Dynamics of Soil Microbial N-Cycling Strategies in Response to Cadmium Stress

Microbiome engineering to palliate microbial dysbiosis occurring in agroecosystems

Plant health and productivity are closely tied to the fluctuations of soil microbiomes, which regulate biogeochemical processes and plant-soil interactions. However, environmental and anthropogenic stressors, including climate change, intensive agricultural practices, and industrial activities, disrupt these microbial communities. This microbial imbalance reduces soil fertility, plant health, and biodiversity, threatening agroecosystem sustainability. This review explores the mechanisms driving microbial dysbiosis in soil and plant environments. Plants under stress release chemical signals through root exudates, dynamically recruiting beneficial microbes to counteract microbial imbalances. Moreover, this review evaluates traditional methods to alleviate these stress-induced microbial alterations, such as microbial inoculants and organic soil amendments, alongside innovative strategies like phage therapy, CRISPR, and small RNA-based technologies. Despite these advancements, the practical implementation of microbiome interventions faces significant challenges. These include regulatory hurdles, economic constraints, and the need for long-term field studies to validate efficacy and ensure environmental safety.

Glyphosate and urea co-exposure: Impacts on soil nitrogen cycling

Glyphosate, the most widely utilized herbicide, frequently coexists with nitrogen fertilizers such as urea in soil environments. Nitrogen cycling is a key process for maintaining soil ecological functions and nutrient balance. However, the effects of co-exposure to glyphosate and urea on this process have remained unclear. This study investigated the impact of co-exposure to glyphosate (10 mg/kg) and urea (260.87 or 347.83 mg/kg, equivalent to 180 or 240 kg N/ha) on soil nitrogen cycling through a 98-day incubation experiment. Soil nutrients, enzyme activities, bacterial community structure, and functional genes were analyzed. NH4+-N and NO3--N contents significantly decreased by 44.70-53.43 % and 36.74-49.12 %, respectively. Co-exposure reduced bacterial diversity and altered nitrogen cycling genes, decreasing nifH while increasing amoA and nosZ, indicating reduced nitrogen input potential and increased inorganic nitrogen loss. Enzyme analysis confirmed excessive activation of nitrification and denitrification, lowering nitrogen availability. Partial least squares structural equation modeling (PLS-SEM) showed co-exposure indirectly decreased NH4+-N and NO3--N via enhanced nitrate and nitrite reductase activities. The study highlights the complex interactions between herbicides and fertilizers in soil environments and underscores the need for further research to understand the implications for wider soil health and crop production in agriculture systems.

Biotic and abiotic drivers of soil carbon, nitrogen and phosphorus and metal dynamic changes during spontaneous restoration of Pb-Zn mining wastelands

The biotic and abiotic mechanisms that drive important biogeochemical processes (carbon, nitrogen, phosphorus and metals dynamics) in metal mine revegetation remains elusive. Metagenomic sequencing was used to explored vegetation, soil properties, microbial communities, functional genes and their impacts on soil processes during vegetation restoration in a typical Pb-Zn mine. The results showed a clear niche differentiation between bacteria, fungi and archaea. Compared to bacteria and fungi, the archaea richness were more tightly coupled with natural restoration changes. The relative abundances of CAZyme-related, denitrification-related and metal resistance genes reduced, while nitrification, urease, inorganic phosphorus solubilisation, phosphorus transport, and phosphorus regulation -related genes increased. Redundancy analysis, hierarchical partitioning analysis, relative-importance analysis and partial least squares path modelling, indicated that archaea diversity, primarily influenced by available lead, directly impacts carbon dynamics. Functional genes, significantly affected by available cadmium, directly alter nitrogen dynamics. Additionally, pH affects phosphorus dynamics through changes in bacterial diversity, while metal dynamics are directly influenced by vegetation. These insights elucidate natural restoration mechanisms in mine and highlight the importance of archaea in soil processes.

Cadmium-Induced Responses and Tolerance Mechanisms of Aerobic Methanotrophs in Rice Paddy Soils

Paddy fields are major sources of atmospheric methane and are at risk of cadmium (Cd) contamination. Aerobic methanotrophs, which serve as biological methane sinks, play a key role in methane cycling, but their responses to Cd stress remain poorly understood. Here, we examined the relationship between Cd pollution levels and aerobic methane oxidation potential in paddy soils. We evaluated methanotrophic enrichments under Cd exposure, applied metagenomic sequencing to identify functional microbes, and investigated Cd tolerance mechanisms in pure culture. Aerobic methane oxidation rates were positively correlated with Cd levels in paddy soils from South China, with Methylocystis and Methylomonas emerging as dominant genera possessing diverse Cd tolerance genes. Notably, interspecific differences in Cd tolerance were observed among methanotrophic strains. The faster-growing Methylomonas sp., endowed with more robust antioxidant defenses and extracellular polymeric substances synthesis genes, exhibited Cd resistance through markedly enhanced loosely bound extracellular polymeric substances production, in contrast to the Cd-sensitive Methylobacter sp. Gene knockout experiments confirmed the essential roles of glutathione synthase, glutathione peroxidase, and exosortase in exopolysaccharide extrusion for Cd detoxification. These findings advance our understanding of the methane cycle in Cd-contaminated rice paddies and suggest potential strategies to mitigate methane emissions while addressing Cd detoxification.

Cadmium inhibits carbon and nitrogen cycling through soil microbial biomass and reduces soil nitrogen availability

Microbial mediated carbon and nitrogen cycling response to cadmium are often observed in soil; however, a unified framework of this response has not yet been established. By analyzing 1232 observations from 166 publications, we found that cadmium decreased microbial biomass carbon (-16 %) and nitrogen (-21 %), dissolved organic nitrogen (-27 %), nitrification rate (-17 %), microbial respiration rate (-12 %), and β-1,4-glucosidase (-21 %) and urease (-16 %) activities, but increased microbial metabolic quotient (+11 %) and fungal-to-bacterial ratio (+39 %). The cadmium impact was concentration-dependent, becoming more pronounced at higher concentrations. Increasing cadmium concentration reduced soil N mineralization rate and total N content, but increased microbial biomass carbon-to-nitrogen ratio. These results indicate that cadmium reduced carbon and nitrogen assimilation into microbial biomass and limited soil inorganic nitrogen production. Soil bulk density drove soil microbial biomass and nitrogen availability response to cadmium. Lower soil bulk density and higher initial carbon and clay contents and soil pH reduced the negative impact of cadmium on microbial biomass and nitrogen availability, suggesting that anthropogenic activities that enhance soil quality may mitigate the inhibitory effect of cadmium on soil carbon and nitrogen cycling. Our analysis provides critical implications for improving our understanding of the ecological consequences of cadmium on soil carbon and nitrogen cycling.

The influences of heavy metals on soil microbial C, N, P cycling and heavy metal resistance under different fertilization regimes

Heavy metal pollution changes microbial heavy metal resistance and ecological functions of carbon (C), nitrogen (N), phosphorus (P), sulfur (S) cycling, although the connections between these changes have been insufficiently explored. The study investigated the effects of varying levels of heavy metal pollution and nutrient on microbial heavy metal resistance and C, N, P, S cycling in soils. The results indicated that heavy metal pollution significantly enhanced microbial metabolic potentials, such as denitrification, Dissimilatory nitrate reduction (DNRA), P uptake and transport, as well as resistance to Cu, Cd, Pb, and As. Heavy metals and pH were identified as major factors affecting these microbial functions. The diversity and evenness of host microorganisms carrying functional genes and heavy metal resistance genes (MRGs) were significantly affected by heavy metal pollution, but this effect was alleviated with the nutrient increased. In low-nutrient soils, a strong correlation between nitrogen degradation and Zn resistance was observed due to heavy metal pollution. As nutrients increased, the close correlations between hemicellulose, P uptake and transport, nitrogen degradation and Zn resistance were also observed. Bradyrhizobium, Nitrospira, Steroidobacter, and Luteitalea might play important roles in regulating C, N, P cycling and heavy metal resistance. This study revealed the adjustment mechanisms of microbial heavy metals resistance and ecological functions under heavy metal pollution and identified the primary host microorganisms.

Bacterivorous protists inhibit nitrification and N2O emissions in cadmium polluted soils via negative feedback loops

Understanding the soil nitrogen (N) process under increasing anthropogenic activities, i.e., heavy metal pollution and N fertilization is essential for optimizing soil N management and tackling environmental problems. However, few studies assess how ubiquitous soil protists influence N process from a multitrophic perspective. Here, we conducted microcosm experiments to investigate how phagotrophic protists (Colpoda steinii) influence the autochthonous bacterial flora proxy for N process to drive the N transformation processes under different Cd pollution levels (0-3 mg kg-1) with or without N fertilization. Because of hormesis, Cd stimulated the net nitrification rate and N2O emissions by up to 65 % and 100 %, respectively, and this stimulation was stronger after N addition. However, protists attenuated and even reversed the stimulation of Cd on the net nitrification rate and N2O flux, especially after N addition by correspondingly reducing N fertilization-enhanced nitrifiers and denitrifiers, which were also metabolically active under Cd pollution. With this negative feedback loop, protists reduced the net nitrification rate and N2O emissions by up to 91 % and 36 %, respectively. This study offers novel insights to assess the effects of heavy metal pollution on soil nutrient cycling regarding soil predation, providing strategies for increasing N-use efficiency in agricultural ecosystems.

Edaphic factors mediate the response of nitrogen cycling and related enzymatic activities and functional genes to heavy metals: A review

Soil nitrogen (N) transformations control N availability and plant production and pose environmental concerns when N is lost, raising issues such as soil acidification, water contamination, and climate change. Former studies suggested that soil N cycling is chiefly regulated by microbial activity; however, emerging evidence indicates that this regulation is disrupted by heavy metal (HM) contamination, which alters microbial communities and enzyme functions critical to N transformations. Environmental factors like soil organic carbon, soil texture, water content, temperature, soil pH, N fertilization, and redox status play significant roles in modulating the response of soil N cycling to HM contamination. This review examines how different HMs affect soil N processes, including N fixation, mineralization, nitrification, denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and immobilization, as well as microbial activities and functional genes related to soil N transformations. The review additionally outlines the impact of HMs on environmental degradation, including the risk of soil N losses (e.g., leaching, runoff, and gaseous emissions) and depletion of soil fertility, thus threatening the sustainability of the ecosystem. The effect of edaphic factors and fertilization on soil N cycling response to HM contamination was also examined. The effect of phytoremediation, a sustainable approach to remediate HM polluted soils, on N cycling was also reviewed. Thus, this review underscores the importance of increasing research and innovative strategies to combat HM pollution's effects to enhance soil health, boost crop yields, and protect soil stability and productivity.

Lanthanum and cerium added to soil influence microbial carbon and nitrogen cycling genes

The soil microbiome plays an important role in carbon (C) and nitrogen (N) processing and storage and is influenced by rare earth elements (REEs), which can have both direct and indirect effects on plant metabolic processes. Using conventional physicochemical methods and metagenomic-based analyses, we investigated REEs effects on soil respiration, soil mineral N, soil microbial community structure and functional genes related to C and N metabolism. High doses of cerium (0.16 and 0.32 mmol kg-1 soil) increased CO2 net production rate by 59 and 42%, and N2O net production rate by 255 and 609%, respectively, compared to no REEs. Similarly, high doses of lanthanum (0.16 and 0.32 mmol kg-1 soil) increased CO2 net production rate by 47 and 39%, and N2O net production rate by 105 and 187%, respectively. Increased soil respiration from altered relative abundances of key soil microorganisms associated with soil N cycling and organic matter degradation and functional genes encoding enzymes involved in C and N metabolism, accelerated N mineralization. Elevated REEs levels substantially increased the relative abundances of functional genes related to cellulose, chitin, glucans, hemicellulose, lignin, and peptidoglycan degradation. REEs also influenced multiple functional genes associated with the N cycle. The abundance of genes responsible for organic N degradation and synthesis, such as asnB, gdh_K15371, glsA, and gs, increased with elevated cerium and lanthanum concentrations. Similarly, the abundances of denitrification genes, including narl, narJ, narZ, and nosZ, also rose with increasing amounts of cerium and lanthanum. However, the decrease in narB and nirB gene abundance with increasing REE concentrations was attributed to the reduction of nitrate to amino groups. Our findings highlight the influence of REEs on key soil microorganisms associated with soil N cycling and organic matter degradation and key functional genes in soil C and N metabolism, with implications for agriculture, environmental protection, and human health.

Interactive effects of microplastics and cadmium on soil properties, microbial communities and bok choy growth

The simultaneous presence of microplastics (MPs) and cadmium (Cd) in soil environments has raised concerns regarding their potential interactive effects on soil-plant ecosystems. This study explores how polyethylene (PE) at concentrations of 0.5 % (w/w), 1 % (w/w), and 2 % (w/w), and Cd at concentrations of 3 mg kg-1 and 12 mg kg-1, either alone or combined, impact soil physicochemical properties, microbial community structures, and bok choy growth through a 40-day pot experiment. Our findings reveal that the addition of 2 % (w/w) PE significantly increased soil organic carbon (SOC). However, when 2 % PE coexisted with Cd, SOC levels decreased, potentially due to a reduction in enzyme activity (β-1,4-glucosidase). PE increased the proportion of 1-2 mm soil aggregates, while the coexistence of 2 % PE and Cd significantly increased the content of soil aggregates larger than 2 mm. The coexistence of PE and Cd increased available potassium (AK) in the soil by approximately 13 % to 41 %. Regarding bok choy growth, the aboveground biomass under 2 % PE was approximately 210 % of that under 0.5 % PE, possibly because of the enhancement in soil nutrients. The presence of Cd, however, reduced the chlorophyll content of bok choy by approximately 18 % to 34 %. Notably, the coexistence of high PE concentration (2 % w/w) and low Cd concentration (3 mg kg-1) resulted in the highest aboveground biomass among all coexistence treatments. Furthermore, the addition of PE and Cd significantly altered the structure of soil bacterial and fungal communities, with fungi showing a greater response. Bacteria were significantly associated with soil inorganic N content and plant growth. This study provides new insights into the interactions of microplastics and Cd within microbial-soil-plant systems.

Interactions between arsenic and nitrogen regulate nitrogen availability and arsenic mobility in flooded paddy soils

In paddy soils, arsenic (As) stress influences nitrogen (N) transformation while application of N fertilizers during rice cropping affects As transformation. However, specific interactive effects between As and N in flooded paddy soils on As mobility and N availability were unclear. Here, we examined N and As dynamics in flooded paddy soils treated with four As levels (0, 30, 80 and 150 mg kg-1) and three urea additions (0, 4 and 8 mmol N kg-1). Arsenic contamination inhibited diazotrophs (nifH) and fungi but promoted AOA and denitrification genes (narG, nirK, nirS), decreasing dissolved organic N, NH4+-N and NO3--N. Besides, urea application stimulated As- and Fe-reducing bacteria (arrA and Geo) coupled with anammox. On Day 28, the addition of 8 mmol N kg-1 increased total As concentrations in solutions of soils treated with 30 and 80 mg As kg-1 by 2.4 and 1.8 times compared with the nil-N control. In contrast, at 150 mg As kg-1, it decreased the total As concentration in soil solution by 63 % through facilitating As(III) oxidation coupled with NO3--N reduction. These results indicate that As contamination decreases N availability, but urea application affects As mobility, depending on As contamination level.

Enhanced mobilization of soil heavy metals by the enantioselective herbicide R-napropamide compared to its S-isomer: Analyses of abiotic and biotic drivers

Chiral herbicides applied to agricultural soils are typically mildly to moderately contaminated with heavy metals (HMs), necessitating a thorough investigation into their effects on soil HMs availability. This study evaluated the effect of the chiral herbicide napropamide (NAP) on HMs bioavailability in different soil types, including weakly alkaline clay in Northeast China, neutral sandy loam in Zhejiang, and weakly acidic clay loam in Sichuan, China. The results demonstrate significant differences in the availability of HMs (Cd, Pb, Zn, and Ni) in the soil following enantiomer treatments, with variation ranges of 4.57-45.67 %, 5.03-96.21 %, 2.92-52.30 %, and 10.57-29.79 %, respectively. Overall, R-NAP enhanced the bioavailability of HMs more effectively than S-NAP, specifically by significantly activating available iron 3.33-191.97 % and markedly affecting soil pH and cation exchange capacity. Additionally, R-NAP influenced biotic processes by enriching dominant microbial communities, such as Chitinophaga, Niabella, and Promicromonospora, and by constructing more stable microbial networks. Notably, bioavailable Fe plays a dual regulatory role, affecting both the abiotic and biotic processes affected by soil NAP. In summary, although R-NAP is commonly used in agriculture, it poses a greater risk of HMs contamination in crops, highlighting the need for careful application and management. This study provides a fundamental theoretical basis for the judicious use of chiral herbicides in agricultural soils with mild-to-moderate HMs contamination.

Copper and cadmium co-contamination increases the risk of nitrogen loss in red paddy soils

The microbiome plays a crucial role in soil nitrogen (N) cycling and in regulating its bioavailability. However, the functional and genomic information of microorganisms encoding N cycling in response to copper (Cu) and cadmium (Cd) contamination is largely unknown. Here, metagenomics and genome binning were used to examine microbial N cycling in Cu and Cd co-contaminated red paddy soils collected from a polluted watershed in southern China. The results showed that soil Cu and Cd concentrations induced more drastic changes in microbial N functional and taxonomic traits than soil general properties. Soil Cu and Cd co-contamination stimulated microbial nitrification, denitrification, and dissimilatory nitrate reduction processes mainly by increasing the abundance of Nitrospira (phylum Nitrospirota), while inhibiting N fixation by decreasing the abundance of Desulfobacca. These contrasting changes in microbial N cycling processes suggested a potential risk of N loss in paddy soils. A high-quality genome was identified as belonging to Nitrospirota with the highest abundance in heavily contaminated soils. This novel Nitrospirota strain possessed metabolic capacities for N transformation and metal resistance. These findings elucidate the genetic mechanisms underlying soil N bioavailability under long-term Cu and Cd contamination, which is essential for maintaining agricultural productivity and controlling heavy metal pollution.

Applying kitchen compost promoted soil chrysene degradation by optimizing microbial community structure

Chrysene, as a high molecular weight polycyclic aromatic hydrocarbon (PAH), has become an important factor in degrading soil quality and constraining the safe production of food crops. Compost has been widely used to amend contaminated soil. However, to date, the main components of kitchen compost that enhance the biodegradation of chrysene in the soil remain unidentified. Thus, in this study, the enhancing effect and mechanisms of kitchen compost (KC) and kitchen compost-derived dissolved organic matter (KCOM) on chrysene removal from soil were investigated through cultivation experiments combined with high-throughput sequencing technology. Additionally, the key components influencing the degradation of chrysene were identified. The results showed that KCOM was the main component of compost that promoted the degradation of chrysene. The average degradation rate of chrysene in 1% KC- and 1% KCOM-treated soil increased by 27.20% and 24.18%, respectively, at different levels of chrysene pollution compared with the control treatment (CK). KC and KCOM significantly increased soil nutrient content, accelerated humification of organic matter, and increased microbial activity in the chrysene-contaminated soil. Correlation analyses revealed that the application of KC and KCOM optimized the microbial community by altering soil properties and organic matter structure. This optimization enhanced the degradation of soil chrysene by increasing the abundance of chrysene-degrading functional bacteria from the genera Bacillus, Arthrobacter, Pseudomonas, Lysinibacillus, and Acinetobacter. This study provides insight into the identification of key components that promote chrysene degradation and into the microbial-enhanced remediation of chrysene-contaminated soil.

Nitrogen utilization efficiency assessment during bioremediation of petroleum-contaminated loess soils: insights from metagenomic analysis

Nitrogen addition is commonly used to remediate total petroleum hydrocarbons (TPH) in petroleum-contaminated soils. However, acceptable exogenous nitrogen dosages and their utilization efficiency for the degradation of hydrocarbons in oil-polluted soils are not well understood. This study compared the hydrocarbon bioremediation capacity by applying different doses of NH4Cl as a stimulant in soils contaminated with TPH at 8553 and 17090 mg/kg. The results showed acceptable exogenous nitrogen levels ranging from 60 to 360 mg N/kg soil, and the optimal nitrogen dosage for TPH remediation was 136 mg N/kg in soils with different TPH concentrations. The nitrogen availability efficiency (NAE) and nitrogen polarization factor availability (NPFA) in the 136 mg N/kg addition treatments were 6.69 and 20.47 mg/mg in 8533 mg/kg TPH-polluted soil, and 6.03 and 31.11 mg/mg in 17090 mg/kg TPH-polluted soil, respectively. Metagenomic analysis revealed that the application of 136 mg/kg nitrogen facilitated ammonia oxidation and nitrite reduction to nitric oxide, and induced soil microorganisms to undergo regulatory or adaptive changes in energy supply and metabolic state, which could aid in restoring the ecological functions of petroleum-contaminated soils. These findings underscore that 136 mg/kg of nitrogen dosage application is optimal for remediation of petroleum-contaminated soils irrespective of the TPH concentrations. This exogenous nitrogen application dosage for TPH remediation aligns with the nitrogen requirements for crop growth in agriculture.

The critical role of organic matter for cadmium-lead interactions in soil: Mechanisms and risks

Understanding the interaction mechanisms between complex heavy metals and soil components is a prerequisite for effectively forecasting the mobility and availability of contaminants in soils. Soil organic matter (SOM), with its diverse functional groups, has long been a focal point of research interest. In this study, four soils with manipulated levels of SOM, cadmium (Cd) and lead (Pb) were subjected to a 90-day incubation experiment. The competitive interactions between Cd and Pb in soils were investigated using Fourier transform infrared spectrometer (FTIR), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and X-ray adsorption near-edge structure (XANES) analysis. Our results indicate that Pb competed with Cd for adsorption sites on the surface of SOM, particularly on carboxyl and hydroxyl functional groups. Approximately 22.6 % of Cd adsorption sites on humus were occupied by Pb. The use of sequentially extracted exchangeable heavy metals as indicators for environment risk assessments, considering variations in soil physico-chemical properties and synergistic or antagonistic effects between contaminants, provides a better estimation of metal bioavailability and its potential impacts. Integrating comprehensive contamination characterization of heavy metal interactions with the soil organic phase is an important advancement to assess the environmental risks of heavy metal dynamics in soil compared to individual contamination assessments.

Response patterns of the microbiome during hexavalent chromium remediation by Tagetes erecta L

Chromium pollution, particularly hexavalent chromium [Cr(VI)], may threaten the environment and human health. This study investigated the potential of Tagetes erecta L. (Aztec marigold) for phytoremediation of soil contaminated with Cr(VI), and focused on the effects of varying concentrations of Cr(VI) on both the physicochemical properties of soil and microbiome of Tagetes erecta L. We observed that Tagetes erecta L. showed tolerance to Cr(VI) stress and maintained normal growth under these conditions, as indicated by bioconcentration factors of 0.33-0.53 in shoots and 0.39-0.70 in roots. Meanwhile, the structure and diversity of bacterial communities were significantly affected by Cr(VI) pollution. Specifically, Cr(VI) had a more significant effect on the microbial community structure in the endophytic of Tagetes erecta L. than in the rhizosphere (p < 0.05). The genera Devosia and Methylobacillus were positively correlated with Cr(VI) concentrations. Biomarkers such as Bacilli and Pseudonocardia were identified under the different Cr(VI)-contaminated treatments using LEfSe. In addition, the interaction and stability of the endophytic microbiome were enhanced under Cr(VI) stress. This study explored the interactions between heavy metals, microorganisms, and plants, providing valuable insights for developing in situ bioremediation of Cr(VI)-contaminated soils.

Effects of combined microplastics and heavy metals pollution on terrestrial plants and rhizosphere environment: A review

Microplastics (MPs) can enter the soil environment through industry, agricultural production and daily life sources. Their interaction with heavy metals (HMs) poses a significant threat to a variety of terrestrial ecosystems, including agricultural ones, thereby affecting crop quality and threatening human health. This review initially addresses the impact of single and combined contamination with MPs and HMs on soil environment, including changes in soil physicochemical properties, microbial community structure and diversity, fertility, enzyme activity and resistance genes, as well as alterations in heavy metal speciation. The article further explores the effects of this pollution on the growth characteristics of terrestrial plants, such as plant biomass, antioxidant systems, metabolites and photosynthesis. In general, the combined contaminants tend to significantly affect soil environment and terrestrial plant growth, i.e., the impact of combined contaminants on plants weight ranged from -87.5% to 4.55%. Similarities and differences in contamination impact levels stem from the variations in contaminant types, sizes and doses of contaminants and the specific plant growth environments. In addition, MPs can not only infiltrate plants directly, but also significantly affect the accumulation of HMs in terrestrial plants. The heavy metals concentration in plants under the treatment of MPs were 70.26%-36.80%. The co-occurrence of these two pollution types can pose a serious threat to crop productivity and safety. Finally, this study proposes suggestions for future research aiming to address current gaps in knowledge, raises awareness about the impact of combined MPs + HMs pollution on plant growth and eco-environmental security.

Variations in different preceding crops on the soil environment, bacterial community richness and diversity of tobacco-planting soil

Tobacco (Nicotiana tabacum L.) is a major cash crop, and soil quality played a significant role in the yield and quality of tobacco. Most farmers cultivate tobacco in rotation with other crops to improve the soil characteristics. However, the effects of different previous crops on the soil's nutrient status and bacterial community for tobacco cultivation still need to be determined. Three treatments were assessed in this study, i.e., tobacco-planting soil without treatment (CK), soil with barley previously cultivated (T1), and soil with rapeseed previously cultivated (T2). The soil physical and chemical properties and the 16S rRNA gene sequence diversity of the bacterial community were analyzed. The effects of different crops on the physical and chemical properties of tobacco-planting soil and the diversity and richness of the bacterial community were comprehensively discussed. The results of this study showed that different previously cultivated crops altered the nutrient status of the soil, with changes in the ratio of NH4 +-N to NO3 --N having the most significant impact on tobacco. In CK, the ratio of NH4 +-N to NO3 --N was 1:24.2, T1-1:9.59, and T2-1:11.10. The composition of the bacterial community in tobacco-planting soil varied significantly depending on the previously cultivated crops. The richness and diversity of the bacterial community with different crops were considerably higher than without prior cultivation of different crops. The dominant bacteria in different treatments were Actinobacteriota, Proteobacteria, and Chloroflexi with their relative abundance differed. In conclusion, our study revealed significant differences in nutrient status, bacterial community diversity, and the richness of tobacco-planting soil after the preceding cultivation of different crops. Suitable crops should be selected to be previously cultivated in tobacco crop rotations in near future for sustainable agriculture.

Chemotaxis-mediated degradation of PAHs and heterocyclic PAHs under low-temperature stress by Pseudomonas fluorescens S01: Insights into the mechanisms of biodegradation and cold adaptation

As wellknown persistent contaminants, polycyclic aromatic hydrocarbons (PAHs) and heterocyclic polyaromatic hydrocarbons (Heterocyclic PAHs)'s fates in cryogenic environments are remains uncertain. Herein, strain S01 was identified as Pseudomonas fluorescens, a novel bacterium tolerant to low temperature and capable of degrading PAHs and heterocyclic PAHs. Strain S01 exhibited growth at 5-40 ℃ and degradation rate of mixed PAHs and heterocyclic PAHs reached 52% under low-temperature. Through comprehensive metabolomic, genomic, and transcriptomic analyses, we reconstructed the biodegradation pathway for PAHs and heterocyclic PAHs in S01 while investigating its response to low temperature. Further experiments involving deletion and replacement of methyl-accepting chemotaxis protein (MCP) confirmed its crucial role in enabling strain S01's adaptation to dual stress of low temperature and pollutants. Additionally, our analysis revealed that MCP was upregulated under cold stress which enhanced strain S01's motility capabilities leading to increased biofilm formation. The establishment of biofilm promoted preservation of distinct cellular membrane stability, thereby enhancing energy metabolism. Consequently, this led to heightened efficiency in pollutant degradation and improved cold resistance capabilities. Our findings provide a comprehensive understanding of the environmental fate of both PAHs and heterocyclic PAHs under low-temperature conditions while also shedding light on cold adaptation mechanism employed by strain S01.

Effect and potential mechanisms of sludge-derived chromium, nickel, and lead on soil nitrification: Implications for sustainable land utilization of digested sludge

Increasing occurrence of heavy metals (HMs) in sewage sludge threatens its widespread land utilization in China due to its potential impact on nutrient cycling in soil, requiring a better understanding of HM-induced impacts on nitrification. Herein, lab-scale experiments were conducted over 185-day, evaluating the effect of sludge-derived chromium (Cr3+), nickel (Ni2+), and lead (Pb2+) on soil nitrification at different concentrations. Quantitative polymerase chain reaction and linear regression results revealed an inhibitory sequence of gene abundance by HMs' labile fraction: ammonia-oxidizing bacteria (AOB)-ammonia monooxygenase (amoA)> nitrite oxidoreductase subunit alpha (nxrA)> nitrite oxidoreductase subunit beta (nxrB). The toxicity of HMs' incremental labile fraction decreased in the order of Ni2+>Cr3+>Pb2+, with respective threshold values of 5.01, 24.03 and 38.42 mg·kg-1. Furthermore, extending incubation time reduced HMs inhibition on ammonia oxidation, mainly related to their fraction bound to carbonate minerals. Random Forest analysis, variation partitioning analysis, and Mantel test indicated that soil physicochemical properties primarily affected nitrification genes, especially in the test of Cr3+ on AOB-amoA, nxrA, nxrB, Ni2+ for complete ammonia-oxidizing bacteria-amoA, and Pb2+ for nxrA and nxrB. These findings underline the importance of labile HMs fractions and soil physicochemical properties to nitrification, guiding the establishment of HM control standards for sludge utilization.

Multimedia distribution, partitioning, sources, comprehensive toxicity risk and co-occurrence network characteristics of trace elements in a typical Chinese shallow lake with high antibiotic risk

Although the combined pollution of trace elements and antibiotics has received extensive attention, the fate and toxicity risk of trace elements with high antibiotic risk are still unclear. The multimedia distributions, partitioning, sources, toxicity risks and co-occurrence network characteristics of trace elements in surface water (SW), overlying water (OW), pore water (PW) and sediment (Sedi) samples of 61 sites from Baiyangdian (BYD) Lake were investigated. The trace elements in the SW and OW are derived mainly from traffic and agricultural sources, and those in PW and Sedi samples are primarily from lithogenic and industrial sources. The total toxicity risk index (TRI) of nine trace elements (ΣTRI) in Sedi samples showed a very high toxicity risk (18.35 ± 8.84), and a high combined pollution toxicity risk (ΣΣTRI) was observed in PW (149.17 ± 97.52) and Sedi samples (46.37 ± 24.00). The co-occurrence network from SW to PW became more vulnerable. Generally, total antibiotics and TP may be keystones of trace elements in water and sediment. The high antibiotic risk significantly influenced ΣΣTRI in water samples but not in Sedi samples. The findings provide new implications for the monitoring and control of combined antibiotic-trace element pollution in shallow lakes.

Coexistence of microplastics and Cd alters soil N transformation by affecting enzyme activity and ammonia oxidizer abundance

Interactions between heavy metal and microplastics represent a serious threat to ecosystems and human health, but the effect of their coexistence on the soil N transformation processes is unclear. The mechanism in which metal-polluted soil reacts to additional microplastics stress and their toxicology interactions on soil N transformation were determined by investigating the dynamics of soil microbial N transformation in response to Cd stress and different doses of polythene (PE) microplastics by conducting a 14 days aerobic 15N microcosmic incubation experiment. The gross nitrification rates (n_gross) were decreased by 7.47% and 12.5% in the 1% and 2% (w/w) PE groups, respectively, through the direct effect on enzyme activity (β-glucosidase, N-acetylglucosaminidase, and leucine-aminopeptidase) and the abundance and community composition of ammonia oxidizer. It also exerted indirect effect by reducing nitrification substrate concentrations. PE microplastics (>1% [w/w]) significantly increased the gross N immobilization rate, and this change could have been driven by C/N stoichiometry. Cd stress alone led to a rapid short-term mineralization-immobilization turnover (1.67 times of the control). However, such effect was offset when Cd coexisted with PE microplastics, possibly because Cd was directly adsorbed by PE microplastics, and/or microplastics satisfied the C demand by microorganisms under Cd stress. Our findings demonstrated that the coexistence of microplastics and Cd significantly altered soil N nitrification and immobilization, which would change the N bioavailability in soil and alter the effect N cycling on the ecological environment.

Cadmium accumulation in brown rice (Oryza sativa L.) depends on environmental factors and nutrient transport: A three-year field study

Cadmium (Cd) accumulation in brown rice is a complex process in agroecosystems and is influenced by multiple factors, such as climate, soil properties, and nutrient transport. However, during the Cd transport process (soil-root-straw-brown rice), it remains unclear how Cd concentration in brown rice (BCd) is causal relationship to environmental factors and nutrient transport. The differences in precipitation, soil properties, nutrient transport, and Cd transport were studied through a three-year fixed-point field trial and linked them to the standard of Cd and nutrient absorption and transport processes. The results showed that the available Cd concentration (ACd), and BCd in 2020 were lower than those in 2019 and 2021, but monthly precipitation (MP) was higher in 2020 than in 2019 and 2021. The MP and niche metrics were significantly negatively associated with ACd and BCd. However, the relationship between the form and location of different nutrient elements and Cd in roots, Cd in straws, and BCd also varied during the transport of nutrient elements and Cd from soil to root to straw to brown rice. Structural equation modelling analysis showed that nitrogen (N 15.5 %), phosphorus (P 14.1 %), silicon (Si 4.2 %), and iron (Fe 7.6 %) transport were more closely related to BCd than to potassium (K), calcium (Ca), magnesium (Mg), and manganese (Mn). The increase in MP significantly inhibited the increase in BCd, whereas the MP led to a decrease in BCd by affecting the transport of N and Fe. Among them, Si, Fe, and BCd had indirect causal relationships, whereas N, P, and BCd had direct causal relationships. Particularly, P is a crucial nutrient in reducing BCd in the Cd transport process. Our results highlight a strong causal relationship between environmental factors and nutrient transport and BCd, and provide a theoretical basis for fertiliser application in Cd-contaminated agroecosystems.

Cadmium reduced methane emissions by stimulating methane oxidation in paddy soils

Flooded rice paddy fields are a significant source of anthropogenic methane (CH4) emissions. Cadmium (Cd) is one of the most common and toxic contaminants in paddy soils. However, little is known about how the soil microbial communities associated with CH4 emissions respond to the increasing Cd-stress in paddies. In this study, we employed isotopically 13C-labelled CH4, high-throughput sequencing analysis, and gene quantification analysis to reveal the effect and mechanism of Cd on CH4 emissions in paddy soils. Results showed that 4.0 mg kg-1 Cd addition reduced CH4 emissions by 16-99% in the four tested paddy soils, and significantly promoted the transformation of 13CH4 to 13CO2. Quantitative polymerase chain reaction (qPCR) demonstrated that Cd addition increased the abundances of pmoA gene, the ratios of methanogens to methanotrophs (mcrA/pmoA) showed a positive correlation with CH4 emissions (R2 = 0.798, p < 0.01). Furthermore, the composition of the microbial community containing the pmoA gene was barely affected by Cd addition (p > 0.05). This observation was consistent with the findings of a pure incubation experiment where methanotrophs exhibited high tolerance to Cd. We argue that microbial feedback to Cd stress amplifies the contribution of methanotrophs to CH4 oxidation in rice fields through the complex interactions occurring among soil microbes. Our study highlights the overlooked association between Cd and CH4 dynamics, offering a better understanding of the role of rice paddies in global CH4 cycling.

Immobilization of zinc and cadmium by biochar-based sulfidated nanoscale zero-valent iron in a co-contaminated soil: Performance, mechanism, and microbial response

Mining and smelting of mineral resources causes excessive accumulation of potentially toxic metals (PTMs) in surrounding soils. Here, biochar-based sulfidated nanoscale zero-valent iron (SNZVI/BC) was designed via a one-step liquid phase reduction method to immobilize cadmium (Cd) and zinc (Zn) in a copolluted arable soil. A 60 d soil incubation experiment revealed that Cd and Zn immobilization efficiency by 6 % SNZVI/BC (25.2-26.2 %) was higher than those by individual SNZVI (13.9-18.0 %) or biochar (14.0-19.3 %) based on the changes in diethylene triamine pentaacetic acid (DTPA)-extractable PTM concentrations in soils, exhibiting a synergistic effect. Cd2+ or Zn2+ replaced isomorphously Fe2+ in amorphous ferrous sulfide, as revealed by XRD, XPS, and high-resolution TEM-EDS, forming metal sulfide precipitates and thus immobilizing PTMs. PTM immobilization was further enhanced by adsorption by biochar and oxidation products (Fe2O3 and Fe3O4) of SNZVI via precipitation and surface complexation. SNZVI/BC also increased the concentration of dissolved organic carbon and soil pH, thus stimulating the abundances of beneficial bacteria, i.e., Bacilli, Clostridia, and Desulfuromonadia. These functional bacteria further facilitated microbial Fe(III) reduction, production of ammonium and available potassium, and immobilization of PTMs in soils. The predicted function of the soil microbial community was improved after supplementation with SNZVI/BC. Overall, SNZVI/BC could be a promising functional material that not only immobilized PTMs but also enhanced available nutrients in cocontaminated soils.

Enhancing plant growth in biofertilizer-amended soil through nitrogen-transforming microbial communities

Biofertilizers have immense potential for enhancing agricultural productivity. However, there is still a need for clarification regarding the specific mechanisms through which these biofertilizers improve soil properties and stimulate plant growth. In this research, a bacterial agent was utilized to enhance plant growth and investigate the microbial modulation mechanism of soil nutrient turnover using metagenomic technology. The results demonstrated a significant increase in soil fast-acting nitrogen (by 46.7%) and fast-acting phosphorus (by 88.6%) upon application of the bacterial agent. This finding suggests that stimulated soil microbes contribute to enhanced nutrient transformation, ultimately leading to improved plant growth. Furthermore, the application of the bacterial agent had a notable impact on the accumulation of key genes involved in nitrogen cycling. Notably, it enhanced nitrification genes (amo, hao, and nar), while denitrification genes (nir and nor) showed a slight decrease. This indicates that ammonium oxidation may be the primary pathway for increasing fast-acting nitrogen in soils. Additionally, the bacterial agent influenced the composition and functional structure of the soil microbial community. Moreover, the metagenome-assembled genomes (MAGs) obtained from the soil microbial communities exhibited complementary metabolic processes, suggesting mutual nutrient exchange. These MAGs contained widely distributed and highly abundant genes encoding plant growth promotion (PGP) traits. These findings emphasize how soil microbial communities can enhance vegetation growth by increasing nutrient availability and regulating plant hormone production. This effect can be further enhanced by introducing inoculated microbial agents. In conclusion, this study provides novel insights into the mechanisms underlying the beneficial effects of biofertilizers on soil properties and plant growth. The significant increase in nutrient availability, modulation of key genes involved in nitrogen cycling, and the presence of MAGs encoding PGP traits highlight the potential of biofertilizers to improve agricultural practices. These findings have important implications for enhancing agricultural sustainability and productivity, with positive societal and environmental impacts.

Arsenic pollution from human activities drives changes in soil microbial community characteristics

Soil arsenic (As) pollution not only decreases plant productivity but also soil quality, in turn hampering sustainable agricultural development. Despite the negative effects of As contamination on rice yield and quality being reported widely, the responses of microbial communities and co-occurrence networks in paddy soil to As pollution have not been explored. Here, based on high-throughput sequencing technologies, we investigated bacterial abundance and diversity in paddy soils with different levels of As contamination, and constructed associated microbial co-occurrence networks. As pollution reduced soil bacterial diversity significantly (p < 0.001). In addition, bioavailable As concentrations were negatively correlated with Actinobacteria and Acidobacteria relative abundance (p < 0.05). Conversely, As pollution had a positive relationship with Chloroflexi, Betaproteobacteria, and Bacteroidetes relative abundance (p < 0.05). Firmicutes relative abundance decreased with an increase in total As concentration. The ecological clusters and key groups in bacterial co-occurrence networks exhibited distinct trends with an increase in As pollution. Notably, Acidobacteria play an important role in maintaining microbial networks in As contaminated soils. Overall, we provide empirical evidence that As contamination influences soil microbial community structure, posing a threat to soil ecosystem health and sustainable agriculture.

Metagenomics reveals taxon-specific responses of soil nitrogen cycling under different fertilization regimes in heavy metal contaminated soil

Soil deficiency, cyclic erosion, and heavy metal pollution have led to fertility loss and ecological function decline in mining areas. Fertilization is an important way to rapidly replenish soil nutrients, which have a major influence on the soil nitrogen cycling process, but different fertilization regimes have different impacts on soil properties and microbial functional potentials. Here, metagenomic sequencing was used to investigate the different responses of key functional genes of microbial nitrogen cycling to fertilization regimes and explore the potential effects of soil physicochemical properties on the key functional genes. The results indicated that AC-HH (ammonium chloride-high frequency and concentration) treatment significantly increased the gene abundance of norC (13.40-fold), nirK (5.46-fold), and napA (5.37-fold). U-HH (urea-high frequency and concentration) treatment significantly increased the gene abundance of hao (6.24-fold), pmoA-amoA (4.32-fold) norC (7.00-fold), nosZ (3.69-fold), and nirK (6.88-fold). Functional genes were distributed differently among the 10 dominant phyla. The nifH and nifK genes were distributed only in Proteobacteria. The hao gene was distributed in Gemmatimonadetes, Nitrospirae and Proteobacteria. Fertilization regimes caused changes in functional redundancy in soil, and nirK and nirB, which are involved in denitrification, were present in different genera. Fertilization regimes with high frequency and high concentration were more likely to increase the gene abundance at the genus level. In summary, this study provides insights into the taxon-specific response of soil nitrogen cycling under different fertilization regimes, where changes in fertilization regimes affect microbial nitrogen cycling by altering soil physicochemical properties in a complex dynamic environment.

Naturally aged polylactic acid microplastics stunted pakchoi (Brassica rapa subsp. chinensis) growth with cadmium in soil

Biodegradable microplastics (BMPs) and cadmium (Cd) are posing threats to agro-systems especially to plants and current studies mostly used virgin BMPs to explore their ecological effects. However, effects of naturally aged BMPs and their combined effects with Cd on pakchoi are yet to be unraveled. Therefore, this study incubated naturally aged polylactic acid (PLA) MPs through soil aging process and investigated the single and combined effects of Cd and PLA MPs (virgin and aged) on pakchoi (Brassica rapa subsp. chinensis) morphology, antioxidant systems and soil microbial activities. Our results found that after being deposited in soil for six months, aged PLA (PLAa) MPs formed with a fractured surface, demonstrating more detrimental effects on pakchoi than virgin ones. PLA/PLAa MPs and Cd stunted pakchoi growth, caused oxidative stress and altered the biophysical environment in soil, separately. Moreover, co-existence of PLA/PLAa MPs and Cd caused greater damages to pakchoi than applied alone. The co-presence of PLAa MPs and Cd inhibited pakchoi biomass accumulation rate by 92.2 % compared with the no-addition group. The results unraveled here emphasized BMPs, especially aged BMPs, could trigger negative effects on agro-systems with heavy metals. These findings will give reference to future holistic assessments of BMPs' ecological effects.

Niche differentiation and influencing factors of nitrite oxidation bacteria Nitrospira in sediments of the Luan River estuary in China

In the estuarine sediment, the nitrite oxidation process mediated by bacteria significantly influences nitrification. Nitrospira is the most widely distributed nitrite-oxidizing bacteria (NOB) and can adapt to various environments. In this study, the Nitrospira-specific primer nxrB 169F-638R was used to analyze the microbial communities in the sediments of low-, middle-, and high-level zones in the Luan River estuary. The structure of the microbial community and its response to environmental factors were also assessed. The abundance and diversity of Nitrospira were the highest in the low-level zone and lowest in the high-level zone. Lineage II and lineage IV were the dominant Nitrospira at 43.58% and 32.09%, respectively. The distribution pattern of Nitrospira was also affected by complex environmental factors, such as the concentration of NH4+, Fe, and Cu cations. This study provides novel insights into the niche differentiation and adaptation strategies of Nitrospira in an estuarine sediment environment and will help to facilitate single-step nitrification.

Sewage sludge application stimulated soil N2O emissions with a low heavy metal pollution risk in Eucalyptus plantations

Sewage sludge (SS) has been extensively used as an alternative fertilizer in forest plantations, which are beneficial in supplying timbers and mitigating climate change. However, whether the extra nitrogen (N) applied by SS would enhance the soil nitrous oxide (N₂O) emission, an important greenhouse gas, in forest plantations have not been well understood. The objective of this study is to evaluate the ecological effects of SS application on soils, by investigating the soil N₂O emission and the toxicity of the potentially toxic elements (PTEs) in soil. A field fertilization experiment was conducted in Eucalyptus plantations with four fertilization rates (0 kg m^-2, 1.5 kg m^-2, 3.0 kg m^-2, and 4.5 kg m^-2). The soil N₂O emissions were monitored at a soil depth of 0-10 cm using static chamber method, soil chemical properties, and PTEs were determined at soil depths of 0-10 cm, 10-20 cm, and 20-40 cm. The average soil N₂O emission rate was 8.1 μg N₂O-N h^-1 m^-2 in plots without SS application (control). The application of SS significantly increased the soil N₂O emissions by 7-10 times as to control. The increased N₂O emissions were positively related to the soil total phosphorus and nitrogen and negatively correlated with copper and zinc, which increased with the SS application. However, the potential ecological risk index (E_i) and the comprehensive potential ecological risk index (RI) of PTEs were lower than 40 and 150 respectively, which indicating a low toxicity of PTEs to soil health. After seven months of SS application, the priming effects of SS on soil N₂O emissions gradually diminished. These findings suggest that the application of SS may increase N₂O emissions at the initial stages of application (<7 months) and may have a low PTEs pollution risk, even at a high SS addition rate (4.5 kg m^-2).

Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil

Viruses are critical for regulating microbial communities and biogeochemical processes affecting carbon/nutrient cycling. However, the role of soil phages in controlling microbial physiological traits and intrinsic dissolved organic matter (DOM) properties remains largely unknown. Herein, microcosm experiments with different soil phage concentrates (including no-added phages, inactive phages, and three dilutions of active phages) at two temperatures (15 °C and 25 °C) were conducted to disclose the nutrient and DOM dynamics associated with viral lysing. Results demonstrated three different phases of viral impacts on CO2 emission at both temperatures, and phages played a role in maintaining Q10 within bounds. At both temperatures, microbial nutrient limitations (especially P limitation) were alleviated by viral lysing as determined by extracellular enzyme activity (decreased Vangle with active phages). Additionally, the re-utilization of lysate-derived DOM by surviving microbes stimulated an increase of microbial metabolic efficiency and recalcitrant DOM components (e.g., SUV254, SUV260 and HIX). This research provides direct experimental evidence that the "viral shuttle" exists in soils, whereby soil phages increase recalcitrant DOM components. Our findings advance the understanding of viral controls on soil biogeochemical processes, and provide a new perspective for assessing whether soil phages provide a net "carbon sink" vs. "carbon source" in soils.

Heavy metal effects on multitrophic level microbial communities and insights for ecological restoration of an abandoned electroplating factory site

The response of soil microbes to heavy metal pollution provides a metric to evaluate the soil health and ecological risks associated with heavy metal contamination. However, a multitrophic level perspective of how soil microbial communities and their functions respond to long-term exposure of multiple heavy metals remains unclear. Herein, we examined variations in soil microbial (including protists and bacteria) diversity, functional guilds and interactions along a pronounced metal pollution gradient in a field surrounding an abandoned electroplating factory. Given the stressful soil environment resulting from extremely high heavy metal concentrations and low nutrients, beta diversity of protist increased, but that of bacteria decreased, at high versus low pollution sites. Additionally, the bacteria community showed low functional diversity and redundancy at the highly polluted sites. We further identified indicative genus and "generalists" in response to heavy metal pollution. Predatory protists in Cercozoa were the most sensitive protist taxa with respect to heavy metal pollution, whereas photosynthetic protists showed a tolerance for metal pollution and nutrient deficiency. The complexity of ecological networks increased, but the communication among the modules disappeared with increasing metal pollution levels. Subnetworks of tolerant bacteria displaying functional versatility (Blastococcus, Agromyces and Opitutus) and photosynthetic protists (microalgae) became more complex with increasing metal pollution levels, indicating their potential for use in bioremediation and restoration of abandoned industrial sites contaminated by heavy metals.

Soil physiochemical properties and bacterial community changes under long-term polycyclic aromatic hydrocarbon stress in situ steel plant soils

In situ soils were collected at two depths in Jinan and Hangzhou steel plants, which both have a long history of operation and polycyclic aromatic hydrocarbons (PAHs) contamination. The richness of 16 S rRNA gene and bacterial community of the soil were determined by real-time PCR and high-throughput sequencing. Soil physicochemical properties, PAHs contamination characteristics, and their interrelationships were also analyzed. In general, the PAHs contamination decreased with increasing soil depths. The physicochemical properties and PAH concentration of soil had synergistic impacts on the composition of the bacterial community. The long-term higher PAHs stress in Hangzhou contaminated soil (982 mg kg^-1) increased the bacterial abundance and diversity, while that of Jinan contaminated soil (63 mg kg^-1) decreased bacterial abundance and diversity. The pH value, sand content of the soil were positively correlated (P < 0.05) with the bacterial diversity including Simpson, Shannon, Observed_species and Chao1 indexes., and the other soil properties exhibited negative correlations with different strengths. The abundances of Curvibacter, Pseudomonas, Thiobacillus, Lysobacter, and Limnobacter were positively correlated with the PAHs concentration (P < 0.01). Additionally, the network structure of the PAHs-contaminated soils was more complex compared to that of uncontaminated soils, with stronger linkages and correlations between the different bacteria. These findings provide a theoretical basis for microbial remediation of PAHs-polluted soil.

Bidirectional potential effects of DON transformation in vadose zones on groundwater nitrate contamination: Different contributions to nitrification and denitrification

The main cause of groundwater nitrate contamination is the continual downward migration of dissolved nitrogen (N) in vadose zone with leachate. In recent years it has been found that dissolved organic N (DON) rise to forefront due to its great migration capacity and environmental effects. However, it remains unknown how the transformation behaviors of DONs with different properties in vadose zone profile may impact N forms distribution and groundwater nitrate contamination. To address the issue, we conducted a series of 60-day microcosm incubation experiments to investigate the effects of various DONs transformation behaviors on the distribution of N forms, microbial communities, and functional genes. The results revealed that urea and amino acids mineralized immediately after substrates addition. By contrast, amino sugars and proteins caused less dissolved N throughout entire incubation period. The transformation behaviors could substantially alter the microbial communities. Moreover, we discovered that amino sugars remarkably increased the absolute abundances of denitrification function genes. These results delineated that DONs with unique characteristics (such as amino sugar) promoted different N geochemical processes in distinct ways: different contributions to nitrification and denitrification. This can provide new insights for nitrate non-point source pollution control in groundwater.

Trade-offs between fertilizer-N availability and Cd pollution potential under crop straw incorporation by 15 N stable isotopes in rice

Application of crop residues and chemical nitrogen (N) fertilizer is a conventional practice for achieving high yield in a rice system. However, the fallacious combination of N fertilizers with crop straw not only significantly reduces the N use efficiencies (NUEs) but also leads to serious environmental problems. The present study employed five treatments including no N fertilization and no straw incorporation (ck), N fertilization incorporation only (S0), N fertilization with 40% straw (S₄₀), N fertilization with 60% straw (S₆₀), and N fertilization with 100% straw (S₁₀₀) to improve N use efficiency as well as reduced Cd distribution in rice. The crop yields were largely enhanced by fertilization ranging from 13 to 52% over the straw addition treatments. Compared with ck, N fertilizer input significantly decreased soil pH, while DOC contents were raised in response to straw amendment, reaching the highest in S₆₀ and S₁₀₀ treatments, respectively. Moreover, straw addition substantially impacted the Cd accumulation and altered the bacterial community structure. The soil NH₄⁺-N concentration under S₀ performed the maximum in yellow soil, while the minimum in black soil compared to straw-incorporated pots. In addition, the soil NO₃^--N concentration in straw-incorporated plots tended to be higher than that in straw-removed plots in both soils, indicating that crop straw triggering the N mineralization was associated with native soil N condition. Furthermore, the NUE increased with ¹⁵ N uptake in the plant, and the residual ¹⁵ N in soil was increased by 26.8% with straw addition across four straw application rates. Overall, our study highlights the trade-offs between straw incorporation with N fertilizer in eliminating potential Cd toxicity, increasing fertilizer-N use efficiencies and help to provide a feasible agricultural management.

Active tailings disturb the surrounding vegetation soil fungal community: Diversity, assembly process and co-occurrence patterns

Soil fungi play an important role in the soil biogeochemical cycle and are important biological indicators for the ecological remediation of mine tailings contaminated sites, therefore understanding the characteristics of soil fungal communities is a key aspect of pollution remediation. However, the influence of biological factors on the characteristics of fungal community diversity; assembly mechanisms and co-occurrence patterns of fungal community along environmental gradients around tailings are not well understood. In this study, soil samples from forest, agriculture and grass around tailings were collected to reveal the assembly mechanisms and co-occurrence patterns of soil fungal community and to quantify the contribution of abiotic and biotic factors to fungal diversity. The results suggest that vegetation types and Cu concentration together drive the distribution of fungal diversity. We found that Exophiala has potential as a biomarker species indicative of restoration progress. Increased environmental stress accelerates the process of changing fungal community assemblages from stochastic to deterministic, while also allowing fungal communities tend to resist tailings-induced environmental stresses through species coexistence. Together, this study provides new insights into the influence of biological factors on fungal community diversity, as well as revealing mechanisms of fungal community assembly and co-occurrence patterns, which are important for understanding the maintenance mechanisms of fungal community diversity and ecological remediation of tailings-contaminated soils.

Nitrogen transformation promotes the anaerobic degradation of PAHs in water level fluctuation zone of the Three Gorges Reservoir in Yangtze River, China: Evidences derived from in-situ experiment

Polycyclic aromatic hydrocarbons (PAHs) pose a great threat to human health and ecological system safety. The interception of nitrogen is common found in the riparian zone. However, there is no evidence on how nitrogen addition affects the anaerobic degradation of PAHs in soil of the water-level-fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR) in Yangtze River, China. Here, we investigated the PAHs degradation rate, the variation of key functional genes and microbial communities after nitrogen addition in soil that experienced a flooding period of water-level-fluctuation. The results revealed that the ∑16PAHs were decreased 16.19 %-36.65 % and more 3-5-rings PAHs were biodegraded with nitrogen addition in WLFZ. The most genes involved in PAHs-anaerobic degradation and denitrification were up-regulated by nitrate addition, and phyla Firmicutes, Actinobacteria and Proteobacteria were more advantages in nitrogen addition groups. The Tax4Fun based genome function analysis revealed that the microbial activity of PAHs-degradation increased with nitrate addition. The co-occurrence network analysis indicated that nitrogen addition accelerated the metabolism of nitrogen and PAHs. It is the first time to provide the direct experimental evidences that nitrogen transformation in the WLFZ soil promotes anaerobic PAHs degradation. This work is of importance to understand the effect of nitrogen intercepted in the WLFZ soil of TGR in Yangtze River, China.

Effects of microplastics on cadmium accumulation by rice and arbuscular mycorrhizal fungal communities in cadmium-contaminated soil

Both microplastics (MPs) and cadmium (Cd) are common contaminants in soil-rice systems, but their combined effects remain unknown. Thereby, we explored the effects of three MPs, i.e., polyethylene terephthalate (PET), polylactic acid (PLA), and polyester (PES), on Cd accumulation in rice and the community diversity and structure of arbuscular mycorrhizal fungi (AMF) in soil spiked with or without Cd. Results showed that 2% PLA decreased shoot biomass (-28%), but PET had a weaker inhibitive effect. Overall, Cd alone did not significantly change shoot and root biomass and increased root biomass in combination with 0.2% PES. MPs generally increased soil Cd availability but decreased Cd accumulation in rice tissues. Both MPs and Cd improved the bioavailability and uptake of Fe and Mn in rice roots. MPs altered the diversity and community composition of AMF, depending on their type and dose and co-existing Cd. Overall, 2% PLA caused the most distinct changes in soil properties, plant growth and Cd accumulation, and AMF communities, but showed no synergistic interactions with Cd. In conclusion, MPs can mediate rice performance and Cd accumulation via altering soil properties, nutrient uptake, and root mycorrhizal communities, and biodegradable PLA MPs thought environment-friendly can exhibit higher phytotoxicity than conventional MPs.

Response mechanisms of bacterial communities and nitrogen cycle functional genes in millet rhizosphere soil to chromium stress

Introduction

A growing amount of heavy metal contamination in soil disturbs the ecosystem's equilibrium, in which microbial populations play a key role in the nutrient cycle of soils. However, given the different sensitivity of microbial communities to different spatial and temporal scales, microbial community structure and function also have varied response mechanisms to different heavy metal contaminated habitats.

Methods

In this study, samples were taken prior to Cr stress (CK) and 6 h and 6 days after Cr stress (Cr_6h, Cr_6d) in laboratory experiments. High-throughput sequencing revealed trends in the structure and diversity of the bacterial communities, and real-time fluorescence quantitative polymerase chain reaction (qPCR) was used to analyze trends in nitrogen cycle functional genes (AOA-amoA, AOB-amoA, narG, nirK, and nifH).

Results

The findings showed that (1) the composition structure of the soil bacterial community changed considerably in Cr-stressed soils; α-diversity showed significant phase transition characteristic from stress to stability (p < 0.05). (2) With an overall rising tendency, the abundance of the nitrogen cycle functional genes (AOA-amoA and AOB-amoA) decreased considerably before increasing, and α-diversity dramatically declined (p < 0.05). (3) The redundancy analysis (RDA) and permutational multivariate analysis of variance (PERMANOVA) tests results showed that the soil physicochemical parameters were significantly correlated with the nitrogen cycle functional genes (r: 0.4195, p < 0.01). Mantel analysis showed that available nitrogen (N), available potassium (K), and available phosphorus (P) were significantly correlated with nifH (p = 0.006, 0.008, 0.004), and pH was highly significantly correlated with nifH (p = 0.026). The PLS-ME (partial least squares path model) model further demonstrated a significant direct effect of the soil physicochemical parameters on the nitrogen cycling functional genes.

Discussion

As a result, the composition and diversity of the bacterial community and the nitrogen cycle functional genes in Cr-stressed agricultural soils changed considerably. However, the influence of the soil physicochemical parameters on the functional genes involved in the nitrogen cycle was greater than that of the bacterial community. and Cr stress affects the N cycling process in soil mainly by affecting nitrification. This research has significant practical ramifications for understanding the mechanisms of microbial community homeostasis maintenance, nitrogen cycle response mechanisms, and soil remediation in heavy metal-contaminated agricultural soils.

Conceptual methodological framework for the resilience of biogeochemical services to heavy metals stress

The idea of linking stressors, services providing units (SPUs), and ecosystem services (ES) is ubiquitous in the literature, although is currently not applied in areas contaminated with heavy metals (HMs), This integrative literature review introduces the general form of a deterministic conceptual model of the cross-scale effect of HMs on biogeochemical services by SPUs with a feedback loop, a cross-scale heuristic concept of resilience, and develops a method for applying the conceptual model. The objectives are 1) to identify the clusters of existing research about HMs effects on ES, biodiversity, and resilience to HMs stress, 2) to map the scientific fields needed for the conceptual model's implementation, identify institutional constraints for inter-disciplinary cooperation, and propose solutions to surpass them, 3) to describe how the complexity of the cause-effect chain is reflected in the research hypotheses and objectives and extract methodological consequences, and 4) to describe how the conceptual model can be implemented. A nested analysis by CiteSpace of a set of 16,176 articles extracted from the Web of Science shows that at the highest level of data aggregation there is a clear separation between the topics of functional traits, stoichiometry, and regulating services from the typical issues of the literature about HMs, biodiversity, and ES. Most of the resilience to HMs stress agenda focuses on microbial communities. General topics such as the biodiversity-ecosystem function relationship in contaminated areas are no longer dominant in the current research, as well as large-scale problems like watershed management. The number of Web of Science domains that include the analyzed articles is large (26 up to 87 domains with at least ten articles, depending on the sub-set), but thirteen domains account for 70-80% of the literature. The complexity of approaches regarding the cause-effect chain, the stressors, the biological and ecological hierarchical level and the management objectives was characterized by a detailed analysis of 60 selected reviews and 121 primary articles. Most primary articles approach short causal chains, and the number of hypotheses or objectives by article tends to be low, pointing out the need for portfolios of complementary research projects in coherent inter-disciplinary programs and innovation ecosystems to couple the ES and resilience problems in areas contaminated with HMs. One provides triggers for developing innovation ecosystems, examples of complementary research hypotheses, and an example of technology transfer. Finally one proposes operationalizing the conceptual methodological model in contaminated socio-ecological systems by a calibration, a sensitivity analysis, and a validation phase.

Submerged zone and vegetation drive distribution of heavy metal fractions and microbial community structure: Insights into stormwater biofiltration system

Biofiltration system is a widely used stormwater treatment option that is effective in removing heavy metals. The concentration and distribution of heavy metal fractions in biofiltration filter media, as well as the microbiota composition affected by the design parameters, are relatively novel concepts that require further research. A laboratory-scale column study was conducted to investigate the microbial community and the fractionation of heavy metals (Pb, Cu, Cr, and Cd) extracted from filter media samples, subjected to the presence of vegetation, submerged zone (SZ), and major environmental parameters (pH, water content). Sequential extractions revealed that, compared to the three other fractions (exchangeable fraction, reducible fraction, and oxidizable fraction), the residual fraction was the most represented for each metal (41 - 82 %). As a result, vegetation was found to reduce pH value, and significantly decrease the concentration of the exchangeable fraction of Pb in the middle layer, and the oxidizable fraction of Pb, Cu, Cd, and Cr in the middle and bottom layers (p < 0.05). The formation of an anoxic environment by submerged zone settlements resulted in a significant decrease in the concentration of reducible fractions and a significant increase in the concentration of oxidizable fractions for four heavy metals (p < 0.05). In addition, the analysis of the microbiota showed that the diversity and richness of microorganisms increased in the presence of SZ and plants. The dominant phylum in biofiltration was Proteobacteria, followed by Firmicutes, Bacteroidetes, Acidobacteria, and Actinobacteria as major phyla. Heavy metal fractions could regulate the structure of microbial communities in biofiltration. The findings of this study would enrich our understanding of the improvement of multi-metal-contaminated runoff treatment and highlight the impact of design parameters and heavy metal fractionation on microbial community structure in the biofiltration system.

Structural and functional characteristics of soil microbial communities in response to different ecological risk levels of heavy metals

Objective

The potential ecological risk index (RI) is the most commonly used method to assess heavy metals (HMs) contamination in soils. However, studies have focused on the response of soil microorganisms to different concentrations, whereas little is known about the responses of the microbial community structures and functions to HMs at different RI levels.

Methods

Here, we conducted soil microcosms with low (L), medium (M) and high (H) RI levels, depending on the Pb and Cd concentrations, were conducted. The original soil was used as the control (CK). High-throughput sequencing, qPCR, and Biolog plate approaches were applied to investigate the microbial community structures, abundance, diversity, metabolic capacity, functional genes, and community assembly processes.

Result

The abundance and alpha diversity indices for the bacteria at different RI levels were significantly lower than those of the CK. Meanwhile, the abundance and ACE index for the fungi increased significantly with RI levels. Acidobacteria, Basidiomycota and Planctomycetes were enriched as the RI level increased. Keystone taxa and co-occurrence pattern analysis showed that rare taxa play a vital role in the stability and function of the microbial community at different RI levels. Network analysis indicates that not only did the complexity and vulnerability of microbial community decrease as risk levels increased, but that the lowest number of keystone taxa was found at the H level. However, the microbial community showed enhanced intraspecific cooperation to adapt to the HMs stress. The Biolog plate data suggested that the average well color development (AWCD) reduced significantly with RI levels in bacteria, whereas the fungal AWCD was dramatically reduced only at the H level. The functional diversity indices and gene abundance for the microorganisms at the H level were significantly lower than those the CK. In addition, microbial community assembly tended to be more stochastic with an increase in RI levels.

Conclusion

Our results provide new insight into the ecological impacts of HMs on the soil microbiome at different risk levels, and will aid in future risk assessments for Pb and Cd contamination.

Individual and combined contamination of oxytetracycline and cadmium inhibited nitrification by inhibiting ammonia oxidizers

Introduction

The large-scale development of animal husbandry and industrialization lead to more and more serious co-contamination from heavy metals and antibiotics in soils. Ecotoxic effects of residues from antibiotics and heavy metals are of increasing concern.

Materials and Methods

In this study, oxytetracycline (OTC) and cadmium (Cd) were selected as target pollutants to evaluate the individual and combined effects on nitrification process using four different soil types sampled from North to South China through a 56-day incubation experiment.

Results and Discussion

The results demonstrated that the contaminations of OTC and Cd, especially combined pollution had significant inhibitory effects on net nitrification rates (NNRs) as well as on AOA and AOB abundance. The toxic effects of contaminants were greatly enhanced with increasing OTC concentration. AOB was more sensitive than AOA to exogenous contaminants. And the interaction effects of OTC and Cd on ammonia oxidizers were mainly antagonistic. Furthermore, Cd contaminant (with or without OTC) had indirect effects on nitrification activity via inhibiting mineral N and AOA/AOB, while OTC alone indirectly inhibited nitrification activity by inhibiting ammonia oxidizers. The results could provide theoretical foundation for exploring the eco-environmental risks of antibiotics and heavy metals, as well as their toxic effects on nitrification processes.

Enhancing network complexity and function of soil bacteria by thiourea-modified biochar under cadmium stress in post-mining area

Cadmium (Cd) pollution cause severe stress to soil microorganisms and biochar utilized for its ability to immobilize Cd in the soil effectively. However, the influence of biochar on the structure and function of the bacterial network under Cd stress is unclear. This research reports a pot experiment conducted to investigate the impact of 2.0% Italian poplar bark biochar (PB), 2.0% thiourea-modified biochar (TP), and control treatment (CK) on the complexity, stability and functional properties of the bacterial community under Cd stress. The results showed that: (1) Biochar increased the diversity of soil bacterial consortia under Cd stress (p < 0.05), and the diversity index demonstrated as order of CK < PB < TP; (2) Compared with CK network, the nodes number of PB and TP treatments networks were much higher, while the modularity and transitivity increased by 0.04% and 37.6%, 2.45% and 1.12%, respectively. The biochar amendment increased the stability and complexity of the network; (3) PICRUSt2 prediction results show that Xenobiotics biodegradation and metabolism membrane transport of TP treatment increased 62.52% and 53.62% compared with CK, respectively, which could be related to the decrease in Cd content according to principal component analysis. (4) The reduction of leaching Cd content caused network complexity and bacterial function changes by biochar amendment. TP amendment enhanced the complexity and stability of soil bacterial community under Cd stress, which will provide a scientific basis for in situ remediations of Cd-contaminated soils.

Microbial interactions enhanced environmental fitness and expanded ecological niches under dibutyl phthalate and cadmium co-contamination

Co-contamination of organic pollutants and heavy metals is universal in the natural environment. Dibutyl phthalate (DBP), a typical plasticizer, frequently coexists with cadmium (Cd) in nature. However, little attention has been given to the impacts of co-contamination by DBP and Cd on microbial communities or the responses of microbes. To address this, a microcosm experiment was conducted by supplying the exogenous DBP-degrading bacterium Glutamicibacter nicotianae ZM05 to investigate the interplay among DBP-Cd co-contamination, the exogenous DBP-degrading bacterium G. nicotianae ZM05, and indigenous microorganisms. To adapt to co-contamination stress, microbial communities adjust their diversity, interactions, and functions. The stability of the microbial community decreased under co-contamination, as evidenced by lower diversity, simpler network, and fewer ecological niches. Microbial interactions were strengthened, as evidenced by enriched pathways related to microbial communications. Meanwhile, interactions between microorganisms enhanced the environmental fitness of the exogenous DBP-degrading bacterium ZM05. Based on co-occurrence network prediction and coculture experiments, metabolic interactions between the non-DBP-degrading bacterium Cupriavidus metallidurans ZM16 and ZM05 were proven. Strain ZM16 utilized protocatechuic acid, a DBP downstream metabolite, to relieve acid inhibition and adsorbed Cd to relieve toxic stress. These findings help to explain the responses of bacterial and fungal communities to DBP-Cd co-contamination and provide new insights for the construction of degrading consortia for bioremediation.

Rhizobacteria communities reshaped by red mud based passivators is vital for reducing soil Cd accumulation in edible amaranth

Red mud (RM) was constantly reported to immobilize soil cadmium (Cd) and reduce Cd uptake by crops, but few studies investigated whether and how RM influenced rhizobacteria communities, which was a vital factor determining Cd bioavailability and plant growth. To address this concern, high-throughput sequencing and bioinformatics were used to analyze microbiological mechanisms underlying RM application reducing Cd accumulation in edible amaranth. Based on multiple statistical models (Detrended correspondence analysis, Bray-Curtis, weighted UniFrac, and Phylogenetic tree), this study found that RM reduced Cd content in plants not only through increasing rhizosphere soil pH, but by reshaping rhizobacteria communities. Special taxa (Alphaproteobacteria, Gammaproteobacteria, Actinobacteriota, and Gemmatimonadota) associated with growth promotion, anti-disease ability, and Cd resistance of plants preferentially colonized in the rhizosphere. Moreover, RM distinctly facilitated soil microbes' proliferation and microbial biofilm formation by up-regulating intracellular organic metabolism pathways and down-regulating cell motility metabolic pathways, and these microbial metabolites/microbial biofilm (e.g., organic acid, carbohydrates, proteins, S^2-, and PO₄^3-) and microbial cells immobilized rhizosphere soil Cd via the biosorption and chemical chelation. This study revealed an important role of reshaped rhizobacteria communities acting in reducing Cd content in plants after RM application.

Structural, metabolic, and functional characteristics of soil microbial communities in response to benzo[a]pyrene stress

Understanding the characteristics of soil microbes responding to benzo[a]pyrene (BaP) helps to deepen the knowledge of the risks of BaP to soil ecosystem. In this study, the structural, metabolic, and functional responses of soil microbial communities to BaP (8.11 mg kg^-1) were investigated. Analysis of microbial community structure based on 16 S rRNA and ITS gene sequencing indicated that BaP addition enriched microbes associated with aromatic compound degradation (Sphingomonas, Bacilli, Fusarium) and oligotrophs (Blastocatellaceae, Rokubacteriales), but inhibited Cyanobacteria involved in nitrogen-fixing process. Network analysis showed that the bacterial community enhanced intraspecific cooperation, while fungal community mainly altered the keystone taxa under BaP stress. Biolog EcoPlate assay demonstrated that microbial metabolism of carbon sources, especially nitrogen-containing sources, was stimulated by BaP addition. Functional analysis based on enzyme activity tests, functional gene quantification, and function annotation showed that nitrogen-cycling processes, especially nitrogen fixation, were significantly inhibited. These results suggest that BaP-tolerant microbes may establish cooperative relationships and compete for resources and ecological niches with sensitive microbes, especially those associated with nitrogen cycling, ultimately leading to enhanced carbon source utilization and restricted nitrogen cycling. This study clearly elucidates the adaptation strategies and functional shifts of soil microbial communities to BaP contamination.