Microbial degradation of hydrocarbons in the environment

Variations in cuticular hydrocarbons of Calliphora vicina (Diptera: Calliphoridae) empty puparia: Insights for estimating late postmortem intervals

Necrophagous flies, particularly blowflies, serve as vital indicators in forensic entomology and ecological studies, contributing to minimum postmortem interval estimations and environmental monitoring. The study investigates variations in the predominant cuticular hydrocarbons (CHCs) viz. n-C25, n-C27, n-C28, and n-C29 of empty puparia of Calliphora vicina Robineau-Desvoidy, 1830, (Diptera: Calliphoridae) across diverse environmental conditions, including burial, above-ground and indoor settings, over 90 days. Notable trends include a significant decrease in n-C25 concentrations in buried and above-ground conditions over time, while n-C27 concentrations decline in buried and above-ground conditions but remain stable indoors. Burial conditions show significant declines in n-C27 and n-C29 concentrations over time, indicating environmental influences. Conversely, above-ground conditions exhibit uniform declines in all hydrocarbons. Indoor conditions remain relatively stable, with weak correlations between weathering time and CHC concentrations. Additionally, machine learning techniques, specifically Extreme Gradient Boosting (XGBoost), are employed for age estimation of empty puparia, yielding accurate predictions across different outdoor and indoor conditions. These findings highlight the subtle responses of CHC profiles to environmental stimuli, underscoring the importance of considering environmental factors in forensic entomology and ecological research. The study advances the understanding of insect remnant degradation processes and their forensic implications. Furthermore, integrating machine learning with entomological expertise offers standardized methodologies for age determination, enhancing the reliability of entomological evidence in legal contexts and paving the way for future research and development.

Dispersant addition, but not nutrients, stimulated blooms of multiple hydrocarbonoclastic genera in nutrient-replete coastal marine surface waters

The range of impacts of chemical dispersants on indigenous marine microbial communities and their activity remains poorly constrained. We tested the response of nearshore surface waters chronically exposed to oil leakage from a downed platform and supplied with nutrients by the Mississippi River to Corexit dispersant and nutrient additions. As assessed using 14C-labeled tracers, hexadecane mineralization potential was orders of magnitude higher in all unamended samples than in previously assessed bathypelagic communities. Nutrient additions stimulated microbial mortality but did not affect community composition and had no generalizable effect on hydrocarbon mineralization potential. By contrast, Corexit amendments caused a rapid shift in community composition and a drawdown of inorganic nitrogen and orthophosphate though no generalizable effect on hydrocarbon mineralization potential. The hydrocarbonoclastic community's response to dispersants is largely driven by the relative availability of organic substrates and nutrients, underscoring the role of environmental conditions and multiple interacting stressors on hydrocarbon degradation potential.

Metabolic Changes in Pseudomonas oleovorans Isolated from Contaminated Construction Material Exposed to Varied Biocide Treatments

Biocide resistance poses a significant challenge in industrial processes, with bacteria like Pseudomonas oleovorans exhibiting intrinsic resistance to traditional antimicrobial agents. In this study, the impact of biocide exposure on the metabolome of two P. oleovorans strains, namely, P. oleovorans P4A, isolated from contaminated coating material, and P. oleovorans 1045 reference strain, were investigated. The strains were exposed to 2-Methylisothiazol-3(2H)-one (MI) MIT, 1,2-Benzisothiazol-3(2H)-one (BIT), and 5-chloro-2-methyl-isothiazol-3-one (CMIT) at two different sub-inhibitory concentrations and the lipids and polar and semipolar metabolites were analyzed by ultra-high performance liquid chromatography quadrupole time-of-flight mass spectrometry UPLC-Q-TOF/MS. Exposure to the BIT biocide induced significant metabolic modifications in P. oleovorans. Notable changes were observed in lipid and metabolite profiles, particularly in phospholipids, amino acid metabolism, and pathways related to stress response and adaptation. The 1045 strain showed more pronounced metabolic alterations than the P4A strain, suggesting potential implications for lipid, amino acid metabolism, energy metabolism, and stress adaptation. Improving our understanding of how different substances interact with bacteria is crucial for making antimicrobial chemicals more effective and addressing the challenges of resistance. We observed that different biocides trigged significantly different metabolic responses in these strains. Our study shows that metabolomics can be used as a tool for the investigation of metabolic mechanisms underlying biocide resistance, and thus in the development of targeted biocides. This in turn can have implications in combating biocide resistance in bacteria such as P. oleovorans.

High temperature and solar radiation in the Red Sea enhance the dissolution of crude oil from surface films

The Red Sea is a hotspot of biodiversity susceptible to oil pollution. Besides, it is one of the warmest seas on the Earth with highly transparent waters. In this study, we estimated the oil dissolution rates under natural sunlight spectra and temperature conditions using coastal oil slicks collected after the 2019 Sabiti oil spill in the Red Sea. Optical analyses revealed the significant interactive effect of sunlight and temperature in enhancing the dissolution of oil into dissolved organic matter (DOM). The highest oil dissolution rate (38.68 g C m-3 d-1) was observed in full-spectrum sunlight. Oil dissolution significantly enhanced total organic carbon (TOC) and polycyclic aromatic hydrocarbons (PAHs) in seawater. High nucleic acid (HNA) bacteria, likely the oil degraders, proliferated from 30 to 70 - 90% after 4 days. The heavier stable carbon isotopic composition of methane (δ13C-CH4) and lighter stable carbon isotopic composition of carbon dioxide (δ13C-CO2) indicate the putative role of bacterial processes in the natural degradation of crude oil. The results indicated that the combined effect of temperature and solar radiation enhanced the biological and photochemical dissolution of oil on the Red Sea surface.

Implementation of in situ aerobic cometabolism for groundwater treatment: State of the knowledge and important factors for field operation

In situ aerobic cometabolism of groundwater contaminants has been demonstrated to be a valuable bioremediation technology to treat many legacy and emerging contaminants in dilute plumes. Several well-designed and documented field studies have shown that this technology can concurrently treat multiple contaminants and reach very low cleanup goals. Fundamentally different from metabolism-based biodegradation of contaminants, microorganisms that cometabolically degrade contaminants do not obtain sufficient carbon and energy from the degradation process to support their growth and require an exogenous growth supporting primary substrate. Successful applications of aerobic cometabolic treatment therefore require special considerations beyond conventional in situ bioremediation, such as competitive inhibition between growth-supporting primary substrate(s) and contaminant non-growth substrates, toxic effects resulting from contaminant degradation, and differences in microbial population dynamics exhibited by biostimulated indigenous consortia versus bioaugmentation cultures. This article first provides a general review of microbiological factors that are likely to affect the rate of aerobic cometabolic biodegradation. We subsequently review fourteen well documented field-scale aerobic cometabolic bioremediation studies and summarize the underlying microbiological factors that may affect the performance observed in these field studies. The combination of microbiological and engineering principles gained from field testing leads to insights and recommendations on planning, design, and operation of an in situ aerobic cometabolic treatment system. With a vision of more aerobic cometabolic treatments being considered to tackle large, dilute plumes, we present several novel topics and future research directions that can potentially enhance technology development and foster success in implementing this technology for environmental restoration.

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

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

Simultaneous removal of crude oil and heavy metals by highly adapted bacterial strain Cutibacterium sp. NL2 isolated from Algerian oilfield

Investigating the ability of bacteria to simultaneously enhance hydrocarbon removal and reduce heavy metals' toxicity is necessary to design more effective bioremediation strategies. A bacterium (NL2 strain) isolated from an Algerian oilfield was cultivated on crude oil as sole carbon and energy sources. Molecular analyses of the 16S rRNA gene sequence placed the strain within the Cutibacterium genera. This isolate was able to tolerate up to 60% of crude oil as sole carbon source. Chemical analyses (GC-MS) evidenced that strain NL2 was able to degrade 92.22% of crude oil (at optimal growing conditions: pH 10, 44 °C, 50 g L-1 NaCl, and 20% of crude oil (v/v) as sole carbon source) in only 7 days. NL2 isolate was also able to produce biosurfactants with reduction of surface tension of growing media (29.4 mN m-1). On the other hand, NL2 strain was able to tolerate high lead (Pb) and copper (Cu) concentrations (up to 60 mM). In fact, NL2 cultivated in the presence of 20% of crude oil, and 0.48 mM of Pb was able to reduce Pb concentration by a 41.36%. In turn, when cultivated on high Pb concentration (15 mM), the strain was able to remove 35.19% of it and 86.25% of crude oil, both in a time frame of 7 days. Our findings suggest that Cutibacterium strain NL2 is able to efficiently use and remove a wide range of crude oil substrates in presence of high Pb concentration. Accordingly, NL2 strain is of extreme interest from a biotechnological standpoint.

Modelling fuel oil transformation on geographically different seacoasts and assessing their self-cleansing capacity

The present paper considers the results of long-term (up to 17 years) in situ and laboratory research carried out on oiled French, Spanish, and Russian seacoasts. The objective of this research is to quantify the influence of geographical factors on the rates of natural transformation of the heavy fuel oil stranded ashore and to develop an empirical statistical model in order to evaluate the self-cleansing capacity of the coastal environment. In a number of field campaigns, 363 samples of weathered oil slicks and tar balls have been collected and analysed with the use of thin-layer chromatography combined with optical and gravimetric methods. The results obtained have been subjected to multiple nonlinear regression analyses. It has been shown that heavy fuel oil natural attenuation is more active in continental or estuarine environments influenced by nutrient-rich freshwater runoff and characterised by a higher number of sunny days, solar irradiation, and large temperature fluctuations. On the oceanic coasts, especially in sectors with low hydrodynamic energy, these processes take more time. The resulting model allows for the identification and mapping of the most vulnerable seacoasts, characterised by a low potential to degrade oil pollution. This information may be used in the contingency plans in order to optimise clean-up techniques and associated costs.

Microbiome single cell atlases generated with a commercial instrument

Single cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, we present EASi-seq (Easily Accessible Single microbe sequencing). By adapting the single cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbes' genomes. EASi-seq allows thousands of microbes to be sequenced per run and, as we show, can generate detailed atlases of human and environmental microbiomes. The ability to capture large shotgun genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, we develop a companion bioinformatic pipeline that clusters microbes by similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, we demonstrate integration of metagenomic contigs with the EASi-seq datasets to reduce capture bias and increase coverage. Overall, EASi-seq enables high quality single cell genomic data for microbiome samples using an accessible workflow that can be run on a commercially available platform.

PAH residues and toxicity levels two years after an extensive oil spill on the northeast Brazilian coast

The most extensive oil spill ever recorded in tropical oceans occurred between August 2019 and March 2020, affecting approximately 3000 km of the Brazilian coast. This study assessed the chemical contamination and toxicity of sediments collected from affected reef areas during two sampling surveys conducted 17 and 24 months after the peak of oil slick inputs. Our results indicated that neither PAH levels nor measured toxicity showed a significant contribution from the spilled oil, with concentrations and biological effects indistinguishable from those in unaffected areas. Similarly, no differences were observed between seasons. Furthermore, there was no discernible relationship between sediment toxicity results and the measured PAH concentrations. Therefore, while biological responses indicated toxicity in most assessed areas, these responses are likely related to other local sources. This evidence suggests a natural oil attenuation process contributing to local environmental recovery. Nonetheless, further investigation is needed for other areas affected by oil spills.

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.

Unraveling the plethora of toxicological implications of nanoparticles on living organisms and recent insights into different remediation strategies: A comprehensive review

Increased use of nanoscale particles have benefited many industries, including medicine, electronics, and environmental cleaning. These particles provide higher material performance, greater reactivity, and improved drug delivery. However, the main concern is the generation of nanowastes that can spread in different environmental matrices, posing threat to our environment and human health. Nanoparticles (NPs) have the potential to enter the food chain through a variety of pathways, including agriculture, food processing, packaging, and environmental contamination. These particles can negatively impact plant and animal physiology and growth. Due to the assessment of their environmental damage, nanoparticles are the particles of size between 1 and 100 nm that is the recent topic to be discussed. Nanoparticles' absorption, distribution, and toxicity to plants and animals can all be significantly influenced by their size, shape, and surface chemistry. Due to their absorptive capacity and potential to combine with other harmful substances, they can alter the metabolic pathways of living organisms. Nevertheless, despite the continuous research and availability of data, there are still knowledge gaps related to the ecotoxicology, prevalence and workable ways to address the impact of nanoparticles. This review focuses on the impact of nanoparticles on different organisms and the application of advanced techniques to remediate ecosystems using hyperaccumulator plant species. Future considerations are explored around nano-phytoremediation, as an eco-friendly, convenient and cost effective technology that can be applied at field scales.

Functional response of microbial communities in lab-controlled oil-contaminated marine sediment

Crude oil contamination is one of the biggest problems in modern society. As oil enters into contact with the environment, especially if the point of contact is a body of water, it begins a weathering process by mixing and spreading. This is dangerous to local living organisms' communities and can impact diversity. However, despite unfavorable conditions, some microorganisms in these environments can survive using hydrocarbons as a nutrient source. Thus, understanding the local community dynamics of contaminated areas is essential. In this work, we analyzed the 16S rRNA amplicon sequencing and metatranscriptomic data of uncontaminated versus contaminated shallow marine sediment from publicly available datasets. We investigated the local population's taxonomic composition, species diversity, and fluctuations over time. Co-expression analysis coupled with functional enrichment showed us a prevalence of hydrocarbon-degrading functionality while keeping a distinct transcriptional profile between the late stages of oil contamination and the uncontaminated control. Processes related to the degradation of aromatic compounds and the metabolism of propanoate and butanoate were coupled with evidence of enhanced activity such as flagellar assembly and two-component system. Many enzymes of the anaerobic toluene degradation pathways were also enriched in our results. Furthermore, our diversity and taxonomical analyses showed a prevalence of the class Desulfobacteria, indicating interesting targets for bioremediation applications on marine sediment.

Methylated cycloalkanes fuel a novel genus in the Porticoccaceae family (Ca. Reddybacter gen. nov)

Cycloalkanes are abundant and toxic compounds in subsurface petroleum reservoirs and their fate is important to ecosystems impacted by natural oil seeps and spills. This study focuses on the microbial metabolism of methylcyclohexane (MCH) and methylcyclopentane (MCP) in the deep Gulf of Mexico. MCH and MCP are often abundant cycloalkanes observed in petroleum and will dissolve into the water column when introduced at the seafloor via a spill or natural seep. We conducted incubations with deep Gulf of Mexico (GOM) seawater amended with MCH and MCP at four stations. Within incubations with active respiration of MCH and MCP, we found that a novel genus of bacteria belonging to the Porticoccaceae family (Candidatus Reddybacter) dominated the microbial community. Using metagenome-assembled genomes, we reconstructed the central metabolism of Candidatus Reddybacter, identifying a novel clade of the particulate hydrocarbon monooxygenase (pmo) that may play a central role in MCH and MCP metabolism. Through comparative analysis of 174 genomes, we parsed the taxonomy of the Porticoccaceae family and found evidence suggesting the acquisition of pmo and other genes related to the degradation of cyclic and branched hydrophobic compounds were likely key events in the ecology and evolution of this group of organisms.

Degradation of polypropylene by fungi Coniochaeta hoffmannii and Pleurostoma richardsiae

The urgent need for better disposal and recycling of plastics has motivated a search for microbes with the ability to degrade synthetic polymers. While microbes capable of metabolizing polyurethane and polyethylene terephthalate have been discovered and even leveraged in enzymatic recycling approaches, microbial degradation of additive-free polypropylene (PP) remains elusive. Here we report the isolation and characterization of two fungal strains with the potential to degrade pure PP. Twenty-seven fungal strains, many isolated from hydrocarbon contaminated sites, were screened for degradation of commercially used textile plastic. Of the candidate strains, two identified as Coniochaeta hoffmannii and Pleurostoma richardsiae were found to colonize the plastic fibers using scanning electron microscopy (SEM). Further experiments probing degradation of pure PP films were performed using C. hoffmannii and P. richardsiae and analyzed using SEM, Raman spectroscopy and Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR). The results showed that the selected fungi were active against pure PP, with distinct differences in the bonds targeted and the degree to which each was altered. Whole genome and transcriptome sequencing was conducted for both strains and the abundance of carbohydrate active enzymes, GC content, and codon usage bias were analyzed in predicted proteomes for each. Enzymatic assays were conducted to assess each strain's ability to degrade naturally occurring compounds as well as synthetic polymers. These investigations revealed potential adaptations to hydrocarbon-rich environments and provide a foundation for further investigation of PP degrading activity in C. hoffmannii and P. richardsiae.

Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy)

Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.

Interactions between microplastics and contaminants: A review focusing on the effect of aging process

Microplastics (MPs) in the environment are a major global concern due to their persistent nature and wide distribution. The aging of MPs is influenced by several processes including photodegradation, thermal degradation, biodegradation and mechanical fragmentation, which affect their interaction with contaminants. This comprehensive review aims to summarize the aging process of MPs and the factors that impact their aging, and to discuss the effects of aging on the interaction of MPs with contaminants. A range of characterization methods that can effectively elucidate the mechanistic processes of these interactions are outlined. The rate and extent of MPs aging are influenced by their physicochemical properties and other environmental factors, which ultimately affect the adsorption and aggregation of aged MPs with environmental contaminants. Pollutants such as heavy metals, organic matter and microorganisms have a tendency to accumulate on MPs through adsorption and the interactions between them impact their environmental behavior. Aging enhances the specific surface area and oxygen-containing functional groups of MPs, thereby affecting the mechanism of interaction between MPs and contaminants. To obtain a more comprehensive understanding of how aging affects the interactions, this review also provides an overview of the mechanisms by which MPs interact with contaminants. In the future, there should be further in-depth studies of the potential hazards of aged MPs in different environments e.g., soil, sediment, aquatic environment, and effects of their interaction with environmental pollutants on human health and ecology.

Functional redundancy in response to runoff input upholds microbial community in hydrocarbon-contaminated land-sea continuum

An experimental approach mimicking the land-sea continuum in microcosms was developed in order to determine the effect of the terrigenous inputs by soil runoff on the microbial functional potential in hydrocarbon (HC) contaminated marine coastal sediment. We hypothesized that the coalescent event increases the functional potential of microbial communities in marine coastal sediments, influencing the fate of HC in marine coastal ecosystems. The microbial functional potential including the HC degradation ability was assessed by DNA-array to compare the sediment receiving or not terrigenous inputs. The removal of HC and the functional gene richness in sediment was unchanged with the terrigenous inputs. However, the gene variants (GVs) composition was modified indicating functional redundancy. In addition, functional indicators including GVs related to sulfite reduction, denitrification and polyaromatic degradation were identified in higher proportion in sediment receiving terrigenous inputs. The terrigenous inputs modified the functional co-occurrence networks, showing a reorganization of the GVs associations with an increase of the network complexity. Different keystone GVs ensuring similar functions were identified in networks with or without terrigenous inputs, further confirming functional redundancy. We argue that functional redundancy maintains the structure of microbial community in hydrocarbon-contaminated land-sea continuum mixing zone. Our results provide helpful functional information for the monitoring and management of coastal environment affected by human land-based activities.

Microbiome single cell atlases generated with a commercial instrument

Single cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, we present EASi-seq (Easily Accessible Single microbe sequencing). By adapting the single cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbes' genomes. EASi-seq allows thousands of microbes to be sequenced per run and, as we show, can generate detailed atlases of human and environmental microbiomes. The ability to capture large shotgun genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, we develop a companion bioinformatic pipeline that clusters microbes by similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, we demonstrate integration of metagenomic contigs with the EASi-seq datasets to reduce capture bias and increase coverage. Overall, EASi-seq enables high quality single cell genomic data for microbiome samples using an accessible workflow that can be run on a commercially available platform.

Effects of marine diesel on microbial diversity and activity in high Arctic beach sediments

Global warming induced sea ice loss increases Arctic maritime traffic, enhancing the risk of ecosystem contamination from fuel spills and nutrient loading. The impact of marine diesel on bacterial metabolic activity and diversity, assessed by colorimetric assay, 16S rRNA and metagenomic sequencing, of Northwest Passage (Arctic Ocean) beach sediments was assessed with nutrient amendment at environmentally relevant temperatures (5 and 15 °C). Higher temperature and nutrients stimulated microbial activity, while diesel reduced it, with metabolism inhibited at and above 0.01 % (without nutrients) and at 1 % (with nutrients) diesel inclusions. Diesel exposure significantly decreased microbial diversity and selected for Psychrobacter genus. Microbial hydrocarbon degradation, organic compound metabolism, and exopolysaccharide production gene abundances increased under higher diesel concentrations. Metagenomic binning recovered nine MAGs/bins with hydrocarbon degradation genes. We demonstrate a nutrients' rescue-type effect in diesel contaminated microbial communities via enrichment of microorganisms with stress response, aromatic compound, and ammonia assimilation metabolisms.

Anoxygenic phototrophic purple non-sulfur bacteria: tool for bioremediation of hazardous environmental pollutants

The extraordinary metabolic flexibility of anoxygenic phototrophic purple non-sulfur bacteria (PNSB) has been exploited in the development of various biotechnological applications, such as wastewater treatment, biohydrogen production, improvement of soil fertility and plant growth, and recovery of high-value compounds. These versatile microorganisms can also be employed for the efficient bioremediation of hazardous inorganic and organic pollutants from contaminated environments. Certain members of PNSB, especially strains of Rhodobacter sphaeroides and Rhodopseudomonas palustris, exhibit efficient remediation of several toxic and carcinogenic heavy metals and metalloids, such as arsenic, cadmium, chromium, and lead. PNSB are also known to utilize diverse biomass-derived lignocellulosic organic compounds and xenobiotics. Although biodegradation of some substituted aromatic compounds by PNSB has been established, available information on the involvement of PNSB in the biodegradation of toxic organic pollutants is limited. In this review, we present advancements in the field of PNSB-based bioremediation of heavy metals and organic pollutants. Furthermore, we highlight that the potential role of PNSB as a promising bioremediation tool remains largely unexplored. Thus, this review emphasizes the necessity of investing extensive research efforts in the development of PNSB-based bioremediation technology.

Cuticular hydrocarbons as weathering biomarkers of empty puparia of the forensically important blowfly Calliphora vicina Robineau-Desvoidy, 1830 (Diptera: Calliphoridae) in soil v/s under room conditions

Forensic entomology uses the age of insects, such as blow flies, to determine a minimum post-mortem interval (PMImin). Recent research has focused on using the analysis of specific cuticular hydrocarbons (CHCs) in adult insects and their empty puparia to estimate their age, as it has been shown that their profile changes are consistent with age. The current work is based on the weathering of five CHCs from empty puparia of Calliphora vicina that were stored in soil (field/outdoor) and non-soil (room/indoor conditions) based pupariation media for a total of six months. The experiment was conducted in a controlled environment chamber at a constant temperature of 25 ± 2 °C under constant darkness. Gas chromatography-mass spectrometry (GC-MS) was used to analyze the cuticular hydrocarbons after they were extracted in n-Hexane. n-Pentacosane, n-Hexacosane, n-Heptacosane, n-Octacosane, and n-Nonacosane were the five CHCs investigated. Results showed that CHCs weathered more quickly in the soil than in the non-soil environment. It was also found that the abundance of Heptacosane increased in the samples during the fifth month when stored in a non-soil medium, while the abundances of all five CHCs were not detected after eight weeks onwards in soil pupation medium.

Does Caulerpa prolifera with Its Bacterial Coating Represent a Promising Association for Seawater Phytoremediation of Diesel Hydrocarbons?

Anthropic diesel-derived contamination of Mediterranean coastal waters is of great concern. Nature-based solutions such as phytoremediation are considered promising technologies to remove contaminants from marine environments. The aim of this work was to investigate the tolerance of the Mediterranean autochthonous seaweed Caulerpa prolifera (Forsskal) Lamouroux to diesel fuel and its hydrocarbon degradation potential. Changes in C. prolifera traits, including its associated bacterial community abundance and structure, were determined by fluorescence microscopy and next-generation sequencing techniques. Thalli of C. prolifera artificially exposed to increasing concentration of diesel fuel for 30 days and thalli collected from three natural sites with different levels of seawater diesel-derived hydrocarbons were analysed. Gas chromatography was applied to determine the seaweed hydrocarbon degradation potential. Overall, in controlled conditions the lower concentration of diesel (0.01%) did not affect C. prolifera survival and growth, whereas the higher concentration (1%) resulted in high mortality and blade damages. Similarly, only natural thalli, collected at the most polluted marine site (750 mg L^-1), were damaged. A higher abundance of epiphytic bacteria, with a higher relative abundance of Vibrio bacteria, was positively correlated to the health status of the seaweed as well as to its diesel-degradation ability. In conclusion, C. prolifera tolerated and degraded moderate concentrations of seawater diesel-derived compounds, especially changing the abundance and community structure of its bacterial coating. The protection and exploitation of this autochthonous natural seaweed-bacteria symbiosis represents a useful strategy to mitigate the hydrocarbon contamination in moderate polluted Mediterranean costal environments.

A novel technology of solarization and phytoremediation enhanced with biosurfactant for the sustainable treatment of PAH-contaminated soil

Hydrocarbon-contaminated land has been a significant issue throughout Nigeria's Niger Delta since the discovery of crude oil in 1956. This paper proposes a novel and sustainable technique involving soil solarization, phytoremediation and biosurfactant to treat polycyclic aromatic hydrocarbon (PAH) contamination. The treatment effect on PAH reduction, plant growth, rhizosphere microorganisms and their enzymatic activities was evaluated. Twenty-eight days of solarization was carried out before the introduction of Chromolaena odorata seedlings for an 84-day phytoremediation period using a 4 × 4 (vegetated) and 2 × 4 (non-vegetated) cell microcosms to simulate the Niger Delta's subtropical conditions. Soil solarization resulted in significant PAH reduction (p ≤ 0.01) of phenanthrene, fluoranthene and benzo(a)pyrene with means reduction of 60.0%, 38.7% and 36.1% compared to their non-solarized counterparts with 18.0%, 18.0% and 18.8% at 95% CI (32.7, 51.3), (15.4, 26.1) and (8.0, 26.6), respectively. In post-solarization, all solarized and vegetated treatment groups significantly reduced (p ≤ 0.01) PAHs compared to their respective counterparts, while biosurfactant contribution in this combination was negligible (p ≥ 0.05). The growth parameters of C. odorata, total soil/rhizosphere heterotrophic microorganisms and their enzymatic activities of dehydrogenase and urease increased in all solarized treatments indicating essential biochemical processes. The novel and successful integration of soil solarization and phytoremediation using indigenous C. odorata as a combined technique to treat even the most recalcitrant form of hydrocarbons (PAHs) brings up new opportunities for a sustainable method of cleaning up contaminated land in Nigeria's oil-rich Niger Delta.

Hydrocarbons and other risks in a beekeeping area of México: the precautionary principle for prevention and biotechnology for remediation

The Yucatan Peninsula is the most important beekeeping region. However, the presence of hydrocarbons and pesticides violates the human right to a healthy environment twice over; it can affect human beings directly due to its toxicological characteristics, but it also constitutes a risk, not very well dimensioned, regarding the loss of biodiversity of the ecosystem via the impact on pollination. On the other hand, the precautionary principle obliges the authorities to prevent damage to the ecosystem that may be caused by the productive activity of individuals. Although there are studies that separately warn about the decrease of bees in the Yucatan due to industrial activity, this work has the novelty of presenting an intersectoral analysis of the risk that includes the soy industry, the swine industry and the tourist industry. The latter incorporates a new risk not considered until now, which is the presence of hydrocarbons in the ecosystem. Additionally, we can demonstrate that hydrocarbons, such as diesel and gasoline, should be avoided when using no genetically modified organisms (GMOs) in bioreactors. The objective of this work was to propose the precautionary principle around the risks in a beekeeping area and to propose biotechnology without using GMOs.

Deep relationships between bacterial community and polycyclic aromatic hydrocarbons in soil profiles near typical coking plants

Bacterial communities play an important role in maintaining the normal functioning of ecosystems; therefore, it is important to understand the effects of polycyclic aromatic hydrocarbons (PAHs) on the bacterial community. In addition, understanding the metabolic potential of bacterial communities for PAHs is important for the remediation of PAH-contaminated soils. However, the deep relationship between PAHs and bacterial community in coking plants is not clear. In this study, we determined the bacterial community and the concentration of PAHs in three soil profiles contaminated by coke plants in Xiaoyi Coking Park, Shanxi, China, using 16S rRNA and gas chromatography coupled with mass spectrometry, respectively. The results show that 2 ~ 3 rings PAHs are the main PAHs and Acidobacteria (23.76%) was the dominant bacterial community in three soil profiles. Statistical analysis showed that there were significant differences in the composition of bacterial communities at different depths and different sites. Redundancy analysis (RDA) and variance partitioning analysis (VPA) illustrate the influence of environmental factors (including PAHs, soil organic matter (SOM), and pH) on the vertical distribution of soil bacterial community, and PAHs were the main factors affecting the bacterial community in this study. The co-occurrence networks further indicated correlations between bacterial community and PAHs and found that Nap has the greatest effect on bacterial community compared with other PAHs. In addition, some operational taxonomic units (OTUs, OTU2, and OTU37) have the potential to degrade PAHs. PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used for further study on the potential of microbial PAHs degradation from a genetic perspective, which showed that different PAH metabolism genes were present in the genomes of bacterial communities in the three soil profiles, and a total of 12 PAH degradation-related genes were isolated, mainly dioxygenase and dehydrogenase genes.

High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean

Species within the genus Alcanivorax are well known hydrocarbon-degraders that propagate quickly in oil spills and natural oil seepage. They are also inhabitants of the deep-sea and have been found in several hydrothermal plumes. However, an in-depth analysis of deep-sea Alcanivorax is currently lacking. In this study, we used multiple culture-independent techniques to analyze the microbial community composition of hydrothermal plumes in the Northern Tonga arc and Northeastern Lau Basin focusing on the autecology of Alcanivorax. The hydrothermal vents feeding the plumes are hosted in an arc volcano (Niua), a rear-arc caldera (Niuatahi) and the Northeast Lau Spreading Centre (Maka). Fluorescence in situ hybridization revealed that Alcanivorax dominated the community at two sites (1210-1565 mbsl), reaching up to 48% relative abundance (3.5 × 104 cells/ml). Through 16S rRNA gene and metagenome analyses, we identified that this pattern was driven by two Alcanivorax species in the plumes of Niuatahi and Maka. Despite no indication for hydrocarbon presence in the plumes of these areas, a high expression of genes involved in hydrocarbon-degradation was observed. We hypothesize that the high abundance and gene expression of Alcanivorax is likely due to yet undiscovered hydrocarbon seepage from the seafloor, potentially resulting from recent volcanic activity in the area. Chain-length and complexity of hydrocarbons, and water depth could be driving niche partitioning in Alcanivorax.

From ecological functions to ecosystem services: linking coastal lagoons biodiversity with human well-being

In this review we highlight the relevance of biodiversity that inhabit coastal lagoons, emphasizing how species functions foster processes and services associated with this ecosystem. We identified 26 ecosystem services underpinned by ecological functions performed by bacteria and other microbial organisms, zooplankton, polychaetae worms, mollusks, macro-crustaceans, fishes, birds, and aquatic mammals. These groups present high functional redundancy but perform complementary functions that result in distinct ecosystem processes. Because coastal lagoons are located in the interface between freshwater, marine and terrestrial ecosystems, the ecosystem services provided by the biodiversity surpass the lagoon itself and benefit society in a wider spatial and historical context. The species loss in coastal lagoons due to multiple human-driven impacts affects the ecosystem functioning, influencing negatively the provision of all categories of services (i.e., supporting, regulating, provisioning and cultural). Because animals' assemblages have unequal spatial and temporal distribution in coastal lagoons, it is necessary to adopt ecosystem-level management plans to protect habitat heterogeneity and its biodiversity, ensuring the provision of services for human well-being to multi-actors in the coastal zone.

The effects of nitrogen and phosphorus nutrients on the bioremediation of oil-contaminated waters by Gracilariopsis persica in the coastal areas of Bandar Abbas

This study investigated the influence of nitrogen and phosphorus on the bioremediation of crude oil by Gracilariopsis persica in littoral zone waters. In order to determine the role of nitrogen in bioremediation, urea, ammonium, and nitrate were used with and without phosphorus, with the result that nitrogen had no significant effect on the degradation of oil by Gracilariopsis persica in the littoral zone. Nearly 90 % of the crude oil used in this study was degraded by treatments with added phosphorus and nitrogen. A significant increase in the degradation of oil-contaminated water was observed after the application of phosphorus. Comparatively to the application of phosphorus alone, nitrogen and phosphorus together increased the rate of biodegradation by the algal species. Based on the results of the study, nitrogen and phosphorus have complementary effects on the bioremediation of oil by Gracilariopsis persica.

Fungal bioproducts for petroleum hydrocarbons and toxic metals remediation: recent advances and emerging technologies

Petroleum hydrocarbons and toxic metals are sources of environmental contamination and are harmful to all ecosystems. Fungi have metabolic and morphological plasticity that turn them into potential prototypes for technological development in biological remediation of these contaminants due to their ability to interact with a specific contaminant and/or produced metabolites. Although fungal bioinoculants producing enzymes, biosurfactants, polymers, pigments and organic acids have potential to be protagonists in mycoremediation of hydrocarbons and toxic metals, they can still be only adjuvants together with bacteria, microalgae, plants or animals in such processes. However, the sudden accelerated development of emerging technologies related to the use of potential fungal bioproducts such as bioinoculants, enzymes and biosurfactants in the remediation of these contaminants, has boosted fungal bioprocesses to achieve higher performance and possible real application. In this review, we explore scientific and technological advances in bioprocesses related to the production and/or application of these potential fungal bioproducts when used in remediation of hydrocarbons and toxic metals from an integral perspective of biotechnological process development. In turn, it sheds light to overcome existing technological limitations or enable new experimental designs in the remediation of these and other emerging contaminants.

Exploring quantitative structure-property relationship models for environmental fate assessment of petroleum hydrocarbons

The rate and extent of biodegradation of petroleum hydrocarbons in the different aquatic environments is an important element to address. The major avenue for removing petroleum hydrocarbons from the environment is thought to be biodegradation. The present study involves the development of predictive quantitative structure-property relationship (QSPR) models for the primary biodegradation half-life of petroleum hydrocarbons that may be used to forecast the biodegradation half-life of untested petroleum hydrocarbons within the established models' applicability domain. These models use easily computable two-dimensional (2D) descriptors to investigate important structural characteristics needed for the biodegradation of petroleum hydrocarbons in freshwater (dataset 1), temperate seawater (dataset 2), and arctic seawater (dataset 3). All the developed models follow OECD guidelines. We have used double cross-validation, best subset selection, and partial least squares tools for model development. In addition, the small dataset modeler tool has been successfully used for the dataset with very few compounds (dataset 3 with 17 compounds), where dataset division was not possible. The resultant models are robust, predictive, and mechanistically interpretable based on both internal and external validation metrics (R² range of 0.605-0.959. Q²_(Loo) range of 0.509-0.904, and Q²_F1 range of 0.526-0.959). The intelligent consensus predictor tool has been used for the improvement of the prediction quality for test set compounds which provided superior outcomes to those from individual partial least squares models based on several metrics (Q²_F1 = 0.808 and Q²_F2 = 0.805 for dataset 1 in freshwater). Molecular size and hydrophilic factor for freshwater, frequency of two carbon atoms at topological distance 4 for temperate seawater, and electronegative atom count relative to size for arctic seawater were found to be the most significant descriptors responsible for the regulation of biodegradation half-life of petroleum hydrocarbons.

Hydrocarbons in the water and bottom sediments of Sivash Bay (the Azov Sea) during its salinization

Sivash Bay is a unique hypersaline lagoon located in the northern part of the Crimean Peninsula. In 2014, due to political events in connection with the closure of the North Crimean Canal, the inflow of fresh water to Sivash Bay has been significantly reduced. As a result, there has been a steady increase in salinity since 2014 to the present. The main purpose of this work was to determine the spatial distribution and qualitative composition of hydrocarbons (aliphatic hydrocarbons, n-alkanes, polycyclic aromatic hydrocarbons) in the water and bottom sediments of the hypersaline Sivash Bay under increasing water salinity. The analysis of the physico-chemical parameters of Sivash Bay in 2020 showed the continued salinization and change of physico-chemical conditions of the lagoon. At the same time, spatially, the change in salinity affected only the total content and qualitative composition of hydrocarbons in the water. The content of the studied classes of hydrocarbons in the bottom sediments did not demonstrate a reliable correlation with the concentration of salts. There was also no statistically significant dependence of Eh and pH of bottom sediments on salinity. In accordance with the composition of n-alkanes and polyaromatic hydrocarbons, as well as on the basis of PCA analysis, it is possible to make a conclusion on natural, mainly autochthonous, sources of this class of substances and low toxicity of bottom sediments of the bay. Low concentrations and composition of hydrocarbons indicate an insignificant input of pollutants of anthropogenic origin in Sivash Bay during its salinization.

Bacillus subtilis and Bifidobacteria bifidum Fermentation Effects on Various Active Ingredient Contents in Cornus officinalis Fruit

Microbial fermentation has been widely used to improve the quality and functional composition of food and edibles; however, the approach has rarely been applied to traditional Chinese medicines. In this study, to understand the effect of microbial fermentation on the active ingredients of traditional Chinese medicines, we used Bifidobacterium bifidum and Bacillus subtilis to ferment the traditional Chinese medicine, Cornus officinalis fruit (COF), and determined the levels of active ingredients using HPLC (high-performance liquid chromatography). According to the results, both B. subtilis and B. bifidum substantially increased the amount of gallic acid in the COF culture broth after fermentation; however, the two species of bacteria had no effect on the loganin content. Moreover, the B. subtilis fermentation reduced the contents of ursolic acid and oleanolic acid in the COF broth, whereas the B. bifidum fermentation did not. This study contributes to a better understanding of the mechanism by which microbial fermentation alters the active ingredient levels of traditional Chinese medicines, and suggests that fermentation may potentially improve their functional ingredients.

Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation

Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.

Influence of bioaugmentation in crude oil contaminated soil by Pseudomonas species on the removal of total petroleum hydrocarbon

This study aimed to carry out the bioaugmentation of crude oil/motor oil contaminated soil. The mixture of novel strains Pseudomonas aeruginosa PP3 and Pseudomonas aeruginosa PP4 were used in this bioaugmentation studies. The four different bioaugmentation systems (BS 1-4) were carried out in this experiment labelled as BS 1 (Crude oil contaminated soil), BS 2 (BS 1 + bacterial consortia), BS 3 (Motor oil sludge contaminated soil), and BS 4 (BS 3 + bacterial consortia). The total petroleum hydrocarbon (TPH) was investigated for monitor the effectiveness of bioaugmentation process. The highest TPH removal rate was recorded on BS 4 (9091 mg Kg ^-1) was about 67% followed by 52% on BS 2 (8584 mg Kg ^-1) respectively. The percentage of biodegradation efficiency (BE) of residual crude and motor oil contaminated soil were evaluated by GCMS analysis and the results showed that 65% (BS 2) and 83% (BS 4) respectively. Further the bioaugmented soil was subjected to the plant cultivation (Lablab purpureus) and the results revealed that the L. purpureus was rapidly grown in the systems BS 4 and BS 2 than the system BS 1 and BS 2 which was due to the lesser biodegradation of the crude oil contents. In resultant, it can be concluded that the soil was suitable for the cultivation of plant. Overall, this study revealed that the selected bacterial consortia were effectively degraded the hydrocarbon and act as a potential bioremediator in the hydrocarbon polluted soil in a short period.

Utilization of a biosurfactant foam/nanoparticle mixture for treatment of oil pollutants in soil

Oil contamination has become a primary environmental concern due to increased exploration, production, and use. When oil enters the soil, it may attach or adsorb to soil particles and stay in the soil for an extended period, contaminating the soil and surrounding areas. Nanoparticles have been widely used for the treatment of organic pollutants in the soil. Surfactant foam has effectively been employed to remediate various soil contaminants or recover oil compounds. In this research, a mixture of biosurfactant foam/nanoparticle was utilized for remediation of oil-contaminated soil. The results demonstrated that the biosurfactant/nanoparticle mixture and nitrogen gas formed high-quality and stable foams. The foam stability depended on the foam quality, biosurfactant concentration, and nanoparticle dosage. The pressure gradient change in the soil column relied on the flowrate (N₂ gas + surfactant/nanoparticle mixture), foam quality, and biosurfactant concentration. The optimal conditions to obtain good quality and stable foams and high oil removal efficiency involved 1 vol% rhamnolipid, 1 wt% nanoparticle, and 1 mL/min flowrate. Biosurfactant foam/nanoparticle mixture was effectively used to remediate oil-contaminated soil, whereas the highest treatment efficiency was 67%, 59%, and 52% for rhamnolipid biosurfactant foam/nanoparticle, rhamnolipid biosurfactant/nanoparticle, and only rhamnolipid biosurfactant, respectively. The oil removal productivity decreased with the increase of flowrate due to the shorter contact time between the foam mixture and oil droplets. The breakthrough curves of oil pollutants in the soil column also suggested that the foam mixture's maximum oil treatment efficiency was higher than biosurfactant/nanoparticle suspension and only biosurfactant.

Dissemination of metaldehyde catabolic pathways is driven by mobile genetic elements in Proteobacteria

Bioremediation of metaldehyde from drinking water using metaldehyde-degrading strains has recently emerged as a promising alternative. Whole-genome sequencing was used to obtain full genomes for metaldehyde degraders Acinetobacter calcoaceticus E1 and Sphingobium CMET-H. For the former, the genetic context of the metaldehyde-degrading genes had not been explored, while for the latter, none of the degrading genes themselves had been identified. In A. calcoaceticus E1, IS91 and IS6-family insertion sequences (ISs) were found surrounding the metaldehyde-degrading gene cluster located in plasmid pAME76. This cluster was located in closely-related plasmids and associated to identical ISs in most metaldehyde-degrading β- and γ-Proteobacteria, indicating horizontal gene transfer (HGT). For Sphingobium CMET-H, sequence analysis suggested a phytanoyl-CoA family oxygenase as a metaldehyde-degrading gene candidate due to its close homology to a previously identified metaldehyde-degrading gene known as mahX. Heterologous gene expression in Escherichia coli alongside degradation tests verified its functional significance and the degrading gene homolog was henceforth called mahS. It was found that mahS is hosted within the conjugative plasmid pSM1 and its genetic context suggested a crossover between the metaldehyde and acetoin degradation pathways. Here, specific replicons and ISs responsible for maintaining and dispersing metaldehyde-degrading genes in α, β and γ-Proteobacteria through HGT were identified and described. In addition, a homologous gene implicated in the first step of metaldehyde utilisation in an α-Proteobacteria was uncovered. Insights into specific steps of this possible degradation pathway are provided.

Biotreatment of oily sludge by a bacterial consortium: Effect of bioprocess conditions on biodegradation efficiency and bacterial community structure

We studied the biodegradation of oily sludge generated by a petroleum plant in Bahrain by a bacterial consortium (termed as AK6) under different bioprocess conditions. Biodegradation of petroleum hydrocarbons in oily sludge (C₁₁-C₂₉) increased from 24% after two days to 99% after 9 days of incubation in cultures containing 5% (w/v) of oily sludge at 40°C. When the nitrogen source was excluded from the batch cultures, hydrocarbon biodegradation dropped to 45% within 7 days. The hydrocarbon biodegradation decreased also by increasing the salinity to 3% and the temperature above 40°C. AK6 tolerated up to 50% (w/v) oily sludge and degraded 60% of the dichloromethane-extractable oil fraction. Illumina-MiSeq analyses revealed that the AK6 consortium was mainly composed of Gammaproteobacteria (ca. 98% of total sequences), with most sequences belonging to Klebsiella (77.6% of total sequences), Enterobacter (16.7%) and Salmonella (5%). Prominent shifts in the bacterial composition of the consortium were observed when the temperature and initial sludge concentration increased, and the nitrogen source was excluded, favoring sequences belonging to Pseudomonas and Stenotrophomonas. The AK6 consortium is endowed with a strong oily sludge tolerance and biodegradation capability under different bioprocess conditions, where Pseudomonas spp. appear to be crucial for hydrocarbon biodegradation.

Characterization of petroleum degrading bacteria and its optimization conditions on effective utilization of petroleum hydrocarbons

Hydrocarbon contamination is continuing to be a serious environmental problem because of their toxicity. Hydrocarbon components have been known to be carcinogens and neurotoxic organic pollutants. The physical and chemical methods of petroleum removal have become ineffective and also are very costly. Therefore, bioremediation is considered the promising technology for the treatment of these contaminated sites since it is cost-effective and will lead to complete mineralization.The current study also concentrates on bioremediation of petroleum products by bacterium isolated from petroleum hydrocarbon contaminated soil. The current work shows that bacterial strains obtained from a petroleum hydrocarbon contaminated environment may degrade petroleum compounds. Two strains Bacillus licheniformis ARMP2 and Pseudomonas aeruginosa ARMP8 were identified as petroleum-degrading bacteria of the isolated bacterial colonies. The best growth conditions for the ARMP2 strain were determined to be pH 9, temperature 29 °C with sodium nitrate as its nitrogen source, whereas for the ARMP8 strain the optimal growth was found at pH 7, temperature 39 °C, and ammonium chloride as the nitrogen source. Both strains were shown to be effective at degrading petroleum chemicals confirmed by GCMS. Overall petroleum product degradation efficiency of the strains ARMP2 and ARMP8 was about 88 % and 73 % respectively in 48 h.The strains Bacillus licheniformis ARMP2 and Pseudomonas aeruginosa ARMP8 were shown to be effective at degrading petroleum compounds in the current study. Even greater results might be obtained if the organisms were utilised in consortia or the degradation time period was extended.

Spatial heterogeneity in chemical composition and stability of glomalin-related soil protein in the coastal wetlands

GRSP is widely distributed in coastal wetlands, and there is a tendency for it to degrade with increasing burial depth. However, the dynamic changes in the chemical composition and stability of GRSP during the burial process are still unclear. The purpose of this study is to clarify the chemical composition and accumulation characteristics of GRSP during the burial process in the Zhangjiang estuary. In a field study, soil cores to the depth of 100 cm were collected in the estuary from mangrove forests dominated by Kandelia obovata and Avicennia marina, and from mudflat. The results showed that the concentration of GRSP in mangrove forest soil was significantly higher than that in the mudflat (p < 0.05), and the C/N ratio of GRSP increased with depth at all sites. Analysis of Fourier transform infrared (FTIR) data showed that the degradation rates of the GRSP's compositions varied with increasing burial depth, with microbial action and pH possibly being the main factors affecting degradation. Values of recalcitrance index (RI) showed that the stability of GRSP increased with increasing depth, and the contribution of GRSP to soil organic carbon (SOC) also increased. This suggests that the burial process plays a role in screening and storing the stable components of GRSP. Overall, our findings suggest that the concentration and chemical composition of GRSP vary dynamically according to habitat and burial processes. In addition, the improved stability of GRSP could contribute to carbon sequestration in coastal wetlands.

Converging alfalfa (Medicago sativa L.) and petroleum hydrocarbon acclimated ACC-deaminase containing bacteria for phytoremediation of petroleum hydrocarbon contaminated soil

Plant assisted bioremediation of petroleum hydrocarbon contaminated soil is considered an effective green technology whereby accelerated degradation occurs due to converged effect of microorganisms and plants. However, survival and growth of microbes and plants under stress conditions is challenging task for success of the technology. In this study, plant growth promoting bacteria containing 1-aminocyclopropane-1-carboxylate (ACC)-deaminase activity and tolerance to petroleum hydrocarbon contamination were used in association with alfalfa for bioremediation of petroleum hydrocarbon contaminated soil. Eight pre-isolated bacterial isolates from soil having previous history of petroleum contamination were used in convergence with alfalfa on sand soil which was artificially contaminated (10 g crude oil per kg^-1 of coarse textured soil). Combined effect of bacteria and plants on the degradation of petroleum hydrocarbons under controlled conditions of light and temperature was observed for a period of 60 days. The results of the study revealed that four bacterial isolates Bacillus subtilis strain PM32Y, Bacillus cereus strain WZ3S1, Bacillus sp. strain SM73 and Bacillus sp. strain WZ3S3 in association with alfalfa significantly degraded petroleum hydrocarbons. The most significant biodegradation (47%) of petroleum hydrocarbons was recorded in the experimental unit receiving PM32Y inoculation in association with alfalfa. Biodegradation of petroleum hydrocarbons was 33% with alone inoculation (without alfalfa) of PM32Y. The study revealed that combined use of bacteria and alfalfa plant is more efficient than alone application of either bacteria or plants for degradation of petroleum hydrocarbons.

Copiotrophic taxa in pig manure mitigate nitrogen limitation of soil microbial communities

Microbial nitrogen (N) limitation is a common problem in terrestrial ecosystems. Pig manure, a type of solid waste, is increasingly applied to improve soil N availability in agriculture through inputs of organic matter and inorganic N. Pig manure application also introduces a lot of exogenous microorganisms, which have distinctly different N requirements and metabolic properties, into the resident soil microbial community. However, the impacts of these manure-borne microorganisms on soil N cycling have not been well determined. Here, we investigated effects of manure-borne microorganisms on the N limitation of soil microorganisms using an ecoenzymatic stoichiometry analysis. We monitored microbial communities over a 90-day period in a laboratory-controlled experiment with four treatments: (1) non-sterilized soil mixed with non-sterilized manure (S-M), (2) non-sterilized soil mixed with sterilized manure (S-sM), (3) sterilized soil mixed with non-sterilized manure (sS-M), and (4) non-sterilized soil without manure addition (S, the control). The microbial N limitations were significantly mitigated in both S-M and sS-M. By contrast, the S-sM and S showed high levels of microbial N limitation, likely stemming from differences in the microbial functional composition. We found chitin-degrading bacteria were the dominant copiotrophic manure-borne bacteria associated with N mineralization, and they may improve soil N availability. We further identified several copiotrophic manure-borne bacteria in S-M and sS-M, and their abundances had significantly negative correlation with the level of N limitation and significantly positive correlation with the stoichiometric homeostasis. As these copiotrophic taxa can maintain homeostasis through regulating enzymatic activities, our results indicate that copiotrophic taxa in pig manure contribute to the mitigation of soil microbial N limitation. Our study also highlights the invasiveness capacity of manure-borne microorganisms in soil and evaluates the biotic effects of manure application on soil N cycling.

Recovery of Macrobenthic Food Web on Rocky Shores Following the Hebei Spirit Oil Spill as Revealed by C and N Stable Isotopes

The impact of large-scale oil spills on organisms can lead to modifications of the food web structure. To assess the effects of the Hebei Spirit oil-spill accident on the trophic structure of the macrobenthic community on intertidal rocky shores along Taean Peninsula on the western coast of Republic of Korea 4 years after the Hebei Spirit oil spill, we analyzed carbon and nitrogen stable isotope ratios of macrobenthic consumers and their potential food sources in two heavily oil-impacted and one non-impacted sites. The results show no significant differences in isotopic ratios of feeding groups and their potential food sources between the polluted and reference sites, suggesting similar trophic structures given similar resource use by consumers. Similar isotopic niches and substantial overlap areas of feeding groups between the affected and reference sites suggest that the oil-impacted sites have re-achieved the trophic functions of the natural ecosystem. This study provides valuable information on the ecological processes of trophic recovery in coastal ecosystems impacted by oil spills.

Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation

Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.

Hydrocarbon bioremediation on Arctic shorelines: Historic perspective and roadway to the future

Climate change has become one of the greatest concerns of the past few decades. In particular, global warming is a growing threat to the Canadian high Arctic and other polar regions. By the middle of this century, an increase in the annual mean temperature of 1.8 °C-2.7 °C for the Canadian North is predicted. Rising temperatures lead to a significant decrease of the sea ice area covered in the Northwest Passage. As a consequence, a surge of maritime activity in that region increases the risk of hydrocarbon pollution due to accidental fuel spills. In this review, we focus on bioremediation approaches on Arctic shorelines. We summarize historical experimental spill studies conducted at Svalbard, Baffin Island, and the Kerguelen Archipelago, and review contemporary studies that used modern omics techniques in various environments. We discuss how omics approaches can facilitate our understanding of Arctic shoreline bioremediation and identify promising research areas that should be further explored. We conclude that specific environmental conditions strongly alter bioremediation outcomes in Arctic environments and future studies must therefore focus on correlating these diverse parameters with the efficacy of hydrocarbon biodegradation.

Biodegradation of petroleum hydrocarbons in a weathered, unsaturated soil is inhibited by peroxide oxidants

Field-weathered crude oil-containing soils have a residual concentration of hydrocarbons with complex chemical structure, low solubility, and high viscosity, often poorly amenable to microbial degradation. Hydrogen peroxide (H₂O₂)-based oxidation can generate oxygenated compounds that are smaller and/or more soluble and thus increase petroleum hydrocarbon biodegradability. In this study, we assessed the efficacy of H₂O₂-based oxidation under unsaturated soil conditions to promote biodegradation in a field-contaminated and weathered soil containing high concentrations of total petroleum hydrocarbons (25200 mg TPH kg^-1) and total organic carbon (80900 mg TOC kg^-1). Microcosms amended with three doses of 48 g H₂O₂ kg^-1 soil (unactivated or Fe²⁺-activated) or 24 g sodium percarbonate kg^-1 soil and nutrients did not show substantial TPH changes during the experiment. However, 7.6-41.8% of the TOC concentration was removed. Furthermore, production of DOC was enhanced and highest in the microcosms with oxidants, with approximately 20-40-fold DOC increase by the end of incubation. In the absence of oxidants, biostimulation led to > 50% TPH removal in 42 days. Oxidants limited TPH biodegradation by diminishing the viable concentration of microorganisms, altering the composition of the soil microbial communities, and/or creating inhibitory conditions in soil. Study's findings underscore the importance of soil characteristics and petroleum hydrocarbon properties and inform on potential limitations of combined H₂O₂ oxidation and biodegradation in weathered soils.

Complete Genome Report of a Hydrocarbon-Degrading Sphingobium yanoikuyae S72

Sphingobium yanoikuyae S72 was isolated from the rhizosphere of sorghum plant in Mexico and we evaluated its survival and role in the degradation of some selected monoaromatic hydrocarbons and polycyclic aromatic hydrocarbons (PAHs) using minimal medium (Bushnell Hass medium (BH)) in which each of the hydrocarbons (naphthalene, phenanthrene, xylene, toluene, and biphenyl) served as sole carbon source. Gas column chromatography–mass spectrometry analysis was used to evaluate the effect of S72’s growth in the medium with the hydrocarbons. The genome of the S72 was sequenced to determine the genetic basis for the degradation of the selected hydrocarbon in S72. The genome was assembled de novo with Spades assembler and Velvet assembler and the obtained contigs were reduced to 1 manually using Consed software. Genome annotation was carried out Prokka version 1.12, and gene calling and further annotation was carried out with NCBI PGAAP. Pangenome analysis and COG annotation were done with bacteria pangenome analysis tool (BPGA) and with PATRIC online server, respectively. S72 grew effectively in the culture medium with the hydrocarbon with concentration ranging from 20–100 mg/mL for each hydrocarbon tested. S72 degraded biphenyl by 85%, phenanthrene by 93%, naphthalene by 81%, xylene by 19%, and toluene by 30%. The sequenced S72 genome was reduced to 1 contig and genome analysis revealed the presence of genes essential for the degradation of hydrocarbons in S72. A total of 126 unique genes in S72 are associated with the degradation of hydrocarbons and xenobiotics. S72 grew effectively in the tested hydrocarbon and shows good degradation efficiency. S72 will therefore be a good candidate for bioremediation of hydrocarbon contaminated soil.

Oil Absorbent Polypropylene Particles Stimulate Biodegradation of Crude Oil by Microbial Consortia

Oil absorbent particles made from surface-modified polypropylene can be used to facilitate the removal of oil from the environment. In this study, we investigated to what extent absorbed oil was biodegraded and how this compared to the biodegradation of oil in water. To do so, we incubated two bacterial communities originating from the Niger Delta, an area subject to frequent oil spills, in the presence and absence of polypropylene particles. One community evolved from untreated soil whereas the second evolved from soil pre-exposed to oil. We observed that the polypropylene particles stimulated the growth of biofilms and enriched species from genera Mycobacterium, Sphingomonas and Parvibaculum. Cultures with polypropylene particles degraded more crude oil than those where the oil was present in suspension regardless of whether they were pre-exposed or not. Moreover, the community pre-exposed to crude oil had a different community structure and degraded more oil than the one from untreated soil. We conclude that the biodegradation rate of crude oil was enhanced by the pre-exposure of the bacterial communities to crude oil and by the use of oil-absorbing polypropylene materials. The data show that bacterial communities in the biofilms growing on the particles have an enhanced degradation capacity for oil.