Genomic Analysis Of Pseudomonas Sp.Rs-198 And Its Interaction Mechanism With Plant Rhizosphere

Soil salinization in Xinjiang is becoming more and more serious,which has seriously affected the production of pepper,cotton,tomato and other major economic crops.Although the total phosphorus content in Xinjiang soil is very high,most of them are unavailable form,which is hard to be utilized by root.The phosphorus fertilizer can alleviate the phosphorus deficiency problem temporarily,the applied phosphorus fertilizers are easily chelated by the metal ions in the soil,resulting a low fertilizer utilization rate,which caused the waste of phosphorus resources.Many studies have reported that rhizobacteria is an environmentally friendly and sustainable agricultural strategy to saline soil,only a small part of them are working on the salt tolerance of pepper plants induced by rhizobacteria.Therefore,the interaction mechanism between Rs-198 and plant rhizosphere under the pot and plot experimental conditions were studied in this work.With the help of whole genome sequencing,the genomic characteristics of the rhizosphere growth promoting strain Rs-198,and its metabolic pathways related to salt and promoting growth property were analyzed.Finally,combined the growth promoting effects and whole genome data,the interaction mechanism between Rs-198 and plant roots was revealed.The present work was comparing the different response of the underground and aboveground of pepper plant to salt stress with or without bacteria Pseudomonas sp.Rs-198 application.It was found that inoculation of Rs-198 performed better aboveground fresh weights by increased 10.90%and underground fresh weights increased by 8.81%significantly at 150 mM salt stress conditions,respectively.Significantly increasing in total N and total P also obtained in non inoculated plants.It was also observed that protein,total soluble sugar concentrations,CAT activity,POD activity and PPO activity of plants under Rs-198 inoculation treatments were significantly improved than those of non inoculated pepper plant.More interesting,the underground showed more severe changes in accumulating N,P,proline,betaine and antioxidant enzymatic activities than aboveground under salt stress with or without application of Rs-198.While aboveground expressed higher sensitivity in TSS and soluble proteins for the main synthesis of protein and sugar happened in the leaf,and they also limited by carbohydrate availability from reduced photosynthesis in the leaf.There are abundant phosphorus which can not be uptaked by plants in salinized soil,the present study was designed to analyze the P element content in rhizosphere soil of pepper and cotton plant and its effect on microbial diversity and community structure.Results showed that the application of Rs-198increased the pepper and cotton nutrients of N,P and K in root,stems and leaves.However,the Na content in pepper and cotton root were significantly decreased by 59.71%and 59.87%after Rs-198inoculation.Therefore,the microbial diversity of pepper rhizosphere soil was analyzed as representative,and it was observed that Rs-198 application can decrease the abundance of Latescibacteria at both bulk and rhizosphere soil,the gene abundance of Blastococcus,AKYG587 and Pseudomonas were significantly increased in bulk soil,where as the abundance of Solirubrobacter,Roseiflexus,Actinoplanes and Skermanella decreased at gene level.In the functional prediction analysis,the treatment of Rs-198 significantly reduced the exogenous biodegradation,lipid metabolism,amino acid metabolism and other enzymes related to plant stress in the soil ecosystem.In addition,carbohydrate metabolism and amino acid metabolism in non rhizosphere soil were higher than rhizosphere soil,while coenzyme,vitamin metabolism and energy metabolism enzyme in rhizosphere soil were relatively higher.Further analysis showed that Rs-198 inoculation increased the contents of available P,Ca₂-P,Ca₈-P,iron-P,aluminum-P and total-P by 34.28%,32.68%,18.04%,9.90%,14.51%and 9.01%.In addition,the content of available P was positively correlated with Ca₂-P and Ca₈-P,and negatively correlated with O-P.It is speculated that Rs-198 can regulate the rhizosphere bacterial activities,transform insoluble phosphorus into soluble phosphorus,increase the content of available phosphorus in soil and promote the growth of plants.The Rs-198 strain was mixed with Bacillus,and provide different bacteria at tomato growth process,in order to facilitate the specific nutrition needed in the specific growth stage.The treatments of Rs-198,B.amyloliquefaciens M and B.mojavensis L alone also produced statistically higher tomato fruit yields over controls by 24.24%,20.67%and 18.30%.The three and four bacteria co-inoculation increased fruit yield by 32.51%and 33.27%over the control,respectively.The levels of N,P,K,Mg,Na,Mn,Cu,Zn were increased when Rs-198 was supplied to the plants.The co-inoculation with three microbes significantly increased fruit Ca,Na,Mn and B concentration in compared to non inoculated control plant.Co-inoculation with four microbes had the highest Fe and Na content.In general,the combination of three microbes gave the highest biomass and yield without the disease presence.More importantly,compared with other strains and combinations,Rs-198 strain can significantly improve the content macronutrient and micronutrient contents in tomato fruit in any condition.Therefore,Rs-198 strain has significant growth promoting effect in both single inoculation and combination inoculation.Giiven the excellent property of Rs-198,the whole genomic characteristics of the rhizosphere growth promoting strain Rs-198 was sequenced by the combination of second and third-generation sequencing.The results show that the Pseudomonas sp.Rs-198 genome has a total of 6321565?bp with 60%G?+?C content,5564 functional genes.It was found that the genome of Rs-198 has multiple genes and metabolic pathways related to the growth promoting property by databases of KEGG,GO and IntEnz.The results are as follows:many enzymes related to the synthesis of low molecular organic acids were found in the pathway of carbon metabolism,the products of which were malic acid,acetic acid,gluconic acid?pqqABCDEFf and gdhA?,etc.These low molecular acids were closely related to the phosphorus solubility of Rs-198;Two key enzymes?Monooxygenase iaaM,amidase amiE?in indoleacetamide pathway of indole-3-acetic acid?IAA?biosynthesis were also identified in tryptophan metabolism;The salt tolerance related key genes beta/betB for betaine synthesis and treY/treZ and treS genes related to trehalose synthesis,gene kdpBDEF which regulates osmotic pressure cell wall synthesis and compatible solute accumulation,and gene NhaACP which is related to Na⁺/H⁺antipoter protein were also found;Many transporters were found in the ABC transport pathway and two-component system of strain Rs-198for cell material and energy exchange,substrate binding protein PstSCA of phosphorus transport system,lipopolysaccharide transporter and lipoprotein transporter corresponding coding genes can also be found in the ABC transport pathway of Rs-198.In summary,the correlation between Rs-198 and salt tolerance,growth promotion of pepper plants,soil microbial diversity and P content of soil nutrient elements in the rhizosphere of pepper were obtained,and the interaction mechanism between PGPR and plants were revealed.The whole genome data of Rs-198 and a number of genes related to growth promotion and salt tolerance were obtained.This study has important scientific theoretical significance and practical application value on reasonable application of Rs-198 to rhizosphere.