Sphingomonas suaedae sp. nov., a chitin-degrading strain isolated from rhizosphere soil of Suaeda salsa

Zhang, Hui; Xu, Liang; Zhang, Jinxin; Sun, Junsong

doi:10.1099/ijsem.0.004238

“…Rhizobacterial metabolites, including phenazines, phenolics, and pyrrole-type, are responsible for their antimicrobial activity [ 16 ]. Sphingomonas , a genus of rod-shaped bacteria, are known for their ability to survive in harsh environments and digest environmental toxins and industrial pollutants [ 17 , 18 ]. Sphingomonas strains contain high concentrations of dihydrosphingosine, a long-chain sphingolipid, and polyamines.…”

Section: Introductionmentioning

confidence: 99%

Phytochemical and biological assessment of secondary metabolites isolated from a rhizosphere strain, Sphingomonas sanguinis DM of Datura metel

Awad,

Hammad,

El-Mashtoly

et al. 2024

BMC Complement Med Ther

2

0

1

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Background The plant roots excrete a large number of organic compounds into the soil. The rhizosphere, a thin soil zone around the roots, is a hotspot for microbial activity, making it a crucial component of the soil ecosystem. Secondary metabolites produced by rhizospheric Sphingomonas sanguinis DM have sparked significant curiosity in investigating their possible biological impacts. Methods A bacterial strain has been isolated from the rhizosphere of Datura metel. The bacterium’s identification, fermentation, and working up have been outlined. The ethyl acetate fraction of the propagated culture media of Sphingomonas sanguinis DM was fractioned and purified using various chromatographic techniques. The characterization of the isolated compounds was accomplished through the utilization of various spectroscopic techniques, such as UV, MS, 1D, and 2D-NMR. Furthermore, the evaluation of their antimicrobial activity was conducted using the agar well diffusion method, while cytotoxicity was assessed using the MTT test. Results The extract from Sphingomonas sanguinis DM provided two distinct compounds: n-dibutyl phthalic acid (1) and Bis (2-methyl heptyl) phthalate (2) within its ethyl acetate fraction. Furthermore, the 16S rRNA gene sequence of Sphingomonas sanguinis DM has been registered under the NCBI GenBank database with the accession number PP422198. The bacterial extract exhibited its effect against gram-positive bacteria, inhibiting Streptococcus mutans (12.6 ± 0.6 mm) and Staphylococcus aureus (10.6 ± 0.6 mm) compared to standard antibiotics. Conversely, compound 1 showed a considerable effect against phytopathogenic fungi such as Alternaria alternate (56.3 ± 10.6 mm) and Fusarium oxysporum (21.3 ± 1.5 mm) with a MIC value of 17.5 µg/mL. However, it was slightly active against Klebsiella pneumonia (11.0 ± 1.0 mm). Furthermore, compound 2 was the most active metabolite, having a significant antimicrobial efficacy against Rhizoctonia solani (63.6 ± 1.1 mm), Pseudomonas aeruginosa (16.7 ± 0.6 mm), and Alternaria alternate (20.3 ± 0.6 mm) with MIC value at 15 µg/mL. In addition, compound 2 exhibited the most potency against hepatocellular (HepG-2) and skin (A-431) carcinoma cell lines with IC50 values of 107.16 µg/mL and 111.36 µg/mL, respectively. Conclusion Sphingomonas sanguinis DM, a rhizosphere bacterium of Datura metel, was studied for its phytochemical and biological characteristics, resulting in the identification of two compounds with moderate antimicrobial and cytotoxic activities.

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“…Saline-alkaline soils cover a wide area of the planet and harbour considerable bacterial diversity with many new species described recently [6,[9][10][11][12][13][14][15]. During a survey of the cultivated bacterial diversity in saline soil in northern China, two strains with high 16S rRNA gene similarities to Ruania strains were isolated from saline soil.…”

Section: Introductionmentioning

confidence: 99%

Ruania suaedae sp. nov. and Ruania halotolerans sp. nov., two actinobacteria isolated from saline soil, and reclassification of Haloactinobacterium kanbiaonis as Occultella kanbiaonis comb. nov.

Xu

¹

,

Shang

²

,

Tian

³

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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Two Gram-stain-positive, non-motile, strictly aerobic, yellow-coloured, rod-shaped bacterial strains, designated LR1S40T and M4N3S171T, were isolated from rhizosphere and bulk saline soil of Suaeda salsa collected in Inner Mongolia, China. Phylogenetic trees based on 16S rRNA gene and whole genome sequences showed that the two strains clustered tightly with strains of the genus Ruania . Strains LR1S40T and M4N3S171T had 95.5% 16S rRNA gene similarity to each other, and strain LR1S40T had 98.8, 98.7, 97.4 and <97.0% similarity to Ruania alkalisoli RN3S43T, Ruania rhizosphaerae LNNU 22110T, Ruania alba YIM 93306T and all other current type strains, while strain M4N3S171T had 98.6 and <97.0% similarity to R. alba YIM 93306T, and all other current type strains, respectively. The average nucleotide identity based on blast (ANIb) and digital DNA–DNA hybridization (dDDH) values of LR1S40T and M4N3S171T with each other and to the other type strains of Ruania were well below the threshold values (95% for ANIb, 70% for dDDH) for differentiating a species. Diphosphatidylglycerol and phosphatidylglycerol were the major polar lipids in both strains. The predominant menaquinone in both strains was both MK-8. The genome of strain LR1S40T consisted of a 3557440 bp circular chromosome, with a G+C content of 71.1 mol%, while the genome of strain M4N3S171T consisted of 4270413 bp, with a G+C content of 67.6 mol%. The phylogenetic, physiological and phenotypic characteristics allowed discrimination of the two strains from their relatives. The names Ruania suaedae sp. nov. [type strain LR1S40T (=CGMCC 1.19028T=KCTC 49726T)] and Ruania halotolerans sp. nov. [type strain M4N3S171T (=CGMCC 1. 19142T=KCTC 49727T)] are therefore proposed. During the publication of Haloactinobacterium kanbiaonis , Haloactinobacterium glacieicola (type strain T3246-1T), which was selected as the reference strain for the identification of H. kanbiaonis , was reclassified as Occultella glacieicola . The two phylogenetic trees showed that H. kanbiaonis HY164T tightly clustered with Occultella aeris F300T, and had the highest 16S rRNA gene similarity (99.8%) to O. aeris F300T. Based on the phylogenetic analysis and the publication record, Haloactinobacterium kanbiaonis should be reclassified as Occultella kanbiaonis comb. nov.

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“…The closest relatives of some of the newly described taxa were previously isolated from aquatic environments, such as Rhizobacter profundi DS48-6-5 T ( 74 ), isolated from freshwater sediment in Korea; Aquabacterium pictum W35 T ( 75 ), isolated from Tama River in Japan; Aquincola tetriaricarbonis L10 T ( 76 ), isolated from contaminated groundwater (Germany); or Flavobacterium album HYN0059 T ( 77 ), isolated from a freshwater lake (Korea). Other closest relatives were described in different types of soils, such as Hymenobacter psychrotolerans Tibet-IIU11 T ( 78 ) in permafrost sediment in China, Sphingomonas suaedae XS-10 T ( 79 ) in the rhizosphere of Suaeda salsa (China), Phenylobacterium immobile E T ( 80 ) in chloridazon-contaminated soil, and Phenylobacterium muchangoponense A8 T ( 81 ) in beach soil (Korea), or Pseudomonas campi S1-A32-2 T ( 82 ) in grassland soil. Mesorhizobium qingshengii CCBAU 33460 T ( 83 ), the closest type strain to isolate J428, was isolated from root nodules of Astragalus sinicus .…”

Section: Discussionmentioning

confidence: 99%

Culturomics of Bacteria from Radon-Saturated Water of the World’s Oldest Radium Mine

Kapinusova

¹

,

Jani

²

,

Smrhova

³

et al. 2022

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The mine Svornost in Jáchymov (Joachimstahl), Czech Republic is a former silver-uranium mine and the world’s first and for a long time only radium mine, nowadays the deepest mine devoted to the extraction of water which is saturated with radon and has therapeutic benefits given its chemical properties. This healing water, which is approximately 13 thousand years old, is used under medical supervision for the treatment of patients with neurological and rheumatic disorders.

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Sphingomonas suaedae sp. nov., a chitin-degrading strain isolated from rhizosphere soil of Suaeda salsa

Cited by 17 publications

References 46 publications

Phytochemical and biological assessment of secondary metabolites isolated from a rhizosphere strain, Sphingomonas sanguinis DM of Datura metel

Phytochemical and biological assessment of secondary metabolites isolated from a rhizosphere strain, Sphingomonas sanguinis DM of Datura metel

Ruania suaedae sp. nov. and Ruania halotolerans sp. nov., two actinobacteria isolated from saline soil, and reclassification of Haloactinobacterium kanbiaonis as Occultella kanbiaonis comb. nov.

Culturomics of Bacteria from Radon-Saturated Water of the World’s Oldest Radium Mine

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