MAPK Cascades in Plant Microbiota Structure and Functioning

Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules that coordinate diverse biological processes such as plant innate immunity and development. Recently, MAPK cascades have emerged as pivotal regulators of the plant holobiont, influencing the assembly of normal plant microbiota, essential for maintaining optimal plant growth and health. In this review, we provide an overview of current knowledge on MAPK cascades, from upstream perception of microbial stimuli to downstream host responses. Synthesizing recent findings, we explore the intricate connections between MAPK signaling and the assembly and functioning of plant microbiota. Additionally, the role of MAPK activation in orchestrating dynamic changes in root exudation to shape microbiota composition is discussed. Finally, our review concludes by emphasizing the necessity for more sophisticated techniques to accurately decipher the role of MAPK signaling in establishing the plant holobiont relationship.

The core microbiota across the green lineage

The study of plant-microbe interactions and the characterization of plant-associated microbiota has been the focus of plant researchers in the last decades due to its importance for plant health in natural conditions. Here, I explore the persistent core microbiota associated with different plant species and across different environments by performing a meta-analysis of publicly available datasets. Intra-specific analyses revealed that diverse plant genotypes growing in similar habitats interact with a common set of microbial groups but that some of these core groups are species- or environment-specific. Furthermore, interspecific meta-analysis demonstrates the conservation of seven bacterial orders across diverse photosynthetic organisms, including microalgae, suggesting a conserved capacity for interaction with these core microbes throughout evolutionary history. However, the specific functions of these core members and whether these functions are conserved across hosts remain largely unexplored. I therefore discuss the importance of understanding the roles of the core microbiota and propose future research directions, including the exploration of microbial interactions across different kingdoms. By investigating the core microbiota and its functions, it will be possible to leverage this knowledge for sustainable agricultural management and conservation goals.

Pesticide interference and additional effects on plant microbiomes

Pesticides are essential to modern human production activities, particularly those increasing global food production and quality; however, corresponding pesticide contamination is becoming more prominent. Plant microbiomes, containing different assemblages of microbial communities in the rhizosphere, endosphere, and phyllosphere, in addition to the mycorrhizal microbiome, substantially impact plant health and productivity. Therefore, the relationships among pesticides, plant microbiomes, and plant communities are important to evaluate the ecological safety of pesticides. To date, the majority of research efforts aimed at understanding the effects of pesticides on microbial communities have focused on single niche microbiomes. However, a comprehensive review of the effects of pesticides on microbial communities and co-occurrence patterns in different ecological niches is still lacking. This review fills this gap by providing an overview of the effects of pesticides on plant microbial communities across ecological niches. Specifically, we discuss the potential feedback and risks associated with these effects on plant health. Through a thorough examination of the available literature, we provide a comprehensive perspective of the impacts of pesticides on plant microbiomes, which may facilitate the development of effective strategies to mitigate these effects.

Inter-Kingdom Networks of Canola Microbiome Reveal Bradyrhizobium as Keystone Species and Underline the Importance of Bulk Soil in Microbial Studies to Enhance Canola Production

The subterranean microbiota of plants is of great importance for plant growth and health, as root-associated microbes can perform crucial ecological functions. As the microbial environment of roots is extremely diverse, identifying keystone microorganisms in plant roots, rhizosphere, and bulk soil is a necessary step towards understanding the network of influence within the microbial community associated with roots and enhancing its beneficial elements. To target these hot spots of microbial interaction, we used inter-kingdom network analysis on the canola growth phase of a long-term cropping system diversification experiment conducted at four locations in the Canadian Prairies. Our aims were to verify whether bacterial and fungal communities of canola roots, rhizosphere, and bulk soil are related and influenced by diversification of the crop rotation system; to determine whether there are common or specific core fungi and bacteria in the roots, rhizosphere, and bulk soil under canola grown in different environments and with different levels of cropping system diversification; and to identify hub taxa at the inter-kingdom level that could play an important ecological role in the microbiota of canola. Our results showed that fungi were influenced by crop diversification, which was not the case on bacteria. We found no core microbiota in canola roots but identified three core fungi in the rhizosphere, one core mycobiota in the bulk soil, and one core bacterium shared by the rhizosphere and bulk soil. We identified two bacterial and one fungal hub taxa in the inter-kingdom networks of the canola rhizosphere, and one bacterial and two fungal hub taxa in the bulk soil. Among these inter-kingdom hub taxa, Bradyrhizobium sp. and Mortierella sp. are particularly influential on the microbial community and the plant. To our knowledge, this is the first inter-kingdom network analysis utilized to identify hot spots of interaction in canola microbial communities.

Inter-organismal phytohormone networks in plant-microbe interactions

Phytohormones are produced by plants and play central roles in interactions with pathogenic and beneficial microbes as well as plant growth and development. Each phytohormone pathway consists of its biosynthesis, transport, perception, and signaling and is intertwined with each other at various levels to form phytohormone networks in plants. Different kinds of microbes also produce phytohormones that exert physiological roles within microbes and manipulate phytohormone networks in plants by using phytohormones, their mimics, and proteinaceous effectors. In turn, plant-derived phytohormones can directly or indirectly through plant signaling networks affect microbial metabolism and community assembly. Therefore, phytohormone networks in plants and microbes are connected through plant and microbial phytohormones and other molecules to form inter-organismal phytohormone networks. In this review, we summarize recent progress on molecular mechanisms of inter-organismal phytohormone networks and discuss future steps necessary for advancing our understanding of phytohormone networks.

Lipopolysaccharide O-antigen molecular and supramolecular modifications of plant root microbiota are pivotal for host recognition

Lipopolysaccharides, the major outer membrane components of Gram-negative bacteria, are crucial actors of the host-microbial dialogue. They can contribute to the establishment of either symbiosis or bacterial virulence, depending on the bacterial lifestyle. Plant microbiota shows great complexity, promotes plant health and growth and assures protection from pathogens. How plants perceive LPS from plant-associated bacteria and discriminate between beneficial and pathogenic microbes is an open and urgent question. Here, we report on the structure, conformation, membrane properties and immune recognition of LPS isolated from the Arabidopsis thaliana root microbiota member Herbaspirillum sp. Root189. The LPS consists of an O-methylated and variously acetylated D-rhamnose containing polysaccharide with a rather hydrophobic surface. Plant immunology studies in A. thaliana demonstrate that the native acetylated O-antigen shields the LPS from immune recognition whereas the O-deacylated one does not. These findings highlight the role of Herbaspirillum LPS within plant-microbial crosstalk, and how O-antigen modifications influence membrane properties and modulate LPS host recognition.

Microbial interactions within the plant holobiont

Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera

BACKGROUND

Within the root endosphere, fungi are known to be important for plant nutrition and resistance to stresses. However, description and understanding of the rules governing community assembly in the fungal fraction of the plant microbiome remains scarce.

METHODS

We used an innovative DNA- and RNA-based analysis of co-extracted nucleic acids to reveal the complexity of the fungal community colonizing the roots of an Agrostis stolonifera population. The normalized RNA/DNA ratio, designated the 'mean expression ratio', was used as a functional trait proxy. The link between this trait and phylogenetic relatedness was measured using the Blomberg's K statistic.

RESULTS

Fungal communities were highly diverse. Only ∼1.5% of the 635 OTUs detected were shared by all individuals, however these accounted for 33% of the sequence number. The endophytic fungal communities in plant roots exhibit phylogenetic clustering that can be explained by a plant host effect acting as environmental filter. The 'mean expression ratio' displayed significant but divergent phylogenetic signals between fungal phyla.

DISCUSSION

These results suggest that environmental filtering by the host plant favours the co-existence of related and similar OTUs within the Basidiomycota community assembly, whereas the Ascomycota and Glomeromycota communities seem to be impacted by competitive interactions which promote the co-existence of phylogenetically related but ecologically dissimilar OTUs.

Is the plant-associated microbiota of Thymus spp. adapted to plant essential oil?

We examined whether the microbiota of two related aromatic thyme species, Thymus vulgaris and Thymus citriodorus, differs in relation to the composition of the respective essential oil (EO). A total of 576 bacterial isolates were obtained from three districts (leaves, roots and rhizospheric soil). They were taxonomically characterized and inspected for tolerance to the EO from the two thyme species. A district-related taxonomic pattern was found. In particular, high taxonomic diversity among the isolates from leaves was detected. Moreover, data obtained revealed a differential pattern of resistance of the isolates to EOs extracted from T. vulgaris and T. citriodorus, which was interpreted in terms of differing chemical composition of the EO of their respective host plants. In conclusion, we suggest that bacterial colonization of leaves in Thymus spp. is influenced by the EO present in leaf glandular tissue as one of the selective forces shaping endophytic community composition.

Deciphering the Pathobiome: Intra- and Interkingdom Interactions Involving the Pathogen Erysiphe alphitoides

Plant-inhabiting microorganisms interact directly with each other, forming complex microbial interaction networks. These interactions can either prevent or facilitate the establishment of new microbial species, such as a pathogen infecting the plant. Here, our aim was to identify the most likely interactions between Erysiphe alphitoides, the causal agent of oak powdery mildew, and other foliar microorganisms of pedunculate oak (Quercus robur L.). We combined metabarcoding techniques and a Bayesian method of network inference to decipher these interactions. Our results indicate that infection with E. alphitoides is accompanied by significant changes in the composition of the foliar fungal and bacterial communities. They also highlight 13 fungal operational taxonomic units (OTUs) and 13 bacterial OTUs likely to interact directly with E. alphitoides. Half of these OTUs, including the fungal endophytes Mycosphaerella punctiformis and Monochaetia kansensis, could be antagonists of E. alphitoides according to the inferred microbial network. Further studies will be required to validate these potential interactions experimentally. Overall, we showed that a combination of metabarcoding and network inference, by highlighting potential antagonists of pathogen species, could potentially improve the biological control of plant diseases.