Analysis Of Endophytic Community In The Healthy And Bacterial Blight Diseased Rice Leaves And Identification Of Physiologic Race And Haplotype Of Xanthomonas Oryzae Pv.oryzae Strains From Southern China

Plant microbiome is a significant ally for the plant in controlling the colonization/infection by plant pathogens.Analysis of microbial populations opens the avenue on the role of microbiome in plant disease.The crop rice is threatened by the causal agent of Bacterial blight（BB）caused by a gram-negative bacteria Xanthomonas oryzae pv.oryzae.None have yet been investigated for the potential effect of the endophytic microbiome in their pathology.To understand possible consequences of BB on the endophytic microbiome and the potential effect of the microbiome in their pathology,the endophytic bacterial and fungal community of the healthy and BB leaves of rice firstly which were collected in naturally regenerated rice in Yunnan Province,China were assessed by culture-independent approaches.In comparisons with healthy leaves of rice,bacterial community structure of BB leaves revealed that the relative abundance of Proteobacteria increased in the BB leaves.Pantoea and Pseudomonas belong to Proteobacteria,Curtobacterium belong to Actinobacteria,the OTUs OTU₃65assigned to Enterobacteriaceae family and OTU₁4 assigned Gammaproteobacteria class were obviously abundant in BB leaves.Endophytic fungal communities dominated by Ascomycota and Basidiomycota phylum.Ascomycota showed more abundant in BB leaves,while Basidiomycota decreased in BB leaves with significantly difference.Khuskia,Pseudopithomyces,Leptosphaerulina,Trichoglossum,Aureobasidium,Cladosporium,Myrothecium and Paraphaeosphaeria genus were mainly abundant fungal genera in BB leaves.30 bacterial strains were isolated from the BB leaves which collected from the different field of Yunnan and Guangdong province,China.Among them,10strains including 9 Pantoea strains and one Pseudomonas strain were identified as inhibitor to the BB pathogen Xoo.Nine Pantoea strains showed very close identities with each other.There strains of nine Pantoea sp.named MSMHa,MSMHe and MSZFNJa have several plant beneficial traits such as IAA product,nitrogen-fixing and ACC Deaminase indicating these three strains probably have rice-promotion growth ability.Interestingly,Inoculation of ZFZa,GDYCa and MSMHa with PXO99^A on rice in different proportions showed that the lesion length on rice leaves caused by PXO99^A was significantly shorter than Inoculation of PXO99^A alone demonstrating these strains have obvious disease-relieved ability and probably act as a biocontrol factor of BB.In order to clarify Xoo pathogen population structure and genotypic diversity in southern China,we analyzed the physiologic race of Xoo isolated from five Provinces（Guangdong,Yunnan,Guangxi,Zhejiang,Hubei）by pathotypic reaction of Xoo to six near-isogenic rice line（IRBB5,IRBB13,IRBB3,IRBB14,IRBB2 and IR24）and haplotypes indicated by various avrBs3/pthA genes employing SphⅠfragment of tal4 gene as probe.We get the conclusion that 6 physiologic races and 10 haplotypes were identified in 51 Xoo strains in southern China.Physiologic races include R1,R8,R9,R17,R18,and R19,of which R17,R18,and R19 are new physiologic races,and R8 accounts for up to 78.43%.The 10haplotypes were clustered intoⅠ-Ⅳ,and the proportion of ClusterIV was 67.31%.In summary,this study revealed the main endophytic bacteria and fungal communities in healthy and BB-infected rice leaves and the antagonism to Xoo and rice-promotion growth ability of pantoea sp.Moreover,we identify physiologic races and genotypes population structure of Xoo in southern China.This study provides a scientific basis for further exploration of endophytic microbiome,rice bacterial blight pathogenesis and its biocontrol.