Microbial population dynamics associated with crude-oil biodegradation in diverse soils

Spatial distribution of PAHs and microbial communities in intertidal sediments of the Pearl River Estuary, South China

The exploration of sediment pollution caused by PAHs and its impact on microbial communities can provide valuable insights for the remediation of sediments. The spatial distribution of PAHs and their impact on the microbial community within the Pearl River Estuary were investigated in this study. The findings revealed that the total concentration ranges of 16 PAHs were between 24.26 and 3075.93 ng/g, with naphthalene, fluorene, and phenanthrene potentially exerting adverse biological effects. More PAHs were found to accumulate in subsurface sediments, and their average accumulation rates gradually decreased as the number of rings in PAHs increased, ranging from 180 % for 2-ring to 36 % for 6-ring. The phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Chloroflexi were found to dominate both surface and subsurface sediments The correlation between microbial genera and PAHs contents was weak in sediments with low levels of PAHs contamination, while a more significant positive relationship was observed in sediments with high levels of PAHs contamination. The physicochemical properties of sediments, such as pH, soil structure and Cu significantly influence bacterial community composition in highly contaminated sediments. Additionally, the network analysis revealed that certain bacterial genera, including Novosphingobium, Robiginitalea and Synechococcus_CC9902, played a pivotal role in the degradation of PAHs. These findings are significant in comprehending the correlation between bacterial communities and environmental factors in intertidal ecosystems, and establish a scientific foundation for bioremediation of intertidal zones.

Trends in Antarctic soil fungal research in the context of environmental changes

Antarctic soils represent one of the most pristine environments on Earth, where highly adapted and often endemic microbial species withstand multiple extremes. Specifically, fungal diversity is extremely low in Antarctic soils and species distribution and diversity are still not fully characterized in the continent. Despite the unique features of this environment and the international interest in its preservation, several factors pose severe threats to the conservation of inhabiting ecosystems. In this light, we aimed to provide an overview of the effects on fungal communities of the main changes endangering the soils of the continent. Among these, the increasing human presence, both for touristic and scientific purposes, has led to increased use of fuels for transport and energy supply, which has been linked to an increase in unintentional environmental contamination. It has been reported that several fungal species have evolved cellular processes in response to these soil contamination episodes, which may be exploited for restoring contaminated areas at low temperatures. Additionally, the effects of climate change are another significant threat to Antarctic ecosystems, with the expected merging of previously isolated ecosystems and their homogenization. A possible reduction of biodiversity due to the disappearance of well-adapted, often endemic species, as well as an increase of biodiversity, due to the spreading of non-native, more competitive species have been suggested. Despite some studies describing the specialization of fungal communities and their correlation with environmental parameters, our comprehension of how soil communities may respond to these changes remains limited. The majority of studies attempting to precisely define the effects of climate change, including in situ and laboratory simulations, have mainly focused on the bacterial components of these soils, and further studies are necessary, including the other biotic components.

Assessment and Biodegradation of Polycyclic Aromatic Hydrocarbons in Soil and Water Around Petroleum Products Depot Suleja, Nigeria

Petroleum contamination constitutes a frequent incidence in various petroleum depots in Nigeria. In this study, the polycyclic aromatic hydrocarbons (PAHs) present in soil and water in communities around Petroleum Products Marketing Company (PPMC) Suleja, Nigeria, were evaluated and degraded using indigenous microorganisms. The samples sites were divided into 7 plots from where samples of water and soil were obtained: one within the PPMC depot, five from communities surrounding the depot, and the control 93,000 km from the depot. The microbial counts were determined using spread plate inoculation technique on minimal salt media. The microbial isolates were characterized and identified based on their cultural, biochemical, and molecular characteristics. The potential of the microbial isolates to utilize 0.05 mL of diesel, kerosene, engine oil, and crude oil was determined in a Bushnell Haas Broth, and the biodegradation was determined by total viable cell counts and spectrophotometry. The ability of the isolates to mineralize PAHs was also evaluated in a minimum salt media. The bacterial isolates were species of Streptococcus, Pseudomonas, Staphylococcus, Proteus, Escherichia, and Bacillus, while species of Penicillium, Aspergillus, Mucor, and Rhizopus were isolated among the fungi. Aspergillus niger strain ATCC 1015 and Bacillus thuringiensis strain M43 showed high capacity to utilize the 16 priority PAHs. The pahE1 gene was used by Bacillus thuringiensis, Pseudomonas aeruginosa and A. niger, while Penicillium notatum used pahE2 gene for the degradation of the PAH. The current study identified microbial isolates that can utilize priority PAHs, making them beneficial for oil spill bioremediation in tropical environments.

Unravelling the role of the group 6 soluble di-iron monooxygenase (SDIMO) SmoABCD in alkane metabolism and chlorinated alkane degradation

Soluble di-iron monooxygenases (SDIMOs) are multi-component enzymes catalysing the oxidation of various substrates. These enzymes are characterized by high sequence and functional diversity that is still not well understood despite their key role in biotechnological processes including contaminant biodegradation. In this study, we analysed a mutant of Rhodoccocus aetherivorans BCP1 (BCP1-2.10) characterized by a transposon insertion in the gene smoA encoding the alpha subunit of the plasmid-located SDIMO SmoABCD. The mutant BCP1-2.10 showed a reduced capacity to grow on propane, lost the ability to grow on butane, pentane and n-hexane and was heavily impaired in the capacity to degrade chloroform and trichloroethane. The expression of the additional SDIMO prmABCD in BCP1-2.10 probably allowed the mutant to partially grow on propane and to degrade it, to some extent, together with the other short-chain n-alkanes. The complementation of the mutant, conducted by introducing smoABCD in the genome as a single copy under a constitutive promoter or within a plasmid under a thiostreptone-inducible promoter, allowed the recovery of the alkanotrophic phenotype as well as the capacity to degrade chlorinated n-alkanes. The heterologous expression of smoABCD allowed a non-alkanotrophic Rhodococcus strain to grow on pentane and n-hexane when the gene cluster was introduced together with the downstream genes encoding alcohol and aldehyde dehydrogenases and a GroEL chaperon. BCP1 smoA gene was shown to belong to the group 6 SDIMOs, which is a rare group of monooxygenases mostly present in Mycobacterium genus and in a few Rhodococcus strains. SmoABCD originally evolved in Mycobacterium and was then acquired by Rhodococcus through horizontal gene transfer events. This work extends the knowledge of the biotechnologically relevant SDIMOs by providing functional and evolutionary insights into a group 6 SDIMO in Rhodococcus and demonstrating its key role in the metabolism of short-chain alkanes and degradation of chlorinated n-alkanes.

Residual hydrocarbons in long-term contaminated soils: implications to risk-based management

Petroleum hydrocarbon (PHC) contamination is a widespread and severe environmental issue affecting many countries' resource sectors. PHCs are mixtures of hydrocarbon compounds with varying molar masses that naturally attenuate at different rates. Lighter fractions attenuate first, followed by medium-molar-mass constituents, while larger molecules remain for longer periods. This results in significant regulatory challenges concerning residual hydrocarbons in long-term contaminated soils. This study examined the potential risks associated with residual PHC and its implications for risk-based management of heavily contaminated soils (23,000-26,000 mg PHC/kg). Ecotoxicological properties, such as seedling emergence and growth of two native plant species-small Flinders grass (Iseilema membranaceum) and ruby saltbush (Enchylaena tomentosa)-and earthworm survival tests in PHC-contaminated soils, were assessed. Additionally, the effects of aging on the attenuation of PHC in contaminated soils were evaluated. Toxicity responses of plant growth parameters were determined as no-observed-effect concentrations: 75%-100% for seedling emergence, < 25%-75% for plant shoot height, and 75%-100% for earthworm survival. After 42 weeks of aging, the total PHC levels in weathered soils decreased by 14% to 30% and by 67% in diesel-spiked soil due to natural attenuation. Dehydrogenase enzyme activity in soils increased during the initial aging period. Furthermore, a clear shift of bacterial communities was observed in the soils following aging, including enrichment of PHC-resistant and -utilizing bacteria-for example, Nocardia sp. This study underscores the potential of natural attenuation for eco-friendly and cost-effective soil management, underlining that its success depends on site-specific factors like water content and nutrient availability. Therefore, we recommend detailed soil assessments to evaluate these conditions prior to adopting a risk-based management approach.

Genomic analysis and biodesulfurization potential of a new carbon-sulfur bond cleaving Tsukamurella sp. 3OW

Direct combustion of sulfur-enriched liquid fuel oil causes sulfur oxide emission, which is one of the main contributors to air pollution. Biodesulfurization is a promising and eco-friendly method to desulfurize a wide range of thiophenic compounds present in fuel oil. Previously, numerous bacterial strains from genera such as Rhodococcus, Corynebacterium, Gordonia, Nocardia, Mycobacterium, Mycolicibacterium, Paenibacillus, Shewanella, Sphingomonas, Halothiobacillus, and Bacillus have been reported to be capable of desulfurizing model thiophenic compounds or fossil fuels. In the present study, we report a new desulfurizing bacterium, Tsukamurella sp. 3OW, capable of desulfurization of dibenzothiophene through the carbon-sulfur bond cleavage 4S pathway. The bacterium showed a high affinity for the hydrocarbon phase and broad substrate specificity towards various thiophenic compounds. The overall genome-related index analysis revealed that the bacterium is closely related to Tsukamurella paurometabola species. The genomic pool of strain 3OW contains 57 genes related to sulfur metabolism, including the key dszABC genes responsible for dibenzothiophene desulfurization. The DBT-adapted cells of the strain 3OW displayed significant resilience and viability in elevated concentrations of crude oil. The bacterium showed a 19 and 37% reduction in the total sulfur present in crude and diesel oil, respectively. Furthermore, FTIR analysis indicates that the oil's overall chemistry remained unaltered following biodesulfurization. This study implies that Tsukamurella paurometabola species, previously undocumented in the context of biodesulfurization, has good potential for application in the biodesulfurization of petroleum oils.

Oil-Contaminated Soil Remediation with Biodegradation by Autochthonous Microorganisms and Phytoremediation by Maize (Zea mays)

Biological methods are currently the most commonly used methods for removing hazardous substances from land. This research work focuses on the remediation of oil-contaminated land. The biodegradation of aliphatic hydrocarbons and PAHs as a result of inoculation with biopreparations B1 and B2 was investigated. Biopreparation B1 was developed on the basis of autochthonous bacteria, consisting of strains Dietzia sp. IN118, Gordonia sp. IN101, Mycolicibacterium frederiksbergense IN53, Rhodococcus erythropolis IN119, Rhodococcus globerulus IN113 and Raoultella sp. IN109, whereas biopreparation B2 was enriched with fungi, such as Aspergillus sydowii, Aspergillus versicolor, Candida sp., Cladosporium halotolerans, Penicillium chrysogenum. As a result of biodegradation tests conducted under ex situ conditions for soil inoculated with biopreparation B1, the concentrations of TPH and PAH were reduced by 31.85% and 27.41%, respectively. Soil inoculation with biopreparation B2 turned out to be more effective, as a result of which the concentration of TPH was reduced by 41.67% and PAH by 34.73%. Another issue was the phytoremediation of the pre-treated G6-3B2 soil with the use of Zea mays. The tests were carried out in three systems (system 1-soil G6-3B2 + Zea mays; system 2-soil G6-3B2 + biopreparation B2 + Zea mays; system 3-soil G6-3B2 + biopreparation B2 with γ-PGA + Zea mays) for 6 months. The highest degree of TPH and PAH reduction was obtained in system 3, amounting to 65.35% and 60.80%, respectively. The lowest phytoremediation efficiency was recorded in the non-inoculated system 1, where the concentration of TPH was reduced by 22.80% and PAH by 18.48%. Toxicological tests carried out using PhytotoxkitTM, OstracodtoxkitTM and Microtox® Solid Phase tests confirmed the effectiveness of remediation procedures and showed a correlation between the concentration of petroleum hydrocarbons in the soil and its toxicity. The results obtained during the research indicate the great potential of bioremediation practices with the use of microbial biopreparations and Zea mays in the treatment of soils contaminated with petroleum hydrocarbons.

Impacts of Arctic diesel contamination on microbial community composition and degradative gene abundance during hydrocarbon biodegradation with and without nutrients: A case study of seven sub-Arctic soils

Although a number of studies have assessed hydrocarbon degradation or microbial responses in petroleum contaminated soils, few have examined both and/or assessed impacts in multiple soils simultaneously. In this study petroleum hydrocarbon biodegradation and microbial activity was monitored in seven sub-Arctic soils at similar levels (∼3500-4000 mg/kg) of Arctic diesel (DSL), amended with moisture and nutrients (70 mg-N/kg, 78 mg-P/kg), and incubated at site-representative summer temperatures (∼7 °C) under water unsaturated conditions. Total petroleum hydrocarbon (TPH) biodegradation extents (42.7-85.4 %) at 50 days were slightly higher in nutrient amended (DSL + N,P) than unamended (DSL) systems in all but one soil. Semi-volatile (C₁₀-C₁₆) hydrocarbons were degraded to a greater extent (40-80 %) than non-volatile (C₁₆-C₂₄) hydrocarbons (20-40 %). However, more significant shifts in microbial diversity and relative abundance of genera belonging to Actinobacteria and Proteobacteria phyla were observed in DSL + N,P than in DSL systems in all soils. Moreover, higher abundance of the alkane degrading gene alkB were observed in DSL + N,P systems than in DSL systems for all soils. The more significant microbial community response in the DSL + N,P systems indicate that addition of nutrients may have influenced the microbial community involved in degradation of carbon sources other than the diesel compounds, such as the soil organic matter or degradation intermediates of diesel compounds. Nocardioides, Arthrobacter, Marmoricola, Pseudomonas, Polaromonas, and Massilia genera were present in high relative abundance in the DSL systems suggesting those genera contained hydrocarbon degraders. Overall, the results suggest that the extents of microbial community shifts or alkB copy number increases may not be closely correlated to the increase in hydrocarbon biodegradation and thus bioremediation performance between various treatments or across different soils.

Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments

Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.

Magnetic susceptibility as a proxy for detection of total petroleum hydrocarbons in contaminated wetlands

Soil petroleum hydrocarbon contamination in the wetlands could cause ecological risk, especially through leakage into water reservoirs. So, the detection of the spatial variability of total petroleum hydrocarbons (TPH) in these soils is very crucial. The variability of TPH and its associations with magnetic susceptibility (χ_lf) in contaminated soils around the Shadegan pond in southern Iran was investigated. TPH varied from 2.1 to 18.1% (w/w), by the variation of χ_lf from 14.08 to 713.93 × 10^-8 m³ kg^-1. The highest variability (coefficient of variation, CV = 107.12%) was obtained for χ_lf indicating significant impacts of magnetic minerals induced by crude oil contamination. High positive correlations were detected among TPH, χ_lf, and different forms of iron (Fe_d: extracted by CBD, Fe_o: extracted by oxalate, and Fe_t: total iron). The results of mineralogy by powdery XRD and scanning electron microscopy (SEM), also revealed the formation of ferrimagnetic minerals (magnetite, maghemite) during the biodegradation of petroleum hydrocarbons. The stepwise multiple regression analysis showed that χ_lf and Fe_d made a great contribution and could explain about 74% of TPH variability in the studied sites. For the extension of this cost-effective and rapid technique, further work is needed to assay saturation isothermal remnant magnetization and isothermal remanet magnetization in contaminated sites.

Rhodococcus strains as a good biotool for neutralizing pharmaceutical pollutants and obtaining therapeutically valuable products: Through the past into the future

Active pharmaceutical ingredients present a substantial risk when they reach the environment and drinking water sources. As a new type of dangerous pollutants with high chemical resistance and pronounced biological effects, they accumulate everywhere, often in significant concentrations (μg/L) in ecological environments, food chains, organs of farm animals and humans, and cause an intense response from the aquatic and soil microbiota. Rhodococcus spp. (Actinomycetia class), which occupy a dominant position in polluted ecosystems, stand out among other microorganisms with the greatest variety of degradable pollutants and participate in natural attenuation, are considered as active agents with high transforming and degrading impacts on pharmaceutical compounds. Many representatives of rhodococci are promising as unique sources of specific transforming enzymes, quorum quenching tools, natural products and novel antimicrobials, biosurfactants and nanostructures. The review presents the latest knowledge and current trends regarding the use of Rhodococcus spp. in the processes of pharmaceutical pollutants’ biodegradation, as well as in the fields of biocatalysis and biotechnology for the production of targeted pharmaceutical products. The current literature sources presented in the review can be helpful in future research programs aimed at promoting Rhodococcus spp. as potential biodegraders and biotransformers to control pharmaceutical pollution in the environment.

A metagenomic portrait of the microbial community responsible for two decades of bioremediation of poly-contaminated groundwater

Biodegradation of pollutants is a sustainable and cost-effective solution to groundwater pollution. Here, we investigate microbial populations involved in biodegradation of poly-contaminants in a pipeline for heavily contaminated groundwater. Groundwater moves from a polluted park to a treatment plant, where an aerated bioreactor effectively removes the contaminants. While the biomass does not settle in the reactor, sediment is collected afterwards and used to seed the new polluted groundwater via a backwash cycle. The pipeline has successfully operated since 1999, but the biological components in the reactor and the contaminated park groundwater have never been described. We sampled seven points along the pipeline, representing the entire remediation process, and characterized the changing microbial communities using genome-resolved metagenomic analysis. We assembled 297 medium- and high-quality metagenome-assembled genome sequences representing on average 46.3% of the total DNA per sample. We found that the communities cluster into two distinct groups, separating the anaerobic communities in the park groundwater from the aerobic communities inside the plant. In the park, the community is dominated by members of the genus Sulfuricurvum, while the plant is dominated by generalists from the order Burkholderiales. Known aromatic compound biodegradation pathways are four times more abundant in the plant-side communities compared to the park-side. Our findings provide a genome-resolved portrait of the microbial community in a highly effective groundwater treatment system that has treated groundwater with a complex contamination profile for two decades.

Vertical distribution characteristics and interactions of polycyclic aromatic compounds and bacterial communities in contaminated soil in oil storage tank areas

Polycyclic aromatic compound (PAC) contamination in soil as a result of oil spills is a serious issue because of the huge global demand for fossil energy. This study assessed the vertical variation in polycyclic aromatic hydrocarbons (PAHs), derivatives of PAHs (dPAHs) and bacterial community structure in deep soil with long-term contamination by oil spillage. Our results suggest that the content of total PACs ranged from 1196.6 μg/kg to 14980.9 μg/kg and decreased with depth at all sites. PAHs were the most abundant PACs, with a mean concentration of 6640.7 μg/kg, followed by oxygenated PAHs (mean 156.3 μg/kg) and nitrated PAHs (mean 33.4 μg/kg). PAHs are mainly low molecular weight PACs such as naphthalene, fluorene and phenanthrene, while derivatives of PAHs are all low molecular weight PACs and mainly oxygenated PAHs. Low molecular weight PAHs were an important source of dPAHs under specific conditions. The bacterial community structure showed higher bacterial diversity and lower bacterial richness in shallow soil (2-6 m in depth) than in deep soil (8-10 m in depth). Spearman's analysis confirmed that dramatic bacterial community shifts are a response to contamination. At the genus level, the presence of PACs highly selected for Pseudomonas, belonging to Proteobacteria. Moreover, functional predictions based on Tax4Fun revealed that soil with long-term contamination had a strong potential for PAC degradation. In addition, statistical analysis showed that oxidation-reduction potential (Eh) was closely related to variations of bacterial community composition and function. Finally, Ramlibacter, Pseudomonas, Pseudonocardia, c_MB-A2-108, f_Amb-16S-1323, and Qipengyuania were identified by cooccurrence network analysis as keystone taxa contributing to the maintenance of bacterial ecological function. Together, our results provide evidence of tight bacterial effects of PAHs and dPAHs and a more complete understanding of the fate of PACs in deep contaminated soils.

Biomineralization of cyanobacteria Synechocystis pevalekii improves the durability properties of cement mortar

Microbially induced calcium carbonate precipitation (MICCP) is considered a novel eco-friendly technique to enhance the structural properties of cementitious-based material. Maximum studies have emphasized using ureolytic bacteria to improve the durability properties of building structures. In this study, the role of photoautotrophic bacteria Synechocystis pevalekii BDHKU 35101 has been investigated for calcium carbonate precipitation in sand consolidation, and enhancing mechanical and permeability properties of cement mortar. Both live and UV-treated S. pevalekii cells were used to treat the mortar specimens, and the results were compared with the control. The compressive strength of mortar specimens was significantly enhanced by 25.54% and 15.84% with live and UV-treated S. pevalekii cells at 28-day of curing. Water absorption levels were significantly reduced in bacterial-treated mortar specimens compared to control at 7 and 28-day curing. Calcium carbonate precipitation was higher in live-treated cells than in UV-treated S. pevalekii cells. Calcium carbonate precipitation by S. pevalekii cells was confirmed with SEM-EDS, XRD, and TGA analysis. These results suggest that S. pevalekii can serve as a low-cost and environment friendly MICCP technology to improve the durability properties of cementitious materials. 

Cyanobacterial Synechocystis pevalekii cells induced calcification on cement mortar.

Both live and UV-treated cells increased the compressive strength and reduced the water absorption.

Biomineralization by S. pevalekii serves as a low-cost and eco-friendly MICCP technology.

Complex impacts of hydraulic fracturing return fluids on soil microbial community respiration, structure, and functional potentials

The consequences of soils exposed to hydraulic fracturing (HF) return fluid, often collectively termed flowback and produced water (FPW), are poorly understood, even though soils are a common receptor of FPW spills. Here, we investigate the impacts on soil microbiota exposed to FPW collected from the Montney Formation of western Canada. We measured soil respiration, microbial community structure, and functional potentials under FPW exposure across a range of concentrations, exposure time, and soil types (luvisol and chernozem). We find that soil type governs microbial community response upon FPW exposure. Within each soil, FPW exposure led to reduced biotic soil respiration, and shifted microbial community structure and functional potentials. We detect substantially higher species richness and more unique functional genes in FPW-exposed soils than in FPW-unexposed soils, with metagenome-assembled genomes (e.g., Marinobacter persicus) from luvisol soil exposed to concentrated FPW being most similar to genomes from HF/FPW sites. Our data demonstrate the complex impacts of microbial communities following FPW exposure, and highlight the site-specific effects in evaluation of spills and agricultural reuse of FPW on the normal soil functions. This article is protected by copyright. All rights reserved.

Evaluation of the Effectiveness of the Biopreparation in Combination with the Polymer γ-PGA for the Biodegradation of Petroleum Contaminants in Soil

Biodegradation is a method of effectively removing petroleum hydrocarbons from the natural environment. This research focuses on the biodegradation of aliphatic hydrocarbons, monoaromatic hydrocarbons such as benzene, toluene, ethylbenzene, and all three xylene isomers (BTEX) and polycyclic aromatic hydrocarbons (PAHs) as a result of soil inoculation with a biopreparation A1 based on autochthonous microorganisms and a biopreparation A1 with the addition of γ-PGA. The research used biopreparation A1 made of the following strains: Dietzia sp. IN133, Gordonia sp. IN138 Mycolicibacterium frederiksbergense IN53, Rhodococcus erythropolis IN119, Rhodococcus sp. IN136 and Pseudomonas sp. IN132. The experiments were carried out in laboratory conditions (microbiological tests, respirometric tests, and in semi-technical conditions (ex-situ prism method). The biodegradation efficiency was assessed on the basis of respirometric tests, chromatographic analyses and toxicological tests. As a result of inoculation of AB soil with the biopreparation A1 within 6 months, a reduction of total petroleum hydrocarbons (TPH) (66.03%), BTEX (80.08%) and PAHs (38.86%) was achieved and its toxicity was reduced. Inoculation of AB soil with the biopreparation A1 with the addition of γ-PGA reduced the concentration of TPH, BTEX and PAHs by 79.21%, 90.19%, and 51.18%, respectively, and reduced its toxicity. The conducted research has shown that the addition of γ-PGA affects the efficiency of the biodegradation process of petroleum pollutants, increasing the degree of TPH biodegradation by 13.18%, BTEX by 10.11% and PAHs by 12.32% compared to pure biopreparation A1.

Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes

Antarctic soils generally have low temperatures and limited availability of liquid water and nutrients. However, animals can increase the nutrient availability of ice-free areas by transferring nutrients from marine to terrestrial ecosystems, mainly through their excreta. In this study, we employed shotgun metagenomics and population genome binning techniques to study the diversity of microbial communities in Antarctic soils impacted by marine pinnipeds and birds relative to soils with no evident animal presence. We obtained ~285,000 16S rRNA gene-carrying metagenomic reads representing ~60 phyla and 100 metagenome-assembled genomes (MAGs) representing eight phyla. Only nine of these 100 MAGs represented previously described species, revealing that these soils harbor extensive novel diversity. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla in all samples, with Rhodanobacter being one of the most abundant genera in the bird-impacted soils. Further, the relative abundance of genes related to denitrification was at least double in soils impacted by birds than soils without animal influence. These results advance our understanding of the microbial populations and their genes involved in nitrous oxide emissions in ice-free coastal Antarctic soils impacted by marine animals and reveal novel microbial diversity associated with these ecosystems.

Bioremediation of Polycyclic Aromatic Hydrocarbons from Industry Contaminated Soil Using Indigenous Bacillus spp

Polycyclic aromatic hydrocarbons (PAHs) are reportedly toxic, ubiquitous and organic compounds that can persist in the environment and are released largely due to the incomplete combustion of fossil fuel. There is a range of microorganisms that are capable of degrading low molecular weight PAHs, such as naphthalene; however, fewer were reported to degrade higher molecular weight PAHs. Bacillus spp. has shown to be effective in neutralizing polluted streams containing hydrocarbons. Following the growing regulatory requirement to meet the PAH specification upon disposal of contaminated soil, the following study aimed to identify potential Bacillus strains that could effectively remediate low and high molecular weight PAHs from the soil. Six potential hydrocarbon-degrading strains were formulated into two prototypes and tested for the ability to remove PAHs from industry-contaminated soil. Following the dosing of each respective soil system with prototypes 1 and 2, the samples were analyzed for PAH concentration over 11 weeks against an un-augmented control system. After 11 weeks, the control system indicated the presence of naphthalene (3.11 µg·kg−1), phenanthrene (24.47 µg·kg−1), fluoranthene (17.80 µg·kg−1) and pyrene (28.92 µg·kg−1), which illustrated the recalcitrant nature of aromatic hydrocarbons. The soil system dosed with prototype 2 was capable of completely degrading (100%) naphthalene, phenanthrene and pyrene over the experimental period. However, the accumulation of PAHs, namely phenanthrene, fluoranthene and pyrene, were observed using prototype 1. The results showed that prototype 2, consisting of a combination of Bacillus cereus and Bacillus subtilis strains, was more effective in the biodegradation of PAHs and intermediate products. Furthermore, the bio-augmented system dosed with prototype 2 showed an improvement in the overall degradation (10–50%) of PAHs, naphthalene, phenanthrene and pyrene, over the un-augmented control system. The following study demonstrates the potential of using Bacillus spp. in a bioremediation solution for sites contaminated with PAHs and informs the use of biological additives for large-scale environmental remediation.

Responses to Ecopollutants and Pathogenization Risks of Saprotrophic Rhodococcus Species

Under conditions of increasing environmental pollution, true saprophytes are capable of changing their survival strategies and demonstrating certain pathogenicity factors. Actinobacteria of the genus Rhodococcus, typical soil and aquatic biotope inhabitants, are characterized by high ecological plasticity and a wide range of oxidized organic substrates, including hydrocarbons and their derivatives. Their cell adaptations, such as the ability of adhering and colonizing surfaces, a complex life cycle, formation of resting cells and capsule-like structures, diauxotrophy, and a rigid cell wall, developed against the negative effects of anthropogenic pollutants are discussed and the risks of possible pathogenization of free-living saprotrophic Rhodococcus species are proposed. Due to universal adaptation features, Rhodococcus species are among the candidates, if further anthropogenic pressure increases, to move into the group of potentially pathogenic organisms with "unprofessional" parasitism, and to join an expanding list of infectious agents as facultative or occasional parasites.

Erosion reduces soil microbial diversity, network complexity and multifunctionality

While soil erosion drives land degradation, the impact of erosion on soil microbial communities and multiple soil functions remains unclear. This hinders our ability to assess the true impact of erosion on soil ecosystem services and our ability to restore eroded environments. Here we examined the effect of erosion on microbial communities at two sites with contrasting soil texture and climates. Eroded plots had lower microbial network complexity, fewer microbial taxa, and fewer associations among microbial taxa, relative to non-eroded plots. Soil erosion also shifted microbial community composition, with decreased relative abundances of dominant phyla such as Proteobacteria, Bacteroidetes, and Gemmatimonadetes. In contrast, erosion led to an increase in the relative abundances of some bacterial families involved in N cycling, such as Acetobacteraceae and Beijerinckiaceae. Changes in microbiota characteristics were strongly related with erosion-induced changes in soil multifunctionality. Together, these results demonstrate that soil erosion has a significant negative impact on soil microbial diversity and functionality.

Assessment of the Suitability of Melilotus officinalis for Phytoremediation of Soil Contaminated with Petroleum Hydrocarbons (TPH and PAH), Zn, Pb and Cd Based on Toxicological Tests

The article presents issues related to the possibility of using toxicological tests as a tool to monitor the progress of soil treatment contaminated with petroleum substances (TPH, PAH), Zn, Pb and Cd in bio-phytoremediation processes. In order to reduce the high content of petroleum pollutants (TPH = 56,371 mg kg⁻¹ dry mass, PAH = 139.3 mg kg⁻¹ dry mass), the technology of stepwise soil treatment was applied, including basic bioremediation and inoculation with biopreparations based of indigenous non-pathogenic species of bacteria, fungi and yeasts. As a result of basic bioremediation in laboratory conditions (ex-situ method), the reduction of petroleum pollutants TPH by 33.9% and PAH by 9.5% was achieved. The introduction of inoculation with biopraparation-1 prepared on the basis of non-pathogenic species of indigenous bacteria made it possible to reduce the TPH content by 86.3%, PAH by 40.3%. The use of a biopreparation-1 enriched with indigenous non-pathogenic species of fungi and yeasts in the third series of inoculation increased to an increase in the degree of biodegradation of aliphatic hydrocarbons with long carbon chains and PAH by a further 28.9%. In the next stage of soil treatment after biodegradation processes, which was characterized by an increased content of heavy metals (Zn, Pb, Cd) and naphthalene, chrysene, benzo(a)anthracene and benzo(ghi)perylene belonging to polycyclic aromatic hydrocarbons, phytoremediation with the use of Melilotus officinalis was applied. After the six-month phytoremediation process, the following was achieved: Zn content by 25.1%, Pb by 27.9%, Cd by 23.2% and TPH by 42.2% and PAH by 49.9%. The rate of removal of individual groups of hydrocarbons was in the decreasing order: C₁₂–C₁₈ > C₆–C₁₂ > C₁₈–C₂₅ > C₂₅–C₃₆. PAHs tended to be removed in the following order: chrysene > naphthalene > benzo(a)anthracene > benzo(ghi)perylene. The TF and BCF coefficients were calculated to assess the capacity of M. officinalis to accumulate metal in tissues, uptake from soil and transfer from roots to shoots. The values of TF translocation coefficients were, respectively, for Zn (0.44), Pb (0.12), Cd (0.40). The calculated BCF concentration factors (BCF_roots > BCF_shoots) show that heavy metals taken up by M. officinalis are mainly accumulated in the root tissues in the following order Zn > Pb > Cd, revealing a poor metal translocation from the root to the shoots. This process was carried out in laboratory conditions for a period of 6 months. The process of phytoremediation of contaminated soil using M. officinalis assisted with fertilization was monitored by means of toxicological tests: Microtox, Ostracodtoxkit F^TM, MARA and Phytotoxkit^TM. The performed phytotoxicity tests have indicated variable sensitivity of the tested plants on contaminants occurring in the studied soils, following the sequence: Lepidium sativum < Sorghum saccharatum < Sinapis alba. The sensitivity of toxicological tests was comparable and increased in the order: MARA < Ostracodtoxkit F^TM < Microtox. The results of the toxicological monitoring as a function of the time of soil treatment, together with chemical analyses determining the content of toxicants in soil and biomass M. officinalis, clearly confirmed the effectiveness of the applied concept of bioremediation of soils contaminated with zinc, lead and cadmium in the presence of petroleum hydrocarbons.

Appropriate human intervention stimulates the development of microbial communities and soil formation at a long-term weathered bauxite residue disposal area

Bauxite residue discharged to disposal areas, which could generate environmental pollution issues. Long-term natural restoration may improve the physicochemical properties of the residues, in turn supporting vegetation establishment, and effectively managing pollution. Nevertheless, the effects of short-term human intervention on soil formation in the weathered disposal areas are still relatively unknown. Thus, residue samples with different depths from different regions including no vegetation, sparse vegetation, complete vegetation coverage, and complete vegetation coverage following sewage sludge treatment were selected to analyze microbial community using Illumina high-throughput sequencing technology and evaluate soil formation process. Long-term weathering changed pH, the fraction of water-stable aggregates and nutrient concentrations, whilst promoting Proteobacteria, Chloroflexi, Acidobacteria and Planctomycete populations. Sewage sludge addition enhanced aggregate stability and significantly changed microbial community diversity. Sewage sludge application enriched the relative abundances of Proteobacteria and Bacteroidetes, whilst decreasing the relative abundance of Acidobacteria, which may be due to variation in environmental factors. Canonical correspondence analysis revealed that pH and EC were the main factors affecting microbial structure, followed by organic carbon content and aggregate stability. The results enhance the understanding of soil formation in bauxite residue and reveal the potential benefit of human intervention in ecological reconstruction at disposal areas.

Rhizosphere assisted bioengineering approaches for the mitigation of petroleum hydrocarbons contamination in soil

The high demand for petroleum oil has led to hydrocarbon contamination in soil, including agricultural lands, and many other ecosystems across the globe. Physical and chemical treatments are effective strategies for the removal of high contamination levels and are useful for small areas, although with concerns of cost-effectiveness. Alternatively, several bacteria belonging to the Phylum: Proteobacteria, Bacteroidetes, Actinobacteria, Nocardioides, or Firmicutes are used for biodegradation of different hydrocarbons - aliphatic, polyaromatic hydrocarbons (PAH), and asphaltenes in the oil-contaminated soil. The rhizoremediation strategy with plant-microbe interactions has prospects to achieve the desired result in the field conditions. However, adequate biostimulation, and bioaugmentation with the suitable plant-microbe combination, and efficiency under a toxic environment needs to be evaluated. Modifying the microbiomes to achieve better biodegradation of contaminants is an upcoming strategy popularly known as microbiome engineering. In this review, rhizoremediation for the successful removal of the hydrocarbons have been critically discussed, with challenges for making it a feasible technology.HIGHLIGHTSPetroleum hydrocarbon contamination has increased around the globe.Rhizoremediation has the potential for the mitigation of pollutants from the contaminated sites.An accurate and detailed analysis of the physio-chemical and climatic conditions of the contaminated sites must be focused on.The suitable plant and bacteria, with other major considerations, may be employed for in-situ remediation.The appropriate data should be obtained using the omics approach to help toward the success of the rhizoremediation strategy.

Microbial diversity and co-occurrence patterns in deep soils contaminated by polycyclic aromatic hydrocarbons (PAHs)

Numerous studies have enriched our knowledge of the microbial community composition and metabolic versatility of contaminated soil. However, there remains a substantial gap regarding the bioassembly patterns of the indigenous microbial community distribution in contaminated deep soils. Herein, the indigenous microbial community structure diversity, function, and co-occurrence relationships in aged PAH-contaminated deep soil collected from an abandoned chemical facility were investigated using high-throughput sequencing. The results showed that the dominant phyla in all samples were responsible for PAH degradation and included Proteobacteria (20.86%-81.37%), Chloroflexi (2.03%-28.44%), Firmicutes (3.06%-31.16%), Actinobacteria (2.92%-11.91%), Acidobacteria (0.41%-12.68%), and Nitrospirae (0.81%-9.21%). Eighty biomarkers were obtained by linear discriminant analysis of effect size (LEfSe), and most of these biomarkers were PAH degraders. Functional predictions using Tax4Fun indicated that the aged contaminated soil has the potential for PAH degradation. Statistical analysis showed that in contrast with the PAH concentration, edaphic properties (nutrients and pH) were significantly correlated (r > 0.25, P < 0.01) with the bacterial community and functional composition. Co-occurrence network analysis (modularity index of 0.781) revealed non-random assembly patterns of the bacterial communities in the PAH-contaminated soils. The modules in the network were mainly involved in carbon and nitrogen cycles, organic substance degradation, and biological electron transfer processes. Microbes from the same module had strong ecological linkages. Additionally, SAR202 clade, Thermoanaerobaculum, Nitrospira, and Xanthomonadales, which were identified as keystone species, played an irreplaceable role in the network. Overall, our results suggested that environmental factors such as nutrients and pH, together with ecological function, are the main factors driving the assembly of microbial communities in aged PAH-contaminated deep soils.

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.

Geo-distribution pattern of microbial carbon cycling genes responsive to petroleum contamination in continental horizontal oilfields

Contamination significantly affects soil microbial community structures, and the metabolisms of organic contaminants might particularly alter soil carbon cycling by shaping microbial carbon cycling genes. Although numerous studies have discussed the impacts of petroleum contamination on soil bacterial communities and relevant degrading genes, there is no work addressing how soil carbon cycling genes are affected by petroleum contamination. In this study, 77 soil samples were collected from five typical oilfields horizontally located in China to explore the influence of environmental variables and petroleum contamination on microbial carbon cycling genes. Results from Geochip suggested a geographic-determined distribution of carbon cycling genes. Although no significant correlation was observed between carbon cycling genes and soil physio-chemical properties for all soils, some relationships were identified in specific oilfield. Principle component analysis indicated that soil physio-chemical properties, rather than petroleum contamination disturbance, are the key factors determining the degree of sample dispersion, whereas environmental variables predominantly control the degree of sample aggregation. Co-occurrence ecological network analysis revealed a more complex interactions of all functional genes in petroleum-contaminated soils, and carbon cycling genes were grouped with nitrogen related genes in petroleum-contaminated communities. Soil moisture and heterogeneity were identified as the main drivers for the abundance and diversity of carbon cycling genes, particularly in petroleum-contaminated soils. These results are attributing to the fewer impacts of petroleum contamination on the diversity of carbon cycling genes than soil physio-chemical properties, and soil carbon cycling genes are mainly driven by geographic location and petroleum contamination together. Our findings provide deeper insight into the influence of petroleum contamination in soil microbial functions related to carbon cycling.

Transcriptome analysis of crude oil degrading Pseudomonas aeruginosa strains for identification of potential genes involved in crude oil degradation

In the microbial world, bacteria are the most effective agents in petroleum hydrocarbons (PHs) degradation, utilization/mineralization and they serve as essential degraders of crude oil contaminated environment. Some genes and traits are involved in the hydrocarbon utilization process for which transcriptome analyses are important to identify differentially expressed genes (DEGs) among different conditions, leading to a new understanding of genes or pathways associated with crude oil degradation. In this work, three crude oil utilizing Pseudomonas aeruginosa strains designated as N002, TP16 and J001 subjected to transcriptome analyses revealed a total of 81, 269 and 137 significant DEGs. Among them are 80 up-regulated genes and one downregulated gene of N002, 121 up- regulated and 148 down-regulated genes of TP16, 97 up-regulated and 40 down-regulated genes of J001 which are involved in various metabolic pathways. TP16 strain has shown more number of DEGs upon crude oil treatment in comparison to the other two strains. Through quantitative real time polymerase chain reaction (qRT-PCR), the selected DEGs of each strain from transcriptome data were substantiated. The results have shown that the up- regulated and down-regulated genes observed by qRT-PCR were consistent with transcriptome data. Taken together, our transcriptome results have revealed that TP16 is a potential P. aeruginosa strain for functional analysis of identified potential DEGs involved in crude oil degradation.

Transcriptome profiling reveals the molecular processes for survival of Lysinibacillus fusiformis strain 15-4 in petroleum environments

A bacterial strain designated Lysinibacillus fusiformis 15-4 was isolated from oil-free soil on the Qinghai-Tibet Plateau, which can grow well utilizing petroleum hydrocarbons as a carbon source at a lower temperature. To deeply characterize the molecular adaptations and metabolic processes of this strain when grown in a petroleum-containing environment, transcriptome analysis was performed. A total of 4664 genes and the expression of 3969 genes were observed in strain 15-4. When the strain was grown in petroleum-containing medium, 2192 genes were significantly regulated, of which 1312 (60%) were upregulated and 880 (40%) were downregulated. This strain degraded and adapted to petroleum via modulation of diverse molecular processes, including improvements in transporter activity, oxidoreductase/dehydrogenase activity, two-component system/signal transduction, transcriptional regulation, fatty acid catabolism, amino acid metabolism, and environmental stress responses. Many strain-specific genes were involved in the oxidation of hydrocarbon compounds, such as several luciferase family alkane monooxygenase genes, flavin-utilizing monooxygenase family genes, and flavoprotein-like family alkanesulfonate monooxygenase genes. Several cold shock protein genes were also induced suggesting adaptation to cold environments and the potential for petroleum degradation at low temperatures. The results obtained in this study may broaden our understanding of molecular adaptation of bacteria to hydrocarbon-containing environments and may provide valuable data for further study of L. fusiformis.

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.

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.

Bacteria with Different Assemblages in the Soil Profile Drive the Diverse Nutrient Cycles in the Sugarcane Straw Retention Ecosystem

Straw retention, an alternative to artificial fertilization, commonly mitigates soil degradation and positively affects soil fertility. In this study, we investigated the succession of soil bacteria during two sugarcane straw retention treatments (control (CK) and sugarcane straw retention (SR)) and at four depths (0–10, 10–20, 20–30, and 30–40 cm) in fallow soil in a sugarcane cropping system. Using an Illumina MiSeq (16S rRNA) and soil enzyme activity, we explored the SR influence on soil bacterial communities and enzyme activities and its inclusive impact on soil fertility, with an emphasis on topsoil (0–10 cm) and subsoil (10–40 cm). Our results show that SR effectively improved soil fertility indicators (C, N, and P), including enzyme activities (C and N cycling), throughout the soil profile: these soil parameters greatly improved in the topsoil compared to the control. Sugarcane straw retention and soil depth (0–10 cm vs. 10–40 cm) were associated with little variation in bacterial species richness and alpha diversity throughout the soil profile. Subsoil and topsoil bacterial communities differed in composition. Compared to the CK treatment, SR enriched the topsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, and Nitrospirae, while the subsoil was depleted in Nitrospirae and Acidobacteria. Similarly, SR enriched the subsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, Gemmatimonadetes, and Bacteroidetes, while the topsoil was depleted in Acidobacteria, Gemmatimonadetes, and Planctomycetes compared to the CK. At the genus level, SR enriched the topsoil with Gp1, Gp2, Gp5, Gp7, Gemmatimonas, Kofleria, Sphingomonas, and Gaiella, which decompose lignocellulose and contribute to nutrient cycling. In summary, SR not only improved soil physicochemical properties and enzyme activities but also enriched bacterial taxa involved in lignocellulosic decomposition and nutrient cycling (C and N) throughout the soil profile. However, these effects were stronger in topsoil than in subsoil, suggesting that SR enhanced fertility more in topsoil than in subsoil in fallow land.

Study on the influence of soil microbial community on the long-term heavy metal pollution of different land use types and depth layers in mine

To understand the importance of the response of soil microbial communities to the stress of heavy metals around mining areas by assessing the feedback of soil ecosystems in different soil habitats, this article selected different land use types (Mining area, Dressing area, Heap mine area, Tailings area and Vegetable field) and surface soil samples of different depths (0-10 cm, 10-20 cm, 20-30 cm) as the variables related to the mining activities in the Shizishan mining area in Tongling, Anhui Province, China. Soil physicochemical properties and heavy metal concentrations of the different land use types and soil depths were compared. Illumina MiSeq. 2500 Sequencing Technology was used to analyze the abundance and structural diversity of the microbial community in soil samples. The relationship between mine soil pollution characteristics and microbial community were investigated. The results showed that soil physicochemical properties and heavy metals significantly affected the microbial community. The microbial community structure was significantly variable in vertical soil depth-layer habitats. The relative abundance (1%) of the soil microbial community at the phylum level was represented by a total of 14 phyla, where the two most dominant phyla were Proteobacteria (41.71%) and Firmicutes (20.44%). The two bacteria were positively related with Cu, Zn, Pb, and pH but negatively associated with soil organic matter (SOM), available potassium (AK), and moisture content (MC). Therefore, Proteobacteria and Firmicutes were highly resistant to heavy metals. These results increased our understanding of microbial variation and assembly pattern under different land use types in heavy metals contaminated mining soils.

Influence of bacterial community composition and soil factors on the fate of phenanthrene and benzo[a]pyrene in three contrasting farmland soils

The fate of polycyclic aromatic hydrocarbons (PAHs) determines their potential risk in soil, which may be directly affected by abiotic conditions and indirectly through the changes in decomposer communities. In comparison, the indirect effects on the fate remain largely elusive. In this study, the fate of phenanthrene and benzo[a]pyrene and the corresponding bacterial changes were investigated in three contaminated farmland soils using a ¹⁴C tracer method and Miseq sequencing. The results showed that most benzo[a]pyrene was consistently extractable with dichloromethane (DCM) after the 60-day incubation (60.4%-78.2%), while phenanthrene was mainly mineralized to CO₂ during the 30-day incubation (40.4%-58.7%). Soils from Guangzhou (GZ) showed a different distribution pattern of ¹⁴C-PAHs exemplified by low mineralization and disparate bound residue formation. The PAH fate in the Shenyang (SY) and Nanjing (NJ) soils were similar to each other than to that in the GZ soil. The fate in the GZ soil seemed to be linked to the distinct edaphic properties, such as organic matter content, however soil microbial community could have influenced the distribution pattern of PAHs. This potential role of microorganisms was reflected by the unique changes in the copy numbers of Gram positive RHD_α gene, and by the distinct shifts in bacterial community composition during the incubation. A quite different shift in bacterial communities was found in the GZ microcosms which may influence PAH mineralization and non-extractable residue (NER) formation.

Synergistic plant-microbes interactions in the rhizosphere: a potential headway for the remediation of hydrocarbon polluted soils

Soil pollution is an unavoidable evil; many crude-oil exploring communities have been identified to be the most ecologically impacted regions around the world due to hydrocarbon pollution and their concurrent health risks. Several clean-up technologies have been reported on the removal of hydrocarbons in polluted soils but most of them are either very expensive, require the integration of advanced mechanization and/or cannot be implemented in small scale. However, "Bioremediation" has been reported as an efficient, cost-effective and environment-friendly technology for clean-up of hydrocarbon"s contaminated soils. Here, we suggest the implementation of synergistic mechanism of bioremediation such as the use of rhizosphere mechanism which involves the actions of plant and microorganisms, which involves the exploitation of plant and microorganisms for effective and speedy remediation of hydrocarbon"s contaminated soils. In this mechanism, plant"s action is synergized with the soil microorganisms through the root rhizosphere to promote soil remediation. The microorganisms benefit from the root metabolites (exudates) and the plant in turn benefits from the microbial recycling/solubilizing of mineral nutrients. Harnessing the abilities of plants and microorganisms is a potential headway for cost-effective clean-up of hydrocarbon"s polluted sites; such technology could be very important in countries with great oil producing activities/records over many years but still developing.

The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil

Planococcus maritimus Y42, isolated from the petroleum-contaminated soil of the Qaidam Basin, can use crude oil as its sole source of carbon and energy at 20 °C. The genome of P. maritimus strain Y42 has been sequenced to provide information on its properties. Genomic analysis shows that the genome of strain Y42 contains one circular DNA chromosome with a size of 3,718,896 bp and a GC content of 48.8%, and three plasmids (329,482; 89,073; and 12,282 bp). Although the strain Y42 did not show a remarkably higher ability in degrading crude oil than other oil-degrading bacteria, the existence of strain Y42 played a significant role to reducing the overall environmental impact as an indigenous oil-degrading bacterium. In addition, genome annotation revealed that strain Y42 has many genes responsible for hydrocarbon degradation. Structural features of the genomes might provide a competitive edge for P. maritimus strain Y42 to survive in oil-polluted environments and be worthy of further study in oil degradation for the recovery of crude oil-polluted environments.

16S metagenomic analysis reveals adaptability of a mixed-PAH-degrading consortium isolated from crude oil-contaminated seawater to changing environmental conditions

A bacterial consortium, named SWO, was enriched from crude oil-contaminated seawater from Phrao Bay in Rayong Province, Thailand, after a large oil spill in 2013. The bacterial consortium degraded a polycyclic aromatic hydrocarbon (PAH) mixture consisting of phenanthrene, anthracene, fluoranthene, and pyrene (50 mg L^-1 each) by approximately 73%, 69%, 52%, and 48%, respectively, within 21 days. This consortium exhibited excellent adaptation to a wide range of environmental conditions. It could degrade a mixture of four PAHs under a range of pH values (4.0-9.0), temperatures (25 °C-37 °C), and salinities (0-10 g L^-1 with NaCl). In addition, this consortium degraded 20-30% of benzo[a]pyrene and perylene (10 mg L^-1 each), high molecular weight PAHs, in the presence of other PAHs within 35 days, and degraded 40% of 2% (v/v) crude oil within 20 days. The 16S rRNA gene amplicon sequencing analysis demonstrated that Pseudomonas and Methylophaga were the dominant genera of consortium SWO in almost all treatments, while Pseudidiomarina, Thalassospira and Alcanivorax were predominant under higher salt concentrations. Moreover, Pseudomonas and Alcanivorax were dominant in the crude oil-degradation treatment. Our results suggest that the consortium SWO maintained its biodegradation ability by altering the bacterial community profile upon encountering changes in the environmental conditions.

Effects of permafrost collapse on soil bacterial communities in a wet meadow on the northern Qinghai-Tibetan Plateau

Background

Permafrost degradation may develop thermokarst landforms, which substantially change physico–chemical characteristics in the soil as well as the soil carbon stock. However, little is known about changes of bacterial community among the microfeatures within thermokarst area.

Results

We investigated bacterial communities using the Illumina sequencing method and examined their relationships with soil parameters in a thermokarst feature on the northern Qinghai-Tibetan Plateau. We categorized the ground surface into three different micro-relief patches based on the type and extent of permafrost collapse (control, collapsing and subsided areas). Permafrost collapse significantly decreased the soil carbon density and moisture content in the upper 10 cm samples in the collapsing areas. The highest loading factors for the first principal component (PC) extracted from the soil parameters were soil carbon and nitrogen contents, while soil moisture content and C:N ratios were the highest loading factors for the second PC. The relative abundance of Acidobacteria decreased with depth. Bacterial diversity in subsided areas was higher than that in control areas.

Conclusions

Bacterial community structure was significantly affected by pH and depth. The relative abundance of Gemmatimonadetes and Firmicutes were significantly correlated with the first and second PCs extracted from multiple soil parameters, suggesting these phyla could be used as indicators for the soil parameters in the thermokarst terrain.

Electronic supplementary material

The online version of this article (10.1186/s12898-018-0183-y) contains supplementary material, which is available to authorized users.

Potential of dissimilatory nitrate reduction pathways in polycyclic aromatic hydrocarbon degradation

This study investigates the potential of an indigenous estuarine microbial consortium to degrade two polycyclic aromatic hydrocarbons (PAHs), naphthalene and fluoranthene, under nitrate-reducing conditions. Two physicochemically diverse sediment samples from the Lima Estuary (Portugal) were spiked individually with 25 mg L^-1 of each PAH in laboratory designed microcosms. Sediments without PAHs and autoclaved sediments spiked with PAHs were run in parallel. Destructive sampling at the beginning and after 3, 6, 12, 30 and 63 weeks incubation was performed. Naphthalene and fluoranthene levels decreased over time with distinct degradation dynamics varying with sediment type. Next-generation sequencing (NGS) of 16 S rRNA gene amplicons revealed that the sediment type and incubation time were the main drivers influencing the microbial community structure rather than the impact of PAH amendments. Predicted microbial functional analyses revealed clear shifts and interrelationships between genes involved in anaerobic and aerobic degradation of PAHs and in the dissimilatory nitrate-reducing pathways (denitrification and dissimilatory nitrate reduction to ammonium - DNRA). These findings reinforced by clear biogeochemical denitrification signals (NO₃^- consumption, and NH₄⁺ increased during the incubation period), suggest that naphthalene and fluoranthene degradation may be coupled with denitrification and DNRA metabolism. The results of this study contribute to the understanding of the dissimilatory nitrate-reducing pathways and help uncover their involvement in degradation of PAHs, which will be crucial for directing remediation strategies of PAH-contaminated anoxic sediments.

Characterization of the genome of a Nocardia strain isolated from soils in the Qinghai-Tibetan Plateau that specifically degrades crude oil and of this biodegradation

A strain of Nocardia isolated from crude oil-contaminated soils in the Qinghai-Tibetan Plateau degrades nearly all components of crude oil. This strain was identified as Nocardia soli Y48, and its growth conditions were determined. Complete genome sequencing showed that N. soli Y48 has a 7.3 Mb genome and many genes responsible for hydrocarbon degradation, biosurfactant synthesis, emulsification and other hydrocarbon degradation-related metabolisms. Analysis of the clusters of orthologous groups (COGs) and genomic islands (GIs) revealed that Y48 has undergone significant gene transfer events to adapt to changing environmental conditions (crude oil contamination). The structural features of the genome might provide a competitive edge for the survival of N. soli Y48 in oil-polluted environments and reflect the adaptation of coexisting bacteria to distinct nutritional niches.

Organic carbon availability limiting microbial denitrification in the deep vadose zone

Microbes in the deep vadose zone play an essential role in the mitigation of nitrate leaching; however, limited information is available on the mechanisms of microbial denitrification due to sampling difficulties. We experimentally studied the factors that affect denitrification in soils collected down to 10.5 meters deep along the soil profile. After an anoxic pre-incubation, denitrification rates moderately increased and the N₂ O/(N₂ O + N₂ ) ratios declined while the microbial abundance and diversity did not change significantly in most of the layers. Denitrification rate was significantly enhanced and the abundance of the denitrification genes was simultaneously elevated by the increased availability of organic carbon in all studied layers, to a greater extent in the subsurface layers than in the surface layers, suggesting the severe scarcity of carbon in the deep vadose zone. The genera Pseudomonas and Bacillus, which are made up of a number of species that have been previously identified as denitrifiers in soil, were the major taxa that respond to carbon addition. Overall, our results suggested that the limited denitrification in the deep vadose zone is not because of the lack of denitrifiers, but due to the low abundance of denitrifiers which is caused by low carbon availability.

Aerobic degradation of crude oil by microorganisms in soils from four geographic regions of China

A microcosm experiment was conducted for 112 d by spiking petroleum hydrocarbons into soils from four regions of China. Molecular analyses of soils from microcosms revealed changes in taxonomic diversity and oil catabolic genes of microbial communities. Degradation of total petroleum hydrocarbons (TPHs) in Sand from the Bohai Sea (SS) and Northeast China (NE) exhibited greater microbial mineralization than those of the Dagang Oilfield (DG) and Xiamen (XM). High-throughput sequencing and denaturing gradient gel electrophoresis (DGGE) profiles demonstrated an obvious reconstruction of the bacterial community in all soils. The dominant phylum of the XM with clay soil texture was Firmicutes instead of Proteobacteria in others (DG, SS, and NE) with silty or sandy soil texture. Abundances of alkane monooxygenase gene AlkB increased by 10- to 1000-fold, relative to initial values, and were positively correlated with rates of degradation of TPHs and n-alkanes C13-C30. Abundances of naphthalene dioxygenase gene Nah were positively correlated with degradation of naphthalene and total tricyclic PAHs. Redundancy analysis (RDA) showed that abiotic process derived from geographical heterogeneity was the primary effect on bioremediation of soils contaminated with oil. The optimization of abiotic and biotic factors should be the focus of future bioremediation of oil contaminated soil.

Effects of stand age and soil properties on soil bacterial and fungal community composition in Chinese pine plantations on the Loess Plateau

The effects of Chinese pine (Pinus tabuliformis) on soil variables after afforestation have been established, but microbial community changes still need to be explored. Using high-throughput sequencing technology, we analyzed bacterial and fungal community composition and diversity in soils from three stands of different-aged, designated 12-year-old (PF1), 29-year-old (PF2), and 53-year-old (PF3), on a Chinese pine plantation and from a natural secondary forest (NSF) stand that was almost 80 years old. Abandoned farmland (BL) was also analyzed. Shannon index values of both bacterial and fungal community in PF1 were greater than those in PF2, PF3 and NSF. Proteobacteria had the lowest abundance in BL, and the abundance increased with stand age. The abundance of Actinobacteria was greater in BL and PF1 soils than those in other sites. Among fungal communities, the dominant taxa were Ascomycota in BL and PF1 and Basidiomycota in PF2, PF3 and NSF, which reflected the successional patterns of fungal communities during the development of Chinese pine plantations. Therefore, the diversity and dominant taxa of soil microbial community in stands 12 and 29 years of age appear to have undergone significant changes; afterward, the soil microbial community achieved a relatively stable state. Furthermore, the abundances of the most dominant bacterial and fungal communities correlated significantly with organic C, total N, C:N, available N, and available P, indicating the dependence of these microbes on soil nutrients. Overall, our findings suggest that the large changes in the soil microbial community structure of Chinese pine plantation forests may be attributed to the phyla present (e.g., Proteobacteria, Actinobacteria, Ascomycota and Basidiomycota) which were affected by soil carbon and nutrients in the Loess Plateau.

Mechanisms of distinct activated carbon and biochar amendment effects on petroleum vapour biofiltration in soil

We studied the effects of two percent by weight activated carbon versus biochar amendments in 93 cm long sand columns on the biofiltration of petroleum vapours released by a non-aqueous phase liquid (NAPL) source. Activated carbon greatly enhanced, whereas biochar slightly reduced, the biofiltration of volatile petroleum hydrocarbons (VPHs) over 430 days. Sorbent amendment benefitted the VPH biofiltration by retarding breakthrough during the biodegradation lag phase. Subsequently, sorbent amendment briefly reduced the mineralization of petroleum hydrocarbons by limiting their bioavailability. During the last and longest study period, when conditions became less supportive of microbial growth, because of inorganic nutrient scarcity, the sorbents again improved the pollution attenuation by preventing the degrading microorganisms from being overloaded with VPHs. A 16S rRNA gene based analysis showed sorbent amendment effects on soil microbial communities. Nocardioidaceae benefitted the most from petroleum hydrocarbons in activated carbon amended soil, whereas Pseudomonadacea predominated in unamended soil. Whilst the degrading microorganisms were overloaded with VPHs in the unamended soil, the reduced mobility and bioavailability of VPHs in the activated carbon amended soil led to the emergence of communities with higher specific substrate affinity, which removed bioavailable VPHs effectively at low concentrations. A numerical pollutant fate model reproduced these experimental observations by considering sorption effects on the pollutant migration and bioavailability for growth of VPH degrading biomass, which is limited by a maximum soil biomass carrying capacity. Activated carbon was a much stronger sorbent for VPHs than biochar, which explained the diverging effects of the two sorbents in this study.

Polychlorinated Biphenyl (PCB)-Degrading Potential of Microbes Present in a Cryoconite of Jamtalferner Glacier

Aiming to comprehensively survey the potential pollution of an alpine cryoconite (Jamtalferner glacier, Austria), and its bacterial community structure along with its biodegrading potential, first chemical analyses of persistent organic pollutants, explicitly polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) as well as polycyclic aromatic hydrocarbons (PAHs), revealed a significant contamination. In total, 18 PCB congeners were detected by high resolution gas chromatography/mass spectrometry with a mean concentration of 0.8 ng/g dry weight; 16 PAHs with an average concentration of 1,400 ng/g; and 26 out of 29 OCPs with a mean concentration of 2.4 ng/g. Second, the microbial composition was studied using 16S amplicon sequencing. The analysis revealed high abundances of Proteobacteria (66%), the majority representing α-Proteobacteria (87%); as well as Cyanobacteria (32%), however high diversity was due to 11 low abundant phyla comprising 75 genera. Biodegrading potential of cryoconite bacteria was further analyzed using enrichment cultures (microcosms) with PCB mixture Aroclor 1242. 16S rDNA analysis taxonomically classified 37 different biofilm-forming and PCB-degrading bacteria, represented by Pseudomonas, Shigella, Subtercola, Chitinophaga, and Janthinobacterium species. Overall, the combination of culture-dependent and culture-independent methods identified degrading bacteria that can be potential candidates to develop novel bioremediation strategies.

Shift in microbial group during remediation by enhanced natural attenuation (RENA) of a crude oil-impacted soil: a case study of Ikarama Community, Bayelsa, Nigeria

Acute and chronic pollution of environments with crude oil does not bode well for biota living within the vicinity of polluted environments. This is due to environmental and public health concerns on the negative impact of crude oil pollution on living organisms. Enhancing microbial activities by adding nutrients and other amendments had proved effective in pollutant removal during bioremediation. This study was carried out to determine how microbial group respond during remediation by enhanced natural attenuation (RENA) during a field-scale bioremediation. Crude oil-polluted soil samples were collected (before, during, and after remediation) from a site undergoing remediation by enhanced natural attenuation (RENA) at Ikarama Community, Bayelsa State, Nigeria, and were analyzed for total petroleum hydrocarbon (TPH), polyaromatic hydrocarbon (PAH), and a shift in microbial community. The gas chromatography-flame ionization detector (GC-FID) results showed that the pollutant concentrations (TPH and PAH) reduced by 98 and 85%, respectively, after the remediation. Culturable hydrocarbon utilizing bacteria (CHUB) was highest (8.3 × 10⁴ cfu/g) for sample collected during the remediation studies, whilst sample collected after remediation had low CHUB (6.1 × 10⁴ cfu/g) compared to that collected before remediation (7.7 × 10⁴ cfu/g). Analysis of 16S rRNA of the isolated CHUB showed they belonged to eight bacterial genera namely: Achromobacter, Alcaligenes, Azospirillus, Bacillus, Lysinibacillus, Ochrobactrum, Proteus, and Pusillimonas, with Alcaligenes as the dominant genus. In this study, it was observed that the bacterial community shifted from mixed group (Gram-positive and -negative) before and during the remediation, to only the latter group after the remediation studies. The betaproteobacteria groups were the dominant isolated bacterial phylotype. This study showed that RENA is an effective method of reducing pollutant concentration in crude oil-polluted sites, and could be applied to other polluted sites in the Niger Delta region of Nigeria to mitigate the devastating effects of crude oil pollution.