● Rhizosphere microbial network in crater had higher complexity than in volcanic cone. ● Bacteria were more prone to enrichment than fungi in volcanic soils. ● The bacteria exhibited greater resistance and resilience than fungi.
Volcanic eruptions are significant natural disturbances that provide valuable opportunities to study their impacts on soil microorganisms. However, no previous studies have compared the rhizosphere microbial communities of Boehmeria nivea L. in volcanic craters and cones. To address this gap, we conducted a comprehensive investigation using Illumina MiSeq high-throughput sequencing to compare the rhizosphere microbial communities in volcanic craters and cones. Principal Coordinate Analysis revealed significant differences in the rhizosphere microbial communities between the crater and cone. The bacterial communities in the rhizosphere of the crater exhibited higher diversity and evenness compared to the cones. Moreover, the cones displayed more intricate bacterial networks than the crater (nodes 556 vs. 440). Conversely, fungal networks were more complex in the crater than the cone (nodes 943 vs. 967). Additionally, bacterial communities demonstrated greater stability than fungal ones within these volcanic soils (avgK 241.1 vs. 499.7) and (avgCC 1.047 vs. 1.092). Furthermore, the Structural Equation Model demonstrated a direct positive impact of alpha diversity on soil microbial community multifunctionality in the crater (λ = 0.920, P < 0.001). Our findings have presented the opportunity to investigate the characteristics of the rhizosphere microbial communities of Boehmeria nivea L. in the crater and cone.
● The Transformer model precisely predicts soil health status from high-throughput sequencing data. ● The SMOTE algorithm addresses data imbalance issues, improving model accuracy. ● Transfer learning validates the model on small samples, strengthening its generalization capabilities.
Inhibiting the occurrence of soil-borne diseases is considered as the most favorable approach for promoting sustainable agricultural development. Constructing soil disease prediction models can serve precision agriculture. However, the analysis results of the meta-framework often contradict each other, causing inconsistency in the important features of machine learning results. Therefore, it is necessary to compare the classification accuracy of various machine learning models and further optimize the features of the models to enhance their classification accuracy. Here, we conducted a comparison of eight common machine learning algorithms (XGBoost, CatBoost, Decision Tree, LGBM, Naïve Byes, Perceptron, Logistic, and Random Forest) at the levels of family, genus, and class. The important features of the model were extracted based on the differences in model accuracy and important features, followed by an interpretable analysis of these important features using feature importance. Subsequently, the data underwent resampling using the SMOTE algorithm, and the results show that the SMOTE-Transformer model performs well, surpassing the training results of the voting and stacking strategies, with an accuracy reaching 90%. We have also deployed the SMOTE-Transformer model on sequencing data, which has an accuracy of over 80%. The construction of SMOTE-Transformer model provides a new idea for soil microbial data analysis by greatly improving the accuracy and robustness of soil microbial data processing tools.
● Bacterial and fungal necromass in soil showed opposite trends with rice growth. ● The contribution of GRSP increased but ASs decreased to SOC with rice growth. ● Microbial residues were mainly influenced by living microbial biomass.
Microbial residues play an important role in soil organic carbon (SOC) sequestration. Paddy fields are important agricultural ecosystems involved in the carbon cycle; however, microbial residues change with rice growth in soil from double-season rice, and the influence of these residues on SOC sequestration is uncertain. Here, we investigated the microbial residues (amino sugars (AS) and glomalin-related soil protein (GRSP)) content and their contribution to SOC during the tillering stage (TS), heading stage (HS), and ripening stage (RS) in both early- and late-season rice in a double-cropping rice-growing area wherein the straw is returned after the early-season rice is harvested. Microbial biomass significantly increased from the early- to the late-season. In addition, the content of bacterial residues decreased (7.94%, P=0.008), while the fungal residues increased (8.15%, P<0.001) in the late-season compared with the early-season, suggesting that bacterial residues were recycled more rapidly than fungal residues. Amino sugar content and its contribution to SOC decreased from the TS to the RS in the late-season soil, probably because of the nutrient requirements of the rapidly growing rice. The contribution of GRSP to SOC increased by 10.5%, whereas that of ASs decreased by 4.5% from the early- to the late-season. Living soil microbes rather than soil physicochemical properties were the main factors influencing microbial residue accumulation. The results of this study provide a theoretical basis from a microbial perspective which will facilitate future efforts to enhance SOC sequestration during paddy field management.
● Bridge constructions decreased soil bacterial alpha and beta diversity. ● Bridge constructions reduced soil microbial biomass carbon and nitrogen. ● Stochastic process dominates soil bacterial community assembly. ● Bridge constructions increased the relative importance of stochasticity.
Soils in mangrove ecosystems are home to diverse and unique microbes, which support many crucial ecosystem services. Despite their vulnerability, the impact of bridge construction on the soil microbiome in mangroves is poorly understood. This study assessed the bacterial community profiles and microbial biomass in mangrove soils under different bridge construction techniques: Sheet Pile Cofferdam (SP) and Steel Casing Pipe (SC), compared to the non-disturbed (ND) counterpart. Bridge construction significantly decreased the alpha diversity and caused biotic homogenization of soil bacterial communities, indicating a loss of microbial biodiversity due to human disturbance. Bridge construction also reduced the microbial biomass carbon and nitrogen. The assembly of soil bacterial communities was dominated by stochastic processes, and bridge construction increased the relative importance of stochasticity. However, the impacts on ecological networks varied with the construction technique, with SC soils showing higher network complexity and stability compared to the ND habitats. Changes in soil bacterial communities were primarily attributed to the shifts in soil pH and nutrient levels. This study identified the effects of sea-crossing bridge construction on the soil microbiome in mangrove ecosystems, aiding in careful planning and environmental impact assessments to minimize the negative effects of urbanization on mangrove ecosystems.
● Egg hatching of the soil collembolan Folsomia candida and the effects of per- and polyfluoroalkyl substances were investigated. ● New and effective laboratory methods for egg hatching studies with soil collembolans were established.
Per- and polyfluoroalkyl compounds (PFASs) have been used industrially worldwide and are persistent organic pollutants in many soils. Twenty eggs laid by synchronized adults of the collembolan Folsomia candida were added to each Petri dish containing compressed soil substrate mixed with perfluorooctanoic acid (PFOA), heptafluorobutyric acid (PFBA), or 6:2 chlorinated polyfluoroalkyl ether sulfonic acid (F-53B), and after 25 d of exposure the number hatched declined on average by 6.9%−49.7%, 10.3%−24.1%, and 3.4%−18.6%, respectively. PFASs delayed the peak of hatching by one day, and at different concentrations reduced the number of eggs hatched during the peak by 16.7%−30% and 23.3%−43.2% in PFOA and PFBA treatments, respectively. In the presence of F-53B the number of eggs hatched declined by 73.3% but the number of individuals increased by 29.3% at higher concentrations. The characteristics of egg hatching were stable and sensitive to PFASs, and may be suitable for use as indicators in the screening of contaminated soils for environmental risk assessment.
● We estimated the effect of three crop strategies on soil health based on 63 functional genes in long-term fields. ● The keystone microbial phylotypes support the agroecosystem sustainability. ● Rotation management thrives keystone phylotypes and soil functions. ● Rotation with soybean is beneficial for the subsequent crops.
Given the often-independent study of microbial diversity and function, the comprehensive impact of various cropping patterns on both aspects, as well as the interconnections between them, remains unclear. This gap constrainsus from evaluating the impact of soil microbiome shifts on soil health across varying agricultural management regimes. Here, we examined the associations between microbial diversity and soil multifunctionality in three long-term cropping patterns: continuous soybean cropping, soybean-corn rotation, and continuous corn cropping. We targeted 63 functional genes associated with carbon, nitrogen, phosphorus and sulfur cycling to assess soil multifunctionality. Our study demonstrated that the biodiversity and interactions of keystone phylotypes had significant positive associations with multiple soil functional genes, such as organic carbon degradation and fixation, nitrogen fixation and phosphorus solubilization. The analysis of retrieved complete genome revealed that the keystone bacteria identified in our study harbored these functional genes. Moreover, these keystone phylotypes showed associations with the dissipation of herbicide residues. Above all, we revealed that rotation of soybean with corn cropping enhanced a greater diversity of keystone phylotypes and thus fueled soil functions. Collectively, our results highlighted the importance of rotation with soybean in maintaining soil health, which could give a mechanism-based guidance for a sustainable agroecosystem.
● Soil respiration rates ( R s) were measured in New Zealand dairy grassland. ● Both season and soil type significantly affected R s. ● Soil temperature and soil type dominated overall R s.
Soil respiration (Rs), the CO2 release from root respiration and microbial metabolism, affects global soil carbon storage and cycling. Only few studies have looked at Rs in the southern hemisphere, especially regarding the interaction between soil type and environmental factors on Rs in dairy grassland. We investigated the relationship between Rs and soil temperature (Ts), soil water content (SWC), soil type, and other environmental factors based on summer and winter measurements at four sites in New Zealand. Across sites, soil respiration rates ranged from 0.29 to 14.58 with a mean of 5.38 ± 0.13 (mean ± standard error) µmol CO2 m−2 s−1. Mean summer Rs was 86.5% higher than mean winter Rs, largely driven by organic/gley and pumice soils while ultic soils showed very little seasonal temperature sensitivity. Overall mean Rs in organic/gley soils was 108.0% higher than that in ultic soils. The high Rs rate observed in organic/gley was likely due to high soil organic matter content, while low Rs in ultic and pallic soils resulted from high clay content and low hydraulic conductance. Soil temperature drove overall Rs. Our findings indicate that soil type and soil temperature together best explain Rs. This implies that a mere classification of land use type may be insufficient for global C models and should be supplemented with soil type information, at least locally.
● Disease-suppressive soils exhibit enhanced soil nutrient status. ● Soil available phosphorus is a distinct feature of disease-suppressive soil. ● Rhizosphere hosts heightened microbial function for disease suppression. ● The soil microbial role in disease suppression is linked to nutrient cycling.
The role of soil nutrient status in disease suppression is of increasing interest for the control of soil-borne diseases. Here, we explored the soil chemical properties, composition, and functional traits of soil microbiomes in pair-located orchards that appeared suppressive or conducive to the occurrence of banana Fusarium wilt using mainly amplicon sequencing and metagenomic approaches. The enhancement of soil available phosphorus, succeeded by increments in soil nitrogen and carbon, played a pivotal role in the suppression of the disease. Additionally, in therhizosphere of suppressive sites, there was an observed increase in the disease-suppressing function of the soil microbiome, which was found to be correlated with specific nutrient-related functions. Notably, this enhancement involved the presence of key microbes such as Blastocatella and Bacillus. Our results highlight the significant roles of soil nutrient status and soil microbiome in supporting the soil-related disease suppressiveness.
● Compound biological bait can replace commercial bait to ensure fish growth. ● The compound biogenic bait can effectively improve the water and soil environment. ● The key microbiome induced by compound biogenic bait plays an important role.
Traditional commercial aquatic fish bait (CA) is not conducive to the scientific breeding of rice and fish in cocropping systems, and excessive feeding easily causes environmental pollution in rice fields. In this study, an environment-friendly compound biogenic bait (CB) mixed with plant-derived (PB) and animal-derived (AB) baits was proposed. The rice–crucian carp cocropping system was used as the research object, and the soil microorganisms and fish gut microorganisms were sequenced with high throughput, respectively, to verify the effect of CB application and the microbial mechanism underlying its functional effect. The results showed that the AB and PB components in CB maintain the growth of fish by improving the metabolism-related functions of fish gut microbiome and reducing the abundance of intestinal pathogenic bacteria, including Actinomadura. In particular, the PB components induced soil microbiome, such as Pseudonocardia, that participate in soil nutrient cycling and increase dissolved oxygen in water, which is key for improving rice quality and yield. This is the first study to focus on how different bait components drive key microbial communities to regulate animal–plant–environment relationships in the integrated planting and breeding patterns of paddy fields.
● We identified a sporocarp as Agrocybe dura growing next to a living corn using PacBio sequencing. ● The mycoparasitism of Trichoderma spp. on A. dura were revealed by the co-occurrence network analysis. ● For long-read HTS data, we updated a bioinformatic pipeline to enhance fungal taxonomic resolution.
In forests, fungal sporocarps house the diverse fungicolous fungi; however, the relationships of sporocarps and associated fungal communities are rarely explored in agroecosystems. In a corn field near Gongzhuling City, Jilin Province, China, we found an epigeous sporocarp with agaricoid morphology that could grow next to the living corn plants. Using PacBio metabarcoding combined with an updated bioinformatic pipeline, we surveyed the fungal community profile along its cap, rhizomorph and hyphosphere soil at a much-improved taxonomic resolution. We identified the sporocarp, at a high probability, as Agrocybe dura, and this mushroom was significantly negatively correlated with Trichoderma hamatum and T. harzianum in the co-occurrence network. Fungal diversity in hyphosphere habitat was significantly higher than that in cap and rhizomorph habitats. Consistent with the pattern in fungal diversity, the node number, edge number, network diameter and average degree were significantly higher in hyphosphere habitat than other habitats. However, both the negative and positive cohesion were significantly higher in rhizomorph habitat than other habitats. Moreover, the z-c plot identified A. dura as the only network hub, linking multiple fungal species. The results give us a glimpse of the ecological relevance of saprobic mushrooms across the extensive northeastern black soil region of China. Our findings will aid in the assessment and forecasting of fungal diversity hotspots and their relationships with soil fertility in the ‘Golden Corn Belt’ of northeast China.
● We examined the development of soil nematodes ecological indices from the perspective of functional traits. ● We found that soil nematode energy flow analyses based on multiple functional traits quantify the dynamics of energy flow across multiple-trophic levels to provide a more comprehensive perspective. ● We conducted comparative analyses of the sensitivities of NMF and energy flow to verify that the energy flow analyses are more sensitive and have greater potential to reveal soil health and ecosystem function. ● Future in-depth studies of functional traits and energy flow analysis can help us achieve informed soil management practices, sustainable agriculture, and healthier soil ecosystems.
This paper examines the development of ecological indices for soil nematodes from the perspective of functional traits. It emphasizes the increasing significance of integrating multiple functional traits to achieve a more accurate assessment of soil health. Ecological indices based on life history strategies, feeding habits, and body size provide useful tools for assessing soil health. However, these indices do not fully capture the dynamics of energy flow across multiple-trophic levels in the soil food web, which is critical for a deeper understanding of the intrinsic properties of soil health. By combining functional traits such as functional group, body size, feeding preference and metabolic rate, nematode energy flow analyses provide a more comprehensive perspective. This approach establishes a direct correlation between changes in the morphology, physiology, and metabolism of soil organisms and alterations in their habitat environment. We conducted comparative analyses of the sensitivity of nematode metabolic footprints and energy flow to latitudinal variation using a nematode dataset from the northeastern black soil region in China. The findings suggest that energy flow analyses are more sensitive to latitude and have greater potential to reveal soil health and ecosystem function. Therefore, future research should prioritize the development of automated and efficient methods for analyzing nematode traits. This will enhance the application of energy flow analyses in nematode food webs and support the development of sustainable soil management and agricultural practices.
● Tourism development influenced the ecological network of microbial communities. ● Regulating mechanism of intra- and inter-domain networks was clarified. ● Macrophyte coverage reduces microbial network complexity and stability. ● Landscaping may promote nitrogen and phosphorus cycle in wetland watershed.
Numerous urban wetland parks have been established, yet the understanding of microbial interactions in response to tourism development is still limited. This study aims to elucidate the impact of tourism development on the complexity and stability of molecular ecological networks within the microbial communities of wetland sediments. Through an analysis of sediments properties, microorganism intra- and inter-domain co-occurrence characteristics in three different wetland functional areas (conservation, landscaping, and recreation areas), we found that tourism development influenced sediment physicochemical properties. These changes regulated the diversity and ecological networks of archaeal and bacterial communities. Specifically, areas with landscaping (LA) exhibited reduced network connectivity and robustness, suggesting that macrophyte coverage diminishes the complexity and stability of microbial communities in wetland parks. Notably, the transition from conservation areas (CA) to LA strengthened the correlations between microbial network modules and sediment total nitrogen (TN) and total phosphorus (TP), potentially enhancing the nitrogenand phosphorus cycles in wetlands. Structural equation modeling analysisrevealed that both abiotic factors (TC, TP, TN, K, Mg, pH) and biotic factors (archaeal and bacterial α-diversity) can influence interdomain network complexity, accounting for 42% of the variation. Among these factors, sediment TN exerted the largest positive effect on network complexity (37.9%), while Mg had the most negative impact (59.8%). This study provides valuable insights for ecological assessments of urban wetlands and can inform strategies for effective wetland ecosystem management.
● Community structure and composition of AMF shifted under different fertilization. ● Soil physicochemical properties played important roles in contributing plant diversity and biomass. ● Fertilization affected plant and AMF communities through changing soil abiotic properties. ● Acaulospora and Diversispora were highly linked with plant communities.
Arbuscular mycorrhizal fungi (AMF) represent a crucial component of soil microorganisms, playing pivotal roles in promoting plant growth by enhancing nutrient availability. However, the responses of AMF communities to different fertilization regimes and their correlations with plant communities in the context of anthropogenic disturbances in alpine meadow ecosystems remain largely unexplored. In this study, we investigated the effects of nitrogen, phosphorus, and combined nitrogen-phosphorus fertilization on AMF communities and their interconnections with plant diversity and biomass based on a seven-year long-term experiment conducted on the Qinghai-Tibet Plateau. Our results showed significant shifts in AMF community structure and composition under different fertilization treatments, while the richness of AMF exhibited no remarkable alterations. Notably, soil pH decreased, and electrical conductivity increased with the increasing nitrogen fertilizer application, emerging as pivotal abiotic factors in predicting plant richness and biomass. Fascinatingly, Acaulospora exhibited a positive correlation with plant richness, serving as an important bioindicator of plant richness, while Diversispora emerged as the primary bioindicator of plant biomass. Our findings shed light on potential correlations between AMF community composition and both plant and soil abiotic factors, driven by nitrogen and phosphorus fertilization. We advocate for the critical significance of balanced fertilization in sustaining beneficial plant–soil–AMF interactions in natural ecosystems as well as agricultural soils.
● Fungi outperformed bacterial in maintaining the microbial co-occurrence networks. ● Fungi showed different elevational network co-occurrence pattern from bacteria. ● Distinct biotic/abiotic factors influenced bacterial and fungal network dynamics.
The interplay between soil micro-organisms in mountain ecosystems critically influences soil biogeochemical cycles and ecosystem processes. However, factors affecting the co-occurrence patterns of soil microbial communities remain unclear. In an attempt to understand how these patterns shift with elevation and identify the key explanatory factors underpinning these changes, we studied soil bacterial and fungal co-occurrence networks on Mt. Seorak, Republic of Korea. Amplicon sequencing was used to target the 16S rRNA gene and ITS2 region for bacteria and fungi, respectively. In contrast to bacteria, we found that fungi were predominantly situated in the core positions of the network, with significantly weakened co-occurrence with increasing elevation. The different co-occurrence patterns of fungal and bacterial communities could be resulted from their distinct responses to various environments. Both abiotic and biotic factors contributed significantly to shaping co-occurrence networks of bacterial and fungal communities. Fungal richness, bacterial community composition (indicated by PCoA1), and soil pH were the predominant factors influencing the variation in the entire microbial co-occurrence network. Biotic factors, such as the composition and diversity of bacterial communities, significantly influenced bacterial co-occurrence networks. External biotic and abiotic factors, including climatic and vegetative conditions, had a significant influence on fungal co-occurrence networks. These findings enhance our understanding of soil microbiota co-occurrences and deepen our knowledge of soil microbiota responses to climatic changes across elevational gradients in mountain ecosystems.
● Biosolids boost OM mineralization, enhancing soil health. ● Moderate biosolid doses improve soil conditions effectively. ● SQI w, with Nmin, efficiently gauges soil quality, simplifying monitoring.
Economic development triggers environmental pollution. To address this issue and mitigate its consequences on the environment and human health, urban wastewater treatment plants are commonly employed to produce treated water and biosolids. However, biosolid disposals pose issues due to space limits and leachate contamination. This study investigates the potential of using biosolids as an organic amendment to remediate soil contaminated with leachate from an open dump in Mexico. Treatments with different doses of biosolids were tested (control, without addition of biosolids; high, medium, and low doses, with a C/N = 8, 10, 12 respectively). The physicochemical and biological characteristics of the soil and biosolids were analyzed, and the dynamics of carbon and nitrogen mineralization over time were studied. The developed soil quality index, primarily based on the mineralized nitrogen indicator, differentiated soil quality among treatments, showing values of moderate quality for the treatments (high, medium, and low doses (0.56, 0.48, 0.40, respectively) and low quality for the control (0.34)). The use of biosolids as an organic amendment improved soil quality by increasing organic matter and microbial growth. Soil quality indices emerges as a practical tool for monitoring the remediation of leachate-contaminated open dump soils in Mexico and similar contexts worldwide.
