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Girard L, Lood C, De Mot R, van Noort V, Baudart J. Genomic diversity and metabolic potential of marine Pseudomonadaceae. Front Microbiol 2023; 14:1071039. [PMID: 37168120 PMCID: PMC10165715 DOI: 10.3389/fmicb.2023.1071039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/21/2023] [Indexed: 05/13/2023] Open
Abstract
Recent changes in the taxonomy of the Pseudomonadaceae family have led to the delineation of three new genera (Atopomonas, Halopseudomonas and Stutzerimonas). However, the genus Pseudomonas remains the most densely populated and displays a broad genetic diversity. Pseudomonas are able to produce a wide variety of secondary metabolites which drives important ecological functions and have a great impact in sustaining their lifestyles. While soilborne Pseudomonas are constantly examined, we currently lack studies aiming to explore the genetic diversity and metabolic potential of marine Pseudomonas spp. In this study, 23 Pseudomonas strains were co-isolated with Vibrio strains from three marine microalgal cultures and rpoD-based phylogeny allowed their assignment to the Pseudomonas oleovorans group (Pseudomonas chengduensis, Pseudomonas toyotomiensis and one new species). We combined whole genome sequencing on three selected strains with an inventory of marine Pseudomonas genomes to assess their phylogenetic assignations and explore their metabolic potential. Our results revealed that most strains are incorrectly assigned at the species level and half of them do not belong to the genus Pseudomonas but instead to the genera Halopseudomonas or Stutzerimonas. We highlight the presence of 26 new species (Halopseudomonas (n = 5), Stutzerimonas (n = 7) and Pseudomonas (n = 14)) and describe one new species, Pseudomonas chaetocerotis sp. nov. (type strain 536T = LMG 31766T = DSM 111343T). We used genome mining to identify numerous BGCs coding for the production of diverse known metabolites (i.e., osmoprotectants, photoprotectants, quorum sensing molecules, siderophores, cyclic lipopeptides) but also unknown metabolites (e.g., ARE, hybrid ARE-DAR, siderophores, orphan NRPS gene clusters) awaiting chemical characterization. Finally, this study underlines that marine environments host a huge diversity of Pseudomonadaceae that can drive the discovery of new secondary metabolites.
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Affiliation(s)
- Léa Girard
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Léa Girard,
| | - Cédric Lood
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - Julia Baudart
- Laboratoire de Biodiversité et Biotechnologie Microbiennes, Sorbonne Université, CNRS, Observatoire Océanologique, Banyuls-sur-Mer, France
- *Correspondence: Julia Baudart,
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Zhang M, Li A, Yao Q, Xiao B, Zhu H. Pseudomonas oligotrophica sp. nov., a Novel Denitrifying Bacterium Possessing Nitrogen Removal Capability Under Low Carbon–Nitrogen Ratio Condition. Front Microbiol 2022; 13:882890. [PMID: 35668762 PMCID: PMC9164167 DOI: 10.3389/fmicb.2022.882890] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/25/2022] [Indexed: 01/02/2023] Open
Abstract
Pseudomonas is a large and diverse genus within the Gammaproteobacteria known for its important ecological role in the environment. These bacteria exhibit versatile features of which the ability of heterotrophic nitrification and aerobic denitrification can be applied for nitrogen removal from the wastewater. A novel denitrifying bacterium, designated JM10B5aT, was isolated from the pond water for juvenile Litopenaeus vannamei. The phylogenetic, genomic, physiological, and biochemical analyses illustrated that strain JM10B5aT represented a novel species of the genus Pseudomonas, for which the name Pseudomonas oligotrophica sp. nov. was proposed. The effects of carbon sources and C/N ratios on denitrification performance of strain JM10B5aT were investigated. In addition, the results revealed that sodium acetate was selected as the optimum carbon source for denitrification of this strain. Besides, strain JM10B5aT could exhibit complete nitrate removal at the low C/N ratio of 3. Genomic analyses revealed that JM10B5aT possessed the functional genes including napA, narG, nirS, norB, and nosZ, which might participate in the complete denitrification process. Comparative genomic analyses indicated that many genes related to aggregation, utilization of alkylphosphonate and tricarballylate, biosynthesis of cofactors, and vitamins were contained in the genome of strain JM10B5aT. These genomic features were indicative of its adaption to various niches. Moreover, strain JM10B5aT harbored the complete operons required for the biosynthesis of vibrioferrin, a siderophore, which might be conducive to the high denitrification efficiency of denitrifying bacterium at low C/N ratio. Our findings demonstrated that the strain JM10B5aT could be a promising candidate for treating wastewater with a low C/N ratio.
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Affiliation(s)
- Mingxia Zhang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Anzhang Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Guangdong BOWOTE BioSciTech, Co., Ltd., Zhaoqing, China
| | - Qing Yao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Botao Xiao
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Botao Xiao
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- *Correspondence: Honghui Zhu
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Transcriptional profiling of biofilms formed on chilled beef by psychrotrophic meat spoilage bacterium, Pseudomonas fragi 1793. Biofilm 2021; 3:100045. [PMID: 33718862 PMCID: PMC7921472 DOI: 10.1016/j.bioflm.2021.100045] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas fragi is the predominant bacterial species associated with spoiled aerobically stored chilled meat worldwide. It readily forms biofilms on meat under refrigerated temperature conditions used in the meat industry. Biofilm growth leads to slime development on meat which in turn becomes a major quality defect. To understand the genetic regulation that aids P. fragi to survive under chilled conditions used in the meat industry, as well to obtain an overview of the transcriptomic behavior of this organism when grown as biofilms, RNA sequencing was carried out for the main stages of the P. fragi 1793 biofilm. RNA was extracted at different stages of the biofilm cycle namely initiation, maturation and dispersal. At the same time, the biofilm growth was assessed by fluorescent staining and imaging using confocal laser scanning microscope. The results of RNA sequencing were verified by qRT-PCR using twelve genes that were most significantly up and down regulated at each stage. Differential expression analysis at biofilm maturation revealed 332 significantly upregulated genes and 37 downregulated genes relative to initiation. Differential expression analysis at biofilm dispersal reveled 658 upregulated and 275 downregulated genes relative to initiation. During biofilm maturation and dispersal, genes coding for flp family type IVb pilin, ribosome modulation factor, creatininase were the most upregulated genes while genes encoding for iron uptake systems including TonB-dependent siderophore receptor and taurine transport were significantly down regulated. The results show that protein synthesis and cellular multiplication cease after the biofilm population maximum has reached.
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Bahmid NA, Heising J, Fogliano V, Dekker M. Packaging Design Using Mustard Seeds as a Natural Antimicrobial: A Study on Inhibition of Pseudomonas fragi in Liquid Medium. Foods 2020; 9:E789. [PMID: 32560102 PMCID: PMC7353601 DOI: 10.3390/foods9060789] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/03/2020] [Accepted: 06/10/2020] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas fragi is the dominant spoilage organism in various foods, especially in spoiled milk, fish, and meats. Its growth can be inhibited by releasing allyl isothiocyanate (AITC) from ground mustard seeds in food packages. This paper aims to investigate the antimicrobial potential of ground mustard seeds against P. fragi growth and the effectiveness of released AITC concentration from mustard seeds on microbial inhibition of the spoilage bacteria growing in the liquid medium. The AITC concentration in the headspace and the liquid medium was measured and the growth of P. fragi in the liquid medium was monitored. Depending on the concentration of AITC, not only growth was inhibited but a reduction of the total count of P. fragi was even observed. The inactivation rate (k) of P. fragi was estimated using first-order inactivation kinetics and the minimum gaseous-released AITC to inactivate P. fragi was determined. Higher AITC concentration in the headspace and liquid medium was observed when using a higher amount of ground mustard seeds and a lower food to headspace ratio. Increasing the amount of ground mustard seeds (>100 mg per 10 mL liquid medium) led to full inactivation of P. fragi in 48 hours. By using an inhibition sigmoid Emax model, the minimum gaseous-released AITC for inactivation of P. fragi in 48 hours was observed around 15 µg/L headspace. These results indicate that inhibition of the spoilage bacteria and extending the shelf life using ground mustard seeds is only possible by applying a careful design of the packaging system.
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Affiliation(s)
- Nur Alim Bahmid
- Food Quality and Design Group, Wageningen University and Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands; (N.A.B.); (J.H.); (V.F.)
- Agriculture and Forestry Faculty, Universitas Sulawesi Barat, Majene 91412, Indonesia
| | - Jenneke Heising
- Food Quality and Design Group, Wageningen University and Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands; (N.A.B.); (J.H.); (V.F.)
| | - Vincenzo Fogliano
- Food Quality and Design Group, Wageningen University and Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands; (N.A.B.); (J.H.); (V.F.)
| | - Matthijs Dekker
- Food Quality and Design Group, Wageningen University and Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands; (N.A.B.); (J.H.); (V.F.)
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Wickramasinghe NN, Ravensdale J, Coorey R, Chandry SP, Dykes GA. The Predominance of Psychrotrophic Pseudomonads on Aerobically Stored Chilled Red Meat. Compr Rev Food Sci Food Saf 2019; 18:1622-1635. [DOI: 10.1111/1541-4337.12483] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Nirmani N. Wickramasinghe
- School of Public HealthCurtin Univ. Perth Western Australia 6845 Australia
- Dept. of Agriculture and FoodCSIRO Werribee Victoria 3030 Australia
| | - Joshua Ravensdale
- School of Public HealthCurtin Univ. Perth Western Australia 6845 Australia
| | - Ranil Coorey
- School of Molecular an Health SciencesCurtin Univ. Perth Western Australia 6845 Australia
| | - Scott P. Chandry
- Dept. of Agriculture and FoodCSIRO Werribee Victoria 3030 Australia
| | - Gary A. Dykes
- School of Public HealthCurtin Univ. Perth Western Australia 6845 Australia
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Sood U, Hira P, Kumar R, Bajaj A, Rao DLN, Lal R, Shakarad M. Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa. Front Microbiol 2019; 10:53. [PMID: 30787911 PMCID: PMC6372532 DOI: 10.3389/fmicb.2019.00053] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/14/2019] [Indexed: 12/11/2022] Open
Abstract
Genomic information for outlier strains of Pseudomonas aeruginosa is exiguous when compared with classical strains. We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. It clustered with the outlier group, hence we scaled up the analyses to understand the differences in environmental and clinical outlier strains. We identified eight new regions of genomic plasticity and a plasmid pCR1 with a VirB/D4 complex followed by trimeric auto-transporter that can induce virulence phenotype in the genome of strain CR1. Virulence genotype analysis revealed that strain CR1 lacked hemolytic phospholipase C and D, three genes for LPS biosynthesis and had reduced antibiotic resistance genes when compared with clinical strains. Genes belonging to proteases, bacterial exporters and DNA stabilization were found to be under strong positive selection, thus facilitating pathogenicity and survival of the outliers. The outliers had the complete operon for the production of vibrioferrin, a siderophore present in plant growth promoting bacteria. The competence to acquire multidrug resistance and new virulence factors makes these strains a potential threat. However, we identified major regulatory hubs that can be used as drug targets against both the classical and outlier groups.
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Affiliation(s)
- Utkarsh Sood
- Department of Zoology, University of Delhi, New Delhi, India
- PhiXGen Private Limited, Gurugram, India
| | - Princy Hira
- Department of Zoology, University of Delhi, New Delhi, India
| | - Roshan Kumar
- Department of Zoology, University of Delhi, New Delhi, India
- PhiXGen Private Limited, Gurugram, India
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD, United States
| | - Abhay Bajaj
- Department of Zoology, University of Delhi, New Delhi, India
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | | | - Rup Lal
- Department of Zoology, University of Delhi, New Delhi, India
- PhiXGen Private Limited, Gurugram, India
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