Pseudonocardia acidicola sp. nov., a novel actinomycete isolated from peat swamp forest soil

Pseudonocardia spirodelae sp. nov., isolated from duckweed and formal proposal to reclassify Pseudonocardia antarctica as a later heterotypic synonym of Pseudonocardia alni and reclassify Pseudonocardia carboxydivorans as Pseudonocardia alni subsp. carboxydivorans

A novel Pseudonocardia strain DW16-2T, isolated from duckweed (Spirodela polyrhiza), was taxonomically studied in detail. The analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to Pseudonocardia carboxydivorans Y8T (98.8%), followed by Pseudonocardia tropica YIM 61452T (98.7%), Pseudonocardia antarctica DVS 5a1T (98.7%) and Pseudonocardia alni DSM 44104T (98.7%). The average nucleotide identity (ANI) based on blast and digital DNA-DNA hybridization (dDDH) relatedness values between strain DW16-2T and their closest type strains were below the threshold values for identifying a novel species. Morphological, physiological and chemotaxonomic features of strain DW16-2T were typical for the genus Pseudonocardia by forming extensively branched substrate mycelium and aerial mycelium that fragmented into rod-shaped spore, with a smooth surface. The whole-cell hydrolysates of strain DW16-2T contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were arabinose, galactose, glucose and a trace amount of ribose. The polar lipids contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified phospholipids. The menaquinone (MK) was MK-8(H4). The cellular fatty acids (>5 %) were iso-C16 : 0, iso-C16 : 1 H, summed feature 3: C16 : 1 ω7c/C16 : 1 ω6c; C16 : 1 ω6c/C16 : 1 ω7c, C17 : 1 ω8c and anteiso-C17 : 0. Characterization based on chemotaxonomic, phenotypic, genotypic and phylogenetic evidence demonstrated that strain DW16-2T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia spirodelae sp. nov. (type strain DW16-2T = TBRC 16418T = NBRC 115857T) is proprosed. In addition, the comparison of the whole genome sequences suggested that P. alni and P. antarctica belong to the same species and P. carboxydivorans is a subspecies of P. alni. Therefore, it is proposed that P. antarctica Prabahar et al. 2004 is reclassified as a later heterotypic synonym of P. alni (Evtushenko et al. 1989) Warwick et al. 1994, and P. carboxydivorans Park et al. 2008 is proposed as a subspecies of P. alni (Evtushenko et al. 1989) Warwick et al. 1994.

Effects of storage durations on flavour and bacterial communities in Liupao tea

Long-term storage of Liupao tea is conducive to improving its flavour and commercial value. Although bacterial communities influence Liupao tea flavour, their impact during storage remains unclear. The aroma compounds and bacterial communities were determined by headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) and Illumina Nova6000 analysis. A total of 18 differential flavour compounds were significantly altered with Liupao tea storage duration, particularly after 9 years of storage. Flavour compounds with sweet notes increased, while those associated with pungent note decreased. The composition and diversity of bacteria remarkable changed after 9 years of tea storage. Six core functional bacteria were identified as contributing to the flavour characteristics of Liupao tea during long-term storage. Our findings provide novel insights that bacteria drive the formation of flavour characteristics during Liupao tea storage duration, and Liupao tea stored for more than 9 years have the best flavour.

Streptomyces macrolidinus sp. nov., a novel soil actinobacterium with potential anticancer and antimalarial activity

A novel actinomycete, strain RY43-2^T, belonging to the genus Streptomyces, was isolated from a peat swamp forest soil collected from Rayong Province, Thailand. The strain was characterized by using a polyphasic approach. The cell-wall peptidoglycan contained ll-diaminopimelic. Ribose and glucose were detected in its whole-cell hydrolysates. The strain contained anteiso-C_15:0, iso-C_14:0 and iso-C_16:0 as the predominant fatty acids, and MK-9(H₄), MK-9(H₆) and MK-9(H₈) as the major menaquinones. The phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, three unidentified ninhydrin-positive phospholipids and two unidentified phospholipids. Strain RY43-2^T showed the highest 16S rRNA gene similarity to Streptomyces misionensis JCM 4497^T (98.9 %) and Streptomyces lichenis LCR6-01^T (98.9 %). The draft genome of RY43-2^T was 6.7 Mb with 6078 coding sequences with an average G+C content of 70.8 mol%. Genomic analysis revealed that the average nucleotide identity (ANI) values based on blast (ANIb) and MUMmer (ANIm) between strain RY43-2^T and S. misionensis JCM 4497^T were 80.1 and 86.1%, respectively. The ANIb and ANIm values between strain RY43-2^T and S. lichenis LCR6-01^T were 77.0 and 85.5%, respectively. The digital DNA-DNA hybridization values were 25.2 and 23.0% in comparison with the draft genomes of S. misionensis JCM 4497^T and S. lichenis LCR6-01^T, respectively. The results of taxonomic analysis suggested that strain RY43-2^T represented a novel species of the genus Streptomyces for which the name Streptomyces macrolidinus sp. nov. is proposed. The type strain is RY43-2^T (=TBRC 7286^T=NBRC 115640^T). Strain RY43-2^T exhibited antimicrobial activity against Enterococcus faecium ATCC 51559, Colletotrichum capsici BMGC 106 and Colletotrichum gloeosporioides BMGC 107 with the minimum inhibitory concentration values of 25.0, 12.5, and 6.25 µg ml^-1. It also exhibited potent antimalarial activity against Plasmodium falciparum K1 with IC₅₀ of 0.0031 µg ml^-1. In addition, it showed cytotoxicity against Vero, KB, MCF-7 and NCI-H187 with IC₅₀ values of 0.0347, 6.15, 3.36 and 0.0352 µg ml^-1, respectively.

Pseudonocardia terrae sp. nov., an actinobacterium isolated from rice rhizosphere soil in Thailand

A novel actinomycete, designated strain RS11V-5T, was isolated from rhizosphere soil of Oryza sativa L. collected from Roi Et Province, Thailand, and its taxonomic position was evaluated. Cells of strain RS11V-5T were Gram-stain-positive, aerobic, and non-motile. Whole-cell hydrolysates contained meso-diaminopimelic acid, arabinose, galactose, glucose and ribose. MK-8(H4) was detected as the predominant menaquinone of this strain. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylmethylethanolamine, hydroxy-phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminolipid and an unidentified glycolipid. The major fatty acids were iso-C16 : 0, C16 : 0 and C16 : 1 ω7c/C16 : 1 ω6c. Phylogenetic analyses based on the 16S rRNA gene sequences showed that strain RS11V-5T belonged to the genus Pseudonocardia and had high 16S rRNA sequence similarity of 99.3 % to Pseudonocardia kujensis KCTC 29062T and less than 98.4 % to other members of the genus Pseudonocardia . The DNA G+C content of the strain RS11V-5T was 73.3 mol%. Strain RS11V-5T showed 46.5 % digital DNA–DNA hybridization, 92.2 % orthologous average nucleotide identity (OrthoANI), 90.2 % ANI based on blast and 92.7 % ANI based on MUMmer to P. kujensis KCTC 29062T. Based its phenotypic, genotypic, phylogenetic and chemotaxonomic characteristics, strain RS11V-5T represents a novel species of the genus Pseudonocardia , for which the name Pseudonocardia terrae sp. nov. is proposed. The type strain is RS11V-5T (=TBRC 15286T=NBRC 115296T).

Pseudonocardia humida sp. nov., an Actinomycete Isolated from Mangrove Soil Showing Distinct Distribution Pattern of Biosynthetic Gene Clusters

A novel actinomycete strain, designated S2-4^T, was isolated from a mangrove soil sample, and a polyphasic approach was employed to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene indicated that strain S2-4^T formed a unique clade next to that harboring Pseudonocardia dioxanivorans CB1190^T, which shared the highest sequence similarity (98.20%) with the new isolate. Phylogenetic analysis based on core genes of genomic sequences displayed a different scenario, exhibiting closer phylogenetic relationship of strain S2-4^T with several species with 16S rRNA gene sequence similarities ranging from 96.95 to 98.06%, which was confirmed by the phylogenetic tree reconstructed based on genomic sequences. Further, substantial differences between the genotypic properties of strain S2-4^T and its closest neighbors, including digital DNA-DNA hybridization, average nucleotide identity, and distribution patterns of biosynthetic gene clusters (BGC), indicated the taxonomic position of strain S2-4^T as a novel species of the genus Pseudonocardia. Accordingly, strain S2-4^T was observed to show a different distribution pattern of a predicted BGC encoding ectoine by comparative genomic analysis, which could be strongly linked to its unique habitat distinct from where its close neighbors were isolated. The major cellular fatty acids were iso-C_15:0, C_21:0, and iso-C_16:0. The predominant menaquinone was MK-8(H₄). The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidyl-N-monomethylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides, and two unidentified glycolipids. Here, we propose a novel species of the genus Pseudonocardia: Pseudonocardia humida sp. nov. with the type strain S2-4^T (= JCM 34291^T = CGMCC 4.7706^T).