Characterization of hydrocarbon-degrading microbial populations in contaminated and pristine Alpine soils

Real-time in situ detection of petroleum hydrocarbon pollution in soils via a novel optical methodology

Petroleum hydrocarbon (PHC) contamination in soils is considered one of the most serious problems currently, of which the detection and identification is a fairly significant but challenging work. Conventional methods to do such work usually need complex sample pretreatment, consume much time and fail to do the in-situ detection. This paper set out to create a novel systematic methodology to realize the goals accurately and efficiently. Based on laser-induced breakdown spectroscopy (LIBS) and self-improved machine learning methods, the innovative methodology only uses extremely simple devices to do the real-time in situ detection and identification work and even realize the quantitative analysis of pollution level accurately. In the study, clean soils mixed with petroleum were served as polluted samples, clean soils to be the blank group for comparison. Based on the elemental information from the spectra obtained by LIBS, machine learning methods were improved and helped optimized the algorithm to identify the PHC polluted soil samples for the first time. Furthermore, a novel model was designed to perform the quantitative analysis of the concentration of PHC pollution in soils, which can be applied to detect the degree of PHC contamination in soils accurately. Finally, the harmful volatile component of the PHC polluted soils was also successfully and identified despite its extremely minimal content in the air. The newly-designed methodology is novel and efficient, which has extensive application prospect in the real-time in situ detection of petroleum hydrocarbon pollution.

Pseudomonas and Pseudarthrobacter are the key players in synergistic phenanthrene biodegradation at low temperatures

Hydrocarbon contamination, including contamination with polycyclic aromatic hydrocarbons (PAHs), is a major concern in Antarctica due to the toxicity, recalcitrance and persistence of these compounds. Under the Antarctic Treaty, nonindigenous species are not permitted for use in bioremediation at polluted sites in the Antarctic region. In this study, three bacterial consortia (C13, C15, and C23) were isolated from Antarctic soils for phenanthrene degradation. All isolated bacterial consortia demonstrated phenanthrene degradation percentages ranging from 45 to 85% for 50 mg/L phenanthrene at 15 ℃ within 5 days. Furthermore, consortium C13 exhibited efficient phenanthrene degradation potential across a wide range of environmental conditions, including different temperature (4-30 ℃) and water availability (without polyethylene glycol (PEG) 6000 or 30% PEG 6000 (w/v)) conditions. Sequencing analysis of 16S rRNA genes revealed that Pseudomonas and Pseudarthrobacter were the dominant genera in the phenanthrene-degrading consortia. Moreover, six cultivable strains were isolated from these consortia, comprising four strains of Pseudomonas, one strain of Pseudarthrobacter, and one strain of Paeniglutamicibacter. These isolated strains exhibited the ability to degrade 50 mg/L phenanthrene, with degradation percentages ranging from 4 to 22% at 15 ℃ within 15 days. Additionally, the constructed consortia containing Pseudomonas spp. and Pseudarthrobacter sp. exhibited more effective phenanthrene degradation (43-52%) than did the individual strains. These results provide evidence that Pseudomonas and Pseudarthrobacter can be potential candidates for synergistic phenanthrene degradation at low temperatures. Overall, our study offers valuable information for the bioremediation of PAH contamination in Antarctic environments.

Sulfonamide Per- and Polyfluoroalkyl Substances Can Impact Microorganisms Used in Aromatic Hydrocarbon and Trichloroethene Bioremediation

Per- and polyfluoroalkyl substances (PFASs) from aqueous film forming foams (AFFFs) can hinder bioremediation of co-contaminants such as trichloroethene (TCE) and benzene, toluene, ethylbenzene, and xylene (BTEX). Anaerobic dechlorination can require bioaugmentation of Dehalococcoides, and for BTEX, oxygen is often sparged to stimulate in situ aerobic biodegradation. We tested PFAS inhibition to TCE and BTEX bioremediation by exposing an anaerobic TCE-dechlorinating coculture, an aerobic BTEX-degrading enrichment culture, and an anaerobic toluene-degrading enrichment culture to n-dimethyl perfluorohexane sulfonamido amine (AmPr-FHxSA), perfluorohexane sulfonamide (FHxSA), perfluorohexanesulfonic acid (PFHxS), or nonfluorinated surfactant sodium dodecyl sulfate (SDS). The anaerobic TCE-dechlorinating coculture was resistant to individual PFAS exposures but was inhibited by >1000× diluted AFFF. FHxSA and AmPr-FHxSA inhibited the aerobic BTEX-degrading enrichment. The anaerobic toluene-degrading enrichment was not inhibited by AFFF or individual PFASs. Increases in amino acids in the anaerobic TCE-dechlorinating coculture compared to the control indicated stress response, whereas the BTEX culture exhibited lower concentrations of all amino acids upon exposure to most surfactants (both fluorinated and nonfluorinated) compared to the control. These data suggest the main mechanisms of microbial toxicity are related to interactions with cell membrane synthesis as well as protein stress signaling.

Degradation and enhanced oil recovery potential of Alcanivorax borkumensis through production of bio-enzyme and bio-surfactant

Microbial enhanced oil recovery (EOR) has become the focus of oilfield research due to its low cost, environmental friendliness and sustainability. The degradation and EOR capacity of A. borkumensis through the production of bio-enzyme and bio-surfactant were first investigated in this study. The total protein concentration, acetylcholinesterase, esterase, lipase, alkane hydroxylase activity, surface tension, and emulsification index (EI) were determined at different culture times. The bio-surfactant was identified as glycolipid compound, and the yield was 2.6 ± 0.2 g/L. The nC12 and nC13 of crude oil were completely degraded, and more than 40.0 % of nC14-nC24 was degraded by by A. borkumensis. The results of the microscopic etching model displacement and core flooding experiments showed that emulsification was the main mechanism of EOR. A. borkumensis enhanced the recovery rate by 20.2 %. This study offers novel insights for the development of environmentally friendly and efficient oil fields.

Revisiting the role of Acinetobacter spp. in side-stream enhanced biological phosphorus removal (S2EBPR) systems

We piloted the incorporation of side-stream enhanced biological phosphorus removal (S2EBPR) with A/B stage short-cut nitrogen removal processes to enable simultaneous carbon-energy-efficient nutrients removal. This unique configuration and system conditions exerted selective force on microbial populations distinct from those in conventional EBPR. Interestingly, effective P removal was achieved with the predominance of Acinetobacter (21.5 ± 0.1 %) with nearly negligible level of known conical PAOs (Ca. Accumulibacter and Tetrasphaera were 0.04 ± 0.10 % and 0.47 ± 0.32 %, respectively). Using a combination of techniques, such as fluorescence in situ hybridization (FISH) coupled with single cell Raman spectroscopy (SCRS), the metabolic tracing of Acinetobacter-like cells exerted PAO-like phenotypic profiling. In addition, comparative metagenomics analysis of the closely related Acinetobacter spp. revealed the EBPR relevant metabolic pathways. Further oligotyping analysis of 16s rRNA V4 region revealed sub-clusters (microdiversity) of the Acinetobacter and revealed that the sub-group (oligo type 1, identical (100 % alignment identity) hits from Acinetobacter_midas_s_49494, and Acinetobacter_midas_s_55652) correlated with EBPR activities parameters, provided strong evidence that the identified Acinetobacter most likely contributed to the overall P removal in our A/B-shortcut N-S2EBPR system. To the best of our knowledge, this is the first study to confirm the in situ EBPR activity of Acinetobacter using combined genomics and SCRS Raman techniques. Further research is needed to identify the specific taxon, and phenotype of the Acinetobacter that are responsible for the P-removal.

Metagenomic analysis reveals the microbial response to petroleum contamination in oilfield soils

The response of the microbes to total petroleum hydrocarbons (TPHs) in three types of oilfield soils was researched using metagenomic analysis. The ranges of TPH concentrations in the grassland, abandoned well, working well soils were 1.16 × 102-3.50 × 102 mg/kg, 1.14 × 103-1.62 × 104 mg/kg, and 5.57 × 103-3.33 × 104 mg/kg, respectively. The highest concentration of n-alkanes and 16 PAHs were found in the working well soil of Shengli (SL) oilfield compared with those in Nanyang (NY) and Yanchang (YC) oilfields. The abandoned well soils showed a greater extent of petroleum biodegradation than the grassland and working well soils. Α-diversity indexes based on metagenomic taxonomy showed higher microbial diversity in grassland soils, whereas petroleum-degrading microbes Actinobacteria and Proteobacteria were more abundant in working and abandoned well soils. RDA demonstrated that low moisture content (MOI) in YC oilfield inhibited the accumulation of the petroleum-degrading microbes. Synergistic networks of functional genes and Spearman's correlation analysis showed that heavy petroleum contamination (over 2.10 × 104 mg/kg) negatively correlated with the abundance of the nitrogen fixation genes nifHK, however, in grassland soils, low petroleum content facilitated the accumulation of nitrogen fixation genes. A positive correlation was observed between the abundance of petroleum-degrading genes and denitrification genes (bphAa vs. nirD, todC vs. nirS, and nahB vs. nosZ), whereas a negative correlation was observed between alkB (alkane- degrading genes) and amo (ammonia oxidation), hao (nitrification). The ecotoxicity of petroleum contamination, coupled with petroleum hydrocarbons (PH) degradation competing with nitrifiers for ammonia inhibited ammonia oxidation and nitrification, whereas PH metabolism promoted the denitrification process. Moreover, positive correlations were observed between the abundance of amo gene and MOI, as well as between the abundance of the dissimilatory nitrate reduction gene nirA and clay content. Thus, improving the soil physicochemical properties is a promising approach for decreasing nitrogen loss and alleviating petroleum contamination in oilfield soils.

Production of enzymes for the removal of odorous substances in plant biomass

Residual plant biomass collected from agricultural, technical or biopharmaceutical processes contains odorous substances. The latter are often unacceptable for customers if the biomass is used in sustainable products such as building materials, paints, glues or flame-resistant foils. The objective of this study was to identify enzymes that can prevent the formation or facilitate the degradation of odorous substances such as butanol, eugenol or ethyl acetate and their derivatives in residual biomass. We used plant cell packs (PCPs) as a small-scale screening platform to assess the expression of enzymes that break down odorous substances in tobacco biomass. First, we compiled a list of volatile compounds in residual plant biomass that may give rise to undesirable odors, refining the list to 10 diverse compounds representing a range of odors. We then selected five monomeric enzymes (a eugenol oxidase, laccase, oxidase, alkane mono-oxidase and ethyl acetate hydrolase) with the potential to degrade these substances. We transiently expressed the proteins in PCPs, targeting different subcellular compartments to identify optimal production conditions. The maximum yield we achieved was ∼20 mg kg-1 for Trametes hirsute laccase targeted to the chloroplast. Our results confirm that enzymes for the removal of odorous substances can be produced in plant systems, facilitating the upcycling of residual biomass as an ingredient for sustainable products.

Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments

Petroleum hydrocarbon (PH) pollution has mostly been caused by oil exploration, extraction, and transportation activities in colder regions, particularly in the Arctic and Antarctic regions, where it serves as a primary source of energy. Due to the resilience feature of nature, such polluted environments become the realized ecological niches for a wide community of psychrophilic hydrocarbonoclastic bacteria (PHcB). In contrast, to other psychrophilic species, PHcB is extremely cold-adapted and has unique characteristics that allow them to thrive in greater parts of the cold environment burdened with PHs. The stated group of bacteria in its ecological niche aids in the breakdown of litter, turnover of nutrients, cycling of carbon and nutrients, and bioremediation. Although such bacteria are the pioneers of harsh colder environments, their growth and distribution remain under the influence of various biotic and abiotic factors of the environment. The review discusses the prevalence of PHcB community in colder habitats, the metabolic processes involved in the biodegradation of PH, and the influence of biotic and abiotic stress factors. The existing understanding of the PH metabolism by PHcB offers confirmation of excellent enzymatic proficiency with high cold stability. The discovery of more flexible PH degrading strategies used by PHcB in colder environments could have a significant beneficial outcome on existing bioremediation technologies. Still, PHcB is least explored for other industrial and biotechnological applications as compared to non-PHcB psychrophiles. The present review highlights the pros and cons of the existing bioremediation technologies as well as the potential of different bioaugmentation processes for the effective removal of PH from the contaminated cold environment. Such research will not only serve to investigate the effects of pollution on the basic functional relationships that form the cold ecosystem but also to assess the efficacy of various remediation solutions for diverse settings and climatic conditions.

Bacteria degrading both n-alkanes and aromatic hydrocarbons are prevalent in soils

This study was undertaken to determine the distribution of soil bacteria capable of utilizing both n-alkanes and aromatic hydrocarbons. These microorganisms have not been comprehensively investigated so far. Ten contaminated (4046-43,861 mg of total petroleum hydrocarbons (TPH) kg-1 of dry weight of soil) and five unpolluted (320-2754 mg TPH kg-1 of dry weight of soil) soil samples from temperate, arid, and Alpine soils were subjected to isolation of degraders with extended preferences and shotgun metagenomic sequencing (selected samples). The applied approach allowed to reveal that (a) these bacteria can be isolated from pristine and polluted soils, and (b) the distribution of alkane monooxygenase (alkB) and aromatic ring hydroxylating dioxygenases (ARHDs) encoding genes is not associated with the contamination presence. Some alkB and ARHD genes shared the same taxonomic affiliation; they were most often linked with the Rhodococcus, Pseudomonas, and Mycolicibacterium genera. Moreover, these taxa together with the Paeniglutamicibacter genus constituted the most numerous groups among 132 culturable strains growing in the presence of both n-alkanes and aromatic hydrocarbons. All those results indicate (a) the prevalence of the hydrocarbon degraders with extended preferences and (b) the potential of uncontaminated soil as a source of hydrocarbon degraders applied for bioremediation purposes.

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

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

Online detection of alkanes by a biological-phase microextraction and biosensing (BPME-BS) device

Oil spill incidents occur frequently and threaten ecosystems and human health. Solid-phase microextraction allows direct alkane extraction from environmental matrices to improve the limit of detection but is unable to measure alkanes on site. A biological-phase microextraction and biosensing (BPME-BS) device was developed by immobilising an alkane chemotactic Acinetobacter bioreporter ADPWH_alk in agarose gel to achieve online alkane quantification with the aid of a photomultiplier. The BPME-BS device had a high enrichment factor (average 7.07) and a satisfactory limit of detection (0.075 mg/L) for alkanes. The quantification range was 0.1-100 mg/L, comparable to a gas chromatography flame ionisation detector and better than a bioreporter without immobilisation. ADPWH_alk cells in the BPME-BS device maintained good sensitivity under a wide range of environmental conditions, including pH (4.0-9.0), temperature (20-40 °C), and salinity (0.0-3.0%), and its response remained stable within 30 days at 4 °C. In a 7-day continual measurement, the BPME-BS device successfully visualised the dynamic concentration of alkanes, and a 7-day field test successfully captured an oil spill event, helping in source apportionment and on-scene law enforcement. Our work proved that the BPME-BS device is a powerful tool for online alkane measurement, showing substantial potential for fast detection and rapid response to oil spills on site and in situ.

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.

Genome-resolved metagenomics reveals depth-related patterns of microbial community structure and functions in a highly stratified, AMD overlaying mine tailings

Acid mine drainage (AMD) is a worldwide environmental problem, yet bioremediation is hampered by a limited knowledge of the reductive microbial processes in the AMD ecosystem. Here, we generate extensive metagenome and geochemical datasets to investigate how microbial populations and metabolic capacities driving major element cycles are structured in a highly stratified, AMD overlaying tailings environment. The results demonstrated an explicit depth-dependent differentiation of microbial community composition and function profiles between the surface and deeper tailings layers, paralleling the dramatic shifts in major physical and geochemical properties. Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers. Genome-resolved metagenomics retrieved 406 intermediate or high-quality genomes spanning 26 phyla, including major new groups (e.g., Patescibacteria and DPANN). Metabolic models involving nitrogen, sulfur, iron, and carbon cycles were proposed based on the functional potentials of the abundant microbial genomes, emphasizing syntrophy and the importance of lesser-known taxa in the degradation of complex carbon compounds. These results have implications for in situ AMD bioremediation.

Unravelling the genetic potential for hydrocarbon degradation in the sediment microbiome of Antarctic islands

Hydrocarbons may have a natural or anthropogenic origin and serve as a source of carbon and energy for microorganisms in Antarctic soils. Herein, 16S rRNA gene and shotgun sequencing were employed to characterize taxonomic diversity and genetic potential for hydrocarbon degradation of the microbiome from sediments of sites located in two Antarctic islands subjected to different temperatures, geochemical compositions, and levels of presumed anthropogenic impact, named: Crater Lake/Deception Island (pristine area), Whalers Bay and Fumarole Bay/Deception Island (anthropogenic-impacted area), and Hannah Point/Livingston Island (anthropogenic-impacted area). Hydrocarbon concentrations were measured for further correlation analyses with biological data. The majority of the hydrocarbon-degrading genes were affiliated to the most abundant bacterial groups of the microbiome: Proteobacteria and Actinobacteria. KEGG annotation revealed 125 catabolic genes related to aromatic hydrocarbon (styrene, toluene, ethylbenzene, xylene, naphthalene, and polycyclic hydrocarbons) and aliphatic (alkanes and cycloalkanes) pathways. Only aliphatic hydrocarbons, in low concentrations, were detected in all areas, thus not characterizing the areas under study as anthropogenically impacted or nonimpacted. The high richness and abundance of hydrocarbon-degrading genes suggest that the genetic potential of the microbiome from Antarctic sediments for hydrocarbon degradation is driven by natural hydrocarbon occurrence.

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Background

Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. 

Results

Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria.

Conclusion

Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08906-w.

Coupling biostimulation and phytoremediation for the restoration of petroleum hydrocarbon-contaminated soil

Total petroleum hydrocarbons (TPH) continue to be among the most common pollutants in soil worldwide. Bioremediation and phytoremediation have become sustainable ways of dealing with TPH contamination and biostimulation-assisted phytoremediation is considered as a potential approach for the treatment of pollutants. In this study, the response surface was used to optimize the single-factor biological stimulation experiment of moisture content, leavening agent content and compound fertilizer content and got the best experimental plan of biological stimulation. It was found that TPH degradation rate was 28.6% by biostimulation after 70 days. Further, from 20 kinds of plant seeds, 5 kinds of suitable or growth and high germination rate were selected for petroleum hydrocarbon degradation experiment. In the phytoremediation, peanut was selected as the best plant species by measuring the TPH degradation rate, bacteria count, growth of test plants, germination rate and amount of catalase in the soil and it could achieved 31.1% degradation rate of petroleum hydrocarbons after 70 days. Finally, the artificial biostimulation and phytoremediation combined degradation experiment of petroleum hydrocarbons-contaminated soil was designed and it achieved 38.9% TPH degradation rate after 70 days.

Pollution and edaphic factors shape bacterial community structure and functionality in historically contaminated soils

Studies about biodegradation potential in soils often refer to artificially contaminated and simplified systems, overlooking the complexity associated with contaminated sites in a real context. This work aims to provide a holistic view on microbiome assembly and functional diversity in the model site SIN Brescia-Caffaro (Italy), characterized by historical and uneven contamination by organic and inorganic compounds. Here, physical and chemical analyses and microbiota characterization were applied on one-hundred-twenty-seven soil samples to unravel the environmental factors driving bacterial community assembly and biodegradation potential in three former agricultural fields. Chemical analyses showed a patchy distribution of metals, metalloids and polychlorinated biphenyls (PCB) and allowed soil categorization according to depth and area of collections. Likewise, the bacterial community structure, described by molecular fingerprinting and 16S rRNA gene analyses, was significantly different according to collection site and depth. Pollutant concentrations (i.e., hexachloro-biphenyls, arsenic and mercury), nitrogen content and parameters related to soil texture were identified as main drivers of microbiota assembly, being significantly correlated to bacterial community composition. Moreover, bacteria putatively involved in the aerobic degradation of PCBs were enriched over the total bacterial community in topsoils, where the highest activity was recorded using fluorescein hydrolysis as proxy. Metataxonomic analyses revealed the presence of bacteria having metabolic pathways related to PCB degradation and tolerance to heavy metals and metalloids in the topsoil samples collected in all areas. Overall, the provided dissection of soil microbiota structure and its degradation potential in the SIN Brescia-Caffaro can contribute to target specific areas for rhizoremediation implementation. Metagenomics studies could be implemented in the future to understand if specific degradative pathways are present in historically polluted sites characterized by the co-occurrence of multiple classes of contaminants.

Valorization of Small Alkanes by Biocatalytic Oxyfunctionalization

The oxidation of alkanes into valuable chemical products is a vital reaction in organic synthesis. This reaction, however, is challenging, owing to the inertness of C-H bonds. Transition metal catalysts for C-H functionalization are frequently explored. Despite chemical alternatives, nature has also evolved powerful oxidative enzymes (e. g., methane monooxygenases, cytochrome P450 oxygenases, peroxygenases) that are capable of transforming C-H bonds under very mild conditions, with only the use of molecular oxygen or hydrogen peroxide as electron acceptors. Although progress in alkane oxidation has been reviewed extensively, little attention has been paid to small alkane oxidation. The latter holds great potential for the manufacture of chemicals. This Minireview provides a concise overview of the most relevant enzyme classes capable of small alkanes (C_<6 ) oxyfunctionalization, describes the essentials of the catalytic mechanisms, and critically outlines the current state-of-the-art in preparative applications.

Evaluating the aerobic xylene-degrading potential of the intrinsic microbial community of a legacy BTEX-contaminated aquifer by enrichment culturing coupled with multi-omics analysis: uncovering the role of Hydrogenophaga strains in xylene degradation

To develop effective bioremediation strategies, it is always important to explore autochthonous microbial community diversity using substrate-specific enrichment. The primary objective of this present study was to reveal the diversity of aerobic xylene-degrading bacteria at a legacy BTEX-contaminated site where xylene is the predominant contaminant, as well as to identify potential indigenous strains that could effectively degrade xylenes, in order to better understand the underlying facts about xylene degradation using a multi-omics approach. Henceforward, parallel aerobic microcosms were set up using different xylene isomers as the sole carbon source to investigate evolved bacterial communities using both culture-dependent and independent methods. Research outcome showed that the autochthonous community of this legacy BTEX-contaminated site has the capability to remove all of the xylene isomers from the environment aerobically employing different bacterial groups for different xylene isomers. Interestingly, polyphasic analysis of the enrichments disclose that the community composition of the o-xylene-degrading enrichment community was utterly distinct from that of the m- and p-xylene-degrading enrichments. Although in each of the enrichments Pseudomonas and Acidovorax were the dominant genera, in the case of o-xylene-degrading enrichment Rhodococcus was the main player. Among the isolates, two Hydogenophaga strains, belonging to the same genomic species, were obtained from p-xylene-degrading enrichment, substantially able to degrade aromatic hydrocarbons including xylene isomers aerobically. Comparative whole-genome analysis of the strains revealed different genomic adaptations to aromatic hydrocarbon degradation, providing an explanation on their different xylene isomer-degrading abilities.

Natural attenuation of oil in marine environments: A review

Natural attenuation is an important process for oil spill management in marine environments. Natural attenuation affects the fate of oil by physical, chemical, and biological processes, which include evaporation, dispersion, dissolution, photo-oxidation, emulsification, oil particle aggregation, and biodegradation. This review examines the cumulative knowledge regarding these natural attenuation processes as well as their simulation and prediction using modelling approaches. An in-depth discussion is provided on how oil type, microbial community and environmental factors contribute to the biodegradation process. It describes how our understanding of the structure and function of indigenous oil degrading microbial communities in the marine environment has been advanced by the application of next generation sequencing tools. The synergetic and/or antagonist effects of oil spill countermeasures such as the application of chemical dispersants, in-situ burning and nutrient enrichment on natural attenuation were explored. Several knowledge gaps were identified regarding the synergetic and/or antagonistic effects of active response countermeasures on the natural attenuation/biodegradation process. This review highlighted the need for field data on both the effectiveness and potential detrimental effects of oil spill response options to support modelling and decision-making on their selection and application.

Hydrocarbon biodegradation potential of microbial communities from high Arctic beaches in Canada's Northwest Passage

Sea ice loss is opening shipping routes in Canada's Northwest Passage, increasing the risk of an oil spill. Harnessing the capabilities of endemic microorganisms to degrade oil may be an effective remediation strategy for contaminated shorelines; however, limited data exists along Canada's Northwest Passage. In this study, hydrocarbon biodegradation potential of microbial communities from eight high Arctic beaches was assessed. Across high Arctic beaches, community composition was distinct, potential hydrocarbon-degrading genera were detected and microbial communities were able to degrade hydrocarbons (hexadecane, naphthalene, and alkanes) at low temperature (4 °C). Hexadecane and naphthalene biodegradation were stimulated by nutrients, but nutrients had little effect on Ultra Low Sulfur Fuel Oil biodegradation. Oiled microcosms showed a significant enrichment of Pseudomonas and Rhodococcus. Nutrient-amended microcosms showed increased abundances of key hydrocarbon biodegradation genes (alkB and CYP153). Ultimately, this work provides insight into hydrocarbon biodegradation on Arctic shorelines and oil-spill remediation in Canada's Northwest Passage.

Bacterial communities and their bioremediation capabilities in oil-contaminated agricultural soils

Rapid industrialization and development in petrochemical industries have resulted in increased hydrocarbon pollution causing substantial damage to the natural ecosystems including agricultural soils. In the recent, past efforts have been made to treat the contaminated soils using microorganisms by natural processes. Soil bacteria, known for their potential to degrade the soil contaminants, play a vital role in maintaining soil health. In the current study, we observed the influence of hydrocarbon contamination on the physicochemical characteristics and enzymatic activities of the soil. Proteobacteria (30.48%), Actinobacteria (13.91%), and Acidobacteria (12.57%) flourished in the non-contaminated soil whereas contaminated sites were dominated by Proteobacteria (44.02 ± 15.65%). In contrast, the sites experiencing the different degrees of exposure to the hydrocarbon pollution allowed specific augmentation of bacterial taxa (in decreasing order of exposure time), viz. Proteobacteria (60.47%), Firmicutes (32.48%), and Bacteroidetes(13.59%), based on culture-independent approach that suggested their potential role in hydrocarbon degradation as compared to the non-contaminated site. The imputation of metabolic function also supported the positive correlation to the exposure to hydrocarbon pollution, with site 2 being highly abundant for gene families involved in xenobiotics biodegradation. The study provides insights into bacterial community structure with special emphasis on their efficiency to degrade hydrocarbons. The results from the study can help in designing appropriate biodegradation strategies to mitigate the serious problems of oil contamination in agricultural soil.

Metagenomic Analysis for Evaluating Change in Bacterial Diversity in TPH-Contaminated Soil after Soil Remediation

Soil washing and landfarming processes are widely used to remediate total petroleum hydrocarbon (TPH)-contaminated soil, but the impact of these processes on soil bacteria is not well understood. Four different states of soil (uncontaminated soil (control), TPH-contaminated soil (CS), after soil washing (SW), and landfarming (LF)) were collected from a soil remediation facility to investigate the impact of TPH and soil remediation processes on soil bacterial populations by metagenomic analysis. Results showed that TPH contamination reduced the operational taxonomic unit (OTU) number and alpha diversity of soil bacteria. Compared to SW and LF remediation techniques, LF increased more bacterial richness and diversity than SW, indicating that LF is a more effective technique for TPH remediation in terms of microbial recovery. Among different bacterial species, Proteobacteria were the most abundant in all soil groups followed by Actinobacteria, Acidobacteria, and Firmicutes. For each soil group, the distribution pattern of the Proteobacteria class was different. The most abundant classed were Alphaproteobacteria (16.56%) in uncontaminated soils, Deltaproteobacteria (34%) in TPH-contaminated soils, Betaproteobacteria (24%) in soil washing, and Gammaproteobacteria (24%) in landfarming, respectively. TPH-degrading bacteria were detected from soil washing (23%) and TPH-contaminated soils (21%) and decreased to 12% in landfarming soil. These results suggest that soil pollution can change the diversity of microbial groups and different remediation techniques have varied effective ranges for recovering bacterial communities and diversity. In conclusion, the landfarming process of TPH remediation is more advantageous than soil washing from the perspective of bacterial ecology.

A New Ciboria sp. for Soil Mycoremediation and the Bacterial Contribution to the Depletion of Total Petroleum Hydrocarbons

A Ciboria sp. strain (Phylum Ascomycota) was isolated from hydrocarbon-polluted soil of an abandoned oil refinery in Italy. The strain was able to utilize diesel oil as a sole carbon source for growth. Laboratory-scale experiments were designed to evaluate the use of this fungal strain for treatment of the polluted soil. The concentration of total petroleum hydrocarbons (TPH) in the soil was 8,538 mg/kg. Mesocosms containing the contaminated soil were inoculated with the fungal strain at 1 or 7%, on a fresh weight base ratio. After 90 days of incubation, the depletion of TPH contamination was of 78% with the 1% inoculant, and 99% with the 7% inoculant. 16S rDNA and ITS metabarcoding of the bacterial and fungal communities was performed in order to evaluate the potential synergism between fungi and bacteria in the bioremediation process. The functional metagenomic prediction indicated Arthrobacter, Dietzia, Brachybacerium, Brevibacterium, Gordonia, Leucobacter, Lysobacter, and Agrobacterium spp. as generalist saprophytes, essential for the onset of hydrocarbonoclastic specialist bacterial species, identified as Streptomyces, Nocardoides, Pseudonocardia, Solirubrobacter, Parvibaculum, Rhodanobacter, Luteiomonas, Planomicrobium, and Bacillus spp., involved in the TPH depletion. The fungal metabolism accelerated the onset of specialist over generalist bacteria. The capacity of the Ciboria sp. to deplete TPH in the soil in treatment was also ascertained.

Analysis of column reactor results with organic decay by native organic microbiota and varying permeability

Field bio-remediation techniques (FBRT) can be a low cost method to avoid the removal of top layers of soil which are rich in organic matter and bio diversity. The use of native microorganisms in FBRT is preferable because non-indigenous species can transfer their genetic material to the environment with negative impacts on the local ecological equilibrium. Petroleum Produced Water (PPW) is an important pollutant source in onshore production areas. However, due to high sodium concentrations in PPW and the occurrence of organic matter in dissolved and dispersed forms, obtaining pollutant transport parameters may be a difficult task. Results of column tests performed using a natural soil permeated by PPW are presented. All the samples presented a permeability decrease over time and the total hydrocarbon petroleum (TPH) breakthrough curves presented evidence of biological decay. Soil samples underwent biological characterization after tests (Metagenomic analyses and cultural media tests). Curves were modelled in an incremental way using a non-constant decay rate to better simulate the growing process of the microorganisms and consider the occurrence of varying velocity/permeability. Biological characterization results indicate the native organisms that are potentially more able to degrade PPW, including four bacteria (Bacillus and Lysinibacillus genus) and two fungi species (Malassezia and Talaromyces genus) that have not previously been mentioned in the consulted literature. The obtained results contribute to the development of more sustainable FBRTs focusing on native microorganisms, already adapted to the local environmental conditions.

Response of soil bacterial communities to high petroleum content in the absence of remediation procedures

Oil spills are events that frequently lead to petroleum pollution. This pollution may cause stress to microbial communities, which require long adaption periods. Soil petroleum pollution is currently considered one of the most serious environmental problems. In the present work, processes occurring in the bacterial communities of three soil samples with different physicochemical characteristics, artificially polluted with 12% of crude oil, were investigated in 120-day laboratory experiment. It was found that the total petroleum hydrocarbon content did not decrease during this time; however, the proportion of petroleum fractions was altered. Petroleum pollution led to a short-term decrease in the bacterial 16S rRNA gene copy number. On the basis of amplicon sequencing analysis, it was concluded that bacterial community successions were similar in the three soils investigated. Thus, the phyla Actinobacteria and Proteobacteria and candidate TM7 phylum (Saccaribacteria) were predominant with relative abundances ranging from 35 to 58%, 25 to 30%, and 15 to 35% in different samples, respectively. The predominant operational taxonomic units (OTUs) after pollution belonged to the genera Rhodococcus and Mycobacterium, families Nocardioidaceae and Sinobacteraceae, and candidate class ТМ7-3. Genes from the alkIII group encoding monoxygenases were the most abundant compared with other catabolic genes from the alkI, alkII, GN-PAH, and GP-PAH groups, and their copy number significantly increased after pollution. The copy numbers of expressed genes involved in the horizontal transfer of catabolic genes, FlgC, TraG, and OmpF, also increased after pollution by 11-33, 16-63, and 11-71 times, respectively. The bacterial community structure after a high level of petroleum pollution changed because of proliferation of the cells that initially were able to decompose hydrocarbons, and in the second place, because proliferation of the cells that received these catabolic genes through horizontal transfer.

Effect of natural microbiome and culturable biosurfactants-producing bacterial consortia of freshwater lake on petroleum-hydrocarbon degradation

Freshwater lake ecosystem is a reservior of valuable microbial diversity. It needs to be explored for addressing key environmental issues like petroleum-hydrocarbon contamination. In this work, the microbial communities (pre and post enriched with petroleum-hydrocarbons) from different layers of freshwater lake, i.e. surface water, sediments and deepwater, were explored through metagenomic and culture-dependent approaches. A total of 41 bacterial phyla were retrieved from pre-enriched samples, which were significantly reduced in enriched samples where Proteobacteria were dominant (87% to 100%) followed by Bacteroidetes (7.37%) and Verrucomicrobia (3.06%). The most dominant hydrocarbon-degrading genera were extensively verified as Pseudomonas (48.65%), Acinetobacter (45.38%), Stenotrophomonas (3.16%) and Brevundimonas (2.07%) in surface water (S1WCC); Acinetobacter (62.46%), Aeromonas (10.7%), Sphingobacterium (5.20%) and Pseudomonas (4.23%) in sediment (S2MCC); and Acinetobacter (46.57%), Pseudomonas (13.10%), Comamonas (12.93%), Flavobacterium (12.18%) and Enterobacter (9.62%) in deep water (S4WCC). Additionally, the maximum biodegradation of petroleum-hydrocarbons (i.e. used engine oil or UEO) was achieved by microbiome of S2MCC (67.60 ± 0.08%) followed by S4WCC (59.70 ± 0.12%), whereas only 36.80 ± 0.10% degradation was achieved by S1WCC microbiome. On the other hand, UEO degradation by cultivable biosurfactant-producing single cultures such as Pseudomonas sp. S2WE, Pseudomonas sp. S2WG, Pseudomonas sp. S2MS, Ochrobactrum sp. S1MM and Bacillus nealsonii S2MT showed 31.10 ± 0.08% to 40.50 ± 0.11% biodegradation. Comparatively, the biodegradation efficiency was found higher (i.e. 42.20 ± 0.12% to 56.10 ± 0.12%) in each consortia comprising of two, three, four, and five bacterial cultures. Conclusively, the isolated culturable biosurfactants-producing bacterial consortium of freshwater lake demonstrated >80% contribution in the total petroleum-hydrocarbons degradation by the natural microbiome of the ecosystem.

Response of bacterial and fungal communities to high petroleum pollution in different soils

Petroleum pollution of soils is a major environmental problem. Soil microorganisms can decompose a significant fraction of petroleum hydrocarbons in soil at low concentrations (1-5%). This characteristic can be used for soil remediation after oil pollution. Microbial community dynamics and functions are well studied in cases of moderate petroleum pollution, while cases with heavy soil pollution have received much less attention. We studied bacterial and fungal successions in three different soils with high petroleum contents (6 and 25%) in a laboratory experiment. The proportion of aliphatic and aromatic compounds decreased by 4-7% in samples with 6% pollution after 120 days of incubation but remained unchanged in samples with 25% hydrocarbons. The composition of the microbial community changed significantly in all cases. Oil pollution led to an increase in the relative abundance of bacteria such as Actinobacteria and the candidate TM7 phylum (Saccaribacteria) and to a decrease in that of Bacteroidetes. The gene abundance (number of OTUs) of oil-degrading bacteria (Rhodococcus sp., candidate class TM7-3 representative) became dominant in all soil samples, irrespective of the petroleum pollution level and soil type. The fungal communities in unpolluted soil samples differed more significantly than the bacterial communities. Nonmetric multidimensional scaling revealed that in the polluted soil, successions of fungal communities differed between soils, in contrast to bacterial communities. However, these successions showed similar trends: fungi capable of lignin and cellulose decomposition, e.g., from the genera Fusarium and Mortierella, were dominant during the incubation period.

Powdered activated carbon - Membrane bioreactor (PAC-MBR): Impacts of high PAC concentration on micropollutant removal and microbial communities

In this study, the effect of a high concentration of powdered activated carbon (PAC) on pollutant removal and microbial communities was systematically investigated. Micropollutant removal by the 'control' MBR (without PAC addition) was pollutant-specific and was mainly controlled by their molecular properties. The PAC-MBR achieved enhanced removal of micropollutant by 10% (ofloxacin) to 40% (caffeine). Analysis of the microbial communities in the sludge samples collected from both MBRs indicated an increase in the abundance of 24 (out of 31) genera following PAC addition. Notably, bacterial diversity enriched, particularly in the anoxic zone of the PAC-MBR, indicating a positive impact of recirculating mixed liquor containing PAC from the aerobic to the anoxic zone. In addition, PAC improved the abundance of Comamonas and Methanomethylovorans (up to 2.5%) that can degrade recalcitrant micropollutants. According to the quantitative PCR (qPCR) analysis, the copies of functional genes (nirS, nosZ and narG) increased in PAC-MBR. This study demonstrated that MBR could be operated at a high PAC concentration without compromising the pollutant removal and microbial community evolution during wastewater treatment.

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.

Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain

Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.

Response Surface Methodology Optimization and Kinetics of Diesel Degradation by a Cold-Adapted Antarctic Bacterium, Arthrobacter sp. Strain AQ5-05

Petroleum hydrocarbons, notably diesel oil, are the main energy source for running amenities in the Antarctic region and are the major cause of pollution in this area. Diesel oil spills are one of the major challenges facing management of the Antarctic environment. Bioremediation using bacteria can be an effective and eco-friendly approach for their remediation. However, since the introduction of non-native organisms, including microorganisms, into the Antarctic or between the distinct biogeographical regions within the continent is not permitted under the Antarctic Treaty, it is crucial to discover native oil-degrading, psychrotolerant microorganisms that can be used in diesel bioremediation. The primary aim of the current study is to optimize the conditions for growth and diesel degradation activity of an Antarctic local bacterium, Arthrobacter sp. strain AQ5-05, using the Plackett-Burman approach and response surface method (RSM) via a central composite design (CCD) approach. Based on this approach, temperature, pH, and salinity were calculated to be optimum at 16.30 °C, pH 7.67 and 1.12% (w/v), respectively. A second order polynomial regression model very accurately represented the experimental figures’ interpretation. These optimized environmental conditions increased diesel degradation from 34.5% (at 10 °C, pH 7.00 and 1.00% (w/v) salinity) to 56.4%. Further investigation of the kinetics of diesel reduction by strain AQ5-05 revealed that the Teissier model had the lowest RMSE and AICC values. The calculated values for the Teissier constants of maximal growth rate, half-saturation rate constant for the maximal growth, and half inhibition constants (μmax, Ks, and Ki), were 0.999 h−1, 1.971% (v/v) and 1.764% (v/v), respectively. The data obtained therefore confirmed the potential application of this cold-tolerant strain in the bioremediation of diesel-contaminated Antarctic soils at low temperature.

Microbial lipases and their industrial applications: a comprehensive review

Lipases are very versatile enzymes, and produced the attention of the several industrial processes. Lipase can be achieved from several sources, animal, vegetable, and microbiological. The uses of microbial lipase market is estimated to be USD 425.0 Million in 2018 and it is projected to reach USD 590.2 Million by 2023, growing at a CAGR of 6.8% from 2018. Microbial lipases (EC 3.1.1.3) catalyze the hydrolysis of long chain triglycerides. The microbial origins of lipase enzymes are logically dynamic and proficient also have an extensive range of industrial uses with the manufacturing of altered molecules. The unique lipase (triacylglycerol acyl hydrolase) enzymes catalyzed the hydrolysis, esterification and alcoholysis reactions. Immobilization has made the use of microbial lipases accomplish its best performance and hence suitable for several reactions and need to enhance aroma to the immobilization processes. Immobilized enzymes depend on the immobilization technique and the carrier type. The choice of the carrier concerns usually the biocompatibility, chemical and thermal stability, and insolubility under reaction conditions, capability of easy rejuvenation and reusability, as well as cost proficiency. Bacillus spp., Achromobacter spp., Alcaligenes spp., Arthrobacter spp., Pseudomonos spp., of bacteria and Penicillium spp., Fusarium spp., Aspergillus spp., of fungi are screened large scale for lipase production. Lipases as multipurpose biological catalyst has given a favorable vision in meeting the needs for several industries such as biodiesel, foods and drinks, leather, textile, detergents, pharmaceuticals and medicals. This review represents a discussion on microbial sources of lipases, immobilization methods increased productivity at market profitability and reduce logistical liability on the environment and user.

Enhanced bioremediation of diesel range hydrocarbons in soil using biochar made from organic wastes

Hydrocarbon contamination due to anthropogenic activities is a major environmental concern worldwide. The present study focuses on biochar prepared from fruit and vegetable waste and sewage sludge using a thermochemical approach and its application for the enhanced bioremediation (biostimulation and bioaugmentation) of diesel-polluted soil. The biochar was characterized using FTIR (Fourier-transform infrared spectroscopy), elemental analysis, surface area analysis, and pore analysis. Adsorption experiments showed that hydrocarbon degradation was attributed to biological processes rather than adsorption. The study found that various biochar amendments could significantly increase the rate of hydrocarbon biodegradation with removal efficiencies > 70%. Bioaugmentation using cow dung further improved the removal efficiency to 82%. Treatments showing the highest degree of removal efficiency indicated the presence of 27 different bacteria phyla with Proteobacteria and Actinobacteria as the most abundant phyla. The present study concludes that biochar amendments have great potential for enhancing the bioremediation of soils contaminated with diesel range hydrocarbons.

Functional Gene Diversity of Selected Indigenous Hydrocarbon-Degrading Bacteria in Aged Crude Oil

Crude oil pollution has consistently deteriorated all environmental compartments through the cycle of activities of the oil and gas industries. However, there is a growing need to identify microbes with catabolic potentials to degrade these pollutants. This research was conducted to identify bacteria with functional degradative genes. A crude oil-polluted soil sample was obtained from an aged spill site at Imo River, Ebubu, Komkom community, Nigeria. Bacteria isolates were obtained and screened for hydrocarbon degradation potential by turbidometry assay. Plasmid and chromosomal DNA of the potential degraders were further screened for the presence of selected catabolic genes (C230, Alma, Alkb, nahAC, and PAHRHD_(GP)) and identified by molecular typing. Sixteen (16) out of the fifty (50) isolates obtained showed biodegradation activity in a liquid broth medium at varying levels. Bacillus cereus showed highest potential for this assay with an optical density of 2.450 @ 600 nm wavelength. Diverse catabolic genes resident in plasmids and chromosomes of the isolates and, in some cases, both plasmid and chromosomes of the same organism were observed. The C230 gene was resident in >50% of the microbial population tested, while other genes occurred in lower proportions with the least observed in nahAC and PAHRHD. These organisms can serve as potential bioremediation agents.

Potential Enhancement of the In-Situ Bioremediation of Contaminated Sites through the Isolation and Screening of Bacterial Strains in Natural Hydrocarbon Springs

Petroleum hydrocarbon contamination (PHC) is an issue of major concern worldwide. These compounds represent the most common environmental pollutants and their cleaning up is mandatory. The main goal of this research was to analyze microbial communities in a site in southern Italy characterized by the presence of hydrocarbons of natural origin by using a multidisciplinary approach based on microbiological, geological and hydrological investigations. Bacterial communities of two springs, the surrounding soils, and groundwater were studied through a combination of molecular and culture-dependent methodologies to explore the biodiversity at the study site, to isolate microorganisms with degradative abilities, and to assess their potential to develop effective strategies to restore the environmental quality. Next-generation sequencing revealed the dominance of species of the Proteobacteria phylum but also the presence of other autochthonous hydrocarbon-oxidizing microorganisms affiliated to other phyla (e.g., species of the genera Flavobacterium and Gordonia). The traditional cultivation-based approach led to the isolation and identification of 11 aerobic hydrocarbon-oxidizing proteobacteria, some of which were able to grow with phenanthrene as the sole carbon source. Seven out of the 11 isolated bacterial strains produced emulsion with diesel fuel (most of them showing emulsifying capacity values greater than 50%) with a high stability after 24 h and, in some cases, after 48 h. These results pave the way for further investigations finalized at (1) exploiting both the degradation ability of the bacterial isolates and/or microbial consortia to remediate hydrocarbon-contaminated sites and (2) the capability to produce molecules with a promoting effect for oil polluted matrices restoration.

Pesticide-tolerant bacteria isolated from a biopurification system to remove commonly used pesticides to protect water resources

In this study, we selected and characterized different pesticide-tolerant bacteria isolated from a biomixture of a biopurification system that had received continuous applications of a pesticides mixture. The amplicon analysis of biomixture reported that the phyla Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were predominant. Six strains grew in the presence of chlorpyrifos and iprodione. Biochemical characterization showed that all isolates were positive for esterase, acid phosphatase, among others, and they were identified as Pseudomonas, Rhodococcus and Achromobacter based on molecular and proteomic analysis. Bacterial growth decreased as both pesticide concentrations increased from 10 to 100 mg L^-1 in liquid culture. The Achromobacter sp. strain C1 showed the best chlorpyrifos removal rate of 0.072–0.147 d^-1 a half-life of 4.7–9.7 d and a maximum metabolite concentration of 2.10 mg L^-1 at 120 h. On the other hand, Pseudomonas sp. strain C9 showed the highest iprodione removal rate of 0.100–0.193 d^-1 a half-life of 4–7 d and maximum metabolite concentration of 0.95 mg L^-1 at 48 h. The Achromobacter and Pseudomonas strains showed a good potential as chlorpyrifos and iprodione-degrading bacteria.

Bioremediation of PAH-Contaminated Soils: Process Enhancement through Composting/Compost

Bioremediation of contaminated soils has gained increasing interest in recent years as a low-cost and environmentally friendly technology to clean soils polluted with anthropogenic contaminants. However, some organic pollutants in soil have a low biodegradability or are not bioavailable, which hampers the use of bioremediation for their removal. This is the case of polycyclic aromatic hydrocarbons (PAHs), which normally are stable and hydrophobic chemical structures. In this review, several approaches for the decontamination of PAH-polluted soil are presented and discussed in detail. The use of compost as biostimulation- and bioaugmentation-coupled technologies are described in detail, and some parameters, such as the stability of compost, deserve special attention to obtain better results. Composting as an ex situ technology, with the use of some specific products like surfactants, is also discussed. In summary, the use of compost and composting are promising technologies (in all the approaches presented) for the bioremediation of PAH-contaminated soils.

Comparative Genomics of the Rhodococcus Genus Shows Wide Distribution of Biodegradation Traits

The genus Rhodococcus exhibits great potential for bioremediation applications due to its huge metabolic diversity, including biotransformation of aromatic and aliphatic compounds. Comparative genomic studies of this genus are limited to a small number of genomes, while the high number of sequenced strains to date could provide more information about the Rhodococcus diversity. Phylogenomic analysis of 327 Rhodococcus genomes and clustering of intergenomic distances identified 42 phylogenomic groups and 83 species-level clusters. Rarefaction models show that these numbers are likely to increase as new Rhodococcus strains are sequenced. The Rhodococcus genus possesses a small “hard” core genome consisting of 381 orthologous groups (OGs), while a “soft” core genome of 1253 OGs is reached with 99.16% of the genomes. Models of sequentially randomly added genomes show that a small number of genomes are enough to explain most of the shared diversity of the Rhodococcus strains, while the “open” pangenome and strain-specific genome evidence that the diversity of the genus will increase, as new genomes still add more OGs to the whole genomic set. Most rhodococci possess genes involved in the degradation of aliphatic and aromatic compounds, while short-chain alkane degradation is restricted to a certain number of groups, among which a specific particulate methane monooxygenase (pMMO) is only found in Rhodococcus sp. WAY2. The analysis of Rieske 2Fe-2S dioxygenases among rhodococci genomes revealed that most of these enzymes remain uncharacterized.

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.

A Rotational Slurry Bioreactor Accelerates Biodegradation of A-Fuel in Oil-Contaminated Soil Even under Low Temperature Conditions

An effective bioaugmentation system for oil-contaminated soil under low-temperature conditions was developed with a rotational slurry bioreactor. Mixtures of two Rhodococcus oil-degraders, strain A and C, which are officially permitted to be used in bioaugmentation in Japan, were inoculated and A-fuel oil was added to a final concentration of 2500 and 5000 mg/kg-slurry. Decomposition tests were carried out for the inoculated samples and non-inoculated samples by rotating at 15 °C, the annual average temperature of Japan. The residue of A-fuel oil and the number of bacteria were measured every two days. After 6 days of treatment, more than 95% of the oil was removed in the inoculated samples, which was more than three times faster than a previous degradation experiment without rotation. A semi-continuous treatment was performed by removing 90% of the treated slurry, then adding the same amount of contaminated slurry into the system without additional degraders. Ninety-four percent of A-fuel oil was successfully degraded after 6 days by this repeated treatment. This could drastically reduce the cost of preparing the degraders. Strikingly, semi-continuous treatment showed oil removal in the non-inoculated samples, indicating that the rotational slurry conditions could efficiently promote biodegradation by indigenous degraders. Our rotational slurry bioreactor accelerated the removal of oil contamination without adding further degraders provides an efficient and cost-effective method of removal of A-fuel oil using a semi-continuous system, which can be used in practical applications in areas with a cooler climate.

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

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

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

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

A new framework for approaching precision bioremediation of PAH contaminated soils

Bioremediation is a sustainable treatment strategy which remains challenging to implement especially in heterogeneous environments such as soil and sediment. Herein, we present a novel precision bioremediation framework that integrates amplicon based metagenomic analysis and chemical profiling. We applied this approach to samples obtained at a site contaminated with polycyclic aromatic hydrocarbons (PAHs). Geobacter spp. were identified as biostimulation targets because they were one of the most abundant genera and previously identified to carry relevant degradative genes. Mycobacterium and Sphingomonads spp. were identified as bioaugmentation and genetic bioaugmentation targets, respectively, due to their positive associations with PAHs and their high abundance and species diversity at all sampling locations. Overall, this case study suggests this framework can help identify bacterial targets for precision bioremediation. However, it is imperative that we continue to build our databases as the power of metagenomic based approaches remains limited to microorganisms currently in our databases.