Genomic and transcriptomic analyses provide new insights into the allelochemical degradation preference of a novel Acinetobacter strain.

A novel n-alkane- and phenolic acid-degrading Acinetobacter strain (designated C16S1T) was isolated from rhizosphere soil. The strain was identified as a novel species named Acinetobacter suaedae sp. nov. using a polyphasic taxonomic approach. Strain C16S1T showed preferential degradation of three compounds: p-hydroxybenzoate (PHBA) > ferulic acid (FA) > n-hexadecane. In a medium containing two or three of these allelochemicals, coexisting n-hexadecane and PHBA accelerated each other's degradation and that of FA. FA typically hindered the degradation of n-hexadecane but accelerated PHBA degradation. The upregulated expression of n-hexadecane- and PHBA-degrading genes induced, by their related substrates, was mutually enhanced by coexisting PHBA or n-hexadecane; in contrast, expression of both gene types was reduced by FA. Coexisting PHBA or n-hexadecane enhanced the upregulation of FA-degrading genes induced by FA. The expressions of degrading genes affected by coexisting chemicals coincided with the observed degradation efficiencies. Iron shortage limited the degradation efficiency of all three compounds and changed the degradation preference of Acinetobacter. The present study demonstrated that the biodegradability of the chemicals, the effects of coexisting chemicals on the expression of degrading genes and the strain's growth, the shortage of essential elements, and the toxicity of the chemicals were the four major factors affecting the removal rates of the coexisting allelochemicals.

Taxonomic characterization and comparative genomic analysis of a novel Devosia species revealed that phenolic acid-degrading traits are ubiquitous in the Devosia genus.

Phenolic acids (PAs) are widely distributed allelochemicals in various environments. To better understand the fate of PAs in environments, a halotolerant PAs-degrading bacterium (named strain RR2S18T) isolated from rhizosphere soil was identified as a novel species of Devosia, named Devosia rhizosphaerae sp. nov. The strain initially degraded PAs into central ring-fission intermediates (protocatechuic acid) using the CoA-dependent non-ß-oxidation pathway. The produced ring-fission intermediates were then consecutively degraded by an ortho-cleavage reaction and the ß-ketoadipic acid pathway. A comparative genomics analysis of 62 Devosia strains revealed that PAs-degrading genes were ubiquitous in their genomes, indicating that PAs degradation is universal among members of this genus. The analysis also suggested that the genes involved in CoA-dependent non-ß-oxidation are inherent to Devosia strains, while those involved in ring-fission and ß-ketoadipic acid pathways were obtained by horizontal gene transfer.

Aquibacillus rhizosphaerae sp. nov., an Indole Acetic Acid (IAA)-producing Halotolerant Bacterium Isolated from the Rhizosphere Soil of Kalidium cuspidatum.

A bacterium (named strain LR5S19T) was isolated from the rhizosphere soil of the halophyte Kalidium cuspidatum in Baotou, Inner Mongolia, China. Strain LR5S19T was Gram-stain-positive, motile with a polar flagellum, rod shaped, and spore forming at the terminal position in swollen sporangia, and it grew at 10-40 ℃ (optimum 30 ℃), pH 6.0-9.0 (optimum pH 7.0), and in the presence of 1.0-15.0% (w/v) NaCl (optimum 2.0%). The phylogenetic analysis of the 16S rRNA gene showed that strain LR5S19T shared the highest similarity (96.7%) with A. koreensis JCM 12387T, followed by A. kalidii HU2P27T (96.2%), A. sediminis BH258T (96.1%), and 'A. salsiterrae' 3ASR75-54T (96.0%). The ANIb, AAI and dDDH values between strain LR5S19T and its closely related type strains were 69.3-73.8%, 65.4-72.4% and 19.2-20.3%, respectively. The major polar lipids in strain LR5S19T consisted of diphosphatidylglycerol, phosphatidylglycerol, and three unidentified phospholipids, while MK-7 was the major respiratory quinone. The major fatty acids of the strain were anteiso-C15:0 and iso-C15:0. Based on phylogenomic and phenotypic results, strain LR5S19T should be classified as a novel species within the genus Aquibacillus, for which Aquibacillus rhizosphaerae sp. nov. is proposed. The type strain is LR5S19T (= CGMCC 1.62028T = KCTC 43434T). The comparative genomic analysis revealed that all eight members of Aquibacillus could utilize D-glucose via the glycolysis-gluconeogenesis pathway or the pentose phosphate pathway and use the tricarboxylic acid cycle as the metabolic center. The potassium ion transport proteins and compatible solute synthesis pathways in all the members likely also help them cope with hypersaline environments.

Idiomarina rhizosphaerae sp. nov. isolated from rhizosphere soil of Kalidium cuspidatum, and reclassification of Idiomarina andamanensis as Pseudidiomarina andamanensis comb. nov., and Idiomarina mangrovi as Pseudidiomarina mangrovi comb. nov.

A Gram-stain-negative, strictly aerobic, gliding motile, non-spore forming, rod-shaped indole-3-acetic acid producing bacterial strain, designated M1R2S28T, was isolated from the rhizosphere soil of Kalidium cuspidatum, in Tumd Right Banner, Inner Mongolia, China. Strain M1R2S28T grew at pH 5.0-10.0 (optimum 8.0), 10-45 °C (optimum 37 °C), in the presence of 0-20% (w/v) NaCl (optimum 5%). The phylogenetic trees based on the 16S rRNA gene sequences and the core-genome both revealed that strain M1R2S28T clustered tightly with Idiomarina loihiensis L2-TRT, and shared 99.3, 99.2, 98.7, and < 98.7% of the 16S rRNA gene sequence similarities with I. loihiensis L2-TRT, I. abyssalis KMM 227 T, I. ramblicola R22T, and all the other current type strains. The strain contained ubiquinone-8 (Q-8) as the sole respiratory quinone. Its major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid, and three unidentified lipids. Its major fatty acids were iso-C15:0, iso-C17:0, and iso-C17:1 ω9c. The genomic DNA G + C content was 46.8%. The average nucleotide identity based on BLAST (ANIb) and the digital DNA-DNA hybridization (dDDH) values of strain M1R2S28T to I. loihiensis L2-TRT, I. ramblicola R22T, and I. abyssalis KMM 227 T were 93.0, 82.9, and 81.8%, and 51.2, 26.0, and 25.0%, respectively. The phylogenetic and physiological results allowed the discrimination of strain M1R2S28T from its phylogenetic relatives. Idiomarina rhizosphaerae sp. nov. is, therefore, proposed with strain M1R2S28T (= CGMCC 1.19026 T = KCTC 92133 T) as the type strain. Additionally, based on the phylogenomic and genomic analysis results, Idiomarina andamanensis and Idiomarina mangrovi were transferred into genus Pseudidiomarina and be named Pseudidiomarina andamanensis comb. nov. and Pseudidiomarina mangrovi comb. nov., respectively.

Corynebacterium kalidii sp. nov, an endophyte from a shoot of the halophyte Kalidium cuspidatum.

A Gram-stain-positive, non-motile, rod-shaped bacterial strain designated LD5P10T was isolated from a root of Kalidium cuspidatum, in Tumd Right Banner, Inner Mongolia, China. The strain grew at 4-40 â„ƒ (optimum 30 â„ƒ), and pH 5.0-10.0 (optimum pH 8.0), and in the presence of 0-16.0% (w/v) NaCl (optimum 2.0%). The strain was positive for catalase, and urease, and negative for nitrate reduction, and oxidase. The phylogenetic trees based on the 16S rRNA gene sequences and the whole genome sequence both revealed that strain LD5P10T clustered tightly with Corynebacterium glyciniphilum AJ 3170T and shared 98.1, 98.1, and < 98.1% of the 16S rRNA gene sequence similarities with strains C. glyciniphilum AJ 3170T, C. variabile DSM 20132T, and all the other current type strains. Strain LD5P10T contained MK-9 as the major respiratory quinone. Its major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphoglycolipid, two unidentified lipids, and two unidentified phospholipids. Its major fatty acids were C16:0 and C18:1 ω9c. The genomic DNA G + C content was 69.0%. The average nucleotide identity based on BLAST (ANIb), amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values of strain LD5P10T to C. glyciniphilum AJ 3170T and C. variabile DSM 20132T were 82.9 and 76.4%, 85.3 and 69.4%, and 25.8 and 20.9%, respectively. The phylogenetic, physiological, and phenotypic results allowed the discrimination of strain LD5P10T from its phylogenetic relatives. Corynebacterium kalidii sp. nov. is, therefore, proposed with strain LD5P10T (= CGMCC 1.19144T = JCM 35048T) as the type strain.

Acuticoccus kalidii sp. nov., a 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing endophyte from a root of Kalidium cuspidatum.

A 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing, Gram-stain-negative, strictly aerobic, non-motile, yellow-reddish, oval-shaped bacterial strain, designated M5D2P5T, was isolated from a root of Kalidium cuspidatum, in Tumd Right Banner, Inner Mongolia, PR China. M5D2P5T grew at 10-40 °C (optimum 30-35 °C), pH 5.0-10.0 (optimum pH 8.0) and with 0-7% NaCl (optimum 3.0 %). The strain was positive for catalase and oxidase. The phylogenetic trees based on 16S rRNA gene sequences indicated that M5D2P5T clustered with Acuticoccus yangtzensis JL1095T, and shared 98.0, 97.3, 97.2, 96.9 and less than 96.9 % 16S rRNA gene similarities to A. yangtzensis JL1095T, Acuticoccus mangrovi B2012T, Acuticoccus sediminis PTG4-2T, Acuticoccus kandeliae J103T, and all the other type strains, respectively. However, the phylogenomic tree showed it clustered with A. kandeliae J103T. M5D2P5T contained Q-10 as the major respiratory quinone, as well as two minor respiratory quinones, Q-7 and Q-8. Its major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified glycolipid, and four unidentified lipids. The genomic DNA G+C content was 66.5 %. The digital DNA-DNA hybridization score and the average nucleotide identity based on blast values of M5D2P5T to A. yangtzensis JL1095T, A. kandeliae J103T, A. mangrovi B2012T, and A. sediminis PTG4-2T, were 20.8, 23.7, 20.7, and 21.5 %, and 73.3, 79.5, 74.4, and 73.7 %, respectively. The phylogenetic and phenotypic characteristics allowed the discrimination of M5D2P5T from its phylogenetic relatives. The novel species Acuticoccus kalidii sp. nov. is therefore proposed, and the type strain is M5D2P5T (=CGMCC 1.19149T=KCTC 92132T).

Sinomicrobium kalidii sp. nov., an indole-3-acetic acid-producing endophyte from a shoot of halophyte Kalidium cuspidatum.

To better understand the effects of endophytic bacteria on halophytes, a bacteria that produced indole-3-acetic acid and 1-aminocyclopropane-1-carboxylic acid deaminase, designated HD2P242T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. The cells of strain HD2P242T were Gram-stain-negative, strictly aerobic, motile by gliding, non-spore-forming and rod-shaped. Strain HD2P242T grew at pH 6.0-9.0 (optimum, pH 7.0) and 10-45 °C (optimum 37 °C), in the presence of 0-8 % (w/v) NaCl (optimum, 4 %). The strain was positive for oxidase and catalase. The phylogenetic trees based on the 16S rRNA gene sequences and the whole genome sequences both showed that strain HD2P242T clustered with Sinomicrobium pectinilyticum 5DNS001T and S. oceani SCSIO 03483T, and had 95.6, 94.3 and <94.3 % 16S rRNA gene similarities to S. pectinilyticum 5DNS001T, S. oceani SCSIO 03483T and all the other current type strains. Strain HD2P242T contained menaquinone 6 as its sole respiratory quinone. Its major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and an unidentified lipid. The major fatty acids were iso-C17 : 0, iso-C16 : 0 3-OH, anteiso-C17 : 0 and summed feature 6 (C19 : 1 ω9c and/or C19 : 1 ω11c). The genome consisted of a 5 364 211 bp circular chromosome, with a G+C content of 45.1 mol%, predicting 4391 coding sequence genes, 47 tRNA genes and two rRNA operons. The average nucleotide identity based on blast and the digital DNA-DNA hybridization values of strain HD2P242T with S. oceani SCSIO 03483T and S. pectinilyticum 5DNS001T were 73.8 and 77.0%, and 22.3 and 22.2%, respectively. The comparative genome analysis showed that the pan-genomes of strain HD2P242T and three Sinomicrobium type strains possessed 4236 clusters, whereas the core genome possessed 2162 clusters, which accounted for 52.3 % of all the clusters. The genomic analysis revealed that all four Sinomicrobium members could utilize d-glucose by the glycolysis-gluconeogenesis pathway or the pentose phosphate pathway. The tricarboxylic acid cycle was utilized as a metabolic centre. The phylogenetic, physiological and phenotypic characteristics allowed the discrimination of strain HD2P242T from its phylogenetic relatives. Therefore, Sinomicrobium kalidii sp. nov. is proposed, and the type strain is HD2P242T (=CGMCC 1.19025T=KCTC 92136T).

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.

Ruania suaedae sp. nov. and Ruania halotolerans sp. nov., two actinobacteria isolated from saline soil, and reclassification of Haloactinobacterium kanbiaonis as Occultella kanbiaonis comb. nov.

Two Gram-stain-positive, non-motile, strictly aerobic, yellow-coloured, rod-shaped bacterial strains, designated LR1S40T and M4N3S171T, were isolated from rhizosphere and bulk saline soil of Suaeda salsa collected in Inner Mongolia, China. Phylogenetic trees based on 16S rRNA gene and whole genome sequences showed that the two strains clustered tightly with strains of the genus Ruania. Strains LR1S40T and M4N3S171T had 95.5% 16S rRNA gene similarity to each other, and strain LR1S40T had 98.8, 98.7, 97.4 and <97.0% similarity to Ruania alkalisoli RN3S43T, Ruania rhizosphaerae LNNU 22110T, Ruania alba YIM 93306T and all other current type strains, while strain M4N3S171T had 98.6 and <97.0% similarity to R. alba YIM 93306T, and all other current type strains, respectively. The average nucleotide identity based on blast (ANIb) and digital DNA-DNA hybridization (dDDH) values of LR1S40T and M4N3S171T with each other and to the other type strains of Ruania were well below the threshold values (95% for ANIb, 70% for dDDH) for differentiating a species. Diphosphatidylglycerol and phosphatidylglycerol were the major polar lipids in both strains. The predominant menaquinone in both strains was both MK-8. The genome of strain LR1S40T consisted of a 3557440 bp circular chromosome, with a G+C content of 71.1 mol%, while the genome of strain M4N3S171T consisted of 4270413 bp, with a G+C content of 67.6 mol%. The phylogenetic, physiological and phenotypic characteristics allowed discrimination of the two strains from their relatives. The names Ruania suaedae sp. nov. [type strain LR1S40T (=CGMCC 1.19028T=KCTC 49726T)] and Ruania halotolerans sp. nov. [type strain M4N3S171T (=CGMCC 1. 19142T=KCTC 49727T)] are therefore proposed. During the publication of Haloactinobacterium kanbiaonis, Haloactinobacterium glacieicola (type strain T3246-1T), which was selected as the reference strain for the identification of H. kanbiaonis, was reclassified as Occultella glacieicola. The two phylogenetic trees showed that H. kanbiaonis HY164T tightly clustered with Occultella aeris F300T, and had the highest 16S rRNA gene similarity (99.8%) to O. aeris F300T. Based on the phylogenetic analysis and the publication record, Haloactinobacterium kanbiaonis should be reclassified as Occultella kanbiaonis comb. nov.

Description and characterization of three endophytic Bacillaceae from the halophyte Suaeda salsa: Paenalkalicoccus suaedae gen. nov., sp. nov., Cytobacillus suaedae sp. nov., and Bacillus suaedae sp. nov.

Three strains of members of the family Bacillaceae, which can inhibit the growth of some Gram-stain-positive strains, designated M4U3P1T, HD4P25T and RD4P76T, were isolated from Suaeda salsa halophytes in Baotou, Inner Mongolia, PR China. A phylogenetic analysis based on the 16S rRNA gene and the whole genome sequences revealed that HD4P25T clustered with Cytobacillus luteolus YIM 93174T with a similarity of 98.4 %, and RD4P76T shared the highest similarity of 16S rRNA gene with Bacillus mesophilus SA4T (97.5 %). M4U3P1T clustered with strains of genera Salipaludibacillus and Alkalicoccus based on whole-genome sequence analyses, but its 16S rRNA gene had the highest similarity to 'Evansella tamaricis' EGI 80668 (96.1 %). The average nucleotide's identity by blast (ANIb) and digital DNA-DNA hybridization (dDDH) values of the three isolated strains to their close relatives were well below the threshold value for identifying a novel species.On the basis of the phylogenetic, physiological and phenotypic results, Paenalkalicoccus suaedae gen. nov., sp. nov. [type strain M4U3P1T (=CGMCC 1.17076T=JCM 33851T)], Cytobacillus suaedae sp. nov. [type strain HD4P25T (=CGMCC 1.18651T =JCM 34524T)], and Bacillus suaedae sp. nov. [type strain RD4P76T (=CGMCC 1.18659T=JCM 34525T)] were proposed, respectively. All three species are ubiquitous in the bulk saline-alkaline soils, but only the species represented by strain RD4P76T was widely distributed in the rhizosphere soil, the above-ground part and the roots of S. salsa. The species represented by M4U3P1T can be detected in the roots of S. salsa, and rarely detected in the above-ground parts of S. salsa. The species represented by HD4P25T was rarely detected in the interior of S. salsa. The three strains could inhibit some of the Gram-stain-positive bacteria (i.e. members of the genera Planococcus, Zhihengliuella and Sanguibacter) in the saline-alkali soil. A genomic analysis of these three strains revealed that they can synthesize different antagonistic compounds, such as aminobenzoate and bacitracin or subtilisin.

Marinilactibacillus kalidii sp. nov., an Indole Acetic Acid-Producing Endophyte Isolated from a Shoot of Halophyte Kalidium cuspidatum.

A Gram-stain-positive, facultatively anaerobic, non-sporulating, motile with single polar flagellum, rod-shaped, indole-3-acetic acid (IAA)-producing bacterium, named M4U5P12T, was isolated from a shoot of Kalidium cuspidatum, Inner Mongolia, China. Strain M4U5P12T grew at pH 6.0-11.0 (optimum 7.5), 4-40 °C (optimum 25 °C), and in the presence of 0-15% (w/v) NaCl (optimum 4%). Positive for catalase, urease, methyl red (M.R.) reaction, and hydrolysis of starch; and negative for oxidase, Voges-Proskauer (V-P) test, and hydrolysis of cellulose. The phylogenetic trees based on the 16S rRNA gene sequences and the whole genome sequences both revealed that it clustered with Marinilactibacillus piezotolerans JCM 12337T (99.3%) and Marinilactibacillus psychrotolerans M13-2T (99.1%). The dDDH and ANIb values of strain M4U5P12T to M. piezotolerans DSM 16108T and M. psychrotolerans M13-2T were 19.3 and 18.9%, and 74.3 and 74.0%, respectively. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, and two unidentified lipids. The major fatty acids were C16:0, C18:1 ω9c, C16:1 ω9c, and C15:1 ω5c. The genomic DNA G + C content was 37.3%. On the basis of physiological, phenotypic, and phylogenetic characteristics, strain M4U5P12T should be classified as a novel species. Therefore, Marinilactibacillus kalidii sp. nov. is proposed, and the type strain is M4U5P12T (= CGMCC 1.17696T = KCTC 43247T).

Ignatzschineria rhizosphaerae sp. nov. Isolated from Rhizosphere Soil of the Halophyte Kalidium cuspidatum.

A Gram-staining negative, non-motile, aerobic, rod-shaped bacterium, designated strain HR5S32T, was isolated from rhizosphere soil of the halophyte Kalidium cuspidatum, in Tumd Right Banner, Inner Mongolia, northern China. Strain HR5S32T grew at 10-40 °C (optimum 30 °C), pH 6.0-10.0 (optimum pH 9.0), and 0-12% (w/v) NaCl (optimum 2%). It was positive for catalase, methyl red test, Voges-Proskauer test, and nitrate reduction, but negative to oxidase, urease and hydrolysis of Tween 80. The phylogenetic trees based on the 16S rRNA gene sequences and whole genome both showed that strain HR5S32T was most closely related to Ignatzschineria indica FFA1T (= KCTC 22643 T). Ubiquinone-8 (Q-8) was the major respiratory quinone. Phosphatidylglycerol, phosphatidylethanolamine, and phospholipid were the major polar lipids. Its major fatty acids were Summed features 8 (C18:1 ω6c and/or C18:1 ω7c), C16:0, Summed features 3 (C16:1ω6c and/or C16:1 ω7c), and C14:0. The genome consisted of a 3,074,733 bp circular chromosome, with a G + C content of 38.8%, predicting 2,763 coding sequence genes, 70 tRNA genes and 6 rRNA. The values of the average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) values of strain HR5S32T to I. indica FFA1T were 74.6% and 22.0%, respectively, hence significantly lower than the thresholds of 95% for ANI and 70% for DDH for species delineation. The results of phenotypic, physiological, genotypic, and phylogenetic tests allowed the differentiation of strain HR5S32T from its closely related species. Ignatzschineria rhizosphaerae sp. nov. is therefore proposed, and the type strain is HR5S32T (= CGMCC 1.19435 T = KCTC 92093 T).

Aquibacillus kalidii sp. nov., an indole acetic acid-producing endophyte from a shoot of Kalidium cuspidatum, and reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011.

A Gram-stain-positive, strictly aerobic, motile, endospore-forming, milk-white, indole acetic acid-producing, rod-shaped bacterial strain, designated as HU2P27T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. Strain grew at 10-40 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 0-14.0 % NaCl (optimum, 5.0-8.0 %). The strain tested positive for oxidase, catalase and nitrate reductase. The phylogenetic trees based on the 16S rRNA gene sequence and the core genome both showed that strain HU2P27T clustered with Aquibacillus koreensis BH30097T, sharing 97.7 % and <97.0 % of 16S rRNA gene similarity with A. koreensis BH30097T and any other type strain. Strain HU2P27T contained MK-7 as the major respiratory quinone. Its major fatty acids were anteiso-C15 : 0 and iso-C15 : 0, and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and four unidentified phospholipids. The genomic DNA G+C content was 36.0 mol%. The average nucleotide identity, amino acid identity and digital DNA-DNA hybridization values of strain HU2P27T with A. koreensis BH30097T were 71.7, 69.2 and 19.4%, respectively. The phylogenetic, physiological and phenotypic results allowed the discrimination of strain HU2P27T from its phylogenetic relatives. The name Aquibacillus kalidii sp. nov. is therefore proposed. The type strain is strain HU2P27T (=CGMCC 1.18646T=KCTC 43248T). Based on the results of 16S rRNA gene and genome analyses, we propose the reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011.

Gracilibacillus suaedae sp. nov., an indole acetic acid-producing endophyte isolated from a root of Suaeda salsa.

A Gram-stain-positive, facultatively anaerobic, spore-forming, motile with unipolar biflagella, rod-shaped, indole acetic acid-producing bacterium, named LD4P30T, was isolated from a root of Suaeda salsa collected in Inner Mongolia, northern China. Strain LD4P30T grew at pH 6.0-11.0 (optimum, pH 7.0), 10-40 °C (35 °C) and in the presence of 1-15% (w/v) NaCl (5%). The strain was positive for oxidase and negative for catalase. The major cellular fatty acids of strain LD4P30T were iso-C15:0, C15:1 ω5c and anteiso-C15:0; the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol; and menaquinone-7 was the only respiratory quinone. The genomic DNA G+C content was 36.7 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain LD4P30T clustered with Gracilibacillus thailandensis TP2-8T, Gracilibacillus saliphilus YIM 91119T and Gracilibacillus lacisalsi BH312T, and showed 99.0, 98.9, 98.0 and <97.7% 16S rRNA gene similarity to G. thailandensis TP2-8T, G. saliphilus YIM 91119T, G. lacisalsi BH312T and all other current type strains, respectively. The digital DNA-DNA hybridization and average nucleotide identity based on blast values between strain LD4P30T and G. saliphilus YIM 91119T, G. thailandensis TP2-8T and G. lacisalsi BH312T were 44.9, 44.7 and 44.4%, and 91.1, 91.0 and 90.8%, respectively. Based on its phenotypic, physiological and phylogenetic characteristics, strain LD4P30T represents a novel species, for which the name Gracilibacillus suaedae is proposed. The type strain is LD4P30T (=CGMCC 1.17697T=KCTC 82375T).

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

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, named SJ-16T, was isolated from desert soil collected in Inner Mongolia, northern PR China. Strain SJ-16T 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-16T clustered with Luteimonas chenhongjianii 100111T and Luteimonas terrae THG-MD21T, and had 98.8, 98.6, 98.3 and <97.9 % of 16S rRNA gene sequence similarity to strains L. chenhongjianii 100111T, L. terrae THG-MD21T, L. aestuarii B9T and all other type strains of the genus Luteimonas, respectively. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 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-16T to L. chenhongjianii 100111T, L. terrae THG-MD21T, L. rhizosphaerae 4-12T and L. aestuarii B9T 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-16T represents a novel species of the genus Luteimonas, for which the name Luteimonas deserti is proposed. The type strain is SJ-16T (=CGMCC 1.17694T=KCTC 82207T).

Ruania alkalisoli sp. nov., Isolated from Saline-Alkaline Soil.

A Gram-positive, strictly aerobic, ivory-colored, rod-shaped bacterial strain, designated RN3S43T, was isolated from saline-alkaline soil, in Tumd Right Banner, Inner Mongolia, China. Strain RN3S43T grew at 10-40 °C (optimum 30 °C), pH 6.0-10.0 (optimum pH 9.0), and 0-12.5% NaCl (optimum 2-4%). It was positive to oxidase, catalase, urease, and nitrate reductase. The methyl red and Voges-Proskauer tests were negative. The phylogenetic trees based on the 16S rRNA gene sequences and genome both showed that strain RN3S43T clustered with Ruania alba YIM 93306 T and shared 95.5% and < 95.0% of 16S rRNA gene similarities with R. alba YIM 93306 T and all the other type strains. MK-8 was the major respiratory quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and an unidentified lipid were the major polar lipids. The major fatty acids were anteiso-C15:0 and iso-C15:0. The genome consisted of a 4,448,708-bp circular chromosome, with a G+C content of 68.2%, predicting 3,911 coding sequence genes, 44 tRNA genes and two rRNA operons. The average nucleotide identity (ANI), amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values of strain RN3S43T to R. alba YIM 93306T were 79.0%, 79.2%, and 23.4%, respectively. The results of phylogenetic, physiological, and phenotypic tests allowed the discrimination of strain RN3S43T from its phylogenetic relatives. Ruania alkalisoli sp. nov. is therefore proposed, and the type strain is RN3S43T (=CGMCC 1.18652T = KCTC 49471T).

Sphingomonas suaedae sp. nov., a chitin-degrading strain isolated from rhizosphere soil of Suaeda salsa.

A Gram-stain-negative, aerobic, chitin-degrading, motile bacterial strain with a single polar flagellum, designated XS-10T, was isolated from saline soil sampled from the rhizosphere of Suaeda salsa, Tumd Right Banner, Inner Mongolia, PR China. Strain XS-10T grew at 10-40 °C (optimum, 35 °C), pH 5.0-9.0 (optimum, pH 8.0) and 0-12.5% NaCl (optimum 2.0 %). The phylogenetic analysis based on both the 16S rRNA gene and the phylogenomic tree revealed that strain XS-10T formed a clade with Sphingomonas turrisvirgatae MCT13T and Sphingomonas koreensis JSS-26T, sharing 98.4 and 97.5 % 16S rRNA gene similarities to S. koreensis JSS-26T and S. turrisvirgatae MCT13T, respectively. Spermidine and Q-10 were the major polyamine and the major respiratory quinone, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, two unidentified lipids and an unidentified aminophospholipid. The major fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and C17 : 1 ω6c. The genome of strain XS-10T consisted of a 4 154 291 bp chromosome with a DNA G+C content of 65.5 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values of strain XS-10T with S. turrisvirgatae MCT13T and S. koreensis JSS-26T were 77.8 and 78.6 %, 75.9 and 76.3 %, and 22.0 and 22.9 %, respectively. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain XS-10T is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas suaedae sp. nov. is proposed. The type strain is XS-10T (=CGMCC 1.17078T=JCM 33850T).

Lysobacter alkalisoli sp. nov., a chitin-degrading strain isolated from saline-alkaline soil.

Strains of Lysobacter, thought to play vital roles in the environment for their high enzyme production capacity, are ubiquitous in various ecosystems. During an analysis of bacterial diversity in saline soil, a Gram-stain-negative, aerobic, chitin-degrading bacterial strain, designated SJ-36T, was isolated from saline-alkaline soil sampled at Tumd Right Banner, Inner Mongolia, PR China. Strain SJ-36T grew at 4-40 °C (optimum, 30 °C), pH 5.0-10.0 (optimum, pH 7.0-8.0) and 0-6 % NaCl (optimum, 1.0 %). Oxidase and catalase activities were positive. A phylogenetic tree based on 16S rRNA gene sequences and the phylogenomic tree both showed that strain SJ-36T formed a tight clade with Lysobacter maris KMU-14T (sharing 97.6 % 16S rRNA gene similarity) and Lysobacter aestuarii S2-CT (97.8 %). The major polar lipids of strain SJ-36T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified lipids and one unidentified phospholipid. The major fatty acids were iso-C15 : 0 (37.5 %), summed feature 9 (14.0 %; iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and iso-C11 : 0 (10.6 %). Q-8 was the predominant ubiquinone. Its genomic DNA G+C content was 66.6 mol%. The average nucleotide identity values of strain SJ-36T to L. maris KMU-14T, L. aestuarii S2-CT and other type strains were 81.5, 79.1 and <79.0 %, respectively. The results of physiological, phenotypic and phylogenetic characterizations allowed the discrimination of strain SJ-36T from its phylogenetic relatives. Lysobacter alkalisoli sp. nov. is therefore proposed with strain SJ-36T (=CGMCC 1.16756T=KCTC 43039T) as the type strain.

Echinicola soli sp. nov., isolated from alkaline saline soil.

Strains of Echinicola, thought to play vital roles in the environment for their high enzyme production capacity during decomposition of polysaccharides, are ubiquitous in hypersaline environments. A Gram-negative, non-spore forming, gliding, aerobic bacterial strain, designated LN3S3T, was isolated from alkaline saline soil sampled in Tumd Right Banner, Inner Mongolia, northern PR China. Strain LN3S3T grew at 10-40 °C (optimum, 30 °C), pH 5.0-9.0 (optimum, pH 8.0) and with 0-12.5 % NaCl (optimum, 2.0 %). A phylogenetic tree based on the 16S rRNA gene sequences showed that strain LN3S3T clustered with Echinicola rosea JL3085T and Echinicola strongylocentroti MEBiC08714T, sharing 97.0, 96.7 and <96.50 % of 16S rRNA gene sequence similarities to E. rosea JL3085T, E. strongylocentroti MEBiC08714T and all other type strains. MK-7 was the major respiratory quinone, while phosphatidylethanolamine, two unidentified phospholipids, an unidentified aminophospholipid, an unidentified lipid and two unidentified aminolipids were the major polar lipids. Its major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The genome consisted of a circular 5 550 304 bp long chromosome with a DNA G+C content of 44.0 mol%. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values of strain LN3S3T to E. rosea JL3085T and E. strongylocentroti MEBiC08714T were 82.5 and 81.5 %, 87.5 and 86.0 %, and 39.1 and 35.1 %, respectively. Based on physiological, genotypic and phylogenetic analyses, strain LN3S3T could be discriminated from its phylogenetic relatives. Echinicola soli sp. nov. is therefore proposed with strain LN3S3T (=CGMCC 1.17081T=KCTC 72458T) as the type strain.

Flavobacterium alkalisoli sp. nov., isolated from rhizosphere soil of Suaeda salsa.

A Gram-negative, strictly aerobic, gliding motility, none-spore forming, yellow, rods bacterial strain, designated XS-5T, was isolated from rhizosphere soil of Suaeda salsa, in Tumd Right Banner, Inner Mongolia, PR China. A phylogenetic tree based on the 16S rRNA gene sequences and the phylogenomic tree both showed that strain XS-5T clustered with Flavobacterium beibuense F44-8T (shared 97.2 % of 16S rRNA gene similarity) and Flavobacterium rakeshii FCS-5T (97.6 %), and shared <96.0 % of 16S rRNA gene similarities with all other type strains. Strain XS-5T contained MK-6 as the major respiratory quinone. Its major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified lipid; and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0, iso-C15 : 0 3-OH, Summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c), and Summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl). The genome consisted of a 3 985 855 bp circular chromosome, with a G+C content of 37.9 mol%, predicting 3616 coding sequences genes, 45 tRNA genes and three rRNA operons. The average nucleotide identity, amino acid identity and digital DNA-DNA hybridization values of strain XS-5T to F. beibuense F44-8T and F. rakeshii FCS-5T were 79.2 and 79.2 %, 81.7 and 81.6 %, 22.3 and 22.2 %, respectively. The results of phylogenetic, physiological and biochemical tests allowed the discrimination of strain XS-5T from its phylogenetic relatives. Flavobacterium alkalisoli sp. nov. is therefore proposed with strain XS-5T (=CGMCC 1.17077T=KCTC 72459T) as the type strain.