Microbial community composition and degradation potential of petroleum-contaminated sites under heavy metal stress

Psychrophilic insights into petroleum degradation: Gene abundance dynamics

Petroleum degradation by psychrophiles can be enhanced on the basis of omics analyses, which offer better sensitivity than traditional biochemical methods do. A metagenomic analysis focusing on gene abundance comparisons may provide new guidance to optimize soil decontamination under cold environmental conditions. The soil used in this study was sampled from Dalian, from which an indigenous consortium was isolated. The degradative soil systems, initially categorized into control (DLC) and experimental (DLD) groups, were kept at room temperature (20 ± 5 °C) for six weeks. The DLD group was subsequently transferred to a low-temperature environment (5-10 °C) for 90 days and renamed DDL. A petroleum removal rate of 74.59 % was achieved in the process from DLD to DDL groups. Each soil sample was subjected to analysis and metagenomic sequencing. The abundance of genes of interest was compared between pathways to determine trends. The findings demonstrate that psychrophilic degradation is more effective than natural remediation is. The soil microbial community structure displayed site specificity, with 802 genes in DDL associated with 249 pathways, indicating greater abundance of psychrophilic genes in DDL than in DLC. The abundance of key genes was at different orders of magnitude but showed similar trends. The abundance of genes associated with hydrocarbon-related metabolism surpassed that of genes associated with sphingolipid, fatty acid, or benzene metabolism. This study provides valuable insights into psychrophilic microbe-driven petroleum degradation and indicates the need for precise supplementation of biosurfactants to improve remediation efficiency.

A novel immobilized bacteria consortium enhanced remediation efficiency of PAHs in soil: Insights into key removal mechanism and main driving factor

The remediation of sites co-contaminated with polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs) poses challenges for efficient and ecofriendly restoration methods. In this study, three strains (Pseudomonas sp. PDC-1, Rhodococcus sp. RDC-1, and Enterobacter sp. EDC-1) were isolated from sites contaminated with PAHs and HMs. The constructed bacteria consortium was then immobilized using biochar, bentonite, and peat. The immobilized bacteria consortium (IBC) demonstrated efficient removal ability of phenanthrene (58.1 %-73.4 %) and benzo[a]pyrene (69.6 %-83.5 %) during 60 days. Additionally, the IBC decreased soil bacterial richness and diversity, but increased the relative abundance of Proteobacteria phylum and Ochrobactrum genus, which were capable of degrading PAHs. Soil microbial co-occurrence network with IBC was classified into three main modules, and 14 genera were identified as keystone taxa linked to PAHs degradation and HMs resistance. The IBC enhanced the dioxygenase metabolic pathways for PAHs degradation, including phthalic acid and salicylic acid pathways, which became the main driving factor affecting PAHs removal efficiency based on the structural equation modeling analysis. This study confirmed the potential application of the constructed IBC in the bioremediation of soil co-contaminated with PAHs-HMs, and provides insights into key removal mechanism and main driving factor of the enhanced elimination of PAHs.

Co-pollution risk of petroleum hydrocarbons and heavy metals in typically polluted estuarine wetlands: Insights from the Xiaoqing River

Excessive accumulation of total petroleum hydrocarbons (TPH) and heavy metals (HMs) in sediments poses a significant threat to the estuarine ecosystem. In this study, the spatial and temporal distribution, ecological risks, sources, and their impacts on the microbial communities of TPH and nine HMs in the estuarine sediments of the Xiaoqing River were determined. Results showed that the spatial distribution of TPH and HMs were similar but opposite in temporal. Ni, Cr, Pb, and Co concentrations were similar to the reference values (RVs). However, the other five HMs (Cu, Zn, Cd, As, and Hg) and TPH concentrations were 2.00-763.44 times higher than RVs; hence, this deserves attention, particularly for Hg. Owing to the water content of the sediments, Hg was mainly concentrated on the surface during the wet season and on the bottom during the dry season. Moreover, because of weak hydrodynamics and upstream pollutant sinks, TPH-HMs in the river were higher than those in the estuary. TPH and HM concentrations were negatively correlated with microbial diversity. Structural equation modeling showed that HMs (path coefficient = -0.50, p < 0.001) had a negative direct effect on microbial community structure and a positive indirect effect on TPH. The microbial community (path coefficient = 0.31, 0.01 < p < 0.05) was significantly correlated with TPH. In summary, this study explores both the chemical analysis of pollutants and their interaction with microbial communities, providing a better understanding of the co-pollution of TPH and HMs in estuarine sediments.

Bacteria-Triggered Mineralization of Silica Shells with Nanochannels for Biocatalysis in Harsh Conditions

Biocatalytic processes using microorganisms are considered efficient and economically and environmentally friendly reactions. However, the viability and function of these microorganisms are prone to being hindered by various practical environments. Here, we reported a bacteria-induced nanochannel structure that endowed the microorganism with biocatalytic ability in harsh conditions. We revealed that the bacteria could trigger the fusion of silica nanoparticles on their surface by the secreted alkaline metabolite, resulting in silica shells with nanochannels on bacteria (bacteria@nSiO2). The nanochannel structure in silica shells endowed bacteria with biocatalytic ability in multiple harsh conditions. We revealed that these nanochannels could influence the mass transfer from the extracellular to the intracellular environment, which protected the bacteria from excessive toxic substance while preserving the mass exchange during biocatalysis. This feature ensured bacteria@nSiO2 with efficient bioactivity under harsh conditions for industrial catalysis and degradation of pollution, which cannot be achieved by corresponding native bacteria. Using the crude oil spill as a practical example, we presented that bacteria@nSiO2 could degrade highly concentrated crude oil, which any reported bacteria cannot achieve. This work emphasized the role of nanochannels in the regulation of cellular functions for enhanced biocatalysis. It also demonstrated a bacteria-triggered nanostructure formation, which is a promising methodology for nanotechnology and provides a strategy for more advanced organism-material hybrids.

A comprehensive assessment of heavy metals, VOCs and petroleum hydrocarbon in different soil layers and groundwater at an abandoned Al/Cu industrial site

Compound pollution at industrial sites impedes urban development, especially when there is a lack of understanding about the spatial variations of internal pollution in industrial areas producing light-weight materials. In this study, spatial distribution and ecological risks of potentially toxic elements (PTEs), volatile organic compounds (VOCs), and petroleum hydrocarbons (C10-40) in the soil and groundwater of an Al/Cu (aluminum/copper) industrial site have been analyzed comprehensively. Results revealed the progressive clustering of pollutants in different soil layers, which indicated varying levels of penetration and migration of pollutants from the surface downward. Furthermore, severity of pollution varied according to pollutant type, with Cu (5-10,228 mg kg-1) often exceeding the background levels significantly (>40). Cd (0.03-2.60 mg kg-1) and Hg (0.01-3.73 mg kg-1) were found at elevated concentrations in deeper soil layers, suggesting distinct variations of PTEs across different soil depths. Among the more hazardous VOCS, polychlorinated biphenyls (1.80-234 μg kg-1) were particularly prevalent in the deeper layers of soil. Petroleum hydrocarbons (C10-40) were widely detected (6-582 mg kg-1), showing significant migration potential from surface to deep soil. These findings suggest that prolonged industrial activities lead to deep-seated accumulation of pollutants, which also impacts the groundwater, contributing to long-term dispersion of contaminants. Furthermore, multivariate statistical analysis indicated certain positive correlations among the distribution of Cu, Pb and petroleum hydrocarbons, indicating possible coupling of these pollutants. Severe Cu pollution caused an ecological risk in the surface soil layer (covering >20 % area of high pollution site, contributing >40 % ecological risk). While the Hg and Cd posed significant risks in the deeper soil layers, showing higher risk coefficients and mobility. The study provides crucial insights into the transformation of urban areas with a history of industrial uses into community spaces and highlights the risks posed by the remaining pollutants.

Impact of Temperature Elevation on Microbial Communities and Antibiotic Degradation in Cold Region Soils of Northeast China

This study systematically investigated the effects of temperature changes on the degradation of antibiotics in soil, as well as the alterations in microbial community structure and aggregation, through a field warming experiment in a greenhouse. Compared to non-warming soil, the warming treatment significantly accelerated the degradation rate of tetracyclines during soil freezing and mitigated the impact of environmental fluctuations on soil microbial communities. The greenhouse environment promoted the growth and reproduction of a wide range of microbial taxa, but the abundance of Myxococcota was positively correlated with antibiotic concentrations in both treatments, suggesting a potential specific association with antibiotic degradation processes. Long-term warming in the greenhouse led to a shift in the assembly process of soil microbial communities, with a decrease in dispersal limitation and an increase in the drift process. Furthermore, co-occurrence network analysis revealed a more loosely structured microbial community in the greenhouse soil, along with the emergence of new characteristic taxa. Notably, more than 60% of the key taxa that connected the co-occurrence networks in both groups belonged to rare taxa, indicating that rare taxa play a crucial role in maintaining community structure and function.

Combined toxicity of Cd and aniline to soil bacteria varying with exposure sequence

Joint toxicity of organic-metal co-contamination can vary depending on organisms, toxicants, and even the sequence of exposure. This study examines how the combined toxicity of aniline (An) and cadmium (Cd) to soil bacteria in microcosms changes when the order of contaminant introduction is altered. Through analyzing biodiversity, molecular ecological network, functional redundancy, functional genes and pathways, we find the treatment of Cd followed by An brings about the strongest adverse impact to the bacterial consortium, followed by the reverse-ordered exposure and the simple mixture of the two chemicals. On the level of individual organisms, exposure sequence also affects the bacteria that are otherwise resistant to the standalone toxicity of both An and Cd. The dynamic behavior of aniline-cadmium composite is interpreted by considering the tolerance of organisms to individual chemicals, the interactions of the two toxicants, the recovery time, as well as the priority effect. The overall effect of the composite contamination is conceptualized by treating the chemicals as environmental filters screening the growth of the community.

Long-Term Contaminant Exposure Alters Functional Potential and Species Composition of Soil Bacterial Communities in Gulf Coast Prairies

Environmental pollution is a persistent threat to coastal ecosystems worldwide, adversely affecting soil microbiota. Soil microbial communities perform critical functions in many coastal processes, yet they are increasingly subject to oil and heavy metal pollution. Here, we assessed how small-scale contamination by oil and heavy metal impacts the diversity and functional potential of native soil bacterial communities in the gulf coast prairie dunes of a barrier island in South Texas along the northern Gulf of Mexico. We analyzed the bacterial community structure and their predicted functional profiles according to contaminant history and examined linkages between species diversity and functional potential. Overall, contaminants altered bacterial community compositions without affecting richness, leading to strongly distinct bacterial communities that were accompanied by shifts in functional potential, i.e., changes in predicted metabolic pathways across oiled, metal, and uncontaminated environments. We also observed that exposure to different contaminants can either lead to strengthened or decoupled linkages between species diversity and functional potential. Taken together, these findings indicate that bacterial communities might recover their diversity levels after contaminant exposure, but with consequent shifts in community composition and function. Furthermore, the trajectory of bacterial communities can depend on the nature or type of disturbance.

The influence of benzene on the composition, diversity and performance of the anodic bacterial community in glucose-fed microbial fuel cells

Bioelectrochemical systems offer unique opportunities to remove recalcitrant environmental pollutants in a net positive energy process, although it remains challenging because of the toxic character of such compounds. In this study, microbial fuel cell (MFC) technology was applied to investigate the benzene degradation process for more than 160 days, where glucose was used as a co-metabolite and a control. We have applied an inoculation strategy that led to the development of 10 individual microbial communities. The electrochemical dynamics of MFC efficiency was observed, along with their 1H NMR metabolic fingerprints and analysis of the microbial community. The highest power density of 120 mW/m2 was recorded in the final period of the experiment when benzene/glucose was used as fuel. This is the highest value reported in a benzene/co-substrate system. Metabolite analysis confirmed the full removal of benzene, while the dominance of fermentation products indicated the strong occurrence of non-electrogenic reactions. Based on 16S rRNA gene amplicon sequencing, bacterial community analysis revealed several petroleum-degrading microorganisms, electroactive species and biosurfactant producers. The dominant species were recognised as Citrobacter freundii and Arcobacter faecis. Strong, positive impact of the presence of benzene on the alpha diversity was recorded, underlining the high complexity of the bioelectrochemically supported degradation of petroleum compounds. This study reveals the importance of supporting the bioelectrochemical degradation process with auxiliary substrates and inoculation strategies that allow the communities to reach sufficient diversity to improve the power output and degradation efficiency in MFCs beyond the previously known limits. This study, for the first time, provides an outlook on the syntrophic activity of biosurfactant producers and petroleum degraders towards the efficient removal and conversion of recalcitrant hydrophobic compounds into electricity in MFCs.

Synergistic removal of total petroleum hydrocarbons and antibiotic resistance genes in Yellow River Delta wetlands contaminated soil composting regulated by biogas slurry addition

The interactive effects between the emerging contaminant antibiotic resistance genes (ARGs) and the traditional pollutant total petroleum hydrocarbons (TPHs) in contaminated soils remain unclear. The synergistic removal of TPHs and ARGs from composted contaminated soil, along with the microbial mechanisms driven by the addition of biogas slurry, have not yet been investigated. This study explored the impact of biogas slurry on the synergistic degradation mechanisms and bacterial community dynamics of ARGs and TPHs in compost derived from contaminated soil. The addition of biogas slurry resulted in a reduction of targeted ARGs and mobile genetic elements (MGEs) by 9.96%-95.70% and 13.32%-97.66%, respectively. Biogas slurry changed the succession of bacterial communities during composting, thereby reducing the transmission risk of ARGs. Pseudomonas, Cellvibrio, and Devosia were identified as core microorganisms in the synergistic degradation of ARGs and TPHs. According to the partial least squares path model, temperature and NO3- indirectly influenced the removal of ARGs and TPHs by directly regulating the abundance and composition of host microbes and MGEs. In summary, the results of this study contribute to the high-value utilization of biogas slurry and provide methodological support for the low-cost remediation of contaminated soils.

Metals and polycyclic aromatic hydrocarbons pollutants in industrial parks under valley landforms in Tibetan Plateau: Spatial pattern, ecological risk and interaction with soil microorganisms

The spatial patterns of pollutants produced by industrial parks are affected by many factors, but the interactions among polycyclic aromatic hydrocarbons (PAHs), metals, and soil microorganisms in the valley landforms of the Tibetan Plateau are poorly understood. Thus, this study systematically investigated the distribution and pollution of metals and PAHs in soil around an industrial park in the typical valley landform of the Tibetan Plateau and analyzed and clarified the interaction among metals, PAHs, and microorganisms. The results were as follows: metal and PAH concentrations were affected by wind direction, especially WN-ES and S-N winds; Cd (2.86-54.64 mg·kg-1) had the highest soil concentrations of the metals screened, followed by variable concentrations of Cu, Pb, and Zn; the pollution levels of metals and PAHs in the S-N wind direction were lower than those in the WN-ES wind direction; the Cd content of Avena sativa in the agricultural soil around the factory exceeded its enrichment ability and food safety standards; the closer to the center of the park, the higher the ecological risk of PAHs; and the TEQ and MEQ values of the PAHs were consistent with their concentration distributions. The results of the soil microbial diversity and co-occurrence network in the dominant wind direction showed that metal and PAH pollution weakened the robustness of soil microbial communities. Additionally, the diversity and robustness of soil microbial communities at the S wind site were higher than those at the ES wind site, which might be attributed to the lower metal content of the former than the latter, which plays a negative role in the biodegradation of PAHs. The results of this study provide insights into the site selection, pollutant supervision, and environmental remediation of industrial parks in typical landforms.

Reduced graphene oxide promotes the biodegradation of sulfamethoxazole by white-rot fungus Phanerochaete chrysosporium under cadmium stress

The biodegradation of antibiotics in aquatic environment is consistently impeded by the widespread presence of heavy metals, necessitating urgent measures to mitigate or eliminate this environmental stress. This work investigated the degradation of sulfamethoxazole (SMX) by the white-rot fungus Phanerochaete chrysosporium (WRF) under heavy metal cadmium ion (Cd2+) stress, with a focus on the protective effects of reduced graphene oxide (RGO). The pseudo-first-order rate constant and removal efficiency of 5 mg/L SMX in 48 h by WRF decrease from 0.208 h-1 and 55.6% to 0.08 h-1 and 28.6% at 16 mg/L of Cd2+, while these values recover to 0.297 h-1 and 72.8% by supplementing RGO. The results demonstrate that RGO, possessing excellent biocompatibility, effectively safeguard the mycelial structure of WRF against Cd2+ stress and provide protection against oxidative damage to WRF. Simultaneously, the production of manganese peroxidase (MnP) by WRF decreases to 38.285 U/L in the presence of 24 mg/L Cd2+, whereas it recovers to 328.51 U/L upon the supplement of RGO. RGO can induce oxidative stress in WRF, thereby stimulating the secretion of laccase (Lac) and MnP to enhance the SMX degradation. The mechanism discovered in this study provides a new strategy to mitigate heavy metal stress encountered by WRF during antibiotic degradation.

Toxic metal contamination effects mediated by hotspot intensity of soil enzymes and microbial community structure

Metal contamination from mine waste is a widespread threat to soil health. Understanding of the effects of toxic metals from mine waste on the spatial patterning of rhizosphere enzymes and the rhizosphere microbiome remains elusive. Using zymography and high-throughput sequencing, we conducted a mesocosm experiment with mine-contaminated soil, to compare the effects of different concentrations of toxic metals on exoenzyme kinetics, microbial communities, and maize growth. The negative effects of toxic metals exerted their effects largely on enzymatic hotspots in the rhizosphere zone, affecting both resistance and the area of hotspots. This study thus revealed the key importance of such hotspots in overall changes in soil enzymatic activity under metal toxicity. Statistical and functional guild analysis suggested that these enzymatic changes and associated microbial community changes were involved in the inhibition of maize growth. Keystone species of bacteria displayed negative correlations with toxic metals and positive correlations with the activity of enzymatic hotspots, suggesting a potential role. This study contributes to an emerging paradigm, that changes both in the activity of soil enzymes and soil biota - whether due to substrate addition or in this case toxicity - are largely confined to enzymatic hotspot areas.

Bioavailability (BA)-based risk assessment of soil heavy metals in provinces of China through the predictive BA-models

The real biological effect is not generated by the total content of heavy metals (HMs), but rather by bioavailable content. A new bioavailability-based ecological risk assessment (BA-based ERA) framework was developed for deriving bioavailability-based soil quality criteria (BA-based SQC) and accurately assessing the ecological risk of soil HMs at a multi-regional scale in this study. Through the random forest (RF) models and BA-based ERA framework, the 217 BA-based SQC for HMs in 31 Chinese provinces were derived and the BA-based ERA was comprehensively assessed. This study found that bioavailable HMs extraction methods (BHEMs) and total HMs content play the predominant role in affecting HMs (As, Cd, Cr, Cu, Ni, Pb, and Zn) bioavailability by explaining 27.55-56.11% and 9.20-62.09% of the variation, respectively. The RF model had accurate and stable prediction ability for the bioavailability of soil HMs with the mean R2 and RMSE of 0.83 and 0.43 for the test set, respectively. The results of BA-based ERA showed that bioavailability could avoid the overestimation of ecological risks to some extent after reducing the uncertainty of soil differences. This study confirmed the feasibility of using bioavailability for ERA and will utilised to revise the soil environmental standards based on bioavailability for HMs.

Metagenomic insight on consortium degradation of soil weathered petroleum and its supplement based on gene abundance change

Petroleum biodegradation is of importance for the mitigation of secondary pollutants from soil chemical remediation. Describing the gene abundance change of the petroleum degradation emerged as an important practice for success. In this study, an indigenous consortium with targeting-enzyme was utilized to develop a degradative system that was later subjected to metagenomic analysis on the soil microbial community. Centering on ko00625 pathway, abundance change of dehydrogenase gene was firstly found increasing from groups D, DS to DC in turn, just in an opposite direction with that of oxygenase. In addition, gene abundance of responsive mechanism went rising with degradative process as well. This finding sufficiently promoted that equal attention should be paid to both degradative and responsive processes. Hydrogen donor system was innovatively built on the consortium-used soil to satisfy the demand of dehydrogenase gene tendency and to sustain further petroleum degradation. Anaerobic pine-needle soil was supplemented to this system, bi-functionally serving as dehydrogenase substrate with nutrients and hydrogen donor. In doing so, two successive degradations optimally achieved the total removal rate 75.6-78.7% for petroleum hydrocarbon. The conception on the gene abundance changes and its corresponding supplement helps industries of concern to develop geno-tag guided framework.