Three novel Luteimonas species from a root and rhizosphere soil of Kalidium cuspidatum: Luteimonas endophytica sp. nov., Luteimonas rhizosphaericola sp. nov. and Luteimonas kalidii sp. nov

Three Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated RD2P54T, M1R5S18T and M1R5S59T, were isolated from a root and rhizosphere soil of Kalidium cuspidatum, in Baotou, PR China. The three strains showed 94.1–98.7 % 16S rRNA gene sequence similarities to Luteimonas strains, indicating they belonged to the genus Luteimonas . The phylogenomic tree based on core genomes showed that strain RD2P54T tightly clustered with Luteimonas salinisoli SJ-92T, while strains M1R5S18T and M1R5S59T clustered with each other and with Luteimonas viscosa XBU10T and Luteimonas saliphila SJ-9T. Though strains M1R5S18T and M1R5S59T showed high 16S rRNA similarity (99.4 %) to each other, the low average nucleotide identity based on blast (ANIb; 88.6 %) and digital DNA–DNA hybridization (dDDH; 31.6 %) values between them indicated that they belonged to two different species. The ANIb and dDDH values of strains RD2P54T, M1R5S18T and M1R5S59T with their closely neighbours are well below the delineation threshold values for identifying strains as representing different species. All three strains take iso-C15 : 0 and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1  ω9c) as major fatty acids, and ubiquinone-8 as the sole respiratory quinone. The major polar lipids of all three strains are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on phenotypic and phylogenetic data, these three strains should be considered to represent three novel species of the genus Luteimonas , for which the names Luteimonas endophytica sp. nov. (type strain RD2P54T=CGMCC 1.61535T =KCTC 92470T), Luteimonas rhizosphaericola sp. nov. (type strain M1R5S18T=CGMCC 1.61537T =KCTC 92469T) and Luteimonas kalidii sp. nov. (type strain M1R5S59T=CGMCC 1.61536T =KCTC 92471T) are proposed.

Luteimonas suaedae sp. nov., a novel bacterium isolated from rhizosphere of Suaeda aralocaspica (Bunge) Freitag & Schütze

Light yellowish-white colonies of a bacterial strain, designated LNNU 24178T, were isolated from the rhizosphere soil of halophyte Suaeda aralocaspica (Bunge) Freitag and Schütze grown at Shihezi district, Xinjiang, PR China. Cells were Gram-stain-negative, non-flagellum-forming, rod-shaped and non-motile. The results of phylogenetic analysis based on the 16S rRNA gene sequence indicated that LNNU 24178T represented a member of the genus Luteimonas and shared the highest sequence similarity with Luteimonas yindakuii CGMCC 1.13927T (97.1 %) and lower sequence similarity (< 97.0 %) to other known species. The genomic DNA G+C content of LNNU 24178T was 68.8 %. The average nucleotide identity (ANI) values between LNNU 24178T and Luteimonas yindakuii CGMCC 1.13927T, Luteimonas mephitis DSM 12574T, Luteimonas arsenica 26-35T and Luteimonas huabeiensis HB2T were 78.7, 78.6, 78.4 and 80.0 %, respectively. The digital DNA-DNA hybridisation (dDDH) values between LNNU 24178T and L. yindakuii CGMCC 1.13927T, L. mephitis DSM 12574T, L. arsenica 26-35T and L. huabeiensis HB2T were 22.0, 22.3, 22.2 and 23.5 %, respectively. The respiratory quinone detected in LNNU 24178T was ubiquinone-8 (Q-8). The major fatty acids (> 5.0 %) of LNNU 24178T were identified as iso-C15 : 0 (33.9 %), iso-C17 : 0 (8.7 %), iso-C11 : 0 (6.2 %), iso-C16 : 0 (5.7 %), C16 : 0 (5.3 %) and summed feature 9 (iso-C17 : 1ω9c/10-methyl C16 : 0) (21.1 %). The major polar lipids of LNNU 24178T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), one unidentified phospholipid (PL), one unidentified glycolipid (GL) and three unidentified lipids. According to the data obtained from phenotypic, chemotaxonomic and phylogenetic analyses, strain LNNU 24178T represents a novel species of the genus Luteimonas, for which the name Luteimonas suaedae sp. nov. is proposed, with LNNU 24178T (= CGMCC 1.17331T= KCTC 62251T) as the type strain.

Description and genome analysis of Luteimonas viscosa sp. nov., a novel bacterium isolated from soil of a sunflower field

Strain XBU10^T was isolated from a soil sample of a sunflower plot in Inner Mongolia, China. The isolate was a Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, and its colonies were bright yellow in colour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XBU10^T belonged to the genus Luteimonas of the family Lysobacteraceae and was most closely related to Luteimonas panaciterrae Gsoil 068^T (97.8%), Luteimonas marina FR1330^T (97.6%), Luteimonas aquatica RIB1-20^T (97.4%) and Luteimonas huabeiensis HB2^T (97.2%). Growth occurred at 4-40 °C (optimum, 28-30 °C), with 0-5.0% (w/v) NaCl (optimum, 0.5%) and at pH 6.0-10.0 (optimum, pH 7.0 - 8.0). The chemotaxonomic characteristics of strain XBU10^T, which had Q-8 as its predominant quinone and iso-C_17:1 ω9c, iso-C_15:0, iso-C_17:0 and iso-C_16:0 as its major fatty acids, were consistent with classification in the genus Luteimonas. The polar lipid profile of strain XBU10^T comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, two unidentified aminophospholipids and three unidentified polar lipids. The genome of strain XBU10^T was 4.17 Mbp with a G + C content of 69.9%. Its genome sequence showed genes encoding alkaline phosphatase and catalase. Protein-coding genes related to carbohydrate-active enzymes were also observed. Average nucleotide identity (ANI) values between XBU10^T and other species of the genus Luteimonas were found to be low (ANIm < 88.0%, ANIb < 85.0% and OrthoANIu < 85.0%). Furthermore, digital DNA-DNA hybridization (dDDH) and average amino acid identity (AAI) values between strain XBU10^T and the closely related species ranged from 20.3 to 28.9% and from 64.2 to 82.3%, respectively. Based on the results of our phylogenetic, phenotypic, genotypic and chemotaxonomic analyses, it is concluded that strain XBU10^T represents a novel species within the genus Luteimonas, for which the name Luteimonas viscosa sp. nov. is proposed. The type strain is XBU10^T (= CGMCC 1.12158^T = KCTC 23878^T).

Luteimonas deserti sp. nov., a novel strain isolated from desert soil

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, named SJ-16^T, was isolated from desert soil collected in Inner Mongolia, northern PR China. Strain SJ-16^T grew at pH 6.0-11.0 (optimum, pH 8.0-9.0), 4-40 °C (optimum, 30-35 °C) and in the presence of 0-8 % (w/v) NaCl (optimum, 0-2 %). The strain was negative for catalase and positive for oxidase. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SJ-16^T clustered with Luteimonas chenhongjianii 100111^T and Luteimonas terrae THG-MD21^T, and had 98.8, 98.6, 98.3 and <97.9 % of 16S rRNA gene sequence similarity to strains L. chenhongjianii 100111^T, L. terrae THG-MD21^T, L. aestuarii B9^T and all other type strains of the genus Luteimonas, respectively. The major cellular fatty acids were iso-C_15 : 0, iso-C_16 : 0, summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c) and summed feature 9 (C_16 : 0 10-methyl and/or iso-C_17 : 1  ω9c). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids, and ubiquinone-8 was the only respiratory quinone. The genomic DNA G+C content was 69.3 mol%. The digital DNA-DNA hybridization and average nucleotide identity values of strain SJ-16^T to L. chenhongjianii 100111^T, L. terrae THG-MD21^T, L. rhizosphaerae 4-12^T and L. aestuarii B9^T were 36.9, 37.5, 24.0 and 21.1 %, and 80.9, 80.6, 80.7 and 76.3 %, respectively. Based on phenotypic, physiological and phylogenetic results, strain SJ-16^T represents a novel species of the genus Luteimonas, for which the name Luteimonas deserti is proposed. The type strain is SJ-16^T (=CGMCC 1.17694^T=KCTC 82207^T).

Luteimonas weifangensis sp. nov., Isolated from Bensulfuron-Methyl Contaminated Watermelon Soil

A Gram-stain-negative bacterium, designated WF-2^T, was isolated from bensulfuron-methyl contaminated watermelon soil in Weifang, Shandong province, China. Cells of strain WF-2^T were strictly aerobic, non-motile and rod-shaped. Strain WF-2^T grew optimally at 30 °C, pH 7.0. Strain WF-2^T possessed ubiquinone-8 (Q-8) as the predominant respiratory quinone. The major cellular fatty acids of the strain WF-2^T (> 5.0%) were iso-C_15:0, anteiso-C_15:0, iso-C_16:0, C_16:0, iso-C_17:0, and summed feature 9 (iso-C_17:1 ω9c/C_16:0 10-methyl). The polar lipids consisted of two unidentified lipids, three unidentified phospholipids, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidyl glycolipid. Phylogenetic analysis based on 16S rRNA g^Tne sequences revealed that WF-2^T was a member of the genus Luteimonas and showed the highest sequence similarity to Luteimonas lumbrici 1.1416^T (98.6%) and Lysobacter pocheonensis Gsoil 193^T (97.9%), lower sequence similarity (< 97.0%) to other known species. The genomic DNA G + C content of WF-2^T was 69.2 mol%. Average nucleotide identity (ANI) and the digital DNA-DNA hybridizations (DDH) between strains WF-2^T and L. lumbrici 1.1416^T were 81.9% and 24.7%, respectively. Based on the phylogenetic, chemotaxonomic and phenotypic data presented here, a new species with the name Luteimonas weifangensis sp. nov. is proposed. The type strain is WF-2^T (= KCTC 62441^T = CGMCC 1.13633^T).

Luteimonas chenhongjianii, a novel species isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae)

Two Gram-stain-negative, strictly aerobic, bright-yellow-pigmented and rod-shaped bacteria (strains 100069 and 100111^T) with a single polar flagellum were isolated from the rectal contents of plateau pika (Ochotona curzoniae). Based on the results of nearly full-length 16S rRNA gene sequence and phylogenetic analyses, strains 100069 and 100111^T belong to the genus Luteimonas, and are closest to Luteimonas rhizosphaerae 4-12^T (98.02 % similarity), Luteimonas aestuarii B9^T (97.8 %) and Luteimonas terrae THG-MD21^T (97.74 %). The DNA G+C contents of these two isolates were 68.30 mol% and 68.29 mol%, respectively. The highest average nucleotide identity (ANI) value between strain 100111^T and its closely related species was 83.34 %, well below the threshold of 95-96 %. The major cellular fatty acids were iso-C_11 : 0, iso-C_15 : 0 and iso-C_17 : 1  ω9. Polar lipid content was dominated by diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. Ubiquinone-8 (Q-8) was the predominant respiratory quinone. These two isolates grew optimally at 35-37 °C, pH 7.0-8.0 and with 1.0 % (w/v) NaCl. The results of ANI analysis and other characteristics obtained from our polyphasic study showed that strains 100069 and 100111^T represent a novel species in genus Luteimonas, for which the name Luteimonas chenhongjianii sp. nov. (type strain 100111^T=DSM 104077^T=CGMCC 1.16429^T) is proposed.

Luteimonas gilva sp. nov., isolated from farmland soil

A Gram-stain-negative, rod-shaped bacterium, strain H23^T, was isolated from farmland soil sampled in Enshi City, Hubei Province, PR China. The isolate grew optimally at 28-32 °C, pH 8.0 and with 0.5 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, strain H23^T belonged to the genus Luteimonas with the highest degree of 16S rRNA gene sequence similarity to Luteimonas cucumeris Y4^T (97.41 %). The DNA G+C content was 65.88 mol%. The average nucleotide identity and the Genome-to-Genome Distance Calculator results also showed low relatedness (below 95 and 70 %, respectively) between strain H23^T and type strains in the genus Luteimonas. Ubiquinone-8 was the predominant quinone. The major fatty acids were iso-C_15 : 0, iso-C_16 : 0, iso-C_17 : 0 and iso-C_17 : 1 ω9c. Polar lipids were dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unidentified phospholipids. Low digital DNA-DNA hybridization values, as well as physiological and biochemical differences, such as no casein hydrolysis, being catalase-negative, and tesing positive for cystine arylamidase, α-chymotrypsin and N-acetyl-β-glucosaminidase, could distinguish strain H23^T from its closely related species. Strain H23^T is considered to represent a novel species in the genus Luteimonas, for which the name Luteimonas gilva sp. nov. is proposed, with strain H23^T (=CCTCC AB 2019255^T=KCTC 72593^T) as the type strain.

Luteimonas yindakuii sp. nov. isolated from the leaves of Dandelion (Taraxacum officinale) on the Qinghai-Tibetan Plateau

Two strains (S-1072^T and 1626) of Gram-stain-negative, oxidase- and catalase-positive, aerobic, rod-shaped, motile bacteria with a single polar flagellum, were isolated from the leaves of Dandelion (Taraxacum officinale) on the Qinghai-Tibet Plateau of China. The cells grew optimally at 28 °C, pH 7.0 and with 0.5 % (w/v) NaCl on brain-heart infusion agar. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains S-1072^T and 1626 belong to the genus Luteimonas, sharing the highest similarity with Luteimonas arsenica CCTCC AB 2014326^T (97.0 %), Luteimonas terricola CGMCC 1.8985^T (96.9 %) and Luteimonas aestuarii KCTC 22048^T (96.6 %). The phylogenomic tree indicated that strains S-1072^T and 1626 were most closely related to Luteimonas abyssi CGMCC 1.12611^T. The biochemical characteristics revealed that strains S-1072^T and 1626 could neither produce trypsin nor produce acid from d-glucose, N-acetylglucosamine and maltose, distinguishing them from four closest relatives. The DNA G+C contents of strains S-1072^T and 1626 were 69.2 and 69.3 mol% respectively. The digital DNA-DNA hybridization values of our isolates with their four closely related species were below the 70 % threshold. The predominant menaquinone was Q-8 (98.7 %) and the major polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids (>10 %) were iso-C_15 : 0, iso-C_16 : 0 and summed feature 9 (10-methyl C_16 : 0 and/or iso-C_17 : 1 ω9c). Based on the data obtained, strains S-1072^T and 1626 should be classified as a novel species of the genus Luteimonas, for which the name Luteimonas yindakuii sp. nov. is proposed. The type strain is S-1072^T (=CGMCC 1.13927^T=JCM 33487^T).

Luteimonas lumbrici sp. nov., a novel bacterium isolated from wormcast

A Gram-stain-negative, yellow-green bacterium, designated 1.1416^T, was isolated from wormcast of Eisenia foetida. The strain was non-motile, rod-shaped, and grew optimally on NA medium at 30 °C, pH 7.0 and with 0 % (w/v) NaCl. On the basis of the 16S rRNA gene sequence and phylogenetic analysis, 1.1416^T showed the highest degree of 16S rRNA gene sequence similarity to Luteimonas arsenica 26-35^T (96.2 %), followed by Luteimonas lutimaris G3^T (96.1 %). The respiratory quinone of 1.1416^T was ubiquinone-8 (Q-8), and its major cellular fatty acids were iso-C_15 : 0 (39.8 %), summed feature 9 (iso-C_17 : 1  ω9c or C_16 : 0 10-methyl) (18.6 %). The major polar lipids of 1.1416^T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and six unidentified phospholipids. The genomic DNA G+C content of 1.1416^T was 71.0 mol%. According to the results of the phenotypic and chemotaxonomic phylogenetic analyses, strain 1.1416^T represents a novel species of the genus Luteimonas, for which the name Luteimonas lumbrici sp. nov. is proposed, with strain 1.1416^T (=KCTC 62979^T=CCTCC AB 2018348^T) as the type strain.