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- Transfer learning enables predictions in soil-borne diseases
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Abstract: Abstract 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 metaframework 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. 
PubDate: 2024-07-26
DOI: 10.1007/s42832-024-0258-y
- Characterization of microbial structure and function in the rhizosphere of
Boehmeria nivea L.: A comparative study of volcanic cone and crater-
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Abstract: Abstract 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 (γ = 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. 
PubDate: 2024-07-26
DOI: 10.1007/s42832-024-0259-x
- Late-season rice increased the contribution of glomalin rather than amino
sugar to soil organic carbon in a double-season paddy soil-
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Abstract: Abstract 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. 
PubDate: 2024-07-18
DOI: 10.1007/s42832-024-0254-2
- Effects of per- and polyfluoroalkyl substances (PFASs) on hatching of
Folsomia candida (Collembola) on soil-
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Abstract: Abstract 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. 
PubDate: 2024-07-05
DOI: 10.1007/s42832-024-0253-3
- Long-term cropping rotation with soybean enhances soil health as evidenced
by improved nutrient cycles through keystone phylotypes interaction-
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Abstract: Abstract 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 constrains us 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. 
PubDate: 2024-06-06
DOI: 10.1007/s42832-024-0251-5
- Soil nutrient levels are associated with suppression of banana Fusarium
wilt disease-
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Abstract: Abstract 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 the rhizosphere 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. 
PubDate: 2024-06-06
DOI: 10.1007/s42832-024-0247-1
- Sporocarp-associated fungal co-occurrence networks in a corn field
revealed by long-read high-throughput sequencing-
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Abstract: Abstract 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. 
PubDate: 2024-06-06
DOI: 10.1007/s42832-024-0245-3
- Enhancing biomass and ecological sustainability in rice–fish cocropping
systems through the induction of functional microbiota with compound
biogenic bait-
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Abstract: Abstract 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. 
PubDate: 2024-06-06
DOI: 10.1007/s42832-024-0252-4
- Soil type and temperature determine soil respiration seasonal dynamics in
dairy grassland-
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Abstract: Abstract Soil respiration rates (Rs) were measured in New Zealand dairy grassland. Both season and soil type significantly affected Rs. Soil temperature and soil type dominated overall Rs. 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. 
PubDate: 2024-06-06
DOI: 10.1007/s42832-024-0250-6
- Advancements in assessing soil health through functional traits and energy
flow analysis of soil nematodes-
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Abstract: Abstract 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. 
PubDate: 2024-05-17
DOI: 10.1007/s42832-024-0228-4
- Effects of tourism development on ecological network and function of
sediment microbial communities in the urban wetland park-
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Abstract: Abstract 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 nitrogen and phosphorus cycles in wetlands. Structural equation modeling analysis revealed 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. 
PubDate: 2024-05-13
DOI: 10.1007/s42832-024-0249-z
- Elevational dynamics in soil microbial co-occurrence: Disentangling biotic
and abiotic influences on bacterial and fungal networks on Mt. Seorak-
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Abstract: Abstract 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. 
PubDate: 2024-05-06
DOI: 10.1007/s42832-024-0246-2
- Unraveling fertilization effects on the dynamics of arbuscular mycorrhizal
fungal community in the Qinghai-Tibet Alpine Meadow-
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Abstract: Abstract 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. 
PubDate: 2024-05-06
DOI: 10.1007/s42832-024-0248-0
- Development of a soil quality index “SQI” from a former open dump:
Dynamics of C and N mineralization-
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Abstract: Abstract Biosolids boost OM mineralization, enhancing soil health. Moderate biosolid doses improve soil conditions effectively. SQIw, 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. 
PubDate: 2024-04-24
DOI: 10.1007/s42832-024-0234-6
- The core phoD-harboring bacteria promote wheat phosphorus uptake by
enhancing alkaline phosphatase activity under long-term fertilization-
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Abstract: Abstract Soil pH was the key factor influencing the phoD-harboring bacterial networks. Identification of a cluster positively linked to ALP activity and plant P uptake. Low soil pH resulted in a severe loss of phoD-harboring bacterial core cluster. Fertilization treatments profoundly influence the bacterial communities associated with soil organic phosphorus (P) mineralization and alkaline phosphatase (ALP) activity. However, the relationships among the phoD-harboring bacterial communities associated with soil organic P mineralization, soil ALP activity, and plant P uptake under long-term fertilization remain unexplored. This study investigated these associations at the wheat rapid growth stage in a 40-year fertilization experiment. NPK fertilization led to a significant decrease in the diversity of phoD-harboring bacteria, which could be partially mitigated by the addition of organic materials. Soil pH emerged as the key factor influencing the structure and diversity of the phoD-harboring bacterial community. Furthermore, fertilizations involving manure additions resulted in more stable and cooperative phoD-harboring bacterial co-occurrence networks, compared to NPK fertilization. A functional phoD-harboring bacterial cluster, comprising genera Nostoc, Bradyrhizobium, and Pseudomonas, was identified, showing a positive association with soil ALP activity and plant P uptake. In summary, our study highlights the significant role of the identified core cluster of phoD-harboring bacteria in maintaining soil ALP activity and promoting plant P uptake, in decades of fertilization. Moreover, this study inferred a list of phoD-harboring bacterial genera from the core cluster, with established links to both plant P uptake and soil organic P mineralization. These findings offer valuable insights for sustainable agricultural practices. 
PubDate: 2024-04-23
DOI: 10.1007/s42832-024-0227-5
- Hg-mining-induced soil pollution by potentially toxic metal(loid)s
presents a potential environmental risk and threat to human health: A
global meta-analysis-
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Abstract: Abstract Agricultural activities may promote the conversion of inorganic Hg to MeHg in soil. Hg and As present an extremely and a moderately contaminated level, respectively. The human health risks posed by As, Hg, and Ni merit more attention. Pokeweed may be considered as a potential Hg hyperaccumulator. Soil pollution caused by potentially toxic metal(loid)s (PTMs) near mercury (Hg) mines has attracted extensive attention, yet the status and potential health risks of PTM contamination in soils near Hg mining sites have rarely been investigated on a large scale. Global data on methylmercury (MeHg), Hg, Cd, Cr, As, Pb, Cu, Zn, Mn, and Ni concentrations in soils from Hg mining areas were obtained from published research articles (1999–2023). Based on the database, pollution levels, spatial distributions, and potential health risks were investigated. Results indicated that the average percentage of MeHg to total Hg in agricultural soils (0.19%) was significantly higher than that in non-agricultural soils (0.013%). Indeed, 72.4% of these study sites were extremely contaminated with Hg. Approximately 45% of the examined sites displayed a moderate level of As contamination or even more. Meanwhile, the examined sites in Spain and Turkey exhibited considerably higher pollution levels of Hg and As than other regions. The mean hazard indices of the nine PTMs were 2.91 and 0.59 for children and adults, with 85.6% and 13.3% of non-carcinogenic risks for children and adults that exceeded the safe level of 1, respectively. In addition, 70.2% and 56.7% of the total cancer risks through exposure to five carcinogenic PTMs in children and adults, respectively, exceeded the safety level. As and Hg showed a high exceedance of non-carcinogenic risks, while As and Ni were the leading contributors to carcinogenic risks. This study demonstrates the urgent necessity for controlling PTM pollution and reducing the health risks in soils near Hg mining sites and provides an important basis for soil remediation. 
PubDate: 2024-04-23
DOI: 10.1007/s42832-024-0233-7
- Metals are overlooked in the evolution of antibiotic resistance
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Abstract: Abstract Metals are increasingly important risk factors for the evolution of antibiotic resistance in environments. The rapid development of antibiotic resistance is occurring at a global scale. We therefore stride into the post-antibiotic era and have to battle antibiotic resistance in the Anthropocene. Metals are widely used and their pollution is widespread worldwide. More importantly, metal-induced co-selection greatly expands the environmental resistomes and increases the health risk of antibiotic resistance in environments. Here, we reviewed the metal-induced co-selection and their increasingly important roles in the development of antibiotic resistance. In particular, we highlight the metal-rich environments that maintain reservoirs for high-risk antibiotic resistance genes with horizontally transferable potentials. We also call for considerations and further investigations of other co-selective agents and the efficacy of metal-based interventions to better manage and combat the global antibiotic resistance crisis within the One Health framework. 
PubDate: 2024-04-12
DOI: 10.1007/s42832-024-0244-4
- Revisiting soil fungal biomarkers and conversion factors: Interspecific
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Abstract: Abstract Refined conversion factors for soil fungal biomarkers are proposed. High interspecific variability is present in all fungal biomarkers. A modeling approach supports the validity of biomarker estimates in diverse soils. ITS1 copies vary strongly, but are fungal-specific with least phylogenetic bias. A combination of fungal biomarkers will reveal soil fungal physiology and activity. The abundances of fungi and bacteria in soil are used as simple predictors for carbon dynamics, and represent widely available microbial traits. Soil biomarkers serve as quantitative estimates of these microbial groups, though not quantifying microbial biomass per se. The accurate conversion to microbial carbon pools, and an understanding of its comparability among soils is therefore needed. We refined conversion factors for classical fungal biomarkers, and evaluated the application of quantitative PCR (qPCR, rDNA copies) as a biomarker for soil fungi. Based on biomarker contents in pure fungal cultures of 30 isolates tested here, combined with comparable published datasets, we propose average conversion factors of 95.3 g fungal C g−1 ergosterol, 32.0 mg fungal C µmol−1 PLFA 18:2ω6,9 and 0.264 pg fungal C ITS1 DNA copy−1. As expected, interspecific variability was most pronounced in rDNA copies, though qPCR results showed the least phylogenetic bias. A modeling approach based on exemplary agricultural soils further supported the hypothesis that high diversity in soil buffers against biomarker variability, whereas also phylogenetic biases impact the accuracy of comparisons in biomarker estimates. Our analyses suggest that qPCR results cover the fungal community in soil best, though with a variability only partly offset in highly diverse soils. PLFA 18:2ω6,9 and ergosterol represent accurate biomarkers to quantify Ascomycota and Basidiomycota. To conclude, the ecological interpretation and coverage of biomarker data prior to their application in global models is important, where the combination of different biomarkers may be most insightful. 
PubDate: 2024-04-12
DOI: 10.1007/s42832-024-0243-5
- Experimental warming increases respiration and affects microbial
communities of soil wetlands at different elevations of the Argentinean
Puna-
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Abstract: Abstract Under warming soil respiration was higher, but soil microbial biomass was lower. Warming effect on soil respiration was higher in soil from the highest elevation. Soil respiration was higher in soil with higher soil carbon content. Warming increased biomass-specific respiration and enzyme activity. The Q10 did not differ among soils from different elevations. Global warming is expected to increase the rate of soil carbon (C) efflux through enhanced soil microbial processes, mainly in systems, such as high elevation wetlands, storing large quantities of soil organic C. Here, we assessed the impact of experimental warming on respiration and microbial communities of high Andean wetland soils of the Puna region located at three different elevations (3 793, 3 862, 4 206 m a.s.l.). We incubated soils at 10°C and 25°C for 68 days and measured the soil respiration rate and its temperature sensitivity (Q10). Furthermore, we measured biomass and composition and enzymatic activity of soil microbial communities, and initial and final soil C content. Although warming increased soil respiration rates, with more pronounced effect in soils sampled from 4 206 m a.s.l., Q10 did not differ between elevations. Soil C content was higher at the highest elevation. Soil microbial biomass, but not enzymatic activity, was lower for warmed soil samples. However, the biomass-specific respiration and biomass-specific enzymatic activity were higher under warming, and in soil from the highest elevation wetland. These results suggest that, in the short-term, warming could stimulate resource allocation to respiration rather than microbial growth, probably related to a reduction in the microbial carbon use efficiency. Simultaneously, soils with higher soil C concentrations could release more CO2, despite the similar Q10 in the different wetlands. Overall, the soil of these high Andean wetlands could become C sources instead of C sinks, in view of forecasted increasing temperatures, with C-losses at regional scale. 
PubDate: 2024-04-11
DOI: 10.1007/s42832-024-0242-6
- Abiotic plant stress mitigation by Trichoderma species
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Abstract: Abstract Ascomycetes of the genus Trichoderma are beneficial fungi that promote plant growth. Several fungal species can mitigate abiotic stress in plants. Trichoderma spp. induce salt stress tolerance and drought protection in plants. Soil contamination by heavy metals can be bioremediated by Trichoderma. Trichoderma can detoxify pesticides and other pollutants in soils. Plants drive both carbon and nitrogen cycling and mediate complex biotic interactions with soil microorganisms. Climate change and the resulting temperature variations, altered precipitation, and water shortages in soils, affect the performance of plants. Negative effects of abiotic stress are reflected in changes of plant morphology associated with biochemical alterations and inadequate adaptation to rapid ecological change. Accumulation of chemical agents, derived from pesticides, salinity due to chemical fertilization, and accumulation of heavy metals, are recurrent problems in agricultural soils. Trichoderma spp. are soil fungi interacting with roots and in this way helping plants to cope with abiotic stresses by increasing root branching, shoot growth and productivity. In part, such fungal effects on the host plant are consequences of the activation of fine-tuned molecular mechanisms mediated by phytohormones, by profound biochemical changes that include production of osmolytes, by the activity of the redox-enzymatic machinery, as well by as complex processes of detoxification. Here, we summarize the most recent advances regarding the beneficial effects of Trichoderma in mitigating the negative effects on plant performance caused by different environmental and chemical factors associated with global change and agricultural practices that provoke abiotic stress. Additionally, we present new perspectives and propose further research directions in the field of Trichoderma-plant interactions when the two types of organism cooperate. 
PubDate: 2024-04-11
DOI: 10.1007/s42832-024-0240-8
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