Microbiome profiling reveals that Pseudomonas antagonises parasitic nodule colonisation of cheater rhizobia in Lotus.

Nodule microbiota are dominated by symbiotic nitrogen-fixing rhizobia, however, other non-rhizobial bacteria also colonise this niche. Although many of these bacteria harbour plant-growth-promoting functions, it is not clear whether these less abundant nodule colonisers impact root-nodule symbiosis. We assessed the relationship between the nodule microbiome and nodulation as influenced by the soil microbiome, by using a metabarcoding approach to characterise the communities inside nodules of healthy and starved Lotus species. A machine learning algorithm and network analyses were used to identify nodule bacteria of interest, which were re-inoculated onto plants in controlled conditions to observe their potential functionality. The nodule microbiome of all tested species differed according to inoculum, but only that of Lotus burttii varied with plant health. Amplicon sequence variants representative of Pseudomonas species were the most indicative non-rhizobial signatures inside healthy L. burttii nodules and negatively correlated with Rhizobium sequences. A representative Pseudomonas isolate co-colonised nodules infected with a beneficial Mesorhizobium, but not with an ineffective Rhizobium isolate and another even reduced the number of ineffective nodules induced on Lotus japonicus. Our results show that nodule endophytes influence the overall outcome of the root-nodule symbiosis, albeit in a plant host-specific manner.

Mesorhizobium norvegicum sp. nov., a rhizobium isolated from a Lotus corniculatus root nodule in Norway.

Strain 10.2.2T was isolated from a root nodule of a Lotus corniculatus plant growing near Skammestein (Norway). Phenotypic and chemotaxonomic characterization revealed that colonies grown on yeast-mannitol broth agar were circular, convex and slimy. Growth occurred at 28 °C in 0-1 % NaCl and in a pH range from above 4 to 10. Cells were resistant to kanamycin and phosphomycin. They could assimilate carbon sources such as l-lysine, d-mannose, d-mannitol, and l-alanine. Major fatty acids found in the organism were 11-methyl C18  :  1ω7c, C16  :  0, C18  :  1ω7c, C18  :  0 and C19  :  0 cyclo ω8c. Genome sequencing and characterization of the genome revealed its size to be 8.27 Mbp with a G+C content of 62.4 mol%. Phylogenetic analyses based on the 16S rRNA gene and housekeeping gene alignments placed this strain within the genus Mesorhizobium. Pairwise genome-wide average nucleotide identity values supported that strain 10.2.2T represents a new species, for which we propose the name Mesorhizobium norvegicum sp. nov. with the type strain 10.2.2T (=DSM 108834T=LMG 31153T).