Introduction
Soil, rhizosphere, and the rhizoplane, including also internal root
tissue, represent complex ecosystems where various organisms interact
and influence positively, neutrally, or negatively each other’s growth,
development, and ecological functions. These interactions are essential
for ecosystem functioning and have profound implications for plant
health and productivity. Microbes in the roots and rhizosphere can
directly and indirectly affect plant growth and development by providing
several services to both plants and ecosystems, such as facilitating the
nutrient acquisition, promoting hormone synthesis, suppressing
pathogens, inducing systemic resistance, contributing to the cycling of
organic matter, nitrogen fixation, and degradation of pollutants, thus
influencing overall soil fertility and ecosystem sustainability. Such
microbes can have various degrees of biotic interaction with plants from
free-living commensal to plant symbionts, and include different groups,
from bacteria to fungi. Within the plant symbionts are rhizobia, a group
of nitrogen-fixing bacteria that can establish mutualistic symbiotic
associations with leguminous plants. These bacteria reside within
specialized structures called nodules on plant roots and convert
atmospheric nitrogen into ammonia, which can be utilized by the host
plant. Sinorhizobium meliloti , a model rhizobial species,
exhibits a broad host range and forms symbiotic associations with
leguminous (Fabaceae ) genera such as Medicago ,Melilotus , and Trigonella . S. meliloti possesses
peculiar genetic and physiological traits, allowing it to efficiently
colonize plant roots, establish nodules, and fix nitrogen . Several
studies have shown the large genetic and symbiotic diversity of S.
meliloti strains, highlighting the importance of rhizobial genotype x
plant genotype partnership for successful symbiotic plant growth
promotion and nitrogen fixation . Tough the attention has mainly been
focused on discovering the genomic determinants of such symbiotic
diversity , recently the focus has shifted to transcriptional variation,
as closer proxy to phenotypic differences . Here, for S.
meliloti , we detected the transcriptomic signatures of wide genotype x
genotype interaction in response to the treatment with the symbiotic
inducer luteolin and with plant root exudates from three alfalfa
(Medicago sativa L.) varieties. In addition, to decipher the
extent of epistatic interaction among the main set of symbiotic genes
and the rest of the genome, a hybrid S. meliloti strain was
constructed by mobilizing the megaplasmid harbouring most of symbiotic
genes .This hybrid strain allowed to discover a large number of unique
transcriptional signatures related to intragenomic regulatory
interactions which can explain part of strain and plant
genotype-specific features of symbiosis.
While many details are known on rhizobia-plant interaction, few studies
have investigated the interaction between rhizobia and the other
relevant components of the root microbiome, i.e. fungi . Fungi play a
crucial role in plant-microbe interactions and soil ecosystem
functioning. They form intricate associations with plant as free-living
organisms in the rhizosphere or, forming interactions with plant roots
as endophytes. Rhizospheric fungi contribute to nutrient cycling by
decomposing organic matter, releasing nutrients, and enhancing nutrient
uptake by plants . They can also act as biocontrol agents, suppressing
plant pathogens and promoting plant growth. Furthermore, rhizospheric
fungi influence soil structure and stability, affecting water retention
and root penetration. Their interactions with plants and soil make them
key players in ecological processes and agricultural sustainability.
Concerning nitrogen-fixing symbiosis, arbuscular mycorrhizal fungi have
shown multiple mutualistic effects with S. meliloti and the host
plant M. truncatula and extensive effects of microbial mutualists
on gene expression. Among the most studied fungi related to plant
growth, used also as bioinoculant, Trichoderma spp. hold a
special attention. They are a group of filamentous fungi, known for
their multifunctional roles in the soil ecosystem. They are widely
recognized as biocontrol agents against plant pathogens due to their
ability to produce a diverse array of antimicrobial compounds and
compete for resources. Trichoderma spp. can also promote plant
growth by enhancing nutrient availability, stimulating root development,
and inducing systemic resistance. Additionally, they contribute to the
decomposition of organic matter, thereby influencing nutrient cycling
and soil structure. The biocontrol and growth-promoting properties ofTrichoderma spp. make them valuable components of sustainable
agriculture and integrated pest management strategies . Unlike
arbuscular mycorrhizal fungi, as R. irregularis , free-living
filamentous fungi as Trichoderma can be easily grown invitro and they are also well-established models with available
genome sequences, as well as methods for the study of their secretome .
The deciphering of the relationships and molecular signals taking place
in the rhizosphere among rhizobia and Trichoderma will then offer
in perspective numerous potentialities in providing testable
experimental models for understanding and exploiting plant-microbiome
interaction and dissecting mutualistic and antagonistic effects down to
the molecular level.
However, it is becoming more and more clear that mutualistic effects
have a strong intraspecific genotype component, i.e. different
combinations of partner’s genotypes may lead to significant changes in
the outcome of the association (e.g. quality of the symbiosis in
rhizobium-legume association) . No data have been reported so far on
genotype-by-genotype interactions between rhizobia and rhizospheric
fungi and how this can affect the quality of the symbiosis withM. sativa as host plant .
Here, we report the results of a study aimed at determining the effect
different Trichoderma species may have on the symbiotic
nitrogen-fixer S. meliloti and the presence of
genotype-by-genotype interaction between strains of S. melilotiand species of Trichoderma . By combining microbiological
observation, physiological, metabolic, and transcriptomic analyses, we
show the existence of rhizobial strain-specific response toTrichoderma species, with the presence of either synergistic,
neutral, or antagonistic interactions depending on the
rhizobium-Trichoderma combination. These interactions determine
changes in gene expression of a large fraction of the rhizobial genomes
(up to 23.45 % of total genes) and are also reflected in host plant
growth-promoting phenotypes. These results provide novel insights into
the well-known mutualism between rhizobia and host legumes, emphasizing
the role of the molecular dialogue taking place in the plant
rhizosphere. Moreover, evidence presented here give a proof-of-concept
that careful analysis of microbial interactions can be key for
successful development of community-mimicking bioinoculants (also
referred to as synthetic communities) in agriculture.