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Gagnon JC, Beauregard-Tousignant S, Marcil JS, Lazar CS. Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada. Genes (Basel) 2023; 14:1529. [PMID: 37628582 PMCID: PMC10454208 DOI: 10.3390/genes14081529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.
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Affiliation(s)
- Jean-Christophe Gagnon
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
- Interuniversity Research Group in Limnology/Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Montréal, QC H3C 3P8, Canada
| | - Samuel Beauregard-Tousignant
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
| | - Jean-Sébastien Marcil
- Derena Geosciences, Quebec, QC G7A 3Y5, Canada;
- Ressources Utica Inc., Quebec, QC G1V 4M7, Canada
| | - Cassandre Sara Lazar
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
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Abril AG, Calo-Mata P, Böhme K, Villa TG, Barros-Velázquez J, Pazos M, Carrera M. Shotgun Proteomics Analysis, Functional Networks, and Peptide Biomarkers for Seafood-Originating Biogenic-Amine-Producing Bacteria. Int J Mol Sci 2023; 24:ijms24097704. [PMID: 37175409 PMCID: PMC10178689 DOI: 10.3390/ijms24097704] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Biogenic amine-producing bacteria are responsible for the production of basic nitrogenous compounds (histamine, cadaverine, tyramine, and putrescine) following the spoilage of food due to microorganisms. In this study, we adopted a shotgun proteomics strategy to characterize 15 foodborne strains of biogenic-amine-producing bacteria. A total of 10,673 peptide spectrum matches belonging to 4081 peptides and corresponding to 1811 proteins were identified. Relevant functional pathways were determined, and strains were differentiated into hierarchical clusters. An expected protein-protein interaction network was created (260 nodes/1973 interactions). Most of the determined proteins were associated with networks/pathways of energy, putrescine metabolism, and host-virus interaction. Additionally, 556 peptides were identified as virulence factors. Moreover, 77 species-specific peptide biomarkers corresponding to 64 different proteins were proposed to identify 10 bacterial species. This represents a major proteomic dataset of biogenic-amine-producing strains. These results may also be suitable for new treatments for food intoxication and for tracking microbial sources in foodstuffs.
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Affiliation(s)
- Ana González Abril
- Department of Food Technology, Spanish National Research Council (CSIC), Institute of Marine Research (IIM-CSIC), 36208 Vigo, Spain
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Tomás G Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Manuel Pazos
- Department of Food Technology, Spanish National Research Council (CSIC), Institute of Marine Research (IIM-CSIC), 36208 Vigo, Spain
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council (CSIC), Institute of Marine Research (IIM-CSIC), 36208 Vigo, Spain
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Abril AG, Quintela-Baluja M, Villa TG, Calo-Mata P, Barros-Velázquez J, Carrera M. Proteomic Characterization of Virulence Factors and Related Proteins in Enterococcus Strains from Dairy and Fermented Food Products. Int J Mol Sci 2022; 23:ijms231810971. [PMID: 36142880 PMCID: PMC9503237 DOI: 10.3390/ijms231810971] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/08/2022] [Accepted: 09/16/2022] [Indexed: 01/23/2023] Open
Abstract
Enterococcus species are Gram-positive bacteria that are normal gastrointestinal tract inhabitants that play a beneficial role in the dairy and meat industry. However, Enterococcus species are also the causative agents of health care-associated infections that can be found in dairy and fermented food products. Enterococcal infections are led by strains of Enterococcus faecalis and Enterococcus faecium, which are often resistant to antibiotics and biofilm formation. Enterococci virulence factors attach to host cells and are also involved in immune evasion. LC-MS/MS-based methods offer several advantages compared with other approaches because one can directly identify microbial peptides without the necessity of inferring conclusions based on other approaches such as genomics tools. The present study describes the use of liquid chromatography−electrospray ionization tandem mass spectrometry (LC−ESI−MS/MS) to perform a global shotgun proteomics characterization for opportunistic pathogenic Enterococcus from different dairy and fermented food products. This method allowed the identification of a total of 1403 nonredundant peptides, representing 1327 proteins. Furthermore, 310 of those peptides corresponded to proteins playing a direct role as virulence factors for Enterococcus pathogenicity. Virulence factors, antibiotic sensitivity, and proper identification of the enterococcal strain are required to propose an effective therapy. Data are available via ProteomeXchange with identifier PXD036435. Label-free quantification (LFQ) demonstrated that the majority of the high-abundance proteins corresponded to E. faecalis species. Therefore, the global proteomic repository obtained here can be the basis for further research into pathogenic Enterococcus species, thus facilitating the development of novel therapeutics.
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Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
- Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain
| | - Marcos Quintela-Baluja
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain
- Correspondence:
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Morinière L, Mirabel L, Gueguen E, Bertolla F. A Comprehensive Overview of the Genes and Functions Required for Lettuce Infection by the Hemibiotrophic Phytopathogen Xanthomonas hortorum pv. vitians. mSystems 2022; 7:e0129021. [PMID: 35311560 PMCID: PMC9040725 DOI: 10.1128/msystems.01290-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/07/2022] [Indexed: 12/25/2022] Open
Abstract
The successful infection of a host plant by a phytopathogenic bacterium depends on a finely tuned molecular cross talk between the two partners. Thanks to transposon insertion sequencing techniques (Tn-seq), whole genomes can now be assessed to determine which genes are important for the fitness of several plant-associated bacteria in planta. Despite its agricultural relevance, the dynamic molecular interaction established between the foliar hemibiotrophic phytopathogen Xanthomonas hortorum pv. vitians and its host, lettuce (Lactuca sativa), remains completely unknown. To decipher the genes and functions mobilized by the pathogen throughout the infection process, we conducted a Tn-seq experiment in lettuce leaves to mimic the selective pressure occurring during natural infection. This genome-wide screening identified 170 genes whose disruption caused serious fitness defects in lettuce. A thorough examination of these genes using comparative genomics and gene set enrichment analyses highlighted that several functions and pathways were highly critical for the pathogen's survival. Numerous genes involved in amino acid, nucleic acid, and exopolysaccharide biosynthesis were critical. The xps type II secretion system operon, a few TonB-dependent transporters involved in carbohydrate or siderophore scavenging, and multiple genes of the carbohydrate catabolism pathways were also critical, emphasizing the importance of nutrition systems in a nutrient-limited environment. Finally, several genes implied in camouflage from the plant immune system and resistance to immunity-induced oxidative stress were strongly involved in host colonization. As a whole, these results highlight some of the central metabolic pathways and cellular functions critical for Xanthomonas host adaptation and pathogenesis. IMPORTANCE Xanthomonas hortorum was recently the subject of renewed interest, as several studies highlighted that its members were responsible for diseases in a wide range of plant species, including crops of agricultural relevance (e.g., tomato and carrot). Among X. hortorum variants, X. hortorum pv. vitians is a reemerging foliar hemibiotrophic phytopathogen responsible for severe outbreaks of bacterial leaf spot of lettuce all around the world. Despite recent findings, sustainable and practical means of disease control remain to be developed. Understanding the host-pathogen interaction from a molecular perspective is crucial to support these efforts. The genes and functions mobilized by X. hortorum pv. vitians during its interaction with lettuce had never been investigated. Our study sheds light on these processes by screening the whole pathogen genome for genes critical for its fitness during the infection process, using transposon insertion sequencing and comparative genomics.
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Affiliation(s)
- Lucas Morinière
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
| | - Laurène Mirabel
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
| | - Erwan Gueguen
- Université Lyon, Université Claude Bernard Lyon 1, INSA, CNRS, UMR Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - Franck Bertolla
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
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