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Microorganisms
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Biodegradation and Environmental Microbiomes
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Biodegradation and Environmental Microbiomes

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

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 54939

Special Issue Editors

Prof. Dr. Shuangjiang Liu

E-Mail Website
Guest Editor
1. State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
2. State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, China
Interests: environmental and gut microbiomes; microbial cultivation; microbe-host interaction
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Hongzhi Tang

E-Mail Website
Guest Editor
State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
Interests: environmental microbiology; bioremediation; synthetic biology; biodegradation; biotransformation
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jiandong Jiang

E-Mail Website
Guest Editor
Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
Interests: biodegradation; bioremediation; catabolism; dehalogenation; biotransformation
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Xiaolei Wu

E-Mail Website
Guest Editor
Institute of Ecology, Peking University, Beijing 100871, China
Interests: petroleum degradation; microbial enhanced oil recovery; xenobiotic compound degradation; microbial culture; wastewater treatment
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The Earth is unique, and we human beings rely on its air, water, and land. Industrialization and human activities have improved our daily life at the cost of nature resources and environmental quality. Air pollution, water eutrophication, and land deterioration challenge our sustainable development, and new technologies are needed to address these challenges. Biodegradation and bioremediation are promising technologies that can return humanity to a sustainable development. Microbe, or microbiome (the sum of all microbes in a defined environment) is the main driving force for biodegradation and bioremediation. This Special Issue will cover new understandings of 1) what the nature and degree of air, water, and land pollution are, 2) how pollutants are degraded by natural or engineered microbes/microbiomes, and 3) successful large-scale implementation of biotechnologies for an improved environment. Both research articles and reviews are welcome.

Prof. Dr. Shuang-Jiang Liu
Prof. Dr. Hong-Zhi Tang
Prof. Dr. Jian-Dong Jiang
Prof. Dr. Xiao-Lei Wu
Guest Editors

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
  • bioremediation
  • engineered microbiomes
  • synthetic biology
  • microbial diversity and interaction
  • wastewater
  • polluted soil
  • air pollution

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Published Papers (18 papers)

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Editorial

Jump to: Research, Review

3 pages, 185 KiB  
Editorial
Special Issue “Biodegradation and Environmental Microbiomes”: Editorial
by Shuang-Jiang Liu
Microorganisms 2023, 11(5), 1253; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11051253 - 10 May 2023
Viewed by 908
Abstract
The Earth is unique, and we as human beings rely on its air, water, and land [...] Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)

Research

Jump to: Editorial, Review

14 pages, 2058 KiB  
Article
New Insights into the Effect of Fipronil on the Soil Bacterial Community
by Suzana Eiko Sato Guima, Francine Piubeli, Maricy Raquel Lindenbah Bonfá and Rodrigo Matheus Pereira
Microorganisms 2023, 11(1), 52; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11010052 - 23 Dec 2022
Cited by 3 | Viewed by 2180
Abstract
Fipronil is a broad-spectrum insecticide with remarkable efficacy that is widely used to control insect pests around the world. However, its extensive use has led to increasing soil and water contamination. This fact is of concern and makes it necessary to evaluate the [...] Read more.
Fipronil is a broad-spectrum insecticide with remarkable efficacy that is widely used to control insect pests around the world. However, its extensive use has led to increasing soil and water contamination. This fact is of concern and makes it necessary to evaluate the risk of undesirable effects on non-target microorganisms, such as the microbial community in water and/or soil. Studies using the metagenomic approach to assess the effects of fipronil on soil microbial communities are scarce. In this context, the present study was conducted to identify microorganisms that can biodegrade fipronil and that could be of great environmental interest. For this purpose, the targeted metabarcoding approach was performed in soil microcosms under two environmental conditions: fipronil exposure and control (without fipronil). After a 35-day soil microcosm period, the 16S ribosomal RNA (rRNA) gene of all samples was sequenced using the ion torrent personal genome machine (PGM) platform. Our study showed the presence of Proteobacteria, Actinobacteria, and Firmicutes in all of the samples; however, the presence of fipronil in the soil samples resulted in a significant increase in the concentration of bacteria from these phyla. The statistical results indicate that some bacterial genera benefited from soil exposure to fipronil, as in the case of bacteria from the genus Thalassobacillus, while others were affected, as in the case of bacteria from the genus Streptomyces. Overall, the results of this study provide a potential contribution of fipronil-degrading bacteria. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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14 pages, 3458 KiB  
Article
Degrading Characterization of the Newly Isolated Nocardioides sp. N39 for 3-Amino-5-methyl-isoxazole and the Related Genomic Information
by Lei Yan, Bin Liang, Meng-Yuan Qi, Ai-Jie Wang and Zhi-Pei Liu
Microorganisms 2022, 10(8), 1496; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10081496 - 25 Jul 2022
Cited by 3 | Viewed by 1648
Abstract
3-amino-5-methyl-isoxazole (3A5MI) is a persistent and harmful intermediate in the degradation of antibiotic sulfamethoxazole. It was accumulated in the environments day by day and has caused great environmental risks due to its refractory characteristic. Microbial degradation is economic and environmentally friendly and a [...] Read more.
3-amino-5-methyl-isoxazole (3A5MI) is a persistent and harmful intermediate in the degradation of antibiotic sulfamethoxazole. It was accumulated in the environments day by day and has caused great environmental risks due to its refractory characteristic. Microbial degradation is economic and environmentally friendly and a promising method to eliminate this pollutant. In this study, a bacterial strain, Nocardioides sp. N39, was isolated. N39 can grow on 3A5MI as the sole carbon, nitrogen and energy resource. The effect of different factors on 3A5MI degradation by N39 was explored, including initial 3A5MI concentration, temperature, pH value, dissolved oxygen and additional carbon or nitrogen source. The degradation ability of N39 to various 3A5MI analogs was also explored. Nevertheless, the degrading ability of N39 for 3A5MI is not permanent, and long-term storage would lead to the loss of this ability. This may result from the mobile genetic elements in the bacterium according to the genomic comparison of N39 and its degrading ability-lost strain, N40. Despite this, N39 could support a lot of useful information about the degradation of 3A5MI and highlight the importance of studies about the environmental effects and potential degradation mechanism. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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9 pages, 1460 KiB  
Article
Tire Ground Rubber Biodegradation by a Consortium Isolated from an Aged Tire
by Sarelia M. Castañeda Alejo, Kevin Tejada Meza, María R. Valderrama Valencia, Armando J. Arenazas Rodríguez and Christian J. Málaga Espinoza
Microorganisms 2022, 10(7), 1414; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10071414 - 14 Jul 2022
Cited by 5 | Viewed by 2766
Abstract
Rubber is a natural product, the main car tire component. Due to the characteristics acquired by this material after its vulcanization process, its degradation under natural conditions requires very long times, causing several environmental problems. In the present work, the existence of a [...] Read more.
Rubber is a natural product, the main car tire component. Due to the characteristics acquired by this material after its vulcanization process, its degradation under natural conditions requires very long times, causing several environmental problems. In the present work, the existence of a bacterial consortium isolated from a discarded tire found within the Socabaya River with the ability to degrade shredded tire rubber without any chemical pretreatment is explored. Taking into consideration the complex chemical composition of a rubber tire and the described benefits of the use of pretreatments, the study is developed as a preliminary analysis. The augmentative growth technique was used, and the level of degradation was quantified as a percentage through the analysis of microbial respiration. Schiff’s test and the use of comparative photographs of scanning electron microscopy (SEM) were also used. The consortium using next generation genetic sequencing was analyzed. A 4.94% degradation point was obtained after 20 days of experimentation, and it was found that the consortium was mostly made up with Delftia tsuruhatensis with 69.12% of the total genetic readings of the consortium and the existence of 15% of unidentified microbial strains at the genre level. The role played by the organisms in the degradation process is unknown. However, the positive results in the tests carried out show that the consortium had action on the shredded tire, showing a mineralization process. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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13 pages, 3830 KiB  
Article
Sphingomonas Relies on Chemotaxis to Degrade Polycyclic Aromatic Hydrocarbons and Maintain Dominance in Coking Sites
by Meng Zhou, Zishu Liu, Jiaqi Wang, Yuxiang Zhao and Baolan Hu
Microorganisms 2022, 10(6), 1109; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10061109 - 27 May 2022
Cited by 15 | Viewed by 1985
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are organic pollutants widely present in industrial sites. Microbial degradation is an effective method of removing PAHs. The identification of microorganisms that have important ecological functions at the site is of great significance for PAH removal. We collected soil [...] Read more.
Polycyclic aromatic hydrocarbons (PAHs) are organic pollutants widely present in industrial sites. Microbial degradation is an effective method of removing PAHs. The identification of microorganisms that have important ecological functions at the site is of great significance for PAH removal. We collected soil samples at three depths in the range of 0–100 cm at 70-day intervals at the coking site and explored the degradation of PAHs. We combined molecular ecology networking, metagenomics, and genome assembly to search for microorganisms that persist, dominate, and affect the microbial community construction in the degradation process and analyzed their adaptation strategies. The results showed that 15.78 mg/kg of PAHs naturally decayed, and 13.33 mg/kg of PAHs migrated from 30–100 cm to 0–30 cm in the soil. Sphingomonas, which occupied a niche advantage, was both the core and keystone microorganism, and its spatial distribution pattern and temporal change dynamics were consistent with those of PAHs. We assembled the genome of Sphingomonas sp., revealing its multiple potential for degrading PAHs and other pollutants. Additionally, flagellar assembly and bacterial chemotaxis genes ranked high in the assembled genome of Sphingomonas sp., which might help it obtain a competitive advantage in the soil. The findings underscored the strategy of Sphingomonas to maintain dominance, enriched the understanding of PAH-degrading microorganisms in site soil, and provided references for the remediation of PAHs. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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10 pages, 2265 KiB  
Article
Biodegradation of Quinoline by a Newly Isolated Salt-Tolerating Bacterium Rhodococcus gordoniae Strain JH145
by Yinhu Jiang, Fuyin Zhang, Siqiong Xu, Pan Yang, Xiao Wang, Xuan Zhang, Qing Hong, Jiguo Qiu, Cuiwei Chu and Jian He
Microorganisms 2022, 10(4), 797; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10040797 - 09 Apr 2022
Cited by 6 | Viewed by 1642
Abstract
Quinoline is a typical nitrogen-heterocyclic compound with high toxicity and carcinogenicity which exists ubiquitously in industrial wastewater. In this study, a new quinoline-degrading bacterial strain Rhodococcus sp. JH145 was isolated from oil-contaminated soil. Strain JH145 could grow with quinoline as the sole carbon [...] Read more.
Quinoline is a typical nitrogen-heterocyclic compound with high toxicity and carcinogenicity which exists ubiquitously in industrial wastewater. In this study, a new quinoline-degrading bacterial strain Rhodococcus sp. JH145 was isolated from oil-contaminated soil. Strain JH145 could grow with quinoline as the sole carbon source. The optimum growth temperature, pH, and salt concentration were 30 °C, 8.0, and 1%, respectively. 100 mg/L quinoline could be completely removed within 28 h. Particularly, strain JH145 showed excellent quinoline biodegradation ability under a high-salt concentration of 7.5%. Two different quinoline degradation pathways, a typical 8-hydroxycoumarin pathway, and a unique anthranilate pathway were proposed based on the intermediates identified by liquid chromatography–time of flight mass spectrometry. Our present results provided new candidates for industrial application in quinoline-contaminated wastewater treatment even under high-salt conditions. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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17 pages, 3354 KiB  
Article
Dynamic Microstructure Assembly Driven by Lysinibacillus sp. LF-N1 and Penicillium oxalicum DH-1 Inoculants Corresponds to Composting Performance
by Haiyan Duan, Cong Fu, Guilin Du, Shiqiu Xie, Min Liu, Baoguo Zhang, Jiping Shi and Junsong Sun
Microorganisms 2022, 10(4), 709; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10040709 - 25 Mar 2022
Cited by 5 | Viewed by 1643
Abstract
The effects of Lysinibacillus sp. LF-N1 and Penicillium oxalicum DH-1 inoculants (LFPO group) on compost succession and the microbial dynamic structure of co-composting wheat straw and cow manure composting were investigated. The inoculants contributed to longer thermophilic stages, higher temperatures (62.8 °C) and [...] Read more.
The effects of Lysinibacillus sp. LF-N1 and Penicillium oxalicum DH-1 inoculants (LFPO group) on compost succession and the microbial dynamic structure of co-composting wheat straw and cow manure composting were investigated. The inoculants contributed to longer thermophilic stages, higher temperatures (62.8 °C) and lower microbial diversity in the LFPO treatment compared to the control group (CK). Moreover, LFPO inoculation increased the germination index and accelerated organic matter and lignocellulose degradation in the compost. Microbial analysis confirmed that the inoculants effectively altered the microbial communities. The predominant biomarkers for bacteria and fungi in inoculated compost were members of Lysinibacillus and Penicillium, respectively. Functional prediction showed greater lignocellulose degradation and less pathogen accumulation in the LFPO group. The cooccurrence network analysis showed that the network structure in LFPO compost was greatly simplified compared to that in CK. Bacterial cluster A was dominated by Lysinibacillus, and fungal cluster B was represented by Penicillium, which were significantly correlated with temperature and lignocellulose degradation, respectively (p < 0.05). These results demonstrated that the LF-N1 and DH-1 inoculants drove the bacterial and fungal assemblies to induce physicochemical property changes during cocomposting. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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15 pages, 2114 KiB  
Article
Harnessing Paenarthrobacter ureafaciens YL1 and Pseudomonas koreensis YL2 Interactions to Improve Degradation of Sulfamethoxazole
by Lan Yu, Yingning Wang, Xiaoqing Shan, Fang Ma and Haijuan Guo
Microorganisms 2022, 10(3), 648; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10030648 - 18 Mar 2022
Cited by 9 | Viewed by 2131
Abstract
Sulfamethoxazole (SMX) is a widespread and persistent pollutant in the environment. Although the screening and analysis of SMX-degrading bacteria have been documented, the interaction mechanisms of functional microorganisms are still poorly understood. This study constructed a consortium with strain YL1 and YL2 supplied [...] Read more.
Sulfamethoxazole (SMX) is a widespread and persistent pollutant in the environment. Although the screening and analysis of SMX-degrading bacteria have been documented, the interaction mechanisms of functional microorganisms are still poorly understood. This study constructed a consortium with strain YL1 and YL2 supplied with SMX as the sole carbon and energy source. The coexisting mechanism and the removal of SMX of the consortium were investigated. The total oxidizable carbon (TOC) removal rate of the combined bacterial system was 38.94% compared to 29.45% for the single bacterial system at the same biomass. The mixed bacterial consortium was able to resist SMX at concentrations up to 400 mg/L and maintained a stable microbial structure at different culture conditions. The optimum conditions found for SMX degradation were 30 °C, pH 7.0, a shaking speed of 160 r·min−1, and an initial SMX concentration of 200 mg·L−1. The degradation of SMX was accelerated by the addition of YL2 for its ability to metabolize the key intermediate, 4-aminophenol. The removal rate of 4-aminophenol by strain YL2 reached 19.54% after 5 days. Genome analysis revealed that adding riboflavin and enhancing the reducing capacity might contribute to the degradation of SMX. These results indicated that it is important for the bioremediation of antibiotic-contaminated aquatic systems to understand the metabolism of bacterial communities. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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12 pages, 2992 KiB  
Article
Biodegradation of Tetracycline Antibiotics by the Yeast Strain Cutaneotrichosporon dermatis M503
by Hao Tan, Delong Kong, Qingyun Ma, Qingqing Li, Yiqing Zhou, Xu Jiang, Zhiye Wang, Rebecca E. Parales and Zhiyong Ruan
Microorganisms 2022, 10(3), 565; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10030565 - 05 Mar 2022
Cited by 9 | Viewed by 2378
Abstract
In this study, the Cutaneotrichosporon dermatis strain M503 was isolated and could efficiently degrade tetracycline, doxycycline, and chlorotetracyline. The characteristics of tetracycline degradation were investigated under a broad range of cultural conditions. Response surface methodology (RSM) predicted that the highest degradation rate of [...] Read more.
In this study, the Cutaneotrichosporon dermatis strain M503 was isolated and could efficiently degrade tetracycline, doxycycline, and chlorotetracyline. The characteristics of tetracycline degradation were investigated under a broad range of cultural conditions. Response surface methodology (RSM) predicted that the highest degradation rate of tetracycline could be obtained under the following conditions: 39.69 °C, pH of 8.79, and inoculum dose of 4.0% (v/v, ~3.5 × 106 cells/mL in the medium). In accordance with the five identified degradation products of tetracycline, two putative degradation pathways, which included the shedding of methyl and amino groups, were proposed. Moreover, the well diffusion method showed that the strain of M503 decreases the antibacterial potency of tetracycline, doxycycline, and chlorotetracycline. These findings proposed a putative mechanism of tetracycline degradation by a fungus strain and contributed to the estimation of the fate of tetracycline in the aquatic environment. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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14 pages, 2314 KiB  
Article
The Leaf Microbiome of Tobacco Plants across Eight Chinese Provinces
by Haiyang Hu, Yunli Liu, Yiqun Huang, Zhan Zhang and Hongzhi Tang
Microorganisms 2022, 10(2), 450; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020450 - 16 Feb 2022
Cited by 7 | Viewed by 2690
Abstract
Leaf microorganism communities play significant roles in the process of plant growth, but the microbiome profiling of crop leaves is still a relatively new research area. Here, we used 16S rDNA sequencing to profile the microbiomes of 78 primary dried tobacco leaf samples [...] Read more.
Leaf microorganism communities play significant roles in the process of plant growth, but the microbiome profiling of crop leaves is still a relatively new research area. Here, we used 16S rDNA sequencing to profile the microbiomes of 78 primary dried tobacco leaf samples from 26 locations in eight Chinese provinces. Our analyses revealed that the national leaf microbial communities contain 4473 operational taxonomic units (OTU) representing 1234 species, but there is a small, national core microbiome with only 14 OTU representing nine species. The function of this core microbiome is related to processes including nitrogen fixation, detoxification of diverse pollutants, and heavy-metal reduction. The leaf microorganism communities are obviously affected by local environments but did not exhibit obvious relationships to single ecological factors (e.g., temperature, precipitation). Our findings enhance the understanding of microbial diversity of tobacco leaves, which could be utilized for a variety of bioprocess, agricultural, and environmental detoxification applications. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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12 pages, 1582 KiB  
Article
Biological Nitrogen Removal Database: A Manually Curated Data Resource
by Tanyaradzwa R. Ngara, Peiji Zeng and Houjin Zhang
Microorganisms 2022, 10(2), 431; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020431 - 12 Feb 2022
Cited by 3 | Viewed by 1828
Abstract
Biological nitrogen removal (BNR) technologies are the most effective approaches for the remediation of environmental nitrogen pollutants from wastewater treatment plants (WWTPs). Presently, research is going on to elucidate the structure and function of BNR microbial communities and optimizing BNR treatment systems to [...] Read more.
Biological nitrogen removal (BNR) technologies are the most effective approaches for the remediation of environmental nitrogen pollutants from wastewater treatment plants (WWTPs). Presently, research is going on to elucidate the structure and function of BNR microbial communities and optimizing BNR treatment systems to enhance nitrogen removal efficiency. The literature on BNR microbial communities and experimental datasets is not unified across various repositories, while a uniform resource for the collection, annotation, and structuring of these BNR datasets is still unavailable. Herein, we present the Biological Nitrogen Removal Database (BNRdb), an integrated resource containing various manually curated BNR-related data. At present, BNRdb contains 23,308 microbial strains, 46 gene families, 24 enzymes, 18 reactions, 301 BNR treatment datasets, 860 BNR-associated next-generation sequencing datasets, and 6 common BNR bioreactor systems. BNRdb provides a user-friendly interface enabling interactive data browsing. To our knowledge, BNRdb is the first BNR data resource that systematically integrates BNR data from archaeal, bacterial, and fungal communities. We believe that BNRdb will contribute to a better understanding of BNR process and nitrogen bioremediation research. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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16 pages, 3451 KiB  
Article
Degradation of Decabromodiphenyl Ether in an Aerobic Clay Slurry Microcosm Using a Novel Immobilization Technique
by Jung-Shan Hsu, Ting-Yu Yu, Da-Jiun Wei, Wann-Neng Jane and Yi-Tang Chang
Microorganisms 2022, 10(2), 402; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020402 - 09 Feb 2022
Cited by 8 | Viewed by 2008
Abstract
A novel chitosan immobilization technique that entraps photocatalyst and microbes was developed and applied to decompose decabromodiphenyl ether (BDE-209) in a clay slurry microcosm. The optimized conditions for immobilization were obtained by mixing 1.2% (w/v) chitosan dissolved in 1% [...] Read more.
A novel chitosan immobilization technique that entraps photocatalyst and microbes was developed and applied to decompose decabromodiphenyl ether (BDE-209) in a clay slurry microcosm. The optimized conditions for immobilization were obtained by mixing 1.2% (w/v) chitosan dissolved in 1% (v/v) acetic acid with nano-TiO2 particles and the BDE-209-degrading bacterial mixed culture. This aqueous mixture was injected into 1% (w/v) water solution containing sodium tripolyphosphate to form spherical immobilized beads. The surface of the immobilized beads was reinforced by 0.25% (v/v) glutaraldehyde cross-linking. These beads had enough mechanical strength during BDE-209 degradation to maintain their shape in the system at a stirring rate of 200-rpm, while undergoing continuous 365 nm UVA irradiation. This novel TiO2-Yi-Li immobilized chitosan beads system allowed a successful simultaneous integration of photolysis, photocatalysis and biodegradation to remove BDE-209. The remaining percentage of BDE-209 was 41% after 70 days of degradation using this system. The dominant bacteria in the BDE-209-degrading bacterial mixed culture during remediation were Chitinophaga spp., Methyloversatilis spp., Terrimonas spp. and Pseudomonas spp. These bacteria tolerated the long-term UVA irradiation and high-level free radicals present, while utilizing BDE-209 as their primary carbon resource. This new method has great potential for the treatment of a range of pollutants. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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16 pages, 1956 KiB  
Article
The Response Regulator FlmD Regulates Biofilm Formation in Comamonas testosteroni through the Transcriptional Activator SoxR
by Yunhao Wang, Zhou Huang, Nan Zhou, Chang Liu, Chengying Jiang, Defeng Li and Shuangjiang Liu
Microorganisms 2022, 10(2), 356; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020356 - 04 Feb 2022
Cited by 1 | Viewed by 2069
Abstract
Biofilm formation is a survival strategy by which microorganisms adapt to environmental challenges. It is regulated by various signals, such as the second messenger c-di-GMP. We previously found that the Flm chemosensory pathway could respond to chemical signals and regulate biofilm formation. [...] Read more.
Biofilm formation is a survival strategy by which microorganisms adapt to environmental challenges. It is regulated by various signals, such as the second messenger c-di-GMP. We previously found that the Flm chemosensory pathway could respond to chemical signals and regulate biofilm formation. This regulation is independent of c-di-GMP. A previous study revealed that the response regulator FlmD is involved in biofilm formation; however, how chemical signals are transmitted downstream of FlmD remained unclear. In the present study, transcriptome analysis and gel shift assay reveal that SoxR, a transcriptional activator of the efflux transporter acrAB-tolC operon, mediates the downstream signaling of FlmD. Phosphorylated FlmD interacts with SoxR and disrupts the interaction between SoxR and the acrAB-tolC operon. It causes a decrease in the expression of acrAB-tolC operon. The downregulation of acrA, acrB, or tolC gene expression results in making less biofilm formation. In conclusion, we identified that the transcription regulator SoxR plays a role in the c-di-GMP independent regulation of biofilm formation in Comamonas testosteroni. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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14 pages, 2493 KiB  
Article
The Odor Release Regularity of Livestock and Poultry Manure and the Screening of Deodorizing Strains
by Haixia Ma, Feier Li, Evode Niyitanga, Xicun Chai, Shipeng Wang and Yutao Liu
Microorganisms 2021, 9(12), 2488; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9122488 - 30 Nov 2021
Cited by 9 | Viewed by 3426
Abstract
Human living environments and health are seriously affected by the odor produced from fermentation of livestock and poultry manure. In order to reduce the odor pollution caused by livestock and poultry manure, efficient strains were screened and two methods were tried in this [...] Read more.
Human living environments and health are seriously affected by the odor produced from fermentation of livestock and poultry manure. In order to reduce the odor pollution caused by livestock and poultry manure, efficient strains were screened and two methods were tried in this study. The orthogonal test design was used to analyze the gas produced by pig manure under different conditions of temperature, time, wheat straw doping amount and calcium carbonate doping amount. Then, according to ammonia, hydrogen sulfide and comprehensive odor removal effects, the high efficiency of deodorizing strains were screened. The results showed that pig manure produced the least odor when the temperature was 20 °C, added 0% calcium carbonate, 20% wheat straw and waited for 48 h. Three strains were screened to inhibit the odor production of pig manure: Paracoccus denitrificans, Bacillus licheniformis and Saccharomyces cerevisiae, showed that their highest removal rate of ammonia and hydrogen sulfide gas could reach 96.58% and 99.74% among them; while for three strains of end-control pig manure stench: Pichia kudriavzevii, P. denitrificans and Bacillus subtilis, the highest removal rate of ammonia and hydrogen sulfide gas reached 85.91% and 90.80% among them. This research provides bacteria resources as the high-efficiency deodorizing function for the source suppression and the end treatment of the odor gas of pig manure, which has high application value for the control of odor pollution. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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18 pages, 1685 KiB  
Article
Exploration of Microalgal Species for Nutrient Removal from Anaerobically Digested Swine Wastewater and Potential Lipids Production
by Zhihui Chen, Yunhua Xiao, Tan Liu, Mingmin Yuan, Gang Liu, Jun Fang and Bo Yang
Microorganisms 2021, 9(12), 2469; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9122469 - 30 Nov 2021
Cited by 17 | Viewed by 2110
Abstract
Bio-treatment of anaerobically treated swine wastewater (ADSW) mediated by microalgae has been deemed as a promising strategy. In the present study, six microalgal strains were used to conduct batch experiments in 0~100% ADSW in order to evaluate their potentials for nutrient removal and [...] Read more.
Bio-treatment of anaerobically treated swine wastewater (ADSW) mediated by microalgae has been deemed as a promising strategy. In the present study, six microalgal strains were used to conduct batch experiments in 0~100% ADSW in order to evaluate their potentials for nutrient removal and biodiesel production. Two strains, Chlorella vulgaris FACHB-8 and Chlorella sp. FACHB-31, were selected based on their better growth performances, higher tolerance to wastewater (up to 100%), and better nutrient removal abilities. The capacity of each strain to remove TN, TP, NH4+-N, as well as lipid production and biomass composition in 100% ADSW were further examined. After 15 days of culture, 87.68~89.85%, 92.61~93.68%, and 97.02~97.86% of the nitrogen, phosphorus, and ammonia nitrogen were removed by Chlorella sp. FACHB-31 and C. vulgaris FACHB-8. Their lipid content and lipid productivities were 29.63~33.33% and 18.91~23.10 mg L−1 d−1, respectively. Proteins were both the major biomass fraction followed by lipids and then carbohydrates. Their fatty acid profiles both mainly consisted of C-16:0, C-18:1, C-18:0, and C-18:2. Taken together, our results suggest that C. vulgaris FACHB-8 and Chlorella sp. FACHB-31 are potential candidates for biodiesel production by using ADSW as a good feedstock. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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Review

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16 pages, 1318 KiB  
Review
Current Advances in Biodegradation of Polyolefins
by Ni Zhang, Mingzhu Ding and Yingjin Yuan
Microorganisms 2022, 10(8), 1537; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10081537 - 29 Jul 2022
Cited by 16 | Viewed by 3938
Abstract
Polyolefins, including polyethylene (PE), polypropylene (PP) and polystyrene (PS), are widely used plastics in our daily life. The excessive use of plastics and improper handling methods cause considerable pollution in the environment, as well as waste of energy. The biodegradation of polyolefins seems [...] Read more.
Polyolefins, including polyethylene (PE), polypropylene (PP) and polystyrene (PS), are widely used plastics in our daily life. The excessive use of plastics and improper handling methods cause considerable pollution in the environment, as well as waste of energy. The biodegradation of polyolefins seems to be an environmentally friendly and low-energy consumption method for plastics degradation. Many strains that could degrade polyolefins have been isolated from the environment. Some enzymes have also been identified with the function of polyolefin degradation. With the development of synthetic biology and metabolic engineering strategies, engineered strains could be used to degrade plastics. This review summarizes the current advances in polyolefin degradation, including isolated and engineered strains, enzymes and related pathways. Furthermore, a novel strategy for polyolefin degradation by artificial microbial consortia is proposed, which would be helpful for the efficient degradation of polyolefin. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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20 pages, 806 KiB  
Review
Microbial Consortia Are Needed to Degrade Soil Pollutants
by Ting Zhang and Houjin Zhang
Microorganisms 2022, 10(2), 261; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020261 - 24 Jan 2022
Cited by 33 | Viewed by 6490
Abstract
Soil pollution is one of the most serious environmental problems globally due to the weak self-purification ability, long degradation time, and high cost of cleaning soil pollution. The pollutants in the soil can be transported into the human body through water or dust, [...] Read more.
Soil pollution is one of the most serious environmental problems globally due to the weak self-purification ability, long degradation time, and high cost of cleaning soil pollution. The pollutants in the soil can be transported into the human body through water or dust, causing adverse effects on human health. The latest research has shown that the clean-up of soil pollutants through microbial consortium is a very promising method. This review provides an in-depth discussion on the efficient removal, bio-adsorption, or carbonated precipitation of organic and inorganic pollutants by the microbial consortium, including PAHs, BPS, BPF, crude oil, pyrene, DBP, DOP, TPHP, PHs, butane, DON, TC, Mn, and Cd. In view of the good degradation ability of the consortium compared to single strains, six different synergistic mechanisms and corresponding microorganisms are summarized. The microbial consortium obtains such activities through enhancing synergistic degradation, reducing the accumulation of intermediate products, generating the crude enzyme, and self-regulating, etc. Furthermore, the degradation efficiency of pollutants can be greatly improved by adding chemical materials such as the surfactants Tween 20, Tween 80, and SDS. This review provides insightful information regarding the application of microbial consortia for soil pollutant removal. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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25 pages, 1671 KiB  
Review
Current Advances in the Biodegradation and Bioconversion of Polyethylene Terephthalate
by Xinhua Qi, Wenlong Yan, Zhibei Cao, Mingzhu Ding and Yingjin Yuan
Microorganisms 2022, 10(1), 39; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010039 - 26 Dec 2021
Cited by 32 | Viewed by 9853
Abstract
Polyethylene terephthalate (PET) is a widely used plastic that is polymerized by terephthalic acid (TPA) and ethylene glycol (EG). In recent years, PET biodegradation and bioconversion have become important in solving environmental plastic pollution. More and more PET hydrolases have been discovered and [...] Read more.
Polyethylene terephthalate (PET) is a widely used plastic that is polymerized by terephthalic acid (TPA) and ethylene glycol (EG). In recent years, PET biodegradation and bioconversion have become important in solving environmental plastic pollution. More and more PET hydrolases have been discovered and modified, which mainly act on and degrade the ester bond of PET. The monomers, TPA and EG, can be further utilized by microorganisms, entering the tricarboxylic acid cycle (TCA cycle) or being converted into high value chemicals, and finally realizing the biodegradation and bioconversion of PET. Based on synthetic biology and metabolic engineering strategies, this review summarizes the current advances in the modified PET hydrolases, engineered microbial chassis in degrading PET, bioconversion pathways of PET monomers, and artificial microbial consortia in PET biodegradation and bioconversion. Artificial microbial consortium provides novel ideas for the biodegradation and bioconversion of PET or other complex polymers. It is helpful to realize the one-step bioconversion of PET into high value chemicals. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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