Isolation and characterization of a hydrocarbonoclastic bacterial enrichment from total petroleum hydrocarbon contaminated sediments: potential candidates for bioaugmentation in bio-based processes

Groups of Geomicrobiological Indicators Are Spread across Gas-Hydrate and Non-Gas-Hydrate Areas in the Northern Part of the Sea of Japan

The bioindication of oil and gas fields is a field of geomicrobiology that is mainly devoted to the detection of hydrocarbon-oxidizing microbial indicator species or functional genes in total DNA. However, it appears promising to use the physiological properties of microorganisms detection deposit type of hydrocarbons, in particular their ability to oxidize hydrocarbons under aerobic and anaerobic conditions. In this study, the most promising approach in this area was the method used for assessing the anaerobic degradation of hydrocarbons. When comparing molecular genetics and cultured methods of bioindication, it can be concluded that molecular biomarkers of functional genes for the anaerobic destruction of hydrocarbons (masD) make it possible to separate areas with traditional and gas-hydrate types of deposits. Using cultured methods, we found that representatives of the Nocardiaceae family of the phylum Actinomycetota were tied to the areas where gas hydrates were found. The ability of aerobic and facultative anaerobic hydrocarbon-oxidizing microorganisms to anaerobically utilize hydrocarbons was determined with cultured methods. For the first time, this ability was revealed for the genera Stenotrophomonas, Psychrobacter, Micrococcus and Peribacillus. The wide distribution of this ability that we found in strains isolated from both study regions suggests its prominent role in the destruction of hydrocarbons in marine sediments.

Effects of oil contamination on plant growth and development: a review

Oil spills generate several environmental impacts and have become more common with the increase in petroleum extraction, refining, transportation, and trade. In soil, oil contamination increases water and nutrient availability and compaction, directly affecting plant growth and development. Different aspects of phytotoxicity can be observed and will vary according to the characteristics of soil and plants. Oil-contaminated soil also results in negative effects on biomass and changes in leaves and roots. Investigating the effects of oil contamination on plant growth and development can aid in the conservation of plant species and in the development of techniques such as bioremediation and biomonitoring. Thus, this review aims to discuss the main effects of oil contamination on plants, such as environmental stress and morphological, physiological, and anatomical changes, and the strategies developed by plants to survive contamination, as well as to identify plants with phytoremediation potential that can assist in removing oil from the environment.

A New Ciboria sp. for Soil Mycoremediation and the Bacterial Contribution to the Depletion of Total Petroleum Hydrocarbons

A Ciboria sp. strain (Phylum Ascomycota) was isolated from hydrocarbon-polluted soil of an abandoned oil refinery in Italy. The strain was able to utilize diesel oil as a sole carbon source for growth. Laboratory-scale experiments were designed to evaluate the use of this fungal strain for treatment of the polluted soil. The concentration of total petroleum hydrocarbons (TPH) in the soil was 8,538 mg/kg. Mesocosms containing the contaminated soil were inoculated with the fungal strain at 1 or 7%, on a fresh weight base ratio. After 90 days of incubation, the depletion of TPH contamination was of 78% with the 1% inoculant, and 99% with the 7% inoculant. 16S rDNA and ITS metabarcoding of the bacterial and fungal communities was performed in order to evaluate the potential synergism between fungi and bacteria in the bioremediation process. The functional metagenomic prediction indicated Arthrobacter, Dietzia, Brachybacerium, Brevibacterium, Gordonia, Leucobacter, Lysobacter, and Agrobacterium spp. as generalist saprophytes, essential for the onset of hydrocarbonoclastic specialist bacterial species, identified as Streptomyces, Nocardoides, Pseudonocardia, Solirubrobacter, Parvibaculum, Rhodanobacter, Luteiomonas, Planomicrobium, and Bacillus spp., involved in the TPH depletion. The fungal metabolism accelerated the onset of specialist over generalist bacteria. The capacity of the Ciboria sp. to deplete TPH in the soil in treatment was also ascertained.

Degradation of BTEX mixture by a new Pseudomonas putida strain: role of the quorum sensing in the modulation of the upper BTEX oxidative pathway

A new Pseudomonas putida strain (AQ8) was isolated from a decommissioned oil refinery's soil in Italy and characterized for its ability to degrade BTEX. The draft genome of the new strain was sequenced and annotated for genes that encode enzymes putatively involved in BTEX degradation and quorum sensing. The strain was transformed with a plasmid expressing lactonase, which cleaves the autoinducer quorum sensing signal molecule, the acyl-homoserine lactone, to obtain a quorum sensing minus strain. P. putida AQ8 depleted the 40% on average of all the components of the initial BTEX concentration in 36 h. The quorum sensing minus strain, in the same time interval, depleted only the 10% of the initial BTEX concentration. The role of quorum sensing in regulating the expression of the annotated benzene/toluene dioxygenase gene (benzA) and biphenyl/toluene/benzene dioxygenase (bphA) genes, which are involved in BTEX degradation, was studied by quantitative RT-real-time quantitative (q)PCR analysis. The qPCR data showed decreased levels of expression of the benzA and bphA genes in the quorum sensing minus strain. Our results showed, for the first time, quorum sensing modulation of the level of transcription of dioxygenase genes in the upper BTEX oxidation pathway.

Determination of biological markers of organic substances in sediment and soil samples by gas chromatography

Once they reach the environment, petroleum hydrocarbons undergo various chemical, physico-chemical and biochemical transformation processes. Organic compounds which are not or are very poorly subject to these processes are thermodynamically the most stable isomers and they are called biological markers (biomarkers). This paper presents the results of the determination of organic substances in twelve samples taken in the area of the city of Banja Luka (Bosnia and Herzegovina). Two soil samples were taken in the Banja Luka city heating plant area and ten river sediment and soil samples were taken in the upper and lower basin of the Vrbas river in the Banja Luka city area. The aim of this study was to determine the biomarkers of oil-type pollutants in contaminated samples as well as the type of organic substances in samples taken near the contaminated area. Assisted solvent extraction was used to isolate the total petroleum hydrocarbons (TPH) from all twelve samples. Fractionation of the extracts into saturated and aromatic hydrocarbon fractions was performed by column chromatography. The fractions were analyzed by gas chromatography-mass spectrometry (GC-MS). On basis of the obtained chromatograms, biomarkers of petroleum pollutants and specific correlation parameters of organic substances in the samples were determined. The dominance of n-alkanes with odd C atoms as well as the presence of an unresolved complex mixture (UCM) on chromatograms of saturated and aromatic hydrocarbons showed the presence of anthropogenic organic substances of petroleum origin in the analyzed samples. Based on the obtained chromatograms, it can be concluded that microbial degradation of hydrocarbons in all samples occurred.

A New Thioalkalivibrio sp. Strain Isolated from Petroleum-Contaminated Brackish Estuary Sediments: A New Candidate for Bio-Based Application for Sulfide Oxidation in Halo-Alkaline Conditions

A new halo-alkaline sulfur-oxidising bacterial strain was isolated from brackish estuary sediments contaminated by total petroleum hydrocarbon. The isolate was classified as a new strain of Thioalkalivibrio sulfidiphilus sp., showing a higher capability of adaptation to pH and a higher optimal sodium concentration for growth, when compared to Thioalkalivibrio sulfidiphilus sp. HL-EbGr7, type strain of the species. The strain was capable to grow in saline concentrations up to 1.5 M Na+ and pH up to 10. The genome of the new isolate was sequenced and annotated. The comparison with the genome of Thioalkalivibrio sulfidiphilus sp. HL-EbGr7 showed a duplication of an operon encoding for a putative primary sodium extruding pump and the presence of a sodium/proton antiporter with optimal efficiency at halo-alkaline conditions. The new strain was able to oxidize sulfide at halo-alkaline conditions at the rate of 1 mmol/mg-N/h, suitable for industrial applications dedicated to the recovery of alkaline scrubber for H2S emission absorption and abatement.

Use of a Zeolite and Molecular Sieve to Restore Homeostasis of Soil Contaminated with Cobalt

Since contamination of soil with cobalt disturbs the soil’s biological balance, various types of compounds are being sought that could be used to restore the homeostasis of contaminated soil. The aim of the study was to determine the use of a Bio.Zeo.S.01 zeolite and molecular sieve in restoring the microbiological and biochemical balance of soil contaminated with cobalt. Soil samples were contaminated with cobalt (CoCl2·6H2O) at 0, 20, 80 mg·kg−1, and a Bio.Zeo.S.01 zeolite and molecular sieve were introduced at 0 and 15 g·kg−1. The soils on which the experiment was conducted were loamy sand and sandy clay loam. The experiment was carried out in two series on soil with and without a crop sown in it. The multiplication of microorganisms and the soil enzymes’ activity were determined on days 25 and 50 (harvest) of the experiment, and the yield of the underground and above-ground parts of maize and chemical and physical properties of soil were determined on the day of harvest. It was found that the microorganisms’ multiplication, enzyme activity, and maize yield were significantly disturbed by the excess of cobalt in the soil regardless of the soil type. The zeolite Bio.Zeo.S.01 used in the study had a smaller impact on microorganisms and soil enzyme activity than the molecular sieve. Cobalt accumulated more in the roots than in the above-ground parts of maize. An addition of sorbents decreased the accumulation of cobalt in maize grown only on sandy clay loam.

Fungal proliferation and hydrocarbon removal during biostimulation of oily sludge with high total petroleum hydrocarbon

A laboratory-scale study was conducted to investigate the effect of bioaugmentation (BA) and biostimulation (BS) on the remediation of oily sludge with high total petroleum hydrocarbon (TPH) content (269,000 mg/kg d.w. sludge). TPH concentration significantly decreased by 30.4% (P < 0.05) in the BS treatment after 13-week incubation, and 17.0 and 9.1% of TPH was removed in the BA and control treatments (amended with sterile water only), respectively. Aliphatic and other fractions (i.e., saturated n-alkanes and cyclic saturated alkanes) were reduced in the BS treatment, whereas no decrease in aromatic hydrocarbons occurred in any treatment. Gas chromatography-mass spectrometry analysis of aliphatic fractions showed that low-chain-length alkanes (C8-C20) were the most biodegradable fractions. The BS treatment supported fungal proliferation, with Sordariomycetes and Eurotiomycetes as the dominant classes. BS increased fungal diversity and decreased fungal abundance, and changed bacterial community structure. The findings show the potential of using BS to treat oily sludge with high TPH content. Graphical abstract.

Comparing Bioremediation Approaches for Agricultural Soil Affected with Petroleum Crude: A Case Study

The aim of work was to check and make comparison of efficacy for five approaches for petroleum crude contaminated agricultural soil remediation by making use of soil microcosms. Concerning the published literature in our information, this is the first report comparing five approaches i.e. abiotic losses, native microbial flora, nutrient amendments and pre-adapted native microbial culture and concurrent amendments of nutrients + pre-adapted native microbial culture for agricultural soil bioremediation using Pseudomonas aeruginosa NCIM 5514 by performing soil microcosm experiments. 96.00 ± 0.18% degradation of petroleum hydrocarbon fractions in 60 days of the experiment was observed when nutrients and P. aeruginosa NCIM 5514 were applied concomitantly. In nutrients- and P. aeruginosa NCIM 5514-added microcosm reduction in nitrogen, organic carbon, and phosphorus was noted. P. aeruginosa NCIM 5514, can be applied as a prospective bioremediation agent to remediate petroleum crude contaminated soil.

Hydrocarbonoclastic Ascomycetes to enhance co-composting of total petroleum hydrocarbon (TPH) contaminated dredged sediments and lignocellulosic matrices

Four new Ascomycete fungi capable of degrading diesel oil were isolated from sediments of a river estuary mainly contaminated by shipyard fuels or diesel oil. The isolates were identified as species of Lambertella, Penicillium, Clonostachys, and Mucor. The fungal candidates degraded and adsorbed the diesel oil in suspension cultures. The Lambertella sp. isolate displayed the highest percentages of oxidation of diesel oil and was characterised by the capacity to utilise the latter as a sole carbon source. This isolate showed extracellular laccase and Mn-peroxidase activities in the presence of diesel oil. It was tested for capacity to accelerate the process of decontamination of total petroleum hydrocarbon contaminated sediments, co-composted with lignocellulosic residues and was able to promote the degradation of 47.6% of the TPH contamination (54,074 ± 321 mg TPH/Kg of sediment) after two months of incubation. The response of the bacterial community during the degradation process was analysed by 16S rRNA gene meta-barcoding.