Depth matters: effects of precipitation regime on soil microbial activity upon rewetting of a plant-soil system

Integrated enzyme activities and untargeted metabolome to reveal the mechanism that allow long-term biochar-based fertilizer substitution improves soil quality and maize yield

Biochar-based fertilizer has potential benefits in improving soil quality and crop yield, but the biological mechanisms of soil microbial enzymes interacting with related metabolisms still need to be further investigated. In this study, we combined enzymology and untargeted metabolomics to investigate how biochar-based fertilizer substitution affects soil quality and crop yield by regulating soil enzymes and metabolites in dry-crop farmland. Our findings showed that biochar-based fertilizer substitution enhanced the activities of enzymes related to carbon, nitrogen, and phosphorus cycling, as well as influenced metabolite composition. The identified differential metabolites were enriched into 10 metabolic pathways including linoleic acid metabolism, fatty acid biosynthesis, styrene degradation, ABC transporters, biosynthesis of unsaturated fatty acids, glutathione metabolism, glycine, serine and threonine metabolism, phenylalanine metabolism, pyrimidine metabolism, and arachidonic acid metabolism. Substantial soil quality index improvement was demonstrated, with at least 63.46% increased, under biochar-based fertilizer application, while maize yield was increased by at least 11.16%, compared to conventional fertilizer. Model analysis elucidated mechanisms underlying soil quality and maize yield enhancement, emphasizing the importance of intrinsic regulation through the release of carbon- and nitrogen-related enzymes (e.g., α-glucosidase (α-GC), N-acetyl-β-D-glucosidase (NAG), and leucine aminopeptidase (LAP)) and specific metabolites (e.g., stearic acid, arachidonic acid, and melibiose). Moreover, the key role of soil quality factors was highlighted, with soil organic carbon (SOC), microbial biomass, and available nutrients playing a fundamental role in contributing to the increase in maize yield. The above findings illustrated that biochar-based fertilizer is crucial in modulating soil microbial activity and their metabolites, and their interactions in the soil are essential for promoting improved soil quality and crop yield.

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

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

Periodic flooding alters ecological processes and carbon metabolism efficiency of riparian soil microbial communities in the three Gorges Reservoir area, China

Soil microbial communities are the most active components in the riparian biota, and are critical in driving carbon cycling. The periodic flooding in riparian zones is a primary driving force in the changes of soil microbial community structures and function. However, whether such events can induce changes in microbial carbon metabolism efficiency has not been fully revealed, especially in large reservoirs that experience counter-seasonal water level fluctuations (WLFs). In this study, high-throughput sequencing and the 18O-H2O cultivation method were applied to investigate the soil microbial community and carbon metabolism in a tributary riparian zone in China's Three Gorges Reservoir, which has experienced large WLFs. Three elevations in the riparian zone (155, 165, and 170 m) were selected as treatments for different flooding intensities. As the frequency of flooding decreased, soil enzyme activity decreased first and then increased. In contrast, soil water content, fungal α-diversity, microbial co-occurrence network complexity, average variation degree, βNTI, and total cohesion decreased slowly. The assembly mechanism of microbial communities is primarily governed by homogeneous dispersion. This suggests that periodic flooding significantly alters microbial ecological processes. Additionally, we found that decreased extracellular enzyme activity increases microbial carbon use efficiency and decreases the metabolic quotient, promoting soil carbon storage. This study enhances our understanding of the response and mechanisms of soil microbial communities to periodic flooding. It provides a theoretical foundation for soil ecosystem management and conservation.

The Response Mechanism of the cbbM Carbon Sequestration Microbial Community in the Alpine Wetlands of Qinghai Lake to Changes in Precipitation

The dramatic changes in precipitation patterns on the Tibetan Plateau affected the carbon-sequestering microbial communities within wetland ecosystems, which were closely related to the responses and adaptation mechanisms of alpine wetland ecosystems to climate change. This study focused on wetland soils subjected to different precipitation gradient treatments and employed high-throughput sequencing technology to analyze the soil cbbM carbon-sequestering microbial communities. The results indicated that Proteobacteria were the dominant microbial community responsible for carbon sequestration in the Wayan Mountain wetland. A 50% increase in precipitation significantly raised the soil moisture content, while a 50% reduction and a 25% increase in precipitation notably enhanced the total soil carbon content. The 25% reduction in precipitation increased the differences in microbial community composition, whereas both the 50% increase and the 50% reduction in precipitation decreased these differences. The soil pH and temperature had the most significant impact on the carbon-sequestering microbial communities. In conclusion, changes in precipitation affect the cbbM carbon sequestration characteristics of soil microbial communities, and a moderate reduction in water input benefited carbon sequestration in wetlands.

Dynamic response of soil microbial communities and network to hymexazol exposure

Fungicides are an essential component of current agricultural practices, but their extensive use has raised concerns about their effects on non-target soil microorganisms, which carry out essential ecosystem functions. However, despite the complexity of microbial communities, many studies investigating their response to fungicides focus only on bacteria or fungi at one point in time. In this study, we used amplicon sequencing to assess the effect of the fungicide hymexazol on the diversity, composition, and co-occurrence network of soil bacteria, fungi, and protists at 7, 21, and 60 days after application. We found that hymexazol had very little effect on microbial alpha-diversity, but that microbial community composition and OTU differential abundance were altered over the duration of the experiment, even after hymexazol concentrations were undetectable. The co-occurrence patterns within and between microbial kingdoms were affected by hymexazol dose, suggesting that indirect effects may play a role in the microbial community response. Nitrogen cycling was also affected, with a transient hymexazol-associated increase in the abundance of ammonia-oxidizing microorganisms and soil nitrate concentration. These findings highlight that the effects of fungicides on soil microorganisms are dynamic and extensive, spanning several taxonomic kingdoms.

Species mixtures enhance fine root biomass but inhibit root decay under throughfall manipulation in young natural boreal forests

Fine roots play crucial roles in terrestrial biogeochemical cycles. Although biodiversity loss and changes in precipitation are two major drivers of global change, our understanding of their effects on fine root biomass (FRB), root functional traits, and fine root decay (FRD) remains incomplete. We manipulated precipitation in young boreal forests dominated by Populus tremuloides, Pinus banksiana, and their relatively even mixtures using 25 % addition, ambient, and 25 % reduction in throughfall during the growing season. We collected root samples using soil core and trunk-traced methods to quantify FRB and root traits, and we simulated fine root decay using an in-situ experiment over 531 days. We found that compared to the average of single-species-dominated stands, species mixtures increased FRB by 41 % under ambient throughfall, by 89 % under throughfall reduction and by 71 % under throughfall addition. Root surface area, fine root volume, and root length density responded to species mixtures similarly to FRB. Meanwhile, species mixtures reduced FRD across all water treatments. There was a positive relationship between the effect of species mixtures on the FRD of absorptive roots and those on the FRB. Our results highlight that species mixtures could modify carbon cycling by enhancing fine root biomass accumulation and reducing its decomposition of young boreal forests under changing precipitation.

Exploring the Rhizospheric Microbial Communities under Long-Term Precipitation Regime in Norway Spruce Seed Orchard

The rhizosphere is the hotspot for microbial enzyme activities and contributes to carbon cycling. Precipitation is an important component of global climate change that can profoundly alter belowground microbial communities. However, the impact of precipitation on conifer rhizospheric microbial populations has not been investigated in detail. In the present study, using high-throughput amplicon sequencing, we investigated the impact of precipitation on the rhizospheric soil microbial communities in two Norway Spruce clonal seed orchards, Lipová Lhota (L-site) and Prenet (P-site). P-site has received nearly double the precipitation than L-site for the last three decades. P-site documented higher soil water content with a significantly higher abundance of Aluminium (Al), Iron (Fe), Phosphorous (P), and Sulphur (S) than L-site. Rhizospheric soil metabolite profiling revealed an increased abundance of acids, carbohydrates, fatty acids, and alcohols in P-site. There was variance in the relative abundance of distinct microbiomes between the sites. A higher abundance of Proteobacteria, Acidobacteriota, Ascomycota, and Mortiellomycota was observed in P-site receiving high precipitation, while Bacteroidota, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadota, and Basidiomycota were prevalent in L-site. The higher clustering coefficient of the microbial network in P-site suggested that the microbial community structure is highly interconnected and tends to cluster closely. The current study unveils the impact of precipitation variations on the spruce rhizospheric microbial association and opens new avenues for understanding the impact of global change on conifer rizospheric microbial associations.

Response Characteristics and Community Assembly Mechanisms of nirS-Type Denitrifiers in the Alpine Wetland under Simulated Precipitation Conditions

The nitrogen cycling process in alpine wetlands is profoundly affected by precipitation changes, yet the dynamic response mechanism of denitrifiers to long-term precipitation shifts in the alpine wetland of the Qinghai-Tibet Plateau remains enigmatic. Utilizing high-throughput sequencing analysis of nirS-type functional genes, this study delved into the dynamic response mechanism of nirS-type denitrifiers to precipitation changes in the alpine wetland of Qinghai Lake. The findings revealed that nirS-type denitrifiers in the alpine wetland of Qinghai Lake were primarily Proteobacteria, and Alpha diversity exhibited a negative correlation with the precipitation gradient, with deterministic processes predominating in the community assembly of denitrifying microbes. A 50% increase in rainfall shifted the community assembly process of denitrifiers from deterministic to stochastic. Dominant microflora at the genus level responded significantly to precipitation changes, with aerobic bacteria comprising the majority of differentially abundant taxa (55.56%). As precipitation increased, the complexity of the microbial interaction network decreased, and a 25% reduction in precipitation notably elevated the relative abundance of three key functional groups: chemoheterotrophic, aerobic chemoheterotrophic, and nitrogen fixation. Precipitation notably emerged as the primary regulator of nirS-type denitrifiers in the alpine wetland of Qinghai Lake, accounting for 51% of the variation in community composition. In summary, this study offers a fresh perspective for investigating the ecological processes of nitrogen cycling in alpine ecosystems by examining the diversity and community composition of nirS-type denitrifiers in response to precipitation changes.

Land use modified impacts of global change factors on soil microbial structure and function: A global hierarchical meta-analysis

Nitrogen cycling in terrestrial ecosystems is critical for biodiversity, vegetation productivity and biogeochemical cycling. However, little is known about the response of functional nitrogen cycle genes to global change factors in soils under different land uses. Here, we conducted a multiple hierarchical mixed effects meta-analyses of global change factors (GCFs) including warming (W+), mean altered precipitation (MAP+/-), elevated carbon dioxide concentrations (eCO2), and nitrogen addition (N+), using 2706 observations extracted from 200 peer-reviewed publications. The results showed that GCFs had significant and different effects on soil microbial communities under different types of land use. Under different land use types, such as Wetland, Tundra, Grassland, Forest, Desert and Agriculture, the richness and diversity of soil microbial communities will change accordingly due to differences in vegetation cover, soil management practices and environmental conditions. Notably, soil bacterial diversity is positively correlated with richness, but soil fungal diversity is negatively correlated with richness, when differences are driven by GCFs. For functional genes involved in nitrification, eCO2 in agricultural soils and the interaction of N+ with other GCFs in grassland soils stimulate an increase in the abundance of the AOA-amoA gene. In agricultural soil, MAP+ increases the abundance of nifH. W+ in agricultural soils and N+ in grassland soils decreased the abundance of nifH. The abundance of the genes nirS and nirK, involved in denitrification, was mainly negatively affected by W+ and positively affected by eCO2 in agricultural soil, but negatively affected by N+ in grassland soil. This meta-analysis was important for subsequent research related to global climate change. Considering data limitations, it is recommended to conduct multiple long-term integrated observational experiments to establish a scientific basis for addressing global changes in this context.

Soil fungal community has higher network stability than bacterial community in response to warming and nitrogen addition in a subtropical primary forest

Global change factors are known to strongly affect soil microbial community function and composition. However, as of yet, the effects of warming and increased anthropogenic nitrogen deposition on soil microbial network complexity and stability are still unclear. Here, we examined the effects of experimental warming (3°C above ambient soil temperature) and nitrogen addition (5 g N m-2 year-1) on the complexity and stability of the soil microbial network in a subtropical primary forest. Compared to the control, warming increased |negative cohesion|:positive cohesion by 7% and decreased network vulnerability by 5%; nitrogen addition decreased |negative cohesion|:positive cohesion by 10% and increased network vulnerability by 11%. Warming and decreased soil moisture acted as strong filtering factors that led to higher bacterial network stability. Nitrogen addition reduced bacterial network stability by inhibiting soil respiration and increasing resource availability. Neither warming nor nitrogen addition changed fungal network complexity and stability. These findings suggest that the fungal community is more tolerant than the bacterial community to climate warming and nitrogen addition. The link between bacterial network stability and microbial community functional potential was significantly impacted by nitrogen addition and warming, while the response of soil microbial network stability to climate warming and nitrogen deposition may be independent of its complexity. Our findings demonstrate that changes in microbial network structure are crucial to ecosystem management and to predict the ecological consequences of global change in the future.

IMPORTANCE

Soil microbes play a very important role in maintaining the function and health of forest ecosystems. Unfortunately, global change factors are profoundly affecting soil microbial structure and function. In this study, we found that climate warming promoted bacterial network stability and nitrogen deposition decreased bacterial network stability. Changes in bacterial network stability had strong effects on bacterial community functional potentials linked to metabolism, nitrogen cycling, and carbon cycling, which would change the biogeochemical cycle in primary forests.

Distinct microbial communities under different rock-associated microhabitats in the Qaidam Desert

Hypolithic communities, which occupy highly specialised microhabitats beneath translucent rocks in desert and arid environments, have assembly mechanisms and ecosystem functions are not fully understood. Thus, in this study, we aimed to examine the microbial community structure, assembly, and function of light-accessible (under quartz, calcite, and hypolithic lichen-dominated biocrusts) and light-inaccessible microhabitats (under basalt and adjacent soil) in the Qaidam Desert, China. The results showed that hypolithic communities have different characteristics compared with microbial communities of light-inaccessible microhabitats. Notably, hypolithic bacterial communities were dominated by Cyanobacteria, whereas light-inaccessible microhabitats showed a predominance of Bacteroidetes and Proteobacteria. Although the class Dothideomycetes (phylum: Ascomycota) dominated the fungal communities between the two microhabitat types, Sordariomycetes were more prevalent in light-accessible microhabitats. Network and robustness analyses showed that hypolithic communities were less complex and more resilient than microbial communities in light-inaccessible microhabitats. Our results indicated that deterministic processes, specifically homogeneous selection, govern the establishment of bacterial and fungal communities in light-accessible and light-inaccessible microhabitats. The hypolithic community showed an increased frequency of phylotypes that exhibited increased tolerance to functional stress response pathways. In contrast to light-inaccessible microhabitats, light-accessible microhabitats showed a slight decrease and a notable increase in the prevalence of carbon fixation pathways in prokaryotes and carbon fixation in photosynthetic organisms, respectively. For fungi, light-accessible microhabitats enriched saprotrophic and ectomycorrhizal groups. These results highlight the importance of complex and diverse microhabitats in desert regions, which serve as vital shelters for microbes. Combining future research on interactions between hypolithic communities and environments may enhance our current understanding of their pivotal roles in sustaining desert ecosystems. This knowledge then be applied to design and implement informed conservation efforts to preserve these unique rock-associated microhabitats in desert ecosystems.

Soil microbial community fragmentation reveals indirect effects of fungicide exposure mediated by biotic interactions between microorganisms

Fungicides are used worldwide to improve crop yields, but they can affect non-target soil microorganisms which are essential for ecosystem functioning. Microorganisms form complex communities characterized by a myriad of interspecies interactions, yet it remains unclear to what extent non-target microorganisms are indirectly affected by fungicides through biotic interactions with sensitive taxa. To quantify such indirect effects, we fragmented a soil microbial community by filtration to alter biotic interactions and compared the effect of the fungicide hymexazol between fractions in soil microcosms. We postulated that OTUs which are indirectly affected would exhibit a different response to the fungicide across the fragmented communities. We found that hymexazol primarily affected bacterial and fungal communities through indirect effects, which were responsible for more than 75% of the shifts in relative abundance of the dominant microbial OTUs after exposure to an agronomic dose of hymexazol. However, these indirect effects decreased for the bacterial community when hymexazol doses increased. Our results also suggest that N-cycling processes such as ammonia oxidation can be impacted indirectly by fungicide application. This work sheds light on the indirect impact of fungicide exposure on soil microorganisms through biotic interactions, which underscores the need for higher-tier risk assessment. ENVIRONMENTAL IMPLICATION: In this study, we used a novel approach based on the fragmentation of the soil microbial community to determine to which extent fungicide application could indirectly affect fungi and bacteria through biotic interactions. To assess off-target effects of fungicide on soil microorganisms, we selected hymexazol, which is used worldwide to control a variety of fungal plant pathogens, and exposed arable soil to the recommended field rate, as well as to higher rates. Our findings show that at least 75% of hymexazol-impacted microbial OTUs were indirectly affected, therefore emphasizing the importance of tiered risk assessment.

Soil extracellular enzyme stoichiometry reveals the nutrient limitations in soil microbial metabolism under different carbon input manipulations

Changes in the quality and quantity of litter and root inputs due to climate change and human activities can influence below-ground biogeochemical processes in forest ecosystems. However, it is unclear whether and how much aboveground litter and root inputs affect soil microbial metabolism and nutrient limitation mechanisms. In this study, according to a 4-years field manipulation experiment, litter and root manipulations (control (CK), double litter input (DL), no litter (NL), no root (NR), and no inputs (NI)) were set up to analyze the extracellular enzyme activities and stoichiometric ratios characteristics of 0-10 cm and 10-20 cm soils, explore the metabolic limitations of microorganisms, and clarify the main driving factors restricting nutrient limitation. The results showed that the enzyme activities associated with the C cycling (β-1,4-glucosidase (BG), cellulose disaccharide hydrolase (CBH)) and N cycling (β-1,4-N-acetylglucosaminidase (NAG), leucine aminopeptidase (LAP)) in DL treatment were significantly higher than those in NR treatment. Moreover, enzyme activities related to P cycling are significantly higher in comparison to other treatments. The acid phosphatase (AP), which is related to the P cycle, showed the highest activity under NR treatment. In addition, there was no significant difference in soil microbial metabolic limitation by the different carbon inputs, which did not change the original nutrient limitation pattern. The main drivers of microbial nutrient metabolic limitation included soil physicochemical properties, soil total nutrients, and available nutrients, among which soil SWC and pH presented the greatest influence on microbial C limitation and soil total nutrients showed the greatest influence on microbial N limitation. Changes in soil carbon input altered soil extracellular enzyme activities and their stoichiometric ratios by affecting soil physicochemical properties, total nutrients. This study provides data for the understanding of material cycling in forest ecosystems under environmental change.

Uranium bioavailability in soil pore water: A long-term investigation in a contaminated soil mesocosm

Uranium in soil can exist in both (IV) and (VI) oxidation states, distributed among different soil fractions (exchangeable, carbonate, oxidizable, reducible, and residual). Following its release from these fractions, uranium enters the soil pore water, becoming bioavailable and potentially posing risks due to its radio and chemical toxicity. Given the significant health and environmental risks associated with uranium, it is crucial to understand its behaviour in contaminated soil pore water and how it changes over time, especially in response to seasonal variations. To address this issue, study was designed to investigate the temporal changes in uranium availability in soil pore water, with a special focus on effect of seasonal variations and biogeochemical reactions that govern the bioavailability of uranium in a contaminated soil mesocosm. This field investigation was carried out for two consecutive years, and revealed that, seasonal variation has a significant effect on the bioavailability of the uranium in the upper soil layers (<30 cm). The biogenic NO3- induced oxidative dissolution of uranium was found to be the predominant reaction causing the dissolution of uranium into soil pore water, followed by ion-exchange in upper layer, whereas at higher depths (30 cm < d < 70 cm) bioavailability is predominantly controlled by ion-exchange reaction. Furthermore, the study shows that at upper layers bioavailability is high during the summer, which is attributed to higher rate of biogenic denitrification and ion exchange reactions. Fast vertical migration of uranium in the soil column is attributed to formation of stable mobile species such as hydroxo‑carbonato ((UO2)xCO3(OH)y-), hydroxo (UO2)x(OH)y and carbonato (UO2CO3) complexes, identified by speciation modelling. For the first time, this study reports the process controlling uranium behaviour in soil pore water and the effect of seasonal variation on it in a contaminated soil. The findings are essential for assessing its potential radiological impact and remediation planning.

Metagenomics reveals effects of fluctuating water conditions on functional pathways in plant litter microbial community

Climate change modifies environmental conditions, resulting in altered precipitation patterns, moisture availability and nutrient distribution for microbial communities. Changes in water availability are projected to affect a range of ecological processes, including the decomposition of plant litter and carbon cycling. However, a detailed understanding of microbial stress response to drought/flooding is missing. In this study, an intermittent lake is taken up as a model for changes in water availability and how they affect the functional pathways in microbial communities of the decomposing Phragmites australis litter. The results show that most enriched functions in both habitats belonged to the classes of Carbohydrates and Clustering-based subsystems (terms with unknown function) from SEED subsystems classification. We confirmed that changes in water availability resulted in altered functional makeup of microbial communities. Our results indicate that microbial communities under more frequent water stress (due to fluctuating conditions) could sustain an additional metabolic cost due to the production or uptake of compatible solutes to maintain cellular osmotic balance. Nevertheless, although prolonged submergence seemed to have a negative impact on several functional traits in the fungal community, the decomposition rate was not affected.

Dynamic Response of the cbbL Carbon Sequestration Microbial Community to Wetland Type in Qinghai Lake

The soil carbon storage in the Qinghai-Tibet Plateau wetlands is affected by microbiota and wetland types, but the response mechanisms of carbon sequestration microorganisms on the Qinghai-Tibet Plateau to different wetland types are still poorly described. To explore the differences in carbon sequestration microbial communities in different wetlands and the main influencing factors, this study took a marsh wetland, river source wetland and lakeside wetland of Qinghai Lake as the research objects and used high-throughput sequencing to study the functional gene, cbbL, of carbon sequestration microorganisms. The results showed that the dominant bacterial group of carbon sequestration microorganisms in marsh and river source wetlands was Proteobacteria, and the dominant bacterial group in the lakeside wetland was Cyanobacteria. The alpha diversity, relative abundance of Proteobacteria and total carbon content were the highest in the marsh wetland, followed by the river source wetland, and they were the lowest in the lakeside wetland. In addition, the physical and chemical characteristics of the three wetland types were significantly different, and the soil temperature and moisture and total carbon content were the most important factors affecting the community structures of carbon-sequestering microorganisms. There was little difference in the total nitrogen contents between the marsh wetland and river source wetland. However, the total nitrogen content was also an important factor affecting the diversity of the carbon sequestration microbial community. In summary, the wetland type significantly affects the process of soil carbon sequestration. Compared with the riverhead and lakeside wetlands, the marsh wetland has the highest carbon storage.

Similarities and differences in the microbial structure of surface soils of different vegetation types

Background

Soil microbial community diversity serves as a highly sensitive indicator for assessing the response of terrestrial ecosystems to various changes, and it holds significant ecological relevance in terms of indicating ecological alterations. At the global scale, vegetation type acts as a major driving force behind the diversity of soil microbial communities, encompassing both bacterial and fungal components. Modifications in vegetation type not only induce transformations in the visual appearance of land, but also influence the soil ecosystem's material cycle and energy flow, resulting in substantial impacts on the composition and performance of soil microbes.

Methods

In order to examine the disparities in the structure and diversity of soil microbial communities across distinct vegetation types, we opted to utilize sample plots representing four specific vegetation types. These included a woodland with the dominant tree species Drypetes perreticulata, a woodland with the dominant tree species Horsfieldia hainanensis, a Zea mays farmland and a Citrus reticulata fields. Through the application of high-throughput sequencing, the 16S V3_V4 region of soil bacteria and the ITS region of fungi were sequenced in this experiment. Subsequently, a comparative analysis was conducted to explore and assess the structure and dissimilarities of soil bacterial and fungal communities of the four vegetation types were analyzed comparatively.

Results

Our findings indicated that woodland soil exhibit a higher richness of microbial diversity compared to farmland soils. There were significant differences between woodland and farmland soil microbial community composition. However, all four dominant phyla of soil fungi were Ascomycota across the four vegetation types, but the bacterial dominant phyla were different in the two-farmland soil microbial communities with the highest similarity. Furthermore, we established a significant correlation between the nutrient content of different vegetation types and the relative abundance of soil microorganisms at both phyla and genus levels. This experiment serves as a crucial step towards unraveling the intricate relationships between plants, soil microbes, and soil, as well as understanding the underlying driving mechanism.

The influence of precipitation timing and amount on soil microbial community in a temperate desert ecosystem

Introduction

Global climate change may lead to changes in precipitation patterns. This may have a significant impact on the microbial communities present in the soil. However, the way these communities respond to seasonal variations in precipitation, particularly in the context of increased precipitation amounts, is not yet well understood.

Methods

To explore this issue, a five-year (2012-2016) field study was conducted at the northeast boundary of the Ulan Buh Desert, examining the effects of increased precipitation during different periods of the growing season on both bacterial and fungal communities. The study included five precipitation pattern treatments: a control group (C), as well as groups receiving 50 and 100% of the local mean annual precipitation amount (145 mm) during either the early growing season (E50 and E100) or the late growing season (L50 and L100). The taxonomic composition of the soil bacterial and fungal communities was analyzed using Illumina sequencing.

Results

After 5 years, the bacterial community composition had significantly changed in all treatment groups, with soil bacteria proving to be more sensitive to changes in precipitation timing than to increased precipitation amounts within the desert ecosystem. Specifically, the alpha diversity of bacterial communities in the late growing season plots (L50 and L100) decreased significantly, while no significant changes were observed in the early growing season plots (E50 and E100). In contrast, fungal community composition remained relatively stable in response to changes in precipitation patterns. Predictions of bacterial community function suggested that the potential functional taxa in the bacterial community associated with the cycling of carbon and nitrogen were significantly altered in the late growing season (L50 and L100).

Discussion

These findings emphasize the importance of precipitation timing in regulating microbial communities and ecosystem functions in arid regions experiencing increased precipitation amounts.

Carbendazim Modulates the Metabolically Active Bacterial Populations in Soil and Rhizosphere

The impact of fungicide residues on non-target soil bacterial communities is relatively unexplained. We hypothesize that the persistence of fungicide residues in the soil will affect the soil bacterial populations. Persistence depends on biotic and abiotic factors, primarily determined by agricultural activities. Activities such as fallow soil (F), farmyard manure (FYM) amendment, rice straw (RS) mulching, and cultivation of maize (Zea mays) and clover (Trifolium alexandrinum) were used as treatments. The soil CO2 efflux showed no effect of Carbendazim on dormant bacteria (unwatered condition). However, in irrigated condition, Carbendazim enhanced the CO2 efflux by 8, 164, 131, 249, and 182% in fallow, FYM, RS, maize, and Trifolium treatments, respectively. However, 16S rRNA metagenome study after 30 days of carbendazim treatment showed that maize rhizosphere microflora was most susceptible, decreasing the Shannon diversity index from 0.321 to 0.165. Diversity indices generally increased in maize and RS treatments, and Proteobacteria was the most prominent bacterial phyla in the maize rhizosphere. The microbial communities separated into distinct groups on the Principal Co-ordinate analysis (PCoA) plot. The separation on scale 1 (35%) and scale 2 (13%) was based, respectively, on microbial activity and carbendazim treatments. Functionally Maize+Carbendazim treatment showed the highest enzyme activities dehydrogenase (82.25%), acid phosphatase (78.10%), alkaline phosphatase (48.26%), β-glucosidase (59.99%), protease (126.65%), and urease (50.66%) compared to fallow soil. Overall, Carbendazim enhanced non-target bacterial activity in metabolically active niches, while it did not affect the dormant microflora. Thus, organic amendments and cultivation of fungicide-contaminated soil may help render the contaminant through bacterial activity.

Land degradation vulnerability mapping in a west coast river basin of India using analytical hierarchy process combined machine learning models

Assessment and modelling of land degradation are crucial for the management of natural resources and sustainable development. The current study aims to evaluate land degradation by integrating various parameters derived from remote sensing and legacy data with analytical hierarchy process (AHP) combined machine learning models for the Mandovi river basin of western India. Various land degradation conditioning factors comprising of topographical, vegetation, pedological, and climatic variables were considered. Integration of the factors was performed through weighted overlay analysis to generate the AHP-based land degradation map. The output of AHP was then used with land degradation conditioning factors to build AHP combined gradient boosting machine (AHP-GBM), random forest (AHP-RF), and support vector machine (AHP-SVM) model. The model performances were assessed through an area under the receiver operating characteristic (AUC). The AHP-RF model recorded the highest AUC (0.996) followed by AHP-SVM (0.987), AHP (0.977), and AHP-GBM (0.975). The study revealed that AHP combined with RF could significantly improve the model performance over solo AHP. High rainfall with high slopes and improper land use were the major causes of land degradation in the study area. The findings of the current study will aid the policymakers to formulate land degradation action plans through implementing appropriate soil and water conservation measures.

Responses of bacterial community and N-cycling functions stability to different wetting-drying alternation frequencies in a riparian zone

Wetting-drying alternation (WD) of the soil is one of the key characteristics of riparian zones shaped by dam construction, profoundly impacting the soil microenvironment that determines the bacterial community. Knowledge concerning the stability of bacterial community and N-cycling functions in response to different frequencies of WD remains unclear. In this study, samples were taken from a riparian zone in the Three Gorges Reservoir (TGR) and an incubation experiment was conducted including four treatments: constant flooding (W), varied wetting-drying alternation frequencies (WD1 and WD2), and constant drying (D) (simulating water level of 145 m, 155 m, 165 m, and 175 m in the riparian zone respectively). The results revealed that there was no significant difference in the diversity among the four treatments. Following the WD1 and WD2 treatments, the relative abundances of Proteobacteria increased, while those of Chloroflexi and Acidobacteriota decreased compared to the W treatment. However, the stability of bacterial community was not affected by WD. Relative to the W treatment, the stability of N-cycling functions estimated by resistance, which refers to the ability of functional genes to adapt to changes in the environment, decreased following the WD1 treatment, but showed no significant change following the WD2 treatment. Random forest analysis showed that the resistances of the nirS and hzo genes were core contributors to the stability of N-cycling functions. This study provides a new perspective for investigating the impacts of wetting-drying alternation on soil microbes.

Cover cropping impacts on soil water and carbon in dryland cropping system

Incorporating cover crops into the rotation is a practice applied across many parts of the globe to enhance soil biological activities. In dryland farming, where crop production is highly dependent on rainfall and soil water storage, cover cropping can affect soil water, yet its effects on soil hydrological and biological health require further investigation. The objective of this study was to evaluate the effect of different timing of summer sorghum cover crop termination on soil water, total and labile organic carbon, arbuscular mycorrhizal fungi and their mediating effects on wheat yield. Through on-farm trial, soil characteristics along with wheat biomass, yield and grain quality were monitored. In comparison with the control (fallow), the early terminated cover crop was the most effective at retaining greater soil water at wheat sowing by 1~4% in 0-45cm soil profile. An increase in water use efficiency, yield and grain protein by 10%, 12% and 5% was observed under early termination. Under late terminated summer cover crop, there was 7% soil water depletion at wheat planting which resulted in 61% decline in yield. However, late-terminated cover crop achieved the greatest gain in soil total and particulate organic carbon by 17% and 72% and arbuscular mycorrhizal fungal Group A and B concentration by 356% and 251%. Summer cover crop incorporation resulted in a rapid gain in labile organic carbon, which constituted hotspots for arbuscular mycorrhizal fungi growth, conversely, fungal activities increased labile organic carbon availability. The combined effect of increased soil water at sowing and over the growing season, organic carbon, and microbial activities contributed to greater yield. The findings suggest that summer cover cropping with timely termination can have implications in managing soil water at sowing time and enhancing soil water storage during the season, soil carbon, and facilitating microbial activities while enhancing productivity in the dryland cropping system.

Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands : Soil Microbial Diversity Relationships

Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Here we assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea and explored how environmental factors influence these relationships. We sampled soil along a 1500-km-long aridity gradient in temperate grasslands of Inner Mongolia (China) and sequenced the 16S rRNA gene of bacteria and archaea and the ITS2 gene of fungi. The diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between different microbial functional groups were evaluated using α-diversity and co-occurrence networks based on microbial abundance. Our results indicate insignificant correlations among the diversity patterns of bacterial, fungal, and archaeal domains using α-diversity but mostly positive correlations among diversity patterns of microbial functional groups based on α-diversity and co-occurrence networks along the aridity gradient. These results suggest that studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights on patterns that cannot be accessed using only overall microbial α-diversity. Increase in aridity weakens the diversity correlations between bacteria and fungi and between bacterial and archaeal functional groups, but strengthens the positive diversity correlations between bacterial functional groups and between fungal functional groups and the negative diversity correlations between bacterial and fungal functional groups. These variations of the diversity correlations are associated with the different responses of microbes to environmental factors, especially aridity. Our findings demonstrate the complex responses of microbial community structure to environmental conditions (especially aridity) and suggest that understanding diversity correlations and co-occurrence patterns between soil microbial groups is essential for predicting changes in microbial communities under future climate change in arid regions.

Diversity and assembly of active bacteria and their potential function along soil aggregates in a paddy field

Numerous studies have found that soil microbiomes differ at the aggregate level indicating they provide spatially heterogeneous habitats for microbial communities to develop. However, an understanding of the assembly processes and the functional profile of microbes at the aggregate level remain largely rudimentary, particularly for those active members in soil aggregates. In this study, we investigated the diversity, co-occurrence network, assembly process and predictive functional profile of active bacteria in aggregates of different sizes using H₂¹⁸O-based DNA stable isotope probing (SIP) and 16S rRNA gene sequencing. Most of the bacterial reads were active with 91 % of total reads incorporating labelled water during the incubation. The active microbial community belonged mostly of Proteobacteria and Actinobacteria, with a relative abundance of 55.32 % and 28.12 %, respectively. Assembly processes of the active bacteria were more stochastic than total bacteria, while the assembly processes of total bacteria were more influenced by deterministic processes. Furthermore, many functional profiles such as environmental information processing increased in active bacteria (19.39 %) compared to total bacteria (11.22 %). After incubation, the diversity and relative abundance of active bacteria of certain phyla increased, such as Proteobacteria (50.70 % to 59.95 %), Gemmatimonadetes (2.63 % to 4.11 %), and Bacteroidetes (1.50 % to 2.84 %). In small macroaggregates (SMA: 0.25-2 mm), the active bacterial community and its assembly processes differed from that of other soil aggregates (MA: microaggregates, <0.25 mm; LMA: large macroaggregates, 2-4 mm). For functional profiles, the relative abundance of important functions, such as amino acid metabolism, signal transduction and cell motility, increased with incubation days and/or in SMA compared to other aggregates. This study provides robust evidence that the community of active bacteria and its assembly processes in soil aggregates differed from total bacteria, and suggests the importance of dominant active bacteria (such as Proteobacteria) for the predicted functional profiles in the soil ecosystem.

Effect of Drought on the Development of Deschampsia caespitosa (L.) and Selected Soil Parameters during a Three-Year Lysimetric Experiment

This work presents results from a field experiment which was focused on the impact of the drought period on microbial activities in rhizosphere and non-rhizosphere soil. To demonstrate the effect of drought, the pot experiment lasted from 2012 to 2015. Fifteen lysimeters (plastic containers) were prepared in our area of interest. These lysimeters were filled with the subsoil and topsoil from this area and divided into two groups. The first group consisted of two variants: V1 (control) and V2 (84 kg N/ha), which were not stressed by drought. The second group consisted of three variants, V3 (control), V4 (84 kg N/ha), and V5 (84 kg N/ha + 1.25 L lignohumate/ha), which were stressed by drought every year of the experiment for 30 days. Changes in the soil moisture content caused by drought significantly affect the growth of Deschampsia caespitosa L., the microbial activity, and the soil’s capacity to retain nutrients. The measured basal respiration and dehydrogenase activity values confirm the significant effect of drought on microbial activity. These values were demonstrably higher in the period before drought simulation by more than 60%. On the other hand, significant differences between microbial activities in the rhizosphere and non-rhizosphere soil were not found. We did not find a clear effect of drought on the formation of soil water repellency.

Soil fungal community characteristics vary with bamboo varieties and soil compartments

Soil fungi play an important role in nutrient cycling, mycorrhizal symbiosis, antagonism against pathogens, and organic matter decomposition. However, our knowledge about the community characteristics of soil fungi in relation to bamboo varieties is still limited. Here, we compared the fungal communities in different soil compartments (rhizosphere vs. bulk soil) of moso bamboo (Phyllostachys edulis) and its four varieties using ITS high-throughput sequencing technology. The fungal α diversity (Shannon index) in bulk soil was significantly higher than that in rhizosphere soil, but it was not affected by bamboo variety or interactions between the soil compartment and bamboo variety. Soil compartment and bamboo variety together explained 31.74% of the variation in fungal community diversity. Soil compartment and bamboo variety were the key factors affecting the relative abundance of the major fungal taxa at the phylum and genus levels. Soil compartment mainly affected the relative abundance of the dominant fungal phylum, while bamboo variety primarily influenced the dominant fungal genus. Network analysis showed that the fungal network in rhizosphere soil was more complex, stable, and connected than that in bulk soil. A FUNGuild database analysis indicated that both soil compartment and bamboo variety affect fungal functions. Our findings provide new insights into the roles of both soil compartments and plant species (including variety) in shaping soil fungal communities.

Untangling microbial diversity and assembly patterns in rare earth element mine drainage in South China

Ion-adsorption rare earth element (REE) deposits are the main reservoirs of REEs worldwide, and are widely exploited in South China. Microbial diversity is essential for maintaining the performance and function of mining ecosystems. Investigating the ecological patterns underlying the REE mine microbiome is essential to understand ecosystem responses to environmental changes and to improve the bioremediation of mining areas. We applied 16S rRNA and ITS gene sequence analyses to investigate the composition characteristics of prokaryotic (bacteria, archaea) and fungal communities in a river impacted by REE acid mine drainage (REE-AMD). The river formed a unique micro-ecosystem, including the main prokaryotic taxa of Proteobacteria, Acidobacteria, Crenarchaeota, and Euryarchaeota, as well as the main fungal taxa of Ascomycota, Basidiomycota, and Chytridiomycota. Analysis of microbial diversity showed that, unlike prokaryotic communities that responded drastically to pollution disturbances, fungal communities were less affected by REE-AMD, but fluctuated significantly in different seasons. Ecological network analysis revealed that fungal communities have lower connectivity and centrality, and higher modularity than prokaryotic networks, indicating that fungal communities have more stable network structures. The introduction of REE-AMD mainly reduced the complexity of the community network and the number of keystone species, while the proportion of negative prokaryotic-fungal associations in the network increased. Ecological process analysis revealed that, compared to the importance of environmental selection for prokaryotes, stochastic processes might have contributed primarily to fungal communities in REE mining areas. These findings confirm that the different assembly mechanisms of prokaryotic and fungal communities are key to the differences in their responses to environmental perturbations. The findings also provide the first insights into microbiota assembly patterns in REE-AMD and important ecological knowledge for the formation and development of microbial communities in REE mining areas.

Environmental selection dominates over dispersal limitation in shaping bacterial biogeographical patterns across different soil horizons of the Qinghai-Tibet Plateau

Soil microbial biogeographical patterns have been widely explored from horizontal to vertical scales. However, studies of microbial vertical distributions were still limited (e.g., how soil genetic horizons influence microbial distributions). To shed light on this question, we investigated soil bacterial communities across three soil horizons (topsoil: horizon A; midsoil: horizon B; subsoil: horizon C) of 60 soil profiles along a 3500 km transect in the Qinghai-Tibet Plateau. We found that bacterial diversity was highest in the topsoil and lowest in the subsoil, and community composition significantly differed across soil horizons. The network complexity decreased from topsoil to subsoil. There were significant geographical/environmental distance-decay relationships (DDR) in three soil horizons, with a lower slope from topsoil to subsoil due to the decreased environmental heterogeneity. Variation partitioning analysis (VPA) showed that bacterial community variations were explained more by environmental than spatial factors. Although environmental selection processes played a dominant role, null model analysis revealed that deterministic processes (mainly variable selection) decreased with deeper soil horizons, while stochastic processes (mainly dispersal limitation) increased from topsoil to subsoil. These results suggested that microbial biogeographical patterns and community assembly processes were soil horizon dependent. Our study provides new insights into the microbial vertical distributions in large-scale alpine regions and highlights the vital role of soil genetic horizons in affecting microbial community assembly, which has implications for understanding the pedogenetic process and microbial responses to extreme environment under climate change.

Effects of Land Use on the Soil Microbial Community in the Songnen Grassland of Northeast China

Land use change obviously changes the plant community composition and soil properties of grasslands and thus affects multiple functions and services of grassland ecosystems. However, the response mechanisms of soil microorganisms, key drivers of the nutrient cycle and other soil functions during changes in grassland use type and associated vegetation are not well understood. In this study, Illumina high-throughput sequencing was used to analyze the changes in the soil microbial community structure of four grassland use types: exclosure (EL), mowed land (ML), grazed land (GL), and farmland (FL) in the Songnen Plain of Northeast China. The results showed that the FL and EL had significantly higher soil total nitrogen (TN) and lower soil electrical conductivity (EC) and pH than GL and ML. In contrast, the GL and ML had higher soil bulk density (BD) and organic matter, respectively, than the other land use types. In addition, the values of the Shannon diversity and Pielou’s evenness indexes were highest in the EL of all the land use types. Based on the high-throughput sequencing results, we observed high levels of α diversity in the FL for both bacteria and fungi. A structural equation model (SEM) revealed that pH and EC had a direct and positive effect on the bacterial community structure and composition. In addition, plant taxonomic diversity (according to the Shannon diversity and Pielou’s evenness indexes) indirectly affected the bacterial community composition via soil pH and EC. Notably, fungal composition was directly and positively correlated with soil nutrients and the value of Pielou’s evenness index changed with land use type. In conclusion, soil properties and/or plant diversity might drive the changes in the soil microbial community structure and composition in different grassland use types.

A Drying-Rewetting Cycle Imposes More Important Shifts on Soil Microbial Communities than Does Reduced Precipitation

Global changes will result in altered precipitation patterns, among which the increasing frequency of drought events has the highest deleterious potential for agriculture. Soil microbes have shown some promise to help crops adapt to drought events, but it is uncertain how crop-associated microorganisms will respond to altered precipitation patterns. To investigate this matter, we conducted a field experiment where we seeded two wheat cultivars (one resistant to water stress and the other sensitive) that were subjected to four precipitation exclusion (PE) regimes (0%, 25%, 50%, and 75% exclusion). These cultivars were sampled seven times (every 2 weeks, from May to August) within one growing season to investigate short-term microbiome responses to altered precipitation regimes and seasonality using 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. One of the most striking features of the data set was the dramatic shift in microbial community diversity, structure, and composition together with a doubling of the relative abundance of the archaeal ammonia oxidizer genus Nitrososphaera following an important drying-rewetting event. Comparatively small but significant effects of PE and wheat cultivar on microbial community diversity, composition, and structure were observed. Taken together, our results demonstrate an uneven response of microbial taxa to decreasing soil water content, which was dwarfed by drying-rewetting events, to which soil bacteria and archaea were more sensitive than fungi. Importantly, our study showed that an increase in drying-rewetting cycles will cause larger shifts in soil microbial communities than a decrease in total precipitation, suggesting that under climate changes, the distribution of precipitation will be more important than small variations in the total quantity of precipitation. IMPORTANCE Climate change will have a profound effect on the precipitation patterns of global terrestrial ecosystems. Seasonal and interannual uneven distributions of precipitation will lead to increasing frequencies and intensities of extreme drought and rainfall events, which will affect crop productivity and nutrient contents in various agroecosystems. However, we still lack knowledge about the responses of soil microbial communities to reduced precipitation and drying-rewetting events in agroecosystems. Our results demonstrated an uneven response of the soil microbiome and a dramatic shift in microbial community diversity and structure to a significant drying-rewetting event with a large increase in the relative abundance of archaeal ammonia oxidizers. These findings highlight the larger importance of rewetting of dry soils on microbial communities, as compared to decreased precipitation, with potential for changes in the soil nitrogen cycling.

Influence of different irrigation methods on the alfalfa rhizosphere soil fungal communities in an arid region

Xinjiang is the largest arid and saline agricultural region in China. The common irrigation methods in this area are traditional flood irrigation and drip irrigation. In this study, we investigated the effects of these two irrigation methods on the fungal diversity, community structures, and functions in alfalfa rhizosphere soil as well as the associated environmental factors in northern Tianshan Mountain (Xinjiang, China). Soil enzyme activities (urease and neutral phosphatase) were significantly higher in the drip-irrigated alfalfa rhizosphere soil than in the flood-irrigated alfalfa rhizosphere soil, whereas the fungal alpha diversity in the drip-irrigated alfalfa rhizosphere soil was significantly lower than that in the flood-irrigated alfalfa rhizosphere soil. Six dominant fungal phyla were identified (>0.1%), with Ascomycota being the most abundant in all soils, followed by Basidiomycota (5.47%), Mortierellomycota (1.07%), Glomeromycota (0.55%), Rozellomycota (0.27%), and Chytridiomycota (0.14%). Ascomycota and Glomeromycota species were significantly less abundant in drip-irrigated alfalfa rhizosphere soil than in flood-irrigated alfalfa rhizosphere soil. A LEFSe analysis identified Cladosporiaceae (20.8%) species as the most abundant marker fungi in drip-irrigated alfalfa rhizosphere soil. Of the 13 fungal functional groups identified on the basis of the functional annotation using the FUNGuild database, Ectomycorrhizal (22.29%) was the primary functional group. Compared with flood irrigation, drip irrigation significantly decreased the relative abundance of Ectomycorrhizal and Arbuscular_Mycorrhizal, while increasing the relative abundance of Plant_Pathogen, although not significantly (P = 0.19). Available potassium was revealed to be the main environmental factor influencing soil enzyme activities, fungal alpha diversity, fungal community structures, and fungal functions in response to the different irrigation methods. In conclusion, drip irrigation may be more appropriate than flood irrigation in the Tianshan dryland agricultural area for enhancing soil enzyme activities, but it may also increase the abundance of plant pathogenic fungi in the soil.

Effects of Drought on the Growth of Lespedeza davurica through the Alteration of Soil Microbial Communities and Nutrient Availability

Lespedeza davurica (Laxm.) is highly important for reducing soil erosion and maintaining the distinctive natural scenery of semiarid grasslands in northwest China. In this study, a pot experiment was conducted to investigate the effects of drought (20% water-holding capacity) on biomass and its allocation, root characteristics, plant hormones, and soil microbial communities and nutrients after L. davurica was grown in a greenhouse. Drought reduced the total biomass of L. davurica but increased the root:shoot biomass ratio. In addition, drought altered the composition and structure of microbial communities by limiting the mobility of nutrients in non-rhizosphere soils. In particular, drought increased the relative abundances of Basidiomycota, Acidobacteria, Actinobacteria, Coprinellus, Humicola and Rubrobacter, which were closely positively related to the soil organic carbon, pH, available phosphorus, ammonia nitrogen (N) and nitrate N under drought conditions. Furthermore, soil fungi could play a more potentially significant role than that of bacteria in the response of L. davurica to drought. Consequently, our study uncovered the effects of drought on the growth of L. davurica by altering soil microbial communities and/or soil nutrients, thus providing new insights for forage production and natural grassland restoration on the Loess Plateau of China.

A global meta-analysis of the impacts of exotic plant species invasion on plant diversity and soil properties

Plant diversity and biogeochemical cycles are rapidly changing in response to exotic plant species invasion. However, there are conflicting conclusions regarding the quantification of such changes in the soil properties and plant diversity. Moreover, the relationships between soil properties and plant diversity are unclear. Here, a global meta-analysis was conducted on the impact of exotic species invasion on soil physicochemistry, microbial activity, and plant diversity using data from 123 published reports and 332 samples. Exotic species invasion significantly enhanced the soil pH, soil microbial activity, and soil nutrient content. The impact was more substantial for grass than for shrub and tree. Exotic species invasion did not significantly affect soil texture, but significantly reduced the plant diversity, richness, and evenness by 36.97%, 64.72%, and 47.21%, respectively. Soil pH, soil organic carbon, and total nitrogen were significantly correlated with plant diversity reduction. The response ratio of plant richness and evenness gradually increased with precipitation. However, the response ratio of phosphatase, microbial biomass nitrogen, microbial biomass phosphorus, total nitrogen, and soil moisture gradually decreased with precipitation. Overall, exotic species invasion significantly increased the soil nutrient content and soil microbial activity, but significantly decreased plant diversity. These effects were influenced by exotic species types and precipitation.

Trends in Microbial Community Composition and Function by Soil Depth

Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.

Effects of Land-Use Type and Flooding on the Soil Microbial Community and Functional Genes in Reservoir Riparian Zones

Ecological processes (e.g., nutrient cycling) in riparian zones are often affected by land-use type and flooding. The extent to which land-use types and flooding conditions affect soil microorganisms and their ecological functions in riparian zones is not well known. By using high-throughput sequencing and quantitative PCR (q-PCR), we tested the effects of three land-use types (i.e., forest, wetland, and grassland) and two flooding conditions (i.e., landward locations and waterward locations within the land-use types) on soil microbial communities and microbial functional genes in the riparian zones of a reservoir. Land-use type but not flooding significantly affected soil microbial community composition at the phylum level, while both land-use type and flooding significantly affected the orders Nitrosotaleales and Nitrososphaerales. Alpha diversity was higher in the wetland and forest regardless of flooding conditions. Functional gene abundance differed among the three land-use types. Archaeal amoA (AOA) and nirS genes were more abundant in the wetland than in the grassland or forest. Bacterial amoA (AOB), nirK, nirS, and nosZ genes were more abundant in the waterward location than in the landward location but only in the wetland. Soil pH, moisture, and concentrations of soil organic matter and total soil nitrogen were significantly associated with the composition of archaeal and bacterial communities as well as with their gene abundance. This study revealed that soil microorganisms putatively involved in nitrogen cycling in riparian zones were more affected by land-use type than flooding.

Soil microbial community responses to the application of a combined amendment in a historical zinc smelting area

Farmland soils that surround a historical zinc smelting area in northwestern Guizhou, China, are characterized by high levels of heavy metal accumulation. Previous studies have mainly focused on the potential risk evaluations of heavy metals in soil and crops. However, at present, the effects of amendment applications on the bioavailability of heavy metals and on microbial community in the heavily contaminated soils of the mining region are still unclear. A pot experiment was conducted to determine the effect of applying a combined amendment (e.g. lime, sepiolite, and vermicompost) on the diversity and composition of microbial community in the contaminated soil. The results showed that the contents of DTPA- and TCLP-extractable heavy metals (e.g. Cd, Pb, and Zn) decreased and that the pH, SWC, EC, and soil available nutrient (e.g. AN, AP, and AK) contents increased after the application of the combined amendment. Furthermore, application of the combined amendment decreased the diversity of soil bacterial and fungal communities and increased the relative abundances of the dominant bacterial and fungal communities such as Proteobacteria, Bacteroidetes, and Ascomycota; however, the relative abundances of Acidobacteria and Actinobacteria decreased. Redundancy analysis (RDA) and structural equation model (SEM) analysis showed that the bioavailability of heavy metals decreased and that soil physicochemical characteristics improved and had positive or negative effects on the diversity and composition of soil microbial community.

Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity

BACKGROUND

Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks.

RESULTS

We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses.

CONCLUSIONS

Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.

Unraveling negative biotic interactions determining soil microbial community assembly and functioning

Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.

Divergent responses of CO2 and CH4 fluxes to changes in the precipitation regime on the Tibetan Plateau: Evidence from soil enzyme activities and microbial communities

Carbon fluxes (CO₂ and CH₄) are important indicators of the response of alpine meadow ecosystems to global climate change. Alpine meadows on the Qinghai-Tibet Plateau are sensitive to climate change. Although the temporal allocation of precipitation can vary, its intensity is expected to increase, and its frequency is expected to decrease in the future. In this study, a manipulative field experiment was conducted to investigate how carbon fluxes are altered in response to moderate and severe changes in the precipitation regime. Fluctuations in CH₄ flux were large under a severely altered precipitation regime (range of -0.048-0.038 mg m^-2 h^-1). Severe changes in the precipitation regime significantly reduced soil CH₄ uptake by approximately 54.3%. This was probably affected by the decrease in the dissolved organic carbon concentration and changes in the microbial community (mainly Gammaproteobacteria), which were induced by variation in soil water conditions under various precipitation regimes. Under moderate changes in the precipitation regime, the average value of CO₂ fluxes (ecosystem respiration) was 698.21 ± 35.19 mg m^-2 h^-1, which was significantly decreased by 20.7% compared with the control. This likely stems from the suppression of enzyme activity (particularly α-1,4-glucosidase and β-1,4-glucosidase) and the alteration of microbial community structure in this treatment, which led to a decrease in organic matter breakdown and a reduction in the release of CO₂ to the atmosphere. However, CO₂ fluxes were slightly (i.e., not significantly) decreased under the severely altered precipitation regime. Such different responses of CO₂ flux are probably driven by differences in microbial strategies. This study not only increases our understanding of the mechanisms underlying the adaptation of alpine meadow ecosystems to global climate change but also provides new insight into the carbon source/sink functions of alpine meadows.

Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System

Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre- and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.

Impact of land use on soil function and bacterial community in the Brazilian savanna

Land use systems have a great impact on soil function and microbial diversity in tropical soils. Our study aimed to evaluate soil biochemical indicators and community composition and to assess the relationship between soil biochemical and microbial indicators and bacterial diversity of three agroecosystems (pine forest, soya and sugarcane) and native Cerrado forest in the Brazilian savanna. Soil biochemical indicators (soil organic matter and enzymes) and high-throughput sequencing of 16S rDNA were performed in two topsoil depths (0-5 cm and 5-10 cm). Soil microbial and enzyme activity showed that agricultural soil usage has a negative impact on soil function compared to native and pine forests. Results also revealed higher enzyme activities in 0-5 cm depth compared to 5-10 cm depth, but enzymatic activities depend on land use systems. Soil bacterial community was affected by land use systems and depth, revealing changes in structure and abundance of bacterial composition. Alpha-diversity indexes were higher in the agricultural systems than in the forests, however they showed a significant negative correlation with most of the studied soil microbial and biochemical indicators. Our research had brought new relevant information about the relationship between the soil biochemical indicators and the bacterial diversity in the Brazilian Cerrado.

Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil

In agricultural settings, microbes and antimicrobial resistance genes (ARGs) have the potential to be transferred across diverse environments and ecosystems. The consequences of these microbial transfers are unclear and understudied. On dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. To determine the extent of both taxonomic and resistance similarity during these transitions, we collected fresh manure, manure from pits, and field soil across 15 different dairy farms for three consecutive seasons. We used a combination of shotgun metagenomic sequencing and functional metagenomics to quantitatively interrogate taxonomic and ARG compositional variation on farms. We found that as the microbiome transitions from fresh dairy cow manure to manure pits, microbial taxonomic compositions and resistance profiles experience distinct restructuring, including decreases in alpha diversity and shifts in specific ARG abundances that potentially correspond to fresh manure going from a gut-structured community to an environment-structured community. Further, we did not find evidence of shared microbial community or a transfer of ARGs between manure and field soil microbiomes. Our results suggest that fresh manure experiences a compositional change in manure pits during storage and that the storage of manure in manure pits does not result in a depletion of ARGs. We did not find evidence of taxonomic or ARG restructuring of soil microbiota with the application of manure to field soils, as soil communities remained resilient to manure-induced perturbation.IMPORTANCE The addition of dairy cow manure-stored in manure pits-to field soil has the potential to introduce not only organic nutrients but also mammalian microbial communities and antimicrobial resistance genes (ARGs) to soil communities. Using shotgun sequencing paired with functional metagenomics, we showed that microbial community composition changed between fresh manure and manure pit samples with a decrease in gut-associated pathobionts, while ARG abundance and diversity remained high. However, field soil communities were distinct from those in manure in both microbial taxonomic and ARG composition. These results broaden our understanding of the transfer of microbial communities in agricultural settings and suggest that field soil microbial communities are resilient against the deposition of ARGs or microbial communities from manure.

Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles

Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO₂ pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO₂ emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO₂ production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.

The bacterial community structure and N-cycling gene abundance in response to dam construction in a riparian zone

Dam construction has significantly altered riparian hydrological regime and environmental conditions in the reservoir region, yet knowledge concerning how bacterial community and N-cycling genes respond to these changes remains limited. In this study, we investigated the bacterial community composition, network structure and N-cycling genes in the water level fluctuation zones (WLFZs) of the Three Gorges Reservoir (TGR). Here, samples collected from five different water levels were divided into three groups: waterward sediments, interface sediments, and landward soils. Our results show that higher contents of NO₂^--N, SOC, DOC, NH₄⁺-N, and TP were characterized in waterward and interface sediments whereas higherNO₃^--N content was observed in landward soils. The α-diversity of bacterial community decreased gradually from waterward sediments to landward soils. Compared with waterward sediments and landward soils, the interface sediments showed a unique bacterial community pattern with diverse primary producers as well as N-cycling microbes. The interface sediments also had a much more complex co-occurrence network and a higher possible community stability. Among all of N-cycling genes, higher abundances of nrfA and AOA amoA genes were observed in interface sediments. The dissimilarity in bacterial community composition and N-cycling gene abundance was mainly driven by water-level. Moreover, random forest model revealed that AOA amoA and nirS genes were the most sensitive indicators in response to water level fluctuations. Overall, this study suggests distinct abundance, diversity, and network structure of microbes in riparian sediments and soils across the gradient of water levels and enhances our understanding with respect to comprehensive effects of dam construction on nitrogen cycle.

History of petroleum disturbance triggering the depth-resolved assembly process of microbial communities in the vadose zone

Biogeochemical gradient forms in vadose zone, yet little is known about the assembly processes of microbial communities in this zone under petroleum disturbance. This study collected vadose zone soils at three sites with 0, 5, and 30 years of petroleum contamination to unravel the vertical microbial community successions and their assembly mechanisms. The results showed that petroleum hydrocarbons exhibited higher concentrations at the long-term contaminated site, showing negative impacts on some soil properties, retarding in the surface soils and decreasing along soil depth. Cultivable fraction of heterotrophic bacteria and microbial α-diversity decreased along depth in vadose zones with short-term/no contamination history, but exhibited an opposite trend with long-term contamination history. Petroleum contamination intensified the vertical heterogeneity of microbial communities based on the contamination time. Microbial co-occurrence network revealed the lowest species co-occurrence pattern at the long-term contaminated site. The distance-decay patterns and null model analysis together suggested distinct assembly mechanisms at three sites, where dispersal limitation (42-45%) was higher and variable and homogenizing selections were lower (37-38%) in vadose zones under petroleum disturbance than those in the uncontaminated vadose zone. Our findings help to better understand the subsurface biogeochemical cycles and bioremediation of petroleum-contaminated vadose zones.

Towards a mechanistic understanding of soil nitrogen availability responses to summer vs. winter drought in a semiarid grassland

More frequent and intense drought events resulting from climate change are anticipated to become important drivers of change for terrestrial ecosystem function by affecting water and nutrient cycles. In semiarid grasslands, the responses of soil nitrogen availability to severe drought and the underlying mechanisms are largely unknown. Moreover, the responses and mechanisms may vary between summer and winter drought. We examined soil nitrogen availability responses to extreme reductions in precipitation over summer and winter using a field experiment in a semiarid grassland located in northeast China, and we explored the mechanisms by examining associated changes in abiotic factors (soil property responses) and biotic factors (plant and soil microbial responses). The results demonstrated that both the summer and winter severe drought treatments significantly reduced plant and microbial biomass, whereas summer drought also changed soil microbial community structure. Summer drought, winter drought and combined summer and winter drought decreased the resistance of soil nitrogen availability by 38.7 ± 11.1%, 43.3 ± 11.4% and 43.8 ± 6.0%, respectively. While both changes in abiotic factors (reduced soil water content and total nitrogen content) and biotic factors (reduced plant and microbial biomass) explained the resistance of soil nitrogen availability to drought over summer, only changes in biotic factors (reduced plant and microbial biomass) explained the legacy effect of winter drought. Our results highlight that severe drought can have important consequences for nitrogen cycling in semiarid grasslands, and that both the effects of summer and winter drought must be accounted for in predicting these responses.

Enhanced biotreatability of petroleum hydrocarbon-contaminated mining waste coupled with the attenuation of acid drainage production

A biostimulation study was conducted on mining waste residue with nutrient (nitrogen and phosphorus) and/or liming agent (ash or CaCO₃ ) amendment to assess petroleum hydrocarbon (PHC) biodegradation efficiency by indigenous microorganisms. Compounds accumulated and/or released by treated samples were also monitored to determine the potential for acid mine drainage production during biostimulation. The potential for natural attenuation (i.e., the biodegradation of PHC contamination) was initially low but increased significantly upon nutrient addition. The best results were obtained when nutrient addition was coupled with the addition of a liming agent, notably CaCO₃ , which contributed to maintaining near-neutral pH values. In fact, during treatment without a liming agent, pH decreased due to the oxidation of sulfide minerals, resulting in acid mine drainage production with increased metals released into sample leachates. Sulfur- and iron-oxidizing bacteria were detected primarily in samples not amended with liming agents, and the predominant organisms were affiliated with Acidithiobacillus spp. and Acidiphilium spp. Overall, the results of the present study demonstrated that amendment with a liming agent when treating PHC-contaminated mining waste residue contributes to maintaining a pH close to neutrality, mitigates sulfate release, and reduces the release of metals without negatively affecting the activity of PHC degraders.

Application of stabilized sludge to extensive green roofs in Shanghai: Feasibility and nitrogen leaching control

Extensive green roofs, in which commercial compost is usually used as organic component, have great potential to mitigate some environmental problems caused by urbanization, but carry risks of nutrients leaching into downstream aquatic. Stabilized sludge (SS) from wastewater treatment plants could be potentially used as nutrient component for green roof, but the effects on effluent quality are uncertain. To investigate the problem, a pilot experiment was conducted under field conditions, the effluent quality of green roof using SS was compared with green roofs using peat soil and controlled release fertilizer. In the field experiment, the nutrient concentrations in effluent of the green roof using SS (TN, NO₃^--N, NH₄⁺-N and TP were 3.27 mg/L, 1.75 mg/L, 1.14 mg/L and 0.34 mg/L, respectively) were not significantly different from the green roofs using peat soil and controlled release fertilizer, and the chemical oxygen demand level (92 mg/L) was lower than the roofs using compost or commercial substrate. To reduce the environmental risks caused by the application of SS to green roofs, a laboratory test was carried out to analyze the effects of biochar and dual-substrate structure on nitrogen leaching. The results showed that both biochar and dual-substrate reduced nitrogen leaching, and nitrogen leaching from green roofs using SS was a combined effect of organic nitrogen mineralization during dry period and biological processes during wet period. A high temperature and low humidity environment which is common in green roofs reduced nitrate accumulation during dry period, and nitrate was transformed to other substances in gaseous form by denitrification, which tended to occur in long duration, low intensity rainfall events. The results suggest that the application of stabilized sludge to green roofs is feasible in area where average rain intensity is not high, preferably combined with amendment of biochar and a dual-substrate structure.

Temperature-Induced Annual Variation in Microbial Community Changes and Resulting Metabolome Shifts in a Controlled Fermentation System

We are rapidly increasing our understanding on the spatial distribution of microbial communities. However, microbial functioning, as well as temporal differences and mechanisms causing microbial community shifts, remains comparably little explored. Here, using Chinese liquor fermentation as a model system containing a low microbial diversity, we studied temporal changes in microbial community structure and functioning. For that, we used high-throughput sequencing to analyze the composition of bacteria and fungi and analyzed the microbially derived metabolome throughout the fermentation process in all four seasons in both 2018 and 2019. We show that microbial communities and the metabolome changed throughout the fermentation process in each of the four seasons, with metabolome diversity increasing throughout the fermentation process. Across seasons, bacterial and fungal communities as well as the metabolome driven by 10 indicator microorganisms and six metabolites varied even more. Daily average temperature in the external surroundings was the primary determinant of the observed temporal microbial community and metabolome changes. Collectively, our work reveals critical insights into patterns and processes determining temporal changes of microbial community composition and functioning. We highlight the importance of linking taxonomic to functional changes in microbial ecology to enable predictions of human-relevant applications.IMPORTANCE We used Chinese liquor fermentation as a model system to show that microbiome composition changes more dramatically across seasons than throughout the fermentation process within seasons. These changes translate to differences in the metabolome as the ultimate functional outcome of microbial activity, suggesting that temporal changes in microbiome composition are translating into functional changes. This result is striking as it suggests that microbial functioning, despite controlled conditions in the fermentors, fluctuates over season along with external temperature differences, which threatens a reproducible food taste. As such, we believe that our study provides a stepping-stone into novel taxonomy-functional studies that promote future work in other systems and that also is relevant in applied settings to better control surrounding conditions in food production.

Seasonal Microbial Community Characteristic and Its Driving Factors in a Copper Tailings Dam in the Chinese Loess Plateau

A combined soil bacterial and fungal community survey was conducted for a copper tailings dam in the Chinese Loess Plateau. We investigated the seasonal differences in the composition and function of soil microbial community to examine the key environmental factors influencing soil microorganisms during restorative ecological processes. Significant seasonal differences were found in the community structure of both bacterial and fungal communities. Bacterial community abundance and fungal community (Shannon index) measurements were highest in summer. Soil nitrite nitrogen (NO₂ ^--N) was the dominant factor influencing both bacterial and fungal communities. The bacterial community composition was significantly affected by NO₂ ^--N and ammonium nitrogen (NH₄ ⁺-N) in spring, and fungal community structure was significantly affected by soil water content in autumn. Moreover, the fungal community exhibited significant functional feature differences among seasons, whereas bacterial community functional groups remained similar. This study aimed to clarify the adaptation response of microbes applying different approaches used in ecological restoration approaches specific to mining areas, and to identify the natural biofertility capacity of the microbial communities that colonize soil ecosystems.