Dealing with complex contamination: A novel approach with a combined bio-phytoremediation strategy and effective analytical techniques.

Phytoremediation is a sustainable technology capable of efficiently removing low or moderate contamination. However, complex pollution conditions can drastically reduce efficiency, as plants can show themselves sensitive to organic contaminants, growing slowly and thus impairing metals' absorption. In cases where the action of indigenous bacteria degrading hydrocarbons and promoting plant growth is not sufficient, more sophisticated strategies are necessary. This investigation aims to evaluate the effectiveness of a train of technologies that sees advanced phytoremediation in combination with other biological approaches to remediate soil from a disused industrial area contaminated by N-containing compounds, alkyl aromatic hydrocarbons, copper, and nickel. In particular, a stepwise procedure was used with a pre-treatment (landfarming and bioaugmentation), significantly affecting the soil's fertility, increasing germinability up to 85%, and allowing the plants to extract the metals adequately. Furthermore, with EDTA as a mobilizing agent, nickel absorption has increased up to 36% in Helianthus annuus and up to 88% in Zea mays. For copper, an increase of up to 262% in Helianthus annuus and up to 202% in Zea Mays was obtained. Analysis through Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry highlighted the biodegradation of some of the N-containing compounds recording, after phytoremediation, a decrease of up to almost 90%. Metagenomic analysis of the soil showed a typical microbial population of oxidizing hydrocarbon strains with a prevalence of the Nocardiaceae family (43%). The results obtained appear to confirm the usefulness of the approach developed, and the employed cutting-edge analytical techniques allowed a top-notch characterization of the remediation scenario.

Use of Shotgun Metagenomics to Assess the Microbial Diversity and Hydrocarbons Degrading Functions of Auto-Mechanic Workshops Soils Polluted with Gasoline and Diesel Fuel.

Bioaugmentation is a valuable technique for oil recovery. This study investigates the composition and functions of microbial communities in gasoline- and diesel-contaminated soils of garages Matoko (SGM) and Guy et Paul (SGP) originating from auto mechanic workshops as well as the concentration of soil enzymes ß-glucosidase, ß-glucosaminidase, and acid phosphatase. The work aimed to evaluate the presence of petroleum-hydrocarbon-degrading bacteria for the development of foreseen bioremediation of oil-contaminated soils. Microbial diversity, as given by shotgun metagenomics, indicated the presence of 16 classes, among which Actinobacteria and Gammaproteobacteria dominated, as well as more than 50 families, including the dominant Gordoniaceae (26.63%) in SGM and Pseudomonadaceae (57.89%) in SGP. The dominant bacterial genera in the two soils were, respectively, Gordonia (26.7%) and Pseudomonas (57.9%). The exploration of the bacterial metabolic abilities using HUMANn2 allowed to detect genes and pathways involved in alkanes and aromatic hydrocarbons in the two contaminated soils. Furthermore, enzymes ß-glucosidase, ß-glucosaminidase, and acid phosphatase were found in high concentrations ranging between 90.27 ± 5.3 and 804.17 ± 20.5 µg pN/g soil/h, which indicated active microbial metabolism. The high diversity of microorganisms with a hydrocarbon degradation genetic package revealed that the bacteria inhabiting the two soils are likely good candidates for the bioaugmentation of oil-contaminated soils.

Diverse plant promoting bacterial species differentially improve tomato plant fitness under water stress.

Introduction: Food crops are increasingly susceptible to the challenging impacts of climate change, encompassing both abiotic and biotic stresses, that cause yield losses. Root-associated microorganisms, including plant growth-promoting bacteria (PGPB), can improve plant growth as well as plant tolerance to environmental stresses. The aims of this work were to characterize bacteria isolated from soil and roots of tomato plants grown in open field. Methods: Biochemical and molecular analyses were used to evaluate the PGP potential of the considered strains on tomato plants in controlled conditions, also assessing their effects under a water deficit condition. The isolated strains were classified by 16S gene sequencing and exhibited typical features of PGPB, such as the release of siderophores, the production of proteases, and phosphorous solubilization. Inoculating tomato plants with eleven selected strains led to the identification of potentially interesting strains that increased shoot height and dry weight. Three strains were then selected for the experiment under water deficit in controlled conditions. The tomato plants were monitored from biometric and physiological point of view, and the effect of inoculation at molecular level was verified with a targeted RT-qPCR based approach on genes that play a role under water deficit condition. Results: Results revealed the PGP potential of different bacterial isolates in tomato plants, both in well-watered and stressed conditions. The used integrated approach allowed to obtain a broader picture of the plant status, from biometric, eco-physiological and molecular point of view. Gene expression analysis showed a different regulation of genes involved in pathways related to abscisic acid, osmoprotectant compounds and heat shock proteins, depending on the treatments. Discussion: Overall, results showed significant changes in tomato plants due to the bacterial inoculation, also under water deficit, that hold promise for future field applications of these bacterial strains, suggesting that a synergistic and complementary interaction between diverse PGPB is an important point to be considered for their exploitation.

The 'microbiome counterattack': Insights on the soil and root-associated microbiome in diverse chickpea and lentil genotypes after an erratic rainfall event.

Legumes maintain soil fertility thanks to their associated microbiota but are threatened by climate change that causes soil microbial community structural and functional modifications. The core microbiome associated with different chickpea and lentil genotypes was described after an unexpected climatic event. Results showed that chickpea and lentil bulk soil microbiomes varied significantly between two sampling time points, the first immediately after the rainfall and the second 2 weeks later. Rhizobia were associated with the soil of the more productive chickpea genotypes in terms of flower and fruit number. The root-associated bacteria and fungi were surveyed in lentil genotypes, considering that several parcels showed disease symptoms. The metabarcoding analysis revealed that reads related to fungal pathogens were significantly associated with one lentil genotype. A lentil core prokaryotic community common to all genotypes was identified as well as a genotype-specific one. A higher number of specific bacterial taxa and an enhanced tolerance to fungal diseases characterized a lentil landrace compared to the commercial varieties. This outcome supported the hypothesis that locally adapted landraces might have a high recruiting efficiency of beneficial soil microbes.

Great Abilities of Shinella zoogloeoides Strain from a Landfarming Soil for Crude Oil Degradation and a Synergy Model for Alginate-Bead-Entrapped Consortium Efficiency.

Oil contamination is of great concern worldwide and needs to be properly addressed. The present work aimed to contribute to the development of bacterial consortia for oil recovery. We investigated the community structure of a landfarming-treated soil (LF2) by metagenomics to unravel the presence of hydrocarbon degraders. Moreover, we isolated Shinella zoogloeoides LFG9 and Bacillus swezeyi LFS15 from LF2 and combined them with Pseudomonas guguanensis SGPP2 isolated from an auto mechanic workshop soil to form the mixed consortium COG1. Bacterial isolates were tested for biosurfactant production. Additionally, the bioremediation potential of COG1 was studied as free and entrapped consortia by gas chromatography-mass spectrometry, in comparison to the single strains. Results revealed the presence of Actinobacteria (66.11%), Proteobacteria (32.21%), Gammaproteobacteria (5.39%), Actinomycetales (65.15%), Burkholderiales (13.92%), and Mycobacterium (32.22%) taxa, indicating the presence of hydrocarbon degraders in soil LF2. All three isolated strains were biosurfactant producers capable of degrading crude oil components within 14 days. However, Shinella zoogloeoides LFG9 performed best and was retained as candidate for further bioremediation investigation. In addition, COG1 performed better when immobilized, with entrapment effectiveness manifested by increased fatty acids and aromatic compound degradation. Attempt to improve crude oil biodegradation by adding surfactants failed as sodium dodecyl sulfate restrained the immobilized consortium performance.

Nature-Based Solutions for Restoring an Agricultural Area Contaminated by an Oil Spill.

A feasibility study is presented for a bioremediation intervention to restore agricultural activity in a field hit by a diesel oil spill from an oil pipeline. The analysis of the real contaminated soil was conducted following two approaches. The first concerned the assessment of the biodegradative capacity of the indigenous microbial community through laboratory-scale experimentation with different treatments (natural attenuation, landfarming, landfarming + bioaugmentation). The second consisted of testing the effectiveness of phytoremediation with three plant species: Zea mays (corn), Lupinus albus (lupine) and Medicago sativa (alfalfa). With the first approach, after 180 days, the different treatments led to biodegradation percentages between 83 and 96% for linear hydrocarbons and between 76 and 83% for branched ones. In case of contamination by petroleum products, the main action of plants is to favor the degradation of hydrocarbons in the soil by stimulating microbial activity thanks to root exudates. The results obtained in this experiment confirm that the presence of plants favors a decrease in the hydrocarbon content, resulting in an improved degradation of up to 18% compared with non-vegetated soils. The addition of plant growth-promoting bacteria (PGPB) isolated from the contaminated soil also promoted the growth of the tested plants. In particular, an increase in biomass of over 50% was found for lupine. Finally, the metagenomic analysis of the contaminated soil allowed for evaluating the evolution of the composition of the microbial communities during the experimentation, with a focus on hydrocarbon- oxidizing bacteria.

37Cl-compound specific isotope analysis and assessment of functional genes for monitoring monochlorobenzene (MCB) biodegradation under aerobic conditions.

A laboratory approach was adopted in this study to explore the potential of 37Cl-CSIA in combination with 13C-CSIA and Biological Molecular Tools (BMTs) to estimate the occurrence of monochloroenzene (MCB) aerobic biodegradation. A new analytical method for 37Cl-CSIA of MCB was developed in this study. This methodology using a GC-IRMS allowed to determine δ37Cl values within an internal error of ±0.3‰. Samples from a heavily MCB contaminated site were collected and MCB aerobic biodegradation microcosms with indigenous cultures in natural and enhanced conditions were set up. The microcosms data show a negligible fractionation for 13C associated to MCB mass decrease of >95% over the incubation time. Conversely, an enrichment factor of -0.6±0.1‰ was estimated for 37Cl, which is a reflection of a secondary isotope effect. Moreover, the dual isotope approach showed a pattern for aerobic degradation which differ from the theoretical trend for reductive dehalogenation. Quantitative Polymerase Chain Reaction (qPCR) results showed a significant increase in todC gene copy number with respect to its initial levels for both natural attenuation and biostimulated microcosms, suggesting its involvement in the MCB aerobic degradation, whereas phe gene copy number increased only in the biostimulated ones. Indeed, 37Cl fractionation in combination with the dual carbon­chlorine isotope approach and the todC gene copy number represent valuable indicators for a qualitative assessment of MCB aerobic biodegradation in the field.