Ji-Quan Sun

Two bacterial strains, designated M5D2P9 ^T and M5D2P17 ^T , were isolated from a root of the halophyte Kalidium cuspidatum in Baotou, Inner Mongolia, China. Phylogenetic trees based on the 16S rRNA gene sequences and core genomes both showed that strains M5D2P9 ^T and M5D2P17 ^T formed a stable cluster with Sinomicrobium strains. Both strains shared the highest similarity with Sinomicrobium pectinilyticum 5DNS001 ^T , with values of 97.7 and 97.9%, respectively. The average nucleotide identity based on blast (ANIb) and digital DNA–DNA hybridization (dDDH) values between the two strains were 88.8 and 39.6%, respectively. The ANIb and dDDH between the two strains and S. pectinilyticum 5DNS001 ^T were 85.3 and 85.9% and 22.1 and 20.9%, respectively. The predominant isoprenoid quinone of strain M5D2P9 ^T was menaquinone 6 (MK-6), while that of strain M5D2P17 ^T was menaquinone 7 (MK-7) and MK-6 as a minor component. The polar lipid profiles of strains M5D2P9 ^T and M5D2P17 ^T were composed of phosphatidylethanolamine, unidentified aminolipid and unidentified phospholipid. Based on phenotypic and phylogenetic analyses, these two strains should be considered as two novel species of the genus Sinomicrobium , for which the names Sinomicrobium endophyticum sp. nov. (type strain M5D2P9 ^T =CGMCC 1.65541 ^T =JCM 38147 ^T ) and Sinomicrobium halophytocola sp. nov. (type strain M5D2P17 ^T =CGMCC 1.65542 ^T =JCM 38148 ^T ) are proposed.

Phenolic acids (PAs), which can exert toxic effects on seed germination and plant growth, are the most common allelopathic substances found in soils. To better understand the degradation fates of PAs in the rhizosphere of halophytes, five haloalkaliphilic PA-degrading bacteria, which were identified as three novel species of Kocuria (namely, Kocuria rhizosphaerae sp. nov., Kocuria kalidii sp. nov., and Kocuria rhizosphaericola sp. nov.), were obtained from the rhizosphere and bulk soil of the halophyte Kalidium cuspidatum. All five Kocuria strains could efficiently degrade ferulic acid (FA) and cinnamic acid (CA) under saline-alkaline conditions. Genomic and transcriptomic analyses revealed that the acrylic groups of FA and CA were first converted to a carboxyl via the coenzyme A (CoA)-dependent non-β-oxidation pathway by the five Kocuria strains. However, the five Kocuria strains selected different aromatic ring-cleavage ways for the degradation of the benzoic derivatives intermediates of the two compounds. The protocatechuate result from FA was then thoroughly degraded through an aromatic ring-opening reaction catalyzed by protocatechuate 3,4-dioxygenase (PcaGH), and the β-ketoadipic acid pathway. At the same time, the yield of benzoate originated from CA was subsequently converted to catechol by the benzoate 1,2-dioxygenase system (BenABCD) or phenylacetyl-CoA epoxidase (PaaABCD) and further completed the ring-cleavage by catechol 1,2-dioxygenase or catechol 2,3-dioxygenase (two non-PcaGH dioxygenases). The comparative genomic analysis revealed that the genes for phenolic acids hydroxylation, protocatechuate 3,4-dioxygenation, and those involved in the β-ketoadipic acid pathways are universal in the Kocuria strains. It is also demonstrated that the Kocuria strains maintain their osmotic balance by accumulating potassium, rather than biosynthesizing organic osmoprotectants, under hypersaline conditions.

Two bacteria, designated strain M1R2S20^T and RD2P27^T, were isolated from rhizosphere soil and a root of Kalidium cuspidatum in Baotou, Inner Mongolia, China. Phylogenetic analyses based on the 16S rRNA gene sequences revealed that strains M1R2S20^T and RD2P27^T were tightly clustered and both shared the highest 16S rRNA gene similarities (98.6 and 98.5 %) to Novosphingobium fluoreni ACCC 19180^T and less than 97.8% similarities with all other current type strains. Values of the digital DNA–DNA hybridization (dDDH), the average nucleotide identity based on the blast method (ANIb) and the average amino acid identity (AAI) of the two strains and their closely related species were 32.2, 79.0, and 84.5%, which were lower than the threshold values (70% for dDDH, 95% for ANIb and 95% for AAI). The major fatty acids of strains M1R2S20^T and RD2P27^T were C_18 : 1  ω7c and summed feature 3 (C_16 : 1  ω6c and/or C_16 : 1  ω7c). The only quinone was ubiquinone-10. Spermidine was the predominant polyamine. The genomic DNA G+C contents for strain M1R2S20^T and RD2P27^T were 62.4 and 62.7%. The phenotypic, chemotaxonomic and phylogenetic results supported that strains M1R2S20^T and RD2P27^T could be identified as two novel species within the genus Novosphingobium, for which the name Novosphingobium rhizovicinum sp. nov. and Novosphingobium kalidii sp. nov. are proposed. The type strains are N. rhizovicinum M1R2S20^T (=CGMCC 1.62060^T=KCTC 8106^T) and N. kalidii RD2P27^T (=CGMCC 1.62131^T=KCTC 8107^T).

Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1–9 prophages and 17–60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.

Three Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated RD2P54^T, M1R5S18^T and M1R5S59^T, 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 RD2P54^T tightly clustered with Luteimonas salinisoli SJ-92^T, while strains M1R5S18^T and M1R5S59^T clustered with each other and with Luteimonas viscosa XBU10^T and Luteimonas saliphila SJ-9^T. Though strains M1R5S18^T and M1R5S59^T 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 RD2P54^T, M1R5S18^T and M1R5S59^T with their closely neighbours are well below the delineation threshold values for identifying strains as representing different species. All three strains take iso-C_15 : 0 and summed feature 9 (C_16 : 0 10-methyl and/or iso-C_17 : 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 RD2P54^T=CGMCC 1.61535^T =KCTC 92470^T), Luteimonas rhizosphaericola sp. nov. (type strain M1R5S18^T=CGMCC 1.61537^T =KCTC 92469^T) and Luteimonas kalidii sp. nov. (type strain M1R5S59^T=CGMCC 1.61536^T =KCTC 92471^T) are proposed.

A bacterium (named strain LR5S19^T) was isolated from the rhizosphere soil of the halophyte Kalidium cuspidatum in Baotou, Inner Mongolia, China. Strain LR5S19^T 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 LR5S19^T shared the highest similarity (96.7%) with A. koreensis JCM 12387^T, followed by A. kalidii HU2P27^T (96.2%), A. sediminis BH258^T (96.1%), and ‘A. salsiterrae’ 3ASR75-54^T (96.0%). The ANIb, AAI and dDDH values between strain LR5S19^T 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 LR5S19^T 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-C_15:0 and iso-C_15:0. Based on phylogenomic and phenotypic results, strain LR5S19^T should be classified as a novel species within the genus Aquibacillus, for which Aquibacillus rhizosphaerae sp. nov. is proposed. The type strain is LR5S19^T (= CGMCC 1.62028^T = KCTC 43434^T). 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.