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Xanthomonas indica sp. nov., a Novel Member of Non-Pathogenic Xanthomonas Community from Healthy Rice Seeds

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Abstract

Xanthomonas is a major group of pathogenic bacteria infecting staple food crops like rice. Increasingly it is being recognized that non-pathogenic Xanthomonas (NPX) are also important members of a healthy plant microbiome. However, the vast majority of the species described in this genus are of pathogenic nature, and only a few NPX species have been reported till now. Genomic and taxonogenomic analysis of NPX is needed for the management of this important group of bacteria. In this study, two yellow-pigmented bacterial isolates were obtained from healthy rice seeds in Punjab, India. The isolates designated PPL560T and PPL568 were identified as members of the genus Xanthomonas based on biochemical tests and 16S rRNA gene sequence analysis retrieved from the whole-genome sequences. Isolates formed a distinct monophyletic lineage with Xanthomonas sontii and Xanthomonas sacchari as the closest relatives in the phylogenetic tree based on core gene content shared by the representative species of the genus Xanthomonas. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridization values calculated against other species of Xanthomonas were below their respective cut-offs. In planta studies revealed that PPL560T and PPL568 are non-pathogenic to rice plants upon leaf clip inoculation. The absence of type III secretion system-related genes and effectors further supported their non-pathogenic status. Herein, we propose Xanthomonas indica sp. nov. as novel species of the genus Xanthomonas with PPL560T = MTCC 13185 = CFBP 9039 = ICMP 24394 as its type strain and PPL568 as another constituent member.

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Data Availability

The whole-genome sequences of PPL560T and PPL568 are deposited in NCBI under the accession numbers JAKJPQ000000000 and JAKLXA000000000, respectively. Pure cultures of the strains are submitted in Microbial Type Culture Collection and Gene Bank (MTCC), International Collection of Microorganisms from Plants (ICMP) and French Collection for Plant-associated Bacteria (CIRM-CFBP) culture collection with accession numbers, PPL560T = MTCC 13185 = CFBP 9039 = ICMP 24394 and PPL568 = MTCC 13186 = CFBP 9040 = ICMP 24395.

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Not applicable.

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Funding

This work is supported by a project entitled “Deciphering the mechanism(s) of host-endophytes co-evolution, enhanced secondary metabolite production and crop productivity. Grant Number: NBRI-IMTECH-MLP48. This work is also supported by a project entitled “Megagenomics and metagenomics insights into adaptation and evolution of fruit microbiome” (GAP0187 – grant number BT/HRD/NBA/38/14/2018-19) by the Department of Biotechnology (DBT), the government of India. We acknowledge Council of Scientific and Industrial Research (CSIR) fellowship to RR.

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Authors and Affiliations

  1. Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India

    Rekha Rana, Tanu Saroha, Kanika Bansal, Amandeep Kaur & Prabhu B. Patil

  2. The Academy of Scientific and Innovative Research, Ghaziabad, India

    Rekha Rana & Tanu Saroha

  3. CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India

    Vishnu Narayanan Madhavan & Hitendra K. Patel

  4. Indian Institute of Science Education and Research, Tirupati, India

    Ramesh V. Sonti

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  1. Rekha Rana
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  2. Vishnu Narayanan Madhavan
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  3. Tanu Saroha
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Contributions

RR isolated the strains, performed identification, and genome analysis. RR and TS did phylogenetic analysis. VNM did the plant virulence assay. RR and AK carried out biochemical tests. RR drafted the manuscript with inputs from KB, AK, TS, RVS, HKP and PBP. PBP planned and participated in the design of the study along with RR, KB, HKP, and RVS. PBP, HKP, and RVS applied for funding and coordinated the study. All authors read and approve the manuscript.

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Correspondence to Prabhu B. Patil.

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Rana, R., Madhavan, V.N., Saroha, T. et al. Xanthomonas indica sp. nov., a Novel Member of Non-Pathogenic Xanthomonas Community from Healthy Rice Seeds. Curr Microbiol 79, 304 (2022). https://doi.org/10.1007/s00284-022-03001-5

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