Microbial functional gene patterns related to soil greenhouse gas emissions in oil contaminated areas

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.

Spatial distribution of volatile organic compounds in contaminated soil and distinct microbial effect driven by aerobic and anaerobic conditions

The vertical distribution of 35 volatile organic compounds (VOCs) was investigated in soil columns from two obsolete industrial sites in Eastern China. The total concentrations of ΣVOCs in surface soils (0-20 cm) were 134-1664 ng g-1. Contamination of VOCs in surface soil exhibited remarkable variability, closely related to previous production activities at the sampling sites. Additionally, the concentrations of ΣVOCs varied with increasing soil depth from 0 to 10 m. Soils at depth of 2 m showed ΣVOCs concentrations of 127-47,389 ng g-1. Among the studied VOCs, xylene was the predominant contaminant in subsoils (2 m), with concentrations ranging from n.d. to 45,400 ng g-1. Chlorinated alkanes and olefins demonstrated a greater downward migration ability compared to monoaromatic hydrocarbons, likely due to their lower hydrophobicity. As a result, this vertical distribution of VOCs led to a high ecological risk in both the surface and deep soil. Notably, the risk quotient (RQ) of xylene in subsoil (2 m, RQ up to 319) was much higher than that in surface soil. Furthermore, distinct effects of VOCs on soil microbes were observed under aerobic and anaerobic conditions. Specifically, after the 30-d incubation of xylene-contaminated soil, Ilumatobacter was enriched under aerobic condition, whereas Anaerolineaceae was enriched under anaerobic condition. Moreover, xylene contamination significantly affected methylotrophy and methanol oxidation functions for aerobic soil (t-test, p < 0.05). However, aromatic compound degradation and ammonification were significantly enhanced by xylene in anaerobic soil (t-test, p < 0.05). These findings suggest that specific VOC compound has distinct microbial ecological effects under different oxygen content conditions in soil. Therefore, when conducting soil risk assessments of VOCs, it is crucial to consider their ecological effects at different soil depths.

Urbanization-driven forest soil greenhouse gas emissions: Insights from the role of soil bacteria in carbon and nitrogen cycling using a metagenomic approach

Increasing population densities and urban sprawl have induced greenhouse gas (GHG) emissions from the soil, and the soil microbiota of urban forests play a critical role in the production and consumption of GHGs, supporting green development. However, the function and potential mechanism of soil bacteria in GHG emissions from forests during urbanization processes need to be better understood. Here, we measured the fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in Cinnamomum camphora forest soils along an urbanization gradient. 16S amplicon and metagenomic sequencing approaches were employed to examine the structure and potential functions of the soil bacterial community involved in carbon (C) and nitrogen (N) cycling. In this study, the CH4 and CO2 emissions from urban forest soils (sites U and G) were significantly greater than those from suburban soils (sites S and M). The N2O emissions in the urban center (site U) were 24.0 % (G), 13.8 % (S), and 13.5 % (M) greater than those at the other three sites. These results were related to the increasing bacterial alpha diversity, interactions, and C and N cycling gene abundances (especially those involved in denitrification) in urban forest soils. Additionally, the soil pH and metal contents (K, Ca, Mg) affected key bacterial populations (such as Methylomirabilota, Acidobacteriota, and Proteobacteria) and indicators (napA, nosZ, nrfA, nifH) involved in reducing N2O emissions. The soil heavy metal contents (Fe, Cr, Pb) were the main contributors to CH4 emissions, possibly by affecting methanogens (Desulfobacterota) and methanotrophic bacteria (Proteobacteria, Actinobacteriota, and Patescibacteria). Our study provides new insights into the benefits of conservation-minded urban planning and close-to-nature urban forest management and construction, which are conducive to mitigating GHG emissions and supporting urban sustainable development by mediating the core bacterial population.

Bioremediation of Diesel-Contaminated Soil by Fungal Solid-State Fermentation

To address the poor removal of diesel in soil by indigenous microorganisms, we proposed a fungal solid-state fermentation (SSF) method for bioremediation. We screened Pycnoporus sanguineus 5.815, Trametes versicolor 5.996, and Trametes gibbosa 5.952 for their diesel-degrading abilities, with Trametes versicolor 5.996 showing the most promise. The fungal inoculum was obtained through SSF using wood chips and bran. Trametes versicolor 5.996 was applied to two treatments: natural attenuation (NA, diesel-contaminated soil) and bioremediation (BR, 10% SSF added to diesel-contaminated soil). Over 20 days, NA removed 12.9% of the diesel, while BR achieved a significantly higher 38.3% degradation rate. BR also increased CO2 and CH4 emissions but reduced N2O emissions. High-throughput sequencing indicated SSF significantly enriched known diesel-degrading microorganisms like Ascomycota (83.82%), Proteobacteria (46.10%), Actinobacteria (27.88%), Firmicutes (10.35%), and Bacteroidota (4.66%). This study provides theoretical support for the application of fungal remediation technology for diesel and improves understanding of microbiologically mediated diesel degradation and soil greenhouse gas emissions.

Regulating the biodegradation of petroleum hydrocarbons with different carbon chain structures by composting systems

Composting can decrease petroleum hydrocarbons in petroleum contaminated soils, however the microbial degradation mechanisms and regulating method for biodegradation of petroleum hydrocarbons with different carbon chain structures in the composting system have not yet been investigated. This study analyzed variations of total petroleum hydrocarbon concentrations with C ≤ 16 and C > 16, Random Forest model was applied to identify the key microorganisms for degrading the petroleum hydrocarbon components with specific structure in biomass-amended composting. Regulating method for biodegradation of petroleum hydrocarbons with different carbon chain structures was proposed by constructing the influence paths of "environmental factors-key microorganisms- total petroleum hydrocarbons". The results showed that composting improved the degradation rate of C ≤ 16 fraction and C > 16 fraction of petroleum hydrocarbons by 67.88 % and 61.87 %, respectively. Analysis of the microbial results showed that the degrading bacteria of the C ≤ 16 fraction had degradation advantages in the heating phase of the compost, while the C > 16 fraction degraded better in the cooling phase. Moreover, microorganisms that specifically degraded C > 16 fractions were significantly associated with total nitrogen and nitrate nitrogen. The biodegradation of C ≤ 16 fraction was regulated by organic matter, moisture content, and temperature. The composting system modified by biogas slurry was effective in removing of petroleum hydrocarbons with different carbon chain structures in soil by regulating the metabolic potential of the 46 key microorganisms. This study given their expected importance to achieve the purpose of treating waste with waste and contributing to soil utilization as well as pollution remediation.

Response of the soil microbial community to petroleum hydrocarbon stress shows a threshold effect: research on aged realistic contaminated fields

Introduction

Microbes play key roles in maintaining soil ecological functions. Petroleum hydrocarbon contamination is expected to affect microbial ecological characteristics and the ecological services they provide. In this study, the multifunctionalities of contaminated and uncontaminated soils in an aged petroleum hydrocarbon-contaminated field and their correlation with soil microbial characteristics were analyzed to explore the effect of petroleum hydrocarbons on soil microbes.

Methods

Soil physicochemical parameters were determined to calculate soil multifunctionalities. In addition, 16S high-throughput sequencing technology and bioinformation analysis were used to explore microbial characteristics.

Results

The results indicated that high concentrations of petroleum hydrocarbons (565-3,613 mg•kg^-1, high contamination) reduced soil multifunctionality, while low concentrations of petroleum hydrocarbons (13-408 mg•kg^-1, light contamination) might increase soil multifunctionality. In addition, light petroleum hydrocarbon contamination increased the richness and evenness of microbial community (p < 0.01), enhanced the microbial interactions and widened the niche breadth of keystone genus, while high petroleum hydrocarbon contamination reduced the richness of the microbial community (p < 0.05), simplified the microbial co-occurrence network, and increased the niche overlap of keystone genus.

Conclusion

Our study demonstrates that light petroleum hydrocarbon contamination has a certain improvement effect on soil multifunctionalities and microbial characteristics. While high contamination shows an inhibitory effect on soil multifunctionalities and microbial characteristics, which has significance for the protection and management of petroleum hydrocarbon-contaminated soil.

Community response of soil microorganisms to combined contamination of polycyclic aromatic hydrocarbons and potentially toxic elements in a typical coking plant

Both polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) of coking industries impose negative effects on the stability of soil ecosystem. Soil microbes are regarded as an essential moderator of biochemical processes and soil remediation, while their responses to PAHs-PTEs combined contamination are largely unknown. In the present study, soil microbial diversity and community composition in the typical coking plant under the chronic co-exposure of PAHs and PTEs were investigated and microbial interaction networks were built to reveal microbial co-occurrence patterns. The results indicated that the concentrations of PAHs in the soil inside the coking plant were significantly higher than those outside the plant. The mean concentration of ∑16PAHs was 2894.4 ng·g^-1, which is 5.58 times higher than that outside the plant. The average Hg concentration inside the coking plant was 22 times higher than the background value of Hebei province. The soil fungal community inside the coking plant showed lower richness compared with that of outside community, and there are significant difference in the bacterial and fungal community composition between inside and outside of coking plant (p < 0.01). Predicted contribution of different environmental factors to each dominant species based on random forest identified 20 and 25 biomarkers in bacteria and fungi, respectively, that were highly sensitive to coking plant soil in operation, such as Betaproteobacteria，Sordariomycetes and Dothideomycetes. Bacterial and fungal communities were shaped by the soil chemical properties (pH), PTEs (Hg), and PAHs together in the coking plant soils. Furthermore, the bacterial and fungal interaction patterns were investigated separately or jointly by intradomain and interdomain networks. Competition is the main strategy based on the co-exclusion pattern in fungal community, and the competitive relationship inside the coking plant is more complex than that outside the plant. In contrast, cooperation is the dominant strategy in bacterial networks based on the co-occurrence pattern. The present study provided insights into microbial response strategies and the interactions between bacteria and fungi under long-term combined contamination.

Deciphering the diversity, composition, function, and network complexity of the soil microbial community after repeated exposure to a fungicide boscalid

Boscalid is a novel, highly effective carboximide fungicide that has been substantially and irrationally applied in greenhouses. However, little is known about the residual characteristics of boscalid and its ecological effects in long-term polluted greenhouse soils. Therefore, actual boscalid pollution status in greenhouse soils was simulated by repeatedly introducing boscalid into the soil under laboratory conditions. The degradation characteristics of boscalid, and its effects on the diversity, composition, function, and co-occurrence patterns of the soil microbial community were systematically investigated. Boscalid degraded slowly, with its degradation half-lives ranging from 31.5 days to 180.1 days in the soil. Boscalid degradation was further delayed by repeated treatment and increasing its initial concentration. Boscalid significantly decreased soil microbial diversity, particularly at the recommended dosage. Amplicon sequencing analysis showed that boscalid altered the soil microbial community and further stimulated the phylum Proteobacteria and four potential boscalid-degrading bacterial genera, Sphingomonas, Starkeya, Citrobacter, and Castellaniella. Although the network analysis revealed that boscalid significantly reduced the microbial network complexity, it enhanced the vital roles of Proteobacteria by increasing its proportion and strengthening the relationships among the internal bacteria in the network. The soil microbial function in the boscalid treatment were simulated at the recommended dosage and two-fold recommended dosage but showed an inhibition-recovery-stimulation trend at the five-fold recommended dosage with an increase in treatment frequency. Moreover, the expression of nitrogen cycling functional genes, nifH, AOA amoA, AOB amoA, nirK, and nirS in all boscalid treatments displayed an inhibition-recovery-stimulation trend during the entire experimental period, and the effects were more pronounced at the five-fold recommended dosage. In conclusion, repeated boscalid treatments delayed degradation, reduced soil microbial diversity and network complexity, disturbed soil microbial community, and interfered with soil microbial function.

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.

Response and contribution of bacterial and archaeal communities to eutrophication in urban river sediments

Excessive loading of nitrogen (N) and phosphorus (P) that leads to eutrophication mutually interacts with sediment microbial community. To unravel the microbial community structures and interaction networks in the urban river sediments with the disturbance of N and P loadings, we used high-throughput sequencing analysis and ecological co-occurrence network methods to investigate the responses of diversity and community composition of bacteria and archaea and identify the keystone species in river sediments. The alpha-diversity of archaea significantly decreased with the increased total nitrogen (TN), whereas the operational taxonomic unit (OTU) number of bacteria increased with the increase of available phosphorus (AP). The beta-diversity of archaea and bacteria was more sensitive to N content than P content. The relative abundance of predominant bacterial and archaeal taxa varied differently in terms of different N and P contents. Complexity and connectivity of bacteria and archaea interaction networks showed significant variations with eutrophication, and competition between bacteria became more significant with the increase of N content. The sensitive and the highest connective species (keystone species) were identified for different N and P loadings. Total carbon (TC), water content (WC), microbial alpha-diversity and interaction networks played pivotal roles in the N and P transformation in urban river sediments.

Microbial compositional and functional traits of BTEX and salinity co-contaminated shallow groundwater by produced water

Intrusion of salinity and petroleum hydrocarbons (e.g., benzene, toluene, ethylbenzene, and xylenes, BTEX) into shallow groundwater by so-called 'produced water' (the water associated with oil and gas production) has recently drawn much attention. However, how this co-contamination affects the groundwater microbial community remains unknown. Herein, geochemical methods (e.g., ion ratios) and high-throughput sequencing (amplicon and shotgun metagenomic) were used to study the contaminant source, hydrogeochemical conditions, microbial community and function in salinity and BTEX co-contaminated shallow groundwater in an oil field, northwest China. The desulfurization coefficient (100rSO₄^2-/rCl^-), coefficient of sodium and chloride (rNa⁺/rCl^-), and coefficient of magnesium and chloride (rMg²⁺/rCl^-) revealed an intrusion of produced water into groundwater, resulting in elevated levels of salinity and BTEX. The consumption of terminal electron acceptors (e.g., NO₃^-, Fe³⁺, and SO₄^2-) was likely coupled with BTEX degradation. Relative to the bacteria, decreased archaeal diversity and enriched community in produced water-contaminated groundwater suggested that archaea were more susceptible to elevated BTEX and salinity. Relative to the nitrate and sulfate reduction genes, the abundance of marker genes encoding fermentation (acetate and hydrogen production) and methanogenesis (aceticlastic and methylotrophic) was more proportional to BTEX concentration. The produced water intrusion significantly enriched the salt-tolerant anaerobic fermentative heterotroph Woesearchaeia in shallow groundwater, and its co-occurrence with BTEX-degrading bacteria and methanogen Methanomicrobia suggested mutualistic interactions among the archaeal and bacterial communities to couple BTEX degradation with fermentation and methanogenesis. This study offers a first insight into the microbial community and function in groundwater contaminated by produced water.

The dominant microbial metabolic pathway of the petroleum hydrocarbons in the soil of shale gas field: Carbon fixation instead of CO2 emissions

In shale gas mining areas, indigenous microorganisms degrade organic pollutants such as petroleum hydrocarbons into carbon dioxide (CO₂) and water (H₂O) through aerobic metabolism. A large quantity of CO₂ emissions will exacerbate the "Greenhouse effect". Based on the clean sieved soil and oil-based drilling fluid in the shale gas mining area, this experiment set three concentration gradients (3523 ± 159 mg/kg, 8715 ± 820 mg/kg and 22,031 ± 1533 mg/kg) to treat the soil, and each group was disposed for the same amount of time (63 days). By analyzing the dynamic changes of microbial diversity and the abundance of key functional genes for carbon fixation, the impact of petroleum hydrocarbons on carbon fixation potential was discovered, and the natural attenuation law of petroleum hydrocarbons in contaminated soil was explored. It provided the scientific research basis of ecology for the carbon cycle, carbon allocation, and carbon fixation in microbial remediation of petroleum hydrocarbon contaminated soil. The results obtained indicated the following: i) The removal rate of petroleum hydrocarbons under high-concentration pollution (45.33 ± 3.90%) was significantly lower than low and medium-concentration pollution. The TPH concentration removal rate of each group was the largest in the early stage of culture (1-5d), and there was no significant correlation between the TPH content and the community composition (R² = 0.0736, P > 0.05). ii) Composition and function of Carbon Fixation associated microbiota were assessed by 16S rRNA sequencing and PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) analysis. The main carbon fixation pathway in this study is the reductive citric acid cycle, because there was no shortage of enzymes that can affect subsequent reactions.

Oil contamination drives the transformation of soil microbial communities: Co-occurrence pattern, metabolic enzymes and culturable hydrocarbon-degrading bacteria

The land-based oil extraction activity has led to serious pollution of the soil. While microbes may play an important role in the remediation of contaminated soils, ecological effects of oil pollution on soil microbial relationships remain poorly understood. Here, typical contaminated soils and undisturbed soils from seven oilfields of China were investigated in terms of their physicochemical characteristics, indigenous microbial assemblages, bacterial co-occurrence patterns, and metabolic enzymes. Network visualization based on k-core decomposition illustrated that oil pollution reduced correlations between co-existing bacteria. The core genera were altered to those related with oil metabolism (Pseudarthrobacter, Alcanivorax, Sphingomonas, Chromohalobacter and Nocardioides). Under oil pollution pressure, the indigenous bacteria Gammaproteobacteria was domesticated as biomarker and the enzyme expression associated with the metabolism of toxic benzene, toluene, ethylbenzene, xylene and polycyclic aromatic hydrocarbons was enhanced. Functional pathways of xenobiotics biodegradation were also stimulated under oil contamination. Finally, twelve culturable hydrocarbon-degrading microbes were isolated from these polluted soils and classified into Stenotrophomonas, Delftia, Pseudomonas and Bacillus. These results show that the soil microbial communities are transformed under oil pollution stress, and also provide useful information for future bioremediation processes.

Dynamics of bacterial functional genes and community structures during rhizoremediation of diesel-contaminated compost-amended soil

The objective of this study was to characterize the effects of organic soil amendment (compost) on bacterial populations associated with petroleum hydrocarbon (PH) degradation and nitrous oxide (N₂O) dynamics via pot experiments. Soil was artificially contaminated with diesel oil at total petroleum hydrocarbon (TPH) concentration of 30,000 mg·kg-soil^-1 and compost was mixed with the contaminated soil at a 1:9 ratio (w/w). Maize seedlings were planted in each pot and a total of ten pots with two treatments (compost-amended and unamended) were prepared. The pot experiment was conducted for 85 days. The compost-amended soil had a significantly higher TPH removal efficiency (51.1%) than unamended soil (21.4%). Additionally, the relative abundance of the alkB gene, which is associated with PH degradation, was higher in the compost-amended soil than in the unamended soil. Similarly, cnorB and nosZ (which are associated with nitric oxide (NO) and N₂O reduction, respectively) were also highly upregulated in the compost-amended soil. Moreover, the compost-amended soil exhibited higher richness and evenness indices, indicating that bacterial diversity was higher in the amended soil than in the unamended soil. Therefore, our findings may contribute to the development of strategies to enhance remediation efficiency and greenhouse gas mitigation during the rhizoremediation of diesel-contaminated soils.

Hydrocarbon transformation pathways and soil organic carbon stability in the biostimulation of oil-contaminated soil: Implications of 13C natural abundance

Mineralization, assimilation, and humification are key processes to detoxify oil-contaminated soil by biostimulation remediation strategies, and these processes are affected by stimulants. In this study, we investigated the effects of either inorganic salts or organic stimulants (organic compost and sawdust) on hydrocarbon transformation. Total petroleum hydrocarbons (TPH) and hydrocarbon components were determined by gravimetry and gas chromatography, and the ¹³C of CO₂, microbial biomass carbon (MBC), and humus were measured by stable isotope mass spectrometry. The results showed that organic compost was the most beneficial for the dissipation of hydrocarbons. After 60 days of remediation, the removal rates of TPH, saturates, aromatics, C7-C30 n-alkanes, and 16 PAHs were 35.7%, 39.6%, 15.9%, 80.5%, and 8.8%, respectively. A total of 84.7%-88.5% of the removed hydrocarbons were mineralized in all the treatments. The hydrocarbon degradation pathway in the control soil (without stimulant addition) was "assimilation → humification → mineralization". The hydrocarbon transformation pathways in the biostimulation treatments were "assimilation → mineralization → humification". The soil organic carbon (SOC) stability decreased during remediation, which was attributed to the enhanced microbial activity and the removal of recalcitrant hydrocarbons.

The stability of soil organic carbon across topographies in a tropical rainforest

Mechanisms of soil organic carbon (SOC) stability are still unclear in forest ecosystems. In order to unveil the influences of topography on the SOC stability, a 60ha dynamic plot of a tropical montane rainforest was selected in Jianfengling, in Hainan Island, China and soil was sampled from 60 quadrats. The chemical fractions of the SOC were detected with 13C CPMAS/NMR and path analyses explore the mechanisms of SOC stability in different topographies. The chemical fractions of the SOC comprised alkyl carbon > O-alkyl carbon > carboxyl carbon > aromatic carbon. The decomposition index (DI) values were greater than 1 in the different topographies, with an average DI value was 1.29, which indicated that the SOC in the study area was stable. Flat and top areas (together named RF) had more favorable nutrients and silt contents compared with steep and slight steep areas (together named RS). The influencing factors of SOC stability varied across the topographies, where SOC, soil moisture (SM) and ammoniacal nitrogen (NH₄⁺-N, AN) were the main influencing factors in the RF, while SM and AN were the main factors in the RS. Greater SOC and AN strengthened the SOC stability, while higher soil moisture lowered SOC stability. The inertia index was higher in the RS than the RF areas, indicating that local topography significantly affects SOC content and SOC stability by changing soil environmental factors. Topography cannot be neglected in considering SOC stability and future C budgets.

Transmembrane transport mechanism of n-hexadecane by Candida tropicalis: Kinetic study and proteomic analysis

Yeasts are the most predominant petroleum hydrocarbon-degrading fungi isolated from petroleum-contaminated soil. However, information of the transmembrane transport of petroleum hydrocarbon into yeast cells is limited. The present study was designed to explore the transmembrane transport mechanisms of the typical petroleum hydrocarbon n-hexadecane in Candida tropicalis cells with petroleum hydrocarbon biodegradation potential. Yeast cells were treated with n-hexadecane in different scenarios, and the percentage of intracellular n-hexadecane and transport dynamics were investigated accordingly. The intracellular concentration of n-hexadecane increased within 15 min, and transportation was inhibited by NaN₃, an ATPase inhibitor. The uptake kinetics of n-hexadecane were well fitted by the Michaelis-Menten model, and Kt values ranged from 152.49 to 194.93 mg/L. All these findings indicated that n-hexadecane might cross the yeast cells in an energy-dependent manner and exhibit an affinity with the cell transport system. Moreover, the differentially expressed membrane proteins induced by n-hexadecane were identified and quantified by tandem mass tag labeling coupled with liquid chromatography tandem mass spectrometry analysis. The proteome analysis results demonstrated that energy production and conversion accounted for a large proportion of the functional classifications of the differentially expressed proteins, providing further evidence that sufficient energy supply is essential for transmembrane transport. Protein functional analysis also suggested that differentially expressed proteins associated with transmembrane transport processes are clearly enriched in endocytosis and phagosome pathways (p < 0.05), and the analysis supported the notion that the underlying transmembrane transport mechanism might be associated with endocytosis and phagosome pathways, revealing a new mechanism of n-hexadecane internalization by Candida tropicalis.

History of petroleum disturbance triggering the depth-resolved assembly process of microbial communities in the vadose zone

Biogeochemical gradient forms in vadose zone, yet little is known about the assembly processes of microbial communities in this zone under petroleum disturbance. This study collected vadose zone soils at three sites with 0, 5, and 30 years of petroleum contamination to unravel the vertical microbial community successions and their assembly mechanisms. The results showed that petroleum hydrocarbons exhibited higher concentrations at the long-term contaminated site, showing negative impacts on some soil properties, retarding in the surface soils and decreasing along soil depth. Cultivable fraction of heterotrophic bacteria and microbial α-diversity decreased along depth in vadose zones with short-term/no contamination history, but exhibited an opposite trend with long-term contamination history. Petroleum contamination intensified the vertical heterogeneity of microbial communities based on the contamination time. Microbial co-occurrence network revealed the lowest species co-occurrence pattern at the long-term contaminated site. The distance-decay patterns and null model analysis together suggested distinct assembly mechanisms at three sites, where dispersal limitation (42-45%) was higher and variable and homogenizing selections were lower (37-38%) in vadose zones under petroleum disturbance than those in the uncontaminated vadose zone. Our findings help to better understand the subsurface biogeochemical cycles and bioremediation of petroleum-contaminated vadose zones.

Geo-distribution pattern of microbial carbon cycling genes responsive to petroleum contamination in continental horizontal oilfields

Contamination significantly affects soil microbial community structures, and the metabolisms of organic contaminants might particularly alter soil carbon cycling by shaping microbial carbon cycling genes. Although numerous studies have discussed the impacts of petroleum contamination on soil bacterial communities and relevant degrading genes, there is no work addressing how soil carbon cycling genes are affected by petroleum contamination. In this study, 77 soil samples were collected from five typical oilfields horizontally located in China to explore the influence of environmental variables and petroleum contamination on microbial carbon cycling genes. Results from Geochip suggested a geographic-determined distribution of carbon cycling genes. Although no significant correlation was observed between carbon cycling genes and soil physio-chemical properties for all soils, some relationships were identified in specific oilfield. Principle component analysis indicated that soil physio-chemical properties, rather than petroleum contamination disturbance, are the key factors determining the degree of sample dispersion, whereas environmental variables predominantly control the degree of sample aggregation. Co-occurrence ecological network analysis revealed a more complex interactions of all functional genes in petroleum-contaminated soils, and carbon cycling genes were grouped with nitrogen related genes in petroleum-contaminated communities. Soil moisture and heterogeneity were identified as the main drivers for the abundance and diversity of carbon cycling genes, particularly in petroleum-contaminated soils. These results are attributing to the fewer impacts of petroleum contamination on the diversity of carbon cycling genes than soil physio-chemical properties, and soil carbon cycling genes are mainly driven by geographic location and petroleum contamination together. Our findings provide deeper insight into the influence of petroleum contamination in soil microbial functions related to carbon cycling.

Biogas slurry as an activator for the remediation of petroleum contaminated soils through composting mediated by humic acid

Soil pollution caused by petroleum hydrocarbons is a widespread environmental problem. Composting is one of the cost-effective solutions for petroleum hydrocarbons removal but limited by low efficiency of bioremediation, leading to high phytotoxicity. Given that biogas slurry as nutrients can alter the microbial activity, the aim of this study was to investigate the role of biogas slurry on the remediation of petroleum contaminated soils in composting. Herein, we added biogas slurry into the composting of hydrocarbon contaminated soil to investigate its effect on the biodegradation of petroleum hydrocarbons, humic acid (HA) transformation and the safety of product. The results showed that biogas slurry addition improved the degradation of organic matter and total petroleum hydrocarbons (TPH) (especially C > 16), but also increased 18.0% of germination index and the humification degree of HA. The estrone from biogas slurry was removed during composting and did not affect the phytotoxicity level of compost. Redundancy analysis and structural equation modeling indicated that TPH degradation was significantly related to the humification of HA components and total nitrogen from biogas slurry, which contributed to composting safety. Therefore, biogas slurry could be a possible activator for the remediation of petroleum contaminated soils through composting mediated by HA transformation, which is beneficial to obtain the composts with a lower phytotoxicity and higher maturity for soil application.

Intensive land uses modify assembly process and potential metabolic function of edaphic bacterial communities in the Yellow River Delta, China

Coastal reclamation is a global threat to natural ecosystems, disturbing biological community structure, diversity and ecological function through habitat conversion. We have limited insights into the changes brought about by coastal reclamation for different land-use types. We used the Yellow River Delta (YRD) as a model because it is a region with intensive land reclamation, and we investigated the structural and functional variations of bacterial communities and their relations to edaphic properties under different land-use types. Our results showed that the high soil organic carbon (SOC), nitrate concentrations and salinity were found in oil field, aquaculture pond and salt pan, respectively, and low values in natural wetland. Land use was found to have significant influence on bacterial community diversity. To investigate the phylogenetic conservation of specific traits, we analyzed the relationship between soil bacterial assembly processes and edaphic properties. Bacterial traits phylogenetically conserved, and differs in depth. Our findings suggest that SOC served as a deep trait due to it negative correlation with deeper branches of phylogenetic clustering, while nitrate functioned as a shallow trait due to its positive correlation with phylogenetic clustering at finer branches. Soil salinity acted as a complex trait effected on both finer and deeper branches. Further potential functional gene co-occurrence network analysis revealed that land reclamation induced shifts of metabolic function by altering the functional gene connectivity. We found that the photosynthesis pathway was enriched in hub modules related to oil field (OF), while methane metabolism was enriched in hub modules linked to sea cucumber pond (CP1). In addition, two-component systems (TCS) were enriched with nitrate, ammonia, SOC and salinity-related modules. Therefore, our study highlights the importance of integrating multi-function and multi-process identification and prediction of coastal diverse reclamation impacts on coastal ecosystems.

The effects of crude oil on microbial nitrogen cycling in coastal sediments

Crude oil could affect certain critical microbial processes of nitrogen cycling (N-cycling) in coastal sediments, and disturb the nitrogen balance. However, the understanding of the effects of crude oil on coastal sediments N-cycling under human disturbance was still limited. In this study, two sediments (named SY and HB with heavy and slight pollution, respectively) were sampled from Hangzhou Bay, China. After an incubation with exposure to different amounts of crude oil in above two sediments for 30 days, we found that crude oil affected microbial N-cycling in multiple levels. Potential rate measurements revealed that crude oil stimulated potential denitrification and N₂O emissions in both sediments, which showed a higher influence on denitrification rates in higher concentration of oil. Quantitative PCR revealed that crude oil greatly increased abundances of bacterial and archaeal 16S rRNA genes and N-cycling genes (nirS, nosZ, nrfA, part of AOA and AOB amoA). On the other hand, only a few genes (16S rRNA and nrfA) showed higher transcriptional activities in oil-addition treatments. Results about relative changes of N-cycling genes revealed that the variations of N-cycling genes in oil-addition treatments were related to sediment types but not crude oil concentrations, and the genes in HB were more sensitive to crude oil than SY. Network analysis of N-cycling genes found that crude oil decreased the complexity of N-cycling gene networks in SY, while increased complexity in HB, and led to more competition among N-cycling microbes. Our findings help to look into the effects of crude oil on key N-cycling processes, and improve the understanding of the interactions among N-cycling under crude oil contamination.

Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

BACKGROUND

Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37 °C) and thermophilic (55 °C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted.

RESULTS

In total, 78 bacterial and archaeal MAGs representing the most abundant members of the communities, and featuring defined quality criteria were selected and characterized in detail. Determination of MAG abundances under the tested conditions by mapping of the obtained metagenome sequence reads to the MAGs revealed that MAG abundance profiles were mainly shaped by the temperature but also by the OLR. However, the OLR effect was more pronounced for the mesophilic systems as compared to the thermophilic ones. In contrast, metatranscriptome mapping to MAGs subsequently normalized to MAG abundances showed that under thermophilic conditions, MAGs respond to increased OLRs by shifting their transcriptional activities mainly without adjusting their proliferation rates. This is a clear difference compared to the behavior of the microbiome under mesophilic conditions. Here, the response to increased OLRs involved adjusting of proliferation rates and corresponding transcriptional activities. The analysis led to the identification of MAGs positively responding to increased OLRs. The most outstanding MAGs in this regard, obviously well adapted to higher OLRs and/or associated conditions, were assigned to the order Clostridiales (Acetivibrio sp.) for the mesophilic biofilm and the orders Bacteroidales (Prevotella sp. and an unknown species), Lachnospirales (Herbinix sp. and Kineothrix sp.) and Clostridiales (Clostridium sp.) for the thermophilic biofilm. Genome-based metabolic reconstruction and transcriptional profiling revealed that positively responding MAGs mainly are involved in hydrolysis of grass silage, acidogenesis and / or acetogenesis.

CONCLUSIONS

An integrated -omics approach enabled the identification of new AD biofilm keystone species featuring outstanding performance under stress conditions such as increased OLRs. Genome-based knowledge on the metabolic potential and transcriptional activity of responsive microbiome members will contribute to the development of improved microbiological AD management strategies for biomethanation of renewable biomass.

Mixing effect of polylactic acid microplastic and straw residue on soil property and ecological function

Microplastics have become a contaminant of increasing concern in soils. Although biodegradable plastics were considered as alternatives of traditional plastics, some evidence showed that biodegradable plastics might produce more microplastics. Until now, the effect of biodegradable microplastics on soil functions and processes, as well as microbial communities is uncertain. Based on high throughput sequencing, enzymatic activity assay and dynamic analysis of soil carbon and nitrogen, we investigated the effects of biodegradable polylactic acid microplastics (PLA MPs) on soil microbiota and related ecological processes under conditions of high or low carbon content. The results showed that PLA MPs had no significant effect on the overall diversity and composition of bacterial communities or related ecosystem functions and processes. However, co-occurrence network analysis revealed that PLA MPs impacted the interactions between constituent species, which might have legacy effect on soil bacterial communities and functions. Our data also revealed that PLA MPs could trade off the priming effect of carbon source. Our results provided an integrated picture in understanding the effects of PLA MPs on soil microbes, properties and ecological functions, which will help to further understand the effects of MPs on terrestrial ecosystems.

Disturbance, carbon physicochemical structure, and soil microenvironment codetermine soil organic carbon stability in oilfields

The stability of soil organic carbon (SOC) is crucial for soil quality, fertility, and natural attenuation processes of pollutants. The physicochemical structures of SOC were believed to control its stability, yet has become controversial. Here we hypothesized that disturbance intensity and variations in the soil environment can also influence the SOC stability, and conducted a case study with oil contaminated soils to quantify the contributions to SOC stability of various factors including contamination level, carbon physicochemical structure, and soil properties. Oil contamination led to increased SOC stability, as suggested by appreciably decreased soil CO₂ fluxes, the enrichment of the δ¹³C in the oil contaminated soils, as well as analysis of soil aggregates and humic substances. Redundancy analysis indicated that overall SOC stability were highly correlated to microaggregate (M2), HA/FA, Fe, soil porosity, EC, pH, and total petroleum hydrocarbon (TPH) in oilfields. Variance partitioning analysis showed that carbon physicochemical structure (S), soil properties (P), and oil contamination (O) could explain the variance of overall SOC stability by up to 90%, while 18% of the variation was explained by S × P and 43% by S × P × O. These results show that multiple factors of the disturbance, carbon physicochemical structure, and soil properties should be essential for future studies of SOC stability.

Insights into Biodegradation Related Metabolism in an Abnormally Low Dissolved Inorganic Carbon (DIC) Petroleum-Contaminated Aquifer by Metagenomics Analysis

In petroleum-contaminated aquifers, biodegradation is always associated with various types of microbial metabolism. It can be classified as autotrophic (such as methanogenic and other carbon fixation) and heterotrophic (such as nitrate/sulfate reduction and hydrocarbon consumption) metabolism. For each metabolic type, there are several key genes encoding the reaction enzymes, which can be identified by metagenomics analysis. Based on this principle, in an abnormally low dissolved inorganic carbon (DIC) petroleum-contaminated aquifer in North China, nine groundwater samples were collected along the groundwater flow, and metagenomics analysis was used to discover biodegradation related metabolism by key genes. The major new finding is that autotrophic metabolism was revealed, and, more usefully, we attempt to explain the reasons for abnormally low DIC. The results show that the methanogenesis gene, Mcr, was undetected but more carbon fixation genes than nitrate reduction and sulfate genes were found. This suggests that there may be a considerable number of autotrophic microorganisms that cause the phenomenon of low concentration of dissolved inorganic carbon in contaminated areas. The metagenomics data also revealed that most heterotrophic, sulfate, and nitrate reduction genes in the aquifer were assimilatory sulfate and dissimilatory nitrate reduction genes. Although there was limited dissolved oxygen, aerobic degrading genes AlkB and Cdo were more abundant than anaerobic degrading genes AssA and BssA. The metagenomics information can enrich our microorganic knowledge about petroleum-contaminated aquifers and provide basic data for further bioremediation.