Pseudomonas eucalypticola sp. nov., a producer of antifungal agents isolated from Eucalyptus dunnii leaves

AbstractPseudomonas are ubiquitously occurring microorganisms and are known for their ability to produce antimicrobials. An endophytic bacterial strain NP-1 T, isolated from Eucalyptus dunnii leaves, exhibits antifungal properties against five tested phytopathogenic fungi. The strain is a Gram-negative rod-shaped bacterium containing a single polar flagellum. It is strictly aerobic, grows at 4–37 °C, 2–5% NaCl, and pH 3–7. The 16S rRNA sequence analysis showed that NP-1 T belongs to the Pseudomonas genus. Phylogenetic analysis based on four concatenated partial genes (16S rDNA, gyrB, rpoB and rpoD) and the phylogenomic tree indicated that NP-1 T belongs to Pseudomonas fluorescens lineage but is distinct from any known Pseudomonas species. The G + C mol % of NP-1 T genome is 63.96, and the differences between NP-1 T and related species are larger than 1. The digital DNA-DNA hybridization and tetranucleotide signatures are 23.8 and 0.97, which clearly separates strain NP-1 T from its closest neighbours, Pseudomonas coleopterorum and Pseudomonas rhizosphaerae. Its phenotypic and chemotaxonomic features confirmed its differentiation from related taxa. The results from this polyphasic approach support the classification of NP-1 T as a novel species of Pseudomonas, and the name of Pseudomonas eucalypticola is thus proposed for this strain, whose type is NP-1 T (= CCTCC M2018494T = JCM 33572 T).

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Arthrobacter nitroguajacolicus sp. nov., a novel 4-nitroguaiacol-degrading actinobacterium

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.02923-0 ◽

2004 ◽

Vol 54 (3) ◽

pp. 773-777 ◽

Cited By ~ 36

Author(s):

Ludmila Kotoučková ◽

Peter Schumann ◽

Eva Durnová ◽

Cathrin Spröer ◽

Ivo Sedláček ◽

...

Keyword(s):

Dna Hybridization ◽

Novel Species ◽

Single Species ◽

Growth Cycle ◽

Nitroaromatic Compounds ◽

Bacterial Isolates ◽

Rrna Sequence ◽

16S Rrna Sequence ◽

Arthrobacter Aurescens ◽

16S Rrna Sequence Analysis

Three bacterial isolates from soil, capable of degradation or transformation of nitroaromatic compounds and displaying a rod–coccus growth cycle, were studied by a polyphasic approach. On the basis of 16S rRNA sequence analysis and of chemotaxonomic characteristics, such as type A3α peptidoglycan with an interpeptide bridge Ala–Thr–Ala, the major menaquinone MK-9(H2) and fatty acid composition, the isolates were assigned to the genus Arthrobacter. DNA–DNA hybridization, riboprinting and phenotypic studies revealed that the three strains constitute a single species, distinct from phylogenetically neighbouring Arthrobacter aurescens and Arthrobacter ilicis. A novel species, Arthrobacter nitroguajacolicus sp. nov., with the type strain G2-1T (=CCM 4924T=DSM 15232T) is proposed.

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Streptomyces gilvifuscus sp. nov., an actinomycete that produces antibacterial compounds isolated from soil

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.000447 ◽

2015 ◽

Vol 65 (Pt_10) ◽

pp. 3493-3500 ◽

Cited By ~ 7

Author(s):

Tuan Manh Nguyen ◽

Jaisoo Kim

Keyword(s):

Fatty Acids ◽

Dna Hybridization ◽

Type Strain ◽

Novel Species ◽

Gram Stain ◽

Rrna Sequence ◽

16S Rrna Sequence ◽

Antibacterial Compounds ◽

Cellular Fatty Acids ◽

16S Rrna Sequence Analysis

This study describes a novel actinomycete, designated T113T, which was isolated from forest soil in Pyeongchang-gun, Republic of Korea, and is an aerobic, Gram-stain-positive actinobacterium that forms flexibilis chains of smooth, elliptical or short rod-shaped spores. The results of 16S rRNA sequence analysis indicated that strain T113T exhibited high levels of similarity to previously characterized species of the genus Streptomyces (98.19–98.89 %, respectively). However, the results of phylogenetic and DNA–DNA hybridization analyses confirmed that the organism represented a novel member of the genus Streptomyces. Furthermore, using chemotaxonomic and phenotypic analyses it was demonstrated that the strain exhibited characteristics similar to those of other members of the genus Streptomyces. The primary cellular fatty acids expressed by this strain included anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C16 : 0. While diphosphatidylglycerol and phosphatidylethanolamine were the predominant lipids expressed by strain T113T, moderate amounts of phosphatidylinositol and phosphatidylinositol mannoside were also detected. Whole-cell hydrolysates contained glucose and ribose, and the predominant menaquinone detected was MK-9 (H6); however, moderate amounts of MK-9 (H8) and trace amounts of MK-10 (H2) and MK-10 (H4) were also detected. We therefore propose that strain T113T be considered as representing a novel species of the genus Streptomyces and propose the name Streptomyces gilvifuscus sp. nov. for this species, with strain T113T ( = KEMB 9005-213T = KACC 18248T = NBRC 110904T) being the type strain.

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Flavobacterium ginsengisoli sp. nov., isolated from soil of a ginseng field

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.053819-0 ◽

2013 ◽

Vol 63 (Pt_11) ◽

pp. 4289-4293 ◽

Cited By ~ 16

Author(s):

Yeon-Ju Kim ◽

Sang-Rae Kim ◽

Ngoc-Lan Nguyen ◽

Deok-Chun Yang

Keyword(s):

Novel Species ◽

Strictly Aerobic ◽

Biochemical Tests ◽

16S Rrna Sequence ◽

Phenotypic Data ◽

Content Type ◽

Link Type ◽

16S Rrna Sequence Analysis ◽

Physiological And Biochemical ◽

Motile By Gliding

A novel bacterial strain, designated DCY54T, was isolated from a field cultivated with ginseng in Yongin, Republic of Korea. Cells were Gram-reaction-negative, yellow-pigmented, rod-shaped, non-spore-forming, and strictly aerobic. They were motile by gliding and produced flexirubin-type pigments. Growth occurred optimally at 25–30 °C, at pH 5.0–7.0 and in the presence of 0–1 % NaCl. The 16S rRNA sequence analysis demonstrated that strain DCY54T was most closely related to Flavobacterium defluvii EMB117T (96.9 %). The only isoprenoid quinone of strain DCY 54T was menaquinone-6 (MK-6) and the major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The major cellular fatty acids (>15 %) were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. The DNA G+C content was 33.3 mol%. Phylogenetic inference and phenotypic data supported affiliation of strain DCY54T to the genus Flavobacterium . Several physiological and biochemical tests differentiated strain DCY54T from the species of the genus Flavobacterium with validly published names. On the basis of data from a polyphasic study, strain DCY54T represents a novel species of the genus Flavobacterium for which the name Flavobacterium ginsengisoli sp. nov. is proposed. The type strain is DCY54T ( = KCTC 23318T = JCM 17336T).

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Marinomonas alcarazii sp. nov., M. rhizomae sp. nov., M. foliarum sp. nov., M. posidonica sp. nov. and M. aquiplantarum sp. nov., isolated from the microbiota of the seagrass Posidonia oceanica

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.027227-0 ◽

2011 ◽

Vol 61 (9) ◽

pp. 2191-2196 ◽

Cited By ~ 34

Author(s):

Patricia Lucas-Elío ◽

Ester Marco-Noales ◽

Elena Espinosa ◽

Mónica Ordax ◽

María M. López ◽

...

Keyword(s):

Fatty Acid ◽

Dna Hybridization ◽

Novel Species ◽

Posidonia Oceanica ◽

Major Fatty Acid ◽

Bacterial Strains ◽

16S Rrna Sequence ◽

Minor Fatty Acid ◽

16S Rrna Sequence Analysis ◽

Fatty Acid Compositions

Five novel Gram-reaction-negative aerobic marine bacterial strains with DNA G+C contents <50 mol% were isolated from the seagrass Posidonia oceanica. 16S rRNA sequence analysis indicated that they belonged to the genus Marinomonas. Major fatty acid compositions, comprising C10 : 0 3-OH, C16 : 0, C16 : 1ω7c and C18 : 1ω7c, supported the affiliation of these strains to the genus Marinomonas. Strains IVIA-Po-14bT, IVIA-Po-145T and IVIA-Po-155T were closely related to Marinomonas pontica 46-16T, according to phylogenetic analysis. However, DNA–DNA hybridization values <35 % among these strains revealed that they represented different species. Further differences in the phenotypes and minor fatty acid compositions were also found among the strains. Another two strains, designated IVIA-Po-181T and IVIA-Po-159T, were found to be closely related to M. dokdonensis DSW10-10T but DNA–DNA relatedness levels <40 % in pairwise comparisons, as well as some additional differences in phenotypes and fatty acid compositions supported the creation of two novel species. Accordingly, strains IVIA-Po-14bT ( = CECT 7730T = NCIMB 14671T), IVIA-Po-145T ( = CECT 7377T = NCIMB 14431T), IVIA-Po-155T ( = CECT 7731T = NCIMB 14672T), IVIA-Po-181T ( = CECT 7376T = NCIMB 14433T) and IVIA-Po-159T ( = CECT 7732T = NCIMB 14673T) represent novel species, for which the names Marinomonas alcarazii sp. nov., Marinomonas rhizomae sp. nov., Marinomonas foliarum sp. nov., Marinomonas posidonica sp. nov. and Marinomonas aquiplantarum sp. nov. are proposed, respectively.

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Pseudomonas coleopterorum sp. nov., a cellulase-producing bacterium isolated from the bark beetle Hylesinus fraxini

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.000344 ◽

2015 ◽

Vol 65 (Pt_9) ◽

pp. 2852-2858 ◽

Cited By ~ 23

Author(s):

Esther Menéndez ◽

Martha H. Ramírez-Bahena ◽

Anna Fabryová ◽

José M. Igual ◽

Oldrich Benada ◽

...

Keyword(s):

Bark Beetle ◽

Dna Hybridization ◽

Gene Sequence ◽

Novel Species ◽

Housekeeping Genes ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Respiratory Quinone ◽

Arginine Dihydrolase

We isolated a strain coded Esc2AmT during a study focused on the microbial diversity of adult specimens of the bark beetle Hylesinus fraxini. Its 16S rRNA gene sequence had 99.4 % similarity with respect to its closest relative, Pseudomonas rhizosphaerae IH5T. The analysis of partial sequences of the housekeeping genes rpoB, rpoD and gyrB confirmed that strain Esc2AmT formed a cluster with P. rhizosphaerae IH5T clearly separated from the remaining species of the genus Pseudomonas. Strain Esc2AmT had polar flagella and could grow at temperatures from 4 °C to 30 °C. The respiratory quinone was Q9 and the main fatty acids were C16 : 0, C18 : 1ω7c and/or C18 : 1ω6c in summed feature 8 and C16 : 1ω7c and/or C16 : 1ω6c in summed feature 3. DNA–DNA hybridization results showed 51 % relatedness with respect to P. rhizosphaerae IH5T. Oxidase, catalase and urease-positive, the arginine dihydrolase system was present but nitrate reduction and β-galactosidase production were negative. Aesculin hydrolysis was positive. Based on the results from the genotypic, phenotypic and chemotaxonomic analyses, we propose the classification of strain Esc2AmT as representing a novel species of the genus Pseudomonas, for which we propose the name Pseudomonas coleopterorum sp. nov. The type strain is Esc2AmT ( = LMG 28558T = CECT 8695T).

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Acquisition of an Agrobacterium Ri Plasmid and Pathogenicity by Other α-Proteobacteria in Cucumber and Tomato Crops Affected by Root Mat

Applied and Environmental Microbiology ◽

10.1128/aem.70.5.2779-2785.2004 ◽

2004 ◽

Vol 70 (5) ◽

pp. 2779-2785 ◽

Cited By ~ 13

Author(s):

S. A. Weller ◽

D. E. Stead ◽

J. P. W. Young

Keyword(s):

Pathogenicity Test ◽

Agrobacterium Radiobacter ◽

Rrna Sequence ◽

16S Rrna Sequence ◽

Ri Plasmid ◽

Fatty Acid Profiling ◽

Transformation Rates ◽

16S Rrna Sequence Analysis ◽

Average Transformation

ABSTRACT Root mat of cucumbers and tomatoes has previously been shown to be caused by Agrobacterium radiobacter strains harboring a root-inducing Ri plasmid (pRi). Nine other pRi-harboring α-Proteobacteria have subsequently been isolated from root mat-infected crops. Fatty acid profiling and partial 16S rRNA sequence analysis identified three of these strains as being in the genus Ochrobactrum, five as being in the genus Rhizobium, and one as being in the genus Sinorhizobium. An in vitro pathogenicity test involving inoculation of cucumber cotyledons was developed. All pRi-harboring α-Proteobacteria induced typical root mat symptoms from the cotyledons. Average transformation rates for rhizogenic Ochrobactrum (46%) and Rhizobium (44%) strains were lower than those observed for rhizogenic A. radiobacter strains (64%). However, individual strains from these three genera all had transformation rates comparable to those observed from cotyledons inoculated with a rhizogenic Sinorhizobium strain (75%).

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Pyrrolnitrin Biosynthesis From Rhizospheric Serratia Spp. With Antifungal Activity and Binding Interactions of PrnF With Ligands

10.21203/rs.3.rs-56362/v1 ◽

2020 ◽

Author(s):

Shraddha P. Pawar ◽

Ambalal B. Chaudhari

Keyword(s):

Antifungal Activity ◽

Phytopathogenic Fungi ◽

Bacterial Strains ◽

Rrna Sequence ◽

16S Rrna Sequence ◽

Protein Model ◽

Stenotrophomonas Rhizophila ◽

K 12 ◽

Layer Chromatography

Abstract Pyrrolnitrin (PRN) from rhizobacteria displays a key role in biocontrol of phytopathogenic fungi in rhizospheric soil. Therefore, different rhizospheric soils were investigated for the prevalence of PRN producer in minimal salt (MS) medium containing tryptophan (0.2 M NaCl; pH 8) using three successive enrichments. Of 12% isolates, only five bacterial strains had shown PRN secretion, screened with Thin Layer Chromatography (Rf 0.8) and antifungal activity (27 mm) against phytopathogen. The phenetic and 16S rRNA sequence revealed the close affiliation of isolates (KMB, M-2, M-11, TW3, and TO2) to Stenotrophomonas rhizophila (KY800458), Enterobacter spp. (KY800455), Brevibacillus parabrevis (KY800454), Serratia marcescens (KY800456) and Serratia nemtodiphila (KY800457). Purified compound from isolates was characterised using UV, IR, HPLC, LCMS and GCMS as PRN. However, BLASTn hit of prn gene sequences from both Serratia species showed 99% similarity with NADPH dependent FMN reductase component (prnF). The homology protein model of prnF was developed from translated sequence of S. marcescens TW3 with chromate reductase of Escherichia coli K-12. Docking with FMN and NADPH was performed. The study demonstrated the possible role of prnF NADPH dependent FMN reductases in prnD for supply of reduced flavin in rhizobacterial strain of Serratia spp. which may pave a way to understand PRN production.

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Mycobacterium neoaurumBacteremia in a Hemodialysis Patient

Canadian Journal of Infectious Diseases ◽

10.1155/2003/840103 ◽

2003 ◽

Vol 14 (1) ◽

pp. 45-48 ◽

Cited By ~ 8

Author(s):

Marissa L Becker ◽

Amar A Suchak ◽

Joyce N Wolfe ◽

Ryan Zarychanski ◽

Amin Kabani ◽

...

Keyword(s):

Sequence Analysis ◽

16S Rrna ◽

Hemodialysis Patient ◽

Immunocompromised Host ◽

Blood Cultures ◽

Clinical Suspicion ◽

Diabetic Woman ◽

Rrna Sequence ◽

16S Rrna Sequence ◽

16S Rrna Sequence Analysis

Bacteremia due toMycobacterium neoaurum, a rapidly growing mycobacterium, is described in a diabetic woman on hemodialysis. This is the first reported case of M neoaurum bacteremia in Canada. The organism initially grew on standard BacT/Alert SA aerobic blood cultures, and was subsequently positively identified using 16S rRNA sequence analysis. The present case serves to reinforce the need for a high index of clinical suspicion of infections caused by unusual microorganisms in the context of an immunocompromised host.

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Newly Isolated Alkane Hydroxylase and Lipase Producing Geobacillus and Anoxybacillus Species Involved in Crude Oil Degradation

Catalysts ◽

10.3390/catal10080851 ◽

2020 ◽

Vol 10 (8) ◽

pp. 851 ◽

Cited By ~ 1

Author(s):

Durratul Fatini Yusoff ◽

Raja Noor Zaliha Raja Abd Rahman ◽

Malihe Masomian ◽

Mohd Shukuri Mohamad Ali ◽

Thean Chor Leow

Keyword(s):

Crude Oil ◽

Oil Spills ◽

Oil Degradation ◽

Alkane Hydroxylase ◽

Rrna Sequence ◽

16S Rrna Sequence ◽

Crude Oil Degradation ◽

16S Rrna Sequence Analysis ◽

First Time ◽

Poly Aromatic Hydrocarbons

Isolation and studies of novel, crude oil biodegrading thermophilic strains may provide a wider knowledge in understanding their role in petroleum degradation. In this study, the screening of ten new thermophilic strains revealed that all strains were alkane hydroxylase producers and seven of them produced lipase concurrently. Three best strains were characterized and identified through 16S rRNA sequence analysis as Geobacillus sp. D4, Geobacillus sp. D7, and Anoxybacillus geothermalis D9 with GenBank accession numbers MK615934.1, MK615935.1, and MK615936.1, respectively. Gas chromatography (GC) analysis showed that all three strains were able to breakdown various compounds in crude oil such as alkanes, toxic poly-aromatic hydrocarbons (PAHs), organosulfur, carboxylic acids, alkene, resins, organosilicon, alcohol, organochlorine, and ester. For the first time, alkane hydroxylase and lipase activity as well as crude oil degradation by A. geothermalis species were reported. Geobacillus sp. D7 is the best alkane degrader followed by A. geothermalis D9 and Geobacillus sp. D4 with 17.3%, 13.1%, and 12.1% biodegradation efficiency (BE%), respectively. The potential of thermophiles isolated can be explored further for bioremediation of sites polluted by petroleum and oil spills.

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