1
|
Xiang Y, Xiong W, Yang Z, Xu R, Zhang Y, Wu M, Ye Y, Peng H, Sun W, Wang D. Metagenomic insights into the toxicity of carbamazepine to functional microorganisms in sludge anaerobic digestion. Sci Total Environ 2024; 919:170780. [PMID: 38340855 DOI: 10.1016/j.scitotenv.2024.170780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Contaminants of emerging concern (CECs) contained in sludge, such as carbamazepine, may be toxic to microorganisms and affect the biogenesis of methane during anaerobic digestion. In this study, different scales of anaerobic digesters were constructed to investigate the inhibitory effect of carbamazepine. Results showed that carbamazepine reduced methane production by 11.3 % and 62.1 % at concentrations of 0.4 and 2 mg/g TS, respectively. Carbamazepine hindered the dissolution of organic matter and the degradation of protein. Carbamazepine inhibited some fermentative bacteria, especially uncultured Aminicenantales, whose abundance decreased by 9.5-93.4 % under carbamazepine stress. It is worth noting that most prior studies investigated the effects of CECs only based on well-known microorganisms, ignoring the metabolisms of uncultured microorganisms. Genome-predicted metabolic potential suggested that 54 uncultured metagenome-assembled genomes (MAGs) associated with acidogenesis or acetogenesis. Therein, uncultured Aminicenantales related MAGs were proved to be acetogenic fermenters, their significant reduction may be an important reason for the decrease of methane production under carbamazepine stress. The toxicity of carbamazepine to microorganisms was mainly related to the overproduction of reactive oxygen species. This study elucidates the inhibition mechanism of carbamazepine and emphasizes the indispensable role of uncultured microorganisms in anaerobic digestion.
Collapse
Affiliation(s)
- Yinping Xiang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Weiping Xiong
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China.
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Rui Xu
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, PR China
| | - Yanru Zhang
- Fujian Key Laboratory of Pollution Control & Resource Reuse, College of Environmental and Resource Sciences, Fujian Normal University, Fuzhou 350007, PR China
| | - Mengru Wu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Yuhang Ye
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Haihao Peng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Weimin Sun
- Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou 510650, PR China
| | - Dongbo Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| |
Collapse
|
2
|
Gurbich TA, Almeida A, Beracochea M, Burdett T, Burgin J, Cochrane G, Raj S, Richardson L, Rogers AB, Sakharova E, Salazar GA, Finn RD. MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues. J Mol Biol 2023; 435:168016. [PMID: 36806692 PMCID: PMC10318097 DOI: 10.1016/j.jmb.2023.168016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023]
Abstract
An increasingly common output arising from the analysis of shotgun metagenomic datasets is the generation of metagenome-assembled genomes (MAGs), with tens of thousands of MAGs now described in the literature. However, the discovery and comparison of these MAG collections is hampered by the lack of uniformity in their generation, annotation and storage. To address this, we have developed MGnify Genomes, a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes. Genomes within a biome-specific catalogue are organised into species clusters. For species that contain multiple conspecific genomes, the highest quality genome is selected as the representative, always prioritising an isolate genome over a MAG. The species representative sequences and annotations can be visualised on the MGnify website and the full catalogue and associated analysis outputs can be downloaded from MGnify servers. A suite of online search tools is provided allowing users to compare their own sequences, ranging from a gene to sets of genomes, against the catalogues. Seven biomes are available currently, comprising over 300,000 genomes that represent 11,048 non-redundant species, and include 36 taxonomic classes not currently represented by cultured genomes. MGnify Genomes is available at https://www.ebi.ac.uk/metagenomics/browse/genomes/.
Collapse
Affiliation(s)
- Tatiana A Gurbich
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Alexandre Almeida
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Martin Beracochea
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Josephine Burgin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Shriya Raj
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Lorna Richardson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Alexander B Rogers
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Ekaterina Sakharova
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Gustavo A Salazar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
| |
Collapse
|
3
|
Lodhi AF, Zhang Y, Adil M, Deng Y. Design and application of a novel culturing chip (cChip) for culturing the uncultured aquatic microorganisms. Arch Microbiol 2023; 205:285. [PMID: 37442830 DOI: 10.1007/s00203-023-03613-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 05/18/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
Culturing uncultured microorganisms is an important aspect of microbiology. Once cultured, these microorganisms can be a source of useful antibiotics, enzymes etc. In this study, we have designed a novel culturing chip (cChip) to facilitate the growth of uncultured aquatic bacterial community by concentrating the samples. cChip was optimized for microbial growth using known bacteria in the laboratory as a pre-experiment. Then microorganisms from a freshwater lake were concentrated and inoculated, before putting the inoculated cChip in a simulated lake environment and further sub-culturing on laboratory media. High-throughput sequencing and traditional culturing were also performed for comparison. These three methods were able to detect 265 genera of microorganisms in the sample, of which 78.87% were detected by high-throughput sequencing, 30.94% by cChip, while only 6.42% were obtained by traditional culture. Moreover, all microorganisms obtained by traditional culture were also cultured using the cChip. A total of 45 new strains were isolated from the cChip, and their 16S rRNA gene sequences were 91.35% to 98.7% similar to their closest relatives according to NCBI GenBank database. We conclude that the design and simple operation of cChip can improve the culture efficiency of traditional culture by almost 5 times. To the best of our knowledge, this is the first report comparing a novel culturing method with high-throughput sequencing data and traditional culturing of the same samples.
Collapse
Affiliation(s)
- Adil Farooq Lodhi
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
- Department of Microbiology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Ying Zhang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Maria Adil
- Department of Microbiology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| |
Collapse
|
4
|
Zhao J, Shakir Y, Deng Y, Zhang Y. Use of modified ichip for the cultivation of thermo-tolerant microorganisms from the hot spring. BMC Microbiol 2023; 23:56. [PMID: 36869305 PMCID: PMC9983152 DOI: 10.1186/s12866-023-02803-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Thermostable microorganisms are extremophiles. They have a special genetic background and metabolic pathway and can produce a variety of enzymes and other active substances with special functions. Most thermo-tolerant microorganisms from environmental samples have resisted cultivation on artificial growth media. Therefore, it is of great significance to isolate more thermo-tolerant microorganisms and study their characteristics to explore the origin of life and exploit more thermo-tolerant enzymes. Tengchong hot spring in Yunnan contains a lot of thermo-tolerant microbial resources because of its perennial high temperature. The ichip method was developed by D. Nichols in 2010 and can be used to isolate so-called "uncultivable" microorganisms from different environments. Here, we describe the first application of modified ichip to isolate thermo-tolerant bacteria from hot springs. RESULTS In this study, 133 strains of bacteria belonging to 19 genera were obtained. 107 strains of bacteria in 17 genera were isolated by modified ichip, and 26 strains of bacteria in 6 genera were isolated by direct plating methods. 25 strains are previously uncultured, 20 of which can only be cultivated after being domesticated by ichip. Two strains of previously unculturable Lysobacter sp., which can withstand 85 °C, were isolated for the first time. Alkalihalobacillus, Lysobacter and Agromyces genera were first found to have 85 °C tolerance. CONCLUSION Our results indicate that the modified ichip approach can be successfully applied in a hot spring environment.
Collapse
Affiliation(s)
- Juntian Zhao
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yasmeen Shakir
- Department of Biochemistry, Hazara University, Mansehra, Pakistan
| | - Yulin Deng
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Ying Zhang
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| |
Collapse
|
5
|
Hu B, Xu P, Ma L, Chen D, Wang J, Dai X, Huang L, Du W. One cell at a time: droplet-based microbial cultivation, screening and sequencing. Mar Life Sci Technol 2021; 3:169-188. [PMID: 37073344 PMCID: PMC10077293 DOI: 10.1007/s42995-020-00082-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Microbes thrive and, in turn, influence the earth's environment, but most are poorly understood because of our limited capacity to reveal their natural diversity and function. Developing novel tools and effective strategies are critical to ease this dilemma and will help to understand their roles in ecology and human health. Recently, droplet microfluidics is emerging as a promising technology for microbial studies with value in microbial cultivating, screening, and sequencing. This review aims to provide an overview of droplet microfluidics techniques for microbial research. First, some critical points or steps in the microfluidic system are introduced, such as droplet stabilization, manipulation, and detection. We then highlight the recent progress of droplet-based methods for microbiological applications, from high-throughput single-cell cultivation, screening to the targeted or whole-genome sequencing of single cells.
Collapse
Affiliation(s)
- Beiyu Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Peng Xu
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 USA
| | - Liang Ma
- Department of Biomedical Devices, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510320 China
| | - Dongwei Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- Department of Biomedical Devices, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510320 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 100049 China
| |
Collapse
|
6
|
Abstract
The study of metagenomics from high throughput sequencing data processed through Waikato Environment for Knowledge Analysis (WEKA) is gaining momentum in recent years. Therefore, we report an analysis of metagenome data generated using T-RFLP followed by using the SMO (Sequential minimal optimization) algorithm in WEKA to identify the total amount of cultured and uncultured microorganism present in the sample collected from multiple sources.
Collapse
Affiliation(s)
- Pritee Chunarkar Patil
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed University, Pune, Maharashtra, India
| | - Pradnya Suresh Panchal
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed University, Pune, Maharashtra, India
| | - Shweta Madiwale
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed University, Pune, Maharashtra, India
| | - Vidya Sunil Tale
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed University, Pune, Maharashtra, India
| |
Collapse
|