Genome insights into the pharmaceutical and plant growth promoting features of the novel species Nocardia alni sp. nov

Abstract

Background Recent studies highlighted the biosynthetic potential of nocardiae to produce diverse novel natural products comparable to that of Streptomyces, thereby making them an attractive source of new drug leads. Many of the 119 Nocardia validly named species were isolated from natural habitats but little is known about the diversity and the potential of the endophytic nocardiae of root nodule of actinorhizal plants. Results The taxonomic status of an actinobacterium strain, designated ncl2T, was established in a genome-based polyphasic study. The strain was Gram-stain-positive, produced substrate and aerial hyphae that fragmented into coccoid and rod-like elements and showed chemotaxonomic properties that were also typical of the genus Nocardia. It formed a distinct branch in the Nocardia 16S rRNA gene tree and was most closely related to the type strains of Nocardia nova (98.6%), Nocardia jiangxiensis (98.4%), Nocardia miyuensis (97.8%) and Nocardia vaccinii (97.7%). A comparison of the draft genome sequence generated for the isolate with the whole genome sequences of its closest phylogenetic neighbours showed that it was most closely related to the N. jiangxiensis, N. miyuensis and N. vaccinii strains, a result underpinned by average nucleotide identity and digital DNA-DNA hybridization data. Corresponding taxogenomic data, including those from a pan-genome sequence analysis showed that strain ncl2T was most closely related to N. vaccinii DSM 43285T. A combination of genomic, genotypic and phenotypic data distinguished these strains from one another. Consequently, it is proposed that strain ncl2T (= DSM 110931T = CECT 30122T) represents a new species within the genus Nocardia, namely Nocardia alni sp. nov. The genomes of the N. alni and N. vaccinii strains contained 36 and 29 natural product-biosynthetic gene clusters, respectively, many of which were predicted to encode for a broad range of novel specialised products, notably antibiotics. Genome mining of the N. alni strain and the type strains of its closest phylogenetic neighbours revealed the presence of genes associated with direct and indirect mechanisms that promote plant growth. The core genomes of these strains mainly consisted of genes involved in amino acid transport and metabolism, energy production and conversion and transcription. Conclusions Our genome-based taxonomic study showed that isolate ncl2T formed a new centre of evolutionary variation within the genus Nocardia. This novel endophytic strain contained natural product biosynthetic gene clusters predicted to synthesize novel specialised products, notably antibiotics and genes associated with the expression of plant growth promoting compounds.

A Complete Genome of Nocardia terpenica NC_YFY_NT001 and Pan-Genomic Analysis Based on Different Sources of Nocardia spp. Isolates Reveal Possibly Host-Related Virulence Factors

“…K (transcription) and E (amino acid transport and metabolism) play an important role in the growth and colonization of Nocardia , so they account for a relatively large proportion in all COG classification, whether in cloud gene, shell gene or core gene. 40 The core genome is different from the variable genome (cloud and shell genomes), representing genes that exist in all strains. In our study, core genome was enriched in “J: Translation, ribosomal structure and biogenesis” (48 genes), “S: Function unknown” (40 genes), “E: Amino acid transport and metabolism” (37 genes) and “K: transcription” (33 genes).…”

Nocardia noduli sp. nov., a novel actinobacterium with biotechnological potential

“…Strain ncl1 T was isolated from a surfaced sterilized root nodule of an Alnus glutinosa tree growing in Leazes Park, Newcastle upon Tyne, UK, as described by Nouioui et al ( 2022 ). An active culture of the strain was obtained following growth on yeast extract-malt extract agar (International Streptomyces project [ISP] medium 2 (Shirling and Gottlieb 1966 )).…”

“…Nocardia are well known as serious causal agents of progressive invasive infections of humans and animals, notably mycetoma and nocardiosis (Conville et al 2018 ), but are also seen to be successful saprophytes as they degrade complex organic compounds (Luo et al 2014 ), and as attractive sources of new drug leads (Männle et al 2020 ). Nocardia strains have been isolated from diverse ecological settings (Goodfellow and Maldonaldo 2012 ), notably from soil, sediments, sponges and wastewater treatment plants (Goodfellow and Maldonado 2012 ), as well as from coastal marine foams (Wright et al 2021 ) and healthy plant tissues (Kaewkla and Franco 2010 ), including nodules of actinorhizal plants (Ghodhbane-Gtari et al 2014 ) thereby suggesting they may be beneficial for plant growth (Nouioui et al 2022 ).…”

Root Nodule Microsymbionts of Native Coriaria myrtifolia in Algeria

“…Numerous are the studies which reported the isolation of non-Frankia actinobacteria from actinorhizal root nodules 18,20,34,[37][38][39][40][41][42][43][44][45] as it was shown before for legume nodules which contain both rhizobial and non-rhizobial bacteria. 46,47 Three type strains; Micromonospora coriariae 42 ; Nocardia casuarinae 44 and Nocardia alni 48 have been isolated respectively from Coriaria; Casuarina and Alnus root nodules. Interestingly, a Micromonospora strain isolated in the present study is very closely related to M. coriariae species suggesting a widespread occurrence of members of this species within C. myrtifolia root nodules.…”