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Biotechnologies for the Environment: Strategies for Containment and Depletion of...
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Biotechnologies for the Environment: Strategies for Containment and Depletion of Pollution in Wastewaters, Air, Soils and Sediments

A special issue of Water (ISSN 2073-4441). This special issue belongs to the section "Water Quality and Contamination".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 17433

Special Issue Editor

Dr. Simona Di Gregorio

E-Mail Website
Guest Editor
Department of Biology, University of Pisa, 56126 Pisa, Italy
Interests: soil remediation; environmental biotechnology; wastewater treatment; ecology environmental analysis; environmental pollution; environmental impact assessment
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With an increasing awareness of the hostile effects of pollutants on the biosphere, reclamation or remediation of different environmental compartments contaminated by persisting and emerging pollutants is nowadays of global concern. Environmental biotechnologies have emerged as sustainable approaches to contain and eventually solve the problem worldwide. Environmental biotechnologies are based on the exploitation of microbial activities as catalysts of reactions for environment decontamination. The knowledge of microbial activity can be exploited for wastewater treatment, for gaseous emission removal, and for biodegradation of environmental organic pollutants and is crucial for the control of environmental pollution. The implementation of aerobic as well as anaerobic microbial activities exploited for their catabolic ability to treat biodegradable waste or pollutants has become an efficient, economical, and environmentally friendly technique that calls for a continuous multidisciplinary discussion between specialists in the environmental sector. This Special Issue aims to be a tool of comparison by addressing aspects such as mitigation and remediation of persistent, emerging, and other contaminants; sources, transport, and fate of persistent and emerging contaminants; toxicology and eco-toxicology of persistent contaminants; and molecular approaches dedicated to the study of the microbial ecology of contaminated matrices and to the restoration of biodiversity and resilience.

Dr. Simona Di Gregorio
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Water is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • dynamics and diversity of microbial populations
  • ecotoxicity of polluted environmental matrices
  • degradation/transformation of persistent contaminants
  • degradation/transformation of emerging contaminants
  • isolation and characterization of new microbial strains for pollution depletion
  • bioremediation
  • bioaugmentation
  • in situ and ex situ treatment
  • myco-remediation
  • micro and nanoplastics in the environment

Published Papers (6 papers)

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Research

34 pages, 8723 KiB  
Article
Anaerobic Digestion of the Organic Fraction of Municipal Solid Waste in Plug-Flow Reactors: Focus on Bacterial Community Metabolic Pathways
by Elena Rossi, Simone Becarelli, Isabella Pecorini, Simona Di Gregorio and Renato Iannelli
Water 2022, 14(2), 195; https://doi.org/10.3390/w14020195 - 11 Jan 2022
Cited by 13 | Viewed by 3209
Abstract
The aim of this study is to investigate the performance of a pilot-scale plug-flow reactor (PFR) as a biorefinery system to recover chemicals (i.e., volatile fatty acids (VFAs)), and biogas during the dry thermophilic anaerobic digestion (AD) of the organic fraction of municipal [...] Read more.
The aim of this study is to investigate the performance of a pilot-scale plug-flow reactor (PFR) as a biorefinery system to recover chemicals (i.e., volatile fatty acids (VFAs)), and biogas during the dry thermophilic anaerobic digestion (AD) of the organic fraction of municipal solid waste (OFMSW). The effects of the hydraulic retention time (HRT) on both outputs were studied, reducing the parameter from 22 to 16 days. In addition, VFA variation along the PFR was also evaluated to identify a section for a further valorization of VFA-rich digestate stream. A particular focus was dedicated for characterizing the community responsible for the production of VFAs during hydrolysis and acidogenesis. The VFA concentration reached 4421.8 mg/L in a section located before the end of the PFR when the HRT was set to 16 days. Meanwhile, biogas production achieved 145 NLbiogas/d, increasing 2.7 times when compared to the lowest HRT tested. Defluviitoga sp. was the most abundant bacterial genus, contributing to 72.7% of the overall bacterial population. The genus is responsible for the hydrolysis of complex polysaccharides at the inlet and outlet sections since a bimodal distribution of the genus was found. The central zone of the reactor was distinctly characterized by protein degradation, following the same trend of propionate production. Full article
(This article belongs to the Special Issue Biotechnologies for the Environment: Strategies for Containment and Depletion of Pollution in Wastewaters, Air, Soils and Sediments)
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24 pages, 7017 KiB  
Article
Innovative Culturomic Approaches and Predictive Functional Metagenomic Analysis: The Isolation of Hydrocarbonoclastic Bacteria with Plant Growth Promoting Capacity
by Ilaria Chicca, Simone Becarelli, Giacomo Bernabei, Giovanna Siracusa and Simona Di Gregorio
Water 2022, 14(2), 142; https://doi.org/10.3390/w14020142 - 6 Jan 2022
Cited by 7 | Viewed by 2395
Abstract
Innovative culturomic approaches were adopted to isolate hydrocarbonoclastic bacteria capable of degrading diesel oil, bitumen and a selection of polycyclic aromatic hydrocarbons (PAH), e.g., pyrene, anthracene, and dibenzothiophene, from a soil historically contaminated by total petroleum hydrocarbons (TPH) (10,347 ± 98 mg TPH/kg). [...] Read more.
Innovative culturomic approaches were adopted to isolate hydrocarbonoclastic bacteria capable of degrading diesel oil, bitumen and a selection of polycyclic aromatic hydrocarbons (PAH), e.g., pyrene, anthracene, and dibenzothiophene, from a soil historically contaminated by total petroleum hydrocarbons (TPH) (10,347 ± 98 mg TPH/kg). The culturomic approach focussed on the isolation of saprophytic microorganisms and specialist bacteria utilising the contaminants as sole carbon sources. Bacterial isolates belonging to Pseudomonas, Arthrobacter, Achromobacter, Bacillus, Lysinibacillus, Microbacterium sps. were isolated for their capacity to utilise diesel oil, bitumen, pyrene, anthracene, dibenzothiphene, and their mixture as sole carbon sources. Pseudomonas, Arthrobacter, Achromobacter and Microbacterium sps. showed plant growth promoting activity, producing indole-3-acetic acid and expressing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity. In parallel to the culturomic approach, in the microbial community of interest, bacterial community metabarcoding and predictive functional metagenomic analysis were adopted to confirm the potentiality of the isolates in terms of their functional representativeness. The combination of isolation and molecular approaches for the characterisation of a TPH contaminated soil microbial community is proposed as an instrument for the construction of an artificial hydrocarbonoclastic microbiota for environmental restoration. Full article
(This article belongs to the Special Issue Biotechnologies for the Environment: Strategies for Containment and Depletion of Pollution in Wastewaters, Air, Soils and Sediments)
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21 pages, 4483 KiB  
Article
Ascomycetes versus Spent Mushroom Substrate in Mycoremediation of Dredged Sediments Contaminated by Total Petroleum Hydrocarbons: The Involvement of the Bacterial Metabolism
by Simone Becarelli, Giovanna Siracusa, Ilaria Chicca, Giacomo Bernabei and Simona Di Gregorio
Water 2021, 13(21), 3040; https://doi.org/10.3390/w13213040 - 1 Nov 2021
Cited by 5 | Viewed by 2111
Abstract
Two mycoremediation approaches for the depletion of the total petroleum hydrocarbons in dredged sediments were compared: co-composting with spent mushroom substrate (SMS) from Pleurotus ostreatus and bioaugmentation with Lambertella sp. MUT 5852, an ascomycetes autochthonous to the sediment, capable of utilizing diesel oil [...] Read more.
Two mycoremediation approaches for the depletion of the total petroleum hydrocarbons in dredged sediments were compared: co-composting with spent mushroom substrate (SMS) from Pleurotus ostreatus and bioaugmentation with Lambertella sp. MUT 5852, an ascomycetes autochthonous to the sediment, capable of utilizing diesel oil its sole carbon source. After 28 days of incubation, 99% depletion was observed in presence of Lambertella sp. MUT 5852. No total petroleum hydrocarbon depletion was observed in sediment co-composting with the SMS after 60 days of incubation. 16S rDNA metabarcoding of the bacterial community was performed to evaluate the potential synergism between fungi and bacteria in the bioremediation process. The functional metagenomic prediction approach indicated that the biodiversity of the bacterial genera potentially involved in the degradation of TPH was higher in sediment bioaugmented with Lambertella sp. MUT 5852, which resulted in being mandatory for TPH depletion. Mechanisms of co-substrate inhibition of the hydrocarburoclastic bacterial species, due to the bioavailable organic matter of the SMS, are suggested to be involved in the observed kinetics of TPH depletion, failing in the case of SMS and successful in the case of Lambertella sp. MUT 5852. Full article
(This article belongs to the Special Issue Biotechnologies for the Environment: Strategies for Containment and Depletion of Pollution in Wastewaters, Air, Soils and Sediments)
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9 pages, 1749 KiB  
Article
A Microcosm Treatability Study for Evaluating Wood Mulch-Based Amendments as Electron Donors for Trichloroethene (TCE) Reductive Dechlorination
by Edoardo Masut, Alessandro Battaglia, Luca Ferioli, Anna Legnani, Carolina Cruz Viggi, Matteo Tucci, Marco Resitano, Alessandro Milani, Camilla de Laurentiis, Bruna Matturro, Maria Letizia Di Franca, Simona Rossetti and Federico Aulenta
Water 2021, 13(14), 1949; https://doi.org/10.3390/w13141949 - 15 Jul 2021
Cited by 3 | Viewed by 2603
Abstract
In this study, wood mulch-based amendments were tested in a bench-scale microcosm experiment in order to assess the treatability of saturated soils and groundwater from an industrial site contaminated by chlorinated ethenes. Wood mulch was tested alone as the only electron donor in [...] Read more.
In this study, wood mulch-based amendments were tested in a bench-scale microcosm experiment in order to assess the treatability of saturated soils and groundwater from an industrial site contaminated by chlorinated ethenes. Wood mulch was tested alone as the only electron donor in order to assess its potential for stimulating the biological reductive dechlorination. It was also tested in combination with millimetric iron filings in order to assess the ability of the additive to accelerate/improve the bioremediation process. The efficacy of the selected amendments was compared with that of unamended control microcosms. The results demonstrated that wood mulch is an effective natural and low-cost electron donor to stimulate the complete reductive dechlorination of chlorinated solvents to ethene. Being a side-product of the wood industry, mulch can be used in environmental remediation, an approach which perfectly fits the principles of circular economy and addresses the compelling needs of a sustainable and low environmental impact remediation. The efficacy of mulch was further improved by the co-presence of iron filings, which accelerated the conversion of vinyl chloride into the ethene by increasing the H2 availability rather than by catalyzing the direct abiotic dechlorination of contaminants. Chemical analyses were corroborated by biomolecular assays, which confirmed the stimulatory effect of the selected amendments on the abundance of Dehalococcoides mccartyi and related reductive dehalogenase genes. Overall, this paper further highlights the application potential and environmental sustainability of wood mulch-based amendments as low-cost electron donors for the biological treatment of chlorinated ethenes. Full article
(This article belongs to the Special Issue Biotechnologies for the Environment: Strategies for Containment and Depletion of Pollution in Wastewaters, Air, Soils and Sediments)
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17 pages, 1332 KiB  
Article
Optimization of an Autochthonous Bacterial Consortium Obtained from Beach Sediments for Bioremediation of Petroleum Hydrocarbons
by Rafaela Perdigão, C. Marisa R. Almeida, Filipa Santos, Maria F. Carvalho and Ana P. Mucha
Water 2021, 13(1), 66; https://doi.org/10.3390/w13010066 - 31 Dec 2020
Cited by 20 | Viewed by 3659
Abstract
Oil spill pollution remains a serious concern in marine environments and the development of effective oil bioremediation techniques are vital. This work is aimed at developing an autochthonous hydrocarbon-degrading consortium with bacterial strains with high potential for hydrocarbons degradation, optimizing first the growth [...] Read more.
Oil spill pollution remains a serious concern in marine environments and the development of effective oil bioremediation techniques are vital. This work is aimed at developing an autochthonous hydrocarbon-degrading consortium with bacterial strains with high potential for hydrocarbons degradation, optimizing first the growth conditions for the consortium, and then testing its hydrocarbon-degrading performance in microcosm bioremediation experiments. Bacterial strains, previously isolated from a sediment and cryopreserved in a georeferenced microbial bank, belonged to the genera Pseudomonas, Rhodococcus and Acinetobacter. Microcosms were assembled with natural seawater and petroleum, for testing: natural attenuation (NA); biostimulation (BS) (nutrients addition); bioaugmentation with inoculum pre-grown in petroleum (BA/P) and bioaugmentation with inoculum pre-grown in acetate (BA/A). After 15 days, a clear blending of petroleum with seawater was observed in BS, BA/P and BA/A but not in NA. Acetate was the best substrate for consortium growth. BA/A showed the highest hydrocarbons degradation (66%). All bacterial strains added as inoculum were recovered at the end of the experiment. This study provides an insight into the capacity of autochthonous communities to degrade hydrocarbons and on the use of alternative carbon sources for bacterial biomass growth for the development of bioremediation products to respond to oil spills. Full article
(This article belongs to the Special Issue Biotechnologies for the Environment: Strategies for Containment and Depletion of Pollution in Wastewaters, Air, Soils and Sediments)
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16 pages, 1780 KiB  
Article
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
by Simone Becarelli, Salvatore La China, Alla Lapidus, Andrey Prijibelski, Dmitrii Polev, Giulio Petroni and Simona Di Gregorio
Water 2020, 12(5), 1385; https://doi.org/10.3390/w12051385 - 13 May 2020
Cited by 1 | Viewed by 2684
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Biotechnologies for the Environment: Strategies for Containment and Depletion of Pollution in Wastewaters, Air, Soils and Sediments)
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