Plant-soil Microbe Interactions Research Articles

Does Bidens pilosa L. Affect Carbon and Nitrogen Contents, Enzymatic Activities, and Bacterial Communities in Soil Treated with Different Forms of Nitrogen Deposition?

The deposition of nitrogen in soil may be influenced by the presence of different nitrogen components, which may affect the accessibility of soil nitrogen and invasive plant-soil microbe interactions. This, in turn, may alter the success of invasive plants. This study aimed to clarify the influences of the invasive plant Bidens pilosa L. on the physicochemical properties, carbon and nitrogen contents, enzymatic activities, and bacterial communities in soil in comparison to the native plant Pterocypsela laciniata (Houtt.) Shih treated with simulated nitrogen deposition at 5 g nitrogen m-2 yr-1 in four forms (nitrate, ammonium, urea, and mixed nitrogen). Monocultural B. pilosa resulted in a notable increase in soil pH but a substantial decrease in the moisture, electrical conductivity, ammonium content, and the activities of polyphenol oxidase, β-xylosidase, FDA hydrolase, and sucrase in soil in comparison to the control. Co-cultivating B. pilosa and P. laciniata resulted in a notable increase in total soil organic carbon content in comparison to the control. Monocultural B. pilosa resulted in a notable decrease in soil bacterial alpha diversity in comparison to monocultural P. laciniata. Soil FDA hydrolase activity and soil bacterial alpha diversity, especially the indices of Shannon's diversity, Simpson's dominance, and Pielou's evenness, exhibited a notable decline under co-cultivated B. pilosa and P. laciniata treated with nitrate in comparison to those treated with ammonium, urea, and mixed nitrogen.

Pioneer plants enhance soil multifunctionality by reshaping underground multitrophic community during natural succession of an abandoned rare earth mine tailing

Spontaneous natural succession in metal mine tailings is fundamental to the rehabilitation of bare tailing. Here, an abandoned rare earth element (REE) mine tailing with spontaneous colonisation by pioneer plants with different functional traits was selected. Soil nutrient cycling, fertility, organic matter decomposition as well as underground organismal communities and their multitrophic networks were investigated. Compared with the bare tailing, the colonisation with Lycopodium japonicum, Miscanthus sinensis, and Dicranopteris dichotoma increased soil multifunction by 222%, 293%, and 525%, respectively. This was accompanied by significant changes in soil bacterial and protistan community composition and increased soil multitrophic network complexity. Rhizospheres of different plant species showed distinct microbial community composition compared to that of bare tailing. Some WPS-2, Chloroflexi, and Chlorophyta were mainly present in the bare tailing, while some Proteobacteria and Cercozoa were predominantly seen in the rhizosphere. Pearson correlation and Random Forest revealed the biotic factors driving soil multifunction. Structural equation modelling further revealed that pioneer plants improved soil multifunction primarily by decreasing the microbial biodiversity and increasing the multitrophic network complexity. Overall, this highlights the importance of subterrestrial organisms in accelerating soil rehabilitation during natural succession and provides options for the ecological restoration of degraded REE mining areas.

Unlocking the Secrets of Soil: Exploring the Microbiome and Its Applications—Part 2

AbstractThe term “microbiome” refers to a collective assembly of microorganisms within a specific environment, including fungi, bacteria, and viruses, influencing dynamic functions within the system. Microbes play a pivotal role in the production of various food items, wines, and medicinal compounds. Their significance in agriculture and ecology is monumental, which will be explored in this two‐part article. In this second part part, we’ll discuss the microbiome’s role in plant adaptation and driving the biogeochemical processes in soil across scales, mathematical and statistical modeling of plant–soil–microbe interactions, and areas of future research.

Early production of switchgrass (Panicum virgatum L.) and willow (Salix spp.) indicates carbon accumulation potential in Appalachian reclaimed mine and agriculture soil

AbstractThe production of bioproduct feedstocks such as switchgrass (Panicum virgatum L.) and willow (Salix spp.) on degraded lands provides an opportunity to grow dedicated bioenergy crops with the potential to capture and store carbon in the soil while reducing competition with land for food production. However, how the production of these crops alters plant–soil–microbe interactions that govern soil C accumulation in highly degraded soil is underexplored. The objectives of this study were to examine select biological and chemical properties related to stable soil organic matter (SOM) production from the growth of switchgrass and willow on marginal soil over two growing seasons and whether biochar amendment can positively affect these parameters. To address our objectives, paired former surface mined lands and non‐mine impacted marginal agriculture sites were selected across West Virginia, USA, and biochar and unamended control treatments were imposed. Through the first two growing seasons, microbial activity and demand for carbon (C) increased and was accompanied by a shift in extracellular enzyme investment for decomposition‐associated enzymes. Mineral‐associated organic matter C increased over the two growing seasons, and this increase was greater in the mine sites compared to the agriculture sites. Compared to each site's previous land use, C losses were observed under bioproduct systems in the agriculture, but not the mine sites. Biochar amendments did not impact microbial activity but did increase the C:N of SOM. Overall, our results suggest that the early growth of switchgrass and willow can result in C accumulation in marginal and highly degraded lands.

Soil Microbial Biomass and Bacterial Diversity Enhanced through Fallow Cover Cropping in Rice–Fish Coculture

Traditional rice production is often reliant on the unsustainable practice of utilizing intensive inputs in monoculture cropping systems. Alternatives fallow cover cropping and rice–fish coculture (RFC) offer promising solutions. However, the potential of fallow cover cropping in RFC remains underexplored, and its impact on soil microbes is poorly understood. In this study, assessments of soil–plant–microbe interactions were conducted across three cover cropping systems: Chinese milk vetch (Astragalus sinicus L.) single cropping (CM), Rapeseed (Brassica napus L.) single cropping (RP), and a combination of Chinese milk vetch and rapeseed intercropping (CM_RP). These systems were evaluated with and without nitrogen (N) addition, encompassing both the RFC and rice monoculture (RMC) systems. The findings indicate a notable increase in soil microbial biomass nitrogen (MBN) with CM. Soil microbial biomass carbon (MBC), influenced more by N-fertilizer than crop species, decreased with N addition. In the RFC system, the soil bacterial co-occurrence network exhibited more connections, yet negative links increased. CM_RP displayed similarities to CM without N but shifted closer to RP with N addition. N addition in intercropping significantly increased the root–shoot ratio (R/S) of A. sinicus, associated with decreased aboveground biomass and total root length. Compared to RMC, RFC with N addition reduced the relative abundance of Anaerolineaceae in CM while increasing Bacillus and Pontibacter across cover cropping systems. Overall, with N addition, both RFC and RMC showed decreased soil bacterial diversity indices. Changes in soil bacterial diversity correlated significantly with soil MBC, MBN, and plant R/S. Continuous fallow cover cropping altered soil microbial biomass and affected cover crop biomass distribution, impacting bacterial composition in paddy soil. These results shed light on how bacterial communities respond to N addition and fallow cover cropping in RFC and RMC systems, offering insights for sustainable nutrient management in paddy systems.

Genetic relatedness can alter the strength of plant-soil interactions.

Intraspecific variation may play a key role in shaping the relationships between plants and their interactions with soil microbial communities. The soil microbes of individual plants can generate intraspecific variation in the responsiveness of the plant offspring, yet have been much less studied. To address this need, we explored how the relatedness of seedlings from established clones of Solidago altissima altered the plant-soil interactions of the seedlings. Seedlings of known parentage were generated from a series of 24 clones grown in a common garden. Seedlings from these crosses were inoculated with soils from maternal, paternal, or unrelated clones and their performance compared to sterilized control inocula. We found that soil inocula influenced by S. altissima clones had an overall negative effect on seedling biomass. Furthermore, seedlings inoculated with maternal or paternal soils tended to experience larger negative effects than seedlings inoculated with unrelated soils. However, there was much variation among individual crosses, with not all responding to relatedness. Our data argue that genetic relatedness to the plant from which the soil microbial inoculum was obtained may cause differential impacts on establishing seedlings, encouraging the regeneration of non-kin adjacent to established clones. Such intraspecific variation represents a potentially important source of heterogeneity in plant-soil microbe interactions with implications for maintaining population genetic diversity.

Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet

BackgroundThe rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenced by root exudates. Here, we investigated the impact of root exudates on the microbiota composition, interactions, and assembly processes, and rhizosheath structure in pearl millet using four distinct lines with contrasting soil aggregation abilities.ResultsUtilizing 16S rRNA gene and ITS metabarcoding for microbiota profiling, coupled with FTICR-MS metabonomic analysis of metabolite composition in distinct plant compartments and root exudates, we revealed substantial disparities in microbial diversity and interaction networks. The ß-NTI analysis highlighted bacterial rhizosphere turnover driven primarily by deterministic processes, showcasing prevalent homogeneous selection in root tissue (RT) and root-adhering soil (RAS). Conversely, fungal communities were more influenced by stochastic processes. In bulk soil assembly, a combination of deterministic and stochastic mechanisms shapes composition, with deterministic factors exerting a more pronounced role. Metabolic profiles across shoots, RT, and RAS in different pearl millet lines mirrored their soil aggregation levels, emphasizing the impact of inherent plant traits on microbiota composition and unique metabolic profiles in RT and exudates. Notably, exclusive presence of antimicrobial compounds, including DIMBOA and H-DIMBOA, emerged in root exudates and RT of low aggregation lines.ConclusionsThis research underscores the pivotal influence of root exudates in shaping the root-associated microbiota composition across pearl millet lines, entwined with their soil aggregation capacities. These findings underscore the interconnectedness of root exudates and microbiota, which jointly shape rhizosheath structure, deepening insights into soil–plant-microbe interactions and ecological processes shaping rhizosphere microbial communities. Deciphering plant–microbe interactions and their contribution to soil aggregation and microbiota dynamics holds promise for the advancement of sustainable agricultural strategies.46mkfZGLAk7WD-UFCK_cLiVideo

Soil–plant–microbe interactions in the rhizosphere: incremental amplification induced by localized fertilization

Soil–plant–microbe interactions in the rhizosphere: incremental amplification induced by localized fertilization

Global patterns and drivers of plant-soil microbe interactions.

Plant-soil feedback (PSF) is an important mechanism determining plant community dynamics and structure. Understanding the geographic patterns and drivers of PSF is essential for understanding the mechanisms underlying geographic plant diversity patterns. We compiled a large dataset containing 5969 observations of PSF from 202 studies to demonstrate the global patterns and drivers of PSF for woody and non-woody species. Overall, PSF was negative on average and was influenced by plant attributes and environmental settings. Woody species PSFs did not vary with latitude, but non-woody PSFs were more negative at higher latitudes. PSF was consistently more positive with increasing aridity for both woody and non-woody species, likely due to increased mutualistic microbes relative to soil-borne pathogens. These findings were consistent between field and greenhouse experiments, suggesting that PSF variation can be driven by soil legacies from climates. Our findings call for caution to use PSF as an explanation of the latitudinal diversity gradient and highlight that aridity can influence plant community dynamics and structure across broad scales through mediating plant-soil microbe interactions.

Soil Bacterial Diversity Responds to Long-Term Establishment of Perennial Legumes in Warm-Season Grassland at Two Soil Depths.

The introduction of rhizoma peanut (RP Arachis glabrata Benth) into bahiagrass (Paspalum notatum Flüggé) may require time to develop stable plant-soil microbe interactions as the microbial legacy of the previous plant community may be long-lasting. A previous study showed that <2 years of introducing rhizoma peanut into bahiagrass pastures minimally affected soil bacterial diversity and community composition. In this study, we compared the effects of the long-term inclusion of rhizoma peanut (>8 years) into bahiagrass on soil bacterial diversity and community composition against their monocultures at 0 to 15 and 15 to 30 cm soil depths using next-generation sequencing to target bacterial 16S V3-V4 regions. We observed that a well-established RP-bahiagrass mixed stand led to a 36% increase in bacterial alpha diversity compared to the bahiagrass monoculture. There was a shift from a soil bacterial community dominated by Proteobacteria (~26%) reported in other bahiagrass and rhizoma peanut studies to a soil bacterial community dominated by Firmicutes (39%) in our study. The relative abundance of the bacterial genus Crossiella, known for its antimicrobial traits, was enhanced in the presence of RP. Differences in soil bacterial diversity and community composition were substantial between 0 to 15 and 15 to 30 cm soil layers, with N2-fixing bacteria belonging to the phylum Proteobacteria concentrated in 0 to 15 cm. Introducing RP into bahiagrass pastures is a highly sustainable alternative to mineral N fertilizer inputs. Our results provide evidence that this system also promotes greater soil microbial diversity and is associated with unique taxa that require further study to better understand their contributions to healthy pastures.

Maize (Zea mays L.) root exudation profiles change in quality and quantity during plant development – A field study

Deciphering root exudate composition of soil-grown plants is considered a crucial step to better understand plant–soil–microbe interactions affecting plant growth performance. In this study, two genotypes of Zea mays L. (WT, rth3) differing in root hair elongation were grown in the field in two substrates (sand, loam) in custom-made, perforated columns inserted into the field plots. Root exudates were collected at different plant developmental stages (BBCH 14, 19, 59, 83) using a soil-hydroponic-hybrid exudation sampling approach. Exudates were characterized by LC-MS based non-targeted metabolomics, as well as by photometric assays targeting total dissolved organic carbon, soluble carbohydrates, proteins, amino acids, and phenolics. Results showed that plant developmental stage was the main driver shaping both the composition and quantity of exuded compounds. Carbon (C) exudation per plant increased with increasing biomass production over time, while C exudation rate per cm² root surface area h−1 decreased with plant maturity. Furthermore, exudation rates were higher in the substrate with lower nutrient mobility (i.e., loam). Surprisingly, we observed higher exudation rates in the root hairless rth3 mutant compared to the root hair-forming WT sibling, though exudate metabolite composition remained similar. Our results highlight the impact of plant developmental stage on the plant–soil–microbe interplay.

The Impacts of Elevated CO2 Levels on Environmental Risk of Heavy Metal Pollution in Agricultural Soils: Applicable Remediation Approaches for Integrated Benefits

Heavy metal pollution in agricultural fields is a serious health concern because of the high bioavailability and persistent toxicity of heavy metals. Much progress has recently been made with respect to elucidating the impacts of climate change (e.g., elevated atmospheric CO2 concentrations) on the environmental behavior of heavy metal pollutants and the associated ecological and health risks. The microbiological responses to elevated CO2 levels are primarily mediated by the C balance in agricultural activities; however, the underlying mechanisms involved in plant–soil–microbe interactions under heavy metal stress are still unclear. Thus, in this study, the challenges and perspectives with regard to controlling heavy metal pollution and optimizing crop yields while reducing greenhouse emissions in agricultural ecosystems responsive to elevated CO2 levels are discussed. Considering the integrated benefits of intensive agriculture and food security under a future changing climate, the summarized findings provided in this study may help to develop applicable remediation approaches for sustainably managing heavy metal polluted soils.

The Effects of Localized Plant–Soil–Microbe Interactions on Soil Nitrogen Cycle in Maize Rhizosphere Soil under Long-Term Fertilizers

Long-term fertilization can result in changes in the nitrogen (N) cycle in maize rhizosphere soil. However, there have been few reports on the impacts of plant–soil–microbe regulatory mechanisms on the N cycle in soil. In this study, soil samples were collected from a long-term experimental site located at Jilin Agricultural University, Changchun City, Jilin Province, Northeast China. We then analyzed the changes in the functional genes related to the N cycle, soil enzyme activity, and maize root exudates under long-term fertilizer application using metagenomics and liquid chromatography analysis. We aimed to investigate the response of the N cycle to long-term fertilizers, the interaction among plant, soil, and microbes, and the effect of the plant–soil–microbe system on the N cycle. Long-term fertilization had a significant effect on soil N contents, N2O emissions, and enzyme activity related to the N cycle in maize rhizosphere soil. The functional genes of the N cycle were mainly enriched in the N degradation pathway in maize rhizosphere soil. N fertilizer application decreased the abundance of functional genes related to N fixation and degradation, denitrification, and assimilatory nitrate reduction (ANRA) and increased the abundance of functional genes participating in dissimilatory nitrate reduction (DNRA) and anaerobic ammonia oxidation/hydroxylamine oxidation. The soil environment was positively related to soil enzyme activity and negatively related to the microbial community composition and amino acids in root exudates. The contribution rate of microorganisms to the N cycle was the highest (r2 = 0.900), followed by amino acids (r2 = 0.836) and the soil environment (r2 = 0.832). Therefore, we concluded that N fertilizer is the main factor limiting the soil N cycle and that microorganisms are the main factor regulating the N cycle in the plant–soil–microorganism system.

Warming affects herbaceous germination, early survival, and growth by shifting plant-soil microbe interactions in an alpine ecosystem

Warming affects herbaceous germination, early survival, and growth by shifting plant-soil microbe interactions in an alpine ecosystem

The Effect of Wool Mulch on Plant Development in the Context of the Physical and Biological Conditions in Soil.

Mulching techniques can comprise a solution that better utilizes precipitation and irrigation water in such a manner that mitigates soil degradation and drought damage; however, there are still gaps in the literature with regard to the effect of the use of mulch materials on the development of plant-soil-microbe interactions. Waste fibers, as alternative biodegradable mulch materials, are becoming increasingly prominent. The effect of wool mulch (WM) on water use efficiency, with regard to pepper seedlings, was investigated in different soil types (sand, clay loam, peat) in a pot experiment. Two semi-field experiments were also set up to investigate the effect of WM-plant interactions on sweet pepper yields, as compared with agro textiles and straw mulches. Soil parameters (moisture, temperature, DHA, β-glucosidase enzymes, permanganate-oxidizable carbon) were measured during the growing season. The effect of WM on yield and biomass was more significant with the less frequent irrigation and the greater water-holding capacity of soils. Microbiological activity was significantly higher in the presence of plants, and because of the water retention of WM, the metabolic products of roots and the more balanced soil temperature were caused by plants. In the sandy soil, the straw mulch had a significantly better effect on microbiological parameters and yields than the agro textiles and WM. In soils with a higher water capacity, WM is a sustainable practice for improving the biological parameters and water use efficiency of soil. The effect of WM on yields cannot solely be explained by the water retention of the mulch; indeed, the development of biological activity and plant-soil-microbe interactions in the soil are also contributing factors.

Soil–Plant–Microbe Interactions Determine Soil Biological Fertility by Altering Rhizospheric Nutrient Cycling and Biocrust Formation

Understanding soil–plant–microbe inter- and intra- interactions are essential for ensuring proper soil health, quality, and soil-mediated ecosystem services (e.g., nutrient cycling) required for human–plant–animal life. Intensive and unsustainable farming practices can decrease soil microbial biodiversity, fertility, and quality leading to soil degradation, impaired nutrient cycling, and the incapability of soil to support plant growth. Under such a context, soil biological fertility can appear as a regenerative component that has the potential to harmonize and improve soil’s physical, chemical, and biological parameters. This study defines and discusses the microbiome in the rhizosphere, microbial nutrient cycling, and biological soil crusts as the major components of soil biological fertility, and explores the answers to the following questions: (i) how does the rhizosphere promote plant growth, development, and nutrient cycling through soil microorganisms (e.g., bacteria, fungi)? (ii) How can soil microorganisms regulate macronutrient cycling and facilitate biocrust formation? This review reveals that soil biological fertility is crucial for increasing crop resilience and productivity as well as sustainability in agriculture. Additionally, the reintroduction of plant growth promoting rhizobacteria, a quantitative estimation of the root exudate’s composition, identifying the spatiotemporal dynamics of potassium solubilizing bacteria and establishing biological soil crusts in agricultural lands remain the major tasks for improving soil biological fertility and the transition towards regenerative agriculture.

A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology.

Microbial soil communities form commensal relationships with plants to promote the growth of both parties. The optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. However, investigation in this field is hindered by a lack of model microbial community systems and efficient approaches for building these communities. Two key challenges in developing standardized model communities are maintaining community diversity over time and storing/resuscitating these communities after cryopreservation, especially considering the different growth rates of organisms. Here, a model synthetic community (SynCom) of 16 soil microorganisms commonly found in the rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, has been developed and optimized for in vitro experiments. The model soil community grows reproducibly between replicates and experiments, with a high community α-diversity being achieved through growth in low-nutrient media and through the adjustment of the starting composition ratios for the growth of individual organisms. The community can additionally be cryopreserved with glycerol, allowing for easy replication and dissemination of this in vitro system. Furthermore, the SynCom also grows reproducibly in fabricated ecosystem devices (EcoFABs), demonstrating the application of this community to an existing in vitro plant-microbe system. EcoFABs allow reproducible research in model plant systems, offering the precise control of environmental conditions and the easy measurement of plant microbe metrics. Our results demonstrate the generation of a stable and diverse microbial SynCom for the rhizosphere that can be used with EcoFAB devices and can be shared between research groups for maximum reproducibility. IMPORTANCE Microbes associate with plants in distinct soil communities to the benefit of both the soil microbes and the plants. Interactions between plants and these microbes can improve plant growth and health and are therefore a field of study in sustainable agricultural research. In this study, a model community of 16 soil bacteria has been developed to further the reproducible study of plant-soil microbe interactions. The preservation of the microbial community has been optimized for dissemination to other research settings. Overall, this work will advance soil microbe research through the optimization of a robust, reproducible model community.

Mechanisms of Biochar Effects on Plant Growth of Seepweed (Suaeda salsa) and Hybrid Sorrel (Rumex patientia × Rumex tianschanicus) in a Coastal Saline Soil over Two Cropping Seasons: Soil–Plant–Microbe Interactions

Mechanisms of Biochar Effects on Plant Growth of Seepweed (Suaeda salsa) and Hybrid Sorrel (Rumex patientia × Rumex tianschanicus) in a Coastal Saline Soil over Two Cropping Seasons: Soil–Plant–Microbe Interactions

How does building healthy soils impact sustainable use of water resources in irrigated agriculture?

As blue water resources become increasingly scarce with more frequent droughts and overuse, irrigated agriculture faces significant challenges to reduce its water footprint while maintaining high levels of crop production. Building soil health has been touted as an important means of enhancing the resilience of agroecosystems to drought, mainly with a focus in rainfed systems reliant on green water through increases in infiltration and soil water storage. Yet, green water often contributes only a small fraction of the total crop water budget in irrigated agricultural regions. To scope the potential for how soil health management could impact water resources in irrigated systems, we review how soil health affects soil water flows, plant–soil–microbe interactions, and plant water capture and productive use. We assess how these effects could interact with irrigation management to help make green and blue water use more sustainable. We show how soil health management could (1) optimize green water availability (e.g., by increasing infiltration and soil water storage), (2) maximize productive water flows (e.g., by reducing evaporation and supporting crop growth), and (3) reduce blue water withdrawals (e.g., by minimizing the impacts of water stress on crop productivity). Quantifying the potential of soil health to improve water resource management will require research that focuses on outcomes for green and blue water provisioning and crop production under different irrigation and crop management strategies. Such information could be used to improve and parameterize finer scale crop, soil, and hydraulic models, which in turn must be linked with larger scale hydrologic models to address critical water-resources management questions at watershed or regional scales. While integrated soil health-water management strategies have considerable potential to conserve water—especially compared to irrigation technologies that enhance field-level water use efficiency but often increase regional water use—transitions to these strategies will depend on more than technical understanding and must include addressing interrelated structural and institutional barriers. By scoping a range of ways enhancing soil health could improve resilience to water limitations and identifying key research directions, we inform research and policy priorities aimed at adapting irrigated agriculture to an increasingly challenging future.

Impact of key parameters involved with plant-microbe interaction in context to global climate change.

Anthropogenic activities have a critical influence on climate change that directly or indirectly impacts plant and microbial diversity on our planet. Due to climate change, there is an increase in the intensity and frequency of extreme environmental events such as temperature rise, drought, and precipitation. The increase in greenhouse gas emissions such as CO2, CH4, NOx, water vapor, increase in global temperature, and change in rainfall patterns have impacted soil–plant-microbe interactions, which poses a serious threat to food security. Microbes in the soil play an essential role in plants’ resilience to abiotic and biotic stressors. The soil microbial communities are sensitive and responsive to these stressors. Therefore, a systemic approach to climate adaptation will be needed which acknowledges the multidimensional nature of plant-microbe-environment interactions. In the last two scores of years, there has been an enhancement in the understanding of plant’s response to microbes at physiological, biochemical, and molecular levels due to the availability of techniques and tools. This review highlights some of the critical factors influencing plant-microbe interactions under stress. The association and response of microbe and plants as a result of several stresses such as temperature, salinity, metal toxicity, and greenhouse gases are also depicted. New tools to study the molecular complexity of these interactions, such as genomic and sequencing approaches, which provide researchers greater accuracy, reproducibility, and flexibility for exploring plant-microbe–environment interactions under a changing climate, are also discussed in the review, which will be helpful in the development of resistant crops/plants in present and future.