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Reiche T, Hageskal G, Hoel S, Tøndervik A, Nærdal GK, Heggeset TMB, Haugen T, Trøen HH, Jakobsen AN. Disinfection in a salmon processing plant: Impact on bacterial communities and efficacy towards foodborne bacteria and biofilms. Int J Food Microbiol 2024; 424:110853. [PMID: 39116462 DOI: 10.1016/j.ijfoodmicro.2024.110853] [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: 05/04/2024] [Revised: 07/19/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024]
Abstract
Salmon aquaculture is the fastest growing food production system in the world. Deficiencies in the quality or safety of salmon can have global repercussions. Controlling food safety aspects during production is therefore essential. Here, we investigate the state of hygiene in a salmon processing plant using next generation sequencing and classical culture-dependent methods to characterize the surface microbiota before and after cleaning and disinfection (C&D) at ten surface sampling points. Total aerobic counts revealed an average reduction in the bacterial loads of 1.1 log CFU/cm2 by C&D. The highest relative abundance in the core microbiota before C&D was assigned to Acinetobacter, Mycoplasmataceae, Pseudomonas and Enterobacteriaceae in descending order. After C&D, we observed a significant increase in the relative abundance of Pseudomonas (p < 0.05). However, variations were found between conveyors, processing machines and drains. To assess the efficacy of commercial disinfectants, we performed susceptibility assays using advanced robotic high-throughput technologies and included foodborne bacteria which may affect food safety and spoilage. These included 128 Pseudomonas isolates, 46 Aeromonas isolates and 59 Enterobacterales isolates sampled from the salmon processing plant. Generally, minimum inhibitory concentrations (MICs) of the disinfectants were below the user concentration recommended by the producer for most isolates. BacTiter-Glo biofilm assays revealed that 30 min exposure to six out of eight commercial disinfectants resulted in an average reduction of relative luminescence >95 % in 59 single-species biofilms selected for screening. However, disinfection alone may not always be sufficient to eradicate biofilms completely. C&D routines must therefore be continuously assessed to maintain food safety and quality. The results from this study can contribute to understand and improve the state of hygiene in salmon processing environments.
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Affiliation(s)
- Thorben Reiche
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim 7012, Norway.
| | - Gunhild Hageskal
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim 7034, Norway
| | - Sunniva Hoel
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim 7012, Norway
| | - Anne Tøndervik
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim 7034, Norway
| | - Guro Kruge Nærdal
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim 7034, Norway
| | | | - Tone Haugen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim 7034, Norway
| | - Hanne Hein Trøen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim 7034, Norway
| | - Anita Nordeng Jakobsen
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim 7012, Norway
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2
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Yin J, Li J, Xie H, Wang Y, Zhao J, Wang L, Wu L. Unveiling cold Code: Acinetobacter calcoaceticus TY1's adaptation strategies and applications in nitrogen treatment. BIORESOURCE TECHNOLOGY 2024; 413:131449. [PMID: 39244103 DOI: 10.1016/j.biortech.2024.131449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 09/01/2024] [Accepted: 09/04/2024] [Indexed: 09/09/2024]
Abstract
Overcoming low nitrogen removal efficiency at low temperatures is a challenge in biological treatment. This study investigated the cold-tolerant heterotrophic nitrification-aerobic denitrification by Acinetobacter calcoaceticus TY1. Transcriptomic and biochemical analyses indicated that strain TY1 upregulated genes for energy production, assimilation, cell motility, and antioxidant enzyme production under cold stress, maintaining functions such as energy supply, nitrogen utilization, and oxidative defense. Increasing the synthesis of extracellular polysaccharides, unsaturated fatty acids, and medium-chain fatty acids and secreting large amounts of antioxidant enzymes ensured cell membrane flexibility while enhancing the antioxidant system. Immobilization experiments showed that biofilms accelerated the removal of nitrogen pollutants and demonstrated good stability, with carriers being reusable to five times, maintaining high ammonia nitrogen (63.90 %) and total nitrogen (50.66 %) removal rates. These findings reveal the cold tolerance mechanisms of strain TY1 and its excellent practical potential as a candidate for wastewater treatment in cold regions.
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Affiliation(s)
- Jiahui Yin
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Junyi Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Hongliang Xie
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Yongman Wang
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Jialin Zhao
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Lixin Wang
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Linhui Wu
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China; Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle, Hohhot 010021, PR China.
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3
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Mittal P, Sinha AK, Pandiyan A, Kumari L, Ray MK, Pavankumar TL. A type II toxin-antitoxin system is responsible for the cell death at low temperature in Pseudomonas syringae Lz4W lacking RNase R. J Biol Chem 2024; 300:107600. [PMID: 39059490 PMCID: PMC11375266 DOI: 10.1016/j.jbc.2024.107600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/17/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
RNase R (encoded by the rnr gene) is a highly processive 3' → 5' exoribonuclease essential for the growth of the psychrotrophic bacterium Pseudomonas syringae Lz4W at low temperature. The cell death of a rnr deletion mutant at low temperature has been previously attributed to processing defects in 16S rRNA, defective ribosomal assembly, and inefficient protein synthesis. We recently showed that RNase R is required to protect P. syringae Lz4W from DNA damage and oxidative stress, independent of its exoribonuclease activity. Here, we show that the processing defect in 16S rRNA does not cause cell death of the rnr mutant of P. syringae at low temperature. Our results demonstrate that the rnr mutant of P. syringae Lz4W, complemented with a RNase R deficient in exoribonuclease function (RNase RD284A), is defective in 16S rRNA processing but can grow at 4 °C. This suggested that the processing defect in ribosomal RNAs is not a cause of the cold sensitivity of the rnr mutant. We further show that the rnr mutant accumulates copies of the indigenous plasmid pLz4W that bears a type II toxin-antitoxin (TA) system (P. syringae antitoxin-P. syringae toxin). This phenotype was rescued by overexpressing antitoxin psA in the rnr mutant, suggesting that activation of the type II TA system leads to cold sensitivity of the rnr mutant of P. syringae Lz4W. Here, we report a previously unknown functional relationship between the cold sensitivity of the rnr mutant and a type II TA system in P. syringae Lz4W.
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Affiliation(s)
- Pragya Mittal
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India; Celtic Renewables Ltd, Edinburgh Napier University, Edinburgh, UK.
| | - Anurag K Sinha
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India; National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Apuratha Pandiyan
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Leela Kumari
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Malay K Ray
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Theetha L Pavankumar
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India; Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA; Department of Molecular and Cellular Biology, University of California, Davis, California, USA.
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4
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Pavankumar TL. RNase R vs. PNPase: selecting the best-suited exoribonuclease for environmental adaptation. Extremophiles 2024; 28:35. [PMID: 39052080 DOI: 10.1007/s00792-024-01350-6] [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: 02/28/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024]
Abstract
3' → 5' exoribonucleases play a critical role in many aspects of RNA metabolism. RNase R, PNPase, and RNase II are the major contributors to RNA processing, maturation, and quality control in bacteria. Bacteria don't seem to have dedicated RNA degradation machineries to process different classes of RNAs. Under different environmental and physiological conditions, their roles can be redundant and sometimes overlapping. Here, I discuss why PNPase and RNase R may have switched their physiological roles in some bacterial species to adapt to environmental conditions, despite being biochemically distinct exoribonucleases.
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Affiliation(s)
- Theetha L Pavankumar
- Department of Microbiology and Molecular Genetics, and Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616, USA.
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5
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Moreno-Pino M, Manrique-de-la-Cuba MF, López-Rodríguez M, Parada-Pozo G, Rodríguez-Marconi S, Ribeiro CG, Flores-Herrera P, Guajardo M, Trefault N. Unveiling microbial guilds and symbiotic relationships in Antarctic sponge microbiomes. Sci Rep 2024; 14:6371. [PMID: 38493232 PMCID: PMC10944490 DOI: 10.1038/s41598-024-56480-w] [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: 09/12/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Marine sponges host diverse microbial communities. Although we know many of its ecological patterns, a deeper understanding of the polar sponge holobiont is still needed. We combine high-throughput sequencing of ribosomal genes, including the largest taxonomic repertoire of Antarctic sponge species analyzed to date, functional metagenomics, and metagenome-assembled genomes (MAGs). Our findings show that sponges harbor more exclusive bacterial and archaeal communities than seawater, while microbial eukaryotes are mostly shared. Furthermore, bacteria in Antarctic sponge holobionts establish more cooperative interactions than in sponge holobionts from other environments. The bacterial classes that established more positive relations were Bacteroidia, Gamma- and Alphaproteobacteria. Antarctic sponge microbiomes contain microbial guilds that encompass ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and sulfur-oxidizing bacteria. The retrieved MAGs showed a high level of novelty and streamlining signals and belong to the most abundant members of the main microbial guilds in the Antarctic sponge holobiont. Moreover, the genomes of these symbiotic bacteria contain highly abundant functions related to their adaptation to the cold environment, vitamin production, and symbiotic lifestyle, helping the holobiont survive in this extreme environment.
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Affiliation(s)
- Mario Moreno-Pino
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | | | - Génesis Parada-Pozo
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile
- Millenium Nucleus in Marine Agronomy of Seaweed Holobionts (MASH), Puerto Montt, Chile
| | | | | | - Patricio Flores-Herrera
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile
| | - Mariela Guajardo
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile.
- Millenium Nucleus in Marine Agronomy of Seaweed Holobionts (MASH), Puerto Montt, Chile.
- FONDAP Center IDEAL- Dynamics of High Latitude Marine Ecosystem, Valdivia, Chile.
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6
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Yang P, Yuan P, Liu W, Zhao Z, Bernier MC, Zhang C, Adhikari A, Opiyo SO, Zhao L, Banks F, Xia Y. Plant Growth Promotion and Plant Disease Suppression Induced by Bacillus amyloliquefaciens Strain GD4a. PLANTS (BASEL, SWITZERLAND) 2024; 13:672. [PMID: 38475518 DOI: 10.3390/plants13050672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Botrytis cinerea, the causative agent of gray mold disease (GMD), invades plants to obtain nutrients and disseminates through airborne conidia in nature. Bacillus amyloliquefaciens strain GD4a, a beneficial bacterium isolated from switchgrass, shows great potential in managing GMD in plants. However, the precise mechanism by which GD4a confers benefits to plants remains elusive. In this study, an A. thaliana-B. cinerea-B. amyloliquefaciens multiple-scale interaction model was used to explore how beneficial bacteria play essential roles in plant growth promotion, plant pathogen suppression, and plant immunity boosting. Arabidopsis Col-0 wild-type plants served as the testing ground to assess GD4a's efficacy. Additionally, bacterial enzyme activity and targeted metabolite tests were conducted to validate GD4a's potential for enhancing plant growth and suppressing plant pathogens and diseases. GD4a was subjected to co-incubation with various bacterial, fungal, and oomycete pathogens to evaluate its antagonistic effectiveness in vitro. In vivo pathogen inoculation assays were also carried out to investigate GD4a's role in regulating host plant immunity. Bacterial extracellular exudate (BEE) was extracted, purified, and subjected to untargeted metabolomics analysis. Benzocaine (BEN) from the untargeted metabolomics analysis was selected for further study of its function and related mechanisms in enhancing plant immunity through plant mutant analysis and qRT-PCR analysis. Finally, a comprehensive model was formulated to summarize the potential benefits of applying GD4a in agricultural systems. Our study demonstrates the efficacy of GD4a, isolated from switchgrass, in enhancing plant growth, suppressing plant pathogens and diseases, and bolstering host plant immunity. Importantly, GD4a produces a functional bacterial extracellular exudate (BEE) that significantly disrupts the pathogenicity of B. cinerea by inhibiting fungal conidium germination and hypha formation. Additionally, our study identifies benzocaine (BEN) as a novel small molecule that triggers basal defense, ISR, and SAR responses in Arabidopsis plants. Bacillus amyloliquefaciens strain GD4a can effectively promote plant growth, suppress plant disease, and boost plant immunity through functional BEE production and diverse gene expression.
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Affiliation(s)
- Piao Yang
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Pu Yuan
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Wenshan Liu
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Zhenzhen Zhao
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Matthew C Bernier
- Campus Chemical Instrument Center, Mass Spectrometry and Proteomics Facility, The Ohio State University, Columbus, OH 43210, USA
| | - Chunquan Zhang
- College of Agriculture and Applied Sciences, Alcorn State University, Lorman, MS 39096, USA
| | - Ashna Adhikari
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Stephen Obol Opiyo
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Lijing Zhao
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Fredrekis Banks
- College of Agriculture and Applied Sciences, Alcorn State University, Lorman, MS 39096, USA
| | - Ye Xia
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA
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7
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Mittal P, Sipani R, Pandiyan A, Sulthana S, Sinha AK, Hussain A, Ray MK, Pavankumar TL. Exoribonuclease RNase R protects Antarctic Pseudomonas syringae Lz4W from DNA damage and oxidative stress. Appl Environ Microbiol 2023; 89:e0116823. [PMID: 37905926 PMCID: PMC10686088 DOI: 10.1128/aem.01168-23] [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] [Accepted: 08/30/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE Bacterial exoribonucleases play a crucial role in RNA maturation, degradation, quality control, and turnover. In this study, we have uncovered a previously unknown role of 3'-5' exoribonuclease RNase R of Pseudomonas syringae Lz4W in DNA damage and oxidative stress response. Here, we show that neither the exoribonuclease function of RNase R nor its association with the RNA degradosome complex is essential for this function. Interestingly, in P. syringae Lz4W, hydrolytic RNase R exhibits physiological roles similar to phosphorolytic 3'-5' exoribonuclease PNPase of E. coli. Our data suggest that during the course of evolution, mesophilic E. coli and psychrotrophic P. syringae have apparently swapped these exoribonucleases to adapt to their respective environmental growth conditions.
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Affiliation(s)
- Pragya Mittal
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Rashmi Sipani
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Apuratha Pandiyan
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Shaheen Sulthana
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Anurag K. Sinha
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Ashaq Hussain
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Malay K. Ray
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Theetha L. Pavankumar
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
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8
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Musialowski M, Kowalewska Ł, Stasiuk R, Krucoń T, Debiec-Andrzejewska K. Metabolically versatile psychrotolerant Antarctic bacterium Pseudomonas sp. ANT_H12B is an efficient producer of siderophores and accompanying metabolites (SAM) useful for agricultural purposes. Microb Cell Fact 2023; 22:85. [PMID: 37120505 PMCID: PMC10149013 DOI: 10.1186/s12934-023-02105-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Bacterial siderophores are chelating compounds with the potential of application in agriculture, due to their plant growth-promoting (PGP) properties, however, high production and purification costs are limiting factors for their wider application. Cost-efficiency of the production could be increased by omitting purification processes, especially since siderophores accompanying metabolites (SAM) often also possess PGP traits. In this study, the metabolism versatility of Pseudomonas sp. ANT_H12B was used for the optimization of siderophores production and the potential of these metabolites and SAM was characterized in the context of PGP properties. RESULTS The metabolic diversity of ANT_H12B was examined through genomic analysis and phenotype microarrays. The strain was found to be able to use numerous C, N, P, and S sources, which allowed for the design of novel media suitable for efficient production of siderophores in the form of pyoverdine (223.50-512.60 μM). Moreover, depending on the culture medium, the pH of the siderophores and SAM solutions varied from acidic (pH < 5) to alkaline (pH > 8). In a germination test, siderophores and SAM were shown to have a positive effect on plants, with a significant increase in germination percentage observed in beetroot, pea, and tobacco. The PGP potential of SAM was further elucidated through GC/MS analysis, which revealed other compounds with PGP potential, such as indolic acetic acids, organic acids, fatty acids, sugars and alcohols. These compounds not only improved seed germination but could also potentially be beneficial for plant fitness and soil quality. CONCLUSIONS Pseudomonas sp. ANT_H12B was presented as an efficient producer of siderophores and SAM which exhibit PGP potential. It was also shown that omitting downstream processes could not only limit the costs of siderophores production but also improve their agricultural potential.
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Affiliation(s)
- M Musialowski
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Ł Kowalewska
- Department of Plant Anatomy and Cytology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, 02-096, Warsaw, Poland
| | - R Stasiuk
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - T Krucoń
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - K Debiec-Andrzejewska
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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9
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Thompson TP, Megaw J, Kelly SA, Hopps J, Gilmore BF. Microbial communities of halite deposits and other hypersaline environments. ADVANCES IN APPLIED MICROBIOLOGY 2022; 120:1-32. [PMID: 36243451 DOI: 10.1016/bs.aambs.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Large regions of Earth's surface are underlain by salt deposits that evaporated from ancient oceans and are populated by extreme halophilic microbes. While the microbiology of ancient evaporites has been well studied, the ecology of halite deposits and more recently formed NaCl "salticle" stalactite structures (speleothems) in a Triassic halite mine are less well characterized. The microbiome of Kilroot Salt Mine was profiled using conventional and enhanced culturing techniques. From this, 89 halophilic archaeal isolates from six known genera, and 55 halophilic or halotolerant bacterial isolates from 18 genera were obtained. Culture-independent metagenomic approaches also revealed that culturing techniques were inadvertently biased toward specific taxa, and the need for optimized isolation procedures are required to enhance cultivation diversity. Speleothems formed from saturated brines are unique structures that have the potential to entomb haloarchaea cells for thousands of years within fluid inclusions. The presence of such fluid inclusions, alongside the high abundance of genes related to glycerol metabolism, biofilm formation, and persister cell formation is highly suggestive of an environmental niche that could promote longevity and survivability. Finally, previous studies reporting the discovery of novel biocatalysts from the Kilroot mine microbiome, suggests that this environment may be an untapped source of chemical diversity with high biodiscovery potential.
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Affiliation(s)
- Thomas P Thompson
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, United Kingdom.
| | - Julianne Megaw
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Stephen A Kelly
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, United Kingdom
| | - Jason Hopps
- Irish Salt Mining & Exploration Company Ltd., Carrickfergus, United Kingdom
| | - Brendan F Gilmore
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, United Kingdom
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10
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Sivasankar P, Poongodi S, Sivakumar K, Al-Qahtani WH, Arokiyaraj S, Jothiramalingam R. Exogenous production of cold-active cellulase from polar Nocardiopsis sp. with increased cellulose hydrolysis efficiency. Arch Microbiol 2022; 204:218. [PMID: 35333982 DOI: 10.1007/s00203-022-02830-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 03/08/2022] [Indexed: 12/01/2022]
Abstract
The present work was designed to isolate and characterise the actinobacteria in the Polar Front region of the Southern Ocean waters and species of Nocardiopsis and Streptomyces were identified. Among those, the psychrophilic actinobacterium, Nocardiopsis dassonvillei PSY13 was found to have good cellulolytic activity and it was further studied for the production and characterisation of cold-active cellulase enzyme. The latter was found to have a specific activity of 6.36 U/mg and a molar mass of 48 kDa with a 22.9-fold purification and 5% recovery at an optimum pH of 7.5 and a temperature of 10 °C. Given the importance of psychrophilic actinobacteria, N. dassonvillei PSY13 can be further exploited for its benefits, meaning that the Southern Ocean harbours biotechnologically important microorganisms that can be further explored for versatile biotechnological and industrial applications.
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Affiliation(s)
- Palaniappan Sivasankar
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965, Poznan, Poland. .,Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India.
| | - Subramaniam Poongodi
- Department of Microbiology, Shri Sakthikailassh Women's College, Salem, 636 003, Tamil Nadu, India
| | - Kannan Sivakumar
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India
| | - Wahidah H Al-Qahtani
- Department of Food Sciences & Nutrition, College of Food & Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Selvaraj Arokiyaraj
- Department of Food Science and Biotechnology, Sejong University, Seoul, South Korea
| | - R Jothiramalingam
- Department of Food Sciences & Nutrition, College of Food & Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
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11
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Abstract
Water is the cellular milieu, drives all biochemistry within Earth's biosphere and facilitates microbe-mediated decay processes. Instead of reviewing these topics, the current article focuses on the activities of water as a preservative-its capacity to maintain the long-term integrity and viability of microbial cells-and identifies the mechanisms by which this occurs. Water provides for, and maintains, cellular structures; buffers against thermodynamic extremes, at various scales; can mitigate events that are traumatic to the cell membrane, such as desiccation-rehydration, freeze-thawing and thermal shock; prevents microbial dehydration that can otherwise exacerbate oxidative damage; mitigates against biocidal factors (in some circumstances reducing ultraviolet radiation and diluting solute stressors or toxic substances); and is effective at electrostatic screening so prevents damage to the cell by the intense electrostatic fields of some ions. In addition, the water retained in desiccated cells (historically referred to as 'bound' water) plays key roles in biomacromolecular structures and their interactions even for fully hydrated cells. Assuming that the components of the cell membrane are chemically stable or at least repairable, and the environment is fairly constant, water molecules can apparently maintain membrane geometries over very long periods provided these configurations represent thermodynamically stable states. The spores and vegetative cells of many microbes survive longer in the presence of vapour-phase water (at moderate-to-high relative humidities) than under more-arid conditions. There are several mechanisms by which large bodies of water, when cooled during subzero weather conditions remain in a liquid state thus preventing potentially dangerous (freeze-thaw) transitions for their microbiome. Microbial life can be preserved in pure water, freshwater systems, seawater, brines, ice/permafrost, sugar-rich aqueous milieux and vapour-phase water according to laboratory-based studies carried out over periods of years to decades and some natural environments that have yielded cells that are apparently thousands, or even (for hypersaline fluid inclusions of mineralized NaCl) hundreds of millions, of years old. The term preservative has often been restricted to those substances used to extend the shelf life of foods (e.g. sodium benzoate, nitrites and sulphites) or those used to conserve dead organisms, such as ethanol or formaldehyde. For living microorganisms however, the ultimate preservative may actually be water. Implications of this role are discussed with reference to the ecology of halophiles, human pathogens and other microbes; food science; biotechnology; biosignatures for life and other aspects of astrobiology; and the large-scale release/reactivation of preserved microbes caused by global climate change.
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Affiliation(s)
- John E. Hallsworth
- Institute for Global Food SecuritySchool of Biological SciencesQueen’s University Belfast19 Chlorine GardensBelfastBT9 5DLUK
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12
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Hallsworth JE, Mancinelli RL, Conley CA, Dallas TD, Rinaldi T, Davila AF, Benison KC, Rapoport A, Cavalazzi B, Selbmann L, Changela H, Westall F, Yakimov MM, Amils R, Madigan MT. Astrobiology of life on Earth. Environ Microbiol 2021; 23:3335-3344. [PMID: 33817931 DOI: 10.1111/1462-2920.15499] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 11/29/2022]
Abstract
Astrobiology is mistakenly regarded by some as a field confined to studies of life beyond Earth. Here, we consider life on Earth through an astrobiological lens. Whereas classical studies of microbiology historically focused on various anthropocentric sub-fields (such as fermented foods or commensals and pathogens of crop plants, livestock and humans), addressing key biological questions via astrobiological approaches can further our understanding of all life on Earth. We highlight potential implications of this approach through the articles in this Environmental Microbiology special issue 'Ecophysiology of Extremophiles'. They report on the microbiology of places/processes including low-temperature environments and chemically diverse saline- and hypersaline habitats; aspects of sulphur metabolism in hypersaline lakes, dysoxic marine waters, and thermal acidic springs; biology of extremophile viruses; the survival of terrestrial extremophiles on the surface of Mars; biological soils crusts and rock-associated microbes of deserts; subsurface and deep biosphere, including a salticle formed within Triassic halite; and interactions of microbes with igneous and sedimentary rocks. These studies, some of which we highlight here, contribute to our understanding of the spatiotemporal reach of Earth'sfunctional biosphere, and the tenacity of terrestrial life. Their findings will help set the stage for future work focused on the constraints for life, and how organisms adapt and evolve to circumvent these constraints.
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Affiliation(s)
- John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 7BL, UK
| | - Rocco L Mancinelli
- Bay Area Environmental Research Institute, NASA Ames Research Center, Mountain View, CA, 94035, USA
| | | | - Tiffany D Dallas
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 7BL, UK
| | - Teresa Rinaldi
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, 00185, Italy
| | | | - Kathleen C Benison
- Department of Geology and Geography, West Virginia University, Morgantown, WV, 26506-6300, USA
| | - Alexander Rapoport
- Laboratory of Cell Biology, Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Str., 1-537, Riga, LV-1004, Latvia
| | - Barbara Cavalazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, 40126, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.,Italian Antarctic National Museum (MNA), Mycological Section, Genoa, 16128, Italy
| | - Hitesh Changela
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.,Department of Earth and Planetary Science, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Frances Westall
- CNRS, Ctr Biophys Mol UPR 4301, Rue Charles Sadron, CS 80054, Orleans, F-45071, France
| | - Michail M Yakimov
- Institute of Marine Biological Resources and Biotechnology, IRBIM-CNR, Messina, 98122, Italy
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (CBMSO, CSICUAM), Cantoblanco, Madrid, 28049, Spain.,Centro de Astrobiología (CAB, INTA-CSIC), Torrejón de Ardoz, 28055, Spain
| | - Michael T Madigan
- School of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
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13
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Sorokin DY, Messina E, Smedile F, La Cono V, Hallsworth JE, Yakimov MM. Carbohydrate‐dependent sulfur respiration in halo(alkali)philic archaea. Environ Microbiol 2021; 23:3789-3808. [DOI: 10.1111/1462-2920.15421] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/03/2021] [Accepted: 02/01/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology Russian Academy of Sciences Moscow Russia
- Department of Biotechnology Delft University of Technology Delft The Netherlands
| | - Enzo Messina
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - Francesco Smedile
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - Violetta La Cono
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, Northern Ireland BT9 5DL UK
| | - Michail M. Yakimov
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
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