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.

The role of cosubstrate and mixing on fungal biofilm efficiency in the removal of tannins

Tannins are polyphenolic compounds produced by plants and they are used in industrial vegetable tanning of leather. Tannins represent one of the low biodegradability substances in tannery wastewaters with high recalcitrant soluble chemical oxygen demand, furthermore high concentration of tannins can inhibit biological treatment. In the present study, four novel rotating submerged packed bed reactors were inoculated with a selected fungal strain to reach a biological degradation of tannins in non-sterile conditions. The selected fungal strain, Aspergillus tubingensis MUT 990, was immobilised in polyurethane foam cubes carriers and inserted inside a submerged rotating cage reactors. The reactors were feed with a solution composed of four tannins: Quebracho (Schinopsis spp.), Wattle (Mimosa spp.), Chestnut (Castanea spp.) and Tara (Caesalpinia spp.). Four reactors with a volume of 4 L each were used, the co-substrate was pure malt extract, the hydraulic retention time was 24 h and the pH setpoint was 5.5. The reactors configuration was chosen to allow the study of the effect of rotation and the co-substrate addition on tannins removal. The experiment lasted two months and it was achieved 80% of chemical oxygen demand and up to 90% dissolved organic carbon removal, furthermore it was detected an important tannase activity.

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.

Respirometric techniques coupled with laboratory-scale tests for kinetic and stoichiometric characterisation of fungal and bacterial tannin-degrading biofilms

In environmental biotechnology applications for wastewater treatment, bacterial-based bioprocesses are mostly implemented; on the contrary, the application of fungal-based bioprocesses, is still challenging under non-sterile conditions. In a previous laboratory-scale study, we showed that when specific tannins are used as the sole carbon source, fungi can play a key role in the microbial community, under non-sterile conditions and in the long term. In a previous study, an engineered ecosystem, based on fungal tannin biodegradation, was successfully tested in a laboratory-scale bioreactor under non-sterile conditions. In the present study, a kinetic and stoichiometric characterisation of the biomass developed therein was performed through the application of respirometric techniques applied to the biomass collected from the above-mentioned reactor. To this aim, a respirometric set-up was specifically adapted to obtain valuable information from tannin-degrading fungal biofilms. A mathematical model was also developed and applied to describe both the respirometric profiles and the experimental data collected from the laboratory-scale tests performed in the bioreactor. The microbial growth was described through a Monod-type kinetic equation as a first approach. Substrate inhibition, decay rate and tannin hydrolysis process were included to better describe the behaviour of immobilised biomass selected in the tannin-degrading bioreactor. The model was implemented in AQUASIM using the specific tool Biofilm Compartment to simulate the attached fungal biofilm. Biofilm features and transport parameters were either measured or assumed from the literature. Key kinetic and stoichiometric unknown parameters were successfully estimated, overcoming critical steps for scaling-up a novel fungal-based technology for tannins biodegradation.

Stability of fungal biomass continuously fed with tannic acid in a non-sterile moving-packed bed reactor

A number of bacteria and fungi are known to degrade tannins. In this study, the efficiency of the white-rot fungus, Bjerkandera adusta MUT 2295, was evaluated for the treatment of a synthetic solution prepared with tannic acid. Tests were performed in continuously fed, bench-scale, packed-bed reactors, operated under non-sterile conditions with biomass immobilized within PolyUrethane Foam cubes (PUFs). The main parameters monitored to evaluate the process efficiency were: soluble Chemical Oxygen Demand (sCOD), Total Organic Carbon (TOC) removal, and activities. of Tannase and Lignin Peroxidase. At the end of the process, additional parameters were evaluated, including the increase of fungal dry weight and the presence of ergosterol. The reactor was operative for 210 days, with maximum sCOD and TOC removal of 81% and 73%, respectively. The reduction of sCOD and TOC were positively correlated with the detection of Tannase and Lignin Peroxidase (LiP) activities. Increases in biomass within the PUF cubes was associated with increases in ergosterol concentrations. This study proved that the fungal-based system tested was efficient for the degradation of tannic acid over a period of time, and under non-sterile conditions.

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

Seven hydrocarbonoclastic new bacterial isolates were isolated from dredged sediments of a river estuary in Italy. The sediments were contaminated by shipyard activities since decades, mainly ascribable to the exploitation of diesel oil as the fuel for recreational and commercial navigation of watercrafts. The bacterial isolates were able to utilize diesel oil as sole carbon source. Their metabolic capacities were evaluated by GC-MS analysis, with reference to the depletion of both the normal and branched alkanes, the nC18 fatty acid methyl ester and the unresolved complex mixture of organic compounds. They were taxonomically identified as different species of Stenotrophomonas and Pseudomonas spp. by the combination of amplified ribosomal DNA restriction analysis (ARDRA) and repetitive sequence-based PCR (REP-PCR) analysis. The metabolic activities of interest were analyzed both in relation to the single bacterial strains and to the combination of the latter as a multibacterial species system. After 6 days of incubation in mineral medium with diesel oil as sole carbon source, the Stenotrophomonas sp. M1 strain depleted 43-46 % of Cn-alkane from C28 up to C30, 70 % of the nC18 fatty acid methyl ester and the 46 % of the unresolved complex mixture of organic compounds. On the other hand, the Pseudomonas sp. NM1 strain depleted the 76 % of the nC18 fatty acid methyl ester, the 50 % of the unresolved complex mixture of organic compounds. The bacterial multispecies system was able to completely deplete Cn-alkane from C28 up to C30 and to deplete the 95 % of the unresolved complex mixture of organic compounds. The isolates, either as single strains and as a bacterial multispecies system, were proposed as candidates for bioaugmentation in bio-based processes for the decontamination of dredged sediments.

Polycyclic aromatic hydrocarbon-contaminated soils: bioaugmentation of autochthonous bacteria and toxicological assessment of the bioremediation process by means of Vicia faba L

Two bacterial strains, Achromobacter sp. (ACH01) and Sphingomonas sp. (SPH01), were isolated from a heavily polycyclic aromatic hydrocarbon (PAH)-contaminated soil (5431.3 ± 102.3 ppm) for their capacity to use a mixture of anthracene, pyrene, phenanthrene and fluorene as sole carbon sources for growth and for the capacity to produce biosurfactants. The two strains were exploited for bioaugmentation in a biopile pilot plant to increase the bioavailability and the degradation of the residual PAH contamination (99.5 ± 7.1 ppm) reached after 9 months of treatment. The denaturing gel gradient electrophoresis (DGGE) profile of the microbial ecology of the soil during the experimentation showed that the bioaugmentation approach was successful in terms of permanence of the two strains in the soil in treatment. The bioaugmentation of the two bacterial isolates positively correlated with the PAH depletion that reached 7.9 ± 2 ppm value in 2 months of treatment. The PAH depletion was assessed by the loss of the phyto-genotoxicity of soil elutriates on the model plant Vicia faba L., toxicological assessment adopted also to determine the minimum length of the decontamination process for obtaining both the depletion of the PAH contamination and the detoxification of the soil at the end of the process. The intermediate phases of the bioremediation process were the most significant in terms of toxicity, inducing genotoxic effects and selective DNA fragmentation in the stem cell niche of the root tip. The selective DNA fragmentation can be related to the selective induction of cell death of mutant stem cells that can compromise offsprings.