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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 (31 July 2022) | Viewed by 28197

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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,

A sharp decline in the quality of the environment makes it extremely urgent to search for ways to prevent and neutralize anthropogenic pollution of natural ecosystems. Freeing the biosphere from eco-pollutants will, 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 been recently concentrated mainly in the field of applied microbiology, which supports the search for rational ways of biodegradation and for effective biodegraders of new 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 studies of the characteristics of microorganisms in contaminated environments, so-called extremotolerant microorganisms or stress-tolerants, which play the role of a primary response system to unfavorable or potentially dangerous environmental changes and initiate their adaptive responses at the earliest stages. We look forward to your input.

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

Published Papers (13 papers)

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Editorial

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4 pages, 212 KiB

Open AccessEditorial

Special Issue “Microbial Biodegradation and Biotransformation”

by Irina Ivshina and Elena Tyumina

Microorganisms 2023, 11(4), 1047; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11041047 - 17 Apr 2023

Viewed by 1061

Abstract

The current state of the environment is a major concern [...] Full article

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

Research

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13 pages, 929 KiB

Open AccessArticle

Arthrospira platensis as Bioremediator of Rhenium Mono- and Polymetallic Synthetic Effluents

by Inga Zinicovscaia, Liliana Cepoi, Ludmila Rudi, Tatiana Chiriac, Nikita Yushin and Dmitrii Grozdov

Microorganisms 2022, 10(11), 2109; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10112109 - 26 Oct 2022

Cited by 1 | Viewed by 1114

Abstract

Rhenium is a scarce and highly important metal for industry and technology. In the present study, the cyanobacterium Arthrospira platensis (Spirulina) was used to remove rhenium and related elements (Mo and Cu) from mono- and polymetallic synthetic effluents. Metal ions in different concentrations were added to the culture medium on the first, third, and fifth days of biomass growth, and their uptake by the biomass was traced using ICP-AES technique. The accumulation of rhenium in the biomass was dependent on the chemical composition of the effluents, and the highest uptake of 161 mg/kg was achieved in the Re-Cu system. The presence of rhenium, copper, and molybdenum affected the productivity of Spirulina biomass and its biochemical composition (proteins, carbohydrates, lipids, phycobiliproteins, the content of chlorophyll α and β-carotene). With the growth of biomass in the presence of rhenium or rhenium and molybdenum, a pronounced increase in productivity and protein content was observed. The presence of copper in systems has a negative effect on biomass productivity and biochemical composition. Arthrospira platensis may be of interest as a bioremediator of rhenium-containing effluents of various chemical compositions. Full article

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

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13 pages, 2970 KiB

Open AccessArticle

Polysiloxane Coatings Biodeterioration in Nature and Laboratory

by Maxim Danilaev, Galina Yakovleva, Sergey Karandashov, Vladimir Kuklin, Hong Quan Le, William Kurdy and Olga Ilinskaya

Microorganisms 2022, 10(8), 1597; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10081597 - 08 Aug 2022

Cited by 3 | Viewed by 1519

Abstract

Objects and structures made of organic glass require protection from damage caused by external factors. Light, humidity, temperature, dust pollution and, undoubtedly, microorganisms lead to the deterioration of optical and mechanical properties. Polysiloxane-based protective coatings, consisting of silicon–oxygen backbones linked together with organic side groups attached to the silicon atoms, are widely used. However, the polysiloxane coatings themselves also cannot avoid deterioration during operation that implies the constant development of new protective materials. Here, we created a new cross-linked polysiloxane that covers organic glasses to enhance their resistance to aggressive external factors, and investigated its own resistance to damage induced by micromycetes in natural tropical conditions and in the laboratory. It has been established that the surface of coatings in the tropics is prone to fouling with micromycetes, mainly of the genera Aspergillus and Penicillium, which produce oxalic, malic, lactic, and citric acids contributing to the biodeterioration of polysiloxane. The testing of monolithic polycarbonate, polymethyl methacrylate, and triplex coated with polysiloxane showed that they retained significant resistance to abrasion and transparency at a level of more than 90% under aggressive natural conditions. Under artificial laboratory conditions, the infection of samples with micromycete spores also revealed their growth on surfaces and a similar trend of damage. Full article

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

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17 pages, 2458 KiB

Open AccessArticle

Hydrocarbons Biodegradation by Rhodococcus: Assimilation of Hexadecane in Different Aggregate States

by Luong Thi Mo, Puntus Irina, Suzina Natalia, Nechaeva Irina, Akhmetov Lenar, Filonov Andrey, Akatova Ekaterina, Alferov Sergey and Ponamoreva Olga

Microorganisms 2022, 10(8), 1594; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10081594 - 08 Aug 2022

Cited by 7 | Viewed by 1974

Abstract

The aim of our study was to reveal the peculiarities of the adaptation of rhodococci to hydrophobic hydrocarbon degradation at low temperatures when the substrate was in solid states. The ability of actinobacteria Rhodococcus erythropolis (strains X5 and S67) to degrade hexadecane at 10 °C (solid hydrophobic substrate) and 26 °C (liquid hydrophobic substrate) is described. Despite the solid state of the hydrophobic substrate at 10 °C, bacteria demonstrate a high level of its degradation (30–40%) within 18 days. For the first time, we show that specialized cellular structures are formed during the degradation of solid hexadecane by Rhodococcus at low temperatures: intracellular multimembrane structures and surface vesicles connected to the cell by fibers. The formation of specialized cellular structures when Rhodococcus bacteria are grown on solid hexadecane is an important adaptive trait, thereby contributing to the enlargement of a contact area between membrane-bound enzymes and a hydrophobic substrate. Full article

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

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14 pages, 2051 KiB

Open AccessArticle

Antiscalants Used in Seawater Desalination: Biodegradability and Effects on Microbial Diversity

by Ashraf Al-Ashhab, Amer Sweity, Luna Al-Hadidi, Moshe Herzberg and Zeev Ronen

Microorganisms 2022, 10(8), 1580; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10081580 - 05 Aug 2022

Cited by 7 | Viewed by 2761

Abstract

Antiscalants are organic polymers widely used for scale inhibition in seawater desalination. While they are susceptible to biodegradation, they provide nutrients for bacterial cell growth and energy for the microbes that assimilate and degrade them. This paper shows the biodegradability of three commercial antiscalants (polyacrylate—CA, polyphosphonate—PP, and carboxylated dendrimers—DN) applied in seawater reverse osmosis desalination (SWRO) as well as analyzing the antiscalant’s effects on microbial diversity using microbial cultures grown in seawater, under semi-continuous batch conditions. Nutritional uptake and contribution of the antiscalants to microbial growth were investigated by measuring DOC, TDN, NO₃⁻, NO₂⁻, PO₄⁻, NH₄⁺, and TP of the filtered samples of the incubated batch, twice a month, for twelve months. The microbial community was estimated by 16S rRNA sequencing. The main changes in the microbial communities were determined by the incubation period. However, bacterial orders of the antiscalant treatments differed significantly from the control treatment, namely Planctomycetales, Clostridiales, Sphingobacteriales, Rhodobacterales, and Flavobacteriales, and other unclassified bacterial orders, which were found in various relative abundances dependent on incubation times. The results showed the PP antiscalant to be the least biodegradable and to have the least effect on the bacterial community composition compared to the control. This result emphasizes the need to reassess the suitability criteria of antiscalants, and to further monitor their long-term environmental effects. Full article

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

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15 pages, 1343 KiB

Open AccessArticle

“Unity and Struggle of Opposites” as a Basis for the Functioning of Synthetic Bacterial Immobilized Consortium That Continuously Degrades Organophosphorus Pesticides

by Elena Efremenko, Nikolay Stepanov, Olga Maslova, Olga Senko, Aysel Aslanli and Ilya Lyagin

Microorganisms 2022, 10(7), 1394; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10071394 - 11 Jul 2022

Cited by 13 | Viewed by 1434

Abstract

This work was aimed at the development of an immobilized artificial consortium (IMAC) based on microorganisms belonging to the Gram-positive and Gram-negative bacterial cells capable of jointly carrying out the rapid and effective degradation of different organophosphorus pesticides (OPPs): paraoxon, parathion, methyl parathion, diazinon, chlorpyrifos, malathion, dimethoate, and demeton-S-methyl. A cryogel of poly(vinyl alcohol) was applied as a carrier for the IMAC. After a selection was made between several candidates of the genera Rhodococcus and Pseudomonas, the required combination of two cultures (P. esterophilus and R. ruber) was found. A further change in the ratio between the biomass of the cells inside the granules of IMAC, increasing the packing density of cells inside the same granules and decreasing the size of the granules with IMAC, gave a 225% improvement in the degradation activity of the cell combination. The increase in the velocity and the OPP degradation degree was 4.5 and 16 times greater than the individual P. esterophilus and R. ruber cells, respectively. Multiple uses of the obtained IMAC were demonstrated. The increase in IMAC lactonase activity confirmed the role of the cell quorum in the action efficiency of the synthetic biosystem. The co-inclusion of natural strains in a carrier during immobilization strengthened the IMAC activities without the genetic enhancement of the cells. Full article

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

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16 pages, 3944 KiB

Open AccessArticle

A Novel Organophosphorus Acid Anhydrolase from Deep Sea Sediment with High Degradation Efficiency for Organophosphorus Pesticides and Nerve Agent

by Xiaofang Zheng, Li Wang, Lihong Qi and Zhiyang Dong

Microorganisms 2022, 10(6), 1112; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10061112 - 27 May 2022

Cited by 9 | Viewed by 1803

Abstract

Organophosphorus compounds (OPCs), including highly toxic nerve agents and pesticides, have been used widely in agricultural and military applications. However, they have aroused widespread concern because they persistently pollute the environment and threaten human life. Organophosphorus acid anhydrolase (OPAA) is a promising enzyme that can detoxify OPCs. Here, a novel OPAA (OPAA114644) was isolated and characterized from deep-sea sediment (−3104 m). It exhibited excellent alkaline stability, and the loss of activity was less than 20% in the pH range 5.0–9.0, even after being incubated for 30 d at 4 °C. It also exhibited high salt tolerance, and its enzymatic activity increased by approximately fourfold in the presence of 20% NaCl (w/v). Additionally, OPAA114644 exhibited high degradation efficiency for soman, dichlorvos, paraoxon, coumaphos, and chlorpyrifos with a concentration of up to 250 mg/L, with the degradation rate being 100%, 100%, 100%, 80% and 51%, respectively, in 20 min under optimal conditions. Notably, OPAA114644 dissolved in different solutions, such as 20% NaCl, 1 mM SDS, 0.05% soap, 10% methanol, and tap water, could efficiently decontaminate the residual paraoxon on the surfaces of glasses, cotton tissues, and apples. These results indicate that OPAA114644 has excellent potential for the biodegradation and bioremediation of OPCs pollution and represents a real application of OPAA in the decontamination and detoxification of foods and clothes, and in the remediation of sites such as floors. Deep-sea sediment might also be an abundant resource for various functional microorganisms and enzymes. Full article

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

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12 pages, 2620 KiB

Open AccessArticle

Cellular Modifications of Rhodococci Exposed to Separate and Combined Effects of Pharmaceutical Pollutants

by Irina Ivshina, Grigory Bazhutin, Semyon Tyan, Maxim Polygalov, Maria Subbotina and Elena Tyumina

Microorganisms 2022, 10(6), 1101; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10061101 - 26 May 2022

Cited by 4 | Viewed by 1735

Abstract

Actinomycetes of the genus Rhodococcus (class Actinomycetia) are dominant dwellers of biotopes with anthropogenic load. They serve as a natural system of primary response to xenobiotics in open ecosystems, initiate defensive responses in the presence of pollutants, and are regarded as ideal agents capable of transforming and degrading pharmaceuticals. Here, the ability of selected Rhodococcus strains to co-metabolize nonsteroidal anti-inflammatory drugs (ibuprofen, meloxicam, and naproxen) and information on the protective mechanisms of rhodococci against toxic effects of pharmaceuticals, individually or in a mixture, have been demonstrated. For the first time, R. ruber IEGM 439 provided complete decomposition of 100 mg/L meloxicam after seven days. It was shown that versatile cellular modifications occurring at the early development stages of nonspecific reactions of Rhodococcus spp. in response to separate and combined effects of the tested pharmaceuticals included changes in electrokinetic characteristics and catalase activity; transition from unicellular to multicellular life forms accompanied by pronounced morphological abnormalities; changes in the average size of vegetative cells and surface area-to-volume ratio; and the formation of linked cell assemblages. The obtained data are considered as adaptation mechanisms in rhodococci, and consequently their increased resistance to separate and combined effects of ibuprofen, meloxicam, and naproxen. Full article

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

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19 pages, 3062 KiB

Open AccessArticle

Assessment of Metal Accumulation by Arthrospira platensis and Its Adaptation to Iterative Action of Nickel Mono- and Polymetallic Synthetic Effluents

by Liliana Cepoi, Inga Zinicovscaia, Ludmila Rudi, Tatiana Chiriac, Svetlana Djur, Nikita Yushin and Dmitrii Grozdov

Microorganisms 2022, 10(5), 1041; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10051041 - 17 May 2022

Cited by 8 | Viewed by 1796

Abstract

Cyanobacteria-mediated wastewater remediation is an economical, efficient, and eco-friendly technology. The present work deals with the bioaccumulation performance of Arthrospira platensis (Spirulina) grown for four cycles in a medium containing nickel mono- and polymetallic synthetic effluents. The metal uptake by spirulina biomass was evaluated using neutron activation analysis. The effects of effluents on biomass production, protein, and phycobiliprotein content were assessed. Metal accumulation in the biomass depended on the effluent composition and metal ion concentrations. Nickel accumulation in the biomass was directly proportional to its concentration in effluents, and maximum uptake (1310 mg/kg) was attained in the Ni/Cr/Fe system. In the same system, biomass accumulated 110 times more chromium and 4.7 times more iron than control. The highest accumulation of copper (2870 mg/kg) was achieved in the Ni/Cu/Zn/Mo system and zinc (1860 mg/kg)—in the Ni/Cu/Zn/Sr system. In biomass grown in the media loaded with nickel and also chromium, iron, copper, strontium, zinc, and molybdenum, a decrease in productivity (on average by 10%) during the first cycle of cultivation and moderate reduction of protein content (by 15–27%) was observed. The presence of metals in the cultivation media inhibited phycobiliprotein synthesis, especially of phycocyanin, and promoted the synthesis of allophycocyanin. The maximum reduction of phycocyanin content was 77%, and the increase of allophycocyanin content—by 45%. Arthrospira platensis may be deemed as bioremediation of nickel-polluted wastewaters of complex composition. Full article

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

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26 pages, 4226 KiB

Open AccessArticle

Biodegradation, Decolorization, and Detoxification of Di-Azo Dye Direct Red 81 by Halotolerant, Alkali-Thermo-Tolerant Bacterial Mixed Cultures

by Islam M. Kamal, Nourtan F. Abdeltawab, Yasser M. Ragab, Mohamed A. Farag and Mohammed A. Ramadan

Microorganisms 2022, 10(5), 994; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10050994 - 09 May 2022

Cited by 18 | Viewed by 3159

Abstract

Azo dyes impact the environment and deserve attention due to their widespread use in textile and tanning industries and challenging degradation. The high temperature, pH, and salinity used in these industries render industrial effluent decolorization and detoxification a challenging process. An enrichment technique was employed to screen for cost-effective biodegraders of Direct Red 81 (DR81) as a model for diazo dye recalcitrant to degradation. Our results showed that three mixed bacterial cultures achieved ≥80% decolorization within 8 h of 40 mg/L dye in a minimal salt medium with 0.1% yeast extract (MSM-Y) and real wastewater. Moreover, these mixed cultures showed ≥70% decolorization within 24 h when challenged with dye up to 600 mg/L in real wastewater and tolerated temperatures up to 60 °C, pH 10, and 5% salinity in MSM-Y. Azoreductase was the main contributor to DR81 decolorization based on crude oxidative and reductive enzymatic activity of cell-free supernatants and was stable at a wide range of pH and temperatures. Molecular identification of azoreductase genes suggested multiple AzoR genes per mixed culture with a possible novel azoreductase gene. Metabolite analysis using hyphenated techniques suggested two reductive pathways for DR81 biodegradation involving symmetric and asymmetric azo-bond cleavage. The DR81 metabolites were non-toxic to Artemia salina nauplii and Lepidium sativum seeds. This study provided evidence for DR81 degradation using robust stress-tolerant mixed cultures with potential use in azo dye wastewater treatment. Full article

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

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17 pages, 1993 KiB

Open AccessArticle

Process Development for Benzyl Alcohol Production by Whole-Cell Biocatalysis in Stirred and Packed Bed Reactors

by Carlos J. C. Rodrigues and Carla C. C. R. de Carvalho

Microorganisms 2022, 10(5), 966; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10050966 - 03 May 2022

Cited by 7 | Viewed by 2633

Abstract

The ocean is an excellent source for new biocatalysts due to the tremendous genetic diversity of marine microorganisms, and it may contribute to the development of sustainable industrial processes. A marine bacterium was isolated and selected for the conversion of benzaldehyde to benzyl alcohol, which is an important chemical employed as a precursor for producing esters for cosmetics and other industries. Enzymatic production routes are of interest for sustainable processes. To overcome benzaldehyde low water solubility, DMSO was used as a biocompatible cosolvent up to a concentration of 10% (v/v). A two-phase system with n-hexane, n-heptane, or n-hexadecane as organic phase allowed at least a 44% higher relative conversion of benzaldehyde than the aqueous system, and allowed higher initial substrate concentrations. Cell performance decreased with increasing product concentration but immobilization of cells in alginate improved four-fold the robustness of the biocatalyst: free and immobilized cells were inhibited at concentrations of benzyl alcohol of 5 and 20 mM, respectively. Scaling up to a 100 mL stirred reactor, using a fed-batch approach, enabled a 1.5-fold increase in benzyl alcohol productivity when compared with batch mode. However, product accumulation in the reactor hindered the conversion. The use of a continuous flow reactor packed with immobilized cells enabled a 9.5-fold increase in productivity when compared with the fed-batch stirred reactor system. Full article

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

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15 pages, 11590 KiB

Open AccessArticle

Coupled Adsorption and Biodegradation of Trichloroethylene on Biochar from Pine Wood Wastes: A Combined Approach for a Sustainable Bioremediation Strategy

by Marta M. Rossi, Bruna Matturro, Neda Amanat, Simona Rossetti and Marco Petrangeli Papini

Microorganisms 2022, 10(1), 101; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010101 - 04 Jan 2022

Cited by 11 | Viewed by 2491

Abstract

Towards chlorinated solvents, the effectiveness of the remediation strategy can be improved by combining a biological approach (e.g., anaerobic reductive dechlorination) with chemical/physical treatments (e.g., adsorption). A coupled adsorption and biodegradation (CAB) process for trichloroethylene (TCE) removal is proposed in a biofilm–biochar reactor (BBR) to assess whether biochar from pine wood (PWB) can support a dechlorinating biofilm by combining the TCE (100 µM) adsorption. The BBR operated for eight months in parallel with a biofilm reactor (BR)—no PWB (biological process alone), and with an abiotic biochar reactor (ABR)—no dechlorinating biofilm (only an adsorption mechanism). Two flow rates were investigated. Compared to the BR, which resulted in a TCE removal of 86.9 ± 11.9% and 78.73 ± 19.79%, the BBR demonstrated that PWB effectively adsorbs TCE and slows down the release of its intermediates. The elimination of TCE was quantitative, with 99.61 ± 0.79% and 99.87 ± 0.51% TCE removal. Interestingly, the biomarker of the reductive dechlorination process, Dehalococcoides mccartyi, was found in the BRR (9.2 × 10⁵ 16S rRNA gene copies/g), together with the specific genes tceA, bvcA, and vcrA (8.16 × 10⁶, 1.28 × 10⁵, and 8.01 × 10³ gene copies/g, respectively). This study suggests the feasibility of biochar to support the reductive dechlorination of D. mccartyi, opening new frontiers for field-scale applications. Full article

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

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Review

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17 pages, 1817 KiB

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Degradation of Triclosan in the Water Environment by Microorganisms: A Review

by Yiran Yin, Hao Wu, Zhenghai Jiang, Jingwei Jiang and Zhenmei Lu

Microorganisms 2022, 10(9), 1713; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10091713 - 25 Aug 2022

Cited by 12 | Viewed by 3089

Abstract

Triclosan (TCS), a kind of pharmaceuticals and personal care products (PPCPs), is widely used and has had a large production over years. It is an emerging pollutant in the water environment that has attracted global attention due to its toxic effects on organisms and aquatic ecosystems, and its concentrations in the water environment are expected to increase since the COVID-19 pandemic outbreak. Some researchers found that microbial degradation of TCS is an environmentally sustainable technique that results in the mineralization of large amounts of organic pollutants without toxic by-products. In this review, we focus on the fate of TCS in the water environment, the diversity of TCS-degrading microorganisms, biodegradation pathways and molecular mechanisms, in order to provide a reference for the efficient degradation of TCS and other PPCPs by microorganisms. Full article

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

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