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Xia R, Sun M, Balcázar JL, Yu P, Hu F, Alvarez PJJ. Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes. THE ISME JOURNAL 2023:10.1038/s41396-023-01408-x. [PMID: 37069233 DOI: 10.1038/s41396-023-01408-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023]
Abstract
The earthworm gut virome influences the structure and function of the gut microbiome, which in turn influences worm health and ecological functions. However, despite its ecological and soil quality implications, it remains elusive how earthworm intestinal phages respond to different environmental stress, such as soil pollution. Here we used metagenomics and metatranscriptomics to investigate interactions between the worm intestinal phages and their bacteria under different benzo[a]pyrene (BaP) concentrations. Low-level BaP (0.1 mg kg-1) stress stimulated microbial metabolism (1.74-fold to control), and enhanced the antiphage defense system (n = 75) against infection (8 phage-host pairs). Low-level BaP exposure resulted in the highest proportion of lysogenic phages (88%), and prophages expressed auxiliary metabolic genes (AMGs) associated with nutrient transformation (e.g., amino acid metabolism). In contrast, high-level BaP exposure (200 mg kg-1) disrupted microbial metabolism and suppressed the antiphage systems (n = 29), leading to the increase in phage-bacterium association (37 phage-host pairs) and conversion of lysogenic to lytic phages (lysogenic ratio declined to 43%). Despite fluctuating phage-bacterium interactions, phage-encoded AMGs related to microbial antioxidant and pollutant degradation were enriched, apparently to alleviate pollution stress. Overall, these findings expand our knowledge of complex phage-bacterium interactions in pollution-stressed worm guts, and deepen our understanding of the ecological and evolutionary roles of phages.
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Affiliation(s)
- Rong Xia
- Soil Ecology Lab, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, 210095, China
| | - Mingming Sun
- Soil Ecology Lab, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, 210095, China.
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), 17003, Girona, Spain
- University of Girona, 17004, Girona, Spain
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310085, China.
| | - Feng Hu
- Soil Ecology Lab, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, 210095, China
| | - Pedro J J Alvarez
- Civil and Environmental Engineering Department, Rice University, Houston, TX, 77005, USA
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Ndoye B, Shafiei R, Sanaei NS, Cleenwerck I, Somda MK, Dicko MH, Tounkara LS, Guiro AT, Delvigne F, Thonart P. Acetobacter senegalensis Isolated from Mango Fruits: Its Polyphasic Characterization and Adaptation to Protect against Stressors in the Industrial Production of Vinegar: A Review. J Appl Microbiol 2022; 132:4130-4149. [PMID: 35182093 DOI: 10.1111/jam.15495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 02/03/2022] [Accepted: 02/12/2022] [Indexed: 11/26/2022]
Abstract
It has been more than a decade since Acetobacter senegalensis was isolated, identified, and described as a thermotolerant strain of acetic acid bacteria. It was isolated from mango fruits in Senegal and used for industrial vinegar production in developing countries, mainly in sub-Saharan Africa. The strain was tested during several spirit vinegar fermentation processes at relatively high temperatures in accordance with African acclimation. The upstream fermentation process had significant stress factors, which are highlighted in this review so that the fermentation process can be better controlled. Due to its high industrial potential, this strain was extensively investigated by diverse industrial microbiologists worldwide; they concentrated on its microbiological, physiological, and genomic features. A research group based in Belgium proposed an important project for the investigation of the whole-genome sequence of A. senegalensis. It would use a 454-pyrosequencing technique to determine and corroborate features that could give this strain significant diverse bioindustrial applications. For instance, its application in cocoa bean fermentation has made it a more suitable acetic acid bacterium for the making of chocolate than Acetobacter pasteurianus. Therefore, in this paper, we present a review that summarizes the current research on A. senegalensis at its microbial and genomic levels and also its specific bioindustrial applications, which can provide economic opportunities for African agribusiness.
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Affiliation(s)
- Bassirou Ndoye
- University of Sine Saloum El Hadji Ibrahima Niasse (USSEIN), BP, Kaolack, Senegal.,Walloon Centre of Industrial Biology, Gembloux Agro-Bio Tech, University of Liège, Belgique
| | - Rasoul Shafiei
- Department of Cell, Molecular Biology and Microbiology, Faculty of Biological Sciences and Technology, University of Isfahan, Isfahan, Iran
| | - Nastaran Shah Sanaei
- Department of Cell, Molecular Biology and Microbiology, Faculty of Biological Sciences and Technology, University of Isfahan, Isfahan, Iran
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Marius K Somda
- Biochemistry, Biotechnology, Food Technology and Nutrition Laboratory, University Pr Joseph Ki Zerbo, PO, Ouagadougou, Burkina Faso
| | - Mamoudou Hama Dicko
- Biochemistry, Biotechnology, Food Technology and Nutrition Laboratory, University Pr Joseph Ki Zerbo, PO, Ouagadougou, Burkina Faso
| | | | - Amadou Tidiane Guiro
- University of Sine Saloum El Hadji Ibrahima Niasse (USSEIN), BP, Kaolack, Senegal
| | - Frank Delvigne
- Walloon Centre of Industrial Biology, Gembloux Agro-Bio Tech, University of Liège, Belgique
| | - Philippe Thonart
- Walloon Centre of Industrial Biology, Gembloux Agro-Bio Tech, University of Liège, Belgique
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Yang H, Chen T, Wang M, Zhou J, Liebl W, Barja F, Chen F. Molecular biology: Fantastic toolkits to improve knowledge and application of acetic acid bacteria. Biotechnol Adv 2022; 58:107911. [PMID: 35033586 DOI: 10.1016/j.biotechadv.2022.107911] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/27/2021] [Accepted: 01/09/2022] [Indexed: 12/24/2022]
Abstract
Acetic acid bacteria (AAB) are a group of gram-negative, obligate aerobic bacteria within the Acetobacteraceae family of the alphaproteobacteria class, which are distributed in a wide variety of different natural sources that are rich in sugar and alcohols, as well as in several traditionally fermented foods. Their capabilities are not limited to the production of acetic acid and the brewing of vinegar, as their names suggest. They can also fix nitrogen and produce various kinds of aldehydes, ketones and other organic acids by incomplete oxidation (also referred to as oxidative fermentation) of the corresponding alcohols and/or sugars, as well as pigments and exopolysaccharides (EPS). In order to gain more insight into these organisms, molecular biology techniques have been extensively applied in almost all aspects of AAB research, including their identification and classification, acid resistance mechanisms, oxidative fermentation, EPS production, thermotolerance and so on. In this review, we mainly focus on the application of molecular biological technologies in the advancement of research into AAB while presenting the progress of the latest studies using these techniques.
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Affiliation(s)
- Haoran Yang
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tao Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin, China
| | - Jingwen Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | | | - François Barja
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Sciences III, Geneva, Switzerland
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.
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Almeida OGG, Gimenez MP, De Martinis ECP. Comparative pangenomic analyses and biotechnological potential of cocoa-related Acetobacter senegalensis strains. Antonie van Leeuwenhoek 2021; 115:111-123. [PMID: 34817761 DOI: 10.1007/s10482-021-01684-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/06/2021] [Indexed: 10/19/2022]
Abstract
Acetobacter senegalensis belongs to the group of acetic acid bacteria (AAB) that present potential biotechnological applications, for production of D-gluconate, cellulose and acetic acid. AAB can overcome heat and acid stresses by using strategies involving the overexpression of heat-shock proteins and enzymes from the complex pyrroquinoline-ADH, besides alcohol dehydrogenases (ADH). Nonetheless, the isolation of A. senegalensis and other AAB from food may be challenging due to presence of viable but non-culturable (VBNC) cells and due to uncertainties about nutritional requirements. To contribute for a better understanding of the ecology of AAB, this paper reports on the pangenome analysis of five strains of A. senegalensis recently isolated from a Brazilian spontaneous cocoa fermentation. The results showed biosynthetic clusters exclusively found in some cocoa-related AAB, such as those related to terpene pathways, which are important for flavour development. Genes related to oxidative stress were conserved in all the genomes, with multiple clusters. Moreover, there were genes coding for ADH and putative ABC transporters distributed in core, shell and cloud genomes, while chaperonin-encoding genes were present only in the core and soft-core genomes. Regarding quorum sensing, a response regulator gene was in the shell genome, and the gene encoding for acyl-homoserine lactone efflux protein was in the soft-core genome. There were quorum quenching-related genes, mainly encoding for lactonases, but also for acylases. Moreover, A. senegalensis did not have determinants of virulence or antibiotic resistance, which are good traits for strains intended to be applied in food fermentation.
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Affiliation(s)
- O G G Almeida
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Universidade de São Paulo, Avenida do Café s/n, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - M P Gimenez
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Universidade de São Paulo, Avenida do Café s/n, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - E C P De Martinis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Universidade de São Paulo, Avenida do Café s/n, Ribeirão Preto, São Paulo, 14040-903, Brazil.
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Proteomic perspectives on thermotolerant microbes: an updated review. Mol Biol Rep 2021; 49:629-646. [PMID: 34671903 DOI: 10.1007/s11033-021-06805-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Thermotolerant microbes are a group of microorganisms that survive in elevated temperatures. The thermotolerant microbes, which are found in geothermal heat zones, grow at temperatures of or above 45°C. The proteins present in such microbes are optimally active at these elevated temperatures. Hence, therefore, serves as an advantage in various biotechnological applications. In the last few years, scientists have tried to understand the molecular mechanisms behind the maintenance of the structural integrity of the cell and to study the stability of various thermotolerant proteins at extreme temperatures. Proteomic analysis is the solution for this search. Applying novel proteomic tools determines the proteins involved in the thermostability of microbes at elevated temperatures. METHODS Advanced proteomic techniques like Mass spectrometry, nano-LC-MS, protein microarray, ICAT, iTRAQ, and SILAC could enable the screening and identification of novel thermostable proteins. RESULTS This review provides up-to-date details on the protein signature of various thermotolerant microbes analyzed through advanced proteomic tools concerning relevant research articles. The protein complex composition from various thermotolerant microbes cultured at different temperatures, their structural arrangement, and functional efficiency of the protein was reviewed and reported. CONCLUSION This review provides an overview of thermotolerant microbes, their enzymes, and the proteomic tools implemented to characterize them. This article also reviewed a comprehensive view of the current proteomic approaches for protein profiling in thermotolerant microbes.
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