Rhizobium dioscoreae sp. nov., a plant growth-promoting bacterium isolated from yam (Dioscorea species)

Ouyabe, Michel; Tanaka, Naoto; Shiwa, Yuh; Fujita, Nobuyuki; Kikuno, Hidehiko; Pachakkil, Babil; Shiwachi, Hironobu

doi:10.1099/ijsem.0.004381

Cited by 18 publications

(6 citation statements)

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“…However, despite its importance, yam remains an “orphan crop” ( Kennedy, 2003 ). We recently reported the growth of yams in low fertile alkaline soil on Miyako Island, Okinawa, Japan, which was achieved by the absorption of nitrogen from the air by plant growth-promoting bacteria (PGPB) ( Shiwachi et al , 2015 ; Rezaei et al , 2016 , 2017 ; Takada et al , 2017 , 2018 ; Ouyabe et al , 2019a , 2019b , 2019c , 2020 ). The involvement of PGPB isolated from yams in nitrogen fixation, phosphate solubilization, indole acetic acid (IAA) production, and siderophore production was demonstrated.…”

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

et al. 2022

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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.

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

et al. 2022

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“…(ASV 87, found in 5.8% of Bombus spp.) are soil dwelling microbes involved in nitrogen fixation ( Eskin, Vessey & Tian, 2014 ; Ouyabe et al, 2020 ). However, each group of bacteria was found exclusively in either honey bees or bumble bees, suggesting little to no transmission of such bacteria between these two groups of bees.…”

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Honey bees and bumble bees occupying the same landscape have distinct gut microbiomes and amplicon sequence variant-level responses to infections

Amiri,

M. Keady,

Lim

2023

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The gut microbiome of bees is vital for the health of their hosts. Given the ecosystem functions performed by bees, and the declines faced by many species, it is important to improve our understanding of the amount of natural variation in the gut microbiome, the level of sharing of bacteria among co-occurring species (including between native and non-native species), and how gut communities respond to infections. We conducted 16S rRNA metabarcoding to discern the level of microbiome similarity between honey bees (Apis mellifera, N = 49) and bumble bees (Bombus spp., N = 66) in a suburban-rural landscape. We identified a total of 233 amplicon sequence variants (ASVs) and found simple gut microbiomes dominated by bacterial taxa belonging to Gilliamella, Snodgrassella, and Lactobacillus. The average number of ASVs per species ranged from 4.00–15.00 (8.79 ± 3.84, mean ± SD). Amplicon sequence variant of one bacterial species, G. apicola (ASV 1), was widely shared across honey bees and bumble bees. However, we detected another ASV of G. apicola that was either exclusive to honey bees, or represented an intra-genomic 16S rRNA haplotype variant in honey bees. Other than ASV 1, honey bees and bumble bees rarely share gut bacteria, even ones likely derived from outside environments (e.g., Rhizobium spp., Fructobacillus spp.). Honey bee bacterial microbiomes exhibited higher alpha diversity but lower beta and gamma diversities than those of bumble bees, likely a result of the former possessing larger, perennial hives. Finally, we identified pathogenic or symbiotic bacteria (G. apicola, Acinetobacter sp. and Pluralibacter sp.) that associate with Trypanosome and/or Vairimorpha infections in bees. Such insights help to determine bees’ susceptibility to infections should gut microbiomes become disrupted by chemical pollutants and contribute to our understanding of what constitutes a state of dysbiosis.

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“…In a 2014 study, the whole genomes of nine Proteobacteria were compared to identify a list of genes that may play a role in the endophytic activity. So yet, only a few of those genes have undergone experimental testing to determine whether they are involved in endophytic colonisation (Shen et al, 2013;Ouyabe et al, 2019). In this study, we have documented some mechanisms involved in plant endophyte interaction at the molecular level.…”

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confidence: 99%

Interaction between bacterial endophytes and host plants

et al. 2023

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Endophytic bacteria are mainly present in the plant’s root systems. Endophytic bacteria improve plant health and are sometimes necessary to fight against adverse conditions. There is an increasing trend for the use of bacterial endophytes as bio-fertilizers. However, new challenges are also arising regarding the management of these newly discovered bacterial endophytes. Plant growth-promoting bacterial endophytes exist in a wide host range as part of their microbiome, and are proven to exhibit positive effects on plant growth. Endophytic bacterial communities within plant hosts are dynamic and affected by abiotic/biotic factors such as soil conditions, geographical distribution, climate, plant species, and plant-microbe interaction at a large scale. Therefore, there is a need to evaluate the mechanism of bacterial endophytes’ interaction with plants under field conditions before their application. Bacterial endophytes have both beneficial and harmful impacts on plants but the exact mechanism of interaction is poorly understood. A basic approach to exploit the potential genetic elements involved in an endophytic lifestyle is to compare the genomes of rhizospheric plant growth-promoting bacteria with endophytic bacteria. In this mini-review, we will be focused to characterize the genetic diversity and dynamics of endophyte interaction in different host plants.

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Rhizobium dioscoreae sp. nov., a plant growth-promoting bacterium isolated from yam (Dioscorea species)

Cited by 18 publications

References 40 publications

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

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

Honey bees and bumble bees occupying the same landscape have distinct gut microbiomes and amplicon sequence variant-level responses to infections

Interaction between bacterial endophytes and host plants

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