Description of a novel species of Leclercia, Leclercia tamurae sp. nov. and proposal of a novel genus Silvania gen. nov. containing two novel species Silvania hatchlandensis sp. nov. and Silvania confinis sp. nov. isolated from the rhizosphere of oak

• Published in: BMC microbiology Vol. 22; no. 1; pp. 289 - 18
• Main Authors: Maddock, Daniel, Arnold, Dawn, Denman, Sandra, Brady, Carrie
• Format: Journal Article
• Language: English
• Published: London BioMed Central 02.12.2022; BioMed Central Ltd; BMC
• Subjects: Acute oak decline; Annotations; Bacteria; Bacteria, Phytopathogenic; Biological Microscopy; Biomedical and Life Sciences; Clusters; Composition; Decline; Disease; Diseases and pests; Enterobacter; Enterobacterales; Enterobacteriaceae; Enterobacteriaceae - genetics; Environmental aspects; Fatty acids; Gammaproteobacteria; Gene sequencing; Genes; Genetic aspects; Genetic diversity; Genomes; Host range; Identification and classification; Immunomodulation; Leclercia; Life Sciences; Microbiology; Mycology; New species; Oak; Parasitology; Parks & recreation areas; Phylogenetics; Phylogeny; Physiological aspects; Plant growth; Plant growth promoting bacteria; Plant growth-promoting traits; Quercus; Recovery; Rhizosphere; RNA, Ribosomal, 16S - genetics; rRNA 16S; Signs and symptoms; Species classification; Taxonomy; Trees; Virology; Virulence; Virulence (Microbiology); Whole genome sequencing; United Kingdom; United Kingdom > UK; Acute oak decline; Plant growth promoting bacteria; Rhizosphere; Plant growth-promoting traits; Silvania; Leclercia; Enterobacteriaceae
• ISSN: 1471-2180; 1471-2180
• DOI: 10.1186/s12866-022-02711-x

Background Acute Oak Decline (AOD) is a decline disease first reported on native oaks in the UK, but in recent years reports from further afield such as Europe and the Middle East, indicate that the distribution and host range is increasing at an alarming rate. The stem weeping symptoms of the disease partially develop due to polymicrobial-host interaction, caused by several members of the order Enterobacterales. While investigating the rhizosphere soil of AOD-unaffected trees, termed ‘healthy’ trees, and diseased oaks suffering from Acute Oak Decline (AOD), an enrichment method designed for enhanced recovery of Enterobacterales led to the recovery of several isolates that could not be classified as any existing species. These isolates showed a close relationship to the genus Leclercia , of which both species are of clinical importance, but the type species Leclercia adecarboxylata also displays plant growth-promoting properties in the rhizosphere. Results Partial sequencing of four housekeeping genes revealed similarity to the genus Leclercia with varying degrees of relatedness. As such a complete polyphasic approach was used to determine the true taxonomic position of these isolates. This involved whole genome sequencing, phylogenomic analysis, phylogenetic analysis of both the 16S rRNA and four housekeeping gene sequences, combined with phenotypic testing and fatty acid analysis. Both the phylogenomic and phylogenetic analyses separated the isolates into four clusters, two of which were contained in the Leclercia clade. The remaining two clusters formed a separate lineage far removed from any currently defined species. Further investigation into the role of the isolates as plant growth-promoting bacteria as well as plant pathogens was investigated computationally, revealing a number of plant growth-promoting traits as well as virulence genes related to motility, adhesion and immune modulation. Conclusion Based on the genotypic and phenotypic data presented here, these isolates could be differentiated from each other and their closest neighbours. As such we propose the description of Leclercia tamurae sp. nov. (type strain H6S3 T  = LMG 32609 T  = CCUG 76176 T ), Silvania gen. nov., Silvania hatchlandensis sp. nov. (type strain H19S6 T  = LMG 32608 T  = CCUG 76185 T ) and Silvania confinis sp. nov. (type strain H4N4 T  = LMG 32607 T  = CCUG 76175 T ). Due to their interesting protein annotations and alignments, these species warrant further investigation for their role in relation to plant health.