Diversity and plant growth-promoting functions of diazotrophic/N-scavenging bacteria isolated from the soils and rhizospheres of two species of Solanum

Abstract

Studies of the interactions between plants and their microbiome have been conducted worldwide in the search for growth-promoting representative strains for use as biological inputs for agriculture, aiming to achieve more sustainable agriculture practices. With a focus on the isolation of plant growth-promoting (PGP) bacteria with ability to alleviate N stress, representative strains that were found at population densities greater than 104 cells g-1 and that could grow in N-free semisolid media were isolated from soils under different management conditions and from the roots of tomato (Solanum lycopersicum) and lulo (Solanum quitoense) plants that were grown in those soils. A total of 101 bacterial strains were obtained, after which they were phylogenetically categorized and characterized for their basic PGP mechanisms. All strains belonged to the Proteobacteria phylum in the classes Alphaproteobacteria (61% of isolates), Betaproteobacteria (19% of isolates) and Gammaproteobacteria (20% of isolates), with distribution encompassing nine genera, with the predominant genus being Rhizobium (58.4% of isolates). Strains isolated from conventional horticulture (CH) soil composed three bacterial genera, suggesting a lower diversity for the diazotrophs/N scavenger bacterial community than that observed for soils under organic management (ORG) or secondary forest coverture (SF). Conversely, diazotrophs/N scavenger strains from tomato plants grown in CH soil comprised a higher number of bacterial genera than did strains isolated from tomato plants grown in ORG or SF soils. Furthermore, strains isolated from tomato were phylogenetically more diverse than those from lulo. BOX-PCR fingerprinting of all strains revealed a high genetic diversity for several clonal representatives (four Rhizobium species and one Pseudomonas species). Considering the potential PGP mechanisms, 49 strains (48.5% of the total) produced IAA (2.96-193.97 μg IAA mg protein-1), 72 strains (71.3%) solubilized FePO4 (0.40-56.00 mg l-1), 44 strains (43.5%) solubilized AlPO4 (0.62-17.05 mg l-1), and 44 strains produced siderophores (1.06-3.23). Further, 91 isolates (90.1% of total) showed at least one PGP trait, and 68 isolates (67.3%) showed multiple PGP traits. Greenhouse trials using the bacterial collection to inoculate tomato or lulo plants revealed increases in plant biomass (roots, shoots or both plant tissues) elicited by 65 strains (54.5% of the bacterial collection), of which 36 were obtained from the tomato rhizosphere, 15 were obtained from the lulo rhizosphere, and 14 originated from samples of soil that lacked plants. In addition, 18 strains showed positive inoculation effects on both Solanum species, of which 12 were classified as Rhizobium spp. by partial 16S rRNA gene sequencing. Overall, the strategy adopted allowed us to identify the variability in the composition of culturable diazotroph/N-scavenger representatives from soils under different management conditions by using two Solanum species as trap plants. The present results suggest the ability of tomato and lulo plants to enrich their belowground microbiomes with rhizobia representatives and the potential of selected rhizobial strains to promote the growth of Solanum crops under limiting N supply.

Fig 1

Qualitative and quantitative distribution of bacterial strains isolated from different sources and from soils under different management conditions according to phylogenetic positioning at the genus level (1A), relative abundance (1B) and isolation source (1C). The chart legend indicates the identified genus and respective classes. BS, soil; TR, tomato unwashed roots; LR, lulo unwashed roots; SF, secondary forest soil with no agricultural use; CH, horticulture soil under conventional management; ORG, horticulture soil under organic management.

Fig 2. Dendrogram representing the genotype diversity and genetic relationships estimated by the cluster analysis of BOX-PCR fingerprints of diazotrophic/N-scavenging bacteria isolated from different sources and from soils under different management conditions.

Dendogram was constructed using the Jaccard coefficient (2% tolerance in terms of band size) with the UPGMA algorithm. Isolation sources: BS (soil); LR (lulo unwashed roots), TR (tomato unwashed roots). Soil management conditions: CH (horticulture under conventional management); ORG (horticulture under organic management); SF (secondary forest with no agricultural use).

Fig 3. Qualitative representation of plant growth-promoting traits observed for diazotrophic/N-scavenging bacteria isolated from different sources and from soils under different management conditions.

(A) Venn diagram showing unique and shared plant growth-promoting (PGP) traits detected for the bacterial strains studied. (B) Quantitative distribution of bacterial strains according to isolation source and PGP traits. (C) Quantitative distribution of bacterial strains according to phylogenetic position at the genus level and PGP traits.

Fig 4. Accumulation of biomass of the root system or aerial tissues of lulo and tomato plants grown under N-limiting conditions in response to the inoculation of 101 different diazotrophic/N-scavenging bacteria.

(A, C) Root dry weight (g plant^-1) of tomato (S. lycopersicum) and lulo (S. quitoense) plants, respectively. (B, D) Shoot dry weight (g plant^-1) of tomato (S. lycopersicum) and lulo (S. quitoense) plants, respectively. The mean values plotted in the same color represent groups that do not significantly differ at p < 0.05 according to the Scott-Knott algorithm. The bars refer to the maximum and minimum values for each plot. RDW, root dry weight; SDW, shoot dry weight.