Mbp In Size Research Articles

Genomic analyses of the southern and eastern yellowjacket wasps (Hymenoptera: Vespidae) reveal evolutionary signatures of social life

Abstract Insects have evolved remarkably complex social systems. Social wasps are particularly noteworthy because they display gradations in social behaviors. Here, we sequence the genomes of two highly diverged Vespula wasps, V. squamosa and V. maculifrons Buysson (Hymenoptera: Vespidae), to gain greater insight into the evolution of sociality. Both V. squamosa and V. maculifrons are social wasps that live in large colonies characterized by distinct queen and worker castes. However, V. squamosa is a facultative social parasite, and V. maculifrons is its frequent host. We found that the genomes of both species were ~200 Mbp in size, similar to the genome sizes of congeneric species. Analyses of gene expression from members of different castes and developmental stages revealed similarities in expression patterns among immature life stages. We also found evidence of DNA methylation within the genome of both species by directly analyzing DNA sequence reads. Moreover, genes that were highly and uniformly expressed were also relatively highly methylated. We further uncovered evidence of differences in patterns of molecular evolution in the two taxa, consistent with V. squamosa exhibiting alterations in evolutionary pressures associated with its facultatively parasitic or polygyne life history. Finally, rates of gene evolution were correlated with variation in gene expression between castes and developmental stages, as expected if more highly expressed genes were subject to stronger levels of selection. Overall, this study expands our understanding of how social behavior relates to genome evolution in insects.

Dolosigranulum savutiense sp. nov., isolated from human upper respiratory samples collected in Botswana.

Four strains (MSK211, MSK294T, MSK312, MSK433) of a novel Dolosigranulum species were cultured from nasopharyngeal swabs collected from mother-infant dyads in southern Botswana. These strains grew optimally on tryptic soy agar with 5% sheep blood solid medium and in fastidious bacteria broth. Colonies on tryptic soy agar with 5% sheep blood agar appeared grey or white with a flat, smooth surface and variable alpha haemolysis. Cells were Gram-positive, non-spore-forming, non-motile cocci that lacked catalase or oxidase activity. Major fatty acids were C16 : 0 (palmitic acid), C18 : 1 ω9c (oleic acid), and C18 : 0 (stearic acid). Analyses of 16S rRNA gene sequences identified these strains as belonging to the genus Dolosigranulum (family Carnobacteriaceae), which currently contains only a single validly published species (Dolosigranulum pigrum). Whole-genome sequencing revealed that the genomes of these strains are 1.98-2.07 Mbp in size and have a G+C content of 39.6-39.9 mol%. Comparisons of these genomes to publicly available genomes of D. pigrum yielded average nucleotide identities and in silico DNA-DNA hybridization values of 92.3-92.9% and 49.1-51.4%, respectively. These results indicate that these strains represent a novel species of Dolosigranulum, for which we propose the name Dolosigranulum savutiense sp. nov., with the type strain MSK294T (=DSM 117171T=JCM 36673T).

Delving deep into the draft genome of Mangrovibacter sp. SLW1, isolated from Sundarbans mangrove

Mangrovibacter sp. SLW1, a Gram-negative, aerobic, motile bacterium, was isolated from mangrove litterfall in Sundarbans mangrove. The draft genome is 5.5 Mbp in size with 49.45 mol% guanine-cytosine (GC) content. The linear chromosome of the bacterium consists of 27 contigs with 7339 coding sequences. The detailed in silico analyses of the genome of Mangrovibacter sp. SLW1 provide information on ecological adaptation. The genome is a reservoir for multiple heavy metals and metalloid resistance gene clusters as well as exhibit metabolic capabilities for utilization of a wide range of carbohydrates. It also encodes for tris-catecholate siderophore and can regulate uptake of iron thereby may influence plant growth such as mangrove vegetation.

Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream.

A Gram-strain-negative, aerobic, yellow-colored, non-motile, and rod-shaped bacterial strain, designated IMCC34852T, was isolated from a freshwater stream in the Republic of Korea. Cellular growth occurred at 10-37°C, pH 6.0-9.0, and with 0-0.5% (w/v) NaCl. The 16S rRNA gene sequence analysis showed that strain IMCC34852T belonged to the genus Flavobacterium and that the strain was most closely related to F. cheonhonense ARSA-15T (97.6%), F. buctense T7T (96.7%), F. silvisoli RD-2-33T (96.1%), and F. paronense KNUS1T (96.1%). The whole-genome sequence of strain IMCC34852T was 3.2 Mbp in size, with a DNA G + C content 37.3%. The average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) values between strain IMCC34852T and its related species were all below 79.8% and 22.7%, respectively, which are significantly lower than the thresholds of 95% for ANI and 70% for DDH for species delineation. The major respiratory quinone of strain IMCC34852T was menaquinone-6 (MK-6) and the predominant cellular fatty acids were iso-C15:0 (32.6%), iso-C16:0 (11.7%), iso-C15:1 G (10.3%), and iso-C14:0 (6.7%). The major polar lipids of the strain were phosphatidylethanolamine, two unidentified aminolipids and six unidentified lipids. Based on these results, it was concluded that strain IMCC34852T represents a novel species in the genus Flavobacterium, for which the name Flavobacterium rivulicola sp. nov is proposed. The type strain of the proposed novel species is IMCC34852T (= KACC 23133T = KCTC 82066T = NBRC 114419T).

Ignisphaera cupida sp. nov., a hyperthermophilic hydrolytic archaeon from a hot spring of Uzon (Kamchatka), and emended description of the genus Ignisphaera

A novel strictly anaerobic hyperthermophilic archaeon, strain 4213-coT, was isolated from a terrestrial hot spring in the Uzon Caldera, Kamchatka (Russian Federation). Coccoid cells were present singly, in pairs, or aggregates, and occasionally were motile. The strain grew at 75–100 °C and within a pH range of 5.4–8.2 with the optimum at 92 °C and pH 6.4–6.7. Strain 4213-coT was a chemoorganoheterotroph, growing on proteinaceous substrates and mono-, di- and polysaccharides (starch, guar gum, xanthan gum). It did not require sodium chloride for growth. The complete genome of strain 4213-coT was 1.74 Mbp in size; its G+C content was 36.18 %. Genome analysis allowed to identify 25 genes encoding glycosidases involved in polysaccharide hydrolysis as well as genes of ADP-forming acetate-CoA ligase, lactate dehydrogenase and two [NiFe] hydrogenases responsible for acetate, lactate and hydrogen formation during fermentation. Moreover gene cluster encoding archaellum subunits was found. According to the phylogenomic analysis strain 4213-coT formed a species-level phylogenetic lineage within Ignisphaera genus. Our phylogenomic analysis also supports the delineation of the Ignisphaera genus into a separate family Ignisphaeraceae, as recently published. Here we propose a novel species Ignisphaera cupida, sp. nov. with type strain 4213-coT (=JCM 39446T=VKM B-3715T=UQM 41593T). Ecogenomic analysis showed that representatives of the Ignisphaera are thermophilic archaea, the majority of them were found in terrestrial hot springs and deep-sea hydrothermal vents. This study allowed a better understanding of physiology and ecology of Ignisphaeraceae – a rather understudied archaeal group.

Taklimakanibacter deserti gen. nov., sp. nov. and Taklimakanibacter lacteus sp. nov., isolated from desert soil.

Two Gram-stain-negative, aerobic, milk-white coloured, non-motile, short rod-shaped bacteria, designated as strains SYSU D60010T and SYSU D60012T, were isolated from sand samples collected from the Taklimakan Desert of Xinjiang Province in China. Both strains were positive for oxidase, catalase and nitrate reduction, but negative for amylase, H2S production, hydrolysis of gelatin and cellulase. Strains SYSU D60010T and SYSU D60012T grew well at 28 °C, at pH 7 and had the same NaCl tolerance range of 0-1 % (w/v). The major fatty acids (>5 %) of strains SYSU D60010T and SYSU D60012T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), iso-C19 : 0 cyclo ω8c, C16 : 0 and iso-C18 : 1 2-OH. Q-10 was the only respiratory ubiquinone. Strains SYSU D60010T and SYSU D60012T showed high 16S rRNA gene sequence similarities to Aestuariivirga litoralis SYSU M10001T (94.2 and 94.1 %), Rhodoligotrophos jinshengii BUT-3T (92.0 and 91.9 %) and Rhodoligotrophos appendicifer 120-1T (91.8 and 91.7 %), and the genomes were 7.4 and 5.8 Mbp in size with DNA G+C contents of 62.8 and 63.0 mol%, respectively. Phylogenetic, phenotypic and chemotaxonomic characteristics indicated that these two strains represent a novel genus and two novel species within the family Aestuariivirgaceae. We propose the name Taklimakanibacter deserti gen. nov., sp. nov. for strain SYSU D60010T, representing the type strain of this species (=KCTC 52783T =NBRC 113344T) and Taklimakanibacter lacteus gen. nov., sp. nov. for strain SYSU D60012T, representing the type strain of this species (=KCTC 52785T=NBRC 113128T).

Draft genome of carotenoid-producing endophytic Pseudomonas sp. 102515 from Taxus chinensis.

Here, we report the draft genome sequence of endophytic Pseudomonas sp. 102515 isolated from Taxus chinensis collected from Logan, UT, USA. The genome is composed of 36 contigs and around 4.9 Mbp in size. The GC content is 66% with an N50 length of 918.9 kbp and L50 count of 2.

Eupransor demetentiae gen. nov., sp. nov., a novel fructophilic lactic acid bacterium from bumble bees.

Strain LMG 33000T was isolated from a Bombus lapidarius gut sample. It shared the highest percentage 16S rRNA sequence identity, average amino acid identity, and amino acid identity of conserved genes with Convivina intestini LMG 28291T (95.86 %, 69.9 and 76.2 %, respectively), and the highest percentage OrthoANIu value with Fructobacillus fructosus DSM 20349T (71.4 %). Phylogenomic analyses by means of 107 or 120 conserved genes consistently revealed Convivina as nearest neighbour genus. The draft genome of strain LMG 33000T was 1.44 Mbp in size and had a DNA G+C content of 46.1 mol%. Genomic and physiological analyses revealed that strain LMG 33000T was a typical obligately fructophilic lactic acid bacterium that lacked the adhE and aldh genes and that did not produce ethanol during glucose or fructose metabolism. In contrast, Convivina species have the adhE and aldh genes in their genomes and produced ethanol from glucose and fructose metabolism, which is typical for heterofermentative lactic acid bacteria. Moreover, strain LMG 33000T exhibited catalase activity, an unusual characteristic among lactic acid bacteria, that is not shared with Convivina species. Given its position in the phylogenomic trees, and the difference in genomic percentage G+C content and in physiological and metabolic characteristics between strain LMG 33000T and Convivina species, we considered it most appropriate to classify strain LMG 33000T into a novel genus and species within the Lactobacillaceae family for which we propose the name Eupransor demetentiae gen. nov., sp. nov., with LMG 33000T (=CECT 30958T) as the type strain.

Klenkia sesuvii sp. nov., isolated from leaves of halophyte Sesuvium portulacastrum.

During a study on the diversity of culturable actinobacteria from coastal halophytes in Thailand, strain LSe6-5T was isolated from leaves of sea purslane (Sesuvium portulacastrum L.), and a polyphasic approach was employed to determine its taxonomic position. The 16S rRNA gene sequences analysis indicated that the strain was most closely related to Klenkia brasiliensis Tu 6233T (99.2 %), Klenkia marina YIM M13156T (99.1 %), and Klenkia terrae PB261T (98.7 %). The genome of strain LSe6-5T was estimated to be 4.33 Mbp in size, with DNA G+C contents of 74.3%. A phylogenomic tree based on whole-genome sequences revealed that strain LSe6-5T formed a clade with Klenkia marina DSM 45722T, indicating their close relationship. However, the average nucleotide identity (ANI)-blast, ANI-MUMmer, and dDDH values between strain LSe6-5T with K. marina DSM 45722T (87.1, 88.9, and 33.0 %) were below the thresholds of 95-96 % ANI and 70 % dDDH for identifying a novel species. Furthermore, strain LSe6-5T showed morphological and chemotaxonomic characteristics of the genus Klenkia. Cells were motile, rod-shaped, and Gram-stain-positive. Optimal growth of strain LSe6-5T occurred at 28 °C, pH 7.0, and 0-3 % NaCl. The whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, with galactose, glucose, mannose, and ribose as whole-cell sugars. The predominant menaquinones were MK-9(H4) and MK-9(H0). The polar lipid profile was composed of diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, an unidentified phospholipid, and an unidentified lipid. Major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, and iso-C17 : 0. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, it is supported that strain LSe6-5T represents a novel species of the genus Klenkia, for which the name Klenkia sesuvii sp. nov. is proposed. The type strain is strain LSe6-5T (=TBRC 16417T= NBRC 115929T).

Sinomonas terricola sp. nov., a plant-beneficial bacterium isolated from litchi rhizosphere soil in Guangdong, China.

A novel plant-beneficial bacterium strain, designated as JGH33T, which inhibited Peronophythora litchii sporangia germination, was isolated on Reasoner's 2A medium from a litchi rhizosphere soil sample collected in Gaozhou City, Guangdong Province, PR China. Cells of strain JGH33T were Gram-stain-positive, aerobic, non-motile, bent rods. The strain grew optimally at 30-37 °C and pH 6.0-8.0. Sequence similarity analysis based on 16S rRNA genes indicated that strain JGH33T exhibited highest sequence similarity to Sinomonas albida LC13T (99.2 %). The genomic DNA G+C content of the isolate was 69.1 mol%. The genome of JGH33T was 4.7 Mbp in size with the average nucleotide identity value of 83.45 % to the most related reference strains, which is lower than the species delineation threshold of 95 %. The digital DNA-DNA hybridization of the isolate resulted in a relatedness value of 24.9 % with its closest neighbour. The predominant respiratory quinone of JGH33T was MK-9(H2). The major fatty acids were C15 : 0 anteiso (43.4 %), C16 : 0 iso (19.1 %) and C17 : 0 anteiso (19.3 %), and the featured component was C18 : 3 ω6c (1.01 %). The polar lipid composition of strain JGH33T included diphosphatidylglycerol, phosphatidylglycerol, dimannosylglyceride, phosphatidylinositol and glycolipids. On the basis of polyphasic taxonomy analyses data, strain JGH33T represents a novel species of the genus Sinomonas, for which the name Sinomonas terricola sp. nov. is proposed, with JGH33T (=JCM 35868T=GDMCC 1.3730T) as the type strain.

Desertivirga arenae gen. nov., sp. nov. and Desertivirga brevis sp. nov., isolated from desert soil, and reclassification of Pedobacter xinjiangensis as Desertivirga xinjiangensis comb. nov. and Pedobacter mongoliensis as Paradesertivirga mongoliensis gen.nov., comb. nov.

Two novel bacterial strains, designated as SYSU D00823T and SYSU D00873T, were isolated from sandy soil of the Gurbantunggut Desert in Xinjiang, north-west China. SYSU D00823T and SYSU D00873T shared 99.0 % 16S rRNA gene sequence identity, and were both most closely related to Pedobacter xinjiangensis 12157T with 96.1 % and 96.0 % similarities, respectively. Phylogenetic and phylogenomic analyses revealed that the two isolates and P. xinjiangensis 12157T formed a separate distinct cluster in a stable subclade with the nearby species Pedobacter mongoliensis 1-32T, as well as the genera Pararcticibacter and Arcticibacter. Furthermore, P. mongoliensis 1-32T formed a separate deep-branching lineage and did not form a cluster with members of the genus Pedobacter. The average nucleotide identity and digital DNA-DNA hybridization values between SYSU D00823T and SYSU D00873T and related species were well below the thresholds for species delineation (<81.0 % and <24.0 %, respectively). The genomes of SYSU D00823T and SYSU D00873T were 6.19 and 6.43 Mbp in size with 40.4 % and 40.5 % DNA G+C contents, respectively. The predominant fatty acids (>10 %) of SYSU D00823T and SYSU D00873T were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). Menaquinone-7 was the only respiratory quinone. The major polar lipids were phosphatidylethanolamine, glycosphingolipid, aminoglycolipid/glycolipid, aminophospholipid and three or four unidentified polar lipids. These data indicated that strains SYSU D00823T and SYSU D00873T should be assigned to two novel species of a new genus within the family Sphingobacteriaceae, for which the names Desertivirga arenae gen. nov., sp. nov. and Desertivirga brevis sp. nov. are proposed. The type strains are SYSU D00823T (=CGMCC 1.18630T=MCCC 1K04973T=KCTC 82278T) and SYSU D00873T (=CGMCC 1.18629T=MCCC 1K04974T=KCTC 82281T), respectively. Accordingly, the reclassification of P. xinjiangensis as Desertivirga xinjiangensis comb. nov., and P. mongoliensis as Paradesertivirga mongoliensis gen. nov., comb. nov. are also proposed.

Draft genome sequences of 21 Pedobacter strains isolated from amphibian specimens.

The genomes of 21 Pedobacter strains isolated from the European salamander Salamandra salamandra and different Madagascan frog species were sequenced using Illumina sequencing. Here, we report their draft genome sequences (~4.7-7.2 Mbp in size) to allow comparative genomics and taxonomic assignment of these strains.

Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads.

Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in natural sediments, but due to their capability for long-distance electron transport, they exert a disproportionately large impact on the biogeochemistry of their environment. Current available genomes of marine cable bacteria are highly fragmented and incomplete, hampering the elucidation of their unique electrogenic physiology. Here, we present a metagenomic pipeline that combines Nanopore long-read and Illumina short-read shotgun sequencing. Starting from a clonal enrichment of a cable bacterium, we recovered a circular metagenome-assembled genome (5.09 Mbp in size), which represents a novel cable bacterium species with the proposed name Candidatus Electrothrix scaldis. The closed genome contains 1109 novel identified genes, including key metabolic enzymes not previously described in incomplete genomes of cable bacteria. We examined in detail the factors leading to genome closure. Foremost, native, non-amplified long reads are crucial to resolve the many repetitive regions within the genome of cable bacteria, and by analysing the whole metagenomic assembly, we found that low strain diversity is key for achieving genome closure. The insights and approaches presented here could help achieve genome closure for other keystone micro-organisms present in complex environmental samples at low abundance.

Whole genome sequencing of Streptomyces antnestii sp. nov. with a potency to become an industrial strain.

Streptomyces Strain San01 is isolated from the soil of ant-nest found in the tea estate of Darjeeling, India. The morphology, biochemical, as well as the molecular characteristics, proved that San01 belonged to the genus Streptomyces. The average nucleotide identity (ANI) value between the genome sequence of the studied strain and its closest phylogenetic neighbors were very low and also could be distinguished from its closest neighbour with broad range of phenotypic data. The draft genome sequence of isolate San01 (NZ_RZYA00000000.1) was estimated to be 9.12 Mbp in size with 71.2% of GC content and it encompasses 39 biosynthetic gene clusters that emphasize the biotechnological potential of this isolate.Based on the phenotypic, genetic and genomic data, isolate San01 (=JCM 34633 = NCTC 14543) merits to be recognized as a type strain of a novel species and hereby propose the name Streptomyces antnestii sp. nov. Incidentally, this is the first report on Streptomyces genomes from Darjeeling, India.

First Report and Genome Resource of Monilinia vaccinii-corymbosi, causal agent of Mummy Berry Disease of Black Huckleberry (Vaccinium membranaceum).

Monilinia vacccinii-corymbosi (phylum Ascomycota, family Sclerotiniaceae) causes fruit disease 'mummy berry' on berry crops and responsible for yield losses and quality of fruits. We reported mummy berry disease of black huckleberry (Vaccinium membranaceum) first time in British Columbia, Canada. We have performed sequencing and genome assembly of M. vacccinii-corymbosi from infected fruits of huckleberry. The resulting genome was 33.8 Mbp in size and consisted of 2,437 scaffolds with an N50 of 33,816 bp. To our best knowledge, this is the first report of resource announcement of whole genome sequence of mummy berry pathogen (M. vacccinii-corymbosi) infecting black huckleberry. The genome resource will be valuable for future studies to understand the genomic structure of pathogen, and mechanisms associated with black huckleberry-M. vacccinii-corymbosi interactions.

Draft genome sequence of Streptomyces poriferorum RTGN2, a bacterial endophyte isolated from Alnus glutinosa root nodules.

Herein is reported the draft genome sequence of Streptomyces poriferum RTGN2, a bacterial isolate of Alnus glutinosa root nodules, collected from Saltwell Park, Gateshead, United Kingdom. The assembly is 9.5 Mbp in size, composed of 187 contigs, with a N50 of 189,630 bp, presenting a GC content of 71.2%.

Draft genome sequence of Amycolatopsis camponoti RTGN1, a bacterial endophyte isolated from Alnus glutinosa root nodules.

Here, we report the draft genome sequence of Amycolatopsis camponoti RTGN1, a bacterial endophyte of Alnus glutinosa root nodules, collected from Saltwell Park, United Kingdom. The genome is 11.9 Mbp in size, composed of 147 contigs, with an N50 of 179,211 bp and presenting a GC content of 70.9%.

Genomic characterization and comparative genomic analysis of pathogenic Vibrio isolated from aquaculture-grown white-leg shrimp (Penaeus vannamei) in Guangdong and Jiangsu, China

The proliferation of opportunistic pathogens Vibrio parahaemolyticus, Vibrio alginolyticus, and Vibrio owensii have impeded the rapid development of aquaculture farming. The study aimed to analyze the whole genome of pathogenic Vibrio strains associated with hepatopancreatic necrosis in Penaeus vannamei. The analysis included genomic characterization, virulence genes profiling, antibiotic resistance genes (ARGs) identification, antimicrobial resistance phenotypes, clustered regularly interspaced short palindromic repeats (CRISPR) and prophage prediction, multi-locus sequence typing, and pan-genome analysis of Vibrio isolates from Guangdong and Jiangsu provinces, China. Sequence analysis of the specimens revealed 29 V. parahaemolyticus isolates, three V. alginolyticus isolates, and one V. owensii isolate. Their genomes are 4.9–5.9 Mbp in size, with a GC content of 44.4–45.4%. Each Vibrio isolate harbored >120 virulence genes. Out of the 33 isolates, 13 (39%) demonstrated multidrug-resistant (MDR). Notably, at least 14 isolates exhibited heightened resistance to sulfamethoxazole, erythromycin, and amoxicillin, with a cumulative detection of 20 ARGs. Nevertheless, no significant correlation was found between the composition of ARGs and the observed antimicrobial resistance phenotypes. All Vibrio isolates differed in the presence of prophage and CRISPR sequences; and two of these prophages harbored virulence genes but not ARGs. The study identified 17 distinct sequence types (STs) in V. parahaemolyticus isolates, primarily ST415 (n = 5), while two Vibrio isolates were classified as ST3. Using the 117 V. parahaemolyticus strains available in the National Center for Biotechnology Information database as a reference, pan-genomic analysis and phylogenetic analysis of the core genome revealed that clinical isolates of the same STs clustered into the same clade, irrespective of isolation date and geographic origins. In summary, these data enhance our understanding of the molecular characteristics and epidemiological risk of Vibrio strains in southern China, especially regarding shrimp aquaculture.

Streptomyces silvisoli sp. nov., a polyene producer, and Streptomyces tropicalis sp. nov., two novel actinobacterial species from peat swamp forests in Thailand.

Two novel actinobacterial strains, designated RB6PN23T and K1PA1T, were isolated from peat swamp soil samples in Thailand and characterized using a polyphasic taxonomic approach. The strains were filamentous Gram-stain-positive bacteria containing ll-diaminopimelic acid in their whole-cell hydrolysates. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strain RB6PN23T was most closely related to Streptomyces rubrisoli (99.1 % sequence similarity) and Streptomyces ferralitis (98.5%), while strain K1PA1T showed 98.8 and 98.7% sequence similarities to Streptomyces coacervatus and Streptomyces griseoruber, respectively. However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were below the species-level thresholds (95-96 % ANI and 70 % dDDH). The genomes of strains RB6PN23T and K1PA1T were estimated to be 7.88 Mbp and 7.39 Mbp in size, respectively, with DNA G+C contents of 70.2 and 73.2 mol%. Moreover, strains RB6PN23T and K1PA1T encode 37 and 24 putative biosynthetic gene clusters, respectively, and in silico analysis revealed that these new species have a high potential to produce unique natural products. Genotypic and phenotypic characteristics confirmed that strains RB6PN23T and K1PA1T represented two novel species in the genus Streptomyces. The names proposed for these strains are Streptomyces silvisoli sp. nov. (type strain RB6PN23T=TBRC 17040T=NBRC 116113T) and Streptomyces tropicalis sp. nov. (type strain K1PA1T=TBRC 17041T=NBRC 116114T). Additionally, a giant linear polyene compound, neotetrafibricin A, exhibiting antifungal activity in strain RB6PN23T, was identified through HPLC and quadrupole time-of-flight MS analysis. The crude extract from the culture broth of strain RB6PN23T exhibited strong antifungal activity against Fusarium verticillioides, Fusarium fujikuroi and Bipolaris zeicola. This finding suggests that strain RB6PN23T could be a promising candidate for biological control of fungal diseases.

Hufsiella ginkgonis gen. nov., sp. nov. and Hufsiella arboris sp. nov., isolated from tree barks.

Two Gram-staining-negative, aerobic, rod-shaped, bacteria that formed pale-pinkish colonies, designated HMF7056T and HMF7647T were isolated from Ginkgo (Ginkgo biloba) and Korean cornel dogwood (Cornus offcinalis), respectively. Phylogenetic analyses based on sequences of 16S rRNA genes and 92 core genes indicated that two strains represent novel species within the family Sphingobacteriaceae. HMF7056T and HMF7647T showed high 16S rRNA sequence similarities to Daejeonella lutea N7d-4T (93.9 % and 95.7 %, respectively). The genomes of HMF7056T and HMF7647T were 5.2 and 4.8 Mbp in size with 50.5 and 42.5 % DNA G+C contents, respectively. Menaquinone-7 was the main respiratory quinone. The predominant fatty acids of HMF7056T and HMF7647T were iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The major polar lipid of both strains was phosphatidylethanolamine. The average nucleotide identity and digital DNA-DNA hybridization values of HMF7056T, HMF7647T and related species were well below the threshold limit for species delineation (<68.9 and <20.8 %, respectively). The average amino acid identity values of HMF7056T, HMF7647T with related type strains were below 67.8 and 68.3 %, respectively. On the basis of the results of phenotypic and phylogenetic characterizations, the two strains are considered to represent members of a novel genus of the family Sphingobacteriaceae, for which the names Hufsiella ginkgonis gen. nov., sp. nov. and Hufsiella arboris sp. nov. are proposed. The type strains are HMF7056T (=KCTC 72282T =NBRC 113964T) and HMF7647T (=KCTC 72283T =NBRC 113965T), respectively.