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Innovative Treatments for the Improvement of Bioremediation Processes

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A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Environmental and Green Processes".

Deadline for manuscript submissions: closed (21 February 2022) | Viewed by 11912

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Special Issue Editor

Dr. Ana Rita Lopes

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Guest Editor

Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, PA 15213-3890, USA
Interests: environmental microbiology; microbial ecology; bioremediation; biocatalysts; green biotechnology; biotransformation; white biotechnology; bacterial genomics

Special Issue Information

Dear Colleagues,

Intense human activity has led to the spread of different pollutants in Earth ecosystems, impacting fauna and flora, consequently impacting human health. These pollutants are diverse in their structure and origin, including naturally occurring and synthetically created compounds (e.g., antibiotics, metals, petroleum hydrocarbons, pesticides, plastics, perfluorinated compounds). Hence, their treatment is complex and faces different physicochemical and biological challenges; these include the bioavailability or accessibility of the pollutant, its biodegradability and the potential accumulation of toxic compounds as a result of the biodegradation of the parent compound. In addition, the adaptability and maintenance of the degrading organism(s), among others, result in the need for an in-depth characterization of the degrading organism(s) (e.g., growth kinetics, metabolic activity, and genetic makeup). This complexity urges us to create solutions that integrate knowledge gathered from distinct fields, such as microbiology, plant biology, chemistry, geology, environmental engineering, and bioengineering, among others. The solutions might be driven by the identification of novel biological routes to degrade a pollutant or by the development of a new bioremediation tool. The latter might result from the modification of a known biocatalyst (e.g., organism, enzyme) or the combination of biological and chemical processes, creating a hybrid system that overcomes the drawbacks of both, maximizing the efficiency of the remediation process.

This Special Issue on "Innovative Treatments for the Improvement of Bioremediation Processes" seeks high-quality research and case studies focusing on developing and applying novel bioremediation strategies.

Topics include but are not limited to:

Identification and characterization of novel degrading metabolic pathways;
Development of novel bioremediation treatments, modifying existing biocatalysts (e.g., microorganism(s), enzyme(s));
Development of hybrid bioremediation systems coupling chemical and biological strategies, optimizing the activity of existing biocatalysts (e.g., plant, microorganism(s), enzyme(s)).

Dr. Ana Rita Lopes
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. Processes is an international peer-reviewed open access monthly 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 2400 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

bioremediation
degradation pathways
redox processes
phytoremediation
biostimulation
green biotechnology
environmental engineering
geochemistry
biocatalysts

Published Papers (4 papers)

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Research

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21 pages, 4407 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Transfer of Potentially Toxic Elements in the Soil-Plant System in Magnesite Mining and Processing Areas

by Lenka Štofejová, Juraj Fazekaš and Danica Fazekašová

Processes 2022, 10(4), 720; https://doi.org/10.3390/pr10040720 - 8 Apr 2022

Cited by 3 | Viewed by 1393

Abstract

Mining activities, ore concentrations, and transport processes generate large amounts of pollutants, including hazardous elements, which are released into the environment. This work presents the results of experimental research aimed at evaluating the environmental risks of soil and plant contamination in two magnesite mining and processing areas in the Slovak Republic, and assesses the phytoremediation potential of dominant plant species. Eleven potentially toxic elements in the soil were investigated using X-ray fluorescence spectrometry (Cd, Pb, Cr, Zn, Cu, As, Ni, Mn, Mg, Fe) and atomic absorption spectrometry (Hg). In plants, potentially toxic elements were investigated using inductively coupled plasma mass spectrometry (Cu, As, Cd, Pb) and inductively coupled plasma atomic emission spectrometry (Cr, Zn, Mn, Mg). Selected soil parameters (pH, redox potential, and soil organic matter) were also investigated. Soil contamination was evaluated using environmental indices (geoaccumulation index—I_geo, enrichment factor—EF, contamination factor—C_f, degree of contamination—C_d). The phytoremediation potential of plants was evaluated using the bioconcentration factor (BCF) and the translocation factor (TF). The soil reaction in the studied areas indicated a strong alkalization of the soil. The soils in Jelšava-Lubeník were significantly contaminated with Cr, As, Mn, and Mg. The most significant enrichment based on the average values of EF was found to be in the order of Cd > Mg > Zn > Cu > As > Cr > Ni > Pb > Fe > Hg > Mn. The observed values of C_f and C_d indicated a high degree of soil contamination. In Košice, the soils were found to be significantly contaminated with Cr, Mn, Mg, and Ni. The most significant enrichment was found in the order of Cd > Mn > Ni > Pb > Zn > Mg > Cu > As > Fe > Cr > Hg. Very high C_f was found for Pb and Cr. The results of correlation and hierarchical cluster analyses suggest a similar origin of pollutants caused by significant anthropogenic interventions due to magnesite mining and processing. The investigated dominant plant species, Phragmites australis, Agrostis stolonifera, Elytrigia repens, and Taraxacum officinale are able to accumulate high concentrations of the monitored potentially toxic elements without more serious load or damage. The results of BCF and TF confirmed that P. australis and T. officinale appeared to be suitable accumulators in the phytoextraction process. In the case of E. repens and A. stolonifera it was confirmed that they accumulate and immobilize high concentrations of potentially toxic elements, especially in the roots, establishing the suitability of their use in phytostabilization processes. Full article

(This article belongs to the Special Issue Innovative Treatments for the Improvement of Bioremediation Processes)

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17 pages, 4042 KiB

Open AccessFeature PaperArticle

Towards Computationally Guided Design and Engineering of a Neisseria meningitidis Serogroup W Capsule Polymerase with Altered Substrate Specificity

by Subhadra Paudel, James Wachira and Pumtiwitt C. McCarthy

Processes 2021, 9(12), 2192; https://doi.org/10.3390/pr9122192 - 6 Dec 2021

Cited by 1 | Viewed by 2382

Abstract

Heavy metal contamination of drinking water is a public health concern that requires the development of more efficient bioremediation techniques. Absorption technologies, including biosorption, provide opportunities for improvements to increase the diversity of target metal ions and overall binding capacity. Microorganisms are a key component in wastewater treatment plants, and they naturally bind metal ions through surface macromolecules but with limited capacity. The long-term goal of this work is to engineer capsule polymerases to synthesize molecules with novel functionalities. In previously published work, we showed that the Neisseria meningitidis serogroup W (NmW) galactose–sialic acid (Gal–NeuNAc) heteropolysaccharide binds lead ions effectively, thereby demonstrating the potential for its use in environmental decontamination applications. In this study, computational analysis of the NmW capsule polymerase galactosyltransferase (GT) domain was used to gain insight into how the enzyme could be modified to enable the synthesis of N-acetylgalactosamine–sialic acid (GalNAc–NeuNAc) heteropolysaccharide. Various computational approaches, including molecular modeling with I-TASSER and molecular dynamics (MD) simulations with NAMD, were utilized to identify key amino acid residues in the substrate binding pocket of the GT domain that may be key to conferring UDP-GalNAc specificity. Through these combined strategies and using BshA, a UDP-GlcNAc transferase, as a structural template, several NmW active site residues were identified as mutational targets to accommodate the proposed N-acetyl group in UDP-GalNAc. Thus, a rational approach for potentially conferring new properties to bacterial capsular polysaccharides is demonstrated. Full article

(This article belongs to the Special Issue Innovative Treatments for the Improvement of Bioremediation Processes)

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13 pages, 858 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Evaluation of the PGPR Capacity of Four Bacterial Strains and Their Mixtures, Tested on Lupinus albus var. Dorado Seedlings, for the Bioremediation of Mercury-Polluted Soils

by Daniel González, Carlota Blanco, Agustín Probanza, Pedro A. Jiménez and Marina Robas

Processes 2021, 9(8), 1293; https://doi.org/10.3390/pr9081293 - 26 Jul 2021

Cited by 10 | Viewed by 2604

Abstract

Soil contamination by mercury, which is one of the most toxic heavy metals due to its bioaccumulative capacity, poses a risk to the environment as well as health. The Almadén mining district in Ciudad Real, Spain is one of the most heavily-polluted sites in the world, making the soils unusable. Bioremediation, and more specifically phyto-rhizoremediation, based on the synergistic interaction established between plant and Plant Growth Promoting Rhizobacteria (PGPR), improves the plant’s ability to grow, mobilize, accumulate, and extract contaminants from the soil. The objective of this study is to evaluate the plant growth-promoting ability of four PGPR strains (and mixtures), isolated from the bulk soil and rhizosphere of naturally grown plants in the Almadén mining district, when they are inoculated in emerged seeds of Lupinus albus, var. Dorado in the presence of high concentrations of mercury. After 20 days of incubation and subsequent harvesting of the seedlings, biometric measurements were carried out at the root and aerial levels. The results obtained show that the seeds treatment with PGPR strains improves plants biometry in the presence of mercury. Specifically, strain B2 (Pseudomonas baetica) and B1 (Pseudomonas moraviensis) were those that contributed the most to plant growth, both individually and as part of mixtures (CS5 and CS3). Thus, these are postulated to be good candidates for further in situ phyto-rhizoremediation tests of mercury-contaminated soils. Full article

(This article belongs to the Special Issue Innovative Treatments for the Improvement of Bioremediation Processes)

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Review

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14 pages, 614 KiB

Open AccessReview

Synthetic Biology: A New Era in Hydrocarbon Bioremediation

by Valentina Jiménez-Díaz, Aura Marina Pedroza-Rodríguez, Oswaldo Ramos-Monroy and Laura C. Castillo-Carvajal

Processes 2022, 10(4), 712; https://doi.org/10.3390/pr10040712 - 6 Apr 2022

Cited by 7 | Viewed by 4685

Abstract

Crude oil is a viscous dark liquid resource composed by a mix of hydrocarbons which, after refining, is used for the elaboration of distinct products. A major concern is that many petroleum components are highly toxic due to their teratogenic, hemotoxic, and carcinogenic effects, becoming an environmental concern on a global scale, which must be solved through innovative, efficient, and sustainable techniques. One of the most widely used procedures to totally degrade contaminants are biological methods such as bioremediation. Synthetic biology is a scientific field based on biology and engineering principles, with the purpose of redesigning and restructuring microorganisms to optimize or create new biological systems with enhanced features. The use of this discipline offers improvement of bioremediation processes. This article will review some of the techniques that use synthetic biology as a platform to be used in the area of hydrocarbon bioremediation. Full article

(This article belongs to the Special Issue Innovative Treatments for the Improvement of Bioremediation Processes)

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