Luteimonas gilva sp. nov., isolated from farmland soil

Luteimonas salinilitoris sp. nov., isolated from the shore soil of saline lake in Tibet of China

Five aerobic, Gram-stain-negative bacterial strains, designated as C3-2-a3T, B3-2-R+30, C3-2-a4, C3-2-M3 and C3-2-M8, were isolated from the coastal soil of LungmuCo Lake in the Tibet Autonomous Region, PR China. Phylogenetic analyses based on 16S rRNA genes and genomes indicated that these isolates belonged to the genus Luteimonas and showed a high similarity to Luteimonas suaedae LNNU 24178T (99.01%), Luteimonas endophytica RD2P54T (98.80%) and Luteimonas salinisoli SJ-92T (97.67%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain C3-2-a3T and related reference strains Luteimonas suaedae LNNU 24178T, Luteimonas endophytica RD2P54T and Luteimonas salinisoli SJ-92T were 91.89, 83.11 and 83.86% and 46.90, 26.90 and 28.20%, respectively. All values were below the thresholds for delineating species, supporting their classification as novel species of the genus Luteimonas. The genomic DNA G+C content of strains C3-2-a3T was 68.39%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified phospholipids. The predominant respiratory quinone was ubiquinone-8 (Q-8), aligning with the characteristics of members of the genus Luteimonas. The major fatty acids (>10.0%) of strain C3-2-a3T were identified as iso-C11 :  0, iso-C15 :  0, iso-C16 : 0 and iso-C17 : 1  ω9c. Based on the results of phenotypic, physiological, chemotaxonomic and genotypic characterizations, we propose that the isolates represent a novel species of genus Luteimonas, for which the name Luteimonas salinilitoris sp. nov is proposed. The type strain is C3-2-a3T (=CGMCC 1.14507T=KCTC 8642T).

Chitiniphilus purpureus sp. nov., a novel chitin-degrading bacterium isolated from crawfish pond sediment

A novel Gram-stain-negative, curved rod-shaped, motile and chitin-degrading strain, designated CD1T, was isolated from crawfish pond sediment in Caidian District (30° 58' N 114° 03' E), Wuhan City, Hubei Province, PR China. Growth of this strain was observed at 15-40°C (optimum between 28 and 30 °C), at pH 7.0-9.0 (optimum between pH 7.0 and 8.0) and with 0-1 % (w/v) NaCl (optimum at 0 %). With respect to the 16S rRNA gene sequences, strain CD1T had the highest similarity (96.91-97.25 %) to four type strains of the genera 'Chitinolyticbacter' and Chitiniphilus within the family Chitinibacteraceae. The phylogenetic trees based on genome sequences and 16S rRNA gene sequences indicated that strain CD1T was close to members of these two genera, in particular to the genus Chitiniphilus. The genomic DNA G+C content of strain CD1T was 64.8 mol%. The average nucleotide identity and the Genome-to-Genome Distance Calculator results showed low relatedness (below 95 and 70 %, respectively) between strain CD1T and the closely related type strains. Ubiquinone-8 was the predominant quinone. The major cellular fatty acids were C10 : 0, C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The polar lipid profile was composed of a mixture of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified lipids, two unidentified phospholipids, two unidentified aminolipids and an unidentified aminoglycolipid. On the basis of the evidences presented in this study, strain CD1T represents a novel species of the genus Chitiniphilus, for which the name Chitiniphilus purpureus sp. nov. is proposed, with strain CD1T (=CCTCC AB 2022395T=KCTC 92850T) as the type strain.

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.

Insight into bacterial community profiles of oil shale and sandstone in ordos basin by culture-dependent and culture-independent methods

To promote the exploitation of unconventional oil resources by indigenous microorganisms, the bacterial community profiles of oil shale and sandstone in Ordos Basin were investigated using Illumina Miseq sequencing combined with the culture-based method, which was performed and reported in this literature for the first time. A total of 601 operational taxonomic units (OTUs) were obtained from collected samples, the predominant phylum present in all samples was Proteobacteria (76.96%-93.07%). Discriminatory bacterial community profiles existed in those samples by culture-dependent and culture-independent methods, with variations not only in diversity indices but also in the abundance of bacteria at different genus levels. The dominant genera in cultured sandstone sample (SCB), uncultured sandstone sample (SUB), cultured shale sample (YCB), uncultured shale sample (YUB) were Enhydrobacter (71.62%), Acidovorax (42.44%), Pseudomonas (40.13%), Variovorax (70.02%), respectively. Both sample sources and culturing methods were the principal factors affecting the variation, while the communities' structures were favored primarily by culture-dependent or culture-independent approaches. The high abundance of hydrocarbon degradation-related genes was exhibited in YCB, which reveals a great potential for utilization of the culture-dependent method in shale oil exploitation. This study provided guidance for the exploitation of shale oil and sandstone oil by artificial utilization of indigenous bacteria.

Luteimonas saliphila sp. nov. and Luteimonas salinisoli sp. nov., two novel strains isolated from saline soils

Two Gram-stain-negative, motile with single polar flagellum, rod-shaped bacterial strains, named SJ-9T and SJ-92T, were isolated from saline soils from Inner Mongolia, PR China. SJ-9T and SJ-92T grew at pH 6.5–10.0 and 7.0–11.0, 10–35 °C, and in the presence of 0–5 % and 0–8 % NaCl, respectively. Both strains were positive for oxidase, and negative for catalase. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that SJ-9T clustered with Luteimonas marina FR1330T (sharing 97.9 % 16S rRNA gene similarity), Luteimonas huabeiensis HB2T (96.5 %), ‘Luteimonas wenzhouensis’ YD-1 (96.6 %), and Luteimonas composti CC-YY255T (95.1 %), and shared low 16S rRNA gene similarities (<97.0 %) with all the other type strains; while SJ-92T clustered with Luteimonas aestuarii B9T (98.2 %), and shared low 16S rRNA gene similarities (<98.0 %) with all the other type strains. The two strains shared 97.4 % 16S rRNA gene similarity with each other. The major cellular fatty acids of both strains are iso-C15 : 0 and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c). The major polar lipids of both strains are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The only respiratory quinone for both strains is ubiquinone-8 (Q-8). The genomic DNA G+C contents are 69.3 and 70.4 mol%, respectively. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity by blast (ANIb) values between the two strains were 22.6 and 77.5 %, while the values between SJ-9T and ‘L. wenzhouensis’ YD-1, L. marina FR1330T, and L. huabeiensis HB2T were 38.1, 39.2, and 21.9 %, and 82.5, 84.4, and 78.5 %, while those between SJ-92T and L. aestuarii B9T were 21.3 and 76.7 %. On the basis of the phenotypic, physiological and phylogenetic results, SJ-9T and SJ-92T represent two novel species of the genus Luteimonas , for which the names Luteimonas saliphila [type stain SJ-9T (=CGMCC 1.17377T=KCTC 82248T)] and Luteimonas salinisoli [type strain SJ-92T (=CGMCC 1.17695T=KCTC 82208T)] are proposed.

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).

Pseudomarimonas arenosa gen. nov., sp. nov. isolated from marine sand

A novel Gram-negative, aerobic, non-motile, rod-shaped, bacterial strain (CAU 1598^T) was isolated from marine sand. Strain CAU 1598^T grew well at 30 °C, pH 6.5-7.0 and with 3 % NaCl (w/v). Phylogeny results based on 16S rRNA gene sequencing indicated that the identified strain had the highest similarity (94.3%) to Pseudoxanthomonas putridarboris, indicating that strain CAU 1598^T belongs to the family Xanthomonadaceae. Further, the fatty acid profile of the strain was primarily composed of C_16:0, iso-C_15 : 0, iso-C_16 : 0, summed feature 3 (consisting of C_16 : 1  ω7c/iso-C_15 : 0 2-OH) and summed feature 9 (consisting of iso-C_17 : 1  ω9c and/or C_16 : 0 10-methyl), with ubiquinone-8 as the major isoprenoid quinone. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphoglycolipid, an unidentified aminolipid and an unidentified lipid. The G+C content of the bacterial genome was 62.6 mol% and its 5.4 Mb length encompassed 144 contigs and 4236 protein-coding genes. These phenotypic, chemotaxonomic and phylogenetic data indicate that CAU 1598^T belongs to a new genus and species, for which the name Pseudomarimonas arenosa gen. nov., sp. nov. is proposed. The type strain is CAU 1598^T (=KCTC 82406^T=MCCC 1K05673^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).