Diversity of bacterial communities along a petroleum contamination gradient in desert soils

Sustainable strategies for combating hydrocarbon pollution: Special emphasis on mobil oil bioremediation

The global rise in industrialization and vehicularization has led to the increasing trend in the use of different crude oil types. Among these mobil oil has major application in automobiles and different machines. The combustion of mobil oil renders a non-usable form that ultimately enters the environment thereby causing problems to environmental health. The aliphatic and aromatic hydrocarbon fraction of mobil oil has serious human and environmental health hazards. These components upon interaction with soil affect its fertility and microbial diversity. The recent advancement in the omics approach viz. metagenomics, metatranscriptomics and metaproteomics has led to increased efficiency for the use of microbial based remediation strategy. Additionally, the use of biosurfactants further aids in increasing the bioavailability and thus biodegradation of crude oil constituents. The combination of more than one approach could serve as an effective tool for efficient reduction of oil contamination from diverse ecosystems. To the best of our knowledge only a few publications on mobil oil have been published in the last decade. This systematic review could be extremely useful in designing a micro-bioremediation strategy for aquatic and terrestrial ecosystems contaminated with mobil oil or petroleum hydrocarbons that is both efficient and feasible. The state-of-art information and future research directions have been discussed to address the issue efficiently.

Microbiome profile of soil and rhizosphere plants growing in traditional oil mining land in Wonocolo, Bojonegoro, Indonesia

Traditional oil mining poses negative effects on the environment through pollution with crude oil. One of the traditional mining sites in Wonocolo, Bojonegoro, Indonesia was reported to contaminate the surrounding area with a high level of crude oil. Therefore, this study aims to examine the microbiome profiles of contaminated soil and the rhizosphere of naturalized plants growing at the sites. It was conducted in Wonocolo, Bojonegoro to obtain an insight into the possible remediation efforts of using indigenous hydrocarbon-degrading bacteria and naturalized plants as in situ remediation agents. The results showed that the soil located close to the oil well-contained a high level of crude oil at 24.8%, and exhibited a distinct microbiome profile compared to those located further which had lower crude oil contamination of 14.15, 10.89, and 4.9%. Soil with the highest level of crude oil contamination had a comparatively higher relative abundance of assA, an anaerobic alkene-degrading gene. Meanwhile, the rhizosphere of the two naturalized plants, Muntingia calabura, and Pennisetum purpureum, exhibited indifferent microbiome profiles compared to the soil. They were found to contain less abundant hydrocarbon-degrading genes, such as C230, PAH-RHD-GP, nahAc, assA, and alkB suggesting that these naturalized plants might not be a suitable tool for in-situ remediation.

Taxonomic and functional trait-based approaches suggest that aerobic and anaerobic soil microorganisms allow the natural attenuation of oil from natural seeps

Natural attenuation, involving microbial adaptation, helps mitigating the effect of oil contamination of surface soils. We hypothesized that in soils under fluctuating conditions and receiving oil from seeps, aerobic and anaerobic bacteria as well as fungi could coexist to efficiently degrade hydrocarbons and prevent the spread of pollution. Microbial community diversity was studied in soil longitudinal and depth gradients contaminated with petroleum seeps for at least a century. Hydrocarbon contamination was high just next to the petroleum seeps but this level drastically lowered from 2 m distance and beyond. Fungal abundance and alpha-diversity indices were constant along the gradients. Bacterial abundance was constant but alpha-diversity indices were lower next to the oil seeps. Hydrocarbon contamination was the main driver of microbial community assemblage. 281 bacterial OTUs were identified as indicator taxa, tolerant to hydrocarbon, potentially involved in hydrocarbon-degradation or benefiting from the degradation by-products. These taxa belonging to lineages of aerobic and anaerobic bacteria, have specific functional traits indicating the development of a complex community adapted to the biodegradation of petroleum hydrocarbons and to fluctuating conditions. Fungi are less impacted by oil contamination but few taxa should contribute to the metabolic complementary within the microbial consortia forming an efficient barrier against petroleum dissemination.

Adaptive changes of sediment microbial communities associated with cleanup of oil spills in Nigerian mangrove forests

The objectives of this study were to assess the influence on microbial communities resulting from i) the physical removal of free oil (pre-treatment or post-treatment), and ii) the level of oiling within a contaminated former mangrove forest. Sediment samples were collected before and after the removal of free oil. Before the process of remediation, a highly biodiverse mangrove microbiome which had adapted to history of recurring oil spills was observed. After removing the surface oil, the microbial diversity of the sediments reduced, with members of the phyla Firmicutes and Proteobacteria becoming dominant. This indicates that while water flushing reduced overall microbial diversity, it stimulated the growth of a more specialized bacterial community reported to be involved in hydrocarbon biodegradation. These results provide new insights on microbial communities and their succession in mangrove forest sediments, that will be useful for monitoring oil cleaning programs using water flushing to remove free oil.

Characterization of bacterial community in oil-contaminated soil and its biodegradation efficiency of high molecular weight (>C40) hydrocarbon

In this study, two biosurfactant producing Pseudomonas aeruginosa sp. were isolated from motor oil contaminated soil for crude oil, alkane and PAH degradation studies. Metagenomics analysis identified as proteobacteria phyla was the dominant. Isolated two bacterial species were well grown in mineral salt medium with 1% of crude oil, alkanes (dotriacontane and tetratetracontane) and PAH (pyrene, benzopyrene and anthracene) as sole carbon sources. Total biodegradation efficiency (BE) of strains PP3 and PP4 in Crude oil degradation evaluated by the analysis of gas chromatography and mass spectrometry was 50% and 86% respectively. BE of PP3, PP4 and mixed consortium in alkane biodegradation were 46%, 47% and 36%, respectively. BE of PP3, PP4 and mixed consortium in PAH biodegradation were 22%, 48% and 35%, respectively. Based on the results revealed that strain pp4 was more efficient bacteria to degrade the crude oil, alkane and PAH than pp3. This was due to the higher production of biosurfactant by PP4 than PP3 and also confirmed in the test of emulsification index (E₂₄). FTIR results showed that the produced biosurfactant could partially solubilize the crude oil hydrocarbons, alkanes and PAH and confirmed as glycolipid (rhamnolipid) in nature. Thus, the obtained results from the GCMS showed that all hydrocarbons were utilized by bacteria as carbon source for biosurfactant production and utilize the high molecular weight hydrocarbons. Based on the present study we can suggest that identified potential biosurfactant producing bacteria are used for biodegradation of high molecular weight hydrocarbon (>C40).

Characteristics of Microbial Community and Function With the Succession of Mangroves

In this study, 16S high-throughput and metagenomic sequencing analyses were employed to explore the changes in microbial community and function with the succession of mangroves (Sonneratia alba, Rhizophora apiculata, and Bruguiera parviflora) along the Merbok river estuary in Malaysia. The sediments of the three mangroves harbored their own unique dominant microbial taxa, whereas R. apiculata exhibited the highest microbial diversity. In general, Gammaproteobacteria, Actinobacteria, Alphaproteobacteria, Deltaproteobacteria, and Anaerolineae were the dominant microbial classes, but their abundances varied significantly among the three mangroves. Principal coordinates and redundancy analyses revealed that the specificity of the microbial community was highly correlated with mangrove populations and environmental factors. The results further showed that R. apiculata exhibited the highest carbon-related metabolism, coinciding with the highest organic carbon and microbial diversity. In addition, specific microbial taxa, such as Desulfobacterales and Rhizobiales, contributed the highest functional activities related to carbon metabolism, prokaryote carbon fixation, and methane metabolism. The present results provide a comprehensive understanding of the adaptations and functions of microbes in relation to environmental transition and mangrove succession in intertidal regions. High microbial diversity and carbon metabolism in R. apiculata might in turn facilitate and maintain the formation of climax mangroves in the middle region of the Merbok river estuary.

Natural attenuation of legacy hydrocarbon spills in pristine soils is feasible despite difficult environmental conditions in the monsoon tropics

The Kimberley region of Western Australia is a National Heritage listed region that is internationally recognised for its environmental and cultural significance. However, petroleum spills have been reported at a number of sites across the region, representing an environmental concern. The region is also characterised as having low soil nutrients, high temperatures and monsoonal rain - all of which may limit the potential for natural biodegradation of petroleum. Therefore, this work evaluated the effect of legacy petroleum hydrocarbons on the indigenous soil microbial community (across the domains Archaea, Bacteria and Fungi) at three sites in the Kimberley region. At each site, soil cores were removed from contaminated and control areas and analysed for total petroleum hydrocarbons, soil nutrients, pH and microbial community profiling (using16S rRNA and ITS sequencing on the Illumina MiSeq Platform). The presence of petroleum hydrocarbons decreased microbial diversity across all kingdoms, altered the structure of microbial communities and increased the abundance of putative hydrocarbon degraders (e.g. Mycobacterium, Acremonium, Penicillium, Bjerkandera and Candida). Microbial community shifts from contaminated soils were also associated with an increase in soil nutrients (notably Colwell P and S). Our study highlights the long-term effect of legacy hydrocarbon spills on soil microbial communities and their diversity in remote, infertile monsoonal soils, but also highlights the potential for natural attenuation to occur in these environments.

Impacts of partially hydrolyzed polyacrylamide (HPAM) on microbial mats from a constructed wetland treating oilfield produced water

Constructed wetlands have been successfully used in the treatment of produced water brought to the surface in large quantities during oil extraction activities. However, with the increasing use of partially hydrolyzed polyacrylamide (HPAM) in enhancing oil recovery, the impacts of HPAM on the biological processes of wetlands is still unknown. Microbial mats in wetlands play a key role in hydrocarbon degradation. Here, we compared the bacterial communities of four wetland microbial mats after flooding with different concentrations of HPAM. Two mats (i.e. the HPAM-free and the 500 ppm HPAM pre-exposed mats) were selected to further investigate the effect of HPAM on respiration and biodegradation activities. The field mats exhibited clear differences in their bacterial community structure, where Cyanobacteria and Alphaproteobacteria became dominant in the presence of HPAM. In the laboratory experiments, the generated CO₂ by the HPAM-free and the 500 ppm HPAM pre-exposed mats did not vary significantly when HPAM was added, although CO₂ values were slightly higher in the presence of oil. Both mats were still able to degrade between 15 ± 14.4 to 50 ± 13.0% of C₁₀ to C₃₀ alkanes in 28 days, and this degradation was not affected by HPAM addition. The HPAM concentration decreased by 22-34% of the initial amount after 28 days of incubation in the HPAM-free mat, versus only 7-18.4% decrease in the 500 ppm HPAM pre-exposed mat. We conclude that the wetland microbial mats seem to have become well adapted to HPAM and could maintain their respiration and hydrocarbon degradation activities.

Mixing of plant litters strengthens their remediation effects on crude oil-contaminated soil

To investigate the effects of the mixing of litters on their remediation efficiency in petroleum-contaminated soil, litters from two common plants in the petroleum-contaminated region of Northern Shaanxi, China, Bothriochloa ischaemum (L.) Keng and Sophora davidii Kom. ex Pavol., and their mixture were mixed with 45 g/kg petroleum-contaminated soil. Based on these, a 150-day simulated remediation experiment was conducted at 25 °C and consistent moisture conditions. The effects on the degradation of petroleum components and the restoration of nutrient contents, pH, and enzymatic activity in the disturbed soil were detected. The effects of the litter treatments on the community structure and carbon source utilization characteristics of soil microorganisms were also studied. The results indicated that all litter treatments significantly accelerated the degradation of petroleum components, while the mixing of litter exhibited significant synergistic effects, leading to significantly higher degradation rates of saturated hydrocarbons, aromatic hydrocarbons, and nonhydrocarbon substances than the observed rates in the single-litter treatments and the predicted rates based on the single-litter treatments. Litter treatment significantly increased the N and P contents and enzymatic activity of contaminated soil. The effects of mixed litter on soil chemical and biological properties fell between the effects of the 2 types of single-litter treatments. However, the mixing of litters exhibited significant synergistic effects in supplementing available P and increasing sucrase, dehydrogenase, lignin peroxidase, and laccase activity, while it exhibited significant antagonistic effects in supplementing nitrate nitrogen and increasing urease, phosphatase, polyphenol oxidase, and manganese peroxidase activity. Litter treatment significantly altered the community structure of soil microorganisms. The relative abundances of some petroleum-degrading microbial phyla or genera in mixed litter-treated soil were significantly different from those in single litter-treated soils, which might contribute to the strengthened remediation effects of mixed litter treatment. The results might provide a theoretical basis for the more effect utilization of biomass resources in the remediation of petroleum-contaminated soil.

Simulation of Microbial Response to Accidental Diesel Spills in Basins Containing Brackish Sea Water and Sediment

The brackish Baltic Sea is under diesel oil pollution risk due to heavy ship traffic. The situation is exasperated by densely distributed marinas and a vigorous although seasonal recreational boating. The seasonality and physical environmental variations hamper the monitoring of microbial communities in response to diesel oil spills. Hence, an 8-week simulation experiment was established in metal basins (containing 265 L sea water and 18 kg quartz sand or natural shore sand as the littoral sediment) to study the effect of accidental diesel oil spills on microbial communities. Our results demonstrated that microbial communities in the surface water responded to diesel oil contamination, whereas those in the littoral sediment did not, indicating that diesel oil degradation mainly happened in the water. Diesel oil decreased the abundance of bacteria and fungi, but increased bacterial diversity in the water. Time was the predominant driver of microbial succession, attributable to the adaption strategies of microbes. Bacteria were more sensitive to diesel oil contamination than fungi and archaea. Diesel oil increased relative abundances of bacterial phyla, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Flavobacteriia and Cytophagia, and fungal phylum Ascomycota in the surface water. Overall, this study improves the understanding of the immediate ecological impact of accidental diesel oil contamination, providing insights into risk management at the coastal area.

Clonal integration in Phragmites australis alters soil microbial communities in an oil-contaminated wetland

Clonal plants can share information and resources among connected ramets (asexual individuals). Such clonal integration can promote ramet growth, which may further influence soil microbial communities in the rooting zone. Crude oil contamination can negatively affect plant growth and alter soil microbial community composition. However, we still know little about how clonal integration affects soil microbial communities, especially under crude oil contamination. In a coastal wetland, ramets of the rhizomatous plant Phragmites australis in circular plots (60 cm in diameter) were subjected to 0, 5 and 10 mm depth of crude oil, and the rhizomes at the edge of the plots were either severed (preventing clonal integration) or left intact (allowing clonal integration). After three years of treatment, we analysed in each plot soil physiochemical properties and soil microbial community composition. The alpha-diversity of the soil microbial communities did not differ between intact and severed plots, but was overall lower in 10-mm than in 0-mm and 5-mm oil plots. Considering all three oil treatments together, soil microbial community dissimilarity (beta-diversity) was positively correlated with soil property distance in both severed and intact plots. Considering the three oil treatments separately, this pattern was also observed in 10-mm oil plots, but not in 0-mm or 5-mm oil plots. The soil microbial community composition was more sensitive to the oil addition than to the clonal integration. Moreover, the relative abundance of the nitrogen-cycling bacterial taxa was lower in intact than in severed plots, and that of the oil-degrading bacterial taxa increased with increasing oil-addition levels. Our results indicate that clonal integration and oil contamination can influence soil microbial communities independently through changing the relative abundance of the component bacteria taxa, which has important implications for ecosystem functions of the soil food web mediated by clonal plants.

Distribution of Bacterial Communities in Petroleum-Contaminated Soils from the Dagang Oilfield, China

Diversity in bacterial communities was investigated along a petroleum hydrocarbon content gradient (0–0.4043 g/g) in surface (5–10 cm) and subsurface (35–40 cm) petroleum-contaminated soil samples from the Dagang Oilfield, China. Using 16S rRNA Illumina high-throughput sequencing technology and several statistical methods, the bacterial diversity of the soil was studied. Subsequently, the environmental parameters were measured to analyze its relationship with the community variation. Nonmetric multidimensional scaling and analysis of similarities indicated a significant difference in the structure of the bacterial community between the nonpetroleum-contaminated surface and subsurface soils, but no differences were observed in different depths of petroleum-contaminated soil. Meanwhile, many significant correlations were obtained between diversity in soil bacterial community and physicochemical properties. Total petroleum hydrocarbon, total organic carbon, and total nitrogen were the three important factors that had the greatest impacts on the bacterial community distribution in the long-term petroleum-contaminated soils. Our research has provided references for the bacterial community distribution along a petroleum gradient in both surface and subsurface petroleum-contaminated soils of oilfield areas.

Characterizations of microbial diversity and machine oil degrading microbes in machine oil contaminated soil

Microbial diversity in machine oil contaminated soil was determined by high-throughput amplicon sequencing technology. The diversity of culturable microbes in the contaminated soil was further characterized using polymerase chain reaction method. Proteobacteria and Bacteroidetes were the most dominant phyla and occupied 52.73 and 16.77%, respectively, while the most abundant genera were Methylotenera (21.62%) and Flavobacterium (3.06%) in the soil. In the culturable microbes, the major phyla were Firmicutes (46.15%) and Proteobacteria (37.36%) and the most abundant genera were Bacillus (42.86%) and Aeromonas (34.07%). Four isolated microbes with high machine oil degradation efficiency were selected to evaluate their characteristics on the oil degradation. All of them reached their highest oil degradation rate after 7 days of incubation. Most of them significantly increased their oil degradation rate by additional carbon or organic nitrogen source in the incubation medium. The oil degradation rate by combination of the four microbes at the same inoculation level was also higher than the rate from each individual microbe. The protocol and findings of this study are very useful for developing micro-bioremediation method to eliminate machine oil contaminants from soil.

Variation in pickleweed root-associated microbial communities at different locations of a saline solid waste management unit contaminated with petroleum hydrocarbons

The main purpose of this study was to explore the potential influences of pickleweed vegetation on the abundance, diversity and metabolic activities of microbial communities in four distinct areas of a petroleum-contaminated solid waste management unit (SWMU) located in Contra Costa County, northern California. The four areas sampled include two central areas, one of which is central vegetated (CV) and one unvegetated (UV), and two peripheral vegetated areas, one of which is located to the west side of the SWMU (V-West) and one located to the east side (V-East). Measurements were made of total petroleum hydrocarbons (TPH), polyaromatic hydrocarbons (PAH), soil physicochemical properties, and various aspects of microbial communities including metabolic activities, microbial abundances (PLFAs), diversity and composition based on amplicon sequencing. The peripheral V-East and V-West sites had 10-times lower electrical conductivity (EC) than that of the CV and UV sites. The high salinity levels of the CV and UV sites were associated with significant reductions in bacterial and fungal abundances (PLFA) when compared to V-East but not when compared to V-West. TPH levels of CV and UV were not significantly different from those of V-West but were substantially lower than V-East TPH (19,311 mg/kg of dry soil), the high value of which may have been associated with a pipeline that ran through the area. Microbial activities (in terms of soil respiration and the activities of three soil enzymes, i.e., urease, lipase, and phosphatase) were greatest in the vegetated sites compared to the UV site. The prokaryotic community was not diverse as revealed by the Shannon index with no significant variation among the four groups of samples. However, the fungal community of the peripheral sites, V-East and V-West had significantly higher OTU richness and Shannon index. Structure of prokaryotic communities inhabiting the rhizosphere of pickleweed plants at the three sites differed significantly and were also different from those found in the UV region of the central site according to pairwise, global PERMANOVA and ANOSIM analyses. The differences in OTU-based rhizosphere-associated bacterial and fungal communities’ composition were explained mainly by the changes in soil EC and pH. The results suggest that saline TPH-contaminated areas that are vegetated with pickleweed are likely to have increased abundances, diversity and metabolic activities in the rhizosphere compared to unvegetated areas, even in the presence of high salinity.

Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China

Microorganisms play important roles in mangrove ecosystems. However, we know little about the ecological implications of mangrove microbiomes for high productivity and the efficient circulation of elements in mangrove ecosystems. Here, we focused on mangrove sediments located at the Yunxiao National Mangrove Reserve in southeast China, uncovering the mangrove microbiome using the 16S rRNA gene and shotgun metagenome sequencing approaches. Physicochemical assays characterized the Yunxiao mangrove sediments as carbon (C)-rich, sulfur (S)-rich, and nitrogen (N)-limited environment. Then phylogenetic analysis profiling a distinctive microbiome with an unexpected high frequency of Chloroflexi and Nitrospirae appeared to be an adaptive characteristic of microbial structure in S-rich habitat. Metagenome sequencing analysis revealed that the metabolic pathways of N and S cycling at the community-level were routed through ammonification and dissimilatory nitrate reduction to ammonium for N conservation in this N-limited habitat, and dissimilatory sulfate reduction along with polysulfide formation for generating bioavailable S resource avoiding the biotoxicity of sulfide in mangrove sediments. In addition, methane metabolism acted as a bridge to connect C cycling to N and S cycling. Further identification of possible biogeochemical linkers suggested Syntrophobacter, Sulfurovum, Nitrospira, and Anaerolinea potentially drive the coupling of C, N, and S cycling. These results highlighting the adaptive routed metabolism flow, a previously undescribed property of mangrove sediment microbiome, appears to be a defining characteristic of this habitat and may significantly contribute to the high productivity of mangrove ecosystems, which could be used as indicators for the health and biodiversity of mangrove ecosystems.

Habitat-dependent composition of bacterial and fungal communities in biological soil crusts from Oman

Biological soil crusts (biocrusts) occur within drylands throughout the world, covering ~12% of the global terrestrial soil surface. Their occurrence in the deserts of the Arabian Peninsula has rarely been reported and their spatial distribution, diversity, and microbial composition remained largely unexplored. We investigated biocrusts at six different locations in the coastal and central deserts of Oman. The biocrust types were characterized, and the bacterial and fungal community compositions of biocrusts and uncrusted soils were analysed by amplicon sequencing. The results were interpreted based on the environmental parameters of the different sites. Whereas at lowland sites, mainly cyanobacteria-dominated biocrusts were observed, both cyanobacteria- and lichen-dominated biocrusts occurred at mountain sites. The majority of bacterial sequences (32–83% of total sequences) belonged to Actinobacteria, Cyanobacteria, Alphaproteobacteria, and Bacteroidetes, whereas fungal sequences belonged to Ascomycota, Basidiomycota, and Chytridiomycota (>95%). With biocrust development, a notable increase in cyanobacterial and decrease in actinobacterial proportions was observed for cyanobacteria-dominated crusts. In coastal areas, where salinity is high, biocrusts were replaced by a unique marine mat-like microbial community, dominated by halotolerant taxa. Redundancy analysis revealed a significant contribution of soil texture, cover type, carbon content, and elevation to the variations in bacterial and fungal communities. Multivariate analysis placed microbial communities in significantly separated clusters based on their carbon content, elevation and electrical conductivity. We conclude that Oman hosts a variety of cyanobacteria- and lichen-dominated crusts with their bacterial and fungal communities being largely dictated by soil properties and environmental parameters.

Cultivated bacterial diversity associated with the carnivorous plant Utricularia breviscapa (Lentibulariaceae) from floodplains in Brazil

Carnivorous plant species, such as Utricularia spp., capture and digest prey. This digestion can occur through the secretion of plant digestive enzymes and/or by bacterial digestive enzymes. To comprehend the physiological mechanisms of carnivorous plants, it is essential to understand the microbial diversity related to these plants. Therefore, in the present study, we isolated and classified bacteria from different organs of Utricularia breviscapa (stolons and utricles) and from different geographic locations (São Paulo and Mato Grosso). We were able to build the first bacterium collection for U. breviscapa and study the diversity of cultivable bacteria. The results show that U. breviscapa bacterial diversity varied according to the geographic isolation site (São Paulo and Mato Grosso) but not the analyzed organs (utricle and stolon). We reported that six genera were common to both sample sites (São Paulo and Mato Grosso). These genera have previously been reported to be beneficial to plants, as well as related to the bioremediation process, showing that these isolates present great biotechnological and agricultural potential. This is the first report of an Acidobacteria isolated from U. breviscapa. The role of these bacteria inside the plant must be further investigated in order to understand their population dynamics within the host.

Treatment of acidic sulfate-containing wastewater using revolving algae biofilm reactors: Sulfur removal performance and microbial community characterization

Industries such as mining operations are facing challenges of treating sulfur-containing wastewater such as acid mine drainage (AMD) generated in their plant. The aim of this work is to evaluate the use of a revolving algal biofilm (RAB) reactor to treat AMD with low pH (3.5-4) and high sulfate content (1-4 g/L). The RAB reactors resulted in sulfate removal efficiency up to 46% and removal rate up to 0.56 g/L-day, much higher than those obtained in suspension algal culture. The high-throughput sequencing revealed that the RAB reactor contained diverse cyanobacteria, green algae, diatoms, and acid reducing bacteria that contribute the sulfate removal through various mechanisms. The RAB reactors also showed a superior performance of COD, ammonia and phosphorus removal. Collectively, the study demonstrated that RAB-based process is an effective method to remove sulfate in wastewater with small footprint and can be potentially installed in municipal or industrial wastewater treatment facilities.

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios.

Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil

Analyzing the microbial community structure and functions become imperative for ecological processes. To understand the impact of spent engine oil (SEO) contamination on microbial community structure of an agricultural soil, soil microcosms designated 1S (agricultural soil) and AB1 (agricultural soil polluted with SEO) were set up. Metagenomic DNA extracted from the soil microcosms and sequenced using Miseq Illumina sequencing were analyzed for their taxonomic and functional properties. Taxonomic profiling of the two microcosms by MG-RAST revealed the dominance of Actinobacteria (23.36%) and Proteobacteria (52.46%) phyla in 1S and AB1 with preponderance of Streptomyces (12.83%) and Gemmatimonas (10.20%) in 1S and Geodermatophilus (26.24%), Burkholderia (15.40%), and Pseudomonas (12.72%) in AB1, respectively. Our results showed that soil microbial diversity significantly decreased in AB1. Further assignment of the metagenomic reads to MG-RAST, Cluster of Orthologous Groups (COG) of proteins, Kyoto Encyclopedia of Genes and Genomes (KEGG), GhostKOALA, and NCBI's CDD hits revealed diverse metabolic potentials of the autochthonous microbial community. It also revealed the adaptation of the community to various environmental stressors such as hydrocarbon hydrophobicity, heavy metal toxicity, oxidative stress, nutrient starvation, and C/N/P imbalance. To the best of our knowledge, this is the first study that investigates the effect of SEO perturbation on soil microbial communities through Illumina sequencing. The results indicated that SEO contamination significantly affects soil microbial community structure and functions leading to massive loss of nonhydrocarbon degrading indigenous microbiota and enrichment of hydrocarbonoclastic organisms such as members of Proteobacteria and Actinobacteria.

Enantiomer signature and carbon isotope evidence for the migration and transformation of DDTs in arable soils across China

Due to the adverse impact of DDTs on ecosystems and humans, a full fate assessment deems a comprehensive study on their occurrence in soils over a large region. Through a sampling campaign across China, we measured the concentrations, enantiomeric fractions (EFs), compound-specific carbon isotope composition of DDT and its metabolites, and the microbial community in related arable soils. The geographically total DDT concentrations are higher in eastern than western China. The EFs and δ¹³C of o,p’-DDT in soils from western China show smaller deviations from those of racemic/standard compound, indicating the DDT residues there mainly result from atmospheric transport. However, the sources of DDT in eastern China are mainly from historic application of technical DDTs and dicofol. The inverse dependence of o,p’-DDT and p,p’-DDE on temperature evidences the transformation of parent DDT to its metabolites. Initial usage, abiotic parameters and microbial communities are found to be the main factors influencing the migration and transformation of DDT isomers and their metabolites in soils. In addition, a prediction equation of DDT concentrations in soils based on stepwise multiple regression analysis is developed. Results from this study offer insights into the migration and transformation pathways of DDTs in Chinese arable soils, which will allow data-based risk assessment on their use.

Kinetics of nutrient enhanced crude oil degradation by Pseudomonas aeruginosa AKS1 and Bacillus sp. AKS2 isolated from Guwahati refinery, India

Bacterial degradation of crude oil in response to nutrient treatments has been vastly studied. But there is a paucity of information on kinetic parameters of crude oil degradation. Here we report the nutrient stimulated kinetic parameters of crude oil degradation assessed in terms of CO2 production and oil removal by Pseudomonas aeruginosa AKS1 and Bacillus sp. AKS2. The hydrocarbon degradation rate of P. aeruginosa AKS1 in oil only amended sediment was 10.75 ± 0.65 μg CO2-C g(-1) sediment day(-1) which was similar to degradation rate in sediments with no oil. In presence of both inorganic N & P, the degradation rate increased to 47.22 ± 1.32 μg CO2-C g(-1) sediment day(-1). The half-saturation constant (Ks) and maximum degradation rate (Vmax) for P. aeruginosa AKS1 under increasing N and saturating P concentration were 13.57 ± 0.53 μg N g(-1) sediment and 39.36 ± 1.42 μg CO2-C g(-1) sediment day(-1) respectively. The corresponding values at increasing P and a constant N concentration were 1.60 ± 0.13 μg P g(-1) sediment and 43.90 ± 1.03 μg CO2-C g(-1) sediment day(-1) respectively. Similarly the degradation rate of Bacillus sp. AKS2 in sediments amended with both inorganic nutrients N & P was seven fold higher than the rates in oil only or nutrient only treated sediments. The Ks and Vmax estimates of Bacillus sp. AKS2 under increasing N and saturating P concentration were 9.96 ± 1.25 μg N g(-1) sediment and 59.96 ± 7.56 μg CO2-C g(-1) sediment day(-1) respectively. The corresponding values for P at saturating N concentration were 0.46 ± 0.24 μg P g(-1) sediment and 63.63 ± 3.54 μg CO2-C g(-1) sediment day(-1) respectively. The rates of CO2 production by both isolates were further stimulated when oil concentration was increased above 12.5 mg g(-1) sediment. However, oil degradation activity declined at oil concentration above 40 mg g(-1) sediment when treated with constant nutrient: oil ratio. Both isolates exhibited alkane hydroxylase activity but aromatic degrading catechol 1, 2-dioxygenase and catechol 2, 3-dioxygenase activities were shown by P. aeruginosa AKS1 only.

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates

Background

Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation.

Results

Taxonomic profiling was carried out by two different complementary approaches i.e. 16S rDNA and lowest common ancestor. The community profiling revealed the enrichment of phylum “Proteobacteria” and genus “Chromobacterium,” respectively for polluted soil sample. Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions.

Conclusion

To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0669-8) contains supplementary material, which is available to authorized users.

EDTA addition enhances bacterial respiration activities and hydrocarbon degradation in bioaugmented and non-bioaugmented oil-contaminated desert soils

The low number and activity of hydrocarbon-degrading bacteria and the low solubility and availability of hydrocarbons hamper bioremediation of oil-contaminated soils in arid deserts, thus bioremediation treatments that circumvent these limitations are required. We tested the effect of Ethylenediaminetetraacetic acid (EDTA) addition, at different concentrations (i.e. 0.1, 1 and 10 mM), on bacterial respiration and biodegradation of Arabian light oil in bioaugmented (i.e. with the addition of exogenous alkane-degrading consortium) and non-bioaugmented oil-contaminated desert soils. Post-treatment shifts in the soils' bacterial community structure were monitored using MiSeq sequencing. Bacterial respiration, indicated by the amount of evolved CO2, was highest at 10 mM EDTA in bioaugmented and non-bioaugmented soils, reaching an amount of 2.2 ± 0.08 and 1.6 ± 0.02 mg-CO2 g(-1) after 14 days of incubation, respectively. GC-MS revealed that 91.5% of the C14-C30 alkanes were degraded after 42 days when 10 mM EDTA and the bacterial consortium were added together. MiSeq sequencing showed that 78-91% of retrieved sequences in the original soil belonged to Deinococci, Alphaproteobacteria, Gammaproteobacteia and Bacilli. The same bacterial classes were detected in the 10 mM EDTA-treated soils, however with slight differences in their relative abundances. In the bioaugmented soils, only Alcanivorax sp. MH3 and Parvibaculum sp. MH21 from the exogenous bacterial consortium could survive until the end of the experiment. We conclude that the addition of EDTA at appropriate concentrations could facilitate biodegradation processes by increasing hydrocarbon availability to microbes. The addition of exogenous oil-degrading bacteria along with EDTA could serve as an ideal solution for the decontamination of oil-contaminated desert soils.

Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes

Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs) were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA) indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

Effect of petroleum on decomposition of shrub-grass litters in soil in Northern Shaanxi of China

The impacts of petroleum contamination on the litter decomposition of shrub-grass land would directly influence nutrient cycling, and the stability and function of ecosystem. Ten common shrub and grass species from Yujiaping oil deposits were studied. Litters from these species were placed into litterbags and buried in petroleum-contaminated soil with 3 levels of contamination (slight, moderate and serious pollution with petroleum concentrations of 15, 30 and 45 g/kg, respectively). A decomposition experiment was then conducted in the lab to investigate the impacts of petroleum contamination on litter decomposition rates. Slight pollution did not inhibit the decomposition of any litters and significantly promoted the litter decomposition of Hippophae rhamnoides, Caragana korshinskii, Amorpha fruticosa, Ziziphus jujuba var. spinosa, Periploca sepium, Medicago sativa and Bothriochloa ischaemum. Moderate pollution significantly inhibited litter decomposition of M. sativa, Coronilla varia, Artemisia vestita and Trrifolium repens and significantly promoted the litter decomposition of C. korshinskii, Z. jujuba var. spinosa and P. sepium. Serious pollution significantly inhibited the litter decomposition of H. rhamnoides, A. fruticosa, B. ischaemum and A. vestita and significantly promoted the litter decomposition of Z. jujuba var. spinosa, P. sepium and M. sativa. In addition, the impacts of petroleum contamination did not exhibit a uniform increase or decrease as petroleum concentration increased. Inhibitory effects of petroleum on litter decomposition may hinder the substance cycling and result in the degradation of plant communities in contaminated areas.