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Giovannini M, Vieri W, Bosi E, Riccardi C, Lo Giudice A, Fani R, Fondi M, Perrin E. Functional Genomics of a Collection of Gammaproteobacteria Isolated from Antarctica. Mar Drugs 2024; 22:238. [PMID: 38921549 PMCID: PMC11205219 DOI: 10.3390/md22060238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile conditions, but knowledge on the molecular mechanisms underlying this process remains limited. The Italian Collection of Antarctic Bacteria (Collezione Italiana Batteri Antartici (CIBAN)), managed by the University of Messina, represents a valuable repository of cold-adapted bacterial strains isolated from various Antarctic environments. In this study, we sequenced and analyzed the genomes of 58 marine Gammaproteobacteria strains from the CIBAN collection, which were isolated during Italian expeditions from 1990 to 2005. By employing genome-scale metrics, we taxonomically characterized these strains and assigned them to four distinct genera: Pseudomonas, Pseudoalteromonas, Shewanella, and Psychrobacter. Genome annotation revealed a previously untapped functional potential, including secondary metabolite biosynthetic gene clusters and antibiotic resistance genes. Phylogenomic analyses provided evolutionary insights, while assessment of cold-shock protein presence shed light on adaptation mechanisms. Our study emphasizes the significance of CIBAN as a resource for understanding Antarctic microbial life and its biotechnological potential. The genomic data unveil new horizons for insight into bacterial existence in Antarctica.
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Affiliation(s)
- Michele Giovannini
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Walter Vieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Emanuele Bosi
- Department of Earth, Environment and Life Sciences—DISTAV, University of Genoa, Corso Europa 26, I-16132 Genova, Italy;
| | - Christopher Riccardi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA 90089, USA
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council, (CNR.ISP), Spianata San Raineri 86, I-98122 Messina, Italy;
- Italian Collection of Antarctic Bacteria, National Antarctic Museum (CIBAN-MNA), I-98122 Messina, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, I-90133 Palermo, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Elena Perrin
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
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Camacho KF, de Melo Carlos L, Bernal SPF, de Oliveira VM, Ruiz JLM, Ottoni JR, Vieira R, Neto A, Rosa LH, Passarini MRZ. Antarctic marine sediment as a source of filamentous fungi-derived antimicrobial and antitumor compounds of pharmaceutical interest. Extremophiles 2024; 28:21. [PMID: 38532228 DOI: 10.1007/s00792-024-01339-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/07/2024] [Indexed: 03/28/2024]
Abstract
Antarctica harbors a microbial diversity still poorly explored and of inestimable biotechnological value. Cold-adapted microorganisms can produce a diverse range of metabolites stable at low temperatures, making these compounds industrially interesting for biotechnological use. The present work investigated the biotechnological potential for antimicrobial and antitumor activity of filamentous fungi and bacteria isolated from marine sediment samples collected at Deception Island, Antarctica. A total of 89 microbial isolates were recovered from marine sediments and submitted to an initial screening for L-glutaminase with antitumoral activity and for antimicrobial metabolites. The isolates Pseudogymnoascus sp. FDG01, Pseudogymnoascus sp. FDG02, and Penicillium sp. FAD33 showed potential antiproliferative action against human pancreatic carcinoma cells while showing no toxic effect on non-tumor cells. The microbial extracts from unidentified three bacteria and four filamentous fungi showed antibacterial activity against at least one tested pathogenic bacterial strain. The isolate FDG01 inhibited four bacterial species, while the isolate FDG01 was active against Micrococcus luteus in the minimal inhibitory concentration of 0.015625 μg mL -1. The results pave the way for further optimization of enzyme production and characterization of enzymes and metabolites found and reaffirm Antarctic marine environments as a wealthy source of compounds potentially applicable in the healthcare and pharmaceutical industry.
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Affiliation(s)
- Karine Fernandes Camacho
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Foz Do Iguaçu, PR, 85870-650, Brazil
| | - Layssa de Melo Carlos
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Foz Do Iguaçu, PR, 85870-650, Brazil
| | - Suzan Prado Fernandes Bernal
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Foz Do Iguaçu, PR, 85870-650, Brazil
| | | | - Jorge Luiz Maria Ruiz
- Laboratório de Biotecnologia da Saúde, Universidade Federal da Integração Latino-Integração Latino-Americana - UNILA, Foz Do Iguaçu, PR, 85870-650, Brazil
| | - Júlia Ronzella Ottoni
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Foz Do Iguaçu, PR, 85870-650, Brazil
| | - Rosemary Vieira
- Instituto de Geociências, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Arthur Neto
- Instituto de Geociências, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Luiz Henrique Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Michel Rodrigo Zambrano Passarini
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Foz Do Iguaçu, PR, 85870-650, Brazil.
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Cao Y, Zhao Q, Jiang F, Geng Y, Song H, Zhang L, Li C, Li J, Li Y, Hu X, Huang J, Tian S. Interactions between inhalable aged microplastics and lung surfactant: Potential pulmonary health risks. ENVIRONMENTAL RESEARCH 2024; 245:117803. [PMID: 38043900 DOI: 10.1016/j.envres.2023.117803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/10/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
The relationship between microplastics (MPs) and human respiratory health has garnered significant attention since inhalation constitutes the primary pathway for atmospheric MP exposure. While recent studies have revealed respiratory risks associated with MPs, virgin MPs used as plastic surrogates in these experiments did not represent the MPs that occur naturally and that undergo aging effects. Thus, the effects of aged MPs on respiratory health remain unknown. We herein analyzed the interaction between inhalable aged MPs with lung surfactant (LS) extracted from porcine lungs vis-à-vis interfacial chemistry employing in-vitro experiments, and explored oxidative damage induced by aged MPs in simulated lung fluid (SLF) and the underlying mechanisms of action. Our results showed that aged MPs significantly increased the surface tension of the LS, accompanied by a diminution in its foaming ability. The stronger adsorptive capacity of the aged MPs toward the phospholipids of LS appeared to produce increased surface tension, while the change in foaming ability might have resulted from a variation in the protein secondary structure and the adsorption of proteins onto MPs. The adsorption of phospholipid and protein components then led to the aggregation of MPs in SLF, where the aged MPs exhibited smaller hydrodynamic diameters in comparison with the unaged MPs, likely interacting with biomolecules in bodily fluids to exacerbate health hazards. Persistent free radicals were also formed on aged MPs, inducing the formation of reactive oxygen species such as superoxide radicals (O2•-), hydrogen peroxide (HOOH), and hydroxyl radicals (•OH); this would lead to LS lipid peroxidation and protein damage and increase the risk of respiratory disease. Our investigation was the first-ever to reveal a potential toxic effect of aged MPs and their actions on the human respiratory system, of great significance in understanding the risk of inhaled MPs on lung health.
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Affiliation(s)
- Yan Cao
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Qun Zhao
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Fanshu Jiang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Yingxue Geng
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Haoran Song
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Linfeng Zhang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Chen Li
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Jie Li
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.
| | - Yingjie Li
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Xuewei Hu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Jianhong Huang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Senlin Tian
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.
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Buckner DK, Anderson MJ, Wisnosky S, Alvarado W, Nuevo M, Williams AJ, Ricco AJ, Anamika, Debic S, Friend L, Hoac T, Jahnke L, Radosevich L, Williams R, Wilhelm MB. Quantifying Global Origin-Diagnostic Features and Patterns in Biotic and Abiotic Acyclic Lipids for Life Detection. ASTROBIOLOGY 2024; 24:1-35. [PMID: 38150549 DOI: 10.1089/ast.2023.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Lipids are a geologically robust class of organics ubiquitous to life as we know it. Lipid-like soluble organics are synthesized abiotically and have been identified in carbonaceous meteorites and on Mars. Ascertaining the origin of lipids on Mars would be a profound astrobiological achievement. We enumerate origin-diagnostic features and patterns in two acyclic lipid classes, fatty acids (i.e., carboxylic acids) and acyclic hydrocarbons, by collecting and analyzing molecular data reported in over 1500 samples from previously published studies of terrestrial and meteoritic organics. We identify 27 combined (15 for fatty acids, 12 for acyclic hydrocarbons) molecular patterns and structural features that can aid in distinguishing biotic from abiotic synthesis. Principal component analysis (PCA) demonstrates that multivariate analyses of molecular features (16 for fatty acids, 14 for acyclic hydrocarbons) can potentially indicate sample origin. Terrestrial lipids are dominated by longer straight-chain molecules (C4-C34 fatty acids, C14-C46 acyclic hydrocarbons), with predominance for specific branched and unsaturated isomers. Lipid-like meteoritic soluble organics are shorter, with random configurations. Organic solvent-extraction techniques are most commonly reported, motivating the design of our novel instrument, the Extractor for Chemical Analysis of Lipid Biomarkers in Regolith (ExCALiBR), which extracts lipids while preserving origin-diagnostic features that can indicate biogenicity.
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Affiliation(s)
- Denise K Buckner
- Department of Geological Sciences, University of Florida, Gainesville, Florida, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Morgan J Anderson
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Axient Corporation, Huntsville, Alabama, USA
| | - Sydney Wisnosky
- Axient Corporation, Huntsville, Alabama, USA
- Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - Walter Alvarado
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Michel Nuevo
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Amy J Williams
- Department of Geological Sciences, University of Florida, Gainesville, Florida, USA
| | - Antonio J Ricco
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Electrical Engineering-Integrated Circuits Laboratory, Stanford University, Stanford, California, USA
| | - Anamika
- Department of Space Studies, University of North Dakota, Grand Forks, North Dakota, USA
| | - Sara Debic
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Trinh Hoac
- Axient Corporation, Huntsville, Alabama, USA
| | - Linda Jahnke
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | | | - Ross Williams
- Civil & Environmental Engineering & Earth Sciences, Notre Dame University, Notre Dame, Indiana, USA
| | - Mary Beth Wilhelm
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
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Zappa S, Berne C, Morton RI, De Stercke J, Brun YV. The HmrABCX pathway regulates the transition between motile and sessile lifestyles in Caulobacter crescentus by a HfiA-independent mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571505. [PMID: 38168291 PMCID: PMC10760086 DOI: 10.1101/2023.12.13.571505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Through its cell cycle, the bacterium Caulobacter crescentus switches from a motile, free-living state, to a sessile surface-attached cell. During this coordinated process, cells undergo irreversible morphological changes, such as shedding of their polar flagellum and synthesis of an adhesive holdfast at the same pole. In this work, we used genetic screens to identify genes involved in the regulation of the motile to sessile lifestyle transition. We identified a predicted hybrid histidine kinase that inhibits biofilm formation and activates the motile lifestyle: HmrA (Holdfast and motility regulator A). Genetic screens and genomic localization led to the identification of additional genes that regulate the proportion of cells harboring an active flagellum or a holdfast and that form a putative phosphorelay pathway with HmrA. Further genetic analysis indicates that the Hmr pathway is independent of the holdfast synthesis regulator HfiA and may impact c-di-GMP synthesis through the diguanylate cyclase DgcB pathway. Finally, we provide evidence that the Hmr pathway is involved in the regulation of sessile-to-motile lifestyle as a function of environmental stresses, namely excess copper and non-optimal temperatures.
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Affiliation(s)
- Sébastien Zappa
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
| | - Cecile Berne
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
| | - Robert I. Morton
- Department of Biology, Indiana University, Bloomington, IN, USA
- Present address: Boston Scientific, Yokneam, Northern, ISRAEL
| | - Jonathan De Stercke
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
- Present address: Unité de Recherche en Biologie des Micro-organismes, Université de Namur, 61 rue de Bruxelles, B-5000 Namur, BELGIUM
| | - Yves V. Brun
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
- Department of Biology, Indiana University, Bloomington, IN, USA
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6
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Cao Y, Tian S, Geng Y, Zhang L, Zhao Q, Chen J, Li Y, Hu X, Huang J, Ning P. Interactions between CuO NPs and PS: The release of copper ions and oxidative damage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166285. [PMID: 37586511 DOI: 10.1016/j.scitotenv.2023.166285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/29/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Copper oxide nanoparticles (CuO NPs) can adversely affect lung health possibly by inducing oxidative damage through the release of copper ions. However, the migration and transformation processes of CuO NPs in lung lining fluid is still unclear, and there are still conflicting reports of redox reactions involving copper ions. To address this, we examined the release of copper ions from CuO NPs in simulated lung fluid supplemented with pulmonary surfactant (PS), and further analyzed the mechanisms of PS-CuO NPs interactions and the health hazards. The results showed that the phospholipid of PS was adsorbed on the particle surface, which not only induced aggregation of the particles but also provided a reaction environment for the interaction of PS with CuO NPs. PS was able to promote the release of ions from CuO NPs, of which the protein was a key component. Lipid peroxidation, protein destabilization, and disruption of the interfacial chemistry also occurred in the PS-CuO NPs interactions, during which copper ions were present only as divalent cations. Meanwhile, the contribution of the particle surface cannot be neglected in the oxidative damage to the lung caused by CuO NPs. Through reacting with biomolecules, CuO NPs accomplished ion release and induced oxidative damage associated with PS. This research was the first to reveal the mechanism of CuO NPs releasing copper ions and inducing lipid oxidative damage in the presence of PS, which provides a new idea of transition metal-induced health risk in human body.
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Affiliation(s)
- Yan Cao
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Senlin Tian
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Yingxue Geng
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Linfeng Zhang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Qun Zhao
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
| | - Jie Chen
- Faculty of Land Resource Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650093, China
| | - Yingjie Li
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Xuewei Hu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Jianhong Huang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Ping Ning
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
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Grigorov AS, Skvortsova YV, Bychenko OS, Aseev LV, Koledinskaya LS, Boni IV, Azhikina TL. Dynamic Transcriptional Landscape of Mycobacterium smegmatis under Cold Stress. Int J Mol Sci 2023; 24:12706. [PMID: 37628885 PMCID: PMC10454040 DOI: 10.3390/ijms241612706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Bacterial adaptation to cold stress requires wide transcriptional reprogramming. However, the knowledge of molecular mechanisms underlying the cold stress response of mycobacteria is limited. We conducted comparative transcriptomic analysis of Mycobacterium smegmatis subjected to cold shock. The growth of M. smegmatis cultivated at 37 °C was arrested just after exposure to cold (acclimation phase) but later (by 24 h) was resumed at a much slower rate (adaptation phase). Transcriptomic analyses revealed distinct gene expression patterns corresponding to the two phases. During the acclimation phase, differential expression was observed for genes associated with cell wall remodeling, starvation response, and osmotic pressure stress, in parallel with global changes in the expression of transcription factors and the downregulation of ribosomal genes, suggesting an energy-saving strategy to support survival. At the adaptation phase, the expression profiles were recovered, indicating restoration of the processes repressed earlier. Comparison of transcriptional responses in M. smegmatis with those in other bacteria revealed unique adaptation strategies developed by mycobacteria. Our findings shed light on the molecular mechanisms underlying M. smegmatis survival under cold stress. Further research should clarify whether the discovered transcriptional mechanisms exist in other mycobacterial species, including pathogenic Mycobacterium tuberculosis, which could be important for transmission control.
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Affiliation(s)
- Artem S. Grigorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | | | | | | | | | | | - Tatyana L. Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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Rolfe CA, Anderson NM, Glenn Black D, Lee A. Barotolerance of acid-adapted and cold-adapted bacterial isolates of E. coli O157:H7, Salmonella spp., and L. monocytogenes in an acidic buffer model. J Food Prot 2023:100116. [PMID: 37321452 DOI: 10.1016/j.jfp.2023.100116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
The fruit and vegetable juice industry has shown a growing trend in minimally processed juices. A frequent technology used in the production of functional juices is cold pressure, which refers to the application of high pressure processing (HPP) at low temperatures to inactivate foodborne pathogens. HPP juice manufacturers are required to demonstrate a 5-log reduction of the pertinent microorganism to comply with FDA Juice HACCP. However, there is no consensus on validation study approaches for bacterial strain selection or their preparation. Individual bacterial strains were grown using three different growth conditions: neutral, cold-adapted, and acid-adapted. Approximately 6.0 - 7.0 log CFU/mL of the matrix-adapted bacterial strains were inoculated individually into buffered peptone water (BPW) at pH 3.50 ± 0.10 (HCl adjusted) and treated at sublethal pressures of 500 MPa for E. coli O157:H7 and 200 MPa for Salmonella spp. and L. monocytogenes (180 s, 4°C). Analyses were conducted at 0, 24 and 48 h (4°C storage) post-HPP on non-selective media. E. coli O157:H7 exhibited greater barotolerance than Salmonella spp. and L. monocytogenes. In neutral growth conditions, E. coli O157:H7 strain TW14359 demonstrated the greatest resistance (2.94 ± 0.64 log reduction) and E. coli O157:H7 strain SEA13B88 was significantly more sensitive (P <0.05). Salmonella isolates, neutral and acid-adapted, expressed similar barotolerance to one another. Cold-adapted S. Cubana and S. Montevideo showed greater resistance compared to other cold-adapted strains. Acid-adapted L. monocytogenes strain MAD328 had <1.00 ± 0.23 log reduction while acid-adapted L. monocytogenes strains CDC and Scott A were significantly more sensitive (P <0.05) with reductions of 2.13 ± 0.48 and 3.43 ± 0.50 log CFU/mL, respectively. These results suggested, under the conditions tested, bacterial strain and preparation methods influence HPP efficacy and should be considered when conducting validation studies.
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Affiliation(s)
- Catherine A Rolfe
- U. S. Food and Drug Administration, 6502 South Archer Road, Bedford Park, IL 60501; Institute for Food Safety and Health, Illinois Institute of Technology, 6502 South Archer Road, Bedford Park, IL 60501.
| | - Nathan M Anderson
- U. S. Food and Drug Administration, 6502 South Archer Road, Bedford Park, IL 60501
| | - Darryl Glenn Black
- U. S. Food and Drug Administration, 6502 South Archer Road, Bedford Park, IL 60501
| | - Alvin Lee
- Institute for Food Safety and Health, Illinois Institute of Technology, 6502 South Archer Road, Bedford Park, IL 60501
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9
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Tian H, Liu J, Zhang Y, Liu Q. Stress response and signalling of a low-temperature bioaugmentation system in decentralized wastewater treatment: Degradation characteristics, community structure, and bioaugmented mechanisms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 342:118257. [PMID: 37290305 DOI: 10.1016/j.jenvman.2023.118257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/10/2023]
Abstract
Low temperatures present challenges for stable wastewater treatment operations in cold regions. Low-temperature effective microorganisms (LTEM) were added as a bioaugmentation strategy at a decentralized treatment facility to improve performance. The effects of a low-temperature bioaugmentation system (LTBS) with LTEM at low temperatures (4 °C) on organic pollutant performance, microbial community changes, and the metabolic pathways of functional genes and functional enzymes were studied. To explore the bioaugmentation mechanism of LTBS based on stress response and signalling. The results showed that the start-up time of the LTBS (S2) with LTEM was shorter (8 days) and that it removed COD and NH4+-N at higher rates (87 % and 72 %, respectively) at 4 °C. LTEM effectively degraded complex macromolecular organics into small molecular organics, and decomposing sludge flocs and the changing the extracellular polymeric substances (EPS) structure removed more organics and nitrogen. LTEM and local microbial communities (nitrifying and denitrifying bacteria) improved the ability of organic matter degradation and denitrification of the LTBS and formed a core microbial community dominated by LTEM (Bacillus and Pseudomonas). Finally, based on the functional enzymes and metabolic pathways of the LTBS, a low-temperature strengthening mechanism consisting of 6 cold stress responses and signal pathways under low temperatures was formed. This study demonstrated that the LTEM-dominated LTBS could provide an engineering alternative for future decentralized wastewater treatment in cold regions.
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Affiliation(s)
- Hongyu Tian
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing, 100083, China; Key Laboratory of Urban Stormwater System and Water Environment (Beijing University of Civil Engineering and Architecture), Ministry of Education, Beijing, 100044, China
| | - Jianwei Liu
- Beijing Engineering Research Center of Sustainable Urban Sewage System Construction and Risk Control, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China; Key Laboratory of Urban Stormwater System and Water Environment (Beijing University of Civil Engineering and Architecture), Ministry of Education, Beijing, 100044, China.
| | - Yuxiu Zhang
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing, 100083, China.
| | - Qianqian Liu
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing, 100083, China
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Zheng B, He S, Zhao L, Li J, Du Y, Li Y, Shi J, Wu Z. Does temperature favour the spread of Raphidiopsis raciborskii, an invasive bloom-forming cyanobacterium, by altering cellular trade-offs? HARMFUL ALGAE 2023; 124:102406. [PMID: 37164561 DOI: 10.1016/j.hal.2023.102406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/08/2023] [Accepted: 02/14/2023] [Indexed: 05/12/2023]
Abstract
As a tropical filamentous cyanobacterium, Raphidiopsis raciborskii has attracted much attention due to its expansion and toxin production. However, the mechanisms of its expansion to temperate regions have not been studied in detail. To address the potential strategies, the physiological and metabolomic profiles of R. raciborskii FACHB 1096 isolated from a temperate lake in China were determined and measured at different temperatures (10 °C, 15 °C, 20 °C, 25 °C, and 32 °C). The results demonstrated that temperature significantly changed cell viability, chlorophyll a content, specific growth rate, Chl a fluorescence, and filamentous shape of R. raciborskii. Low temperature decreased cell viability, specific growth rate, and photosynthetic efficiency, while the proportion of akinete and carbon fixation per unit cell were significantly increased compared with high temperature (32 °C). A constructed unimodal model indicated that filament length, cell volume, and cell length/width of R. raciborskii were significantly reduced in both high and low temperature environments. Under low-temperature conditions, R. raciborskii suffered different degrees of oxidative damage and produced corresponding antioxidant substances to resist oxidative stress, suggesting that low temperature changes the metabolic level of the cells, causing the cells to gradually switch from development to defense. Metabolomic data further confirmed that temperature change induced shifts in metabolic pathways in R. raciborskii, including starch and sucrose metabolic pathways, glutathione metabolic pathways, and the pentose phosphate pathways (PPP), as well as metabolic pathways related to the tricarboxylic acid (TCA) cycle. Our results indicated that the trade-offs of R. raciborskii cells among the growth, cell size, and metabolites can be significantly regulated by temperature, with broad implications for its global expansion in temperate waterbodies.
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Affiliation(s)
- Baohai Zheng
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Shuhan He
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Lu Zhao
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jiaxin Li
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yuxin Du
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yuxin Li
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Junqiong Shi
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Zhongxing Wu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, 400715, China.
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11
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Ban GH, Lee JI, Kang DH. Effects of storage temperature on microbiota shifts in raw milk biofilm developed on stainless steel. Food Microbiol 2023; 110:104163. [DOI: 10.1016/j.fm.2022.104163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022]
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12
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Fadiji AE, Yadav AN, Santoyo G, Babalola OO. Understanding the plant-microbe interactions in environments exposed to abiotic stresses: An overview. Microbiol Res 2023; 271:127368. [PMID: 36965460 DOI: 10.1016/j.micres.2023.127368] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/07/2023] [Accepted: 03/19/2023] [Indexed: 03/27/2023]
Abstract
Abiotic stress poses a severe danger to agriculture since it negatively impacts cellular homeostasis and eventually stunts plant growth and development. Abiotic stressors like drought and excessive heat are expected to occur more frequently in the future due to climate change, which would reduce the yields of important crops like maize, wheat, and rice which may jeopardize the food security of human populations. The plant microbiomes are a varied and taxonomically organized microbial community that is connected to plants. By supplying nutrients and water to plants, and regulating their physiology and metabolism, plant microbiota frequently helps plants develop and tolerate abiotic stresses, which can boost crop yield under abiotic stresses. In this present study, with emphasis on temperature, salt, and drought stress, we describe current findings on how abiotic stresses impact the plants, microbiomes, microbe-microbe interactions, and plant-microbe interactions as the way microorganisms affect the metabolism and physiology of the plant. We also explore crucial measures that must be taken in applying plant microbiomes in agriculture practices faced with abiotic stresses.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Ajar Nath Yadav
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich 58030, Mexico
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
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13
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Dopson M, González-Rosales C, Holmes DS, Mykytczuk N. Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies. Front Microbiol 2023; 14:1149903. [PMID: 37007468 PMCID: PMC10050440 DOI: 10.3389/fmicb.2023.1149903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/16/2023] [Indexed: 03/17/2023] Open
Abstract
Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH < 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, “Ferrovum myxofaciens,” and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of “omics” techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.
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Affiliation(s)
- Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- *Correspondence: Mark Dopson
| | - Carolina González-Rosales
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastian, Santiago, Chile
| | - Nadia Mykytczuk
- Goodman School of Mines, Laurentian University, Sudbury, ON, Canada
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14
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Lü J, Wang S, Liu B, Song X. Spatiotemporal heterogeneity of nitrogen transformation potentials in a freshwater estuarine system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160335. [PMID: 36414069 DOI: 10.1016/j.scitotenv.2022.160335] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/31/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Under the influence of water diversion, the microbial community composition of estuarine waters and sediments might have complex spatiotemporal variations. Microbial interactions with N are significant for lake water quality. Therefore, the largest lake receiving seasonal water diversion in the North China Plain was selected as the study area. Based on 16S rRNA high-throughput sequencing and metagenomic sequencing techniques, this study analysed temporal (June-December) and spatial (estuary-pelagic zone) changes in the microbial community and functional gene composition of water and sediment. The results showed that the water microbial community composition had temporality, while sediment microbes had spatiality. The main causes of temporality in the aquatic microbial community were temperature and nitrate-N concentration, while those of sediment were flow velocity and N content. Additionally, there were complex interactions between microbial communities and N. In water, temporal variation in the relative abundance of N-related functional genes might have indirectly contributed to inorganic N composition in June (nitrite-N > ammonia-N > nitrate-N) and August (nitrite-N > nitrate-N > ammonia-N). High nitrate-N concentrations in December influenced the microbial community composition. In sediment, the estuary had higher N functional genes than the pelagic estuary, creating a relatively active N cycle and reducing total N levels in the estuary. This study revealed a potentially overlooked N sink and a flow velocity threshold that has great impacts on microbial community composition. This research contributes to a deeper understanding of the estuarine N cycle under the influence of water diversions, with implications for the calculation of global N balances and the management of lake water environments.
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Affiliation(s)
- Jiali Lü
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China; Sino-Danish College of University of Chinese Academy of Sciences, Beijing 101408, China; Sino-Danish Centre for Education and Research, Beijing 101408, China; Key Laboratory of Water Cycle & Related Land Surface Processes, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 999017, Denmark
| | - Shiqin Wang
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China; Xiongan Institute of Innovation, Chinese Academy of Science, China.
| | - Binbin Liu
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China; Xiongan Institute of Innovation, Chinese Academy of Science, China
| | - Xianfang Song
- Sino-Danish College of University of Chinese Academy of Sciences, Beijing 101408, China; Sino-Danish Centre for Education and Research, Beijing 101408, China; Key Laboratory of Water Cycle & Related Land Surface Processes, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
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15
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Górecki I, Kołodziejczyk A, Harasymczuk M, Młynarczyk G, Szymanek-Majchrzak K. The Impact of Harsh Stratospheric Conditions on Survival and Antibiotic Resistance Profile of Non-Spore Forming Multidrug Resistant Human Pathogenic Bacteria Causing Hospital-Associated Infections. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2787. [PMID: 36833485 PMCID: PMC9956888 DOI: 10.3390/ijerph20042787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Bacteria are constantly being lifted to the stratosphere due to air movements caused by weather phenomena, volcanic eruptions, or human activity. In the upper parts of the atmosphere, they are exposed to extremely harsh and mutagenic conditions such as UV and space radiation or ozone. Most bacteria cannot withstand that stress, but for a fraction of them, it can act as a trigger for selective pressure and rapid evolution. We assessed the impact of stratospheric conditions on the survival and antibiotic resistance profile of common non-spore-forming human pathogenic bacteria, both sensitive and extremely dangerous multidrug-resistant variants, with plasmid-mediated mechanisms of resistance. Pseudomonas aeruginosa did not survive the exposure. In the case of strains that were recovered alive, the survival was extremely low: From 0.00001% of Klebsiella pneumoniae carrying the ndm-1 gene and methicillin-resistant Staphylococcus aureus mecA-positive with reduced susceptibility to vancomycin (MRSA/VISA), to a maximum of 0.001% of K. pneumoniae sensitive to all common antibiotics and S. aureus sensitive to vancomycin (MRSA/VSSA). We noticed a tendency towards increased antibiotic susceptibility after the stratospheric flight. Antimicrobial resistance is a current real, global, and increasing problem, and our results can inform current understandings of antibiotic resistance mechanisms and development in bacteria.
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Affiliation(s)
- Ignacy Górecki
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego, Str. 5, 02-004 Warsaw, Poland
| | - Agata Kołodziejczyk
- Analog Astronaut Training Center, Morelowa Str. 1F/4, 30-222 Cracow, Poland
- Space Technology Centre, AGH University of Technology, Czarnowiejska Str. 36, 30-054 Cracow, Poland
| | - Matt Harasymczuk
- Analog Astronaut Training Center, Morelowa Str. 1F/4, 30-222 Cracow, Poland
| | - Grażyna Młynarczyk
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego, Str. 5, 02-004 Warsaw, Poland
| | - Ksenia Szymanek-Majchrzak
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego, Str. 5, 02-004 Warsaw, Poland
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16
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An G, Yan R, Fu Z, Chen Z, Guo Y, Yang J, Zhou Y. Adaptation of anammox consortia in microbial fuel cell to low temperature: Microbial community and predictive functional profiling. BIORESOURCE TECHNOLOGY 2023; 370:128565. [PMID: 36596367 DOI: 10.1016/j.biortech.2022.128565] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
The purpose of this study was to explore the tolerance mechanism of anammox consortia in microbial fuel cell (MFC) system at low temperature. Data showed that nearly 80 % total nitrogen removal was achieved after the temperature decreased from 30 °C to 15 °C. The nitrogenremovalrate (NRR) of the system was decreased by 26.3 %, from 0.441 kgN·m-3·d-1 at 30 °C to 0.325 kgN·m-3·d-1 at 15 °C. Isotope experiment in 15NH4+-containing reactor found that much more 29N2 were produced than 30N2, confirming that anammox was the main 15NH4+ removal pathway and electrochemical oxidation participate in this process. High throughput sequencing analysis indicated the low temperature stimulated the enrichment of heterotrophic bacteria, such as Comamonadaceae and Rhodobacteraceae. While the relative abundance of Candidatus Brocadia, typical anammox bacteria, decreased significantly. Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis showed that the low temperature induced a more efficient expression in synthesis of unsaturated fatty acids (UFAs) and ABC membrane transports. This study indicates that anammox consortia are likely to maintain high nitrogen removal performance of MFC system by changing the proportion of membrane composition and EPS exportation.
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Affiliation(s)
- Geer An
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
| | - Rong Yan
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China; Inner Mongolia Lvchuang Environmental Protection Technology Co., Ltd., Hohhot 010051, China
| | - Zhimin Fu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China.
| | - Zepeng Chen
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
| | - Yaru Guo
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
| | - Jun Yang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
| | - Yongheng Zhou
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
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17
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Pastore MA, Classen AT, English ME, Frey SD, Knorr MA, Rand K, Adair EC. Soil microbial legacies influence freeze–thaw responses of soil. Funct Ecol 2023. [DOI: 10.1111/1365-2435.14273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Melissa A. Pastore
- Rubenstein School of Environment and Natural Resources University of Vermont Burlington Vermont USA
- Gund Institute for Environment University of Vermont Burlington Vermont USA
| | - Aimée T. Classen
- Gund Institute for Environment University of Vermont Burlington Vermont USA
- Ecology and Evolutionary Biology Department University of Michigan Ann Arbor Michigan USA
- University of Michigan Biological Station Pellston Michigan USA
| | - Marie E. English
- Rubenstein School of Environment and Natural Resources University of Vermont Burlington Vermont USA
| | - Serita D. Frey
- Department of Natural Resources and the Environment University of New Hampshire Durham New Hampshire USA
| | - Melissa A. Knorr
- Department of Natural Resources and the Environment University of New Hampshire Durham New Hampshire USA
| | - Karin Rand
- Rubenstein School of Environment and Natural Resources University of Vermont Burlington Vermont USA
| | - E. Carol Adair
- Rubenstein School of Environment and Natural Resources University of Vermont Burlington Vermont USA
- Gund Institute for Environment University of Vermont Burlington Vermont USA
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18
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Grivokostopoulos NC, Makariti IP, Tsadaris S, Skandamis PN. Impact of population density and stress adaptation on the internalization of Salmonella in leafy greens. Food Microbiol 2022; 106:104053. [PMID: 35690446 DOI: 10.1016/j.fm.2022.104053] [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: 03/02/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022]
Abstract
Salmonella enterica is capable of entering the interior of leafy greens and establishing in the apoplastic area, a phenomenon known as internalization. The ability of internalized bacteria to evade common disinfection practices poses a well-established risk. Our aim was to study the effect of: i) inoculum size and ii) prior adaptation of Salmonella to sublethal stresses, on the internalization of the pathogen in four leafy vegetables. Spinach, lettuce, arugula and chicory were inoculated, by immersion for 2 min at room temperature with: i) Salmonella Enteritidis at 3.0, 4.0, 5.0, 6.0, 7.0 log CFU/mL and ii) non-adapted or adapted S. Enteritidis to acid (in TSB with 1% glucose, incubated for 24 h at 37 °C), cold (in TSB for 7 days at 4 °C), starvation (0.85% NaCl of pH 6.6, 48 h at 37 °C) or desiccation (1.5 h at 42 °C, 4 days at 21 °C) stress at appx 3.5 log CFU/mL). Inoculated leafy greens were subsequently stored at 5 °C and 20 °C for 2 h and 48 h (n = 2 × 2). Population of internalized Salmonella, after surface decontamination with 1% w/v AgNO3, was assessed on selective media. Even the lowest initial bacterial inoculum was adequate for internalization of Salmonella to occur in leafy vegetables. Non-adapted Salmonella inoculum of 7.0 (maximum) and 3.0 log CFU/mL (lowest inoculation level tested) after short storage (2 h) resulted in 3.7-4.3 and 1.3-1.5 log CFU/g internalized bacterial population, respectively. Colonization (including both attachment and internalization processes), as well as internalization process, were positively correlated to initial inoculum level. These processes reached a different plateau beyond which, no further increase in internalization was observed. Adaptation of the pathogen to mild stresses enhanced internalization (P < 0.05), with desiccation- and acid-adapted Salmonella demonstrating the highest internalization capacity, regardless of the vegetable and storage temperature. These findings could contribute to further elucidation of colonization capacity of Salmonella in leafy vegetables and assist in selecting the proper conditions that contribute to the prevention of fresh produce contamination with Salmonella.
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Affiliation(s)
- N C Grivokostopoulos
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - I P Makariti
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - S Tsadaris
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - P N Skandamis
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece.
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19
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Zhao Y, Min H, Luo K, Zhang R, Chen Q, Chen Z. Transcriptomics and proteomics revealed the psychrotolerant and antibiotic-resistant mechanisms of strain Pseudomonas psychrophila RNC-1 capable of assimilatory nitrate reduction and aerobic denitrification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153169. [PMID: 35051480 DOI: 10.1016/j.scitotenv.2022.153169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Aerobic denitrification has been proved to be profoundly affected by temperature and antibiotics, but little is known about how aerobic denitrifiers respond to temperature and antibiotic stress. In this study, the nitrate reduction performance and the intracellular metabolism by a psychrotolerant aerobic denitrifying bacteria, named Pseudomonas psychrophila RNC-1, were systematically investigated at different temperatures (10 °C, 20 °C, 30 °C) and different sulfamethoxazole (SMX) concentrations (0 mg/L, 0.1 mg/L, 0.5 mg/L, 1.0 mg/L, and 5.0 mg/L). The results showed that strain RNC-1 performed satisfactory nitrate removal at 10 °C and 20 °C, but its growth was significantly inhibited at 30 °C. Nitrate removal by strain RNC-1 was slightly promoted in the presence of 0.5 mg/L SMX, whereas it was significantly suppressed with 5.0 mg/L SMX. Nitrogen balance analysis indicated that assimilatory nitrate reduction and dissimilatory aerobic denitrification jointly dominated in the nitrate removal process of strain RNC-1, in which the inhibition effected on assimilation process was much higher than that on the aerobic denitrification process under SMX exposure. Further transcriptomics and proteomics analysis revealed that the psychrotolerant mechanism of strain RNC-1 could be attributed to the up-regulation of RNA translation, energy metabolism, ABC transporters and the over-expression of cold shock proteins, while the down-regulation of oxidative phosphorylation pathway was the primary reason for the deteriorative cell growth at 30 °C. The promotion of nitrate reduction with 0.5 mg/L SMX was related to the up-regulation of amino acid metabolism pathways, while the down-regulation of folate cycle, glycolysis/gluconeogenesis and bacterial chemotaxis pathways were responsible for the inhibition effect at 5.0 mg/L SMX. This work provides a mechanistic understanding of the metabolic adaption of strain RNC-1 under different stress, which is of significance for its application in nitrogen contaminated wastewater treatment processes.
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Affiliation(s)
- Yuanyi Zhao
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China; College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China
| | - Hongchao Min
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Kongyan Luo
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China; College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China
| | - Ruijie Zhang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China.
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China.
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20
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Kouba V, Bachmannová C, Podzimek T, Lipovová P, van Loosdrecht MCM. Physiology of anammox adaptation to low temperatures and promising biomarkers: A review. BIORESOURCE TECHNOLOGY 2022; 349:126847. [PMID: 35167904 DOI: 10.1016/j.biortech.2022.126847] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
The adaptation of bacteria involved in the anaerobic ammonium oxidation (anammox) to low temperatures in the mainstream of WWTP will unlock substantial treatment savings. However, their adaptation mechanisms have begun to be revealed only very recently. This study reviewed the state-of-the-art knowledge on these mechanisms from -omics studies, crucially including metaproteomics and metabolomics. Anammox bacteria adapt to low temperatures by synthesizing both chaperones of RNA and proteins and chemical chaperones. Furthermore, they preserve energy for the core metabolism by reducing biosynthesis in general. Thus, in this study, a number of biomarkers are proposed to help practitioners assess the extent of anammox bacteria adaptation and predict the decomposition of biofilms/granules or slower growth. The promising biomarkers also include unique ladderane lipids. Further proteomic and metabolomic studies are necessary for a more detailed understanding of anammox low-temperature adaptation, thus easing the transition to more cost-effective and sustainable wastewater treatment.
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Affiliation(s)
- V Kouba
- University of Chemistry and Technology Prague, Department of Water Technology and Environmental Engineering, Technická 5, 166 28 Prague, Czechia.
| | - Ch Bachmannová
- University of Chemistry and Technology Prague, Department of Water Technology and Environmental Engineering, Technická 5, 166 28 Prague, Czechia
| | - T Podzimek
- University of Chemistry and Technology Prague, Department of Biochemistry and Microbiology, Technická 5, 166 28 Prague, Czechia
| | - P Lipovová
- University of Chemistry and Technology Prague, Department of Biochemistry and Microbiology, Technická 5, 166 28 Prague, Czechia
| | - M C M van Loosdrecht
- The Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
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21
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Ijaq J, Chandra D, Ray MK, Jagannadham MV. Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation. Front Genet 2022; 13:825269. [PMID: 35360867 PMCID: PMC8963723 DOI: 10.3389/fgene.2022.825269] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/07/2022] [Indexed: 11/28/2022] Open
Abstract
Exploring the molecular mechanisms behind bacterial adaptation to extreme temperatures has potential biotechnological applications. In the present study, Pseudomonas sp. Lz4W, a Gram-negative psychrophilic bacterium adapted to survive in Antarctica, was selected to decipher the molecular mechanism underlying the cold adaptation. Proteome analysis of the isolates grown at 4°C was performed to identify the proteins and pathways that are responsible for the adaptation. However, many proteins from the expressed proteome were found to be hypothetical proteins (HPs), whose function is unknown. Investigating the functional roles of these proteins may provide additional information in the biological understanding of the bacterial cold adaptation. Thus, our study aimed to assign functions to these HPs and understand their role at the molecular level. We used a structured insilico workflow combining different bioinformatics tools and databases for functional annotation. Pseudomonas sp. Lz4W genome (CP017432, version 1) contains 4493 genes and 4412 coding sequences (CDS), of which 743 CDS were annotated as HPs. Of these, from the proteome analysis, 61 HPs were found to be expressed consistently at the protein level. The amino acid sequences of these 61 HPs were submitted to our workflow and we could successfully assign a function to 18 HPs. Most of these proteins were predicted to be involved in biological mechanisms of cold adaptations such as peptidoglycan metabolism, cell wall organization, ATP hydrolysis, outer membrane fluidity, catalysis, and others. This study provided a better understanding of the functional significance of HPs in cold adaptation of Pseudomonas sp. Lz4W. Our approach emphasizes the importance of addressing the “hypothetical protein problem” for a thorough understanding of mechanisms at the cellular level, as well as, provided the assessment of integrating proteomics methods with various annotation and curation approaches to characterize hypothetical or uncharacterized protein data. The MS proteomics data generated from this study has been deposited to the ProteomeXchange through PRIDE with the dataset identifier–PXD029741.
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Affiliation(s)
- Johny Ijaq
- Metabolomics Facility, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Deepika Chandra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Malay Kumar Ray
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - M. V. Jagannadham
- Metabolomics Facility, School of Life Sciences, University of Hyderabad, Hyderabad, India
- *Correspondence: M. V. Jagannadham,
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22
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Reghu S, Miyako E. Nanoengineered Bifidobacterium bifidum with Optical Activity for Photothermal Cancer Immunotheranostics. NANO LETTERS 2022; 22:1880-1888. [PMID: 35179380 DOI: 10.1021/acs.nanolett.1c04037] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
There is substantial interest regarding the understanding and designing of nanoengineered bacteria to combat various fatal diseases. Here, we report the nanoengineering of Bifidobacterium bifidum using Cremophor EL to encapsulate organic dye molecules by simple incubation and washing processes while maintaining the bacterial morphology and viability. The prepared functional bacteria exhibit characteristics such as optical absorbance, unique fluorescence, powerful photothermal conversion, low toxicity, excellent tumor targeting, and anticancer efficacy. They also displayed significant in vivo fluorescent expression in implanted colorectal cancerous tumors. Moreover, the powerful photothermal conversion of the functional bacteria could be spatiotemporally evoked by biologically penetrable near-infrared laser for effective tumor regression in mice, with the help of immunological responses. Our study demonstrates that a nanoengineering approach can provide the strong physicochemical traits and attenuation of living bacterial cells for cancer immunotheranostics.
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Affiliation(s)
- Sheethal Reghu
- Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Eijiro Miyako
- Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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23
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Ríos‐López AL, Heredia N, García S, Merino‐Mascorro JÁ, Solís‐Soto LY, Dávila‐Aviña JE. Effect of phenolic compounds and cold shock on survival and virulence of
Escherichia coli
pathotypes. J Food Saf 2022. [DOI: 10.1111/jfs.12966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ana L. Ríos‐López
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas Universidad Autónoma de Nuevo León San Nicolás de los Garza Mexico
| | - Norma Heredia
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas Universidad Autónoma de Nuevo León San Nicolás de los Garza Mexico
| | - Santos García
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas Universidad Autónoma de Nuevo León San Nicolás de los Garza Mexico
| | - José Á. Merino‐Mascorro
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas Universidad Autónoma de Nuevo León San Nicolás de los Garza Mexico
| | - Luisa Y. Solís‐Soto
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas Universidad Autónoma de Nuevo León San Nicolás de los Garza Mexico
| | - Jorge E. Dávila‐Aviña
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas Universidad Autónoma de Nuevo León San Nicolás de los Garza Mexico
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24
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Puig-Castellví F, Midoux C, Guenne A, Conteau D, Franchi O, Bureau C, Madigou C, Jouan-Rimbaud Bouveresse D, Kroff P, Mazéas L, Rutledge DN, Gaval G, Chapleur O. Metataxonomics, metagenomics and metabolomics analysis of the influence of temperature modification in full-scale anaerobic digesters. BIORESOURCE TECHNOLOGY 2022; 346:126612. [PMID: 34954354 DOI: 10.1016/j.biortech.2021.126612] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Full-scale anaerobic digesters' performance is regulated by modifying their operational conditions, but little is known about how these modifications affect their microbiome. In this work, we monitored two originally mesophilic (35 °C) full-scale anaerobic digesters during 476 days. One digester was submitted to sub-mesophilic (25 °C) conditions between days 123 and 373. We characterized the effect of temperature modification using a multi-omics (metataxonomics, metagenomics, and metabolomics) approach. The metataxonomics and metagenomics results revealed that the lower temperature allowed a substantial increase of the sub-dominant bacterial population, destabilizing the microbial community equilibrium and reducing the biogas production. After restoring the initial mesophilic temperature, the bacterial community manifested resilience in terms of microbial structure and functional activity. The metabolomic signature of the sub-mesophilic acclimation was characterized by a rise of amino acids and short peptides, suggesting a protein degradation activity not directed towards biogas production.
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Affiliation(s)
- Francesc Puig-Castellví
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 75005 Paris, France; Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France
| | - Cédric Midoux
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France; Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France; Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, 78350, Jouy-en-Josas, France
| | - Angéline Guenne
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France
| | | | - Oscar Franchi
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France; Universidad Adolfo Ibanez, Facultad de ingeniería y ciencias, 2520000 Viña del mar, Chile
| | - Chrystelle Bureau
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France
| | - Céline Madigou
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France
| | | | | | - Laurent Mazéas
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France
| | - Douglas N Rutledge
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 75005 Paris, France; National Wine and Grape Industry Centre, Charles Sturt University, 2650 Wagga Wagga, Australia
| | | | - Olivier Chapleur
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France.
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25
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Li X, Li D, Ma S, Yang Y. Integration of transcriptomic and proteomic analyses of cold shock response in Kosmotoga olearia, a typical thermophile with an incredible minimum growth temperature at 20 °C. Braz J Microbiol 2022; 53:71-88. [PMID: 34997565 PMCID: PMC8882551 DOI: 10.1007/s42770-021-00662-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 11/19/2021] [Indexed: 01/09/2023] Open
Abstract
Kosmotoga olearia TBF 19.5.1 is a typical thermophile with optimal growth at 65 °C and also exhibits visible growth at an incredible minimum temperature (20 °C). It is considered an ideal model for investigating the evolutionary transition from thermophiles to mesophiles within Thermotogae. However, knowledge relevant to molecular mechanisms of K. olearia responding to cold shock is still limited. In this study, transcriptomics and proteomics were integrated to investigate the global variations at the transcript and protein level during cold shock in K. olearia. As a result, total 734 differentially expressed genes and 262 differentially expressed proteins were identified. The cold-responsive genes and proteins were associated with signaling transduction, transcription, translation and repair, cell wall/membrane reconstruction, amino acid biosynthesis, and stress response. However, most genes and proteins, involved in carbon metabolism, fatty acid biosynthesis, and energy production, were repressed. This work provides the first integrative transcriptomics and proteomics analyses of the cold shock response in K. olearia, and it offered new insights into the mechanisms of cold adaptation and post-transcriptional regulation of the distinctive thermophile within Thermotogae.
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Affiliation(s)
- Xia Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China ,Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041 China
| | - Dan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China ,School of Liquor-Making Engineering, Sichuan University Jinjiang College, Meishan, 620680 China
| | - Shichun Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041 China
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China
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26
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Yu Q, Feng T, Yang J, Su W, Zhou R, Wang Y, Zhang H, Li H. Seasonal distribution of antibiotic resistance genes in the Yellow River water and tap water, and their potential transmission from water to human. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118304. [PMID: 34627965 DOI: 10.1016/j.envpol.2021.118304] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/05/2021] [Accepted: 10/05/2021] [Indexed: 05/25/2023]
Abstract
The prevalence and transmission of antibiotic resistance genes (ARGs) and opportunistic pathogens in water environments can pose great threat to public health. However, the dissemination of ARGs and opportunistic pathogens from water environments to humans has been poorly explored. Here, we employed 16S rRNA gene sequencing and high-throughput quantitative PCR techniques to explore the seasonal distribution of ARGs and opportunistic pathogens in the Yellow River water (source water) and tap water, as well as their relationships with healthy humans at Lanzhou, China. Physiochemical analysis was applied to detect water quality parameters and heavy metal contents. The absolute abundance and diversity of ARGs in the Yellow River and tap water demonstrated distinct seasonal patterns. In winter, the Yellow river water had the highest ARG abundance and diversity, while tap water owned the lowest. Mobile genetic elements (MGEs) were the predominant driver of ARG profiles in both the Yellow river and tap water. Null model analysis showed that ARG assembly in the Yellow River was more influenced by stochastic processes than tap water and this was independent of seasons. Total organic carbon and arsenic contents exhibited positive correlations with many ARGs. Opportunistic pathogens Aeromonas and Pseudomonas may be potential hosts for ARGs. Approximately 80% of detected ARGs were shared between water samples and the human gut. These persistent ARGs could not be entirely eliminated through drinking water treatment processes. Thus, it is crucial to protect sources of tap water from anthropogenic pollution and improve water treatment technologies to reduce the dissemination of ARGs and ensure drinking-water biosafety for human health.
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Affiliation(s)
- Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Tianshu Feng
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Rui Zhou
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Yijie Wang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Hong Zhang
- Anhui Microanaly Gene Co., Ltd., Hefei, 230601, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou, 730000, China; Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.
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27
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Rizvi A, Ahmed B, Khan MS, Umar S, Lee J. Psychrophilic Bacterial Phosphate-Biofertilizers: A Novel Extremophile for Sustainable Crop Production under Cold Environment. Microorganisms 2021; 9:2451. [PMID: 34946053 PMCID: PMC8704983 DOI: 10.3390/microorganisms9122451] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/18/2022] Open
Abstract
Abiotic stresses, including low-temperature environments, adversely affect the structure, composition, and physiological activities of soil microbiomes. Also, low temperatures disturb physiological and metabolic processes, leading to major crop losses worldwide. Extreme cold temperature habitats are, however, an interesting source of psychrophilic and psychrotolerant phosphate solubilizing bacteria (PSB) that can ameliorate the low-temperature conditions while maintaining their physiological activities. The production of antifreeze proteins and expression of stress-induced genes at low temperatures favors the survival of such organisms during cold stress. The ability to facilitate plant growth by supplying a major plant nutrient, phosphorus, in P-deficient soil is one of the novel functional properties of cold-tolerant PSB. By contrast, plants growing under stress conditions require cold-tolerant rhizosphere bacteria to enhance their performance. To this end, the use of psychrophilic PSB formulations has been found effective in yield optimization under temperature-stressed conditions. Most of the research has been done on microbial P biofertilizers impacting plant growth under normal cultivation practices but little attention has been paid to the plant growth-promoting activities of cold-tolerant PSB on crops growing in low-temperature environments. This scientific gap formed the basis of the present manuscript and explains the rationale for the introduction of cold-tolerant PSB in competitive agronomic practices, including the mechanism of solubilization/mineralization, release of biosensor active biomolecules, molecular engineering of PSB for increasing both P solubilizing/mineralizing efficiency, and host range. The impact of extreme cold on the physiological activities of plants and how plants overcome such stresses is discussed briefly. It is time to enlarge the prospects of psychrophilic/psychrotolerant phosphate biofertilizers and take advantage of their precious, fundamental, and economical but enormous plant growth augmenting potential to ameliorate stress and facilitate crop production to satisfy the food demands of frighteningly growing human populations. The production and application of cold-tolerant P-biofertilizers will recuperate sustainable agriculture in cold adaptive agrosystems.
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Affiliation(s)
- Asfa Rizvi
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India; (A.R.); (S.U.)
| | - Bilal Ahmed
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Korea
| | - Mohammad Saghir Khan
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India;
| | - Shahid Umar
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India; (A.R.); (S.U.)
| | - Jintae Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Korea
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28
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Shimada S, Nakai R, Aoki K, Kudoh S, Imura S, Shimoeda N, Ohno G, Watanabe K, Miyazaki Y, Ishii Y, Tateda K. Characterization of the First Cultured Psychrotolerant Representative of Legionella from Antarctica Reveals Its Unique Genome Structure. Microbiol Spectr 2021; 9:e0042421. [PMID: 34668737 PMCID: PMC8528123 DOI: 10.1128/spectrum.00424-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Culture-independent analysis shows that Legionella spp. inhabit a wide range of low-temperature environments, but to date, no psychrotolerant or psychrophilic strains have been reported. Here, we characterized the first cultivated psychrotolerant representative, designated strain TUM19329T, isolated from an Antarctic lake using a polyphasic approach and comparative genomic analysis. A genome-wide phylogenetic tree indicated that this strain was phylogenetically separate at the species level. Strain TUM19329T shared common physiological traits (e.g., Gram-negative, limited growth on buffered charcoal-yeast extract α-ketoglutarate [BCYEα] agar with l-cysteine requirements) with its relatives, but it also showed psychrotolerant growth properties (e.g., growth at 4°C to 25°C). Moreover, this strain altered its own cellular fatty acid composition to accumulate unsaturated fatty acid at a lower temperature, which may help maintain the cell membrane fluidity. Through comparative genomic analysis, we found that this strain possessed massive mobile genetic elements compared with other species, amounting to up to 17% of the total genes. The majority of the elements were the result of the spread of only a few insertion sequences (ISs), which were spread throughout the genome by a "copy-and-paste" mechanism. Furthermore, we found metabolic genes, such as fatty acid synthesis-related genes, acquired by horizontal gene transfer (HGT). The expansion of ISs and HGT events may play a major role in shaping the phenotype and physiology of this strain. On the basis of the features presented here, we propose a new species-Legionella antarctica sp. nov.-represented by strain TUM19329T (= GTC 22699T = NCTC 14581T). IMPORTANCE This study characterized a unique cultivated representative of the genus Legionella isolated from an Antarctic lake. This psychrotolerant strain had some common properties of known Legionella species but also displayed other characteristics, such as plasticity in fatty acid composition and an enrichment of mobile genes in the genome. These remarkable properties, as well as other factors, may contribute to cold hardiness, and this first cultivated cold-tolerant strain of the genus Legionella may serve as a model bacterium for further studies. It is worth noting that environmentally derived 16S rRNA gene phylotypes closely related to the strain characterized here have been detected from diverse environments outside Antarctica, suggesting a wide distribution of psychrotolerant Legionella bacteria. Our culture- and genome-based findings may accelerate the ongoing studies of the behavior and pathogenicity of Legionella spp., which have been monitored for many years in the context of public health.
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Affiliation(s)
- Sho Shimada
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
- Department of Respiratory Medicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido, Japan
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Sakae Kudoh
- National Institute of Polar Research, Research Organization of Information and Systems, Tokyo, Japan
- Department of Polar Science, The Graduate University for Advanced Studies, SOKENDAI, Tokyo, Japan
| | - Satoshi Imura
- National Institute of Polar Research, Research Organization of Information and Systems, Tokyo, Japan
- Department of Polar Science, The Graduate University for Advanced Studies, SOKENDAI, Tokyo, Japan
| | | | | | - Kentaro Watanabe
- National Institute of Polar Research, Research Organization of Information and Systems, Tokyo, Japan
| | - Yasunari Miyazaki
- Department of Respiratory Medicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
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29
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Homeoviscous Adaptation of the Acinetobacter baumannii Outer Membrane: Alteration of Lipooligosaccharide Structure during Cold Stress. mBio 2021; 12:e0129521. [PMID: 34425709 PMCID: PMC8406137 DOI: 10.1128/mbio.01295-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To maintain optimal membrane dynamics, cells from all domains of life must acclimate to various environmental signals in a process referred to as homeoviscous adaptation. Alteration of the lipid composition is critical for maintaining membrane fluidity, permeability of the lipid bilayer, and protein function under diverse conditions. It is well documented, for example, that glycerophospholipid content varies substantially in both Gram-negative and Gram-positive bacteria with changes in growth temperature. However, in the case of Gram-negative bacteria, far less is known concerning structural changes in lipopolysaccharide (LPS) or lipooligosaccharide (LOS) during temperature shifts. LPS/LOS is anchored at the cell surface by the highly conserved lipid A domain and localized in the outer leaflet of the outer membrane. Here, we identified a novel acyltransferase, termed LpxS, involved in the synthesis of the lipid A domain of Acinetobacter baumannii. A. baumannii is a significant, multidrug-resistant, opportunistic pathogen that is particularly difficult to clear from health care settings because of its ability to survive under diverse conditions. LpxS transfers an octanoate (C8:0) fatty acid, the shortest known secondary acyl chain reported to date, replacing a C12:0 fatty acid at the 2' position of lipid A. Expression of LpxS was highly upregulated under cold conditions and likely increases membrane fluidity. Furthermore, incorporation of a C8:0 acyl chain under cold conditions increased the effectiveness of the outer membrane permeability barrier. LpxS orthologs are found in several Acinetobacter species and may represent a common mechanism for adaptation to cold temperatures in these organisms. IMPORTANCE To maintain cellular fitness, the composition of biological membranes must change in response to shifts in temperature or other stresses. This process, known as homeoviscous adaptation, allows for maintenance of optimal fluidity and membrane permeability. Here, we describe an enzyme that alters the fatty acid content of A. baumannii LOS, a major structural feature and key component of the bacterial outer membrane. Although much is known regarding how glycerophospholipids are altered during temperature shifts, our understanding of LOS or LPS alterations under these conditions is lacking. Our work identifies a cold adaptation mechanism in A. baumannii, a highly adaptable and multidrug-resistant pathogen.
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30
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Liu X, Lin S, Liu T, Zhou Y, Wang W, Yao J, Guo Y, Tang K, Chen R, Benedik MJ, Wang X. Xenogeneic silencing relies on temperature-dependent phosphorylation of the host H-NS protein in Shewanella. Nucleic Acids Res 2021; 49:3427-3440. [PMID: 33693785 PMCID: PMC8034616 DOI: 10.1093/nar/gkab137] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 12/20/2022] Open
Abstract
Lateral gene transfer (LGT) plays a key role in shaping the genome evolution and environmental adaptation of bacteria. Xenogeneic silencing is crucial to ensure the safe acquisition of LGT genes into host pre-existing regulatory networks. We previously found that the host nucleoid structuring protein (H-NS) silences prophage CP4So at warm temperatures yet enables this prophage to excise at cold temperatures in Shewanella oneidensis. However, whether H-NS silences other genes and how bacteria modulate H-NS to regulate the expression of genes have not been fully elucidated. In this study, we discovered that the H-NS silences many LGT genes and the xenogeneic silencing of H-NS relies on a temperature-dependent phosphorylation at warm temperatures in S. oneidensis. Specifically, phosphorylation of H-NS at Ser42 is critical for silencing the cold-inducible genes including the excisionase of CP4So prophage, a cold shock protein, and a stress-related chemosensory system. By contrast, nonphosphorylated H-NS derepresses the promoter activity of these genes/operons to enable their expression at cold temperatures. Taken together, our results reveal that the posttranslational modification of H-NS can function as a regulatory switch to control LGT gene expression in host genomes to enable the host bacterium to react and thrive when environmental temperature changes.
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Affiliation(s)
- Xiaoxiao Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Shituan Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianlang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiqing Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiquan Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianyun Yao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Ran Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Michael J Benedik
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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Craig K, Johnson BR, Grunden A. Leveraging Pseudomonas Stress Response Mechanisms for Industrial Applications. Front Microbiol 2021; 12:660134. [PMID: 34040596 PMCID: PMC8141521 DOI: 10.3389/fmicb.2021.660134] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/12/2021] [Indexed: 12/25/2022] Open
Abstract
Members of the genus Pseudomonas are metabolically versatile and capable of adapting to a wide variety of environments. Stress physiology of Pseudomonas strains has been extensively studied because of their biotechnological potential in agriculture as well as their medical importance with regards to pathogenicity and antibiotic resistance. This versatility and scientific relevance led to a substantial amount of information regarding the stress response of a diverse set of species such as Pseudomonas chlororaphis, P. fluorescens, P. putida, P. aeruginosa, and P. syringae. In this review, environmental and industrial stressors including desiccation, heat, and cold stress, are cataloged along with their corresponding mechanisms of survival in Pseudomonas. Mechanisms of survival are grouped by the type of inducing stress with a focus on adaptations such as synthesis of protective substances, biofilm formation, entering a non-culturable state, enlisting chaperones, transcription and translation regulation, and altering membrane composition. The strategies Pseudomonas strains utilize for survival can be leveraged during the development of beneficial strains to increase viability and product efficacy.
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Affiliation(s)
- Kelly Craig
- AgBiome Inc., Research Triangle Park, NC, United States
| | | | - Amy Grunden
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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32
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Liu Q, Li W, Liu D, Li L, Li J, Lv N, Liu F, Zhu B, Zhou Y, Xin Y, Dong X. Light stimulates anoxic and oligotrophic growth of glacial Flavobacterium strains that produce zeaxanthin. ISME JOURNAL 2021; 15:1844-1857. [PMID: 33452478 DOI: 10.1038/s41396-020-00891-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 01/17/2023]
Abstract
Bacteria that inhabit glaciers usually produce carotenoids. Here, we report that a group of zeaxanthin-producing glacial Flavobacterium exhibited light-promoted growth. Of the tested 47 strains, 45 showed increased growths but two died under illumination at 50 μmol photon m-2 s-1. Light stimulation occurred mainly in either anoxic or nutrient-poor cultures, while the same levels of light promotion were found for that grown at 14 and 7 °C. Pigment assays identified overrepresentative zeaxanthin but trace retinal in the light promoted 45 strains, while flexirubin was exclusively in the light-lethal two. Genomic analysis revealed the gene cluster for zeaxanthin synthesis in the 45 strains, in which 37 strains also harbored the proteorhodopsin gene prd. Transcriptomic analysis found that light-induced expressions of both the zeaxanthin synthesis and proteorhodopsin genes. Whereas, deletion of the prd gene in one strain did not diminish light promotion, inhibition of zeaxanthin synthesis did. In comparison, no light promotion was determined in a glacier Cryobacterium luteum that produced a non-zeaxanthin-type carotenoid. Therefore, light stimulation on the glacial Flavobacterium is mostly likely related to zeaxanthin, which could provide better photoprotection and sustain membrane integrity for the organisms living in cold environments.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,China General Microorganism Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Wei Li
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Di Liu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingyan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Na Lv
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fei Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuguang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,China General Microorganism Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
| | - Yuhua Xin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,China General Microorganism Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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33
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Bioactive Secondary Metabolites from Psychrophilic Fungi and Their Industrial Importance. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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34
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Bacillus cereus Decreases NHE and CLO Exotoxin Synthesis to Maintain Appropriate Proteome Dynamics During Growth at Low Temperature. Toxins (Basel) 2020; 12:toxins12100645. [PMID: 33036317 PMCID: PMC7601483 DOI: 10.3390/toxins12100645] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 12/02/2022] Open
Abstract
Cellular proteomes and exoproteomes are dynamic, allowing pathogens to respond to environmental conditions to sustain growth and virulence. Bacillus cereus is an important food-borne pathogen causing intoxication via emetic toxin and/or multiple protein exotoxins. Here, we compared the dynamics of the cellular proteome and exoproteome of emetic B. cereus cells grown at low (16 °C) and high (30 °C) temperature. Tandem mass spectrometry (MS/MS)-based shotgun proteomics analysis identified 2063 cellular proteins and 900 extracellular proteins. Hierarchical clustering following principal component analysis indicated that in B. cereus the abundance of a subset of these proteins—including cold-stress responders, and exotoxins non-hemolytic enterotoxin (NHE) and hemolysin I (cereolysin O (CLO))—decreased at low temperature, and that this subset governs the dynamics of the cellular proteome. NHE, and to a lesser extent CLO, also contributed significantly to exoproteome dynamics; with decreased abundances in the low-temperature exoproteome, especially in late growth stages. Our data therefore indicate that B. cereus may reduce its production of secreted protein toxins to maintain appropriate proteome dynamics, perhaps using catabolite repression to conserve energy for growth in cold-stress conditions, at the expense of virulence.
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35
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Yi Z, Cao X, Li H, Jian H, Xu X, Yu L, Tang X. Genomic analysis of Microbacterium sediminis YLB-01 T reveals backgrounds related to its deep-sea environment adaptation. Mar Genomics 2020; 56:100818. [PMID: 33632425 DOI: 10.1016/j.margen.2020.100818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 08/14/2020] [Accepted: 08/27/2020] [Indexed: 11/27/2022]
Abstract
Microbacterium sediminis YLB-01T, a piezotolerant and psychrotolerant actinomycete, was isolated from deep-sea sediment of the South-West Indian Ocean and could be a good model for understanding the adaptation of extremophiles to the benthic piezosphere. Here, we report the analysis of the complete genome sequence of strain YLB-01T. The genome sequence consists of a single circular chromosome comprising 2,792,195 bp and a linear plasmid comprising 127,669 bp with G + C content of 71.76 and 68.49 mol%, respectively. In this regard, strain YLB-01T possesses the smallest genome size but the highest G + C content among the genus Microbacterium sequenced to date. As the first complete genome sequence of the genus Microbacterium isolated from deep-sea environment, the strain YLB-01T genome is unique or enriched in genes involved in xenobiotics biodegradation and metabolism, compatible solutes, and transposases, some of which might be related to bacterial enhancement of ecological fitness in the deep sea.
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Affiliation(s)
- Zhiwei Yi
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xiaorong Cao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Hong Li
- China National Accreditation Insititute for Conformity Assessment, No. 8 Nanhuashi Dajie Chongwen District, Beijing 10086, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiashutong Xu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Libo Yu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xixiang Tang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; China Ocean Sample Respository (Biology), Xiamen 361005, China.
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36
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Pattanayak S, Priyadarsini S, Paul A, Kumar PR, Sahoo PK. Diversity of virulence-associated genes in pathogenic Aeromonas hydrophila isolates and their in vivo modulation at varied water temperatures. Microb Pathog 2020; 147:104424. [PMID: 32771658 DOI: 10.1016/j.micpath.2020.104424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/13/2020] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
Abstract
Most environmental parameters have no consistent effect on the expression of bacterial genes responsible for their virulence. However, as fish are poikilothermic, the possibility of temperature variation having a pronounced effect on the expression of virulence-associated gene(s) of bacteria infecting the host needs to be investigated. In this study, the diversity of virulence genes in seven Aeromonas hydrophila isolates collected from diseased fish from different parts of India was characterized, and the effect of temperature variation on the extent of expression of their virulence was investigated. All bacterial isolates were screened for a total of nine bacterial virulent genes {aerolysin, hemolysin, cytoen, outer membrane protein TS (Omp TS), elastase, flagellin, lipase, β hemolysin and type 3 secretion system}, and the diversity in their presence or absence were marked at a particular in vitro condition. Three bacterial isolates (nos. 1, 7 and 2) were selected for further study, based on their ability to cause varied mortalities (20-100%) in Labeo rohita juveniles in intraperitoneal challenge study. Further, three isolates were injected intraperitoneally into L. rohita fingerlings at three different temperatures (i.e., 20, 28 and 37 °C) and at 6 h post-challenge, the kidney samples were collected to measure the levels of all nine bacterial virulence genes using semi-quantitative PCR. The maximum level of amplicons of virulence genes in all three A. hydrophila isolates was noticed at 28 °C as compared to 37 °C and 20 °C. It was also observed that haemolysin played a more prominent role in the expression of virulence, when compared to cytoen gene. Hence, it was concluded that water temperature does play a crucial role in governing virulence gene expression, and a temperature of 28 °C would be considered as suitable for looking into the pathogenicity of A. hydrophila for conducting any challenge study with this organism in tropical environment.
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Affiliation(s)
- Sabyasachi Pattanayak
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Swatismita Priyadarsini
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Anirban Paul
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - P Rajesh Kumar
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - P K Sahoo
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India.
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Zhang W, Cao S, Ding W, Wang M, Fan S, Yang B, Mcminn A, Wang M, Xie BB, Qin QL, Chen XL, He J, Zhang YZ. Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics. MICROBIOME 2020; 8:47. [PMID: 32241287 PMCID: PMC7119284 DOI: 10.1186/s40168-020-00826-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/13/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND The Arctic and Antarctic are the two most geographically distant bioregions on earth. Recent sampling efforts and following metagenomics have shed light on the global ocean microbial diversity and function, yet the microbiota of polar regions has not been included in such global analyses. RESULTS Here a metagenomic study of seawater samples (n = 60) collected from different depths at 28 locations in the Arctic and Antarctic zones was performed, together with metagenomes from the Tara Oceans. More than 7500 (19%) polar seawater-derived operational taxonomic units could not be identified in the Tara Oceans datasets, and more than 3,900,000 protein-coding gene orthologs had no hits in the Ocean Microbial Reference Gene Catalog. Analysis of 214 metagenome assembled genomes (MAGs) recovered from the polar seawater microbiomes, revealed strains that are prevalent in the polar regions while nearly undetectable in temperate seawater. Metabolic pathway reconstruction for these microbes suggested versatility for saccharide and lipids biosynthesis, nitrate and sulfate reduction, and CO2 fixation. Comparison between the Arctic and Antarctic microbiomes revealed that antibiotic resistance genes were enriched in the Arctic while functions like DNA recombination were enriched in the Antarctic. CONCLUSIONS Our data highlight the occurrence of dominant and locally enriched microbes in the Arctic and Antarctic seawater with unique functional traits for environmental adaption, and provide a foundation for analyzing the global ocean microbiome in a more complete perspective. Video abstract.
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Affiliation(s)
- Weipeng Zhang
- College of Marine Life Science, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373 China
| | - Shunan Cao
- The Key Laboratory for Polar Science SOA, Polar Research Institute of China, Shanghai, 200136 China
| | - Wei Ding
- College of Marine Life Science, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003 China
| | - Meng Wang
- College of Marine Life Science, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003 China
| | - Shen Fan
- College of Marine Life Science, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003 China
| | - Bo Yang
- College of Marine Life Science, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003 China
| | - Andrew Mcminn
- College of Marine Life Science, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003 China
| | - Min Wang
- College of Marine Life Science, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003 China
| | - Bin-bin Xie
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237 China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237 China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237 China
| | - Jianfeng He
- The Key Laboratory for Polar Science SOA, Polar Research Institute of China, Shanghai, 200136 China
| | - Yu-Zhong Zhang
- College of Marine Life Science, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373 China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237 China
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38
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Skowron K, Wałecka-Zacharska E, Grudlewska K, Kwiecińska-Piróg J, Wiktorczyk N, Kowalska M, Paluszak Z, Kosek-Paszkowska K, Brożek K, Korkus J, Gospodarek-Komkowska E. Effect of Selected Environmental Factors on the Microbicidal Effectiveness of Radiant Catalytic Ionization. Front Microbiol 2020; 10:3057. [PMID: 32038531 PMCID: PMC6989485 DOI: 10.3389/fmicb.2019.03057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023] Open
Abstract
The aim of this study was the assessment of the effect of time exposure, temperature, distance, and organic contaminants on radiant catalytic ionization (RCI) microbicidal effectiveness. The number of all examined bacteria decreased together with time exposure of RCI. The lowest recovery was obtained, both from the rubber surface (6.36 log CFU × cm-2) and steel (6.04 log CFU × cm-2) in the case of Escherichia coli O157:H7. On the other hand, Staphylococcus aureus was isolated in the largest number (rubber: 7.88 log CFU × cm-2, steel: 7.79 log CFU × cm-2). Among the tested environmental conditions, the greatest bacterial population was re-isolated at 4°C (distance: 0.5 m, time: 24 h), whereas the lowest population was found at a distance of 0.5 m (temperature: 20°C, time: 24 h) and on surfaces without contamination. In the samples treated with RCI, the bacterial population was the lowest on non-contaminated surfaces, ranging from 3.76 log CFU × cm-2 (E. coli O157:H7) to 5.58 log CFU × cm-2 (S. aureus) for the rubber, and from 3.26 log CFU × cm-2 (E. coli O157:H7) to 5.20 log CFU × cm-2 (S. aureus) for the stainless steel. The highest bacteria number was isolated from surfaces contaminated with meat and fish pulp. The lowest bacterial reduction caused by RCI was found in the case of rubber contaminated with meat-fish pulp (24 h, 0.5 m, 20°C). The reduction rate was equal to 0.89 log CFU × cm-2 for S. aureus, 1.17 log CFU × cm-2 for Listeria monocytogenes, 1.43 log CFU × cm-2 for Salmonella Enteritidis and 1.61 log CFU × cm-2 for E. coli O157:H7. In turn, the greatest bacterial reduction was found in the case of non-contaminated steel (24 h, 0.5 m, 37°C). The reduction rate was equal to 4.52 log CFU × cm-2 for L. monocytogenes, 3.61 log CFU × cm-2 for S. Enteritidis, 2.98 log CFU × cm-2 for E. coli O157:H7 and 2.77 log CFU × cm-2 for S. aureus. RCI allows the inactivation of pathogens from stainless steel and rubber surfaces. Its efficacy is species-dependent and affected by environmental factors.
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Affiliation(s)
- Krzysztof Skowron
- Department of Microbiology, Collegium Medicum of L. Rydygier in Bydgoszcz, Nicolaus Copernicus University in Toruñ, Bydgoszcz, Poland
| | - Ewa Wałecka-Zacharska
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Katarzyna Grudlewska
- Department of Microbiology, Collegium Medicum of L. Rydygier in Bydgoszcz, Nicolaus Copernicus University in Toruñ, Bydgoszcz, Poland
| | - Joanna Kwiecińska-Piróg
- Department of Microbiology, Collegium Medicum of L. Rydygier in Bydgoszcz, Nicolaus Copernicus University in Toruñ, Bydgoszcz, Poland
| | - Natalia Wiktorczyk
- Department of Microbiology, Collegium Medicum of L. Rydygier in Bydgoszcz, Nicolaus Copernicus University in Toruñ, Bydgoszcz, Poland
| | - Maria Kowalska
- Department of Food Analytics and Environmental Protection, Faculty of Chemical Technology and Engineering, UTP University of Sciences and Technology in Bydgoszcz, Bydgoszcz, Poland
| | - Zbigniew Paluszak
- Department of Microbiology and Food Technology, UTP University of Sciences and Technology in Bydgoszcz, Bydgoszcz, Poland
| | - Katarzyna Kosek-Paszkowska
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Klaudia Brożek
- Department of Microbiology, Collegium Medicum of L. Rydygier in Bydgoszcz, Nicolaus Copernicus University in Toruñ, Bydgoszcz, Poland
| | - Jakub Korkus
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Collegium Medicum of L. Rydygier in Bydgoszcz, Nicolaus Copernicus University in Toruñ, Bydgoszcz, Poland
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Kowallis KA, Duvall SW, Zhao W, Childers WS. Manipulation of Bacterial Signaling Using Engineered Histidine Kinases. Methods Mol Biol 2020; 2077:141-163. [PMID: 31707657 DOI: 10.1007/978-1-4939-9884-5_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two-component systems allow bacteria to respond to changes in environmental or cytosolic conditions through autophosphorylation of a histidine kinase (HK) and subsequent transfer of the phosphate group to its downstream cognate response regulator (RR). The RR then elicits a cellular response, commonly through regulation of transcription. Engineering two-component system signaling networks provides a strategy to study bacterial signaling mechanisms related to bacterial cell survival, symbiosis, and virulence, and to develop sensory devices in synthetic biology. Here we focus on the principles for engineering the HK to identify unknown signal inputs, test signal transmission mechanisms, design small molecule sensors, and rewire two-component signaling networks.
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Affiliation(s)
| | - Samuel W Duvall
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Zhao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - W Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA. .,Chevron Science Center, University of Pittsburgh, Pittsburgh, PA, USA.
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40
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Inactivation of Listeria Monocytogenes at various growth temperatures by ultrasound pretreatment and cold plasma. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2019.108635] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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41
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Magnetoreception in Microorganisms. Trends Microbiol 2019; 28:266-275. [PMID: 31753537 DOI: 10.1016/j.tim.2019.10.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 11/24/2022]
Abstract
Magnetoreception is the sense whereby organisms geolocate and navigate in response to the Earth's magnetic field lines. For decades, magnetotactic bacteria have been the only known magnetoreceptive microorganisms. The magnetotactic behaviour of these aquatic prokaryotes is due to the biomineralization of magnetic crystals. While an old report alleged the existence of microbial algae with similar behaviour, recent discoveries have demonstrated the existence of unicellular eukaryotes able to sense the geomagnetic field, and have revealed different mechanisms and strategies involved in such a sensing. Some ciliates can be magnetically guided after predation of magnetotactic bacteria, while some flagellates acquired this sense through symbiosis with magnetic bacteria. A report has even suggested that some magnetotactic protists could biomineralize magnetic crystals.
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Bianco A, Deguillaume L, Chaumerliac N, Vaïtilingom M, Wang M, Delort AM, Bridoux MC. Effect of endogenous microbiota on the molecular composition of cloud water: a study by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Sci Rep 2019; 9:7663. [PMID: 31113999 PMCID: PMC6529453 DOI: 10.1038/s41598-019-44149-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/07/2019] [Indexed: 11/23/2022] Open
Abstract
A cloud water sample collected at the puy de Dôme observatory (PUY) has been incubated under dark conditions, with its endogenous microbiota at two different temperatures (5 and 15 °C), and the change in the molecular organic composition of this sample was analyzed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Microorganisms were metabolically active and strongly modified the dissolved organic matter since they were able to form and consume many compounds. Using Venn diagrams, four fractions of compounds were identified: (1) compounds consumed by microbial activity; (2) compounds not transformed during incubation; (3) compounds resulting from dark chemistry (i.e., hydrolysis and Fenton reactions) and, finally, (4) compounds resulting from microbial metabolic activity. At 15 °C, microorganisms were able to consume 58% of the compounds initially present and produce 266 new compounds. For this cloud sample, the impact of dark chemistry was negligible. Decreasing the temperature to 5 °C led to the more efficient degradation of organic compounds (1716 compounds vs. 1094 at 15 °C) but with the less important production of new ones (173). These transformations were analyzed using a division into classes based on the O/C and H/C ratios: lipid-like compounds, aliphatic/peptide-like compounds, carboxylic-rich alicyclic molecule (CRAM)-like structures, carbohydrate-like compounds, unsaturated hydrocarbons, aromatic structures and highly oxygenated compounds (HOCs). Lipid-like, aliphatic/peptide-like and CRAMs-like compounds were the most impacted since they were consumed to maintain the microbial metabolism. On the contrary, the relative percentages of CRAMs and carbohydrates increased after incubation.
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Affiliation(s)
- Angelica Bianco
- Université Clermont Auvergne, CNRS Laboratoire de Météorologie Physique, F-63000, Clermont-Ferrand, France.,CEA, DAM, DIF, F-91297, Arpajon, France
| | - Laurent Deguillaume
- Université Clermont Auvergne, CNRS Laboratoire de Météorologie Physique, F-63000, Clermont-Ferrand, France.
| | - Nadine Chaumerliac
- Université Clermont Auvergne, CNRS Laboratoire de Météorologie Physique, F-63000, Clermont-Ferrand, France
| | - Mickaël Vaïtilingom
- Université Clermont Auvergne, CNRS Laboratoire de Météorologie Physique, F-63000, Clermont-Ferrand, France.,Laboratoire de Recherche en Géosciences et Energies (LaRGE), Departement of Physics, Université des Antilles, Pointe-à-Pitre, France
| | - Miao Wang
- Université Clermont Auvergne, CNRS Laboratoire de Météorologie Physique, F-63000, Clermont-Ferrand, France
| | - Anne-Marie Delort
- Université Clermont Auvergne, CNRS, SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, F-63000, Clermont-Ferrand, France
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Bale NJ, Rijpstra WIC, Sahonero-Canavesi DX, Oshkin IY, Belova SE, Dedysh SN, Sinninghe Damsté JS. Fatty Acid and Hopanoid Adaption to Cold in the Methanotroph Methylovulum psychrotolerans. Front Microbiol 2019; 10:589. [PMID: 31024466 PMCID: PMC6460317 DOI: 10.3389/fmicb.2019.00589] [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: 10/12/2018] [Accepted: 03/07/2019] [Indexed: 12/31/2022] Open
Abstract
Three strains of aerobic psychrotolerant methanotrophic bacteria Methylovulum psychrotolerans, isolated from geographically remote low-temperature environments in Northern Russia, were grown at three different growth temperatures, 20, 10 and 4°C and were found to be capable of oxidizing methane at all temperatures. The three M. psychrotolerans strains adapted their membranes to decreasing growth temperature by increasing the percent of unsaturated fatty acid (FAs), both for the bulk and intact polar lipid (IPL)-bound FAs. Furthermore, the ratio of βOH-C16:0 to n-C16:0 increased as growth temperature decreased. The IPL head group composition did not change as an adaption to temperature. The most notable hopanoid temperature adaptation of M. psychrotolerans was an increase in unsaturated hopanols with decreasing temperature. As the growth temperature decreased from 20 to 4°C, the percent of unsaturated M. psychrotolerans bulk-FAs increased from 79 to 89 % while the total percent of unsaturated hopanoids increased from 27 to 49 %. While increased FA unsaturation in response to decreased temperature is a commonly observed response in order to maintain the liquid-crystalline character of bacterial membranes, hopanoid unsaturation upon cold exposition has not previously been described. In order to investigate the mechanisms of both FA and hopanoid cold-adaption in M. psychrotolerans we identified genes in the genome of M. psychrotolerans that potentially code for FA and hopanoid desaturases. The unsaturation of hopanoids represents a novel membrane adaption to maintain homeostasis upon cold adaptation.
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Affiliation(s)
- Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, and Utrecht University, Texel, Netherlands
| | - W Irene C Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, and Utrecht University, Texel, Netherlands
| | - Diana X Sahonero-Canavesi
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, and Utrecht University, Texel, Netherlands
| | - Igor Y Oshkin
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Svetlana E Belova
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Svetlana N Dedysh
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, and Utrecht University, Texel, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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Koo H, Hakim JA, Morrow CD, Crowley MR, Andersen DT, Bej AK. Metagenomic Analysis of Microbial Community Compositions and Cold-Responsive Stress Genes in Selected Antarctic Lacustrine and Soil Ecosystems. Life (Basel) 2018; 8:life8030029. [PMID: 29997353 PMCID: PMC6161096 DOI: 10.3390/life8030029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 11/16/2022] Open
Abstract
This study describes microbial community compositions, and various cold-responsive stress genes, encompassing cold-induced proteins (CIPs) and cold-associated general stress-responsive proteins (CASPs) in selected Antarctic lake water, sediment, and soil metagenomes. Overall, Proteobacteria and Bacteroidetes were the major taxa in all metagenomes. Prochlorococcus and Thiomicrospira were highly abundant in waters, while Myxococcus, Anaeromyxobacter, Haliangium, and Gloeobacter were dominant in the soil and lake sediment metagenomes. Among CIPs, genes necessary for DNA replication, translation initiation, and transcription termination were highly abundant in all metagenomes. However, genes for fatty acid desaturase (FAD) and trehalose synthase (TS) were common in the soil and lake sediment metagenomes. Interestingly, the Lake Untersee water and sediment metagenome samples contained histone-like nucleoid structuring protein (H-NS) and all genes for CIPs. As for the CASPs, high abundances of a wide range of genes for cryo- and osmo-protectants (glutamate, glycine, choline, and betaine) were identified in all metagenomes. However, genes for exopolysaccharide biosynthesis were dominant in Lake Untersee water, sediment, and other soil metagenomes. The results from this study indicate that although diverse microbial communities are present in various metagenomes, they share common cold-responsive stress genes necessary for their survival and sustenance in the extreme Antarctic conditions.
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Affiliation(s)
- Hyunmin Koo
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Michael R Crowley
- Department of Genetics, Heflin Center Genomics Core, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Dale T Andersen
- Carl Sagan Center, SETI Institute, Mountain View, California, CA 94043, USA.
| | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Ricke SC, Dawoud TM, Kim SA, Park SH, Kwon YM. Salmonella Cold Stress Response: Mechanisms and Occurrence in Foods. ADVANCES IN APPLIED MICROBIOLOGY 2018; 104:1-38. [PMID: 30143250 DOI: 10.1016/bs.aambs.2018.03.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Since bacteria in foods often encounter various cold environments during food processing, such as chilling, cold chain distribution, and cold storage, lower temperatures can become a major stress environment for foodborne pathogens. Bacterial responses in stressful environments have been considered in the past, but now the importance of stress responses at the molecular level is becoming recognized. Documenting how bacterial changes occur at the molecular level may help to achieve the in-depth understanding of stress responses, to predict microbial fate when they encounter cold temperatures, and to design and develop more effective strategies to control pathogens in food for ensuring food safety. Microorganisms differ in responding to a sudden downshift in temperature and this, in turn, impacts their metabolic processes and can cause various structural modifications. In this review, the fundamental aspects of bacterial cold stress responses focused on cell membrane modification, DNA supercoiling modification, transcriptional and translational responses, cold-induced protein synthesis including CspA, CsdA, NusA, DnaA, RecA, RbfA, PNPase, KsgA, SrmB, trigger factors, and initiation factors are discussed. In this context, specific Salmonella responses to cold temperature including growth, injury, and survival and their physiological and genetic responses to cold environments with a focus on cross-protection, different gene expression levels, and virulence factors will be discussed.
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Affiliation(s)
- Steven C Ricke
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States; Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Food Science, University of Arkansas, Fayetteville, AR, United States.
| | - Turki M Dawoud
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States; Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Sun Ae Kim
- Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Food Science, University of Arkansas, Fayetteville, AR, United States; Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Si Hong Park
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States; Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Young Min Kwon
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States; Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
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Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa. G3-GENES GENOMES GENETICS 2018; 8:1439-1454. [PMID: 29563189 PMCID: PMC5940138 DOI: 10.1534/g3.118.200112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
When subjected to rapid drops of temperature (cold shock), Neurospora responds with a temporary shift in its morphology. This report is the first to examine this response genetically. We report here the results of a screen of selected mutants from the Neurospora knockout library for alterations in their morphological response to cold shock. Three groups of knockouts were selected to be subject to this screen: genes previously suspected to be involved in hyphal development as well as knockouts resulting in morphological changes; transcription factors; and genes homologous to E. coli genes known to alter their expression in response to cold shock. A total of 344 knockout strains were subjected to cold shock. Of those, 118 strains were identified with altered responses. We report here the cold shock morphologies and GO categorizations of strains subjected to this screen. Of strains with knockouts in genes associated with hyphal growth or morphology, 33 of 131 tested (25%) showed an altered response to cold shock. Of strains with knockouts in transcription factor genes, 30 of 145 (20%) showed an altered response to cold shock. Of strains with knockouts in genes homologous to E. coli genes which display altered levels of transcription in response to cold shock, a total of 55 of 68 tested (81%) showed an altered cold shock response. This suggests that the response to cold shock in these two organisms is largely shared in common.
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Bacteria from Antarctic environments: diversity and detection of antimicrobial, antiproliferative, and antiparasitic activities. Polar Biol 2018. [DOI: 10.1007/s00300-018-2300-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Firdaus-Raih M, Hashim NHF, Bharudin I, Abu Bakar MF, Huang KK, Alias H, Lee BKB, Mat Isa MN, Mat-Sharani S, Sulaiman S, Tay LJ, Zolkefli R, Muhammad Noor Y, Law DSN, Abdul Rahman SH, Md-Illias R, Abu Bakar FD, Najimudin N, Abdul Murad AM, Mahadi NM. The Glaciozyma antarctica genome reveals an array of systems that provide sustained responses towards temperature variations in a persistently cold habitat. PLoS One 2018; 13:e0189947. [PMID: 29385175 PMCID: PMC5791967 DOI: 10.1371/journal.pone.0189947] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/05/2017] [Indexed: 01/01/2023] Open
Abstract
Extremely low temperatures present various challenges to life that include ice formation and effects on metabolic capacity. Psyhcrophilic microorganisms typically have an array of mechanisms to enable survival in cold temperatures. In this study, we sequenced and analysed the genome of a psychrophilic yeast isolated in the Antarctic region, Glaciozyma antarctica. The genome annotation identified 7857 protein coding sequences. From the genome sequence analysis we were able to identify genes that encoded for proteins known to be associated with cold survival, in addition to annotating genes that are unique to G. antarctica. For genes that are known to be involved in cold adaptation such as anti-freeze proteins (AFPs), our gene expression analysis revealed that they were differentially transcribed over time and in response to different temperatures. This indicated the presence of an array of adaptation systems that can respond to a changing but persistent cold environment. We were also able to validate the activity of all the AFPs annotated where the recombinant AFPs demonstrated anti-freeze capacity. This work is an important foundation for further collective exploration into psychrophilic microbiology where among other potential, the genes unique to this species may represent a pool of novel mechanisms for cold survival.
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Affiliation(s)
- Mohd Firdaus-Raih
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- * E-mail:
| | - Noor Haza Fazlin Hashim
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Izwan Bharudin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Mohd Faizal Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Malaysia Genome Institute, Jalan Bangi Lama, Kajang, Selangor, Malaysia
| | - Kie Kyon Huang
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Halimah Alias
- Malaysia Genome Institute, Jalan Bangi Lama, Kajang, Selangor, Malaysia
| | - Bernard K. B. Lee
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Mohd Noor Mat Isa
- Malaysia Genome Institute, Jalan Bangi Lama, Kajang, Selangor, Malaysia
| | - Shuhaila Mat-Sharani
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Malaysia Genome Institute, Jalan Bangi Lama, Kajang, Selangor, Malaysia
| | - Suhaila Sulaiman
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Lih Jinq Tay
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Radziah Zolkefli
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Yusuf Muhammad Noor
- Malaysia Genome Institute, Jalan Bangi Lama, Kajang, Selangor, Malaysia
- Department of Biosciences Engineering, Faculty of Chemical & Natural Resources Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Douglas Sie Nguong Law
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Siti Hamidah Abdul Rahman
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Rosli Md-Illias
- Department of Biosciences Engineering, Faculty of Chemical & Natural Resources Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Nazalan Najimudin
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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Pittera J, Jouhet J, Breton S, Garczarek L, Partensky F, Maréchal É, Nguyen NA, Doré H, Ratin M, Pitt FD, Scanlan DJ, Six C. Thermoacclimation and genome adaptation of the membrane lipidome in marine Synechococcus. Environ Microbiol 2017; 20:612-631. [PMID: 29124854 DOI: 10.1111/1462-2920.13985] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/20/2017] [Accepted: 11/02/2017] [Indexed: 12/01/2022]
Abstract
The marine cyanobacteria of the genus Synechococcus are important primary producers, displaying a wide latitudinal distribution that is underpinned by diversification into temperature ecotypes. The physiological basis underlying these ecotypes is poorly known. In many organisms, regulation of membrane fluidity is crucial for acclimating to variations in temperature. Here, we reveal the detailed composition of the membrane lipidome of the model strain Synechococcus sp. WH7803 and its response to temperature variation. Unlike freshwater strains, membranes are almost devoid of C18, mainly containing C14 and C16 chains with no more than two unsaturations. In response to cold, we observed a rarely observed process of acyl chain shortening that likely induces membrane thinning, along with specific desaturation activities. Both of these mechanisms likely regulate membrane fluidity, facilitating the maintenance of efficient photosynthetic activity. A comprehensive examination of 53 Synechococcus genomes revealed clade-specific gene sets regulating membrane lipids. In particular, the genes encoding desaturase enzymes, which is a key to the temperature stress response, appeared to be temperature ecotype-specific, with some of them originating from lateral transfers. Our study suggests that regulation of membrane fluidity has been among the important adaptation processes for the colonization of different thermal niches by marine Synechococcus.
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Affiliation(s)
- Justine Pittera
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Juliette Jouhet
- Institut de Biosciences et Biotechnologies de Grenoble, CEA Grenoble, Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, 38054 Grenoble cedex 9, France
| | - Solène Breton
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Laurence Garczarek
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Frédéric Partensky
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Éric Maréchal
- Institut de Biosciences et Biotechnologies de Grenoble, CEA Grenoble, Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, 38054 Grenoble cedex 9, France
| | - Ngoc A Nguyen
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Hugo Doré
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Morgane Ratin
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Frances D Pitt
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Christophe Six
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
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Jousse C, Dalle C, Canet I, Lagrée M, Traïkia M, Lyan B, Mendes C, Sancelme M, Amato P, Delort AM. Metabolomic study of the response to cold shock in a strain of Pseudomonas syringae isolated from cloud water. Metabolomics 2017; 14:11. [PMID: 30830325 DOI: 10.1007/s11306-017-1295-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/07/2017] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Active microorganisms have been recently discovered in clouds, thus demonstrating the capacity of microorganisms to exist in harsh environments, including exposure to UV and oxidants, osmotic and cold shocks, etc. It is important to understand how microorganisms respond to and survive such stresses at the metabolic level. OBJECTIVES The objective of this work is to assess metabolome modulation in a strain of Pseudomonas syringae isolated from cloud water and facing temperature downshift from 17 to 5 °C by identifying key molecules and pathways of the response/adaptation to cold shock. METHODS Bacterial extracts from suspensions of cells grown at 17 °C and further incubated in microcosms at 5 and 17 °C to mimic cloud conditions were analysed by combining LC-MS and NMR; the results were evaluated in comparison to similar suspensions kept at constant temperature. The differences in the metabolome profiles were deciphered using multivariate statistics (PLS-DA). RESULTS Key cold shock biomarkers were observed, including cryoprotectants (trehalose, glucose, glycerol, carnitine, glutamate), antioxidants (glutathione and carnitine) and their precursors, alkaloids (bellendine and slaframine) and metabolites involved in energy metabolism (ATP, carbohydrates). Furthermore, new short peptides (nine dipeptides and a tetrapeptide) were found that have no known function. CONCLUSIONS This study shows that in response to cold temperatures, Pseudomonas syringae PDD-32b-74 demonstrates numerous metabolism modifications to counteract the impacts of low temperatures.
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Affiliation(s)
- Cyril Jousse
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Céline Dalle
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Isabelle Canet
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
| | - Marie Lagrée
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Mounir Traïkia
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Bernard Lyan
- Université Clermont Auvergne - INRA, UNH, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Cédric Mendes
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Martine Sancelme
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
| | - Pierre Amato
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
| | - Anne-Marie Delort
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France.
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France.
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