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Microbial Biodegradation and Biotransformation 2.0

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (15 November 2023) | Viewed by 22180

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Prof. Dr. Irina Ivshina

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Institute of Ecology and Genetics of Microorganisms UB RAS – Perm Federal Research Center UB RAS, Perm, Russia
Interests: microbial diversity; microbial chemistry; bioconversion of organic pollutants; immobilization of microorganisms; biocatalysts based on actinobacteria; applied biocatalysis; biotechnology
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Dr. Elena A. Tyumina

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Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia
Interests: microbial biodegradation; biotechnology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Microbial Biodegradation and Biotransformation”.

A sharp decline in the quality of the environment makes it extremely urgent to search for ways to prevent and neutralize the anthropogenic pollution of natural ecosystems. Freeing the biosphere from ecopollutants could, as an unsolved problem, be in the spotlight for a long time. Xenobiotics are a “time bomb”. In this regard, the efforts of most researchers have recently been mainly concentrated in the field of applied microbiology, supporting the search for rational ways for the biodegradation and effective biodegraders of novel xenobiotic compounds continuously entering the environment. Their harmful effects are enhanced due to the simultaneous presence of many other active xenobiotics in the system, with varying degrees of degradability and toxicity.

All this makes it necessary to expand and intensify the study of the characteristics of microorganisms in contaminated environments, so-called extremotolerant or stress-tolerant microorganisms, which play the role of a primary response system to unfavorable or potentially dangerous environmental changes, initiating their adaptive responses at the earliest stages. We look forward to your contributions.

Prof. Dr. Irina Ivshina
Dr. Elena A. Tyumina
Guest Editors

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Keywords

biodegradation
biotransformation
bioremediation
hydrocarbons
xenobiotics
biodegradation genes
biocatalysts
biodegradative pathways
pharmaceutically active compounds
terpenoids

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Published Papers (9 papers)

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Research

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15 pages, 4371 KiB

Open AccessArticle

Ideonella sakaiensis Can Metabolize Bisphenol A as a Carbon Source

by Cristian-Emilian Pop, György Deák, Cristina Maria, Gina Ghiță, Alexandru Anton Ivanov, Sergiu Fendrihan, Dan Florin Mihăilescu and Maria Mernea

Microorganisms 2023, 11(12), 2891; https://doi.org/10.3390/microorganisms11122891 - 30 Nov 2023

Viewed by 2043

Abstract

Bisphenol A and its analogues represent a significant environmental and public health hazard, particularly affecting the endocrine systems of children and newborns. Due to the growing need for non-pathogenic biodegradation microbial agents as environmentally friendly and cost-effective solutions to eliminate endocrine disruptors, this study aimed to investigate the degradation of bisphenol A by Ideonella sakaiensis, based on its currently understood unique enzymatic machinery that is already well known for degrading polyethylene terephthalate. The present study provides novel insights into the metabolic competence and growth particularities of I. sakaiensis. The growth of I. sakaiensis exposed to bisphenol A exceeded that in the control conditions, starting with 72 h in a 70% nutrient-rich medium and starting with 48 h in a 100% nutrient-rich medium. Computational modeling showed that bisphenol A, as well as its analogue bisphenol S, are possible substrates of PETase and MHETase. The use of bisphenol A as a carbon and energy source through a pure I. sakaiensis culture expands the known substrate spectra and the species’ potential as a new candidate for bisphenol A bioremediation processes. Full article

(This article belongs to the Special Issue Microbial Biodegradation and Biotransformation 2.0)

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20 pages, 3135 KiB

Open AccessArticle

Metabolic Profiling and Comparative Proteomic Insight in Respect of Amidases during Iprodione Biodegradation

by Pamela Donoso-Piñol, Gabriela Briceño, Joseph A. M. Evaristo, Fábio C. S. Nogueira, Barbara Leiva, Claudio Lamilla, Heidi Schalchli and María Cristina Diez

Microorganisms 2023, 11(10), 2367; https://doi.org/10.3390/microorganisms11102367 - 22 Sep 2023

Cited by 2 | Viewed by 1434

Abstract

The fungicide iprodione (IPR) (3-(3,5-dichlorophenyl) N-isopropyl-2,4-dioxoimidazolidine-1-carboxamide) is a highly toxic compound. Although IPR has been restricted, it is still being applied in many places around the world, constituting an environmental risk. The biodegradation of IPR is an attractive option for reducing its residues. In this study, we isolated thirteen IPR-tolerant bacteria from a biopurification system designed to treat pesticides. A study of biodegradation using different strains was comparatively evaluated, and the best degradation rate of IPR was presented by Achromobacter sp. C1 with a half-life (T_1/2) of 9 days. Based on a nano-LC-MS/MS analysis for the strains, proteins solely expressed in the IPR treatment were identified by highlighting the strain Achromobacter sp. C1, with 445 proteins primarily involved in the biosynthesis of secondary metabolites and microbial metabolism in diverse environments. Differentially expressed protein amidases were involved in six metabolic pathways. Interestingly, formamidase was inhibited while other cyclases, i.e., amidase and mandelamide hydrolase, were overexpressed, thereby minimizing the effect of IPR on the metabolism of strain C1. The dynamic changes in the protein profiles of bacteria that degrade IPR have been poorly studied; therefore, our results offer new insight into the metabolism of IPR-degrading microorganisms, with special attention paid to amidases. Full article

(This article belongs to the Special Issue Microbial Biodegradation and Biotransformation 2.0)

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12 pages, 1744 KiB

Open AccessArticle

Isolation and Characterization of the Wastewater Micropollutant Phenacetin-Degrading Bacterium Rhodococcus sp. Strain PNT-23

by Yaxuan Yuan, Kexin Wang, Yihe Liu, Maoting Jiang, Yinhu Jiang and Jiguo Qiu

Microorganisms 2023, 11(8), 1962; https://doi.org/10.3390/microorganisms11081962 - 31 Jul 2023

Viewed by 1762

Abstract

Phenacetin, an antipyretic and analgesic drug, poses a serious health risk to both humans and aquatic organisms, which is of concern since this micropollutant is frequently detected in various aquatic environments. However, rare pure bacterial cultures have been reported to degrade phenacetin. Therefore, in this study, the novel phenacetin-degrading strain PNT-23 was isolated from municipal wastewater and identified as a Rhodococcus sp. based on its morphology and 16S rRNA gene sequencing. The isolated strain could completely degrade 100 mg/L phenacetin at an inoculum concentration of OD₆₀₀ 1.5 within 80 h, utilizing the micropollutant as its sole carbon source for growth. Strain PNT-23 exhibited optimal growth in LB medium at 37 °C and a pH of 7.0 with 1% NaCl, while the optimal degradation conditions in minimal medium were 30 °C and a pH of 7.0 with 1% NaCl. Two key intermediates were identified during phenacetin biodegradation by the strain PNT-23: N-acetyl-4-aminophenol and 4-aminophenol. This study provides novel insights into the biodegradation of phenacetin using a pure bacterium culture, expands the known substrate spectra of Rhodococcus strains and presents a potential new candidate for the microbial removal of phenacetin in a diverse range of environments. Full article

(This article belongs to the Special Issue Microbial Biodegradation and Biotransformation 2.0)

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15 pages, 2880 KiB

Open AccessArticle

Phenol Degradation by Pseudarthrobacter phenanthrenivorans Sphe3

by Stamatia Asimakoula, Orfeas Marinakos, Epameinondas Tsagogiannis and Anna-Irini Koukkou

Microorganisms 2023, 11(2), 524; https://doi.org/10.3390/microorganisms11020524 - 18 Feb 2023

Cited by 21 | Viewed by 2829

Abstract

Phenol poses a threat as one of the most important industrial environmental pollutants that must be removed before disposal. Biodegradation is a cost-effective and environmentally friendly approach for phenol removal. This work aimed at studying phenol degradation by Pseudarthrobacter phenanthrenivorans Sphe3 cells and also, investigating the pathway used by the bacterium for phenol catabolism. Moreover, alginate-immobilized Sphe3 cells were studied in terms of phenol degradation efficiency compared to free cells. Sphe3 was found to be capable of growing in the presence of phenol as the sole source of carbon and energy, at concentrations up to 1500 mg/L. According to qPCR findings, both pathways of ortho- and meta-cleavage of catechol are active, however, enzymatic assays and intermediate products identification support the predominance of the ortho-metabolic pathway for phenol degradation. Alginate-entrapped Sphe3 cells completely degraded 1000 mg/L phenol after 192 h, even though phenol catabolism proceeds slower in the first 24 h compared to free cells. Immobilized Sphe3 cells retain phenol-degrading capacity even after 30 days of storage and also can be reused for at least five cycles retaining more than 75% of the original phenol-catabolizing capacity. Full article

(This article belongs to the Special Issue Microbial Biodegradation and Biotransformation 2.0)

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14 pages, 1247 KiB

Open AccessArticle

Bioremediation of Oil-Contaminated Soil of the Republic of Kazakhstan Using a New Biopreparation

by Tatiana Vyacheslavovna Funtikova, Lenar Imametdinovich Akhmetov, Irina Filippovna Puntus, Pavel Alexeevich Mikhailov, Nurbol Orynbasaruly Appazov, Roza Abdibekovna Narmanova, Andrey Evgenievich Filonov and Inna Petrovna Solyanikova

Microorganisms 2023, 11(2), 522; https://doi.org/10.3390/microorganisms11020522 - 18 Feb 2023

Cited by 7 | Viewed by 2955

Abstract

A new biopreparation is developed to clean soils from oil pollution in the arid climate of the Republic of Kazakhstan. The biopreparation includes bacterial strains R. qingshengii F2-1, R. qingshengii F2-2, and P. alloputida BS3701. When using the biopreparation in a liquid mineral medium with 15% crude oil, laboratory studies have revealed degradation of 48% n-alkanes and 39% of PAHs after 50 days. The effectiveness of the biopreparation has been demonstrated in field experiments in the soil contaminated with 10% crude oil at the K-Kurylys landfill, Republic of Kazakhstan. During the six-month field experiment, the number of oil degraders reached 10⁷ CFU/g soil, which degraded 70% of crude oil by the end of the experiment. Full article

(This article belongs to the Special Issue Microbial Biodegradation and Biotransformation 2.0)

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14 pages, 1330 KiB

Open AccessArticle

Indigenous Yeasts from Rose Oil Distillation Wastewater and Their Capacity for Biotransformation of Phenolics

by Mila Rusanova, Krasimir Rusanov, Veronika Butterweck and Ivan Atanassov

Microorganisms 2023, 11(1), 201; https://doi.org/10.3390/microorganisms11010201 - 12 Jan 2023

Cited by 1 | Viewed by 2529

Abstract

The indigenous yeasts associated with the spontaneous fermentation of phenolic-rich rose oil distillation wastewater (RODW) generated after the industrial distillation of rose oil were studied. The ITS-rDNA sequence analysis of the samples collected from RODW fermented at semi-sterile conditions, a waste deposition lagoon and endophytic yeasts isolated from industrially cultivated Rosa damascena suggests that the spontaneous RODW fermentation is caused by yeasts from the genus Cyberlindnera found also as endophytes in the rose flowers. Phylogenetic analysis based on the nucleotide sequences of the translation elongation factor (TEF1α) and 18S- and 26S- rRNA genes further confirmed the taxonomic affiliation of the RODW yeast isolates with the genus Cyberlindnera. The RODW fermentation capacity of a selected set of indigenous yeast isolates was studied and compared with those of common yeast strains. The indigenous yeast isolates demonstrated a superior growth rate, resulting in a nearly double reduction in the phenolic content in the fermented RODW. The indigenous yeasts’ fermentation changed the RODW phenolics’ composition. The levels of some particular phenolic glycosides decreased through the depletion and fermentation of their sugar moiety. Hence, the relative abundance of the corresponding aglycons and other phenolic compounds increased. The capacity for the biotransformation of RODW phenolics by indigenous yeasts is discussed. Full article

(This article belongs to the Special Issue Microbial Biodegradation and Biotransformation 2.0)

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13 pages, 2169 KiB

Open AccessArticle

Characterization of Latex-Clearing Protein and Aldehyde Dehydrogenases Involved in the Utilization of poly(cis-1,4-isoprene) by Nocardia farcinica NBRC 15532

by Natsuhei Suzuki, Daito Suda, Nguyen Thi Thuy Ngan, Namiko Gibu, Nguyen Lan Huong, To Kim Anh and Daisuke Kasai

Microorganisms 2022, 10(12), 2324; https://doi.org/10.3390/microorganisms10122324 - 24 Nov 2022

Cited by 4 | Viewed by 1947

Abstract

Microbial degradation of natural rubber and synthetic poly(cis-1,4-isoprene) is expected to become an alternative treatment system for waste from poly(cis-1,4-isoprene) products including scrap tires. Nocardia farcinica NBRC 15,532, a gram-positive rubber-degrading bacterium, can utilize poly(cis-1,4-isoprene) as the sole source of carbon and energy to produce oligo-isoprene metabolites containing aldehyde and keto end groups. A homology-based search of the genome revealed a gene encoding a latex-clearing protein (Lcp). Gene disruption analysis indicated that this gene is essential for the utilization of poly(cis-1,4-isoprene) in this strain. Further analysis of the genome sequence identified aldehyde dehydrogenase (ALDH) genes as potential candidates for oxidative degradation of oligo-isoprene aldehydes. Based on the enzymatic activity of the ALDH candidates, NF2_RS14000 and NF2_RS14385 may be involved in the degradation of oligo-isoprene aldehydes. Analysis of the reaction products revealed that these ALDHs oxidized tri- to penta-isoprene aldehydes, which were generated by the reaction of Lcp. Based on the inability of ALDH gene deletion mutants, we concluded that NF2_RS14000 is mainly involved in the utilization of poly(cis-1,4-isoprene) and the oxidative degradation of oligo-isoprene aldehydes in Nocardia farcinica NBRC 15,532. Full article

(This article belongs to the Special Issue Microbial Biodegradation and Biotransformation 2.0)

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16 pages, 3031 KiB

Open AccessArticle

Guts Bacterial Communities of Porcellio dilatatus: Symbionts Predominance, Functional Significance and Putative Biotechnological Potential

by Catarina Coelho, Igor Tiago and António Veríssimo

Microorganisms 2022, 10(11), 2230; https://doi.org/10.3390/microorganisms10112230 - 11 Nov 2022

Cited by 1 | Viewed by 1663

Abstract

Terrestrial isopods are effective herbivorous scavengers with an important ecological role in organic matter cycling. Their guts are considered to be a natural enrichment environment for lignocellulosic biomass (LCB)-degrading bacteria. The main goal of this work was to assess the structural diversity of Porcellio dilatatus gut bacterial communities using NGS technologies, and to predict their functional potential using PICRUSt2 software. Pseudomonadota, Actinomycetota, Bacillota, Cyanobacteria, Mycoplasmatota, Bacteroidota, Candidatus Patescibacteria and Chloroflexota were the most abundant phyla found in P. dilatatus gut bacterial communities. At a family level, we identified the presence of eleven common bacterial families. Functionally, the P. dilatatus gut bacterial communities exhibited enrichment in KEGG pathways related to the functional module of metabolism. With the predicted functional profile of P. dilatatus metagenomes, it was possible to envision putative symbiotic relationships between P. dilatatus gut bacterial communities and their hosts. It was also possible to foresee the presence of a well-adapted bacterial community responsible for nutrient uptake for the host and for maintaining host homeostasis. Genes encoding LCB-degrading enzymes were also predicted in all samples. Therefore, the P. dilatatus digestive tract may be considered a potential source of LCB-degrading enzymes that is not to be neglected. Full article

(This article belongs to the Special Issue Microbial Biodegradation and Biotransformation 2.0)

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Review

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30 pages, 1564 KiB

Open AccessReview

Iron Compounds in Anaerobic Degradation of Petroleum Hydrocarbons: A Review

by Ana R. Castro, Gilberto Martins, Andreia F. Salvador and Ana J. Cavaleiro

Microorganisms 2022, 10(11), 2142; https://doi.org/10.3390/microorganisms10112142 - 29 Oct 2022

Cited by 11 | Viewed by 3951

Abstract

Waste and wastewater containing hydrocarbons are produced worldwide by various oil-based industries, whose activities also contribute to the occurrence of oil spills throughout the globe, causing severe environmental contamination. Anaerobic microorganisms with the ability to biodegrade petroleum hydrocarbons are important in the treatment of contaminated matrices, both in situ in deep subsurfaces, or ex situ in bioreactors. In the latter, part of the energetic value of these compounds can be recovered in the form of biogas. Anaerobic degradation of petroleum hydrocarbons can be improved by various iron compounds, but different iron species exert distinct effects. For example, Fe(III) can be used as an electron acceptor in microbial hydrocarbon degradation, zero-valent iron can donate electrons for enhanced methanogenesis, and conductive iron oxides may facilitate electron transfers in methanogenic processes. Iron compounds can also act as hydrocarbon adsorbents, or be involved in secondary abiotic reactions, overall promoting hydrocarbon biodegradation. These multiple roles of iron are comprehensively reviewed in this paper and linked to key functional microorganisms involved in these processes, to the underlying mechanisms, and to the main influential factors. Recent research progress, future perspectives, and remaining challenges on the application of iron-assisted anaerobic hydrocarbon degradation are highlighted. Full article

(This article belongs to the Special Issue Microbial Biodegradation and Biotransformation 2.0)

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