Beneficial Plant-microbe Interactions Research Articles

Three separate pathways in Rhizobium leguminosarum maintain phosphatidylcholine biosynthesis, which is required for symbiotic nitrogen fixation with clover.

Understanding the molecular mechanisms of symbiotic nitrogen fixation has important implications for sustainable agriculture. The presence of the phospholipid phosphatidylcholine (PC) in the membrane of rhizobia is critical for the establishment of productive nitrogen-fixing root nodules on legume plants. The reasons for the PC requirement are unknown. Here, we employed Rhizobium leguminosarum and clover as model system for a beneficial plant-microbe interaction. We found that R. leguminosarum produces PC by three distinct pathways. The relative contribution of these pathways to PC formation was determined in an array of single, double, and triple mutant strains. Several of the PC biosynthesis enzymes were purified and biochemically characterized. Most importantly, we demonstrated the essential role of PC formation by R. leguminosarum in nitrogen fixation and pinpointed a specific enzyme indispensable for plant-microbe interaction. Our study offers profound insights into bacterial PC biosynthesis and its pivotal role in biological nitrogen fixation.

Specific responses in soil metabolite alteration and fungal community decline to the long-term monocropping of lisianthus

Continuous cropping obstacle (CCO) is becoming a serious threat to the quality production of lisianthus (Eustoma grandiflorum). However, investigations of the causal mechanism of CCO in lisianthus are still lacking. To this end, soil biotic dynamics and metabolites alterations were illuminated using metagenomic sequencing and metabolomic profiling along a chronosequence that has cultivated lisianthus from 2 weeks to 6 years. Soil EC and nutrient contents increased significantly as the cultivation duration prolonged. Fungal community has undergone significant decline in their diversity and biomass. Nevertheless, no apparent accumulation of pathogenicity-related microbes was observed along the investigated chronosequence. The alterations of soil metabolites along the chronosequence reflect the decline of microbial activity, the accumulation of phytotoxic compounds and the loss of metabolite involved in beneficial plant-microbe interactions. As a result, lisianthus plants in the longer continuous cropping soil experienced stressful condition as evidenced by the increasing trend of stress responsive metabolites and the overall soil function deterioration as indicated by soil enzymes. Hierarchical partitioning analysis showed that the investigated factors can explain a total of 92.25 % of the variations in the soil function degradation. Of which, soil metabolite alteration was the most important factor in explaining the CCO development, covering 24.55 % of the explainable variations. Spearman's correlation results further implied that soil metabolite alteration is the main driver in the development of CCO in lisianthus, especially by mediating the plant-microbes interactions. Our findings revealed a general pattern of soil biotic and abiotic response to the continuous monocropping of lisianthus and suggest that the overcome of the CCO in lisianthus requires further studies focusing on the crucial metabolites and their interactions with microbes.

The potential of Pseudomonas fluorescens SBW25 to produce viscosin enhances wheat root colonization and shapes root-associated microbial communities in a plant genotype-dependent manner in soil systems.

Understanding parameters governing microbiome assembly on plant roots is critical for successfully exploiting beneficial plant-microbe interactions for improved plant growth under low-input conditions. While it is well-known from in vitro studies that specialized metabolites are important for plant-microbe interactions, e.g., root colonization, studies on the ecological role under natural soil conditions are limited. This might explain the often-low translational power from laboratory testing to field performance of microbial inoculants. Here, we showed that viscosin synthesis potential results in a differential impact on the microbiome assembly dependent on wheat cultivar, unlinked to colonization potential. Overall, our study provides novel insights into factors governing microbial assembly on plant roots, and how this has a derived but differential effect on the bacterial and protist communities.

Interactions between an arbuscular mycorrhizal inoculum and the root-associated microbiome in shaping the response of Capsicum annuum “Locale di Senise” to different irrigation levels

Abstract Background and aims The use of root-associated microorganisms emerge as a sustainable tool to enhance crop tolerance and productivity under climate change, particularly in drought-affected areas. Here, the impact of an inoculum based on arbuscular mycorrhizal fungi (AMF) was evaluated on pepper (Capsicum annuum L.) cultivation at varying water irrigation treatments (well-watered, reduced irrigation and rain-fed) under open-field conditions. Methods Agronomic and ecophysiological parameters, as well as biochemical analyses on stress markers and phytohormones in leaves and on fruit quality traits, were evaluated, along with the shifts in soil- and root-associated microbial communities. Results Rain-fed water treatment caused reduced fruit sizes, while no differences were detected among well-watered and reduced irrigation. Reduced irrigation did not cause a reduction in stomatal conductance. The highest AM fungal colonization rates were observed under reduced irrigation, and the enhanced flavonoid content and reduced oxidative stress markers in AMF-inoculated plants suggested a synergistic effect of AM fungal inoculation in boosting plant tolerance against stress. A shift in microbial community composition in the different irrigation treatments, associated with different enzymatic activity, highlighted the potential role of microbial dynamics in plant stress response under water-limited conditions. Conclusion The study suggests that a reduced irrigation comes along with beneficial impacts on pepper root associated microbes, while not impairing crop performance and yields, indicating a potential of saving water. All together, our results imply that optimization of irrigation and beneficial plant–microbe interactions, such as AM fungal symbiosis, can improve pepper physiological and productivity features under climate change.

Beneficial Plant–Microbe Interactions and Stress Tolerance in Maize

Beneficial microbes are crucial for improving crop adaptation and growth under various stresses. They enhance nutrient uptake, improve plant immune responses, and help plants tolerate stresses like drought, salinity, and heat. The yield potential of any crop is significantly influenced by its associated microbiomes and their potential to improve growth under different stressful environments. Therefore, it is crucial and exciting to understand the mechanisms of plant–microbe interactions. Maize (Zea mays L.) is one of the primary staple foods worldwide, in addition to wheat and rice. Maize is also an industrial crop globally, contributing 83% of its production for use in feed, starch, and biofuel industries. Maize requires significant nitrogen fertilization to achieve optimal growth and yield. Maize plants are highly susceptible to heat, salinity, and drought stresses and require innovative methods to mitigate the harmful effects of environmental stresses and reduce the use of chemical fertilizers. This review summarizes our current understanding of the beneficial interactions between maize plants and specific microbes. These beneficial microbes improve plant resilience to stress and increase productivity. For example, they regulate electron transport, downregulate catalase, and upregulate antioxidants. We also review the roles of plant growth-promoting rhizobacteria (PGPR) in enhancing stress tolerance in maize. Additionally, we explore the application of these microbes in maize production and identify major knowledge gaps that need to be addressed to utilize the potential of beneficial microbes fully.

Plant-microbe Interactions and their Potential Application in Improving Disease Resistance in Vegetable Crops

Microorganisms have a substantial impact on the environment and have been observed to either immunize or infect organisms from all kingdoms. Plants and microorganisms have undergone co-evolution and engage in interactions within their natural environment. Plant microbiota, often known as plant-associated microorganisms, are essential components of plant existence. Similar to other living systems, the plant body interacts with a range of living and non-living factors as it develops in an intricate environment. The plant microbiome can sustain disease suppression by providing essential tasks to their host, such as stress tolerance, vitality, and development. Plants and microorganisms have evolved molecular systems to mutually interact and derive advantages from their interaction. This symbiotic relationship is advantageous for both the microorganisms and the plants. Various pathways have been explored and are currently being utilized to achieve agricultural, environmental, and health benefits, based on this molecular interaction. Plant-associated microorganisms serve a vital role in the growth and development of plants. Microorganisms stimulate plant growth by directly increasing nutrient uptake and stimulating hormone production. The potential benefits of these mutually beneficial interactions between plants and microbes could be connected to develop microbial inoculants for application in agricultural biotechnology. In general, the utilization of microorganisms and the establishment of beneficial plant-microbe interactions offer promising and environmentally favourable approaches for sustainable and organic agriculture worldwide.

The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype

Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.

Integration of transcriptome, metabolome and high-throughput amplicon sequencing to compare the performance of wild and cultivated psammosilene tunicoides to reveal the beneficial plant-microbe interactions for domestication

Psammosilene tunicoides is an herbal medicine with analgesic, anti-inflammatory and immunoregulatory properties, and it is listed as an International Union for the Conservation of Nature (IUCN) endangered species. The plants have been domesticated in some areas of Yunnan Province, China, for commercial and medical use. However, the performance of domesticated plants and the negative effects of domestication remain unclear. Multi-omics analyses were performed to compare the performance between wild P. tunicoides (WP) and cultivated P. tunicoides (CP). Transcriptomic and metabolomic data were generated from the roots, while microbiome data were obtained from the rhizospheres. The transcriptomic data showed that there were different patterns of gene expression between the WP and CP. The genes HMGS, HMGR, MPD and SQS, which are involved in the biosynthesis of triterpenoid saponins, were significantly more highly expressed in the WP than in the CP. The metabolomic analysis also found that significantly more triterpenoids were produced in the WP compared with the CP. The microbiome data showed that most of the plant growth-promoting rhizobacteria (PGPR), such as Burkholderia-Caballeronia-Paraburkholderia and others, were enriched in the WP type, while some pathogenic microorganisms were enriched in the CP type. A weighted gene co-expression network analysis revealed that the accumulation of triterpenoid saponins positively correlated with the modules of genes that primarily participated in the plant hormone signal transduction pathway and the PGPR in modules. This indicated that the triterpenoid saponins may function as signaling molecules to recruit the functional microbes. The regulatory “plant-microbe” network of microorganisms and the genes associated with triterpenes was detected in P. tunicoides. This suggests that the management of these interactions should be considered as a sustainable tool to enhance the performance of domesticated plants.

From salty to thriving: plant growth promoting bacteria as nature's allies in overcoming salinity stress in plants.

Soil salinity is one of the main problems that affects global crop yield. Researchers have attempted to alleviate the effects of salt stress on plant growth using a variety of approaches, including genetic modification of salt-tolerant plants, screening the higher salt-tolerant genotypes, and the inoculation of beneficial plant microbiome, such as plant growth-promoting bacteria (PGPB). PGPB mainly exists in the rhizosphere soil, plant tissues and on the surfaces of leaves or stems, and can promote plant growth and increase plant tolerance to abiotic stress. Many halophytes recruit salt-resistant microorganisms, and therefore endophytic bacteria isolated from halophytes can help enhance plant stress responses. Beneficial plant-microbe interactions are widespread in nature, and microbial communities provide an opportunity to understand these beneficial interactions. In this study, we provide a brief overview of the current state of plant microbiomes and give particular emphasis on its influence factors and discuss various mechanisms used by PGPB in alleviating salt stress for plants. Then, we also describe the relationship between bacterial Type VI secretion system and plant growth promotion.

Microbe-Responsive Proteomes During Plant–Microbe Interactions Between Rice Genotypes and the Multifunctional Methylobacterium oryzae CBMB20

BackgroundRice is colonized by plant growth promoting bacteria such as Methylobacterium leading to mutually beneficial plant–microbe interactions. As modulators of the rice developmental process, Methylobacterium influences seed germination, growth, health, and development. However, little is known about the complex molecular responsive mechanisms modulating microbe-driven rice development. The application of proteomics to rice-microbe interactions helps us elucidate dynamic proteomic responses mediating this association.ResultsIn this study, a total of 3908 proteins were detected across all treatments of which the non-inoculated IR29 and FL478 share up to 88% similar proteins. However, intrinsic differences appear in IR29 and FL478 as evident in the differentially abundant proteins (DAPs) and their associated gene ontology terms (GO). Successful colonization of M. oryzae CBMB20 in rice resulted to dynamic shifts in proteomes of both IR29 and FL478. The GO terms of DAPs for biological process in IR29 shifts in abundance from response to stimulus, cellular amino acid metabolic process, regulation of biological process and translation to cofactor metabolic process (6.31%), translation (5.41%) and photosynthesis (5.41%). FL478 showed a different shift from translation-related to response to stimulus (9%) and organic acid metabolic acid (8%). Both rice genotypes also showed a diversification of GO terms due to the inoculation of M. oryzae CBMB20. Specific proteins such as peptidyl-prolyl cis–trans isomerase (A2WJU9), thiamine thiazole synthase (A2YM28), and alanine—tRNA ligase (B8B4H5) upregulated in IR29 and FL478 indicate key mechanisms of M. oryzae CBMB20 mediated plant growth promotion in rice.ConclusionsInteraction of Methylobacterium oryzae CBMB20 to rice results in a dynamic, similar, and plant genotype-specific proteomic changes supporting associated growth and development. The multifaceted CBMB20 expands the gene ontology terms and increases the abundance of proteins associated with photosynthesis, diverse metabolic processes, protein synthesis and cell differentiation and fate potentially attributed to the growth and development of the host plant. The specific proteins and their functional relevance help us understand how CBMB20 mediate growth and development in their host under normal conditions and potentially link subsequent responses when the host plants are exposed to biotic and abiotic stresses.

Epigenetic control is involved in molecular dialogue in plant-microbe symbiosis.

This article is a Commentary on Vigneaud et al. (2023), 238: 2561–2577.

Fragmentation disrupts microbial effects on native plant community productivity

Abstract Anthropogenic habitat fragmentation—the breaking up of natural landscapes—is a pervasive threat to biodiversity and ecosystem function world‐wide. Fragmentation results in a mosaic of remnant native habitat patches embedded in human‐modified habitat known as the ‘matrix’. By introducing novel environmental conditions in matrix habitats and reducing connectivity of native habitats, fragmentation can dramatically change how organisms experience their environment. The effects of fragmentation can be especially important in urban landscapes, which are expanding across the globe. Despite this surging threat and the importance of microbiomes for ecosystem services, we know very little about how fragmentation affects microbiomes and even less about their consequences for plant–microbe interactions in urban landscapes. By combining field surveys, microbiome sequencing and experimental mesocosms, we (1) investigated how microbial community diversity, composition and functional profiles differed between 15 native pine rockland fragments and the adjacent urban matrix habitat, (2) identified habitat attributes that explained significant variation in microbial diversity of native core habitat compared to urban matrix and (3) tested how changes in urbanized and low connectivity microbiomes affected plant community productivity. We found urban and native microbiomes differed substantively in diversity, composition and functional profiles, including symbiotic fungi decreasing 81% and pathogens increasing 327% in the urban matrix compared to native habitat. Furthermore, fungal diversity rapidly declined as native habitats became increasingly isolated, with ~50% of variation across the landscape explained by habitat connectivity alone. Interestingly, microbiomes from native habitats increased plant productivity by ~300% while urban matrix microbiomes had no effect, suggesting that urbanization may decouple beneficial plant–microbe interactions. In addition, microbial diversity within native habitats explained significant variation in plant community productivity, with higher productivity linked to more diverse microbiomes from more connected, larger fragments. Synthesis. Taken together, our study not only documents significant changes in microbial diversity, composition and functions in the urban matrix, but also supports that two aspects of habitat fragmentation—the introduction of a novel urban matrix and reduced habitat connectivity—disrupt microbial effects on plant community productivity, highlighting preservation of native microbiomes as critical for productivity in remnant fragments.

Reviewing and renewing the use of beneficial root and soil bacteria for plant growth and sustainability in nutrient-poor, arid soils.

A rapidly increasing human population coupled with climate change and several decades of over-reliance on synthetic fertilizers has led to two pressing global challenges: food insecurity and land degradation. Therefore, it is crucial that practices enabling both soil and plant health as well as sustainability be even more actively pursued. Sustainability and soil fertility encompass practices such as improving plant productivity in poor and arid soils, maintaining soil health, and minimizing harmful impacts on ecosystems brought about by poor soil management, including run-off of agricultural chemicals and other contaminants into waterways. Plant growth promoting bacteria (PGPB) can improve food production in numerous ways: by facilitating resource acquisition of macro- and micronutrients (especially N and P), modulating phytohormone levels, antagonizing pathogenic agents and maintaining soil fertility. The PGPB comprise different functional and taxonomic groups of bacteria belonging to multiple phyla, including Proteobacteria, Firmicutes, Bacteroidetes, andActinobacteria,among others. This review summarizes many of the mechanisms and methods these beneficial soil bacteria use to promote plant health and asks whether they can be further developed into effective, potentially commercially available plant stimulants that substantially reduce or replace various harmful practices involved in food production and ecosystem stability. Our goal is to describe the various mechanisms involved in beneficial plant-microbe interactions and how they can help us attain sustainability.

Plant growth and microbial responses from urban agriculture soils amended with excavated local sediments and municipal composts

Abstract With increasing urbanization and critical issues of food insecurity emerging globally, urban agriculture is expanding as an agroecosystem with a distinct soil type. Growing food in cities is challenged by legacy contaminants in soils, which necessitates the use of imported, safe soils and composts. To promote the long-term sustainability of urban agriculture, we examined the agronomic potential of constructing safe, locally sourced soils to support food production. We collected composts from four municipal composting facilities in New York City: Big Reuse, Long Island City, Queens (BRL), New York Department of Sanitation, Fresh Kills, Staten Island (DNY), Lower Eastside Ecology Center (LES) and Queens Botanic Garden (QBG). We then created two types of constructed soils using each compost: 100% pure compost and a 50:50 blend of compost and clean excavated sediments from the New York City Clean Soil Bank. We then assessed the growth of tomato, pepper and kale in the constructed soils within a plant growth chamber facility. We found Clean Soil Bank sediments enhanced tomato aboveground biomass production by 98%, kale aboveground biomass production by 50% and pepper plant height by 52% when mixed with compost from BRL. At the same time, Clean Soil Bank Sediments decreased tomato plant height by 16% and aboveground biomass production by 29% in LES compost and tomato plant height by 18% in QBG compost, likely due to compost properties. The addition of Clean Soil Bank sediments showed no decline in the symbiosis of arbuscular mycorrhizal fungi across all composts, which is an important beneficial plant–microbe interaction in agroecosystems. A positive ecosystem service was found when Clean Soil Bank sediments were added to municipal composts, with up to a 74% decrease in greenhouse gas emissions of soil CO2 in BRL compost. The results indicate that urban agricultural soils can be constructed using clean, locally sourced materials, such as composted organic waste and excavated sediments from city development sites to support sustainable urban agriculture while enhancing ecosystem services.

Wheat genome architecture influences interactions with phytobeneficial microbial functional groups in the rhizosphere.

Wheat has undergone a complex evolutionary history, which led to allopolyploidization and the hexaploid bread wheat Triticum aestivum. However, the significance of wheat genomic architecture for beneficial plant-microbe interactions is poorly understood, especially from a functional standpoint. In this study, we tested the hypothesis that wheat genomic architecture was an overriding factor determining root recruitment of microorganisms with particular plant-beneficial traits. We chose five wheat species representing genomic profiles AA (Triticum urartu), BB {SS} (Aegilops speltoides), DD (Aegilops tauschii), AABB (Triticum dicoccon) and AABBDD (Triticum aestivum) and assessed by qPCR their ability to interact with free-nitrogen fixers, 1-aminocyclopropane-1-carboxylate deaminase producers, 2,4-diacetylphloroglucinol producers and auxin producers via the phenylpyruvate decarboxylase pathway, in combination with Illumina MiSeq metabarcoding analysis of N fixers (and of the total bacterial community). We found that the abundance of the microbial functional groups could fluctuate according to wheat genomic profile, as did the total bacterial abundance. N fixer diversity and total bacterial diversity were also influenced significantly by wheat genomic profile. Often, rather similar results were obtained for genomes DD (Ae. tauschii) and AABBDD (T. aestivum), pointing for the first time that the D genome could be particularly important for wheat-bacteria interactions. This article is protected by copyright. All rights reserved.

Ethylene: A Master Regulator of Plant-Microbe Interactions under Abiotic Stresses.

The plant phytohormone ethylene regulates numerous physiological processes and contributes to plant-microbe interactions. Plants induce ethylene production to ward off pathogens after recognition of conserved microbe-associated molecular patterns (MAMPs). However, plant immune responses against pathogens are essentially not different from those triggered by neutral and beneficial microbes. Recent studies indicate that ethylene is an important factor for beneficial plant-microbial association under abiotic stress such as salt and heat stress. The association of beneficial microbes with plants under abiotic stresses modulates ethylene levels which control the expression of ethylene-responsive genes (ERF), and ERFs further regulate the plant transcriptome, epi-transcriptome, Na+/K+ homeostasis and antioxidant defense mechanisms against reactive oxygen species (ROS). Understanding ethylene-dependent plant-microbe interactions is crucial for the development of new strategies aimed at enhancing plant tolerance to harsh environmental conditions. In this review, we underline the importance of ethylene in beneficial plant-microbe interaction under abiotic stresses.

Understanding plant-microbe interaction of rice and soybean with two contrasting diazotrophic bacteria through comparative transcriptome analysis.

Understanding the beneficial plant-microbe interactions is becoming extremely critical for deploying microbes imparting plant fitness and achieving sustainability in agriculture. Diazotrophic bacteria have the unique ability to survive without external sources of nitrogen and simultaneously promote host plant growth, but the mechanisms of endophytic interaction in cereals and legumes have not been studied extensively. We have studied the early interaction of two diazotrophic bacteria, Gluconacetobacter diazotrophicus (GAB) and Bradyrhizobium japonicum (BRH), in 15-day-old seedlings of rice and soybean up to 120 h after inoculation (hai) under low-nitrogen medium. Root colonization of GAB in rice was higher than that of BRH, and BRH colonization was higher in soybean roots as observed from the scanning electron microscopy at 120 hai. Peroxidase enzyme was significantly higher at 24 hai but thereafter was reduced sharply in soybean and gradually in rice. The roots of rice and soybean inoculated with GAB and BRH harvested from five time points were pooled, and transcriptome analysis was executed along with control. Two pathways, "Plant pathogen interaction" and "MAPK signaling," were specific to Rice-Gluconacetobacter (RG), whereas the pathways related to nitrogen metabolism and plant hormone signaling were specific to Rice-Bradyrhizobium (RB) in rice. Comparative transcriptome analysis of the root tissues revealed that several plant-diazotroph-specific differentially expressed genes (DEGs) and metabolic pathways of plant-diazotroph-specific transcripts, viz., chitinase, brassinosteroid, auxin, Myeloblastosis (MYB), nodulin, and nitrate transporter (NRT), were common in all plant-diazotroph combinations; three transcripts, viz., nitrate transport accessory protein (NAR), thaumatin, and thionin, were exclusive in rice and another three transcripts, viz., NAC (NAM: no apical meristem, ATAF: Arabidopsis thaliana activating factor, and CUC: cup-shaped cotyledon), ABA (abscisic acid), and ammonium transporter, were exclusive in soybean. Differential expression of these transcripts and reduction in pathogenesis-related (PR) protein expression show the early interaction. Based on the interaction, it can be inferred that the compatibility of rice and soybean is more with GAB and BRH, respectively. We propose that rice is unable to identify the diazotroph as a beneficial microorganism or a pathogen from an early response. So, it expressed the hypersensitivity-related transcripts along with PR proteins. The molecular mechanism of diazotrophic associations of GAB and BRH with rice vis-à-vis soybean will shed light on the basic understanding of host responses to beneficial microorganisms.

Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT.

Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla Chlorophyta and Streptophyta that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na+/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.

Breeding toward improved ecological plant-microbiome interactions.

Domestication processes, amplified by breeding programs, have allowed the selection of more productive genotypes and more suitable crop lines capable of coping with the changing climate. Notwithstanding these advancements, the impact of plant breeding on the ecology of plant-microbiome interactions has not been adequately considered yet. This includes the possible exploitation of beneficial plant-microbe interactions to develop crops with improved performance and better adaptability to any environmental scenario. Here we discuss the exploitation of customized synthetic microbial communities in agricultural systems to develop more sustainable breeding strategies based on the implementation of multiple interactions between plants and their beneficial associated microorganisms.

Interaction networks reveal highly antagonistic endophytic bacteria in native maize seeds from traditional milpa agroecosystems.

Milpas are traditional Mesoamerican agroecosystems maintained with ancestral practices. Maize landraces are grown in polyculture, creating highly productive and diverse ecosystems. Recent studies suggest that milpas maintain beneficial plant-microbe interactions that are probably absent in modern agroecosystems; however, direct comparisons of the microbiome of plants between traditional and modern agroecosystems are still needed. Here, we studied seed-endophytic bacterial communities from native maize landraces from milpas and hybrid varieties. First, we quantified the abundance of culturable endophytic microbes; next, we assessed pairwise antagonistic interaction networks between bacterial isolates; finally, we compared bacterial community structure by 16S rRNA amplicon sequencing. We found that seeds from native maize landraces harbour a higher endophytic microbial load, including more bacterial strains with antagonistic activity against soil-borne bacteria, and overall harbour more diverse bacterial communities than the hybrid varieties. Noteworthy, most of the seed-endophytic strains with antagonistic activity corresponded to Burkholderia spp. that were only found in native maize seeds, through both culture-dependent and independent strategies. Altogether, our results support that crop modernization alters the functions and structure of plant-associated microbes; we propose native maize from milpas could serve as a model for understanding plant-microbe interactions and the effect of modernization.