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Microorganisms
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Biodegradation and Environmental Microbiomes
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Biodegradation and Environmental Microbiomes

A topical collection in Microorganisms (ISSN 2076-2607). This collection belongs to the section "Environmental Microbiology".

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Editors

Prof. Dr. Hongzhi Tang

E-Mail Website
Collection 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
Collection 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
Collection 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

Topical Collection Information

Dear Colleagues,

This Topic Collection is the continuation of our previous Special Issue "Biodegradation and Environmental Microbiomes".

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 Topic Collection 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. Hongzhi Tang
Prof. Dr. Jiandong Jiang
Prof. Dr. Xiaolei Wu
Collection Editors

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Related Special Issue

Published Papers (9 papers)

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2024

Jump to: 2023, 2022

16 pages, 5888 KiB  
Article
Development and Characterization of Ammonia Removal Moving Bed Biofilms for Landfill Leachate Treatment
by Rossana Petrilli, Attilio Fabbretti, Kathleen Pucci, Graziella Pagliaretta, Valerio Napolioni and Maurizio Falconi
Microorganisms 2024, 12(12), 2404; https://doi.org/10.3390/microorganisms12122404 (registering DOI) - 23 Nov 2024
Viewed by 211
Abstract
Urbanization growth has intensified the challenge of managing and treating increasing amounts of municipal solid waste (MSW). Landfills are commonly utilized for MSW disposal because of their low construction and operation costs. However, this practice produces huge volumes of landfill leachate, a highly [...] Read more.
Urbanization growth has intensified the challenge of managing and treating increasing amounts of municipal solid waste (MSW). Landfills are commonly utilized for MSW disposal because of their low construction and operation costs. However, this practice produces huge volumes of landfill leachate, a highly polluting liquid rich in ammoniacal nitrogen (NH3-N), organic compounds, and various heavy metals, making it difficult to treat in conventional municipal wastewater treatment plants (WWTPs). In recent years, research has shown that microbial biofilms, developed on carriers of different materials and called “moving bed biofilm reactors” (MBBRs), may offer promising solutions for bioremediation. This study explored the biofilm development and the nitrification process of moving bed biofilms (MBBs) obtained from high ammonia-selected microbial communities. Using crystal violet staining and confocal laser-scanning microscopy, we followed the biofilm formation stages correlating nitrogen removal to metagenomic analyses. Our results indicate that MBBs unveiled a 10-fold more enhanced nitrification rate than the dispersed microbial community present in the native sludge of the Porto Sant’Elpidio (Italy) WWTP. Four bacterial families, Chitinophagaceae, Comamonadaceae, Sphingomonadaceae, and Nitrosomonadaceae, accumulate in structured biofilms and significantly contribute to the high ammonium removal rate of 80% in 24 h as estimated in leachate-containing wastewaters. Full article
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17 pages, 3284 KiB  
Article
Different Roles of Dioxin-Catabolic Plasmids in Growth, Biofilm Formation, and Metabolism of Rhodococcus sp. Strain p52
by Xu Wang, Yanan Wu, Meng Chen, Changai Fu, Hangzhou Xu and Li Li
Microorganisms 2024, 12(8), 1700; https://doi.org/10.3390/microorganisms12081700 - 17 Aug 2024
Viewed by 846
Abstract
Microorganisms harbor catabolic plasmids to tackle refractory organic pollutants, which is crucial for bioremediation and ecosystem health. Understanding the impacts of plasmids on hosts provides insights into the behavior and adaptation of degrading bacteria in the environment. Here, we examined alterations in the [...] Read more.
Microorganisms harbor catabolic plasmids to tackle refractory organic pollutants, which is crucial for bioremediation and ecosystem health. Understanding the impacts of plasmids on hosts provides insights into the behavior and adaptation of degrading bacteria in the environment. Here, we examined alterations in the physiological properties and gene expression profiles of Rhodococcus sp. strain p52 after losing two conjugative dioxin-catabolic megaplasmids (pDF01 and pDF02). The growth of strain p52 accelerated after pDF01 loss, while it decelerated after pDF02 loss. During dibenzofuran degradation, the expression levels of dibenzofuran catabolic genes on pDF01 were higher compared to those on pDF02; accordingly, pDF01 loss markedly slowed dibenzofuran degradation. It was suggested that pDF01 is more beneficial to strain p52 under dibenzofuran exposure. Moreover, plasmid loss decreased biofilm formation, especially after pDF02 loss. Transcriptome profiling revealed different pathways enriched in upregulated and downregulated genes after pDF01 and pDF02 loss, indicating different adaptation mechanisms. Based on the transcriptional activity variation, pDF01 played roles in transcription and anabolic processes, while pDF02 profoundly influenced energy production and cellular defense. This study enhances our knowledge of the impacts of degradative plasmids on native hosts and the adaptation mechanisms of hosts, contributing to the application of plasmid-mediated bioremediation in contaminated environments. Full article
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13 pages, 3189 KiB  
Article
The Phylogeny and Metabolic Potentials of a Lignocellulosic Material-Degrading Aliiglaciecola Bacterium Isolated from Intertidal Seawater in East China Sea
by Hongcai Zhang, Zekai Wang, Xi Yu, Junwei Cao, Tianqiang Bao, Jie Liu, Chengwen Sun, Jiahua Wang and Jiasong Fang
Microorganisms 2024, 12(1), 144; https://doi.org/10.3390/microorganisms12010144 - 11 Jan 2024
Cited by 4 | Viewed by 1512
Abstract
Lignocellulosic materials are composed of cellulose, hemicellulose and lignin and are one of the most abundant biopolymers in marine environments. The extent of the involvement of marine microorganisms in lignin degradation and their contribution to the oceanic carbon cycle remains elusive. In this [...] Read more.
Lignocellulosic materials are composed of cellulose, hemicellulose and lignin and are one of the most abundant biopolymers in marine environments. The extent of the involvement of marine microorganisms in lignin degradation and their contribution to the oceanic carbon cycle remains elusive. In this study, a novel lignin-degrading bacterial strain, LCG003, was isolated from intertidal seawater in Lu Chao Harbor, East China Sea. Phylogenetically, strain LCG003 was affiliated with the genus Aliiglaciecola within the family Alteromonadaceae. Metabolically, strain LCG003 contains various extracellular (signal-fused) glycoside hydrolase genes and carbohydrate transporter genes and can grow with various carbohydrates as the sole carbon source, including glucose, fructose, sucrose, rhamnose, maltose, stachyose and cellulose. Moreover, strain LCG003 contains many genes of amino acid and oligopeptide transporters and extracellular peptidases and can grow with peptone as the sole carbon and nitrogen source, indicating a proteolytic lifestyle. Notably, strain LCG003 contains a gene of dyp-type peroxidase and strain-specific genes involved in the degradation of 4-hydroxy-benzoate and vanillate. We further confirmed that it can decolorize aniline blue and grow with lignin as the sole carbon source. Our results indicate that the Aliiglaciecola species can depolymerize and mineralize lignocellulosic materials and potentially play an important role in the marine carbon cycle. Full article
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2023

Jump to: 2024, 2022

19 pages, 6832 KiB  
Article
Microbiological Characterization of the Biofilms Colonizing Bioplastics in Natural Marine Conditions: A Comparison between PHBV and PLA
by Anna Marín, Patricia Feijoo, Rosa de Llanos, Belén Carbonetto, Pedro González-Torres, José Tena-Medialdea, José R. García-March, José Gámez-Pérez and Luis Cabedo
Microorganisms 2023, 11(6), 1461; https://doi.org/10.3390/microorganisms11061461 - 31 May 2023
Cited by 8 | Viewed by 3011
Abstract
Biodegradable polymers offer a potential solution to marine pollution caused by plastic waste. The marine biofilms that formed on the surfaces of poly(lactide acid) (PLA) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) were studied. Bioplastics were exposed for 6 months to marine conditions in the Mediterranean Sea, [...] Read more.
Biodegradable polymers offer a potential solution to marine pollution caused by plastic waste. The marine biofilms that formed on the surfaces of poly(lactide acid) (PLA) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) were studied. Bioplastics were exposed for 6 months to marine conditions in the Mediterranean Sea, and the biofilms that formed on their surfaces were assessed. The presence of specific PLA and PHBV degraders was also studied. PHBV showed extensive areas with microbial accumulations and this led to higher microbial surface densities than PLA (4.75 vs. 5.16 log CFU/cm2). Both polymers’ surfaces showed a wide variety of microbial structures, including bacteria, fungi, unicellular algae and choanoflagellates. A high bacterial diversity was observed, with differences between the two polymers, particularly at the phylum level, with over 70% of bacteria affiliated to three phyla. Differences in metagenome functions were also detected, revealing a higher presence of proteins involved in PHBV biodegradation in PHBV biofilms. Four bacterial isolates belonging to the Proteobacteria class were identified as PHBV degraders, demonstrating the presence of species involved in the biodegradation of this polymer in seawater. No PLA degraders were detected, confirming its low biodegradability in marine environments. This was a pilot study to establish a baseline for further studies aimed at comprehending the marine biodegradation of biopolymers. Full article
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11 pages, 1677 KiB  
Article
Expression and Characterization of 3,6-Dihydroxy-picolinic Acid Decarboxylase PicC of Bordetella bronchiseptica RB50
by Cansheng Yuan, Lingling Zhao, Lu Tong, Lin Wang, Zhuang Ke, Ying Yang and Jian He
Microorganisms 2023, 11(4), 854; https://doi.org/10.3390/microorganisms11040854 - 27 Mar 2023
Cited by 1 | Viewed by 1582
Abstract
Picolinic acid (PA) is a typical mono-carboxylated pyridine derivative produced by human/animals or microorganisms which could be served as nutrients for bacteria. Most Bordetella strains are pathogens causing pertussis or respiratory disease in humans and/or various animals. Previous studies indicated that Bordetella strains [...] Read more.
Picolinic acid (PA) is a typical mono-carboxylated pyridine derivative produced by human/animals or microorganisms which could be served as nutrients for bacteria. Most Bordetella strains are pathogens causing pertussis or respiratory disease in humans and/or various animals. Previous studies indicated that Bordetella strains harbor the PA degradation pic gene cluster. However, the degradation of PA by Bordetella strains remains unknown. In this study, a reference strain of genus Bordetella, B. bronchiseptica RB50, was investigated. The organization of pic gene cluster of strain RB50 was found to be similar with that of Alcaligenes faecalis, in which the sequence similarities of each Pic proteins are between 60% to 80% except for PicB2 (47% similarity). The 3,6-dihydroxypicolinic acid (3,6DHPA) decarboxylase gene (BB0271, designated as picCRB50) of strain RB50 was synthesized and over-expressed in E. coli BL21(DE3). The PicCRB50 showed 75% amino acid similarities against known PicC from Alcaligenes faecalis. The purified PicCRB50 can efficiently transform 3,6DHPA to 2,5-dihydroxypyridine. The PicCRB50 exhibits optimal activities at pH 7.0, 35 °C, and the Km and kcat values of PicCRB50 for 3,6DHPA were 20.41 ± 2.60 μM and 7.61 ± 0.53 S−1, respectively. The present study provided new insights into the biodegradation of PA by pathogens of Bordetella spp. Full article
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19 pages, 4647 KiB  
Article
Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome
by Nazima Habibi, Saif Uddin, Hanan Al-Sarawi, Ahmed Aldhameer, Anisha Shajan, Farhana Zakir, Nasreem Abdul Razzack and Faiz Alam
Microorganisms 2023, 11(2), 531; https://doi.org/10.3390/microorganisms11020531 - 20 Feb 2023
Cited by 13 | Viewed by 3979
Abstract
Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting [...] Read more.
Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were Woeseia, Nitrosopumilus, and Rhizophagus, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA p > 0.05; ANOSIM-0.05, p > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs. Full article
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15 pages, 3416 KiB  
Article
Biodegradation of Oil by a Newly Isolated Strain Acinetobacter junii WCO-9 and Its Comparative Pan-Genome Analysis
by Shijie Jiang, Qingfeng Fan, Zeying Zhang, Yunfeng Deng, Lihong Wang, Qilin Dai, Jin Wang, Min Lin, Jian Zhou, Zhijian Long, Guiqiang He and Zhengfu Zhou
Microorganisms 2023, 11(2), 407; https://doi.org/10.3390/microorganisms11020407 - 6 Feb 2023
Cited by 4 | Viewed by 2334
Abstract
Waste oil pollution and the treatment of oily waste present a challenge, and the exploitation of microbial resources is a safe and efficient method to resolve these problems. Lipase-producing microorganisms can directly degrade waste oil and promote the degradation of oily waste and, [...] Read more.
Waste oil pollution and the treatment of oily waste present a challenge, and the exploitation of microbial resources is a safe and efficient method to resolve these problems. Lipase-producing microorganisms can directly degrade waste oil and promote the degradation of oily waste and, therefore, have very significant research and application value. The isolation of efficient oil-degrading strains is of great practical significance in research into microbial remediation in oil-contaminated environments and for the enrichment of the microbial lipase resource library. In this study, Acinetobacter junii WCO-9, an efficient oil-degrading bacterium, was isolated from an oil-contaminated soil using olive oil as the sole carbon source, and its enzyme activity of ρ-nitrophenyl decanoate (ρ-NPD) decomposition was 3000 U/L. The WCO-9 strain could degrade a variety of edible oils, and its degradation capability was significantly better than that of the control strain, A junii ATCC 17908. Comparative pan-genome and lipid degradation pathway analyses indicated that A. junii isolated from the same environment shared a similar set of core genes and that the species accumulated more specific genes that facilitated resistance to environmental stresses under different environmental conditions. WCO-9 has accumulated a complete set of oil metabolism genes under a long-term oil-contamination environment, and the compact arrangement of abundant lipase and lipase chaperones has further strengthened the ability of the strain to survive in such environments. This is the main reason why WCO-9 is able to degrade oil significantly more effectively than ATCC 17908. In addition, WCO-9 possesses a specific lipase that is not found in homologous strains. In summary, A. junii WCO-9, with a complete triglyceride degradation pathway and the specific lipase gene, has great potential in environmental remediation and lipase for industry. Full article
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2022

Jump to: 2024, 2023

13 pages, 3079 KiB  
Article
Predicting the Postmortem Interval Based on Gravesoil Microbiome Data and a Random Forest Model
by Chunhong Cui, Yang Song, Dongmei Mao, Yajun Cao, Bowen Qiu, Peng Gui, Hui Wang, Xingchun Zhao, Zhi Huang, Liqiong Sun and Zengtao Zhong
Microorganisms 2023, 11(1), 56; https://doi.org/10.3390/microorganisms11010056 - 24 Dec 2022
Cited by 13 | Viewed by 3069
Abstract
The estimation of a postmortem interval (PMI) is particularly important for forensic investigations. The aim of this study was to assess the succession of bacterial communities associated with the decomposition of mouse cadavers and determine the most important biomarker taxa for estimating PMIs. [...] Read more.
The estimation of a postmortem interval (PMI) is particularly important for forensic investigations. The aim of this study was to assess the succession of bacterial communities associated with the decomposition of mouse cadavers and determine the most important biomarker taxa for estimating PMIs. High-throughput sequencing was used to investigate the bacterial communities of gravesoil samples with different PMIs, and a random forest model was used to identify biomarker taxa. Redundancy analysis was used to determine the significance of environmental factors that were related to bacterial communities. Our data showed that the relative abundance of Proteobacteria, Bacteroidetes and Firmicutes showed an increasing trend during decomposition, but that of Acidobacteria, Actinobacteria and Chloroflexi decreased. At the genus level, Pseudomonas was the most abundant bacterial group, showing a trend similar to that of Proteobacteria. Soil temperature, total nitrogen, NH4+-N and NO3−-N levels were significantly related to the relative abundance of bacterial communities. Random forest models could predict PMIs with a mean absolute error of 1.27 days within 36 days of decomposition and identified 18 important biomarker taxa, such as Sphingobacterium, Solirubrobacter and Pseudomonas. Our results highlighted that microbiome data combined with machine learning algorithms could provide accurate models for predicting PMIs in forensic science and provide a better understanding of decomposition processes. Full article
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15 pages, 3079 KiB  
Article
Role of Indigenous Bacteria in Corrosion of Two Types of Carbon Steel
by Mihaela Marilena Stancu
Microorganisms 2022, 10(12), 2451; https://doi.org/10.3390/microorganisms10122451 - 12 Dec 2022
Cited by 2 | Viewed by 2113
Abstract
This study aimed to investigate the presence of both aerobic and anaerobic bacteria in a water sample collected from a nuclear power plant and establish if the indigenous bacteria or the products of their metabolic activities could initiate the corrosion of two different [...] Read more.
This study aimed to investigate the presence of both aerobic and anaerobic bacteria in a water sample collected from a nuclear power plant and establish if the indigenous bacteria or the products of their metabolic activities could initiate the corrosion of two different types of carbon steel (i.e., A570, 1045). The aerobic (heterotrophic, iron-oxidizing) and anaerobic (sulfate-reducing) bacteria were detected in low numbers in the water sample. Three bacterial strains were isolated by the enrichment procedure from this sample. Based on phenotypic and genotypic characteristics, the isolated bacteria were identified as Stenotrophomonas maltophilia IBBCn1 (MT893712), Stenotrophomonas maltophilia IBBCn2 (MT893713), and Bacillus thuringiensis IBBCn3 (MT893714). The bacteria existing in the water sample were able to initiate the corrosion of carbon steel A570 and 1045. The sulfate-reducing bacteria were detected in higher numbers than the heterotrophic bacteria and iron-oxidizing bacteria at the end of the biocorrosion experiments. The carbon steel coupons revealed macroscopic and microscopic changes in the surface characteristics, and these changes could be due to biofilm formation on their surfaces and the accumulation of the corrosion products. The corrosion rate varied from one type of carbon steel to another, depending on the incubation conditions and the chemical composition of the coupons. Full article
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