Novosphingobium malaysiense sp. nov. isolated from mangrove sediment

Genomic-based taxonomic classification of the order Sphingomonadales

The order Sphingomonadales strains are globally distributed in various biomes and are renowned for their biodegradable and biosynthesis capabilities. At present, it consists of 4 families and 49 genera making it the third largest order within the class Alphaproteobacteria. However, their taxonomy remains complex, especially due to polyphyly in the family Sphingomonadaceae. In this study, we collected 429 Sphingomonadales type strain genomes, reconstructed robust phylogenomic relationships, and proposed delineation thresholds at the genus and family levels based on average amino acid identities (AAI) and evolutionary distances (ED). Based on the maximum-likelihood and Bayesian phylogenomic trees reconstructed by two molecular sets determined by orthologous sequence identity and the Genome Taxonomy Database, the consensus degree values were all higher than 90%, revealing that those phylogenomic trees had similar topological structures. By confirming monophyletic taxa and determining stable nodes, we reclassified the order Sphingomonadales into thirteen families including nine novel ones. AAI calculations indicated that the average intra-family AAI values ranged from 0.62 to 0.84, while inter-family ones were 0.51 to 0.60. ED summaries demonstrated that the average and median intra-family ED values were 0.16 to 0.57, and inter-family ones ranged from 0.50 to 1.22. Comparisons of AAI and ED values calculated by using genomic and phylogenetic analyses supported that those 13 families were significantly separated with p values < 2.2×10-16. Thus, it was speculated that the AAI and ED thresholds for distinguishing different families were <0.6 and >0.5, respectively. Additionally, we reclassified 163 species into new genera with their phylogenetic topologies, according to the previous genus AAI and ED boundaries of 0.7 and 0.4. Our study is the first genomic-based study of the order Sphingomonadales and will promote further insights into the evolution of this order.

Novosphingobium beihaiensis sp. nov., a novel pesticide-tolerant bacterium isolated from mangrove sediments

A novel Novosphingobium species, designated strain B2638T, was isolated from mangrove sediments which was collected from Beibu Gulf, Beihai, P. R. China. The isolate could grow in the presence of chlorpyrifos. Phylogenetic analysis based on 16S rRNA gene sequence revealed that the isolate belonged to the genus Novosphingobium, showing 99.9% sequence similarity with N. decloroationis 502str22T and less than 98% similarity with other type strain of species of this genus. Molecular typing by BOX-PCR divided strain B2638T and N. declorationis 502str22T into two clusters and indicated that they were not identical. Genomic comparison referenced by values of the DNA-DNA hybridization (dDDH) and the average nucleotide identity (ANI) between strain B2638T and its close phylogenetic neighbors were 20.0-29.5% and 75.3-85.3%, respectively, that were lower than proposed thresholds for bacterial species delineation. The major fatty acids (> 10%) were identified as C18:1 ω7c, C17:1 iso ω9c and C16:0. The main polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, phosphatidyl glycerol, unidentified lipid and unidentified aminolipid. Results from phenotypic, chemotaxonomic and genotypic analyses proposed that strain B2638T (= MCCC 1K07406T = KCTC 72968 T) is represented a novel species in the genus Novosphingobium, for which the names Novosphingobium beihaiensis sp. nov. is proposed.

Novosphingobium album sp. nov., Novosphingobium organovorum sp. nov. and Novosphingobium mangrovi sp. nov. with the organophosphorus pesticides degrading ability isolated from mangrove sediments

Members of the genus Novosphingobium were frequently isolated from polluted environments and possess great bioremediation potential. Here, three species, designated B2637^T, B2580^T and B1949^T, were isolated from mangrove sediments and might represent novel species in the genus Novosphingobium based on a polyphasic taxonomy study. Phylogenomic analysis revealed that strains B2580^T, B1949^T and B2637^T clustered with Novosphingobium naphthalenivorans NBRC 102051^T, 'N. profundi' F72 and N. decolorationis 502str22^T, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between isolates and their closely related species were less than 94 and 54 %, respectively, all below the threshold of species discrimination. The sizes of the genomes of isolates B2580^T, B2637^T and B1949^T ranged from 4.4 to 4.6 Mb, containing 63.3-66.4 % G+C content. Analysis of their genomic sequences identified genes related to pesticide degradation, heavy-metal resistance, nitrogen fixation, antibiotic resistance and sulphur metabolism, revealing the biotechnology potential of these isolates. Except for B2637^T, B1949^T and B2580^T were able to grow in the presence of quinalphos. Results from these polyphasic taxonomic analyses support the affiliation of these strains to three novel species within the genus Novosphingobium, for which we propose the name Novosphingobium album sp. nov. B2580^T (=KCTC 72967^T=MCCC 1K04555^T), Novosphingobium organovorum sp. nov. B1949^T (=KCTC 92158^T=MCCC 1K03763^T) and Novosphingobium mangrovi sp. nov. B2637^T (KCTC 72969^T=MCCC 1K04460^T).

Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid

A novel bacterial strain, designated GeG2T, was isolated from soils of the native Cerrado, a highly biodiverse savanna-like Brazilian biome. 16S rRNA gene analysis of GeG2T revealed high sequence identity (100%) to the alphaproteobacterium Novosphingobium rosa; however, comparisons with N. rosa DSM 7285T showed several distinctive features, prompting a full characterization of the new strain in terms of physiology, morphology, and, ultimately, its genome. GeG2T cells were Gram-stain-negative bacilli, facultatively anaerobic, motile, positive for catalase and oxidase activities, and starch hydrolysis. Strain GeG2T presented planktonic-sessile dimorphism and cell aggregates surrounded by extracellular matrix and nanometric spherical structures were observed, suggesting the production of exopolysaccharides (EPS) and outer membrane vesicles (OMVs). Despite high 16S rDNA identity, strain GeG2T showed 90.38% average nucleotide identity and 42.60% digital DNA-DNA hybridization identity with N. rosa, below species threshold. Whole-genome assembly revealed four circular replicons: a 4.1 Mb chromosome, a 2.7 Mb extrachromosomal megareplicon, and two plasmids (212.7 and 68.6 kb). The megareplicon contains a few core genes and plasmid-type replication/maintenance systems, consistent with its classification as a chromid. Genome annotation shows a vast repertoire of carbohydrate-active enzymes and genes involved in the degradation of aromatic compounds, highlighting the biotechnological potential of the new isolate. Chemotaxonomic features, including polar lipid and fatty acid profiles, as well as physiological, molecular, and whole-genome comparisons showed significant differences between strain GeG2T and N. rosa, indicating that it represents a novel species, for which the name Novosphingobium terrae is proposed. The type strain is GeG2T (= CBMAI 2313T = CBAS 753 T).

Novosphingobium aureum sp. nov., a marine bacterium isolated from salt flat sediment

A Gram-stain-negative, aerobic, pale yellow-coloured, rod-shaped marine bacterium designated strain YJ-S2-02^T was isolated from salt flat sediment sampled in Yongyu-do, Republic of Korea. Strain YJ-S2-02^T grew at pH 6.0-9.0 (optimum, pH 7.0), 10-40 °C (optimum, 30 °C) and with optimum 1 % (w/v) NaCl. The 16S rRNA gene sequence analysis indicated that strain YJ-S2-02^T was closely related to Novosphingobium naphthalenivorans NBRC 102051^T (97.8 %) followed by Novosphingobium mathurense SM117^T (97.5 %), Novosphingobium indicum H25^T (97.3 %), Novosphingobium pentaromativorans US6-1^T (96.8 %), Novosphingobium fontis STM-14^T (96.6 %), Novosphingobium endophyticum EGI60015^T (96.5 %), Novosphingobium naphthae D39^T (96.5 %) and Novosphingobium malaysiense MUSC 273^T (95.9 %). The average nucleotide identity and estimated DNA-DNA hybridization values between YJ-S2-02^T and related type strains were 77.0-77.9 % and 19.1-24.0 %. Strain YJ-S2-02^T was characterized as having Q-10 as the predominant respiratory quinone and the principal fatty acids (>10 %) were summed feature 8 (C_18 : 1  ω6c/ω7c, 20.7 %), C_18 : 3  ω6c (16.3 %) and C_17 : 1  ω6c (11.8 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingolipids and two unidentified lipids. The DNA G+C content of strain YJ-S2-02^T was 65.6 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, YJ-S2-02^T should be classified as representing a novel species within the genus Novosphingobium, for which name Novosphingobium aureum is proposed, with the type strain YJ-S2-02^T (=KACC 21677^T =KCTC 72891^T=JCM 33996^T).

Kaustia mangrovi gen. nov., sp. nov. isolated from Red Sea mangrove sediments belongs to the recently proposed Parvibaculaceae family within the order Rhizobiales

We isolated a novel strain, R1DC25T, described as Kaustia mangrovi gen. nov. sp. nov. from the sediments of a mangrove forest on the coast of the Red Sea in Saudi Arabia. This isolate is a moderately halophilic, aerobic/facultatively anaerobic Gram-stain-negative bacterium showing optimum growth at between 30 and 40 °C, at a pH of 8.5 and with 3-5 % NaCl. The genome of R1DC25T comprises a circular chromosome that is 4 630 536 bp in length, with a DNA G+C content of 67.3 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis of 120 concatenated single-copy genes revealed that R1DC25T represents a distinct lineage within the family Parvibaculaceae in the order Rhizobiales within the class Alphaproteobacteria. R1DC25T showing 95.8, 95.3 and 94.5 % 16S rRNA gene sequence identity with Rhodoligotrophos appendicifer, Rhodoligotrophos jinshengii and Rhodoligotrophos defluvii, respectively. The predominant quinone was Q-10, and the polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, as well as several distinct aminolipids and lipids. The predominant cellular fatty acids were C19 : 0 cyclo ω8c, a combination of C18 : 1ω7c and/or C18 : 1ω6c and C16 : 0. On the basis of the differences in the phenotypic, physiological and biochemical characteristics from its known relatives and the results of our phylogenetic analyses, R1DC25T (=KCTC 72348T;=JCM 33619T;=NCCB 100699T) is proposed to represent a novel species in a novel genus, and we propose the name Kaustia mangrovi gen. nov., sp. nov. (Kaustia, subjective name derived from the abbreviation KAUST for King Abdullah University of Science and Technology; mangrovi, of a mangrove).

Novosphingobium ovatum sp. nov., isolated from a freshwater mesocosm

A bacterial strain, designated FSY-8^T, was isolated from a freshwater mesocosm in Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain FSY-8^T were aerobic, Gram-stain-negative, rod-shaped, non-motile and formed yellow coloured colonies on Reasoner's 2A agar. Growth occurred at 20-40 °C (optimum, 30-37 °C) and pH 5-7 (optimum, pH 6) and in the presence of 0-0.5 % NaCl (optimum, 0 %, w/v). The major fatty acids (>10 %) of strain FSY-8^T were summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c) and summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, diphosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 64.8 mol %. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-8^T formed a phylogenetic lineage in the genus Novosphingobium. Strain FSY-8^T showed 71.6-77.2 % average nucleotide identity and 19.9-22.8 % digital DNA-DNA hybridization identity with the strains of other Novosphingobium species. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-8^T should be classified in a novel species of the genus Novosphingobium, for which the name Novosphingobium ovatum sp. nov. is proposed. The type strain is FSY-8^T (=BCRC 81051^T=LMG 30053^T=KCTC 52812^T).

Novosphingobium umbonatum sp. nov., isolated from a freshwater mesocosm

A bacterial strain designated FSY-9^T was isolated from a freshwater mesocosm in Taiwan and characterized to determine its taxonomic affiliation. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-9^T formed a phylogenetic lineage in the genus Novosphingobium. Strain FSY-9^T was most closely related to Novosphingobium humi R1-4^T with a 97.2 % 16S rRNA gene sequence similarity. Strain FSY-9^T showed 71.3-72.6 % average nucleotide identity and 17.7-23.0 % digital DNA-DNA hybridization identity with the strains of other Novosphingobium species. Cells of strain FSY-9^T were facultatively anaerobic, Gram-negative, rod-shaped, non-motile and formed light yellow coloured colonies. Growth occurred at 15-37 °C and pH 5.5-7, and in the presence of 0-0.5 % NaCl. The major fatty acids (>10 %) of strain FSY-9^T were summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c), C_18 : 1ω7c and C_16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, sphingoglycolipid, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 61.5 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-9^T should be classified as a novel species of the genus Novosphingobium, for which the name Novosphingobium umbonatum sp. nov. is proposed. The type strain is FSY-9^T (=BCRC 81052^T=LMG 30054^T=KCTC 52813^T).

Kinetics of hydrocarbon degradation by a newly isolated heavy metal tolerant bacterium Novosphingobium panipatense P5:ABC

This study report kinetics of PAHs and crude oil degradation by a newly isolated multiple heavy metal tolerant Novosphingobium panipatense P5:ABC. The isolate showed hydrocarbon degrading enzyme activities namely alkane hydroxylase, catechol 1,2-dioxygenase and catechol 2,3-dioxygenase. The level of C23O activity was 9.63 times higher than C12O thus suggesting active involvement of meta-cleavage pathway. The data of biodegradation of hydrocarbons fitted well to the first order kinetic model. The degradation rate was highest for phenanthrene followed by crude oil, and fluoranthene. We have further reported the estimate of fundamental kinetic parameters, half-saturation constant (K_s) and maximum degradation rates (V_max) for biodegradation of phenanthrene and fluoranthene. Overall characterization underscores the potential of Novosphingobium in bioremediation of crude oil polluted sites.

Description of novel members of the family Sphingomonadaceae: Aquisediminimonas profunda gen. nov., sp. nov., and Aquisediminimonas sediminicola sp. nov., isolated from freshwater sediment

Two Gram-stain-negative bacterial strains, DS48-3^T and CH68-4^T, were isolated from freshwater sediment taken from the Daechung Reservoir, Republic of Korea. Cells of strains DS48-3^T and CH68-4^T were aerobic, non-motile, non-spore-forming and rod-shaped. Strain DS48-3^T was isolated from a sediment surface sample at a depth of 48 m from the Daechung Reservoir and was most closely related to the genus Sphingopyxis according to 16S rRNA gene sequence analysis (94.5-95.9 % similarity). Strain CH68-4^T was isolated from the very bottom of a 67-cm-long sediment core collected from Daechung Reservoir at a water depth of 17 m and was most closely related to the genus Sphingopyxis (16S rRNA gene sequence similarity of 93.7-95.0 %). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the two strains formed a separate lineage within the order Sphingomonadales showing similarity values below 95.9 % with their closest phylogenetic neighbours, and sharing 97.3 % similarity with each other. The combined genotypic and phenotypic data showed that strains DS48-3^T and CH68-4^T could be distinguished from all genera within the family Sphingomonadaceae and represented two distinct species of a novel genus, Aquisediminimonas profunda gen. nov., sp. nov. (type strain DS48-3^T=KCTC 52068^T=CCTCC AB 2018061^T) and Aquisediminimonas sediminicola sp. nov. (type strain CH68-4^T=KCTC 62205^T=CCTCC AB 2018062^T).

Streptomyces monashensis sp. nov., a novel mangrove soil actinobacterium from East Malaysia with antioxidative potential

A new Streptomyces species discovered from Sarawak mangrove soil is described, with the proposed name - Streptomyces monashensis sp. nov. (strain MUSC 1JT). Taxonomy status of MUSC 1JT was determined via polyphasic approach. Phylogenetic and chemotaxonomic properties of strain MUSC 1JT were in accordance with those known for genus Streptomyces. Based on phylogenetic analyses, the strains closely related to MUSC 1JT were Streptomyces corchorusii DSM 40340T (98.7%), Streptomyces olivaceoviridis NBRC 13066T (98.7%), Streptomyces canarius NBRC 13431T (98.6%) and Streptomyces coacervatus AS-0823T (98.4%). Outcomes of DNA-DNA relatedness between strain MUSC 1JT and its closely related type strains covered from 19.7 ± 2.8% to 49.1 ± 4.3%. Strain MUSC 1JT has genome size of 10,254,857 bp with DNA G + C content of 71 mol%. MUSC 1JT extract exhibited strong antioxidative activity up to 83.80 ± 4.80% in the SOD assay, with significant cytotoxic effect against colon cancer cell lines HCT-116 and SW480. Streptomyces monashensis MUSC 1JT (=DSM 103626T = MCCC 1K03221T) could potentially be a producer of novel bioactive metabolites; hence discovery of this new species may be highly significant to the biopharmaceutical industry as it could lead to development of new and useful chemo-preventive drugs.

Novosphingobium arvoryzae sp. nov., isolated from a flooded rice field

A bacterial strain, designated Jyi-02^T, was isolated from a flooded rice field in Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain Jyi-02^T were aerobic, Gram-stain-negative, rod-shaped, non-motile and formed yellowish orange coloured colonies. Growth occurred at 10-40 °C (optimum, 20 °C) and pH 5.0-9.0 (optimum, pH 7.0) and in the presence of 0-1.0 % NaCl (optimum, 0 %, w/v). The major fatty acids (>10 %) of strain Jyi-02^T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C14 : 0 2-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, sphingoglycolipid, an uncharacterized phospholipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 64.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Jyi-02^T belonged to the genus Novosphingobium and had closest phylogenetic similarity to Novosphingobium soli CC-TPE-1^T (97.8 %). The DNA-DNA relatedness of strain Jyi-02^T with respect to valid published species of the genus Novosphingobium was less than 35 %. Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Novosphingobium. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Jyi-02^T represents a novel species in the genus Novosphingobium, for which the name Novosphingobium arvoryzae sp. nov. is proposed. The type strain is Jyi-02^T (=BCRC 80537^T=KCTC 32422^T).

Novosphingobium lubricantis sp. nov., isolated from a coolant lubricant emulsion

A yellow-pigmented, Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain KSS165-70^T) was isolated from a coolant lubricant emulsion. The 16S rRNA gene sequence analysis of strain KSS165-70^T showed high sequence similarity to the type strains of Novosphingobium subterraneum (98.1 %), Novosphingobium lentum (97.9 %) and Novosphingobium taihuense (97.8 %). Sequence similarities to type strains of all other Novosphingobium species were below 97.5 %. Ubiquinone Q-10 was detected as the major respiratory quinone. The predominant fatty acid C18 : 1ω7c and the typical 2-hydroxy fatty acid C14 : 0 2-OH were detected. The polar lipid profile contained the major lipids diphosphatidylglycerol, phosphatedylethanolamine, sphingoglycolipid, phosphatidylcholine and two unidentified phospholipids. The polyamine pattern contained the major compound spermidine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, and ubiquinone, polar lipid and fatty acid composition revealed that strain KSS165-70^T represents a new species of the genus Novosphingobium. For this reason, we propose the name Novosphingobium lubricantis sp. nov. with the type strain KSS165-70^T (=CIP 111490^T=CCM 8814^T).

Novosphingobium ipomoeae sp. nov., isolated from a water convolvulus field

A bacterial strain designated Tese-5T was isolated from a water convolvulus field in Taiwan and characterized using the polyphasic taxonomic approach. Strain Tese-5T was an aerobic, Gram-stain-negative, non-motile, rod-shaped bacterium and formed bright yellow coloured colonies. Strain Tese-5T grew at 15-35 °C (optimum, 30 °C), with 0-1.0 % NaCl (optimum, 0-0.5 %) and at pH 5.5-7 (optimum, pH 6). The major fatty acids (>10 %) of strain Tese-5T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid profile comprised phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and sphingoglycolipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 65.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Tese-5T belonged to the genus Novosphingobium and showed the highest levels of sequence similarity to Novosphingobium chloroacetimidivorans BUT-14T and Novosphingobium mathurense SM117T (96.3 %). Phenotypic characteristics of the novel strain also differed from those of the closest-related species of the genus Novosphingobium. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Tese-5T represents a novel species in the genus Novosphingobium, for which the name Novosphingobium ipomoeaesp. nov. is proposed. The type strain is Tese-5T (=BCRC 80904T=LMG 28838T=KCTC 42656T).

Streptomyces colonosanans sp. nov., A Novel Actinobacterium Isolated from Malaysia Mangrove Soil Exhibiting Antioxidative Activity and Cytotoxic Potential against Human Colon Cancer Cell Lines

Streptomyces colonosanans MUSC 93J^T, a novel strain isolated from mangrove forest soil located at Sarawak, Malaysia. The bacterium was noted to be Gram-positive and to form light yellow aerial and vivid yellow substrate mycelium on ISP 2 agar. The polyphasic approach was used to determine the taxonomy of strain MUSC 93J^T and the strain showed a range of phylogenetic and chemotaxonomic properties consistent with those of the members of the genus Streptomyces. Phylogenetic and 16S rRNA gene sequence analysis indicated that closely related strains include Streptomyces malachitofuscus NBRC 13059^T (99.2% sequence similarity), Streptomyces misionensis NBRC 13063^T (99.1%), and Streptomyces phaeoluteichromatogenes NRRL 5799^T (99.1%). The DNA–DNA relatedness values between MUSC 93J^T and closely related type strains ranged from 14.4 ± 0.1 to 46.2 ± 0.4%. The comparison of BOX-PCR fingerprints indicated MUSC 93J^T exhibits a unique DNA profile. The genome of MUSC 93J^T consists of 7,015,076 bp. The DNA G + C content was determined to be 69.90 mol%. The extract of strain MUSC 93J^T was demonstrated to exhibit potent antioxidant activity via ABTS, metal chelating, and SOD assays. This extract also exhibited anticancer activity against human colon cancer cell lines without significant cytotoxic effect against human normal colon cells. Furthermore, the chemical analysis of the extract further emphasizes the strain is producing chemo-preventive related metabolites. Based on this polyphasic study of MUSC 93J^T, it is concluded that this strain represents a novel species, for which the name Streptomyces colonosanans sp. nov. is proposed. The type strain is MUSC 93J^T (= DSM 102042^T = MCCC 1K02298^T).

Novosphingobium guangzhouense sp. nov., with the ability to degrade 1-methylphenanthrene

A novel Gram-stain-negative, flagellated, rod-shaped, yellow-pigmented aerobic bacterium, strain SA925T, that is capable of degrading 1-methylphenanthrene was isolated from oil-polluted soil collected from a refinery located in Guangzhou, China. Phylogenetic analysis based on the 16S rRNA gene sequence demonstrated that strain SA925T belongs to the genus Novosphingobium and is evolutionarily close to the type strains of Novosphingobium gossypii (98.5 % similarity), Novosphingobium panipatense (98.2 %), Novosphingobium mathurense (98.0 %) and Novosphingobium pentaromativorans (96.5 %). The G+C content of the genomic DNA was 60.2 mol%. DNA-DNA hybridization experiments between strain SA925T and the closest strain, Novosphingobium gossypii JM-1396T, revealed a low level of relatedness (35.5 %). Strain SA925T grew at 10-35 °C, at pH 6.0-8.0 and in the presence of 0-4 % (w/v) NaCl. The major fatty acids were C18 : 1ω7c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipid profiles mainly consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylethanolamine and sphingoglycolipid (the characteristic polar lipid). The predominant ubiquinone was Q-10. The major polyamine was spermidine. Based on the phylogenetic, phenotypic and physiological characteristics, strain SA925T was considered to represent a novel species of the genus Novosphingobium, for which the name Novosphingobium guangzhouense sp. nov. is proposed. The type strain is SA925T (=DSM 32207T=GDMCC 1.1110T).

Novosphingobium profundi sp. nov. isolated from a deep-sea seamount

A marine bacterial strain, F72^T, was isolated from a solitary scleractinian coral, collected in Yap seamounts in the Pacific Ocean. Strain F72^T is a Gram-negative, light-yellow-pigmented, motile, rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain F72^T is related to the genus Novosphingobium and has high 16S rRNA gene sequence similarities with the type strains of Novosphingobium pentaromativorans US6-1^T (97.7 %), Novosphingobium panipatense SM16^T (97.6 %), Novosphingobium mathurense SM117^T (97.2 %) and Novosphingobium barchaimii LL02^T (97.1 %). Ubiquinone Q-10 was detected as the dominant quinone. The predominant cellular fatty acids were C_18:1ω7c and C_17:1ω6c. The genomic DNA G+C content of strain F72^T was 63.4 mol %. The polar lipids profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine, sphingoglycolipid and one uncharacterized lipid. Strain F72^T shared DNA relatedness of 25 % with N. pentaromativorans JCM 12182^T, 31 % with N. panipatense DSM 22890^T, 21 % with N. mathurense DSM 23374^T and 26 % with N. barchaimii DSM 25411^T. Combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies demonstrated that the strain F72^T is a representative of a novel species of the genus Novosphingobium, for which we propose the name Novosphingobium profundi sp. nov. (type strain F72^T = KACC 18566^T = CGMCC 1.15390^T).

Streptomyces antioxidans sp. nov., a Novel Mangrove Soil Actinobacterium with Antioxidative and Neuroprotective Potentials

A novel strain, Streptomyces antioxidans MUSC 164^T was recovered from mangrove forest soil located at Tanjung Lumpur, Malaysia. The Gram-positive bacterium forms yellowish-white aerial and brilliant greenish yellow substrate mycelium on ISP 2 agar. A polyphasic approach was used to determine the taxonomy status of strain MUSC 164^T. The strain showed a spectrum of phylogenetic and chemotaxonomic properties consistent with those of the members of the genus Streptomyces. The cell wall peptidoglycan was determined to contain LL-diaminopimelic acid. The predominant menaquinones were identified as MK-9(H₆) and MK-9(H₈), while the identified polar lipids consisted of aminolipid, diphosphatidylglycerol, glycolipid, hydroxyphosphatidylethanolamine, phospholipid, phosphatidylinositol, phosphatidylethanolamine, phosphatidylglycerol and lipid. The cell wall sugars consist of galactose, glucose and ribose. The predominant cellular fatty acids (>10.0%) were identified as iso-C_15:0 (34.8%) and anteiso-C_15:0(14.0%). Phylogenetic analysis identified that closely related strains for MUSC 164^T as Streptomyces javensis NBRC 100777^T (99.6% sequence similarity), Streptomyces yogyakartensis NBRC 100779^T (99.6%) and Streptomyces violaceusniger NBRC 13459^T (99.6%). The DNA–DNA relatedness values between MUSC 164^T and closely related type strains ranged from 23.8 ± 0.3% to 53.1 ± 4.3%. BOX-PCR fingerprints comparison showed that MUSC 164^T exhibits a unique DNA profile, with DNA G + C content determined to be 71.6 mol%. Based on the polyphasic study of MUSC 164^T, it is concluded that this strain represents a novel species, for which the name Streptomyces antioxidans sp. nov. is proposed. The type strain is MUSC 164^T (=DSM 101523^T = MCCC 1K01590^T). The extract of MUSC 164^T showed potent antioxidative and neuroprotective activities against hydrogen peroxide. The chemical analysis of the extract revealed that the strain produces pyrazines and phenolic-related compounds that could explain for the observed bioactivities.

Streptomyces malaysiense sp. nov.: A novel Malaysian mangrove soil actinobacterium with antioxidative activity and cytotoxic potential against human cancer cell lines

Actinobacteria from the unique intertidal ecosystem of the mangroves are known to produce novel, bioactive secondary metabolites. A novel strain known as MUSC 136^T (=DSM 100712^T = MCCC 1K01246^T) which was isolated from Malaysian mangrove forest soil has proven to be no exception. Assessed by a polyphasic approach, its taxonomy showed a range of phylogenetic and chemotaxonomic properties consistent with the genus of Streptomyces. Phylogenetically, highest similarity was to Streptomyces misionensis NBRC 13063^T (99.6%) along with two other strains (>98.9% sequence similarities). The DNA–DNA relatedness between MUSC 136^T and these type strains ranged from 22.7 ± 0.5% to 46.5 ± 0.2%. Overall, polyphasic approach studies indicated this strain represents a novel species, for which the name Streptomyces malaysiense sp. nov. is proposed. The potential bioactivities of this strain were explored by means of antioxidant and cytotoxic assays. Intriguingly, MUSC 136^T exhibited strong antioxidative activities as evaluated by a panel of antioxidant assays. It was also found to possess high cytotoxic effect against HCT-116 cells, which probably mediated through altering p53 protein and intracellular glutathione levels. Chemical analysis of the extract using GC-MS further affirms that the strain produces chemopreventive related metabolites.

Streptomyces humi sp. nov., an actinobacterium isolated from soil of a mangrove forest

A novel Streptomyces strain, MUSC 119(T), was isolated from a soil collected from a mangrove forest. Cells of MUSC 119(T) stained Gram-positive and formed light brownish grey aerial mycelium and grayish yellowish brown substrate mycelium on ISP 2 medium. A polyphasic approach was used to determine the taxonomic status of strain MUSC 119(T), which shows a range of phylogenetic and chemotaxonomic properties consistent with those of the genus Streptomyces. The cell wall peptidoglycan consisted of LL-diaminopimelic acid. The predominant menaquinones were identified as MK-9(H8), MK-9(H6) and MK-9(H4). The polar lipid profile consisted of phosphatidylinositol, phosphatidylethanolamine, glycolipids, diphosphatidylglycerol and four phospholipids. The predominant cellular fatty acids were anteiso-C15:0, iso-C16:0, and anteiso-C17:0. The cell wall sugars were glucose, mannose, ribose and rhamnose. The phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain MUSC119(T) to be closely related to Streptomyces rhizophilus JR-41(T) (99.0 % sequence similarity), S. panaciradicis 1MR-8(T) (98.9 %), S. gramineus JR-43(T) (98.8 %) and S. graminisoli JR-19(T) (98.7 %). These results suggest that MUSC 119(T) should be placed within the genus Streptomyces. DNA-DNA relatedness values between MUSC 119(T) to closely related strains ranged from 14.5 ± 1.3 to 27.5 ± 0.7 %. The G+C content was determined to be 72.6 mol %. The polyphasic study of MUSC 119(T) showed that this strain represents a novel species, for which the name Streptomyces humi sp. nov. is proposed. The type strain of S. humi is MUSC 119(T) (=DSM 42174(T) = MCCC 1K00505(T)).

Evaluation of Antioxidative and Cytotoxic Activities of Streptomyces pluripotens MUSC 137 Isolated from Mangrove Soil in Malaysia

Streptomyces pluripotens MUSC 137 was isolated from mangrove soil obtained from Tanjung Lumpur, Pahang, Malaysia. We investigated the phylogenetic, genomic, biochemical, and phenotypic characteristics of this strain. Uniquely adapted microorganisms from mangrove habitats have previously yielded compounds of biopharmaceutical interest. In order to examine the bioactivities possessed by the strain, fermentation extract was prepared through solvent extraction method prior to bioactivities screenings. Antioxidant activity was examined via DPPH assay while the cytotoxic effect was assessed by means of examining the activity of the extract against selected human cancer cell lines, namely colon cancer cells (HCT-116, Caco-2, SW480, and HT-29), breast cancer cell (MCF-7), lung cancer cell (A549), prostate cancer cell (DU145), and cervical cancer cell (Ca Ski). The results revealed MUSC 137 possesses significant antioxidant activity and demonstrates cytotoxic effect against several cancer cell lines tested. The results indicated MCF-7 cells were most susceptible to the extract with the lowest IC₅₀ (61.33 ± 17.10 μg/mL), followed by HCT-116 and A549. Additionally, selective index (SI) showed that MUSC 137 extract was less toxic against normal cell lines when compared to MCF-7 and HCT-116 cells. The extract was further subjected to chemical analysis using GC–MS and revealed the presence of deferoxamine and pyrrolizidines related compounds which may account for the antioxidant and cytotoxic properties observed.

Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum

A Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a yellow pigment, was isolated from the healthy internal stem tissue of post-harvest cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit at the E. V. Smith Research Center in Tallassee (Macon county), AL, USA. 16S rRNA gene sequence analysis of strain JM-1396T showed high sequence similarity values to the type strains of Novosphingobium mathurense, Novosphingobium panipatense (both 98.6 %) and Novosphingobium barchaimii (98.5 %); sequence similarities to all other type strains of species of the genus Novosphingobium were below 98.3 %. DNA–DNA pairing experiments of the DNA of strain JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T showed low relatedness values of 8 % (reciprocal 7 %), 24 % (reciprocal 26 %) and 19 % (reciprocal 25 %), respectively. Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid, C14 : 0 2-OH (11.7 %), were detected as typical components. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern contained the major compound spermidine and only minor amounts of other polyamines. All these data revealed that strain JM-1396T represents a novel species of the genus Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov. with the type strain JM-1396T ( = LMG 28605T = CCM 8569T = CIP 110884T).

Presence of antioxidative agent, Pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro- in newly isolated Streptomyces mangrovisoli sp. nov

A novel Streptomyces, strain MUSC 149(T) was isolated from mangrove soil. A polyphasic approach was used to study the taxonomy of MUSC 149(T), which shows a range of phylogenetic and chemotaxonomic properties consistent with those of the members of the genus Streptomyces. The diamino acid of the cell wall peptidoglycan was LL-diaminopimelic acid. The predominant menaquinones were identified as MK9(H8) and MK9(H6). Phylogenetic analysis indicated that closely related strains include Streptomyces rhizophilus NBRC 108885(T) (99.2% sequence similarity), S. gramineus NBRC 107863(T) (98.7%) and S. graminisoli NBRC 108883(T) (98.5%). The DNA-DNA relatedness values between MUSC 149(T) and closely related type strains ranged from 12.4 ± 3.3% to 27.3 ± 1.9%. The DNA G + C content was determined to be 72.7 mol%. The extract of MUSC 149(T) exhibited strong antioxidant activity and chemical analysis reported identification of an antioxidant agent, Pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro-. These data showed that metabolites of MUSC 149(T) shall be useful as preventive agent against free-radical associated diseases. Based on the polyphasic study of MUSC 149(T), the strain merits assignment to a novel species, for which the name S. mangrovisoli sp. nov. is proposed. The type strain is MUSC 149(T) (=MCCC 1K00699(T)=DSM 100438(T)).

Streptomyces gilvigriseus sp. nov., a novel actinobacterium isolated from mangrove forest soil

A novel Streptomyces, strain MUSC 26(T), was isolated from mangrove soil at Tanjung Lumpur, Malaysia. The bacterium was observed to be Gram-positive and to form grayish yellow aerial and substrate mycelium on ISP 7 agar. A polyphasic approach was used to study the taxonomy of strain MUSC 26(T), which shows a range of phylogenetic and chemotaxonomic properties consistent with those of the members of the genus Streptomyces. The cell wall peptidoglycan was determined to contain LL-diaminopimelic acid. The predominant menaquinones were identified as MK-9 (H8) and MK-9(H6). The polar lipids detected were identified as diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylmethylethanolamine and hydroxyphosphatidylmethylethanolamine. The predominant cellular fatty acids (>10.0 %) were identified as anteiso-C15:0 (31.4 %), iso-C16:0 (16.3 %), iso-C15:0 (13.9 %) and anteiso-C17:0 (12.6 %). The cell wall sugars were found to be galactose, glucose, mannose, ribose and rhamnose. These results suggest that MUSC 26(T) should be placed within the genus Streptomyces. Phylogenetic analysis indicated that closely related strains include Streptomyces qinglanensis 172205(T) (96.5 % sequence similarity), S. sodiiphilus YIM 80305(T) (96.5 %) and S. rimosus subsp. rimosus ATCC 10970(T) (96.4 %). DNA-DNA relatedness values between MUSC 26(T) and closely related type strains ranged from 17.0 ± 2.2 to 33.2 ± 5.3 %. Comparison of BOX-PCR fingerprints indicated MUSC 26(T) presents a unique DNA profile. The DNA G+C content was determined to be 74.6 mol%. Based on this polyphasic study of MUSC 26(T), it is concluded that this strain represents a novel species, for which the name Streptomyces gilvigriseus sp. nov. is proposed. The type strain is MUSC 26(T) (=DSMZ 42173(T) = MCCC 1K00504(T)).

Novosphingobium marinum sp. nov., isolated from seawater

A Gram-stain-negative, aerobic, short rod-shaped bacterium, strain LA53T, was isolated from a deep-sea water sample collected from the eastern Pacific Ocean. Strain LA53T grew in the presence of 0–7.0 % (w/v) NaCl and at 15-37 °C; optimum growth was observed with 1.0–2.0 % (w/v) NaCl and at 35 °C. Chemotaxonomic analysis showed ubiquinone-10 as the predominant respiratory quinone, C18 : 1ω7c and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) as major fatty acids, and diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid as major polar lipids. The genomic DNA G+C content was 57.7 mol%. Phylogenetic analyses revealed that strain LA53T belongs to the genus Novosphingobium . 16S rRNA gene sequence similarities between strain LA53T and the type strains of species of the genus Novosphingobium with validly published names ranged from 93.1 to 96.3 %. In addition, strain LA53T could be differentiated from Novosphingobium pentaromativorans DSM 17173T and Novosphingobium indicum DSM 23608T as well as the type strain of the type species of the genus, Novosphingobium capsulatum DSM 30196T, by some phenotypic characteristics, including hydrolysis of substrates, utilization of carbon sources and susceptibility to antibiotics. On the basis of phenotypic and genotypic data, strain LA53T represents a novel species within the genus Novosphingobium , for which the name Novosphingobium marinum sp. nov. is proposed. The type strain is LA53T ( = CGMCC 1.12918T = JCM 30307T).

Sinomonas humi sp. nov., an amylolytic actinobacterium isolated from mangrove forest soil

Strain MUSC 117(T) was isolated from mangrove soil of the Tanjung Lumpur forest in Pahang, Malaysia. This bacterium was yellowish-white pigmented, Gram-staining-positive, rod-coccus shaped and non-motile. On the basis of 16S rRNA gene sequence, strain MUSC 117(T) exhibited highest sequence similarity to Sinomonas atrocyanea DSM 20127(T) (98.0 %), Sinomonas albida LC13(T) (97.9 %) and Sinomonas soli CW 59(T) (97.8 %), and lower (<97.6 %) sequence similarity to other species of the genus Sinomonas. DNA-DNA hybridization experiments revealed a low level of DNA-DNA relatedness (less than 27 %) between strain MUSC 117(T) and closely related species. Chemotaxonomically, the peptidoglycan type was A3α, containing the amino acids lysine, serine, glycine, alanine, glutamic acid and muramic acid. The whole-cell sugars detected were rhamnose, ribose, glucose, galactose and a smaller amount of mannose. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and five unidentified glycolipids. The major fatty acids (>10.0 %) of the cell membrane were anteiso-C15 : 0 (39.4 %), C18 : 1ω7c (17.7 %), anteiso-C17 : 0 (17.2 %) and iso-C16 : 0 (11.4 %). The predominant respiratory quinones detected were MK-9(H2) and MK-9. The DNA G+C content was 67.3 mol%. A comparison of BOX-PCR fingerprints indicated that strain MUSC 117(T) represented a unique DNA profile. Results based on a polyphasic approach showed that strain MUSC 117(T) represents a novel species of the genus Sinomonas, for which the name Sinomonas humi sp. nov. is proposed. The type strain of Sinomonas humi sp. nov. is MUSC 117(T) ( = DSM 29362(T) = MCCC 1K00410(T) = NBRC 110653(T)).

Proposal of Novosphingobium rhizosphaerae sp. nov., isolated from the rhizosphere

A yellow, Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1T) was isolated from the rhizosphere of a field-grown Zea mays plant in Auburn, AL, USA. 16S rRNA gene sequence analysis of strain JM-1T showed high sequence similarity to the type strains of Novosphingobium capsulatum (98.9 %), Novosphingobium aromaticivorans (97.4 %), Novosphingobium subterraneum (97.3 %) and Novosphingobium taihuense (97.1 %); sequence similarities to all other type strains of species of the genus Novosphingobium were below 97.0 %. DNA–DNA hybridizations of strain JM-1T and N. capsulatum DSM 30196T, N. aromaticivorans SMCC F199T and N. subterraneum SMCC B0478T showed low similarity values of 33 % (reciprocal: 21 %), 14 % (reciprocal 16 %) and 36 % (reciprocal 38 %), respectively. Ubiquinone Q-10 was detected as the major respiratory quinone. The predominant fatty acid was C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid C14 : 0 2-OH (11.7 %) was detected. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, and ubiquinone, polar lipid and fatty acid composition revealed that strain JM-1T represents a novel species of the genus Novosphingobium . For this species we propose the name Novosphingobium rhizosphaerae sp. nov. with the type strain JM-1T ( = LMG 28479T = CCM 8547T).

Streptomyces pluripotens sp. nov., a bacteriocin-producing streptomycete that inhibits meticillin-resistant Staphylococcus aureus

Two novel actinobacteria, strains MUSC 135(T) and MUSC 137, were isolated from mangrove soil at Tanjung Lumpur, Malaysia. The 16S rRNA gene sequence similarity and DNA-DNA relatedness between strains MUSC 135(T) and MUSC 137 were 100 % and 83±3.2 %, confirming that these two strains should be classified in the same species. Strain MUSC 135(T) exhibited a broad-spectrum bacteriocin against the pathogens meticillin-resistant Staphylococcus aureus (MRSA) strain ATCC BAA-44, Salmonella typhi ATCC 19430(T) and Aeromonas hydrophila ATCC 7966(T). A polyphasic approach was used to study the taxonomy of MUSC 135(T), and it showed a range of phylogenetic and chemotaxonomic properties consistent with those of the genus Streptomyces. The diamino acid of the cell-wall peptidoglycan was ll-diaminopimelic acid. The predominant menaquinones were MK-9(H6), MK-9(H4) and MK-9(H8). Polar lipids detected were a lipid, an aminolipid, a phospholipid, phosphatidylinositol, phosphatidylethanolamine and two glycolipids. The predominant cellular fatty acids (>10.0 %) were anteiso-C15 : 0 (20.8 %), iso-C16 : 0 (18.0 %), iso-C15 : 0 (12.2 %) and anteiso-C17 : 0 (11.6 %). The whole-cell sugars were ribose, glucose and mannose. These results suggested that MUSC 135(T) should be placed within the genus Streptomyces. Phylogenetic analysis based on the 16S rRNA gene sequence exhibited that the most closely related strains were Streptomyces cinereospinus NBRC 15397(T) (99.18 % similarity), Streptomyces mexicanus NBRC 100915(T) (99.17 %) and Streptomyces coeruleofuscus NBRC 12757(T) (98.97 %). DNA-DNA relatedness between MUSC 135(T) and closely related type strains ranged from 26.3±2.1 to 49.6±2.5 %. BOX-PCR fingerprint comparisons showed that MUSC 135(T) exhibited a unique DNA profile. The DNA G+C content determined was 70.7±0.3 mol%. Based on our polyphasic study of MUSC 135(T), the strain merits assignment to a novel species, for which the name Streptomyces pluripotens sp. nov. is proposed. The type strain is MUSC 135(T) ( = MCCC 1K00252(T) = DSM 42140(T)).