Changes in root-exudate-induced respiration reveal a novel mechanism through which drought affects ecosystem carbon cycling

Pisolithus microcarpus isolates with contrasting abilities to colonise Eucalyptus grandis exhibit significant differences in metabolic signalling

Biotic factors in fungal exudates impact plant-fungal symbioses establishment. Mutualistic ectomycorrhizal fungi play various ecological roles in forest soils by interacting with trees. Despite progress in understanding secreted fungal signals, dynamics of signal production in situ before or during direct host root contact remain unclear. We need to better understand how variability in intra-species fungal signaling at these stages impacts symbiosis with host tissues. Using the ECM model Pisolithus microcarpus, we selected two isolates (Si9 and Si14) with different abilities to colonize Eucalyptus grandis roots. Hypothesizing that distinct early signalling and metabolite profiles between these isolates would influence colonization and symbiosis, we used microdialysis to non-destructively collect secreted metabolites from either the fungus, host, or both, capturing the dynamic interplay of pre-symbiotic signalling over 48 hours. Our findings revealed significant differences in metabolite profiles between Si9 and Si14, grown alone or with a host root. Si9, with lower colonization efficiency than Si14, secreted a more diverse range of compounds, including lipids, oligopeptides, and carboxylic acids. In contrast, Si14's secretions, similar to the host's, included more aminoglycosides. This study emphasizes the importance of intra-specific metabolomic diversity in ectomycorrhizal fungi, suggesting that early metabolite secretion is crucial for establishing successful mutualistic relationships.

A state-of-the-art review of environmental behavior and potential risks of biodegradable microplastics in soil ecosystems: Comparison with conventional microplastics

As the use of biodegradable plastics becomes increasingly widespread, their environmental behaviors and impacts warrant attention. Unlike conventional plastics, their degradability predisposes them to fragment into microplastics (MPs) more readily. These MPs subsequently enter the terrestrial environment. The abundant functional groups of biodegradable MPs significantly affect their transport and interactions with other contaminants (e.g., organic contaminants and heavy metals). The intermediates and additives released from depolymerization of biodegradable MPs, as well as coexisting contaminants, induce alterations in soil ecosystems. These processes indicate that the impacts of biodegradable MPs on soil ecosystems might significantly diverge from conventional MPs. However, an exhaustive and timely comparison of the environmental behaviors and effects of biodegradable and conventional MPs within soil ecosystems remains scarce. To address this gap, the Web of Science database and bibliometric software were utilized to identify publications with keywords containing biodegradable MPs and soil. Moreover, this review comprehensively summarizes the transport behavior of biodegradable MPs, their role as contaminant carriers, and the potential risks they pose to soil physicochemical properties, nutrient cycling, biota, and CO2 emissions as compared with conventional MPs. Biodegradable MPs, due to their great transport and adsorption capacity, facilitate the mobility of coexisting contaminants, potentially inducing widespread soil and groundwater contamination. Additionally, these MPs and their depolymerization products can disrupt soil ecosystems by altering physicochemical properties, increasing microbial biomass, decreasing microbial diversity, inhibiting the development of plants and animals, and increasing CO2 emissions. Finally, some perspectives are proposed to outline future research directions. Overall, this study emphasizes the pronounced effects of biodegradable MPs on soil ecosystems relative to their conventional counterparts and contributes to the understanding and management of biodegradable plastic contamination within the terrestrial ecosystem.

Dry season irrigation promotes nutrient cycling by reorganizing Eucalyptus rhizosphere microbiome

In southern China, seasonal droughts and low soil phosphorus content constrain the productivity of Eucalyptus trees. To understand the rhizosphere microbiome response to the dry season, metagenomic sequencing analysis was used to investigate the 6-year-old Eucalyptus rhizosphere microbiome under four different irrigation and fertilization treatments. The results showed that irrigation and fertilization during the dry season significantly altered the composition of microbiome in the rhizosphere soil of Eucalyptus plantations. The soil physicochemical properties and enzyme activity explained 30.73 % and 29.75 % of the changes in bacterial and fungal community structure in Eucalyptus rhizosphere soil, respectively. Irrigation and fertilization during the dry season significantly altered the physicochemical properties of rhizosphere soil. Compared with the seasonal drought without fertilizer treatment (CK), the dry season irrigation with fertilizer treatment (WF) significantly increased the content of total nitrogen (46.34 %), available nitrogen (37.72 %), available phosphorus (440.9 %), and organic matter (35.34 %). Soil organic matter (OM), pH, and available phosphorus (AP) were key environmental factors influencing the microbial community composition. Moreover, irrigation and fertilization promoted carbon fixation and nitrogen and phosphorus mineralization, increasing soil OM content and the availability of inorganic nitrogen and phosphorus. Meanwhile, compared to the CK, the increase of acid phosphatase (16.81 %), invertase (146.89 %)and urease (59.45 %) in rhizosphere soil under irrigation (W) treatment further proves that dry season irrigation promote the soil carbon, nitrogen and phosphorus cycles. Irrigation and fertilization treatment alleviated the constraints of low phosphorus in southern China's soil, which promoted Eucalyptus productivity. In conclusion, we suggest implementing reasonable irrigation and fertilization strategies in the production practice of Eucalyptus and utilizing microbial resources to improve soil fertility and Eucalyptus productivity.

Soil depth and physicochemical properties influence microbial dynamics in the rhizosphere of two Peruvian superfood trees, cherimoya and lucuma, as shown by PacBio-HiFi sequencing

The characterization of soil microbial communities at different depths is essential to understand their impact on nutrient availability, soil fertility, plant growth and stress tolerance. We analyzed the microbial community at three depths (3 cm, 12 cm, and 30 cm) in the native fruit trees Annona cherimola (cherimoya) and Pouteria lucuma (lucuma), which provide fruits in vitamins, minerals, and antioxidants. We used PacBio-HiFi, a long-read high-throughput sequencing to explore the composition, diversity and putative functionality of rhizosphere bacterial communities at different soil depths. Bacterial diversity, encompassing various phyla, families, and genera, changed with depth. Notable differences were observed in the alpha diversity indices, especially the Shannon index. Beta diversity also varied based on plant type and depth. In cherimoya soils, positive correlations with Total Organic Carbon (TOC) and Cation Exchange Capacity (CEC) were observed, but negative ones with certain cations. In lucuma soils, indices like the Shannon index exhibited negative correlations with several metals and specific soil properties. We proposed that differences between the plant rhizosphere environments may explain the variance in their microbial diversity. This study provides insights into the microbial communities present at different soil depths, highlighting the prevalence of decomposer bacteria. Further research is necessary to elucidate their specific metabolic features and overall impact on crop growth and quality.

Mechanistic and future prospects in rhizospheric engineering for agricultural contaminants removal, soil health restoration, and management of climate change stress

Climate change, food insecurity, and agricultural pollution are all serious challenges in the twenty-first century, impacting plant growth, soil quality, and food security. Innovative techniques are required to mitigate these negative outcomes. Toxic heavy metals (THMs), organic pollutants (OPs), and emerging contaminants (ECs), as well as other biotic and abiotic stressors, can all affect nutrient availability, plant metabolic pathways, agricultural productivity, and soil-fertility. Comprehending the interactions between root exudates, microorganisms, and modified biochar can aid in the fight against environmental problems such as the accumulation of pollutants and the stressful effects of climate change. Microbes can inhibit THMs uptake, degrade organic pollutants, releases biomolecules that regulate crop development under drought, salinity, pathogenic attack and other stresses. However, these microbial abilities are primarily demonstrated in research facilities rather than in contaminated or stressed habitats. Despite not being a perfect solution, biochar can remove THMs, OPs, and ECs from contaminated areas and reduce the impact of climate change on plants. We hypothesized that combining microorganisms with biochar to address the problems of contaminated soil and climate change stress would be effective in the field. Despite the fact that root exudates have the potential to attract selected microorganisms and biochar, there has been little attention paid to these areas, considering that this work addresses a critical knowledge gap of rhizospheric engineering mediated root exudates to foster microbial and biochar adaptation. Reducing the detrimental impacts of THMs, OPs, ECs, as well as abiotic and biotic stress, requires identifying the best root-associated microbes and biochar adaptation mechanisms.

Salt marsh nitrogen cycling: where land meets sea

Salt marshes sit at the terrestrial-aquatic interface of oceans around the world. Unique features of salt marshes that differentiate them from their upland or offshore counterparts include high rates of primary production from vascular plants and saturated saline soils that lead to sharp redox gradients and a diversity of electron acceptors and donors. Moreover, the dynamic nature of root oxygen loss and tidal forcing leads to unique biogeochemical conditions that promote nitrogen cycling. Here, we highlight recent advances in our understanding of key nitrogen cycling processes in salt marshes and discuss areas where additional research is needed to better predict how salt marsh N cycling will respond to future environmental change.

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.

Optimizing irrigation and nitrogen addition to balance grassland biomass production with greenhouse gas emissions: A mesocosm study

Achieving a balance between greenhouse gas mitigation and biomass production in grasslands necessitates optimizing irrigation frequency and nitrogen addition, which significantly influence grassland productivity and soil nitrous oxide emissions, and consequently impact the ecosystem carbon dioxide exchange. This study aimed to elucidate these influences using a controlled mesocosm experiment where bermudagrass (Cynodon dactylon L.) was cultivated under varied irrigation frequencies (daily and every 6 days) with (100 kg ha-1) or without nitrogen addition; measurements of net ecosystem carbon dioxide exchange, ecosystem respiration, soil respiration, and nitrous oxide emissions across two cutting events were performed as well. The findings revealed a critical interaction between water-filled pore space, regulated by irrigation, and nitrogen availability, with the latter exerting a more substantial influence on aboveground biomass growth and ecosystem carbon dioxide exchange than water availability. Moreover, the total dry matter was significantly higher with nitrogen addition compared to without nitrogen addition, irrespective of the irrigation frequency. In contrast, soil nitrous oxide emissions were observed to be significantly higher with increased irrigation frequency and nitrogen addition. The effects of nitrogen addition on soil respiration components appeared to depend on water availability, with autotrophic respiration seeing a significant rise with nitrogen addition under limited irrigation (5.4 ± 0.6 μmol m-2 s-1). Interestingly, the lower irrigation frequency did not result in water stress, suggesting resilience in bermudagrass. These findings highlight the importance of considering interactions between irrigation and nitrogen addition to optimize water and nitrogen input in grasslands for a synergistic balance between grassland biomass production and greenhouse gas emission mitigation.

Synergistic effects of plant genotype and soil microbiome on growth in Lotus japonicus

The biological interactions between plants and their root microbiomes are essential for plant growth, and even though plant genotype (G), soil microbiome (M), and growth conditions (environment; E) are the core factors shaping root microbiome, their relationships remain unclear. In this study, we investigated the effects of G, M, and E and their interactions on the Lotus root microbiome and plant growth using an in vitro cross-inoculation approach, which reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. Results suggested that a large proportion of the root microbiome composition is determined by M and E, while G-related (G, G × M, and G × E) effects were significant but small. In contrast, the interaction between G and M had a more pronounced effect on plant shoot growth than M alone. Our findings also indicated that most microbiome variations controlled by M have little effect on plant phenotypes, whereas G × M interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention to optimize crop yield and resilience.

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.

Rhizosheath drought responsiveness is variety-specific and a key component of belowground plant adaptation

Biophysicochemical rhizosheath properties play a vital role in plant drought adaptation. However, their integration into the framework of plant drought response is hampered by incomplete mechanistic understanding of their drought responsiveness and unknown linkage to intraspecific plant-soil drought reactions. Thirty-eight Zea mays varieties were grown under well-watered and drought conditions to assess the drought responsiveness of rhizosheath properties, such as soil aggregation, rhizosheath mass, net-rhizodeposition, and soil organic carbon distribution. Additionally, explanatory traits, including functional plant trait adaptations and changes in soil enzyme activities, were measured. Drought restricted soil structure formation in the rhizosheath and shifted plant-carbon from litter-derived organic matter in macroaggregates to microbially processed compounds in microaggregates. Variety-specific functional trait modifications determined variations in rhizosheath drought responsiveness. Drought responses of the plant-soil system ranged among varieties from maintaining plant-microbial interactions in the rhizosheath through accumulation of rhizodeposits, to preserving rhizosheath soil structure while increasing soil exploration through enhanced root elongation. Drought-induced alterations at the root-soil interface may hold crucial implications for ecosystem resilience in a changing climate. Our findings highlight that rhizosheath soil properties are an intrinsic component of plant drought response, emphasizing the need for a holistic concept of plant-soil systems in future research on plant drought adaptation.

A trait-based framework linking the soil metabolome to plant-soil feedbacks

By modifying the biotic and abiotic properties of the soil, plants create soil legacies that can affect vegetation dynamics through plant-soil feedbacks (PSF). PSF are generally attributed to reciprocal effects of plants and soil biota, but these interactions can also drive changes in the identity, diversity and abundance of soil metabolites, leading to more or less persistent soil chemical legacies whose role in mediating PSF has rarely been considered. These chemical legacies may interact with microbial or nutrient legacies to affect species coexistence. Given the ecological importance of chemical interactions between plants and other organisms, a better understanding of soil chemical legacies is needed in community ecology. In this Viewpoint, we aim to: highlight the importance of belowground chemical interactions for PSF; define and integrate soil chemical legacies into PSF research by clarifying how the soil metabolome can contribute to PSF; discuss how functional traits can help predict these plant-soil interactions; propose an experimental approach to quantify plant responses to the soil solution metabolome; and describe a testable framework relying on root economics and seed dispersal traits to predict how plant species affect the soil metabolome and how they could respond to soil chemical legacies.

Biodegradable PBAT microplastics adversely affect pakchoi (Brassica chinensis L.) growth and the rhizosphere ecology: Focusing on rhizosphere microbial community composition, element metabolic potential, and root exudates

Biodegradable plastics (BPs) have gained increased attention as a promising solution to plastics pollution problem. However, BPs often exhibited limited in situ biodegradation in the soil environment, so they may also release microplastics (MPs) into soils just like conventional non-degradable plastics. Therefore, it is necessary to evaluate the impacts of biodegradable MPs (BMPs) on soil ecosystem. Here, we explored the effects of biodegradable poly(butylene adipate-co-terephthalate) (PBAT) MPs and conventional polyethylene (PE) MPs on soil-plant (pakchoi) system at three doses (0.02 %, 0.2 %, and 2 %, w/w). Results showed that PBAT MPs reduced plant growth in a dose-dependent pattern, while PE MPs exhibited no significant phytotoxicity. High-dose PBAT MPs negatively affected the rhizosphere soil nutrient availability, e.g., decreased available phosphorus and available potassium. Metagenomics analysis revealed that PBAT MPs caused more serious interference with the rhizosphere microbial community composition and function than PE MPs. In particular, compared with PE MPs, PBAT MPs induced greater changes in functional potential of carbon, nitrogen, phosphorus, and sulfur cycles, which may lead to alterations in soil biogeochemical processes and ecological functions. Moreover, untargeted metabolomics showed that PBAT MPs and PE MPs differentially affect plant root exudates. Mantel tests, correlation analysis, and partial least squares path model analysis showed that changes in plant growth and root exudates were significantly correlated with soil properties and rhizosphere microbiome driven by the MPs-rhizosphere interactions. This work improves our knowledge of how biodegradable and conventional non-degradable MPs affect plant growth and the rhizosphere ecology, highlighting that BMPs might pose greater threat to soil ecosystems than non-degradable MPs.

Plant effects on microbiome composition are constrained by environmental conditions in a successional grassland

BACKGROUND

Below-ground microbes mediate key ecosystem processes and play a vital role in plant nutrition and health. Understanding the composition of the belowground microbiome is therefore important for maintaining ecosystem stability. The structure of the belowground microbiome is largely determined by individual plants, but it is not clear how far their influence extends and, conversely, what the influence of other plants growing nearby is.

RESULTS

To determine the extent to which a focal host plant influences its soil and root microbiome when growing in a diverse community, we sampled the belowground bacterial and fungal communities of three plant species across a primary successional grassland sequence. The magnitude of the host effect on its belowground microbiome varied among microbial groups, soil and root habitats, and successional stages characterized by different levels of diversity of plant neighbours. Soil microbial communities were most strongly structured by sampling site and showed significant spatial patterns that were partially driven by soil chemistry. The influence of focal plant on soil microbiome was low but tended to increase with succession and increasing plant diversity. In contrast, root communities, particularly bacterial, were strongly structured by the focal plant species. Importantly, we also detected a significant effect of neighbouring plant community composition on bacteria and fungi associating with roots of the focal plants. The host influence on root microbiome varied across the successional grassland sequence and was highest in the most diverse site.

CONCLUSIONS

Our results show that in a species rich natural grassland, focal plant influence on the belowground microbiome depends on environmental context and is modulated by surrounding plant community. The influence of plant neighbours is particularly pronounced in root communities which may have multiple consequences for plant community productivity and stability, stressing the importance of plant diversity for ecosystem functioning.

Impacts of seasonality, drought, nitrogen fertilization, and litter on soil fluxes of biogenic volatile organic compounds in a Mediterranean forest

Biogenic volatile organic compounds (BVOCs) play critical roles in ecosystems at various scales, influencing above- and below-ground interactions and contributing to the atmospheric environment. Nonetheless, there is a lack of research on soil BVOC fluxes and their response to environmental changes. This study aimed to investigate the impact of drought, nitrogen (N) fertilization, and litter manipulation on soil BVOC fluxes in a Mediterranean forest. We assessed the effects of drought and N fertilization on soil BVOC exchanges and soil CO2 fluxes over two consecutive years using a dynamic chamber method, and solid-phase microextraction was utilized to quantify soil BVOCs in one year. Our findings revealed that the soil acted as an annual net sink for isoprenoids (1.30-10.33 μg m-2 h-1), with the highest uptake rates observed during summers (25.90 ± 9.36 μg m-2 h-1). The increased summer uptake can be attributed to the significant concentration gradient of BVOCs between atmosphere and soil. However, strong seasonal dynamics were observed, as the soil acted as a source of BVOCs in spring and autumn. The uptake rate of isoprenoids exhibited a significant positive correlation with soil temperature and atmospheric isoprenoid concentrations, while displaying a negative correlation with soil moisture and soil CO2 flux. The effects of drought and N fertilization on soil BVOCs were influenced by the type of VOCs, litter layer, and season. Specifically, drought significantly affected the exchange rate and quantities of sesquiterpenes. N fertilization led to increased emissions of specific BVOCs (α-pinene and camphene) due to the stimulation of litter emissions. These findings underscore the importance of the soil as a sink for atmospheric BVOCs in this dry Mediterranean ecosystem. Future drought conditions may significantly impact soil water content, resulting in drier soils throughout the year, which will profoundly affect the exchange of soil BVOCs between the soil and atmosphere.

Deciphering microbiomes dozens of meters under our feet and their edaphoclimatic and spatial drivers

Microbes inhabiting deep soil layers are known to be different from their counterpart in topsoil yet remain under investigation in terms of their structure, function, and how their diversity is shaped. The microbiome of deep soils (>1 m) is expected to be relatively stable and highly independent from climatic conditions. Much less is known, however, on how these microbial communities vary along climate gradients. Here, we used amplicon sequencing to investigate bacteria, archaea, and fungi along fifteen 18-m depth profiles at 20-50-cm intervals across contrasting aridity conditions in semi-arid forest ecosystems of China's Loess Plateau. Our results showed that bacterial and fungal α diversity and bacterial and archaeal community similarity declined dramatically in topsoil and remained relatively stable in deep soil. Nevertheless, deep soil microbiome still showed the functional potential of N cycling, plant-derived organic matter degradation, resource exchange, and water coordination. The deep soil microbiome had closer taxa-taxa and bacteria-fungi associations and more influence of dispersal limitation than topsoil microbiome. Geographic distance was more influential in deep soil bacteria and archaea than in topsoil. We further showed that aridity was negatively correlated with deep-soil archaeal and fungal richness, archaeal community similarity, relative abundance of plant saprotroph, and bacteria-fungi associations, but increased the relative abundance of aerobic ammonia oxidation, manganese oxidation, and arbuscular mycorrhizal in the deep soils. Root depth, complexity, soil volumetric moisture, and clay play bridging roles in the indirect effects of aridity on microbes in deep soils. Our work indicates that, even microbial communities and nutrient cycling in deep soil are susceptible to changes in water availability, with consequences for understanding the sustainability of dryland ecosystems and the whole-soil in response to aridification. Moreover, we propose that neglecting soil depth may underestimate the role of soil moisture in dryland ecosystems under future climate scenarios.

Biochar Enhances the Resistance of Legumes and Soil Microbes to Extreme Short-Term Drought

Short-term drought events occur more frequently and more intensively under global climate change. Biochar amendment has been documented to ameliorate the negative effects of water deficits on plant performance. Moreover, biochar can alter the soil microbial community, soil properties and soil metabolome, resulting in changes in soil functioning. We aim to reveal the extent of biochar addition on soil nutrients and the soil microbial community structure and how this improves the tolerance of legume crops (peanuts) to short-term extreme drought. We measured plant performances under different contents of biochar, set as a gradient of 2%, 3% and 4%, after an extreme experimental drought. In addition, we investigated how soil bacteria and fungi respond to biochar additions and how the soil metabolome changes in response to biochar amendments, with combined growth experiments, high-throughput sequencing and soil omics. The results indicated that biochar increased nitrites and available phosphorus. Biochar was found to influence the soil bacterial community structure more intensively than the soil fungal community. Additionally, the fungal community showed a higher randomness under biochar addition when experiencing short-term extreme drought compared to the bacterial community. Soil bacteria may be more strongly related to soil nutrient cycling in peanut agricultural systems. Although the soil metabolome has been documented to be influenced by biochar addition independent of soil moisture, we found more differential metabolites with a higher biochar content. We suggest that biochar enhances the resistance of plants and soil microbes to short-term extreme drought by indirectly modifying soil functioning probably due to direct changes in soil moisture and soil pH.

Unveiling changes in rhizosphere-associated bacteria linked to the genotype and water stress in quinoa

Drought is among the main abiotic factors causing agronomical losses worldwide. To minimize its impact, several strategies have been proposed, including the use of plant growth-promoting bacteria (PGPBs), as they have demonstrated roles in counteracting abiotic stress. This aspect has been little explored in emergent crops such as quinoa, which has the potential to contribute to reducing food insecurity. Thus, here we hypothesize that the genotype, water environment and the type of inoculant are determining factors in shaping quinoa rhizosphere bacterial communities, affecting plant performance. To address this, two different quinoa cultivars (with contrasting water stress tolerance), two water conditions (optimal and limiting water conditions) and different soil infusions were used to define the relevance of these factors. Different bacterial families that vary among genotypes and water conditions were identified. Certain families were enriched under water stress conditions, such as the Nocardioidaceae, highly present in the water-sensitive cultivar F15, or the Pseudomonadaceae, Burkholderiaceae and Sphingomonadaceae, more abundant in the tolerant cultivar F16, which also showed larger total polyphenol content. These changes demonstrate that the genotype and environment highly contribute to shaping the root-inhabiting bacteria in quinoa, and they suggest that this plant species is a great source of PGPBs for utilization under water-liming conditions.

A Dual Transcriptomic Approach Reveals Contrasting Patterns of Differential Gene Expression During Drought in Arbuscular Mycorrhizal Fungus and Carrot

While arbuscular mycorrhizal (AM) fungi are known for providing host plants with improved drought tolerance, we know very little about the fungal response to drought in the context of the fungal-plant relationship. In this study, we evaluated the drought responses of the host and symbiont, using the fungus Rhizophagus irregularis with carrot (Daucus carota) as a plant model. Carrots inoculated with spores of R. irregularis DAOM 197198 were grown in a greenhouse. During taproot development, carrots were exposed to a 10-day water restriction. Compared with well-watered conditions, drought caused diminished photosynthetic activity and reduced plant growth in carrot with and without AM fungi. Droughted carrots had lower root colonization. For R. irregularis, 93% of 826 differentially expressed genes (DEGs) were upregulated during drought, including phosphate transporters, several predicted transport proteins of potassium, and the aquaporin RiAQPF2. In contrast, 78% of 2,486 DEGs in AM carrot were downregulated during drought, including the symbiosis-specific genes FatM, RAM2, and STR, which are implicated in lipid transfer from the host to the fungus and were upregulated exclusively in AM carrot during well-watered conditions. Overall, this study provides insight into the drought response of an AM fungus in relation to its host; the expression of genes related to symbiosis and nutrient exchange were downregulated in carrot but upregulated in the fungus. This study reveals that carrot and R. irregularis exhibit contrast in their regulation of gene expression during drought, with carrot reducing its apparent investment in symbiosis and the fungus increasing its apparent symbiotic efforts. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants

Plant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant-mediated processes, such as root exudation, influence soil organic matter turnover in the rhizosphere is essential. In this study, we used 16S rRNA gene amplicon sequencing, rhizosphere metabolomics, and position-specific 13C-pyruvate labeling to examine the effects of three different plant species (Piper auritum, Hibiscus rosa sinensis, and Clitoria fairchildiana) and their associated microbial communities on soil organic carbon turnover in the rhizosphere. Our findings indicate that in these tropical plants, the rhizosphere metabolome is primarily shaped by the response of roots to drought rather than direct shifts in the rhizosphere bacterial community composition. Specifically, the reduced exudation of plant roots had a notable effect on the metabolome of the rhizosphere of P. auritum, with less reliance on neighboring microbes. Contrary to P. auritum, H. rosa sinensis and C. fairchildiana experienced changes in their exudate composition during drought, causing alterations to the bacterial communities in the rhizosphere. This, in turn, had a collective impact on the rhizosphere's metabolome. Furthermore, the exclusion of phylogenetically distant microbes from the rhizosphere led to shifts in its metabolome. Additionally, C. fairchildiana appeared to be associated with only a subset of symbiotic bacteria under drought conditions. These results indicate that plant species-specific microbial interactions systematically change with the root metabolome. As roots respond to drought, their associated microbial communities adapt, potentially reinforcing the drought tolerance strategies of plant roots. These findings have significant implications for maintaining plant health and preference during drought stress and improving plant performance under climate change.

Agricultural tillage practice and rhizosphere selection interactively drive the improvement of soybean plant biomass

Rhizosphere microbes play key roles in plant growth and productivity in agricultural systems. One of the critical issues is revealing the interaction of agricultural management (M) and rhizosphere selection effects (R) on soil microbial communities, root exudates and plant productivity. Through a field management experiment, we found that bacteria were more sensitive to the M × R interaction effect than fungi, and the positive effect of rhizosphere bacterial diversity on plant biomass existed in the bacterial three two-tillage system. In addition, inoculation experiments demonstrated that the nitrogen cycle-related isolate Stenotrophomonas could promote plant growth and alter the activities of extracellular enzymes N-acetyl- d-glucosaminidase and leucine aminopeptidase in rhizosphere soil. Microbe-metabolites network analysis revealed that hubnodes Burkholderia-Caballeronia-Paraburkholderia and Pseudomonas were recruited by specific root metabolites under the M × R interaction effect, and the inoculation of 10 rhizosphere-matched isolates further proved that these microbes could promote the growth of soybean seedlings. Kyoto Encyclopaedia of Genes and Genomes pathway analysis indicated that the growth-promoting mechanisms of these beneficial genera were closely related to metabolic pathways such as amino acid metabolism, melatonin biosynthesis, aerobactin biosynthesis and so on. This study provides field observation and experimental evidence to reveal the close relationship between beneficial rhizosphere microbes and plant productivity under the M × R interaction effect.

Severe Prolonged Drought Favours Stress-Tolerant Microbes in Australian Drylands

Drylands comprise one-third of Earth's terrestrial surface area and support over two billion people. Most drylands are projected to experience altered rainfall regimes, including changes in total amounts and fewer but larger rainfall events interspersed by longer periods without rain. This transition will have ecosystem-wide impacts but the long-term effects on microbial communities remain poorly quantified. We assessed belowground effects of altered rainfall regimes (+ 65% and -65% relative to ambient) at six sites in arid and semi-arid Australia over a period of three years (2016-2019) coinciding with a significant natural drought event (2017-2019). Microbial communities differed significantly among semi-arid and arid sites and across years associated with variation in abiotic factors, such as pH and carbon content, along with rainfall. Rainfall treatments induced shifts in microbial community composition only at a subset of the sites (Milparinka and Quilpie). However, differential abundance analyses revealed that several taxa, including Acidobacteria, TM7, Gemmatimonadates and Chytridiomycota, were more abundant in the wettest year (2016) and that their relative abundance decreased in drier years. By contrast, the relative abundance of oligotrophic taxa such as Actinobacteria, Alpha-proteobacteria, Planctomycetes, and Ascomycota and Basidiomycota, increased during the prolonged drought. Interestingly, fungi were shown to be more sensitive to the prolonged drought and to rainfall treatment than bacteria with Basidiomycota mostly dominant in the reduced rainfall treatment. Moreover, correlation network analyses showed more positive associations among stress-tolerant dominant taxa following the drought (i.e., 2019 compared with 2016). Our result indicates that such stress-tolerant taxa play an important role in how whole communities respond to changes in aridity. Such knowledge provides a better understanding of microbial responses to predicted increases in rainfall variability and the impact on the functioning of semi-arid and arid ecosystems.

Does genotypic diversity of Hydrocotyle vulgaris affect CO2 and CH4 fluxes?

Biodiversity plays important roles in ecosystem functions and genetic diversity is a key component of biodiversity. While effects of genetic diversity on ecosystem functions have been extensively documented, no study has tested how genetic diversity of plants influences greenhouse gas fluxes from plant-soil systems. We assembled experimental populations consisting of 1, 4 or 8 genotypes of the clonal plant Hydrocotyle vulgaris in microcosms, and measured fluxes of CO2 and CH4 from the microcosms. The fluxes of CO2 and CO2 equivalent from the microcosms with the 1-genotype populations of H. vulgaris were significantly lower than those with the 4- and 8-genotype populations, and such an effect increased significantly with increasing the growth period. The cumulative CO2 flux was significantly negatively related to the growth of the H. vulgaris populations. However, genotypic diversity did not significantly affect the flux of CH4. We conclude that genotypic diversity of plant populations can influence CO2 flux from plant-soil systems. The findings highlight the importance of genetic diversity in regulating greenhouse gas fluxes.

Arctic rooting depth distribution influences modelled carbon emissions but cannot be inferred from aboveground vegetation type

The distribution of roots throughout the soil drives depth-dependent plant-soil interactions and ecosystem processes, particularly in arctic tundra where plant biomass, is predominantly belowground. Vegetation is usually classified from aboveground, but it is unclear whether such classifications are suitable to estimate belowground attributes and their consequences, such as rooting depth distribution and its influence on carbon cycling. We performed a meta-analysis of 55 published arctic rooting depth profiles, testing for differences both between distributions based on aboveground vegetation types (Graminoid, Wetland, Erect-shrub, and Prostrate-shrub tundra) and between 'Root Profile Types' for which we defined three representative and contrasting clusters. We further analyzed potential impacts of these different rooting depth distributions on rhizosphere priming-induced carbon losses from tundra soils. Rooting depth distribution hardly differed between aboveground vegetation types but varied between Root Profile Types. Accordingly, modelled priming-induced carbon emissions were similar between aboveground vegetation types when they were applied to the entire tundra, but ranged from 7.2 to 17.6 Pg C cumulative emissions until 2100 between individual Root Profile Types. Variations in rooting depth distribution are important for the circumpolar tundra carbon-climate feedback but can currently not be inferred adequately from aboveground vegetation type classifications.

Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions

Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO2 levels). For this purpose, we combined 18O-water vapor equilibration with quantitative stable isotope probing (termed 'vapor-qSIP') to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO2) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.

Effects of Climate Change on Soil Organic Matter C and H Isotope Composition in a Mediterranean Savannah (Dehesa): An Assessment Using Py-CSIA

Dehesas are Mediterranean agro-sylvo-pastoral systems sensitive to climate change. Extreme climate conditions forecasted for Mediterranean areas may change soil C turnover, which is of relevance for soil biogeochemistry modeling. The effect of climate change on soil organic matter (SOM) is investigated in a field experiment mimicking environmental conditions of global change scenarios (soil temperature increase, +2-3 °C, W; rainfall exclusion, 30%, D; a combination of both, W+D). Pyrolysis-compound-specific isotope analysis (Py-CSIA) is used for C and H isotope characterization of SOM compounds and to forecast trends exerted by the induced climate shift. After 2.5 years, significant δ13C and δ2H isotopic enrichments were detected. Observed short- and mid-chain n-alkane δ13C shifts point to an increased microbial SOM reworking in the W treatment; a 2H enrichment of up to 40‰ of lignin methoxyphenols was found when combining W+D treatments under the tree canopy, probably related to H fractionation due to increased soil water evapotranspiration. Our findings indicate that the effect of the tree canopy drives SOM dynamics in dehesas and that, in the short term, foreseen climate change scenarios will exert changes in the SOM dynamics comprising the biogeochemical C and H cycles.

Progressive drought alters the root exudate metabolome and differentially activates metabolic pathways in cotton (Gossypium hirsutum)

Root exudates comprise various primary and secondary metabolites that are responsive to plant stressors, including drought. As increasing drought episodes are predicted with climate change, identifying shifts in the metabolome profile of drought-induced root exudation is necessary to understand the molecular interactions that govern the relationships between plants, microbiomes, and the environment, which will ultimately aid in developing strategies for sustainable agriculture management. This study utilized an aeroponic system to simulate progressive drought and recovery while non-destructively collecting cotton (Gossypium hirsutum) root exudates. The molecular composition of the collected root exudates was characterized by untargeted metabolomics using Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) and mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Over 700 unique drought-induced metabolites were identified throughout the water-deficit phase. Potential KEGG pathways and KEGG modules associated with the biosynthesis of flavonoid compounds, plant hormones (abscisic acid and jasmonic acid), and other secondary metabolites were highly induced under severe drought, but not at the wilting point. Additionally, the associated precursors of these metabolites, such as amino acids (phenylalanine and tyrosine), phenylpropanoids, and carotenoids, were also mapped. The potential biochemical transformations were further calculated using the data generated by FT-ICR MS. Under severe drought stress, the highest number of potential biochemical transformations, including methylation, ethyl addition, and oxidation/hydroxylation, were identified, many of which are known reactions in some of the mapped pathways. With the application of FT-ICR MS, we revealed the dynamics of drought-induced secondary metabolites in root exudates in response to drought, providing valuable information for drought-tolerance strategies in cotton.

Species phylogeny, ecology, and root traits as predictors of root exudate composition

Root traits including root exudates are key factors affecting plant interactions with soil and thus play an important role in determining ecosystem processes. The drivers of their variation, however, remain poorly understood. We determined the relative importance of phylogeny and species ecology in determining root traits and analyzed the extent to which root exudate composition can be predicted by other root traits. We measured different root morphological and biochemical traits (including exudate profiles) of 65 plant species grown in a controlled system. We tested phylogenetic conservatism in traits and disentangled the individual and overlapping effects of phylogeny and species ecology on traits. We also predicted root exudate composition using other root traits. Phylogenetic signal differed greatly among root traits, with the strongest signal in phenol content in plant tissues. Interspecific variation in root traits was partly explained by species ecology, but phylogeny was more important in most cases. Species exudate composition could be partly predicted by specific root length, root dry matter content, root biomass, and root diameter, but a large part of variation remained unexplained. In conclusion, root exudation cannot be easily predicted based on other root traits and more comparative data on root exudation are needed to understand their diversity.

Above- and belowground linkages during extreme moisture excess: leveraging knowledge from natural ecosystems to better understand implications for row-crop agroecosystems

Above- and belowground linkages are responsible for some of the most important ecosystem processes in unmanaged terrestrial systems including net primary production, decomposition, and carbon sequestration. Global change biology is currently altering above- and belowground interactions, reducing ecosystem services provided by natural systems. Less is known regarding how above- and belowground linkages impact climate resilience, especially in intentionally managed cropping systems. Waterlogged or flooded conditions will continue to increase across the Midwestern USA due to climate change. The objective of this paper is to explore what is currently known regarding above- and belowground linkages and how they impact biological, biochemical, and physiological processes in systems experiencing waterlogged conditions. We also identify key above- and belowground processes that are critical for climate resilience in Midwestern cropping systems by exploring various interactions that occur within unmanaged landscapes. Above- and belowground interactions that support plant growth and development, foster multi-trophic-level interactions, and stimulate balanced nutrient cycling are critical for crops experiencing waterlogged conditions. Moreover, incorporating ecological principles such as increasing plant diversity by incorporating crop rotations and adaptive management via delayed planting dates and adjustments in nutrient management will be critical for fostering climate resilience in row-crop agriculture moving forward.

Integrated Microbiome and Metabolomic Analysis Reveal Responses of Rhizosphere Bacterial Communities and Root exudate Composition to Drought and Genotype in Rice (Oryza sativa L.)

BACKGROUND

As climate change events become more frequent, drought is an increasing threat to agricultural production and food security. Crop rhizosphere microbiome and root exudates are critical regulators for drought adaptation, yet our understanding on the rhizosphere bacterial communities and root exudate composition as affected by drought stress is far from complete. In this study, we performed 16S rRNA gene amplicon sequencing and widely targeted metabolomic analysis of rhizosphere soil and root exudates from two contrasting rice genotypes (Nipponbare and Luodao 998) exposed to drought stress.

RESULTS

A reduction in plant phenotypes was observed under drought, and the inhibition was greater for roots than for shoots. Additionally, drought exerted a negligible effect on the alpha diversity of rhizosphere bacterial communities, but obviously altered their composition. In particular, drought led to a significant enrichment of Actinobacteria but a decrease in Firmicutes. We also found that abscisic acid in root exudates was clearly higher under drought, whereas lower jasmonic acid and L-cystine concentrations. As for plant genotypes, variations in plant traits of the drought-tolerant genotype Luodao 998 after drought were smaller than those of Nipponbare. Interestingly, drought triggered an increase in Bacillus, as well as an upregulation of most organic acids and a downregulation of all amino acids in Luodao 998. Notably, both Procrustes analysis and Mantel test demonstrated that rhizosphere microbiome and root exudate metabolomic profiles were highly correlated. A number of differentially abundant genera responded to drought and genotype, including Streptomyces, Bacillus and some members of Actinobacteria, were significantly associated with organic acid and amino acid contents in root exudates. Further soil incubation experiments showed that Streptomyces was regulated by abscisic acid and jasmonic acid under drought.

CONCLUSIONS

Our results reveal that both drought and genotype drive changes in the compositions of rice rhizosphere bacterial communities and root exudates under the greenhouse condition, and that organic acid exudation and suppression of amino acid exudation to select specific rhizosphere bacterial communities may be an important strategy for rice to cope with drought. These findings have important implications for improving the adaptability of rice to drought from the perspective of plant-microbe interactions.

Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan-Hengduan Mountains

Hybridization caused by frequent environmental changes can lead both to species diversification (speciation) and to speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus, a genus with its trifoliolate lineage in the Himalayan-Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating speciation dynamics based on integrated evidence. We investigated phylogenetic discordance and reticulate evolution in Parthenocissus based on rigorous analyses of plastome and transcriptome data. We focused on reticulations in the trifoliolate lineage in the HHM region using a population-level genome resequencing dataset, incorporating evidence from morphology, distribution, and elevation. Comprehensive analyses confirmed multiple introgressions within Parthenocissus in a robust temporal-spatial framework. Around the HHM region, at least three hybridization hot spots were identified, one of which showed evidence of ongoing speciation reversal. We present a solid case study using an integrative methodological approach to investigate reticulate evolutionary history and its underlying mechanisms in plants. It demonstrates an example of speciation reversal through frequent hybridizations in the HHM region, which provides new perspectives on speciation dynamics in mountainous areas with strong topographic and environmental heterogeneity.

Plant domestication shapes rhizosphere microbiome assembly and metabolic functions

BACKGROUND

The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication builds up specific rhizosphere microbiomes and metabolic functions, as well as the importance of these affected rhizobiomes and relevant root exudates in maintaining plant growth, is not well understood. Here, we firstly investigated the rhizosphere bacterial and fungal communities of domestication and wild accessions of tetraploid wheat using amplicon sequencing (16S and ITS) after 9 years of domestication process at the main production sites in China. We then explored the ecological roles of root exudation in shaping rhizosphere microbiome functions by integrating metagenomics and metabolic genomics approaches. Furthermore, we established evident linkages between root morphology traits and keystone taxa based on microbial culture and plant inoculation experiments.

RESULTS

Our results suggested that plant rhizosphere microbiomes were co-shaped by both host genotypes and domestication status. The wheat genomes contributed more variation in the microbial diversity and composition of rhizosphere bacterial communities than fungal communities, whereas plant domestication status exerted much stronger influences on the fungal communities. In terms of microbial interkingdom association networks, domestication destabilized microbial network and depleted the abundance of keystone fungal taxa. Moreover, we found that domestication shifted the rhizosphere microbiome from slow growing and fungi dominated to fast growing and bacteria dominated, thereby resulting in a shift from fungi-dominated membership with enrichment of carbon fixation genes to bacteria-dominated membership with enrichment of carbon degradation genes. Metagenomics analyses further indicated that wild cultivars of wheat possess higher microbial function diversity than domesticated cultivars. Notably, we found that wild cultivar is able to harness rhizosphere microorganism carrying N transformation (i.e., nitrification, denitrification) and P mineralization pathway, whereas rhizobiomes carrying inorganic N fixation, organic N ammonification, and inorganic P solubilization genes are recruited by the releasing of root exudates from domesticated wheat. More importantly, our metabolite-wide association study indicated that the contrasting functional roles of root exudates and the harnessed keystone microbial taxa with different nutrient acquisition strategies jointly determined the aboveground plant phenotypes. Furthermore, we observed that although domesticated and wild wheats recruited distinct microbial taxa and relevant functions, domestication-induced recruitment of keystone taxa led to a consistent growth regulation of root regardless of wheat domestication status.

CONCLUSIONS

Our results indicate that plant domestication profoundly influences rhizosphere microbiome assembly and metabolic functions and provide evidence that host plants are able to harness a differentiated ecological role of root-associated keystone microbiomes through the release of root exudates to sustain belowground multi-nutrient cycles and plant growth. These findings provide valuable insights into the mechanisms underlying plant-microbiome interactions and how to harness the rhizosphere microbiome for crop improvement in sustainable agriculture. Video Abstract.

Plant root plasticity during drought and recovery: What do we know and where to go?

AIMS

Drought stress is one of the most limiting factors for agriculture and ecosystem productivity. Climate change exacerbates this threat by inducing increasingly intense and frequent drought events. Root plasticity during both drought and post-drought recovery is regarded as fundamental to understanding plant climate resilience and maximizing production. We mapped the different research areas and trends that focus on the role of roots in plant response to drought and rewatering and asked if important topics were overlooked.

METHODS

We performed a comprehensive bibliometric analysis based on journal articles indexed in the Web of Science platform from 1900-2022. We evaluated a) research areas and temporal evolution of keyword frequencies, b) temporal evolution and scientific mapping of the outputs over time, c) trends in the research topics analysis, d) marked journals and citation analysis, and e) competitive countries and dominant institutions to understand the temporal trends of root plasticity during both drought and recovery in the past 120 years.

RESULTS

Plant physiological factors, especially in the aboveground part (such as "photosynthesis", "gas-exchange", "abscisic-acid") in model plants Arabidopsis, crops such as wheat and maize, and trees were found to be the most popular study areas; they were also combined with other abiotic factors such as salinity, nitrogen, and climate change, while dynamic root growth and root system architecture responses received less attention. Co-occurrence network analysis showed that three clusters were classified for the keywords including 1) photosynthesis response; 2) physiological traits tolerance (e.g. abscisic acid); 3) root hydraulic transport. Thematically, themes evolved from classical agricultural and ecological research via molecular physiology to root plasticity during drought and recovery. The most productive (number of publications) and cited countries and institutions were situated on drylands in the USA, China, and Australia. In the past decades, scientists approached the topic mostly from a soil-plant hydraulic perspective and strongly focused on aboveground physiological regulation, whereas the actual belowground processes seemed to have been the elephant in the room. There is a strong need for better investigation into root and rhizosphere traits during drought and recovery using novel root phenotyping methods and mathematical modeling.

Changes in Metal-Chelating Metabolites Induced by Drought and a Root Microbiome in Wheat

The essential metals Cu, Zn, and Fe are involved in many activities required for normal and stress responses in plants and their microbiomes. This paper focuses on how drought and microbial root colonization influence shoot and rhizosphere metabolites with metal-chelation properties. Wheat seedlings, with and without a pseudomonad microbiome, were grown with normal watering or under water-deficit conditions. At harvest, metal-chelating metabolites (amino acids, low molecular weight organic acids (LMWOAs), phenolic acids, and the wheat siderophore) were assessed in shoots and rhizosphere solutions. Shoots accumulated amino acids with drought, but metabolites changed little due to microbial colonization, whereas the active microbiome generally reduced the metabolites in the rhizosphere solutions, a possible factor in the biocontrol of pathogen growth. Geochemical modeling with the rhizosphere metabolites predicted Fe formed Fe-Ca-gluconates, Zn was mainly present as ions, and Cu was chelated with the siderophore 2'-deoxymugineic acid, LMWOAs, and amino acids. Thus, changes in shoot and rhizosphere metabolites caused by drought and microbial root colonization have potential impacts on plant vigor and metal bioavailability.

Type-dependent effects of microplastics on tomato (Lycopersicon esculentum L.): Focus on root exudates and metabolic reprogramming

Much attention has been paid to the prevalence of microplastics (MPs) in terrestrial systems. MPs have been shown to affect the physio-biochemical properties of plants. Different MPs may have distinctive behaviors and diverse effects on plant growth. In the present study, the effects of polystyrene (PS), polyethylene (PE), and polypropylene (PP) MPs on physio-biochemical properties, root exudates, and metabolomics of tomato (Lycopersicon esculentum L.) under hydroponic conditions were investigated. Our results show that MPs exposure has adverse effects on tomato growth. MPs exposure had a significant type-dependent effect (p < 0.001) on photosynthetic gas parameters, chlorophyll content, and antioxidant enzyme activities. After exposure to MPs, the content of low molecular weight organic acids in tomato root exudates was significantly increased, which was considered as a strategy to alleviate the toxicity of MPs. In addition, MPs treatment significantly changed the metabolites of tomato root and leaf. Metabolic pathway analysis showed that MPs treatment had a great effect on amino acid metabolism. We also found that plants exposed to PS and PP MPs produced more significant metabolic reprogramming than those exposed to PE MPs. This study provides important implications for the mechanism studies on the toxic effect of various MPs on crops and their future risk assessment.

Root Exudates Mediate the Processes of Soil Organic Carbon Input and Efflux

Root exudates, as an important form of material input from plants to the soil, regulate the carbon input and efflux of plant rhizosphere soil and play an important role in maintaining the carbon and nutrient balance of the whole ecosystem. Root exudates are notoriously difficult to collect due to their underlying characteristics (e.g., low concentration and fast turnover rate) and the associated methodological challenges of accurately measuring root exudates in native soils. As a result, up until now, it has been difficult to accurately quantify the soil organic carbon input from root exudates to the soil in most studies. In recent years, the contribution and ecological effects of root exudates to soil organic carbon input and efflux have been paid more and more attention. However, the ecological mechanism of soil organic carbon input and efflux mediated by root exudates are rarely analyzed comprehensively. In this review, the main processes and influencing factors of soil organic carbon input and efflux mediated by root exudates are demonstrated. Soil minerals and soil microbes play key roles in the processes. The carbon allocation from plants to soil is influenced by the relationship between root exudates and root functional traits. Compared with the quantity of root exudates, the response of root exudate quality to environmental changes affects soil carbon function more. In the future, the contribution of root exudates in different plants to soil carbon turnover and their relationship with soil nutrient availability will be accurately quantified, which will be helpful to understand the mechanism of soil organic carbon sequestration.

Soil legacy effects of plants and drought on aboveground insects in native and range-expanding plant communities

Soils contain biotic and abiotic legacies of previous conditions that may influence plant community biomass and associated aboveground biodiversity. However, little is known about the relative strengths and interactions of the various belowground legacies on aboveground plant-insect interactions. We used an outdoor mesocosm experiment to investigate the belowground legacy effects of range-expanding versus native plants, extreme drought and their interactions on plants, aphids and pollinators. We show that plant biomass was influenced more strongly by the previous plant community than by the previous summer drought. Plant communities consisted of four congeneric pairs of natives and range expanders, and their responses were not unanimous. Legacy effects affected the abundance of aphids more strongly than pollinators. We conclude that legacies can be contained as soil 'memories' that influence aboveground plant community interactions in the next growing season. These soil-borne 'memories' can be altered by climate warming-induced plant range shifts and extreme drought.

A meta-analysis on morphological, physiological and biochemical responses of plants with PGPR inoculation under drought stress

Plant growth-promoting rhizobacteria (PGPR) can help plants to resist drought stress. However, the mechanisms of how PGPR inoculation affect plant status under drought remain incompletely understood. We performed a meta-analysis of plant response to PGPR inoculation by compiling data from 57 PGPR-inoculation studies, including 2, 387 paired observations on morphological, physiological and biochemical parameters under drought and well-watered conditions. We compare the PGPR effect on plants performances among different groups of controls and treatments. Our results reveal that PGPR enables plants to restore themselves from drought-stressed to near a well-watered state, and that C4 plants recover better from drought stress than C3 plants. Furthermore, PGPR is more effective underdrought than well-watered conditions in increasing plant biomass, enhancing photosynthesis and inhibiting oxidant damage, and the responses of C4 plants to the PGPR effect was stronger than that of C3 plants under drought conditions. Additionally, PGPR belonging to different taxa and PGPR with different functional traits have varying degrees of drought-resistance effects on plants. These results are important to improve our understanding of the PGPR beneficial effects on enhanced drought-resistance of plants.

Is ABA the exogenous vector of interplant drought cuing?

We have recently demonstrated that root cuing from drought-stressed plants increased the survival time of neighboring plants under drought, which came at performance costs under benign conditions. The involvement of abscisic acid (ABA) was implicated from additional experiments in which interplant drought cuing was greatly diminished in ABA-deficient plants. Here, we tested the hypothesis that ABA is the exogenous vector of interplant drought cuing. Pisum sativum plants were grown in rows of three split-root plants. One of the roots of the first plant was subjected to either drought of benign conditions in one rooting vial, while its other root shared its rooting vial with one of the roots of an unstressed neighbor, which in turn shared its other rooting vial with an additional unstressed neighbor. One hour after subjecting one of the roots of the first plant to drought, ABA concentrations were 106% and 145% higher around its other root and the roots of its unstressed neighbor, compared to their respective unstressed controls; however, the absolute concentrations of ABA found in the rooting media were substantially low. The results may indicate that despite its involvement in interplant drought and the commonly observed exchange of ABA between drought-stressed plants and their rhizospheres, ABA is not directly involved in exogenous interplant drought cuing. However, previous studies have shown that even minute concentrations of ABA in the rhizosphere can prevent ABA leakage from roots and thus to significantly increase endogenous ABA levels. In addition, under drought conditions, plants tend to accumulate ABA, which could markedly increase internal ABA concentrations over time and ABA concentrations in close proximity to the root surface might be significantly greater than estimated from entire rooting volumes. Finally, phaseic acid, an ABA degradation product, is known to activate various ABA receptors, which could enhance plant drought tolerance. It is thus feasible that while the role of ABA is limited, its more stable degradation products could play a significant role in interplant drought cuing. Our preliminary findings call for an extensive investigation into the identity and modes of operation of the exogenous vectors of interplant drought cuing.

Compensatory growth as a response to post-drought in grassland

Grasslands are structurally and functionally controlled by water availability. Ongoing global change is threatening the sustainability of grassland ecosystems through chronic alterations in climate patterns and resource availability, as well as by the increasing frequency and intensity of anthropogenic perturbations. Compared with many studies on how grassland ecosystems respond during drought, there are far fewer studies focused on grassland dynamics after drought. Compensatory growth, as the ability of plants to offset the adverse effects of environmental or anthropogenic perturbations, is a common phenomenon in grassland. However, compensatory growth induced by drought and its underlying mechanism across grasslands remains not clear. In this review, we provide examples of analogous compensatory growth from different grassland types across drought characteristics (intensity, timing, and duration) and explain the effect of resource availability on compensatory growth and their underlying mechanisms. Based on our review of the literature, a hypothetic framework for integrating plant, root, and microbial responses is also proposed to increase our understanding of compensatory growth after drought. This research will advance our understanding of the mechanisms of grassland ecosystem functioning in response to climate change.

AMF colonization affects allelopathic effects of Zea mays L. root exudates and community structure of rhizosphere bacteria

Arbuscular mycorrhizal fungi (AMF) widely exist in the soil ecosystem. It has been confirmed that AMF can affect the root exudates of the host, but the chain reaction effect of changes in the root exudates has not been reported much. The change of soil microorganisms and soil enzyme vigor is a direct response to the change in the soil environment. Root exudates are an important carbon source for soil microorganisms. AMF colonization affects root exudates, which is bound to have a certain impact on soil microorganisms. This manuscript measured and analyzed the changes in root exudates and allelopathic effects of root exudates of maize after AMF colonization, as well as the enzymatic vigor and bacterial diversity of maize rhizosphere soil. The results showed that after AMF colonization, the contents of 35 compounds in maize root exudates were significantly different. The root exudates of maize can inhibit the seed germination and seedling growth of recipient plants, and AMF colonization can alleviate this situation. After AMF colonization, the comprehensive allelopathy indexes of maize root exudates on the growth of radish, cucumber, lettuce, pepper, and ryegrass seedlings decreased by 60.99%, 70.19%, 80.83%, 36.26% and 57.15% respectively. The root exudates of maize inhibited the growth of the mycelia of the pathogens of soil-borne diseases, and AMF colonization can strengthen this situation. After AMF colonization, the activities of dehydrogenase, sucrase, cellulase, polyphenol oxidase and neutral protein in maize rhizosphere soil increased significantly, while the bacterial diversity decreased but the bacterial abundance increased. This research can provide a theoretical basis for AMF to improve the stubble of maize and the intercropping mode between maize and other plants, and can also provide a reference for AMF to prevent soil-borne diseases in maize.

Root exudates enhanced rhizobacteria complexity and microbial carbon metabolism of toxic plants

Root exudates and rhizosphere microorganisms play key roles in the colonization of toxic plants under climate change and land degradation. However, how root exudates affect the rhizosphere microorganisms and soil nutrients of toxic plants in degraded grasslands remains unknown. We compared the interaction of soil microbial communities, root exudates, microbial carbon metabolism, and environmental factors in the rhizosphere of toxic and non-toxic plants. Deterministic processes had a greater effect on toxic than non-toxic plants, as root exudates affected rhizosphere microorganisms directly. The 328 up-regulated compounds in root exudates of toxic plants affected the diversity of rhizosphere microorganisms. Rhizosphere bacteria-enriched enzymes were involved in the phenylpropanoid biosynthesis pathway. Root exudates of toxic plants form complex networks of rhizosphere microorganisms, provide high rhizosphere nutrients, and increase microbial carbon metabolism. The interaction between root exudates and rhizosphere microorganisms is the key mechanism that enables toxic plants to spread in degraded grassland habitats.

Plant-microbial responses to reduced precipitation depend on tree species in a temperate forest

Given that global change is predicted to increase the frequency and severity of drought in temperate forests, it is critical to understand the degree to which plant belowground responses cascade through the soil system to drive ecosystem responses to water stress. While most research has focused on plant and microbial responses independently of each other, a gap in our understanding lies in the integrated response of plant-microbial interactions to water stress. We investigated the extent to which divergent belowground responses to reduced precipitation between sugar maple trees (Acer saccharum) versus oak trees (Oak spp.) may influence microbial activity via throughfall exclusion in the field. Evidence that oak trees send carbon belowground to prime microbial activity more than maples under ambient conditions and in response to water stress suggests there is the potential for corresponding impacts of reduced precipitation on microbial activity. As such, we tested the hypothesis that differences in belowground C allocation between oaks and maples would stimulate microbial activity in the oak treatment soils and reduce microbial activity in in the sugar maple treatment soils compared to their respective controls. We found that the treatment led to declines in N mineralization, soil respiration, and oxidative enzyme activity in the sugar maple treatment plot. These declines may be due to sugar maple trees reducing root C transfers to the soil. By contrast, the reduced precipitation treatment enhanced soil respiration, as well as rates of N mineralization and peroxidase activity in the oak rhizosphere. This enhanced activity suggests that oak roots provided optimal rhizosphere conditions during water stress to prime microbial activity to support net primary production. With future changes in precipitation predicted for forests in the Eastern US, we show that the strength of plant-microbial interactions drives the degree to which reduced precipitation impacts soil C and nutrient cycling.

Drought legacies and ecosystem responses to subsequent drought

Climate change is expected to increase the frequency and severity of droughts. These events, which can cause significant perturbations of terrestrial ecosystems and potentially long-term impacts on ecosystem structure and functioning after the drought has subsided are often called 'drought legacies'. While the immediate effects of drought on ecosystems have been comparatively well characterized, our broader understanding of drought legacies is just emerging. Drought legacies can relate to all aspects of ecosystem structure and functioning, involving changes at the species and the community scale as well as alterations of soil properties. This has consequences for ecosystem responses to subsequent drought. Here, we synthesize current knowledge on drought legacies and the underlying mechanisms. We highlight the relevance of legacy duration to different ecosystem processes using examples of carbon cycling and community composition. We present hypotheses characterizing how intrinsic (i.e. biotic and abiotic properties and processes) and extrinsic (i.e. drought timing, severity, and frequency) factors could alter resilience trajectories under scenarios of recurrent drought events. We propose ways for improving our understanding of drought legacies and their implications for subsequent drought events, needed to assess the longer-term consequences of droughts on ecosystem structure and functioning.

Root exudates and rhizosphere soil bacterial relationships of Nitraria tangutorum are linked to k-strategists bacterial community under salt stress

When plants are subjected to various biotic and abiotic stresses, the root system responds actively by secreting different types and amounts of bioactive compounds, while affects the structure of rhizosphere soil bacterial community. Therefore, understanding plant-soil-microbial interactions, especially the strength of microbial interactions, mediated by root exudates is essential. A short-term experiment was conducted under drought and salt stress to investigate the interaction between root exudates and Nitraria tangutorum rhizosphere bacterial communities. We found that drought and salt stress increased rhizosphere soil pH (9.32 and 20.6%) and electrical conductivity (1.38 and 11 times), respectively, while decreased organic matter (27.48 and 31.38%), total carbon (34.55 and 29.95%), and total phosphorus (20 and 28.57%) content of N. tangutorum rhizosphere soil. Organic acids, growth hormones, and sugars were the main differential metabolites of N. tangutorum under drought and salt stress. Salt stress further changed the N. tangutorum rhizosphere soil bacterial community structure, markedly decreasing the relative abundance of Bacteroidota as r-strategist while increasing that of Alphaproteobacteria as k-strategists. The co-occurrence network analysis showed that drought and salt stress reduced the connectivity and complexity of the rhizosphere bacterial network. Soil physicochemical properties and root exudates in combination with salt stress affect bacterial strategies and interactions. Our study revealed the mechanism of plant-soil-microbial interactions under the influence of root exudates and provided new insights into the responses of bacterial communities to stressful environments.

Carbon allocation to root exudates is maintained in mature temperate tree species under drought

Carbon (C) exuded via roots is proposed to increase under drought and facilitate important ecosystem functions. However, it is unknown how exudate quantities relate to the total C budget of a drought-stressed tree, that is, how much of net-C assimilation is allocated to exudation at the tree level. We calculated the proportion of daily C assimilation allocated to root exudation during early summer by collecting root exudates from mature Fagus sylvatica and Picea abies exposed to experimental drought, and combining above- and belowground C fluxes with leaf, stem and fine-root surface area. Exudation from individual roots increased exponentially with decreasing soil moisture, with the highest increase at the wilting point. Despite c. 50% reduced C assimilation under drought, exudation from fine-root systems was maintained and trees exuded 1.0% (F. sylvatica) to 2.5% (P. abies) of net C into the rhizosphere, increasing the proportion of C allocation to exudates two- to three-fold. Water-limited P. abies released two-thirds of its exudate C into the surface soil, whereas in droughted F. sylvatica it was only one-third. Across the entire root system, droughted trees maintained exudation similar to controls, suggesting drought-imposed belowground C investment, which could be beneficial for ecosystem resilience.

Plant-Microbiota Interactions in Abiotic Stress Environments

Abiotic stress adversely affects cellular homeostasis and ultimately impairs plant growth, posing a serious threat to agriculture. Climate change modeling predicts increasing occurrences of abiotic stresses such as drought and extreme temperature, resulting in decreasing the yields of major crops such as rice, wheat, and maize, which endangers food security for human populations. Plants are associated with diverse and taxonomically structured microbial communities that are called the plant microbiota. Plant microbiota often assist plant growth and abiotic stress tolerance by providing water and nutrients to plants and modulating plant metabolism and physiology and, thus, offer the potential to increase crop production under abiotic stress. In this review, we summarize recent progress on how abiotic stress affects plants, microbiota, plant-microbe interactions, and microbe-microbe interactions, and how microbes affect plant metabolism and physiology under abiotic stress conditions, with a focus on drought, salt, and temperature stress. We also discuss important steps to utilize plant microbiota in agriculture under abiotic stress.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Crafting the plant root metabolome for improved microbe-assisted stress resilience

Plants and microbes coinhabit the earth and have coevolved during environmental changes over time. Root metabolites are the key to mediating the dynamic association between plants and microbes, yet the underlying functions and mechanisms behind this remain largely illusive. Knowledge of metabolite-mediated alteration of the root microbiota in response to environmental stress will open avenues for engineering root microbiotas for improved plant stress resistance and health. Here, we synthesize recent advances connecting environmental stresses, the root metabolome and microbiota, and propose integrated synthetic biology-based strategies for tuning the plant root metabolome in situ for microbe-assisted stress resistance, offering potential solutions to combat climate change. The current limitations, challenges and perspectives for engineering the plant root metabolome for modulating microbiota are collectively discussed.

Deciphering the role of specialist and generalist plant-microbial interactions as drivers of plant-soil feedback

Feedback between plants and soil microbial communities can be a powerful driver of vegetation dynamics. Plants elicit changes in the soil microbiome that either promote or suppress conspecifics at the same location, thereby regulating population density-dependence and species co-existence. Such effects are often attributed to the accumulation of host-specific antagonistic or beneficial microbiota in the rhizosphere. However, the identity and host-specificity of the microbial taxa involved are rarely empirically assessed. Here we review the evidence for host-specificity in plant-associated microbes and propose that specific plant-soil feedbacks can also be driven by generalists. We outline the potential mechanisms by which generalist microbial pathogens, mutualists and decomposers can generate differential effects on plant hosts and synthesize existing evidence to predict these effects as a function of plant investments into defence, microbial mutualists and dispersal. Importantly, the capacity of generalist microbiota to drive plant-soil feedbacks depends not only on the traits of individual plants but also on the phylogenetic and functional diversity of plant communities. Identifying factors that promote specialization or generalism in plant-microbial interactions and thereby modulate the impact of microbiota on plant performance will advance our understanding of the mechanisms underlying plant-soil feedback and the ways it contributes to plant co-existence.

Effect of drought on root exudates from Quercus petraea and enzymatic activity of soil

Root exudation is a key process that determines rhizosphere functions and plant-soil relationships. The present study was conducted with the objectives to (1) determine the root morphology of sessile oak seedlings in relation to drought, (2) assess root exudation and its response to drought, and (3) detect possible changes in the activity of soil enzymes in response to drought enhancement. In the experiment, sessile oak seedlings (Quercus petraea Matt.) were used, and two variants of substrate moisture (25% humidity-dry variant and 55% humidity-fresh variant) on which oaks grew were considered. Exudates were collected using a culture-based cuvette system. Results confirmed the importance of drought in shaping the morphology of roots and root carbon exudation of sessile oak. The oak roots in the dry variant responded with a higher increment in length. In the case of roots growing in higher humidity, a higher specific root area and specific root length were determined. Experimental evidence has demonstrated decreased root exudation under dry conditions, which can lead to a change in enzyme activity. In the study, enzyme activity decreased by 90% for β-D-cellobiosidase (CB), 50% for β-glucosidase (BG) and N-acetyl-β-D-glucosaminidase (NAG), 20% for β-xylosidase (XYL) decreased by, and the activity of arylsulphatase (SP) and phosphatase (PH) decreased by 10%.