Flagellimonas baculiformis sp. nov. and Flagellimonas crocea sp. nov., isolated from surface seawater of the Pacific Ocean.

Two Gram-negative, non-spore-forming, non-motile, non-flagellated bacteria, designated strains D6T and DH64T, were isolated from surface water of the Pacific Ocean. For strain D6T, growth occurred at 10-40 °C, pH 5.5-9.0 and in the presence of 0-8.0 % NaCl (w/v). For strain DH64T, growth occurred at 10-40 °C, pH 5.5-8.5 and in the presence of 0.5-8.0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains D6T and DH64T both belonged to the genera Flagellimonas, with the highest sequence identities to Flagellimonas taeanensis JCM 17757T (98.2 %) and Flagellimonas marinaquae JCM 11811T (98.6 %), respectively. The 16S rRNA gene sequence identity between strains D6T and DH64T was 95.9 %. The average amino acid identity and digital DNA-DNA hybridization values between the two strains and the nearest phylogenetic neighbours were 66.7-93.3 % and 16.1-38.5 %, respectively. The major respiratory quinone of both strains was menaquinone-6. The major polar lipid was phosphatidylethanolamine. The major fatty acids were identified similarly as iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. The genomic G+C contents of strains D6T and DH64T were determined to be 45.5 and 42.6 mol%, respectively. The combined genotypic and phenotypic data show that the strains represent two novel species within genera Flagellimonas, for which the names Flagellimonas baculiformis sp. nov. and Flagellimonas crocea sp. nov. are proposed, with type strains D6T (=MCCC M28982T=KCTC 92604T) and DH64T (=MCCC M28986T=KCTC 92975T).

Qipengyuania benthica sp. nov. and Qipengyuania profundimaris sp. nov., two novel Erythrobacteraceae members isolated from deep-sea environments.

Two Gram-stain-negative, rod-shaped and non-motile strains, designated as DY56-A-20T and G39T, were isolated from deep-sea sediment of the Pacific Ocean and deep-sea seawater of the Indian Ocean, respectively. Strain DY56-A-20T was found to grow at 15-37 °C (optimum, 28 °C), at pH 6.0-10.0 (optimum, pH 6.5-7.0) and in 0.5-6.0 % (w/v) NaCl (optimum, 1.0-2.0 %), while strain G39T was found to grow at 10-42 °C (optimum, 35-40 °C), at pH 5.5-10.0 (optimum, pH 6.5-7.0) and in 0-12.0 % (w/v) NaCl (optimum, 1.0-2.0 %). The 16S rRNA gene sequence identity analysis indicated that strain DY56-A-20T had the highest sequence identity with Qipengyuania marisflavi KEM-5T (97.6 %), while strain G39T displayed the highest sequence identity with Qipengyuania citrea H150T (98.8 %). The phylogenomic reconstruction indicated that both strains formed independent clades within the genus Qipengyuania. The digital DNA-DNA hybridization and average nucleotide identity values between strains DY56-A-20T/G39T and Qipengyuania/Erythrobacter type strains were 17.8-23.8 % and 70.7-81.1 %, respectively, which are below species delineation thresholds. The genome DNA G+C contents were 65.0 and 63.5 mol% for strains DY56-A-20T and G39T, respectively. The predominant cellular fatty acids (>10 %) of strain DY56-A-20T were C17 : 1 ω6c, summed feature 8 and summed feature 3, and the major cellular fatty acids of strain G39T were C17 : 1 ω6c and summed feature 8. The major polar lipids in both strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and an unidentified polar lipid. The only respiratory quinone present in both strains was ubiquinone-10. Based on those genotypic and phenotypic results, the two strains represent two novel species belonging to the genus Qipengyuania, for which the names Qipengyuania benthica sp. nov. and Qipengyuania profundimaris sp. nov. are proposed. The type strain of Q. benthica is DY56-A-20T (=MCCC M27941T=KCTC 92309T), and the type strain of Q. profundimaris is G39T (=MCCC M30353T=KCTC 8208T).

Aerobic Anoxygenic Phototrophic Bacteria in the Marine Environments Revealed by Raman/Fluorescence-Guided Single-Cell Sorting and Targeted Metagenomics.

Aerobic anoxygenic phototrophic bacteria (AAPB) contribute profoundly to the global carbon cycle. However, most AAPB in marine environments are uncultured and at low abundance, hampering the recognition of their functions and molecular mechanisms. In this study, we developed a new culture-independent method to identify and sort AAPB using single-cell Raman/fluorescence spectroscopy. Characteristic Raman and fluorescent bands specific to bacteriochlorophyll a (Bchl a) in AAPB were determined by comparing multiple known AAPB with non-AAPB isolates. Using these spectroscopic biomarkers, AAPB in coastal seawater, pelagic seawater, and hydrothermal sediment samples were screened, sorted, and sequenced. 16S rRNA gene analysis and functional gene annotations of sorted cells revealed novel AAPB members and functional genes, including one species belonging to the genus Sphingomonas, two genera affiliated to classes Betaproteobacteria and Gammaproteobacteria, and function genes bchCDIX, pucC2, and pufL related to Bchl a biosynthesis and photosynthetic reaction center assembly. Metagenome-assembled genomes (MAGs) of sorted cells from pelagic seawater and deep-sea hydrothermal sediment belonged to Erythrobacter sanguineus that was considered as an AAPB and genus Sphingomonas, respectively. Moreover, multiple photosynthesis-related genes were annotated in both MAGs, and comparative genomic analysis revealed several exclusive genes involved in amino acid and inorganic ion metabolism and transport. This study employed a new single-cell spectroscopy method to detect AAPB, not only broadening the taxonomic and genetic contents of AAPB in marine environments but also revealing their genetic mechanisms at the single-genomic level.

Biodegradation of low-density polyethylene film by two bacteria isolated from plastic debris in coastal beach.

Low-density polyethylene (LDPE) conduces massive environmental accumulation due to its high production and recalcitrance to environment. In this study, We successfully enriched and isolated two strains, Nitratireductor sp. Z-1 and Gordonia sp. Z-2, from coastal plastic debris capable of degrading LDPE film. After a 30-day incubation at 30 ℃, strains Z-1 and Z-2 decreased the weight of branched-LDPE (BLDPE) film by 2.59 % and 10.27 % respectively. Furthermore, high temperature gel permeation chromatography (HT-GPC) analysis revealed molecular weight reductions of 7.69 % (Z-1) and 23.22 % (Z-2) in the BLDPE film. Scanning electron microscope (SEM) image showed the presence of microbial colonization and perforations on the film's surface. Fourier transform infrared spectroscopy (FTIR) analysis indicated novel functional groups, such as carbonyl and carbon-carbon double bonds in LDPE films. During LDPE degradation, both strains produced extracellular reactive oxygen species (ROS). GC-MS analysis revealed the degradation products included short-chain alkanes, alkanols, fatty acids, and esters. Genomic analysis identified numerous extracellular enzymes potentially involved in LDPE chain scission. A model was proposed suggesting a coordinated role between ROS and extracellular enzymes in the biodegradation of LDPE. This indicates strains Z-1 and Z-2 can degrade LDPE, providing a basis for deeper exploration of biodegradation mechanisms.

A scoping review of hospital to home transitional care programmes for stroke survivors.

AIM: The study was aimed at exploring the current scope of hospital to home transitional care programmes for stroke survivors. BACKGROUND: Stroke survivors face the dilemma of solving many complex problems that leave survivors at high risk for readmission as they discharge from hospital. The transitional care model has proved to be effective in reducing readmissions and mortality, thereby improving health outcomes and enhancing patient satisfaction for survivors with stroke. DESIGN: A scoping review. METHODS: Conducted in accordance with the Joanna Briggs Institute (JBI) Methodology for Scoping Reviews. DATA SOURCES: A comprehensive search was conducted in nine databases, including PubMed, Web of Science, Cochrane Library, EMBASE, CINAHL, Medline, China Knowledge Net-work, Wanfang Database and China Biomedical Literature Database (SinoMed) from January 2014 to June 2023. RESULTS: Title and abstract screening was performed on 10,171 articles resulting in 287 articles for full-text screening. Full-text screening yielded 49 articles that met inclusion criteria. CONCLUSION: This study identified transitional care programmes for stroke survivors, as well as areas for future consideration to be explored in more depth to help improve transitional care for stroke survivors as they transition from hospital to home. IMPLICATIONS FOR THE PROFESSION AND/OR PATIENT CARE: This study demonstrates that multidisciplinary collaboration becomes an integral part of the transitional care model for stroke survivors, which provides comprehensive and precise medical care to them. REPORTING METHOD: PRISMA checklist for scoping reviews. PATIENT AND PUBLIC CONTRIBUTION: No patient or public contribution was part of this study.

Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea.

Thaumarchaeota are among the most abundant prokaryotes in the ocean, playing important roles in carbon and nitrogen cycling. Marine Thaumarchaeota ecotypes exhibit depth-related diversification and seasonal changes. However, transcriptomic activities concerning niche partitioning among thaumarchaeal ecotypes remain unclear. Here, we examined the variations in the distribution and transcriptomic activity of marine Thaumarchaeota ecotypes. Three primary ecotypes were identified: a Nitrosopumilus-like clade; a Nitrosopelagicus-like water column A (WCA) clade, thriving in epipelagic water; and a water column B (WCB) clade, dominant in deep water. Depth-related partitioning of the three ecotypes and the seasonal variability of the WCA and WCB ecotypes were observed. Nutrient concentrations, chlorophyll α and salinity were the primary environmental factors. The relative abundance of the WCA ecotype and its transcript abundance of amoA gene were positively correlated with chlorophyll α and salinity, while the WCB ecotype was positively correlated with nitrate and phosphate. Based on high-quality metagenome-assembled genomes, transcriptomic analysis revealed that the three ecotypes exhibited various co-occurring expression patterns of the elemental cycling genes in the nitrogen, carbon, phosphorus, and sulfur cycles. Our results provide transcriptomic evidence of the niche differentiation of marine Thaumarchaeota ecotypes, highlighting the diverse roles of ecotypes and WCA subclades in biogeochemical cycles.

Microbulbifer zhoushanensis sp. nov., Microbulbifer sediminum sp. nov. and Microbulbifer guangxiensis sp. nov., three marine bacteria isolated from a tidal flat.

Three strains, TT30T, TT37T and L3T, were isolated from tidal flat samples. Cells were Gram-stain-negative, non-motile and rod shaped. Cells of strains TT30T and TT37T were able to grow in a medium containing 1.0-15.0 % (w/v) NaCl (optimum, 3.0 and 4.0 %, respectively), and cells of strain L3T was able to grow in a medium containing 1.0-10.0 % (w/v) NaCl (optimum, 1.0 %). Growth of the three strains was observed at pH 6.0-10.0 and at 10-40 °C. Strains TT30T, TT37T and L3T showed the highest similarity to Microbulbifer hydrolyticus DSM 11525T (97.7 %), M. yueqingensis CGMCC 1.10658T (98.0 %) and M. elongatus DSM 6810T (97.9 %), respectively. Results of phylogenetic analyses indicated that the three isolates represented two distinct lineages within the genus Microbulbifer. The DNA G+C contents of strains TT30T, TT37T and L3T were 61.3, 60.9 and 60.2%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization values among strains TT30T, TT37T and L3T and the reference strains were 84.4-87.4 and 19.6-28.9 %, respectively. Differential phenotypic properties, chemotaxonomic differences, phylogenetic distinctiveness, together with the genomic data, demonstrated that strains TT30T, TT37 T and L3T represent novel species of the genus Microbulbifer, which are named Microbulbifer zhoushanensis sp. nov. (TT30T=KCTC 92167T=MCCC 1K07276T), Microbulbifer sediminum sp. nov. (TT37T=KCTC 92168T=MCCC 1K07277T) and Microbulbifer guangxiensis sp. nov. (L3T=KCTC 92165T=MCCC 1K07278T).

Membranihabitans maritimus sp. nov., a marine bacterium isolated from deep seawater.

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, designated C281T, was isolated from seawater sampled at the Marshallese seamount chain. Results of 16S rRNA gene analysis revealed that strain C281T was most closely related to Membranihabitans marinus CZ-AZ5T with 92.7 % sequence similarity. Phylogenetic analysis indicated that the new isolate represented a novel species by forming a distinctive lineage within the family Saprospiraceae. The DNA G+C content of strain C281T was 38.4 mol%. The genome sizes of strain C281T and the reference strain M. marinus CZ-AZ5T were 5 962 917 and 5 395 999 bp, respectively. The average nucleotide identity and in silico DNA-DNA hybridization values between strains C281T and M. marinus CZ-AZ5T were found to be low (69.3 and 17.6 %, respectively). Different functional genes were found in the genome of strain C281T, such as CZC CBA, polysaccharide utilization loci and linear azol(in)e-containing peptide cluster coding genes. The NaCl range for growth was 0.5-15.0 %. Positive results were obtained for hydrolysis of Tween 60 and urease. MK-7 was the sole respiratory quinone. The major fatty acids were C16 : 1 ω6c and/or C16 : 1 ω7c, iso-C15 : 0 and iso-C15 : 1 F. The major polar lipids of strain C281T were phosphatidylethanolamine, phosphatidylglycerol, two unidentified lipids and five unidentified glycolipids. On the basis of its taxonomic characteristics, the isolate represents a novel species of the genus Membranihabitans, for which the name Membranihabitans maritimus sp. nov. (type strain C281T=KCTC 92171T=MCCC M27001T) is proposed.

Secondary Metabolic Potential of Kutzneria.

Kutzneria is a rare genus of Actinobacteria that harbors a variety of secondary metabolite gene clusters and produces several interesting types of bioactive secondary metabolites. Recent efforts have partially elucidated the biosynthetic pathways of some of these bioactive natural products, suggesting the diversity and specificity of secondary metabolism within this genus. Here, we summarized the chemical structures, biosynthetic pathways, and key metabolic enzymes of the secondary metabolites isolated from Kutzneria strains. In-depth comparative genomic analysis of all six available high-quality Kutzneria genomes revealed that the majority (77%) of the biosynthetic gene cluster families of Kutzneria were untapped and identified homologues of key metabolic enzymes in the putative gene clusters, including cytochrome P450s, halogenases, and flavin-dependent N-hydroxylases. The present study suggests that Kutzneria exhibits great potential to synthesize novel secondary metabolites, encodes a variety of valuable metabolic enzymes, and also provides valuable information for the targeted discovery and biosynthesis of novel natural products from Kutzneria.

Genome-Wide Identification of BES1 Gene Family in Six Cucurbitaceae Species and Its Expression Analysis in Cucurbita moschata.

The BES1 (BRI1-EMSSUPPRESSOR1) gene family play a vital role in the BR (brassinosteroid) signaling pathway, which is involved in the growth and development, biotic, abiotic, and hormone stress response in many plants. However, there are few reports of BES1 in Cucurbita moschata. In this study, 50 BES1 genes were identified in six Cucurbitaceae species by genome-wide analysis, which could be classified into 3 groups according to their gene structural features and motif compositions, and 13 CmoBES1 genes in Cucurbita moschata were mapped on 10 chromosomes. Quantitative real-time PCR analysis showed that the CmoBES1 genes displayed differential expression under different abiotic stress and hormone treatments. Subcellular localization showed that the most of CmoBES1 proteins localized in nucleus and cytoplasm, and transactivation assay indicated 9 CmoBES1 proteins played roles as transcription factors. Our analysis of BES1s diversity, localization, and expression in Curcubitaceae contributes to the better understanding of the essential roles of these transcription factors in plants.

Sphingomicrobium nitratireducens sp. nov., isolated from a tidal flat in Guangxi.

An aerobic, yellow-pigmented and Gram-stain-negative strain, designated as O-35 T, was isolated from a tidal flat sediment collected in Dangjiang Town, the southern China. Colonies of strain O-35 T were circular with 0.5-1.0 mm in diameter, convex and smooth. Cells of strain O-35 T were coccoid-shaped, non-spore forming, non-motile and the strain could reduce nitrate. Growth of strain O-35 T was observed at 15-40 °C (optimum 30 °C), at pH 6.0-9.5 (optimum 7.5-8.0) and in 0.5-5.0% NaCl (optimum 2%, w/v). Strain O-35 T showed 16S rRNA gene sequence identities of 97.3-97.5% with Sphingomicrobium lutaoense CC-TBT-3 T and Sphingomicrobium aestuariivivum AH-M8T, higher than the rest of Sphingomicrobium type strains. Phylogenetic trees based on the 16S rRNA gene and the core-genome sequences demonstrated that strain O-35 T was affiliated within the genus Sphingomicrobium. Overall genome relatedness index calculations revealed that strain O-35 T had < 75.8% of average nucleotide identity and < 19.2% of digital DNA-DNA hybridization values with Sphingomicrobium type strains. The sole isoprenoid quinone was ubiquinone-10. The major fatty acids (> 10%) were summed feature 8, summed feature 3, C16:0 and C18:1 2-OH. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, sphingoglycolipid, two unidentified glycolipids, one unidentified lipid and one unidentified phospholipid. On the basis of the phenotypic, chemotaxonomic and genomic properties, strain O-35 T represents a novel species in the genus Sphingomicrobium, for which the name Sphingomicrobium nitratireducens sp. nov. is proposed. The type strain is O-35 T (= KCTC 92308 T = MCCC 1K07589T).

Pontibrevibacter nitratireducens gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from seawater of the Indian Ocean and intertidal zone.

Two Gram-stain-negative, facultatively anaerobic, non-motile, rod-shaped bacteria, strains h42T and ALG8, were isolated individually from the Indian Ocean and intertidal zone of Zhoushan, China. The results of 16S rRNA gene sequence analysis showed that the sequence similarity between strains h42T and ALG8 was 99.7 %, and the closest related strains were Monaibacterium marinum C7T (97.77 and 97.62 %) and Pontivivens insulae GYSW-23T (95.31 and 95.45 %). Phylogenetic analysis based on 16S rRNA gene sequences shows that these two novel strains belong to a distinct new lineage of the family Rhodobacteraceae in the order Rhodobacterales. The average nucleotide identity and in silico DNA-DNA hybridization values between the two novel strains and M. marinum C7T and P. insulae GYSW-23T were 72.73-78.15 % and 19.70-20.80 %, respectively. The DNA G+C content of strains h42T and ALG8 was 62.36 % and 62.17 mol %. The major fatty acids (>10 %) in strain h42T were C18 : 0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), and in strain ALG8 were C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1ω6c and/or C18 : 1 ω7c). The predominant isoprenoid ubiquinone of the two novel strains was Q-10; their major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified glycolipids, an unidentified aminoglycolipid, an unidentified phospholipid and an unidentified lipid. Based on the results of the morphological, physiological, chemotaxonomic and phylogenetic analysis of these two strains, a novel species of a new genus in the family Rhodobacteraceae is proposed, named as Pontibrevibacter nitratireducens gen. nov., sp. nov. The type strain and non-type strain of P. nitratireducens are h42T (=KCTC 72875T=CGMCC 1.17849T=MCCC 1K04735T) and ALG8 (=KCTC 82194=MCCC 1K04733).

Thiosulfatihalobacter marinus gen. nov. sp. nov., a novel member of the family Roseobacteraceae, isolated from the West Pacific Ocean.

Two strains (GL-11-2T and ZH2-Y79) were isolated from the seawater collected from the West Pacific Ocean and the East China Sea, respectively. Cells were Gram-stain-negative, strictly aerobic, non-motile and rod-shaped. Cells grew in the medium containing 0.5-7.5 % NaCl (w/v, optimum, 1.0-3.0 %), at pH 6.0-8.0 (optimum, pH 6.5-7.0) and at 4-40 °C (optimum, 30 °C). H2S production occurred in marine broth supplemented with sodium thiosulphate. The almost-complete 16S rRNA gene sequences of the two isolates were identical, and exhibited the highest similarity to Pseudoruegeria aquimaris JCM 13603T (97.5 %), followed by Ruegeria conchae TW15T (97.2%), Shimia aestuarii DSM 15283T (97.1 %) and Ruegeria lacuscaerulensis ITI-1157T (97.0 %). Phylogenetic analysis revealed that the isolates were affiliated with the family Roseobacteraceae and represented an independent lineage. The sole isoprenoid quinone was ubiquinone 10. The principal fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and cyclo-C19 : 0 ω8c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol. The DNA G+C content was 62.3 mol%. The orthologous average nucleotide identity, in silico DNA-DNA hybridization and average amino acid identity values among the genomes of strain GL-11-2T and the reference strains were 73.2-79.0, 20.3-22.5 and 66.0-80.8 %, respectively. Strains GL-11-2ᵀ and ZH2-Y79 possessed complete metabolic pathways for thiosulphate oxidation, dissimilatory nitrate reduction and denitrification. Phylogenetic distinctiveness, chemotaxonomic differences and phenotypic properties revealed that the isolates represent a novel genus and species of the family Roseobacteraceae, belonging to the class Alphaproteobacteria, for which the name Thiosulfatihalobacter marinus gen. nov., sp. nov. (type strain, GL-11-2T=KCTC 82723T=MCCC M20691T) is proposed.

Mesobacterium pallidum gen. nov., sp. nov., Heliomarina baculiformis gen. nov., sp. nov. and Oricola indica sp. nov., three novel Alphaproteobacteria members isolated from deep-sea water in the southwest Indian ridge.

Three Gram-staining-negative, aerobic and rod-shaped strains, designated as T40-1T, T40-3T and JL-62T, were isolated from the deep-sea water in the southwest Indian ridge. For strain T40-1T, growth occurred at 15-37 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.5) and in the presence of 0.5-5.0 % NaCl (w/v; optimum, 2.0 %). Strain T40-3T could grow at 15-40 °C (optimum, 28 °C), with 0.5-11.0 % NaCl (optimum, 2.0 %, w/v) at pH 6.0-9.5 (optimum, 8.0). The temperature, pH and salinity ranges for growth of strain JL-62T were 15-40 °C (optimum, 30 °C), pH 5.5-9.0 (optimum, pH 7.5-8.0) and 0.5-9.0 % NaCl (w/v; optimum, 4.0 %). Ubiquinone-10 was the sole ubiquinone in all strains, the major fatty acids (>20 %) were summed feature 8 (C18 : 1 ω7c / C18 : 1 ω6c). The major polar lipids of strains T40-1T and T40-3T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain JL-62T contained phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sulfoquinovosyldiacylglycerol as major polar lipids. Phylogenetic trees based on 16S rRNA gene and core-genomic sequences revealed affiliation of strains T40-1Tand T40-3T to the family Roseobacteraceae and formed two independent clades from other Roseobacteraceae genera, and those two strains had average nucleotide identities of 62.0-72.0 % to their phylogenetically related species which fell into to the genus boundary range, indicating that they represent two novel genera. While strain JL-62T represents a novel species in the genus Oricola belonging to the family Phyllobacteriaceae, which was supported by overall genomic relatedness index calculations. The DNA G+C contents of strains T40-1T, T40-3T and JL-62T were 66.5, 60.1 and 62.1 mol %, respectively. Based on the polyphasic taxonomic data, strains T40-1T (=MCCC M24557T=KCTC 82975T) and T40-3T (=MCCC 1K05135T=KCTC 82976T) are classified as representing two novel genera belonging to the family Roseobacteraceae with the names Mesobacterium pallidum gen. nov., sp. nov. and Heliomarina baculiformis gen. nov., sp. nov. are proposed, and strain JL-62T (=MCCC M24579T=KCTC 82974T) is proposed to represent a novel species within the genus Oricola with the name Oricola indica sp. nov. is proposed.

An atlas of bacterial secondary metabolite biosynthesis gene clusters.

Bacterial secondary metabolites are rich sources of novel drug leads. The diversity of secondary metabolite biosynthetic gene clusters (BGCs) in genome-sequenced bacteria, which will provide crucial information for the efficient discovery of novel natural products, has not been systematically investigated. Here, the distribution and genetic diversity of BGCs in 10 121 prokaryotic genomes (across 68 phyla) were obtained from their PRISM4 outputs using a custom python script. A total of 18 043 BGCs are detected from 5743 genomes with non-ribosomal peptide synthetases (25.4%) and polyketides (15.9%) as the dominant classes of BGCs. Bacterial strains harbouring the largest number of BGCs are revealed and BGC count in strains of some genera vary greatly, suggesting the necessity of individually evaluating the secondary metabolism potential. Additional analysis against 102 strains of discovered bacterial genera with abundant amounts of BGCs confirms that Kutzneria, Kibdelosporangium, Moorea, Saccharothrix, Cystobacter, Archangium, Actinosynnema, Kitasatospora, and Nocardia, may also be important sources of natural products and worthy of priority investigation. Comparative analysis of BGCs within these genera indicates the great diversity and novelty of the BGCs. This study presents an atlas of bacterial secondary metabolite BGCs that provides a lot of key information for the targeted discovery of novel natural products.

Aestuariibaculum sediminum sp. nov., a marine bacterium isolated from a tidal flat in Zhoushan.

A Gram-staining-negative, non-motile, strictly aerobic bacterium, designated as strain TT11T, was isolated from a sediment sample of a tidal flat connected in Zhoushan, China. Cells of strain TT11T are spherical, halotolerant, catalase- and oxidase-positive, and produce carotenoid-like pigments. Colonies were 0.5-1.0 mm diameter, smooth, round, convex and orange-yellow after growth on marine agar at 30 °C for 24 h. Growth of the strain TT11T was observed at 10-40 °C (optimum, 35 °C), at pH 6.0-9.5 (optimum, pH 6.5), and in the presence of 0-8.0% (w/v) NaCl (optimum, 0.5-1.0%). The results of 16S rRNA gene sequence analysis revealed that strain TT11T represents a member of the genus Aestuariibaculum and was closely related to Aestuariibaculum suncheonense SC17T (97.2%) and Aestuariibaculum marinum IP7T (96.8%). The G + C content of the genome was 34.6%. The only respiratory quinone was MK-6. The major fatty acids (> 10%) were iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. The major polar lipids contained phosphatidylethanolamine, phosphoglycolipid, four unidentified aminolipids, four unidentified lipids and two unidentified glycolipids. On the basis of these genomic, chemotaxonomic and phenotypic characteristics, we propose a novel species Aestuariibaculum sediminum sp. nov. with the type strain TT11T (= KCTC 82195T = MCCC 1K04734T).

Luteirhabdus pelagi gen. nov., sp. nov., a novel member of the family Flavobacteriaceae, isolated from the West Pacific Ocean.

A Gram-stain-negative, aerobic, and yellow-pigmented bacterium, designated A3-108T, was isolated from seawater of the West Pacific Ocean. Cells were non-motile and rod-shaped, with carotenoid-type pigments. Strain A3-108T grew at pH 6.0-8.5 (optimum 6.5) and 15-40 °C (optimum 28 °C), in the presence of 0.5-10% (w/v) NaCl (optimum 1.0%). It possessed the ability to produce H2S. Based on the 16S rRNA gene analysis, strain A3-108T exhibited highest similarity with Aureisphaera salina A6D-50T (90.6%). Phylogenetic analysis shown that strain A3-108T affiliated with members of the family Flavobacteriaceae and represented an independent lineage. The principal fatty acids were iso-C15:0, iso-C17:0 3-OH, iso-C15:1 G, and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The sole isoprenoid quinone was MK-6. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified aminolipid and one unidentified lipid. The ANIb, in silico DDH and AAI values among the genomes of strain A3-108T and three reference strains were 67.3-71.1%, 18.7-22.1%, and 58.8-71.4%, respectively. The G + C content was 41.0%. Distinctness of the phylogenetic position as well as differentiating chemotaxonomic and other phenotypic traits revealed that strain A3-108T represented a novel genus and species of the family Flavobacteriaceae, for which the name Luteirhabdus pelagi gen. nov., sp. nov. is proposed (type strain, A3-108T = CGMCC 1.18821T = KCTC 82563T).

Physiological and genomic features of Henriciella with the description of Henriciella mobilis sp. nov.

Strains M65T, M69 and JN25 were isolated from seawater of the West Pacific Ocean. Cells of the three strains were Gram-stain-negative, aerobic and rod-shaped. Cells were motile by means of flagella. On the basis of the results of 16S rRNA gene sequence analysis, strains M65T, M69 and JN25 showed the highest 16S rRNA gene sequence similarity to Henriciella algicola MCS27T (98.8 %), followed by Henriciella marina DSM 19595T (98.4 %), Henriciella barbarensis MCS23T (98.4 %), Henriciella pelagia LA220T (98.3 %), Henriciella aquimarina P38T (98.1 %) and Henriciella litoralis SD10T (97.8 %). The 16S rRNA gene sequence similarities among the isolates were 100 %. Phylogenetic analyses revealed that the isolates fell within a cluster comprising the Henriciella species and represented an independent lineage. The average nucleotide identity and in silico DNA-DNA hybridization values between strain M65T and the type strains of Henriciella species were 73.9-85.8 % and 19.9-22.4 %, respectively. The sole respiratory quinone detected in the three isolates was ubiquinone 10. The principal fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The major polar lipids were glucuronopyranosyldiglyceride, monoglycosyldiglyceride and one unidentified glycolipid. The DNA G+C content was 61.3-61.4 mol%. Phylogenetic distinctiveness, chemotaxonomic differences, together with phenotypic properties, revealed that the isolates could be differentiated from the Henriciella species with validly published names. Therefore, it is proposed that strains M65T, M69 and JN25 represent a novel species of the genus Henriciella, for which the name Henriciella mobilis sp. nov. (type strain, M65T=CGMCC 1.15927T=KCTC 52576T) is proposed.

Euzebya pacifica sp. nov., a novel member of the class Nitriliruptoria.

A Gram-stain-positive, aerobic, chemo-organotrophic, rod-shaped, non-spore-forming strain, which produced convex, circular, pink-pigmented colonies, designated as DY32-46T, was isolated from seawater collected from the Pacific Ocean. DY32-46T was found to grow at 20-40 °C (optimum, 30-35 °C), pH 6.0-8.0 (optimum, pH 6.5) and with 0-5 % (w/v) NaCl (optimum, 1-2 %). The results of chemotaxonomic analysis indicated that the respiratory quinone of DY32-46T was MK-9(H4), and major fatty acids (>10 %) were C17 : 1 ω8c, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C15 : 1 ω6c. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophospholipid, three unidentified glycolipids, three unidentified phospholipids, one unidentified phosphoglycolipid and five unidentified lipids. The DNA G+C content of DY32-46T was 70.6 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences and genomic data indicated that DY32-46T should be assigned to the genus Euzebya. ANI and in silico DNA-DNA hybridization values between strain DY32-46T and type strains of Euzebya species were 73.1-87.2 % and 20.2-32.4 %, respectively. Different phenotypic properties, together with genetic distinctiveness, demonstrated that strain DY32-46T was clearly distinct from recognized species of the genus Euzebya. Therefore, DY32-46T represents a novel species within the genus Euzebya, for which the name Euzebya pacifica sp. nov is proposed. The type strain is DY32-46T (=MCCC 1K03476T=KCTC 49091T).

Alterinioella nitratireducens gen. nov., sp. nov., Isolated from Seawater in the West Pacific Ocean.

A novel Gram-negative, nonspore forming, nonmotile, and short-rod-shaped aerobic bacterium, designated DY48A3-103T, was isolated from a seawater sample collected from the West Pacific Ocean. Strain DY48A3-103T showed oxidase-positive and catalase-positive activities. Growth was observed at 10-37 °C (optimum 30 °C), at pH 6.5-9.5 (optimum 8.0) and in 1-11% NaCl (optimum 3%, w/v). 16S rRNA gene sequence analysis exhibited 96.3%, 96.1%, 96.0%, and 94.9% sequence similarity to the type strains Rhodophyticola porphyridii MA-7-27T, Nioella sediminis JS7-11T, N. nitratireducens SSW136T, and Jannaschia helgolandensis DSM 14858T, respectively. Strain DY48A3-103T and the type strains of phylogenetically related species have 61.7-75.4% AAI values, which fell into to the genus boundary range (60-80% AAI). Phylogenetic trees based on the 16S rRNA gene sequences and the genome sequences of strain DY48A3-103T revealed that it was affiliated to the members of the family Rhodobacteraceae. The G+C content was 65.4%. The sole isoprenoid quinone was Q-10. The predominant polar lipids were phosphatidylcholine and phosphatidylglycerol. Major fatty acids were summed feature 8 (comprising C18:1ω7c and/or C18:1ω6c), C19:0 cyclo ω8c, and C16:0. On the basis of the phenotypic, chemotaxonomic, and genomic properties, strain DY48A3-103t is proposed to represent a novel genus and a novel species, Alterinioella nitratireducens gen. nov., sp. nov., in the family Rhodobacteraceae. The type strain is DY48A3-103T (= KCTC 72738T = MCCC 1K04322T).