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

Microbial diversity and metabolic pathways linked to benzene degradation in petrochemical-polluted groundwater

The rapid advance in shotgun metagenome sequencing has enabled us to identify uncultivated functional microorganisms in polluted environments. While aerobic petrochemical-degrading pathways have been extensively studied, the anaerobic mechanisms remain less explored. Here, we conducted a study at a petrochemical-polluted groundwater site in Henan Province, Central China. A total of twelve groundwater monitoring wells were installed to collect groundwater samples. Benzene appeared to be the predominant pollutant, detected in 10 out of 12 samples, with concentrations ranging from 1.4 μg/L to 5,280 μg/L. Due to the low aquifer permeability, pollutant migration occurred slowly, resulting in relatively low benzene concentrations downstream within the heavily polluted area. Deep metagenome sequencing revealed Proteobacteria as the dominant phylum, accounting for over 63 % of total abundances. Microbial α-diversity was low in heavily polluted samples, with community compositions substantially differing from those in lightly polluted samples. dmpK encoding the phenol/toluene 2-monooxygenase was detected across all samples, while the dioxygenase bedC1 was not detected, suggesting that aerobic benzene degradation might occur through monooxygenation. Sequence assembly and binning yielded 350 high-quality metagenome-assembled genomes (MAGs), with 30 MAGs harboring functional genes associated with aerobic or anaerobic benzene degradation. About 80 % of MAGs harboring functional genes associated with anaerobic benzene degradation remained taxonomically unclassified at the genus level, suggesting that our current database coverage of anaerobic benzene-degrading microorganisms is very limited. Furthermore, two genes integral to anaerobic benzene metabolism, i.e, benzoyl-CoA reductase (bamB) and glutaryl-CoA dehydrogenase (acd), were not annotated by metagenome functional analyses but were identified within the MAGs, signifying the importance of integrating both contig-based and MAG-based approaches. Together, our efforts of functional annotation and metagenome binning generate a robust blueprint of microbial functional potentials in petrochemical-polluted groundwater, which is crucial for designing proficient bioremediation strategies.

Characterization of new diesel-degrading bacteria isolated from freshwater sediments

As the result of diesel's extensive production and use as fuel for transportation, pollution with such complex mixtures of hydrocarbons is a major concern worldwide. The present study's focus was to investigate the presence of diesel-degrading bacteria in different Danube Delta freshwater sediments. Ten bacterial strains capable to grow in a minimal medium with diesel as the sole carbon source were isolated and characterized in this study. Based on the phenotypic and molecular characteristics, the ten strains belong to four genera and seven species, such as Pseudomonas (P. aeruginosa, P. nitroreducens, P. resinovorans, P. multiresinivorans), Acinetobacter (A. tandoii), Bacillus (B. marisflavi), and Stenotrophomonas (S. maltophilia). All these bacteria were excellent biosurfactant producers, and they were able to tolerate saturated hydrocarbons, like n-heptane, n-decane, n-pentadecane, and n-hexadecane. The ten strains possess at least one alkane hydroxylase gene in their genome, and they were also able to tolerate and degrade diesel. Higher biodegradation rates of diesel were acquired for the strains from the genera Pseudomonas, Acinetobacter, and Stenotrophomonas, compared with that obtained for the Bacillus strain. Due to their remarkable potential to degrade diesel and produce biosurfactants, the ten isolated bacteria are attractive candidates for bioremediation of diesel-polluted environments.

Phyto-Beneficial Traits of Rhizosphere Bacteria: In Vitro Exploration of Plant Growth Promoting and Phytopathogen Biocontrol Ability of Selected Strains Isolated from Harsh Environments

Beneficial interactions between plants and some bacterial species have been long recognized, as they proved to exert various growth-promoting and health-protective activities on economically relevant crops. In this study, the growth promoting and antifungal activity of six bacterial strains, Paenarthrobacter ureafaciens, Beijerinckia fluminensis, Pseudomonas protegens, Arthrobacter sp., Arthrobacter defluii, and Arthrobacter nicotinovorans, were investigated. The tested strains resulted positive for some plant growth promoting (PGP) traits, such as indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate-deaminase (ACC-deaminase), siderophore production, and solubilization of phosphates. The effect of the selected bacteria on Arabidopsis thaliana seedlings growth was assessed using different morphological parameters. Bacterial activity against the phytopathogenic fungal species Aspergillus flavus, Fusarium proliferatum, and Fusarium verticillioides was also assessed, since these cause major yield losses in cereal crops and are well-known mycotoxin producers. Strains Pvr_9 (B. fluminensis) and PHA_1 (P. protegens) showed an important growth-promoting effect on A. thaliana coupled with a high antifungal activity on all the three fungal species. The analysis of bacterial broths through ultra performance liquid chromatography-mass spectrometry (UPLC-MS) and liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) confirmed the presence of potential PGP-compounds, among these are desferrioxamine B, aminochelin, asperchrome B, quinolobactin siderophores, and salicylic acid.

A Multidisciplinary Approach to Evaluate the Effectiveness of Natural Attenuation at a Contaminated Site

This study evaluates the natural attenuation of chlorinated hydrocarbons as remediation action in a contaminated site downtown the city of Parma (Italy). To achieve this goal, a combination of new investigation methods (bio-molecular analysis, compound specific isotope analysis, phytoscreening) has been proposed. The approach (named circular multi step) allows to: fully understand the phenomena that occur at the study site, design new investigation activities, and manage best practices. Consequently, each step of the approach improves the conceptual and numerical models with new knowledge. The activities carried out at the study site allowed to detect a contamination of perchloroethylene in a large part of the city of Parma and, of main importance, underneath a kindergarten. The results of the study did not show significant natural attenuation of chlorinated hydrocarbons and that the detected contamination could refer to the same unknown contaminant source. Furthermore, the innovative phytoscreening technique was applied to assess the presence of chlorinated hydrocarbons at the ground level. The plume spread was estimated through numerical modeling starting from potential contaminant sources. This study enhances the knowledge of groundwater flow and contamination in Parma and allows authorities to design new investigation/reclamation activities through management actions.

Natural Surface Hydrocarbons and Soil Faunal Biodiversity: A Bioremediation Perspective

Hydrocarbon pollution threatens aquatic and terrestrial ecosystems globally, but soil fauna in oil-polluted soils has been insufficiently studied. In this research, soil hydrocarbon toxicity was investigated in two natural oil seepage soils in Val D’Agri (Italy) using two different approaches: (i) toxicological tests with Folsomia candida (Collembola) and Eisenia fetida (Oligochaeta) and (ii) analysis of abundance and composition of micro- and meso-fauna. Soil sampling was done along 20 m-transepts starting from the natural oil seepages. Toxicological testing revealed that no exemplars of F. candida survived, whereas specimens of E. fetida not only survived but also increased in weight in soils with higher PAH concentrations, although no reproduction was observed. Analysis on microfauna showed that Nematoda was the most abundant group, with distance from seepages not affecting its abundance. Arthropoda results showed that Acarina, Collembola and Diptera larvae represented the most abundant taxa. The highest divergence in community composition was found between soils situated near seepages and at 5 m and 10 m distance. Arthropoda taxa numbers, total abundance and Acarina were lower in soils with high PAH concentration, while Diptera larvae were not significantly affected. Earthworms, together with Nematoda and Diptera larvae, could therefore represent ideal candidates in PAH degradation studies.