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

Harnessing the Ecological and Genomic Adaptability of the Bacterial Genus Massilia for Environmental and Industrial Applications

The bacterial genus Massilia was first described in 1998, and since then has attracted growing interest due to its ecological plasticity and biotechnological promise. Certain species of the genus Massilia inhabit a variety of ecosystems, from arid deserts to polar glaciers, and exhibit unique adaptations such as resistance to cold and heat. In contaminated environments, some members of Massilia contribute significantly to the detoxification of heavy metals and the degradation of organic pollutants, presenting them as promising agents for bioremediation. In addition, Massilia species improve plant resistance and facilitate pollutant absorption in phytoremediation strategies. New research also highlights their potential as bioindicators of environmental health, given their abundance in anthropogenically influenced ecosystems and airborne microbial communities. In addition to their ecological roles, some Massilia species have potential in biotechnological applications by producing biopolymers and secondary metabolites. Here, we integrate findings across various habitats to present a comprehensive overview of the ecological and biotechnological importance of the genus Massilia. We highlight critical knowledge gaps and propose future research directions to fully harness the potential of this not fully explored bacterial genus to address environmental challenges, including contamination.

Co-occurrence of PFASs, TPHs, and BTEX in subsurface soils: Impacts on native microbial communities and implications for bioremediation

This study investigates the co-occurrence of per- and polyfluoroalkyl substances (PFASs), petroleum hydrocarbons (TPHs) and benzene, toluene, ethylbenzene, and xylene (BTEX) and their effects on the indigenous microbial communities in soils at a contaminated site with a history of petroleum refinery operations. PFASs concentrations were in the range of 5.65-6.73 ng/g, and fluorooctane sulfonate (PFOS) and perfluorobutane sulfonic acid (PFBS) were the dominating compounds. No significant difference was observed in the PFASs concentration profiles between the site and background locations, indicating that PFASs detected in the soil samples were mainly contributed from non-point sources, due to the long-distance transport of PFASs in the region. The concentrations of TPHs and BTEX ranged from 227 to 72,360 mg/kg and 0.06-2109.77 mg/kg, respectively, mainly contributed by the historical refinery activities. The presence of PFASs, TPHs, and BTEX significantly impacted soil microbial community diversity and abundance, altering microbial compositions and enriching bacteria with higher resistance or metabolic capabilities against contamination. Strong correlations were observed between TPHs and its degraders such as Pseudomonas, Azoarcus, and Polaromonas. Significant positive relationship between PFASs and Trichlorobacter implied the potential defluorination capabilities of Trichlorobacter, warranting further investigation. Moreover, the higher energy metabolism including carbon, nitrogen and sulfur metabolisms and higher abundance of metabolic enzymes for alkane, cyclohexane and toluene in the refinery site revealed the potential occurrence of natural biodegradation of contaminants with indigenous microbial community. These findings highlight the complexity of sites contaminated with a mixture of traditional and emerging contaminants, providing valuable insights into the potential for biodegradation of mixed contaminants and underscoring the need for integrated approaches in environmental remediation strategies. This study contributes to understanding the ecological impacts of co-occurring contaminants and emphasizes the importance of considering multiple contaminant types in environmental risk assessments and remediation efforts.

A review of oil spill research in Canadian Arctic marine environments

The Canadian Arctic is a large and diverse geographic area that encompasses a wide variety of environmental conditions and ecosystems. Over recent decades, marine transportation has increased across the Arctic and, as a result, so has the likelihood of an oil spill. The study of oil spills in the Arctic presents unique challenges compared to temperate marine environments, due to remoteness, cold temperatures and the presence of snow and ice throughout much of the year. This review summarizes and discusses the fate of oil in the Canadian Arctic. A brief introduction to the Canadian Arctic and sources of potential petroleum spills is provided, followed by discussions of the behaviour of oil in ice and freezing temperatures, oil-sediment interactions, and the weathering and natural remediation of oil under Arctic conditions. A summary of perspectives concludes the review, with emphasis on possible areas of future work to address research gaps.

Metagenomic survey reveals hydrocarbon biodegradation potential of Canadian high Arctic beaches

BACKGROUND

Decreasing sea ice coverage across the Arctic Ocean due to climate change is expected to increase shipping activity through previously inaccessible shipping routes, including the Northwest Passage (NWP). Changing weather conditions typically encountered in the Arctic will still pose a risk for ships which could lead to an accident and the uncontrolled release of hydrocarbons onto NWP shorelines. We performed a metagenomic survey to characterize the microbial communities of various NWP shorelines and to determine whether there is a metabolic potential for hydrocarbon degradation in these microbiomes.

RESULTS

We observed taxonomic and functional gene evidence supporting the potential of NWP beach microbes to degrade various types of hydrocarbons. The metagenomic and metagenome-assembled genome (MAG) taxonomy showed that known hydrocarbon-degrading taxa are present in these beaches. Additionally, we detected the presence of biomarker genes of aerobic and anaerobic degradation pathways of alkane and aromatic hydrocarbons along with complete degradation pathways for aerobic alkane degradation. Alkane degradation genes were present in all samples and were also more abundant (33.8 ± 34.5 hits per million genes, HPM) than their aromatic hydrocarbon counterparts (11.7 ± 12.3 HPM). Due to the ubiquity of MAGs from the genus Rhodococcus (23.8% of the MAGs), we compared our MAGs with Rhodococcus genomes from NWP isolates obtained using hydrocarbons as the carbon source to corroborate our results and to develop a pangenome of Arctic Rhodococcus. Our analysis revealed that the biodegradation of alkanes is part of the core pangenome of this genus. We also detected nitrogen and sulfur pathways as additional energy sources and electron donors as well as carbon pathways providing alternative carbon sources. These pathways occur in the absence of hydrocarbons allowing microbes to survive in these nutrient-poor beaches.

CONCLUSIONS

Our metagenomic analyses detected the genetic potential for hydrocarbon biodegradation in these NWP shoreline microbiomes. Alkane metabolism was the most prevalent type of hydrocarbon degradation observed in these tidal beach ecosystems. Our results indicate that bioremediation could be used as a cleanup strategy, but the addition of adequate amounts of N and P fertilizers, should be considered to help bacteria overcome the oligotrophic nature of NWP shorelines.

Biodegradation and adsorption of benzo[a]pyrene by fungi-bacterial coculture

In this work, the relationship and kinetics of biodegradation and bio-adsorption of benzo[a]pyrene (BaP) by Bacillus and Ascomycota were explored, and the metabolites of BaP under mixed microbial coculture were analyzed and characterized. The results show that BaP was removed through both biosorption and biodegradation. Under mixed microbial coculture, biosorption played a significant role in the early stage and biodegradation was predominant in the later stage. During the removal of BaP, the fungi exhibited remarkable adsorption capabilities for BaP with an adsorption efficiency (AE) of 38.14 %, while bacteria had a best degradation for BaP with a degradation efficiency (DE) of 56.13 %. Under the mixed microbial culture, the removal efficiency (RE) of BaP by the synergistic action of fungi and bacteria reached up to 76.12 % within 15 days. Kinetics analysis illustrated that the degradation and adsorption process of BaP were well fit to the first-order and the pseudo-second-order kinetic models, respectively. The research on the relationship between degradation and adsorption during microbial removal of BaP, as well as the synergistic effects of fungi and bacteria, will provide a theoretical guidance for two or even synthetic microbial communities.

Urea amendment decouples nitrification in hydrocarbon contaminated Antarctic soil

Hydrocarbon contaminated soils resulting from human activities pose a risk to the natural environment, including in the Arctic and Antarctic. Engineered biopiles constructed at Casey Station, Antarctica, have proven to be an effective strategy for remediating hydrocarbon contaminated soils, with active ex-situ remediation resulting in significant reductions in hydrocarbons, even in the extreme Antarctic climate. However, the use of urea-based fertilisers, whilst providing a nitrogen source for bioremediation, has also altered the natural soil chemistry leading to increases in pH, ammonium and nitrite. Monitoring of the urea amended biopiles identified rising levels of nitrite to be of particular interest, which misaligns with the long term goal of reducing contaminant levels and returning soil communities to a 'healthy' state. Here, we combine amplicon sequencing, microfluidic qPCR on field samples and laboratory soil microcosms to assess the impact of persistent nitrite accumulation (up to 60 months) on nitrifier abundances observed within the Antarctic biopiles. Differential inhibition of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) Nitrobacter and Nitrospira in the cold, urea treated, alkaline soils (pH 8.1) was associated with extensive nitrite accumulation (76 ± 57 mg N/kg at 60 months). When the ratio of Nitrospira:AOB dropped below ∼1:1, Nitrobacter was completely inhibited or absent from the biopiles, and nitrite accumulated. Laboratory soil microcosms (incubated at 7 °C and 15 °C for 9 weeks) reproduced the pattern of nitrite accumulation in urea fertilized soil at the lower temperature, consistent with our longer-term observations from the Antarctic biopiles, and with other temperature-controlled microcosm studies. Diammonium phosphate amended soil did not exhibit nitrite accumulation, and could be a suitable alternative biostimulant to avoid excessive nitrite build-up.

Composition and Diversity of the Endobacteria and Ectobacteria of the Invasive Bark Beetle Hylurgus ligniperda (Fabricius) (Curculionidae: Scolytinae) in Newly Colonized Areas

Hylurgus ligniperda (Fabricius) (Curculionidae: Scolytinae) is a new invasive pest beetle in China, which colonized the Shandong province, causing devastating damage. Originating in Europe, it has spread to Oceania, Asia, North and South America. Bacterial associates have been frequently reported to play a vital role in strengthening the ecological adaptations of bark and ambrosia beetles. The environmental adaptability of H. ligniperda may be supported by their associated bacteria. Bacterial communities colonizing different body parts of insects may have different functions. However, little is known about the bacteria associated with H. ligniperda and their potential involvement in facilitating the adaptation and invasion of the beetles into new environments. In this study, we employed high-throughput sequencing technology to analyze the bacterial communities associated with male and female adults of H. ligniperda by comparing those colonizing the elytra, prothorax, and gut. Results showed that the bacterial communities of male and female adults were similar, and the elytra samples had the highest bacterial diversity and richness, followed by the gut, while the prothorax had the lowest. The dominant phyla were Proteobacteria, Firmicutes, and Actinobacteriota, while the dominant genera were Serratia, Lactococcus, Rhodococcus, unclassified Enterobacteriaceae, and Gordonia. Among these, Rhodococcus and Gordonia were the specific genera of endobacteria and ectobacteria, respectively. Differences in the distribution of associated bacteria may suggest that they have different ecological functions for H. ligniperda. The results of functional prediction showed that bacteria were enriched in terpenoid backbone biosynthesis, degradation of aromatic compounds, limonene and pinene degradation, neomycin, kanamycin and gentamicin biosynthesis, indicating that they may assist their beetles in synthesizing pheromones, degrading toxic secondary metabolites of host trees, and antagonizing pathogenic fungi. These results help us understand the interaction between H. ligniperda and bacteria and highlight possible contributions to the invasion process.

Bioremediation of Diesel-Contaminated Soil by Fungal Solid-State Fermentation

To address the poor removal of diesel in soil by indigenous microorganisms, we proposed a fungal solid-state fermentation (SSF) method for bioremediation. We screened Pycnoporus sanguineus 5.815, Trametes versicolor 5.996, and Trametes gibbosa 5.952 for their diesel-degrading abilities, with Trametes versicolor 5.996 showing the most promise. The fungal inoculum was obtained through SSF using wood chips and bran. Trametes versicolor 5.996 was applied to two treatments: natural attenuation (NA, diesel-contaminated soil) and bioremediation (BR, 10% SSF added to diesel-contaminated soil). Over 20 days, NA removed 12.9% of the diesel, while BR achieved a significantly higher 38.3% degradation rate. BR also increased CO2 and CH4 emissions but reduced N2O emissions. High-throughput sequencing indicated SSF significantly enriched known diesel-degrading microorganisms like Ascomycota (83.82%), Proteobacteria (46.10%), Actinobacteria (27.88%), Firmicutes (10.35%), and Bacteroidota (4.66%). This study provides theoretical support for the application of fungal remediation technology for diesel and improves understanding of microbiologically mediated diesel degradation and soil greenhouse gas emissions.

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.