Nocardioides convexus sp. nov. and Nocardioides anomalus sp. nov., isolated from soil and mineral water

Park, Jinah; Liu, Qingzhen; Maeng, Soohyun; Choi, Won Jung; Chang, Yoonjee; Im, Wan‐Taek

doi:10.1099/ijsem.0.004547

Cited by 20 publications

(8 citation statements)

References 26 publications

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“…The nuclear genome circle diagram was displayed in Figure 5 . Their high GC contents (both at 72.2%) were similar to the description of bacteria classified to the genus Nocardioides [ 46 , 47 ]. A total of four and three contigs were assembled in N39 and N40, respectively, and no gaps were found.…”

Section: Resultssupporting

confidence: 78%

Degrading Characterization of the Newly Isolated Nocardioides sp. N39 for 3-Amino-5-methyl-isoxazole and the Related Genomic Information

Yan

Liang

et al. 2022

Microorganisms

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3-amino-5-methyl-isoxazole (3A5MI) is a persistent and harmful intermediate in the degradation of antibiotic sulfamethoxazole. It was accumulated in the environments day by day and has caused great environmental risks due to its refractory characteristic. Microbial degradation is economic and environmentally friendly and a promising method to eliminate this pollutant. In this study, a bacterial strain, Nocardioides sp. N39, was isolated. N39 can grow on 3A5MI as the sole carbon, nitrogen and energy resource. The effect of different factors on 3A5MI degradation by N39 was explored, including initial 3A5MI concentration, temperature, pH value, dissolved oxygen and additional carbon or nitrogen source. The degradation ability of N39 to various 3A5MI analogs was also explored. Nevertheless, the degrading ability of N39 for 3A5MI is not permanent, and long-term storage would lead to the loss of this ability. This may result from the mobile genetic elements in the bacterium according to the genomic comparison of N39 and its degrading ability-lost strain, N40. Despite this, N39 could support a lot of useful information about the degradation of 3A5MI and highlight the importance of studies about the environmental effects and potential degradation mechanism.

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Section: Resultssupporting

confidence: 78%

Degrading Characterization of the Newly Isolated Nocardioides sp. N39 for 3-Amino-5-methyl-isoxazole and the Related Genomic Information

Yan

Liang

et al. 2022

Microorganisms

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“…S5). The strain had menaquinone with eight isoprene units (MK-8) as the major quinone, consistent with other members of the genus Nocardioides [3–8], and ll -diaminopimelic acid as the diagnostic diamino acid of the cell-wall peptidoglycan.…”

Section: Full-textsupporting

confidence: 78%

“…At the time of writing, the genus consists of 124 species with validly published names (https://lpsn.dsmz.de/genus/nocardioides). Nocardioides species have been isolated from soil of various environments, such as forest, land without vegetation, mountain, ginseng field, and rhizosphere of Cynanchum wilfordii [2][3][4][5][6]. According to phylogenetic analysis of 16S rRNA gene sequences, the genus Nocardioides is closely related to the genus Marmoricola [7]; however, there are remarkable differences in their fatty acid profiles, including the amount of iso-branched-chain fatty acids.…”

mentioning

confidence: 99%

Nocardioides panacis sp. nov., isolated from soil of a ginseng field

Park

Liu

Maeng

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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A bacterial strain designated as G188T was isolated from ginseng field soil in the Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences showed that strain G188T formed a distinct lineage within the genus Nocardioides, family Nocardioidaceae , order Propionibacteriales . Sequence similarity revealed that strain G188T was most closely related to Nocardioides iriomotensis IR27-S3T (97.7 % 16S rRNA similarity). The genome size of strain G188T was 4 901 775 bp, and the genomic DNA G+C content was 72.3 mol%. The average nucleotide identity and DNA–DNA hybridization values with other Nocardioides species were less than 75.6 and 20.1 %, respectively. The main fatty acids of strain G188T were C17 : 0, C17 : 1 ω8c and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylinositol, and the major respiratory quinone was menaquinone 8, supporting that strain G188T was affiliated with the genus Nocardioides . Based on biochemical, chemotaxonomic and phylogenetic analyses, the novel species Nocardioides panacis G188T (KACC 21695T=LMG 31733T) is proposed.

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“…Plant-associated microorganisms were founded previously in rhizospheres -for example, Bradyrhyzobium [23], Nocardioides [32]. Some of the taxa previously reported as typical soil microbiota -Nocardioides [32,33], Pseudonocardia [34,35], Kribbella [36], Pseudolabrys [37]. Except differential analysis limitation, this result can be connected with using of topsoil.…”

Section: Discussionmentioning

confidence: 83%

Microbial features of mature and abandoned soils in refractory clay deposits

et al. 2022

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Processes of soil restoration in anthropogenically disturbed soils is an urgent topic in modern ecology and nature management. Being mediator between mineral soil composition and plant vegetation, soil microbial community is important factor of soil restoration processes. Analysis of main soil nutrition components followed by 16S amplicon sequencing are sufficient methods for primary analysis of novel locations. Here is the primary analysis in a novel location in Northwest Europe (Russia). Main nutrition parameters (pH, P, Na and NH4+) and 16S rDNA Illumina amplicons were explored in abandoned soils from sandy pit quarry (2 sites) and refractory clay mining dumps (4 sites).Microbial communities of mature soils and dumps are variable and different in terms both nutritional and microbial components. pH, N and TOC are strong predictors for microbial composition. Dumps of refractory clays pQ_2 are non-developed soils, highly acidic and form specific microbial community. Differences between dumps and mature soils in both pre-quaternary and quaternary soils are connected with specific bacterial taxa. Those taxa are connected more with plant composition, not the soil properties themselves. The exact changes in microbial community are unique for different soils and areas. Graphical Abstract

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Nocardioides convexus sp. nov. and Nocardioides anomalus sp. nov., isolated from soil and mineral water

Cited by 20 publications

References 26 publications

Degrading Characterization of the Newly Isolated Nocardioides sp. N39 for 3-Amino-5-methyl-isoxazole and the Related Genomic Information

Degrading Characterization of the Newly Isolated Nocardioides sp. N39 for 3-Amino-5-methyl-isoxazole and the Related Genomic Information

Nocardioides panacis sp. nov., isolated from soil of a ginseng field

Microbial features of mature and abandoned soils in refractory clay deposits

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