Fig 1.
Location of sampled fields within the Haut-Bassins and Cascades regions of western Burkina Faso (sampled in 2017, 2018 and 2019).
Source: OpenStreetMap. Table 1 provides a detailed description of the fields.
Table 1.
Geographic and diachronic description of sampled fields and rice developmental stages.
Table 2.
Summary of all sampled isolates and the part constituting the working collection.
Fig 2.
Rarefaction curves (A) and (B), and diversity of isolates obtained from different sites at the genus level (C).
Fig 3.
Distribution of potential endophyte species and genera between two root fractions.
The Venn diagram shows the number of common and specific species of isolates from our collection, obtained from total roots (total microflora, in blue) or from surface sterilised roots (potential endophytes, in yellow). The listings show the total microflora, specific endophytes and shared endophytes at the genus level. The full list of species names is given in S1 Table.
Fig 4.
Bacterial isolate diversity sampled from each culture medium.
A, bar plot representing the number of genera (in brackets) per culture medium. B, Venn diagram showing the number of common and specific genera according to the culture medium.
Fig 5.
Characterization of PGP capacities of isolates in the working collection.
A, proportion of isolates (in percentage) presenting PGP capacities on the basis of the bacterial phyla: Ammonium, ammonia production; Auxin, auxin biosynthesis capacity; Phosphate, phosphate solubilising capacity and Siderophore, siderophore biosynthesis capacity. B, principal component analysis. C, detailed representation of in vitro PGP capacities (y-axis) of the working collection isolates (x-axis) on the basis of the taxonomy. As a majority of isolates had an ammonia production capacity, it was not displayed in part C of the figure.
Fig 6.
Comparison of in vitro measured PGP capacities and in planta PGP effects of 45 representative isolates according to their taxonomy.
Asterisks indicate statistically significant PGP inoculation effects-black for positive and green for negative effects. NH4, ammonium; ABC, auxin biosynthesis capacity; PSC, phosphate solubilisation capacity; SBC, siderophore biosynthesis capacity; TS2 and ORYLUX, rice cultivars, ctrl1 and ctrl2, for controls with non-inoculated plants; Size, plant size (cm); LW, aerial part dry weight (g); RW, root dry weight (g).
Fig 7.
Comparison of the diversity of isolates between the culturable collection and 16S amplicon barcode data from the study of Barro et al. [61] with a cut-off at 0.0001%.
A, phylum level; B, top 50 orders; C, top 50 genera.
Fig 8.
Neighbour joining phylogenetic tree of combined rice bacterial associated microbiota diversity (ASVs and culturable isolates).
The collection isolates are indicated by red circles. ASVs abundance is displayed with circles (blue circles, 1/100 read number (to better highlight the most abundant ones); green circles, log of read number).
Fig 9.
Assessment of PGPR in the rice root microbiome across the studied fields based on a comparison with the corresponding ASVs.
Irrigated conditions, Bama and Karfiguela; and rainfed lowland conditions, Badala and Tengrela. The colour scale represents the number of reads of each ASV.