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Microbial Degradation of Xenobiotics
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Microbial Degradation of Xenobiotics

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

Deadline for manuscript submissions: closed (30 November 2019) | Viewed by 59420

Special Issue Editor

Prof. Dr. Yuji Nagata

E-Mail Website
Guest Editor
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
Interests: microbial degradation of environmental pollutants; evolution and adaptation of bacteria, protein evolution; mobile genetic elements; bacterial genome and metagenome

Special Issue Information

Dear Colleagues,

Xenobiotics have been released into the environment by human activities, and they often cause environmental pollution problems, since most such compounds cannot be readily degraded and have harmful effects on the natural ecosystem, including human beings. However, some microorganisms have been isolated that degrade man-made xenobiotics. Especially, most aerobic xenobiotic-degrading bacterial strains can use such chemicals as their sole sources of carbon and energy, and thus they are excellent models for studying the adaptation and evolution of bacteria in the environment.

Recent genome analyses of the bacterial strains degrading xenobiotics have strongly suggested that they indeed emerged relatively recently by gathering genes for the degradation of xenobiotics, and mobile genetic elements played important roles in the recruitment of the genes. However, the origin of the genes and the evolutionary processes of such bacterial strains remain largely unknown. Ongoing comprehensive genome and metagenome analyses may provide some insights into such mysteries, and the genes for the degradation of xenobiotics can be used as probes to reveal novel mechanisms for the evolution of microorganisms. In addition, enzymes for the degradation of xenobiotics are good materials for studies of protein evolution, since generally they show promiscuous activity and their properties change dramatically with a small number of mutations. On the other hand, the importance of microbial consortia and symbiosis for the degradation of xenobiotics in the environment has also been suggested, and thus studies of xenobiotic degradation may provide some novel concepts into the field of microbial ecology.

For this Special Issue of Microorganisms, we invite you to send contributions encompassing any aspects relating to the evolution and adaptation of microorganisms towards xenobiotics.

Prof. Dr. Yuji Nagata
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. Microorganisms 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 2700 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

  • biodegradation
  • xenobiotics
  • environmental pollutants
  • evolution and adaptation
  • genome and metagenome
  • mobile genetic elements
  • protein evolution
  • microbial consortia
  • symbiosis

Published Papers (15 papers)

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Editorial

Jump to: Research, Review, Other

2 pages, 156 KiB  
Editorial
Special Issue: Microbial Degradation of Xenobiotics
by Yuji Nagata
Microorganisms 2020, 8(4), 487; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8040487 - 30 Mar 2020
Cited by 6 | Viewed by 2420
Abstract
Xenobiotics are released into the environment by human activities, and they often cause problems such as environmental pollution, since most such compounds cannot be readily degraded, and have harmful effects on human beings and the natural ecosystem [...] Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)

Research

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11 pages, 3257 KiB  
Article
A Rotational Slurry Bioreactor Accelerates Biodegradation of A-Fuel in Oil-Contaminated Soil Even under Low Temperature Conditions
by Yuna Miyoshi, Jo Okada, Tomotaka Urata, Masaki Shintani and Kazuhide Kimbara
Microorganisms 2020, 8(2), 291; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8020291 - 20 Feb 2020
Cited by 8 | Viewed by 3029
Abstract
An effective bioaugmentation system for oil-contaminated soil under low-temperature conditions was developed with a rotational slurry bioreactor. Mixtures of two Rhodococcus oil-degraders, strain A and C, which are officially permitted to be used in bioaugmentation in Japan, were inoculated and A-fuel oil was [...] Read more.
An effective bioaugmentation system for oil-contaminated soil under low-temperature conditions was developed with a rotational slurry bioreactor. Mixtures of two Rhodococcus oil-degraders, strain A and C, which are officially permitted to be used in bioaugmentation in Japan, were inoculated and A-fuel oil was added to a final concentration of 2500 and 5000 mg/kg-slurry. Decomposition tests were carried out for the inoculated samples and non-inoculated samples by rotating at 15 °C, the annual average temperature of Japan. The residue of A-fuel oil and the number of bacteria were measured every two days. After 6 days of treatment, more than 95% of the oil was removed in the inoculated samples, which was more than three times faster than a previous degradation experiment without rotation. A semi-continuous treatment was performed by removing 90% of the treated slurry, then adding the same amount of contaminated slurry into the system without additional degraders. Ninety-four percent of A-fuel oil was successfully degraded after 6 days by this repeated treatment. This could drastically reduce the cost of preparing the degraders. Strikingly, semi-continuous treatment showed oil removal in the non-inoculated samples, indicating that the rotational slurry conditions could efficiently promote biodegradation by indigenous degraders. Our rotational slurry bioreactor accelerated the removal of oil contamination without adding further degraders provides an efficient and cost-effective method of removal of A-fuel oil using a semi-continuous system, which can be used in practical applications in areas with a cooler climate. Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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13 pages, 2154 KiB  
Article
Degradation Potential of the Nonylphenol Monooxygenase of Sphingomonas sp. NP5 for Bisphenols and Their Structural Analogs
by Masahiro Takeo, Junichi Akizuki, Aika Kawasaki and Seiji Negoro
Microorganisms 2020, 8(2), 284; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8020284 - 19 Feb 2020
Cited by 15 | Viewed by 3387
Abstract
The nonylphenol-degrading bacterium Sphingomonas sp. strain NP5 has a very unique monooxygenase that can attack a wide range of 4-alkylphenols with a branched side chain. Due to the structural similarity, it can also attack bisphenolic compounds, which are very important materials for the [...] Read more.
The nonylphenol-degrading bacterium Sphingomonas sp. strain NP5 has a very unique monooxygenase that can attack a wide range of 4-alkylphenols with a branched side chain. Due to the structural similarity, it can also attack bisphenolic compounds, which are very important materials for the synthesis of plastics and resins, but many of them are known to or suspected to have endocrine disrupting effects to fish and animals. In this study, to clarify the substrate specificity of the enzyme (NmoA) for bisphenolic compounds, degradation tests using the cell suspension of Pseudomonas putida harboring the nonylphenol monooxygenase gene (nmoA) were conducted. The cell suspension degraded several bisphenols including bisphenol F, bisphenol S, 4,4′-dihydroxybenzophenone, 4,4′-dihydroxydiphenylether, and 4,4′-thiodiphenol, indicating that this monooxygenase has a broad substrate specificity for compounds with a bisphenolic structure. Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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14 pages, 2746 KiB  
Article
On the Ability of Perfluorohexane Sulfonate (PFHxS) Bioaccumulation by Two Pseudomonas sp. Strains Isolated from PFAS-Contaminated Environmental Matrices
by Alessandro Presentato, Silvia Lampis, Andrea Vantini, Flavio Manea, Francesca Daprà, Stefano Zuccoli and Giovanni Vallini
Microorganisms 2020, 8(1), 92; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8010092 - 09 Jan 2020
Cited by 48 | Viewed by 7330
Abstract
PFASs (perfluoroalkyl and polyfluoroalkyl substances) are highly fluorinated, aliphatic, synthetic compounds with high thermal and chemical stability as well as unique amphiphilic properties which make them ingredients in a range of industrial processes. PFASs have attracted consideration due to their persistence, toxicity and [...] Read more.
PFASs (perfluoroalkyl and polyfluoroalkyl substances) are highly fluorinated, aliphatic, synthetic compounds with high thermal and chemical stability as well as unique amphiphilic properties which make them ingredients in a range of industrial processes. PFASs have attracted consideration due to their persistence, toxicity and bioaccumulation tendency in the environment. Recently, attention has begun to be addressed to shorter-chain PFASs, such as perfluorohexane sulfonate [PFHxS], apparently less toxic to and more easily eliminated from lab animals. However, short-chain PFASs represent end-products from the transformation of fluorotelomers whose biotic breakdown reactions have not been identified to date. This means that such emergent pollutants will tend to accumulate and persist in ecosystems. Since we are just learning about the interaction between short-chain PFASs and microorganisms, this study reports on the response to PFHxS of two Pseudomonas sp. strains isolated from environmental matrices contaminated by PFASs. The PFHxS bioaccumulation potential of these strains was unveiled by exploiting different physiological conditions as either axenic or mixed cultures under alkanothrofic settings. Moreover, electron microscopy revealed nonorthodox features of the bacterial cells, as a consequence of the stress caused by both organic solvents and PFHxS in the culturing substrate. Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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16 pages, 2564 KiB  
Article
Enrichment and Analysis of Stable 1,4-dioxane-Degrading Microbial Consortia Consisting of Novel Dioxane-Degraders
by Tanmoy Roy Tusher, Takuya Shimizu, Chihiro Inoue and Mei-Fang Chien
Microorganisms 2020, 8(1), 50; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8010050 - 25 Dec 2019
Cited by 22 | Viewed by 3960
Abstract
Biodegradation of 1,4-dioxane, a water contaminant of emerging concern, has drawn substantial attention over the last two decades. A number of dioxane-degraders have been identified, though many of them are unable to metabolically utilize 1,4-dioxane. Moreover, it is considered more preferable to use [...] Read more.
Biodegradation of 1,4-dioxane, a water contaminant of emerging concern, has drawn substantial attention over the last two decades. A number of dioxane-degraders have been identified, though many of them are unable to metabolically utilize 1,4-dioxane. Moreover, it is considered more preferable to use microbial consortia rather than the pure strains, especially in conventional bioreactors for industrial wastewater treatment. In the present study, a stable 1,4-dioxane-degrading microbial consortium was enriched, namely 112, from industrial wastewater by nitrate mineral salt medium (NMSM). The consortium 112 is capable of utilizing 1,4-dioxane as a sole carbon and energy source, and can completely degrade 1,4-dioxane up to 100 mg/L. From the consortium 112, two 1,4-dioxane-degrading bacterial strains were isolated and identified, in which the Variovorax sp. TS13 was found to be a novel 1,4-dioxane-degrader that can utilize 100 mg/L of 1,4-dioxane. The efficacy of the consortium 112 was increased significantly when we cultured the consortium with mineral salt medium (MSM). The new consortium, N112, could utilize 1,4-dioxane at a rate of 1.67 mg/L·h. The results of the ribosomal RNA intergenic spacer analysis (RISA) depicted that changes in the microbial community structure of consortium 112 was the reason behind the improved degradation efficiency of consortium N112, which was exhibited as a stable and effective microbial consortium with a high potential for bioremediation of the dioxane-impacted sites and contaminated industrial wastewater. Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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12 pages, 2447 KiB  
Article
Isolation and Characterization of Genes Responsible for Naphthalene Degradation from Thermophilic Naphthalene Degrader, Geobacillus sp. JF8
by Daisuke Miyazawa, Le Thi Ha Thanh, Akio Tani, Masaki Shintani, Nguyen Hoang Loc, Takashi Hatta and Kazuhide Kimbara
Microorganisms 2020, 8(1), 44; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8010044 - 24 Dec 2019
Cited by 16 | Viewed by 3555
Abstract
Geobacillus sp. JF8 is a thermophilic biphenyl and naphthalene degrader. To identify the naphthalene degradation genes, cis-naphthalene dihydrodiol dehydrogenase was purified from naphthalene-grown cells, and its N-terminal amino acid sequence was determined. Using a DNA probe encoding the N-terminal region of the [...] Read more.
Geobacillus sp. JF8 is a thermophilic biphenyl and naphthalene degrader. To identify the naphthalene degradation genes, cis-naphthalene dihydrodiol dehydrogenase was purified from naphthalene-grown cells, and its N-terminal amino acid sequence was determined. Using a DNA probe encoding the N-terminal region of the dehydrogenase, a 10-kb DNA fragment was isolated. Upstream of nahB, a gene for dehydrogenase, there were two open reading frames which were designated as nahAc and nahAd, respectively. The products of nahAc and nahAd were predicted to be alpha and beta subunit of ring-hydroxylating dioxygenases, respectively. Phylogenetic analysis of amino acid sequences of NahB indicated that it did not belong to the cis-dihydrodiol dehydrogenase group that includes those of classical naphthalene degradation pathways. Downstream of nahB, four open reading frames were found, and their products were predicted as meta-cleavage product hydrolase, monooxygenase, dehydrogenase, and gentisate 1,2-dioxygenase, respectively. A reverse transcriptase-PCR analysis showed that transcription of nahAcAd was induced by naphthalene. These findings indicate that we successfully identified genes involved in the upper pathway of naphthalene degradation from a thermophilic bacterium. Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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12 pages, 2185 KiB  
Article
Biotransformation of Monocyclic Phenolic Compounds by Bacillus licheniformis TAB7
by Enock Mpofu, Joydeep Chakraborty, Chiho Suzuki-Minakuchi, Kazunori Okada, Toshiaki Kimura and Hideaki Nojiri
Microorganisms 2020, 8(1), 26; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8010026 - 21 Dec 2019
Cited by 8 | Viewed by 4052
Abstract
Bacillus licheniformis strain TAB7 is a bacterium used as a commercial deodorizing agent for compost in Japan. In this work, its ability to biotransform the following monocyclic phenolic compounds was assessed: ferulate, vanillate, p-coumarate, caffeate, protocatechuate, syringate, vanillin, and cinnamate (a precursor [...] Read more.
Bacillus licheniformis strain TAB7 is a bacterium used as a commercial deodorizing agent for compost in Japan. In this work, its ability to biotransform the following monocyclic phenolic compounds was assessed: ferulate, vanillate, p-coumarate, caffeate, protocatechuate, syringate, vanillin, and cinnamate (a precursor for some phenolic compounds). These compounds are abundant in composting material and are reported to have allelopathic properties. They come from sources such as plant material decomposition or agro-industrial waste. Biotransformation assays were carried out in LB supplemented with 0.2 mg/mL of an individual phenolic compound and incubated for up to 15 days followed by extraction and HPLC analysis. The results showed that TAB7 could biotransform ferulate, caffeate, p-coumarate, vanillate, protocatechuate, and vanillin. It, however, had a poor ability to transform cinnamate and syringate. LC-MS/MS analysis showed that ferulate was transformed into 4-vinylguaiacol as the final product, while caffeate was transformed into 4-ethylcatechol. TAB7 genome analysis suggested that, while TAB7 may not mineralize phenolic compounds, it harbored genes possibly encoding phenolic acid decarboxylase, vanillate decarboxylase, and some protocatechuate degradation pathway enzymes, which are involved in the catabolism of phenolic compounds known to have negative allelopathy on some plants. The results thus suggested that TAB7 can reduce such phenolic compounds in compost. Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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17 pages, 2760 KiB  
Article
The Degradative Capabilities of New Amycolatopsis Isolates on Polylactic Acid
by Francesca Decorosi, Maria Luna Exana, Francesco Pini, Alessandra Adessi, Anna Messini, Luciana Giovannetti and Carlo Viti
Microorganisms 2019, 7(12), 590; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7120590 - 20 Nov 2019
Cited by 26 | Viewed by 4367
Abstract
Polylactic acid (PLA), a bioplastic synthesized from lactic acid, has a broad range of applications owing to its excellent proprieties such as a high melting point, good mechanical strength, transparency, and ease of fabrication. However, the safe disposal of PLA is an emerging [...] Read more.
Polylactic acid (PLA), a bioplastic synthesized from lactic acid, has a broad range of applications owing to its excellent proprieties such as a high melting point, good mechanical strength, transparency, and ease of fabrication. However, the safe disposal of PLA is an emerging environmental problem: it resists microbial attack in environmental conditions, and the frequency of PLA-degrading microorganisms in soil is very low. To date, a limited number of PLA-degrading bacteria have been isolated, and most are actinomycetes. In this work, a method for the selection of rare actinomycetes with extracellular proteolytic activity was established, and the technique was used to isolate four mesophilic actinomycetes with the ability to degrade emulsified PLA in agar plates. All four strains—designated SO1.1, SO1.2, SNC, and SST—belong to the genus Amycolatopsis. The PLA-degrading capability of the four strains was investigated by testing their ability to assimilate lactic acid, fragment PLA polymers, and deteriorate PLA films. The strain SNC was the best PLA degrader—it was able to assimilate lactic acid, constitutively cleave PLA, and form a thick and widespread biofilm on PLA film. The activity of this strain extensively eroded the polymer, leading to a weight loss of 36% in one month in mesophilic conditions. Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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11 pages, 1444 KiB  
Article
Identification of A Novel Arsenic Resistance Transposon Nested in A Mercury Resistance Transposon of Bacillus sp. MB24
by Mei-Fang Chien, Ying-Ning Ho, Hui-Erh Yang, Masaru Narita, Keisuke Miyauchi, Ginro Endo and Chieh-Chen Huang
Microorganisms 2019, 7(11), 566; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7110566 - 16 Nov 2019
Cited by 4 | Viewed by 2590
Abstract
A novel TnMERI1-like transposon designated as TnMARS1 was identified from mercury resistant Bacilli isolated from Minamata Bay sediment. Two adjacent ars operon-like gene clusters, ars1 and ars2, flanked by a pair of 78-bp inverted repeat sequences, which resulted [...] Read more.
A novel TnMERI1-like transposon designated as TnMARS1 was identified from mercury resistant Bacilli isolated from Minamata Bay sediment. Two adjacent ars operon-like gene clusters, ars1 and ars2, flanked by a pair of 78-bp inverted repeat sequences, which resulted in a 13.8-kbp transposon-like fragment, were found to be sandwiched between two transposable genes of the TnMERI1-like transposon of a mercury resistant bacterium, Bacillus sp. MB24. The presence of a single transcription start site in each cluster determined by 5′-RACE suggested that both are operons. Quantitative real time RT-PCR showed that the transcription of the arsR genes contained in each operon was induced by arsenite, while arsR2 responded to arsenite more sensitively and strikingly than arsR1 did. Further, arsenic resistance complementary experiments showed that the ars2 operon conferred arsenate and arsenite resistance to an arsB-knocked out Bacillus host, while the ars1 operon only raised arsenite resistance slightly. This transposon nested in TnMARS1 was designated as TnARS1. Multi-gene cluster blast against bacteria and Bacilli whole genome sequence databases suggested that TnMARS1 is the first case of a TnMERI1-like transposon combined with an arsenic resistance transposon. The findings of this study suggested that TnMERI1-like transposons could recruit other mobile elements into its genetic structure, and subsequently cause horizontal dissemination of both mercury and arsenic resistances among Bacilli in Minamata Bay. Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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29 pages, 1218 KiB  
Article
Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway
by Martin Demko, Lukáš Chrást, Pavel Dvořák, Jiří Damborský and David Šafránek
Microorganisms 2019, 7(11), 553; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7110553 - 11 Nov 2019
Cited by 8 | Viewed by 3669
Abstract
In our previous work, we designed and implemented a synthetic metabolic pathway for 1,2,3-trichloropropane (TCP) biodegradation in Escherichia coli. Significant effects of metabolic burden and toxicity exacerbation were observed on single cell and population levels. Deeper understanding of mechanisms underlying these effects [...] Read more.
In our previous work, we designed and implemented a synthetic metabolic pathway for 1,2,3-trichloropropane (TCP) biodegradation in Escherichia coli. Significant effects of metabolic burden and toxicity exacerbation were observed on single cell and population levels. Deeper understanding of mechanisms underlying these effects is extremely important for metabolic engineering of efficient microbial cell factories for biotechnological processes. In this paper, we present a novel mathematical model of the pathway. The model addresses for the first time the combined effects of toxicity exacerbation and metabolic burden in the context of bacterial population growth. The model is calibrated with respect to the real data obtained with our original synthetically modified E. coli strain. Using the model, we explore the dynamics of the population growth along with the outcome of the TCP biodegradation pathway considering the toxicity exacerbation and metabolic burden. On the methodological side, we introduce a unique computational workflow utilising algorithmic methods of computer science for the particular modelling problem. Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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20 pages, 1861 KiB  
Article
Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17
by Lukas Chrast, Katsiaryna Tratsiak, Joan Planas-Iglesias, Lukas Daniel, Tatyana Prudnikova, Jan Brezovsky, David Bednar, Ivana Kuta Smatanova, Radka Chaloupkova and Jiri Damborsky
Microorganisms 2019, 7(11), 498; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7110498 - 28 Oct 2019
Cited by 17 | Viewed by 3920
Abstract
Haloalkane dehalogenases are enzymes with a broad application potential in biocatalysis, bioremediation, biosensing and cell imaging. The new haloalkane dehalogenase DmxA originating from the psychrophilic bacterium Marinobacter sp. ELB17 surprisingly possesses the highest thermal stability (apparent melting temperature Tm,app = 65.9 °C) [...] Read more.
Haloalkane dehalogenases are enzymes with a broad application potential in biocatalysis, bioremediation, biosensing and cell imaging. The new haloalkane dehalogenase DmxA originating from the psychrophilic bacterium Marinobacter sp. ELB17 surprisingly possesses the highest thermal stability (apparent melting temperature Tm,app = 65.9 °C) of all biochemically characterized wild type haloalkane dehalogenases belonging to subfamily II. The enzyme was successfully expressed and its crystal structure was solved at 1.45 Å resolution. DmxA structure contains several features distinct from known members of haloalkane dehalogenase family: (i) a unique composition of catalytic residues; (ii) a dimeric state mediated by a disulfide bridge; and (iii) narrow tunnels connecting the enzyme active site with the surrounding solvent. The importance of narrow tunnels in such paradoxically high stability of DmxA enzyme was confirmed by computational protein design and mutagenesis experiments. Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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17 pages, 1701 KiB  
Article
Bioremediation of Artificial Diesel-Contaminated Soil Using Bacterial Consortium Immobilized to Plasma-Pretreated Wood Waste
by Ravit Farber, Alona Rosenberg, Shmuel Rozenfeld, Gabi Banet and Rivka Cahan
Microorganisms 2019, 7(11), 497; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7110497 - 28 Oct 2019
Cited by 18 | Viewed by 5391
Abstract
Bioaugmentation is a bioremediation option based on increasing the natural in-situ microbial population that possesses the ability to degrade the contaminating pollutant. In this study, a diesel-degrading consortium was obtained from an oil-contaminated soil. The diesel-degrading consortium was grown on wood waste that [...] Read more.
Bioaugmentation is a bioremediation option based on increasing the natural in-situ microbial population that possesses the ability to degrade the contaminating pollutant. In this study, a diesel-degrading consortium was obtained from an oil-contaminated soil. The diesel-degrading consortium was grown on wood waste that was plasma-pretreated. This plasma treatment led to an increase of bacterial attachment and diesel degradation rates. On the 7th day the biofilm viability on the plasma-treated wood waste reached 0.53 ± 0.02 OD 540 nm, compared to the non-treated wood waste which was only 0.34 ± 0.02. Biofilm attached to plasma-treated and untreated wood waste which was inoculated into artificially diesel-contaminated soil (0.15% g/g) achieved a degradation rate of 9.3 mg day−1 and 7.8 mg day−1, respectively. While, in the soil that was inoculated with planktonic bacteria, degradation was only 5.7 mg day−1. Exposing the soil sample to high temperature (50 °C) or to different soil acidity did not influence the degradation rate of the biofilm attached to the plasma-treated wood waste. The two most abundant bacterial distributions at the family level were Xanthomonadaceae and Sphingomonadaceae. To our knowledge, this is the first study that showed the advantages of biofilm attached to plasma-pretreated wood waste for diesel biodegradation in soil. Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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15 pages, 1900 KiB  
Article
Characterization and Transcriptional Regulation of n-Alkane Hydroxylase Gene Cluster of Rhodococcus jostii RHA1
by Namiko Gibu, Daisuke Kasai, Takumi Ikawa, Emiko Akiyama and Masao Fukuda
Microorganisms 2019, 7(11), 479; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7110479 - 23 Oct 2019
Cited by 18 | Viewed by 3822
Abstract
Gram-positive actinomycete Rhodococcus jostii RHA1 is able to grow on C10 to C19 n-alkanes as a sole source of carbon and energy. To clarify, the n-alkane utilization pathway—a cluster of 5 genes (alkBrubA1A2BalkU) which appeared to be involved in [...] Read more.
Gram-positive actinomycete Rhodococcus jostii RHA1 is able to grow on C10 to C19 n-alkanes as a sole source of carbon and energy. To clarify, the n-alkane utilization pathway—a cluster of 5 genes (alkBrubA1A2BalkU) which appeared to be involved in n-alkane degradation—was identified and the transcriptional regulation of these genes was characterized. Reverse transcription-PCR analyses revealed that these genes constituted an operon and were transcribed in the presence of n-alkane. Inactivation of alkB led to the absence of the ability to utilize n-undecane. The alkB mutation resulted in reduction of growth rates on C10 and C12 n-alkanes; however, growths on C13 to C19 n-alkanes were not affected by this mutation. These results suggested that alkB was essential for the utilization of C10 to C12 n-alkanes. Inactivation of alkU showed the constitutive expression of alkB. Purified AlkU is able to bind to the putative promoter region of alkB, suggesting that AlkU played a role in repression of the transcription of alk operon. The results of this study indicated that alkB was involved in the medium-chain n-alkanes degradation of strain RHA1 and the transcription of alk operon was negatively regulated by alkU-encoded regulator. This report is important to understand the n-alkane degradation pathway of R. jostii, including the transcriptional regulation of alk gene cluster. Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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Review

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14 pages, 3328 KiB  
Review
TonB-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation
by Devyani Samantarrai, Annapoorni Lakshman Sagar, Ramurthy Gudla and Dayananda Siddavattam
Microorganisms 2020, 8(3), 359; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8030359 - 03 Mar 2020
Cited by 16 | Viewed by 4489
Abstract
TonB-dependent transport system plays a critical role in the transport of nutrients across the energy-deprived outer membrane of Gram-negative bacteria. It contains a specialized outer membrane TonB-dependent transporter (TBDT) and energy generating (ExbB/ExbD) and transducing (TonB) inner membrane multi-protein complex, called TonB complex. [...] Read more.
TonB-dependent transport system plays a critical role in the transport of nutrients across the energy-deprived outer membrane of Gram-negative bacteria. It contains a specialized outer membrane TonB-dependent transporter (TBDT) and energy generating (ExbB/ExbD) and transducing (TonB) inner membrane multi-protein complex, called TonB complex. Very few TonB complex protein-coding sequences exist in the genomes of Gram-negative bacteria. Interestingly, the TBDT coding alleles are phenomenally high, especially in the genomes of bacteria surviving in complex and stressful environments. Sphingomonads are known to survive in highly polluted environments using rare, recalcitrant, and toxic substances as their sole source of carbon. Naturally, they also contain a huge number of TBDTs in the outer membrane. Out of them, only a few align with the well-characterized TBDTs. The functions of the remaining TBDTs are not known. Predictions made based on genome context and expression pattern suggest their involvement in the transport of xenobiotic compounds across the outer membrane. Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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1 pages, 149 KiB  
Erratum
Erratum: Farber, R.; Rosenberg, A.; Rozenfeld, S.; Banet, G.; Cahan, R. Bioremediation of Artificial Diesel-Contaminated Soil Using Bacterial Consortium Immobilized to Plasma-Pretreated Wood Waste. Microorganisms 2019, 7, 497
by Ravit Farber, Alona Rosenberg, Shmuel Rozenfeld, Gabi Banet and Rivka Cahan
Microorganisms 2019, 7(12), 677; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7120677 - 10 Dec 2019
Cited by 1 | Viewed by 1540
Abstract
The authors wish to make the following erratum in this paper [...] Full article
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
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