Paenibacillus hubeiensis sp. nov.: A Novel Selenium-Resistant Bacterium Isolated from the Rhizosphere of Galinsoga parviflora in a Selenium-Rich Region of Enshi, Hubei Province

Abstract

ES5-4^T, a Gram-positive, motile, aerobic, and rod-shaped strain, was isolated from the rhizosphere of Galinsoga parviflora growing in the selenium-rich ore area of Enshi, Hubei Province, China. This strain can grow at pH levels of 5.0-10.0 and temperatures of 4-42 °C, with optimal growth at pH 7.0 and 28 °C. It was found to resist NaCl up to 5% (w/v), with an optimal growth condition of 0.5-1.0%. The strain exhibited tolerance to selenite (Se⁴⁺) concentrations up to 5000 mg/L. The major fatty acids of the ES5-4^T strain were anteiso-C_15:0 (46.5%) and C_16:0 (21.7%), its predominant respiratory quinone was MK-7, and its polar lipids included diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and an unidentified phospholipid (PL). The presence of the 16S rRNA gene sequence implies that ES5-4^T belongs to a member of the genus Paenibacillus, with the highest sequence similarity of 98.4% to Paenibacillus pabuli NBRC 13638^T. The bac120 tree also confirmed that the strain is within the genus Paenibacillus. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between ES5-4^T and closely related members of the genus Paenibacillus were all below the cutoff levels of 95-96% and 70%, respectively. Based on a polyphasic approach, including phenotypic, chemotaxonomic, and phylogenetic analyses, the ES5-4^T strain is proposed as a novel species of the genus Paenibacillus, for which the name Paenibacillus hubeiensis sp. nov. is proposed. This type strain is designated as ES5-4^T (=GDMCC 1.3540^T = KCTC 43478^T).

Keywords: Paenibacillus hubeiensis sp. nov.; bac120 tree; polyphasic analysis.

Figure 1

Maximum likelihood phylogenetic tree based on 16S rRNA gene sequences showing the position of the ES5-4^T strain. Bootstrap values (expressed as percentages of 1000 replications) of >70 (%) are shown at the branch nodes. GenBank accession numbers are indicated in brackets at the end of the tip labels. Bacillus subtilis NCIB 3610^T is used as the outgroup. Bar = 0.02 substitutions per nucleotide position.

Figure 2

A maximum likelihood tree based on protein sequences of the bac120 gene set, showing the phylogenetic relationship of ES5-4^T in the genus Paenibacillus. Bootstrap values are displayed at the branch nodes. The GenBank assembly accession number is indicated in brackets. The @ symbol at the end of labels indicates an atypical strain that showed 16S rRNA gene similarities of >98.5%. Staphylococcus aureus NCTC 8325^T (GCA000013425.1) is used as an outgroup. Bar = 0.1 substitutions per amino acid position.

Figure 3

The electron microscopy images of the ES5-4^T strain. (A) The TEM images (15,000× magnification) showing the cell morphology of the ES5-4^T strain cultured on TSA media at 28 °C for 2 days. (B) The SEM images (10,000× magnification) showing the cell morphology of the ES5-4^T strain cultured on TSA media at 28 °C for 1 day.

Figure 4

Effects of Se⁴⁺ concentration (20–5000 mg/L) on the colony diameter of the ES5-4^T strain cultured on TSA media at 28 °C for 2 days. Different letters above the column indicate significant differences between treatments (p < 0.05).

Figure 5

The distribution of genes for selenocompound metabolism within the genus Paenibacillus. Type strains are marked in bold. Gradient colors indicate gene numbers (0–3) detected in the relevant gene family.