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

Influence mechanisms underlying the degradation of petroleum hydrocarbons in response to various nitrogen dosages supplementation through metatranscriptomics analysis

Exogenous nitrogen supplementation for the bioremediation of petroleum-contaminated soils is a widely adopted and effective environmentally friendly strategy. However, the mechanism by which varying nitrogen dosages affect hydrocarbon degradation pathways remains unclear. This study conducted bioremediation on soil with a total petroleum hydrocarbon (TPH) content of 17,090 mg/kg over 210 days. The results indicated that low-dosage nitrogen supplementation (136 mg N/kg, LN) achieved a 24.8 % TPH removal, significantly outperforming high-dosage nitrogen treatment (1360 mg N/kg, HN), which achieved only 12.8 % TPH removal. The LN treatment demonstrated nitrogen availability efficiency (NAVE) and nitrogen partial factor availability (NPFA) values of 6.03 mg/mg and 31.11 mg/mg, respectively, compared to -0.90 mg/mg and 1.60 mg/mg for the HN treatment. The metatranscriptomic data were employed to investigate differential gene expression across individual samples and for GO and KEGG functional annotation. The annotation results revealed a significant increase in the number of differentially expressed genes (DEGs) associated with each functional category as the nitrogen dose increased. Notably, the LN treatment upregulated genes such as bbsE, bbsF, golA, and badH, which are crucial for encoding aromatic hydrocarbon degradation. Additionally, pyruvate metabolism genes including aceE, acdA, and atoB were enriched due to the LN treatment. In contrast, the HN treatment promoted soil nitrogen metabolism through enhanced expression of nitrogen cycling-related genes such as narK, narG, narH, nirA, and nirK, contributing to competitive interactions with carbon metabolism and impeding hydrocarbon degradation by soil microorganisms. These results suggest that the regulation of nitrogen application is crucial for enhancing hydrocarbon biodegradation efficiency in petroleum-contaminated soils.

Metagenomic and isotopic insights into carbon fixation by autotrophic microorganisms in a petroleum hydrocarbon impacted red clay aquifer

Autotrophic microorganisms, the pivotal carbon fixers, exhibit a broad distribution across diverse environments, playing critical roles in the process of carbon sequestration. However, insights into their distribution characteristics in aquifers, particularly in those petroleum-hydrocarbon-contaminated (PHC) aquifers that were known for rich in heterotrophs, have been limited. In the study, groundwater samples were collected from red clay aquifers in the storage tank leakage area of a PHC site, a prevalent aquifer type in southern China and other regions. Metagenomics combined with hydrochemical and inorganic carbon isotope analyses were employed to elucidate the presence of microbial carbon fixation and its driving forces. Results showed that there were hundreds of autotrophic microorganisms participating in distinct carbon fixation processes in the red clay PHC aquifers. Reductive tricarboxylic acid (rTCA) and dicarboxylate/4-hydroxybutyrate (DC/4HB), as well as 3-hydroxypropionate (3HP or/and 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB)) were the predominant carbon fixation pathways. The abundances of carbon fixation genes and autotrophic microorganisms were significantly and positively correlated with hydrocarbon concentrations and δ13C of dissolved inorganic carbon (δ13C-DIC) values. This finding indicated that the petroleum hydrocarbon significantly promoted the proliferation of carbon fixation microorganisms, leading to a substantial uptake of inorganic carbon. Therefore, we deduce that this process holds considerable potential for carbon sequestration in PHC-contaminated aquifers.

Characterization the microbial diversity and functional genes in the multi-component contaminated groundwater in a petrochemical site

Microorganisms in groundwater at petroleum hydrocarbon (PHC)-contaminated sites are crucial for PHC natural attenuation. Studies mainly focused on the microbial communities and functions in groundwater contaminated by PHC only. However, due to diverse raw and auxiliary materials and the complex production processes, in some petrochemical sites, groundwater suffered multi-component contamination, but the microbial structure remains unclear. To solve the problem, in the study, a petrochemical enterprise site, where the groundwater suffered multi-component pollution by PHC and sulfates, was selected. Using hydrochemistry, 16S rRNA gene, and metagenomic sequencing analyses, the relationships among electron acceptors, microbial diversity, functional genes, and their interactions were investigated. Results showed that different production processes led to different microbial structures. Overall, pollution reduced species richness but increased the abundance of specific species. The multi-component contamination multiplied a considerable number of hydrocarbon-degrading and sulfate-reducing microorganisms, and the introduced sulfates might have promoted the biodegradation of PHC. PRACTITIONER POINTS: The compound pollution of the site changed the microbial community structure. Sulfate can promote the degradation of petroleum hydrocarbons by hydrocarbon-degrading microorganisms. The combined contamination of petroleum hydrocarbons and sulfates will decrease the species richness but increase the abundance of endemic species.

Spatial heterogeneity plays a vital role in shaping the structure and function of estuarine carbon-fixing bacterial communities

Carbon-fixing bacterial communities are essential drivers of carbon fixation in estuarine ecosystems that critically affect the global carbon cycle. This study compared the abundances of the Calvin cycle functional genes cbbL and cbbM and Reductive tricarboxylic acid cycle gene aclB, as well as compared carbon-fixing bacterial community features in the two estuaries, predicted potential ecological functions of carbon-fixation bacteria, and analyzed their symbiosis strategies in two estuaries having different geographical distributions. Gammaproteobacteria was the dominant carbon-fixing bacterial community in the two estuaries. However, a higher number of Alphaproteobacteria were noted in the Liaohe Estuary, and a higher number of Betaproteobacteria were found in the Yalujiang Estuary. The carbon-fixing functional gene levels exhibited the order of aclB > cbbL > cbbM, and significant effects of Cu, Pb, and petroleum were observed (p < 0.05). Nitrogen-associated nutrient levels are major environmental factors that affect carbon-fixing bacterial community distribution patterns. Spatial factors significantly affected cbbL carbon-fixing functional bacterial community structure more than environmental factors. With the increase in offshore distance, the microbial-led processes of methylotrophy and nitrogen fixation gradually weakened, but a gradual strengthening of methanotrophy and nitrification was observed. Symbiotic network analysis of the microorganisms mediating these ecological processes revealed that the carbon-fixing bacterial community in these two estuaries had a non-random symbiotic pattern, and microbial communities from the same module were strongly linked among the carbon, nitrogen, and sulfur cycle. These findings could advance the understanding of carbon fixation in estuarine ecosystems.

Metagenomic analysis revealed highly diverse carbon fixation microorganisms in a petroleum-hydrocarbon-contaminated aquifer

As one of the ultimate products of hydrocarbon biodegradation, inorganic carbon always be used to evaluate hydrocarbon biodegradation rates in petroleum-hydrocarbon-contaminated (PHC) aquifers. The evaluation method was challenged because of the existence of carbon fixation microorganisms, which may uptake inorganic carbons and consequently cause the biodegradation rates to be underestimated. We wonder if there are carbon fixation microorganisms in PHC aquifers. Although an extremely limited number of carbon fixation microorganisms in PHC sites have been studied in previous studies, the vast majority of microorganisms that participate in carbon fixation have not been systematically identified. To systematically reveal carbon fixation microorganisms and their survival environmental conditions, high-throughput metagenomic sequencing technologies, which are characterized by culture-independent, unbiased, and comprehensive methods for the detection and taxonomic characterization of microorganisms, were introduced to analyze the groundwater samples collected from a PHC aquifer. Results showed that 1041 genera were annotated as carbon fixation microorganisms, which accounted for 49% of the total number of genera in the PHC aquifer. Carbon fixation genes involved in Calvin-Benson-Bassham (CBB), 3-hydroxy propionate (3HP), reductive tricarboxylic acid (rTCA), and Wood-Ljungdahl (WL) cycles accounted for 2%, 41%, 34%, and 23% of the total carbon fixation genes, respectively, and 3HP, rTCA, and WL can be deemed as the dominant carbon fixation pathways. Most of the identified carbon fixation microorganisms are potential hydrocarbon biodegraders, and the most abundant carbon fixation microorganisms, such as Microbacterium, Novosphingobium, and Reyranella, were just the most abundant microorganisms in the aquifer system. It's deduced that most of the microorganisms in the aquifer were facultative autotrophic, and undertaking the dual responsibilities of degrading hydrocarbons to inorganic carbon and uptaking inorganic carbon to biomass.

Enhanced phytoremediation of petroleum-contaminated soil by biochar and urea

Application of bioremediation in petroleum-contaminated soils is limited by its low efficiency. Although biochar and urea are commonly used soil additives, their potential beneficial effect on the bioremediation of petroleum contamination have rarely been discussed. In this study, biochar and urea were combined to test their effects on the phytoremediation of petroleum-contaminated soil in pot experiments. Our results showed that the degradation rate of total petroleum hydrocarbons reached 49.6%, 38.3%, 42.5%, and 77.9% when the soil was treated with biochar, urea, ryegrass, and their integrated application treatment (PBCN), respectively. A number of soil physicochemical properties (e.g., pH, elements, aggregate distribution, and organic matter composition) altered by the treatments were found to be linked to the accelerated degradation of petroleum hydrocarbons. The activities of soil dehydrogenase, lipase, and urease, and the abundances of 16 s rRNA gene and alkane degradation-related genes could be increased simultaneously when biochar, urea, and ryegrass were co-applied. Furthermore, urea significantly reduced soil bacterial α-diversity, while soil bacterial community dissimilation was mainly driven by urea and ryegrass. Lysobacter, xanthomonadaceae, and longimicrobia could be biomarker species in the PBCN group. Soil bacterial network analysis showed that biochar and urea application decreased the network complexity and robustness, while ryegrass behaved inversely. Lastly, soil metabolomic analysis revealed that root soil metabolites were greatly affected by urea-addition during phytoremediation, and co-application of biochar and urea could activate the putative metabolism pathway of petroleum hydrocarbons in root soil (e.g., naphthalene and anthracene degradation, and pyruvate metabolism). In summary, this study confirmed the enhancement of biochar and urea application in the phytoremediation of petroleum-contaminated soil and explored the internal mechanism of the interactive effect, which can potentially improve the development of eco-friendly and cost-effective in-situ bioremediation technology for petroleum-contaminated soils.

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.

Effect of the bacterial community assembly process on the microbial remediation of petroleum hydrocarbon-contaminated soil

Introduction

The accumulation of petroleum hydrocarbons (PHs) in the soil can reduce soil porosity, hinder plant growth, and have a serious negative impact on soil ecology. Previously, we developed PH-degrading bacteria and discovered that the interaction between microorganisms may be more important in the degradation of PHs than the ability of exogenous-degrading bacteria. Nevertheless, the role of microbial ecological processes in the remediation process is frequently overlooked.

Methods

This study established six different surfactant-enhanced microbial remediation treatments on PH-contaminated soil using a pot experiment. After 30 days, the PHs removal rate was calculated; the bacterial community assembly process was also determined using the R language program, and the assembly process and the PHs removal rate were correlated.

Results and discussion

The rhamnolipid-enhanced Bacillus methylotrophicus remediation achieved the highest PHs removal rate, and the bacterial community assembly process was impacted by deterministic factors, whereas the bacterial community assembly process in other treatments with low removal rates was affected by stochastic factors. When compared to the stochastic assembly process and the PHs removal rate, the deterministic assembly process and the PHs removal rate were found to have a significant positive correlation, indicating that the deterministic assembly process of bacterial communities may mediate the efficient removal of PHs. Therefore, this study recommends that when using microorganisms to remediate contaminated soil, care should be taken to avoid strong soil disturbance because directional regulation of bacterial ecological functions can also contribute to efficient removal of pollutants.

Construction of the comprehensive evaluation system of waterbody pollution degree and the response of sedimentary microbial community

This study proposed and established a comprehensive evaluation system for the pollution degree of the waterbody by taking overlying water and sediment as a whole. By dividing different sampling points into three gradients according to the pollution degree, the changes in sedimentary microbes under various pollution gradients were compared. The results showed that microbial diversity, abundance and specific OTUs decreased significantly with the increase in pollution degree. Meanwhile, Firmicutes, Bacteroidota and Caldiseriota increased in the severely polluted group, while Chloroflexi and Acidobacteriota decreased. Spearman correlation analysis and co-occurrence network revealed that COD, pH in overlying water, and Mn, Fe in sediments were the most significant pollution degree evaluation indicators affecting sedimentary microorganisms, which drove the sedimentary microbial communities dominated by Proteobacteria and Firmicutes. FAPROTAX functional prediction indicated that increased pollution levels led to the weakening of functional genes related to nitrogen metabolism and sulfur metabolism and the increase of functional genes related to carbon metabolism in sediment microorganisms. This study not only provided new insights into waterbody pollution evaluation but also verified the feasibility of this evaluation method by the response of sedimentary microbial communities to different pollution degrees.

Comparison of the efficiency and microbial mechanisms of chemical- and bio-surfactants in remediation of petroleum hydrocarbon

Surfactant-enhanced remediation (SER) is one of the most effective methods for petroleum hydrocarbon-contaminated sites compared to single physical and chemical methods. However, biosurfactants are not as commonly used as chemical surfactants, and the actual remediation effects and related mechanisms remain undefined. Therefore, to comprehensively compare the remediation effects and biological mechanisms of biosurfactants and chemical surfactants, soil column leaching experiments including two biosurfactants (rhamnolipids and lipopeptide) and three commercially used chemical surfactants (Tween 80, Triton X-100, and Berol 226SA) were conducted. After seven days of leaching, rhamnolipids exhibited the highest petroleum hydrocarbon removal rate of 61.01%, which was superior to that of chemical surfactants (11.73-18.75%) in n-alkanes C10-C30. Meanwhile, rhamnolipids exhibited a great degradation advantage of n-alkanes C13-C28, which was 1.22-30.55 times that of chemical surfactants. Compared to chemical surfactants, biosurfactants significantly upregulated the soil's biological functions, including soil conductivity (80.90-155.56%), and soil enzyme activities of lipase (90.31-497.10%), dehydrogenase (325.00-655.56%), core enzyme activities of petroleum hydrocarbon degradation, and quorum sensing between species. Biosurfactants significantly changed the composition of Pseudomonas, Citrobacter, Acidobacteriota, and Enterobacter at the genus level. Meanwhile, chemical surfactants had less influence on the bacterial community and interactions between species. Moreover, the biosurfactants enhanced the microbial interactions and centrality of petroleum hydrocarbon degraders in the community based on the network. Overall, this work provides a systematic comparison and understanding of the chemical- and bio-surfactants used in bioremediation. In the future, we intend to apply biosurfactants to practical petroleum hydrocarbon-contaminated fields to observe realistic remediation effects and compare their functional mechanisms.

Response of cbbL-harboring microorganisms to precipitation changes in a naturally-restored grassland

The impact of the long-term uneven precipitation distribution model on the diversity and community composition of soil C-fixing microorganisms in arid and semiarid grasslands remains unclear. In 2015, we randomly set up five experimental plots with precipitation gradients on the natural restoration grassland of the Loess Plateau (natural precipitation, NP; ± 40% natural precipitation: decreased precipitation (DP), DP40; increased precipitation (IP), IP40; ± 80% natural precipitation: DP80; IP80). In the third and fifth years after the experimental layout (spanned two years), we explored the cbbL-genes, which are functional genes in the Calvin cycle, harboring microbial diversity and community composition under different precipitation treatments. The results showed that the increase in mean annual precipitation significantly changed the cbbL-harboring microbial alpha diversity, especially when controlling for 40% natural precipitation. The response of the dominant microbial communities to interannual increased precipitation variation shifted from Gammaproteobacteria (Bradyrhizobium) to Betaproteobacteria (Variovorax). The structural equation model showed that precipitation directly affected the cbbL-harboring microbial diversity and community composition and indirectly by affecting soil NO₃^- (mg N kg ^-1), soil organic matter, dissolved organic N content, and above- and underground biomass. In conclusion, studying how cbbL-harboring microbial diversity and community composition respond to uneven precipitation variability provides new insights into the ecological processes of C-fixing microbes in semi-arid naturally-restored grasslands dominated by the Calvin cycle.

Removal of organochlorine pesticides and metagenomic analysis by multi-stage constructed wetland treating landfill leachate

Constructed wetlands (CWs) can effectively treat landfill leachate (LL). However, there is limited research on the removal of organochlorine pesticides (OCPs) refractory organics during LL treatment in CWs. In this study, multi-stage subsurface flow CWs was used to treat LL, and the removal fate of hexachlorocyclohexane (HCH) and dichlorodiphenyltrichloroethane (DDT) in CWs was investigated. The structural differences between plant roots and substrate microbial communities were compared and the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway of organic matter was analyzed based on metagenomic analysis. The results showed that substrate adsorption (50.55%-72.74%) and microbial degradation (20.38%-27.89%) were the main ways to remove OCPs. The Proteobacteria occupied a dominant position in the CWs system, among which Betaproteobacteria (34.37%-35.90%) were contained in the substrate, and Alphaproteobacteria (21.19%-23.84%) was a more dominant microorganism in plant roots. Formaldehyde assimilation and serine pathway were the main pathways of methane metabolism. This study provides a reference for the removal mechanism of OCPs to promote the application of CWs technology in LL treatment.

Effects of Temperature and Nitrogen Application on Carbon and Nitrogen Accumulation and Bacterial Community Composition in Apple Rhizosphere Soil

Malus sieversii grows on the slopes of the Tianshan Mountains in Xinjiang where the difference in daily temperature is significant. In recent years, the rhizosphere soil health of Malus sieversii has been severely impacted by anthropogenic disturbance and pathogenic infestation. The soil nutrient content and soil microorganism diversity are the main components of soil health. Low temperature has negative effects on soil bacterial community structure by inhibiting the accumulation of carbon and nitrogen. However, the effects of temperature and nitrogen application on soil carbon and nitrogen accumulation and the bacterial community composition in the rhizosphere soil of Malus sieversii are unclear. We set two temperature levels, i.e., low temperature (L) and room temperature (R), combined with no nitrogen (N0) and nitrogen application (N1) to explore the response of plant carbon and nitrogen uptake, rhizosphere soil carbon and nitrogen accumulation and bacterial community composition to temperature and nitrogen fertilization. At the same temperature level, plant 13C abundance (P-Atom13C), plant 15N absolute abundance (P-Con15N), soil 15N abundance (S-Atom15N) and soil urease, protease and glutaminase activities were significantly higher under nitrogen application compared with the no-nitrogen application treatment. The bacterial community diversity and richness indices of the apple rhizosphere soil in the N1 treatment were higher than those in the N0 treatment. The relative abundances of Actinobacteria, Rhodopseudomonas, and Bradyrhizobium were higher in the LN1 treatment than in the LN0 treatment. Redundancy analysis (RDA) showed that plant 13C absolute abundance (P-Con13C) and plant 15N absolute abundance (P-Con15N) were the main factors affecting the soil bacterial community composition. In summary, Nitrogen application can alleviate the effects of low temperature stress on the soil bacterial community and is of benefit for the uptakes of carbon and nitrogen in Malus sieversii plants.