17 research outputs found
Symbiotic and non-symbiotic members of the genus Ensifer (syn. Sinorhizobium) are separated into two clades based on comparative genomics and high-throughput phenotyping
Legume tasters: symbiotic rhizobia host preference and smart inoculant formulations
Mutualistic interactions have great importance in ecology, with genetic information
that takes shape through interactions within the symbiotic partners and
between the partners and the environment. It is known that variation of the
host-associated microbiome contributes to buffer adaptation challenges of the
host’s physiology when facing varying environmental conditions. In agriculture,
pivotal examples are symbiotic nitrogen-fixing rhizobia, known to contribute
greatly to host (legume plants) adaptation and host productivity. A holistic view
of increasing crop yield and resistance to biotic and abiotic stresses is that of
microbiome engineering, the exploitation of a host-associated microbiome
through its rationally designed manipulation with synthetic microbial communities.
However, several studies highlighted that the expression of the desired
phenotype in the host resides in species-specific, even genotype-specific interactions
between the symbiotic partners. Consequently, there is a need to
dissect such an intimate level of interaction, aiming to identify the main genetic
components in both partners playing a role in symbiotic differences/host
preferences. In the present paper, while briefly reviewing the knowledge and
the challenges in plant–microbe interaction and rhizobial studies, we aim to
promote research on genotype x genotype interaction between rhizobia and
host plants for a rational design of synthetic symbiotic nitrogen-fixing microbial
communities to be used for sustainably improving leguminous plants yield.This work was supported by the
grant MICRO4Legumes (“Il microbioma
vegetale simbionte come strumento per il
miglioramento delle leguminose foraggere.
Acronimo”), D.M.n.89267 (Italian Ministry of
Agriculture)
Endogenous histamine in the medial septum-diagonal band comp-lex increases the release of acetylcholine from the hippocampus: a dual probe microdialysis study in the freely moving rat
When biodiversity preservation meets biotechnology: The challenge of developing synthetic microbiota for resilient sustainable crop production
Synthetic plant microbiota challenges in nonmodel species
Plant-associated microbiota are becoming central in the development of ways to improve plant productivity and health. However, most research has focussed mainly on a few model plant species. It is essential to translate discoveries to the many nonmodel crops, allowing the design and application of effective synthetic microbiota
Scent of a Symbiont: The Personalized Genetic Relationships of Rhizobium—Plant Interaction
Many molecular signals are exchanged between rhizobia and host legume plants, some of which are crucial for symbiosis to take place, while others are modifiers of the interaction, which have great importance in the competition with the soil microbiota and in the genotype-specific perception of host plants. Here, we review recent findings on strain-specific and host genotype-specific interactions between rhizobia and legumes, discussing the molecular actors (genes, gene products and metabolites) which play a role in the establishment of symbiosis, and highlighting the need for research including the other components of the soil (micro)biota, which could be crucial in developing rational-based strategies for bioinoculants and synthetic communities’ assemblage
Crossing Bacterial Genomic Features and Methylation Patterns with MeStudio: An Epigenomic Analysis Tool
DNA methylation is one of the most observed epigenetic modifications. It is present in eukaryotes and prokaryotes and is related to several biological phenomena, including gene flow and adaptation to environmental conditions. The widespread use of third-generation sequencing technologies allows direct and easy detection of genome-wide methylation profiles, offering increasing opportunities to understand and exploit the epigenomic landscape of individuals and populations. Here, we present a pipeline named MeStudio, with the aim of analyzing and combining genome-wide methylation profiles with genomic features. Outputs report the presence of DNA methylation in coding sequences (CDSs) and noncoding sequences, including both intergenic sequences and sequences upstream of the CDS. We apply this novel tool, showing the usage and performance of MeStudio, on a set of single-molecule real-time sequencing outputs from strains of the bacterial species Sinorhizobium meliloti
Crossing Bacterial Genomic Features and Methylation Patterns with MeStudio: An Epigenomic Analysis Tool
DNA methylation is one of the most observed epigenetic modifications. It is present in eukaryotes and prokaryotes and is related to several biological phenomena, including gene flow and adaptation to environmental conditions. The widespread use of third-generation sequencing technologies allows direct and easy detection of genome-wide methylation profiles, offering increasing opportunities to understand and exploit the epigenomic landscape of individuals and populations. Here, we present a pipeline named MeStudio, with the aim of analyzing and combining genome-wide methylation profiles with genomic features. Outputs report the presence of DNA methylation in coding sequences (CDSs) and noncoding sequences, including both intergenic sequences and sequences upstream of the CDS. We apply this novel tool, showing the usage and performance of MeStudio, on a set of single-molecule real-time sequencing outputs from strains of the bacterial species Sinorhizobium meliloti
Differential Response of Wheat Rhizosphere Bacterial Community to Plant Variety and Fertilization
The taxonomic assemblage and functions of the plant bacterial community are strongly influenced by soil and host plant genotype. Crop breeding, especially after the massive use of nitrogen fertilizers which led to varieties responding better to nitrogen fertilization, has implicitly modified the ability of the plant root to recruit an effective bacterial community. Among the priorities for harnessing the plant bacterial community, plant genotype-by-microbiome interactions are stirring attention. Here, we analyzed the effect of plant variety and fertilization on the rhizosphere bacterial community. In particular, we clarified the presence in the bacterial community of a varietal effect of N and P fertilization treatment. 16S rRNA gene amplicon sequence analysis of rhizospheric soil, collected from four wheat varieties grown under four N-P fertilization regimes, and quantification of functional bacterial genes involved in the nitrogen cycle (nifH; amoA; nirK and nosZ) were performed. Results showed that variety played the most important role and that treatments did not affect either bacterial community diversity or bacterial phyla abundance. Variety-specific response of rhizosphere bacterial community was detected, both in relation to taxa (Nitrospira) and metabolic functions. In particular, the changes related to amino acid and aerobic metabolism and abundance of genes involved in the nitrogen cycle (amoA and nosZ), suggested that plant variety may lead to functional changes in the cycling of the plant-assimilable nitrogen
Effect of Site and Phenological Status on the Potato Bacterial Rhizomicrobiota
The potato is the fourth major food crop in the world. Its cultivation can encounter problems, resulting in poor growth and reduced yield. Plant microbiota has shown an ability to increase growth and resistance. However, in the development of effective microbiota manipulation strategies, it is essential to know the effect of environmental variables on microbiota composition and function. Here, we aimed to identify the differential impact of the site of cultivation and plant growth stage on potato rhizosphere microbiota. We performed a 16S rRNA gene amplicon sequencing analysis of rhizospheric soil collected from potato plants grown at four sites in central Italy during two phenological stages. Rhizomicrobiota was mainly composed of members of phyla Acidobacteriota, Actinobacteriota, Chloroflexi, and Proteobacteria and was affected by both the site of cultivation and the plant stages. However, cultivation sites overcome the effect of plant phenological stages. The PiCRUST analysis suggested a high abundance of functions related to the biosynthesis of the siderophore enterobactin. The presence of site-specific taxa and functional profiling of the microbiota could be further exploited in long-term studies to evaluate the possibility of developing biomarkers for traceability of the products and to exploit plant growth-promoting abilities in the native potato microbiota