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

Effects of Biochar on Cadmium Availability, Nitrification and Microbial Communities in Soils with Varied pH Levels

Cadmium (Cd) contamination poses severe threats to agricultural productivity and ecosystem health. Biochar has shown promise in immobilizing Cd and enhancing microbial functions, yet its pH-dependent mechanisms remain underexplored. This study aimed to elucidate pH-dependent variations in biochar-mediated cadmium (Cd) immobilization efficiency, nitrification activity, and bacterial community diversity across soils of contrasting pH levels, with mechanistic insights into the synergistic interplay between biochar properties and soil pH. Real-time quantitative PCR (qPCR) and high-throughput sequencing were used to investigate the effects of a 1% (w/w) biochar amendment on ammonia-oxidizing microorganism abundance and microbial diversity in neutral Shandong soil (SD, pH 7.46) and acidic Yunnan soil (YN, pH 5.88). In neutral SD soil, available Cd decreased from 0.22 mg kg-1 (day 0) to 0.1 mg kg-1 (day 56) and stabilized, accompanied by insignificant changes in ammonia-oxidizing bacteria (AOB) abundance. However, nitrification activity was enhanced through the enrichment of Nitrospira (nitrite-oxidizing bacteria within Nitrospirales and Nitrospiraceae). In acidic YN soil, biochar reduced available Cd by 53.37% over 56 days, concurrent with a 34.28% increase in AOB amoA gene abundance (predominantly Nitrosomonadales), driving pH-dependent nitrification enhancement. These findings demonstrated that biochar efficacy was critically modulated by soil pH; the acidic soils require higher biochar dosages (>1% w/w, adjusted to local soil properties and agronomic conditions) for optimal Cd immobilization. Meanwhile, pH-specific nitrifier taxa (Nitrosomonadales in acidic vs. Nitrospira in neutral soils) underpinned biochar-induced nitrification dynamics. The study provided a mechanistic framework for tailoring biochar remediation strategies to soil pH gradients, emphasizing the synergistic regulation of Cd immobilization and microbial nitrogen cycling.

Prevalence of antibiotic resistance genes in mining-impacted farmland environments

Mining activities produce large quantities of tailings and acid mine drainage, which contain varieties of heavy metals, thereby affecting the downstream farmland soils and crops. Heavy metals could induce antibiotic resistance through co-selection pressure. However, the profiles of antibiotic resistance genes (ARGs) in the mining-affected farmland soils and crops are still unclear. Here we investigated contents of heavy metals, ARG abundances, mobile genetic elements (MGEs), and microbial community in mining-affected farmland soils and vegetables from Shangba village (SB), in comparison to a nearby reference village Taiping (TP). Results showed that in SB group, except for Cr, other metals were all above the Chinese Standards. When compared with the reference group, higher ARG abundances were detected in mining-affected farmland soils and vegetables, with great proportions of genes resistant to sulfonamides, chloramphenicols and tetracyclines. In addition, positive correlations were found between the above three ARG classes and heavy metals concentrations (especially Cu, Pb and Zn). Spearman's correlations revealed that there were positive correlations between sul1 and total nitrogen, as well as tetB/P and pH. Additionally, the Shannon index values were different for the samples from two villages (p < 0.05). Proteobacteria and Actinobacteria were dominant phyla in soil samples. Network analysis suggested that multiple genera (belonging to Proteobacteria and Actinobacteria) were positively associated with many ARGs (p < 0.05), implying they might be potential hosts for ARGs. To sum up, this study provided clear evidence that mining activities caused severe heavy metals pollution to the farmland, thus posing co-selection pressure on the persistence of ARGs in the affected farmland environments.

Cadmium contamination decreased bacterial network complexity and stability in coastal reclamation areas

Cadmium(Cd) contamination can exert significantly adverse effects on soil microbiota in reclaimed areas, however, its effects on bacterial network structure are still limitedly understood. Here we collected soil samples from typical reclaimed wetlands (RW) and ditch wetlands (DW) in coastal reclamation areas and examined the effects of Cd contamination on the bacterial network complexity and stability. The results showed that the bacterial networks were destabilized by the Cd contamination, while bacteria in DW soils showed robust invulnerability characterized by higher node constancy and compositional stability compared with RW soils. Soil bacteria resisted Cd stress by forming a network with intensive connections in the module but sparser connections among the modules. Especially, network modularity was higher in DW soils than in RW soils, but made it more vulnerable to nodes removal. In addition, Cd contamination promoted bacterial positive cohesion but decreased negative cohesion in RW soils. Flavobacteriaceae, Xanthomonadaceae, and Alcaligenaceae were identified as core phylotypes, which played pivotal roles in regulating interspecies interactions due to higher contributions to cohesion and significant correlations with soil nutrients. The findings of this work indicate the changes of bacterial network structure and the indispensable role of core phylotypes in regulating interactions and maintaining network sustainability under Cd contamination.

Enhanced phytoremediation of cadmium-contaminated soil using chelating agents and plant growth regulators: effect and mechanism

The heavy metal cadmium (Cd) is a major threat to food safety and human health. Phytoremediation is the most widely used remediation technology, and how to improve the remediation efficiency of phytoremediation has become a key issue. In this study, we constructed an intensive phytoremediation technology for remediation of Cd-contaminated soil with biodegradable chelating agent and plant growth regulator combined with maize and investigated the mechanism of this technology. The results showed that the best remediation effect was achieved in the treatment with 10-6 mol l-1 gibberellic acid (GA3) and 6 mmol kg-1 aspartate diethoxysuccinic acid (AES) combined with maize. In this treatment, the total biomass and extraction efficiency of maize were 3.6 and 8.67 times higher than those of the control, respectively, and the antioxidant enzyme activities of maize were also increased. The soil was enriched with dominant bacterial genera that promote plant growth and metabolism and tolerance to heavy metal stress, which in turn promoted maize growth and Cd accumulation. Structural equation modelling results indicated a large effect of plant Cd concentration and plant antioxidant enzyme activity on plant Cd extraction. The enhanced phytoremediation technology showed good potential for safe use of Cd-contaminated soil.

Impact of waste separation on the biological nitrogen removal in a MSW incineration leachate treatment plant: Performance and microbial community shift

After waste separation program was launched in China in 2019, incineration leachate treatment plants are facing a challenge of effective removal of nitrogen from leachate due to lack of sufficient carbon source. In this study, the performance of a biological incineration leachate treatment process (anaerobic digestion (AD) - two-stage anoxic/aerobic (A/O) process) was evaluated after adopting the waste separation program, and the changes in the microbial community and function was analyzed using 16S rRNA amplicon sequencing technology. Results showed that after the waste separation, the influent chemical oxygen demand (COD) concentration reduced by 90% (from 19,300 to 1780 mg L-1) with the COD/N ratio decreased from 12.3 to 1.4, which led to a decreased nitrogen removal efficiency (NRE) of <65% and a high effluent NO3- accumulation (445.8-986.5 mg N·L-1). By bypassing approximately 60% of the influent to the two-stage A/O process and adding external carbon source (glucose), the mean NRE increased to 86.3 ± 7.4%. Spearman's analysis revealed that refractory compounds in the bypassed leachate were closely related to the variations in bacterial community composition and nitrogen removal function in the two-stage A/O, leading to a weakened correlation of microbial network. KEGG functional pathway predictions based on Tax4Fun also confirmed that the bypassed leachate induced xenobiotic compounds to the two-stage A/O process, the relative abundance of nitrogen metabolism was reduced by 32%, and more external carbon source was required to ensure the satisfactory nitrogen removal of >80%. The findings provide a good guide for regulation of incineration leachate treatment processes after the waste separation.

Long-term surface composts application enhances saline-alkali soil carbon sequestration and increases bacterial community stability and complexity

Organic composts could remediate saline-alkali soils on agricultural land by amending soil micro-environment which is one of the main strategies for resourceful treatment and recycling of livestock manure. However, it was still unknown how long-term surface application of organic composts affects the microhabitat and bacterial community characteristics and assembly processes on the profile. We examined the features of the soil properties, bacterial community, and assembly models after 7-years composts application. Physicochemical indicators, enzyme activities, and bacterial diversity of the saline-alkali farmland were all enhanced by the surface composts application, particularly in the 0-20 cm. The network analysis showed that the surface application of composts significantly enhanced the robustness and topological characteristics of the bacterial community and that bacteria from Acidobacteriota were the keystone of the saline-alkali soils improvement. Composts also greatly increased the ecological niche of the bacterial community, while stochastic processes (mainly dispersal limitation) significantly shaped the bacterial community compared to the control. Structural equation modeling indicated that composts application promoted bacterial community succession, which in turn promoted elevated total organic carbon and improved saline-alkali soils properties. Overall, the study linked the ecological characteristics of soil microhabitats and bacterial communities during the restoration of saline-alkali soils by long-term surface application of composts, providing the management and remediation of saline-alkali agricultural soil with a theoretical foundation and technological support.

Bacteria-loaded biochar for the immobilization of cadmium in an alkaline-polluted soil

The combination of biochar and bacteria is a promising strategy for the remediation of Cd-polluted soils. However, the synergistic mechanisms of biochar and bacteria for Cd immobilization remain unclear. In this study, the experiments were conducted to evaluate the effects of the combination of biochar and Pseudomonas sp. AN-B15, on Cd immobilization, soil enzyme activity, and soil microbiome. The results showed that biochar could directly reduce the motility of Cd through adsorption and formation of CdCO3 precipitates, thereby protecting bacteria from Cd toxicity in the solution. In addition, bacterial growth further induces the formation of CdCO3 and CdS and enhances Cd adsorption by bacterial cells, resulting in a higher Cd removal rate. Thus, bacterial inoculation significantly enhances Cd removal in the presence of biochar in the solution. Moreover, soil incubation experiments showed that bacteria-loaded biochar significantly reduced soil exchangeable Cd in comparison with other treatments by impacting soil microbiome. In particular, bacteria-loaded biochar increased the relative abundance of Bacillus, Lysobacter, and Pontibacter, causing an increase in pH, urease, and arylsulfatase, thereby passivating soil exchangeable Cd and improving soil environmental quality in the natural alkaline Cd-contaminated soil. Overall, this study provides a systematic understanding of the synergistic mechanisms of biochar and bacteria for Cd immobilization in soil and new insights into the selection of functional strain for the efficient remediation of the contaminated environments by bacterial biochar composite.

Effects of uranium mining on soil bacterial communities and functions in the Qinghai-Tibet plateau

The microecological effects of plateau uranium mining are still unknown. In this study, we used 16S rRNA high-throughput sequencing to analyze the impact of plateau uranium mining on the microbial diversity and community structure of tailings soil, tunnel soil, and soil at different depths in an open pit. The results showed that uranium mining significantly reduced soil microbial community richness and diversity indicators, including Chao1, Pielou evenness, and Shannon index (P < 0.05). Uranium mining activities significantly reduced the abundance of RB41, Vicinamidactaceae, and Nitrospira (P < 0.05). Interestingly, the abundance of Thiobacillus, Sphingomonas, and Sulfuriferula significantly increased in the soil samples from various environments and depths during uranium mining (P < 0.05). Beta diversity analysis found that uranium mining resulted in the differentiation of soil microbial communities. Functional enrichment analysis found that uranium mining resulted in the functional enrichment of DNA binding response regulator, DNA helicase, methyl-accepting chemotaxis protein, and Helicase conserved C-terminal domain, whereas cell wall synthesis, nonspecific serine/threonine protein kinase, RNA polymerase sigma-70 factor, and ATP binding cassette transporter were significantly affected by uranium mining (P < 0.05). In addition, we also found that different uranium mining environments and soil depths enriched diverse microbial populations and functions to cope with the environmental pressures that were elicited by uranium mining, including Gaiella, Gemmatimonas, Lysobacter, Pseudomonas, signal transformation histidine kinase, DNA-directed DNA polymerase, and iron complex outer membrane receptor protein functions (P < 0.05). The results have enhanced our understanding of the impact of uranium mining on plateau soil microecological stability and the mechanism of microbial response to uranium mining activities for the first time and aided us in screening microbial strains that can promote the environmental remediation of uranium mining in plateaus.

Chicken manure application alters microbial community structure and the distribution of antibiotic-resistance genes in rhizosphere soil of Cinnamomum camphora forests

The distribution of antibiotic-resistance genes (ARGs) in environmental soil is greatly affected by livestock and poultry manure fertilization, the application of manure will lead to antibiotic residues and ARGs pollution, and increase the risk of environmental pollution and human health. Cinnamomum camphora is an economically significant tree species in Fujian Province, China. Here, through high-throughput sequencing analysis, significant differences in the composition of the bacterial community and ARGs were observed between fertilized and unfertilized rhizosphere soil. The application of chicken manure organic fertilizer significantly increased the relative abundance and alpha diversity of the bacterial community and ARGs. The content of organic matter, soluble organic nitrogen, available phosphorus, nitrate reductase, hydroxylamine reductase, urease, acid protease, β-glucosidase, oxytetracycline, and tetracycline in the soil of C. camphora forests have significant effects on bacterial community and ARGs. Significant correlations between environmental factors, bacterial communities, and ARGs were observed in the rhizosphere soil of C. camphora forests according to Mantel tests. Overall, the findings of this study revealed that chicken manure organic fertilizer application has a significant effect on the bacterial community and ARGs in the rhizosphere soil of C. camphora forests, and several environmental factors that affect the bacterial community and ARGs were identified.

Effect of different types of biochar on soil properties and functional microbial communities in rhizosphere and bulk soils and their relationship with CH4 and N2O emissions

Biochar as an agricultural soil amendment plays vital roles in mediating methane (CH4) and nitrous oxide (N2O) emissions in soils. The link between different types of biochar, bulk soil, and rhizosphere microbial communities in relation to CH4 and N2O emissions is being investigated in this study. The rice pot experiment was conducted using biochar at two temperatures (300°C and 500°C) in combination with three biochar levels (0, 2, 10% w/w). Soil properties and the abundance of genes associated with CH4 and N2O emissions from both rhizosphere and bulk soils were investigated. The study also aimed to examine the structure of microbial communities (pmoA, nosZ) in rhizosphere and bulk soils whereas CH4 and N2O emissions were monitored while growing rice. Results showed that biochar at 300°C and 10% incorporation significantly increased the CH4 emissions by up to 59% rise compared to the control group. Random Forest analysis revealed that the ratio of mcrA/pmoA along with the abundance of mcrA from both rhizosphere and bulk soils, the abundance of AOA, TN, DOC, and the community composition of pmoA-harboring microorganisms from both bulk and rhizosphere soils were important predictors of CH4 emissions. Therefore, the ratio of mcrA/pmoA in rhizosphere soil and the abundance of AOA in bulk soil were the main factors influencing CH4 emissions. Variation Partitioning Analysis (VPA) results indicated that the effects of these factors on bulk soil were 9% of CH4 emissions variations in different treatments, which contributed more than rhizosphere soils' factors. Moreover, random forest analysis results indicated that the abundance of AOB in bulk soil was the most important predictor influencing N2O emissions. The VPA result revealed that the factors in rhizosphere soil could explain more than 28% of the variations in N2O emissions. Our study highlights that rhizosphere soil has a more significant effect than bulk soil on N2O production. Our findings further the understanding of the link between bulk and rhizosphere attributes, and their impact on CH4 and N2O emissions in paddy soils. In summary, we recommend the application of biochar at 500°C and 2% incorporation rate for agricultural production in the area.

Effect of cornstalk biochar on phytoremediation of Pb-contaminated soil by females and males of Populus deltoides (Salicaceae)

Soil pollution with lead (Pb) has become a serious global concern, adversely affecting the forest ecosystem. This study was conducted to investigate the effects of corn straw on the remediation efficiency of Pb-contaminated soil using Populus deltoides. Female and male P. deltoides cuttings were subjected to soil spiked with 900 mg kg-1 Pb and amended with 5% (v/v) corn straw biochar for 90 days. Under Pb stress, the addition of biochar significantly increased the total biomass accumulation by 29% in females and 26% in males. However, without the addition of biochar, the biomass accumulation was significantly reduced by 11% in females and 3% in males under Pb stress. Females showed a higher uptake and accumulation of Pb in roots and leaves, while males accumulated more Pb in roots and stems and exhibited an increased anti-oxidative capacity. Biochar addition alleviated Pb toxicity in both male and female P. deltoides by immobilizing Pb ion in the soil, reducing Pb uptake and translocation, promoting nutrient uptake, and improving the diversity and stability of the soil bacteria community. Under Pb stress, the relative abundances of metal-resistance bacteria significantly increased, such as the abundance of Bacteroidetes in females and the abundances of Actinobacteria, Firmicutes, and Planctomycetes in males. In brief, the males under biochar addition exhibited promising potential as candidates for phytoremediation of Pb-contaminated soil. This study provides new insights into mechanisms underlying sexually differential responses to Pb stress in the presence of biochar amendment.

Chitin and crawfish shell biochar composite decreased heavy metal bioavailability and shifted rhizosphere bacterial community in an arsenic/lead co-contaminated soil

Sustainable management of ever-increasing organic biowaste and arable soil contamination by potentially toxic elements are of concern from both environmental and agricultural perspectives. To tackle the waste issue of crawfish shells and simultaneously minimize the threat of arsenic (As) and lead (Pb) to human health, a pot trial was conducted using chitin (CT), crawfish shell biochar (CSB), crawfish shell powder (CSP), and CT-CSB composite to compare their remediation efficiencies in As/Pb co-contaminated soil. Results demonstrated that addition of all amendments decreased Pb bioavailability, with the greatest effect observed for the CT-CSB treatment. Application of CSP and CSB increased the soil available As concentration, while significant decreases were observed in the CT and CT-CSB treatments. Meanwhile, CT addition was the most effective in enhancing the soil enzyme activities including acid phosphatase, α-glucosidase, N-acetyl-β-glucosaminidase, and cellobiohydrolase, whereas CSB-containing treatments suppressed the activities of most enzymes. The amendments altered the bacterial abundance and composition in soil. For instance, compared to the control, all treatments increased Chitinophagaceae abundance by 2.6-4.7%. The relative abundance of Comamonadaceae decreased by 1.6% in the CSB treatment, while 2.1% increase of Comamonadaceae was noted in the CT-CSB treatment. Redundancy and correlation analyses (at the family level) indicated that the changes in bacterial community structure were linked to bulk density, water content, and As/Pb availability of soils. Partial least squares path modeling further indicated that soil chemical property (i.e., pH, dissolved organic carbon, and cation exchange capacity) was the strongest predictor of As/Pb availability in soils following amendment application. Overall, CT-CSB could be a potentially effective amendment for simultaneously immobilizing As and Pb and restoring soil ecological functions in contaminated arable soils.

The addition of biochar and nitrogen alters the microbial community and their cooccurrence network by affecting soil properties

Biochar plays an important role in reducing the harmful environmental effects of inorganic nitrogen (N) fertilizers on agroecosystems, but the the impact mechanisms of biochar combined with N fertilizers on soil microorganisms are not clear enough. In this study, high-throughput sequencing was used to study the influences of three N fertilizer levels (0 (N0), 90 (N90) and 120 (N120) kg ha^-1) and two biochar levels (0 (B0) and 20 (B20) t ha^-1) on the soil microbial community and symbiotic network among microbial taxa in wheat fields. Compared to the control (B0N0), N fertilizer alone or combined with biochar significantly increased soil total N, available N, and organic matter in topsoil (0-20 cm), and the same results were found only in B20N120 treatment in subsoil (20-40 cm). In addition, bacterial and fungal diversity in topsoil were significantly increased and decreased by all N and biochar treatments, respectively. Moreover, soil bacterial and fungal community compositions also were also changed by N and biochar. Furthermore, biochar weakened the competition and cooperation among microorganisms in topsoil and subsoil, and the keystone species of networks were also changed by biochar. Redundancy analysis showed that soil total N, available N, available P, available K and pH were the main environmental factors driving the changes in bacterial and fungal community structures. These data indicated that the addition of N fertilizer and biochar could improve soil fertility by maintaining the stability of microbial community structures, which can provide reasonable guidance for the sustainable development of agriculture, such as maintaining dryland production.

Synthesis and application of starch-stablized Fe-Mn/biochar composites for the removal of lead from water and soil

Starch-stablized and Fe/Mn bimetals modified biochar derived from corn straw (SFM@CBC and SFM@CBC-350) were firstly prepared, characterized (FTIR, XRD, SEM, EDS, BET and XPS), and applied in Pb removal from water and soil. SFM@CBC and SFM@CBC-350 displayed highly effective adsorption performance of Pb²⁺ from wastewater with the maximum adsorption capacity of 170.91 mg g^-1 and 190.17 mg g^-1, respectively, which were much greater than that of FM@CBC (149.25 mg g^-1) and CBC (101.10 mg g^-1). Studies of adsorption kinetics, isotherms and thermodynamics indicated that the absorption of Pb²⁺ by SFM@CBC and SFM@CBC-350 was spontaneous and endothermic reaction, and it was controlled by monolayer chemisorption. The mechanism studies indicated that Pb²⁺ removal involved with multiple mechanism, including complexation (dominant process confirmed by XPS analysis), physical adsorption, electrostatic attraction, and cation exchange. The reusability test demonstrated that SFM@CBC and SFM@CBC-350 had very good stability and reusability. In addition, in order to further explore Pb removal performance of the modified biochar, SFM@CBC-350 was used in soil-ryegrass pot systems. Compared with the controls, the addition of SFM@CBC-350 reduced Pb content in soil and ryegrass, increased the biomass and total chlorophyll content, reduced the activity of antioxidant enzymes (CAT, SOD, MDA and POD) and ROS fluorescence intensity of ryegrass, thus alleviating Pb stress of ryegrass. Besides, the addition of SFM@CBC-350 could increase the richness and diversity of soil microorganisms, which was beneficial to the growth of ryegrass. Hence, SFM@CBC-350 has the potential of being used as a green, efficient and promising adsorbent in Pb removal from wastewater and soil.

Biochar rebuilds the network complexity of rare and abundant microbial taxa in reclaimed soil of mining areas to cooperatively avert cadmium stress

Understanding the interactions between the soil microbial communities and species is critical in the remediation of heavy metal-contaminated soil. Biochar has been widely applied as a stabilizer in the in situ remediation of cadmium (Cd)-contaminated soils in mining areas. However, the rebuilding of the microbial taxa of rare and abundant species by biochar and their cooperative resistance to Cd stress remains elusive. In this pursuit, the present study envisaged the effects of two types of biochars viz., poplar bark biochar (PB) and thiourea-modified poplar bark biochar (TP) on the rare and abundant bacterial and fungal taxa by using pot experiments. The results demonstrated that the PB and TP treatments significantly reduced the leached Cd content, by 35.13 and 68.05%, respectively, compared with the control group (CK), in the reclaimed soil of the mining area. The application of biochar significantly improved the physicochemical properties like pH and Soil Organic Matter (SOM) of the soil. It was observed that TP treatment was superior to the PB and CK groups in increasing the diversity of the soil abundant and rare species of microbial taxa. Compared with the CK group, the application of PB and TP enhanced and elevated the complexity of the microbial networks of rare and abundant taxa, increased the number and types of network core microorganisms, reshaped the network core microorganisms and hubs, and boosted the microbial resistance to Cd stress. Our results indicate the response of rare and abundant microbial taxa to biochar application and the mechanism of their synergistic remediation of Cd-contaminated soil, thereby providing technical feasibility for in situ remediation of Cd-contaminated soil in mining areas.