screened a Tistrella strain library to identify a potent didemnin B producer, and then introduced a second copy of the didemnin biosynthetic gene cluster into its genome, resulting in a didemnin B titer of approximately 75 mg/L. Next, we developed two straightforward chemical strategies to convert didemnin B into plitidepsin, one of which involved a one-step synthetic route giving over 90 % overall yield. Furthermore, we synthesized 13 new didemnin derivatives and three didemnin probes, enabling research into structure-activity relationships and interactions between didemnin and proteins. Our study highlights the synergistic potential of biosynthesis and chemical synthesis in overcoming the challenge of producing complex natural products sustainably and at scale.

Pseudodonghicola flavimaris sp. nov. and Sedimentitalea xiamensis sp. nov., two novel species belonging to the family Roseobacteraceae.

Two Gram-stain-negative, chemoheterotrophic, aerobic bacteria, designated IC7T and JM2-8T, were isolated from seawater of the Yellow Sea of China and rhizosphere soil of mangroves in Xiamen, Fujian, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that these two novel strains belonged to the family Roseobacteraceae. Strain IC7T formed a coherent lineage within the genus Pseudodonghicola, showing 98.05 % 16S rRNA gene sequence similarity to Pseudodonghicola xiamenensis Y-2T. Strain JM2-8T was most closely related to members of the genus Sedimentitalea, showing 96.51 and 96.73 % 16S rRNA gene sequence similarities to Sedimentitalea nanhaiensis NH52FT and Sedimentitalea todarodis KHS03T, respectively. The two novel strains contained Q-10 as the major quinone, and phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol and phosphatidylcholine as the principal polar lipids. The main fatty acid of strain IC7T was C19 : 0 cyclo ω8c, while the fatty acid profile JM2-8T was dominated by summed feature 8 containing C18 : 1 ω7c and/or C18 : 1 ω6c. The average nucleotide identity and digital DNA-DNA hybridization values between these two novel isolates and their closely related species were below the cut-off values of 95-96 and 70 %, respectively. The combined genotypic and phenotypic data show that strain IC7T represents a novel species of the genus Pseudodonghicola, for which the name Pseudodonghicola flavimaris sp. nov. is proposed, with the type strain IC7T (=MCCC 1A02763T=KCTC 82844T), and strain JM2-8T represents a novel species of the genus Sedimentitalea, for which the name Sedimentitalea xiamensis sp. nov. is proposed, with the type strain JM2-8T (=MCCC 1A17756T=KCTC 82846T).

Sulfurovum mangrovi sp. nov., an obligately chemolithoautotrophic, hydrogen-oxidizing bacterium isolated from coastal marine sediments.

A novel mesophilic, chemolithoautotrophic, hydrogen-oxidizing bacterium, designated strain ST1-3T, was isolated from mud sediment samples collected from mangroves in Jiulong River estuary. The cells were Gram-stain-negative, non-motile and rod-shaped. The temperature, pH and salinity ranges for growth of strain ST1-3T were 4-45 °C (optimum, 35 °C), pH 5.0-8.5 (optimum, pH 7.0) and 0-8.0 % (w/v) NaCl (optimum, 4.0 %). The isolate was an obligate chemolithoautotroph capable of growth using hydrogen as the only energy source, and molecular oxygen, thiosulphate and elemental sulphur as electron acceptors. The major cellular fatty acids of strain ST1-3T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c). The major polar lipids were phosphatidylethanolamine, phosphatidyldimethyl ethanolamine and phosphatidylglycerol. The respiratory quinone was menaquinone-6. The genomic DNA G+C content was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and core genes showed that the novel isolate belonged to the genus Sulfurovum and was most closely related to Sulfurovum lithotrophicum 42BKTT (94.7 % sequence identity). The average nucleotide identity and digital DNA-DNA hybridization values between ST1-3T and S. lithotrophicum 42BKTT were 74.6 and 16.3 %, respectively. On the basis of the phenotypic, phylogenetic and genomic data presented here, strain ST1-3T represents a novel species of the genus Sulfurovum, for which the name Sulfurovum mangrovi sp. nov. is proposed, with the type strain ST1-3T (=MCCC M25234T=KCTC 25639T).

Mangrovimonas aestuarii sp. nov., isolated from tidal flat sediment.

A Gram-stain-negative, rod-shaped and light yellow-pigmented strain designated MBT5T was isolated from tidal flat sediment of an oyster farming area in Quanzhou Bay, PR China. Catalase activity and oxidase activity were positive. Flexirubin-type pigment was absent. Growth was observed at 10-40 °C (optimum, 35 °C), pH 6-9 (optimum, pH 7), and with 1-7 % NaCl (optimum, 2 %, w/v). The 16S rRNA gene of strain MBT5T had maximum sequence similarity values with Meridianimaribacter flavus NH57NT, Mangrovimonas yunxiaonensis LYYY01T and Mangrovimonas futianensis AS18T of 95.6, 95.4 and 94.9 %, respectively. Phylogenetic analysis based on 16S rRNA gene sequences and 120 conserved concatenated proteins indicated that strain MBT5T was affiliated to the genus Mangrovimonas and formed a distinct monophyletic branch. The digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values between strain MBT5T and the type strains of Mangrovimonas were estimated to be 17.3-18.7 %, 70.9-71.5 % and 66.4-68.2 %, respectively. The respiratory quinone was menaquinone-6. The major fatty acids were iso-C15 : 0 and iso-C15 : 1 G. The draft genome size was 2 952 053 bp with a DNA G+C content of 36.5 %. Based on phenotypic, physiological, phylogenetic and genomic data, together with chemotaxonomic characteristics, strain MBT5T represents a novel species, for which the name Mangrovimonas aestuarii sp. nov. is proposed. The type strain is MBT5T (=MCCC 1K06186T=KCTC 92888T=GDMCC 1.3851T).

Bacillus changyiensis sp. nov., isolated from coastal sediment.

Two Gram-stain-positive, facultatively anaerobic, motile, endospore-forming, rod-shaped bacteria, designated CLL-3-40T and CLL-7-23, were isolated from coastal sediment sampled in Changyi, Shandong Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains were related to the genus Bacillus and close to six type strains of species within the Bacillus licheniformis group. In phenotypic characterization tests, strain CLL-3-40T could grow at 15-50 °C (optimum, 37 °C) and in media with pH 5-9 (optimum pH 7.0), and tolerate up to 12 % (w/v) NaCl. The fermentation broth supernatant extracted by ethyl acetate of strain CLL-3-40T could inhibit aquaculture pathogenic vibrios. The predominant cellular fatty acids of strain CLL-3-40T were anteiso-C15 : 0 (30.7 %) and iso-C15 : 0 (31.5 %); the peptidoglycan from cell-wall contained meso-diaminopimelic acid; the predominant quinone was menaquinone 7; and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and two unidentified phospholipids. The digital DNA-DNA hybridization values and average nucleotide identities among strains CLL-3-40T and CLL-7-23 and their close type strains were less than 21.9 and 48.4 %, respectively, thereby indicating that strain CLL-3-40T should represent a novel species of the genus Bacillus. The genomic DNA G+C contents were 38.4 mol% in strain CLL-3-40T and 38.3 mol% in strain CLL-7-23. The 12 biosynthetic gene clusters of strain CLL-3-40T were predicted based on results from the online server antiSMASH. Based upon the consensus of phenotypic and genotypic results, strain CLL-3-40T should be classified as representing a novel species of the genus Bacillus, for which the name Bacillus changyiensis sp. nov. is proposed. The type strain is CLL-3-40T (= MCCC 1A14857T=JCM 35755T).

Galbibacter pacificus sp. nov., isolated from surface seawater of the western Pacific Ocean and transfer of Joostella marina to the genus Galbibacter as Galbibacter orientalis nom. nov. and emended description of the genus Galbibacter.

Two Gram-stain-negative, non-motile, non-spore-forming, strictly aerobic and rod-shaped bacterial strains, CMA-7T and CAA-3, were isolated from surface seawater samples collected from the western Pacific Ocean. Phylogeny of 16S rRNA gene sequences indicated they were related to the genera Galbibacter and Joostella and shared 95.1, 90.9 and 90.8% sequence similarity with G. mesophilus Mok-17T, J. marina DSM 19592T and G. marinus ck-I2-15T, respectively. Phylogenomic analysis showed that the two strains, together with the members of the genera Galbibacter and Joostella, formed a monophyletic clade that could also be considered a monophyletic taxon. This distinctiveness was supported by amino acid identity and percentage of conserved proteins indices, phenotypic and chemotaxonomic characteristics and comparative genomics analysis. Digital DNA‒DNA hybridization values and average nucleotide identities between the two strains and their closest relatives were 18.0-20.8 % and 77.7-79.3 %, respectively. The principal fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, Summed Feature 3 (C16 : 1 ω7c/C16 : 1 ω6c or C16 : 1 ω6c/C16 : 1 ω7c), Summed Feature 9 (iso-C17 : 1 ω9c or C16 : 0 10-methyl), and C15 : 0 3-OH. The predominant respiratory quinone was MK-6. The polar lipids were phosphatidylethanolamine, aminolipid, aminophospholipid, phospholipid, phosphoglycolipid, glycolipid and unknown polar lipid. The genomic DNA G+C content of strains CMA-7T and CAA-3 was both 38.4 mol%. Genomic analysis indicated they have the potential to degrade cellulose and chitin. Based on the polyphasic evidence presented in this study, the two strains represent a novel species within the genus Galbibacter, for which the name Galbibacter pacificus sp. nov. is proposed. The type strain is CMA-7T (=MCCC M28999T = KCTC 92588T). Moreover, the transfer of Joostella marina to the genus Galbibacter as Galbibacter orientalis nom. nov. (type strain En5T = KCTC 12518T = DSM 19592T=CGMCC 1.6973T) is also proposed.

Characterization and Comparative Genomic Analysis of a Deep-Sea Bacillus Phage Reveal a Novel Genus.

As the most abundant biological entities, viruses are the major players in marine ecosystems. However, our knowledge on virus diversity and virus-host interactions in the deep sea remains very limited. In this study, vB_BteM-A9Y, a novel bacteriophage infecting Bacillus tequilensis, was isolated from deep-sea sediments in the South China Sea. vB_BteM-A9Y has a hexametric head and a long, complex contractile tail, which are typical features of myophages. vB_BteM-A9Y initiated host lysis at 60 min post infection with a burst size of 75 PFU/cell. The phage genome comprises 38,634 base pairs and encodes 54 predicted open reading frames (ORFs), of which 27 ORFs can be functionally annotated by homology analysis. Interestingly, abundant ORFs involved in DNA damage repair were identified in the phage genome, suggesting that vB_BteM-A9Y encodes multiple pathways for DNA damage repair, which may help to maintain the stability of the host/phage genome. A BLASTn search of the whole genome sequence of vB_BteM-A9Y against the GenBank revealed no existing homolog. Consistently, a phylogenomic tree and proteome-based phylogenetic tree analysis showed that vB_BteM-A9Y formed a unique branch. Further comparative analysis of genomic nucleotide similarity and ORF homology of vB_BteM-A9Y with its mostly related phages showed that the intergenomic similarity between vB_BteM-A9Y and these phages was 0-33.2%. Collectively, based on the comprehensive morphological, phylogenetic, and comparative genomic analysis, we propose that vB_BteM-A9Y belongs to a novel genus under Caudoviricetes. Therefore, our study will increase our knowledge on deep-sea virus diversity and virus-host interactions, as well as expanding our knowledge on phage taxonomy.

Pseudophaeobacter profundi sp. nov., isolated from the Western Pacific Ocean.

A novel Gram-stain-negative, facultatively anaerobic and heterotrophic bacterium, designated strain ZH257T, was isolated from in situ enrichment samples incubated on the seamount floor of the Western Pacific Ocean. Cells were rod-shaped, oxidase- and catalase- positive, and motile by means of polar flagella. Strain ZH257T grew at 4-37 °C (optimum, 28-32 °C), pH 6.0-9.0 (optimum, pH 7.0) and with 2.0-9.0 % (w/v) NaCl (optimum, 3.0-4.0 %). Strain ZH257T was most closely related to members of the genus Pseudophaeobacter, sharing 99.13, 98.27 and 96.89 % 16S rRNA gene sequence identities with Pseudophaeobacter flagellatus GDMCC 1.2988T, Pseudophaeobacter arcticus DSM 23566T and Pseudophaeobacter leonis DSM 25627T, respectively. The DNA G+C content was 59.2 mol%. The estimated average nucleotide identity and digital DNA-DNA hybridization values between strain ZH257T and its closely related species were 79.61-93.04 % and 23.10-50.20 %, respectively. Strain ZH257T harboured complete denitrification and nitrate assimilation pathways. Strain ZH257T contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) as major fatty acids (>5 %), and Q-10 as the major respiratory quinone. The polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and four unidentified lipids. The combined phenotypic, genotypic and chemotaxonomic data showed that strain ZH257T represents a novel species of the genus Pseudophaeobacter, for which the name Pseudophaeobacter profundi sp. nov. is proposed, with the type strain ZH257T (=MCCC M29024T=KACC 23147T).

Genomic and metabolic insights into the first host-associated isolate of Psychrilyobacter.

Although gut bacteria are vital to their hosts, few studies have focused on marine animals. Psychrilyobacter is frequently related to various marine animals, but its interaction with host remains unknown due to the lack of host-associated isolate or genomic information. Here, we combined cultivation-independent and cultivation-dependent methods to uncover the potential roles of Psychrilyobacter in the host abalone. The high-throughput sequencing and literature compiling results indicated that Psychrilyobacter is widely distributed in marine and terrestrial ecosystems with both host-associated and free-living lifestyles, but with a strong niche preference in the guts of marine invertebrates, especially abalone. By in vitro enrichment that mimicked the gut inner environment, the first host-related pure culture of Psychrilyobacter was isolated from the abalone intestine. Phylogenetic, physiological, and biochemical characterizations suggested that it represents a novel species named Psychrilyobacter haliotis B1. Carbohydrate utilization experiments and genomic evidence indicated that B1 can utilize diverse host-food-related monosaccharides and disaccharides but not polysaccharides, implying its potential role in the downstream fermentation instead of the upstream food degradation in the gut. Particularly, this strain showed potential to colonize the gut and benefit the host via different strategies, such as the short-chain fatty acids generation by fermenting peptides and/or amino acids, and the putative production of diverse vitamins and antibiotics to support the host growth and antipathogenicity. To our knowledge, strain B1 represents the first host-related pure culture of Psychrilyobacter; genomic and metabolic evidence showed some beneficial characteristics of the dominant gut anaerobe to the host. IMPORTANCE Psychrilyobacter is a globally distributed bacterial genus and with an inhabiting preference for guts of marine invertebrates. Due to the difficulty of cultivation and the limited genomic information, its role in host remains largely unknown. We isolated the first host-associated Psychrilyobacter species from abalone gut and uncovered its functional potential to the host through different mechanisms. Our findings provide some insights into the understanding of host-microbe interactions on a core taxon with the marine invertebrates, and the isolate may have an application potential in the protection of marine animals.

Coraliomargarita parva sp. nov., isolated from mangrove sediment and genome-based analysis of the class Opitutae revealed five novel families: Coraliomargaritaceae fam. nov., Pelagicoccaceae fam. nov., Cerasicoccaeae fam. nov., Oceanipulchritudinaceae fam. nov., and Alterococcaeae fam. nov.

Members of the class Opitutae are widely distributed in various environments such as rice paddy soil, freshwater lakes, seawater, marine sediment, and invertebrate digestive tracts. The class currently consists of two orders, Opitutales and Puniceicoccales, represented by the families Opitutaceae and Puniceicoccaceae, respectively, which are primarily delineated on the basis of 16S rRNA gene sequences and limited phenotypic characterizations of a few type strains. The scarcity of 16S rRNA gene and genome sequences generated from the type strains of the class Opitutae constrained our understanding of the ecological distribution and adequate resolution of its taxonomy. Here, an Opitutae strain designated WMMB3T, isolated from a mangrove sediment, was subjected to taxonomic characterization. The 16S rRNA gene of strain WMMB3T shared high sequence similarities with Coraliomargarita akajimensis DSM 45221T and C. sinensis WN38T of 96.1 and 95.9%, respectively. Phylogenetic analysis suggested that strain WMMB3T formed a monophyletic branch affiliated to the genus Coraliomargarita. The average nucleotide identity (ANI) values, digital DNA-DNA hybridization (dDDH) values and average amino acid identity (AAI) values of strain WMMB3T compared between Coraliomargarita members were 71.8-72.5, 20.7, and 68.2-68.7%, respectively, indicating that strain WMMB3T represented a novel species of Coraliomargarita. The genome of strain WMMB3T was 4.5 Mbp with a DNA G + C content of 56.0%. The respiratory quinone was menaquinone-7. The major fatty acids were iso-C14:0, and C18:1ω9c. Based on genomic, phenotypic, and chemotaxonomic characterizations, strain WMMB3T represents a novel species, and Coraliomargarita parva sp. nov. is proposed. Additionally, the phylogenomic analysis of more than 500 genomes of the class Opitutae, encompassing a majority of uncultivated bacteria and a few type strains, was performed using the Genome Taxonomic Database toolkit (GTDB-Tk) to present adequate resolution of the taxonomy. Combined with 16S rRNA gene sequence phylogeny and genomic relatedness, five novel families retrieved mainly from marine habitats were proposed: Coraliomargaritaceae fam. nov., Pelagicoccaceae fam. nov., Cerasicoccaeae fam. nov., Oceanipulchritudinaceae fam. nov., and Alterococcaeae fam. nov. AAI values of 58-60% could be considered as the boundary to delineate families of the class Opitutae. This study provided a new taxonomic framework of the class Opitutae based on the genomic data.

Thermomonas mangrovi sp. nov., isolated from soil of a mangrove nature reserve.

A Gram-stain-negative, non-motile, aerobic and ovoid-rod-shaped bacterial strain, designated as 2C3345T, was isolated from soil of a mangrove nature reserve in Shenzhen, PR China and its taxonomic position was investigated. The 16S rRNA gene sequence of strain 2C3345T exhibited the highest similarity value to that of the type strains Thermomonas aquatica NBRC 113114T (98.4 %), Thermomonas carbonis KCTC 42013T (98.1 %), Thermomonas brevis DSM 15422T (98.0 %) and Thermomonas haemolytica DSM 13605T (97.9 %). Strain 2C3345T grew optimally at 28-30 °C, pH 7.0 and without NaCl. The predominant ubiquinone in 2C3345T was identified as Q-8. The major fatty acids of 2C3345T were iso-C15 : 0, iso-C16 : 0 and summed feature 9 (is0-C17:1ω9c and/or 10-methyl C16:0). The major polar lipids of 2C3345T were phosphatidylcholine (PC), phosphatidylglycerol (PG), diphosphatidglycerol (DPG), phosphatidylethanolamine (PE), an unidentified phospholipid, an unidentified aminolipid and two unidentified lipids. The DNA G+C content of strain 2C3345T was 69.9 %. The draft genome sequence of 2C3345T included 2 888 645 bp in total (N50=310 730 bp) with a medium read coverage of 388.6×and 21 scaffolds. In silico DNA-DNA hybridisation with type strains of species of the genus Thermomonas showed 24.4, 22.4, 24.1 and 23.2% relatedness to T. aquatica NBRC 113114T, T. carbonis KCTC 42013T, T. brevis DSM 15422T and T. haemolytica DSM 13605T, respectively. And the average nucleotide identity by blast (ANIb) values between 2C3345T and these four reference strains were 81.9, 80.0, 81.2 and 80.6 %, respectively, lower than the 95-96% threshold value for dividing prokaryotic species. On the basis of its phenotypic, chemotaxonomic, phylogenetic and phylogenomic properties, strain 2C3345T is considered to represent a novel species within the genus Thermomonas, for which the name Thermomonas mangrovi sp. nov. is proposed. The type strain is 2C3345T (=KCTC 92730T =MCCC 1K08335T).