Shifts in bacterial diversity, interactions and microbial elemental cycling genes under cadmium contamination in paddy soil: Implications for altered ecological function

Ecological characteristics of tall fescue and spatially organized communities: Their contribution to mitigating cadmium damage

The threat of cadmium (Cd) stress to agricultural soil environments, as well as their productivity attracting growing global interest. Tall fescue (Festuca arundinacea Schreb.) is a strong candidate for the remediation of heavy metals in soil. However, the joint analysis of Cd tolerance, physiological responses, and multifaceted plant microbiomes in tall fescue fields has not been extensively researched. Therefore, this study employed microbial sequencing (i.e., 16S and ITS sequencing) to investigate the differences in microbial community structure among various plant compartments of Cd-resistant tall fescue (cv. 'Arid3') and Cd-sensitive tall fescue (cv. 'Barrington'). Furthermore, we examined the mechanism of resistance to Cd by introducing three different bacteria and a fungus that were isolated from the 'Arid3' rhizosheath soil. It highlighted the potential application of enriched taxa such as Delftia, Novosphingobium, Cupriavidus and Torula in enhancing the activity of antioxidant defense systems, increasing the production of osmotic regulatory substances, and stimulating the expression of Cd-resistance genes. This ultimately promoted plant growth and enhanced phytoremediation efficiency. This study shed light on the response mechanism of the tall fescue microbiome to Cd stress and underscored the potential of tall fescue-microbe co-culture in the remediation of heavy metal-contaminated areas.

Precision management of Fusarium fujikuroi in rice through seed coating with an enhanced nanopesticide using a tannic acid-ZnII formulation

Seed coating with fungicides is a common practice in controlling seed-borne diseases, but conventional methods often result in high toxicity to plants and soil. In this study, a nanoparticle formulation was successfully developed using the metal-organic framework UiO-66 as a carrier of the fungicide ipconazole (IPC), with a tannic acid (TA)-ZnII coating serving as a protective layer. The IPC@UiO-66-TA-ZnII nanoparticles provided a controlled release, triggered and regulated by environmental factors such as pH and temperature. This formulation efficiently controlled the proliferation of Fusarium fujikuroi spores, with high penetration into both rice roots and fungal mycelia. The product exhibited high antifungal activity, achieving control efficacy rates of 84.09% to 93.10%, low biotoxicity, and promoted rice growth. Compared to the IPC flowable suspension formula, IPC@UiO-66-TA-ZnII improved the physicochemical properties and enzymatic activities in soil. Importantly, it showed potential for mitigating damage to beneficial soil bacteria. This study provides a promising approach for managing plant diseases using nanoscale fungicides in seed treatment.

Role of key microbial modules for soil carbon sequestration effects in biochar-based remediation of cadmium-contaminated soil

How changes in soil properties and heavy metal toxicity induced during biochar remediation of cadmium (Cd) contaminated soils induce changes in microbial communities, and further, how this process affects the soil carbon sequestration capacity by microorganisms, has not been explored. We prepared virgin biochar (named BC400 and BC600) using rice straw at 400 °C and 600 °C and modified biochar (named MNT-BC400 and MNT-BC600) using co-pyrolysis of montmorillonite and rice straw at the same two temperatures, in an attempt to create different CO2 emission backgrounds during the remediation of cadmium contamination in soil, and to explore the mechanism of soil carbon sequestration capacity during remediation. The results showed that MNT-BC600 was effective in reducing the soil available Cd during incubation without increasing soil carbon emission, whereas soil carbon emission was elevated by 83.10%, 50.19%, and 21.53% in BC400, MNT-BC400, and MNT-BC600 treatments compared to the control group (CK). Microbial carbon use efficiency (CUE) was increased by 20.68%, 18.78%, and 12.73% in BC400, BC600, and MNT-BC600 treatments, respectively. We found that the bacterial module (Bmod#2), dominated by the eutrophic bacteria Proteobacteria and Actinobacteriota, controlled the increase of soil carbon emissions; the bacterial module (Bmod#3) composed of both oligotrophic and eutrophic flora were closely related to soil CUE after remediation; the bacterial module (Bmod#4) consisting of oligotrophic and eutrophic bacteria alone was easily replaced by eutrophic bacteria module (Bmod#2) under eutrophic conditions and had a negative linear relationship with soil CO2 emission, while the switch in Cd form was more likely to affect the community structure of modules containing eutrophic bacteria. These findings provide new insights into the use of biochar for soil remediation and balancing soil carbon sequestration.

The Marine-Origin Exopolysaccharide-Producing Bacteria Micrococcus Antarcticus HZ Inhibits Pb Uptake in Pakchoi (Brassica chinensis L.) and Affects Rhizosphere Microbial Communities

Exopolysaccharides (EPSs) produced by microorganisms play an important role in biotolerance and reducing heavy metal (HM) contamination by limiting the migration of HMs into plants. However, research on the application of EPS-producing marine bacteria for soil heavy metal remediation remains limited, particularly regarding their mechanisms of HM immobilization in soil and impact on plant growth. In this study, the EPS-producing marine bacterium Micrococcus antarcticus HZ was investigated for its ability to immobilize Pb and produce EPSs in soil filtrate. The effects on the growth quality and biomass of pakchoi (Brassica chinensis L.), as well as bacterial communities in inter-root soil contaminated with Pb, were also investigated. The results indicated that HZ could reduce the Pb concentration in the soil filtrate, achieving a removal rate of 43.25-63.5%. The EPS content and pH levels increased in the presence of Pb. Pot experiments showed that adding HZ significantly increased the biomass of pakchoi (9.45-14.69%), vitamin C (Vc) (9.69-12.92%), and soluble protein content (22.58-49.7%). HZ reduced the Pb content in the roots (17.52-47.48%) and leaves (edible tissues) (43.82-52.83%) of pakchoi. HZ increased soil enzyme activities (alkaline phosphatase, dehydrogenase, and urease), and the contents of ammonium nitrogen and nitrate nitrogen. Additionally, HZ also increased the relative abundance of beneficial bacteria (e.g., Proteobacteria, Cyanobacteria, and Chlorobacteria) in the inter-root soil, which have prophylactic and heavy-metal fixation functions. In summary, HZ reduces effective Pb content in edible tissues, roots, and inter-root soil by regulating inter-root soil microbial community structure, increasing soil pH, nitrogen content, and soil enzyme activity, and altering dominant phylum abundance.

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

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

Uptake and translocation of cadmium and trace metals in common rice varieties at different growth stages

Rice (Oryza sativa) is an important nutritional grain for the majority of Asian countries, but it is also a major source of cadmium (Cd) accumulation. A pot experiment was carried out to investigate the Cd uptake and translocation of high Cd (IR-50) and low Cd (White Ponni) rice cultivars in Cd-contaminated soils. The findings revealed that Cd impacts on rice development and growth differed depending on rice cultivars. Soil Cd levels in the seedling stage exceeded the critical levels (3-6 mg kg-1) only 5.0 mg kg-1 Cd treatment for the IR-50 (7.47 mg kg-1). At higher Cd treatments (1.0 and 5.0 mg kg-1), morphometric characteristics and yield of grains showed a declining and increasing trend in both rice varieties, respectively. The accumulation of Cd was higher in soil and roots during seedling and tillering stages, whereas in booting and maturity stages increased in stems and leaves in IR-50 and WP rice varieties. Cd levels in rice grains above the maximum allowable limit (0.4 mg kg-1) only in IR-50 (0.51 mg kg-1) rice cultivar at maturity stage. The EF of Cd were classified as minor enrichment to 'moderate enrichment' in both rice cultivars. TF values exhibited > 1 in booting and maturity stages in both rice cultivars at higher Cd treatments. The study concluded that the IR-50 rice variety exhibited increased Cd intake and transported to various parts of rice plants, particularly grains. The findings indicate that WP rice cultivar is more resistant to Cd toxicity, reducing health hazards for persons who preferred the staple food rice.

R3 strain and Fe-Mn modified biochar reduce Cd absorption capacity of roots and available Cd content of soil by affecting rice rhizosphere and endosphere key flora

Microorganisms have a significant role in regulating the absorption and transportation of Cd in the soil-plant system. However, the mechanism by which key microbial taxa play a part in response to the absorption and transportation of Cd in rice under Cd stress requires further exploration. In this study, the cadmium-tolerant endophytic bacterium Herbaspirillum sp. R3 (R3) and Fe-Mn-modified biochar (Fe-Mn) were, respectively, applied to cadmium-contaminated rice paddies to investigate the effects of key bacterial taxa in the soil-rice system on the absorption and transportation of Cd in rice under different treatments. The results showed that both R3 and Fe-Mn treatments considerably decreased the content of cadmium in roots, stems and leaves of rice at the peak tillering stage by 17.24-49.28% in comparison to the control (CK). The cadmium content reduction effect of R3 treatment is better than that of Fe-Mn treatment. Further analysis revealed that the key bacterial taxa in rice roots under R3 treatment were Sideroxydans and Actinobacteria, and that their abundance showed a substantial positive correlation and a significant negative correlation with the capacity of rice roots to assimilate Cd from the surroundings, respectively. The significant increase in soil pH under Fe-Mn treatment, significant reduction in the relative abundances of Acidobacteria, Verrucomicrobia, Subdivision3 genera incertae sedis, Sideroxydans, Geobacter, Gp1, and Gp3, and the significant increase in the relative abundance of Thiobacillus among the soil bacterial taxa may be the main reasons for the decrease in available Cd content of the soil. In addition, both the R3 and Fe-Mn treatments showed some growth-promoting effects on rice, which may be related to their promotion of transformations of soil available nutrients. This paper describes the possible microbial mechanisms by which strain R3 and Fe-Mn biochar reduce Cd uptake in rice, providing a theoretical basis for the remediation of Cd contamination in rice and soil by utilizing key microbial taxa.

Relationships between high-concentration toxic metals in sediment and evolution of microbial community structure and carbon-nitrogen metabolism functions under long-term stress perspective

Microorganisms are highly sensitive to toxic metal pollution and play an important role in the material cycling and energy flow of the water ecosystem. Herein, 13 sediment samples from Junchong Reservoir (Guangxi Province, China) were collected in December 2021. The spatial distribution of pollution levels for toxic metals and the effects of toxic metals on the composition, functional characteristics, and metabolism of microorganisms were investigated. The results demonstrated that the area is a proximate area to industrial zones with severity of toxic metal pollution. Their mean concentrations of As, Cu, Zn, and Pb were up to 128.79 mg/kg, 57.62 mg/kg, 594.77 mg/kg, and 97.12 mg/kg respectively. There was a strong correlation between As, Cu, Zn, and Pb, with the highest correlation coefficient reaching 0.94. As the level of toxic metal pollution increases, the diversity and abundance of microorganisms gradually decrease. Compared to those with lower pollution levels, the Shannon index in regions with higher pollution levels decreases by up to 0.373, and the Chao index decreases by up to 143.507. However, the relative abundance of Bacteroidota, Patescibacteria, and Chloroflexi increased by 23%, 20%, and 5%, respectively, indicating their higher adaptability to toxic metals. Furthermore, microbial carbon and nitrogen metabolism were also affected by the presence of toxic metals. FAPROTAX analysis demonstrated an abundant reduction of ecologically functional groups associated with carbon and nitrogen transformations under high toxic metal pollution levels. KEGG pathway analysis indicated that carbon fixation and nitrogen metabolism pathways were inhibited with increasing toxic metal concentrations. These findings would contribute to a better understanding of the effects of toxic metal pollution on sediment microbial communities and function, shedding light on the ecological consequences of toxic metal contamination.

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.