Xylophilus rhododendri sp. nov., Isolated from Flower of Royal Azalea, Rhododendron schlippenbachii

A bacterial strain, designated CJ1-R5^T, was isolated from the flower of the royal azalea plant (Rhododendron schlippenbachii) collected in Jeju Island, Republic of Korea. The strain was a Gram-negative, strictly aerobic, motile, rod-shaped bacterium, growing at a temperature range of 4-33 °C (optimum 28-30 °C), pH 5.0-9.0 (optimum pH 7.0-8.0), and 0-1% NaCl (optimum 0%). The 16S rRNA sequence analysis of strain CJ1-R5^T revealed the highest sequence similarity (97.9%) with Xylophilus ampelinus ATCC 33914^T, and sequence similarities of less than 97.2% with other validly named species. Phylogenetic tree analysis based on the 16S rRNA gene sequences showed that strain CJ1-R5^T clustered with Xylophilus ampelinus ATCC 33914^T and two uncultured bacterial clones. The only quinone observed in strain CJ1-R5^T was ubiquinone-8. The polar lipids observed were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid and two unidentified lipids. The major fatty acids were C_16:0, C_17:0 cyclo, and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). The genome size of strain CJ1-R5^T was 5.85 Mbp. The genomic G + C content was 68.4 mol%. ANI and dDDH values between strain CJ1-R5^T and Xylophilus ampelinus ATCC 33914^T were 79.0% and 22.5%, respectively. Based on the polyphasic taxonomic data, strain CJ1-R5^T is considered to represent a novel species, for which the name Xylophilus rhododendri sp. nov. is proposed. The type strain is CJ1-R5^T (= KACC 21265^T = CCTCC AB2020030^T).

Draft genome sequence of Xenophilus sp. E41 isolated from an activated sludge reactor treating wastewater with high cephalexin concentration

OBJECTIVES

This study reports the draft genome sequence of Xenophilus sp. E41, a strain resistant to multiple antimicrobials isolated from an activated sludge reactor treating wastewater with a high cephalexin concentration.

METHODS

Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system. The generated sequence reads were assembled using MEGAHIT in combination with SOAPdenovo. Mauve and CompareM were used to align the Xenophilus sp. E41 genome to other draft genomes of the genus Xenophilus in order to determine their evolutionary relationships. The draft genome was annotated using the Rapid Annotation using Subsystem Technology (RAST) server and the nr database, whilst antimicrobial resistance genes (ARGs) were identified using the SARG 2.0 database, RAST server and nr database.

RESULTS

Xenophilus sp. E41, with a genome length of 5919552bp, harbours seven types of ARGs involving resistance to β-lactams, tetracycline, aminoglycosides, sulfonamides, chloramphenicol, teicoplanin and bleomycin. No virulence factors or plasmids were identified.

CONCLUSION

The genome sequence reported here will provide useful information for a better understanding of antimicrobial resistance profiles in this strain and the genus Xenophilus.

Description of Variovorax humicola sp. nov., isolated from a forest topsoil

Employing a modified cultivation method, we studied two bacterial strains, UC10 and UC38^T, found on the Kyonggi University campus, Suwon in Gyeonggi-Do province, South Korea. These strains were non-spore-forming, Gram-stain-negative, motile and rod-shaped. Growth occurred in the presence of 0-2 % (w/v) NaCl, at pH 4-9 and a temperature range of 4-35 °C. On an R2A agar plate incubated for 5 days at 28 °C, irregular, raised and pale-yellowish colonies were observed. Comparative analysis of nearly full-length 16S rRNA gene sequences indicated that these strains were closely related to Variovorax guangxiensis GXGD002^T, with 98.6 % similarity. Strains UC10 and UC38^T were 98.0 % similar to V.ariovorax soli GH9-3^T; 97.8 % to V.ariovorax dokdonensis DS-43^T; 97.3-97.7 % to V.ariovorax ginsengisoli Gsoil 3165^T; 97.7-98.0 % to V.ariovorax paradoxus IAM 12373^T; 97.4-97.6 % to V.ariovorax defluvii 2C1-b^T; and 97.3-97.4 % to V.ariovorax boronicumulans BAM-48^T. The predominant ubiquinone was Q-8. The primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 0 cyclo. DNA-DNA hybridization assays indicated 89.2-91.4 % genomic DNA similarity between strains UC10 and UC38^T. Moreover, genomic DNA similarity between these novel strains and reference strains of the genus Variovoraxwas less than the 70 %. Based on these results, strain UC38^T was designated a representative of a novel species of the genus Variovorax, with the proposed name Variovorax humicola sp. nov. The type strain is UC38^T (=KACC 18501^T=NBRC 111520^T).

Corticibacter populi gen. nov., sp. nov., a new member of the family Comamonadaceae, from the bark of Populus euramericana

Three novel endophytic strains, designated 17B10-2-12T, 26C10-4-4 and D13-10-4-9, were isolated from the bark of Populus euramericana in Heze, Shandong Province, China. They were Gram-reaction-negative, aerobic, non-motile, short-rod-shaped, oxidase-positive and catalase-negative. A phylogenetic analysis of the 16S rRNA gene showed that the three novel strains clustered with members of the family Comamonadaceae and formed a distinct branch. The isolates shared 100 % similarities among themselves and had the highest sequence similarity with Xenophilus azovorans DSM 13620T (95.2 %) and Xenophilus arseniciresistens YW8T (95.0 %), and less than 95.0 % sequence similarities with members of other species. Their major fatty acids were C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and C16 : 1ω7c/C16 : 1ω6c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unknown aminophospholipids. The predominant quinone was ubiquinone-8 (Q-8). The DNA G+C content was 69.5–70.0 mol%. Based on data from a polyphasic taxonomy study, the three strains represent a novel species of a novel genus of the family Comamonadaceae, for which the name Corticibacter populi gen. nov., sp. nov. is proposed. The type strain is 17B10-2-12T ( = CFCC 12099T = KCTC 42091T).

Xenophilus arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from soil

A Gram-reaction-negative, aerobic, motile, rod-shaped, arsenite [As(III)]-resistant bacterium, designated strain YW8(T), was isolated from agricultural soil. 16S rRNA gene sequence analysis showed over 97% sequence similarity to strains of the environmental species Xenophilus azovorans, Xenophilus aerolatus, Simplicispira metamorpha, Variovorax soli, and Xylophilus ampelinus. However, the phylogenetic tree indicated that strain YW8(T) formed a separate clade from Xenophilus azovorans. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain YW8(T) and its closest phylogenetic neighbours were below 24.2-35.5%, which clearly separated the strain from these closely related species. The major cellular fatty acids of strain YW8(T) were C(16 : 0), C(17 : 0) cyclo, C(18 : 1)ω7c, and summed feature 3(C(16 : 1)ω6c and/or C(16 : 1)ω7c). The genomic DNA G+C content was 69.3 mol%, and the major respiratory quinone was ubiquinone-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, an unknown polar lipid and phosphatidylserine. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of morphological, physiological and biochemical characteristics, phylogenetic position, DNA-DNA hybridization and chemotaxonomic data, strain YW8(T) is considered to represent a novel species of the genus Xenophilus, for which the name Xenophilus arseniciresistens sp. nov. is proposed; the type strain is YW8(T) ( = CCTCC AB2012103(T) = KACC 16853(T)).