The Biodiversity Changes in the Microbial Population of Soils Contaminated with Crude Oil

Potential effects of soil petroleum contamination on decomposition of Artemisia annua plant litter

The accumulation of petroleum contaminants in phytoremediating plants can significantly impact the decomposition of their litter. However, the mechanisms underlying these effects and the potential influence of the contaminant concentration remain unclear. In this study, litter from Artemisia annua plants grown in soil with varying concentrations of petroleum (0, 15, 30, and 45 g kg-1) was collected. The litter samples were then inoculated with soil microorganisms and subjected to an indoor simulation of decomposition under controlled temperature and humidity conditions. Changes in the chemical properties, activities of decomposition-related enzymes in the litter, and decomposition rates were measured. Additionally, structural equation modeling was employed to analyze the mechanism through which soil petroleum contamination affects litter decomposition. The findings revealed several key points: (1) increasing soil petroleum contamination tended to reduce the concentration of carbon and nitrogen in litter while increasing those of lignin and total petroleum hydrocarbons (TPH). (2) Soil petroleum contamination tended to increase the activities of both total lignocellulases and total nutrient cycling-related enzymes in litter. (3) Soil petroleum contamination might indirectly inhibit the activity of lignocellulases by increasing the concentration of lignin and TPH in litter. However, it might also directly accelerate the activity of these enzymes, resulting in contradictory effects on litter decomposition. (4) Finally, A. annua litter produced in soil contaminated with 15 and 30 g kg-1 of petroleum exhibited significantly lower decomposition rates than that from uncontaminated soil.

Emerging organic contaminants in the soil-plant-receptor continuum: transport, fate, health risks, and removal mechanisms

There is a lack of comprehensive reviews tracking emerging organic contaminants (EOCs) within the soil-plant continuum using the source-pathway-receptor-impact-mitigation (SPRIM) framework. Therefore, this review examines existing literature to gain insights into the occurrence, behaviour, fate, health hazards, and strategies for mitigating EOCs within the soil-plant system. EOCs identified in the soil-plant system encompass endocrine-disrupting chemicals, surfactants, pharmaceuticals, personal care products, plasticizers, gasoline additives, flame retardants, and per- and poly-fluoroalkyl substances (PFAS). Sources of EOCs in the soil-plant system include the land application of biosolids, wastewater, and solid wastes rich in EOCs. However, less-studied sources encompass plastics and atmospheric deposition. EOCs are transported from their sources to the soil-plant system and other receptors through human activities, wind-driven processes, and hydrological pathways. The behaviour, persistence, and fate of EOCs within the soil-plant system are discussed, including sorption, degradation, phase partitioning, (bio)transformation, biouptake, translocation, and bioaccumulation in plants. Factors governing the behaviour, persistence, and fate of EOCs in the soil-plant system include pH, redox potential, texture, temperature, and soil organic matter content. The review also discusses the environmental receptors of EOCs, including their exchange with other environmental compartments (aquatic and atmospheric), and interactions with soil organisms. The ecological health risks, human exposure via inhalation of particulate matter and consumption of contaminated food, and hazards associated with various EOCs in the soil-plant system are discussed. Various mitigation measures including removal technologies of EOCs in the soil are discussed. Finally, future research directions are presented.

Functional response of microbial communities in lab-controlled oil-contaminated marine sediment

Crude oil contamination is one of the biggest problems in modern society. As oil enters into contact with the environment, especially if the point of contact is a body of water, it begins a weathering process by mixing and spreading. This is dangerous to local living organisms' communities and can impact diversity. However, despite unfavorable conditions, some microorganisms in these environments can survive using hydrocarbons as a nutrient source. Thus, understanding the local community dynamics of contaminated areas is essential. In this work, we analyzed the 16S rRNA amplicon sequencing and metatranscriptomic data of uncontaminated versus contaminated shallow marine sediment from publicly available datasets. We investigated the local population's taxonomic composition, species diversity, and fluctuations over time. Co-expression analysis coupled with functional enrichment showed us a prevalence of hydrocarbon-degrading functionality while keeping a distinct transcriptional profile between the late stages of oil contamination and the uncontaminated control. Processes related to the degradation of aromatic compounds and the metabolism of propanoate and butanoate were coupled with evidence of enhanced activity such as flagellar assembly and two-component system. Many enzymes of the anaerobic toluene degradation pathways were also enriched in our results. Furthermore, our diversity and taxonomical analyses showed a prevalence of the class Desulfobacteria, indicating interesting targets for bioremediation applications on marine sediment.

Shumkonia mesophila gen. nov., sp. nov., a novel representative of Shumkoniaceae fam. nov. and its potentials for extracellular polymeric substances formation and sulfur metabolism revealed by genomic analysis

A microaerophilic, mesophilic, chemoorganoheterotrophic bacterium, designated Y-P2T, was isolated from oil sludge enrichment in China. Cells of the strain were Gram-stain-negative, non-motile, non-spore-forming, rod-shaped or slightly curved with 0.8-3.0 µm in length and 0.4-0.6 µm in diameter. The strain Y-P2T grew optimally at 25 °C (range from 15 to 30 °C) and pH 7.0 (range from pH 6.0 to 7.5) without NaCl. The major cellular fatty acids were C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The main polar liquids of strain Y-P2T comprised phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The respiratory quinone was Q-10. Acetate and H2 were the fermentation products of glucose. The DNA G + C content was 66.0%. Strain Y-P2T shared the highest 16S rRNA gene sequence similarity (90.3-90.6%) with species within Oceanibaculum of family Thalassobaculaceae in Rhodospirillales. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that strain Y-P2T formed a distinct evolutionary lineage within the order Rhodospirillales. On the basis of phenotypic, phylogenetic and phylogenomic data, we propose that strain Y-P2T represents a novel species in a novel genus, for which Shumkonia mesophila gen. nov., sp. nov., within a new family Shumkoniaceae fam. nov. The type strain is Y-P2T (= CCAM 826 T = JCM 34766 T).

Efficient Bioremediation of Petroleum-Contaminated Soil by Immobilized Bacterial Agent of Gordonia alkanivorans W33

In this article, we report a method for preparing an immobilized bacterial agent of petroleum-degrading bacteria Gordonia alkanivorans W33 by combining high-density fermentation and bacterial immobilization technology and testing its bioremediation effect on petroleum-contaminated soil. After determining the optimal combination of MgCl₂, CaCl₂ concentration, and culture time in the fermentation conditions by conducting a response surface analysis, the cell concentration reached 7.48 × 10⁹ CFU/mL by 5 L fed-batch fermentation. The W33-vermiculite-powder-immobilized bacterial agent mixed with sophorolipids and rhamnolipids in a weight ratio of 9:10 was used for the bioremediation of petroleum-contaminated soil. After 45 days of microbial degradation, 56.3% of the petroleum in the soil with 20,000 mg/kg petroleum content was degraded, and the average degradation rate reached 250.2 mg/kg/d.

Crude oil associated heavy metals (HMs) contamination in agricultural land: Understanding risk factors and changes in soil biological properties

Ecological and human risks of crude oil associated heavy metals (HMs) in the contaminated agricultural lands were evaluated employing different indices. The indices that were employed includes enrichment factor (EF), contamination factor (C_f),pollution load index (PLI), geo-accumulation index (I_geo), ecological risk index (ERI), contamination degree (C_d), Nemerow's pollution index (P_N), exposure factor (ExF), hazard quotient (HQ) and hazard index (HI). Besides, the adverse effects of crude oil associated HMs on the soil biological properties were also analyzed. The results of C_f and EF were found consistent with each other showing the HMs in the decreasing order of contamination as Mn > Zn > Cr > Ni > Cu. The I_geo and ERI fall in the grade (I_geo>5) and (ERI ≥40) respectively. The results of PLI, C_d, P_N and ExF values clearly indicate a high environmental risk of crude oil-associated HMs. The results of the human health risks assessment revealed the maximum level of HMs enters the body via ingestion. There were significant(p < 0.05) decreases (5.7-15.5 folds) in the activities of cellulase (0.194 ± 0.02-0.998 ± 0.1), phosphatase (0.173 ± 0.3-0.612 ± 1.5), catalase (0.328 ± 0.3-2.036 ± 1.5), urease (0.44 ± 0.3-1.80 ± 1.2), dehydrogenase (0.321 ± 0.2-0.776 ± 0.7),polyphenol oxidase (0.21 ± 0.5-0.89 ± 2.5)and peroxidase (0.13 ± 0.4-0.53 ± 1.03)in crude oil-contaminated soil. The Pearson's correlation confirmed the significant negative impact of HMs on the soil's biological properties.

Insights of microbial community evolution under benzisothiazolinone exposure in different soil environments

Benzisothiazolinones (1, 2-benzisothiazoline-3-one; BIT) is widely used to control bacterial and fungal diseases of various crops, and their residues in soil may play an important role in the interaction between soil microorganisms. We studied microbial remediation in five representative soils under different soil conditions (unsterilized, sterilized and flooded) using 16S rRNA gene sequencing to investigate the effect of microorganisms on the degradation of BIT residues in soils to minimize the potentially toxic effects of BIT. High-throughput sequencing data showed that the structure and abundance of bacterial communities in BIT soils changed greatly, which might affect their degradation pathways, while Principal Coordinates Analysis (PCoA) results showed that there was no significant difference in the fungal community in different treatments of the five soils, but the degradation rate of BIT was more influenced by anaerobic microorganisms. Furthermore, Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria were the predominant bacterial phyla, accounting for 93.74% of all OTUs, which played an important role in the degradation of BIT. Lysinibacillus had a high relative abundance (21.10%) under flooded treatment conditions in Jilin soil, and its bioremediation may be a reason for the rapid degradation of BIT in flooded treatment. Besides, only soil organic matter (SOM) and pH among the soil properties had significant effects on the microbial community. Based on the further analysis of bacterial phenotype, some microorganisms related to the biodegradation of BIT were found, mainly belonging to Proteobacteria, Bacteroidetes and Firmicutes. This study provides a useful theoretical basis for the biodegradation of BIT using isolated microorganisms.

Impact of Petroleum Contamination on the Structure of Saline Soil Bacterial Communities

Petroleum contamination may lead to variations in soil microbial community structure and activities. The bioremediation of petroleum-contaminated soil typically depends on the characteristics and activities of oil-degrading microorganisms, which can be introduced or be part of the native soil microbiota. Thus, analyzing the structure of the microbial community and internal relationships in the bioremediation process is critical. Our study characterized the physical and chemical properties, microbial community structure, and microbial diversity of surface soil collected near an oilfield. The total carbon (TC), total organic carbon (TOC), and microbial diversity in oil-contaminated soil was found higher than in uncontaminated samples. Proteobacteria abundance was inhibited with oil pollution, while Actinomycetes abundance was enhanced. Some indigenous hydrocarbon-degrading bactera were enriched by oil pollution, such as Bacillus, Actinomarinales norank, Balneolaceae uncultured, Marinobacter, and Pseudomonas. Furthermore, Rokubacteria, Nitrospirae, and Entotheonellaeota were significant differences in the contaminated group. There were 16 genera with significant differences in the polluted group, such as Woeseia, Pelagibius, Pontibacillus, IS_44, Aliifodinibius, while Halothiobacillus, Algoriphagus, Novosphingobium, etc. had significant differences in the uncontaminated group. Redundancy analysis demonstrated that the responses of the microorganisms to the evaluated environmental factors were different, and TC was the most important driver of microbial community variation. Moreover, TOC was the largest contributor to operational taxonomic unit (OTU) and Chao index variations. Our results provide a theoretical basis for the enhancement of microbial activity in oil-contaminated soil, which might improve bioremediation efficacy.

Combined maize straw-biochar and oxalic acids induced a relay activity of abundant specific degraders for efficient phenanthrene degradation: Evidence based on the DNA-SIP technology

Biochar-oxalic acid composite application (BCOA) have shown to be efficient in the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil, but the functional degraders and the mechanism of improving biodegradation remains unclear. In this study, with the help of stable isotope probing technology of phenanthrene (Phe), we determined that BCOA significantly improved Phe mineralization by 2.1 times, which was ascribed to the increased numbers and abundances of functional degraders. The BCOA increased contents of dissolved organic carbon and available nutrients and decreased pH values in soil, thus promoting the activity, diversity and close cooperation of the functional Phe-degraders, and stimulating their functions associated with Phe degradation. In addition, there is a relay activity among more and diverse functional Phe-degraders in the soil with BCOA. Specifically, Pullulanibacillus persistently participated in Phe-degradation in the soil with BCOA throughout the incubation period. Moreover, Pullulanibacillus, Blastococcus, Alsobacter, Ramlibacter, and Mizugakiibacter were proved to be potential Phe-degraders in soil for the first time. The specific Phe degraders and their relay and cooperation activity in soils as impacted by BCOA were first identified with DNA-stable isotope probing technology. Our findings provided a novel perspective to understand the efficient degradation of PAH in the BCOA treatments, revealed the potential of soil native microbes in the efficient bioremediation of PAH-contaminated natural soil, and provided a basis for the development of in-situ phytoremediation technologies to remediate PAH pollution in future.

Accumulation of nylon microplastics and polybrominated diphenyl ethers and effects on gut microbial community of Chironomus sancticaroli

Microplastics (MP) are emerging contaminants with the capacity to bind and transport hydrophobic organic compounds of environmental concern, such as polybrominated diphenyl ethers (PBDEs). The aim of this study was to investigate the ingestion of nylon (polyamide) MP alone and when associated with PBDEs and their effects on Chironomus sancticaroli larvae survival and microbiome structure. Survival, PBDE uptake and microbial community composition were measured in fourth instar larvae exposed for 96 h to BDEs- 47, 99, 100 and 153 in the presence and absence of 1% w/w MP in sediment. Microbiome community structures were determined through high throughput sequencing of 16S small subunit ribosomal RNA gene (16S rRNA). Initial experiments showed that larvae ingested MP faster at 0.5% w/w MP, while depuration was more efficient at 1% w/w MP, although retention of MP was seen even after 168 h depuration. No mortality was observed as a result of PBDEs and MP exposure. MP had a negative effect on PBDE concentration within larvae (η² = 0.94) and a negative effect on sediment concentrations (η² = 0.48). In all samples, microbial communities were dominated by Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Gammaproteobacteria. Bacterial alpha diversity was not significantly affected by PBDEs or MP exposure. However, the abundance of discrete bacterial taxa was more sensitive to MP (X² = 45.81, p = 0.02), and PBDE exposure. Our results highlight that C. sancticaroli showed no acute response to MPs and PBDEs, but that MPs influenced bacterial microbiome structure even after only short-term acute exposure.

Taxonomic and functional trait-based approaches suggest that aerobic and anaerobic soil microorganisms allow the natural attenuation of oil from natural seeps

Natural attenuation, involving microbial adaptation, helps mitigating the effect of oil contamination of surface soils. We hypothesized that in soils under fluctuating conditions and receiving oil from seeps, aerobic and anaerobic bacteria as well as fungi could coexist to efficiently degrade hydrocarbons and prevent the spread of pollution. Microbial community diversity was studied in soil longitudinal and depth gradients contaminated with petroleum seeps for at least a century. Hydrocarbon contamination was high just next to the petroleum seeps but this level drastically lowered from 2 m distance and beyond. Fungal abundance and alpha-diversity indices were constant along the gradients. Bacterial abundance was constant but alpha-diversity indices were lower next to the oil seeps. Hydrocarbon contamination was the main driver of microbial community assemblage. 281 bacterial OTUs were identified as indicator taxa, tolerant to hydrocarbon, potentially involved in hydrocarbon-degradation or benefiting from the degradation by-products. These taxa belonging to lineages of aerobic and anaerobic bacteria, have specific functional traits indicating the development of a complex community adapted to the biodegradation of petroleum hydrocarbons and to fluctuating conditions. Fungi are less impacted by oil contamination but few taxa should contribute to the metabolic complementary within the microbial consortia forming an efficient barrier against petroleum dissemination.

Land-use types shape soil microbial compositions under rapid urbanization in the Xiong'an New Area, China

For urban planning and infrastructural projects, considerable attention has been paid to the relationship between soil biota, especially protists, and edaphic conditions in various land-use types having different plant species in the Xiong'an New Area of China. To elucidate this relationship, we assessed edaphic variables and soil biota compositions and compared them among 5 habitat types: human-made forests, crop cultivations, arid rivers, Baiyangdian (BYD) Lake, and around oil wells. In all, 12 experimental plots from terrestrial and aquatic ecosystems were assessed using high-throughput sequencing of environmental DNA, targeting the V3-V4 region of the 16S rRNA gene, internal transcribed spacer 1, and V4 region of the 18S rRNA gene for bacteria, fungi, and protists, respectively. The abundance of bacterial and protist communities was higher than fungi, possibly because fungi prefer acidic soil conditions and likely have greater susceptibility to anthropogenic activities. Across all experimental plots, land-use types contributed the most to the β-diversity of soil biota, followed by soil moisture. Diversity and richness were significantly higher at aquatic habitats than at terrestrial habitats. Predictive metagenomic analysis of trophic groups predicted relatively high frequency of functional genes from bacterial metabolism pathways (carbohydrate and amino acid); contrary to expectation, phototrophic protists, but not fungal symbionts and protistan consumers, were the dominant group at the BYD Lake. Geographical coordinates showed significant (P < 0.05) relationships with all microbiome taxa (nodes at network) from all land-use types. Moreover, soil-microbiome relationships were more complex and more intense at crop habitats. Links between protist and fungal taxa were the highest at the petroleum-contaminated sampling sites, indicating the importance of these two soil microbiomes in polluted soil. Thus, our findings suggest that human manipulation and land-use types are crucial factors for soil biota structure and composition across our sampling sites.

Petroleum hydrocarbon rhizoremediation and soil microbial activity improvement via cluster root formation by wild proteaceae plant species

Rhizoremediation potential of different wild plant species for total (aliphatic) petroleum hydrocarbon (TPH)-contaminated soils was investigated. Three-week-old seedlings of Acacia inaequilatera, Acacia pyrifolia, Acacia stellaticeps, Banksia seminuda, Chloris truncata, Hakea prostrata, Hardenbergia violacea, and Triodia wiseana were transplanted in a soil contaminated with diesel and engine oil as TPH at pollution levels of 4,370 (TPH1) and 7,500 (TPH2) mg kg^-1, and an uncontaminated control (TPH0). After 150 days, the presence of TPH negatively affected the plant growth, but the growth inhibition effect varied between the plant species. Plant growth and associated root biomass influenced the activity of rhizo-microbiome. The presence of B. seminuda, C. truncata, and H. prostrata significantly increased the TPH removal rate (up to 30% compared to the unplanted treatment) due to the stimulation of rhizosphere microorganisms. No significant difference was observed between TPH1 and TPH2 regarding the plant tolerance and rhizoremediation potentials of the three plant species. The presence of TPH stimulated cluster root formation in B. seminuda and H. prostrata which was associated with enhanced TPH remediation of these two members of Proteaceae family. These results indicated that B. seminuda, C. truncata, and H. prostrata wild plant species could be suitable candidates for the rhizoremediation of TPH-contaminated soil.

Microbial Degradation of Naphthalene and Substituted Naphthalenes: Metabolic Diversity and Genomic Insight for Bioremediation

Low molecular weight polycyclic aromatic hydrocarbons (PAHs) like naphthalene and substituted naphthalenes (methylnaphthalene, naphthoic acids, 1-naphthyl N-methylcarbamate, etc.) are used in various industries and exhibit genotoxic, mutagenic, and/or carcinogenic effects on living organisms. These synthetic organic compounds (SOCs) or xenobiotics are considered as priority pollutants that pose a critical environmental and public health concern worldwide. The extent of anthropogenic activities like emissions from coal gasification, petroleum refining, motor vehicle exhaust, and agricultural applications determine the concentration, fate, and transport of these ubiquitous and recalcitrant compounds. Besides physicochemical methods for cleanup/removal, a green and eco-friendly technology like bioremediation, using microbes with the ability to degrade SOCs completely or convert to non-toxic by-products, has been a safe, cost-effective, and promising alternative. Various bacterial species from soil flora belonging to Proteobacteria (Pseudomonas, Pseudoxanthomonas, Comamonas, Burkholderia, and Novosphingobium), Firmicutes (Bacillus and Paenibacillus), and Actinobacteria (Rhodococcus and Arthrobacter) displayed the ability to degrade various SOCs. Metabolic studies, genomic and metagenomics analyses have aided our understanding of the catabolic complexity and diversity present in these simple life forms which can be further applied for efficient biodegradation. The prolonged persistence of PAHs has led to the evolution of new degradative phenotypes through horizontal gene transfer using genetic elements like plasmids, transposons, phages, genomic islands, and integrative conjugative elements. Systems biology and genetic engineering of either specific isolates or mock community (consortia) might achieve complete, rapid, and efficient bioremediation of these PAHs through synergistic actions. In this review, we highlight various metabolic routes and diversity, genetic makeup and diversity, and cellular responses/adaptations by naphthalene and substituted naphthalene-degrading bacteria. This will provide insights into the ecological aspects of field application and strain optimization for efficient bioremediation.

Mixing of plant litters strengthens their remediation effects on crude oil-contaminated soil

To investigate the effects of the mixing of litters on their remediation efficiency in petroleum-contaminated soil, litters from two common plants in the petroleum-contaminated region of Northern Shaanxi, China, Bothriochloa ischaemum (L.) Keng and Sophora davidii Kom. ex Pavol., and their mixture were mixed with 45 g/kg petroleum-contaminated soil. Based on these, a 150-day simulated remediation experiment was conducted at 25 °C and consistent moisture conditions. The effects on the degradation of petroleum components and the restoration of nutrient contents, pH, and enzymatic activity in the disturbed soil were detected. The effects of the litter treatments on the community structure and carbon source utilization characteristics of soil microorganisms were also studied. The results indicated that all litter treatments significantly accelerated the degradation of petroleum components, while the mixing of litter exhibited significant synergistic effects, leading to significantly higher degradation rates of saturated hydrocarbons, aromatic hydrocarbons, and nonhydrocarbon substances than the observed rates in the single-litter treatments and the predicted rates based on the single-litter treatments. Litter treatment significantly increased the N and P contents and enzymatic activity of contaminated soil. The effects of mixed litter on soil chemical and biological properties fell between the effects of the 2 types of single-litter treatments. However, the mixing of litters exhibited significant synergistic effects in supplementing available P and increasing sucrase, dehydrogenase, lignin peroxidase, and laccase activity, while it exhibited significant antagonistic effects in supplementing nitrate nitrogen and increasing urease, phosphatase, polyphenol oxidase, and manganese peroxidase activity. Litter treatment significantly altered the community structure of soil microorganisms. The relative abundances of some petroleum-degrading microbial phyla or genera in mixed litter-treated soil were significantly different from those in single litter-treated soils, which might contribute to the strengthened remediation effects of mixed litter treatment. The results might provide a theoretical basis for the more effect utilization of biomass resources in the remediation of petroleum-contaminated soil.

Effects of organic matter addition on chronically hydrocarbon-contaminated soil

Soil is the recipient of organic pollutants as a consequence of anthropogenic activities. Hydrocarbons are contaminants that pose a risk to human and environmental health. Bioremediation of aging contaminated soils is a challenge due to the low biodegradability of contaminants as a result of their interaction with the soil matrix. The aim of this work was to evaluate the effect of both composting and the addition of mature compost on a soil chronically contaminated with hydrocarbons, focusing mainly on the recovery of soil functions and transformations of the soil matrix as well as microbial community shifts. The initial pollution level was 214 ppm of polycyclic aromatic hydrocarbons (PAHs) and 2500 ppm of aliphatic hydrocarbons (AHs). Composting and compost addition produced changes on soil matrix that promoted the release of PAHs (5.7 and 15 % respectively) but not the net PAH elimination. Interestingly, composting stimulated AHs elimination (about 24 %). The lack of PAHs elimination could be attributed to the insufficient PAHs content to stimulate the microbial degrading capacity, and the preferential consumption of easily absorbed C sources by the bacterial community. Despite the low PAH catabolic potential of the aging soil, metabolic shift was driven by the addition of organic matter, which could be monitored by the ratio of Proteobacteria to Actinobacteria combined with E₄/E₆ ratio. Regarding the quality of the soil, the nutrients provided by the exogenous organic matter contributed to the recovery of the global functions and species diversity of the soil along with the reduction of phytotoxicity.

Multimarker approach to assess the exposure of the wild rodent Calomys laucha to a simulated crude oil spill

A mysterious oil spill occurred in the ocean near Brazil in 2019, which affected coastal areas in northeastern Brazil. When oil pollution occurs in coastal zones, organisms such as small mammals can suffer deleterious effects to their health. This study aimed to evaluate the effects of exposure to contaminated sandy soil with different crude oil concentrations in males of the species Calomys laucha. The exposure to crude oil resulted in multiple health issues for the subjects in the very first days of exposure. Furthermore, the exposure resulted in mutagenic damage to bone marrow blood cells and behavioral and morphological alterations, which were almost always in a dose-dependent form. The present study demonstrates the sensibility of the biomarkers used and highlights that small wild mammals such as C. laucha are useful for predicting environmental damage caused by the exposure to crude oil.

The linkage between methane production activity and prokaryotic community structure in the soil within a shale gas field in China

Soil methane generation mainly driven by soil prokaryotic microbes can be coupled with the degradation of petroleum hydrocarbons (PHCs); however, the relationship between prokaryotic community structure and methane production activity in soil with the potential risk of PHC contamination is seldom reported. In this study, 3 soil samples (CS-1 to CS-3) in the area nearby an exploratory gas well and 5 soil samples (DC-1 to DC-5) in a drill cutting dump area were obtained from the Fuling shale gas field (Chongqing City, China). Then, the prokaryotic community structure was examined by Illumina Miseq sequencing, and the linkage between soil methane production rate (MPR) and prokaryotic community composition was analyzed. The results indicated that 2 samples (DC-4 and DC-5) collected from the drill cutting dump area had significantly higher MPR than the other samples, and a significant and positive relationship (r = 0.44, P < 0.05) was found between soil MPR and soil organic matter (OM) content. The prokaryotic community composition in the sample (DC-5) with the highest MPR was different from those in the other samples, and soil OM and MPR were the major factors significantly correlated with the prokaryotic community structure in this soil. The samples (DC-4 and DC-5) with higher MPR had a higher relative abundance of Archaea and different archaeal community structures from the other samples, and the MPR was the sole factor significantly correlated with the archaeal genus composition in this soil. Therefore, both the prokaryotic and archaeal community structures are essential in the determination of soil MPR, and the bacterial genus of Saccharibacteria and the archaeal genus of Methanolobus might be the key contributors for methane generation in this soil from the shale gas field.

High-Level Abundances of Methanobacteriales and Syntrophobacterales May Help To Prevent Corrosion of Metal Sheet Piles

Iron sheet piles are widely used in flood protection, dike construction, and river bank reinforcement. Their corrosion leads to gradual deterioration and often makes replacement necessary. Natural deposit layers on these sheet piles can prevent degradation and significantly increase their life span. However, little is known about the mechanisms of natural protective layer formation. Here, we studied the microbially diverse populations of corrosion-protective deposit layers on iron sheet piles at the Gouderak pumping station in Zuid-Holland, the Netherlands. Deposit layers, surrounding sediment and top sediment samples were analyzed for soil physicochemical parameters, microbially diverse populations, and metabolic potential. Methanogens appeared to be enriched 18-fold in the deposit layers. After sequencing, metagenome assembly and binning, we obtained four nearly complete draft genomes of microorganisms (Methanobacteriales, two Coriobacteriales, and Syntrophobacterales) that were highly enriched in the deposit layers, strongly indicating a potential role in corrosion protection. Coriobacteriales and Syntrophobacterales could be part of a microbial food web degrading organic matter to supply methanogenic substrates. Methane-producing Methanobacteriales could metabolize iron, which may initially lead to mild corrosion but potentially stimulates the formation of a carbonate-rich protective deposit layer in the long term. In addition, Methanobacteriales and Coriobacteriales have the potential to interact with metal surfaces via direct interspecies or extracellular electron transfer. In conclusion, our study provides valuable insights into microbial populations involved in iron corrosion protection and potentially enables the development of novel strategies for in situ screening of iron sheet piles in order to reduce risks and develop more sustainable replacement practices.IMPORTANCE Iron sheet piles are widely used to reinforce dikes and river banks. Damage due to iron corrosion poses a significant safety risk and has significant economic impact. Different groups of microorganisms are known to either stimulate or inhibit the corrosion process. Recently, natural corrosion-protective deposit layers were found on sheet piles. Analyses of the microbial composition indicated a potential role for methane-producing archaea. However, the full metabolic potential of the microbial communities within these protective layers has not been determined. The significance of this work lies in the reconstruction of the microbial food web of natural corrosion-protective layers isolated from noncorroding metal sheet piles. With this work, we provide insights into the microbiological mechanisms that potentially promote corrosion protection in freshwater ecosystems. Our findings could support the development of screening protocols to assess the integrity of iron sheet piles to decide whether replacement is required.

Implications of co-contamination with aged heavy metals and total petroleum hydrocarbons on natural attenuation and ecotoxicity in Australian soils

The bioremediation of historic industrial contaminated sites is a complex process. Co-contamination, often with lead which was commonly added to gasoline until 16 years ago is one of the biggest challenges affecting the clean-up of these sites. In this study, the effect of heavy metals, as co-contaminant, together with total petroleum hydrocarbons (TPH) is reported, in terms of remaining soil toxicity and the structure of the microbial communities. Contaminated soil samples from a relatively hot and dry climate in Western Australia were collected (n = 27). Analysis of soils showed the presence of both contaminants, TPHs and heavy metals. The Microtox test confirmed that their co-presence elevated the remaining ecotoxicity. Toxicity was correlated with the presence of lead, zinc and TPH (0.893, 0.599 and 0.488), respectively, assessed using Pearson Correlation coefficient factor. Next Generation Sequencing of soil bacterial 16S rRNA, revealed a lack of dominate genera; however, despite the variation in soil type, a few genera including Azospirillum spp. and Conexibacter were present in most soil samples (85% and 82% of all soils, respectively). Likewise, many genera of hydrocarbon-degrading bacteria were identified in all soil samples. Streptomyces spp. was presented in 93% of the samples with abundance between 7% and 40%. In contrast, Acinetobacter spp. was found in only one sample but was a dominant member of (45%) of the microbial community. In addition, some bacterial genera were correlated to the presence of the heavy metals, such as Geodermatophilus spp., Rhodovibrio spp. and Rubrobacter spp. which were correlated with copper, lead and zinc, respectively. This study concludes that TPH and heavy metal co-contamination significantly elevated the associated toxicity. This is an important consideration when carrying out risk assessment associated with natural attenuation. This study also improves knowledge about the dynamics of microbial communities in mixed contamination scenarios.

The Emergence of Different Functionally Equivalent PAH Degrading Microbial Communities from a Single Soil in Liquid PAH Enrichment Cultures and Soil Microcosms Receiving PAHs with and without Bioaugmentation

Polycyclic aromatic hydrocarbon (PAHs) are common soil contaminants of concern due to their toxicity toward plants, animals and microorganisms. The use of indigenous or added microbes (bioaugmentation) is commonly used for bioremediation of PAHs. In this work, the biodegradation rates and changes in the bacterial community structure were evaluated. The enrichment culture was useful for unambiguously identifying members of the soil bacterial community associated with PAH degradation and yielded a low diversity community. No significant difference in the rate of PAH degradation was observed between the microcosm receiving only PAHs or PAHs and bioaugmentation. Moreover, identical matches to the bioaugmentation inoculum were only observed at the initial stages of PAH degradation on day 8. After 22 days of incubation, the substantial degradation of all PAHs had occurred in both microcosms and the PAH contaminated soil had statistically significant increases in Alphaproteobacteria. There were also increases in Betaproteobacteria. In contrast, the PAH contaminated and bioaugmented soil was not enriched in PAH degrading Proteobacteria genera and, instead, an increase from 1.6% to 8% of the population occurred in the phylum Bacteroidetes class Flavobacteria, with Flavobacterium being the only identified genus. In addition, the newly discovered genus Ohtaekwangia increased from 0% to 3.2% of the total clones. These results indicate that the same soil microbial community can give rise to different PAH degrading consortia that are equally effective in PAH degradation efficiency. Moreover, these results suggest that the lack of efficacy of bioaugmentation in soils can be attributed to a lack of persistence of the introduced microbes, yet nonetheless may alter the microbial community that arises in response to PAH contamination in unexpected ways.

Effect of the nitrification inhibitor (3, 4-dimethylpyrazole phosphate) on the activities and abundances of ammonia-oxidizers and denitrifiers in a phenanthrene polluted and waterlogged soil

Through a 60-day microcosm incubation, the effect of 3, 4-dimethylpyrazole phosphate (DMPP) on the activities and abundances of ammonia-oxidizers and denitrifiers in phenanthrene-polluted soil was investigated. Five treatments were conducted for clean soil (CK), phenanthrene added (P), phenanthrene and DMPP added (PD), phenanthrene and urea added (PU), and phenanthrene, urea, and DMPP added (PUD) soils. The results indicate that the potential nitrification rate (PNR) in the P treatment was significantly higher than that in the PD treatment only on day 7, whereas the PNR in the PU treatment was significantly higher than that in the PUD treatment on each sampling day. The abundance of soil ammonia-oxidizing bacteria (AOB) in the PU treatment was significantly higher than that in the PUD treatment on each sampling day. Moreover, the abundance of AOB but rather than the ammonia-oxidizing archaea (AOA) had significantly positive correlation with soil PNR (P < 0.05). DMPP showed no obvious effect on the soil denitrification enzyme activity (DEA), which could have inhibited the abundances of denitrification-related narG, nirS, and nirK genes. The results of this study should provide a deeper understanding of the interaction between soil polycyclic aromatic hydrocarbons (PAH) contamination, ammonia oxidization, and denitrification, and offer valuable information for assessing the potential contribution of denitrification for soil PAH elimination.

Microbial diversity changes with rhizosphere and hydrocarbons in contrasting soils

In the ecotoxicological assessment of petroleum hydrocarbon-contaminated soil, microbial community profile is important aspect due to their involvement in soil functions. However, soil physicochemical properties and the inhabiting plants could dictate the microbial composition. A question remains unanswered is, how an integrated approach may be utilized to account for various contrasting soil properties, plant types (reference vs. native) and the nature of the hydrocarbon contamination. In this study, we utilized bacterial DNA profiling techniques to investigate the relationship between soil properties, contaminant and plant species. Results identified that Proteobacteria and Actinobacteria were the most abundant bacteria of the 45 phyla identified in the hydrocarbon-contaminated soil. The bulk and rhizosphere microbiome showed that the contaminated soil originally had quite distinct bacterial communities compared to the artificially contaminated soil (mine soil = 95 genera vs. other soils = 2-29 genera). In these cases, not significantly but the native plant slightly increased bacterial diversity and relative abundance in the same soils. Also, within each site, the bacterial community was significantly altered with the hydrocarbon concentration. In this instance, the influence of the contaminant was strong and also with the soil pH and organic matter. These results would significantly contribute to the novel insights on the molecular technique-based hydrocarbon toxicity assessment and the development of the further integrative approach with other microbial community and their metabolic profile in the contaminated sites.

Novel Butane-Oxidizing Bacteria and Diversity of bmoX Genes in Puguang Gas Field

To investigate the diversity of butane-oxidizing bacteria in soils contaminated by long-term light hydrocarbon microseepage and the influence of butane on the soil microbial community, a quantitative study and identification of butane-oxidizing bacteria (BOB) in soils at the Puguang gas field were performed by DNA-based stable isotope probing (DNA-SIP). For the first time, two phylotypes corresponding to the genera Giesbergeria and Ramlibacter were identified as being directly involved in butane oxidation, in addition to the well-known light hydrocarbon degrader Pseudomonas. Furthermore, bmoX genes were strongly labeled by ¹³C-butane, and their abundances in gas field soils increased by 43.14-, 17.39-, 21.74-, and 30.14-fold when incubated with butane for 6, 9, 12, and 14 days, respectively, indicating that these bmoX-harboring bacteria could use butane as the sole carbon and energy source and they play an important role in butane degradation. We also found that the addition of butane rapidly shaped the bacterial community and reduced the diversity of bmoX genes in the gas field soils. These findings improve our understanding of BOB in the gas field environment and reveal the potential for their applications in petroleum exploration and bioremediation.

Bioremediation of petroleum-contaminated soil using aged refuse from landfills

This study explored the effects and mechanisms of petroleum-contaminated soil bioremediation using aged refuse (AR) from landfills. Three treatments of petroleum-contaminated soil (47.28 mg·g^-1) amended with AR, sterilized aged refuse (SAR) and petroleum-contaminated soil only (as a control) were tested. During 98 days of incubation, changes in soil physicochemical properties, residual total petroleum hydrocarbon (TPH), biodegradation kinetics, enzyme activities and the microbial community were investigated. The results demonstrated that AR was an effective soil conditioner and biostimulation agent that could comprehensively improve the quality of petroleum-contaminated soil and promote microbial growth, with an 74.64% TPH removal rate, 22.36 day half-life for SAR treatment, compared with the control (half-life: 138.63 days; TPH removal rate: 22.40%). In addition, the petroleum-degrading bacteria isolation results demonstrated that AR was also a petroleum-degrading microbial agent containing abundant microorganisms. AR addition significantly improved both the biotic and abiotic conditions of petroleum-contaminated soil without other additives. The cooperation of conditioner addition, biostimulation and bioaugmentation in AR treatment led to better bioremediation effects (half-life: 13.86 days; TPH removal rate: 89.83%). In conclusion, AR amendment is a cost-effective, easy-to-use method facilitating in situ large-scale application while simultaneously recycling huge amounts of AR from landfills.

Remediation of a soil chronically contaminated with hydrocarbons through persulfate oxidation and bioremediation

The impact of remediation combining chemical oxidation followed by biological treatment on soil matrix and microbial community was studied, of a chronically hydrocarbon contaminated soil sourced from a landfarming treatment. Oxidation by ammonium persulfate produced a significant elimination of polycyclic aromatic hydrocarbons (PAHs) and an increase in PAH bioavailability. Organic-matter oxidation mobilized nutrients from the soil matrix. The bacterial populations were affected negatively, with a marked diminution in the diversity indices. In this combined treatment with oxidation and bioremediation working in tandem, the aliphatic-hydrocarbon fractions were largely eliminated along with additional PAHs. The chemical and spectroscopic analyses indicated a change in soil nutrients. In spite of the high residual-sulfate concentration, a rapid recovery of the cultivable bacterial population and the establishment of a diverse and equitable microbial community were obtained. Pyrosequencing analysis demonstrated a marked succession throughout this twofold intervention in accordance with the chemical and biologic shifts observed. These remediation steps produced different effects on the soil physiology. Spectroscopic analysis became a useful tool for following and comparing those treatments, which involved acute changes in a matrix of such chronically hydrocarbon-contaminated soil. The combined treatment increased the elimination efficiency of both the aliphatic hydrocarbons and the PAHs at the expense of the mobilized organic matter, thus sustaining the recovery of the resilient populations throughout the treatment. The high-throughput-DNA-sequencing techniques enabled the identification of the predominant populations that were associated with the changes observed during the treatments.

Rhizospheric microorganisms as a solution for the recovery of soils contaminated by petroleum: A review

Petroleum is currently the world's main energy source, and its demand is expected to increase in coming years. Its intense exploitation can lead to an increase in the number of environmental accidents, such as spills and leaks, and an increase in the generation of environmental liabilities resulting from refining. Due to its hydrophobic characteristics and slow process of biodegradation, petroleum can remain in the environment for a long time and its toxicity can cause a negative impact on both terrestrial and aquatic ecosystems, with the main negative effects related to its carcinogenic potential for both animals and humans. The objective of the present review is to discuss environmental contamination by oil, conventional treatment techniques and bioremediation an alternative tool for recovery petroleum-contaminated soils, focusing on the rhizodegradation process, plant growth-promoting rhizobacteria (PGPR), a phytoremediation strategy in which the microorganisms that colonize the roots of phytoremediatior plants are responsible for the biodegradation of petroleum. These microorganisms can be selected and tested individually or in the form of consortia to evaluate their potential for oil degradation, or even to measure the use of biosurfactants produced by them to constitute tools for the development of environmental recovery strategies and biotechnological application.

The responses of two native plant species to soil petroleum contamination in the Yellow River Delta, China

Petroleum contamination is a significant environmental problem in the Yellow River Delta. The responses of two native salt-tolerant plant species, alfalfa (Medicago sativa) and bristle grass (Setaria uiridis Beauv), to soil petroleum contamination were investigated at five levels between 0 and 2.0% (w/w). Results showed that the total, aboveground and underground plant biomasses of both species were significantly reduced by petroleum contamination (p < 0.05), with the inhibition enhanced with increased petroleum levels. However, the emergence rate of bristle grass was promoted by petroleum contamination. Following 100 days of exposure, the number of soil petroleum degraders increased greatly, with a trend of initial increase followed by a decrease at 1.5% contamination or higher. Compared to bulk soils, bacteria-degrading alkanes, total hydrocarbons and PAHs in alfalfa rhizosphere soils increased by 1.33-4.18-, 0.85-3.01- and 4.12-12.75-fold, respectively, with an increase of 2.80-10.00-, 4.42-14.44- and 7.30-26.00-fold in bristle grass rhizosphere soils, respectively. The greatest number of petroleum degraders in bristle grass rhizosphere soils resulted in the highest petroleum degradation rate. Bristle grass may be the optimal species for petroleum remediation in the studied area.

Dechlorination of three tetrachlorobenzene isomers by contaminated harbor sludge-derived enrichment cultures follows thermodynamically favorable reactions

Dechlorination patterns of three tetrachlorobenzene isomers, 1,2,3,4-, 1,2,3,5-, and 1,2,4,5-TeCB, were studied in anoxic microcosms derived from contaminated harbor sludge. The removal of doubly, singly, and un-flanked chlorine atoms was noted in 1,2,3,4- and 1,2,3,5-TeCB fed microcosms, whereas only singly flanked chlorine was removed in 1,2,4,5-TeCB microcosms. The thermodynamically more favorable reactions were selectively followed by the enriched cultures with di- and/or mono-chlorobenzene as the main end products of the reductive dechlorination of all three isomers. Based on quantitative PCR analysis targeting 16S rRNA genes of known organohalide-respiring bacteria, the growth of Dehalococcoides was found to be associated with the reductive dechlorination of all three isomers, while growth of Dehalobacter, another known TeCB dechlorinator, was only observed in one 1,2,3,5-TeCB enriched microcosm among biological triplicates. Numbers of Desulfitobacterium and Geobacter as facultative dechlorinators were rather stable suggesting that they were not (directly) involved in the observed TeCB dechlorination. Bacterial community profiling suggested bacteria belonging to the phylum Bacteroidetes and the order Clostridiales as well as sulfate-reducing members of the class Deltaproteobacteria as putative stimulating guilds that provide electron donor and/or organic cofactors to fastidious dechlorinators. Our results provide a better understanding of thermodynamically preferred TeCB dechlorinating pathways in harbor environments and microbial guilds enriched and active in anoxic TeCB dechlorinating microcosms.

Comparative Investigation of Bacterial, Fungal, and Archaeal Community Structures in Soils in a Typical Oilfield in Jianghan, China

Agricultural soils in oilfields have high risk for polycyclic aromatic hydrocarbon (PAH) pollution. In this study, from the Jianghan Oilfield (Hubei Province, China) with a history of >50 years, 7 soil samples (OS-1 to OS-7) were collected. Subsequently, the bacterial, archaeal, and fungal community structures were investigated by Illumina MiSeq sequencing, and the relationship between microbial community structure and soil PAH content was analyzed. The results indicated that bacterial and archaeal Chao 1 indices showed a significantly negative relationship with soil PAH content, and only the bacterial Shannon index had a significantly negative relationship with soil PAH content. Moreover, the community structure of bacteria (r ² = 0.9001, p = 0.013) showed a stronger correlation with PAH content than that of fungi (r ² = 0.7357, p = 0.045), and no significant relationship was found between archaeal community structure (r ² = 0.4553, p = 0.262) and soil PAH content. In addition, the relative greater abundances of some bacterial genus belonging to Actinobacteria (Mycobacterium and Micromonospora) and Proteobacteria (Pseudomonas, Lysobacter, Idiomarina, Oxalobacteraceae, and Massilia), fungal genus belonging to Ascomycota (Sordariales and Pleosporales), and archaeal phylum (Euryarchaeota) were detected in the soil samples (OS-3 and OS-5) with greater PAH content. In summary, soil PAHs showed an obvious influence and selectivity on the soil microbiota. Furthermore, compared with fungi and archaea, bacteria was more sensitive to soil PAH pollution, and the diversity indices and community structure of bacteria both might be suitable indicators for assessment of soil PAH stress on the soil ecosystem.