Structures and diversities of bacterial communities in oil-contaminated soil at shale gas well site assessed by high-throughput sequencing

Currently, there is limited understanding of the structures and variabilities of bacterial communities in oil-contaminated soil within shale gas development. The Changning shale gas well site in Sichuan province was focused, and high-throughput sequencing was used to investigate the structures of bacterial communities and functions of bacteria in soil with different degrees of oil pollution. Furthermore, the influences of the environmental factors including pH, moisture content, organic matter, total nitrogen, total phosphorus, oil, and the biological toxicity of the soil on the structures of bacterial communities were analyzed. The results revealed that Proteobacteria and Firmicutes predominated in the oil-contaminated soil. α-Proteobacteria and γ-Proteobacteria were the main classes under the Proteobacteria phylum. Bacilli was the main class in the Firmicutes phylum. Notably, more bacteria were only found in CN-5 which was the soil near the storage pond for abandoned drilling mud, including Marinobacter, Balneola, Novispirillum, Castellaniella, and Alishewanella. These bacteria exhibited resilience to higher toxicity and demonstrated proficiency in oil degradation. The functions including carbohydrate transport and metabolism, energy metabolism, replication, recombination and repair replication, signal transduction mechanisms, and amino acid transport and metabolism responded differently to varying concentrations of oil. The disparities in bacterial genus composition across samples stemmed from a complex play of pH, moisture content, organic matter, total nitrogen, total phosphorus, oil concentration, and biological toxicity. Notably, bacterial richness correlated positively with moisture content, while bacterial diversity showed a significant positive correlation with pH. Acidobacteria exhibited a significant positive correlation with moisture content. Litorivivens and Luteimonas displayed a significant negative correlation with pH, while Rhizobium exhibited a significant negative correlation with moisture content. Pseudomonas, Proteiniphilum, and Halomonas exhibited positive correlations not only with organic matter but also with oil concentration. Total nitrogen exhibited a significant positive correlation with Taonella and Sideroxydans. On the other hand, total phosphorus showed a significant negative correlation with Sphingomonas. Furthermore, Sphingomonas, Gp6, and Ramlibacter displayed significant negative correlations with biological toxicity. The differential functions exhibited no significant correlation with environmental factors but displayed a significant positive correlation with the Proteobacteria phylum. Aridibacter demonstrated a significant positive correlation with cell motility and cellular processes and signaling. Conversely, Pseudomonas, Proteiniphilum, and Halomonas were negatively correlated with differential functions, particularly in amino acid metabolism, carbohydrate metabolism, and membrane transport. Compared with previous research, more factors were considered in this research when studying structural changes in bacterial communities, such as physicochemical properties and biological toxicity of soil. In addition, the correlations of differential functions of communities with environmental factors, bacterial phyla, and genera were investigated.

Surfactant-enhanced bioremediation of petroleum-contaminated soil and microbial community response: A field study

Surfactant-enhanced bioremediation (SEBR) is frequently employed to clean up soil polluted with petroleum hydrocarbons, but few studies have focused on how surfactants affect microbial communities and different fractions of petroleum hydrocarbons, particularly in the field. Here, the surfactants sodium dodecyl benzene sulfonate (SDBS), alpha olefin sulfonate (AOS), Triton X-100 (TX-100), Tween80, and rhamnolipid were combined with the oil-degrading bacterium Pseudomonas sp. SB to remediate oil-contaminated soil in the laboratory. AOS gave the highest removal efficiency (65.1%) of total petroleum hydrocarbons (TPHs). Therefore, AOS was used in a field experiment with Pseudomonas sp. SB and the removal efficiency of TPHs and long-chain hydrocarbons C21-C40 reached 57.4 and 53.0%, respectively, significantly higher than the other treatments. During bioremediation the addition of Pseudomonas sp. SB significantly stimulated the growth of bacterial genera such as Alcanivorax, Luteimonas, Parvibaculum, Stenotrophomonas, and Pseudomonas and AOS further stimulated the growth of Sphingobacterium, Pseudomonas and Alcanivorax. This study validates the feasibility of surfactant-enhanced bioremediation in the field and partly reveals the mechanism of surfactant-enhanced bioremediation from the perspective of changes in different fractions of petroleum and microbial community dynamics.

Level of oxidative stress for the land snail Cepaea nemoralis from aged and bioremediated soil contaminated with petroleum products

Here, we investigated whether the widely distributed snail Cepaea nemoralis could be used as a suitable sentinel animal for assessing the effects of soil contaminants-petroleum oil derivatives-after years of soil ageing and treatment with a bacterial formulation. Oxidative stress was assessed in the foot and hepatopancreas of C. nemoralis L. exposed to soil contaminated with unleaded petrol, spent engine oil or diesel oil and bioremediated with a bacterial formulation (soil was used 2 years after contamination and bioremediation process). We measured total antioxidant capacity, catalase and glutathione transferase activity and concentrations of superoxide anions, hydrogen peroxide and protein carbonyls in the foot and hepatopancreas of snails after 2 and 4 weeks of treatment. The studied antioxidant responses appeared largely to be tissue and remediation process specific, while the concentrations of superoxide anions, hydrogen peroxide and protein carbonyls depended on time of exposure, tissue type and the type of contaminants, but mostly not on the remediation process. Generally, changes in the concentrations of superoxide anions, hydrogen peroxide and protein carbonyls in the hepatopancreas of snails seemed to be a suitable measure to assess the risk of animals exposed to soil contaminated with petroleum substances and used after many years of ageing and treatment with a microbial formulation.

Hydrocarbons removal from real marine sediments: Analysis of degradation pathways and microbial community development during bioslurry treatment

In this study, real marine sediments polluted by petroleum compounds were treated by means of a bioslurry pilot scale reactor. The treatment performance was evaluated by measuring the removal of total petroleum hydrocarbon (TPH), coupled to further analyses required to understand the mechanisms involved in the biodegradation process. The maximum TPH-removal efficiency reached 86 % at the end of experiments. Moreover, high throughput 16S RNA gene sequencing was used to describe the microbiome composition in sediment prior to, and after, bioslurry treatment, in order to identify the taxa mostly entailed in the TPH removal process. The raw sediment was mostly colonized by members of Sulfurimonas genus; after bioslurry treatment, it was noticed a shift in the microbial community composition, with Proteobacteria phylum dominating the remediation environment (high increase in terms of growth for Hydrogenophaga and Sphingorhabdus genera) along with the Phaeodactylibacter genus (Bacteroidetes). Furthermore, the assessment of gaseous emissions from the system allowed to quantify the volatile hydrocarbon component and, consequently, to obtain a more accurate evaluation of TPH-removal pathway by the bioslurry system. Finally, phytotoxicity tests on sediment samples highlighted an increase of the treated sample quality status compared to the untreated one.

Variation of bacterial community and alkane monooxygenase gene abundance in diesel n-alkane contaminated subsurface environment under seasonal water table fluctuation

n-Alkanes, the main component of diesel fuel, are common light non-aqueous phase liquids (LNAPLs) that threaten ecological security. The subsurface from vadose zone, through fluctuating zone, to saturated zone, is a critical multi-interface earth layer which significantly affects the biodegradation processes of n-alkanes. A pilot-scale diesel contaminated aquifer column experiment has been undertaken to investigate the variations of bacterial community and alkane monooxygenase (alkB) gene abundance in these zones due to water-table fluctuations. The n-alkanes formed a layer immediately above the water table, and when this was raised, they were carried upwards through the fluctuating zone into the vadose zone. Water content and n-alkanes component C10-C12 are main factors influencing bacterial community variation in the vadose zone, while C10-C12 is a key driving factor shaping bacterial community in the fluctuating zone. The most abundant bacterial phyla at all three zones were Proteobacteria, Firmicutes and Actinobacteria, but moisture-niche selection determined their relative abundance. The intermittent wetting cycle resulted in higher abundance of Proteobacteria, and lower abundance of Actinobacteria in the vadose and fluctuating zones in comparison to the control column with a static water-table. The abundances of the alkB gene variants were relatively uniform in different zones, probably because the bacterial populations harboring alkB gene are habituated to biogenic n-alkanes rather than responding to diesel fuel contamination. The variation in the bacterial populations with height due to moisture-niche selection had very little effect on the alkB gene abundance, possibly because numerous species in both phyla (Proteobacteria and Actinobacteria) carry an alkB gene variant. Nevertheless, the drop in the water table caused a short-term spike in alkB gene abundance in the saturated zone, which is most likely associated with transport of solutes or colloids from the fluctuating zone to bacteria species in the saturated zone, so a fluctuating water table could potentially increase n-alkane biodegradation function.

The car tank lid bacteriome: a reservoir of bacteria with potential in bioremediation of fuel

Bioprospecting of microorganisms suitable for bioremediation of fuel or oil spills is often carried out in contaminated environments such as gas stations or polluted coastal areas. Using next-generation sequencing (NGS) we analyzed the microbiota thriving below the lids of the fuel deposits of diesel and gasoline cars. The microbiome colonizing the tank lids differed from the diversity found in other hydrocarbon-polluted environments, with Proteobacteria being the dominant phylum and without clear differences between gasoline or diesel-fueled vehicles. We observed differential growth when samples were inoculated in cultures with gasoline or diesel as the main carbon source, as well as an increase in the relative abundance of the genus Pseudomonas in diesel. A collection of culturable strains was established, mostly Pseudomonas, Stenotrophomonas, Staphylococcus, and Bacillus genera. Strains belonging to Bacillus, Pseudomonas, Achromobacter, and Isoptericola genera showed a clear diesel degradation pattern when analyzed by GC-MS, suggesting their potential use for bioremediation and a possible new species of Isoptericola was further characterized as hydrocarbon degrader.

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.

Preliminary insights about the treatment of contaminated marine sediments by means of bioslurry reactor: Process evaluation and microbiological characterization

Contaminated marine sediments represent a critical threat towards human health and ecosystems, since they constitute a potential reservoir of toxic compounds release. In the present study, a bioslurry reactor was studied for the treatment of real marine sediments contaminated by petroleum hydrocarbons. The experimental campaign was divided in two periods: in the first period, microcosm trials were carried out to achieve useful indicators for biological hydrocarbon removal from sediments. The microcosm trials highlighted that the inoculum of halotolerant allochthonous bacteria provided the highest performance followed by autochthonous biomass. Based on the achieved results, in the second experimental period a bioslurry reactor was started up, based on a semisolid stirred tank reactor (STR) operated in batch mode. The process performances have been evaluated in terms of total petroleum hydrocarbon (TPH) removal, coupled with the characterization of microbial community through a Next Generation Sequencing (NGS) and phytotoxicity tests through the Germination Index (GI) with Lepidium Sativum seeds. The achieved results showed good hydrocarbons removal, equal to 40%, with a maximum removal rate of 220 mg_TPH kg^-1 d^-1, but highlighting that high contaminant concentrations might affect negatively the overall removal performance. In general, the observed results were encouraging towards the feasibility of biological treatment of marine sediments contaminated by hydrocarbons. The microbiological analysis allowed the identification of taxa most involved in the degradation of TPH, highlighting after the treatment a shift in the microbial community from that of the raw sediment.

Hydrocarbon biodegradation and transcriptome responses of cellulase, peroxidase, and laccase encoding genes inhabiting rhizospheric fungal isolates

By using the indigenous micro-organisms of the polluted environment to be treated, bioremediation can be a successful strategy. PCR and RT-PCR molecular techniques were applied to examine the evolution of fungal isolates through putative genes f ligninolytic enzymes like lignin peroxidase (LiP), laccase (LaC), manganese peroxidase (MnP), and cellulase (Cx) as a response to polluting of the environment by hydrocarbons. In this study, isolation of rhizospheric fungal isolates, molecular identification, crude oil tolerance, and enzyme excretions were demonstrated. From the date palm rhizosphere, 3 fungal isolates were isolated and characterized morphologically and molecularly by ITS ribosomal RNA (rRNA) sequencing. The isolates were identified as Aspergillus flavus AF15, Trichoderma harzianum TH07, and Fusarium solani FS12 through using the BLAST tool in NCBI. All fungal isolates showed high tolerance to crude oil and survived with various responses at the highest concentration (20%). Aspergillus flavus AF15 and Trichoderma harzianum TH07 demonstrated promising oil-degrading tolerance ability based on the dose inhibition response percentage (DIRP) of the fungal isolates. A. flavus had a powerful capacity to production Cx, LaC, LiP and MnP with a range from 83.7 to 96.3 mL. Molecularly, nine genes of the ligninolytic enzymes, cbh (cbhI.1, cbhI.1, cbhII) lcc, lig (1, 2, 4 and 6) and mnp were tested for presence and expression (by PCR and RT-PCR, respectively). PCR showed that all isolates contained all the nine genes examined, regardless of capacity to enzymes production profiles, so the presence responses of nine genes did not correlate with enzymes-production ability. Gene expression analysis shows a more diverse pattern for tested isolates for example, Aspergillus flavus AF15 had over-expression of lig and mnp genes, Fusarium solani FS12 have a weak signal with lcc gene while, Trichoderma harzianum TH07 showed moderate expression of mnp and lcc genes. The power of the transcription of the gene leads to increased enzyme secretion by fungal isolates. Fungi are important microorganisms in the clean-up of petroleum pollution. They have bioremediation highly potency that is related to their diverse production of these catalytic enzymes.

Specific enrichment of hydrocarbonclastic bacteria from diesel-amended soil on biochar particles

Biochar has been proposed as a suitable biostimulant for the remediation of hydrocarbon contamination, and also has the potential to act as a carrier for hydrocarbonoclastic microorganisms which could bioaugment endogenous microbial communities. However, the evidence regarding the biostimulatory effects of biochars on hydrocarbon bioremediation is somewhat equivocal, possibly due to variability of the physicochemical properties of biochar and soil across studies. Here, we use standard biochars with defined properties produced from softwood pellets (SWP) and rice husk (RH) at pyrolysis temperatures of 550 °C or 700 °C to test the effects of biochar amendment on microbial community composition and hydrocarbon degradation in soil microcosms contaminated with diesel oil. Combining this approach for the first time with specific analysis of microbial community composition using amplicon sequence variants (ASVs), we find that oil contamination causes extreme short-term loss of soil microbial diversity, and highly-specific selection of a limited set of genera defined by 13 ASVs. Biochar ameliorates the short-term loss of diversity, and in the longer term (9 weeks), changes community composition in a type-specific manner. The majority of the 13 selected ASVs are further enriched on biochar particles, although SWP biochars perform better than RH biochar in enrichment of putative hydrocarbonoclastic Aquabacterium spp. However, complete degradation of normal (n) alkanes from the aliphatic hydrocarbon fraction is prevented in the presence of biochar amendment, possibly due to their adsorption onto the char surface. Furthermore, we show that putative hydrocarbon degraders released from diesel-amended soil can subsequently be enriched to high levels on SWP biochar particles in growth medium supplemented with diesel oil as the sole carbon source; these include selected ASVs representing the genera Rhodococcus, Aquabacterium, and Cavicella. This work suggests that use of biochar pre-enriched with endogenous, conditionally-rare hydrocarbon degrading bacteria is a promising strategy for bioaugmentation of diesel-contaminated soils.

Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures

The aim of the present study was to reveal how different microbial communities evolve in diesel fuel/crude oil-contaminated environments under aerobic and microaerobic conditions. To investigate this question, aerobic and microaerobic bacterial enrichments amended with a diesel fuel/crude oil mixture were established and analysed. The representative aerobic enrichment community was dominated by Gammaproteobacteria (64.5%) with high an abundance of Betaproteobacteriales (36.5%), followed by Alphaproteobacteria (8.7%), Actinobacteria (5.6%), and Candidatus Saccharibacteria (4.5%). The most abundant alkane monooxygenase (alkB) genotypes in this enrichment could be linked to members of the genus Rhodococcus and to a novel Gammaproteobacterium, for which we generated a high-quality draft genome using genome-resolved metagenomics of the enrichment culture. Contrarily, in the microaerobic enrichment, Gammaproteobacteria (99%) overwhelmingly dominated the microbial community with a high abundance of the genera Acinetobacter (66.3%), Pseudomonas (11%) and Acidovorax (11%). Under microaerobic conditions, the vast majority of alkB gene sequences could be linked to Pseudomonas veronii. Consequently, results shed light on the fact that the excellent aliphatic hydrocarbon degrading Rhodococcus species favour clear aerobic conditions, while oxygen-limited conditions can facilitate the high abundance of Acinetobacter species in aliphatic hydrocarbon-contaminated subsurface environments.

Bioremediation of Artificial Diesel-Contaminated Soil Using Bacterial Consortium Immobilized to Plasma-Pretreated Wood Waste

Bioaugmentation is a bioremediation option based on increasing the natural in-situ microbial population that possesses the ability to degrade the contaminating pollutant. In this study, a diesel-degrading consortium was obtained from an oil-contaminated soil. The diesel-degrading consortium was grown on wood waste that was plasma-pretreated. This plasma treatment led to an increase of bacterial attachment and diesel degradation rates. On the 7th day the biofilm viability on the plasma-treated wood waste reached 0.53 ± 0.02 OD 540 nm, compared to the non-treated wood waste which was only 0.34 ± 0.02. Biofilm attached to plasma-treated and untreated wood waste which was inoculated into artificially diesel-contaminated soil (0.15% g/g) achieved a degradation rate of 9.3 mg day-1 and 7.8 mg day-1, respectively. While, in the soil that was inoculated with planktonic bacteria, degradation was only 5.7 mg day-1. Exposing the soil sample to high temperature (50 °C) or to different soil acidity did not influence the degradation rate of the biofilm attached to the plasma-treated wood waste. The two most abundant bacterial distributions at the family level were Xanthomonadaceae and Sphingomonadaceae. To our knowledge, this is the first study that showed the advantages of biofilm attached to plasma-pretreated wood waste for diesel biodegradation in soil.

Ecological impact evaluation by constructing in situ microcosm with porous ceramic arrowhead

In recent years, bioremediation has been used as an effective technique for the cleaning of polluted sites. However, bioremediation treatment efficacy varies considerably; thus, characterization of indigenous pollutant-degrading soil microorganisms and assessment of the changes in microbial composition by pollutants are essential for designing efficient bioremediation methods. In this study, an ecological impact evaluation method that is cost-efficient and has low contamination risk was developed to assess the indigenous microbial composition. An "in situ microcosm" was constructed using a porous ceramic arrowhead. Phenol, a common environmental pollutant, was used to assess the evaluation efficacy of this method. Our data showed that phenol gradually percolated into the soil adjacent to the arrowhead and stimulated unique indigenous microorganisms (Bacillus sp., Streptomyces sp., and Cupriavidus sp.). Furthermore, the arrowhead approach enabled efficient evaluation of the ecological impact of phenol on soil microorganisms. Thus, the arrowhead method will contribute to the development of bioremediation methods.

Catabolic Fingerprinting and Diversity of Bacteria in Mollic Gleysol Contaminated with Petroleum Substances

This study focused on the determination of both catabolic and genetic fingerprinting of bacteria inhabiting soil contaminated with car fuels. A surface layer (0–20 cm) of Mollic Gleysol was used for the experiment and was contaminated with car fuels—unleaded 95-octane petrol and diesel at a dose of 15 g per 10 g of soil. The experiment lasted 42 days and was performed at 20 °C. The metabolic potential of soil bacterial communities was evaluated using the Biolog EcoPlate system. The results demonstrated that petroleum substances influenced the structure of the microbial populations and their catabolic activity. The Arthrobacter, Paenibacillus, and Pseudomonas genera were found in diesel-contaminated soil, whilst Bacillus and Microbacterium were found in petrol-contaminated soil. Rhodococcus species were identified in both variants of impurities, suggesting the widest capability of car fuel degradation by this bacterial genus. The contamination with unleaded 95-octane petrol caused rapid inhibition of the metabolic activity of soil bacteria in contrast to the diesel treatment, where high metabolic activity of bacteria was observed until the end of the incubation period. Higher toxicity of petrol in comparison with diesel car fuel was evidenced.

Development of mixed bacterial cultures DAK11 capable for degrading mixture of polycyclic aromatic hydrocarbons (PAHs)

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous and persistent pollutants having mutagenic and carcinogenic properties. Microbial metabolism is an alternative approach for removal of PAHs from polluted environment. Mixed bacterial cultures DAK11 capable for degrading mixture of PAHs was developed from long term polluted marine sediments. DAK11 was able to degrade 500 mg/L of mixture of four PAHs and their degradation efficiency was enhanced by supplementing commercially available NPK fertilizer (0.1%, w/v). Anionic surfactant SDS has enhanced the degradation of PAHs, but DAK11 growth was inhibited in presence of cationic surfactant CTAB. Heavy metals have decreased the rate of degradation, while it was completely inhibited in the presence of Zn²⁺ and CrO₄^2- (1mM). DAK11 was able to degrade PAHs in the presence of mono-aromatic hydrocarbons, lubricant oil and diesel. Lower molecular weight aromatic and aliphatic compounds were identified using GC-MS during metabolism of mixture of PHAs.

Transcriptomic responses of catalase, peroxidase and laccase encoding genes and enzymatic activities of oil spill inhabiting rhizospheric fungal strains

Fungi are well associated with the degradation of hydrocarbons by the production of different enzymes, among which catalases (CBH), laccases (LCC) and peroxidases (LiP and MnP) are of immense importance. In this study, crude oil tolerance and enzyme secretions were demonstrated by rhizospheric fungal strains. Four most abundant strains were isolated from the rhizosphere of grasses growing in aged oil spill sites and identified through morphological characterization and molecular PCR-amplification of 5.8-28S ribosomal rRNA using ITS1 and ITS4 primers. These strains were subjected to crude oil tolerance test at 0-20% concentrations. Presence and transcriptase responses of putative genes lig (1-6), mnp, cbh (1.1, 1.1 and 11), and lcc encoding lignin peroxidase, manganese peroxidase, catalase, and laccase enzymes respectively were also studied in these strains using RT-PCR. In addition, activities of secreted enzymes by each strain were studied in aliquots. The strains were identified as Aspergillus niger asemoA (KY473958), Talaromyces purpurogenus asemoF (KY488463), Trichoderma harzianum asemoJ (KY488466), and Aspergillus flavus asemoM (KY488467) through sequencing and comparing the sequences' data at NCBI BLAST search software. All the isolated strains showed tolerance to crude oil at 20% concentration, but the growth rate reduced with increasing in oil concentrations. All the isolated strains possess the tested genes and lig 1-6 gene was overexpressed in A. niger and T. harzianum while lcc and mnp genes were moderately expressed in all the four strains. Almost 145 U.mL^-1 of lignin and manganese peroxidase, 87 U.mL^-1 of catalase, and 180 U.mL^-1 of laccase enzymes were produced by these strains and it was also observed that these strain mostly produced studied enzymes in response to increasing crude oil concentrations. Considering the robust nature and diverse production of these catalytic enzymes by these strains, they can be exploited for various bioremediation technologies as well as other biotechnological applications.

Identification and Quantification of Volatile Compounds Found in Vinasses from Two Different Processes of Tequila Production

Vinasses are the main byproducts of ethanol distillation and distilled beverages worldwide and are generated in substantial volumes. Tequila vinasses (TVs) could be used as a feedstock for biohydrogen production through a dark fermentative (DF) process due to their high content of organic matter. However, TV components have not been previously assayed in order to evaluate if they may dark ferment. This work aimed to identify and quantify volatile compounds (VC) in TV and determine if the VC profile depends upon the type of production process (whether the stems were initially cooked or not). TVs were sampled from 3 agave stems with a not-cooking (NC) process, and 3 agave stems with a cooking (C) process, and volatile compounds were determined by gas chromatography coupled with mass spectrometry (GC–MS). A total of 111 volatile compounds were identified, the TV from the cooking process (C) showed the higher presence of furanic compounds (furfural and 5-(hydroxymethyl) furfural) and organic acids (acetic acid and butyric acid), which have been reported as potential inhibitors for DF. To our knowledge, this is the first description of the VC composition from TVs. This study could serve as a base for further investigations related to vinasses from diverse sources.

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

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

Biodegradation of hydrocarbon mixtures in surface waters at environmentally relevant levels - Effect of inoculum origin on kinetics and sequence of degradation

Biodegradation is a dominant removal process for many organic pollutants, and biodegradation tests serve as tools for assessing their environmental fate within regulatory risk assessment. In simulation tests, the inoculum is not standardized, varying in microbial quantity and quality, thereby potentially impacting the observed biodegradation kinetics. In this study we investigated the effect of inoculum origin on the biodegradation kinetics of hydrocarbons for five inocula from surface waters varying in urbanization and thus expected pre-exposure to petroleum hydrocarbons. A new biodegradation method for testing mixtures of hydrophobic chemicals at trace concentrations was demonstrated: Aqueous solutions containing 9 hydrocarbons were generated by passive dosing and diluted with surface water resulting in test systems containing native microorganisms exposed to test substances at ng-μg/L levels. Automated Headspace Solid Phase Microextraction coupled to GC-MS was applied directly to these test systems to determine substrate depletion relative to abiotic controls. Lag phases were generally less than 8 days. First order rate constants were within one order of magnitude for each hydrocarbon in four of the five waters but lower in water from a rural lake. The sequence of degradation between the 9 hydrocarbons showed similar patterns in the five waters indicating the potential for using selected hydrocarbons for benchmarking between biodegradation tests. Degradation half-times were shorter than or within one order of magnitude of BioHCwin predictions for 8 of 9 hydrocarbons. These results showed that location choice is important for biodegradation kinetics and can provide a relevant input to aquatic exposure and fate models.

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) by fungal enzymes: A review

Polycyclic aromatic hydrocarbons (PAHs) are a large group of chemicals. They represent an important concern due to their widespread distribution in the environment, their resistance to biodegradation, their potential to bioaccumulate and their harmful effects. Several pilot treatments have been implemented to prevent economic consequences and deterioration of soil and water quality. As a promising option, fungal enzymes are regarded as a powerful choice for degradation of PAHs. Phanerochaete chrysosporium, Pleurotus ostreatus and Bjerkandera adusta are most commonly used for the degradation of such compounds due to their production of ligninolytic enzymes such as lignin peroxidase, manganese peroxidase and laccase. The rate of biodegradation depends on many culture conditions, such as temperature, oxygen, accessibility of nutrients and agitated or shallow culture. Moreover, the addition of biosurfactants can strongly modify the enzyme activity. The removal of PAHs is dependent on the ionization potential. The study of the kinetics is not completely comprehended, and it becomes more challenging when fungi are applied for bioremediation. Degradation studies in soil are much more complicated than liquid cultures because of the heterogeneity of soil, thus, many factors should be considered when studying soil bioremediation, such as desorption and bioavailability of PAHs. Different degradation pathways can be suggested. The peroxidases are heme-containing enzymes having common catalytic cycles. One molecule of hydrogen peroxide oxidizes the resting enzyme withdrawing two electrons. Subsequently, the peroxidase is reduced back in two steps of one electron oxidation. Laccases are copper-containing oxidases. They reduce molecular oxygen to water and oxidize phenolic compounds.

Bioremediation of Polycyclic Aromatic Hydrocarbon (PAHs): A Perspective

Hydrocarbon pollution is a perennial problem not only in India but throughout the globe. A plethora of microorganisms have been reported to be efficient degraders of these recalcitrant pollutants. One of the major concerns of environmental problem is the presence of hydrocarbons due to the various anthropogenic activities. PAHs are ubiquitous in naturei.e.present in soil, water and air. Presence of PAHs in environment creates problem as their presence have deleterious effect on human and animals. They also have the ability to cause the tumors in human and animals. Some of the microorganisms are capable of transforming and degrading these PAHs and remove them from the environment. The present review describes about the sources, structure, fate and toxicity of PAHs as well as different bioremediation techniques involved in the removing of contaminants from the environment which are efficient and cost-effective. The conventional approaches used for removal of PAH are not only environment friendly but also are able to reduce the risk to human and ecosystem.

Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments

The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.

Microbial succession in response to pollutants in batch-enrichment culture

As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl₂. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl₂ affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments.

Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes

With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils to determine the possible influences of oil contamination on microbial interactions and potential functions. Soil samples were obtained from an oil-exploring site located in South China, and the microbial functional genes were analyzed with GeoChip, a high-throughput functional microarray. By building random networks based on null model, we demonstrated that overall network structures and properties were significantly different between contaminated and uncontaminated soils (P < 0.001). Network connectivity, module numbers, and modularity were all reduced with contamination. Moreover, the topological roles of the genes (module hub and connectors) were altered with oil contamination. Subnetworks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships. The potential "keystone" genes, defined as either "hubs" or genes with highest connectivities in the network, were further identified. The network constructed in this study predicted the potential effects of anthropogenic contamination on microbial community co-occurrence interactions.

From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation

Hydrocarbons are worldwide-distributed pollutants that disturb various ecosystems. The aim of this study was to characterize the short-lapse dynamics of soil microbial communities in response to hydrocarbon pollution and different bioremediation treatments. Replicate diesel-spiked soil microcosms were inoculated with either a defined bacterial consortium or a hydrocarbonoclastic bacterial enrichment and incubated for 12 weeks. The microbial community dynamics was followed weekly in microcosms using Illumina 16S rRNA gene sequencing. Both the bacterial consortium and enrichment enhanced hydrocarbon degradation in diesel-polluted soils. A pronounced and rapid bloom of a native gammaproteobacterium was observed in all diesel-polluted soils. A unique operational taxonomic unit (OTU) related to the Alkanindiges genus represented ∼ 0.1% of the sequences in the original community but surprisingly reached >60% after 6 weeks. Despite this Alkanindiges-related bloom, inoculated strains were maintained in the community and may explain the differences in hydrocarbon degradation. This study shows the detailed dynamics of a soil bacterial bloom in response to hydrocarbon pollution, resembling microbial blooms observed in marine environments. Rare community members presumably act as a reservoir of ecological functions in high-diversity environments, such as soils. This rare-to-dominant bacterial shift illustrates the potential role of a rare biosphere facing drastic environmental disturbances. Additionally, it supports the concept of "conditionally rare taxa," in which rareness is a temporary state conditioned by environmental constraints.

Identification and analysis of polyaromatic hydrocarbons (PAHs)--biodegrading bacterial strains from refinery soil of India

Polyaromatic hydrocarbons (PAHs) utilizing bacteria were isolated from soils of seven sites of Mathura refinery, India. Twenty-six bacterial strains with different morphotypes were isolated. These strains were acclimatized to utilize a mixture of four polycyclic aromatic hydrocarbons, i.e., anthracene, fluorene, phenanthrene, and pyrene, each at 50 mg/L concentration as sole carbon source. Out of total isolates, 15 potent isolates were subjected to 16S rDNA sequencing and identified as a member of diverse genera, i.e., Bacillus, Acinetobacter, Stenotrophomonas, Alcaligenes, Lysinibacillus, Brevibacterium, Serratia, and Streptomyces. Consortium of four promising isolates (Acinetobacter, Brevibacterium, Serratia, and Streptomyces) were also investigated for bioremediation of PAH mixture. This consortium was proved to be efficient PAH degrader resulting in 40-70 % degradation of PAH within 7 days. Results of this study indicated that these genera may play an active role in bioremediation of PAHs.

Assessing the hydrocarbon degrading potential of indigenous bacteria isolated from crude oil tank bottom sludge and hydrocarbon-contaminated soil of Azzawiya oil refinery, Libya

The disposal of hazardous crude oil tank bottom sludge (COTBS) represents a significant waste management burden for South Mediterranean countries. Currently, the application of biological systems (bioremediation) for the treatment of COTBS is not widely practiced in these countries. Therefore, this study aims to develop the potential for bioremediation in this region through assessment of the abilities of indigenous hydrocarbonoclastic microorganisms from Libyan Hamada COTBS for the biotreatment of Libyan COTBS-contaminated environments. Bacteria were isolated from COTBS, COTBS-contaminated soil, treated COTBS-contaminated soil, and uncontaminated soil using Bushnell Hass medium amended with Hamada crude oil (1 %) as the main carbon source. Overall, 49 bacterial phenotypes were detected, and their individual abilities to degrade Hamada crude and selected COBTS fractions (naphthalene, phenanthrene, eicosane, octadecane and hexane) were evaluated using MT2 Biolog plates. Analyses using average well colour development showed that ~90 % of bacterial isolates were capable of utilizing representative aromatic fractions compared to 51 % utilization of representative aliphatics. Interestingly, more hydrocarbonoclastic isolates were obtained from treated contaminated soils (42.9 %) than from COTBS (26.5 %) or COTBS-contaminated (30.6 %) and control (0 %) soils. Hierarchical cluster analysis (HCA) separated the isolates into two clusters with microorganisms in cluster 2 being 1.7- to 5-fold better at hydrocarbon degradation than those in cluster 1. Cluster 2 isolates belonged to the putative hydrocarbon-degrading genera; Pseudomonas, Bacillus, Arthrobacter and Brevundimonas with 57 % of these isolates being obtained from treated COTBS-contaminated soil. Overall, this study demonstrates that the potential for PAH degradation exists for the bioremediation of Hamada COTBS-contaminated environments in Libya. This represents the first report on the isolation of hydrocarbonoclastic bacteria from Libyan COTBS and COTBS-contaminated soil.

Potential impact of soil microbial heterogeneity on the persistence of hydrocarbons in contaminated subsurface soils

In situ bioremediation is potentially a cost effective treatment strategy for subsurface soils contaminated with petroleum hydrocarbons, however, limited information is available regarding the impact of soil spatial heterogeneity on bioremediation efficacy. In this study, we assessed issues associated with hydrocarbon biodegradation and soil spatial heterogeneity (samples designated as FTF 1, 5 and 8) from a site in which in situ bioremediation was proposed for hydrocarbon removal. Test pit activities showed similarities in FTF soil profiles with elevated hydrocarbon concentrations detected in all soils at 2 m below ground surface. However, PCR-DGGE-based cluster analysis showed that the bacterial community in FTF 5 (at 2 m) was substantially different (53% dissimilar) and 2-3 fold more diverse than communities in FTF 1 and 8 (with 80% similarity). When hydrocarbon degrading potential was assessed, differences were observed in the extent of (14)C-benzene mineralisation under aerobic conditions with FTF 5 exhibiting the highest hydrocarbon removal potential compared to FTF 1 and 8. Further analysis indicated that the FTF 5 microbial community was substantially different from other FTF samples and dominated by putative hydrocarbon degraders belonging to Pseudomonads, Xanthomonads and Enterobacteria. However, hydrocarbon removal in FTF 5 under anaerobic conditions with nitrate and sulphate electron acceptors was limited suggesting that aerobic conditions were crucial for hydrocarbon removal. This study highlights the importance of assessing available microbial capacity prior to bioremediation and shows that the site's spatial heterogeneity can adversely affect the success of in situ bioremediation unless area-specific optimizations are performed.