Geminicoccus flavidas sp. nov. and Geminicoccus harenae sp. nov., two IAA-producing novel rare bacterial species inhabiting desert biological soil crusts

Zhu-Ming Jiang; Yang Deng; Xue-Fei Han; Jing Su; Hao Wang; Li-Yan Yu; Yu-Qin Zhang

doi:10.3389/fmicb.2022.1034816

Geminicoccus flavidas sp. nov. and Geminicoccus harenae sp. nov., two IAA-producing novel rare bacterial species inhabiting desert biological soil crusts

Front Microbiol. 2022 Oct 31:13:1034816. doi: 10.3389/fmicb.2022.1034816. eCollection 2022.

Authors

Zhu-Ming Jiang^{1

2}, Yang Deng^{1

2}, Xue-Fei Han^{1

2}, Jing Su¹, Hao Wang¹, Li-Yan Yu¹, Yu-Qin Zhang^{1

2}

Affiliations

¹ Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China.
² State Key Laboratory of Dao-di Herb, Beijing, China.

Abstract

Two Gram-staining negative strains (CPCC 101082^T and CPCC 101083^T) were isolated from biological sandy soil crusts samples collected from Badain Jaran desert, China. Both isolates were heterotrophic phototroph, could produce indole-3-acetic acid. The 16S rRNA gene sequences of these two strains were closely related to the members of the family Geminicoccaceae, showing high similarities with Geminicoccus roseus DSM 18922^T (96.9%) and Arboricoccus pini B29T1^T (90.1%), respectively. In phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 101082^T and CPCC 101083^T formed a robust distinct clade with Geminicoccus roseus DSM 18922^T within the family Geminicoccaceae, which indicated that these two isolates could be classified into the genus Geminicoccus. The growth of strain CPCC 101082^T occurred at 15-42°C and pH 4.0-10.0 (optima at 28-37°C and pH 6.0-8.0). The growth of strain CPCC 101083^T occurred at 4-45°C and pH 4.0-10.0 (optima at 25-30°C and pH 6.0-8.0). The major cellular fatty acids of CPCC 101082^T and CPCC 101083^T contained C_18:1 ω7c/C_18:1 ω6c, cyclo-C_19:0 ω8c, and C_16:0. Q-10 was detected as the sole respiratory quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified phospholipid and an unidentified aminolipid were tested in the polar lipids profile. The genomes of the two isolates were characterized as about 5.9 Mbp in size with the G + C content of nearly 68%. The IAA-producing encoding genes were predicated in both genomes. The values of average nucleotide identity were 80.6, 81.2 and 92.4% based on a pairwise comparison of the genomes of strains CPCC 101082^T and CPCC 101083^T and Geminicoccus roseus DSM 18922^T, respectively. On the basis of the genotypic, chemotaxonomic and phenotypic characteristics, the strains CPCC 101082^T (=NBRC 113513^T = KCTC 62853^T) and CPCC 101083^T (=NBRC 113514^T = KCTC 62854^T) are proposed to represent two novel species of the genus Geminicoccus with the names Geminicoccus flavidas sp. nov. and Geminicoccus harenae sp. nov.

Keywords: Geminicoccus flavidas; Geminicoccus harenae; average nucleotide identity; biological soil crusts; pan-genome.