Differential sensitivity of total and active soil microbial communities to drought and forest management

Seasonal variations of profiles of antibiotic resistance genes and virulence factor genes in household dust from Beijing, China revealed by the metagenomics

Household-related microbiome is closely related with human health. However, the knowledge about profiles of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) which are carried by microbes inside homes and their temporal dynamics are rather limited. Here we monitored the seasonal changes of bacterial community (especially pathogenic bacteria), ARGs, and VFGs in household dust samples during two years. Based on metagenomic sequencing, the dust-related bacterial pathogenic community, ARGs, and VFGs all harbored the lowest richness in spring among four seasons. Their structure (except that of VFGs) also exhibited remarkable differences among the seasons. The structural variations of ARGs and VFGs were almost explained by mobile genetic elements (MGEs), bacterial pathogens, and particulate matter-related factors, with MGEs explaining the most. Moreover, the total normalized abundance of ARGs or VFGs showed no significant change across the seasons. Results of metagenomic binning and microbial network both showed that several pathogenic taxa (e.g., Ralstonia pickettii) were strongly linked with numerous ARGs (mainly resistant to multidrug) and VFGs (mainly encoding motility) simultaneously. Overall, these findings underline the significance of MGEs in structuring ARGs and VFGs inside homes along with seasonal variations, suggesting that household dust is a neglected reservoir for ARGs and VFGs.

Global analysis of the adverse effects of micro- and nanoplastics on intestinal health and microbiota of fish

The wide occurrence of micro- and nanoplastics (MPs/NPs) within aquatic ecosystems has raised increasing concerns regarding their potential effects on aquatic organisms. However, the effects of MPs/NPs on intestinal health and microbiota of fish remain controversial, and there is a lack of comprehensive understanding regarding how the impact of MPs/NPs is influenced by MPs/NPs characteristics and experimental designs. Here, we conducted a global analysis to synthesize the effects of MPs/NPs on 47 variables associated with fish intestinal health and microbiota from 118 studies. We found that MPs/NPs generally exerted obvious adverse effects on intestinal histological structure, permeability, digestive function, immune and oxidative-antioxidative systems. By contrast, MPs/NPs showed slight effects on intestinal microbial variables. Further, we observed that the responses of intestinal variables to MPs/NPs were significantly regulated by MPs/NPs characteristics and experimental designs. For instance, polyvinyl chloride plastics showed higher toxicity to fish gut than polyethylene and polystyrene did. Additionally, larval fish appeared to be more sensitive to MPs/NPs than juvenile fish. Collectively, this study highlights the potential impacts of MPs/NPs on intestinal health and microbiota of fish, and underscores the determinant role of MPs/NPs characteristics and experimental designs in MPs/NPs toxicity.

Changes in soil oxidase activity induced by microbial life history strategies mediate the soil heterotrophic respiration response to drought and nitrogen enrichment

Drought and nitrogen deposition are two major climate challenges, which can change the soil microbial community composition and ecological strategy and affect soil heterotrophic respiration (Rh). However, the combined effects of microbial community composition, microbial life strategies, and extracellular enzymes on the dynamics of Rh under drought and nitrogen deposition conditions remain unclear. Here, we experimented with an alpine swamp meadow to simulate drought (50% reduction in precipitation) and multilevel addition of nitrogen to determine the interactive effects of microbial community composition, microbial life strategy, and extracellular enzymes on Rh. The results showed that drought significantly reduced the seasonal mean Rh by 40.07%, and increased the Rh to soil respiration ratio by 22.04%. Drought significantly altered microbial community composition. The ratio of K- to r-selected bacteria (BK:r) and fungi (FK:r) increased by 20 and 91.43%, respectively. Drought increased hydrolase activities but decreased oxidase activities. However, adding N had no significant effect on microbial community composition, BK:r, FK:r, extracellular enzymes, or Rh. A structural equation model showed that the effects of drought and adding nitrogen via microbial community composition, microbial life strategy, and extracellular enzymes explained 84% of the variation in Rh. Oxidase activities decreased with BK:r, but increased with FK:r. Our findings show that drought decreased Rh primarily by inhibiting oxidase activities, which is induced by bacterial shifts from the r-strategy to the K-strategy. Our results highlight that the indirect regulation of drought on the carbon cycle through the dynamic of bacterial and fungal life history strategy should be considered for a better understanding of how terrestrial ecosystems respond to future climate change.

Drought legacy interacts with wildfire to alter soil microbial communities in a Mediterranean climate-type forest

Mediterranean forest ecosystems will be increasingly affected by hotter drought and more frequent and severe wildfire events in the future. However, little is known about the longer-term responses of these forests to multiple disturbances and the forests' capacity to maintain ecosystem function. This is particularly so for below-ground organisms, which have received less attention than those above-ground, despite their essential contributions to forest function. We investigated rhizosphere microbial communities in a resprouting Eucalyptus marginata forest, southwestern Australia, that had experienced a severe wildfire four years previously, and a hotter drought eight years previously. Our aim was to understand how microbial communities are affected over longer-term trajectories by hotter drought and wildfire, singularly, and in combination. Fungal and bacterial DNA was extracted from soil samples, amplified, and subjected to high throughput sequencing. Richness, diversity, composition, and putative functional groups were then examined. We found a monotonic decrease in fungal, but not bacterial, richness and diversity with increasing disturbance with the greatest changes resulting from the combination of drought and wildfire. Overall fungal and bacterial community composition reflected a stronger effect of fire than drought, but the combination of both produced the greatest number of indicator taxa for fungi, and a significant negative effect on the abundance of several fungal functional groups. Key mycorrhizal fungi, fungal saprotrophs and fungal pathogens were found at lower proportions in sites affected by drought plus wildfire. Wildfire had a positive effect on bacterial hydrogen and bacterial nitrogen recyclers. Fungal community composition was positively correlated with live tree height. These results suggest that microbial communities, in particular key fungal functional groups, are highly responsive to wildfire following drought. Thus, a legacy of past climate conditions such as hotter drought can be important for mediating the responses of soil microbial communities to subsequent disturbance like wildfire.

Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms

Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.

Increased belowground tree carbon allocation in a mature mixed forest in a dry versus a wet year

Tree species differ in their carbon (C) allocation strategies during environmental change. Disentangling species-specific strategies and contribution to the C balance of mixed forests requires observations at the individual tree level. We measured a complete set of C pools and fluxes at the tree level in five tree species, conifers and broadleaves, co-existing in a mature evergreen mixed Mediterranean forest. Our study period included a drought year followed by an above-average wet year, offering an opportunity to test the effect of water availability on tree C allocation. We found that in comparison to the wet year, C uptake was lower in the dry year, C use was the same, and allocation to belowground sinks was higher. Among the five major C sinks, respiration was the largest (ca. 60%), while root exudation (ca. 10%) and reproduction (ca. 2%) were those that increased the most in the dry year. Most trees relied on stored starch for maintaining a stable soluble sugars balance, but no significant differences were detected in aboveground storage between dry and wet years. The detailed tree-level analysis of nonstructural carbohydrates and δ13 C dynamics suggest interspecific differences in C allocation among fluxes and tissues, specifically in response to the varying water availability. Overall, our findings shed light on mixed forest physiological responses to drought, an increasing phenomenon under the ongoing climate change.

Microbial inoculants with higher capacity to colonize soils improved wheat drought tolerance

Microbial inoculants have gained increasing attention worldwide as an eco-friendly solution for improving agriculture productivity. Several studies have demonstrated their potential benefits, such as enhanced resistance to drought, salinity, and pathogens. However, the beneficial impacts of inoculants remain inconsistent. This variability is attributed to limited knowledge of the mechanisms by which microbial inoculants affect crop growth and a lack of ecological characteristics of these inoculants that limit our ability to predict their beneficial effects. The first important step is believed to be the evaluation of the inoculant's ability to colonize new habitats (soils and plant roots), which could provide crops with beneficial functions and improve the consistency and efficiency of the inoculants. In this study, we aimed to investigate the impact of three microbial inoculants (two bacterial: P1 and P2, and one fungal: P3) on the growth and stress responses of three wheat varieties in two different soil types under drought conditions. Furthermore, we investigated the impact of microbial inoculants on soil microbial communities. Plant biomass and traits were measured, and high-throughput sequencing was used to characterize bulk and rhizosphere soil microbiomes after exposure to drought stress. Under drought conditions, plant shoot weight significantly increased (11.37%) under P1 treatments compared to uninoculated controls. In addition, total nitrogen enzyme activity increased significantly under P1 in sandy soil but not in clay soil. Importantly, network analyses revealed that P1, consisting of Bacillus paralicheniformis and Bacillus subtilis, emerged as the keystone taxa in sandy soil. Conversely, P2 and P3 failed to establish as keystone taxa, which may explain their insignificant impact on wheat performance under drought conditions. In conclusion, our study emphasizes the importance of effective colonization by microbial inoculants in promoting crop growth under drought conditions. Our findings support the development of microbial inoculants that robustly colonize plant roots for improved agricultural productivity.

Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition

Climate change can alter the flow of nutrients and energy through terrestrial ecosystems. Using an inverse climate change field experiment in the central European Alps, we explored how long-term irrigation of a naturally drought-stressed pine forest altered the metabolic potential of the soil microbiome and its ability to decompose lignocellulolytic compounds as a critical ecosystem function. Drought mitigation by a decade of irrigation stimulated profound changes in the functional capacity encoded in the soil microbiome, revealing alterations in carbon and nitrogen metabolism as well as regulatory processes protecting microorganisms from starvation and desiccation. Despite the structural and functional shifts from oligotrophic to copiotrophic microbial lifestyles under irrigation and the observation that different microbial taxa were involved in the degradation of cellulose and lignin as determined by a time-series stable-isotope probing incubation experiment with 13C-labeled substrates, degradation rates of these compounds were not affected by different water availabilities. These findings provide new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest and will help to improve our understanding of alterations in biogeochemical cycling under a changing climate.

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.

Climate and Soil Microsite Conditions Determine Local Adaptation in Declining Silver Fir Forests

Ongoing climatic change is threatening the survival of drought-sensitive tree species, such as silver fir (Abies alba). Drought-induced dieback had been previously explored in this conifer, although the role played by tree-level genetic diversity and its relationship with growth patterns and soil microsite conditions remained elusive. We used double digest restriction-site-associated DNA sequencing (ddRADseq) to describe different genetic characteristics of five silver fir forests in the Spanish Pyrenees, including declining and non-declining trees. Single nucleotide polymorphisms (SNPs) were used to investigate the relationships between genetics, dieback, intraspecific trait variation (functional dendrophenotypic traits and leaf traits), local bioclimatic conditions, and rhizosphere soil properties. While there were no noticeable genetic differences between declining and non-declining trees, genome-environment associations with selection signatures were abundant, suggesting a strong influence of climate, soil physicochemical properties, and soil microbial diversity on local adaptation. These results provide novel insights into how genetics and diverse environmental factors are interrelated and highlight the need to incorporate genetic data into silver fir forest dieback studies to gain a better understanding of local adaptation.

Plantations thinning: A meta-analysis of consequences for soil properties and microbial functions

Thinning is a widely-used management practice to reduce tree competition and improve wood production and quality in forest plantations. Thinning affects the soil ecosystem by changing the microclimate and plant growth, as well as litter inputs above and belowground, with all the resulting consequences for microbial communities and functions. Although many case studies have been carried out, a comprehensive understanding of the thinning effects on soil properties and microbial communities and functions in plantations remains to be explored. In this study, a meta-analysis was performed on 533 paired observations based on 90 peer-reviewed articles to evaluate the general responses of soil (mainly 0-20 cm depth) physicochemical properties, microbial biomass and community structure, and enzyme activities to thinning. Results showed that thinning increased soil temperature (13 %), moisture (8.0 %), electric conductivity (13 %), and the contents of total nitrogen (TN, 4.1 %), dissolved organic carbon (DOC, 9.7 %), nitrate N (NO₃^--N, 27 %) and available phosphorous (22 %). For microbial properties, thinning decreased the fungi to bacteria ratio (F:B, -28 %) and the gram-positive bacteria to gram-negative bacteria ratio (G+:G-, -12 %), while increased microbial biomass C (7.1 %), microbial respiration (13 %), and nutrient-cycle related enzyme activities, including phenol oxidase (14 %), cellobiohydrolase (21 %), urease (10 %), and acid phosphatase (9 %). In particular, moderate thinning (30-60 % intensity) has higher conservation benefits for soil C and nutrients than light and heavy intensity, thus being recommended as the optimal thinning activity. This meta-analysis suggests that thinning consistently altered soil properties, shifted microbial community compositions from K- to-r strategist dominance, and stimulated microbial activities. These results are essential for optimizing plantation thinning management and provide evidence for applying the macro-ecology theory to ecosystem disturbance in soil microbial ecology.

The effects of mixed-species root zones on the resistance of soil bacteria and fungi to long-term experimental and natural reductions in soil moisture

Mixed forest stands tend to be more resistant to drought than species-specific stands partially due to complementarity in root ecology and physiology. We asked whether complementary differences in the drought resistance of soil microbiomes might contribute to this phenomenon. We experimented on the effects of reduced soil moisture on bacterial and fungal community composition in species-specific (single species) and mixed-species root zones of Norway spruce and European beech forests in a 5-year-old throughfall-exclusion experiment and across seasonal (spring-summer-fall) and latitudinal moisture gradients. Bacteria were most responsive to changes in soil moisture, especially members of Rhizobiales, while fungi were largely unaffected, including ectomycorrhizal fungi (EMF). Community resistance was higher in spruce relative to beech root zones, corresponding with the proportions of drought-favored (more in spruce) and drought-sensitive bacterial taxa (more in beech). The spruce soil microbiome also exhibited greater resistance to seasonal changes between spring (wettest) and fall (driest). Mixed-species root zones contained a hybrid of beech- and spruce-associated microbiomes. Several bacterial populations exhibited either enhanced resistance or greater susceptibility to drought in mixed root zones. Overall, patterns in the relative abundances of soil bacteria closely tracked moisture in seasonal and latitudinal precipitation gradients and were more predictive of soil water content than other environmental variables. We conclude that complementary differences in the drought resistance of soil microbiomes can occur and the likeliest form of complementarity in mixed-root zones coincides with the enrichment of drought-tolerant bacteria associated with spruce and the sustenance of EMF by beech.

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.

Agro-physiological and soil microbial responses to desalinated seawater irrigation in two crops

Irrigation with desalinated seawater (DSW) is a potential solution for addressing water scarcity in semiarid regions across the globe. However, this strategy may compromise the health of agricultural ecosystems due to the high content of phytotoxic elements (mainly boron, B) in this water. Here, a three-year experiment was carried to evaluate the response of the soil's physicochemical and microbiological properties, and plant physiology, to three irrigation water treatments (DSW; fresh water, FW; and their blend (1:1), BW) in the presence or not of organic amendments. Lemon trees (Citrus limon (L.) Burm. fil. cv. Eureka), with a higher sensitivity to B toxicity, and apricot trees (Prunus armeniaca L. cv. 'Búlida'), with a lower one, were used as model plants. Lemon trees irrigated with BW and DSW showed a decline in net photosynthesis and stomatal conductance, and an accumulation of B in leaves that exceeded the toxicity threshold. These effects were stronger in amended soils. In soils cultivated with lemon trees, DSW irrigation increased the water-soluble nitrogen content, the urease activity, and the activity and biomass of the microbial community, and shifted the microbial community structure as compared with the other water treatments. The soil microbial community responses were controlled by the addition of organic amendments. The irrigation of apricots with DSW did not negatively impact plant physiological parameters but increased the soil microbial biomass, as in the case of the lemon tree-soil system. These results suggest that DSW irrigation increases soil microbial biomass in both crop-soil systems but harms the physiological status of the most sensitive crop. Our findings provide an initial approach to evaluate the response of the plant-soil system to DSW.

Silicon and soil microorganisms improve rhizospheric soil health with bacterial community, plant growth, performance and yield

The interaction of silicon and soil microorganisms stimulates crop enhancement to ensure sustainable agriculture. Silicon may potentially increase nutrient availability in rhizosphere with improved plants' growth, development as it does not produce phytotoxicity. The rhizospheric microbiome accommodates a variety of microbial species that live in a small area of soil directly associated with the hidden half plants' system. Plant growth-promoting rhizobacteria (PGPR) play a major role in plant development in response to adverse climatic conditions. PGPRs may enhance the growth, quality, productivity in variety of crops, and mitigate abiotic stresses by reprogramming stress-induced physiological variations in plants via different mechanisms, such as synthesis of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate deaminase, exopolysaccharides, volatile organic compounds, atmospheric nitrogen fixation, and phosphate solubilization. Our article eye upon interactions of silicon and plant microbes which seems to be an opportunity for sustainable agriculture for series of crops and cropping systems in years to come, essential to safeguard the food security for masses.

Moss biocrust accelerates the recovery and resilience of soil microbial communities in fire-affected semi-arid Mediterranean soils

After wildfires in Mediterranean ecosystems, ruderal mosses are pioneer species, stabilizing the soil surface previous to the establishment of vascular vegetation. However, little is known about the implication of pioneer moss biocrusts for the recovery and resilience of soils in early post-fire stages in semi-arid areas. Therefore, we studied the effects of the burgeoning biocrust on soil physicochemical and biochemical properties and the diversity and composition of microbial communities after a moderate-to-high wildfire severity. Seven months after the wildfire, the biocrust softened the strong impact of the fire in soils, affecting the diversity and composition of bacteria and fungi community compared to the uncrusted soils exposed to unfavourable environmental stress. Soil moisture, phosphorous, and enzyme activities representing the altered biogeochemical cycles after the fire, were the main explanatory variables for biocrust microbial community composition under the semi-arid conditions. High bacterial diversity was found in soils under mosses, while long-lasting legacies are expected in the fungal community, which showed greater sensitivity to the fire. The composition of bacterial and fungal communities at several taxonomical levels was profoundly altered by the presence of the moss biocrust, showing a rapid successional transition toward the unburned soil community. Pioneer moss biocrust play an important role improving the resilience of soil microbial communities. In the context of increasing fire intensity, studying the moss biocrust effects on the recovery of soils microbiome is essential to understanding the resistance and resilience of Mediterranean forests to wildfires.

Water Stress, Cadmium, and Plant Genotype Modulate the Rhizosphere Microbiome of Pisum sativum L

Drought and heavy metals seriously affect plant growth and the biodiversity of the associated rhizosphere microbiomes, which, in turn, could be involved in the adaptation of plants to these environmental stresses. Rhizosphere soil was collected from a three-factor pot experiment, where pea line SGE and its Cd-tolerant mutant SGECd^t were cultivated under both optimal and limited water conditions and treated with a toxic Cd concentration. The taxonomic structure of the prokaryotic rhizosphere microbiome was analyzed with the high-throughput sequencing of 16S rRNA amplicon libraries. A permutation test demonstrated statistically significant effects of Cd and water stress but not of pea genotype on the rhizosphere microbiome structure. Phylogenetic isometric log-ratio data transformation identified the taxonomic balances that were affected by abiotic factors and pea genotypes. A small number of significant (log ratio [-3.0:+3.0]) and phylogenetically deep balances characterized water stress, while a larger number of weak (log ratio [-0.8:+0.8]) phylogenetically lower balances described the influence of the plant genotype. Stress caused by cadmium took on an intermediate position. The main conclusion of the study is that the most powerful factor affecting the rhizosphere microbiome was water stress, and the weakest factor was plant genotype since it demonstrated a very weak transformation of the taxonomic structure of rhizosphere microbiomes in terms of alpha diversity indices, beta diversity, and the log ratio values of taxonomic balances.

Moisture Controls the Suppression of Panax notoginseng Root Rot Disease by Indigenous Bacterial Communities

Harnessing indigenous soil microbial suppression is an emerging strategy for managing soilborne plant diseases. Soil moisture is a vital factor in soil microbiomes, but its role in the regulation of microbial suppression is poorly understood. Here, we investigated the correlation of root rot disease of Panax notoginseng with rhizosphere microbial communities mediated by soil moisture gradients from 55% to 100% field capacity (FC); then, we captured the disease-suppressive and disease-inductive microbiomes and validated their functions by a culture experiment with synthetic microbiotas containing keystone species. We found that proper soil moisture at 75% to 95% FC could maintain a disease-suppressive microbiome to alleviate root rot disease. However, extremely low or high soil moistures (>95% FC or <75% FC) could aggravate root rot disease by depleting the disease-suppressive microbiome while enriching the disease-inductive microbiome. Both the low-soil-moisture-enriched pathogen Monographella cucumerina and the high-soil-moisture-enriched pathogen Ilyonectria destructans could synergize with different disease-inductive microbiomes to aggravate disease. Metagenomic data confirmed that low- and high-moisture conditions suppressed antibiotic biosynthesis genes but enriched pathogenicity-related genes, resulting in a change in the soil state from disease suppressive to inductive. This study highlights the importance of soil moisture when indigenous microbial suppression is harnessed for disease control. IMPORTANCE Soilborne diseases pose a major problem in high-intensity agricultural systems due to the imbalance of microbial communities in soil, resulting in the buildup of soilborne pathogens. Harnessing indigenous soil microbial suppression is an emerging strategy for overcoming soilborne plant diseases. In this study, we showed that soil moisture is a key factor in balancing microbiome effects on root rot disease. Proper soil moisture management represent an effective approach to maintain microbial disease resistance by enriching disease-suppressive microbiomes. Conversely, moisture stresses may enrich for a disease-inductive microbiome and aid accumulation of host-specific soilborne pathogens threatening crop production. This work could provide a new strategy for sustainable control of soilborne diseases by enriching the indigenous disease-suppressive microbiome through soil moisture management.

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

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

The active core microbiota of two high-yielding laying hen breeds fed with different levels of calcium and phosphorus

The nutrient availability and supplementation of dietary phosphorus (P) and calcium (Ca) in avian feed, especially in laying hens, plays a vital role in phytase degradation and mineral utilization during the laying phase. The required concentration of P and Ca peaks during the laying phase, and the direct interaction between Ca and P concentration shrinks the availability of both supplements in the feed. Our goal was to characterize the active microbiota of the entire gastrointestinal tract (GIT) (crop, gizzard, duodenum, ileum, caeca), including digesta- and mucosa-associated communities of two contrasting high-yielding breeds of laying hens (Lohmann Brown Classic, LB; Lohmann LSL-Classic, LSL) under different P and Ca supplementation levels. Statistical significances were observed for breed, GIT section, Ca, and the interaction of GIT section x breed, P x Ca, Ca x breed and P x Ca x breed (p &lt; 0.05). A core microbiota of five species was detected in more than 97% of all samples. They were represented by an uncl. Lactobacillus (average relative abundance (av. abu.) 12.1%), Lactobacillus helveticus (av. abu. 10.8%), Megamonas funiformis (av. abu. 6.8%), Ligilactobacillus salivarius (av. abu. 4.5%), and an uncl. Fusicatenibacter (av. abu. 1.1%). Our findings indicated that Ca and P supplementation levels 20% below the recommendation have a minor effect on the microbiota compared to the strong impact of the bird’s genetic background. Moreover, a core active microbiota across the GIT of two high-yielding laying hen breeds was revealed for the first time.

Alfalfa modified the effects of degraded black soil cultivated land on the soil microbial community

Legume alfalfa (Medicago sativa L.) is extensively planted to reduce chemical fertilizer input to the soil and remedy damaged fields. The soil mechanism of these effects is potentially related to the variations in alfalfa-mediated interactions of the soil microbial community. To understand the impact of planting alfalfa on the soil microbial community in degraded black soil cultivated land, a 4-year experiment was conducted in degraded black soil cultivated land. We assessed soil parameters and characterized the functional and compositional diversity of the microbial community by amplicon sequencing that targeted the 16S rDNA gene of bacteria and ITS of fungi in four systems under corn cultivation at the Harbin corn demonstration base (Heilongjiang, China): multiyear corn planting (more than 30 years, MC1); 2 years of alfalfa-corn rotation (OC); 3 years of alfalfa planting (TA); and 4 years of alfalfa planting (FA). It was found out that alfalfa led to changes in the alpha diversity of soil bacteria rather than in fungi in the degraded arable land. The abundance of the bacterial groups Gemmatimonadetes, Actinobacteria, Planctomycetes, and Chloroflexi was increased in OC, while Proteobacteria and Acidobacteria and the fungal group Glomeromycota were increased in TA and FA. OC, TA, and FA significantly increased the pH level but reduced soil electrical conductivity, but they had no impact on soil available nitrogen and soil available potassium at the 0-15 cm soil depth. However, with the years of alfalfa planting, soil available nitrogen and soil available potassium were reduced at the 15-30 cm soil depth. OC, TA, and FA significantly reduced the soil available phosphorus and soil total phosphorus at the 15-30 cm soil depth. There was no significant impact made on soil total nitrogen. FA significantly reduced the soil organic matter at the 15-30 cm soil depth. Planting alfalfa in degraded black soil cultivated land can reduce the salt content of the soil, and the nutrient content of soil planted with alfalfa without fertilization was equivalent to that of degraded corn cultivated land with annual fertilization. Besides, alfalfa recruited and increased contained taxa with the capacity to improve soil nutrient utilization and inhibit the harmful influences of pathogens for subsequent crops. Meanwhile, the planting of alfalfa can modify soil conditions by promoting the proliferation of specific beneficial microbiota groups.

Zero-valent iron-induced successive chemical transformation and biodegradation of lindane in historically contaminated soil: An isotope-informed metagenomic study

Zero-valent iron (ZVI) is widely used to mitigate environmental pollutants such as chlorinated pesticides through reductive reactions accompanied by extensive impacts on the soil microbial community. However, whether and how ZVI changes the biodegradation of target compounds remain poorly understood. Here, we monitor the fate of lindane using a ¹⁴C-labled tracer and evaluate the growth and functions of the bacterial community in ZVI-stressed conditions in a historically γ-hexachlorocyclohexane (lindane)-contaminated soil using a combination of isotopic (¹⁸O-H₂O) and metagenomic methods. ZVI promoted the biomineralization of lindane in a dose-dependent manner. Soil bacteria were inhibited by amendment with ZVI during the initial stages of incubation (first three days) but recovered during the subsequent six weeks. Metagenomic study indicates that the todC1/bedC1 genes involved in the oxidation of dechlorinated lindane intermediates were upregulated in the ¹⁸O-labeled bacterial community but the presence of the lin genes responsible for lindane dechlorination was not confirmed. In addition, the benzoate biodegradation pathway that links to downstream catabolism of lindane was enhanced. These findings indicate successive chemical and biological degradation mechanisms underlying ZVI-enhanced lindane mineralization and provide a scientific basis for the inclusion of an extended bioremediation stage in the environmental application of ZVI materials.

Rhizosphere soil bacterial communities and nitrogen cycling affected by deciduous and evergreen tree species

Deciduous and evergreen trees differ in their responses to drought and nitrogen (N) demand. Whether or not these functional types affect the role of the bacterial community in the N cycle during drought remains uncertain. Two deciduous tree species (Alnus cremastogyne, an N₂-fixing species, and Liquidambar formosana) and two evergreen trees (Cunninghamia lanceolata and Pinus massoniana) were used to assess factors in controlling rhizosphere soil bacterial community and N cycling functions. Photosynthetic rates and biomass production of plants, 16S rRNA sequencing and N-cycling-related genes of rhizosphere soil were measured. The relative abundance of the phyla Actinobacteria and Firmicutes was higher, and that of Proteobacteria, Acidobacteria, and Gemmatimondaetes was lower in rhizosphere soil of deciduous trees than that of evergreen. Beta-diversity of bacterial community also significantly differed between the two types of trees. Deciduous trees showed significantly higher net photosynthetic rates and biomass production than evergreen species both at well water condition and short-term drought. Root biomass was the most important factor in driving soil bacterial community and N-cycling functions than total biomass and aboveground biomass. Furthermore, 44 bacteria genera with a decreasing response and 46 taxa showed an increased response along the root biomass gradient. Regarding N-cycle-related functional genes, copy numbers of ammonia-oxidizing bacteria (AOB) and autotrophic ammonia-oxidizing archaea (AOA), N₂ fixation gene (nifH), and denitrification genes (nirK, nirS) were significantly higher in the soil of deciduous trees than in that of the evergreen. Structural equation models explained 50.2%, 47.6%, 48.6%, 49.4%, and 37.3% of the variability in copy numbers of nifH, AOB, AOA, nirK, and nirS, respectively, and revealed that root biomass had significant positive effects on copy numbers of all N-cycle functional genes. In conclusion, root biomass played key roles in affecting bacterial community structure and soil N cycling. Our findings have important implications for our understanding of plants control over bacterial community and N-cycling function in artificial forest ecosystems.

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.

Multifarious Responses of Forest Soil Microbial Community Toward Climate Change

Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO₂, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.

Soil microbial communities of dryland legume plantations are more complex than non-legumes

Soil microorganisms play a crucial role in the vegetation restoration of dryland plantations and participating in biogeochemical cycles. However, how the co-occurrence networks of soil microbial communities respond to dryland legume and non-legume plantations is unclear. Here, we conducted a comparative analysis of legume (13-, 35-, and 55-years Caragana korshinskii) and non-legume (13- and 55-years Platycladus orientalis) plantations, including plant communities, soil physicochemical properties, and soil microbial communities, in the west of the Loess Plateau, China. The results showed higher richness and diversity, more keystone taxa and positive relationships, and larger connectivity and potential functions existed in soil bacterial and fungal communities of legume plantations. Meanwhile, richer plant communities and higher soil nutrients in legume plantations were found than those in non-legume plantations. We revealed that legume plantations shaped a more complex co-occurrence network, forming a virtuous cycling of "plant-soil-microbe" continuum in legume plantation ecosystems. Our results provided a new perspective on evaluating the ecological value and plantation stability of legume tree species in the vegetation restoration engineering of drylands.

Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience

Current environmental monitoring efforts often focus on known, regulated contaminants ignoring the potential effects of unmeasured compounds and/or environmental factors. These specific, targeted approaches lack broader environmental information and understanding, hindering effective environmental management and policy. Switching to comprehensive, untargeted monitoring of contaminants, organism health, and environmental factors, such as nutrients, temperature, and pH, would provide more effective monitoring with a likely concomitant increase in environmental health. However, even this method would not capture subtle biochemical changes in organisms induced by chronic toxicant exposure. Ecosurveillance is the systematic collection, analysis, and interpretation of ecosystem health-related data that can address this knowledge gap and provide much-needed additional lines of evidence to environmental monitoring programs. Its use would therefore be of great benefit to environmental management and assessment. Unfortunately, the science of ‘ecosurveillance’, especially omics-based ecosurveillance is not well known. Here, we give an overview of this emerging area and show how it has been beneficially applied in a range of systems. We anticipate this review to be a starting point for further efforts to improve environmental monitoring via the integration of comprehensive chemical assessments and molecular biology-based approaches. Bringing multiple levels of omics technology-based assessment together into a systems-wide ecosurveillance approach will bring a greater understanding of the environment, particularly the microbial communities upon which we ultimately rely to remediate perturbed ecosystems.

Functional soil mycobiome across ecosystems

Fungi support a wide range of ecosystem processes such as decomposition of organic matter and plant-soil relationships. Yet, our understanding of the factors driving the metaproteome of fungal communities is still scarce. Here, we conducted a field survey including data on fungal biomass (by phospholipid fatty acids, PLFA), community composition (by metabarcoding of the 18S rRNA gene from extracted DNA) and functional profile (by metaproteomics) to investigate soil fungi and their relation to edaphic and environmental variables across three ecosystems (forests, grasslands, and shrublands) distributed across the globe. We found that protein richness of soil fungi was significantly higher in forests than in shrublands. Among a wide suite of edaphic and environmental variables, we found that soil carbon content and plant cover shaped evenness and diversity of fungal soil proteins while protein richness correlated to mean annual temperature and pH. Functions shifted from metabolism in forests to information processing and storage in shrublands. The differences between the biomes highlight the utility of metaproteomics to investigate functional microbiomes in soil. SIGNIFICANCE: Understanding the structure and the function of fungal communities and the driving factors is crucial to determine the contribution to ecosystem services of fungi and what effect future climate has. While there is considerable knowledge on the ecosystem processes provided by fungi such as decomposition of organic matter and plant-soil relationships, our understanding of the driving factors of the fungal metaproteome is scarce. Here we present the first estimates of fungal topsoil protein diversity in a wide range of soils across global biomes. We report taxonomic differences for genes delivered by amplicon sequencing of the 18S rRNA gene and differences of the functional microbiome based on metaproteomics. Both methods gave a complementary view on the fungal topsoil communities, unveiling both taxonomic and functional changes with changing environments. Such a comprehensive multi-omic analysis of fungal topsoil communities has never been performed before, to our knowledge.

Planting Systems Affect Soil Microbial Communities and Enzymes Activities Differentially under Drought and Phosphorus Addition

The use of phosphorus (P) to alleviate soil nutrient deficiency alters resources in plant and microbial communities, but it remains unknown how mixed and monospecific planting of forest tree species shape soil microbial structure and functions in response to drought and its interplay with phosphorus addition. We investigated the microbial structure and chemical properties of forest soils planted with P. zhennan monoculture, A. cremastogyne monoculture, and their mixed cultures. The three planting systems were exposed to drought (30-35% water reduction) and the combination of drought with P. A well-watered treatment (80-85% water addition) of similar combinations was used as the control. Planting systems shaped the effects of drought on the soil microbial properties leading to an increase in nitrate nitrogen, urease activity, and microbial biomass carbon in the monocultures, but decrease in mixed cultures. In the monoculture of P. zhennan, addition of P to drought-treated soil increased enzyme activities, the concentration of dissolved organic nitrogen, and carbon, leading to increase in the total bacteria, G⁺ bacteria, and arbuscular mycorrhizal fungi. Except in the drought with P addition treatment, the impact of admixing on total phospholipid fatty acids (PLFAs), bacterial PLFA, and fungi PLFA was synergistic in all treatments. Our findings indicated that in monoculture of P. zhennan and its mixed planting with A. cremastogyne, greater biological activities could be established under drought conditions with the addition of P.

Soil Ventilation Benefited Strawberry Growth via Microbial Communities and Nutrient Cycling Under High-Density Planting

In order to increase O₂ concentration in the rhizosphere and reduce the continuous cropping obstacles under high-density cultivation, ventilation is often used to increase soil aeration. Yet, the effect of ventilation on soil microbial communities and nutrient cycling and, further, the extent to which they influence strawberry growth under greenhouse conditions are still poorly understood. Thus, four treatments—no ventilation + low planting density (LD), ventilation + LD, no ventilation + high planting density (HD), and ventilation + HD—of strawberry “Red cheeks” (Fragaria × ananassa Duch. cv. “Benihopp”) were studied in a greenhouse for 3 years. The ventilation pipe (diameter = 10 cm) was buried in the soil at a depth of 15 cm from the surface and fresh air was sent to the root zone through the pipe by a blower. Ten pipes (one pipeline in a row) were attached to a blower. Soil samples were collected using a stainless-steel corer (five-point intra-row sampling) for the nutrient and microbial analyses. The composition and structure of the soil bacterial and fungal communities were analyzed by high-throughput sequencing of the 16S and 18S rRNA genes, and functional profiles were predicted using PICRUSt and FUNGuild, respectively. The results showed that soil ventilation increased the net photosynthetic rate (Pn), transpiration rate (Tr), and water use efficiency (WUE) of strawberry plants across two growth stages [vegetative growth stage (VGS) and fruit development stage (FDS)]. Soil ventilation increased its available nutrient contents, but the available nutrient contents were reduced under the high planting density compared with low planting density. Both the O₂ concentration and O₂:CO₂ ratio were increased by ventilation; these were positively correlated with the relative abundance of Bacilli, Gamma-proteobacteria, Blastocatella, as well as Chytridiomycota and Pezizomycetes. Conversely, ventilation decreased soil CO₂ concentration and the abundance of Beta-proteobacteria and Gemmatimonadetes. The greater planting density increased the relative abundance of Acidobacteria (oligotrophic group). Ventilation altered soil temperature and pH along with carbon and nitrogen functional profiles in the VGS (more nitrogen components) and FDS (more carbon components), which benefited strawberry plant growth under high planting density. The practice of soil ventilation provides a strategy to alleviate hypoxia stress and continuous cropping obstacles for improving crop production in greenhouse settings.

Lower relative abundance of ectomycorrhizal fungi under a warmer and drier climate is linked to enhanced soil organic matter decomposition

The aboveground impacts of climate change receive extensive research attention, but climate change could also alter belowground processes such as the delicate balance between free-living fungal decomposers and nutrient-scavenging mycorrhizal fungi that can inhibit decomposition through a mechanism called the Gadgil effect. We investigated how climate change-induced reductions in plant survival, photosynthesis and productivity alter soil fungal community composition in a mixed arbuscular/ectomycorrhizal (AM/EM) semiarid shrubland exposed to experimental warming (W) and/or rainfall reduction (RR). We hypothesised that increased EM host plant mortality under a warmer and drier climate might decrease ectomycorrhizal fungal (EMF) abundance, thereby favouring the proliferation and activity of fungal saprotrophs. The relative abundance of EMF sequences decreased by 57.5% under W+RR, which was accompanied by reductions in the activity of hydrolytic enzymes involved in the acquisition of organic-bound nutrients by EMF and their host plants. W+RR thereby created an enhanced potential for soil organic matter (SOM) breakdown and nitrogen mineralisation by decomposers, as revealed by 127-190% increases in dissolved organic carbon and nitrogen, respectively, and decreasing SOM content in soil. Climate aridification impacts on vegetation can cascade belowground through shifts in fungal guild structure that alter ecosystem biogeochemistry and accelerate SOM decomposition by reducing the Gadgil effect.

Alteration and the Function of Intestinal Microbiota in High-Fat-Diet- or Genetics-Induced Lipid Accumulation

Diet and host genetics influence the composition of intestinal microbiota, yet few studies have compared the function of intestinal microbiota in the diet- or genotype-induced lipid deposition, which limits our understanding of the role of intestinal bacteria in metabolic disorders. The lipid accumulation in wild-type zebrafish fed with control (CON) or high-fat (HF) diet and two gene-knockout zebrafish lines (cpt1b^–/– or pparab^–/–) fed with control diet was measured after a 4-week feeding experiment. The intestinal microbiota composition of these groups was investigated using 16S ribosomal RNA (rRNA) gene sequencing (DNA-based) and 16S rRNA sequencing (RNA-based). The HF diet or deficiency of two genes induced more weight gain and higher triglyceride content in the liver compared with their control group. 16S rRNA gene sequencing (DNA-based) indicated the decreased abundance of Proteobacteria in the HF group compared with CON, but there was no significant difference in bacterial α diversity among treatments. 16S rRNA sequencing (RNA-based) confirmed the decreased abundance of Proteobacteria and the bacterial α diversity in the HF group compared with CON. Deficiency of cpt1b or pparab showed less change in microbiota composition compared with their wild-type group. Intestinal microbiota of each group was transferred to germ-free zebrafish, and the quantification of Nile red staining indicated that the intestinal microbiota of the HF group induced more lipid accumulation compared with CON, whereas intestinal microbiota of cpt1b^–/– and pparab^–/– zebrafish did not. The results showed that RNA-based bacterial sequencing revealed more bacterial alteration than DNA-based bacterial sequencing. HF diet had a more dominant role in shaping gut microbiota composition to induce lipid accumulation compared with the gene-knockout of cpt1b or pparab in zebrafish, and the transplant of intestinal microbiota from HF-fed fish induced more lipid deposition in germ-free zebrafish. Together, these data suggested that a high-fat diet exerted a more dominant role over the deletion of cpt1b or pparab on the intestinal bacterial composition, which corresponded to lipid accumulation.

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

Climate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events.

Legacies of past ecological disturbances are expected but challenging to demonstrate. Here the authors report a 10-year field experiment in a mountain grassland that shows ecological memory of soil microbial community and functioning in response to recurrent drought.

Keystone taxa-mediated bacteriome response shapes the resilience of the paddy ecosystem to fungicide triadimefon contamination

The increasing input of fungicides has emerged as a global concern for agroecosystem stability and sustainability. Agroecosystem resilience has been linked to microbiome response, however, is not well understood. Focusing on a widespread triazole-class fungicide triadimefon in the paddy ecosystem, we characterized that the soils and sediments were dominant triadimefon reservoirs with the peak level at 195 μg kg^-1 and 31.3 μg kg^-1, respectively, but essential for the resilience of paddy ecosystem to triadimefon. In paddy simulation models, the half-life of triadimefon in soil-sediment was 8.4-28.9 days, while it was prolonged to 86.6-115.5 days after elimination of resident microbial community. Phospholipid fatty acid profiling and high-throughput sequencing showed that the distinctive bacterial community responses contributed to variable degradation of triadimefon in paddy soils and sediments. Sphingomonas and Xanthomonas were identified as positive responders of the keystone taxa in the responsive bacteriome, whereas Enterobacter were negative responders that declined over time. Synthetic assemblages combined with quantitative polymerase chain reaction further validated that Sphingomonas and Xanthomonas were involved in sustaining soil-sediment resilience to triadimefon contamination. Collectively, our results revealed that the shaping of soil and sediment bacteriomes was responsible for the resilience of the paddy agroecosystem to fungicide contamination.

Microbial approaches for remediation of pollutants: Innovations, future outlook, and challenges

Environmental contamination with persistent organic pollutants has emerged as a serious threat of pollution. Bioremediation is a key to eliminate these harmful pollutants from the environment and has gained the interest of researchers during the past few decades. Scientific knowledge upon microbial interactions with individual pollutants over the past decades has helped to abate environmental pollution. Traditional bioremediation approaches have limitations for their applications; hence, it is essential to discover new bioremediation approaches with biotechnological interventions for best results. The developments in various methodologies are expected to increase the efficiency of bioremediation techniques and provide environmentally sound strategies. This paper deals with the profiling of microorganisms present in polluted sites using various techniques such as culture-based approaches and omics-based approaches. Besides this, it also provides up-to-date scientific literature on the microbial electrochemical technologies which are nowadays considered as the best approach for remediation of pollutants. Detailed information about future outlook and challenges to evaluate the effect of various treatment technologies for remediation of pollutants has been discussed.

Resistance and resilience of soil prokaryotic communities in response to prolonged drought in a tropical forest

Global climate changes such as prolonged duration and intensity of drought can lead to adverse ecological consequences in forests. Currently little is known about soil microbial community responses to such drought regimes in tropical forests. In this study, we examined the resistance and resilience of topsoil prokaryotic communities to a prolongation of the dry season in terms of diversity, community structure and co-occurrence patterns in a French Guianan tropical forest. Through excluding rainfall during and after the dry season, a simulated prolongation of the dry season by five months was compared to controls. Our results show that prokaryotic communities increasingly diverged from controls with the progression of rain exclusion. Furthermore, prolonged drought significantly affected microbial co-occurrence networks. However, both the composition and co-occurrence networks of soil prokaryotic communities immediately ceased to differ from controls when precipitation throughfall returned. This study thus suggests modest resistance but high resilience of microbial communities to a prolonged drought in tropical rainforest soils.

Historical forest disturbance mediates soil microbial community responses to drought

Despite the abundance of studies demonstrating the effects of drought on soil microbial communities, the role of land use legacies in mediating these drought effects is unclear. To assess historical land use influences on microbial drought responses, we conducted a drought-rewetting experiment in soils from two adjacent and currently forested watersheds with distinct land use histories: an undisturbed 'reference' site and a 'disturbed' site that was clear-cut and converted to agriculture ~60 years prior. We incubated intact soil cores at either constant moisture or under a drought-rewet treatment and characterized bacterial and fungal communities using amplicon sequencing throughout the experiment. Bacterial alpha diversity decreased following drought-rewetting while fungal diversity increased. Bacterial beta diversity also changed markedly following drought-rewetting, especially in historically disturbed soils, while fungal beta diversity exhibited little response. Additionally, bacterial beta diversity in disturbed soils recovered less from drought-rewetting compared with reference soils. Disturbed soil communities also exhibited notable reductions in nitrifying taxa, increases in putative r-selected bacteria, and reductions in network connectivity following drought-rewetting. Overall, our study reveals historical land use to be important in mediating responses of soil bacterial communities to drought, which will influence the ecosystem-scale trajectories of these environments under ongoing and future climate change.

Bacteria are more sensitive than fungi to moisture in eroded soil by natural grass vegetation restoration on the Loess Plateau

Community composition and respiration rates of bacterial and fungal communities from grass-covered eroded soils of the Loess Plateau responded differently to constant and increasing soil moisture (SM) regimes. The soils were incubated with SM contents of 5%, 30%, and 45% and with wetting processes in the SM ranges from 5% to 30% (5-30%), from 5% to 30% to 45% (5-30-45%) and from 30% to 45% (30-45%); high-throughput sequencing and co-occurrence network analyses were applied to investigate the different responses of the bacterial and fungal communities to changed SM. Our results showed that bacteria were more sensitive than fungi to changes in SM. The dominant bacterial communities converted from Actinobacterial to Proteobacteria and Acidobacteria in 5-30-45% wetting procedure. Firmicutes preferred wet condition and exhibited slow resilience. However, no difference was observed for the Chloroflexi communities across any sample. The obvious difference in fungal composition was found between the wetting process of 5-30-45% and constant 45% SM. During the 5-30-45% procedure, the respiration rate was higher than that at 30-45% procedure after incubation for 24 days. The respiration rate in 5-30% procedure was lower than that of 5-30-45% process after incubation for 16-27 days. The larger effects on bacterial response than on fungi were verified in network analysis. Multiple stepwise regression analysis showed that 84.40% of the variation in bacterial richness and diversity as well as fungal diversity can be explained by changes in soil respiration rate in response to wetting procedure. Understanding the response of difference between bacterial and fungal community composition, phylum-levels networks and respiration rate to changes in SM is essential for the management of plant-soil-water relationship in the ecosystem after natural vegetation restoration on the Loess Plateau.

16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys

Sequencing 16S rRNA gene amplicons is the gold standard to uncover the composition of prokaryotic communities. The presence of multiple copies of this gene makes the community abundance data distorted and gene copy normalization (GCN) necessary for correction. Even though GCN of 16S data provided a picture closer to the metagenome before, it should also be compared with communities of known composition due to the fact that library preparation is prone to methodological biases. Here, we process 16S rRNA gene amplicon data from eleven simple mock communities with DADA2 and estimate the impact of GCN. In all cases, the mock community composition derived from the 16S sequencing differs from those expected, and GCN fails to improve the classification for most of the analysed communities. Our approach provides empirical evidence that GCN does not improve the 16S target sequencing analyses in real scenarios. We therefore question the use of GCN for metataxonomic surveys until a more comprehensive catalogue of copy numbers becomes available.

Response of soil fungal community composition and functions on the alteration of precipitation in the grassland of Loess Plateau

A change in precipitation caused by climate change is an important factor that affects the biodiversity and ecological function of arid and semi-arid regions, but its influence on the composition and function of the soil fungi community in the grasslands of the Loess Plateau remains unclear. To fill this knowledge gap, we conducted an in-situ simulation experiment using five precipitation gradients (natural precipitation, increased and decreased by 40%, and 80%) in a natural restoration grassland for three years. The composition of soil fungal communities and their functions were analyzed using high-throughput sequencing techniques. Although the change of precipitation did not change the diversity index of soil fungi, it changed the composition and function of dominant fungal community groups. Specifically, decreased precipitation resulted in an increase in the relative abundance of Dothideomycetes and Boeremia by up to 12.17% and 9.93%, respectively, while these decreased with increased precipitation. The abundance of Basidiomycota, Glomeromycota, and Agaricomycetes abundance decreased by up to 11.27%, 6.96%, and 11.46% with decreased precipitation, but also decreased by up to 10.9%, 1.73%, and 10.51% with increased precipitation, respectively. However, the abundance of Ascomycota, Pezizomycetes, and norank_Pezizales increased by up to 22.58%, 7.45%, and 6.95% with decreased precipitation, and increased by up to 12.05%, 8.43%, and 5.81% with increased precipitation, respectively. The number of dominant fungal groups with interactive relationships weakened by 34.93% and 8.7% under decreased precipitation by 80% and increased 80%, respectively. Precipitation change had no significant effect on the proportion of saprotrophs, while a decrease of precipitation increased the endophyte-plant pathogens by up to 58.0% and decreased arbuscular mycorrhizal fungi by up to 92.6%. In brief, the dominant soil fungal communities could adapt and respond to climate change by altering the proportion of different dominant fungal groups by responding to moisture patterns with changes in the interrelationships between microbial communities and the proportional distribution of functional groups.

Harnessing the plant microbiome to promote the growth of agricultural crops

The rhizosphere microbiome is composed of diverse microbial organisms, including archaea, viruses, fungi, bacteria as well as eukaryotic microorganisms, which occupy a narrow region of soil directly associated with plant roots. The interactions between these microorganisms and the plant can be commensal, beneficial or pathogenic. These microorganisms can also interact with each other, either competitively or synergistically. Promoting plant growth by harnessing the soil microbiome holds tremendous potential for providing an environmentally friendly solution to the increasing food demands of the world's rapidly growing population, while also helping to alleviate the associated environmental and societal issues of large-scale food production. There recently have been many studies on the disease suppression and plant growth promoting abilities of the rhizosphere microbiome; however, these findings largely have not been translated into the field. Therefore, additional research into the dynamic interactions between crop plants, the rhizosphere microbiome and the environment are necessary to better guide the harnessing of the microbiome to increase crop yield and quality. This review explores the biotic and abiotic interactions that occur within the plant's rhizosphere as well as current agricultural practices, and how these biotic and abiotic factors, as well as human practices, impact the plant microbiome. Additionally, some limitations, safety considerations, and future directions to the study of the plant microbiome are discussed.

A novel constructed carbonate-mineralized functional bacterial consortium for high-efficiency cadmium biomineralization

A stable, urease-producing consortium (UPC) was constructed for high-efficiency cadmium (Cd) ion mineralization via a short-term and efficient acclimation process (five acclimation transfers). 16S rRNA gene high-throughput sequencing and quantitative polymerase chain reaction (qPCR) analyses of the urease subunit C (ureC) gene suggested that the three functional genera, all belonging to the phylum Firmicutes, rapidly increased during the process and finally composed the UPC (70.22-75.41 % of Sporosarcina, 13.83-20.66 % of norank_f_Bacillaceae, and 5.91-13.69 % of unclassified_f_Bacillaceae). The UPC exhibited good adaptability to a wide range of environmental conditions (a pH range of 4.0-11.0, temperature range of 10-45 °C, and Cd concentration range of 0-200 mg L^-1). After 8 h of incubation, 92.87 % of Cd at an initial concentration of 100 mg L^-1 was mineralized by UPC, exhibiting a great improvement as compared to the first acclimated consortium (C-1). Furthermore, although the acclimated consortium had been successively transferred 21 times, the Cd biomineralization efficiency remained stable, and this was consistent with the observed stable microbial community structure. X-ray diffraction (XRD) spectra revealed that Cd was mineralized in a (Ca0.67, Cd0.33)CO₃ phase. This research obtained a promising microbial resource for the biomineralization of Cd or other hazardous heavy metal contaminants.

The Total and Active Bacterial Community of the Chlorolichen Cetraria islandica and Its Response to Long-Term Warming in Sub-Arctic Tundra

Lichens are traditionally defined as a symbiosis between a fungus and a green alga and or a cyanobacterium. This idea has been challenged by the discovery of bacterial communities inhabiting the lichen thalli. These bacteria are thought to contribute to the survival of lichens under extreme and changing environmental conditions. How these changing environmental conditions affect the lichen-associated bacterial community composition remains unclear. We describe the total (rDNA-based) and potentially metabolically active (rRNA-based) bacterial community of the lichen Cetaria islandica and its response to long-term warming using a 20-year warming experiment in an Icelandic sub-Arctic tundra. 16S rRNA and rDNA amplicon sequencing showed that the orders Acetobacterales (of the class Alphaproteobacteria) and Acidobacteriales (of the phylum Acidobacteria) dominated the bacterial community. Numerous amplicon sequence variants (ASVs) could only be detected in the potentially active community but not in the total community. Long-term warming led to increases in relative abundance of bacterial taxa on class, order and ASV level. Warming altered the relative abundance of ASVs of the most common bacterial genera, such as Granulicella and Endobacter. The potentially metabolically active bacterial community was also more responsive to warming than the total community. Our results suggest that the bacterial community of the lichen C. islandica is dominated by acidophilic taxa and harbors disproportionally active rare taxa. We also show for the first time that climate warming can lead to shifts in lichen-associated bacterial community composition.

Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights

Soil is a complex matrix where biotic and abiotic components establish a still unclear network involving bacteria, fungi, archaea, protists, protozoa, and roots that are in constant communication with each other. Understanding these interactions has recently focused on metagenomics, metatranscriptomics and less on metaproteomics studies. Metaproteomic allows total extraction of intracellular and extracellular proteins from soil samples, providing a complete picture of the physiological and functional state of the “soil community”. The advancement of high-performance mass spectrometry technologies was more rapid than the development of ad hoc extraction techniques for soil proteins. The protein extraction from environmental samples is biased due to interfering substances and the lower amount of proteins in comparison to cell cultures. Soil sample preparation and extraction methodology are crucial steps to obtain high-quality resolution and yields of proteins. This review focuses on the several soil protein extraction protocols to date to highlight the methodological challenges and critical issues for the application of proteomics to soil samples. This review concludes that improvements in soil protein extraction, together with the employment of ad hoc metagenome database, may enhance the identification of proteins with low abundance or from non-dominant populations and increase our capacity to predict functional changes in soil.

Drought changed soil organic carbon composition and bacterial carbon metabolizing patterns in a subtropical evergreen forest

Subtropical forests are considerable carbon sinks in the northern hemisphere, yet are increasingly suffering from the impact of extreme drought. To better understand the dynamics and kinetics of forest soil carbon storage under long-term drought, a rainfall-reduction experiment was established in a subtropical evergreen forest of eastern China. Soil organic carbon (SOC) composition, microbial carbon metabolism and the interactions with soil microbial community structure were investigated across different soil aggregate size fractions. After five years' treatment of rainfall reduction, a significant loss of large macroaggregates, as well as an increase of microaggregates by over 100% was observed. Meanwhile, drought changed the composition of SOC, reducing the non-hydrolyzed carbon and humin contents in large- to medium-size macroaggregates. Microbial metabolizing capacity of polymeric compounds was also reduced especially in the above aggregate fractions, whereas the utilization of small-molecular compounds was more impacted in small macroaggregates and microaggregates. The changes in carbon metabolizing patterns were further associated with the abundance changes of specific microbial taxa, revealing the microbially mediated mechanism of soil carbon metabolism under long-term drought. In addition, carbon metabolism in microaggregates was particularly sensitive to the changes of soil moisture, suggesting long-term drought may continually influence the functional resistance of the microbial communities. Taken together, our results provide insights into how biotic and abiotic processes together influence the SOC metabolizing processes, continued monitoring and investigation of which shall contribute to better understanding of the dynamics and kinetics of SOC storage under the impact of long-term drought.

Comparative study of neighboring Holm oak and olive trees-belowground microbial communities subjected to different soil management

It is well-known that different plant species, and even plant varieties, promote different assemblages of the microbial communities associated with them. Here, we investigate how microbial communities (bacteria and fungi) undergo changes within the influence of woody plants (two olive cultivars, one tolerant and another susceptible to the soilborne fungal pathogen Verticillium dahliae, plus wild Holm oak) grown in the same soil but with different management (agricultural versus native). By the use of metabarcoding sequencing we determined that the native Holm oak trees rhizosphere bacterial communities were different from its bulk soil, with differences in some genera like Gp4, Gp6 and Solirubrobacter. Moreover, the agricultural management used in the olive orchard led to belowground microbiota differences with respect to the natural conditions both in bulk soils and rhizospheres. Indeed, Gemmatimonas and Fusarium were more abundant in olive orchard soils. However, agricultural management removed the differences in the microbial communities between the two olive cultivars, and these differences were minor respect to the olive bulk soil. According to our results, and at least under the agronomical conditions here examined, the composition and structure of the rhizospheric microbial communities do not seem to play a major role in olive tolerance to V. dahliae.

Ecological Effects of Heavy Metal Pollution on Soil Microbial Community Structure and Diversity on Both Sides of a River around a Mining Area

The objectives of this study were to understand the characteristics of heavy metal pollution caused by mining activities on the two sides of the Shun'an river and the response of soil microorganisms to the habitats by different contamination levels and vegetation. This paper selected soil samples from the banks of the Shun'an River near the Shizishan mining area, which is at the left of the river, in Tongling, Anhui Province, China. Using Illumina MiSeq 2500 technology, we analyzed the relationship between environmental factors and microbial communities. As the distance from the mining area increased, the heavy metal comprehensive pollution and potential risk value decreased. Additionally, the pollution severity and risk value of the left bank, where the mining area lies, were generally higher than those of the right bank. Because the symmetric sampling points on both banks of the river had similar planting types, their environmental factors and microbial community structure were similar and clustered. However, under different vegetation, the paddy soils tended to have a higher nutrient content and community richness and diversity than the vegetable fields or the abandoned land. It was found that soil microbial communities in this area were mostly affected by pH and Nemerow pollution index (P_N). The pH significantly affected the abundance and structure of most microorganisms. In addition, Proteobacteria, Acidobacteria, and Bacteroidetes had significant tolerance to Zn, Pb, and Cd. By exploring the potential use of these tolerant microorganisms, we seek to provide strains and the theoretical basis for the bioremediation of areas contaminated by heavy metal.

Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality

Biodiversity on the Earth is changing at an unprecedented rate due to a variety of global change factors (GCFs). However, the effects of GCFs on microbial diversity is unclear despite that soil microorganisms play a critical role in biogeochemical cycling. Here, we synthesize 1235 GCF observations worldwide and show that microbial rare species are more sensitive to GCFs than common species, while GCFs do not always lead to a reduction in microbial diversity. GCFs-induced shifts in microbial alpha diversity can be predominately explained by the changed soil pH. In addition, GCF impacts on soil functionality are explained by microbial community structure and biomass rather than the alpha diversity. Altogether, our findings of GCF impacts on microbial diversity are fundamentally different from previous knowledge for well-studied plant and animal communities, and are crucial to policy-making for the conservation of microbial diversity hotspots under global changes.