Analysis of genomic and characterization features of Luteolibacter soli sp. nov., isolated from soil

Jing An; Xiaoqi Xuan; Yanan Wang; Linwei Wu; Jizhong Zhou; Dashuai Mu

doi:10.3389/fmicb.2024.1483195

Analysis of genomic and characterization features of Luteolibacter soli sp. nov., isolated from soil

Front Microbiol. 2024 Sep 13:15:1483195. doi: 10.3389/fmicb.2024.1483195. eCollection 2024.

Authors

Jing An¹, Xiaoqi Xuan¹, Yanan Wang¹, Linwei Wu^{2

3}, Jizhong Zhou^{3

4

5

6}, Dashuai Mu^{1

3

7

8}

Affiliations

¹ Marine College, Shandong University, Weihai, China.
² Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, China.
³ Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States.
⁴ Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States.
⁵ State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
⁶ School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, United States.
⁷ School Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
⁸ Weihai Research Institute of Industrial Technology of Shandong University, Weihai, China.

Abstract

The strain designated as Y139^T is a novel Gram-stain-negative, aerobic, and non-motile bacterium, was isolated from a soil sample in McClain County, Oklahoma, United States. The cells of strain Y139^T were a rod-shaped, with the width of 0.4-0.7 $μm$ and the length of 1.5-2.0 $μm$ . Growth occurred at 20-37°C (optimum, 30°C), pH 5.5-9.5 (optimum, pH 7.0), and 0-1.0% NaCl (w/v) (optimum, 0%). The polar lipid profiles included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine, and an unidentified lipid. The major fatty acids included C_16:0, iso-C_14:0, and C_16:1 ω9c. Menaquinone-9 (MK-9) was recognized as the only respiratory quinone. Strain Y139^T showed the highest 16S rRNA gene sequence similarity to Luteolibacter flavescens MCCC 1K03193^T (98.3%). Phylogenetic analysis positioned it within the genus Luteolibacter. The draft genome of strain Y139^T consisted of 7,106,054 bp, and contained 5,715 open reading frames (ORFs), including 5,656 coding sequences (CDSs) and 59 RNA genes. The genomic DNA G + C content was found to be 62.5%. Comparing strain Y139^T with L. flavescens MCCC 1K03193^T and Luteolibacter arcticus CCTCC AB 2014275^T, the average nucleotide identity (ANI) values were 80.6 and 82.1%, respectively. Following phylogenetic, physiological, biochemical, and chemotaxonomic analyses, a novel species within the genus Luteolibacter, designated as Luteolibacter soli sp. nov., was proposed for strain Y139^T, which was also assigned as the type strain (=KCTC 92644^T = MCCC 1H01451^T). Further analysis of core genes across 9 Luteolibacter species uncovered significant genomic divergence, particularly in those related to cofactor, vitamin, and energy metabolism. Analysis of biogeographic distribution suggested that lake and soil were the main habitats for the genus Luteolibacter. Additionally, the genus Luteolibacter was sensitive to climate warming and precipitation.

Keywords: 16S rRNA gene; Luteolibacter; climate change; genome; phylogenetic.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Natural Science Foundation of China (32470010); Science and Technology Fundamental Resources Investigation Program (Grant nos. 2019FY100700 and 2022FY101100) and the National Natural Science Foundation of China (41876166).