Assembly processes of bacterial and fungal communities in metal(loid)s smelter soil

Impact of soil physicochemical factors and heavy metals on co-occurrence pattern of bacterial in rural simple garbage dumping site

Rural waste accumulation leads to heavy metal soil pollution, impacting microbial communities. However, knowledge gaps exist regarding the distribution and occurrence patterns of bacterial communities in multi-metal contaminated soil profiles. In this study, high-throughput 16 S rRNA gene sequencing technology was used to explore the response of soil bacterial communities to various heavy metal pollution in rural simple waste dumps in karst areas of Southwest China. The study selected three habitats in the center, edge, and uncontaminated areas of the waste dump to evaluate the main factors driving the change in bacterial community composition. Pollution indices reveal severe contamination across all elements, except for moderately polluted lead (Pb); contamination severity ranks as follows: Mn > Cd > Zn > Cr > Sb > V > Cu > As > Pb. Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteriota predominate, collectively constituting over 60% of the relative abundance. Analysis of Chao and Shannon indices demonstrated that the waste dump center boasted the greatest bacterial richness and diversity. Correlation data indicated a predominant synergistic interaction among the landfill's bacterial community, with a higher number of positive associations (76.4%) compared to negative ones (26.3%). Network complexity was minimal at the dump's edge. RDA analysis showed that Pb(explained:46%) and Mn(explained:21%) were the key factors causing the difference in bacterial community composition in the edge area of the waste dump, and AK(explained:42.1%) and Cd(explained:35.2%) were the key factors in the center of the waste dump. This study provides important information for understanding the distribution patterns, co-occurrence networks, and environmental response mechanisms of bacterial communities in landfill soils under heavy metal stress, which helps guide the formulation of rural waste treatment and soil remediation strategies.

Considering the bioavailability and bioaccessibility of metal(loid)s for risk assessment of soils affected by different non-ferrous metal activities in Southwest China

Toxic metal(loid)s released into the soil by non-ferrous metal mining and smelting activities pose a serious threat to residents and the surrounding ecosystem. Considering only total metal(loid) concentrations likely overestimates routine (eco)toxicological risk assessment of soil. We hypothesize that considering metal(loid) bioavailability/accessibility will improve the accuracy of risk assessment. To test this hypothesis, four mining areas in Southwest China, including mining and surrounding sites, were studied. Bioavailability was determined considering metal(loid)s leached by a simulated strong acid rain (SSAR) treatment. In the four areas, the mining site showed higher cumulative releases of metal(loid)s under SSAR treatment than the agricultural field located in the surrounding sites. Thus, the bioavailable metal(loid)s contents were continuously being released during SSAR treatment and likely increased the environmental risk. Ecological and health risk assessment of soil, calculated using total metal(loid)s content, was corrected considering bioavailable/accessible metal(loid)s, which was determined by the heavy metal(loid)s forms and in vitro simulated intestinal stages. Although the corrected indices indicated that the risk of metal(loid)s-contaminated soil was reduced, unfavorable ecological and health risks remained in the four areas. Our study provides new perspectives to better predict the risk of bioavailable/accessible metal(loid)s in non-ferrous metal contaminated and surrounding soils.

Impacts of multiple environmental factors on soil bacterial community assembly in heavy metal polluted paddy fields

Soil microorganisms play pivotal roles in driving essential biogeochemical processes in terrestrial ecosystems, and they are sensitive to heavy metal pollution. However, our understanding of multiple environmental factors interaction in heavy metal polluted paddy fields to shape microbial community assembly remain limited. In the current study, we used 16S rRNA amplicon sequencing to characterize the microbial community composition in paddy soils collected from a typical industry town in Taihu region, eastern China. The results revealed that Cd and Pb were the major pollutant, and Proteobacteria, Acidobacteria and Chloroflexi were the dominate indigenous bacterial phyla. Linear regression and random forest analysis demonstrated that soil pH was the most important predictor of bacterial diversity. Mantel analysis showed that bacterial community structure was mainly driven by pH, CEC, silt, sand, AK, total Cd and DTPA-Cd. The constructed bacterial co-occurrence network, utilizing a random matrix theory-based approach, exhibited non-random with scale-free and modularity features. The major modules within the networks also showed significant correlations with soil pH. Overall, our study indicated that soil physiochemical properties made predominant contribution to bacterial community diversity, structure and their association in Cd/Pb polluted paddy fields. These findings expand our knowledge of the key environmental drivers and co-occurrence patterns of bacterial community in polluted paddy fields.

A novel Biochar-PGPB strategy for simultaneous soil remediation and safe vegetable production

There is currently increasing pressure on agriculture to simultaneously remediate soil and ensure safe agricultural production. In this study, we investigate the potential of a novel combination of biochar and plant growth-promoting bacteria (PGPB) as a promising approach. Two types of biochar, corn stover and rice husk-derived, were used in combination with a PGPB strain, Bacillus sp. PGP5, to remediate Cd and Pb co-contaminated soil and enhance lettuce performance. The contaminated soil was pre-incubated with biochar prior to PGP5 inoculation. The combined application of biochar and PGPB reduced the diethylenetriaminepentaacetic acid (DTPA) -extractable Cd and Pb concentrations in the soil by 46.45%-55.96% and 42.08%-44.83%, respectively. Additionally, this combined application increased lettuce yield by 23.37%-65.39% and decreased Cd and Pb concentrations in the edible parts of the lettuce by 57.39%-68.04% and 13.57%-32.50%. The combined application showed a better promotion on lettuce growth by facilitating chlorophyll synthesis and reducing oxidative stress. These demonstrated a synergistic effect between biochar and PGPB. Furthermore, our study elucidated the specific role of the biochar-PGPB combination in soil microbial communities. Biochar application promoted the survival of PGP5 in the soil. The impact of biochar or PGPB on microbial communities was found to be most significant in the early stage, while the development of plants had a greater influence on rhizosphere microbial communities in later stage. Plants showed a tendency to recruit plant-associated microbes, such as Cyanobacteria, to facilitate growth processes. Notably, the combined application of biochar and PGPB expedited the assembly of microbial communities, enabling them more closely with the rhizosphere microbial communities in late stage of plant development and thus enhancing their effects on promoting plant growth. This study highlights the "accelerating" advantage of the biochar-PGPB combination in the assembly of rhizosphere microbiomes and offers a new strategy for simultaneous soil remediation and safe agricultural production.

Impacts of cadmium accumulation on the diversity, assembly processes, and co-occurrence patterns of archaeal communities in marine sediments

There is limited understanding regarding the changes in the ecological processes and the mechanisms of archaeal community in response to heavy metal contamination in the marine sediments. In this study, sediment samples were collected from 46 locations near harbors, and the concentration of heavy metals and the diversity of archaeal communities were investigated to understand the impact of Cd on archaeal communities. The results demonstrated a significant correlation between the diversity of archaeal community and Cd concentration, particularly showing a linear decrease in the species richness with rising Cd concentration. ANME-1b was identified as a significantly enriched archaeal taxon in the higher Cd environment. Null model and neutral community model indicated that the ecological assembly of archaeal communities in marine sediments was primarily governed by the stochastic processes, with dispersal limitation being the primary factor. The contribution of deterministic process to the assembly of archaeal communities in higher Cd environments increased clearly, accompanied by a notable reduction in species migration rates and widths of ecological niche of archaeal populations. Co-occurrence network analysis revealed an obvious increase in species interactions in higher Cd environments, with an apparent rise in the proportion of competitive relationships and an increase in the number of keystone species. Moreover, archaeal species formed a more complex and stable community to cope with Cd stress. This study provides new insights into the impacts of heavy metals on the ecological processes of marine microorganisms and the underlying mechanisms.

Ecological characteristics of sugar beet plant and rhizosphere soil in response to high boron stress: A study of the remediation potential

High boron (B) stress degrades the soil environment and reduces plant productivity. Sugar beet has a high B demand and potential for remediation of B-toxic soils. However, the mechanism regarding the response of sugar beet plants and rhizosphere soil microbiome to high B stress is not clear. In the potted soil experiment, we set different soil effective B environments (0.5, 5, 10, 30, 50, and 100 mg kg-1) to study the growth status of sugar beets under different B concentrations, as well as the characteristics of soil enzyme activity and microbial community changes. The results showed that sugar beet growth was optimal at 5 mg kg-1 of B. Exceeding this concentration the tolerance index decreased. The injury threshold EC20 was reached at an available B concentration of 35.8 mg kg-1. Under the treatment of 100 mg kg-1, the B accumulation of sugar beet reached 0.22 mg plant-1, and the tolerance index was still higher than 60%, which had not yet reached the lethal concentration of sugar beet. The abundance of Acidobacteriota, Chloroflexi and Patescibacteria increased, which was beneficial to the resistance of sugar beet to high B stress. In summary, under high B stress sugar beet had strong tolerance, enhanced capacity for B uptake and enrichment, and changes in soil microbial community structure. This study provides a theoretical basis for clarifying the mechanism of sugar beet resistance to high B stress and soil remediation.

Contrasting response strategies of sulfate-reducing bacteria in a microbial consortium to As3+ stress under anaerobic and aerobic environments

The sulfate-reducing efficiency of sulfate-reducing bacteria (SRB) is strongly influenced by the presence of oxygen, but little is known about the oxygen tolerance mechanism of SRB and the effect of oxygen on the metalliferous immobilization by SRB. The performance evaluation, identification of bioprecipitates, and microbial and metabolic process analyses were used here to investigate the As3+ immobilization mechanisms and survival strategies of the SRB1 consortium under different oxygen-containing environments. Results indicated that the sulfate reduction efficiency was significantly decreased under aerobic (47.37%) compared with anaerobic conditions (66.72%). SEM analysis showed that under anaerobic and aerobic conditions, the morphologies of mineral particles were different, whereas XRD and XPS analyses showed that the most of As3+ bioprecipitates under both conditions were arsenic minerals such as AsS and As4S4. The abundances of Clostridium_sensu_stricto_1, Desulfovibrio, and Thiomonas anaerobic bacteria were significantly higher under anaerobic than aerobic conditions, whereas the aerobic Pseudomonas showed an opposite trend. Network analysis revealed that Desulfovibrio was positively correlated with Pseudomonas. Metabolic process analysis confirmed that under aerobic conditions the SRB1 consortium generated additional extracellular polymeric substances (rich in functionalities such as Fe-O, SO, CO, and -OH) and the anti-oxidative enzyme superoxide dismutase to resist As3+ stress and oxygen toxicity. New insights are provided here into the oxygen tolerance and detoxification mechanism of SRB and provide a basis for the future remediation of heavy metal(loid)-contaminated environments.

Archaea are better adapted to antimony stress than their bacterial counterparts in Xikuangshan groundwater

Archaea are important ecological components of microbial communities in various environments, but are currently poorly investigated in antimony (Sb) contaminated groundwater particularly on their ecological differences in comparison with bacteria. To address this issue, groundwater samples were collected from Xikuangshan aquifer along an Sb gradient and subjected to 16S rRNA gene amplicon sequencing and bioinformatic analysis. The results demonstrated that bacterial communities were more susceptibly affected by elevated Sb concentration than their archaeal counterparts, and the positive stimulation of Sb concentration on bacterial diversity coincided with the intermediate disturbance hypothesis. Overall, the balance of environmental variables (Sb, pH, and EC), competitive interactions, and stochastic events jointly regulated bacterial and archaeal communities. Linear fitting analysis revealed that Sb significantly drove the deterministic process (heterogeneous selection) of bacterial communities, whereas stochastic process (dispersal limitation) contributed more to archaeal community assembly. In contract, the assembly of Sb-resistant bacteria and archaea was dominated by the stochastic process (undominated), which implied the important role of diversification and drift instead of selection. Compared with Sb-resistant microorganisms, bacterial and archaeal communities showed lower niche width, which may result from the constraints of Sb concentration and competitive interaction. Moreover, Sb-resistant archaea had a higher niche than that of Sb-resistant bacteria via investing on flexible metabolic pathways such as organic metabolism, ammonia oxidation; and carbon fixation to enhance their competitiveness. Our results offered new insights into the ecological adaptation mechanisms of bacteria and archaea in Sb-contaminated groundwater.

Disentangling the impact of biogas slurry topdressing as a replacement for chemical fertilizers on soil bacterial and fungal community composition, functional characteristics, and co-occurrence networks

The application of biogas slurry topdressing with drip irrigation systems can compensate for the limitation of traditional solid organic fertilizer, which can only be applied at the bottom. Based on this, we attempted to define the response of soil bacterial and fungal communities of maize during the tasseling and full maturity stages, by using a no-topdressing control and different ratios of biogas slurry nitrogen in place of chemical fertilizer topdressing. The application of biogas slurry resulted in the emergence of new bacterial phyla led by Synergistota. Compared with pure urea chemical topdressing, the pure biogas slurry topdressing treatment significantly enriched Firmicutes and Basidiomycota communities during the tasseling stage, in addition to affecting the separation of bacterial and fungal α-diversity indices between the tasseling and full maturity stages. Based on the prediction of community composition and function, the changes in bacterial and fungal communities caused by biogas slurry treatment stimulated the ability of microorganisms to decompose refractory organic components, which was conducive to turnover in the soil carbon cycle, and improved multi-element (such as sulfur) cycles; however it may also bring potential risks of heavy metal and pathogenic microbial contamination. Notably, the biogas slurry treatment reduced the correlation and aggregation of bacterial and fungal symbiotic networks, and had a dual effect on ecological randomness. These findings contribute to a deeper comprehension of the alterations occurring in soil microbial communities when substituting chemical fertilizers treated with biogas slurry topdressing, and promote the efficient and sustainable utilization of biogas slurry resources.

Distribution heterogeneity of sediment bacterial community in the river-lake system impacted by nonferrous metal mines: Diversity, composition and co-occurrence patterns

Metal(loid) pollution caused by mining activities can affect microbial communities. However, knowledge of the diversity, composition, and co-occurrence patterns of bacterial communities in aquatic systems impacted by nonferrous metal mines. Here, the metal(loid) contents and bacterial communities in sediments from the Zijiang River (tributary to mainstream) to Dongting Lake were investigated by geochemical and molecular biology methods. The results indicated that the river sediments had lower pH and higher ecological risk of metal(loid)s than the lake sediment. The diversity and composition of bacterial communities in river sediments significantly (p < 0.05) differed from those in lake sediments, showing distributional heterogeneity. The biomarkers of tributary, mainstream, and lake sediments were mainly members of Deltaproteobacteria, Firmicutes, and Nitrospirae, respectively, reflecting species sorting in different habitats. Multivariate statistical analysis demonstrated that total and bioavailable Sb, As, and Zn were positively correlated with bacterial community richness. pH, TOC, TN, and Zn were crucial factors in shaping the distribution difference of bacterial communities. Environment-bacteria network analysis indicated that pH, SO42-, and total and bioavailable As and Sb greatly influenced the bacterial composition at the genus level. Bacteria-bacteria network analysis manifested that the co-occurrence network in mainstream sediments with a higher risk of metal(loid) pollution exhibited higher modularity and connectivity, which might be the survival mechanism for bacterial communities adapted to metal(loid) pollution. This study can provide a theoretical basis for understanding the ecological status of aquatic systems.

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

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

Unveiling the impact and mechanisms of Cd-driven ecological assembly and coexistence of bacterial communities in coastal sediments of Yellow Sea

The microbial community assembly processes and underlying mechanisms in response to heavy metal accumulation in coastal sediments remain underexplored. In this study, the heavy metal concentration in samples were found below the marine sediment quality standards. Through partial Mantel tests and linear regression analysis, Cd was identified as the major influencing factor, displaying strongest correlation with the bacterial community in the sediments. The class Desulfuromonadia was identified as a biomarker which showed enrichment in the sediments with high Cd content. Additionally, the results of null model and the neutral community model demonstrated the prominent role of stochastic processes in the assembly of bacterial community. However, with the increase in Cd concentration, the influence of selection processes intensified, resulting in a decline in species migration rate and subsequent reduction in ecological niche width. Furthermore, the intensified competition and an increase in keystone species among bacterial populations further enhanced the stability of the microbial co-occurrence network in response to high Cd concentration. This study offers an insight into the effects of heavy metal on microbial assembly and coexistence, which are conducive to marine ecosystem management and conservation.

New insights on the effect of non-ferrous metal mining and smelting activities on microbial activity characteristics and bacterial community structure

Mining and smelting activities have brought potentially serious heavy metal(loid)s pollution to their surrounding locale. However, studies on microbial metabolic activities, community structure, and adaptation in soils proximal to non-ferrous metal mining and smelting areas are still lacking. Here the effects of biotic and abiotic characteristics of soil taken from sites surrounding inactive and active non-ferrous metal mine smelting facilities on microbial enzyme activity, microcalorimetry, and high-throughput sequencing of 16S rRNA gene barcoding were studied. Data indicated that the soils were heavily polluted by toxic metal(loid)s, of which As and Cd were the main contaminants. Microbial acid phosphatase activity and microcalorimetric total heat value were sensitive metabolic indicators in the studied areas. Actinobacteriota had the highest relative abundance, followed by Proteobacteria, Chloroflexi, and Acidobacteria. Microbial metabolic activity, bacterial community structure and phenotype varied between inactive and active sites (p < 0.05). Such analyses indicated that electrical conductivity, total As, Cu, and Mn contents, and bioavailable As, Cu, Cd, and Mn concentrations were key factors determining microbial activities, bacterial community structure, and phenotypes. Knowledge of microbial adaptation to heavy metal stressors is important for better understanding the aerial transfer of fugitive heavy metal(loid)s (and possibly microbes) and for designing future strategies for improved soil bioremediation.