Modulation of microbial consortia enriched from different polluted environments during petroleum biodegradation

Improved chickpea growth, physiology, nutrient assimilation and rhizoremediation of hydrocarbons by bacterial consortia

BACKGROUND

Soil pollution by petroleum hydrocarbons (PHCs) reduces yield by changing the physico-chemical properties of soil and plants due to PHCs' biotoxicity and persistence. Thus, removing PHCs from the soil is crucial for ecological sustainability. Microbes-assisted phytoremediation is an economical and eco-friendly solution. The current work aimed to develop and use bacterial consortia (BC) for PHCs degradation and plant growth enhancement in hydrocarbon-contaminated soil. Initially, the enriched microbial cultures (that were prepared from PHCs-contaminated soils from five distinct regions) were obtained via screening through microcosm experiments. Afterward, two best microbial cultures were tested for PHCs degradation under various temperature and pH ranges. After culture optimization, isolation and characterization of bacterial strains were done to construct two BC. These constructed BC were tested in a pot experiment for hydrocarbons degradation and chickpea growth in PHCs contaminated soil.

RESULTS

Findings revealed that PHCs exerted significant phytotoxic effects on chickpea growth and physiology when cultivated in PHCs contaminated soil, reducing agronomic and physiological traits by 13-29% and 12-43%, respectively. However, in the presence of BC, the phytotoxic impacts of PHCs on chickpea plants were reduced, resulting in up to 24 - 35% improvement in agronomic and physiological characteristics as compared to un-inoculated contaminated controls. Furthermore, the bacterial consortia boosted chickpea's nutritional absorption and antioxidant mechanism. Most importantly, chickpea plants phytoremediated 52% of the initial PHCs concentration; however, adding BC1 and BC2 with chickpea plants further increased this removal and remediated 74% and 80% of the initial PHCs concentration, respectively.

CONCLUSION

In general, BC2 outperformed BC1 (with few exceptions) in promoting plant growth and PHCs elimination. Therefore, using multi-trait BC for PHCs degradation and plant growth improvement under PHCs stress may be an efficient and environmentally friendly strategy to deal with PHCs pollution and toxicity.

Bioremediation of oily hypersaline soil via autochthonous bioaugmentation with halophilic bacteria and archaea

Kuwaiti hypersaline soil samples were contaminated with 5 % (w/w) weathered Kuwaiti light crude oil and bioaugmented with autochthonous halophilic hydrocarbonoclastic archaeal and bacterial strains, two each, individually and as consortia. Residual oil contents were determined, and microbial communities were analyzed by culture-dependent and culture-independent approaches initially and seasonally for one year. After one year of the bioremediation process, the mean oil degradation rate was similar across all treated soils including the controlled unbioaugmented one. Oil hydrocarbons were drastically reduced in all soil samples with values ranging from 82.7 % to 93 %. During the bioremediation process, the number of culturable oil-degrading bacteria increased to a range of 142 to 344 CFUx104 g-1 after 12 months of bioaugmentation. Although culture-independent analysis showed a high proportion of inoculants initially, none could be cultured throughout the bioremediation procedure. Within a year, microbial communities changed continually, and 33 species of halotolerant/halophilic hydrocarbonoclastic bacteria were isolated and identified belonged mainly to the three major bacterial phyla Actinobacteria, Proteobacteria, and Firmicutes. The archaeal phylum Halobacterota represented <1 % of the microbial community's relative abundance, which explains why none of its members were cultured. Improving the biodegradability of an already balanced environment by autochthonous bioaugmentation is more involved than just adding the proper oil degraders. This study emphasizes the possibility of a relatively large resistant population, a greater diversity of oil-degrading microorganisms, and the highly selective impacts of oil contamination on hypersaline soil bacterial communities.

Bacterial Diversity in Old Hydrocarbon Polluted Sediments of Ecuadorian Amazon River Basins

The Ecuadorian Amazon rainforest stands out as one of the world's most biodiverse regions, yet faces significant threats due to oil extraction activities dating back to the 1970s in the northeastern provinces. This research investigates the environmental and societal consequences of prolonged petroleum exploitation and oil spills in Ecuador's Amazon. Conducted in June 2015, the study involved a comprehensive analysis of freshwater sediment samples from 24 locations in the Rio Aguarico and Napo basins. Parameters such as water and air temperature, conductivity, soil pH, and hydrocarbon concentrations were examined. Total petroleum hydrocarbon (TPH) concentrations ranged from 9.4 to 847.4 mg kg-1, with polycyclic aromatic hydrocarbon (PAH) levels varying from 10.15 to 711.1 mg kg-1. The pristane/phytane ratio indicated historic hydrocarbon pollution in 8 of the 15 chemically analyzed sediments. Using non-culturable techniques (Illumina), bacterial analyses identified over 350 ASV, with prominent families including Comamonadaceae, Chitinophagaceae, Anaeromyxobacteraceae, Sphingomonadaceae, and Xanthobacteraceae. Bacterial diversity, assessed in eight samples, exhibited a positive correlation with PAH concentrations. The study provides insights into how microbial communities respond to varying levels of hydrocarbon pollution, shedding light on the enduring impact of oil exploitation in the Amazonian region. Its objective is to deepen our understanding of the environmental and human well-being in the affected area, underscoring the pressing need for remedial actions in the face of ongoing ecological challenges.

Distribution and abundance of oil-degrading bacteria in seawater of the Yellow Sea and Bohai Sea, China

Petroleum hydrocarbons are widespread in seawater. As an important sea area in northern China, the content and distribution of petroleum hydrocarbons in seawater need our attention because of the high toxicity and lasting polluting effects on the ecological environment of the Yellow Sea and Bohai Sea. In addition, there are few reports comparing the diversity of oil-degrading bacteria before and after enrichment. Therefore, we collected surface seawater from 10 sites in the Yellow Sea and Bohai Sea in the autumn of 2020 to study the distribution characteristics of total petroleum hydrocarbons (TPH) and the diversity of oil-degrading bacteria. The concentration of TPH was 81.65 μg/L-139.55 μg/L at ten sites in the Bohai Sea and the Yellow Sea, which conformed to the China Grade II water quality standard (GB3097-1997). Moreover, the pristine/phytane (PR/PH) value of most sites was close to 1, indicating that the area was obviously polluted by exogenous petroleum hydrocarbons. We found that oil-degrading bacteria in the seawater of the Yellow Sea and the Bohai Sea had a good degradation effect on C11-C14 short chain alkanes (degradation rate of 59.19-73.22 %) and C1-C4 phenanthrene (degradation rate of 48.19-60.74 %). In terms of the diversity of oil-degrading bacteria, Gammaproteobacteria and Alphaproteobacteria dominated the enriched bacterial communities. Notably, the relative abundance of Alcanivorax changed significantly before and after enrichment. We proposed that surface seawater in the Bohai Sea and Yellow Sea could form oil-degrading bacteria mainly composed of Alcanivorax, which had great potential for oil pollution remediation.

Taxonomic and Predictive Functional Profile of Hydrocarbonoclastic Bacterial Consortia Developed at Three Different Temperatures

Microbial community exhibit shift in composition in response to temperature variation. We report crude oil-degrading activity and high-throughput 16S rRNA gene sequencing (metagenome) profiles of four bacterial consortia enriched at three different temperatures in crude oil-amended Bushnell-Hass Medium from an oily sludge sediment. The consortia were referred to as O (4 ± 2 ℃ in 3% w/v crude oil), A (25 ± 2 ℃ in 1% w/v crude oil), H (25 ± 2 ℃ in 3% w/v crude oil), and X (45 ± 2 ℃ in 3% w/v crude oil). The hydrocarbon-degrading activity was highest for consortium A and H and lowest for consortium O. The metagenome profile revealed the predominance of Proteobacteria (62.12-1.25%) in each consortium, followed by Bacteroidota (18.94-37.77%) in the consortium O, A, and H. Contrarily, consortium X comprised 7.38% Actinomycetota, which was essentially low (< 0.09%) in other consortia, and only 0.41% Bacteroidota. The PICRUSt-based functional analysis predicted major functions associated with the metabolism and 5060 common KEGG Orthology (KOs). A total of 296 KOs were predicted exclusively in consortium X. Additionally, 247 KOs were predicted from xenobiotic biodegradation pathways. This study found that temperature had a stronger influence on the composition and function of the bacterial community than crude oil concentration.

Nature-Based Solutions for Restoring an Agricultural Area Contaminated by an Oil Spill

A feasibility study is presented for a bioremediation intervention to restore agricultural activity in a field hit by a diesel oil spill from an oil pipeline. The analysis of the real contaminated soil was conducted following two approaches. The first concerned the assessment of the biodegradative capacity of the indigenous microbial community through laboratory-scale experimentation with different treatments (natural attenuation, landfarming, landfarming + bioaugmentation). The second consisted of testing the effectiveness of phytoremediation with three plant species: Zea mays (corn), Lupinus albus (lupine) and Medicago sativa (alfalfa). With the first approach, after 180 days, the different treatments led to biodegradation percentages between 83 and 96% for linear hydrocarbons and between 76 and 83% for branched ones. In case of contamination by petroleum products, the main action of plants is to favor the degradation of hydrocarbons in the soil by stimulating microbial activity thanks to root exudates. The results obtained in this experiment confirm that the presence of plants favors a decrease in the hydrocarbon content, resulting in an improved degradation of up to 18% compared with non-vegetated soils. The addition of plant growth-promoting bacteria (PGPB) isolated from the contaminated soil also promoted the growth of the tested plants. In particular, an increase in biomass of over 50% was found for lupine. Finally, the metagenomic analysis of the contaminated soil allowed for evaluating the evolution of the composition of the microbial communities during the experimentation, with a focus on hydrocarbon- oxidizing bacteria.

Dynamic changes in the microbial community in the surface seawater of Jiaozhou Bay after crude oil spills: An in situ microcosm study

The changes in the composition and structure of microbial communities in Jiaozhou Bay are strongly affected by marine oil pollution, but the outcomes of the microbial responses and effects of dispersant application remain unclear. Herein, we performed an in situ microcosm study to investigate the response of the indigenous microbial community under crude oil alone and combined oil and dispersant treatment in the surface seawater of a semi-enclosed marine area of Jiaozhou Bay. The dynamics of the bacterial classification based on 16s rDNA sequencing were used to assess the changes with the crude oil concentration, dispersant use, and time. The crude oil resulted in a high abundance of the genera Pseudohongiella, Cycloclasticus, Marivita, and C1-B045 from the Gammaproteobacteria and Alphaproteobacteria classes, suggesting for hydrocarbon degradation. However, the dispersant treatment was more advantageous for Pacificibacter, Marivita, and Loktanella. Besides accelerating the rate of bacterial community succession, the dispersants had significantly stronger effects on the structure of the bacterial community and the degradation functions than the oil. A higher dose of oil exposure corresponded to fewer dominant species with a high relative abundance. Our study provides information for screening potential degradation bacteria and assessing the risks that oil spills pose to marine ecosystems.

Factors Influencing the Bacterial Bioremediation of Hydrocarbon Contaminants in the Soil: Mechanisms and Impacts

The discharge of hydrocarbons and their derivatives to environments due to human and/or natural activities cause environmental pollution (soil, water, and air) and affect the natural functioning of an ecosystem. To minimize or eradicate environmental pollution by hydrocarbon contaminants, studies showed strategies including physical, chemical, and biological approaches. Among those strategies, the use of biological techniques (especially bacterial biodegradation) is critically important to remove hydrocarbon contaminants. The current review discusses the insights of major factors that enhance or hinder the bacterial bioremediation of hydrocarbon contaminants (aliphatic, aromatic, and polyaromatic hydrocarbons) in the soil. The key factors limiting the overall hydrocarbon biodegradation are generally categorized as biotic factors and abiotic factors. Among various environmental factors, temperature range from 30 to 40°C, pH range from 5 to 8, moisture availability range from 30 to 90%, carbon/nitrogen/phosphorous (C/N/P; 100:20:1) ratio, and 10–40% of oxygen for aerobic degradation are the key factors that show positive correlation for greatest hydrocarbon biodegradation rate by altering the activities of the microbial and degradative enzymes in soil. In addition, the formation of biofilm and production of biosurfactants in hydrocarbon-polluted soil environments increase microbial adaptation to low bioavailability of hydrophobic compounds, and genes that encode for hydrocarbon degradative enzymes are critical for the potential of microbes to bioremediate soils contaminated with hydrocarbon pollutants. Therefore, this review works on the identification of factors for effective hydrocarbon biodegradation, understanding, and optimization of those factors that are essential and critical.

Exploring the diversity and hydrocarbon bioremediation potential of microbial community in the waste sludge of Duliajan oil field, Assam, India

Microbial community analysis of crude oil containing sludge collected from Duliajan oil field, Assam, India, showed the predominance of hydrocarbon-degrading bacteria such as Pseudomonas (20.1%), Pseudoxanthomonas (15.8%), Brevundimonas (1.6%), and Bacillus (0.8%) alongwith anaerobic, fermentative, nitrogen-fixing, nitrate-, sulfate-, and metal-reducing, syntrophic bacteria, and methanogenic archaea. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated gene collection for potential hydrocarbon degradation, lipid, nitrogen, sulfur, and methane metabolism. The culturable microbial community was predominated by Pseudomonas and Bacillus with the metabolic potential for utilizing diverse hydrocarbons, crude oil, and actual petroleum sludge as sole carbon source during growth and tolerating various environmental stresses prevailing in such contaminated sites. More than 90% of the isolated strains could produce biosurfactant and exhibit catechol 2,3-dioxygenase activity. Nearly 30% of the isolates showed alkane hydroxylase activity with the maximum specific activity of 0.54 μmol min^-1 mg^-1. The study provided better insights into the microbial diversity and functional potential within the crude oil containing sludge which could be exploited for in situ bioremediation of contaminated sites.

Microbial approaches for remediation of pollutants: Innovations, future outlook, and challenges

Environmental contamination with persistent organic pollutants has emerged as a serious threat of pollution. Bioremediation is a key to eliminate these harmful pollutants from the environment and has gained the interest of researchers during the past few decades. Scientific knowledge upon microbial interactions with individual pollutants over the past decades has helped to abate environmental pollution. Traditional bioremediation approaches have limitations for their applications; hence, it is essential to discover new bioremediation approaches with biotechnological interventions for best results. The developments in various methodologies are expected to increase the efficiency of bioremediation techniques and provide environmentally sound strategies. This paper deals with the profiling of microorganisms present in polluted sites using various techniques such as culture-based approaches and omics-based approaches. Besides this, it also provides up-to-date scientific literature on the microbial electrochemical technologies which are nowadays considered as the best approach for remediation of pollutants. Detailed information about future outlook and challenges to evaluate the effect of various treatment technologies for remediation of pollutants has been discussed.

Kurstakin molecules facilitate diesel oil assimilation by Acinetobacter haemolyticus strain 2SA through overexpression of alkane hydroxylase genes

Biodegradation is a cost-effective process commonly used to eliminate many xenobiotic hydrocarbons such as diesel oils. However, their hydrophobic character reduces the biodegradation efficiency. In order to overcome this hurdle, kurstakins isolated from Bacillus thuringiensis strain 7SA were used as emulsifying agents. The influence of kurstakin molecules on diesel oil degradation by Acinetobacter haemolyticus strain 2SA was evaluated in the presence and absence of the aforementioned lipopeptide. The degradation rates and gene expressions of alkane hydroxylases were evaluated at days 4, 10, 14 and 21. Results showed that kurstakin molecules increased the hydrophobicity of 2SA. Moreover, diesel oil degradation activities were higher in the presence of kurstakin with 29%, 35%, 29% and 23% improvement at 4th, 10th, 14th and 21st day respectively. Statistical analysis indicated that the difference between the degradation rates in the presence and absence of kurstakin was significant with p = 0.03. The detection of three different hydroxylase genes namely alkB, almA and cyp153 in 2SA genome, might have allowed more efficient degradability of alkanes. According to the real-time PCR results, cyp153 was the most induced gene during diesel oil degradation in the presence and absence of kurstakin. Yet, the three genes demonstrated higher levels of expression in the presence of kurstakin when compared to its absence. This study showed that kurstakins enhance the diesel oil biodegradation rate by increasing the hydrophobicity of 2SA. In addition to their anti-fungal activities, kurstakins can be used as biosurfactant to increase biodegradation of diesel oil.

Effect of consortium bioaugmentation and biostimulation on remediation efficiency and bacterial diversity of diesel-contaminated aged soil

This study aimed to evaluate the effects of consortium bioaugmentation (CB) and various biostimulation options on the remediation efficiency and bacterial diversity of diesel-contaminated aged soil. The bacterial consortium was prepared using strains D-46, D-99, D134-1, MSM-2-10-13, and Oil-4, isolated from oil-contaminated soil. The effects of CB and biostimulation were evaluated in various soil microcosms: CT (water), T1 (CB only), T2 (CB + NH₄NO₃ and KH₂PO_4, nutrients), T3 (CB + activated charcoal, AC), T4 (CB + nutrients + AC), T5 (AC + water), T6 (CB + nutrients + zero-valent iron nanoparticles, nZVI), T7 (CB + nutrients + AC + nZVI), T8 (CB + activated peroxidase, oxidant), T9 (AC + nZVI), and T10 (CB + nZVI + AC + oxidant). Preliminary evaluation of the bacterial consortium revealed 81.9% diesel degradation in liquid media. After 60 days of treatment, T6 demonstrated the highest total petroleum hydrocarbon (TPH) degradation (99.0%), followed by T1 (97.4%), T2 (97.9%), T4 (96.0%), T7 (96.0%), T8 (94.8%), T3 (93.6%), and T10 (86.2%). The lowest TPH degradation was found in T5 (24.2%), T9 (17.2%), and CT (11.7%). Application of CB and biostimulation to the soil microcosms decreased bacterial diversity, leading to selective enrichment of bacterial communities. T2, T6, and T10 contained Firmicutes (50.06%), Proteobacteria (64.69%), and Actinobacteria (54.36%) as the predominant phyla, respectively. The initial soil exhibited the lowest metabolic activity, which improved after treatment. The study results indicated that biostimulation alone is inadequate for remediation of contaminated soil that lacks indigenous oil degraders, suggesting the need for a holistic approach that includes both CB and biostimulation. Graphical Abstract.

Effects of co-contamination of heavy metals and total petroleum hydrocarbons on soil bacterial community and function network reconstitution

Due to the accumulation of heavy metals in soil ecosystems, the response of soil microorganisms to the disturbance of heavy metals were widely studied. However, little was known about the interactions among microorganisms in heavy metals and total petroleum hydrocarbons (TPH) co-contaminated soils. In the present study, the microbiota shifts of 2 different contamination types of heavy metal-TPH polluted soils were investigated. NGS sequencing approach was adopted to illustrate the microbial community structure and to predict community function. Networks were established to reveal the interactions between microbes and environmental pollutants. Results showed that the alpha diversity and OTUs number of soil microbiota were reduced under heavy metals and TPH pollutants. TPH was the major pollutant in HT1 group, in which Proteobacteria phylum increased significantly, including Arenimonas genus, Sphingomonadaceae family and Burkholderiaceae family. Moreover, the function structures based on the KEGG database of HT1 group was enriched in the benzene matter metabolism and bacterial motoricity in microbiota. In contrast, severe Cr-Pb-TPH co-pollutants in HT2 increased the abundance of Firmicutes. In details, the relative abundance of Streptococcus genus and Bacilli class raised sharply. The DNA replication functions in microbiota were enriched under severely contaminated soil as a result of high concentrations of heavy metals and TPH pollutants' damage to bacteria. Furthermore, according to the correlation analysis between microbes and the pollutants, Streptococcus, Neisseria, Aeromonas, Porphyromonas and Acinetobacter were suggested as the bioremediation bacteria for Cr and Pb polluted soils, while Syntrophaceae spp. and Immundisolibacter were suggested as the bioremediation bacteria for TPH polluted soil. The study took a survey on the microbiota shifts of the heavy metals and TPH polluted soils, and the microbe's biomarkers provided new insights for the candidate strains of biodegradation, while further researches are required to verify the biodegradation mechanism of these biomarkers.

Nutrient drip irrigation for refractory hydrocarbon removal and microbial community shift in a historically petroleum-contaminated soil

An adequate amount of nutrients is required to enable biodegradation of refractory hydrocarbons in petroleum-contaminated soil. In this study, a microcosm experiment was conducted using a drip fertigation method for petroleum-contaminated soil remediation. Nitrogen and phosphorus were homogeneously and periodically sprayed into a historically contaminated soil using a modified horticultural drip irrigation device. Various petroleum hydrocarbon fraction contents were then determined by gravimetry and gas chromatography (GC), and changes in the soil microbial community were analyzed by high throughput sequencing. After 90 days of remediation, the removal efficiencies of total petroleum hydrocarbon (TPH), saturates, aromatics, C7-C30 n-alkanes, and 16 PAHs were respectively enhanced by 21.5%, 25.5%, 12.4%, 10.4%, and 19.6% compared with the use of a single nutrient amendment application. The high throughput sequencing result showed that obvious changes had occurred in the soil microbial community compositions during drip fertigation; however, fungi were more sensitive to drip fertigation than bacteria. The resulting predominant bacterial and fungal genera were Dietzia, Nocardioides, Mycobacterium, Sphaerobacter, Leifsonia, and Aspergillus, Scolecobasidium, and Fusarium, respectively. Remediating polluted soils by regular fertigation ensures the automatic addition of even amounts of nutrients, which achieves high refractory hydrocarbon removal efficiencies. It is expected that this method can be applied in the in-situ remediation of petroleum-contaminated soil on a large scale.

Bacterial succession in oil-contaminated soil under phytoremediation with poplars

Petroleum hydrocarbons (PHCs) continue to be among the most common pollutants in soil worldwide. Phytoremediation has become a sustainable way of dealing with PHC contamination. We conducted the off-site phytoremediation of PHC-polluted soil from an oil tanker truck accident, where poplars were used for the phytoremediation of the oil-polluted soil in a boreal climate during a seven-year treatment. The succession of bacterial communities over the entire phytoremediation process was monitored using microbial ecological tools relying on high-throughput 16S rRNA gene sequencing. Upon the successful depletion of PHCs from soil, endophytic communities were analyzed in order to assess the complete plant-associated microbiome after the ecological recovery. The rhizosphere-associated soil exhibited different bacterial dynamics than unplanted soil, but both soils experienced succession of bacteria over time, with diversity being negatively correlated with PHC concentration. In the relatively short growing season in North Europe, seasonal variations in environmental conditions were identified that contributed to the dynamics of bacterial communities. Overall, our study proved that phytoremediation using poplar trees can be used to assist in the removal of PHCs from soils in boreal climate conditions and provides new insight into the succession patterns of bacterial communities associated with these plants.

Vertical response of microbial community and degrading genes to petroleum hydrocarbon contamination in saline alkaline soil

A column microcosm was conducted by amending crude oil into Dagang Oilfield soil to simulate the bioremediation process. The dynamic change of microbial communities and metabolic genes in vertical depth soil from 0 to 80 cm were characterized to evaluate the petroleum degradation potential of indigenous microorganism. The influence of environmental variables on the microbial responds to petroleum contamination were analyzed. Degradation extent of 42.45% of n-alkanes (C8-C40) and 34.61% of 16ΣPAH were reached after 22 weeks. Relative abundance of alkB, nah, and phe gene showed about 10-fold increment in different depth of soil layers. Result of HTS profiles demonstrated that Pseudomonas, Marinobacter and Lactococcus were the major petroleum-degrading bacteria in 0-30 and 30-60 cm depth of soils. Fusarium and Aspergillus were the dominant oil-degrading fungi in the 0-60 cm depth of soils. In 60-80 cm deep soil, anaerobic bacteria such as Bacteroidetes, Lactococcus, and Alcanivorax played important roles in petroleum degradation. Redundancy analysis (RDA) and correlation analysis demonstrated that petroleum hydrocarbons (PHs) as well as soil salinity, clay content, and anaerobic conditions were the dominant effect factors on microbial community compositions in 0-30, 30-60, and 60-80 cm depth of soils, respectively.

Degradation of crude oil by mixed cultures of bacteria isolated from the Qinghai-Tibet plateau and comparative analysis of metabolic mechanisms

This study investigates the biodegradation of crude oil by a mixed culture of bacteria isolated from the Qinghai-Tibet plateau using gas chromatography-mass spectrometer (GC-MS) and the gravimetric method. The results showed that a mixed culture has a stronger ability to degrade hydrocarbon than pure cultures. Once both Nocardia soli Y48 and Rhodococcus erythropolis YF28-1 (8) were present in a culture, the culture demonstrated the highest crude oil removal efficiency of almost 100% after 10 days of incubation at 20 °C. Moreover, further analysis of the degradation mechanisms used by the above strains, which revealed utilization of different n-alkane substrates, indicated the diversity of evolution and variations in different strains, as well as the importance of multiple metabolic mechanisms for alkane degradation. Therefore, it is concluded that a mixed culture of Y48 and YF28-1 (8) strains can provide a more effective method for bioremediation of hydrocarbon-contaminated soil in permafrost regions.

Molecular and Microbiological Insights on the Enrichment Procedures for the Isolation of Petroleum Degrading Bacteria and Fungi

Autochthonous bioaugmentation, by exploiting the indigenous microorganisms of the contaminated environment to be treated, can represent a successful bioremediation strategy. In this perspective, we have assessed by molecular methods the evolution of bacterial and fungal communities during the selective enrichment on different pollutants of a soil strongly polluted by mixtures of aliphatic and polycyclic hydrocarbons. Three consecutive enrichments were carried out on soil samples from different soil depths (0-1, 1-2, 2-3 m), and analyzed at each step by means of high-throughput sequencing of bacterial and fungal amplicons biomarkers. At the end of the enrichments, bacterial and fungal contaminants degrading strains were isolated and identified in order to (i) compare the composition of enriched communities by culture-dependent and culture-independent molecular methods and to (ii) obtain a collection of hydrocarbon degrading microorganisms potentially exploitable for soil bioremediation. Molecular results highlighted that for both bacteria and fungi the pollutant had a partial shaping effect on the enriched communities, with paraffin creating distinct enriched bacterial community from oil, and polycyclic aromatic hydrocarbons generally overlapping; interestingly neither the soil depth or the enrichment step had significant effects on the composition of the final enriched communities. Molecular analyses well-agreed with culture-dependent analyses in terms of most abundant microbial genera. A total of 95 bacterial and 94 fungal strains were isolated after selective enrichment procedure on different pollutants. On the whole, isolated bacteria where manly ascribed to Pseudomonas genus followed by Sphingobacterium, Bacillus, Stenothrophomonas, Achromobacter, and Serratia. As for fungi, Fusarium was the most abundant genus followed by Trichoderma and Aspergillus. The species comprising more isolates, such as Pseudomonas putida, Achromobacter xylosoxidans and Ochromobactrum anthropi for bacteria, Fusarium oxysporum and Fusarium solani for fungi, were also the dominant OTUs assessed in Illumina.

Vertical stratification of bacteria and the chemical compounds in crude oil-contaminated soil layers of the semi-deserted Dzungharian Basin

The largely semi-deserted and deserted Dzungharian Basin sites in the northwest of China geologically represent an extension of the Paleozoic Kazakhstan Block and were once part of an independent continent. For reasons of overdevelopment and unreasonable operations during the process of exploitation and transportation, oil pollutants that were discharged into the soil environment caused serious pollution in this weak ecosystem. To explore the bacterial community composition in detail and their possible origination and potential during the natural attenuation of petroleum contaminants in this type of ecologic niche, GC-MS and high-throughput sequencing techniques were used to resolve the organic compounds and bacterial communities in vertical soil layers. The degradation of petroleum contaminants in semi-deserted and deserted soils mainly occurred in the layer at a depth of 45-55 cm. During this process, aromatic and heterocyclic compounds were significantly enriched in soils. The bacterial communities in this basin exhibited a distinct vertical stratification from the surface layer down to the bottom soil layer. Considering the interaction between the community composition and the geochemical properties, we speculate that the degradation of petroleum contaminants in this semi-deserted and deserted soil might represent a microorganism-mediated process and mainly occur in the deeper soil layer.