Root colonization and plant probiotic function are important traits of plant growth-promoting rhizobacteria (PGPR). Bacillus velezensis SC60, a plant endophytic strain screened from Sesbania cannabina, has a strong colonization ability on various plant roots, which indicates that SC60 has a preferable adaptability to plants. However, the probiotic function of the strain SC60 is not well-understood. Promoting plant growth and suppressing soil-borne pathogens are key to the plant probiotic functions. In this study, the genetic mechanism of plant growth-promoting and antibacterial activity of the strain SC60 was analyzed by biological and bioinformatics methods. The complete genome size of strain SC60 was 3,962,671 bp, with 4079 predicted genes and an average GC content of 46.46%. SC60 was designated as Bacillus velezensis according to the comparative analysis, including average nucleotide polymorphism (ANI), digital DNA–DNA hybridization (dDDH), and phylogenetic analysis. Genomic secondary metabolite analyses indicated two clusters encoding potential new antimicrobials. The antagonism experiments revealed that strain SC60 had the ability to inhibit the growth of a variety of plant pathogens and its closely related strains of Bacillus spp., which was crucial to the rhizospheric competitiveness and growth-promoting effect of the strain. The present results further suggest that B. velezensis SC60 could be used as a PGPR strain to develop new biocontrol agents or microbial fertilizers.

A Gram-stain-negative, short ovoid- to coccus-shaped, aerobic, non-flagellated, and nonmotile strain, designated WN007T, was isolated from the natural saline–alkali wetland soil. Growth occurred at 10–45 °C (optimum 33–37 °C), pH 6.5–10.0 (optimum, pH 7.5–8.0) and with 0–15 % (w/v) NaCl (optimum, 2–4 % NaCl). Catalase- and oxidase-positive. A comparison of the 16S rRNA gene sequence of WN007T showed the highest sequence similarities to Paracoccus chinensis (97.5 %) and Paracoccus niistensis (97.4 %). The major respiratory quinone of strain WN007T was Q10 and the fatty acid profile of strain WN007T contained a predominant amount of summed feature 7 and small quantities of C10 : 0 3OH, C16 : 00 and C18 : 00. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, glycolipid, aminolipid and lipid. The genome revealed that the G+C content was 63.9 mol% and the DNA–DNA relatedness values between strain WN007T and the type strains of P. chinensis CGMCC 1.7655Tand P. niistensis KCTC 22789T were 46.9±2.3 and 42.4±1.7 %, respectively. This was also confirmed by the low average nucleotide identity values (<83.5 %) between strain WN007T and the most closely related recognized Paracoccus species. According to these results, strain WN007T represents a novel species of the genus Paracoccus , for which the name Paracoccus salipaludis sp. nov. is proposed. The type strain is WN007T (=KCTC 52851T=ACCC 19972T).

Root colonization by beneficial rhizobacteria determines their plant beneficial effects. The messenger c-di-GMP is involved in the bacterial transition process between motility and biofilm, which are crucial to the colonization ability of the rhizobacteria. In this study, we identified three GGDEF domain-containing proteins (YdaK, YhcK, and YtrP) and two EAL domain-containing proteins (YuxH and YkuI) in beneficial rhizobacterium Bacillus velezensis SQR9. We found that deficiency of ytrP or ykuI in SQR9 led to impaired biofilm formation, while deficiency of yuxH led to weakened motility. Further investigation showed that YtrP, YuxH, and YkuI all contributed to the root colonization of SQR9 on cucumber root. Further bioinformatics analysis showed that YtrP and YuxH are conserved in plant beneficial Bacillus group, while they do not occur in animal pathogenic Bacillus. This research will be useful for enhancing the beneficial function of Bacillus spp. in agricultural application.

Poly-γ-glutamic acid (γ-PGA) significantly promotes the fertilizer N uptake efficiency of crops and evidently affects soil available N (nitrate, ammonium and glutamate) status. As an adaptive strategy to forage N, root morphology responds variably to soil available N dynamics. Detailed knowledge of how root morphology responds to γ-PGA remains unexplored. A pot trial was conducted to investigate the response of root morphological traits to γ-PGA when applied with CO(NH₂)₂ or (NH₄)₂SO₄. The results showed that γ-PGA significantly improved the dry weight, total carbon and total nitrogen content of roots, and with a higher improvement with CO(NH₂)₂ compared to (NH₄)₂SO₄. γ-PGA significantly increased the root length, total surface area, tips and forks with CO(NH₂)₂. Contrarily, γ-PGA significantly reduced root length, specific root length, specific root area, root volume, tips and forks with (NH₄)₂SO₄, with its inhibition on root growth mainly caused by the high ammonium content in soil. In conclusion, γ-PGA gives opposite effects on root morphological traits when applied with CO(NH₂)₂ or (NH₄)₂SO₄. This finding provides a new insight to reveal the promotion mechanism of γ-PGA on plant N acquisition in the rhizosphere and offers a practical reference for optimizing γ-PGA and fertilizer application management.