Bacterial Community of Water Yam (<i>Dioscorea alata</i> L.) cv. A-19

Abstract

The bacterial community of water yam ( Dioscorea alata L.) cv. A-19 is vital because it may promote plant growth without the need for fertilization. However, the influence of fertilization practices on the composition and proportion of the bacterial community of water yam cv. A-19 has not yet been extensively examined. Therefore, we herein investigated the diversity and composition of the bacterial community of water yam cv. A-19 cultivated with and without chemical fertilization using amplicon community profiling based on 16S rRNA gene sequences. No significant difference was detected in the growth of plants cultivated with or without chemical fertilization. Alpha diversity indices were significantly dependent on each compartment, and a decrease was observed in indices from the belowground (rhizosphere and root) to aboveground compartments (stem and leaf). The bacterial composition of each compartment was clustered into three groups: bulk soil, rhizosphere and root, and stem and leaf. Chemical fertilization did not significantly influence the diversity or composition of the water yam cv. A-19 bacterial community. It remained robust in plants cultivated with chemical fertilization. The amplicon community profiling of bacterial communities also revealed the dominance of two bacterial clades, the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade and Burkholderia-Caballeronia-Paraburkholderia clade, with and without chemical fertilization. This is the first study to characterize the bacterial community of water yam cv. A-19 cultivated with and without chemical fertilization.

Replacement of water yam (Dioscorea alata L.) indigenous root endophytes and rhizosphere bacterial communities via inoculation with a synthetic bacterial community of dominant nitrogen-fixing bacteria

“…Bacterial diversity and abundance in the water yam plants were evaluated using species richness and Shannon indices based on ENS and PCoA as alpha- and beta-diversities, respectively. Analysis of species richness revealed a significantly higher number of species (richness) in the R and Rh samples compared to the BK samples ( Figure 2 ), inconsistent with the results of Kihara et al (2022) who characterized the bacterial communities of water yam cv. A-19 under two different fertilization regimes (with- and without chemical fertilizers) using high-throughput 16 s rRNA amplicon sequencing.…”

“…Moreover, in both experiments, only the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade was found in all sample types, with a relative abundance of >1% in the water yam microbiota at all sampling dates. In Kihara et al (2022), the relative abundance of the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade accounted for 4.62-21.16% across the R, Rh, stem, and leaf samples, while in the present study, the R and Rh communities were also dominated by the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade (1.58-15.37%) across all harvesting dates and treatments. These results suggest that the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade comprises essential core bacteria even under different growth conditions.…”

“…They further revealed that 38.4% of nitrogen in the control plants was derived from the atmosphere. Similarly, a recent study by Kihara et al (2022) The strong association between water yam cv. A-19 plants and their native PGPB was also supported by the core bacteria identified in this study (Tables 4A, B and Supplementary Table 3 were found to be common between the R and Rh samples across all harvesting dates and treatments.…”

“…Previous studies have used microbial abundance to identify key species in the microbiota which high abundant taxa are considered as the core species ( Müller et al, 2016 ; Schmitz et al, 2022 ). Therefore, we defined bacteria showing an abundance of 1% or more in the water yam microbiota as dominant and used these criteria to select dominant NFB in our culturable bacteria library derived from yam plants based on bacterial 16S rRNA metagenomic sequencing data reported by Kihara et al (2022) ( Supplementary Table 1 and Supplementary Figure 1 ). Seventeen (17) strains, previously isolated by Ouyabe et al (2019) , Takada (2020) , and Liswadiratanakul et al (2021) , were selected ( Table 1 ), all of which were related to the genera Neorhizobium and Rhizobium , Enterobacter , Stenotrophomonas , and Ralstonia at a relative abundance in the water yam plants of 21.16, 3.96, 12.53, and 2.10%, respectively.…”

“…Therefore, to further address the difficulties associated with biofertilizer development, five NFB originating from water yam roots were selected based on their dominance (>1% relative abundance) in the water yam microbiota revealed by Kihara et al (2022) and their PGP activities. The PGP effects of a synthetic bacterial inoculant on plant growth and native water yam microbiota were subsequently examined.…”