Pontibacter cellulosilyticus sp. nov., a carboxymethyl cellulose-hydrolysing bacterium isolated from coastal water

Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review

Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.

Pontibacter kalidii sp. nov., isolated from rhizosphere soil of Kalidium foliatum

A Gram-negative, aerobic, gliding motile, rod-shaped bacterium, designated XAAS-72T, was isolated from the rhizosphere soil of Kalidium foliatum sampled in the Xinjiang Uyghur Autonomous Region, PR China. Cells grew at 4-45 °C, pH 5.0-8.0 and 0-8% NaCl, with optimal growth at 20-30 °C, pH 6.0-7.0 and 1-2 % NaCl. Strain XAAS-72T is closely related to members of the genus Pontibacter, namely Pontibacter korlensis CCTCC AB 206081T (97.6%) and Pontibacter flavimaris ACCC 19859T (97.2 %), and <94.6 % related to other currently described Pontibacter strains. The average nucleotide identity values between XAAS-72T and P. korlensis CCTCC AB 206081T and P. flavimaris ACCC 19859T were 77.9 and 86.9 %, respectively; the corresponding digital DNA-DNA hybridization values were 21.7 and 31.8 %. Menaquinone-7 was the predominant respiratory menaquinone. The polar lipids consisted of phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified glycolipids and five unidentified lipids. The major cellular fatty acids were summed feature 4 (containing iso-C17 : 1 I/anteiso-C17 : 1 B), summed feature 3 (containing C16 : 1  ω7c/C16 : 1  ω6c) and iso-C15 : 0. The genome length of strain XAAS-72T was 5 054 860 bp with a genomic DNA G+C content of 54.5 mol%. The phenotypic and genotypic data suggest that strain XAAS-72T represents a novel species of the genus Pontibacter, for which the name Pontibacter kalidii sp. nov. is proposed. The strain is XAAS-72T (CGMCC 16594T=KCTC 72095T).

Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov., isolated from soil

Two Gram-stain-negative, aerobic, yellow and rod-shaped bacteria, designated as strains PBS4-4^T and GMJ5^T, were isolated from soil samples collected in Goyang-si and Paju-si, Gyeonggi-do, Republic of Korea. Strains PBS4-4^T and GMJ5^T were both positive for catalase and oxidase. Strain PBS4-4^T grew at 15-37 °C and pH 5.0-12.0. Strain GMJ5^T grew at 15-37 °C and pH 5.0-11.0. Neither strain required NaCl for growth. 16S rRNA sequence analysis revealed that strains PBS4-4^T and GMJ5^T form a closely related cluster with the genus Chryseobacterium. The average nucleotide identity and digital DNA-DNA hybridization values between strain PBS4-4^T and its closely related strains were 79.4-84.5% and 23.2-28.7 %, respectively. For GMJ5^T, the values were 78.3-79.3% and 22.0-22.6 %, respectively. The major fatty acids shared by both novel strains were iso-C_15 : 0 and summed feature 3 (C_16 : 1 ω7c/C_16 : 1 ω6c). Strain GMJ5^T had one other major fatty acid: iso-C_17 : 0 3OH. Based on phenotypic, genomic and phylogenetic results, strains PBS4-4^T and GMJ5^T represent novel species within the genus Chryseobacterium, and the names Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov. are proposed, respectively. The type strain of C. edaphi is PBS4-4^T (=KACC 22882^T=TBRC 17052^T) and the type strain of C. gilvum is GMJ5^T (=KACC 22883^T=TBRC 17053^T).

Comparative genomic analyses of four novel Ramlibacter species and the cellulose-degrading properties of Ramlibacter cellulosilyticus sp. nov

In this study, four novel bacterial strains, USB13^T, AW1^T, GTP1^T, and HM2^T, were isolated from various environments in Busan and Jeju Island, Republic of Korea. The 16S rRNA sequencing results indicated that the four novel strains belong to the genus Ramlibacter. All four strains were tested for their potential cellulolytic properties, where strain USB13^T was identified as the only novel bacterium and the first within its genus to show cellulolytic activity. When tested, the highest activities of endoglucanase, exoglucanase, β-glucosidase, and filter paper cellulase (FPCase) were 1.91 IU/mL, 1.77 IU/mL, 0.76 IU/mL, and 1.12 IU/mL, respectively at pH 6.0. Comparisons of draft whole genome sequences (WGS) were also made using average nucleotide identity, digital DNA-DNA hybridization values, and average amino acid identity values, while whole genome comparison was visualized using the BLAST Ring Image Generator. The G + C contents of the strains ranged from 67.9 to 69.9%, while genome sizes ranged from 4.31 to 6.15 Mbp. Based on polyphasic evidence, the novel strains represent four new species within the genus Ramlibacter, for which the names Ramlibacter cellulosilyticus sp. nov. (type strain, USB13^T = KACC 21656^T = NBRC 114839^T) Ramlibacter aurantiacus sp. nov. (type strain, AW1^T = KACC 21544^T = NBRC 114862^T), Ramlibacter albus sp. nov. (type strain, GTP1^T = KACC 21702^T = NBRC 114488^T), and Ramlibacter pallidus sp. nov. (type strain, HM2^T = KCTC 82557^T = NBRC 114489^T) are proposed.