Plant-microbiome interactions under a changing world: responses, consequences and perspectives

Warming and rainfall reduction alter soil microbial diversity and co-occurrence networks and enhance pathogenic fungi in dryland soils

In this 9-year manipulative field experiment, we examined the impacts of experimental warming (2 °C, W), rainfall reduction (30 % decrease in annual rainfall, RR), and their combination (W + RR) on soil microbial communities and native vegetation in a semi-arid shrubland in south-eastern Spain. Warming had strong negative effects on plant performance across five coexisting native shrub species, consistently reducing their aboveground biomass growth and long-term survival. The impacts of rainfall reduction on plant growth and survival were species-specific and more variable. Warming strongly altered the soil microbial community alpha-diversity and changed the co-occurrence network structure. The relative abundance of symbiotic arbuscular mycorrhizal fungi (AMF) increased under W and W + RR, which could help buffer the direct negative impacts of climate change on their host plants nutrition and enhance their resistance to heat and drought stress. Indicator microbial taxa analyses evidenced that the marked sequence abundance of many plant pathogenic fungi, such as Phaeoacremonium, Cyberlindnera, Acremonium, Occultifur, Neodevriesia and Stagonosporopsis, increased significantly in the W and W + RR treatments. Moreover, the relative abundance of fungal animal pathogens and mycoparasites in soil also increased significantly under climate warming. Our findings indicate that warmer and drier conditions sustained over several years can alter the soil microbial community structure, composition, and network topology. The projected warmer and drier climate favours pathogenic fungi, which could offset the benefits of increased AMF abundance under warming and further aggravate the severe detrimental impacts of increased abiotic stress on native vegetation performance and ecosystem services in drylands.

Prediction of the global occurrence of maize diseases and estimation of yield loss under climate change

BACKGROUND

Climate change significantly impacts global maize production via yield reduction, posing a threat to global food security. Disease-related crop damage reduces quality and yield and results in economic losses. However, the occurrence of diseases caused by climate change, and thus crop yield loss, has not been given much attention.

RESULTS

This study aims to investigate the potential impact of six major diseases on maize yield loss over the next 20 to 80 years under climate change. To this end, the Maximum Entropy model was implemented, based on Coupled Model Intercomparison Project 6 data. The results indicated that temperature and precipitation are identified as primary limiting factors for disease onset. Southern corn rust was projected to be the most severe disease in the future; with a few of the combined occurrence of all the selected diseases covered in this study were predicted to progressively worsen over time. Yield losses caused by diseases varied per continent, with North America facing the highest loss, followed by Asia, South America, Europe, Africa, and Oceania.

CONCLUSION

This study provides a basis for regional projections and global control of maize diseases under future climate conditions. © 2024 Society of Chemical Industry.

Non-pathogenic microbiome associated to aquatic plants and anthropogenic impacts on this interaction

The microbiota associated with aquatic plants plays a crucial role in promoting plant growth and development. The structure of the plant microbiome is shaped by intricate interactions among hosts, microbes, and environmental factors. Consequently, anthropogenic pressures that disrupt these interactions can indirectly impact the ecosystem services provided by aquatic plants, such as CO2 fixation, provision of food resources, shelter to animals, nutrient cycling, and water purification. Presently, studies on plant-microbiota interactions primarily focus on terrestrial hosts and overlook aquatic environments with their unique microbiomes. Therefore, there is a pressing need for a comprehensive understanding of plant microbiomes in aquatic ecosystems. This review delves into the overall composition of the microbiota associated with aquatic plant, with a particular emphasis on bacterial communities, which have been more extensively studied. Subsequently, the functions provided by the microbiota to their aquatic plants hosts are explored, including the acquisition and mobilization of nutrients, production of auxin and related compounds, enhancement of photosynthesis, and protection against biotic and abiotic stresses. Additionally, the influence of anthropogenic stressors, such as climate change and aquatic contamination, on the interaction between microbiota and aquatic plants is discussed. Finally, knowledge gaps are highlighted and future directions in this field are suggested.

An integrated fast-slow plant and nematode economics spectrum predicts soil organic carbon dynamics during natural restoration

Aboveground and belowground attributes of terrestrial ecosystems interact to shape carbon (C) cycling. However, plants and soil organisms are usually studied separately, leading to a knowledge gap regarding their coordinated contributions to ecosystem C cycling. We explored whether integrated consideration of plant and nematode traits better explained soil organic C (SOC) dynamics than plant or nematode traits considered separately. Our study system was a space-for-time natural restoration chronosequence following agricultural abandonment in a subtropical region, with pioneer, early, mid and climax stages. We identified an integrated fast-slow trait spectrum encompassing plants and nematodes, demonstrating coordinated shifts from fast strategies in the pioneer stage to slow strategies in the climax stage, corresponding to enhanced SOC dynamics. Joint consideration of plant and nematode traits explained more variation in SOC than by either group alone. Structural equation modeling revealed that the integrated fast-slow trait spectrum influenced SOC through its regulation of microbial traits, including microbial C use efficiency and microbial biomass. Our findings confirm the pivotal role of plant-nematode trait coordination in modulating ecosystem C cycling and highlight the value of incorporating belowground traits into biogeochemical cycling under global change scenarios.

Pattern and Process in a Rapidly Changing World: Ideas and Approaches

AbstractScience is as dynamic as the world around us. Our ideas continually change, as do the approaches we use to study science. Few things remain invariant in this changing landscape, but a fascination with pattern and process is one that has endured throughout the history of science. Paying homage to this long-held tradition, the 2023 Vice Presidential Symposium of the American Society of Naturalists focused on the role of pattern and process in ecology and evolution. It brought together a group of early-career researchers working on topics ranging from genetic diversity in microbes to changing patterns of species interactions in the geological record. Their work spanned the taxonomic spectrum from microbes to mammals, the temporal dimension from the Cenozoic to the present, and approaches ranging from manipulative experiments to comparative approaches. In this introductory article, I discuss how these diverse topics are linked by the common thread of elucidating processes underlying patterns and how they collectively generate novel insights into diversity maintenance at different levels of organization.

Interactive Effects of Climate Change and Pathogens on Plant Performance: A Global Meta-Analysis

Plant health is increasingly threatened by abiotic and biotic stressors linked to anthropogenic global change. These stressors are frequently studied in isolation. However, they might have non-additive (antagonistic or synergistic) interactive effects that affect plant communities in unexpected ways. We conducted a global meta-analysis to summarize existing evidence on the joint effects of climate change (drought and warming) and biotic attack (pathogens) on plant performance. We also investigated the effect of drought and warming on pathogen performance, as this information is crucial for a mechanistic interpretation of potential indirect effects of climate change on plant performance mediated by pathogens. The final databases included 1230 pairwise cases extracted from 117 recently published scientific articles (from 2006) on a global scale. We found that the combined negative effects of drought and pathogens on plant growth were lower than expected based on their main effects, supporting the existence of antagonistic interactions. Thus, the larger the magnitude of the drought, the lower the pathogen capacity to limit plant growth. On the other hand, the combination of warming and pathogens caused larger plant damage than expected, supporting the existence of synergistic interactions. Our results on the effects of drought and warming on pathogens revealed a limitation of their growth rates and abundance in vitro but an improvement under natural conditions, where multiple factors operate across the microbiome. Further research on the impact of climate change on traits explicitly defining the infective ability of pathogens would enhance the assessment of its indirect effects on plants. The evaluated plant and pathogen responses were conditioned by the intensity of drought or warming and by moderator categorical variables defining the pathosystems. Overall, our findings reveal the need to incorporate the joint effect of climatic and biotic components of global change into predictive models of plant performance to identify non-additive interactions.

Sphingomonas sp. Hbc-6 alters Arabidopsis metabolites to improve plant growth and drought resistance by manipulating the microbiome

Drought significantly affects crop productivity and poses a considerable threat to agricultural ecosystems. Plant growth-promoting bacteria (PGPB) and plant microbiome play important roles in improving drought resistance and plant performance. However, the response of the rhizosphere microbiota to PGPB during the development of plants and the interaction between inoculum, microbiota, and plants under drought stress remain to be explored. In the present study, we used culturomic, microbiomic, and metabonomic analyses to uncover the mechanisms by which Sphingomonas sp. Hbc-6, a PGPB, promotes Arabidopsis growth and enhances drought resistance. We found that the rhizosphere microbiome assembly was interactively influenced by developmental stage, Hbc-6, and drought; the bacterial composition exhibited three patterns of shifts with developmental stage: resilience, increase, and decrease. Drought diminished microbial diversity and richness, whereas Hbc-6 increased microbial diversity and helped plants recruit specific beneficial bacterial taxa at each developmental stage, particularly during the bolting stage. Some microorganisms enriched by Hbc-6 had the potential to promote carbon and nitrogen cycling processes, and 86.79 % of the isolated strains exhibited PGP characteristics (for example Pseudomonas sp. TA9). They jointly regulated plant physiological metabolism (i.e., upregulated drought resistant-facilitating substances and reduced harmful substances), thereby stimulating the growth of Arabidopsis and increasing plant biomass under drought stress conditions. Collectively, these results indicate that Hbc-6 mediates plant growth and drought resistance by affecting the microbiome. The study thus provides novel insights and strain resources for drought-resistant, high-yielding crop cultivation and breeding.

Elaborating the multifarious role of PGPB for sustainable food security under changing climate conditions

Changing climate creates a challenge to agricultural sustainability and food security by changing patterns of parameters like increased UV radiation, rising temperature, altered precipitation patterns, and higher occurrence of extreme weather incidents. Plants are vulnerable to different abiotic stresses such as waterlogging, salinity, heat, cold, and drought in their natural environments. The prevailing agricultural management practices play a major role in the alteration of the Earth's climate by causing biodiversity loss, soil degradation through chemical and physical degradation, and pollution of water bodies. The extreme usage of pesticides and fertilizers leads to climate change by releasing greenhouse gases (GHGs) and depositing toxic substances in the soil. At present, there is an urgent need to address these abiotic stresses to achieve sustainable growth in agricultural production and fulfill the rising global food demand. Several types of bacteria that are linked with plants can increase plant resistance to stress and lessen the negative effects of environmental challenges. This review aims to explore the environmentally friendly capabilities and prospects of multi-trait plant growth-promoting bacteria (PGPB) in the alleviation of detrimental impacts of harsh environmental conditions on plants.

Partner or perish: tree microbiomes and climate change

Understanding the complex relationships between plants, their microbiomes, and environmental changes is crucial for improving growth and survival, especially for long-lived tree species. Trees, like other plants, maintain close associations with a multitude of microorganisms on and within their tissues, forming a 'holobiont'. However, a comprehensive framework for detailed tree-microbiome dynamics, and the implications for climate adaptation, is currently lacking. This review identifies gaps in the existing literature, emphasizing the need for more research to explore the coevolution of the holobiont and the full extent of climate change impact on tree growth and survival. Advancing our knowledge of plant-microbial interactions presents opportunities to enhance tree adaptability and mitigate adverse impacts of climate changes on trees.

Glycine betaine: A multifaceted protectant against salt stress in Indian mustard through ionic homeostasis, ROS scavenging and osmotic regulation

Salt stress is a prevalent environmental issue that disrupts the redox balance and metabolic processes in plants, leading to reduced crop growth and productivity. Currently, over 6.74 million hectares in India are salt-affected, and about 75% of this land lies in states that are the major cultivators of edible oilseed crops (rapeseed-mustard). Therefore, this study focused on the efficacy of glycine betaine (GB) supplementation in mitigating the detrimental effects of salt stress in Brassica juncea L. (Indian mustard) plants. Indian mustard plants were subjected to salt stress [0, 50, 100, and 150 mM sodium chloride] 20 days after sowing (DAS), while a foliar spray of 20 mM GB was applied to the foliage at 50 and 70 DAS. The data showed that salt stress substantially reduced growth, photosynthetic rate, membrane stability, and yield by significantly increasing lipid peroxidation, ion toxicity, cell death, electrolyte leakage, and reactive oxygen species accumulation that triggered oxidative stress. Supplementation with 20 mM GB provided tolerance to plants against salt-induced toxicity since it substantially increased growth, biomass, water content, nutrient uptake, and photosynthetic efficiency. Additionally, GB enhances the accumulation of osmolytes, enhances the antioxidant defence system, improves ionic balance, and enhances cell viability. Taken together, the obtained data provides deeper insights into the beneficial effect of the exogenous GB application that could have biotechnological uses to enhance crop stress tolerance in challenging environments.

Regional diversity and leaf microbiome interactions of the fungal maize pathogen Exserohilum turcicum in Switzerland: A metagenomic analysis

The spread and adaptation of fungal plant pathogens in agroecosystems are facilitated by environmental homogeneity. Metagenomic sequencing of infected tissues allowed us to monitor eco-evolutionary dynamics and interactions between host, pathogen and plant microbiome. Exserohilum turcicum, the causal agent of northern corn leaf blight (NCLB) in maize, is distributed in multiple clonal lineages throughout Europe. To characterize regional pathogen diversity, we conducted metagenomic DNA sequencing on 241 infected leaf samples from the highly susceptible Swiss maize landrace Rheintaler Ribelmais, collected over 3 years (2016-2018) from an average of 14 agricultural farms within the Swiss Rhine Valley. All major European clonal lineages of E. turcicum were identified. Lineages differ by their mating types which indicates potential for sexual recombination and rapid evolution of new pathogen strains, although we found no evidence of recent recombination. The associated eukaryotic and prokaryotic leaf microbiome exhibited variation in taxonomic diversity between years and locations and is likely influenced by local weather conditions. A network analysis revealed distinct clusters of eukaryotic and prokaryotic taxa that correlates with the frequency of E. turcicum sequencing reads, suggesting causal interactions. Notably, the yeast genus Metschnikowia exhibited a strongly negative association with E. turcicum, supporting its known potential as biological control agent against fungal pathogens. Our findings show that metagenomic sequencing is a useful tool for analysing the role of environmental factors and potential pathogen-microbiome interactions in shaping pathogen dynamics and evolution, suggesting their potential for effective pathogen management strategies.

Characterization of bacterial diversity in rhizospheric soils, irrigation water, and lettuce crops in municipalities near the Bogotá river, Colombia

The use of wastewater in agricultural practices poses a potential risk for the spread of foodborne diseases. Therefore, this study aimed to characterize the bacterial biodiversity in rhizospheric soil, irrigation water, and lettuce crops in three municipalities adjacent to the Bogotá River, Colombia. Samples were collected in Mosquera, Funza, and Cota municipalities, including rhizospheric soil, lettuce leaves, and irrigation water. The total DNA extraction was performed to analyze bacterial diversity through high-throughput sequencing of the 16S ribosomal RNA genes, utilizing the Illumina HiSeq 2500 PE 300 sequencing platform. A total of 198 genera from the rhizospheric soil were detected including a higher abundance of zOTUs such as Bacillus, Streptomyces, and clinically relevant genera such as Mycobacterium and Pseudomonas. In lettuce, the detection of 26 genera of endophytic bacteria showed to Proteobacteria and Firmicutes as the predominant phyla, with Staphylococcus and Bacillus as the most abundant genera. Notably, Funza's crops exhibited the highest abundance of endophytes, approximately 50 %, compared to Cota (20 %). Furthermore, the most abundant bacterial genera in the irrigation water were Flavobacterium and Pseudomonas. The most prevalent Enterobacteriaceae were Serratia, Enterobacter, Citrobacter, Klebsiella, Yersinia, Shigella, Escherichia, and Erwinia. The Bacillus genus was highly enriched in both rhizospheric soils and lettuce crops, indicating its significant contribution as the main endophytic bacterium.

Bacillus species are core microbiota of resistant maize cultivars that induce host metabolic defense against corn stalk rot

BACKGROUND

Microbes colonizing each compartment of terrestrial plants are indispensable for maintaining crop health. Although corn stalk rot (CSR) is a severe disease affecting maize (Zea mays) worldwide, the mechanisms underlying host-microbe interactions across vertical compartments in maize plants, which exhibit heterogeneous CSR-resistance, remain largely uncharacterized.

RESULTS

Here, we investigated the microbial communities associated with CSR-resistant and CSR-susceptible maize cultivars using multi-omics analysis coupled with experimental verification. Maize cultivars resistant to CSR reshaped the microbiota and recruited Bacillus species with three phenotypes against Fusarium graminearum including niche pre-emption, potential secretion of antimicrobial compounds, and no inhibition to alleviate pathogen stress. By inducing the expression of Tyrosine decarboxylase 1 (TYDC1), encoding an enzyme that catalyzes the production of tyramine and dopamine, Bacillus isolates that do not directly suppress pathogen infection induced the synthesis of berberine, an isoquinoline alkaloid that inhibits pathogen growth. These beneficial bacteria were recruited from the rhizosphere and transferred to the stems but not grains of the CSR-resistant plants.

CONCLUSIONS

The current study offers insight into how maize plants respond to and interact with their microbiome and lays the foundation for preventing and treating soil-borne pathogens. Video Abstract.

Protective role of native root-associated bacterial consortium against root-knot nematode infection in susceptible plants

Root-knot nematodes (RKNs) are a global menace to agricultural crop production. The role of root-associated microbes (RAMs) in plant protection against RKN infection remains unclear. Here we observe that cucumber (highly susceptible to Meloidogyne incognita) exhibits a consistently lower susceptibility to M. incognita in the presence of native RAMs in three distinct soils. Nematode infection alters the assembly of bacterial RAMs along the life cycle of M. incognita. Particularly, the loss of bacterial diversity of RAMs exacerbates plant susceptibility to M. incognita. A diverse range of native bacterial strains isolated from M. incognita-infected roots has nematode-antagonistic activity. Increasing the number of native bacterial strains causes decreasing nematode infection, which is lowest when six or more bacterial strains are present. Multiple simplified synthetic communities consisting of six bacterial strains show pronounced inhibitory effects on M. incognita infection in plants. These inhibitory effects are underpinned via multiple mechanisms including direct inhibition of infection, secretion of anti-nematode substances, and regulation of plant defense responses. This study highlights the role of native bacterial RAMs in plant resistance against RKNs and provides a useful insight into the development of a sustainable way to protect susceptible plants.

Life on a leaf: the epiphyte to pathogen continuum and interplay in the phyllosphere

Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant-microbe-microbe interactions on the leaf surface.

From Microbes to Microbiomes: Applications for Plant Health and Sustainable Agriculture

Plant-microbe interaction research has had a transformative trajectory, from individual microbial isolate studies to comprehensive analyses of plant microbiomes within the broader phytobiome framework. Acknowledging the indispensable role of plant microbiomes in shaping plant health, agriculture, and ecosystem resilience, we underscore the urgent need for sustainable crop production strategies in the face of contemporary challenges. We discuss how the synergies between advancements in 'omics technologies and artificial intelligence can help advance the profound potential of plant microbiomes. Furthermore, we propose a multifaceted approach encompassing translational considerations, transdisciplinary research initiatives, public-private partnerships, regulatory policy development, and pragmatic expectations for the practical application of plant microbiome knowledge across diverse agricultural landscapes. We advocate for strategic collaboration and intentional transdisciplinary efforts to unlock the benefits offered by plant microbiomes and address pressing global issues in food security. By emphasizing a nuanced understanding of plant microbiome complexities and fostering realistic expectations, we encourage the scientific community to navigate the transformative journey from discoveries in the laboratory to field applications. As companies specializing in agricultural microbes and microbiomes undergo shifts, we highlight the necessity of understanding how to approach sustainable agriculture with site-specific management solutions. While cautioning against overpromising, we underscore the excitement of exploring the many impacts of microbiome-plant interactions. We emphasize the importance of collaborative endeavors with societal partners to accelerate our collective capacity to harness the diverse and yet-to-be-discovered beneficial activities of plant microbiomes.

Engineering plant-microbe communication for plant nutrient use efficiency

Nutrient availability and efficient use are critical for crop productivity. Current agricultural practices rely on excessive chemical fertilizers, contributing to greenhouse gas emissions and environmental pollution. Rhizosphere microbes facilitate plant nutrient acquisition and contribute to nutrient use efficiency. Thus, engineering plant-microbe communication within the rhizosphere emerges as a promising and sustainable strategy to enhance agricultural productivity. Recent advances in plant engineering have enabled the development of plants capable of selectively enriching beneficial microbes through root exudates. At the same time, synthetic biology techniques have produced microbes capable of improving nutrient availability and uptake by plants. By engineering plant-microbe communication, researchers aim to harness beneficial soil microbes, thereby offering a targeted and efficient approach to optimizing plant nutrient use efficiency.

Unearthing opportunity amid declining plant-beneficial bacteria

Plant-associated microbiomes maintain biodiversity and ecosystem productivity amid global change. Under projected climate change scenarios, the abundance of plant-beneficial bacteria is expected to decrease. Altered plant-associated microbiomes may affect plant tolerance to stress and (agro-)ecosystem productivity. Forward-thinking approaches, like microbiome breeding, offer biotechnological opportunities to understand and mine plant-microbe interactions.

Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought

Mitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers. Differences in community structure were observed between crops and between drought and watered and planted and unplanted treatments within crops. Despite crop-specific communities, drought rhizobiome dynamics were similar across the two crops. The presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought observed only for the bean rhizobiome. The switchgrass rhizobiome was stable despite changes in rhizosphere metabolite profiles between planted and unplanted treatments. We conclude that rhizobiome responses to short-term drought are crop-specific, with possible decoupling of plant exudation from rhizobiome responses.

The Ability of Different Tea Tree Germplasm Resources in South China to Aggregate Rhizosphere Soil Characteristic Fungi Affects Tea Quality

It is generally recognized that the quality differences in plant germplasm resources are genetically determined, and that only a good "pedigree" can have good quality. Ecological memory of plants and rhizosphere soil fungi provides a new perspective to understand this phenomenon. Here, we selected 45 tea tree germplasm resources and analyzed the rhizosphere soil fungi, nutrient content and tea quality. We found that the ecological memory of tea trees for soil fungi led to the recruitment and aggregation of dominant fungal populations that were similar across tea tree varieties, differing only in the number of fungi. We performed continuous simulation and validation to identify four characteristic fungal genera that determined the quality differences. Further analysis showed that the greater the recruitment and aggregation of Saitozyma and Archaeorhizomyces by tea trees, the greater the rejection of Chaetomium and Trechispora, the higher the available nutrient content in the soil and the better the tea quality. In summary, our study presents a new perspective, showing that ecological memory between tea trees and rhizosphere soil fungi leads to differences in plants' ability to recruit and aggregate characteristic fungi, which is one of the most important determinants of tea quality. The artificial inoculation of rhizosphere fungi may reconstruct the ecological memory of tea trees and substantially improve their quality.

Unveiling the influence of salinity on bacterial microbiome assembly of halophytes and crops

BACKGROUND

Climate change and anthropogenic activities intensify salinity stress impacting significantly on plant productivity and biodiversity in agroecosystems. There are naturally salt-tolerant plants (halophytes) that can grow and withstand such harsh conditions. Halophytes have evolved along with their associated microbiota to adapt to hypersaline environments. Identifying shared microbial taxa between halophyte species has rarely been investigated. We performed a comprehensive meta-analysis using the published bacterial 16S rRNA gene sequence datasets to untangle the rhizosphere microbiota structure of two halophyte groups and non-halophytes. We aimed for the identification of marker taxa of plants being adapted to a high salinity using three independent approaches.

RESULTS

Fifteen studies met the selection criteria for downstream analysis, consisting of 40 plants representing diverse halophyte and non-halophyte species. Microbiome structural analysis revealed distinct compositions for halophytes that face high salt concentrations in their rhizosphere compared to halophytes grown at low salt concentrations or from non-halophytes. For halophytes grown at high salt concentrations, we discovered three bacterial genera that were independently detected through the analysis of the core microbiome, key hub taxa by network analysis and random forest analysis. These genera were Thalassospira, Erythrobacter, and Marinobacter.

CONCLUSIONS

Our meta-analysis revealed that salinity level is a critical factor in affecting the rhizosphere microbiome assembly of plants. Detecting marker taxa across high-halophytes may help to select Bacteria that might improve the salt tolerance of non-halophytic plants.

Influence of Drought Stress on the Rhizosphere Bacterial Community Structure of Cassava (Manihot esculenta Crantz)

Drought presents a significant abiotic stress that threatens crop productivity worldwide. Rhizosphere bacteria play pivotal roles in modulating plant growth and resilience to environmental stresses. Despite this, the extent to which rhizosphere bacteria are instrumental in plant responses to drought, and whether distinct cassava (Manihot esculenta Crantz) varieties harbor specific rhizosphere bacterial assemblages, remains unclear. In this study, we measured the growth and physiological characteristics, as well as the physical and chemical properties of the rhizosphere soil of drought-tolerant (SC124) and drought-sensitive (SC8) cassava varieties under conditions of both well-watered and drought stress. Employing 16S rDNA high-throughput sequencing, we analyzed the composition and dynamics of the rhizosphere bacterial community. Under drought stress, biomass, plant height, stem diameter, quantum efficiency of photosystem II (Fv/Fm), and soluble sugar of cassava decreased for both SC8 and SC124. The two varieties' rhizosphere bacterial communities' overall taxonomic structure was highly similar, but there were slight differences in relative abundance. SC124 mainly relied on Gamma-proteobacteria and Acidobacteriae in response to drought stress, and the abundance of this class was positively correlated with soil acid phosphatase. SC8 mainly relied on Actinobacteria in response to drought stress, and the abundance of this class was positively correlated with soil urease and soil saccharase. Overall, this study confirmed the key role of drought-induced rhizosphere bacteria in improving the adaptation of cassava to drought stress and clarified that this process is significantly related to variety.

The underground world of plant disease: Rhizosphere dysbiosis reduces above-ground plant resistance to bacterial leaf spot and alters plant transcriptome

Just as the human gut microbiome is colonized by a variety of microbes, so too is the rhizosphere of plants. An imbalance in this microbial community, known as dysbiosis, can have a negative impact on plant health. This study sought to explore the effect of rhizosphere dysbiosis on the health of tomato plants (Solanum lycopersicum L.), using them and the foliar bacterial spot pathogen Xanthomonas perforans as model organisms. The rhizospheres of 3-week-old tomato plants were treated with either streptomycin or water as a control, and then spray-inoculated with X. perforans after 24 h. Half of the plants that were treated with both streptomycin and X. perforans received soil microbiome transplants from uninfected plant donors 48 h after the streptomycin was applied. The plants treated with streptomycin showed a 26% increase in disease severity compared to those that did not receive the antibiotic. However, the plants that received the soil microbiome transplant exhibited an intermediate level of disease severity. The antibiotic-treated plants demonstrated a reduced abundance of rhizobacterial taxa such as Cyanobacteria from the genus Cylindrospermum. They also showed a down-regulation of genes related to plant primary and secondary metabolism, and an up-regulation of plant defence genes associated with induced systemic resistance. This study highlights the vital role that beneficial rhizosphere microbes play in disease resistance, even against foliar pathogens.

Exploring Aluminum Tolerance Mechanisms in Plants with Reference to Rice and Arabidopsis: A Comprehensive Review of Genetic, Metabolic, and Physiological Adaptations in Acidic Soils

Aluminum (Al) makes up a third of the Earth's crust and is a widespread toxic contaminant, particularly in acidic soils. It impacts crops at multiple levels, from cellular to whole plant systems. This review delves into Al's reactivity, including its cellular transport, involvement in oxidative redox reactions, and development of specific metabolites, as well as the influence of genes on the production of membrane channels and transporters, alongside its role in triggering senescence. It discusses the involvement of channel proteins in calcium influx, vacuolar proton pumping, the suppression of mitochondrial respiration, and the initiation of programmed cell death. At the cellular nucleus level, the effects of Al on gene regulation through alterations in nucleic acid modifications, such as methylation and histone acetylation, are examined. In addition, this review outlines the pathways of Al-induced metabolic disruption, specifically citric acid metabolism, the regulation of proton excretion, the induction of specific transcription factors, the modulation of Al-responsive proteins, changes in citrate and nucleotide glucose transporters, and overall metal detoxification pathways in tolerant genotypes. It also considers the expression of phenolic oxidases in response to oxidative stress, their regulatory feedback on mitochondrial cytochrome proteins, and their consequences on root development. Ultimately, this review focuses on the selective metabolic pathways that facilitate Al exclusion and tolerance, emphasizing compartmentalization, antioxidative defense mechanisms, and the control of programmed cell death to manage metal toxicity.

Impact of Plant-Microbe Interactions with a Focus on Poorly Investigated Urban Ecosystems-A Review

The urbanization process, which began with the Industrial Revolution, has undergone a considerable increase over the past few decades. Urbanization strongly affects ecological processes, often deleteriously, because it is associated with a decrease in green spaces (areas of land covered by vegetation), loss of natural habitats, increased rates of species extinction, a greater prevalence of invasive and exotic species, and anthropogenic pollutant accumulation. In urban environments, green spaces play a key role by providing many ecological benefits and contributing to human psychophysical well-being. It is known that interactions between plants and microorganisms that occur in the rhizosphere are of paramount importance for plant health, soil fertility, and the correct functioning of plant ecosystems. The growing diffusion of DNA sequencing technologies and "omics" analyses has provided increasing information about the composition, structure, and function of the rhizomicrobiota. However, despite the considerable amount of data on rhizosphere communities and their interactions with plants in natural/rural contexts, current knowledge on microbial communities associated with plant roots in urban soils is still very scarce. The present review discusses both plant-microbe dynamics and factors that drive the composition of the rhizomicrobiota in poorly investigated urban settings and the potential use of beneficial microbes as an innovative biological tool to face the challenges that anthropized environments and climate change impose. Unravelling urban biodiversity will contribute to green space management, preservation, and development and, ultimately, to public health and safety.

Agricultural fertilization near marshes impacts the potential for greenhouse gas emissions from wetland ecosystems by modifying microbial communities

Ensuring agricultural security and preserving the health of wetland ecosystems are crucial concerns facing northeast China. However, the adverse effects of environmental pollution, especially nitrogen (N), caused by prolonged agricultural development on the health of marsh wetlands cannot be systematically recognized. To address this issue, an 18-year trial with four different levels of N application was carried out in a typical area of the Northeast region: 0, 6, 12, and 24 gN·m-2·a-1 (referred to as CK, N6, N12, and N24, respectively) to investigate changes in wetland ecological functioning. The results showed that long-term N input significantly enhanced soil N availability. High-level of N addition (N24) significantly reduced soil bacterial richness in October, while fungal diversity was significantly higher in June than in October for both control and N6 treatments. The main environmental factors affecting microorganisms in June were TN, NH4+, and EC, while bacterial and fungal communities were influenced by TN and Leaf Area Index (LAI), respectively, in October. It was found that the AN16S gene was significantly higher in June than in October, indicating that summer is the critical time for N removal in the wetland. N addition significantly reduced the abundance of the NIFH gene and decreased the N fixation potential of the wetland. In June, low and medium levels of N inputs promoted denitrification processes in the wetland and elevated the wetland N2O emission potential. The abundance of NARG, NIRK, and NOSZ genes decreased significantly in October compared to June, indicating a decrease in the wetland N2O emission potential. Additionally, it was observed that soil methanotrophs were positively affected by NH4+ and TN in October, thereby reducing the wetland CH4 emission potential. Our research provides a systematic understanding of the impact of agricultural N pollution on marsh wetlands, which can inform strategies to protect wetland health.

Strigolactones shape the assembly of root-associated microbiota in response to phosphorus availability

Plants rely on strigolactones (SLs) to regulate their development and form symbiotic relationships with microbes as part of the adaptive phosphorus (P) efficiency strategies. However, the impact of SLs on root-associated microbial communities in response to P availability remains unknown. Here, root microbiota of SL biosynthesis (max3-11) and perception (d14-1) were compared to wild-type Col-0 plants under different P concentrations. Using high-throughput sequencing, the relationship between SLs, P concentrations, and the root-associated microbiota was investigated to reveal the variation in microbial diversity, composition, and interaction. Plant genotypes and P availability played important but different roles in shaping the root-associated microbial community. Importantly, SLs were found to attract Acinetobacter in low P conditions, which included an isolated CP-2 (Acinetobacter soli) that could promote plant growth in cocultivation experiments. Moreover, SLs could change the topologic structure within co-occurrence networks and increase the number of keystone taxa (e.g., Rhizobiaceae and Acidobacteriaceae) to enhance microbial community stability. This study reveals the key role of SLs in mediating root-associated microbiota interactions.IMPORTANCEStrigolactones (SLs) play a crucial role in plant development and their symbiotic relationships with microbes, particularly in adapting to phosphorus levels. Using high-throughput sequencing, we compared the root microbiota of plants with SL biosynthesis and perception mutants to wild-type plants under different phosphorus concentrations. These results found that SLs can attract beneficial microbes in low phosphorus conditions to enhance plant growth. Additionally, SLs affect microbial network structures, increasing the stability of microbial communities. This study highlights the key role of SLs in shaping root-associated microbial interactions, especially in response to phosphorus availability.

Recruitment and Aggregation Capacity of Tea Trees to Rhizosphere Soil Characteristic Bacteria Affects the Quality of Tea Leaves

There are obvious differences in quality between different varieties of the same plant, and it is not clear whether they can be effectively distinguished from each other from a bacterial point of view. In this study, 44 tea tree varieties (Camellia sinensis) were used to analyze the rhizosphere soil bacterial community using high-throughput sequencing technology, and five types of machine deep learning were used for modeling to obtain characteristic microorganisms that can effectively differentiate different varieties, and validation was performed. The relationship between characteristic microorganisms, soil nutrient transformation, and tea quality formation was further analyzed. It was found that 44 tea tree varieties were classified into two groups (group A and group B) and the characteristic bacteria that distinguished them came from 23 genera. Secondly, the content of rhizosphere soil available nutrients (available nitrogen, available phosphorus, and available potassium) and tea quality indexes (tea polyphenols, theanine, and caffeine) was significantly higher in group A than in group B. The classification result based on both was consistent with the above bacteria. This study provides a new insight and research methodology into the main reasons for the formation of quality differences among different varieties of the same plant.

Mycobiome mediates the interaction between environmental factors and mycotoxin contamination in wheat grains

Environmental factors significantly impact grain mycobiome assembly and mycotoxin contamination. However, there is still a lack of understanding regarding the wheat mycobiome and the role of fungal communities in the interaction between environmental factors and mycotoxins. In this study, we collected wheat grain samples from 12 major wheat-producing provinces in China during both the harvest and storage periods. Our aim was to evaluate the mycobiomes in wheat samples with varying deoxynivalenol (DON) contamination levels and to confirm the correlation between environmental factors, the wheat mycobiome, and mycotoxins. The results revealed significant differences in the wheat mycobiome and co-occurrence network between contaminated and uncontaminated wheat samples. Fusarium was identified as the main differential taxon responsible for inducing DON contamination in wheat. Correlation analysis identified key factors affecting mycotoxin contamination. The results indicate that both environmental factors and the wheat mycobiome play significant roles in the production and accumulation of DON. Environmental factors can affect the wheat mycobiome assembly, and wheat mycobiome mediates the interaction between environmental factors and mycotoxin contamination. Furthermore, a random forest (RF) model was developed using key biological indicators and environmental features to predict DON contamination in wheat with accuracies exceeding 90 %. The findings provide data support for the accurate prediction of mycotoxin contamination and lay the foundation for the research on biological control technologies of mycotoxin through the assembly of synthetic microbial communities.

Changes in Endophyte Communities across the Different Plant Compartments in Response to the Rice Blast Infection

The rice blast disease, caused by the fungal pathogen, Magnaporthe oryzae (syn. Pyricularia oryzae), poses a significant threat to the global rice production. Understanding how this disease impacts the plant's microbial communities is crucial for gaining insights into hostpathogen interactions. In this study, we investigated the changes in communities of bacterial and fungal endophytes inhabiting different compartments in healthy and diseased plants. We found that both alpha and beta diversities of endophytic communities do not change significantly by the pathogen infection. Rather, the type of plant compartment appeared to be the main driver of endophytic community structures. Although the overall structure seemed to be consistent between healthy and diseased plants, our analysis of differentially abundant taxa revealed the specific bacterial and fungal operational taxonomic units that exhibited enrichment in the root and leaf compartments of infected plants. These findings suggest that endophyte communities are robust to the changes at the early stage of pathogen infection, and that some of endophytes enriched in infected plants might have roles in the defense against the pathogen.

How temperature modulates the expression of pathogenesis-related molecules of the cross-kingdom pathogen Lasiodiplodia hormozganensis

Lasiodiplodia hormozganensis, initially recognized as a fungal plant pathogen, is recognized now acknowledged as a potential threat to humans. However, our understanding of the pathogenesis mechanisms of Lasiodiplodia species remains limited, and the impact of temperature on its pathogenicity is unclear. This study aims to elucidate the effects of temperature on the biology of L. hormozganensis, focusing on the expression of pathogenesis-related molecules and its ability to function as a cross-kingdom pathogen. We conducted experiments at two different temperatures, 25 and 37 °C, analyzing the proteome and transcriptome of L. hormozganensis. Using strain CBS339.90, initially identified as L. theobromae but confirmed through ITS and tef1-α sequence analysis to be L. hormozganensis, we aimed to understand the fungus's protein expression under varying temperature conditions. Results from the functional analysis of the secretome at 25 °C showed a noteworthy presence of proteins related to carbohydrate metabolism, catabolism, plant cell wall degradation, and pathogenesis. However, when grown at 37 °C, the fungus exhibited an increased production of stress response and pathogenesis-related proteins. Our findings identified various pathways crucial for pathogenesis in both plants and humans, suggesting that L. hormozganensis possesses the genetic foundation to infect both hosts. Specific pathogenesis-related proteins, including the phytotoxin snodprot1, aspartic protease aspergillopepsin, and virulence protein SSD1, were also identified. Concluding, we propose a possible mechanism of how L. hormozganensis adapts to different temperatures. The shift in temperature results in the expression of genes that favor human related pathogenesis molecules.

Kinetics-based inference of environment-dependent microbial interactions and their dynamic variation

Microbial communities in nature are dynamically evolving as member species change their interactions subject to environmental variations. Accounting for such context-dependent dynamic variations in interspecies interactions is critical for predictive ecological modeling. In the absence of generalizable theoretical foundations, we lack a fundamental understanding of how microbial interactions are driven by environmental factors, significantly limiting our capability to predict and engineer community dynamics and function. To address this issue, we propose a novel theoretical framework that allows us to represent interspecies interactions as an explicit function of environmental variables (such as substrate concentrations) by combining growth kinetics and a generalized Lotka-Volterra model. A synergistic integration of these two complementary models leads to the prediction of alterations in interspecies interactions as the outcome of dynamic balances between positive and negative influences of microbial species in mixed relationships. The effectiveness of our method was experimentally demonstrated using a synthetic consortium of two Escherichia coli mutants that are metabolically dependent (due to an inability to synthesize essential amino acids) but competitively grow on a shared substrate. The analysis of the E. coli binary consortium using our model not only showed how interactions between the two amino acid auxotrophic mutants are controlled by the dynamic shifts in limiting substrates but also enabled quantifying previously uncharacterizable complex aspects of microbial interactions, such as asymmetry in interactions. Our approach can be extended to other ecological systems to model their environment-dependent interspecies interactions from growth kinetics.IMPORTANCEModeling environment-controlled interspecies interactions through separate identification of positive and negative influences of microbes in mixed relationships is a new capability that can significantly improve our ability to understand, predict, and engineer the complex dynamics of microbial communities. Moreover, the prediction of microbial interactions as a function of environmental variables can serve as valuable benchmark data to validate modeling and network inference tools in microbial ecology, the development of which has often been impeded due to the lack of ground truth information on interactions. While demonstrated against microbial data, the theory developed in this work is readily applicable to general community ecology to predict interactions among macroorganisms, such as plants and animals, as well as microorganisms.

Soil microbiota and herbivory drive the assembly of tomato plant-associated microbial communities through different mechanisms

Plant-associated microbial communities are key to shaping many aspects of plant biology. In this study, we tested whether soil microbial communities and herbivory influence the bacterial community of tomato plants and whether their influence in different plant compartments is driven by microbial spillover between compartments or whether plants are involved in mediating this effect. We grew our plants in soils hosting three different microbial communities and covered (or not) the soil surface to prevent (or allow) passive microbial spillover between compartments, and we exposed them (or not) to herbivory by Manduca sexta. Here we show that the soil-driven effect on aboveground compartments is consistently detected regardless of soil coverage, whereas soil cover influences the herbivore-driven effect on belowground microbiota. Together, our results suggest that the soil microbiota influences aboveground plant and insect microbial communities via changes in plant metabolism and physiology or by sharing microorganisms via xylem sap. In contrast, herbivores influence the belowground plant microbiota via a combination of microbial spillover and changes in plant metabolism. These results demonstrate the important role of plants in linking aboveground and belowground microbiota, and can foster further research on soil microbiota manipulation for sustainable pest management.

Disaster Plant Pathology: Smart Solutions for Threats to Global Plant Health from Natural and Human-Driven Disasters

Disaster plant pathology addresses how natural and human-driven disasters impact plant diseases and the requirements for smart management solutions. Local to global drivers of plant disease change in response to disasters, often creating environments more conducive to plant disease. Most disasters have indirect effects on plant health through factors such as disrupted supply chains and damaged infrastructure. There is also the potential for direct effects from disasters, such as pathogen or vector dispersal due to floods, hurricanes, and human migration driven by war. Pulse stressors such as hurricanes and war require rapid responses, whereas press stressors such as climate change leave more time for management adaptation but may ultimately cause broader challenges. Smart solutions for the effects of disasters can be deployed through digital agriculture and decision support systems supporting disaster preparedness and optimized humanitarian aid across scales. Here, we use the disaster plant pathology framework to synthesize the effects of disasters in plant pathology and outline solutions to maintain food security and plant health in catastrophic scenarios. We recommend actions for improving food security before and following disasters, including (i) strengthening regional and global cooperation, (ii) capacity building for rapid implementation of new technologies, (iii) effective clean seed systems that can act quickly to replace seed lost in disasters, (iv) resilient biosecurity infrastructure and risk assessment ready for rapid implementation, and (v) decision support systems that can adapt rapidly to unexpected scenarios. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application

Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.

Trophic interactions in microbiomes influence plant host population size and ecosystem function

Plant microbiomes that comprise diverse microorganisms, including prokaryotes, eukaryotes and viruses, are the key determinants of plant population dynamics and ecosystem function. Despite their importance, little is known about how species interactions (especially trophic interactions) between microbes from different domains modify the importance of microbiomes for plant hosts and ecosystems. Using the common duckweed Lemna minor, we experimentally examined the effects of predation (by bacterivorous protists) and parasitism (by bacteriophages) within microbiomes on plant population size and ecosystem phosphorus removal. Our results revealed that the addition of predators increased plant population size and phosphorus removal, whereas the addition of parasites showed the opposite pattern. The structural equation modelling further pointed out that predation and parasitism affected plant population size and ecosystem function via distinct mechanisms that were both mediated by microbiomes. Our results highlight the importance of understanding microbial trophic interactions for predicting the outcomes and ecosystem impacts of plant-microbiome symbiosis.

The plant endomicrobiome: Structure and strategies to produce stress resilient future crop

Plants have a microbiome, a diverse community of microorganisms, including bacteria, fungi, and viruses, living inside and on their tissues. Versatile endophytic microorganisms inhabited in every plant part without causing disease and develop endophytic microbiome or endo-microbiome. Plant endo-microbiome are drawn by the nutrient rich micro-environment, and in turn some microbes mutualistically endorse and protect plant from adverse environmental stresses. Plant endo-microbiome interact within well-designed host equilibrium containing xylem, phloem, nutrients, phytohormones, metabolites and shift according to environmental and nutritional change. Plant endo-microbiome regulate and respond to environmental variations, pathogens, herbivores by producing stress regulators, organic acids, secondary metabolites, stress hormones as well as unknown substances and signalling molecules. Endomicrobiome efficiently synthesizes multiple bioactive compounds, stress phytohormones with high competence. The technological innovation as next generation genomics biology and high-throughput multiomics techniques stepping stones on the illumination of critical endo-microbiome communities and functional characterization that aid in improving plant physiology, biochemistry and immunity interplay for best crop productivity. This review article contains deeper insight in endomicrobiome related research work in last years, recruitment, niche development, nutrient dynamics, stress removal mechanisms, bioactive services in plant health development, community architecture and communication, and immunity interplay in producing stress resilient future crop.

Forest top canopy bacterial communities are influenced by elevation and host tree traits

BACKGROUND

The phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the phyllosphere microbiome, host trees of the same species that are subjected to different environmental conditions can still exhibit large degrees of variation in their microbiome diversity and composition. Whether these intra-specific variations in phyllosphere microbiome diversity and composition can be observed over the broader expanse of forest landscapes remains unclear. In this study, we aim to assess the variation in the top canopy phyllosphere bacterial communities between and within host tree species in the temperate European forests, focusing on Fagus sylvatica (European beech) and Picea abies (Norway spruce).

RESULTS

We profiled the bacterial diversity, composition, driving factors, and discriminant taxa in the top canopy phyllosphere of 211 trees in two temperate forests, Veluwe National Parks, the Netherlands and Bavarian Forest National Park, Germany. We found the bacterial communities were primarily shaped by host species, and large variation existed within beech and spruce. While we showed that there was a core microbiome in all tree species examined, community composition varied with elevation, tree diameter at breast height, and leaf-specific traits (e.g., chlorophyll and P content). These driving factors of bacterial community composition also correlated with the relative abundance of specific bacterial families.

CONCLUSIONS

While our results underscored the importance of host species, we demonstrated a substantial range of variation in phyllosphere bacterial diversity and composition within a host species. Drivers of these variations have implications at both the individual host tree level, where the bacterial communities differed based on tree traits, and at the broader forest landscape level, where drivers like certain highly plastic leaf traits can potentially link forest canopy bacterial community variations to forest ecosystem processes. We eventually showed close associations between forest canopy phyllosphere bacterial communities and host trees exist, and the consistent patterns emerging from these associations are critical for host plant functioning.

Traits-based approach: leveraging genome size in plant-microbe interactions

Trait-based approaches have gained growing interest in studying plant-microbe interactions. However, current traits normally considered (e.g., morphological, physiological, or chemical traits) are biased towards those showing large intraspecific variations, necessitating the identification of fewer plastic traits that differ between species. Here, we propose using genome size (the amount of DNA in the nucleus of a cell) as a suitable trait for studying plant-microbiome interactions due to its relatively stable nature, minimally affected by external environmental variations. Emerging evidence suggests that plant genome size affects the plant-associated microbial community, and tissue-specific environments select microbes based on their genome size. These findings pinpoint environmental selection in genome size as an emerging driver of plant-microbiome interactions, potentially impacting ecosystem functions and productivity.

Metabolomics-guided utilization of beneficial microbes for climate-resilient crops

In the rhizosphere, plants and microbes communicate chemically, especially under environmental stress. Over millions of years, plants and their microbiome have coevolved, sharing various chemicals, including signaling molecules. This mutual exchange impacts bacterial communication and influences plant metabolism. Inter-kingdom signal crosstalk affects bacterial colonization and plant fitness. Beneficial microbes and their metabolomes offer eco-friendly ways to enhance plant resilience and agriculture. Plant metabolites are pivotal in this dynamic interaction between host plants and their interacting beneficial microbes. Understanding these associations is key to engineering a robust microbiome for stress mitigation and improved plant growth. This review explores mechanisms behind plant-microbe interactions, the role of beneficial microbes and metabolomics, and the practical applications for addressing climate change's impact on agriculture. Integrating beneficial microbes' activities and metabolomics' application to study metabolome-driven interaction between host plants and their corresponding beneficial microbes holds promise for enhancing crop resilience and productivity.

Soil, rhizosphere, and root microbiome in kiwifruit vine decline, an emerging multifactorial disease

Kiwifruit vine decline syndrome (KVDS) is characterized by severe root system impairment, which leads to irreversible wilting of the canopy. Plants usually collapse rapidly from the appearance of the first aboveground symptoms, without recovery even in the following seasons. The syndrome has been negatively impacting kiwifruit yield in different areas of Italy, the main producing European country, since its first outbreak in 2012. To date, a unique, common causal factor has yet to be found, and the syndrome is referred to as multifactorial. In this article, we investigated the whole biotic community (fungi, bacteria, and oomycetes) associated with the development of KVDS in three different belowground matrices/compartments (soil, rhizosphere, and root). Sampling was performed at both healthy and affected sites located in the main kiwifruit-producing area of Northwestern Italy. To address the multifactorial nature of the syndrome and to investigate the potential roles of abiotic factors in shaping these communities, a physicochemical analysis of soils was also performed. This study investigates the associations among taxonomic groups composing the microbiome and also between biotic and abiotic factors. Dysbiosis was considered as a driving event in shaping KVDS microbial communities. The results obtained from this study highlight the role of the oomycete genus Phytopythium, which resulted predominantly in the oomycete community composition of diseased matrices, though it was also present in healthy ones. Both bacterial and fungal communities resulted in a high richness of genera and were highly correlated to the sampling site and matrix, underlining the importance of multiple location sampling both geographically and spatially. The rhizosphere community associated with KVDS was driven by a dysbiotic process. In addition, analysis of the association network in the diseased rhizosphere revealed the presence of potential cross-kingdom competition for plant-derived carbon between saprobes, oomycetes, and bacteria.

Enriched rhizospheric functional microbiome may enhance adaptability of Artemisia lavandulaefolia and Betula luminifera in antimony mining areas

Dominant native plants are crucial for vegetation reconstruction and ecological restoration of mining areas, though their adaptation mechanisms in stressful environments are unclear. This study focuses on the interactions between dominant indigenous species in antimony (Sb) mining area, Artemisia lavandulaefolia and Betula luminifera, and the microbes in their rhizosphere. The rhizosphere microbial diversity and potential functions of both plants were analyzed through the utilization of 16S, ITS sequencing, and metabarcoding analysis. The results revealed that soil environmental factors, rather than plant species, had a more significant impact on the composition of the rhizosphere microbial community. Soil pH and moisture significantly affected microbial biomarkers and keystone species. Actinobacteria, Proteobacteria and Acidobacteriota, exhibited high resistance to Sb and As, and played a crucial role in the cycling of carbon, nitrogen (N), phosphorus (P), and sulfur (S). The genes participating in N, P, and S cycling exhibited metabolic coupling with those genes associated with Sb and As resistance, which might have enhanced the rhizosphere microbes' capacity to endure environmental stressors. The enrichment of these rhizosphere functional microbes is the combined result of dispersal limitations and deterministic assembly processes. Notably, the genes related to quorum sensing, the type III secretion system, and chemotaxis systems were significantly enriched in the rhizosphere of plants, especially in B. luminifera, in the mining area. The phylogenetic tree derived from the evolutionary relationships among rhizosphere microbial and chloroplast whole-genome resequencing results, infers both species especially B. luminifera, may have undergone co-evolution with rhizosphere microorganisms in mining areas. These findings offer valuable insights into the dominant native rhizosphere microorganisms that facilitate plant adaptation to environmental stress in mining areas, thereby shedding light on potential strategies for ecological restoration in such environments.

Seasonality and longer-term development generate temporal dynamics in the Populus microbiome

Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change.IMPORTANCEMicrobiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.

The soil microbiome of Lolium perenne L. depends on host genotype, is modified by nitrogen level and varies across season

Genotype by environment interactions (G × E) are frequently observed in herbage production. Understanding the underlying biological mechanisms is important for achieving stable and predictive outputs across production environments. The microbiome is gaining increasing attention as a significant contributing factor to G × E. Here, we focused on the soil microbiome of perennial ryegrass (Lolium perenne L.) grown under field conditions and investigated the soil microbiome variation across different ryegrass varieties to assess whether environmental factors, such as seasonality and nitrogen levels, affect the microbial community. We identified bacteria, archaea, and fungi operational taxonomic units (OTUs) and showed that seasonality and ryegrass variety were the two factors explaining the largest fraction of the soil microbiome diversity. The strong and significant variety-by-treatment-by-seasonal cut interaction for ryegrass dry matter was associated with the number of unique OTUs within each sample. We identified seven OTUs associated with ryegrass dry matter variation. An OTU belonging to the Solirubrobacterales (Thermoleophilales) order was associated with increased plant biomass, supporting the possibility of developing engineered microbiomes for increased plant yield. Our results indicate the importance of incorporating different layers of biological data, such as genomic and soil microbiome data to improve the prediction accuracy of plant phenotypes grown across heterogeneous environments.

Host genotype-specific rhizosphere fungus enhances drought resistance in wheat

BACKGROUND

The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses.

RESULTS

Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum).

CONCLUSIONS

Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.

Strategies for breeding crops for future environments

The green revolution successfully increased agricultural output in the early 1960s by relying primarily on three pillars: plant breeding, irrigation, and chemical fertilization. Today, the need to reduce the use of chemical fertilizers, water scarcity, and future environmental changes, together with a growing population, requires innovative strategies to adapt to a new context and prevent food shortages. Therefore, scientists from around the world are directing their efforts to breed crops for future environments to sustainably produce more nutritious food. Herein, we propose scientific avenues to be reinforced in selecting varieties, including crop wild relatives, either for monoculture or mixed cropping systems, taking advantage of plant-microbial interactions, while considering the diversity of organisms associated with crops and unlocking combinatorial nutritional stresses.

Nitrogen starvation modulates the sensitivity of rhizobacterial community to drought stress in Stevia rebaudiana

Alterations in water regimes or nitrogen (N) availability lead to shifts in the assemblage of rhizosphere microbial community; however, how the rhizosphere microbiome response to concurrent changes in water and N availability remains largely unclear. Herein, we investigated the taxonomic and functional characteristics of rhizobacteria associated with stevia (Stevia rebaudiana Bertoni) under varying combinations of water and N levels. Community diversity and predicted functions of rhizobacteria were predominantly altered by drought stress, with N-starvation modulating these effects. Moreover, N fertilization simplified the ecological interactions within rhizobacterial communities and heightened the relative role of stochastic processes on community assembly. In terms of rhizobacterial composition, we observed both common and distinctive changes in drought-responsive bacterial taxa under different N conditions. Generally, the relative abundance of Proteobacteria and Bacteroidetes phyla were depleted by drought stress but the Actinobacteria phylum showed increases. The rhizobacterial responses to drought stress were influenced by N availability, where the positive response of δ-proteobacteria and the negative response of α- and γ-proteobacteria, along with Bacteroidetes, were further heightened under N starvation. By contrast, under N fertilization conditions, an amplified negative or positive response to drought were demonstrated in Firmicutes and Actinobacteria phyla, respectively. Further, the drought-responsive rhizobacteria were mostly phylogenetically similar, but this pattern was modulated under N-rich conditions. Overall, our findings indicate an N-dependent specific restructuring of rhizosphere bacteria under drought stress. These changes in the rhizosphere microbiome could contribute to enhancing plant stress tolerance.

Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?

Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.

Soil warming increases the number of growing bacterial taxa but not their growth rates

Soil microorganisms control the fate of soil organic carbon. Warming may accelerate their activities putting large carbon stocks at risk of decomposition. Existing knowledge about microbial responses to warming is based on community-level measurements, leaving the underlying mechanisms unexplored and hindering predictions. In a long-term soil warming experiment in a Subarctic grassland, we investigated how active populations of bacteria and archaea responded to elevated soil temperatures (+6°C) and the influence of plant roots, by measuring taxon-specific growth rates using quantitative stable isotope probing and 18O water vapor equilibration. Contrary to prior assumptions, increased community growth was associated with a greater number of active bacterial taxa rather than generally faster-growing populations. We also found that root presence enhanced bacterial growth at ambient temperatures but not at elevated temperatures, indicating a shift in plant-microbe interactions. Our results, thus, reveal a mechanism of how soil bacteria respond to warming that cannot be inferred from community-level measurements.

Applied microbiology of the phyllosphere

The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.