Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China

Effects of aeolian deposition on soil properties and microbial carbon metabolism function in farmland of Songnen Plain, China

The effects of wind erosion, one of the crucial causes of soil desertification in the world, on the terrestrial ecosystem are well known. However, ecosystem responses regarding soil microbial carbon metabolism to sand deposition caused by wind erosion, a crucial driver of biogeochemical cycles, remain largely unclear. In this study, we collected soil samples from typical aeolian deposition farmland in the Songnen Plain of China to evaluate the effects of sand deposition on soil properties, microbial communities, and carbon metabolism function. We also determined the reads number of carbon metabolism-related genes by high-throughput sequencing technologies and evaluated the association between sand deposition and them. The results showed that long-term sand deposition resulted in soil infertile, roughness, and dryness. The impacts of sand deposition on topsoil were more severe than on deep soil. The diversity of soil microbial communities was significantly reduced due to sand deposition. The relative abundances of Nitrobacteraceae, Burkholderiaceae, and Rhodanobacteraceae belonging to α-Proteobacteria significantly decreased, while the relative abundances of Streptomycetaceae and Geodermatophilaceae belonging to Actinobacteria increased. The results of the metagenomic analysis showed that the gene abundances of carbohydrate metabolism and carbohydrate-activity enzyme (GH and CBM) significantly decreased with the increase of sand deposition amount. The changes in soil microbial community structure and carbon metabolism decreased soil carbon emissions and carbon cycling in aeolian deposition farmland, which may be the essential reasons for land degradation in aeolian deposition farmland.

Sulfur/zinc co-doped biochar for stabilization remediation of mercury-contaminated soil: Performance, mechanism and ecological risk

In this study, a novel sulfur/zinc co-doped biochar (SZ-BC) stabilizer was successfully developed for the remediation of mercury-contaminated soil. Results from SEM, TEM, FTIR and XRD revealed that biochar (BC) was successfully modified by sulfur and zinc. In the batch adsorption experiments, the sulfur-zinc co-pyrolysis biochar displayed excellent Hg(II) adsorption performance, with the maximum adsorption capacity of SZ-BC (261.074 mg/g) being approximately 16.5 times that of BC (15.855 mg/g). Laboratory-scale static incubation, column leaching, and plant pot experiments were conducted using biochar-based materials. At an additional dosage of 5 % mass ratio, the SZ-BC exhibits the most effective stabilization of mercury in soil, leading to a significant reduction in leaching loss compared to the control group (CK) by 51.30 %. Following 4 weeks of incubation and 2 weeks of leaching with SZ-BC, the residual mercury in the soil increased by 27.84 %. As a result, potential ecological risk index of mercury decreased by 92 % compared to the CK group. In the pot experiment, SZ-BC significantly enhanced the growth of Chinese cabbage, with biomass and root dry weight reaching 3.20 and 2.80 times that of the CK group, respectively. Additionally, the Translocation Factor (TF) and Bioconcentration Factor (BF) were reduced by 44.86 % and 74.43 %, respectively, in the SZ-BC group compared to the CK group. Moreover, SZ-BC can effectively improve enzyme activities and increase microbial communities in mercury-contaminated soils. The mechanisms of adsorption and stabilization were elucidated through electrostatic adsorption, ion exchange, surface complexation, and precipitation. These findings provide a potentially effective material for stabilizing soils contaminated with mercury.

Can Mercury Influence Carbon Dioxide Levels? Implications for the Implementation of the Minamata Convention on Mercury

The Paris Agreement and the Minamata Convention on Mercury are two of the most important environmental conventions being implemented concurrently, with a focus on reducing carbon and mercury emissions, respectively. The relation between mercury and carbon influences the interactions and outcomes of these two conventions. This perspective investigates the link between mercury and CO2, assessing the consequences and exploring the policy implications of this link. We present scientific evidence showing that mercury and CO2 levels are negatively correlated under natural conditions. As a result of this negative correlation, the CO2 level under the current mercury reduction scenario is predicted to be 2.4-10.1 ppm higher than the no action scenario by 2050, equivalent to 1.0-4.8 years of CO2 increase due to human activity. The underlying causations of this negative correlation are complex and need further research. Economic analysis indicates that there is a trade-off between the benefits and costs of mercury reduction actions. As reducing mercury emission may inadvertently undermine efforts to achieve climate goals, we advocate for devising a coordinated implementation strategy for carbon and mercury conventions to maximize synergies and reduce trade-offs.

Bioindicator responses to extreme conditions: Insights into pH and bioavailable metals under acidic metal environments

Acid mine drainage (AMD) caused environmental risks from heavy metal pollution, requiring treatment methods such as chemical precipitation and biological treatment. Monitoring and adapting treatment processes was crucial for success, but cost-effective pollution monitoring methods were lacking. Using bioindicators measured through 16S rRNA was a promising method to assess environmental pollution. This study evaluated the effects of AMD on ecological health using the ecological risk index (RI) and the Risk Assessment Code (RAC) indices. Additionally, we also examined how acidic metal stress affected the diversity of bacteria and fungi, as well as their networks. Bioindicators were identified using linear discriminant analysis effect size (LEfSe), Partial least squares regression (PLS-R), and Spearman analyses. The study found that Cd, Cu, Pb, and As pose potential ecological risks in that order. Fungal diversity decreased by 44.88% in AMD-affected areas, more than the 33.61% decrease in bacterial diversity. Microbial diversity was positively correlated with pH (r = 0.88, p = 0.04) and negatively correlated with bioavailable metal concentrations (r = -0.59, p = 0.05). Similarly, microbial diversity was negatively correlated with bioavailable metal concentrations (bio_Cu, bio_Pb, bio_Cd) (r = 0.79, p = 0.03). Acidiferrobacter and Thermoplasmataceae were prevalent in acidic metal environments, while Puia and Chitinophagaceae were identified as biomarker species in the control area (LDA>4). Acidiferrobacter and Thermoplasmataceae were found to be pH-tolerant bioindicators with high reliability (r = 1, P < 0.05, BW > 0.1) through PLS-R and Spearman analysis. Conversely, Puia and Chitinophagaceae were pH-sensitive bioindicators, while Teratosphaeriaceae was a potential bioindicator for Cu-Zn-Cd metal pollution. This study identified bioindicator species for acid and metal pollution in AMD habitats. This study outlined the focus of biological monitoring in AMD acidic stress environments, including extreme pH, heavy metal pollutants, and indicator species. It also provided essential information for heavy metal bioremediation, such as the role of omics and the effects of organic matter on metal bioavailability.

Soil organic matter degradation and methylmercury dynamics in Hg-contaminated soils: Relationships and driving factors

Biodegradation of soil organic matter (SOM), which involves greenhouse gas (GHG) emissions, plays an essential role in the global carbon cycle. Over the past few decades, this has become an important research focus, particularly in natural ecosystems. SOM biodegradation significantly affects contaminants in the environment, such as mercury (Hg) methylation, producing highly toxic methylmercury (MeHg). However, the potential link between GHG production from SOM turnover in contaminated soils and biogeochemical processes involving contaminants remains unclear. In this study, we investigated the dynamics of GHG, MeHg production, and the relationship between biogeochemical processes in soils from two typical Hg mining sites. The two contaminated soils have different pathways, explaining the significant variations in GHG and MeHg production. The divergence of the microbial communities in these two biogeochemical processes is essential. In addition to the microbial role, abiotic factors such as Hg species can significantly affect MeHg production. On the other hand, we found an inverse relationship between CH4 and MeHg, suggesting that carbon emission reduction policies and management could inadvertently increase the MeHg levels. This highlights the need for an eclectic approach to organic carbon sequestration and contaminant containment. These findings suggest that it is difficult to establish a general pattern to describe and explain the SOM degradation and MeHg production in contaminated soils within the specific scenarios. However, this study provides a case study and helpful insights for further understanding the links between environmental risks and carbon turnover in Hg mining areas.

Selenium- and chitosan-modified biochars reduce methylmercury contents in rice seeds with recruiting Bacillus to inhibit methylmercury production

Biochar could reshape microbial communities, thereby altering methylmercury (MeHg) concentrations in rice rhizosphere and seeds. However, it remains unclear whether and how biochar amendment perturbs microbe-mediated MeHg production in mercury (Hg) contaminated paddy soil. Here, we used pinecone-derived biochar and its six modified biochars to reveal the disturbance. Results showed that selenium- and chitosan-modified biochar significantly reduced MeHg concentrations in the rhizosphere by 85.83% and 63.90%, thereby decreasing MeHg contents in seeds by 86.37% and 75.50%. The two modified bicohars increased the abundance of putative Hg-resistant microorganisms Bacillus, the dominant microbe in rhizosphere. These reductions about MeHg could be facilitated by biochar sensitive microbes such as Oxalobacteraceae and Subgroup_7. Pinecone-derived biochar increased MeHg concentration in rhizosphere but unimpacted MeHg content in seeds was observed. This biochar decreased the abundance in Bacillus but enhanced in putative Hg methylator Desulfovibrio. The increasing MeHg concentration in rhizosphere could be improved by biochar sensitive microbes such as Saccharimonadales and Clostridia. Network analysis showed that Saccharimonadales and Clostridia were the most prominent keystone taxa in rhizosphere, and the three biochars manipulated abundances of the microbes related to MeHg production in rhizosphere by those biochar sensitive microbes. Therefore, selenium- and chitosan-modified biochar could reduce soil MeHg production by these microorganisms, and is helpful in controlling MeHg contamination in rice.

Labile carbon inputs boost microbial contribution to legacy mercury reduction and emissions from industry-polluted soils

Soils is a crucial reservoir influencing mercury (Hg) emissions and soil-air exchange dynamics, partially modulated by microbial reducers aiding Hg reduction. Yet, the extent to which microbial engagements contribute to soil Hg volatilization remains largely unknown. Here, we characterized Hg-reducing bacterial communities in natural and anthropogenically perturbed soil environments and quantified their contribution to soil Hg(0) volatilization. Our results revealed distinct Hg-reducing bacterial compositions alongside elevated mercuric reductase (merA) gene abundance and diversity in soils adjacent to chemical factories compared to less-impacted ecosystems. Notably, solely industry-impacted soils exhibited increased merA gene abundance along Hg gradients, indicating microbial adaption to Hg selective pressure through quantitative changes in Hg reductase and genetic diversity. Microcosm studies demonstrated that glucose inputs boosted microbial involvement and induced 2-8 fold increments in cumulative Hg(0) volatilization in industry-impacted soils. Microbially-mediated Hg reduction contributed to 41.6% of soil Hg(0) volatilization in industry-impacted soils under 25% water-holding capacity and glucose input conditions over a 21-day incubation period. Alcaligenaceae, Moraxellaceae, Nitrosomonadaceae and Shewanellaceae were identified as potential contributors to Hg(0) volatilization in the soil. Collectively, our study provides novel insights into microbially-mediated Hg reduction and soil-air exchange processes, with important implications for risk assessment and management of industrial Hg-contaminated soils.

Accumulation and risk assessment of mercury in soil as influenced by mercury mining/smelting in Tongren, Southwest China

To investigate the influence of mercury (Hg) mining/smelting on the surrounding soil environment, ninety soil samples were collected around Hg mining/smelting areas in Tongren city, Guizhou Province, Southwest China. The total mercury (THg), methylmercury (MeHg), bioavailability and fractions of Hg in the soil and their potential risk were evaluated. The results showed that Hg mining/smelting significantly increased the soil pH and decreased the soil organic matter content (p < 0.05). The THg content in the surrounding soil was much higher than that at the control site, with almost all the samples exceeding the national standard in China (3.4 mg/kg, GB15618-2018). Similarly, the concentrations of MeHg (0.09-2.74 μg/kg) and bioavailable Hg (0.64-62.94 μg/kg) in these soil samples were also significantly higher than those in the control site. However, the MeHg/THg ratio was significantly lower in mining/smelting influenced soils (0.01-0.68%) than in control soils (0.60-3.72%). Fraction analysis revealed that residual (RES-Hg) and organic matter-bounded (OM-Hg) Hg accounted for more than 50% of the THg. Ecological risk assessment revealed that the potential ecological risk for most of the Hg mining/smelting-influenced soils (30.16 ≤ Er ≤ 2280.02) were higher than those at the control site (15.12 ≤ Er ≤ 27.1). In addition, these Hg mining/smelting-influenced soils posed acceptable noncarcinogenic risks to adults (except for two soil samples), with hazard indices (HIs) ranging from 0.04 to 1.11 and a mean HI of 0.44. However, children suffer serious noncarcinogenic risks, with HIs ranging from 0.34 to 7.43 and a mean HI of 3.10.

Toxicity factors to assess the ecological risk for soil microbial communities

The toxicity factor (TF), a critical parameter within the potential ecological risk index (RI), is determined without accounting for microbial factors. It is considerable uncertainty exists concerning its validity for quantitatively assessing the influence of metal(loid)s on microorganisms. To evaluate the suitability of TF, we constructed microcosm experiments with varying RI levels (RI = 100, 200, 300, 500, and 700) by externally adding zinc (Zn), chromium (Cr), copper (Cu), lead (Pb), nickel (Ni), cadmium (Cd), and mercury (Hg) to uncontaminated soil (CK). Quantitative real-time PCR (qPCR) and high-throughput sequencing techniques were employed to measure the abundance and community of bacteria and fungi, and high-throughput qPCR was utilised to quantify functional genes associated with CNPS cycles. The results demonstrated that microbial diversity and function exhibited significant alterations (p < 0.05) in response to increasing RI levels, and the influences on microbial community structure, enzyme activity, and functional gene abundances were different due to the types of metal(loid)s treatments. At the same RI level, significant differences (p < 0.05) were discerned in microbial diversity and function across metal(loid) treatments, and these differences became more pronounced (p < 0.001) at higher levels. These findings suggest that TF may not be suitable for the quantitative assessment of microbial ecological risk. Therefore, we adjusted the TF by following three steps (1) determining the adjustment criteria, (2) deriving the initial TF, and (3) adjusting and optimizing the TF. Ultimately, the optimal adjusted TF was established as Zn = 1.5, Cr = 4.5, Cu = 6, Pb = 4.5, Ni = 5, Cd = 22, and Hg = 34. Our results provide a new reference for quantitatively assessing the ecological risks caused by metal(loid)s to microorganisms.

Corn straw biochar addition elevated phosphorus availability in a coastal salt-affected soil under the conditions of different halophyte litter input and moisture contents

Improving salt-affected soil health using different strategies is of great significance for Sustainable Development Goals. The effects of biochar as a sustainable carbon negative soil amendment on phosphorous (P) pools in the degraded salt-affected soils of the of coastal wetlands (as one of the primary blue carbon ecosystems) with halophyte litter input under different water conditions (the two intrinsic characteristics of coastal wetlands) are poorly understood. Thus, a corn straw derived biochar (CBC) was added into a coastal salt-affected soil collected from the Yellow River Delta to investigate its effect on P fractions and availability under the input of three different local halophyte litters (i.e., Suaeda salsa, Imperata cylindrica and Phragmites australis) and under the unflooded and flooded water conditions. The results showed that the individual input of Suaeda salsa increased soil P availability by 28.2-40.9 %, but Imperata cylindrica and Phragmites australis had little effect on P availability. CBC individual amendment more efficiently enhanced P availability in the unflooded soil than the flooded soil. However, the co-amendment of CBC with litters showed little synergistic effect on P availability. CBC sharply increased the proportion of Ca-bound labile P fraction, but moderately lifted the proportion of Al/Fe-bound mediumly labile P fraction. CBC-enhanced P availability and altered inorganic P fractions were mainly resulted from the provision of labile inherent P by biochar, improved soil properties (i.e., increased CEC), and altered bacterial community composition (i.e., elevated abundance of P-solubilizing and phosphate-accumulating bacteria). These findings give new insights into understanding P biogeochemical cycling in the coastal salt-affected soils amended with biochars, and will be helpful to develop biochar-based technologies for enhancing P pools and improving soil health of the blue carbon ecosystems.

The influence of cysteine in transformation of Cd fractionation and microbial community structure and functional profile in contaminated paddy soil

Remediating cadmium (Cd) contaminated paddy soil is vital for agroecology, food safety, and human health. Soil washing is more feasible to reduce remediation method due to its high efficiency. However, green, low-cost and more efficient washing agents are still required. In this study, we investigated the ability of cysteine as a washing agent for soil washing to remove Cd from contaminated paddy soil. Through a batch experiment, we evaluated the removal efficiency of cysteine as a washing agent by comparing their removal rate with that of a microbial inoculant and sulphuric acid as other washing agents. The transformation of Cd fractionation and microbial community structure and functional profile in paddy soils after cysteine leaching was studied by using sequential extraction and high-throughput sequencing. Results showed that cysteine had better efficiency in the removal of Cd from paddy soil in comparison to sulphuric acid and the microbial inoculant, and could achieve a maximum removal rate of 97 % Cd in paddy soil. Cysteine decreased the proportion of Cd in the exchangeable fraction, carbonate bound fraction, iron and manganese bound fraction, and organic matter bound fraction and was best for the removal of the residual fraction, which contributed to its higher Cd removal ability. Considering the economic benefits of the reagents used, cysteine was shown to be economically feasible for use as a leaching agent. In addition, cysteine could significantly increase the relative abundance of Thermochromatium, Sideroxydans, Streptacidiphilus, and Frankia which promoted the nitrogen and sulfur metabolism in the paddy soil. In summary, this study revealed that cysteine was readily available, cheap, non-toxic, highly efficient, and even has fertilizing properties, making it eco-friendly and ideal for remediation of Cd-contaminated paddy soils. Besides, the health of paddy soils would also benefit from cysteine's promotion of microbial nitrogen and sulfur metabolism.

Assessing microbial degradation potential of methylmercury in different types of paddy soil through short-term incubation

The neurotoxic methylmercury (MeHg) in paddy soils can accumulate in rice grains. Microbial demethylation is an important pathway of MeHg degradation in soil, but the effect of soil type on microbial degradation of MeHg remains unclear. Therefore, we investigated MeHg degradation in eight typical paddy soils and analyzed the associations between soil physiochemical properties and microbial degradation efficiencies of MeHg. Results showed that MeHg was significantly degraded in unsterilized paddy soils, and the microbial degradation efficiency ranged from 10.8% to 64.6% after a 30-day incubation. The high microbial degradation efficiency of MeHg was observed in the soils with high levels of clay content, whereas relatively low degradation efficiency was found in the red paddy soils. We identified that Paenibacillaceae was the most important microbial predictor of MeHg degradation and was positively correlated with the degradation efficiency in the soils. The abundances of these microbial taxa associated with MeHg degradation were positively correlated with clay content. In addition, Eh, pH, and SOC could influence microbial degradation of MeHg by regulating certain microbial communities. Our results indicate that soil type is crucial in driving MeHg degradation, which has important implications for the mitigation of MeHg pollution in various croplands.

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.

Microbial biomarkers of tree water status for next-generation biomonitoring of forest ecosystems

Next-generation biomonitoring proposes to combine machine-learning algorithms with environmental DNA data to automate the monitoring of the Earth's major ecosystems. In the present study, we searched for molecular biomarkers of tree water status to develop next-generation biomonitoring of forest ecosystems. Because phyllosphere microbial communities respond to both tree physiology and climate change, we investigated whether environmental DNA data from tree phyllosphere could be used as molecular biomarkers of tree water status in forest ecosystems. Using an amplicon sequencing approach, we analysed phyllosphere microbial communities of four tree species (Quercus ilex, Quercus robur, Pinus pinaster and Betula pendula) in a forest experiment composed of irrigated and non-irrigated plots. We used these microbial community data to train a machine-learning algorithm (Random Forest) to classify irrigated and non-irrigated trees. The Random Forest algorithm detected tree water status from phyllosphere microbial community composition with more than 90% accuracy for oak species, and more than 75% for pine and birch. Phyllosphere fungal communities were more informative than phyllosphere bacterial communities in all tree species. Seven fungal amplicon sequence variants were identified as candidates for the development of molecular biomarkers of water status in oak trees. Altogether, our results show that microbial community data from tree phyllosphere provides information on tree water status in forest ecosystems and could be included in next-generation biomonitoring programmes that would use in situ, real-time sequencing of environmental DNA to help monitor the health of European temperate forest ecosystems.

Soil core microbiota drive community resistance to mercury stress and maintain functional stability

Soil microbial communities have resistance to environmental stresses and thus can maintain ecosystem functions such as decomposition, nutrient provisioning, and plant pathogen control. However, predominant factors driving community resistance of soil microbiome to heavy metal pollution stresses and ecosystem functional stability are still unclear, limiting our ability to forecast how soil pollution might affect ecosystem sustainability. Here, we conducted microcosm experiments to estimate the importance of soil microbiome in predicting community resistance to heavy metal mercury (Hg) stress in paired paddy and upland fields. We found that community resistance of soil microbiome was strongly correlated with ecosystem functional stability, so were the individual groups of organisms such as bacteria, saprotrophic fungi, and phototrophic protists. The core phylotypes within soil microbiome had a major contribution to community resistance, which was essential for the maintenance of functional stability. Co-occurrence network further confirmed that community resistances of main ecological clusters were positively correlated with ecosystem functional stability. Together, our results provide new insights into the link between community resistance and functional stability, and highlight the importance of core microbiota in driving community resistance to environmental stresses and maintain functional stability.

Soil edaphic factors and climate seasonality explain the turnover of methanotrophic communities in riparian wetlands

Aerobic CH4-oxidizing bacteria (methanotrophs) represent a biological model system for the removal of atmospheric CH4, which is sensitive to the dynamics of water tables. However, little attention has been given to the turnover of methanotrophic communities across wet and dry periods in riparian wetlands. Here, by sequencing the pmoA gene, we investigated the turnover of soil methanotrophic communities across wet and dry periods in typical riparian wetlands that experience intensive agricultural practices. The results demonstrated that the methanotrophic abundance and diversity were significantly higher in the wet period than in the dry period, probably owing to the climatic seasonal succession and associated variation in soil edaphic factors. The co-occurrence patterns of the interspecies association analysis demonstrated that the key ecological clusters (i.e., Mod#1, Mod#2, Mod#4, Mod#5) showed contrasting correlations with soil edaphic properties between wet and dry periods. The linear regression slope of the relationships between the relative abundance of Mod#1 and the carbon to nitrogen ratio was higher in the wet period than in the dry period, whereas the linear regression slope of the relationships between the relative abundance of Mod#2 and soil nitrogen content (i.e., dissolved organic nitrogen, nitrate, and total nitrogen) was higher in the dry period than in the wet period. Moreover, Stegen's null model combined with phylogenetic group-based assembly analysis demonstrated that the methanotrophic community exhibited a higher proportion of drift (55.0%) and a lower contribution of dispersal limitation (24.5%) in the wet period than in the dry period (43.8% and 35.7%, respectively). Overall, these findings demonstrate that the turnover of methanotrophic communities across wet and dry periods were soil edaphic factors and climate dependent.

Distinct assembly processes and environmental adaptation of abundant and rare archaea in Arctic marine sediments

Revealing the ecological processes and environmental adaptation of abundant and rare archaea is a central, but poorly understood, topic in ecology. Here, abundant and rare archaeal diversity, community assembly processes and co-occurrence patterns were comparatively analyzed in Arctic marine sediments. Our findings revealed that the rare taxa exhibited significantly higher diversity compared to the abundant taxa. Additionally, the abundant taxa displayed stronger environmental adaptation than the rare taxa. The co-occurrence network analysis demonstrated that the rare taxa developed more interspecies interactions and modules in response to environmental disturbance. Furthermore, the community assembly of abundant and rare taxa in sediments was primarily controlled by stochastic and deterministic processes, respectively. These findings provide valuable insights into the archaeal community assembly processes and significantly contribute to a deeper understanding of the environmental adaptability of abundant and rare taxa in Arctic marine sediments.

Copper and cadmium co-contamination affects soil bacterial taxonomic and functional attributes in paddy soils

Microorganisms inhabiting heavy metal-contaminated soils have evolved specific metabolic capabilities to survive, which has the potential for effective bioremediation. However, the ecological consequence of copper (Cu) and cadmium (Cd) on bacterial taxonomic and functional attributes of rice field remains unclear. Here, we selected paddy soils along a polluted river in southern China to evaluate the role of Cu and Cd contaminant fractions in regulating bacterial co-occurrence patterns. We also assessed the effects of these heavy metal fractions on the relative abundance of functional genes using shotgun metagenomic analysis. Soil Cu and Cd concentrations in paddy soils gradually decreased from upstream to downstream of the river, and had a greater impact on bacterial communities and metabolic potentials than soil general properties. Soil Cu and Cd contamination led to drastic changes in the cumulative relative abundance of ecological modules in bacterial co-occurrence networks. Bacteria associated with AD3, HSB_OF53-F07 (both belonging to Chloroflexi), Rokubacteriales, and Nitrospira were identified as tolerant to Cu and Cd contamination. The Cu and Cd contaminant fractions were positively correlated with the genes involved in metal resistance, carbon (C) fixation, nitrification, and denitrification, but negatively correlated with the genes related to nitrogen (N) fixation. These results indicated that soil Cu and Cd pollution not only enriched metal resistant genes, but also affected genes related to microbial C and N cycling. This is critical for facilitating microbiome bioremediation of metal-contaminated paddy soils.

The role of phosphorus speciation of biochar in reducing available Cd and phytoavailability in mining area soil: Effect and mechanism

The effect of phosphorus (P) speciation in biochar on soil available Cd and its mechanism to alleviate plant Cd stress remain largely unknown. Here, ammonium polyphosphate (PABC)-, phosphoric acid (PHBC)-, potassium dihydrogen phosphate (PKBC)-, and ammonium dihydrogen phosphate (PNBC)-modified biochar were used to investigate P speciation. The Cd immobilization mechanism of biochar was analyzed by XPS and ³¹P NMR, and the soil quality and the mechanism for the biochar to alleviate Cd stress were also determined. The results demonstrated that PBC (pristine biochar), PABC, PHBC, PKBC, and PNBC reduced the content of soil DTPA-Cd by 14.96 % - 32.19 %, 40.44 % - 47.26 %, 17.52 % - 41.78 %, and 21.90 % - 36.64 %, respectively. The XPS and ³¹P NMR results demonstrated that the orthophosphate on the surface of PABC, PHBC, PKBC, and PNBC accounted for 82.06 %, 62.77 %, 33.1 %, and 54.46 %, respectively, indicating that PABC has the highest passivation efficiency on soil Cd, which was ascribed to the highest orthophosphate content on the biochar surface. Pot experiments revealed that PABC could reduce the Cd content by 4.18, 4.41, 4.43, 2.94, and 2.57 folds in roots, stems, leaves, pods, and grains, respectively, and at the same time increase the dry and fresh weight of soybean and decrease Cd toxicity to soybean by improving the antioxidant system. In addition, application of the P-modified biochars improved the enzyme activity and physicochemical properties of the soil. This study provides a new perspective for studying the effect of P-modified biochars on soil Cd immobilization.

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.

Reduced Antibiotic Resistance in the Rhizosphere of Lupinus albus in Mercury-Contaminated Soil Mediated by the Addition of PGPB

The emergence of antibiotic resistance (AR) poses a threat to the "One Health" approach. Likewise, mercury (Hg) pollution is a serious environmental and public health problem. Its ability to biomagnify through trophic levels induces numerous pathologies in humans. As well, it is known that Hg-resistance genes and AR genes are co-selected. The use of plant-growth-promoting bacteria (PGPB) can improve plant adaptation, decontamination of toxic compounds and control of AR dispersal. The cenoantibiogram, a technique that allows estimating the minimum inhibitory concentration (MIC) of a microbial community, has been postulated as a tool to effectively evaluate the evolution of a soil. The present study uses the metagenomics of 16S rRNA gene amplicons to understand the distribution of the microbial soil community prior to bacterial inoculation, and the cenoantibiogram technique to evaluate the ability of four PGPB and their consortia to minimize antibiotic resistance in the rhizosphere of Lupinus albus var. Orden Dorado grown in Hg-contaminated soils. Results showed that the addition of A1 strain (Brevibacterium frigoritolerans) and its consortia with A2, B1 and B2 strains reduced the edaphic community´s MIC against cephalosporins, ertapenem and tigecycline. The metagenomic study revealed that the high MIC of non-inoculated soils could be explained by the bacteria which belong to the detected taxa,. showing a high prevalence of Proteobacteria, Cyanobacteria and Actinobacteria.

Mercury and Sulfur Redox Cycling Affect Methylmercury Levels in Rice Paddy Soils across a Contamination Gradient

Methylmercury (MeHg) contamination in rice via paddy soils is an emerging global environmental issue. An understanding of mercury (Hg) transformation processes in paddy soils is urgently needed in order to control Hg contamination of human food and related health impacts. Sulfur (S)-regulated Hg transformation is one important process that controls Hg cycling in agricultural fields. In this study, Hg transformation processes, such as methylation, demethylation, oxidation, and reduction, and their responses to S input (sulfate and thiosulfate) in paddy soils with a Hg contamination gradient were elucidated simultaneously using a multi-compound-specific isotope labeling technique (200HgII, Me198Hg, and 202Hg0). In addition to HgII methylation and MeHg demethylation, this study revealed that microbially mediated reduction of HgII, methylation of Hg0, and oxidative demethylation-reduction of MeHg occurred under dark conditions; these processes served to transform Hg between different species (Hg0, HgII, and MeHg) in flooded paddy soils. Rapid redox recycling of Hg species contributed to Hg speciation resetting, which promoted the transformation between Hg0 and MeHg by generating bioavailable HgII for fuel methylation. Sulfur input also likely affected the microbial community structure and functional profile of HgII methylators and, therefore, influenced HgII methylation. The findings of this study contribute to our understanding of Hg transformation processes in paddy soils and provide much-needed knowledge for assessing Hg risks in hydrological fluctuation-regulated ecosystems.

Reduced trace gas oxidizers as a response to organic carbon availability linked to oligotrophs in desert fertile islands

Atmospheric trace gases, such as H₂ and CO, are important energy sources for microbial growth and maintenance in various ecosystems, especially in arid deserts with little organic substrate. Nonetheless, the impact of soil organic C availability on microbial trace gas oxidation and the underlying mechanisms are unclear at the community level. This study investigated the energy and life-history strategies of soil microbiomes along an organic C gradient inside and out of Hedysarum scoparium islands dispersed in the Mu Us Desert, China. Metagenomic analysis showed that with increasing organic C availability from bare areas into "fertile islands", the abundance of trace gas oxidizers (TGOs) decreased, but that of trace gas nonoxidizers (TGNOs) increased. The variation in their abundance was more related to labile/soluble organic C levels than to stable/insoluble organic C levels. The consumption rates of H₂ and CO confirmed that organic C addition, especially soluble organic C addition, inhibited microbial trace gas oxidation. Moreover, microorganisms with distinct energy-acquiring strategies showed different life-history traits. The TGOs had lower 16 S rRNA operon copy numbers, lower predicted maximum growth rates and higher proportions of labile C degradation genes, implying the prevalence of oligotrophs. In contrast, copiotrophs were prevalent in the TGNOs. These results revealed a mechanism for the microbial community to adapt to the highly heterogeneous distribution of C resources by adjusting the abundances of taxa with distinct energy and life-history strategies, which would further affect trace gas consumption and C turnover in desert ecosystems.

Plastispheres as hotspots of microbially-driven methylmercury production in paddy soils

Microplastics (MPs) as emerging contaminants have accumulated extensively in agricultural ecosystems and are known to exert important effects on biogeochemical processes. However, how MPs in paddy soils influence the conversion of mercury (Hg) to neurotoxic methylmercury (MeHg) remains poorly understood. Here, we evaluated the effects of MPs on Hg methylation and associated microbial communities in microcosms using two typical paddy soils in China (i.e., yellow and red soils). Results showed that the addition of MPs significantly increased MeHg production in both soils, which could be related to higher Hg methylation potential in the plastisphere than in the bulk soil. We found significant divergences in the community composition of Hg methylators between the plastisphere and the bulk soil. In addition, the plastisphere had higher proportions of Geobacterales in the yellow soil and Methanomicrobia in the red soil compared with the bulk soil, respectively; and plastisphere also had more densely connected microbial groups between non-Hg methylators and Hg methylators. These microbiota in the plastisphere are different from those in the bulk soil, which could partially account for their distinct MeHg production ability. Our findings suggest plastisphere as a unique biotope for MeHg production and provide new insights into the environment risks of MP accumulation in agricultural soils.

Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes

The earthworm gut virome influences the structure and function of the gut microbiome, which in turn influences worm health and ecological functions. However, despite its ecological and soil quality implications, it remains elusive how earthworm intestinal phages respond to different environmental stress, such as soil pollution. Here we used metagenomics and metatranscriptomics to investigate interactions between the worm intestinal phages and their bacteria under different benzo[a]pyrene (BaP) concentrations. Low-level BaP (0.1 mg kg^-1) stress stimulated microbial metabolism (1.74-fold to control), and enhanced the antiphage defense system (n = 75) against infection (8 phage-host pairs). Low-level BaP exposure resulted in the highest proportion of lysogenic phages (88%), and prophages expressed auxiliary metabolic genes (AMGs) associated with nutrient transformation (e.g., amino acid metabolism). In contrast, high-level BaP exposure (200 mg kg^-1) disrupted microbial metabolism and suppressed the antiphage systems (n = 29), leading to the increase in phage-bacterium association (37 phage-host pairs) and conversion of lysogenic to lytic phages (lysogenic ratio declined to 43%). Despite fluctuating phage-bacterium interactions, phage-encoded AMGs related to microbial antioxidant and pollutant degradation were enriched, apparently to alleviate pollution stress. Overall, these findings expand our knowledge of complex phage-bacterium interactions in pollution-stressed worm guts, and deepen our understanding of the ecological and evolutionary roles of phages.

The microbiome of a brownfield highly polluted with mercury and arsenic

Abandoned brownfields represent a challenge for their recovery. To apply sustainable remediation technologies, such as bioremediation or phytoremediation, indigenous microorganisms are essential agents since they are adapted to the ecology of the soil. Better understanding of microbial communities inhabiting those soils, identification of microorganisms that drive detoxification process and recognising their needs and interactions will significantly improve the outcome of the remediation. With this in mind we have carried out a detailed metagenomic analysis to explore the taxonomic and functional diversity of the prokaryotic and eukaryotic microbial communities in soils, several mineralogically distinct types of pyrometallurgic waste, and groundwater sediments of a former mercury mining and metallurgy site which harbour very high levels of arsenic and mercury pollution. Prokaryotic and eukaryotic communities were identified, which turned out to be more diverse in the surrounding contaminated soils compared to the pyrometallurgic waste. The highest diversity loss was observed in two environments most contaminated with mercury and arsenic (stupp, a solid mercury condenser residue and arsenic-rich soot from arsenic condensers). Interestingly, microbial communities in the stupp were dominated by an overwhelming majority of archaea of the phylum Crenarchaeota, while Ascomycota and Basidiomycota fungi comprised the fungal communities of both stump and soot, results that show the impressive ability of these previously unreported microorganisms to colonize these extreme brownfield environments. Functional predictions for mercury and arsenic resistance/detoxification genes show their increase in environments with higher levels of pollution. Our work establishes the bases to design sustainable remediation methods and, equally important, to study in depth the genetic and functional mechanisms that enable the subsistence of microbial populations in these extremely selective environments.

Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide

Soil contamination is one of the main threats to ecosystem health and sustainability. Yet little is known about the extent to which soil contaminants differ between urban greenspaces and natural ecosystems. Here we show that urban greenspaces and adjacent natural areas (i.e., natural/semi-natural ecosystems) shared similar levels of multiple soil contaminants (metal(loid)s, pesticides, microplastics, and antibiotic resistance genes) across the globe. We reveal that human influence explained many forms of soil contamination worldwide. Socio-economic factors were integral to explaining the occurrence of soil contaminants worldwide. We further show that increased levels of multiple soil contaminants were linked with changes in microbial traits including genes associated with environmental stress resistance, nutrient cycling, and pathogenesis. Taken together, our work demonstrates that human-driven soil contamination in nearby natural areas mirrors that in urban greenspaces globally, and highlights that soil contaminants have the potential to cause dire consequences for ecosystem sustainability and human wellbeing.

Phagotrophic Protists Modulate Copper Resistance of the Bacterial Community in Soil

Protist predation is a crucial biotic driver modulating bacterial populations and functional traits. Previous studies using pure cultures have demonstrated that bacteria with copper (Cu) resistance exhibited fitness advantages over Cu-sensitive bacteria under the pressure of protist predation. However, the impact of diverse natural communities of protist grazers on bacterial Cu resistance in natural environments remains unknown. Here, we characterized the communities of phagotrophic protists in long-term Cu-contaminated soils and deciphered their potential ecological impacts on bacterial Cu resistance. Long-term field Cu pollution increased the relative abundances of most of the phagotrophic lineages in Cercozoa and Amoebozoa but reduced the relative abundance of Ciliophora. After accounting for soil properties and Cu pollution, phagotrophs were consistently identified as the most important predictor of the Cu-resistant (Cu^R) bacterial community. Phagotrophs positively contributed to the abundance of a Cu resistance gene (copA) through influencing the cumulative relative abundance of Cu-resistant and -sensitive ecological clusters. Microcosm experiments further confirmed the promotion effect of protist predation on bacterial Cu resistance. Our results indicate that the selection by protist predation can have a strong impact on the Cu^R bacterial community, which broadens our understanding of the ecological function of soil phagotrophic protists.

Mechanisms and biological effects of organic amendments on mercury speciation in soil-rice systems: A review

Mercury (Hg) pollution is a well-recognized global environmental and health issue and exhibits distinctive persistence, neurotoxicity, bioaccumulation, and biomagnification effects. As the largest global Hg reservoir, the Hg cumulatively stored in soils has reached as high as 250-1000 Gg. Even more concerning is that global soil-rice systems distributed in many countries have become central to the global Hg cycle because they are both a major food source for more than 3 billion people worldwide and the central bridge linking atmospheric and soil Hg circulation. In this review, we discuss the form distribution, transformation, and bioavailability of Hg in soil-rice systems by focusing on the Hg methylation and demethylation pathways and distribution, uptake, and accumulation in rice plants and the effects of Hg on the community structure and ecological functions of microorganisms in soil-rice systems. In addition, we clarify the mechanisms through which commonly used humus and biochar organic amendments influence Hg and its environmental effects in soil-rice systems. The review also elaborates on the advantages of sulfur-modified biochars and their critical role in controlling Hg migration and bioavailability in soils. Finally, we provide key information about Hg pollution in soil-rice systems, which is of great significance for developing appropriate strategies and mitigation planning to limit Hg bioconcentration in rice crops and achieving key global sustainable development goals, such as the guarantee of food security and the promotion of sustainable agriculture.

Phytoremediation: A Novel Approach of Bast Fiber Plants (Hemp, Kenaf, Jute and Flax) for Heavy Metals Decontamination in Soil-Review

Heavy metal pollution in the environment is a major concern for humans as it is non-biodegradable and can have a lot of effects on the environment, humans as well as plants. At present, a solution to this problem is suggested in terms of a new, innovative and eco-friendly technology known as phytoremediation. Bast fiber plants are typically non-edible crops that have a short life cycle. It is one of the significant crops that has attracted interest for many industrial uses because of its constant fiber supply and ease of maintenance. Due to its low maintenance requirements with minimum economic investment, bast fiber plants have been widely used in phytoremediation. Nevertheless, these plants have the ability to extract metals from the soil through their deep roots, combined with their commercial prospects, making them an ideal candidate as a profit-yielding crop for phytoremediation purposes. Therefore, a comprehensive review is needed for a better understanding of the morphology and phytoremediation mechanism of four commonly bast fiber plants, such as hemp (Cannabis sativa), kenaf (Hibiscus cannabinus), jute (Corchorus olitorius) and Flax (Linum usitatissimum). This review article summarizes the existing research on the phytoremediation potential of these plants grown in different toxic pollutants such as Lead (Pb), Cadmium (Cd) and Zinc (Zn). This work also discusses several aids including natural and chemical amendments to improve phytoremediation. The role of these amendments in the bioavailability of contaminants, their uptake, translocation and bioaccumulation, as well as their effect on plant growth and development, has been highlighted in this paper. This paper helps in identifying, comparing and addressing the recent achievements of bast fiber plants for the phytoremediation of heavy metals in contaminated soil.

Responses of soil fungal taxonomic attributes and enzyme activities to copper and cadmium co-contamination in paddy soils

Excess heavy metals, especially copper (Cu) and cadmium (Cd), are common in paddy soils in the red soil hilly areas of southern China. Microorganisms are regulators of soil organic matter accumulation and pollutant transformation. Clarifying the effects of Cu and Cd accumulation on microbial community composition and function is a prerequisite for bioremediation of paddy soil contamination. However, it remains unclear how Cu and Cd contamination affects soil fungal taxonomic attributes and microbial-mediated biogeochemical processes in paddy soils. Here, soil heavy metals, fungal community composition, and soil enzyme activities were determined in paddy fields downstream of a typical mining area in southern China, and the effects of Cu and Cd co-contamination on fungal community diversity and co-occurrence networks, as well as the associations between them were assessed. The concentrations of Cu and Cd in paddy soils decreased from upstream to downstream of the river, and were positively correlated with the Shannon index of fungal communities. Soil Cu and Cd concentrations exhibited a greater impact on the structure and assembly of fungal communities than soil general properties. Increases in soil Cu and Cd concentrations were correlated with drastic changes in the cumulative relative abundance of ecological clusters in fungal co-occurrence networks. Soil Cu and Cd concentrations were positively correlated with the relative abundances of Eurotiomycetes, Pezizomycetes, Ustilaginomycetes, and Kickxellomycetes, respectively, whereas negatively correlated with hydrolase activities related to carbon, nitrogen, and phosphorus cycles. These results confirmed in the field that long-term Cu and Cd enrichment significantly altered the structure and diversity of fungal communities in the subtropical paddy soils, thereby affecting soil nutrient transformation and organic matter accumulation. This can also provide a basis for the bioremediation of heavy metal pollution in paddy soils.

Effects of combined pollution of organic pollutants and heavy metals on biodiversity and soil multifunctionality in e-waste contaminated soil

Electronic waste (e-waste) is increasing globally, but the impact of this source of combined pollution on soil biodiversity and multiple soil functions (i.e., ecosystem multifunctionality) remains unclear. Here, we evaluated the effects of combined pollution on the biodiversity and soil multifunctionality using samples collected from upland and paddy soils chronically contaminated with e-waste. Overall biodiversity, as well as the relative abundance and biodiversity of key ecological clusters, as combined pollution concentrations increased in upland soil, while the opposite was true in paddy soil. Soil multifunctionality followed the same trend. Organic pollutants had significant negative effects on soil multifunctionality and were the main influencing factors in upland soil. Heavy metals had significant positive effects on soil multifunctionality in paddy soil. Moreover, driving soil multifunctionality was overall biodiversity in upland soil but key biodiversity in paddy soil. Importantly, a strong positive association between key organism biodiversity and soil multifunctionality was found in soil with low contamination. However, the relationship between key organism biodiversity and soil multifunctionality weakened or disappeared in highly contaminated soil, whereas overall biodiversity was significantly and positively correlated with multifunctionality. Our results emphasized that severe e-waste contamination would reduce soil biodiversity and soil multifunctionality and warrants high attention.

Long-term mercury contamination does not affect the microbial gene potential for C and N cycling in soils but enhances detoxification gene abundance

Soil microorganisms are key transformers of mercury (Hg), a toxic and widespread pollutant. It remains uncertain, however, how long-term exposure to Hg affects crucial microbial functions, such as litter decomposition and nitrogen cycling. Here, we used a metagenomic approach to investigate the state of soil functions in an agricultural floodplain contaminated with Hg for more than 80 years. We sampled soils along a gradient of Hg contamination (high, moderate, low). Hg concentrations at the highly contaminated site (36 mg kg–1 dry soil on average) were approximately 10 times higher than at the moderately contaminated site (3 mg kg–1 dry soil) and more than 100 times higher than at the site with low contamination (0.25 mg kg–1 dry soil; corresponding to the natural background concentration in Switzerland). The analysis of the CAZy and NCyc databases showed that carbon and nitrogen cycling was not strongly affected with high Hg concentrations, although a significant change in the beta-diversity of the predicted genes was observed. The only functional classes from the CAZy database that were significantly positively overrepresented under higher Hg concentrations were genes involved in pectin degradation, and from the NCyc database dissimilatory nitrate reduction and N-fixation. When comparing between low and high Hg concentrations the genes of the EggNOG functional category of inorganic ion transport and metabolism, two genes encoding Hg transport proteins and one gene involved in heavy metal transport detoxification were among those that were highly significantly overrepresented. A look at genes specifically involved in detoxification of Hg species, such as the mer and hgc genes, showed a significant overrepresentation when Hg contamination was increased. Normalized counts of these genes revealed a dominant role for the phylum Proteobacteria. In particular, most counts for almost all mer genes were found in Betaproteobacteria. In contrast, hgc genes were most abundant in Desulfuromonadales. Overall, we conclude from this metagenomic analysis that long-term exposure to high Hg triggers shifts in the functional beta-diversity of the predicted microbial genes, but we do not see a dramatic change or breakdown in functional capabilities, but rather functional redundancy.

Increased water inputs fuel microbial mercury methylation in upland soils

Mercury (Hg) can be converted to neurotoxic methylmercury (MeHg) by certain microbes typically in anaerobic environments, threatening human health due to its bioaccumulation in food webs. However, it is unclear whether and how Hg can be methylated in legacy aerobic uplands with increasing water. Here, we conducted a series of incubation experiments to investigate the effects of increased water content on MeHg production in two typical upland soils (i.e., long-term and short-term use). Results showed that marked MeHg production occurred in water-saturated upland soils, which was strongly correlated with the proportions of significantly stimulated Hg methylating taxon (i.e., Geobacter). Elevated temperature further enhanced MeHg production by blooming proportions of typical Hg methylators (i.e., Clostridium, Acetonema, and Geobacter). Water saturation could also enhance microbial Hg methylation by facilitating microbial syntrophy between non-Hg methylators and Hg methylators. Taken together, the present work suggests that uplands could turn into a potential MeHg reservoir in response to water inputs resulting from rainfall or anthropogenic irrigation.

Fertilizing-induced changes in the nitrifying microbiota associated with soil nitrification and crop yield

Ammonia oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira (CMX) play pivotal roles in global nitrogen-cycling network. Despite its importance, the driving forces for niche specialization of these nitrifiers, as well as their relative contributions to nitrification and crop yield have not been fully understood. Here, we investigated the niche specialization and environmental prevalence of nitrifying communities, and their importance for the nitrification rate and crop yield across a gradient of nitrogen inputs in a two-decade old field experiment. The results of ¹⁵N-tracer and quantitative PCR revealed that AOB and NOB jointly determined the gross nitrification rates across mineral fertilizer treatments, whereas AOA and AOB contributed more than other nitrifiers to nitrification under with organic fertilizer amendments. Linear regression model revealed that crop yield could be linked with AOB and NOB under inorganic farming but closely associated with CMX under organic management. Amplicon sequencing of these functional genes further demonstrated that mineral and organic fertilizers have distinct influences on the β-diversity and niche breadth of these nitrifying communities, indicating that fertilization triggered niche specialization of nitrifying guilds in agricultural soils. Notably, organic fertilization enhanced the network complexity of these nitrifiers by harboring keystone taxa. Random forest analysis provide robustly evidence for the hypothesis that abundance of functional genes contributed more than a- and β-diversity of these nitrifiers for driving nitrification rates and crop yields. Collectively, these findings provide the empirical evidence for the environmental adaptation and niche specialization of nitrifying communities, and their contributions in nitrification and crop yield when confronted with long-term nitrogen inputs.

Lower abundance of Bacteroides and metabolic dysfunction are highly associated with the post-weaning diarrhea in piglets

Growing evidences show a direct link between diarrhea and disorders of gut microbiota in pigs. However, whether there are microbial markers associated with post-weaning diarrhea remains unknown. In the current study, we compared the microbial community, functions and metabolites between healthy weaned piglets (group H, n=7) and piglets with post-weaning diarrhea (group D, n=7), in order to find out diarrhea associated microbial markers. Each of 7 fecal samples was collected from H and D piglets (weaned at 21 d and sampled at 26 d). The metagenomic and untargeted metabolomic analysis revealed that the microbial composition, function and metabolic profile in D pigs was considerably reshaped, including the reduced abundance and number of Bacteroides, which significantly correlated with the diarrhea status of host. The carbohydrate metabolism, biosynthesis and metabolism, lipid metabolism, amino acid metabolism, and the activity of glycan and carbohydrates digestion related enzymes showed extensively down-regulated in D pigs compared with H pigs. Diarrhea significantly changed the metabolic profiles of fecal microbiota, and most of the altered metabolites were negatively or positively correlated with the change in the abundance of Bacteroides. In conclusion, the lower abundance of Bacteroides and its associated metabolic dysfunction may be regarded as microbial markers of physiological post-weaning diarrhea in piglets.

Evaluation of the oxidative stress alleviation in Lupinus albus var. orden Dorado by the inoculation of four plant growth-promoting bacteria and their mixtures in mercury-polluted soils

Mercury (Hg) pollution is a serious environmental and public health problem. Hg has the ability to biomagnify through the trophic chain and generate various pathologies in humans. The exposure of plants to Hg affects normal plant growth and its stress levels, producing oxidative cell damage. Root inoculation with plant growth-promoting bacteria (PGPB) can help reduce the absorption of Hg, minimizing the harmful effects of this metal in the plant. This study evaluates the phytoprotective capacity of four bacterial strains selected for their PGPB capabilities, quantified by the calculation of the biomercuroremediator suitability index (IIBMR), and their consortia, in the Lupinus albus var. orden Dorado. The oxidative stress modulating capacity in the inoculated plant was analyzed by measuring the activity of the enzymes catalase (CAT), superoxide dismutase (SOD), ascorbate peroxidase (APX), and glutathione reductase (GR). In turn, the phytoprotective capacity of these PGPBs against the bioaccumulation of Hg was studied in plants grown in soils highly contaminated by Hg vs. soils in the absence of Hg contamination. The results of the oxidative stress alleviation and Hg bioaccumulation were compared with the biometric data of Lupinus albus var. orden Dorado previously obtained under the same soil conditions of Hg concentration. The results show that the biological behavior of plants (biometrics, bioaccumulation of Hg, and activity of regulatory enzymes of reactive oxygen species [ROS]) is significantly improved by the inoculation of strains B1 (Pseudomonas moraviensis) and B2 (Pseudomonas baetica), as well as their corresponding consortium (CS5). In light of the conclusions of this work, the use of these strains, as well as their consortium, is postulated as good candidates for their subsequent use in phytostimulation and phytoprotection processes in areas contaminated with Hg.

Can agricultural land use alter the responses of soil biota to antibiotic contamination?

Antibiotics accumulate in soils via various agricultural activities, endangering soil biota that play fundamental roles in maintaining agroecosystem function. However, the effects of land-use heterogeneity on soil biota tolerance to antibiotic stresses are not well understood. In this study, we explored the relationships between antibiotic residues, bacterial communities, and earthworm populations in areas with different land-use types (forest, maize, and peanut fields). The results showed that antibiotic levels were generally higher in maize and peanut fields than in forests. Furthermore, land use modulated the effects of antibiotics on soil bacterial communities and earthworm populations. Cumulative antibiotic concentrations in peanut fields were negatively correlated with bacterial diversity and earthworm abundance, whereas no significant correlations were detected in maize fields. In contrast, antibiotics improved bacterial diversity and richness in forest soils. Generally, earthworm populations showed stronger tolerance to antibiotics than did soil bacterial communities. Agricultural land use differentially modified the responses of the soil bacterial community and earthworm population to antibiotic contamination, and earthworms might provide an alternative for controlling antibiotic contamination.

Stronger responses of soil protistan communities to legacy mercury pollution than bacterial and fungal communities in agricultural systems

Soil pollution is an important stressor affecting biodiversity and ecosystem functioning. However, we lack a holistic understanding of how soil microbial communities respond to heavy metal pollution in agricultural ecosystems. Here, we explored the distribution patterns and inter-kingdom interactions of entire soil microbiome (including bacteria, fungi, and protists) in 47 paired paddy and upland fields along a gradient of legacy mercury (Hg) pollution. We found that the richness and composition of protistan community had stronger responses to Hg pollution than those of bacterial and fungal communities in both paddy and upland soils. Mercury polluted soils harbored less protistan phototrophs but more protistan consumers. We further revealed that long-term Hg pollution greatly increased network complexity of protistan community than that of bacterial and fungal communities, as well as intensified the interactions between protists and the other microorganisms. Moreover, our results consistently indicated that protistan communities had stronger responses to long-term Hg pollution than bacterial and fungal communities in agricultural soils based on structural equation models and random forest analyses. Our study highlights that soil protists can be used as bioindicators of Hg pollution, with important implications for the assessment of contaminated farmlands and the sustainable management of agricultural ecosystems.

Mercury drives microbial community assembly and ecosystem multifunctionality across a Hg contamination gradient in rice paddies

Soil microbial communities are critical for maintaining terrestrial ecosystems and fundamental ecological processes. Mercury (Hg) is a heavy metal that is toxic to microorganisms, but its effects on microbial community assembly and ecosystem multifunctionality in rice paddy ecosystems remain largely unknown. In the current study, we analyzed the microbial community structure and ecosystem multifunctionality of paddy soils across a Hg contamination gradient. The results demonstrated that Hg contamination significantly altered the microbial community structure. The microbial communities were predominantly driven by deterministic selection rather than stochastic processes. The random forest model and variation partition analysis demonstrated that the Hg level was the most important predictor of microbial profiles. Ecosystem multifunctionality decreased across the Hg concentration gradient, and multifunctionality was significantly correlated with soil biodiversity, suggesting that Hg-induced reductions in soil biodiversity led to reduced ecosystem services. A structural equation model showed that Hg contamination directly and indirectly affected ecosystem multifunctionality. The present work broadens our knowledge of the assembly of the microbiome in rice paddies across a Hg contamination gradient and highlights the significance of soil biodiversity in regulating ecosystem functions, especially in Hg-polluted rice paddies.

Contamination with multiple heavy metals decreases microbial diversity and favors generalists as the keystones in microbial occurrence networks

Soil contamination with multiple heavy metals poses threats to human health and ecosystem functioning. Using the Nemerow pollution index, which considers the effects of multiple heavy metals, we compared the diversity and composition of bacteria, fungi and protists and their potential interactions in response to a multi-metal contamination gradient. Multi-metal contamination significantly altered the community composition of bacteria, fungi and protists, and the degree of alteration increased with increasing severity of contamination. The alpha-diversity of bacteria, fungi and protists significantly decreased with increasing contamination level. The dominant generalists, found in all soil samples, were Gammaproteobacteria, Chloroflexi and Bacillus sp, whereas the dominant specialists were Anaerolineaceae, Entoloma sp. and Sandonidae_X sp. The relative abundances of generalists were positively correlated, whereas those of specialists were negatively correlated, with the Nemerow pollution index. In addition, the complexity of the microbial co-occurrence network increased with increasing contamination level. Generalists, rather than specialists, were the keystones in the microbial co-occurrence network and played a crucial role in adaptation to multi-metal contamination through enhanced potential interactions within the entire microbiome. Our results provide insights into the ecological effects of multi-metal contamination on the soil microbiome and will help to develop bio-remediation technologies for contaminated soils.

Speciation of heavy metals in soils and their immobilization at micro-scale interfaces among diverse soil components

Heavy metal (HM) pollution of soils is a globally important ecological and environmental problem. Previous studies have focused on i) tracking pollution sources in HM-contaminated soils, ii) exploring the adsorption capacity and distribution of HMs, and iii) assessing phyto-uptake of HMs and their ecotoxicity. However, few reviews have systematically summarized HM pollution in soil-plant systems over the past decade. Understanding the mechanisms of interaction between HMs and solid soil components is consequently key to effectively controlling and remediating HM pollution. However, the compositions of solid soil phases are diverse, their structures are complex, and their spatial arrangements are heterogeneous, all leading to the formation of soil micro-domains that exhibit different particle sizes and surface properties. The various soil components and their interactions ultimately control the speciation, transformation, and bioavailability of HMs in soils. Over the past few decades, the extensive application of advanced instrumental techniques and methods has greatly expanded our understanding of the behavior of HMs in organic mineral assemblages. In this review, studies investigating the immobilization of HMs by minerals, organic compounds, microorganisms, and their associated complexes are summarized, with a particular emphasis on the interfacial adsorption and immobilization of HMs. In addition, methods for analyzing the speciation and distribution of HMs in aggregates of natural soils with different particle sizes are also discussed. Moreover, we also review the methods for speciating HMs at mineral-organic micro-scale interfaces. Lastly, developmental prospects for HM research at inorganic-organic interfaces are outlined. In future research, the most advanced methods should be used to characterize the interfaces and in situ characteristics of metals and metal complexes. In particular, the roles and contributions of microorganisms in the immobilization of HMs at complex mineral-organic interfaces require significant further investigation.

Microbial assemblies associated with temperature sensitivity of soil respiration along an altitudinal gradient

Identifying the drivers of the response of soil microbial respiration to warming is integral to accurately forecasting the carbon-climate feedbacks in terrestrial ecosystems. Microorganisms are the fundamental drivers of soil microbial respiration and its response to warming; however, the specific microbial communities and properties involved in the process remain largely undetermined. Here, we identified the associations between microbial community and temperature sensitivity (Q₁₀) of soil microbial respiration in alpine forests along an altitudinal gradient (from 2974 to 3558 m) from the climate-sensitive Tibetan Plateau. Our results showed that changes in microbial community composition accounted for more variations of Q₁₀ values than a wide range of other factors, including soil pH, moisture, substrate quantity and quality, microbial biomass, diversity and enzyme activities. Specifically, co-occurring microbial assemblies (i.e., ecological clusters or modules) targeting labile carbon consumption were negatively correlated with Q₁₀ of soil microbial respiration, whereas microbial assemblies associated with recalcitrant carbon decomposition were positively correlated with Q₁₀ of soil microbial respiration. Furthermore, there were progressive shifts of microbial assemblies from labile to recalcitrant carbon consumption along the altitudinal gradient, supporting relatively high Q₁₀ values in high-altitude regions. Our results provide new insights into the link between changes in major microbial assemblies with different trophic strategies and Q₁₀ of soil microbial respiration along an altitudinal gradient, highlighting that warming could have stronger effects on microbially-mediated soil organic matter decomposition in high-altitude regions than previously thought.

Relevance of the microbial community to Sb and As biogeochemical cycling in natural wetlands

Mining activities lead to elevated levels of antimony (Sb) and arsenic (As) in river systems, having adverse effects on the aquatic environment and human health. Microbes inhabiting river sediment can mediate the transformation of Sb and As, thus changing the toxicity and mobility of Sb and As. Compared to river sediments, natural wetlands could introduce distinct geochemical conditions, leading to the formation of different sedimentary microbial compositions between river sediments and wetland sediments. However, whether such changes in microbial composition could influence the microbially mediated geochemical behavior of Sb or As remains poorly understood. In this study, we collected samples from a river contaminated by Sb tailings and a downstream natural wetland to study the influence of microorganisms on the geochemical behavior of Sb and As after the Sb/As-contaminated river entered the natural wetland. We found that the microbial compositions in the natural wetland soil differed from those in the river sediment. The Sb/As contaminant components (Sb(III), As(III), As(V), As_exe) and nutrients (TC) were important determinants of the difference in the compositions of the microbial communities in the two environments. Taxonomic groups were differentially enriched between the river sediment and wetland soil. For example, the taxonomic groups Xanthomonadales, Clostridiales and Desulfuromonadales were important in the wetland and were likely to involve in Sb/As reduction, sulfate reduction and Fe(III) reduction, whereas Burkholderiales, Desulfobacterales, Hydrogenophilales and Rhodocyclales were important taxonomic groups in the river sediments and were reported to involve in Sb/As oxidation and sulfide oxidation. Our results suggest that microorganisms in both river sediments and natural wetlands can affect the geochemical behavior of Sb/As, but the mechanisms of action are different.

Insights into Bacterial Community Structure and Metabolic Diversity of Mercury-Contaminated Sediments from Hyeongsan River, Pohang, South Korea

This study investigated the bacterial community structure and metabolic diversity and their relationship with Hg and other environmental variables in sediments collected from different locations (HSR-1-HSR-6) in the Hyeongsan River estuary in South Korea. The results showed that the highest total mercury (THg) and methylmercury (MeHg) concentrations were in HSR-2, with values of 4585.3 µg/kg and 13.4 µg/kg, respectively. The lowest THg (31.9 µg/kg) and MeHg (0.1 µg/kg) concentrations were found in HSR-1. Sulfate and organic matter (OM) were more influential environmental variables, revealing a positive association with THg and MeHg and negatively affecting bacterial and metabolic diversities. Bacterial and metabolic diversities were also negatively impacted by the THg and MeHg concentrations. Proteobacteria and Bacteroidetes were abundantly distributed in all the sediments. The dominance of Proteobacteria was upscaled in all the heavily Hg-contaminated sites (HSR-2-HSR-6), and it was the only phylum that showed a significant positive correlation with THg, MeHg, and OM. The genera Sulfurovum and Sulfurimonas were abundantly observed in sites with high Hg contamination, whereas Congregibacter, Gaetbulibacter, Ilumatobacter, Methylotenera, Nevskia, and Sediminibacter were only detected in low Hg-contaminated sites (HSR-1). The community-level physiological profile data showed the highest (1.0) average well color development (AWCD) value in HSR-1 and the lowest (0.45) AWCD value in HSR-2. Overall, these results demonstrated the inhibitory effects of THg, MeHg, and other environmental variables on microbial communities and metabolic diversity. These findings broaden the current knowledge on the dynamics of bacterial and metabolic diversities in Hg-contaminated sediments and might be useful in the management of Hg pollution.

Comparative Metagenomic Study of Rhizospheric and Bulk Mercury-Contaminated Soils in the Mining District of Almadén

Soil contamination by heavy metals, particularly mercury (Hg), is a problem that can seriously affect the environment, animals, and human health. Hg has the capacity to biomagnify in the food chain. That fact can lead to pathologies, of those which affect the central nervous system being the most severe. It is convenient to know the biological environmental indicators that alert of the effects of Hg contamination as well as the biological mechanisms that can help in its remediation. To contribute to this knowledge, this study conducted comparative analysis by the use of Shotgun metagenomics of the microbial communities in rhizospheric soils and bulk soil of the mining region of Almadén (Ciudad Real, Spain), one of the most affected areas by Hg in the world The sequences obtained was analyzed with MetaPhlAn2 tool and SUPER-FOCUS. The most abundant taxa in the taxonomic analysis in bulk soil were those of Actinobateria and Alphaproteobacteria. On the contrary, in the rhizospheric soil microorganisms belonging to the phylum Proteobacteria were abundant, evidencing that roots have a selective effect on the rhizospheric communities. In order to analyze possible indicators of biological contamination, a functional potential analysis was performed. The results point to a co-selection of the mechanisms of resistance to Hg and the mechanisms of resistance to antibiotics or other toxic compounds in environments contaminated by Hg. Likewise, the finding of antibiotic resistance mechanisms typical of the human clinic, such as resistance to beta-lactams and glycopeptics (vancomycin), suggests that these environments can behave as reservoirs. The sequences involved in Hg resistance (operon mer and efflux pumps) have a similar abundance in both soil types. However, the response to abiotic stress (salinity, desiccation, and contaminants) is more prevalent in rhizospheric soil. Finally, sequences involved in nitrogen fixation and metabolism and plant growth promotion (PGP genes) were identified, with higher relative abundances in rhizospheric soils. These findings can be the starting point for the targeted search for microorganisms suitable for further use in bioremediation processes in Hg-contaminated environments.

The Proportion of Soil-Borne Fungal Pathogens Increases with Elevated Organic Carbon in Agricultural Soils

Soil-borne fungal phytopathogens are important threats to soil and crop health. However, their community composition and environmental determinants remain unclear. Here, we explored the effects of agricultural fertilization regime (i.e., organic material application) on soil fungal phytopathogens, using data sets from a combination of field survey and long-term experiment. We found that soil organic carbon was the key factor that affected the diversity and relative abundance of fungal phytopathogens in agricultural soils. The dominant genera of phytopathogens including Monographella was also strongly associated with soil organic carbon. In addition, the elevated soil organic carbon enhanced the node proportion of phytopathogens and the positive interactions within the fungal community in the network. Results of the long-term experiment revealed that applications of crop straw and fresh livestock manure significantly increased the proportion of phytopathogens, which were associated with the elevated soil organic carbon. This work offers new insights into the occurrence and environmental factors of fungal phytopathogens in agricultural soils, which are fundamental to control their impacts on the soil and crop systems. IMPORTANCE Fungal phytopathogens are important threats to soil and crop health, but their community composition and environmental determinants remain unclear. We found that soil organic carbon is the key factor of the prevalence of fungal phytopathogens through a field survey, which is also supported by our long-term (6-year) experiment showing the applications of crop straw and fresh livestock manure significantly increased the proportion of fungal phytopathogens. These findings advance our understanding of the occurrence and environmental drivers of soil-borne fungal phytopathogens under agricultural fertilization regime and have important implications for the control of soil-borne pathogens.

Veterinary antibiotics can reduce crop yields by modifying soil bacterial community and earthworm population in agro-ecosystems

Veterinary antibiotics are intensively and widely used in animal farming to treat or prevent diseases, as well as improve growth rate and feed efficiency. Animal manure is an important reservoir of veterinary antibiotics due to their high excretion rates, and thus manure application has been a critical source of veterinary antibiotics in agro-ecosystems. However, how veterinary antibiotics affect agroecosystem functions is still unclearly understood. In this study, we evaluated the effects of veterinary antibiotics on soil bacteria and earthworms in agricultural land with long-term manure application. The potential mechanisms of antibiotic-induced changes in crop yields were also revealed. The results showed that the increasing prevalence of veterinary antibiotics in agro-ecosystems inhibited earthworm abundance and bacterial diversity, and then decreased the bioavailability of soil nutrients. Furthermore, high-dose exposure to veterinary antibiotics improved the abundance of plant pathogenic bacteria. Analysis indicated that veterinary antibiotics played an important underlying role in driving the negative effects on peanut grain yields via disturbing microbe- and earthworm-mediated soil available nutrient contents. The direct toxicity effects of antibiotics on peanut relative yields were stronger than their indirect mediating effects. Additionally, the tradeoffs between antibiotics and agroecosystem functions increased at low exposure levels and then decreased at high exposure levels, which indicated the effects of antibiotics on agroecosystem functions were dose-dependent, except for earthworm biomass. Antibiotic contamination which will impose threats to agricultural sustainability was highlighted and should be paid more attention.

Microbial investigations of new hydrogel-biochar composites as soil amendments for simultaneous nitrogen-use improvement and heavy metal immobilization

Agricultural sustainability is challenging because of increasingly serious and co-existing issues, e.g., poor nitrogen-fertilizer use and heavy metal pollution. Herein, we introduced a new poly(acrylic acid)-grafted chitosan and biochar composite (PAA/CTS/BC) for soil amendment, and provided a first microbial insight into how PAA/CTS/BC amendment simultaneously improved nitrogen cycling and immobilized heavy metals. Our results suggest that the PAA/CTS/BC amendment significantly promoted soil ammonium retention, and reduced nitrate accumulation, nitrous oxide emission and ammonia volatilization during the rice cultivation. The availability of various heavy metals (Fe, Mn, Cu, Zn, Ni, Pb, Cr, and As) markedly decreased in the PAA/CTS/BC amended soil, thereby reducing their accumulation in rice root. The PAA/CTS/BC amendment significantly altered the structure and function of soil microbial communities. Importantly, the co-occurrence networks of microbial communities became more complex and function-specific after PAA/CTS/BC addition. For example, the keystone species related to organic matter degradation, denitrification, and plant resistance to pathogen or stresses were enriched within the network. In addition to direct adsorption, the effects of PAA/CTS/BC on shaping microbial communities played dominant roles in the soil amendment. Our findings provide a promising strategy of simultaneous nitrogen-use improvement and heavy metal immobilization for achieving crop production improvement, pollution control, and climate change mitigation.

Selenium-enriched Bacillus subtilis reduces the effects of mercury-induced on inflammation and intestinal microbes in carp (Cyprinus carpio var. specularis)

Mercury (Hg) is a global pollutant that affects the health of humans and ecosystems. Selenium (Se) is an essential trace element for many organisms including humans. Bacillus subtilis is one of the main probiotics used in aquaculture, and has a certain adsorption effect on heavy metals. The interaction between Hg and Se was rigorously studied, especially due to the observation of the protective effect of Se on Hg toxicity. The objective of this study was to research the effects of Hg, Se, and B. subtilis on inflammation and intestinal microbes in common carp. The common carp was exposed to Hg (0.03 mg/L), and 10⁵ cfu/g Se-rich B. subtilis was added to the feed. After 30 days of feeding, samples were taken to evaluate the growth performance, serological response, inflammatory response, and intestinal microbial changes. In this study, when fish were exposed to Hg, the growth performance of the Se-rich B. subtilis plus 0.03 mg/L Hg fish group was lower than that of the control group and higher than 0.03 mg/L Hg; The levels of serum immunoglobulin M (IgM) and lysozyme (LZM) decreased, but after supplementation with Se-rich B. subtilis, the levels of LZM and IgM increased; Hg treatment significantly upregulated the mRNA expression of interleukin-1β (IL-1β), interleukin-8 (IL-8), tumor necrosis factor-α (TNF-α), and nuclear factor-kB (NF-κB P65), but downregulated the mRNA expression of interleukin-10 (IL-10), transforming growth factor-β (TGF-β) and NF-kappa-B inhibitor alpha (IkBα). However, compared with the Hg group, the Se-rich B. subtilis plus Hg group can significantly increase the mRNA expression levels of IL-1β, IL-8, TNF-α, and NF-κB P65, but reduce the regulation of IL-10, TGF-β, and IkBα expression. Through the analysis of the microbiological, we found that the Hg group was mainly composed of Aeromonas sobria and Aeromonas hydrophila. However, in the Se-rich B. subtilis treatment group, we found that Aeromonas sobria was significantly less than the Hg group. Se-rich B. subtilis improves Hg-induced intestinal microbial changes, alleviates the abundance of Aeromonas, and alleviates the inflammation of the fish. The results of this study show that Se-rich B. subtilis dietary supplements can effectively protect common carp against Hg toxicity.