Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community

Effects of water-saving irrigation on microbial community structures, assembly, and metabolic activities in alfalfa rhizosphere soils

In agricultural areas of arid Xinjiang, China, selecting appropriate irrigation strategies for farmland is essential. Increasing attention is being paid to the ecological effects of different irrigation methods on the soil environment. As a crucial component of soil quality, the microbial community is a key indicator of the impacts of irrigation on the soil environment. To investigate the effects of irrigation treatments on the properties of rhizosphere soil and the underlying microbial community characteristics, this study conducted an alfalfa field experiment applying three water-saving treatments (3750, 4500, and 5250 m3 hm-2) and regular irrigation (6750 m3 hm-2, CK). The results showed that the water-saving treatments increased the soil pH, salinity, available nitrogen, and phosphorus levels. The water-saving treatments decreased the richness and diversity of the bacterial community in the rhizosphere but increased those of the fungal community. The influence of stochastic processes on fungal and bacterial communities assembly under water-saving treatments was more noticeable than that under CK. Compared with CK, water-saving treatments reduced the complexity of microbial network and increased the potential negative interaction between bacteria and fungi. Functional prediction analysis showed that species specificity among treatments may result from a specific selection of rhizosphere functional requirements. This study reveals the effect of controlling irrigation quantity on protecting soil microbial diversity and function and improves the understanding of rhizosphere soil community response affected by different irrigation strategies. The results facilitate the development of effective and beneficial agricultural measures.

Ecosystems have multiple interacting processes that buffer against co-occurring stressors

There are multiple processes that buffer the effects of anthropogenic stressors. Much is known about how single buffering processes (e.g., biodiversity, adaptation) mitigate the effects of stressors on ecosystem properties and functions, but how multiple buffering processes combine to mitigate the effects of multiple co-occurring stressors is poorly understood. We outline how single processes (e.g., cross-tolerance) can buffer the effects of multiple stressors, whereas multiple buffering processes can act jointly across ecological and temporal scales to reduce the effects of single or multiple stressors. Synergistic interactions between multiple buffering processes can further enhance ecosystem resistance to multiple stressors. A wider awareness of interacting buffering processes in ecosystems will enhance our understanding of ecosystem stability in the face of multiple stressors.

Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems

Different microbial communities are impacted disproportionately by environmental disturbances. The degree to which a community can remain unchanged under a disturbance is referred to as resistance1. However, the contributing ecological factors, which infer a community's resistance are unknown. In this study, the impact of historical environmental stability on ecological phenomena and microbial community resistance to shocks was investigated. Three separate methanogenic bioreactor consortia, which were subjected to varying degrees of historical environmental stability, and displayed different levels of resistance to an organic loading rate (OLR) shock were sampled. Their community composition was assessed using high throughput sequencing of 16S rRNA genes and assembly based metagenomics. The effect environmental instability on ecological phenomena such as microbial community assembly, microbial niche breadth and the rare biosphere were assessed in the context of each reactor's demonstrated resistance to an OLR shock. Additionally, metagenome assembled genomes were analysed for functional effects of prolonged stability/instability. The system which was subjected to more environmental instability experienced more temporal variation in community beta diversity and a proliferation of specialists, with more abundant two component regulatory systems. This community was more susceptible to deterministic community assembly and demonstrated a lower degree of resistance, indicating that microbial communities experiencing longer term environmental instability (e.g. variations in pH or temperature) are less able to resist a large disturbance.

Microbial biomass stoichiometry and proportion of Fe organic complexes separately shape the heterogeneity of mixotrophic denitrification and net N2O sinks in iron-carbon amended ecological ditch

Coupling of iron-carbon can form a mixotrophic denitrification and is regarded as a promising solution for purifying nitrate-rich agricultural runoff. However, its prevalence and efficacy of the synergistic augmentation of nitrogen elimination and net N2O sinks remain crucial knowledge gaps in ecological ditches (eco-ditches). Here, we investigated the underlying variability mechanisms by implementing sponge iron (sFe)-coupled Iris hexagonus (IH)- or Myriophyllum aquaticum (MA)-derived biochar produced via microwave-assisted (MW) pyrolysis and conventional pyrolysis. Surprisingly, unamened eco-ditch became net N2O sink while exhibiting a significant increase in total nitrogen (TN) removal rate of 319 % (P < 0.001) compared to soil ditch. The integration of MW pyrolyzed IH-derived biochar with sFe to amend eco-ditch achieved synchronous enhancement in net N2O sinks (P < 0.01) and TN removal rate (P < 0.001), whereas the remaining amended eco-ditches that significantly intensified TN removal performance, were N2O emitters. Such heterogeneity primarily depends on Fe organic complexes (Fep) / the total reactive Fe oxides (Fed) ratio, rather than the prevailing nosZ gene, underscoring that low density metastable reactive iron plays a more important role than biological reactions during the mixotrophic denitrification process. As such, iron oxides are not necessarily a bottleneck for denitrification and contribute to N2O sinks. Conversely, microbial biomass C:(C + N), together with nirK and nosZ genes, mainly explain the TN removal heterogeneity of sFe-biochar eco-ditch. This study revisits the discrepant resilience of iron-carbon coupling to N abatement and N2O sink-induced cooling and has significant practical implications for better understanding the cascading effects of mixotrophic denitrification driven by iron-carbon interactions.

Legacies of temperature fluctuations promote stability in marine biofilm communities

The increasing frequency and intensity of extreme climate events are driving significant biodiversity shifts across ecosystems. Yet, the extent to which these climate legacies will shape the response of ecosystems to future perturbations remains poorly understood. Here, we tracked taxon and trait dynamics of rocky intertidal biofilm communities under contrasting regimes of warming (fixed vs. fluctuating) and assessed how they influenced stability dimensions in response to temperature extremes. Fixed warming enhanced the resistance of biofilm by promoting the functional redundancy of stress-tolerance traits. In contrast, fluctuating warming boosted recovery rate through the selection of fast-growing taxa at the expense of functional redundancy. This selection intensified a trade-off between stress tolerance and growth further limiting the ability of biofilm to cope with temperature extremes. Anticipating the challenges posed by future extreme events, our findings offer a forward-looking perspective on the stability of microbial communities in the face of ongoing climatic change.

Soil CO2 and CH4 response to experimental warming under various tree species compositions in a temperate harwood forest

Under climate change, some forest ecosystems appear to be transitioning into net source of carbon dioxide (CO2), raising questions about the future role of soil respiration rate (Rs), which depends on hydroclimatic conditions. Conversely, well-drained forest soils could become more significant sinks of methane (CH4) under warming. The main objective of this study was to assess the effects of artificial soil warming on Rs and CH4 fluxes in a sugar maple forest at the northern limit of Quebec temperate deciduous forests in eastern Canada, and to evaluate the effect of species composition on soil response to warming. We measured Rs and CH4 fluxes during the snow-free period of 2021 and 2022 in 32 plots distributed across three forest types, half of which were artificially heated by approximately 2 °C with heating cables. Forest soils were a very consistent sink for CH4 and it did not respond to artificial soil warming nor was it sensitive to variations in soil moisture, ionic activity in soil solution and forest types. However, we observed an increase in Rs in response to warming in the heated plots, but only up to a threshold of about 15 °C, beyond which Rs started to slow down in respect to the control plots. We also observed a weakening of the exponential relationship between Rs and soil temperature beyond this threshold. This trend varied across the forest types, with hardwood-beech stands being more sensitive to warming than mixedwoods and other hardwoods. This greater response of hardwood-beech stands to warming resulted in a more significant downshift of Rs, starting from a colder temperature threshold, around 10-12 °C. This study highlights a potential plateauing of Rs despite rising soil temperature, at least in eastern Canada's temperate deciduous forest, but this trend could vary from one forest type to another.

Supplementary Information

The online version contains supplementary material available at 10.1007/s44378-025-00045-4.

Simulated Climate Change Enhances Microbial Drought Resilience in Ethiopian Croplands but Not Forests

Climate change and land-use change represent a dual threat to terrestrial ecosystem functioning. In the tropics, forest conversion to agriculture is occurring alongside warming and more pronounced periods of drought. Rainfall after drought induces enormous dynamics in microbial growth (potential soil carbon storage) and respiration (determining carbon loss), affecting the ecosystem carbon budget. We investigated how legacies of drought and warming affected microbial functional (growth and respiration) and structural (16S and ITS amplicon) responses after drought. Rain shelters and open-top chambers (OTCs) were used to simulate drought and warming in tropical cropland and forest sites in Ethiopia. Rain shelters reduced soil moisture by up to 25 vol%, with a bigger effect in the forest, while OTCs increased soil temperature by up to 6°C in the cropland and also reduced soil moisture but had no clear effect in the forest. Soils from these field treatments were then exposed to a standardized drought cycle to test how microbial community traits had been shaped by the different climate legacies. Microbial growth started increasing immediately after rewetting in all soils, reflecting a resilient response and indicating that microbial communities perceived the perturbation as relatively mild. Fungi recovered faster than bacteria, and the recovery of fungal growth was generally accelerated in soils with a legacy of drought. Microbial community functions and structures were both more responsive in the cropland than in forest soils, and a legacy of drought particularly enhanced microbial growth and respiration responses in the cropland but not the forest. Microbial communities in cropland soils also used carbon with a higher efficiency after rewetting. Together, these results suggest contrasting feedbacks to climate change determined by land use, where croplands will be associated with mitigated losses of soil carbon by microorganisms in response to future cycles of drought, compared to forests where soil carbon reservoirs remain more sensitive.

Mitigating Water Stress in Plants with Beneficial Bacteria: Effects on Growth and Rhizosphere Bacterial Communities

Climate change has reshaped global weather patterns and intensified extreme events, with drought and soil salinity negatively impacting the yield and quality of crop production. To mitigate the detrimental effects of drought stress, the introduction of beneficial plant growth-promoting rhizobacteria (PGPR) has proven to be a promising approach. In this study, we evaluated a synthetic microbial community (SynCom) comprising bacterial strains belonging to the species Bacillus velezensis, Pseudomonas simiae, P. salmasensis, Glutamicibacter halophytocola, and Leclercia sp., which have been demonstrated to promote tomato growth both individually and collectively. The SynCom and most of its individual bacterial strains were shown to mitigate the detrimental effects of polyethylene glycol (PEG)-induced drought stress in vitro in Arabidopsis thaliana seedlings, either by reducing alterations in xylem elements or promoting the formation of new xylem strands. In a greenhouse trial, soil drenching with the SynCom and two individual strains, B. velezensis PSE31B and P. salmasensis POE54, improved the water stress response in soilless-grown tomato plants under a 40% reduced irrigation regime. Additionally, bacterial treatments positively influenced the diversity of rhizosphere bacterial communities, with distinct changes in bacterial composition, which suggest a treatment-specific interplay between the introduced strains and the native microbiome. These findings highlight the potential of microbial consortia and individual PGPR strains as sustainable tools to improve plant resilience to abiotic stresses.

Drought and vegetation restoration patterns shape soil enzyme activity and nutrient limitation dynamics in the loess plateau

Appropriate vegetation restoration measures are beneficial to ecosystem restoration and nutrient retention in ecologically fragile areas. However, the high water consumption of planted forests and the increasing frequency of drought events may reshape or complicate this ecological process. The effects of forest types and drought stress on nutrient limitation remain unclear. In this study, we selected five different vegetation restoration types on the Loess Plateau, China, and applied three drought levels to assess their effects on extracellular enzyme activity, soil microbial biomass, and soil nutrient limitations.We measured the activities of carbon-, nitrogen-, and phosphorus-acquiring enzymes and investigated the relationships among enzyme activity, microbial biomass, and nutrient limitations under drought conditions. Our results showed that vegetation types and drought significantly influenced soil enzymatic activity and stoichiometry. Mixed forests demonstrated higher enzyme activity and nutrient content compared to pure forests, indicating greater resilience under drought conditions. Short-term drought significantly reduced soil enzyme activity and microbial biomass, whereas mild drought stimulated enzyme activity, and moderate drought promoted microbial biomass. Drought markedly decreased microbial carbon and nitrogen content but increased the microbial carbon-to-nitrogen ratio. Furthermore, drought enhanced the correlation between microbial biomass carbon and carbon-acquiring enzymes, but there was no correlation between microbial biomass nitrogen and nitrogen-acquiring enzymes under drought. All vegetation types exhibited nitrogen limitation, and a negative correlation was observed between nitrogen and carbon limitations under drought conditions. Drought significantly exacerbated nitrogen limitation, while its impact on carbon limitation varied with drought severity and vegetation type. Overall, plant communities exhibited distinct nutrient acquisition strategies under drought stress, resulting in complex changes in soil enzyme activities and microbial biomass. This study advances our understanding of microbial nutrient limitations and enzymatic activities under varying vegetation restoration patterns and drought conditions, providing critical insights for enhancing soil resilience and nutrient cycling under climate change.

Grassland bud and shoot demographic responses to single and recurrent droughts vary across an aridity gradient

Clonal demographic traits play important roles in regulating community dynamics. Yet, it remains unclear how the responses of these clonal traits to drought might depend on previous drought exposure, and how drought responses vary among grasslands. We conducted a repeated drought experiment across four grasslands along an aridity gradient in northern China. We assessed the effects of single (precipitation reduction in 2021-2022) versus recurrent (precipitation reduction in 2015-2018 and 2021-2022) drought on bud density, shoot density, and the ratio of bud to shoot density. Drought reduced bud density at all grasslands and shoot density at most grasslands. Drought reduced the ratio of bud-to-shoot density only in the most arid grasslands. Recurrent drought had larger negative effects than a single drought on bud density and composition of bud and shoot at only one of four grasslands, and on shoot density at two of four grasslands. Our results suggest that previous drought exposure can alter the response of plant clonal demographic traits to subsequent drought in some but not all grasslands, and that responses can vary with mean climate.

Dynamic soil columns simulate Arctic redox biogeochemistry and carbon release during changes in water saturation

Thawing Arctic permafrost can induce hydrologic change and alter redox conditions, shifting the balance of soil organic matter (SOM) decomposition. There remains uncertainty about how soil saturation and redox transitions impact dissolved and gas phase carbon fluxes, and efforts to link hydrobiogeochemical processes to ecosystem-scale models are limited. This study evaluates SOM decomposition of Arctic tundra soils using column experiments, water chemistry measurements, microbial community analysis, and a PFLOTRAN reactive transport model. Soil columns from a thermokarst channel (TC) and an upland tundra (UC) were exposed to cycles of saturation and drainage, which controlled carbon emissions. During saturation, an outflow of dissolved organic carbon from the UC soil correlated with elevated reduced iron and decreased pH; during drainage, UC carbon dioxide fluxes were 70% higher than TC fluxes. Intermittent methane release was observed for TC, consistent with higher methanogen abundance. Slower drainage in the TC soil correlated with more subtle biogeochemical changes. PFLOTRAN simulations captured experimental trends in soil carbon fluxes, oxygen concentrations, and water contents. The model was then used to evaluate additional soil water drainage rates. This study emphasizes the importance of considering hydrologic change when evaluating and simulating SOM decomposition in dynamic Arctic tundra environments.

Long-term climate establishes functional legacies by altering microbial traits

Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.

Microbial Carbon Use Efficiency and Growth Rates in Soil: Global Patterns and Drivers

Carbon use efficiency (CUE) of microbial communities in soil quantifies the proportion of organic carbon (C) taken up by microorganisms that is allocated to growing microbial biomass as well as used for reparation of cell components. This C amount in microbial biomass is subsequently involved in microbial turnover, partly leading to microbial necromass formation, which can be further stabilized in soil. To unravel the underlying regulatory factors and spatial patterns of CUE on a large scale and across biomes (forests, grasslands, croplands), we evaluated 670 individual CUE data obtained by three commonly used approaches: (i) tracing of a substrate C by 13C (or 14C) incorporation into microbial biomass and respired CO2 (hereafter 13C-substrate), (ii) incorporation of 18O from water into DNA (18O-water), and (iii) stoichiometric modelling based on the activities of enzymes responsible for C and nitrogen (N) cycles. The global mean of microbial CUE in soil depends on the approach: 0.59 for the 13C-substrate approach, and 0.34 for the stoichiometric modelling and for the 18O-water approaches. Across biomes, microbial CUE was highest in grassland soils, followed by cropland and forest soils. A power-law relationship was identified between microbial CUE and growth rates, indicating that faster C utilization for growth corresponds to reduced C losses for maintenance and associated with mortality. Microbial growth rate increased with the content of soil organic C, total N, total phosphorus, and fungi/bacteria ratio. Our results contribute to understanding the linkage between microbial growth rates and CUE, thereby offering insights into the impacts of climate change and ecosystem disturbances on microbial physiology with consequences for C cycling.

Modeling urban pollutant wash-off processes with ecological memory

Urbanization increases the extent of impervious surfaces, runoff, sediment, and nutrient loadings downstream, leading to the deterioration of urban surface waters. During pollutant wash-off from urban surfaces, the peak concentration of pollutants typically occurs after the rainfall peak. However, current urban wash-off models do not consider this time delay, assuming that the effect of rainfall on the wash-off process is immediate. Ecological memory (EM) is defined as the capacity of past states or experiences to influence the present or future ecological responses of a community ecosystem. In this study, ecological memory was calculated to reflect the lagging impact of rainfall on the wash-off process. Incorporating ecological memory into the original wash-off model improved its performance across all pollutant types and rainfall conditions, with the adjusted R-squared value increasing from -0.01-0.61 to -0.08-0.83. Among the factors impacting ecological memory, rainfall intensity significantly affected the distributions of ecological memory (p < 0.05 according to the Kolmogorov-Smirnov test). The first flush phenomenon, which involves a larger concentration or mass of pollutants in the initial portion of a storm event compared to the rest, showed no significant difference in the distributions of ecological memory between rain events with and without this phenomenon. The improved urban wash-off model can be applied for real-time simulation of urban pollutants and help develop site-specific measures for reducing urban nonpoint source pollution.

Legacy effects of precipitation change: Theories, dynamics, and applications

The intensification of climate-induced precipitation change poses a dual challenge to terrestrial ecosystems: immediate effects on their structure and function, coupled with legacy effects that persist beyond the cessation of precipitation change. Quantifying these legacy effects accurately can greatly assist in assessing the long-term impact of precipitation change. However, their broader understanding is just beginning. Therefore, this review endeavors to synthesize the existing knowledge concerning the legacy effects of precipitation change, elucidating their nature, characteristics, driving factors, and implications, thereby fostering further advancements in this research domain. To begin, we define that precipitation legacies are carried by the information and/or material remnants arising from previous precipitation change, with the enduring impacts of these remnants (precipitation legacy carriers) on the current ecosystem being termed the precipitation legacy effects. To comprehensively investigate the performances of precipitation legacy effects, we introduce a multi-faceted characterization framework, encompassing magnitude, direction, duration, and spatial-temporal variability. This framework is complemented by a proposed sequential analysis approach, spanning the pre-, during, and post-precipitation change phases. Next, we emphasize that the nature of precipitation legacy carriers and the pattern of precipitation change jointly determine the characteristics of precipitation legacy effect. Subsequently, we elucidate the possible carriers of precipitation legacies across species, community, and ecosystem levels, as well as the linkages among these carriers and levels, thereby introducing the underlying formation mechanism of precipitation legacy effects. Lastly, from the perspective of ecosystem stability debt, we propose potential applications of precipitation legacy effects in future climate change research. The viewpoints and methodologies outlined in this review can deepen our comprehension of precipitation legacy effects, contributing to the comprehensive assessment of precipitation impact on soil-vegetation systems and providing guidance for formulating effective strategies to address future climate change.

Paddy-upland rotation combined with manure application: An optimal strategy for enhancing soil multifunctionality

Promoting soil multifunctionality is pivotal for maintaining agricultural productivity and sustainable agriculture, especially with the increasing global population and food demand. The effectiveness of different agricultural practices in enhancing soil multifunctionality and how the combination can maximize soil multifunctionality remains unknown. This study aimed to investigate the different impacts of rotation (paddy-upland rotation and dryland rotation) combined with fertilization (chemical fertilizer and manure) on soil multifunctionality, microbial community structure, and microbial networks. A two-year field experiment was conducted at the Fengqiu National Agro-Ecosystem Observation and Research Station in Henan Province, China, comparing the differences between rice-wheat rotation (paddy-upland rotation) and maize-wheat rotation (dryland rotation) combined with chemical fertilizer and pig manure. This finding revealed that paddy-upland rotation combined with manure application had the optimal effect in enhancing soil multifunctionality with a 216.25 % enhancement while contributing to a yield increase of 222.71 %. Notably, paddy-upland rotation and fertilization significantly promoted the soil bacterial network complexity and robustness, and these network properties were crucial factors in predicting soil multifunctionality. This study provides a new insight for developing a comprehensive strategy combining paddy-upland rotation with manure application in the future, which can help us to better improve soil health and agricultural sustainability.

The strong seasonality of soil microbial community structure in declining Mediterranean pine forests depends more on soil conditions than on tree vitality

The soil microbiome plays an important role in forest functioning. However, the impact of drought-induced dieback and tree death on soil microbial biomass, community structure, and functional composition is unknown. We also lack understanding on how soil microbiota varies seasonally in such declining stands. We used Phospholipid Fatty Acids (PLFA) analysis to quantify soil microbial biomass and study its seasonal changes in three Mediterranean forests showing dieback and dominated by three pine species (Pinus halepensis Mill, Pinus pinaster Ait. and Pinus sylvestris L.). We also measured microclimatic parameters and soil physical and chemical parameters under trees with different vigor, assessed as canopy defoliation degree, and related them to seasonal changes in the soil microbial community. We found marked differences in soil microbial community structure, total biomass, and the relative abundance of major functional groups among forests. First, soil microbial biomass peaked either in the dry summer (P. halepensis) or in autumn (P. pinaster and P. sylvestris). Accordingly, the relative abundance of most functional groups, excluding Arbuscular mycorrhizal fungi, displayed substantial variation between seasons. In addition, the relative abundance of fungi and Gram-positive bacteria exhibited an opposite pattern compared to actinomycetes and Gram-negative bacteria. Second, soil physical and chemical parameters had a significant impact on within-site PLFA variation, although their influence was less important than that of seasonal variation. Third, differences between defoliated and healthy trees were minor and restricted to averaged ratios between different PLFA markers. Overall, the structure, biomass and relative abundance of major functional groups of the soil microbiome vary considerably among stand types and seasons in forests showing ongoing dieback and high mortality. However, while the seasonal dynamics show predictable patterns, which should be accounted for in future studies, the within-site variation is highly variable and mainly depends on soil physical and chemical parameters.

Exploring and exploiting the rice phytobiome to tackle climate change challenges

The future of agriculture is uncertain under the current climate change scenario. Climate change directly and indirectly affects the biotic and abiotic elements that control agroecosystems, jeopardizing the safety of the world's food supply. A new area that focuses on characterizing the phytobiome is emerging. The phytobiome comprises plants and their immediate surroundings, involving numerous interdependent microscopic and macroscopic organisms that affect the health and productivity of plants. Phytobiome studies primarily focus on the microbial communities associated with plants, which are referred to as the plant microbiome. The development of high-throughput sequencing technologies over the past 10 years has dramatically advanced our understanding of the structure, functionality, and dynamics of the phytobiome; however, comprehensive methods for using this knowledge are lacking, particularly for major crops such as rice. Considering the impact of rice production on world food security, gaining fresh perspectives on the interdependent and interrelated components of the rice phytobiome could enhance rice production and crop health, sustain rice ecosystem function, and combat the effects of climate change. Our review re-conceptualizes the complex dynamics of the microscopic and macroscopic components in the rice phytobiome as influenced by human interventions and changing environmental conditions driven by climate change. We also discuss interdisciplinary and systematic approaches to decipher and reprogram the sophisticated interactions in the rice phytobiome using novel strategies and cutting-edge technology. Merging the gigantic datasets and complex information on the rice phytobiome and their application in the context of regenerative agriculture could lead to sustainable rice farming practices that are resilient to the impacts of climate change.

Soil fungi remain active and invest in storage compounds during drought independent of future climate conditions

Microbial growth is central to soil carbon cycling. However, how microbial communities grow under climate change is still largely unexplored. Here we use a unique field experiment simulating future climate conditions (increased atmospheric CO2 and temperature) and drought concomitantly and investigate impacts on soil microbial activity. We trace 2H or 18O applied via water-vapor exchange into membrane (and storage) fatty acids or DNA, respectively, to assess community- and group-level adjustments in soil microbial physiology (replication, storage product synthesis, and carbon use efficiency). We show that, while bacterial growth decreases by half during drought, fungal growth remains stable, demonstrating a remarkable resistance against soil moisture changes. In addition, fungal investment into storage triglycerides increases more than five-fold under drought. Community-level carbon use efficiency (the balance between anabolism and catabolism) is unaffected by drought but decreases in future climate conditions, favoring catabolism. Our results highlight that accounting for different microbial growth strategies can foster our understanding of soil microbial contributions to carbon cycling and feedback on the climate system.

Seasonal dynamics of soil microbiome in response to dry-wet alternation along the Jinsha River Dry-hot Valley

BACKGROUND

Soil microorganisms play a key role in nutrient cycling, carbon sequestration, and other important ecosystem processes, yet their response to seasonal dry-wet alternation remains poorly understood. Here, we collected 120 soil samples from dry-hot valleys (DHVs, ~ 1100 m a.s.l.), transition (~ 2000 m a.s.l.) and alpine zones (~ 3000 m a.s.l.) along the Jinsha River in southwest China during both wet and dry seasons. Our aims were to investigate the bacterial microbiome across these zones, with a specific focus on the difference between wet and dry seasons.

RESULTS

Despite seasonal variations, bacterial communities in DHVs exhibit resilience, maintaining consistent community richness, diversity, and coverage. This suggests that the microbes inhabiting DHVs have evolved adaptive mechanisms to withstand the extreme dry and hot conditions. In addition, we observed season-specific microbial clades in all sampling areas, highlighting their resilience to environmental fluctuations. Notably, we found similarities in microbial clades between soils from DHVs and the transition zones, including the phyla Actinomycetota, Chloroflexota, and Pseudomonadota. The neutral community model respectively explained a substantial proportion of the community variation in DHVs (87.7%), transition (81.4%) and alpine zones (81%), indicating that those were predominantly driven by stochastic processes. Our results showed that migration rates were higher in the dry season than in the wet season in both DHVs and the alpine zones, suggesting fewer diffusion constraints. However, this trend was reversed in the transition zones.

CONCLUSIONS

Our findings contribute to a better understanding of how the soil microbiome responds to seasonal dry-wet alternation in the Jinsha River valley. These insights can be valuable for optimizing soil health and enhancing ecosystem resilience, particularly in dry-hot valleys, in the context of climate change.

Bacterial accumulation dynamics in runoff from extreme precipitation

Extreme precipitation can significantly influence the water quality of surface waters. However, the total amount of bacteria carried by rainfall runoff is poorly understood. Here, thirty rainfall scenarios were simulated by artificial rainfall simulators, with designed rainfall intensity ranging from 19.3 to 250 mm/h. The instantaneous concentration ranges of R2A, nutrient agar (NA) culturable bacteria, and viable bacteria in runoff depended on the types of underlying surfaces. The instantaneous bacterial concentrations in runoff generated by forest lands, grasslands and bare soil were: R2A culturable bacteria = 104.5-6.3, 104.5-6.1, 104.0-5.3 colony-forming units (CFU)/mL, NA culturable bacteria = 104.0-6.0, 103.9-5.8, 103.2-4.9 CFU/mL, and viable bacteria = 106.4-8.0, 107.0-8.9, 106.4-7.6 cells/mL. Based on the measured bacterial instantaneous concentration in runoff, cumulative dynamic models were established, and the maximum amount of culturable bacteria and viable bacteria entering water sources were estimated to be 109.38-11.31 CFU/m2 and 1011.84-13.25 cells/m2, respectively. The model fitting and the bacterial accumulation dynamics were influenced by the rainfall types (p < 0.01). Surface runoff from the underlying surface of forest lands and grasslands had a high microbial risk that persisted even during the "Drought-to-Deluge Transition". Bacterial accumulation models provide valuable insight for predicting microbial risks in catchments during precipitation and can serve as theoretical support for further ensuring the safety of drinking water under the challenge of climate change.

Protists and fungi: Reinforcing urban soil ecological functions against flash droughts

Rising instances of flash droughts are contributing to notable variability in soil moisture across terrestrial ecosystems. These phenomena challenge urban ecosystem services, yet the reaction of soil ecological functions (SEFs) to such events is poorly understood. This study investigates the responses of SEFs (about nutrient metabolism capacity and potential) and the microbiome under two specific scenarios: a flooding-drought sequence and a direct drought condition. Using quantitative microbial element cycling analysis, high-throughput sequencing, and enzyme activity measurements, we found that unlike in forests, the microbial composition in urban soils remained unchanged during flash drought conditions. However, SEFs were affected in both settings. Correlation analysis and Mantel test showed that forest soils exhibited more complex interactions among soil moisture, properties, and microbial communities. Positive linear correlation revealed that bacteria were the sole drivers of SEFs. Interestingly, while multi-threshold results suggested bacterial α diversity impeded the maximization of SEFs in urban soils, fungi and protists had a beneficial impact. Cross-domain network of urban soils had higher number of nodes and edges, but lower average degree and robustness than forest soils. Mantel test revealed that fungi and protist had significant correlations with bacterial composition in forest soils, but not in urban soils. In the urban network, the degree and eigenvector centrality of bacterial, fungal and protistan ASVs were significantly lower compared to those in the forest. These results suggest that the lower robustness of the microbial network in urban soils is attributed to limited interactions among fungi, consumer protists, and bacteria, contributing to the failure of microbial-driven ecological functions. Overall, our findings emphasize the critical role of fungi and protists in shielding urban soils from drought-induced disturbances and in enhancing the resistance of urban ecological functions amidst environmental changes.

Effects of the recovery period after particulate matter pollution events on the dust retention capacity and physiological characteristics of Nerium oleander

Plants are known for their significant dust retention capacity and are widely used to alleviate atmospheric pollution. Urban green plants are exposed to periodic particulate matter pollution stress, and the time intervals between periods of pollution exposure are often inconsistent. The impact of stress memory and pollution intervals on plant dust retention capacity and physiological characteristics during periodic stress is not yet clear. In this study, the common urban landscaping species Nerium oleander L. was selected as the test plant, and stable isotope (15NH4Cl) tracing technology and aerosol generators were used to simulate periodic PM2.5 pollution. This study included two particulate pollution periods (each lasting 14 days) and one recovery period with three different durations (7, 14, and 21 days). The results indicated that periodic particulate matter pollution-induced stress decreased the dust retention capacity of N. oleander leaf surfaces, but particle adsorption to the wax layer was more stable. As the duration of the recovery period increased, leaf particle absorption, which accounted for the greatest proportion of total dust retention, increased, indicating that leaves are the primary organ for dust retention in Nerium oleander L. Root absorption also increased with increasing recovery periods. Prior pollution stress increased oleander physiological and morphological responses, and the plant's air pollution tolerance significantly improved after a recovery period of >14 days.

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.

Bacterial community response to novel and repeated disturbances

Disturbance response and recovery are increasingly important in microbial ecology, as microbes may recover from disturbances differently than macro communities. Past disturbances can alter microbial community structure and their response to subsequent disturbance events, but it remains unclear if the same recovery patterns persist after long-term exposure to stress. Here, we compare bacterial community composition in a community that experienced 2 years of monthly salinity addition disturbances with a community that has not experienced salinity additions. We then track the response and recovery to an additional salinity addition based on past disturbance exposure. We tested the following hypotheses: first, communities with a repeated disturbance history will have a different community composition than communities without a disturbance history; second, communities exposed to repeated disturbances will undergo a different recovery trajectory than communities experiencing a novel disturbance. We find that repeated disturbances alter community composition and affect community response and recovery to a subsequent disturbance after 2 years, primarily through increased resistance. This work enhances our understanding of microbial temporal dynamics and suggests that novel disturbances may pose a threat to microbial community structure and function.

Native Plant Diversity Generates Microbial Legacies That Either Promote or Suppress Non-Natives, Depending on Drought History

Diverse native plant communities resist non-native plants more than species-poor communities, in part through resource competition. The role of soil biota in diversity-invasibility relationships is poorly understood, although non-native plants interact with soil biota during invasions. We tested the responses of non-native plants to soil biota generated by different native plant diversities. We applied well-watered and drought treatments in both conditioning and response phases to explore the effects of 'historical' and 'contemporary' environmental stresses. When generated in well-watered soils, the microbial legacies from higher native diversity inhibited non-native growth in well-watered conditions. In contrast, when generated in drought-treated soils, the microbial legacies from higher native diversity facilitated non-native growth in well-watered conditions. Contemporary drought eliminated microbial legacy effects on non-native growth. We provide a new understanding of mechanisms behind diversity-invasibility relationships and demonstrate that temporal variation in environmental stress shapes relationships among native plant diversity, soil biota and non-native plants.

Evaluation of forest ecosystem resilience to drought considering lagged effects of drought

Drought can cause significant disruption to forest ecosystems and may have long-term impacts on the structure and function of ecosystems after the end of drought. This is the key to quantifying the ability of ecosystem to respond to disturbance events by comprehensively analyzing the impact of drought on vegetation, the lagged effect, and ecosystem resilience to drought. This article takes broad-leaved forests and coniferous forests in multiple temperature zones of China as the object of study, using distributed lagged nonlinear model (DLNM) to construct a systematic method. Our results show that the main sensitive lagged time for coniferous forests and broad-leaved forests is the first 3 months in various temperature zones, with the strongest lagged effect in the month when the drought incidents occur. Coping capacity represents ecosystems to remain stable during droughts, and we quantified the indicator by the ratio of the resistance (the difference between NDVI value before the drought and during the drought) to recovery (the difference between NDVI value after the drought and during the drought). When dealing with intensive drought events, the coping capacity of subtropical broad-leaved forests (-0.67) and tropical broad-leaved forests (-0.88) exhibit the strongest coping capacity (value tends to -1). Overall, vegetation growth in subtropical and tropical regions is less affected by drought compared to temperate and cold temperate zones. The research results help us understand the comprehensive impact of drought on vegetation and the strategies for different vegetation to cope with drought.

Persistent legacy effects on soil metagenomes facilitate plant adaptive responses to drought

Both chronic and acute drought alter the composition and physiology of soil microbiomes, with implications for globally important processes including carbon cycling and plant productivity. When water is scarce, selection favors microbes with thicker peptidoglycan cell walls, sporulation ability, and constitutive osmolyte production (Schimel, Balser, and Wallenstein 2007)-but also the ability to degrade complex plant-derived polysaccharides, suggesting that the success of plants and microbes during drought are inextricably linked. However, communities vary enormously in their drought responses and subsequent interactions with plants. Hypothesized causes of this variation in drought resilience include soil texture, soil chemistry, and historical precipitation patterns that shaped the starting communities and their constituent species (Evans, Allison, and Hawkes 2022). Currently, the physiological and molecular mechanisms of microbial drought responses and microbe-dependent plant drought responses in diverse natural soils are largely unknown (de Vries et al. 2023). Here, we identify numerous microbial taxa, genes, and functions that characterize soil microbiomes with legacies of chronic water limitation. Soil microbiota from historically dry climates buffered plants from the negative effects of subsequent acute drought, but only for a wild grass species native to the same region, and not for domesticated maize. In particular, microbiota with a legacy of chronic water limitation altered the expression of a small subset of host genes in crown roots, which mediated the effect of acute drought on transpiration and intrinsic water use efficiency. Our results reveal how long-term exposure to water stress alters soil microbial communities at the metagenomic level, and demonstrate the resulting "legacy effects" on neighboring plants in unprecedented molecular and physiological detail.

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

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

Enhancement of nitrogen on core taxa recruitment by Penicillium oxalicum stimulated microbially-driven soil formation in bauxite residue

Microbially-driven soil formation process is an emerging technology for the ecological rehabilitation of alkaline tailings. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. Herein, a 1-year field-scale experiment was applied to demonstrate the effect of nitrogen input on the structure and function of the microbiome in alkaline bauxite residue. Results showed that the contents of nutrient components were increased with Penicillium oxalicum (P. oxalicum) incorporation, as indicated by the increasing of carbon and nitrogen mineralization and enzyme metabolic efficiency. Specifically, the increasing enzyme metabolic efficiency was associated with nitrogen input, which shaped the microbial nutrient acquisition strategy. Subsequently, we evidenced that P. oxalicum played a significant role in shaping the assemblages of core bacterial taxa and influencing ecological functioning through intra- and cross-kingdom network analysis. Furthermore, a recruitment experiment indicated that nitrogen enhanced the enrichment of core microbiota (Nitrosomonas, Bacillus, Pseudomonas, and Saccharomyces) and may provide benefits to fungal community bio-diversity and microbial network stability. Collectively, these results demonstrated nitrogen-based coexistence patterns among P. oxalicum and microbiome and revealed P. oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. It will aid in promoting soil formation and ecological rehabilitation of bauxite residue. ENVIRONMENT IMPLICATION: Bauxite residue is a highly alkaline solid waste generated during the Bayer process for producing alumina. Attempting to transform bauxite residue into a stable soil-like substrate using low-cost microbial resources is a highly promising engineering. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. In this study, we evidenced the nitrogen-based coexistence patterns among Penicillium oxalicum and microbiome and revealed Penicillium oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. This study can improve the understanding of core microbes' assemblies that affect the microbiome physiological traits in soil formation processes.

Aridity shapes distinct biogeographic and assembly patterns of forest soil bacterial and fungal communities at the regional scale

Climate change is exacerbating drought in arid and semi-arid forest ecosystems worldwide. Soil microorganisms play a key role in supporting forest ecosystem services, yet their response to changes in aridity remains poorly understood. We present results from a study of 84 forests at four south-to-north Loess Plateau sites to assess how increases in aridity level (1- precipitation/evapotranspiration) shapes soil bacterial and fungal diversity and community stability by influencing community assembly. We showed that soil bacterial diversity underwent a significant downward trend at aridity levels >0.39, while fungal diversity decreased significantly at aridity levels >0.62. In addition, the relative abundance of Actinobacteria and Ascomycota increased with higher aridity level, while the relative abundance of Acidobacteria and Basidiomycota showed the opposite trend. Bacterial communities also exhibited higher similarity-distance decay rates across geographic and environmental gradients than did fungal communities. Phylogenetic bin-based community assembly analysis revealed homogeneous selection and dispersal limitation as the two dominant processes in bacterial and fungal assembly. Dispersal limitation of bacterial communities monotonically increased with aridity levels, whereas homogeneous selection of fungal communities monotonically decreased. Importantly, aridity also increased the sensitivity of microbial communities to environmental disturbance and potentially decreased community stability, as evidenced by greater community similarity-environmental distance decay rates, narrower habitat niche breadth, and lower microbial network stability. Our study provides new insights into soil microbial drought response, with implications on the sustainability of ecosystems under environmental stress.

Quantifying functional redundancy in polysaccharide-degrading prokaryotic communities

BACKGROUND

Functional redundancy (FR) is widely present, but there is no consensus on its formation process and influencing factors. Taxonomically distinct microorganisms possessing genes for the same function in a community lead to within-community FR, and distinct assemblies of microorganisms in different communities playing the same functional roles are termed between-community FR. We proposed two formulas to respectively quantify the degree of functional redundancy within and between communities and analyzed the FR degrees of carbohydrate degradation functions in global environment samples using the genetic information of glycoside hydrolases (GHs) encoded by prokaryotes.

RESULTS

Our results revealed that GHs are each encoded by multiple taxonomically distinct prokaryotes within a community, and the enzyme-encoding prokaryotes are further distinct between almost any community pairs. The within- and between-FR degrees are primarily affected by the alpha and beta community diversities, respectively, and are also affected by environmental factors (e.g., pH, temperature, and salinity). The FR degree of the prokaryotic community is determined by deterministic factors.

CONCLUSIONS

We conclude that the functional redundancy of GHs is a stabilized community characteristic. This study helps to determine the FR formation process and influencing factors and provides new insights into the relationships between prokaryotic community biodiversity and ecosystem functions. Video Abstract.

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

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

Comparative metabolic profiling of the mycelium and fermentation broth of Penicillium restrictum from Peucedanum praeruptorum rhizosphere

Microorganisms in the rhizosphere, particularly arbuscular mycorrhiza, have a broad symbiotic relationship with their host plants. One of the major fungi isolated from the rhizosphere of Peucedanum praeruptorum is Penicillium restrictum. The relationship between the metabolites of P. restrictum and the root exudates of P. praeruptorum is being investigated. The accumulation of metabolites in the mycelium and fermentation broth of P. restrictum was analysed over different fermentation periods. Non-targeted metabolomics was used to compare the differences in intracellular and extracellular metabolites over six periods. There were significant differences in the content and types of mycelial metabolites during the incubation. Marmesin, an important intermediate in the biosynthesis of coumarins, was found in the highest amount on the fourth day of incubation. The differential metabolites were screened to obtain 799 intracellular and 468 extracellular differential metabolites. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the highly enriched extracellular metabolic pathways were alanine, aspartate and glutamate metabolism, glyoxylate and dicarboxylate metabolism, and terpenoid backbone biosynthesis. In addition, the enrichment analysis associated with intracellular and extracellular ATP-binding cassette transporter proteins revealed that some ATP-binding cassette transporters may be involved in the transportation of certain amino acids and carbohydrates. Our results provide some theoretical basis for the regulatory mechanisms between the rhizosphere and the host plant and pave the way for the heterologous production of furanocoumarin.

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.

Drought resistance and resilience of rhizosphere communities in forest soils from the cellular to ecosystem scale - insights from 13C pulse labeling

The link between above- and belowground communities is a key uncertainty in drought and rewetting effects on forest carbon (C) cycle. In young beech model ecosystems and mature naturally dry pine forest exposed to 15-yr-long irrigation, we performed 13C pulse labeling experiments, one during drought and one 2 wk after rewetting, tracing tree assimilates into rhizosphere communities. The 13C pulses applied in tree crowns reached soil microbial communities of the young and mature forests one and 4 d later, respectively. Drought decreased the transfer of labeled assimilates relative to the irrigation treatment. The 13C label in phospholipid fatty acids (PLFAs) indicated greater drought reduction of assimilate incorporation by fungi (-85%) than by gram-positive (-43%) and gram-negative bacteria (-58%). 13C label incorporation was more strongly reduced for PLFAs (cell membrane) than for microbial cytoplasm extracted by chloroform. This suggests that fresh rhizodeposits are predominantly used for osmoregulation or storage under drought, at the expense of new cell formation. Two weeks after rewetting, 13C enrichment in PLFAs was greater in previously dry than in continuously moist soils. Drought and rewetting effects were greater in beech systems than in pine forest. Belowground C allocation and rhizosphere communities are highly resilient to drought.

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

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

Host genotype-specific rhizosphere fungus enhances drought resistance in wheat

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Independent and combined effects of microplastics pollution and drought on soil bacterial community

Global terrestrial ecosystems are simultaneously threatened by multiple environmental pressures, with microplastics (MPs) pollution and drought possibly being the most pressing, both of which may have unanticipated effects on soil organisms. Here, we investigated the responses of diversity, composition and functions of soil bacterial community to MPs pollution (including two MPs types: polyethylene (PE) and polylactic acid (PLA); two MPs sizes: < 20 μm and <300 μm) and drought in microcosms. We found that only 20 μm PLA MPs significantly decreased soil bacterial diversity by 17.4 % and altered soil bacterial community composition, while PE MPs and 300 μm PLA MPs had no significant effects. The copiotrophic bacteria (i.e., Proteobacteria and Firmicutes) were enriched in the 20 μm PLA MPs pollution soils due to the enhanced dissolved organic carbon contents. Moreover, our results showed that the 20 μm PLA MPs also affected the potential phenotypes and functions of soil bacterial community, increasing the potentially pathogenic, stress-tolerant, containing mobile elements and forming biofilms phenotypes, and promoting membrane transport and signal transduction pathways. These results suggested that the effects of MPs on soil bacterial community varied depending on MPs types and sizes. However, drought significantly increased soil bacterial diversity by 10.3 % and affected soil bacterial community composition in the 20 μm PLA MPs pollution soils. We also found that drought inhibited the levels of potentially pathogenic, containing mobile elements and forming biofilms phenotypes in the 20 μm PLA MPs pollution soils. Taken together, these findings reveal that drought may alleviate the adverse effects of MPs pollution on soil bacterial community, which enhances our understanding of the interactive effects of multiple global change factors on agroecosystem functions.

Monotonic trends of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China

To investigate microbial communities and their contributions to carbon and nutrient cycling along water gradients can enhance our comprehension of climate change impacts on ecosystem services. Thus, we conducted an assessment of microbial communities, metagenomic functions, and metabolomic profiles within four ecosystems, i.e., desert grassland (DG), shrub-steppe (SS), forest (FO), and marsh (MA) in the Altai region of Xinjiang, China. Our results showed that soil total carbon (TC), total nitrogen, NH4+, and NO3- increased, but pH decreased with soil water gradients. Microbial abundances and richness also increased with soil moisture except the abundances of fungi and protists being lowest in MA. A shift in microbial community composition is evident along the soil moisture gradient, with Proteobacteria, Basidiomycota, and Evosea proliferating but a decline in Actinobacteria and Cercozoa. The β-diversity of microbiomes, metagenomic, and metabolomic functioning were correlated with soil moisture gradients and have significant associations with specific soil factors of TC, NH4+, and pH. Metagenomic functions associated with carbohydrate and DNA metabolisms, as well as phages, prophages, TE, plasmids functions diminished with moisture, whereas the genes involved in nitrogen and potassium metabolism, along with certain biological interactions and environmental information processing functions, demonstrated an augmentation. Additionally, MA harbored the most abundant metabolomics dominated by lipids and lipid-like molecules and organic oxygen compounds, except certain metabolites showing decline trends along water gradients, such as N'-Hydroxymethylnorcotinine and 5-Hydroxyenterolactone. Thus, our study suggests that future ecosystem succession facilitated by changes in rainfall patterns will significantly alter soil microbial taxa, functional potential, and metabolite fractions.

Microbial regulation of feedbacks to ecosystem change

Microbes are key biodiversity components of all ecosystems and control vital ecosystem functions. Although we have just begun to unravel the scales and factors that regulate microbial communities, their role in mediating ecosystem stability in response to disturbances remains underexplored. Here, we review evidence of how, when, and where microbes regulate or drive disturbance feedbacks. Negative feedbacks dampen the impacts of disturbance, which maintain ecosystem stability, whereas positive feedbacks instead erode stability by amplifying the disturbance. Here we describe the processes underlying the responses to disturbance using a hierarchy of functional traits, and we exemplify how these may drive biogeochemical feedbacks. We suggest that the feedback potential of functional traits at different hierarchical levels is contingent on the complexity and heterogeneity of the environment.

Water Level Fluctuations Modulate the Microbiomes Involved in Biogeochemical Cycling in Floodplains

Drastic changes in hydrological conditions within floodplain ecosystems create distinct microbial habitats. However, there remains a lack of exploration regarding the variations in microbial function potentials across the flooding and drought seasons. In this study, metagenomics and environmental analyses were employed in floodplains that experience hydrological variations across four seasons. Analysis of functional gene composition, encompassing nitrogen, carbon, and sulfur metabolisms, revealed apparent differences between the flooding and drought seasons. The primary environmental drivers identified were water level, overlying water depth, submergence time, and temperature. Specific modules, e.g., the hydrolysis of β-1,4-glucosidic bond, denitrification, and dissimilatory/assimilatory nitrate reduction to ammonium, exhibited higher relative abundance in summer compared to winter. It is suggested that cellulose degradation was potentially coupled with nitrate reduction during the flooding season. Phylogenomic analysis of metagenome-assembled genomes (MAGs) unveiled that the Desulfobacterota lineage possessed abundant nitrogen metabolism genes supported by pathway reconstruction. Variation of relative abundance implied its environmental adaptability to both the wet and dry seasons. Furthermore, a novel order was found within Methylomirabilota, containing nitrogen reduction genes in the MAG. Overall, this study highlights the crucial role of hydrological factors in modulating microbial functional diversity and generating genomes with abundant nitrogen metabolism potentials.

High intensity perturbations induce an abrupt shift in soil microbial state

Soil microbial communities play a pivotal role in regulating ecosystem functioning. But they are increasingly being shaped by human-induced environmental change, including intense "pulse" perturbations, such as droughts, which are predicted to increase in frequency and intensity with climate change. While it is known that soil microbial communities are sensitive to such perturbations and that effects can be long-lasting, it remains untested whether there is a threshold in the intensity and frequency of perturbations that can trigger abrupt and persistent transitions in the taxonomic and functional characteristics of soil microbial communities. Here we demonstrate experimentally that intense pulses of drought equivalent to a 30-year drought event (<15% WHC) induce a major shift in the soil microbial community characterised by significantly altered bacterial and fungal community structures of reduced complexity and functionality. Moreover, the characteristics of this transformed microbial community persisted after returning soil to its previous moisture status. As a result, we found that drought had a strong legacy effect on bacterial community function, inducing an enhanced growth rate following subsequent drought. Abrupt transitions are widely documented in aquatic and terrestrial plant communities in response to human-induced perturbations. Our findings demonstrate that such transitions also occur in soil microbial communities in response to high intensity pulse perturbations, with potentially deleterious consequences for soil health.

Cumulative effects of drought have an impact on net primary productivity stability in Central Asian grasslands

Global warming has exacerbated the threat of drought in Central Asia, amplifying its ecological implications within the region's grassland ecosystems. This has become an increasingly prominent issue that requires attention and action. The temporal link between grassland development and drought is asymmetric. However, a quantitative assessment of the temporal effects of multiscale drought on Central Asian grasslands has yet to be explored. Based on correlation analysis and the coefficient of variation method, this study analysed the cumulative and lag effects of multitimescale drought on grassland NPP (net primary productivity) under different climatic zones, altitudes and water availabilities in Central Asia from 1982 to 2018, and discussed the impact of temporal effects on grassland NPP stability. Our results on the cumulative effects of drought on grasslands indicate the 6.72 months preceding NPP measurement was the duration for which, on average, drought was most strongly correlated with NPP. Additionally, we found a mean lagged effect of 5.36 months, meaning that the monthly drought 5.36 months prior to NPP measurement was, on average, most strongly correlated with NPP. The degree to which grassland NPP was affected by cumulative drought at a given level of water availability was inversely proportional to the number of cumulative drought months. Under different water availabilities, the lagged effect of grassland NPP was stronger in dry areas than in wet areas, and the number of lag months tended to decrease and then increase as the water availability increased. The percentage of areas where grassland NPP was dominated by the cumulative and lagging effects of drought was 30.02% and 69.98%, respectively. The stability of grassland NPP was adversely affected by the drought accumulation effect. The findings of this study contribute to a deeper understanding of the long-term effects of drought on grassland ecosystems. Additionally, it will aid in the development of strategies for mitigating and adapting to drought events, thereby minimizing their negative impacts on agriculture, livestock, and ecosystems.

Extreme summers impact cropland and grassland soil microbiomes

The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond to such disturbances. Here, metagenomics was used to investigate the effects of future climate scenarios (+0.6 °C warming and altered precipitation) on soil microbiomes during the summers of 2014-2019. Unexpectedly, Central Europe experienced extreme heatwaves and droughts during 2018-2019, causing significant impacts on the structure, assembly, and function of soil microbiomes. Specifically, the relative abundance of Actinobacteria (bacteria), Eurotiales (fungi), and Vilmaviridae (viruses) was significantly increased in both cropland and grassland. The contribution of homogeneous selection to bacterial community assembly increased significantly from 40.0% in normal summers to 51.9% in extreme summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), and sporulation (spoIID, spoVK) were identified as potential contributors to drought-enriched taxa, and their expressions were confirmed by metatranscriptomics in 2022. The impact of extreme summers was further evident in the taxonomic profiles of 721 recovered metagenome-assembled genomes (MAGs). Annotation of contigs and MAGs suggested that Actinobacteria may have a competitive advantage in extreme summers due to the biosynthesis of geosmin and 2-methylisoborneol. Future climate scenarios caused a similar pattern of changes in microbial communities as extreme summers, but to a much lesser extent. Soil microbiomes in grassland showed greater resilience to climate change than those in cropland. Overall, this study provides a comprehensive framework for understanding the response of soil microbiomes to extreme summers.

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.

Impact of drought on soil microbial biomass and extracellular enzyme activity

Introduction

With the continuous changes in climate patterns due to global warming, drought has become an important limiting factor in the development of terrestrial ecosystems. However, a comprehensive understanding of the impact of drought on soil microbial activity at a global scale is lacking.

Methods

In this study, we aimed to examine the effects of drought on soil microbial biomass (carbon [MBC], nitrogen [MBN], and phosphorus [MBP]) and enzyme activity (β-1, 4-glucosidase [BG]; β-D-cellobiosidase [CBH]; β-1, 4-N-acetylglucosaminidase [NAG]; L-leucine aminopeptidase [LAP]; and acid phosphatase [AP]). Additionally, we conducted a meta-analysis to determine the degree to which these effects are regulated by vegetation type, drought intensity, drought duration, and mean annual temperature (MAT).

Result and discussion

Our results showed that drought significantly decreased the MBC, MBN, and MBP and the activity levels of BG and AP by 22.7%, 21.2%, 21.6%, 26.8%, and 16.1%, respectively. In terms of vegetation type, drought mainly affected the MBC and MBN in croplands and grasslands. Furthermore, the response ratio of BG, CBH, NAG, and LAP were negatively correlated with drought intensity, whereas MBN and MBP and the activity levels of BG and CBH were negatively correlated with drought duration. Additionally, the response ratio of BG and NAG were negatively correlated with MAT. In conclusion, drought significantly reduced soil microbial biomass and enzyme activity on a global scale. Our results highlight the strong impact of drought on soil microbial biomass and carbon- and phosphorus-acquiring enzyme activity.

Effects of moderate drought extension on bacterial network structure in the rhizosphere soil of Leymus chinensis in semi-arid grasslands

Introduction

Grasslands are home to complex bacterial communities whose dynamic interactions play a crucial role in organic matter and nutrient cycling. However, there is limited understanding regarding the impact of changes in rainfall amount and the duration of dry intervals on bacterial interactions.

Methods

To assess the impact of changes in precipitation volume and dry intervals on bacterial co-occurrence networks, we carried out precipitation manipulation experiments in the Eastern Eurasian Steppe of China.

Results and Discussion

We found that alterations in precipitation and dry intervals did not significantly affect bacterial alpha and beta diversity. However, we observed significant changes in the co-occurrence network structure of bacteria in the rhizosphere ecosystem, with the 12-day dry interval showing the most notable reduction in the number of degrees, edges, and clustering coefficient. Additionally, the study identified putative keystone taxa and observed that the moderately prolonged dry intervals between precipitation events had a major effect on the robustness of bacterial networks. The complexity and stability of the network were found to be positively correlated, and were primarily influenced by soil water content, phosphorous, and aboveground biomass, followed by available phosphorus (AP) and total biomass. These findings have the potential to enhance our comprehension of how bacterial co-occurrence pattern react to variations in dry intervals, by regulating their interactions in water-limited ecosystems. This, in turn, could aid in predicting the impact of precipitation regime alterations on ecosystem nutrient cycling, as well as the feedback between ecosystem processes and global climate change.

Nitrogen inhibitors improve soil ecosystem multifunctionality by enhancing soil quality and alleviating microbial nitrogen limitation

Soil quality (SQI) is a comprehensive indicator reflecting the agricultural productivity of soil, and soil ecosystem multifunctionality (performing multiple functions simultaneously; EMF) can reflect complex biogeochemical processes. However, the effects of enhanced efficiency nitrogen fertilizers (EENFs; urease inhibitors (NBPT), nitrification inhibitors (DCD), and coated controlled-release urea (RCN)) application on the SQI and soil EMF and their relationships are still unclear. Therefore, we conducted a field experiment to study the effects of different EENFs on the SQI, enzyme stoichiometry and soil EMF in semiarid areas of Northwest China (Gansu, Ningxia, Shaanxi, Shanxi). Across the four study sites, DCD and NBPT increased SQI by 7.61-16.80 % and 2.61 %-23.20 % compared to mineral fertilizer, respectively. N fertilizer application (N200 and EENFs) alleviated microbial N limitation, and EENFs alleviated microbial N and C limitations to a greater extent in Gansu and Shanxi. Moreover, nitrogen inhibitors (Nis; DCD and NBPT) improved the soil EMF to a greater extent than N200 and RCN, DCD increased by 205.82-340.00 % and 145.00-215.47 % in Gansu and Shanxi, respectively; NBPT increased by 332.75-778.59 % and 364.44-929.62 % in Ningxia and Shanxi, respectively. A random forest model showed that the microbial biomass carbon (MBC), microbial biomass nitrogen (MBN) and soil water content (SWC) of the SQI factors were the main driving forces of soil EMF. Moreover, SQI improvement could alleviate microbial C and N limitations and promote the improvement of soil EMF. It is worth noting that soil EMF was mainly affected by microbial N limitation rather than C limitation. Overall, NIs application is an effective way to improve the SQI and soil EMF in the semiarid region of Northwest China.

The diversity and abundance of bacterial and fungal communities in the rhizosphere of Cathaya argyrophylla are affected by soil physicochemical properties

Cathaya argyrophylla is an ancient Pinaceae species endemic to China that is listed on the IUCN Red List. Although C. argyrophylla is an ectomycorrhizal plant, the relationship between its rhizospheric soil microbial community and soil properties related to the natural habitat remains unknown. High-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences was used to survey the C. argyrophylla soil community at four natural spatially distributed points in Hunan Province, China, and functional profiles were predicted using PICRUSt2 and FUNGuild. The dominant bacterial phyla included Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, and the dominant genus was Acidothermus. The dominant fungal phyla were Basidiomycota and Ascomycota, while Russula was the dominant genus. Soil properties were the main factors leading to changes in rhizosphere soil bacterial and fungal communities, with nitrogen being the main driver of changes in soil microbial communities. The metabolic capacities of the microbial communities were predicted to identify differences in their functional profiles, including amino acid transport and metabolism, energy production and conversion, and the presence of fungi, including saprotrophs and symbiotrophs. These findings illuminate the soil microbial ecology of C. argyrophylla, and provide a scientific basis for screening rhizosphere microorganisms that are suitable for vegetation restoration and reconstruction for this important threatened species.