Metagenome Analysis of a Hydrocarbon-Degrading Bacterial Consortium Reveals the Specific Roles of BTEX Biodegraders

Taxonomic identification, phenol biodegradation and soil remediation of the strain Rhodococcus sacchari sp. nov. Z13T

Phenols are highly toxic chemicals that are extensively used in industry and produce large amounts of emissions. Notably, phenols released into the soil are highly persistent, causing long-term harm to human health and the environment. In this study, a gram-positive, aerobic, and rod-shaped bacterial strain, Z13T, with efficient phenol degradation ability, was isolated from the soil of sugarcane fields. Based on the physiological properties and genomic features, strain Z13T is considered as a novel species of the genus Rhodococcus, for which the name Rhodococcus sacchari sp. nov. is proposed. The type strain is Z13T (= CCTCC AB 2022327T = JCM 35797T). This strain can use phenol as its sole carbon source. Z13T was able to completely degrade 1200 mg/L phenol within 20 h; the maximum specific growth rate was μmax = 0.93174 h-1, and the maximum specific degradation rate was qmax = 0.47405 h-1. Based on whole-genome sequencing and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, strain Z13T contains a series of phenol degradation genes, including dmpP, CatA, dmpB, pcaG, and pcaH, and can metabolize aromatic compounds. Moreover, the potential of strain Z13T for soil remediation was investigated by introducing Z13T into simulated phenol-contaminated soil, and the soil microbial diversity was analyzed. The results showed that 100% of the phenol in the soil was removed within 7.5 d. Furthermore, microbial diversity analysis revealed an increase in the relative species richness of Oceanobacillus, Chungangia, and Bacillus.

Recruitment and Aggregation Capacity of Tea Trees to Rhizosphere Soil Characteristic Bacteria Affects the Quality of Tea Leaves

There are obvious differences in quality between different varieties of the same plant, and it is not clear whether they can be effectively distinguished from each other from a bacterial point of view. In this study, 44 tea tree varieties (Camellia sinensis) were used to analyze the rhizosphere soil bacterial community using high-throughput sequencing technology, and five types of machine deep learning were used for modeling to obtain characteristic microorganisms that can effectively differentiate different varieties, and validation was performed. The relationship between characteristic microorganisms, soil nutrient transformation, and tea quality formation was further analyzed. It was found that 44 tea tree varieties were classified into two groups (group A and group B) and the characteristic bacteria that distinguished them came from 23 genera. Secondly, the content of rhizosphere soil available nutrients (available nitrogen, available phosphorus, and available potassium) and tea quality indexes (tea polyphenols, theanine, and caffeine) was significantly higher in group A than in group B. The classification result based on both was consistent with the above bacteria. This study provides a new insight and research methodology into the main reasons for the formation of quality differences among different varieties of the same plant.

Risk assessment of Benzene, Toluene, Ethyl benzene, and Xylene (BTEX) in the atmospheric air around the world: A review

Volatile organic compounds, such as BTEX, have been the subject of numerous debates due to their detrimental effects on the environment and human health. Human beings have had a significant role in the emergence of this situation. Even though US EPA, WHO, and other health-related organizations have set standard limits as unhazardous levels, it has been observed that within or even below these limits, constant exposure to these toxic chemicals results in negative consequences as well. According to these facts, various studies have been carried out all over the world - 160 of which are collected within this review article, so that experts and governors may come up with effective solutions to manage and control these toxic chemicals. The outcome of this study will serve the society to evaluate and handle the risks of being exposed to BTEX. In this review article, the attempt was to collect the most accessible studies relevant to risk assessment of BTEX in the atmosphere, and for the article to contain least bias, it was reviewed and re-evaluated by all authors, who are from different institutions and backgrounds, so that the insights of the article remain unbiased. There may be some limitations to consistency or precision in some points due to the original sources, however the attempt was to minimize them as much as possible.

Assessing the impacts of oil contamination on microbial communities in a Niger Delta soil

Oil spills are a global challenge, contaminating the environment with organics and metals known to elicit toxic effects. Ecosystems within Nigeria's Niger Delta have suffered from prolonged severe spills for many decades but the level of impact on the soil microbial community structure and the potential for contaminant bioremediation remains unclear. Here, we assessed the extent/impact of an oil spill in this area 6 months after the accident on both the soil microbial community/diversity and the distribution of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHDGNα) genes, responsible for encoding enzymes involved in the degradation of PAHs, across the impacted area. Analyses confirmed the presence of oil contamination, including metals such as Cr and Ni, across the whole impacted area and at depth. The contamination impacted on the microbial community composition, resulting in a lower diversity in all contaminated soils. Gamma-, Delta-, Alpha- proteobacteria and Acidobacteriia dominated 16S rRNA gene sequences across the contaminated area, while Ktedonobacteria dominated the non-contaminated soils. The PAH-RHDαGN genes were only detected in the contaminated area, highlighting a clear relationship with the oil contamination/hydrocarbon metabolism. Correlation analysis indicated significant positive relationships between the oil contaminants (organics, Cr and Ni), PAH-RHDαGN gene, and the presence of bacteria/archaea such as Anaerolinea, Spirochaetia Bacteroidia Thermoplasmata, Methanomicrobia, and Methanobacteria indicating that the oil contamination not only impacted the microbial community/diversity present, but that the microbes across the impacted area and at depth were potentially playing an important role in degrading the oil contamination present. These findings provide new insights on the level of oil contamination remaining 6 months after an oil spill, its impacts on indigenous soil microbial communities and their potential for in situ bioremediation within a Niger Delta's ecosystem. It highlights the strength of using a cross-disciplinary approach to assess the extent of oil pollution in a single study.

Microbial community response to hydrocarbon exposure in iron oxide mats: an environmental study

Hydrocarbon pollution is a widespread issue in both groundwater and surface-water systems; however, research on remediation at the interface of these two systems is limited. This interface is the oxic-anoxic boundary, where hydrocarbon pollutant from contaminated groundwaters flows into surface waters and iron mats are formed by microaerophilic iron-oxidizing bacteria. Iron mats are highly chemically adsorptive and host a diverse community of microbes. To elucidate the effect of hydrocarbon exposure on iron mat geochemistry and microbial community structure and function, we sampled iron mats both upstream and downstream from a leaking underground storage tank. Hydrocarbon-exposed iron mats had significantly higher concentrations of oxidized iron and significantly lower dissolved organic carbon and total dissolved phosphate than unexposed iron mats. A strong negative correlation between dissolved phosphate and benzene was observed in the hydrocarbon-exposed iron mats and water samples. There were positive correlations between iron and other hydrocarbons with benzene in the hydrocarbon-exposed iron mats, which was unique from water samples. The hydrocarbon-exposed iron mats represented two types, flocculent and seep, which had significantly different concentrations of iron, hydrocarbons, and phosphate, indicating that iron mat is also an important context in studies of freshwater mats. Using constrained ordination, we found the best predictors for community structure to be dissolved oxygen, pH, and benzene. Alpha diversity and evenness were significantly lower in hydrocarbon-exposed iron mats than unexposed mats. Using 16S rDNA amplicon sequences, we found evidence of three putative nitrate-reducing iron-oxidizing taxa in microaerophile-dominated iron mats (Azospira, Paracoccus, and Thermomonas). 16S rDNA amplicons also indicated the presence of taxa that are associated with hydrocarbon degradation. Benzene remediation-associated genes were found using metagenomic analysis both in exposed and unexposed iron mats. Furthermore, the results indicated that season (summer vs. spring) exacerbates the negative effect of hydrocarbon exposure on community diversity and evenness and led to the increased abundance of numerous OTUs. This study represents the first of its kind to attempt to understand how contaminant exposure, specifically hydrocarbons, influences the geochemistry and microbial community of freshwater iron mats and further develops our understanding of hydrocarbon remediation at the land-water interface.

The remediation of polycyclic aromatic hydrocarbon contaminated soil by immobilized microorganisms using distiller's grains

Polycyclic aromatic hydrocarbons are a persistent organic pollutant, and their biodegradation in the soil is often limited due to the limited degradation ability of indigenous bacteria and the low activity of exogenous PAH degrading bacteria. Immobilized microbial technology can protect microorganisms from the impact of harsh environments, and distiller's grains have the potential as carriers for microbial immobilization. This study aims to use distiller's grains as a microbial carrier, investigate the feasibility of immobilized microorganisms using distiller's grains for remediation of PAH contaminated soil; explore the relationship between soil nutrient content, consumption, and PAH degradation rate; and reveal the mechanism of bioremediation from the perspective of soil enzyme activity and microbial community composition. The results showed that after 72 days of remediation, the removal rates of phenanthrene and pyrene in the treatment of immobilized microorganisms in distiller grains reached 91.78% and 58.59%, respectively. Distiller grains can serve as a carrier for microorganisms, providing them with shelter and nutrients to enhance their chance of survival. Additionally, they can regulate the composition of soil particles and improve aeration, thereby increasing the efficiency of PAH degradation in soil.

Groundwater-level fluctuation effects on petroleum hydrocarbons in vadose zones and their potential risks: Laboratory studies

Despite the role of the vadose zone protecting groundwater from contamination, the non-stationarity in this zone makes it difficult to predict the behavior of petroleum hydrocarbons (PH) therein. In laboratory soil columns with sandy and sandy loam soils, we simulated a vadose zone subjected to repeated groundwater-level fluctuation (GLF) to evaluate the behavior of PH under hydrodynamic conditions. The GLF vertically redistributed the PH, the extent of which was pronounced in the sandy soil with a high initial concentration due to the enhanced transport of the immiscible PH through the larger pores. The frequency of GLF did not show a substantial effect on the extent of PH redistribution but largely affected their attenuation. The greater GLF hindered PH volatilization by maintaining a high degree of water saturation, while the subsequent development of a local anaerobic regime inhibited biodegradation, which was more apparent in the sandy loam. Finally, a specific potential risk index was introduced to quantitatively compare the potential risk of PH contamination in different vadose zones exposed to GLF. Overall, the sandy soil contaminated with the higher total PH (TPH) concentration showed markedly higher potential risk indices (i.e., 18.4-29.0%), while the ones comprised of the sandy loam showed 0.6-4.9%, which increased under the greater number of GLF cycles.

Bioremediation of Automotive Residual Oil-Contaminated Soils by Biostimulation with Enzymes, Surfactant, and Vermicompost

Contamination of soils by automotive residual oil represents a global environmental problem. Bioremediation is the technology most suitable to remove this contaminant from the medium. Therefore, this work aimed to evaluate the effectiveness of bioremediation of automotive residual oil-contaminated soils by biostimulation with enzymes, surfactant, and vermicompost. The bioremediation efficiency was examined using a factorial design of 24 to determine the effect of the time, pH and temperature conditions, biostimulation with enzyme-vermicompost, and biostimulation with enzyme-surfactant. Enzymes obtained from Ricinus communis L. seeds, commercial vermicompost, and Triton X-100 were used. Results showed that the highest removal efficiency (99.9%) was achieved at 49 days, with a pH of 4.5, temperature of 37 °C, and using biostimulation with enzyme-vermicompost (3% w/v-5% w/w). The addition of surfactant was not significant in increasing the removal efficiency. Therefore, the results provide adequate conditions to bioremediate automotive residual oil-contaminated soils by biostimulation using enzymes supported with vermicompost.

Meta-omics integration approach reveals the effect of soil native microbiome diversity in the performance of inoculant Azospirillum brasilense

Plant growth promoting bacteria (PGPB) have been used as integrative inputs to minimize the use of chemical fertilizers. However, a holistic comprehension about PGPB-plant-microbiome interactions is still incipient. Furthermore, the interaction among PGPB and the holobiont (host-microbiome association) represent a new frontier to plant breeding programs. We aimed to characterize maize bulk soil and rhizosphere microbiomes in irradiated soil (IS) and a native soil (NS) microbial community gradient (dilution-to-extinction) with Azospirillum brasilense Ab-V5, a PGPB commercial inoculant. Our hypothesis was that plant growth promotion efficiency is a result of PGPB niche occupation and persistence according to the holobiont conditions. The effects of Ab-V5 and NS microbial communities were evaluated in microcosms by a combined approach of microbiomics (species-specific qPCR, 16S rRNA metataxonomics and metagenomics) and plant phenomics (conventional and high-throughput methods). Our results revealed a weak maize growth promoting effect of Ab-V5 inoculation in undiluted NS, contrasting the positive effects of NS dilutions 10^-3, 10^-6, 10^-9 and IS with Ab-V5. Alpha diversity in NS + Ab-V5 soil samples was higher than in all other treatments in a time course of 25 days after sowing (DAS). At 15 DAS, alpha diversity indexes were different between NS and IS, but similar in all NS dilutions in rhizospheric samples. These differences were not persistent at 25 DAS, demonstrating a stabilization process in the rhizobiomes. In NS 10^-3 +Ab-V5 and NS 10^-6 Ab-V5, Ab-V5 persisted in the maize rhizosphere until 15 DAS in higher abundances compared to NS. In NS + Ab-V5, abundance of six taxa were positively correlated with response to (a)biotic stresses in plant-soil interface. Genes involved in bacterial metabolism of riboses and amino acids, and cresol degradation were abundant on NS 10^-3 + Ab-V5, indicating that these pathways can contribute to plant growth promotion and might be a result of Ab-V5 performance as a microbial recruiter of beneficial functions to the plant. Our results demonstrated the effects of holobiont on Ab-V5 performance. The meta-omics integration supported by plant phenomics opens new perspectives to better understanding of inoculants-holobiont interaction and for developing better strategies for optimization in the use of microbial products.

Bacterial community dynamics and associated genes in hydrocarbon contaminated soil during bioremediation using brewery spent grain

Brewery spent grain (BSG) has previously been exploited in bioremediation. However, detailed knowledge of the associated bacterial community dynamics and changes in relevant metabolites and genes over time is limited. This study investigated the bioremediation of diesel contaminated soil amended with BSG. We observed complete degradation of three total petroleum hydrocarbon (TPH C10-C28) fractions in amended treatments as compared to one fraction in the unamended, natural attenuation treatments. The biodegradation rate constant (k) was higher in amended treatments (0.1021k) than in unamended (0.059k), and bacterial colony forming units increased significantly in amended treatments. The degradation compounds observed fitted into the elucidated diesel degradation pathways and quantitative PCR results showed that the gene copy numbers of all three associated degradation genes, alkB, catA and xylE, were significantly higher in amended treatments. High-throughput sequencing of 16S rRNA gene amplicons showed that amendment with BSG enriched autochthonous hydrocarbon degraders. Also, community shifts of the genera Acinetobacter and Pseudomonas correlated with the abundance of catabolic genes and degradation compounds observed. This study showed that these two genera are present in BSG and thus may be associated with the enhanced biodegradation observed in amended treatments. The results suggest that the combined evaluation of TPH, microbiological, metabolite and genetic analysis provides a useful holistic approach to assessing bioremediation.

Assessment of the Microbial Communities in Soil Contaminated with Petroleum Using Next-Generation Sequencing Tools

Microbial communities are known to play a principal role in petroleum degradation. This study tries to determine the composition of bacteria in selected crude oil-contaminated soil from Tabasco and Tamaulipas states, Mexico. We determined the microbial populations living under these conditions. We evaluated the structure and diversity of bacterial communities in the contaminated soil samples. The most abundant phylum is proteobacteria. Next Generation Sequencing (NGS) analysis of the sampled soils from both states revealed that this phylum has the most relative abundance among the identified bacteria phyla. The heatmap represented the relative percentage of each genus within each sample and clustered the four samples into two groups. Moreover, this allowed us to identify many genera in alkaline soil from Tamaulipas, such as Skermanella sp., Azospirillum sp. and Unclassified species from the Rhodospirillaceae family in higher abundance. Meanwhile, in acidic soil from Tabasco, we identified Thalassospira, Unclassified members of the Sphingomonadaceae family and Unclassified members of the Alphaproteobacteria class with higher abundance. Alpha diversity analysis showed a low diversity (Shannon and Simpson index); Chao observed species in both Regions. These results suggest that the bacteria identified in these genera may possess the ability to degrade petroleum, and further studies in the future should elucidate their role in petroleum degradation.

Bioremediation of petroleum hydrocarbon contaminated soil by microorganisms immobilized on sludge modified by non-ionic surfactant

The immobilization of microorganisms on high-quality and inexpensive carriers to remediate oil-contaminated soil is an effective strategy for contaminated soil remediation. Due to the abundance in nutrients, large specific surface area, and fewer pathogens, the composting sludge is considered a high-quality immobilized material. Herein, two non-ionic surfactants, TW-80 and sophorolipid, were used to modify composted sludge. High-efficiency petroleum hydrocarbon-degrading bacteria groups selected in the laboratory were fixed on the modified composting sludge under optimal conditions. The immobilized material was placed in the soil contaminated by petroleum hydrocarbons at an additive amount of 2wt/%, and a simulated remediation experiment was performed for 90 days. Both soil properties and microbial structure were characterized. Surfactant-modified compost sludge enhances the adsorption capacity to petroleum hydrocarbon. The immobilized microorganisms in the modified compost sludge showed a good effect on the remediation of soil contaminated by petroleum hydrocarbons. In addition, immobilized materials also increase the diversity of the microbial community structure in the soil. High-efficiency petroleum hydrocarbon-degrading bacteria immobilized on surfactant-modified compost can effectively promote the degradation of petroleum hydrocarbons in the soil and increase the abundance of microorganisms in the soil. It shows the feasibility of eco-friendly remediation of hydrocarbon-contaminated soil.

Metagenome analyses of microbial population in geotextile fabrics used in permeable reactor barriers for toluene biodegradation

Toluene is one of the hydrocarbons that contaminate soil and groundwater, and has a high cost to remediate, which makes it an environmental pollutant of concern. This study aimed to find bacterial distribution from nonwoven geotextile (GT) fabric specimens in a pilot-scale permeable reactive barrier (PRB). Upon 167 days of incubation with the addition of toluene, the microbial community on the GT surfaces (n = 12) was investigated by the 16S rRNA metagenome sequencing approach. According to taxonomic classification, the Proteobacteria phylum dominated the metagenomes of all the geotextile samples (80-90%). Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database search of the toluene degradation mechanism revealed the susceptible toluene-degrading species. For the toluene-to-benzoate degradation, the Cupriavidus genus, particularly C. gilardii, C. metallidurans, and C. taiwanensis, are likely to be functional. In addition to these species, the Novosphingobium genus was abundantly localized in the GTs, in particular Novosphingobium sp. ABRDHK2. The results suggested the biodegradation potential of these species in toluene remediation. Overall, this work sheds light on the variety of microorganisms found in the geotextile fabrics used in PRBs and the species involved in the biodegradation of toluene from several sources, including soil, sediment, and groundwater.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03460-y.

Biostimulation of Petroleum-Contaminated Soil Using Organic and Inorganic Amendments

The most common approaches for the in-situ bioremediation of contaminated sites worldwide are bioaugmentation and biostimulation. Biostimulation has often proved more effective for chronically contaminated sites. This study examined the effectiveness of optimized water hyacinth compost in comparison with other organic and inorganic amendments for the remediation of crude oil-polluted soils. Water hyacinth was found to be rich in nutrients necessary to stimulate microbial growth and activity. An organic geochemical analysis revealed that all amendments in this study increased total petroleum hydrocarbon (TPH) biodegradation by ≥75% within 56 days, with the greatest biodegradation (93%) occurring in sterilized soil inoculated with optimized water hyacinth compost. This was followed by polluted soil amended with a combination of spent mushroom and water hyacinth composts (SMC + WH), which recorded a TPH biodegradation of 89%. Soil amendment using the inorganic fertilizer NPK (20:10:10) resulted in 86% TPH biodegradation. On the other hand, control samples (natural attenuation) recorded only 4% degradation. A molecular analysis of residual polycyclic aromatic hydrocarbons (PAHs) showed that the 16 PAHs designated by the US EPA as priority pollutants were either completely or highly degraded in the combined treatment (SMC + WH), indicating the potential of this amendment for the environmental remediation of soils contaminated with recalcitrant organic pollutants.

Bioremediation of petroleum-contaminated saline soil by Acinetobacter baumannii and Talaromyces sp. and functional potential analysis using metagenomic sequencing

Microbial remediation is a potential remediation method for petroleum-contaminated soil. In order to explore the petroleum degradation mechanism by microorganisms, the oilfield soil was remedied by Acinetobacter baumannii combined with Talaromyces sp. The degradation mechanism was studied by analyzing soil microbial community and functional genes through metagenomics during the degradation process. The result showed the degradation rate of petroleum was 65.6% after 28 days. The concentration of petroleum decreased from 1220 mg/kg to 420 mg/kg. In the co-culture group, Acinetobacter baumannii became the dominant species, the annotated genes of it at the species level accounted for 7.34% while that of Talaromyces sp. accounted for only 0.34%. Meanwhile, the annotated genes of Bacillus, Halomonas, and Nitriliruptor at the genus level were up-regulated by 1.83%, 0.90%, and 0.71%, respectively. In addition, large functional genes were significantly up-regulated, including the peroxisome, P450 enzyme (CYP53, CYP116, CYP102, CYP645), and biofilm formulation, promoting the oxidation and hydroxylation, and catalyzing the epoxidation of aromatic and aliphatic hydrocarbons. Meanwhile, the degrading genes of alkanes and aromatic hydrocarbons were expressed promotionally, and degradation pathways were deduced. In conclusion, the inoculation of Acinetobacter baumannii combined with Talaromyces sp. accelerated the degradation of petroleum in oilfield soil and improved the growth of indigenous petroleum-degrading bacteria. Many functional genes related to petroleum degradation were promoted significantly. These results proved the co-culture of bacteria-fungi consortium contributes to the bioremediation of petroleum-contaminated soil.

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.