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Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant-Bacteria Interactions.

ABSTRACT: Plant growth-promoting bacteria can improve host plant traits including nutrient uptake and metabolism and tolerance to biotic and abiotic stresses. Understanding the molecular basis of plant-bacteria interactions using dual RNA-seq analyses provides key knowledge of both host and bacteria simultaneously, leading to future enhancements of beneficial interactions. In this study, dual RNA-seq analyses were performed to provide insights into the early-stage interactions between barley seedlings and three novel bacterial strains (two Paenibacillus sp. strains and one Erwinia gerundensis strain) isolated from the perennial ryegrass seed microbiome. Differentially expressed bacterial and barley genes/transcripts involved in plant-bacteria interactions were identified, with varying species- and strain-specific responses. Overall, transcriptome profiles suggested that all three strains improved stress response, signal transduction, and nutrient uptake and metabolism of barley seedlings. Results also suggested potential improvements in seedling root growth via repressing ethylene biosynthesis in roots. Bacterial secondary metabolite gene clusters producing compounds that are potentially associated with interactions with the barley endophytic microbiome and associated with stress tolerance of plants under nutrient limiting conditions were also identified. The results of this study provided the molecular basis of plant growth-promoting activities of three novel bacterial strains in barley, laid a solid foundation for the future development of these three bacterial strains as biofertilisers, and identified key differences between bacterial strains of the same species in their responses to plants.

SUBMITTER: Li T

PROVIDER: S-EPMC8467301 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundBacteria associated with plants can enhance the plants' growth and resistance against phytopathogens. Today, growers aim to reduce the use of mineral fertilizers and pesticides. Since phytopathogens cause severe yield losses in crop production systems, biological alternatives gain more attention. Plant and also seed endophytes have the potential to influence the plant, especially seed-borne bacteria may express their beneficiary impact at initial plant developmental stages. In the current study, we assessed the endophytic seed microbiome of seven genetically diverse barley accessions by 16S rRNA gene amplicon sequencing and verified the in vitro plant beneficial potential of isolated seed endophytes. Furthermore, we investigated the impact of the barley genotype and its seed microbiome on the rhizosphere microbiome at an early growth stage by 16S rRNA gene amplicon sequencing.ResultsThe plant genotype displayed a significant impact on the microbiota in both barley seed and rhizosphere. Consequently, the microbial alpha- and beta-diversity of the endophytic seed microbiome was highly influenced by the genotype. Interestingly, no correlation was observed between the endophytic seed microbiome and the single nucleotide polymorphisms of the seven genotypes. Unclassified members of Enterobacteriaceae were by far most dominant. Other abundant genera in the seed microbiome belonged to Curtobacterium, Paenibacillus, Pantoea, Sanguibacter and Saccharibacillus. Endophytes isolated from barley seeds were affiliated to dominant genera of the core seed microbiome, based on their 16S rRNA gene sequence. Most of these endophytic isolates produced in vitro plant beneficial secondary metabolites known to induce plant resistance.ConclusionAlthough barley accessions representing high genetic diversity displayed a genotype-dependent endophytic seed microbiome, a core seed microbiome with high relative abundances was identified. Endophytic isolates were affiliated to members of the core seed microbiome and many of them showed plant beneficial properties. We propose therefore that new breeding strategies should consider genotypes with high abundance of beneficial microbes.

Project description:The heavy use of mineral fertilizers causes imbalances in the biological processes that take place in soil. Therefore, it is necessary to develop more effective fertilizers or fertilizer complexes that ensure agricultural productivity and soil conservation. There is currently a lack of knowledge regarding the effectiveness of biologically enriched, complex mineral fertilizers for spring barley fertilization. The hypothesis of this study was that bacteria-enriched (Paenibacillus azotofixans, Bacillus megaterium, Bacillus mucilaginosus, and Bacillus mycoides), complex mineral fertilizers (N5P20.5K36) have significant impacts on the yield and potential for economic use of spring barley. Experimental studies were carried out for three years (2020-2022) with sandy loam soil in southern Lithuania. Four different spring barley fertilization scenarios (SCs) were investigated. In SC-1 (control), complex mineral fertilizer (N5P20.5K36) was not applied. In the other SCs, spring barley was sown with a drill and fertilizers were incorporated locally during the sowing operation: fertilization scenario SC-2 used 300 kg ha-1, SC-3 used 150 kg ha-1 preceded by a bacteria-inoculated complex mineral fertilizer (N5P20.5K36), and SC-4 used 300 kg ha-1 with the same bacterial complex. The results showed that the bacterial inoculant increased the efficiency of the mineral fertilizer and had an effect on plant growth in barley. For three consecutive years in the same plots, the bacterial inoculant showed significant positive effects on grain yield (changes of 8.1% in 2020, 6.8% in 2021, and 17.3% in 2022 between SC-2 and SC-4). Comparing the several different fertilizer scenarios from an economic point of view, it was observed that the highest profit per hectare was obtained with SC-4 in all three years of the study. Comparing SC-4 and SC-2, an increase of 13.7% was observed in 2020, followed by 9.1% and 41.9% in 2021 and in 2022, respectively. This study will be useful for farmers, biological inoculant manufacturers, and scientists researching the effectiveness of biological inoculants for growing agricultural crops. We found that it is possible to increase the yield of barley (7-17%) using the same rate of mineral fertilization by enriching it with bacterial inoculants. Further studies should be conducted to determine the effects of the bacterial inoculant on crop yield and soil over a period longer than 3 years.

Dataset Information

Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant-Bacteria Interactions.

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