Plant host and drought shape the root associated fungal microbiota in rice

Rootstocks and drought stress impact the composition and functionality of grapevine rhizosphere bacterial microbiota

The microbiota, a component of the plant holobiont, plays an active role in the response to biotic and abiotic stresses. Nowadays, with recurrent drought and global warming, a growing challenge in viticulture is being addressed by different practices, including the use of adapted rootstocks. However, the relationships between these practices, abiotic stress and the composition and functions of the rhizosphere microbiota remain to be deciphered. This study aimed to unravel the impact of five rootstocks, water management and the combination of both on the rhizosphere bacterial microbiota in grapevines using shotgun metagenomics approach. The results showed that drought impacted the diversity, composition and functionality of the rhizosphere bacterial community. The genera Mycolicibacterium, Mycobacterium and Rhodococcus, and the bacterial functions, including DNA damage repair, fatty acid synthesis, sugar and amino acid transport, oxidative stress reduction, toxin synthesis and detoxification of exogenous compounds were significantly enriched under drought conditions. Rootstocks also significantly affected the rhizosphere bacterial richness but its influence on diversity and functionality compared to water management was weaker. Some taxa and function could be linked to water managements applied. The interaction between rootstocks and water management further influenced the rhizosphere composition, especially under drought conditions, where distinct clustering was observed for specific rootstocks. The results highlight the importance of conducting multifactorial studies to better understand their impact on shaping functional rhizosphere bacterial communities. This study paves the way for future research on beneficial bacterial inoculation and genetic engineering of rootstock to cope with drought stress.

Drought stress mitigation through bioengineering of microbes and crop varieties for sustainable agriculture and food security

Climate change and agriculture are intrinsically connected and sudden changes in climatic conditions adversely impact global food production and security. The climate change-linked abiotic stressors like drought and high temperatures are resulting in crop failure. The most severe abiotic stress drought significantly affect the stomatal closure, production of reactive oxygen species, transpiration, photosynthesis or other physiological processes and plant morphology, and adversely affect plant growth and crop yield. Therefore, there is an exigent need for cost effective and eco-friendly modern technologies to induce drought tolerance in crop plants leading to climate-adapted sustainable agricultural practices for sustained food production. Among many options being pursued in this regard, the use of plant growth promoting microbes (PGPMs) is the most sustainable approach to promote drought stress resilience in crop plants leading to better plant growth and crop productivity. These PGPMs confer drought resistance via various direct or indirect mechanisms including production of antioxidants, enzymes, exopolysaccharides, modulation of phytohormones level, osmotic adjustment by inducing the accumulation of sugars, along with increases in nutrients, water uptake and photosynthetic pigments. However, several technological and ecological challenges limit their use in agriculture and sometimes treatment with plant beneficial microbes fails to produce desired results under field conditions. Thus, development of synthetic microbial communities or host mediated microbiome engineering or development of transgenic plants with the capacity to express desired traits may promote plant survival and growth under drought stress conditions. The present review critically assesses research evidence on the plant growth and stress resilience promoting potentials of PGPMs and their genes as an approach to develop drought resilient plants leading to increased crop productivity. Effective collaboration among scientific communities, policymakers and regulatory agencies is needed to create strong frameworks that both promote and regulate the utilization of synthetic microbial communities and transgenic plants in agriculture.

Oak seedling microbiome assembly under climate warming and drought

Despite that climate change is currently one of the most pervasive challenges, its effects on the plant-associated microbiome is still poorly studied. The aim of this study was to evaluate the impact of the independent and combinatory effect of climate warming and drought on the microbiome assembly of oak from seed to seedling. In a multifactorial experimental set up, acorns were subjected to different temperatures (15 °C, 20 °C, and 25 °C) and soil moisture levels (drought (15%) and control (60%)) from germination until the seedling stage, after which the bacterial and fungal communities associated to the rhizosphere and phyllosphere were characterized by amplicon sequencing and qPCR. The results showed a stronger effect of temperature on fungal than on bacterial diversity and the effect was more pronounced in the phyllosphere. Under drought condition, temperature had a significantly negative effect on phyllosphere fungal diversity. In the rhizosphere, temperature had a significant effect on the fungal community composition which was primarily caused by species turnover. Regardless of temperature, Actinobacteriota was significantly enriched in drought, a group of bacteria known to increase plant drought tolerance. This study provides new insights into the effect of climate change on the plant microbiome in natural ecosystems.

Differential response of bacteria and fungi to drought on the decomposition of Sarcocornia fruticosa woody stems in a saline stream

Inland saline ecosystems suffer multiple stresses (e.g., high radiation, salinity, water scarcity) that may compromise essential ecosystem functions such as organic matter decomposition. Here, we investigated the effects of drought on microbial colonization and decomposition of Sarcocornia fruticosa woody stems across different habitats in a saline watershed: on the dry floodplain, submerged in the stream channel and at the shoreline (first submerged, then emerged). Unexpectedly, weight loss was not enhanced in the submerged stems, while decomposition process differed between habitats. On the floodplain, it was dominated by fungi and high cellulolytic activity; in submerged conditions, a diverse community of bacteria and high ligninolytic activity dominated; and, on the shoreline, enzyme activities were like submerged conditions, but with a fungal community similar to the dry conditions. Results indicate distinct degradation paths being driven by different stress factors: strong water scarcity and photodegradation in dry conditions, and high salinity and reduced oxygen in wet conditions. This suggests that fungi are more resistant to drought, and bacteria to salinity. Overall, in saline watersheds, variations in multiple stress factors exert distinct environmental filters on bacteria and fungi and their role in the decomposition of plant material, affecting carbon cycling and microbial interactions.

Harnessing root-soil-microbiota interactions for drought-resilient cereals

Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.

Harnessing rhizospheric core microbiomes from arid regions for enhancing date palm resilience to climate change effects

Date palm cultivation has thrived in the Gulf Cooperation Council region since ancient times, where it represents a vital sector in agricultural and socio-economic development. However, climate change conditions prevailing for decades in this area, next to rarefication of rain, hot temperatures, intense evapotranspiration, rise of sea level, salinization of groundwater, and intensification of cultivation, contributed to increase salinity in the soil as well as in irrigation water and to seriously threaten date palm cultivation sustainability. There are also growing concerns about soil erosion and its repercussions on date palm oases. While several reviews have reported on solutions to sustain date productivity, including genetic selection of suitable cultivars for the local harsh environmental conditions and the implementation of efficient management practices, no systematic review of the desertic plants' below-ground microbial communities and their potential contributions to date palm adaptation to climate change has been reported yet. Indeed, desert microorganisms are expected to address critical agricultural challenges and economic issues. Therefore, the primary objectives of the present critical review are to (1) analyze and synthesize current knowledge and scientific advances on desert plant-associated microorganisms, (2) review and summarize the impacts of their application on date palm, and (3) identify possible gaps and suggest relevant guidance for desert plant microbes' inoculation approach to sustain date palm cultivation within the Gulf Cooperation Council in general and in Qatar in particular.

Role of Microbes in Alleviating Crop Drought Stress: A Review

Drought stress is an annual global phenomenon that has devastating effects on crop production, so numerous studies have been conducted to improve crop drought resistance. Plant-associated microbiota play a crucial role in crop health and growth; however, we have a limited understanding of the key processes involved in microbiome-induced crop adaptation to drought stress. In this review, we summarize the adverse effects of drought stress on crop growth in terms of germination, photosynthesis, nutrient uptake, biomass, and yield, with a focus on the response of soil microbial communities to drought stress and plant-microbe interactions under drought stress. Moreover, we review the morpho-physiological, biochemical, and molecular mechanisms underlying the mitigation effect of microbes on crop drought stress. Finally, we highlight future research directions, including the characterization of specific rhizosphere microbiome species with corresponding root exudates and the efficiency of rhizobacteria inoculants under drought conditions. Such research will advance our understanding of the complex interactions between crops and microbes and improve crop resistance to drought stress through the application of beneficial drought-adaptive microbes.

Plant-Fungi Interactions: Where It Goes?

Fungi live different lifestyles-including pathogenic and symbiotic-by interacting with living plants. Recently, there has been a substantial increase in the study of phytopathogenic fungi and their interactions with plants. Symbiotic relationships with plants appear to be lagging behind, although progressive. Phytopathogenic fungi cause diseases in plants and put pressure on survival. Plants fight back against such pathogens through complicated self-defense mechanisms. However, phytopathogenic fungi develop virulent responses to overcome plant defense reactions, thus continuing their deteriorative impacts. Symbiotic relationships positively influence both plants and fungi. More interestingly, they also help plants protect themselves from pathogens. In light of the nonstop discovery of novel fungi and their strains, it is imperative to pay more attention to plant-fungi interactions. Both plants and fungi are responsive to environmental changes, therefore construction of their interaction effects has emerged as a new field of study. In this review, we first attempt to highlight the evolutionary aspect of plant-fungi interactions, then the mechanism of plants to avoid the negative impact of pathogenic fungi, and fungal strategies to overcome the plant defensive responses once they have been invaded, and finally the changes of such interactions under the different environmental conditions.

Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance

BACKGROUND

Rice is the second most produced crop worldwide, but is highly susceptible to drought. Micro-organisms can potentially alleviate the effects of drought. The aim of the present study was to unravel the genetic factors involved in the rice-microbe interaction, and whether genetics play a role in rice drought tolerance. For this purpose, the composition of the root mycobiota was characterized in 296 rice accessions (Oryza sativa L. subsp. indica) under control and drought conditions. Genome wide association mapping (GWAS) resulted in the identification of ten significant (LOD > 4) single nucleotide polymorphisms (SNPs) associated with six root-associated fungi: Ceratosphaeria spp., Cladosporium spp., Boudiera spp., Chaetomium spp., and with a few fungi from the Rhizophydiales order. Four SNPs associated with fungi-mediated drought tolerance were also found. Genes located around those SNPs, such as a DEFENSIN-LIKE (DEFL) protein, EXOCYST TETHERING COMPLEX (EXO70), RAPID ALKALINIZATION FACTOR-LIKE (RALFL) protein, peroxidase and xylosyltransferase, have been shown to be involved in pathogen defense, abiotic stress responses and cell wall remodeling processes. Our study shows that rice genetics affects the recruitment of fungi, and that some fungi affect yield under drought. We identified candidate target genes for breeding to improve rice-fungal interactions and hence drought tolerance.

Abundance, diversity, and composition of root-associated microbial communities varied with tall fescue cultivars under water deficit

The plant breeding program has developed many cultivars of tall fescue (Festuca arundinacea) with low maintenance and stress tolerance. While the root-associated microbial community helps confer stress tolerance in the host plant, it is still largely unknown how the microbiota varies with plant cultivars under water stress. The study aimed to characterize drought-responsive bacteria and fungi in the roots and rhizosphere of different tall fescue cultivars. Intact grass-soil cores were collected from six cultivars grown in a field trial under no-irrigation for 3 years. Tall fescue under irrigation was also sampled from an adjacent area as the contrast. Bacterial and fungal communities in roots, rhizosphere, and bulk soil were examined for abundance, diversity, and composition using quantitative-PCR and high-throughput amplicon sequencing of 16S rRNA gene and ITS regions, respectively. Differences in microbial community composition and structure between non-irrigated and irrigated samples were statistically significant in all three microhabitats. No-irrigation enriched Actinobacteria in all three microhabitats, but mainly enriched Basidiomycota in the root endosphere and only Glomeromycota in bulk soil. Tall fescue cultivars slightly yet significantly modified endophytic microbial communities. Cultivars showing better adaptability to drought encompassed more relatively abundant Actinobacteria, Basidiomycota, or Glomeromycota in roots and the rhizosphere. PICRUSt2-based predictions revealed that the relative abundance of functional genes in roots related to phytohormones, antioxidant enzymes, and nutrient acquisition was enhanced under no-irrigation. Significant associations between Streptomyces and putative drought-ameliorating genes underscore possible mechanics for microbes to confer tall fescue with water stress tolerance. This work sheds important insight into the potential use of endophytic microbes for screening drought-adaptive genotypes and cultivars.

Plant microbiota dysbiosis and the Anna Karenina Principle

Microorganisms are associated with all plants, recently leading to the hologenome concept. We reviewed the assembly processes of plant microbiota and analyzed its structure during the emergence of dysbioses. In particular, we discussed the Anna Karenina Principle (AKP) based on Leo Tolstoy's assertion applied to plant microbiota: 'All healthy microbiota are alike; each disease-associated microbiota is sick in its own way.' We propose the AKP to explain how stochastic processes in plant microbiota assembly due to several external stressors could lead to plant diseases. Finally, we propose the AKP to conceptualize plant dysbioses as a transitory loss of host capacity to regulate its microbiota, implying a loss of function that leads to a reduction of the host's fitness.

A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production

The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.

Fungal Endophytes to Combat Biotic and Abiotic Stresses for Climate-Smart and Sustainable Agriculture

The agricultural sustainability concept considers higher food production combating biotic and abiotic stresses, socio-economic well-being, and environmental conservation. On the contrary, global warming-led climatic changes have appalling consequences on agriculture, generating shifting rainfall patterns, high temperature, CO2, drought, etc., prompting abiotic stress conditions for plants. Such stresses abandon the plants to thrive, demoting food productivity and ultimately hampering food security. Though environmental issues are natural and cannot be regulated, plants can still be enabled to endure these abnormal abiotic conditions, reinforcing the stress resilience in an eco-friendly fashion by incorporating fungal endophytes. Endophytic fungi are a group of subtle, non-pathogenic microorganisms establishing a mutualistic association with diverse plant species. Their varied association with the host plant under dynamic environments boosts the endogenic tolerance mechanism of the host plant against various stresses via overall modulations of local and systemic mechanisms accompanied by higher antioxidants secretion, ample enough to scavenge Reactive Oxygen Species (ROS) hence, coping over-expression of defensive redox regulatory system of host plant as an aversion to stressed condition. They are also reported to ameliorate plants toward biotic stress mitigation and elevate phytohormone levels forging them worthy enough to be used as biocontrol agents and as biofertilizers against various pathogens, promoting crop improvement and soil improvement, respectively. This review summarizes the present-day conception of the endophytic fungi, their diversity in various crops, and the molecular mechanism behind abiotic and biotic resistance prompting climate-resilient aided sustainable agriculture.

Cross-inoculation of rhizobiome from a congeneric ruderal plant imparts drought tolerance in maize (Zea mays) through changes in root morphology and proteome

Rhizobiome confer stress tolerance to ruderal plants, yet their ability to alleviate stress in crops is widely debated, and the associated mechanisms are poorly understood. We monitored the drought tolerance of maize (Zea mays) as influenced by the cross-inoculation of rhizobiota from a congeneric ruderal grass Andropogon virginicus (andropogon-inoculum), and rhizobiota from organic farm maintained under mesic condition (organic-inoculum). Across drought treatments (40% field capacity), maize that received andropogon-inoculum produced two-fold greater biomass. This drought tolerance translated to a similar leaf metabolomic composition as that of the well-watered control (80% field capacity) and reduced oxidative damage, despite a lower activity of antioxidant enzymes. At a morphological-level, drought tolerance was associated with an increase in specific root length and surface area facilitated by the homeostasis of phytohormones promoting root branching. At a proteome-level, the drought tolerance was associated with upregulation of proteins related to glutathione metabolism and endoplasmic reticulum-associated degradation process. Fungal taxa belonging to Ascomycota, Mortierellomycota, Archaeorhizomycetes, Dothideomycetes, and Agaricomycetes in andropogon-inoculum were identified as potential indicators of drought tolerance. Our study provides a mechanistic understanding of the rhizobiome-facilitated drought tolerance and demonstrates a better path to utilize plant-rhizobiome associations to enhance drought tolerance in crops.

Current Studies of the Effects of Drought Stress on Root Exudates and Rhizosphere Microbiomes of Crop Plant Species

With the warming global climate, drought stress is considered to be the most important abiotic factor limiting plant growth and yield in the world. Drought stress has serious impacts on crop production. Many researchers have studied the influences of drought stress on crop production and plant physiology; however, few researchers have combined root exudates with root-associated microbiomes for their mutual effects under drought conditions. In this review, we systematically illustrate the impact of drought stress on root exudates and root-associated microbiomes, and then we discuss the mutual regulation of root-associated microbiomes and the host plant in helping the plant adapt to drought. Finally, we construct a framework for the mutual connections between the plant, root exudates, and the microbiome. We hope this review can provide some significant guidelines to promote the study of drought resistance in plants in association with the rhizosphere microbiota.

OUP accepted manuscript

Strigolactones are endogenous plant hormones regulating plant development and are exuded into the rhizosphere when plants experience nutrient deficiency. There, they promote the mutualistic association of plants with arbuscular mycorrhizal fungi that help the plant with the uptake of nutrients from the soil. This shows that plants actively establish—through the exudation of strigolactones—mutualistic interactions with microbes to overcome inadequate nutrition. The signaling function of strigolactones could possibly extend to other microbial partners, but the effect of strigolactones on the global root and rhizosphere microbiome remains poorly understood. Therefore, we analyzed the bacterial and fungal microbial communities of 16 rice genotypes differing in their root strigolactone exudation. Using multivariate analyses, distinctive differences in the microbiome composition were uncovered depending on strigolactone exudation. Moreover, the results of regression modeling showed that structural differences in the exuded strigolactones affected different sets of microbes. In particular, orobanchol was linked to the relative abundance of Burkholderia–Caballeronia–Paraburkholderia and Acidobacteria that potentially solubilize phosphate, while 4-deoxyorobanchol was associated with the genera Dyella and Umbelopsis. With this research, we provide new insight into the role of strigolactones in the interplay between plants and microbes in the rhizosphere.

Drought Sensitivity of Sugarcane Cultivars Shapes Rhizosphere Bacterial Community Patterns in Response to Water Stress

Rhizosphere bacteria, the main functional microorganisms inhabiting the roots of terrestrial plants, play important roles in regulating plant growth and environmental stress resistance. However, limited information is available regarding changes occurring within the structure of the root microbial community and the response mechanisms of host plants that improve adaptability to drought stress. In this study, we conducted an experiment on two sugarcane varieties with different drought tolerance levels under drought and control treatments and analyzed the rhizosphere bacterial communities using 16S rRNA high-throughput sequencing. Correlation analysis results clarified the influence of various factors on the rhizosphere bacterial community structure. Drought stress reduced the diversity of the bacterial community in the rhizosphere of sugarcane. Interestingly, the bacterial community of the drought-sensitive sugarcane cultivar GT39 changed more than that of the drought-tolerant cultivar ZZ9. In addition, ZZ9 had a high abundance of drought-resistant bacteria in the rhizosphere under optimal soil water conditions, whereas GT39 accumulated a large number of drought-resistant bacteria only under drought stress. GT39 mainly relied on Actinobacteria in its response to drought stress, and the abundance of this phylum was positively correlated with soil acid phosphatase and protease levels. In contrast, ZZ9 mainly relied on Bacilli in its response to drought stress, and the abundance of this class was positively correlated with only soil acid phosphatase levels. In conclusion, drought stress can significantly reduce the bacterial diversity and increase the abundance of drought-resistant bacteria in the sugarcane rhizosphere. The high abundance of drought-resistant bacteria in the rhizosphere of drought-tolerant cultivars under non-drought conditions is an important factor contributing to the high drought adaptability of these cultivars. Moreover, the core drought-resistant bacteria of the sugarcane rhizosphere and root exudates jointly affect the resistance of sugarcane to drought.

The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications

Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.

Log-ratio analysis of microbiome data with many zeroes is library size dependent

Microbiome composition data collected through amplicon sequencing are count data on taxa in which the total count per sample (the library size) is an artefact of the sequencing platform, and as a result, such data are compositional. To avoid library size dependency, one common way of analysing multivariate compositional data is to perform a principal component analysis (PCA) on data transformed with the centred log‐ratio, hereafter called a log‐ratio PCA. Two aspects typical of amplicon sequencing data are the large differences in library size and the large number of zeroes. In this study, we show on real data and by simulation that, applied to data that combine these two aspects, log‐ratio PCA is nevertheless heavily dependent on the library size. This leads to a reduction in power when testing against any explanatory variable in log‐ratio redundancy analysis. If there is additionally a correlation between the library size and the explanatory variable, then the type 1 error becomes inflated. We explore putative solutions to this problem.

Quantifying Nutrient Trade in the Arbuscular Mycorrhizal Symbiosis Under Extreme Weather Events Using Quantum-Dot Tagged Phosphorus

Given the current trends in climate change, extreme weather events are expected to increase in strength and frequency. Such events can impact species survival and species interactions. One of the most ubiquitous symbioses on earth is the nutrient exchange partnership between arbuscular mycorrhizal fungi and their host plants. While past work has shown that mycorrhizal fungi can help alleviate stress, it is unknown how phosphorus uptake by plants to fungi is affected by extreme weather events, such as flooding and heat waves. To test this response, we grewMedicago truncatulahost plants with or without mycorrhizal fungi and then exposed them to extreme weather treatments: increasing soil temperature by 12°C, or by flooding the plant roots for 7 days. We measured plant and fungal performance, and quantified phosphorus (P) uptake before and after extreme weather treatments using a technique in which we tagged apatite, a form of rock phosphorus, with fluorescing quantum-dots (QDs) nanoparticles. We then measured fluorescence in root and shoot tissue at harvest. We found that plants and arbuscular mycorrhizal fungi were affected by soil flooding, with plant survival, fungal colonization and QD-apatite uptake decreasing under flooded conditions. We did not see these negative effects in the heat treatment. While the presence of arbuscular mycorrhizal fungi affected plant biomass allocation, leading to an increase in shoot biomass, the symbiosis did not increase plant survival, total biomass or QD uptake in either treatment. More generally, we found host tissue contained roughly 80% more QD-apatite from the pre-treatment compared to the post-treatment nutrient injection. Future studies should focus on various plant-fungal combinations to create databases on which predictive models to extreme weather events can be constructed.

Environmental adaptation of the root microbiome in two rice ecotypes

The root microbiome plays a key role that can influence host plant growth and abiotic stress. While there has been extensive characterization of community structure, spatial compartmentalization, and the impact of drought stresses on the root microbiome in rice and other plants, there is relatively little known about the differences in root microbiome among rice ecotypes in natural upland and lowland fields. Herein, we used two rice ecotypes, upland and irrigated ecotype rice (two Indica and two Japonica genotypes), as a model to explore the responses of the root microbiome under different environmental conditions. We aimed to identify environment-induced adaptation in the root bacterial and fungal composition of rice ecotypes by high-throughput sequencing. Rice from lowland field or upland had significantly altered overall bacterial and fungal community compositions of the two ecotypes, with diversity of both ecotypes greatly decreased from lowland field to upland. The overall response of the root microbiome to upland conditions was taxonomically driven by the enrichment of family Enterobacteriaceae and genera Serratia, and phylum Ascomycota. Interestingly, rice ecotypes specifically enriched root microbes when they were transferred from their original environment, such as the enrichment of class Thermoleophilia and phylum Actinobacteria when the irrigated ecotype rice was moved from lowland to upland field. These results revealed that different environmental conditions and rice ecotypes resulted in a restructuring of root microbiome communities, and suggested the possibility that components responsible for the beneficial attributes in the altered root microbiome might contribute to the adaptation of different ecotypes in natural fields.

Gigaspora margarita and Its Endobacterium Modulate Symbiotic Marker Genes in Tomato Roots under Combined Water and Nutrient Stress

As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF) may be effective in enhancing plant resilience to drought, one of the major limiting factors threatening crop productivity. AMF host their own microbiota and previous data demonstrated that endobacteria thriving in Gigaspora margarita modulate fungal antioxidant responses. Here, we used the G. margarita-Candidatus Glomeribacter gigasporarum system to test whether the tripartite interaction between tomato, G. margarita and its endobacteria may improve plant resilience to combined water/nutrient stress. Tomato plants were inoculated with spores containing endobacteria (B+) or not (B-), and exposed to combined water/nutrient stress. Plants traits, AM colonization and expression of AM marker genes were measured. Results showed that mycorrhizal frequency was low and no growth effect was observed. Under control conditions, B+ inoculated plants were more responsive to the symbiosis, as they showed an up-regulation of three AM marker genes involved in phosphate and lipids metabolism compared with B- inoculated or not-inoculated plants. When combined stress was imposed, the difference between fungal strains was still evident for one marker gene. These results indicate that the fungal endobacteria finely modulate plant metabolism, even in the absence of growth response.

Plant Hosts Modify Belowground Microbial Community Response to Extreme Drought

Climate change causes significant alterations in precipitation and temperature regimes that are predicted to become more extreme throughout the next century. Microorganisms are important members within ecosystems, and how they respond to these changing abiotic stressors has large implications for the functioning of ecosystems, the recycling of nutrients, and the health of the aboveground plant community. Drought stress negatively impacts microbial activity, but the magnitude of this stress response may be dependent on above- and belowground interactions. This study demonstrates that beneficial associations between plants and microbes can enhance tolerance to abiotic stress.

Drought stress negatively impacts microbial activity, but the magnitude of stress responses is likely dependent on a diversity of belowground interactions. Populus trichocarpa individuals and no-plant bulk soils were exposed to extended drought (∼0.03% gravimetric water content [GWC] after 12 days), rewet, and a 12-day “recovery” period to determine the effects of plant presence in mediating soil microbiome stability to water stress. Plant metabolomic analyses indicated that drought exposure increased host investment in C and N metabolic pathways (amino acids, fatty acids, phenolic glycosides) regardless of recovery. Several metabolites positively correlated with root-associated microbial alpha-diversity, but not those of soil communities. Soil bacterial community composition shifted with P. trichocarpa presence and with drought relative to irrigated controls, whereas soil fungal composition shifted only with plant presence. However, root fungal communities strongly shifted with drought, whereas root bacterial communities changed to a lesser degree. The proportion of bacterial water-stress opportunistic operational taxonomic units (OTUs) (enriched counts in drought) was high (∼11%) at the end of drying phases and maintained after rewet and recovery phases in bulk soils, but it declined over time in soils with plants present. For root fungi, opportunistic OTUs were high at the end of recovery in drought treatments (∼17% abundance), although relatively not responsive in soils, particularly planted soils (<0.5% abundance for sensitive or opportunistic). These data indicate that plants modulate soil and root-associated microbial drought responses via tight plant-microbe linkages during extreme drought scenarios, but trajectories after extreme drought vary with plant habitat and microbial functional groups.

IMPORTANCE Climate change causes significant alterations in precipitation and temperature regimes that are predicted to become more extreme throughout the next century. Microorganisms are important members within ecosystems, and how they respond to these changing abiotic stressors has large implications for the functioning of ecosystems, the recycling of nutrients, and the health of the aboveground plant community. Drought stress negatively impacts microbial activity, but the magnitude of this stress response may be dependent on above- and belowground interactions. This study demonstrates that beneficial associations between plants and microbes can enhance tolerance to abiotic stress.