Bacterial, archaeal, and fungal community responses to acid mine drainage-laden pollution in a rice paddy soil ecosystem

Efficient removal of atrazine by iron-modified biochar loaded Acinetobacter lwoffii DNS32

In order to efficiently remove commonly used herbicide atrazine in farmland, an iron-modified biochar (FeMBC) was fabricated via chemical co-precipitation of Fe³⁺ onto corn stalks biochar. The composites of FeMBC and Acinetobacter lwoffii DNS32 (bFeMBC) effectively accelerated the degradation rate of atrazine (100 mg L^-1) in inorganic salt culture solution. TEM，XRD，XPS and FTIR were used to study the basic properties of the Materials. FeMBC promoted the formation of bacterial biofilm, -NH functional group on the surface of bacterial extracellular polymers (EPS) and FeMBC could interact with the aromatic ring of atrazine through Hbonding, which were conducive for microbial capture of atrazine. Meanwhile, the pores (2-10 μm) of FeMBC facilitated the passage of the DNS32 strain and the atrazine molecule, which contributed to the efficient capture and degradation of atrazine by DNS32 strain. BFeMBC amendment helped to maintain the bacterial diversity in the atrazine contaminated soil. The increase of rare bacteria (relative abundance of 0.01%-0.05%) richness plays a certain role in stabilizing nutrient cycling, thereby promoting microbial nutrient utilization activities and has the function of pollutant degradation. This may contribute to the digestion of atrazine and its intermediate metabolites，reducing the stress of microbial in atrazine contaminated soil. bFeMBC amendment may be a promising in situ remediation technique for soil atrazine contamination.

Potentially toxic metal contamination and microbial community analysis in an abandoned Pb and Zn mining waste deposit

Bioindicators have been widely used to assess the contamination of lead/zinc (Pb/Zn) in smelter areas, mining waste disposal areas and in areas containing slags from Pb ore smelting. In this context, the analysis involving microorganisms has gained prominence as a complementary tool in studies aimed at assessing contaminated sites. Therefore, the objective of this study was to assess the contamination of Pb, Zn and cadmium (Cd) in an area where a PbZn smelter operated, using the integration of geochemical and microbial data. The experimental analysis was conducted to characterize the soil collected at three different sites (samples NS, EW and EP). The analysis conducted was physicochemical, metal concentration, metal speciation and analysis of the microbial community through high-throughput sequencing technique. Through the results it was observed that the high concentrations of metals altered the bacterial community present in the soil. Differences were noted between the microbial communities according to the sampling site, especially in sample EP, collected at the margin of the dirt road, which presented higher metal concentrations and microbial diversity. The main phyla detected in the samples were: Proteobacteria, Bacteroidetes and Acidobacteria. Bacteria tolerant to the presence of potentially toxic metals (PTM), such as Rhodoplanes, Kaistobacter, Sphingomonas and Flavisolibacter were identified in the analyzed samples. The phylogenetic groups identified in the study area are similar to those obtained in other studies in metal contaminated areas. The differences between the bacterial communities in each sample indicate that the concentration of PTM may have influenced the microbial community in the soil. Thus, it is noted the importance of the integration of geochemical and microbial data to evaluate the impact of the improper disposal of high PTM concentrated slags in natural soils.

Dissimilatory iron and sulfate reduction by native microbial communities using lactate and citrate as carbon sources and electron donors

The bacterial (dissimilatory) iron and sulfate reduction (BIR and BSR) are intimately linked to the biogeochemical cycling of C, Fe, and S in acid mine drainage (AMD) environments. This study examined the response of native microbial communities to the reduction of iron and sulfate in bench experimental systems. Results showed that the reduction of ferric iron and sulfate took place when the electron acceptors coexist. Existence of Fe(III) can postpone the reduction of sulfate, but can enhance the reduction rate. Cultures grown in the presence of 10 mM iron can reach the final level of sulfate bio-reduction rate (~100%) after 35 days incubation. 16 S rDNA -based microbial community analysis revealed that the three genera Anaeromusa, Acinetobacter and Bacteroides were dominated in the ferric-reducing conditions. SRB (Desulfobulbus, Desulfosporosinus and Desulfovibrio) were dominated in the sulfate reduction process. Results in this study highlighted the highly coupled nature of C, Fe, and S biogeochemical cycles in AMD and provided insights into the potential of environmental remediation by native microbial.

Natural Farming Improves Soil Quality and Alters Microbial Diversity in a Cabbage Field in Japan

Natural farming (NF), an environmentally friendly agricultural practice similar to organic farming, was developed in Japan. Unlike conventional farming, little is known about the influence of NF on soil microbial communities, especially the surface soil. We therefore compared the effect of seven years’ conventional practice (CP), conventional practice without chemicals (CF), and NF on soil properties and microbial community structure at two soil depths (0–10, 10–20 cm) in an experimental cabbage field. Both soil depth and agricultural practice significantly influenced edaphic measures and microbial community structure. NF improved bulk density, pH, electrical conductivity, urease activity, and nitrate reductase activity in topsoil; similar trends were observed in deeper soil. Pyrosequencing demonstrated that the use of pesticides in conventional farming (CP) led to lower microbial abundance and diversity in topsoil than CF. Similarly, NF increased microbial abundance compared to CP. However, distinct taxa were present in the topsoil, but not deeper soil, in each treatment. CP-enriched microbial genera may be related to plant pathogens (e.g., Erwinia and Brenneria) and xenobiotic degraders (e.g., Sphingobacterium and Comamonas). The microbial community structure of NF was distinct to CP/CF, with enrichment of Pedomicrobium and Solirubrobacter, which may prefer stable soil conditions. Network analysis of dominant genera confirmed the more stable, complex microbial network structure of the 0–10 cm than 10–20 cm layer. Flavisolibacter/Candidatus Solibacter and Candidatus Nitrososphaera/Leuconostoc are potentially fundamental taxa in the 0–10 cm and 10–20 cm layer networks, respectively. Overall, we show that NF positively affects soil quality and microbial community composition within sustainable farming systems.

Simultaneous mitigation of tissue cadmium and lead accumulation in rice via sulfate-reducing bacterium

The objectives of this study were to investigate the mechanism responsible for Cd and Pb immobilization by sulfate reduction to sulfide and effectiveness of decreasing Cd²⁺ and Pb²⁺ bioavailability in culture solution and paddy soils via sulfate-reducing bacterium (SRB1-1). The SRB1-1 strain, exhibiting high resistances to Cd²⁺ and Pb²⁺, was isolated from bulk soils in the metal(loid)-contaminated paddy field. During the culture of the SRB1-1 strain, the removal percentages of Cd²⁺ and Pb²⁺ from culture solution reached 99.5% and 76.0% in 72 h, respectively. The surface morphology and composition of metal precipitates formed by SRB1-1 strain were analyzed by transmission electron microscopy (TEM) and further confirmed to be CdS and PbS by X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). When living SRB1-1 strain was applied in Cd and Pb-contaminated soils, the SRB1-1 strain could stably colonize using its resistance to rifampicin, and showed significantly impact on the bacterial community composition. Cd and Pb contents in rice grains were decreased by 29.5% and 26.2%, respectively, while Cd and Pb contents in the roots, culms, leaves, and husk were also decreased ranging from 19.1% to 43%, respectively. Due to growth in highly Cd and Pb contaminated soils, Cd content of the rice grains did not meet the standard for limit of Cd and Pb, but safe production of rice plants may be obtained in slightly or moderately metal(loid)-contaminated soils in the presence of the living SRB1-1 strain. These results indicated that the SRB1-1 strain could effectively reduce the Cd and Pb bioavailability in soils and uptake in rice plants. Our results highlighted the possibility to develop a new bacterial-assisted technique for reduced metal accumulation in rice grains, and also showed potential for effective synergistic bioremediation of SRB1-1 strain and rice plants in metal(loid)-contaminated soils.

Soil aggregate-associated bacterial metabolic activity and community structure in different aged tea plantations

Revealing the dynamics of soil aggregate-associated microbial (particularly bacterial) metabolic activity and community structure is of great importance to maintain the soil health and microbial community stability in tea plantation ecosystems. In this study, the bacterial metabolic activity (as measured by Biolog Eco MicroPlates) and community structure (as measured by high-throughput sequencing) were analyzed in soil aggregates, which were collected at the 0-20 cm depth in four tea plantations with different ages (16, 23, 31, and 53 yrs.) in the areas of Western Sichuan, China. A dry-sieving procedure was adopted to separate soil aggregates into four fractions, including >2, 2-1, 1-0.25, and <0.25 mm. In all the tea plantations, the highest levels of soil bacterial metabolic activity (as indicated by average well color development, AWCD) and community diversity (as indicated by Chao 1 and Shannon indices) appeared in the >2 mm fractions, which indicated that these aggregate fractions with complex bacterial communities not only provided biological buffering, but also prevented the dominance of individual microorganisms through predation or competition. Soil aggregates with >2 mm were concentrated in the 23 yrs. tea plantation, implying that this tea plantation possessed the relatively suitable soil environments to the growth and proliferation of soil bacteria, thus increasing their metabolic activity and community diversity. After 23 yrs. of tea planting, the reduction of the >2 mm fractions in the whole-soil accounted for the degradation of soil bacterial communities to some extent. In the meanwhile, soil microbial quotient (the ratio of soil microbial biomass C to organic C) and pH were also important drivers of the variations in soil bacterial communities during tea planting. This study underscored the requirement for sustainable soil managements which could maintain the soil health and bacterial community stability after 23 yrs. of tea planting in the areas of Western Sichuan, China.

Environmental implications of metal mobility in marine sediments receiving input from a torrent affected by mine discharge

Acid Mine Drainage (AMD) is one of the most important sources of pollution in fluvial systems and can enrich rivers in dissolved and suspended metals of environmental concern. Colloidal particles may favour the transport of metals to the sea, where metals can be accumulated in bottom sediments. The aim of this paper was to evaluate the mobility of metals in the "Baia delle Favole" bottom sediments (Sestri Levante, Italy), which receive the input of the AMD impacted Gromolo Torrent, using chemical speciation (BCR sequential extraction). Basing on the Risk Assessment Code (RAC), our results showed a systematic and widespread high risk classification for Mn, whereas a medium risk is associated to Co, Cu, and Zn in the sediments collected near the mouth of the Gromolo Torrent. Moreover, in these sediments the occurrence of Fe oxyhydroxides has been observed, reflecting an increase of metals in the reducible fraction obtained with BCR.

Bacterial community variations in paddy soils induced by application of veterinary antibiotics in plant-soil systems

Soil bacterial communities have complex regulatory networks, which are mainly associated with soil fertility and ecological functions, and are likely to be disturbed due to antibiotics applications. The impact of antibiotics, particularly in mixtures form, on bacterial communities in different paddy soils is poorly understood. Using pyrosequencing techniques of 16 S rRNA genes, this study investigated the synergistic effects of veterinary antibiotics (sulfadiazine, sulfamethoxazole, trimethoprim, florfenicol, and clarithromycin) on bacterial communities in a soil-bacteria-plant system. Rice was grown under controlled greenhouse conditions where unplanted and planted treatments were doped with 200 µg kg^-1 of combined antibiotics over a period of 3 months. Bacterial richness remained unaltered, while a significant decline was observed in bacterial diversity due to antibiotics in the four paddy soils. Bacteroidetes and Acidobacteria were increased, while Actinobacteria and Firmicutes decreased under antibiotics exposure. Despite antibiotics perturbation, compositional variations were mainly attributed to the different paddy soils which harbor distinct bacterial communities. Haliangium and Gaiella were among the sensitive genera that were negatively correlated to antibiotics perturbation. Additionally, electrical conductivity, total organic carbon, and total nitrogen of soil solution were the key physiochemical indices which significantly influenced the structure of bacterial communities in the paddy soils. These findings expanded our knowledge of effects from synergistic antibiotics application and variations in bacterial communities among different paddy soils.

Monitoring the Activated Sludge Activities Affected by Industrial Toxins via an Early-Warning System Based on the Relative Oxygen Uptake Rate (ROUR) Index

Shock load from industrial wastewater is known to harm the microbial activities of the activated sludge in wastewater treatment plants (WWTPs) and disturb their performance. This study developed a system monitoring the activated sludge activities based on the relative oxygen uptake rate (ROUR) and explored the influential factors with wastewater and the activated sludge samples collected from a typical WWTP in the Taihu Lake of southern Jiangsu province, China. The ROUR was affected by the concentration of toxic substances, mixed liquid suspended solids (MLSS), hydraulic retention time (HRT) and pH. Higher toxin contents significantly decreased the ROUR and the EC50 value of Zn2+, Ni2+, Cr(VI), Cu2+, and Cd2+ was 13.40, 15.54, 97.56, 12.01, and 14.65 mg/L, respectively. The ROUR declined with the increasing HRT and MLSS above 2000 mg/L had buffering capacities for the impacts of toxic substances to some extent. The ROUR remained stable within a broad range pH (6–10), covering most of the operational pH in WWTPs and behaving as an appropriate indicator for monitoring the shock load. A toxicity model assessing and predicting the ROUR was developed and fitted well with experimental data. Coupling the ROUR monitoring system and toxicity model, an online early-warning system was assembled and successfully used for predicting the toxicity of different potential toxic metals. This study provides a new universal toxicity model and an online early-warning system for monitoring the shock load from industrial wastewater, which is useful for improving the performance of WWTPs.

Bacterial community shaped by heavy metals and contributing to health risks in cornfields

Scientists are increasingly aware that heavy metal contamination in soils, especially in farmland ecosystems, can negatively affect human health and alter the bacterial community that plays a critical role in plant growth and heavy metal accumulation. The goal of the present paper was to uncover how various heavy metals and non-metallic elements affect human health and bacterial diversity in cornfields and to explore the contribution of soil bacteria to heavy metal accumulation in crops. Soil samples were collected from five counties in Shandong Province, China, where abnormally high levels of heavy metals and metalloids were caused by mining and heavy industry. We calculated a hazard quotient (HQ) to evaluate the health risk these heavy metals cause and analyzed the soil bacterial community using 16S rRNA gene sequencing. The HQ results showed that As posed the greatest threat to human health followed by Pb although concentrations of all metals did not reach the health risk threshold. Meanwhile, principal component analysis (PCA) and redundancy analysis (RDA) revealed soil bacterial richness was significantly influenced by As, Ni, and Cr as well as pH and phosphorus, but not by the species diversity of aboveground weeds. The most abundant bacteria in our study region were heavy metal tolerant groups, specifically Actinobacteria and Proteobacteria. Moreover, correlation analysis suggested that Actinobacteria might reduce the phytoaccumulation of Cr, Cu, Zn, and Hg in corn, while Proteobacteria might weaken phytoaccumulation of Pb, Ni, As, and Cd. Our results verified that heavy metals play an important role in shaping the soil bacterial community. Using native bacteria in farmland provides a potential biological strategy for reducing the health risk posed by heavy metals related to food consumption.

Migration and fate of metallic elements in a waste mud impoundment and affected river downstream: A case study in Dabaoshan Mine, South China

Fate of metallic elements and their migration mechanisms in a waste mud impoundment and affected downstream were assessed. Physicochemical and mineralogical methods combined with PHREEQC calculation, statistical analysis and review of relevant literatures were employed. Results showed that the waste in mud impoundment had been severely weathered and acidized. Metallic elements exhibited high mobility and activity, with a mobility ranking order of Cd > Zn > Mn > Cu ≈ Cr > As ≈ Pb. Hydraulic transportation originating from elevation variation was the most important driving force for metallic elements migration. Although damming standstill was considered as an effective strategy for controlling coarse suspended particulate pollutants, metallic elements were still transported to the Hengshi River in both dissolved phase and fine suspended particle phase accompanied by the overflow of acid mine drainage. The concentrations of dissolved metallic elements were attenuated significantly along the Hengshi River within 41 km stretch. Precipitation/ co-precipitation of iron oxyhydroxides, especially schwertmannite, ferrihydrite and goethite minerals, were established as the most critical processes for metallic elements attenuation in river water. Accompanied by metals migration in the river, two pollution sensitive sites with notably high content of metals in the stretch of S6-S8 and S10, were identified in gently sloping river stretch.

Phytoextraction and biodegradation of atrazine by Myriophyllum spicatum and evaluation of bacterial communities involved in atrazine degradation in lake sediment

The accumulation of atrazine in lake sediments leads to persistent contamination, which may damage the succeeding submerged plants and create potential threats to the lake eco-environment. In this study, the degradation characteristics of atrazine and its detoxication by Myriophyllum spicatum and the associated bacterial community in lake sediments were evaluated. M. spicatum absorbed more than 18-fold the amount of atrazine in sediments and degraded atrazine to hydroxyatrazine (HA), deelthylatrazine (DEA), didealkylatrazine (DDA), cyanuric acid (CYA) and biuret. The formation of biuret suggested for the first time, the ring opening of atrazine in an aquatic plant. The residual rate of atrazine was 6.5 ± 2.0% in M. spicatum-grown sediment, which was significantly lower than the 18.0 ± 2.5% in unplanted sediments on day 60 (P < 0.05). Moreover, on day 15, the increase in contents of HA, CYA and biuret in M. spicatum-grown sediment indicated that M. spicatum promoted the degradation and removal of atrazine following rapid dechlorination. The colonization of M. spicatum and the addition of atrazine altered the structure of the dominant bacterial community in sediments, including effects on Nitrospirae and Acidobacteria. Based on the maximum amount among the genera of atrazine-degrading bacteria, Acetobacter was most likely responsible for the degradation of atrazine. Our findings reveal the natural attenuation of atrazine by aquatic organisms.

Migration and Fate of Acid Mine Drainage Pollutants in Calcareous Soil

As a major province of mineral resources in China, Shanxi currently has 6000 mines of various types, and acid mine drainage (AMD) is a major pollutant from the mining industry. Calcareous soil is dominant in western North China (including the Shanxi Province), therefore, clarifying the migration behavior of the main AMD pollutants (H⁺, S, Fe, heavy metals) in calcareous soil is essential for remediating AMD-contaminated soil in North China. In this study, the migration behavior of the main pollutants from AMD in calcareous soil was investigated using soil columns containing 20 cm of surficial soil to which different volumes of simulated AMD were added in 20 applications. Filtrate that was discharged from the soil columns and the soil samples from the columns were analyzed. Almost all of the Fe ions (>99%) from the AMD were intercepted in the 0–20 cm depth of the soil. Although >80% of SO₄²⁻ was retained, the retention efficiency of the soil for SO₄²⁻ was lower than it was for Fe. Cu, as a representative of heavy metals that are contained in AMD, was nearly totally retained by the calcareous soil. However, Cu had a tendency to migrate downward with the gradual acidification of the upper soil. In addition, CaCO₃ was transformed into CaSO₄ in AMD-contaminated soil. The outcomes of this study are valuable for understanding the pollution of calcareous soil by AMD and can provide key parameters for remediating AMD-contaminated soil.