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

The bright side of ecological stressors

Ecological stressors are considered to negatively affect biological systems; however, corresponding responses to stressors can be complex, depending on the ecological functions and the number and duration of the stressors. Mounting evidence indicates potential benefits of stressors. Here, we develop an integrative framework to understand stressor-induced benefits by clarifying three categories of mechanisms: seesaw effects, cross-tolerance, and memory effects. These mechanisms operate across various organizational levels (e.g., individual, population, community) and can be extended to an evolutionary context. One remaining challenge is to develop scaling approaches for linking stressor-induced benefits across organizational levels. Our framework provides a novel platform for predicting the consequences of global environmental changes and informing management strategies in conservation and restoration practices.

Shifting microbial communities can enhance tree tolerance to changing climates

Climate change is pushing species outside of their evolved tolerances. Plant populations must acclimate, adapt, or migrate to avoid extinction. However, because plants associate with diverse microbial communities that shape their phenotypes, shifts in microbial associations may provide an alternative source of climate tolerance. Here, we show that tree seedlings inoculated with microbial communities sourced from drier, warmer, or colder sites displayed higher survival when faced with drought, heat, or cold stress, respectively. Microbially mediated drought tolerance was associated with increased diversity of arbuscular mycorrhizal fungi, whereas cold tolerance was associated with lower fungal richness, likely reflecting a reduced burden of nonadapted fungal taxa. Understanding microbially mediated climate tolerance may enhance our ability to predict and manage the adaptability of forest ecosystems to changing climates.

Soil drying legacy does not affect phenanthrene fate in soil but modifies bacterial community response

Alteration of the structure of soil microbial communities following the elimination of hydrophobic organic pollutants (e.g., polycyclic aromatic hydrocarbons, PAHs) is generally assessed using DNA-based techniques, and soil is often required to dry prior to pollutant addition, to facilitate a better mix when establishing microcosms. However, the drying practice may have a legacy effect on soil microbial community structure, which would in turn influence the biodegradation process. Here, we used ¹⁴C-labeled phenanthrene to examine the potential side effects of precedent short-term drought events. The results indicate that the drying practice had legacy effects on soil microbial community structure, illustrated by irreversible shifts in the communities. The legacy effects had no significant impact on phenanthrene mineralization and non-extractable residue formation. However, they altered the response of bacterial communities to PAH degradation, leading to a decrease in the abundance of potential PAH degradation genes plausibly attributed to moderately abundant taxa. Based on a comparison of the varied effects of different drying intensity levels, an accurate description of microbial responses to phenanthrene degradation strongly relies on the establishment of stable microbial communities before PAH amendment. Concurrent alterations in the communities resulting from environmental perturbation could greatly mask minor alterations from the degradation of recalcitrant hydrophobic PAH. In practice, to minimize the legacy effects, a soil equilibration step with a reduced drying intensity is indispensable.

Water quality improvement and consequent N2O emission reduction in hypoxic freshwater utilizing green oxygen-carrying biochar

Declines in dissolved oxygen (DO) levels in aquatic systems worldwide negatively influence biodiversity, nutrient biogeochemistry, drinking water quality, and greenhouse gas emission. As a response, oxygen-carrying dual-modified sediment-based biochar (O-DM-SBC) as a green and sustainable emerging material was utilized for simultaneous hypoxia restoration, water quality improvement, and greenhouse gas reduction. Column incubation experiments were carried out using the water and sediment samples from a tributary of the Yangtze River. The application of O-DM-SBC effectively increased the DO concentration from ~1.99 mg/L to ~6.44 mg/L and decreased the concentrations of TN and NH₄⁺-N by 61.1 % and 78.3 %, respectively, during the 30-day incubation period. Moreover, the N₂O emission was apparently inhibited by O-DM-SBC with a 50.2 % decrease in daily flux under the functional coupling of biochar (SBC) and oxygen nanobubbles (ONBs). Path analysis supported that the treatments (SBC, modification, and ONBs) had joint effects on N₂O emission by changing the concentration and composition of dissolved inorganic nitrogen (e.g., NH₄⁺-N, NO₂^--N and NO₃^--N). The nitrogen-transforming bacteria were found to be significantly promoted by O-DM-SBC at the end of the incubation, while the archaeal community seemed to be more active in the SBC groups without ONB, confirming their different mechanisms. The PICRUSt2 prediction results revealed that most nitrogen metabolism genes including nitrification (i.e., amoABC), denitrification (i.e., nirK and nosZ), and assimilatory nitrate reduction (i.e., nirB and gdhA) were largely enriched in O-DM-SBC, indicating the active nitrogen-cycling network was established, thus achieving simultaneous nitrogen pollution control and N₂O emission reduction. Our findings not only confirm the beneficial effect of O-DM-SBC amendment on nitrogen pollution control and N₂O emission mitigation in hypoxic freshwater, but also contribute to a more comprehensive understanding of the effect of oxygen-carrying biochar on nitrogen cycling microbial communities.

Functional Potential of Soil Microbial Communities and Their Subcommunities Varies with Tree Mycorrhizal Type and Tree Diversity

Soil microbial communities play crucial roles in the earth's biogeochemical cycles. Yet, their genomic potential for nutrient cycling in association with tree mycorrhizal type and tree-tree interactions remained unclear, especially in diverse tree communities. Here, we studied the genomic potential of soil fungi and bacteria with arbuscular (AM) and ectomycorrhizal (EcM) conspecific tree species pairs (TSPs) at three tree diversity levels in a subtropical tree diversity experiment (BEF-China). The soil fungi and bacteria of the TSPs' interaction zone were characterized by amplicon sequencing, and their subcommunities were determined using a microbial interkingdom co-occurrence network approach. Their potential genomic functions were predicted with regard to the three major nutrients carbon (C), nitrogen (N), and phosphorus (P) and their combinations. We found the microbial subcommunities that were significantly responding to different soil characteristics. The tree mycorrhizal type significantly influenced the functional composition of these co-occurring subcommunities in monospecific stands and two-tree-species mixtures but not in mixtures with more than three tree species (here multi-tree-species mixtures). Differentiation of subcommunities was driven by differentially abundant taxa producing different sets of nutrient cycling enzymes across the tree diversity levels, predominantly enzymes of the P (n = 11 and 16) cycles, followed by the N (n = 9) and C (n = 9) cycles, in monospecific stands and two-tree-species mixtures, respectively. Fungi of the Agaricomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes and bacteria of the Verrucomicrobia, Acidobacteria, Alphaproteobacteria, and Actinobacteria were the major differential contributors (48% to 62%) to the nutrient cycling functional abundances of soil microbial communities across tree diversity levels. Our study demonstrated the versatility and significance of microbial subcommunities in different soil nutrient cycling processes of forest ecosystems. IMPORTANCE Loss of multifunctional microbial communities can negatively affect ecosystem services, especially forest soil nutrient cycling. Therefore, exploration of the genomic potential of soil microbial communities, particularly their constituting subcommunities and taxa for nutrient cycling, is vital to get an in-depth mechanistic understanding for better management of forest soil ecosystems. This study revealed soil microbes with rich nutrient cycling potential, organized in subcommunities that are functionally resilient and abundant. Such microbial communities mainly found in multi-tree-species mixtures associated with different mycorrhizal partners can foster soil microbiome stability. A stable and functionally rich soil microbiome is involved in the cycling of nutrients, such as carbon, nitrogen, and phosphorus, and their combinations could have positive effects on ecosystem functioning, including increased forest productivity. The new findings could be highly relevant for afforestation and reforestation regimes, notably in the face of growing deforestation and global warming scenarios.

Plant-soil feedback under drought: does history shape the future?

Plant-soil feedback (PSF) is widely recognised as a driver of plant community composition, but understanding of its response to drought remains in its infancy. Here, we provide a conceptual framework for the role of drought in PSF, considering plant traits, drought severity, and historical precipitation over ecological and evolutionary timescales. Comparing experimental studies where plants and microbes do or do not share a drought history (through co-sourcing or conditioning), we hypothesise that plants and microbes with a shared drought history experience more positive PSF under subsequent drought. To reflect real-world responses to drought, future studies need to explicitly include plant-microbial co-occurrence and potential co-adaptation and consider the precipitation history experienced by both plants and microbes.

Microbial drought resistance may destabilize soil carbon

Droughts are becoming more frequent and intense with climate change. As plants and microbes respond to drought, there may be consequences for the vast stocks of organic carbon stored in soils. If microbes sustain their activity under drought, soils could lose carbon, especially if inputs from plants decline. Empirical and theoretical studies reveal multiple mechanisms of microbial drought resistance, including tolerance and avoidance. Physiological responses allow microbes to acclimate to drought within minutes to days. Along with dispersal, shifts in community composition could allow microbiomes to maintain functioning despite drought. Microbes might also adapt to drier conditions through evolutionary processes. Together, these mechanisms could result in soil carbon losses larger than currently anticipated under climate change.

Microbial community structure and denitrification responses to cascade low-head dams and their contribution to eutrophication in urban rivers

Low-head dams are one of the most common hydraulic facilities, yet they often fragment rivers, leading to profound changes in aquatic biodiversity and river eutrophication levels. Systematic assessments of river ecosystem structure and functions, and their contribution to eutrophication, are however lacking, especially for urban rivers where low-head dams prevail. In this study, we address this gap with a field survey on microbial community structure and ecosystem function, in combination with hydrological, environmental and ecological factors. Our findings revealed that microbial communities showed significant differences among the cascade impoundments, which may be due to the environment heterogeneity resulting from the cascade low-head dams. The alternating lentic-lotic flow environment created by the low-head dams caused nutrient accumulation in the cascade impoundments, enhancing environmental sorting and interspecific competition relationships, and thus possibly contributing to the reduction in sediment denitrification function. Decreased denitrification led to excessive accumulation of nutrients, which may have aggravated river eutrophication. In addition, structural equation model analysis showed that flow velocity may be the key controlling factor for river eutrophication. Therefore, in the construction of river flood control and water storage systems, the location, type and water storage capacity of low-head dams should be fully considered to optimize the hydrodynamic conditions of rivers. To summarize, our findings revealed the cumulative effects of cascade low-head dams in an urban river, and provided new insights into the trade-off between construction and decommissioning of low-head dams in urban river systems.

Different and unified responses of soil bacterial and fungal community composition and predicted functional potential to 3 years’ drought stress in a semiarid alpine grassland

Introduction

Soil microbial communities are key to functional processes in terrestrial ecosystems, and they serve as an important indicator of grasslands status. However, the responses of soil microbial communities and functional potential to drought stress in semiarid alpine grasslands remain unclear.

Methods

Here, a field experiment was conducted under ambient precipitation as a control, −20% and −40% of precipitation to explore the responses of soil microbial diversity, community composition, and predicted functional potential to drought stress in a semiarid alpine grassland located in the northwest of China. Moreover, 16S rRNA gene and ITS sequencing were used to detect bacterial and fungal communities, and the PICRUST and FUNGuild databases were used to predict bacterial and fungal functional groups.

Results

Results showed drought stress substantially changes the community diversity of bacteria and fungi, among which the bacteria community is more sensitive to drought stress than fungi, indicating that the diversity or structure of soil bacteria community could serve as an indicator of alpine grasslands status. However, the fungal community still has difficulty maintaining resistance under excessive drought stress. Our paper also highlighted that soil moisture content, plant diversity (Shannon Wiener, Pieiou, and Simpson), and soil organic matter are the main drivers affecting soil bacterial and fungal community composition and predicted functional potential. Notably, the soil microbial functional potential could be predictable through taxonomic community profiles.

Conclusion

Our research provides insight for exploring the mechanisms of microbial community composition and functional response to climate change (longer drought) in a semiarid alpine grassland.

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

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

Influence of exposure history on the particle retention capacity and physiological responses of Euonymus japonicus Thunb. var. aurea-marginatus Hort

Green plants in urban environments experience cyclical particulate matter stress. And this history of exhaust exposure may generate stress memory in plants, which may alter their subsequent response. Studies combining urban pollution characteristics and stress memory are limited. Therefore, we selected E. japonicus var. aurea-marginatus, a common urban greening tree species in the Yangtze River Delta, and conducted an experiment in three periods: the initial pollution period (S1: 28 days), the recovery period (R: 14 days) and the secondary pollution period (S2: 28 days). The experimental design consisted of an elevated pollution treatment (173 μg•cm^-3) and an ambient control (34 μg•cm^-3) with three replicates. In S2, the net total particle retention and saturated particle retention decreased by 11.5% and 19.3%, respectively, while PM₁₀ and PM_2.5 did not change significantly. E. japonicus var. aurea-marginatus exhibited recovery of chlorophyll levels, slower degradation of carotenoid, faster accumulation of ASA, lower accumulation of MDA, reduced activity of SOD under the second pollution period, and the period had a significant effect on the physiological indicators. Collectively, the effect of autoexhaust exposure history on the particle retention capacity of selected plant varied across particle sizes, and stress memory may confer plant resistance to recurrent exhaust pollution via combined regulations of physiological responses. Fine particles which pose a great risk to human health arise predominantly from vehicular traffic and energy production. So, E. japonicus tends to play a stabilising role in particle retention in industrial, traffic and residential areas.

Prolonged drought regulates the silage quality of maize (Zea mays L.): Alterations in fermentation microecology

Prolonged drought stress caused by global warming poses a tremendous challenge to silage production of maize. Drought during maize growth and development resulted in altered micro-environment for silage fermentation. How fermentation of silage maize responds to moisture scales remains uncharted territory. In this research, Maize water control trials were conducted and the silage quality and microbial community of drought-affected maize were determined. The results showed that drought stress significantly reduced the dry matter but increased root-to-shoot ratio, soluble sugar and malonaldehyde content in maize. Before fermentation, the crude protein, crude ash and acid detergent fiber contents were significantly increased but the ether extract content was decreased under drought. The crude protein and acid detergent fiber were significantly decreased in the drought affected group after fermentation. Furthermore, water stress at maize maturity stage greatly reduced the number of total bacteria in silage fermentation but increased the proportion of the lactobacillus and lactic acid content of silage. Drought stress alters the microbial ecosystem of the fermentation process and reconstitutes the diversity of the bacterial community and its metabolites. This study provides a theoretical basis for the study of changes in silage fermentation as affected by abiotic stresses.

Diversity-triggered bottom-up trophic interactions impair key soil functions under lindane pollution stress

A growing amount of evidence suggests that microbial diversity loss may have negative effects on soil ecosystem function. However, less attention has been paid to the determinants of the relationship between community diversity and soil functioning under pollution stress. Here we manipulated microbial diversity to observe how biotic and abiotic factors influenced soil multi-functions (e.g. lindane degradation, soil respiration and nutrient cycling). Results showed that protist community was more sensitive to dilution, pollution stress, and sodium acetate addition than bacterial and fungal community. Acetate addition accelerated the lindane removal. Any declines in microbial diversity reduced the specialized soil processes (NO₃-N production, and N₂O flux), but increased soil respiration rate. Dilution led to a significant increase in consumers-bacterial and fungi-bacterial interaction as evidenced by co-occurrence network, which possibly played roles in maintaining microbiome stability and resilience. Interestingly, pollution stress and resource availability weaken the relationship between microbial diversity and soil functions through the bottom-up trophic interaction and environmental preference of soil microbiome. Overall, this work provides experimental evidence that loss in microbial diversity, accompanied with changes in trophic interactions mediated biotic and abiotic factors, could have important consequences for specialized soil functioning in farmland ecosystems.

Fungal isolates influence the quality of Peucedanum praeruptorum Dunn

The symbiotic relationship between beneficial microorganisms and plants plays a vital role in natural and agricultural ecosystems. Although Peucedanum praeruptorum Dunn is widely distributed, its development is greatly limited by early bolting. The reason for early bolting in P. praeruptorum remains poorly characterized. We focus on the plant related microorganisms, including endophytes and rhizosphere microorganisms, by combining the traditional isolation and culture method with metagenomic sequencing technology. We found that the OTUs of endophytes and rhizosphere microorganisms showed a positive correlation in the whole growth stage of P. praeruptorum. Meanwhile, the community diversity of endophytic and rhizosphere fungi showed an opposite change trend, and bacteria showed a similar change trend. Besides, the microbial communities differed during the pre- and post-bolting stages of P. praeruptorum. Beneficial bacterial taxa, such as Pseudomonas and Burkholderia, and fungal taxa, such as Didymella and Fusarium, were abundant in the roots in the pre-bolting stage. Further, a strain belonging to Didymella was obtained by traditional culture and was found to contain praeruptorin A, praeruptorin B, praeruptorin E. In addition, we showed that the fungus could affect its effective components when it was inoculated into P. praeruptorum. This work provided a research reference for the similar biological characteristics of perennial one-time flowering plants, such as Saposhnikovia divaricate, Angelica sinensis and Angelica dahurica.

Mitigating abiotic stress: microbiome engineering for improving agricultural production and environmental sustainability

The responses of plants to different abiotic stresses and mechanisms involved in their mitigation are discussed. Production of osmoprotectants, antioxidants, enzymes and other metabolites by beneficial microorganisms and their bioengineering ameliorates environmental stresses to improve food production. Progressive intensification of global agriculture, injudicious use of agrochemicals and change in climate conditions have deteriorated soil health, diminished the microbial biodiversity and resulted in environment pollution along with increase in biotic and abiotic stresses. Extreme weather conditions and erratic rains have further imposed additional stress for the growth and development of plants. Dominant abiotic stresses comprise drought, temperature, increased salinity, acidity, metal toxicity and nutrient starvation in soil, which severely limit crop production. For promoting sustainable crop production in environmentally challenging environments, use of beneficial microbes has emerged as a safer and sustainable means for mitigation of abiotic stresses resulting in improved crop productivity. These stress-tolerant microorganisms play an effective role against abiotic stresses by enhancing the antioxidant potential, improving nutrient acquisition, regulating the production of plant hormones, ACC deaminase, siderophore and exopolysaccharides and accumulating osmoprotectants and, thus, stimulating plant biomass and crop yield. In addition, bioengineering of beneficial microorganisms provides an innovative approach to enhance stress tolerance in plants. The use of genetically engineered stress-tolerant microbes as inoculants of crop plants may facilitate their use for enhanced nutrient cycling along with amelioration of abiotic stresses to improve food production for the ever-increasing population. In this chapter, an overview is provided about the current understanding of plant-bacterial interactions that help in alleviating abiotic stress in different crop systems in the face of climate change. This review largely focuses on the importance and need of sustainable and environmentally friendly approaches using beneficial microbes for ameliorating the environmental stresses in our agricultural systems.

Substrate complexity affects the prevalence and interconnections of antibiotic, metal and biocide resistance genes, integron-integrase genes, human pathogens and virulence factors in anaerobic digestion

Anaerobic digestion (AD) is widely used to treat livestock manure that harbors diverse pollutants (resistance genes (ARGs), metal/biocide resistance genes (MBRGs), integron-integrase genes, human pathogens and pathogen virulence factors (VFs)). However, the interplays of these pollutants and the effects of substrate complexity on pollutants in AD are elusive. This study investigated the dynamics of these pollutants and bacterial communities during AD of swine manure, by metatranscriptomic sequencing and amplicon sequencing of 16 S rRNA and 16 S rRNA gene. The pollutant profiles and bacterial communities differed across AD processes, nevertheless with consistent dominance of ARGs of multi-drugs, tetracycline, aminoglycoside and rifamycin, MBRGs of multi-biocides, multi-metals, copper and arsenic, the integron-integrase gene intI1, potential pathogens of Escherichia coli, Streptococcus gallolyticus and Clostridium perfringens, VFs involved in pathogen adherence, and bacterial phyla of Firmicutes, Bacteroidetes and Proteobacteria. Reduced substrate complexity (replacing a part of swine manure, a complex substrate, with a simple substrate, apple waste or fructose) decreased the prevalence and stochastic turnover of ARGs and MBRGs. Network analyses revealed decreased interplays among pollutants under reduced substrate complexity. Our findings provide a mechanical understanding of diverse pollutants dynamics during AD, and reveal the importance of substrate complexity in controlling prevalence and interplays of pollutants.

Ecoenzymatic stoichiometry reveals stronger microbial carbon and nitrogen limitation in biochar amendment soils: A meta-analysis

Soil extracellular enzyme activities of microbes to acquire carbon (C), nitrogen (N) and phosphorus (P) exert great roles on soil C sequestration and N, P availability. However, a lack of biochar-induced changes of C, N and P acquisition enzyme activities hinders us from understanding if biochar application will lead to microbial C, N and P limitation based on ecoenzymatic stoichiometry. In this study, through ecoenzymatic stoichiometry, a meta-analysis was conducted to evaluate responses of microbial metabolic limitation to biochar amendment by collecting data of ecoenzymatic activities (EEAs) of the C, N and P acquisition from peer-reviewed papers. The results showed that biochar application increased activities of C, N acquisition enzymes significantly by 9.3 % and 15.1 % on average, respectively. But the influence on P acquisition enzymes activities (Acid, neutral or alkaline phosphatase, abbreviated wholly as PHOS) was not significant. Biochar increased ratio of C acquisition enzymes activities (E_C) over P enzymes activities (E_P) and ratio of N enzymes activities (E_N) over E_P, but decreased E_C:E_N, indicating an increased N limitation or a shift from P limitation to N limitation in microbial metabolism. Enzyme vector analysis showed that soil microbial metabolism was limited by C relative to nutrients (N and P) under biochar amendment according to the overall increased vector length (~1.5 %). Wood biochar caused the strongest microbial C limitation, followed by crop residue biochar as indicated by increased enzyme vector length of 3.6 % and 1.2 % on average, respectively. The stronger microbial C limitation was also found when initial soil total organic carbon (SOC) was <20 g·kg^-1. Our results illustrated that available nitrogen and organic carbon should be provided to meet microbial stoichiometric requirements to improve plant productivity, especially in low fertile soils under biochar amendment.

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.

Exogenous Melatonin Reprograms the Rhizosphere Microbial Community to Modulate the Responses of Barley to Drought Stress

The rhizospheric melatonin application-induced drought tolerance has been illuminated in various plant species, while the roles of the rhizosphere microbial community in this process are still unclear. Here, the diversity and functions of the rhizosphere microbial community and related physiological parameters were tested in barley under the rhizospheric melatonin application and drought. Exogenous melatonin improved plant performance under drought via increasing the activities of non-structural carbohydrate metabolism enzymes and activating the antioxidant enzyme systems in barley roots under drought. The 16S/ITS rRNA gene sequencing revealed that drought and melatonin altered the compositions of the microbiome. Exogenous melatonin increased the relative abundance of the bacterial community in carbohydrate and carboxylate degradation, while decreasing the relative abundance in the pathways of fatty acid and lipid degradation and inorganic nutrient metabolism under drought. These results suggest that the effects of melatonin on rhizosphere microbes and nutrient condition need to be considered in its application for crop drought-resistant cultivation.

Soil microbial communities shift along an urban gradient in Berlin, Germany

The microbial communities inhabiting urban soils determine the functioning of these soils, in regards to their ability to cycle nutrients and support plant communities. In an increasingly urbanized world these properties are of the utmost importance, and the microbial communities responsible are worthy of exploration. We used 53 grassland sites spread across Berlin to describe and explain the impacts of urbanity and other environmental parameters upon the diversity and community composition of four microbial groups. These groups were (i) the Fungi, with a separate dataset for (ii) the Glomeromycota, (iii) the Bacteria, and (iv) the protist phylum Cercozoa. We found that urbanity had distinct impacts on fungal richness, which tended to increase. Geographic distance between sites and soil chemistry, in addition to urbanity, drove microbial community composition, with site connectivity being important for Glomeromycotan communities, potentially due to plant host communities. Our findings suggest that many microbial species are well adapted to urban soils, as supported by an increase in diversity being a far more common result of urbanity than the reverse. However, we also found distinctly separate distributions of operational taxonomic unit (OTU)s from the same species, shedding doubt of the reliability of indicator species, and the use of taxonomy to draw conclusion on functionality. Our observational study employed an extensive set of sites across an urbanity gradient, in the region of the German capital, to produce a rich microbial dataset; as such it can serve as a blueprint for other such investigations.

Legacies at work: plant-soil-microbiome interactions underpinning agricultural sustainability

Agricultural intensification has had long-lasting negative legacies largely because of excessive inputs of agrochemicals (e.g., fertilizers) and simplification of cropping systems (e.g., continuous monocropping). Conventional agricultural management focuses on suppressing these negative legacies. However, there is now increasing attention for creating positive above- and belowground legacies through selecting crop species/genotypes, optimizing temporal and spatial crop combinations, improving nutrient inputs, developing intelligent fertilizers, and applying soil or microbiome inoculations. This can lead to enhanced yields and reduced pest and disease pressure in cropping systems, and can also mitigate greenhouse gas emissions and enhance carbon sequestration in soils. Strengthening positive legacies requires a deeper understanding of plant-soil-microbiome interactions and innovative crop, input, and soil management which can help to achieve agricultural sustainability.

Increase in rainfall intensity promotes soil nematode diversity but offset by nitrogen addition in a temperate grassland

Precipitation regime in arid and semi-arid regions is exhibiting a trend of increase in rainfall intensity but reduction in frequency under global climate change. In addition, nitrogen (N) deposition occurs simultaneously in the same regions. Nematodes are the dominant soil biota in terrestrial ecosystems and are involved in various underground processes. How the diversity of nematode communities responds to changing precipitation regime and how N deposition regulates the responses remain unclear. Here, we performed a field experiment initiated in 2012 to examine the effect of changes in the precipitation regime (2 mm precipitation intensity, 5 mm precipitation intensity, 10 mm precipitation intensity, 20 mm precipitation intensity, and 40 mm precipitation intensity) and N addition (10 g N m^-2 yr^-1) on soil nematode community in a semi-arid grassland in Inner Mongolia of China. We found that the abundance and diversity of nematodes increased under the treatments with fewer but stronger precipitation events (the largest abundance of total nematodes was 1458.37 individuals/100 g dry soil occurred under 40 mm intensity treatment). However, N addition reduced nematode diversity under these treatments, which largely offset the positive effects of increased rainfall intensity alone. Soil pH and plant belowground biomass were the main factors affecting nematode diversity. Our results imply that, as a consequence of global climate change, an increase in the intensity of rainfall events in the coming decades may favor the nematode communities within arid and semi-arid ecosystems. However, this positive effect may be largely offset by soil acidification in the regions experiencing heavy N deposition.

Water Deficit History Selects Plant Beneficial Soil Bacteria Differently Under Conventional and Organic Farming

Water deficit tolerance is critical for plant fitness and survival, especially when successive drought events happen. Specific soil microorganisms are however able to improve plant tolerance to stresses, such as those displaying a 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Microorganisms adapted to dry conditions can be selected by plants over time because of properties such as sporulation, substrate preference, or cell-wall thickness. However, the complexity and interconnection between abiotic factors, like drought or soil management, and biotic factors, like plant species identity, make it difficult to elucidate the general selection processes of such microorganisms. Using a pot experiment in which wheat and barley were grown on conventional and organic farming soils, we determined the effect of water deficit history on soil microorganisms by comparing single and successive events of water limitation. The analysis showed that water deficit strongly impacts the composition of both the total microbial community (16S rRNA genes) and one of ACC deaminase-positive (acdS+) microorganisms in the rhizosphere. In contrast, successive dry conditions moderately influence the abundance and diversity of both communities compared to a single dry event. We revealed interactive effects of the farming soil type and the water deficit conditioning treatment. Indeed, possibly due to better nutrient status, plants grown on soils from conventional farming showed higher growth and were able to select more adapted microbial taxa. Some of them are already known for their plant-beneficial properties like the Actinobacteria Streptomyces, but interestingly, some Proteobacteria were also enriched after a water deficit history under conventional farming. Our approach allowed us to identify key microbial taxa promoting drought adaptation of cereals, thus improving our understanding of drought effects on plant-microbe interactions.

How do plants remember drought?

Plants develop both short-term and transgenerational memory of drought stress through epigenetic regulation of transcription for a better response to subsequent exposure. Recurrent spells of droughts are more common than a single drought, with intermittent moist recovery intervals. While the detrimental effects of the first drought on plant structure and physiology are unavoidable, if survived, plants can memorize the first drought to present a more robust response to the following droughts. This includes a partial stomatal opening in the watered recovery interval, higher levels of osmoprotectants and ABA, and attenuation of photosynthesis in the subsequent exposure. Short-term drought memory is regulated by ABA and other phytohormone signaling with transcriptional memory behavior in various genes. High levels of methylated histones are deposited at the drought-tolerance genes. During the recovery interval, the RNA polymerase is stalled to be activated by a pause-breaking factor in the subsequent drought. Drought leads to DNA demethylation near drought-response genes, with genetic control of the process. Progenies of the drought-exposed plants can better adapt to drought owing to the inheritance of particular methylation patterns. However, a prolonged watered recovery interval leads to loss of drought memory, mediated by certain demethylases and chromatin accessibility factors. Small RNAs act as critical regulators of drought memory by altering transcript levels of drought-responsive target genes. Further studies in the future will throw more light on the genetic control of drought memory and the interplay of genetic and epigenetic factors in its inheritance. Plants from extreme environments can give queues to understanding robust memory responses at the ecosystem level.

Per-, poly-fluoroalkyl substances (PFASs) and planktonic microbiomes: Identification of biotic and abiotic regulations in community coalescence and food webs

The importance of per-, poly-fluoroalkyl substances (PFASs) effects on riverine microbiomes is receiving increased recognition in the environmental sciences. However, few studies have explored how PFASs affect microbiomes across trophic levels, specifically through predator-prey interactions. This study examined the community profiles of planktonic archaea, bacteria, fungi, algae, protozoa, and metazoa in a semi-industrial and agricultural river alongside their interactions with 15 detected PFASs. As abiotic factors, PFASs affected community coalescence more than biogenic substances (p < 0.05). For biotic regulations, sub-communities in rare biospheres (including always rare taxa-ART and critically rare taxa-CRT) contributed to spatial community coalescence more than sub-communities in abundant biospheres (always abundant taxa-AAT and critically abundant taxa-CAT) (p < 0.05). Metazoa-bacteria (Modularity = 1.971) and protozoa-fungi (1.723) were determined to be the most stable predator-prey networks. Based on pathway models, short-chain PFBA (C4) was shown to weaken the trophic transfer efficiencies from heterotrophic bacteria (HB) to heterotrophic flagellates (HF) (p < 0.05). Long-chain PFTeDA (C14) promoted HB to amoeba (p < 0.05), which we postulate is the pathway for PFTeDA to enter the microbial food chain. Our preliminary results elucidated the influence of PFASs on planktonic microbial food webs and highlighted the need to consider protecting and remediating riverine ecosystems containing PFASs.

Water deficit affects inter-kingdom microbial connections in plant rhizosphere

The frequency and severity of drought are increasing due to anthropogenic climate change and are already limiting cropping system productivity in many regions around the world. Few microbial groups within plant microbiomes can potentially contribute towards the fitness and productivity of their hosts under abiotic stress events including water deficits. However, microbial communities are complex and integrative work considering the multiple co-existing groups of organisms is needed to better understand how the entire microbiome responds to environmental stresses. We hypothesize that water deficit stress will differentially shape bacterial, fungal, and protistan microbiome composition and influence inter-kingdom microbial interactions in the rhizospheres of corn and sugar beet. We used amplicon sequencing to profile bacterial, fungal, and protistan communities in corn and sugar beet rhizospheres grown under irrigated and water deficit conditions. The water deficit treatment had a stronger influence than host species on bacterial composition, whereas the opposite was true for protists. These results indicate that different microbial kingdoms have variable responses to environmental stress and host factors. Water deficit also influenced intra- and inter-kingdom microbial associations, wherein the protist taxa formed a separate cluster under water deficit conditions. Our findings help elucidate the influence of environmental and host drivers of bacterial, fungal, and protistan community assembly and co-occurrence in agricultural rhizosphere environments.

Drought soil legacy alters drivers of plant diversity-productivity relationships in oldfield systems

Ecosystem functions are threatened by both recurrent droughts and declines in biodiversity at a global scale, but the drought dependency of diversity-productivity relationships remains poorly understood. Here, we use a two-phase mesocosm experiment with simulated drought and model oldfield communities (360 experimental mesocosms/plant communities) to examine drought-induced changes in soil microbial communities along a plant species richness gradient and to assess interactions between past drought (soil legacies) and subsequent drought on plant diversity-productivity relationships. We show that (i) drought decreases bacterial and fungal richness and modifies relationships between plant species richness and microbial groups; (ii) drought soil legacy increases net biodiversity effects, but responses of net biodiversity effects to plant species richness are unaffected; and (iii) linkages between plant species richness and complementarity/selection effects vary depending on past and subsequent drought. These results provide mechanistic insight into biodiversity-productivity relationships in a changing environment, with implications for the stability of ecosystem function under climate change.

The adjustment of life history strategies drives the ecological adaptations of soil microbiota to aridity

Soil microbiota increase their fitness to local habitats by adjusting their life history strategies. Yet, how such adjustments drive their ecological adaptations in xeric grasslands remains elusive. In this study, shifts in the traits that potentially represent microbial life history strategies were studied along two aridity gradients with different climates using metagenomic and trait-based approaches. The results indicated that resource acquisition (e.g., higher activities of β-D-glucosidase and N-acetyl-beta-D-glucosidase, higher degradation rates of cellulose and chitin as well as genes involved in cell motilities, biodegradations, transportations and competitions) and growth yield (e.g., higher biomass and respiration) strategies were depleted with a higher aridity. However, cellular and high growth potential maintenance (e.g., higher metabolic quotients and genes related to DNA replication, transcription, translation, central carbon metabolisms and biosynthesis) and stress tolerance (e.g., genes involved in DNA damage repair, cation transporter, sporulation and osmolyte biosynthesis) strategies were enriched with a higher aridity. This implied that microbiota have lower growth yields but are probably well primed for rapid responses to pulse rainfalls in more arid soils, whereas those in less arid soils may have stronger resource acquisition and growth yield abilities. By integrating a large amount of evidence involved in taxonomic, metagenomic, genomic and biochemical properties, this study demonstrated that the ecological adaptations of soil microbiota to aridity made by adjusting and optimizing their life history strategies are universal in xeric grasslands and provided an underlying mechanistic understanding of soil microbial responses to climate changes.

Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities

The mechanisms underlying microbial community dynamics and co-occurrence patterns along ecological succession are crucial for understanding ecosystem recovery but remain largely unexplored. Here, we investigated community dynamics and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Bacterial community structures became increasingly phylogenetically clustered with soil age at early successional stages and varied less at later successional stages. The dynamics of bacterial community phylogenetic structures were determined by the changes in the soil vegetation cover along succession. The dynamics of fungal community phylogenetic structures did not significantly correlate with soil age, soil properties or vegetation cover, and were mainly attributed to stochastic processes. Along succession, the common decrease in the bacterial co-occurrence complexity and in the average pairwise phylogenetic distances between co-occurring bacteria implied a decrease in potential bacterial cooperation. The increased complexity of fungal co-occurrence along succession was independent of phylogenetic relatedness between co-occurring fungi. This study provides new sights into ecological mechanisms underlying bacterial and fungal community succession.

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

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

Changes in precipitation regime lead to acceleration of the N cycle and dramatic N2O emission

Alpine meadows on the Qinghai-Tibetan Plateau are sensitive to climate change. The precipitation regime in this region has undergone major changes, "repackaging" precipitation from more frequent, smaller events to less frequent, larger events. Nitrous oxide (N₂O) is an important indicator of responses to global change in alpine meadow ecosystems. However, little information is available describing the mechanisms driving the response of N₂O emissions to changes in the precipitation regime. In this study, a manipulative field experiment was conducted to investigate N₂O flux, soil properties, enzyme activity, and gene abundance in response to severe and moderate changes in precipitation regime over two years. Severe changes in precipitation regime led to a 12.6-fold increase in N₂O fluxes (0.0068 ± 0.0018 mg m^-2 h^-1) from Zoige alpine meadows relative to natural conditions (0.0005 ± 0.0029 mg m^-2 h^-1). In addition, severe changes in precipitation regime significantly suppressed the activities of leucine amino peptidase (LAP) and peroxidase (PEO), affected ecoenzymatic stoichiometry, and increased the abundances of gdhA, narI and nirK genes, which significantly promoted organic nitrogen (N) decomposition, denitrification, and anammox processes. The increase in abundance of these genes could be ascribed to changes in the abundance of several dominant bacterial taxa (i.e., Actinobacteria and Proteobacteria) as a result of the altered precipitation regime. Decreases in nitrate and soil moisture caused by severe changes in precipitation may exacerbate N limitation and water deficit, lead to a suppression of soil enzyme activity, and change the structure of microorganism community. The N cycle of the alpine meadow ecosystem may accelerate by increasing the abundance of key N functional genes. This would, in turn, lead to increased N₂O emission. This study provided insights into how precipitation regimes changes affect N cycling, and may also improve prediction of N₂O fluxes in response to changes in precipitation regime.

Ecosystem effects of environmental extremes

[Figure: see text].