Selective pressures of heavy metals on microbial community determine microbial functional roles during composting: Sensitive, resistant and actor

Assembly processes and co-occurrence of bacterial communities in tree rhizosphere under Pb-Zn contamination

Rhizosphere bacteria are critical for supporting plant performance in stressful environments. Understanding the assembly and co-occurrence of rhizosphere bacterial communities contributes significantly to both plant growth and heavy metal accumulation. In this study, Ligustrum lucidum and Melia azedarach were planted in soils with simulated varying levels of Pb-Zn contamination. The Rhizosphere bacterial communities were investigated by using 16S rRNA gene sequencing. The impacts of Pb-Zn contamination on the diversity and structure of the rhizosphere bacterial community were found to be greater than those of both tree species. The variation in bacterial community structure in both trees was mainly driven by the combinations of Pb-Zn and soil properties. Deterministic processes (non-planted, 82 %; L. lucidum, 73 %; M. azedarach, 55 %) proved to be the most important assembly processes for soil bacterial communities, but both trees increased the importance of stochastic processes (18 %, 27 %, 45 %). The rhizosphere co-occurrence networks exhibited greater stability compared to the non-planted soil networks. Rare taxa played a dominant role in maintaining the stability of rhizosphere networks, as most of the keystone taxa within rhizosphere networks belonged to rare taxa. Dissimilarities in the structure and network complexity of rhizosphere bacterial communities were significantly associated with differences in tree biomass and metal accumulation. These variations in response varied between both trees, with L. lucidum exhibiting greater potential for phytoremediation in its rhizosphere compared to M. azedarach. Our results offer valuable insights for designing effective microbe-assisted phytoremediation systems.

Variability in Microbial Communities Driven by Particulate Matter on Human Facial Skin

Microbial communities are known to play an important role in maintaining ecological balance and can be used as an indicator for assessing environmental pollution. Numerous studies have revealed that air pollution can alter the structure of microbial communities, which may increase health risks. Nevertheless, the relationships between microbial communities and particulate matter (PM) caused by air pollution in terms of health risk assessment are not well understood. This study aimed to validate the influences of PM chemical compositions on microbial communities and assess the associated health risks. Our results, based on similarity analysis, revealed that the stability structure of the microbial communities had a similarity greater than 73%. In addition, the altered richness and diversity of microbial communities were significantly associated with PM chemical compositions. Volatile organic compounds (VOCs) and polycyclic aromatic hydrocarbons (PAHs) exerted a positive influence on microbial communities in different environmental variables. Additionally, a stronger linear correlation was observed between hydroxyl radicals (·OH) and the richness of microbial communities. All estimated health risks from PM chemical compositions, calculated under different environmental variables, significantly exceeded the acceptable level by a factor of more than 49. Cr and 1,2-Dibromoethane displayed dual adverse effects of non-carcinogenic and carcinogenic risks. Overall, the study provides insights into the fundamental mechanisms of the variability in microbial communities driven by PM, which may support the crucial role of PM chemical compositions in the risk of microorganisms in the atmospheric environment.

Warming inhibits HgII methylation but stimulates methylmercury demethylation in paddy soils

Inorganic mercury (HgII) can be transformed into neurotoxic methylmercury (MeHg) by microorganisms in paddy soils, and the subsequent accumulation in rice grains poses an exposure risk for human health. Warming as an important manifestation of climate change, changes the composition and structure of microbial communities, and regulates the biogeochemical cycles of Hg in natural environments. However, the response of specific HgII methylation/demethylation to the changes in microbial communities caused by warming remain unclear. Here, nationwide sampling of rice paddy soils and a temperature-adjusted incubation experiment coupled with isotope labeling technique (202HgII and Me198Hg) were conducted to investigate the effects of temperature on HgII methylation, MeHg demethylation, and microbial mechanisms in paddy soils along Hg gradients. We showed that increasing temperature significantly inhibited HgII methylation but promoted MeHg demethylation. The reduction in the relative abundance of Hg-methylating microorganisms and increase in the relative abundance of MeHg-demethylating microorganisms are the likely reasons. Consequently, the net Hg methylation production potential in rice paddy soils was largely inhibited under the increasing temperature. Collectively, our findings offer insights into the decrease in net MeHg production potential associated with increasing temperature and highlight the need for further evaluation of climate change for its potential effect on Hg transformation in Hg-sensitive ecosystems.

Vertical distribution of arsenic and bacterial communities in calcareous farmland amending by organic fertilizer and iron-oxidizing bacteria: Field experiment on concomitant remediation

The migration and transformation mechanisms of arsenic (As) in soil environments necessitate an understanding of its influencing processes. Here, we investigate the subsurface biogeochemical transformation of As and iron (Fe) through amended in the top 20 cm with iron oxidizing bacteria (FeOB) and organic fertilizer (OF). Our comprehensive 400-day field study, conducted in a calcareous soil profile sectioned into 20 cm increments, involved analysis by sequential extraction and assessment of microbial properties. The results reveal that the introduction of additional OF increased the release ratio of As/Fe from the non-specific adsorption fraction (136.47 %) at the subsoil depth (40-60 cm), underscoring the importance of sampling at various depths and time points to accurately elucidate the form, instability, and migration of As within the profile. Examination of bacterial interaction networks indicated a disrupted initial niche in the bottom layer, resulting in a novel cooperative symbiosis. While the addition of FeOB did not lead to the dominance of specific bacterial species, it did enhance the relative abundance of As-tolerant Acidobacteria and Gemmatimonadetes in both surface (39.2 % and 38.76 %) and deeper soils (44.29 % and 23.73 %) compared to the control. Consequently, the amendment of FeOB in conjunction with OF facilitated the formation of poorly amorphous Fe (hydr)oxides in the soil, achieved through abiotic and biotic sequestration processes. Throughout the long-term remediation process, the migration coefficient of bioavailable As within the soil profile decreased, indicating that these practices did not exacerbate As mobilization. This study carries significant implications for enhancing biogeochemical cycling in As-contaminated Sierozem soils and exploring potential bioremediation strategies. ENVIRONMENTAL IMPLICATION: The long-term exposure of sewage irrigation has potential adverse effects on the local ecosystem, causing serious environmental problems. Microorganisms play a vital role in the migration and transformation of arsenic in calcareous soil in arid areas, which highlights the necessity of understanding its dynamics. The vertical distribution, microbial community and fate of arsenic in calcareous farmland soil profile in northwest China were studied through field experiments. The results of this work have certain significance for the remediation of arsenic-contaminated soil in arid areas, and provide new insights for the migration, transformation and remediation of arsenic in this kind of soil.

Inhibition of high sulfur on functional microorganisms and genes in slightly contaminated soil by cadmium and chromium

It is generally accepted that sulfur can passivate the bioavailability of heavy metals in soil, but it is not clear whether high sulfur in cadmium (Cd) and chromium (Cr) contaminated soil has negative effect on soil microbial community and ecological function. In this study, total sulfur (TS) inhibited the Chao 1, Shannon, Phylogenetic diversity (Pd) of bacterial and Pd of fungi in slightly contaminated soil by Cd and Cr around pyrite. TS, total potassium, pH, total chromium, total cadmium, total nitrogen, soil organic matter were the predominant factors for soil microbial community; the contribution of TS in shaping bacterial and fungal communities ranked at first and fifth, respectively. Compared with the low sulfur group, the abundance of sulfur sensitive microorganisms Gemmatimonas, Pseudolabrys, MND1, and Schizothecium were decreased by 68.79-97.22% (p < 0.01) at high sulfur one; the carbon fixation, nitrogen cycling, phosphorus cycling and resistance genes abundance were significantly lower (p < 0.01) at the latter. Such variations were strongly and closely correlated to the suppression of energy metabolism (M00009, M00011, M00086) and carbon fixation (M00173, M00376) functional module genes abundance in the high sulfur group. Collectively, high sulfur significantly suppressed the abundances of functional microorganisms and functional genes in slightly contaminated soil with Cd and Cr, possibly through inhibition of energy metabolism and carbon fixation of functional microorganisms. This study provided new insights into the environmental behavior of sulfur in slightly contaminated soil with Cd and Cr.

Response of fulvic acid linking to redox characteristics on methane and short-chain fatty acids in anaerobic digestion of chicken manure

Fulvic acids (FAs) is formed during the bioconversion of organic matter (OM) to biogas during anaerobic digestion (AD) and has a complex structure and redox function. However, the evolutionary mechanisms of FAs during AD and its interactions with acid and methane production have not been sufficiently investigated, especially at different stages of AD. Intermittent AD experiments by chicken manure and rice husk showed significant structural changes and reduced aromatization of FAs (e.g., O-H stretch6, 14.10-0%; SR, 0.22-0.60). The electron donating capacity (EDC) [9.76-45.39 μmole-/(g C)] and electron accepting capacity (EAC) [2.55-5.20 μmole-/(g C)] of FAs showed a tendency of decreasing and then increasing, and FAs had a stronger electron transfer capacity (ETC) in the methanogenic stage. Correlation analysis showed that the EDC of FAs was influenced by their own structure (C-O stretch2, C-H bend1, C-H bend4, and N-H bend) and also had an inhibitory effect on propionic production, which further inhibited acetic production. The EAC of FAs was affected by molecular weight and had a promoting effect on methane production. Structural equation modelling identified three possible pathways for AD. The C-O stretch2 structure of FAs alone inhibits the production of propionic. In addition, pH can directly affect the EDC of FAs. This study provides a theoretical basis for the structural and functional evolution of FAs in AD of chicken manure on the mechanism of methane production.

Metagenomic binning analyses of swine manure composting reveal mechanism of nitrogen cycle amendment using kaolin

The efficient control of nitrogen loss in composting and the enhancement of product quality have become prominent concerns in current research. The positive role of varying concentrations kaolin in reducing nitrogen loss during composting was revealed using metagenomic binning combined with reverse transcription quantitative polymerase chain reaction. The results indicated that the addition of 0.5 % kaolin significantly (P < 0.05) up-regulated the expression of nosZ and nifH on day 35, while concurrently reducing norB abundance, resulting in a reduction of NH3 and N2O emissions by 61.4 % and 17.5 %, respectively. Notably, this study represents the first investigation into the co-occurrence of nitrogen functional genes and heavy metal resistance genes within metagenomic assembly genomes during composting. Emerging evidence indicates that kaolin effectively impedes the binding of Cu/Zn to nirK and nosZ gene reductases through passivation. This study offers a novel approach to enhance compost quality and waste material utilization.

Microbial-driven mechanisms for the effects of heavy metals on soil organic carbon storage: A global analysis

Heavy metal (HM) enrichment is closely related to soil organic carbon (SOC) pools in terrestrial ecosystems, which are deeply intertwined with soil microbial processes. However, the influence of HMs on SOC remains contentious in terms of magnitude and direction. A global analysis of 155 publications was conducted to integrate the synergistic responses of SOC and microorganisms to HM enrichment. A significant increase of 13.6 % in SOC content was observed in soils exposed to HMs. The response of SOC to HMs primarily depends on soil properties and habitat conditions, particularly the initial SOC content, mean annual precipitation (MAP), initial soil pH, and mean annual temperature (MAT). The presence of HMs resulted in significant decreases in the activities of key soil enzymes, including 31.9 % for soil dehydrogenase, 24.8 % for β-glucosidase, 35.8 % for invertase, and 24.3 % for cellulose. HMs also exerted inhibitory effects on microbial biomass carbon (MBC) (26.6 %), microbial respiration (MR) (19.7 %), and the bacterial Shannon index (3.13 %) but elevated the microbial metabolic quotient (qCO2) (20.6 %). The HM enrichment-induced changes in SOC exhibited positive correlations with the response of MBC (r = 0.70, p < 0.01) and qCO2 (r = 0.50, p < 0.01), while it was negatively associated with β-glucosidase activity (r = 0.72, p < 0.01) and MR (r = 0.39, p < 0.01). These findings suggest that the increase in SOC storage is mainly attributable to the inhibition of soil enzymes and microorganisms under HM enrichment. Overall, this meta-analysis highlights the habitat-dependent responses of SOC to HM enrichment and provides a comprehensive evaluation of soil carbon dynamics in an HM-rich environment.

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.

Mechanism and application of modified bioelectrochemical system anodes made of carbon nanomaterial for the removal of heavy metals from soil

Bioelectrochemical techniques are quick, efficient, and sustainable alternatives for treating heavy metal soils. The use of carbon nanomaterials in combination with electroactive microorganisms can create a conductive network that mediates long-distance electron transfer in an electrode system, thereby resolving the issue of low electron transfer efficiency in soil remediation. As a multifunctional soil heavy metal remediation technology, its application in organic remediation has matured, and numerous studies have demonstrated its potential for soil heavy metal remediation. This is a ground-breaking method for remediating soils polluted with high concentrations of heavy metals using soil microbial electrochemistry. This review summarizes the use of bioelectrochemical systems with modified anode materials for the remediation of soils with high heavy metal concentrations by discussing the mass-transfer mechanism of electrochemically active microorganisms in bioelectrochemical systems, focusing on the suitability of carbon nanomaterials and acidophilic bacteria. Finally, we discuss the emerging limitations of bioelectrochemical systems, and future research efforts to improve their performance and facilitate practical applications. The mass-transfer mechanism of electrochemically active microorganisms in bioelectrochemical systems emphasizes the suitability of carbon nanomaterials and acidophilic bacteria for remediating soils polluted with high concentrations of heavy metals. We conclude by discussing present and future research initiatives for bioelectrochemical systems to enhance their performance and facilitate practical applications. As a result, this study can close any gaps in the development of bioelectrochemical systems and guide their practical application in remediating heavy-metal-contaminated soils.

Effects of an assistive electric field on heavy metal passivation during manure composting

Composting is one of main technologies for treating and thus utilizing livestock manure and sludge. However, heavy metals are major concerns in compost utilization due to their potential environmental hazards and health risks. This study aimed to investigate the effects of electric field-assisted composting on the variations of heavy metals and the affecting factors. The results showed that electric field significantly reduced the contents of bioavailable heavy metals including Mn, Zn, Cu, Ni, and Cd, with their bioavailable concentrations decreasing by 61.7, 63.8, 64.9, 83.7, and 63.8 %, respectively. The heavy metals being transformed into stable states were increased, indicating that the electric field also passivated these heavy metals and reduced their biological toxicity and stabilized their forms. Spearman's correlation analysis revealed that the changes in substances, temperature, and organic matter were the dominant environmental factors affecting the forms of heavy metals. Microbial community analysis indicated an increase in the abundance of metal-resistant bacteria such as Pseudomonas and Bacillus during electric field-assisted composting, with their relative abundances being increased to 2.66 % and 15.63 % in the pile of electric field-assisted composting, respectively, compared to the values of 1.88 % and 4.36 % respectively in the conventional composting. The current study suggests that electric field-assisted composting can significantly reduce the availability of heavy metals in the compost, and thus mitigate the health risks associated with its application.

Cd contamination determined assembly processes and network stability of AM fungal communities in an urban green space ecosystem

The effects of cadmium (Cd) contamination on the assembly mechanism and co-occurrence patterns of arbuscular mycorrhizal (AM) fungal communities remain unclear, especially in urban green spaces. This study sequenced AM fungal communities in greenbelt soils in Zhengzhou (China). The effects of Cd contamination on the AM fungal diversity, community assembly processes, and co-occurrence patterns were explored. We found that (1) an increase in Cd contamination changed the community composition, which resulted in a significant improvement in the diversity of specialists of AM fungi and a significant decrease in the diversity of generalists. (2) Deterministic processes dominated the community assembly of specialists and stochastic processes dominated the community assembly of generalists. (3) Specialists played a more important role than generalists in maintaining the stability of AM fungal networks under Cd contamination. Overall, Cd contamination affected the ecological processes of AM fungi in urban green space ecosystems. However, the effects on the assembly processes and network stability of different AM fungi taxa (specialists and generalists) differed significantly. The present study provides deeper insight into the effect of Cd contamination on the ecological processes of AMF and is helpful in further exploring the ecological risk of Cd contamination in urban green spaces.

The transformation of heavy metal speciation during rapid high-temperature aerobic fermentation of food waste and their potential mechanisms

In this study, the content changes of multiple trace heavy metals (HMs) in food waste using a new rapid high-temperature aerobic fermentation (RTAF) technology and their relationships with different physicochemical factors were researched. The results indicated that the content of HMs in the decomposed products met the industry standards for organic fertilizers (NY/T525-2021, China). Physicochemical factors played an important role in controlling the changes in HM content. The component evolution of dissolved organic matter was studied, and its influences on the transformation of HM speciation showed that the RTAF process converted proteins into humus-like substances. Redundancy analysis revealed that the main factors driving the speciation transformation of HMs were tyrosine-like substances or microbial-derived humus (C3), molecular weight of dissolved organic matter (SUVA254) and humification degree (E250/E365). The increase in humification degree contributed to passivating HMs. The correlation network analysis results showed that the exchangeable HMs (Exc-HMs) were related to Lactobacillus and Pediococcu. Additionally, the cytoskeleton, coenzyme transport and metabolic function of microorganisms affected the Exc-HM content. These research results can provide a scientific basis for the prevention and control of HM pollution during the treatment of food waste.

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.

Differential response of the soil nutrients, soil bacterial community structure and metabolic functions to different risk areas in Lead-Zine tailings

Rapid growth in the mining industry has brought about a large formation of tailings, which result in serious destruction of the ecological environment and severe soil pollution problems. This study assesses soil nutrients, soil bacterial community and soil microbes' metabolic function in heavily polluted areas (W1), moderately polluted areas (W2), lightly polluted areas (W3) and clean areas (CK) using 16S Illumina sequencing. The results of this study showed that compared with CK, a severe loss of soil nutrients and richness of OTUs (Chao1 and ACE indices) were observed with the aggravated pollution of tailings. The Chao1 and ACE indices in the W1 group decreased significantly by 15.53 and 16.03%, respectively, (p < 0.01). Besides, the relative abundance of Actinobacteria and Proteobacteria was high whereas and relative abundance of Chloroflexi in the polluted areas. Among them, W1 groups increased significantly the relative abundance of Actinobacteria and decreased significantly the relative abundance of Chloroflexi, these can be used as indicator phyla for changes in soil community structures under polluted stress. Tax4 Fun analysis showed that W1 groups affected the soil bacterial community and altered the primary types of biological metabolism in polluted areas. Tailings have adverse impacts on soil bacterial community and metabolic functions, and the deterioration in soil quality is dependent on the levels of tailings pollution. Cumulatively, this study provides valuable information on the bacterial community structure and metabolic functions in the tailing polluted soil.

Treatment Options for Municipal Solid Waste by Composting and Its Challenges

Recovery and recycling of municipal solid waste biodegradable fraction (50-55%) are essential for attaining sustainability and a circular economy. Among organic waste treatment methods, composting is used to recycle organic fractions of waste. However, only 10-12% of municipal solid waste is utilized for composting treatment due to a lack of segregation practices and process challenges, including long process periods, odorous and greenhouse gas emissions, nitrogen loss, and low compost quality, which hinders large-scale practice. The current review paper discusses the challenges of composting treatment and its possible solutions. Various strategies were explored to address these challenges, such as utilizing microbial inoculum, additives, and optimization of physicochemical parameters. It also emphasizes the application of metagenomics for exploring key species. The knowledge about the microbial community and biochemical pathways (genome mining) can be exploited for the improvement of treatment efficiency.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01087-4.

Effect of sodium alginate-gelatin-polyvinyl pyrrolidone microspheres on cucumber plants, soil, and microbial communities under lead stress

Lead is highly persistent and toxic in soil, hindering plant growth. Microspheres are a novel, functional, and slow-release preparation commonly used for controlled release of agricultural chemicals. However, their application in the remediation of Pb-contaminated soil has not been studied; furthermore, the remediation mechanism involved has not been systematically assessed. Herein, we evaluated the Pb stress mitigation ability of sodium alginate-gelatin-polyvinyl pyrrolidone composite microspheres. Microspheres effectively attenuated the Pb toxic effect on cucumber seedlings. Furthermore, they boosted cucumber growth, increased peroxidase activity, and chlorophyll content, while reducing malondialdehyde content in leaves. Microspheres promoted Pb enrichment in cucumber, especially in roots (about 4.5 times). They also improved soil physicochemical properties, promoted enzyme activity, and increased soil available Pb concentration in the short term. In addition, microspheres selectively enriched functional (heavy metal-tolerating and plant growth promoting) bacteria to adapt to and resist Pb stress by improving soil properties and nutrients. These results indicated that even a small amount (0.025-0.3 %) of microspheres can significantly reduce the adverse effects of Pb on plants, soil, and bacterial communities. Composite microspheres have shown great value in Pb remediation, and their application potential in phytoremediation is also worth evaluating to expand the application.

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.

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.

Lignite drove phenol precursors to participate in the formation of humic acid during chicken manure composting

This study set out to explore the impact of lignite on preserving organic matter and promoting the formation of humic acid (HA) during chicken manure composting. Composting test was carried out for control (CK), 5 % lignite addition treatment (L1), 10 % addition treatment (L2) and 15 % addition treatment (L3). The results demonstrated that lignite addition effectively reduced the loss of organic matter. The HA content of all lignite-added groups was higher than that of CK, and the highest was 45.44 %. L1 and L2 increased the richness of bacterial community. Network analysis showed higher diversity of HA-associated bacteria in L2 and L3 treatments. Structural equation models revealed that reducing sugar and amino acid contributed to the formation of HA during CK and L1 composting, while polyphenol contributed more to the HA formation during L2 and L3 composting. Furthermore, lignite addition also could promote the direct effect of microorganisms on HA formation. Therefore, the addition of lignite had practical significance to enhance compost quality.

Elaborating the role of rhamnolipids on the formation of humic substances during rice straw composting based on Fenton pretreatment and fungal inoculation

Composting is a green and sustainable way to dispose and reuse agricultural wastes, but the low degradation rate during composting hinders its application. This study was conducted to explore the effect of added surfactant rhamnolipids after Fenton pretreatment and inoculation of fungi (Aspergillus fumigatus) into the compost on the formation of humic substances (HS) during rice straw composting, and explored the effect of this method. The results showed that rhamnolipids speeded up the degradation of organic matter and HS formation during composting. Rhamnolipids promoted the generation of lignocellulose-degrading products after Fenton pretreatment and fungal inoculation. The differential products benzoic acid, ferulic acid, 2, 4-Di-tert-butylphenol and syringic acid were obtained. Additionally, key fungal species and modules were identified using multivariate statistical analysis. Reducing sugars, pH, and total nitrogen were the key environmental factors that affected HS formation. This study provides a theoretical basis for the high-quality transformation of agricultural wastes.

The driving mechanism of passivator islands adsorbing and immobilizing heavy metals during chicken manure composting

The aim of this study was to assess the effectiveness of biochar and montmorillonite islands on heavy metal adsorptive immobilization and identify crucial driving factors and pathways during chicken manure composting. Compared to montmorillonite (6.74 and 89.25 mg/kg), biochar exhibited an obviously higher ability of Cu and Zn enrichment (41.79 and 167.77mg/kg), might be attributed to its abundant active functional groups. Network analysis showed that compared to Cu, core bacteria positively and negatively related to Zn was obviously more and less in passivator islands, respectively, which might explain significantly higher Zn concentration. Structural Equation Model displayed that dissolved organic carbon (DOC), pH and bacteria were critical driving factors. Pretreatment of passivator packages, such as soaking in the solution being rich in DOC and inoculating specific microbial agents accumulating heavy metals via extracellular adsorption /intracellular interception would significantly improve the effectiveness of adsorptive passivation on heavy metals.

Di-n-butyl phthalate stress induces changes in the core bacterial community associated with nitrogen conversion during agricultural waste composting

Nitrogen (N) loss during composting reduces the quality of compost products and causes secondary environmental pollution. Phthalate esters (PAEs) are common pollutants in agricultural wastes. However, little information is currently available on how PAEs affect N conversion during agricultural waste composting. This research systematically analyzed the impact of di-n-butyl phthalate (DBP) pollution on the N conversion and its related microbial community during composting. Our results indicated that DBP stress results in a shorter thermophilic phase, and then slower compost maturation during composting. Notably, DBP stress inhibited the conversion of ammonia to nitrate, but increased the release of NH₃ and N₂O leading to an increased N loss and an elevated greenhouse effect. Furthermore, DBP exposure led to a reduction of bacteria related to NH₄⁺ and NO₃^- conversion and altered the network complexity of the bacterial community involved in N conversion. It also reduced the abundance of a major nitrification gene (amoA) (P < 0.01) and increased the abundance of denitrification genes (nirK and norB) (P < 0.05). Moreover, DBP affected the overall microbial community composition at all tested concentrations. These findings provide theoretical and methodological basis for improving the quality of PAE-contaminated agricultural waste compost products and reducing secondary environmental pollution.

Multi-omics analysis provides insight into the phytotoxicity of chicken manure and cornstalk on seed germination

To minimize environmental risks and the phytotoxic influence of organic materials on crop growth, it is necessary to test their phytotoxicity and maturity when they were used in farmland. However, the stress response of seed germination to chicken manure and cornstalks is not clear. This study used multi-omics analysis to investigate the inhibition mechanism of seed germination by chicken manure and cornstalk. Chicken manure caused destructive inhibition of seed germination with higher phytotoxicity (GI = 0). Cornstalk also had a low GI (8.81 %), while it mainly inhibited radicle growth (RL = 9.39 %) rather than seed germination (GR = 93.33 %). The response of radish seed germination to chicken manure and cornstalk phytotoxic stresses was accompanied by metabolic adjustments of storage substance accumulation, antioxidant enzyme activity change, phytohormone induction, and expression of specific proteins and gene regulation. Combined transcriptomic and proteomic analysis revealed that differential expression of 13,090 (5944 upregulated/7146 downregulated) and 3850 (2389 upregulated/1461 downregulated) genes (DEGs), and 1041 (82 upregulated/932 downregulated) and 575 (111 upregulated/464 downregulated) proteins (DEPs) at chicken manure and cornstalk treatment, respectively. Most down-regulated genes and proteins were involved in phenylpropanoid biosynthesis under chicken manure stress, which caused irreversible inhibition of seed germination. Down-regulation of phytohormone signal transduction-related genes under cornstalk stress resulted in inhibition of radicle growth, but the inhibitory stress was restorable. These findings provide new insight into the phytotoxicity of livestock manure and cornstalk on seed germination.

Effect of biochar addition on copper and zinc passivation pathways mediated by humification and microbial community evolution during pig manure composting

The mobility and bioavailability of Cu and Zn are the main threats associated with the land application of pig manure (PM) compost products. This study investigated the impacts of biochar (BC) concentration on passivation of Cu and Zn associated with the compost maturity. The results indicated that 15% and 10% BC favoured the passivation of Cu and Zn, respectively. BC promoted passivation of Cu by accelerating HA production and optimized the abundance of Firmicutes. BC promoted the passivation of Zn by increasing the high temperature peak and the corresponding pH (8-8.5). A higher level (15% and 20%) of BC altered the dominant bacterial phylum from Firmicutes to Proteobacteria. 20% BC inhibited the passivation of Cu and Zn by reducing the highest temperature and lowering the alkalinity of substrate. These results offer new insights into understanding how the addition of BC could reduce the risk of hazardous products during PM composting.

Soil microbial communities and their co-occurrence networks in response to long-term Pb-Zn contaminated soil in southern China

Mining causes extreme heavy metal (HM) contamination to surrounding environments and poses threats to soil microbial community. The effects of HMs on soil microbial communities are not only related to their total amounts but also associated with the distribution of chemical fractions. However, the effects of chemical fractions on soil microbes and their interactions remain largely unclear. Here we investigated soil physicochemical properties and bacterial and fungal communities of soil samples from the control area and lightly (L), moderately (M), and heavily (H) contaminated areas, respectively, which were collected from long-term Pb-Zn slag contamination area in the southern China. The results showed that bacterial and fungal community composition and structure were significantly affected by HMs, while community diversity was not significantly affected by HMs. The critical environmental factor affecting bacterial and fungal communities was pH, and the impacts of chemical fractions on their changes were more significant than the total amounts of HMs. Variance partitioning analysis (VPA) revealed fungal community changes were mostly driven by HM total amounts, but bacterial community changes were mostly driven by soil chemical properties. Co-occurrence network indicated that interactions among species of fungal network were sparser than that of bacterial network, but fungal network was more stable, due to a more significant number of keystone taxa and a lower percentage of positive associations. These illustrated that the fungal community might serve as indicator taxa for HM-contaminated status, and specific HM-responsive fungal species such as Triangularia mangenotii, Saitozyma podzolica, and Cladosporium endophytica, and genus Rhizophagus can be considered relevant bioindicators due to their less relative abundance in contaminated areas. Additionally, HM-responsive bacterial OTUs representing five genera within Sulfurifustis, Thiobacillus, Sphingomonas, Qipengyuania, and Sulfurirhabdus were found to be tolerant to HM stress due to their high relative abundance in contaminated levels.

Soil bacterial community structure in the habitats with different levels of heavy metal pollution at an abandoned polymetallic mine

Heavy metal pollution caused by mining activities can be harmful to soil microbiota, which are highly sensitive to heavy metal stress. This study aimed to investigate the response of soil bacterial communities to varying levels of heavy metal pollution in four types of habitats (i.e., tailing, remediation, natural recovery, and undisturbed areas) at an abandoned polymetallic mine by high-throughput 16 S rRNA gene sequencing, and to determine the dominant ecological processes and major factors driving the variations in bacterial community composition. The diversity and composition of bacterial communities varied significantly between soil habitats (p < 0.05). Heterogeneous selection played a crucial role in shaping the difference of bacterial community composition between distinct soil habitats. Redundancy analysis and Pearson correlation analysis revealed that the total contents of Cu and Zn were key factors causing the difference in bacterial community composition in the tailing and remediation areas, whereas bioavailable Mn and Cd, total nitrogen, available nitrogen, soil organic carbon, vegetation coverage, and plant diversity were key factors shaping the soil bacterial structure in the undisturbed and natural recovery areas. These findings provide insights into the distribution patterns of bacterial communities in soil habitats with different levels of heavy metal pollution, and the dominant ecological processes and the corresponding environmental drivers, and expand knowledge in bacterial assembly mechanisms in mining regions.

Exploration of bacterial community-induced polycyclic aromatic hydrocarbons degradation and humus formation during co-composting of cow manure waste combined with contaminated soil

To solve polycyclic aromatic hydrocarbons (PAHs) pollution, composting was chosen as a remediation method. During composting, the dissipation of PAHs was carried out by resource utilization of organic solid waste and its degradation by bacteria. This study was conducted by co-composting with contaminated soil and cow manure. The results showed that the degradation rates of naphthalene (Nap), phenanthrene (Phe), and benzo[α]pyrene (BaP) could reach 82.2%, 79.4%, and 59.6% respectively during composting. Cluster analysis indicated that polyphenol oxidase (PPO), laccase, and protease were important drivers of PAHs transformation. The content of humic substances (HS) was 106.67 g/kg in PAH treatment, which was significantly higher than that in the control group at 65 days. The phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) and network analysis was used to infer the degradation mechanism of PAHs by microorganisms. The degradation of PAHs by PPO was found to have a significant contribution to the formation of HS. It was shown that PAHs and metabolic intermediates were more inclined to be oxidized and decomposed by PPO to form quinone, which in turn condensed with amino acids to form HS. Composting could promote the degradation of PAHs while improving the quality of compost, achieving a win-win situation.

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.

Community response of soil microorganisms to combined contamination of polycyclic aromatic hydrocarbons and potentially toxic elements in a typical coking plant

Both polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) of coking industries impose negative effects on the stability of soil ecosystem. Soil microbes are regarded as an essential moderator of biochemical processes and soil remediation, while their responses to PAHs-PTEs combined contamination are largely unknown. In the present study, soil microbial diversity and community composition in the typical coking plant under the chronic co-exposure of PAHs and PTEs were investigated and microbial interaction networks were built to reveal microbial co-occurrence patterns. The results indicated that the concentrations of PAHs in the soil inside the coking plant were significantly higher than those outside the plant. The mean concentration of ∑16PAHs was 2894.4 ng·g^-1, which is 5.58 times higher than that outside the plant. The average Hg concentration inside the coking plant was 22 times higher than the background value of Hebei province. The soil fungal community inside the coking plant showed lower richness compared with that of outside community, and there are significant difference in the bacterial and fungal community composition between inside and outside of coking plant (p < 0.01). Predicted contribution of different environmental factors to each dominant species based on random forest identified 20 and 25 biomarkers in bacteria and fungi, respectively, that were highly sensitive to coking plant soil in operation, such as Betaproteobacteria，Sordariomycetes and Dothideomycetes. Bacterial and fungal communities were shaped by the soil chemical properties (pH), PTEs (Hg), and PAHs together in the coking plant soils. Furthermore, the bacterial and fungal interaction patterns were investigated separately or jointly by intradomain and interdomain networks. Competition is the main strategy based on the co-exclusion pattern in fungal community, and the competitive relationship inside the coking plant is more complex than that outside the plant. In contrast, cooperation is the dominant strategy in bacterial networks based on the co-occurrence pattern. The present study provided insights into microbial response strategies and the interactions between bacteria and fungi under long-term combined contamination.

Exploring the variation of bacterial community and nitrogen transformation functional genes under the pressure of heavy metals in different coastal mariculture patterns

Equilibrium in microbial dynamics and nitrogen transformation in the sediment is critical for maintaining healthy mariculture environment. However, our understanding about the impact of heavy metals on the bacterial community and nitrogen transformation functional genes in different mariculture patterns is still limited. Here, we analyzed 30 sediment samples in the vertical distribution from three different mariculture patterns mainly include open mariculture zone (K), closed mariculture pond (F) and pristine marine area (Q). Illumina MiSeq Sequencing was applied to investigate the bacterial community and structure in the sediment. Quantitative polymerase chain reaction (qPCR) was used to determine the effect of heavy metals on nitrogen transformation functional genes. Results showed that bacterial community and structure varied greatly in different mariculture patterns. Chloroflexi, Proteobacteria and Desulfobacterota were predominant phyla in the coastal mariculture area. High concentrations of heavy metals mainly enriched in the up layer (5-40 cm) of the sediment in the mariculture zone. The abundance of functional genes in the closed mariculture pond was much higher than the open mariculture zone and pristine marine area. And the high abundance of nitrification and denitrification functional genes mainly accumulated at the depth from 5 cm to 40 cm. Heavy metals content such as Fe, Cr, Mn, Ni, As, Cd, Pb and nutrient content NH₄⁺-N, NO₃^--N and NO₂^--N were highly associated with bacterial community and nitrogen transformation functional genes. This study comprehensively elaborated the effect of heavy metals on the bacterial community and nitrogen transformation functional genes in different coastal mariculture patterns, indicating the possible role of closed mariculture pond in reducing nitrogen transformation efficiency, which will provide useful information for preventing pollution risk in the mariculture area.

Heavy Metals Contained Within a Pb-Zn Waste Heap Exhibit Selective Association with Microbial Modules as Revealed by Network Analysis

Heavy metal contamination is a global environmental concern due to its persistence and toxicity. To explore soil microbial interaction mechanisms and their association with heavy metals on a Pb-Zn waste heap, ecological network analysis tools were used to analyze high-throughput data in microbiology. The microbial network was divided into several modules, but heavy metals were associated with specific modules. The heavy metal-tolerant module (M2) had a more negative than positive relationship with the heavy metal-mid-tolerant modules (M1 and M3). Tight coupling between fungal and bacterial operational taxonomic units (OTUs) within M2 was critical for module stability and heavy metal bioremediation. Additionally, members within M2 needed to form a positive relationship to cope with heavy metal contamination (As, Pb, Zn, Cu, and Cd). The study provides fundamental information for a deeper understanding of heavy metal bioremediation mechanisms in the Pb-Zn waste heap.

Effects of Comamonas testosteroni on dissipation of polycyclic aromatic hydrocarbons and the response of endogenous bacteria for soil bioremediation

Bioremediation is a promising method of treating polycyclic aromatic hydrocarbons (PAHs) in contaminated soil; however, the understanding of the efficiency and the way of microbial inoculants work in complex soil environments is limited. Comamonas testosteroni (Ct) strains could efficiently degrade PAHs, especially naphthalene (Nap) and phenanthrene (Phe). This study aimed to explore the functional role of Ct in soil indigenous microorganisms and analyze the effect of Ct addition on PAHs concentration in PAH-contaminated soil. The results showed that inoculation with Ct degraded naphthalene (Nap), phenanthrene (Phe), and benzo [α] pyrene (BaP) significantly; the degradation rates were 63.38%, 81.18%, and 37.98% on day 25, respectively, suggesting that the low molecular weights of Nap and Phe were more easily degraded by microorganisms than those of BaP. We speculated that BaP and Phe might be converted into Nap for further degradation, which is the main reason for the low degradation rate of Nap detected after 10-25 days. Network analysis showed that inoculation with Ct significantly increased bacteria community abundance closely related to PAHs. Structural equation models confirmed that Steroidobacter, as functional bacteria, could affect the degradation of Nap and BaP. Inoculated Ct effectively enhanced the synergy among indigenous bacteria to degrade PAHs. This finding will help understand the function of inoculated Ct strains in PAH-contaminated soil at the laboratory level.

Effect of superphosphate addition on heavy metals speciation and microbial communities during composting

Superphosphate fertilizer (SSP) as an additive can reduce the nitrogen loss and increase available phosphorus in composting but few studies investigated the effect of SSP addition on heavy metal and microbial communities. In this study, different ratios (10%, 18%, 26%) of SSP were added into pig manure composting to assess the changes of heavy metal (Cu, Mn, As, Zn, and Fe) fractions, bacterial and fungal communities as well as their interactions. SSP addition at 18% had lower ecological risk but still increased the bioavailability of Cu, Mn, and Fe in composts compared to control. Adding 18% SSP into compost decreased bacterial number and increased the fungal diversity compared to CK. Redundancy analysis indicated heavy metal fractions correlated significantly with bacterial and fungal community compositions in composting with 18% SSP. Network analysis showed adding 18% SSP increased microbial interaction and positive cooperation especially enhanced the proportion of Proteobacteria and Ascomycota.

Fungal community enhanced humification and influenced by heavy metals in industrial-scale hyperthermophilic composting of municipal sludge

The succession of fungal community and effects of heavy metals on fungi during industrial-scale hyperthermophilic composting of municipal sludge remain unclear. Results showed hyperthermophilic composting enhanced decomposition and humification of municipal sludge in the short terms, while heavy metal concentrations and speciation had no significant change with high copper and zinc levels (101-122 and 292-337 mg/kg, respectively) in compost samples. The fungal community and its ecological assembly displayed dynamic change during hyperthermophilic composting. Some thermophilic-resistant fungi, such as phylum Ascomycota and genera Candida, Aspergillus, Thermomyces and Petriella dominated in hyperthermophilic phase. Heavy metals served important effects on fungal community structure and functions during composting. Some fungal drivers (e.g., Thermomyces, Petriella and Schizophyllum) and keystone fungi (e.g., Candida and Pichia) might be thermophilic- and heavy metal-resistant fungi which played important roles in decomposition and humification of municipal sludge. This study reveals fungal community accelerating humification and its influencing factors during composting.

Large-scale microbiome analysis reveals bacterial community characteristics in typical Chinese herbal slices

Chinese herbal slices (CHSs) are closely associated to microorganisms, whether they are endophytic or epiphytic in plants, or introduced during processing. In this study, the structures and predicted functions of microbial communities in 150 batches of samples from five types of CHSs were investigated by combining pure culture and 16 S rDNA amplicon sequencing. Bile-salt-tolerant gram-negative bacteria were detected in 56.0% of samples, and Salmonella was detected in two batches of Glycyrrhiza slices and in one batch of Rheum slices. The main genera from the Enterobacteriaceae, Bacillaceae, Fibrobacteraceae, and Pseudomonadaceae families were assessed in typical colonies. Amplicon sequencing identified 1200 bacterial genera, including some pharmacopeial-controlled bacteria and many beneficial endophytes of medicinal plants. Around 65% of the genera co-occurred in all five CHSs. In clustering based on different algorithms, the samples from each CHS type were relatively clustered, with some overlap. Ranked from highest to lowest diversity, the CHSs were Rheum, Angelica, Astragalus, Codonopsis, and Glycyrrhiza. Each CHS had its indicator species. Functional annotations suggest that potential microbial transformation uses CHSs as substrates and microbial communities as transformants. Overall, it was demonstrated that, based on their complementary advantages, high-throughput sequencing technology and traditional pure-culture technology together can fully assess the microbial load of CHSs and reduce the misdetection rate. We observed large microbial communities in typical CHSs, demonstrating differences and similarities among different CHS types. These results provide a reference for establishing new microbial limit criteria for CHSs and highlight the importance of further correlating CHS microbial community structure and function.

Coordination of bacterial biomarkers with the dominant microbes enhances triclosan biodegradation in soil amended with food waste compost and cow dung compost

Increasing concerns regarding the micropollutant triclosan (TCS) derive from its potential threats to human health and ecological security. Compost addition have been verified to be effective in soil remediation, however, the biodegradation of TCS under compost amendment in soil remain unclear. This study investigated the removal of TCS in soils amended with food waste compost (FS), cow dung compost (CS) and sludge compost (SS), respectively, explored the key TCS-degraders and biological mechanisms of TCS removal. Compost addition significantly enhanced the removal of TCS (p < 0.05) in the order of FS > CS > SS. The dosage of 20% (w/w) was the most efficient one and the ultimate concentrations of TCS were decreased by 76.67%, 67.90% and 56.79% compared with CK, respectively. The abundance of key dominant bacterial genus (7 in FS and 4 in CS) and fungal genus (3 in FS and CS) was stimulated due to the increase of soil nutrient factors (including dissolved organic carbon, DOC; soil organic matter, SOM; ammonium nitrogen, NH₄⁺; nitrate nitrogen, NO₃^-) and the decrease of pH. A negative correlation between these dominant microbes and TCS concentration indicated their potential effect on TCS degradation. A total of four bacterial biomarkers, namely Saccharomonospora, Aequorivita, Bacillaceae and Fodinicurvataceae (both at family level) were the key TCS-degraders. Structural equation model (SEM) indicated that the improvement of soil nutrient factors in FS and CS promoted TCS biodegradation by improving the activity of bacterial biomarkers, as while, the key dominant microbes showed good tolerance to TCS stress. However, there were no significant biological effects on TCS in SS group. Network analysis further confirmed that it was the coordination of bacterial biomarkers with the dominant microbes that enhanced TCS biodegradation in soil amended with food waste compost and cow dung compost.

How microorganisms tell the truth of potentially toxic elements pollution in environment

Potentially toxic elements (PTEs) posed a major hazard to microbial community in river sediments, but the way how different kinds of microorganisms responses to elements pollution has not been clearly understood. The target of this research was to discriminate the apposite indicators for diagnosing elements pollution based on the sensitivity of microbial abundance, biodiversity, predicted metabolic functions to PTEs (Cu, Cd, Cr, Ni, Pb, Zn, As and Hg). Considering Huaihe River Basin as the main subject, sediment samples were gathered from 135 sites. Ni, Zn and Cd significantly influenced the microbial communities and predicted functions. In general, the microbial sensitivity to PTEs was bacteria > archaea. Geo-accumulation index and potential ecological risk (PER) index suggested Hg and Cd were the significant contaminates and posed the most serious ecological risk in sediments. Structural Equation Model identified the bioindicators 1/nitrate reduction and rara taxa (Azoarcus) as reflect and speculate Hg and Cd pollution, respectively. PER was predicted by 1/nitrate reduction and rare taxa (Phaeodactylibacter and Illumatobacter). Results elucidated the rather role of rare taxa in indicating PTEs pollution. The findings contributed to provide useful reference for bioremediation of contaminated sediments under PTEs stress.

Insights into the associations of copper and zinc with nitrogen metabolism during manure composting with shrimp shell powder

The application of shrimp shell powder (SSP) in manure composting can promote the maturation of compost and reduce the associated environmental risk. This study investigated the response of adding SSP at different levels (CK: 0, L: 5%, M: 10%, and H: 15%) on heavy metal resistance genes (MRGs), nitrogen functional genes, enzymes, and microorganisms. SSP inhibited nitrification and denitrification via decreasing the abundances of functional genes and key enzymes related to Cu, Zn, and MRGs. The nitrate reductase and nitrous-oxide reductase in the denitrification pathway were lower under H. Phylogenetic trees indicated that Burkholderiales sp. had strong relationships with OTU396 and OTU333, with important roles in the nitrogen cycle and plant growth. Redundancy analysis and structural equation modeling showed the complex response between heavy metal and nitrogen that bio-Cu and bio-Zn had positive significantly relationships with nirK-type and amoA-type bacteria, and amoA-type bacteria might be hotspot of cueO.

Soil pH Filters the Association Patterns of Aluminum-Tolerant Microorganisms in Rice Paddies

Soil microbes are considered the second genome of plants. Understanding the distribution and network of aluminum (Al)-tolerant microorganisms is helpful to alleviate Al toxicity to plants in acidic soils. Here, we examined soluble Al³⁺ and bacterial communities carrying Al resistance genes in paddy soils with a soil pH range of 3.6 to 8.7. In the acidic soil with pH <5.1, the content of Al³⁺ increased significantly. There were abundant and diverse Al-tolerant microorganisms in acidic soils, including Clostridium, Bacillus, Paenibacillus, Desulfitobacterium, and Desulfosporosinus, etc. Moreover, compared with neutral and alkaline soils, the network structure of Al-tolerant microorganisms was more complex. The potential roles of major Al-tolerant microbial taxa on each other in the ecological network were identified by a directed network along 0.01 pH steps. The influential taxa in the network had a broader niche and contained more antioxidant functional genes to resist Al stress, indicating their survival advantage over the sensitive taxa. Our study is the first to explore the distribution of Al-tolerant microorganisms in continental paddies and reveal their potential associations mediated by pH, which provides a basis for further utilization of microbial resources in acidic agricultural soils. IMPORTANCE Aluminum (Al) toxicity is the primary limiting factor of crop production in acidic soils with pH <5.0. Numerous studies have focused on the mechanism of Al toxicity and tolerance in plants; however, the effects of Al toxicity on soil microorganisms and their tolerance remain less studied. This study investigated the distribution and association patterns of Al-tolerant microorganisms across continental paddy fields with a soil pH range of 3.6 to 8.7. The results showed that soil pH filters exchangeable Al³⁺ content, diversity, and potential associations of Al-tolerant microbial community. The influential taxa in community network play an important role in Al tolerance and have potential applications in mitigating Al toxicity and promoting crop growth in acidic soils.

Effects of heavy metals stress on chicken manures composting via the perspective of microbial community feedback

Heavy metal pollution was the main risk during livestock manures composting, in which microorganisms played a vital role. However, response strategies of microbial community to heavy metals stress (HMS) remained largely unclear. Therefore, the objective of this study was to reveal the ecological adaptation and counter-effect of bacterial community under HMS during chicken manures composting, and evaluating environmental implications of HMS on composting. The degradation of organic matters (more than 6.4%) and carbohydrate (more than 19.8%) were enhanced under intense HMS, suggesting that microorganisms could quickly adapt to the HMS to ensure smooth composting. Meanwhile, HMS increased keystone nodes and strengthened significant positive correlation relationships between genera (p < 0.05), indicating that bacteria resisted HMS through cooperating during composting. In addition, different bacterial groups performed various functions to cope with HMS. Specific bacterial groups responded to HMS, and certain groups regulated bacterial networks. Therefore, bacterial community had the extraordinary potential to deal with HMS and guarantee chicken manures composting even in the presence of high concentrations of heavy metals.

Responses of heavy metals mobility and resistant bacteria to adding time of activated carbon during chicken manure composting

With the wide application of compost in agriculture, heavy metals (HMs) continue to accumulate in the soil environment, which poses a great threat to the health of the soil environment. Therefore, it is critical for effectively reduce the mobility of HMs. In this study, the influence of activated carbon (AC) addition time on mobility of HMs (Cu, Zn and Pb) and HMs resistant bacteria structure were evaluated during chicken manure composting. The result showed that the addition of AC in the thermophilic period could effectively reduce the mobility of HMs. Subsequently, high-throughput sequencing results showed that the dominant phyla were Proteobacteria, Firmicutes, Actinbacteria, Deinococcus-Thermus, Chloroflexi, Gemmatimonadetes and Bacteroidetes within the sample, which were ubiquitous and abundant in composting. The Redundancy analysis (RDA) results indicated that the mobility of HMs (Cu, Zn and Pb) by superior bacteria fate varied in AC amendment composting. Ultimately, a regulation method is proposed to influence the mobility of HMs by regulating the bacteria community in the AC compost. Our current studies suggest that the addition of AC during compost preparation (thermophilic period) is an effective strategy in regulating the mobility (bioavailability) of HMs, thereby significantly reducing environmental pollution problems.

Give priority to abiotic factor of phosphate additives for pig manure composting to reduce heavy metal risk rather than bacterial contribution

Phosphate additives especially superphosphate can reduce nitrogen loss, and increase phosphorus availability in composting. This study investigated the changes of different heavy metals fractions and their relationship with bacterial community and abiotic factors during pig manure composting with adding equimolar H₃PO₄, H₂SO₄ and K₂HPO₄. Results showed that both acidic and alkaline labile phosphate increased the potential ecological risk of heavy metals compared to control, but K₂HPO₄ decreased the accumulation of exchangeable Zn and Mn by 12% and 15% than that with H₃PO₄ and H₂SO₄ addition. Network analysis showed that K₂HPO₄ enhanced the proportion of negative links in bacterial species with heavy metals, but H₃PO₄ decreased the stability of bacterial network. Redundancy analysis demonstrated that pH was the key factor on metal speciation and risk with phosphate additives than bacterial role. The study presented theoretical basis for additive selection in controlling composting nitrogen fixation and environmental risk.

Microbial community profiles in soils adjacent to mining and smelting areas: Contrasting potentially toxic metals and co-occurrence patterns

Mining and smelting activities have introduced severe potentially toxic metals (PTMs) contamination into surrounding soil settings. Influences of PTMs on microbial diversity have been widely studied. However, variations of microbial communities, network structures and community functions in different levels of PTMs contaminated soils adjacent to mining and smelting aera are still poorly investigated. In this study, microbial communities of soils around different levels of PTMs contamination were comprehensively studied by 16S rRNA gene amplicons high-throughput sequencing. Microbial interactions and module functions were also exploited to ascertain the discrepancies of PTMs concentration levels on microbial ecological functions. Results indicated that the microbial community composition was significantly distinct attributed to the phylum Protebacteria (p = 0.002) dominating in soil with high level PTMs contents but Actinobacteria (p = 0.002) in low level of PTMs-contaminated soil. Microbial α diversity was not significantly influenced by different levels of PTMs contaminations. Microorganisms proactively responded to PTMs content levels by means of strengthening network complexities and modularities among microbe-microbe interactions. The functions of main network modules were predicted associating membrane transport, amino acid metabolism, energy metabolism and carbohydrate metabolism. The PTMs detoxification and anti-oxidation were significantly strengthened at the high level of PTMs contamination. The present study demonstrated that modification of microbial community by the adaptive adjustment of microbial compositions and strengthening their network complexity and modularity.

Inoculation of phosphate-solubilizing bacteria (Bacillus) regulates microbial interaction to improve phosphorus fractions mobilization during kitchen waste composting

Bacillus presents in most composts as core microbial taxa and is widely used as inoculant in composting. However, the role of Bacillus as phosphate-solubilizing bacteria (PSB) inoculant in composting and the response of indigenous bacterial community are unclear. This study used redundancy analysis (RDA), network analysis and structural equation model (SEM) to investigate the dynamics of phosphorus (P) fractions, bacterial community, and microbial interaction in composting with PSB (Bacillus sp. P6) inoculation. Results indicated that Bacillus inoculation increased Olsen P content, organic matter degradation, and bacterial diversity, benefiting P fractions mobilization during composting. RDA showed that pH was the main factor influencing P fractions transformation and bacterial taxa. Network analysis and SEM revealed that Bacillus indirectly improved the contribution of bacterial community on P mobilization by enhancing microbial interactions. Therefore, Bacillus with P solubilizing function may be a potential inoculant to regulate the biotic process of P transformation.

Improving the Strength and Leaching Characteristics of Pb-Contaminated Silt through MICP

Microbial-induced carbonate precipitation (MICP) is an effective technology for repairing sites contaminated by heavy metals. In this work, Sporosarcina pasteurii was cultured and mixed with a cementing fluid as a binder to remediate Pb-contaminated silt. The effects of varying experimental parameters, including Pb concentration and dry density, were also tested and analyzed. The leaching and strength characteristics and the MICP improvement mechanism of the Pb-contaminated silt were studied. Samples with dry densities of 1.50 g/cm3 and 1.55 g/cm3 exhibited the highest unconfined compression strengths (UCS). Scanning electron microscopy showed that not all CaCO3 crystals produced a cementation effect, with some filling pores in an invalid cementation form. The results showed that MICP remediation of low Pb2+ concentration-contaminated silt could meet the relevant Chinese environmental safety standards. Low Pb concentrations helped improve MICP-treated, Pb-contaminated silt strength, whereas high Pb concentrations significantly reduced this strength. Testing to determine the tolerance of an active microbe, Sporosarcina pasteurii, showed that trace amounts of Pb promoted its growth, thus improving the MICP effect, whereas excessive Pb had a toxic effect, which reduced MICP effectiveness. Mercury injection experiments showed that MICP produced CaCO3; this mainly filled soil mesopores and macropores and, thus, improved the soil UCS. Scanning electron microscopy showed that not all CaCO3 crystals produced a cementation effect, with some filling pores in an invalid cementation form. MICP was innovatively applied to silt sites with heavy metal pollutants while considering the soil compaction in actual construction, thus broadening the application scope of MICP, optimizing the construction process, and reducing the construction cost.

Anaerobic digestion of chicken manure: Sequences of chemical structures in dissolved organic matter and its effect on acetic acid production

The use of chicken manure (CM) leads to serious environmental pollution due to the existence of bacteria and insect pests. Anaerobic digestion (AD) is one of the important technologies of CM treatment. However, methane production is limited by the accumulation of short-chain fatty acids (SCFAs) from AD. Therefore, the study explored the possible formation mechanism of acetic acid by understanding the effect of sequences of chemical structure variation in DOM on acetic acid production. The chemical structures of DOM were observed. The tyrosine-like substances (C1, 53.53-29.99%) and humic-like substances (C3, 18.38-5.96%) showed a tendency to decrease. Tryptophan-like substances (C2, 28.09-64.04%) showed the increasing trend. The results indicated that C2 was unwilling to biodegrade. In DOM, the order of biodegradability was C2< C1< C3. AD resulted in the enrichment of N-H in-plane (0-22.75%) and COO- stretch (7.53-18.57%) and the loss of O-H stretch (19.39-13.72%), C-H stretch (4.56%-0), CC stretch (12.04-9.61%) and C-O stretch (10.02-5.03%). Two-dimensional correlation spectroscopy is applied to investigate the sequences of chemical structures in DOM, the order is as follows: CC stretch > COO- stretch > N-H in-plane > C-O stretch. The result confirmed that protein was rapidly decomposed and utilized, which would result in the increase of microorganism metabolism and hydrolysis rate, polysaccharide was hydrolyzed to form phenol and carboxylic acid. Four possible pathways were identified in AD by the structural equation model. C1and hydroxyl can promote propionic and butyric acid formation by the pathway of valeric or iso-butyric acid production and further effected acetic acid production. This study proposed the possible formative mechanisms of acetic acid according to sequences of chemical structures variation in DOM during AD, which can provide the theoretical basis for directional regulating the conversion of different chemical structures of DOM into acetic acid in AD.

Patterns of heavy metal resistant bacterial community succession influenced by biochar amendment during poultry manure composting

The purpose of this study was to investigate the heavy metal resistant bacteria (HMRB) community succession and bacterial activity in poultry manure (PM) composting. Five different concentration of chicken manure biochar (CMB) at 0%, 2%, 4%, 6%, and 10% on a dry weight basis was applied with initial feedstock (poultry manure + wheat straw) and indicated with T1, T2, T3, T4, and T5. In addition, high-throughput sequencing, principal coordinate analysis, and correlation analysis were used to analyze the evolution of HMRB communities during composting. The study indicated that crucial phyla were Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. The bacterial diversity in the CMB amendment treatment was higher than in the control treatment, and T4 treatment has the highest among all CMB applied treatments. Moreover, results from CCA indicated that T4 and T5 treatments quickly enters the high-temperature period which is maintained for 5 days, and is significantly positively correlated with Proteobacteria, and Actinobacteria. These findings offer insight into potential strategies to understand the succession of HMRBs during PM reuse. Overall, the above results show the addition of 6% biochar (T4) was potentially beneficial to enrich the abundance of bacterial community to improve composting environment quality and composting efficiency. In addition, effective to immobilized the heavy metals and HMRB in the end product.

Pollution control in biochar-driven clean composting: Emphasize on heavy metal passivation and gaseous emissions mitigation

Present study was focus on the pollution control aspect of gaseous mitigation and heavy metal passivation as well as their associated bacterial communities driven by apple tree branch biochar (BB) during sheep manure composting. Six treatment was performed with distinct concentration of BB from 0%, 2.5%, 5%, 7.5%, 10%, and 12.5% as T1 to T6. Compared with compost without additive, biochar-based composting recorded faster thermophilic process (4thd) and longer duration (12-14d), lower gaseous emission in terms of ammonia (5.37-10.29 g), nitrous oxide (0.12-0.47 g) and methane (4.38-30.29 g). Notably highest temperature (65.3 ℃) and active thermophilic duration (14d), minimized gaseous volatilization were detected in 10%BB composting. Aspect of non-degradability and enrichment-concentration properties of heavy metals, the total copper (Cu) and zinc (Zn) were increased (from initial 12.71-17.91 to final 16.36-29.36 mg/kg and 107.39-146.58-161.48-211.91 mg/kg). In view of available diethylene triamine pentacetic acid (DTPA) extractable form, DTPA-Cu and DTPA-Zn from 4.29 to 6.57 and 31.66-39.32 mg/kg decreased to 3.75-4.82 and 23.43-40.54 mg/kg, especially the maximized passivation rate of 46.95% and 56.27% were present in 10%BB composting. Additionally, bacterial diversity of biochar-based composting was increased (1817-2310 OTUs) than control (1686 OTUs) and dominant by Firmicutes (52.75%), Bacteroidetes (28.41%) and Actinobacteriota (13.98%). Validated 10% biochar-based composting is the optimal option for effectively control environmental pollution to obtain hygienic composting.