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

• Published in: Current microbiology Vol. 79; no. 10; p. 304
• Main Authors: Rana, Rekha, Madhavan, Vishnu Narayanan, Saroha, Tanu, Bansal, Kanika, Kaur, Amandeep, Sonti, Ramesh V., Patel, Hitendra K., Patil, Prabhu B.
• Format: Journal Article
• Language: English
• Published: New York Springer US 01-10-2022; Springer Nature B.V
• Subjects: Bacteria; Biochemical tests; Biomedical and Life Sciences; Biotechnology; Cereal crops; Deoxyribonucleic acid; DNA; Gene sequencing; Hybridization; Inoculation; Life Sciences; Microbiology; Microbiomes; New species; Nucleotide sequence; Nucleotides; Phylogeny; Plant bacterial diseases; Rice; rRNA 16S; Seeds; Sequence analysis; Xanthomonas
• ISSN: 0343-8651; 1432-0991
• DOI: 10.1007/s00284-022-03001-5

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 PPL560
T
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 PPL560
T
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 PPL560
T
 = MTCC 13185 = CFBP 9039 = ICMP 24394 as its type strain and PPL568 as another constituent member.