Isolation, characterization and determination of biotechnological potential of oil-degrading bacteria from Algerian centre coast

Microbial community enrichment and transition in landfill for the biotransformation of unpretreated low-density polyethylene (LDPE) under aerobic and anaerobic conditions

Low density polyethylene (LDPE), prevalent in single-use plastics, poses a significant environmental challenge due to its limited biodegradation. This study aims to enrich and characterize unpretreated LDPE degrading microorganisms from a nearly 50-year-old municipal landfill under aerobic and anaerobic conditions. Detailed analysis of the microbial communities through 16S rRNA gene based metataxonomy, whole genome metagenomics as well as thorough characterization of LDPE films exposed to the enriched microorganisms are done. Distinct shifts between plastisphere and bulk communities were observed. Shotgun metagenomics enabled reconstruction of thirty high-quality metagenome-assembled genomes (MAGs), revealing genes for plastic and hydrocarbon degradation, and biosurfactant production. Several plastic degradation-associated bacteria were identified, including Pseudomonas, Streptomyces, Burkholderia, Bacillus, Thermobifida, Saccharomonospora, Methylocaldum, Methylobacter, Ilumatobacter, Rubrivivax, and archaeal candidates like Methanosarcina and Nitrosarchaeum were observed. MAGs from Burkholderiales and Chlamydiales showed higher potential for LDPE degradation. Scanning electron microscopy showed biofilm formation on plastics, atomic force microscopy indicated surface topological changes, and Fourier transform infrared spectroscopy revealed increased carbonyl groups. Aerobic enrichments allowed up to 60% weight reduction of LDPE, with a degradation rate of 0.00766 mg/day and reaching half-life in nearly 90.49 days, confirming the biodegradation potential of the microbial community. From these observations, this study suggests two potential mechanisms of LDPE degradation under aerobic and anaerobic conditions by enriched communities. This study highlights role of landfill microbiomes in LDPE degradation, offering valuable insights into microbial succession of plastisphere and contributing to the development of effective plastic-degrading community. Future research could explore optimizing these for large-scale plastic waste management.

High-quality physiology of Alcanivorax borkumensis SK2 producing glycolipids enables efficient stirred-tank bioreactor cultivation

Glycine-glucolipid, a glycolipid, is natively synthesized by the marine bacterium Alcanivorax borkumensis SK2. A. borkumensis is a Gram-negative, non-motile, aerobic, halophilic, rod-shaped γ-proteobacterium, classified as an obligate hydrocarbonoclastic bacterium. Naturally, this bacterium exists in low cell numbers in unpolluted marine environments, but during oil spills, the cell number significantly increases and can account for up to 90% of the microbial community responsible for oil degradation. This growth surge is attributed to two remarkable abilities: hydrocarbon degradation and membrane-associated biosurfactant production. This study aimed to characterize and enhance the growth and biosurfactant production of A. borkumensis, which initially exhibited poor growth in the previously published ONR7a, a defined salt medium. Various online analytic tools for monitoring growth were employed to optimize the published medium, leading to improved growth rates and elongated growth on pyruvate as a carbon source. The modified medium was supplemented with different carbon sources to stimulate glycine-glucolipid production. Pyruvate, acetate, and various hydrophobic carbon sources were utilized for glycolipid production. Growth was monitored via online determined oxygen transfer rate in shake flasks, while a recently published hyphenated HPLC-MS method was used for glycine-glucolipid analytics. To transfer into 3 L stirred-tank bioreactor, aerated batch fermentations were conducted using n-tetradecane and acetate as carbon sources. The challenge of foam formation was overcome using bubble-free membrane aeration with acetate as the carbon source. In conclusion, the growth kinetics of A. borkumensis and glycine-glucolipid production were significantly improved, while reaching product titers relevant for applications remains a challenge.

Identification of cultivable bacterial strains producing biosurfactants/bioemulsifiers isolated from an Algerian oil refinery

Algerian petrochemical industrial areas are usually running spills and leakages of hydrocarbons, which constitutes a major source of toxic compounds in soil such as aromatic hydrocarbons. In this paper, samples of crude oil-polluted soil were collected from Skikda's oil refinery and were subjected to mono and polyaromatic hydrocarbons threshold assessment. Soil physicochemical parameters were determined for each sample to examine their response to pollution. Amid 34 isolated bacteria, eleven strains were selected as best Biosurfactants (Bs)/Bioemulsifiers (Be) producers and were assigned to Firmicutes and Proteobacteria phyla based on molecular identification. Phylogenetic analysis of partial 16S rDNA gene sequences allowed the construction of evolutionary trees by means of the maximum likelihood method. Accordingly, strains were similar to Bacillus spp., Priesta spp., Pseudomonas spp., Enterobacter spp. and Kosakonia spp. with more than 95% similarity. These strains could be qualified candidates for an efficient bioremediation process of severally polluted soils.

Bioremediation by oil degrading marine bacteria: An overview of supplements and pathways in key processes

Oil spillage is one of the most common pollutants which brings greater economic loss and damage to the environment. The intensity and amount of the damage may vary depending on factors such as the type of oil, the location of the spill, and the climatic parameters in the area. As for any pollution management, the guidelines are Reduce, Re-use, Recover and Disposal. Amongst the other remediation processes, Bioremediation is amongst the most significant environmentally friendly and cost-effective approaches for marine biological restoration because it allows complex petroleum hydrocarbons in spilt oil to decompose completely into harmless compounds. Mainly, the necessity and essence of bioremediation were talked about. This review discussed the bacteria identified which are capable of degrading various oil related pollutants and their components. Also, it covered the various media components used for screening and growing the oil degrading bacteria and the pathways that are associated with oil degradation. This article also reviewed the recent research carried out related to the oil degrading bacteria.

Bioremediation of Petroleum Hydrocarbons in Seawater: Prospects of Using Lyophilized Native Hydrocarbon-Degrading Bacteria

This work aimed to develop a bioremediation product of lyophilized native bacteria to respond to marine oil spills. Three oil-degrading bacterial strains (two strains of Rhodococcus erythropolis and one Pseudomonas sp.), isolated from the NW Portuguese coast, were selected for lyophilization after biomass growth optimization (tested with alternative carbon sources). Results indicated that the bacterial strains remained viable after the lyophilization process, without losing their biodegradation potential. The biomass/petroleum ratio was optimized, and the bioremediation efficiency of the lyophilized bacterial consortium was tested in microcosms with natural seawater and petroleum. An acceleration of the natural oil degradation process was observed, with an increased abundance of oil-degraders after 24 h, an emulsion of the oil/water layer after 7 days, and an increased removal of total petroleum hydrocarbons (47%) after 15 days. This study provides an insight into the formulation and optimization of lyophilized bacterial agents for application in autochthonous oil bioremediation.

Untapped Potential of Moving Bed Biofilm Reactors with Different Biocarrier Types for Bilge Water Treatment: A Laboratory-Scale Study

Two labscale aerobic moving bed biofilm reactor (MBBR) systems, with a different type of biocarrier in each (K3 and Mutag BioChip), were operated in parallel for the treatment of real saline bilge water. During the operation, different stress conditions were applied in order to evaluate the performance of the systems: organic/hydraulic load shock (chemical oxygen demand (COD): 9 g L−1; hydraulic retention time (HRT): 48–72 h) and salinity shock (salinity: 40 ppt). At the same time, the microbiome in the biofilm and suspended biomass was monitored through 16S rRNA gene analysis in order to describe the changes in the microbial community. The dominant classes were Alphaproteobacteria (families Rhodospirillaceae and Rhodobacteraceae) and Bacteroidia (family Lentimicrobiaceae), being recorded at high relative abundance in all MBBRs. The structure of the biofilm was examined and visualized with scanning electron microscopy (SEM) analysis. Both systems exhibited competent performance, reaching up to 86% removal of COD under high organic loading conditions (COD: 9 g L−1). In the system in which K3 biocarriers were used, the attached and suspended biomass demonstrated a similar trend regarding the changes observed in the microbial communities. In the bioreactor filled with K3 biocarriers, higher concentration of biomass was observed. Biofilm developed on Mutag BioChip biocarriers presented lower biodiversity, while the few species identified in the raw wastewater were not dominant in the bioreactors. Through energy-dispersive X-ray (EDX) analysis of the biofilm, the presence of calcium carbonate was discovered, indicating that biomineralization occurred.

Isolation and characterization of a novel rhamnolipid producer Pseudomonas sp. LGMS7 from a highly contaminated site in Ain El Arbaa region of Ain Temouchent, Algeria

This study aims to isolate and characterize a novel rhamnolipid producer within the recent bioremediation approaches for treating hydrocarbon-contaminated soils in Algeria. In this context, from a hydrocarbon-contaminated soil, a newly bacterium designated LGMS7 was screened and identified, belonged to the Pseudomonas genus, and was closely related to Pseudomonas mucidolens, with a 16S rRNA sequence similarity of 99.05%. This strain was found to use different hydrocarbons and oils as a sole carbon and energy source for growth. It showed a stable emulsification index E₂₄ (%) of 66.66% ± 3.46 when growing in mineral salts medium (MSM) supplemented with 2% (v/v) glycerol after incubation for 6 days at 30 °C. Interestingly, it was also able to reduce the surface tension of the cell-free supernatant to around 30 ± 0.65 mN m^-1 with a critical micelle concentration (CMC) of 800 mg l^-1. It was found to be able to produce around 1260 ± 0.57 mg l^-1 as the yield of rhamnolipid production. Its biosurfactant has demonstrated excellent stability against pH (pH 2.0-12.0), salinity (0-150 g l^-1), and temperature (-20 to 121 °C). Based on various chromatographic and spectroscopic techniques (i.e., TLC, FTIR, ¹H-NMR), it was found to belong to the glycolipid class (i.e., rhamnolipids). Taken altogether, the strain LGMS7 and its biosurfactant display interesting biotechnological capabilities for the bioremediation of hydrocarbon-contaminated sites. To the best of our knowledge, this is the first study that described the production of biosurfactants by Pseudomonas mucidolens species.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02751-6.

Distributions of chlorinated paraffins and the effects on soil microbial community structure in a production plant brownfield site

The distributions of chlorinated paraffins (CPs) in soils and their ecological effects attract much attention, while site-scale data are still scarce. In this study, a comprehensive investigation was performed to understand the CP distributions at a CP production plant brownfield site, as well as their effects on soil microbial community. Short-, medium- and long-chain CPs (SCCPs, MCCPs, LCCPs) were detected in most samples with total contents ranging ND-5,090, ND-6,670, and ND-1450 ng g^-1 (dw), respectively. A CP-hotspot was observed 10 m beneath the synthesis workshop, indicating the downward migration of CPs. The consistence of soil SCCP congener profiles with commercial product CP-52 suggested the leakage of CP products as the contamination source. Besides CPs, petroleum hydrocarbons (PHC) contamination also occurred beneath the synthesis workshop. Soil microbial community composition and diversity were significantly influenced by SCCPs (p < 0.05) despite their lower contents compared to other concerned contaminants. Microbial network analysis indicated nonrandom co-occurrence patterns, with Acinetobacter, Brevibacterium, Corynebacterium, Microbacterium, Stenotrophomonas, and Variibacter as the keystone genera. Genera from the same module showed significant ecological links (p < 0.05) and were involved in the degradation of PHCs and chlorinated organic contaminants. This study provides the first phylogenetic look at the microbial communities in CP contaminated soils, indicating that the long-term exposure to CPs and PHCs may lead to microbial group assemblages with the potential for degradation.

Innovative, ecofriendly biosorbent-biodegrading biofilms for bioremediation of oil- contaminated water

Immobilization of microorganisms capable of degrading specific contaminants significantly promotes bioremediation processes. In this study, innovative and ecofriendly biosorbent-biodegrading biofilms have been developed in order to remediate oil-contaminated water. This was achieved by immobilizing hydrocarbon-degrading gammaproteobacteria and actinobacteria on biodegradable oil-adsorbing carriers, based on polylactic acid and polycaprolactone electrospun membranes. High capacities for adhesion and proliferation of bacterial cells were observed by scanning electron microscopy. The bioremediation efficiency of the systems, tested on crude oil and quantified by gas chromatography, showed that immobilization increased hydrocarbon biodegradation by up to 23 % compared with free living bacteria. The resulting biosorbent biodegrading biofilms simultaneously adsorbed 100 % of spilled oil and biodegraded more than 66 % over 10 days, with limited environmental dispersion of cells. Biofilm-mediated bioremediation, using eco-friendly supports, is a low-cost, low-impact, versatile tool for bioremediation of aquatic systems.

Cover Crop Impact on Soil Organic Carbon, Nitrogen Dynamics and Microbial Diversity in a Mediterranean Semiarid Vineyard

Cover crop (CC) management in vineyards increases sustainability by improving soil chemical and biological fertility, but knowledge on its effects in semiarid soils is lacking. This study evaluated the effect of leguminous CC management on soil organic carbon (SOC) sequestration, soil nitrate content and microbial diversity in a semiarid vineyard, in comparison to conventional tillage (CT). SOC and nitrate were monitored during vine-growing season; soil respiration, determined by incubation experiments, microbial biomass and diversity was analyzed after CC burial. The microbial diversity was evaluated by bacterial and fungal automated ribosomal intergenic spacer analysis (ARISA) and high-throughput sequencing of 16SrDNA. CC increased nitrate content and, although it had no relevant effect on SOC, almost doubled its active microbial component, which contributes to SOC stabilization. An unexpected stability of the microbial communities under different soil managements was assessed, fungal diversity being slightly enhanced under CT while bacterial diversity increased under CC. The complete nitrifying genus Nitrospira and plant growth-promoting genera were increased under CC, while desiccation-tolerant genera were abundant in CT. Findings showed that temporary CC applied in semiarid vineyards does not optimize the provided ecosystem services, hence a proper management protocol for dry environments should be set up.