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Aziz T, Hangyu H, Naveed M, Shabbir MA, Sarwar A, Nasbeeb J, Zhennai Y, Alharbi M. Genotypic Profiling, Functional Analysis, Cholesterol-Lowering Ability, and Angiotensin I-Converting Enzyme (ACE) Inhibitory Activity of Probiotic Lactiplantibacillus plantarum K25 via Different Approaches. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10258-8. [PMID: 38613617 DOI: 10.1007/s12602-024-10258-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2024] [Indexed: 04/15/2024]
Abstract
Due to its alleged health advantages, several uses in biotechnology and food safety, the well-known probiotic strain Lactiplantibacillus plantarum K25 has drawn interest. This in-depth investigation explores the genetic diversity, makeup, and security characteristics of the microbial genome of L. plantarum K25, providing insightful knowledge about its genotypic profile and functional characteristics. Utilizing cutting-edge bioinformatics techniques like comparative genomics, pan-genomics, and genotypic profiling was carried out to reveal the strain's multidimensional potential in various fields. The results not only add to our understanding of the genetic makeup of L. plantarum K25 but also show off its acceptability in various fields, notably in biotechnology and food safety. The explanation of evolutionary links, which highlights L. plantarum K25's aptitude as a probiotic, is one notable finding from this research. Its safety profile, which is emphasized by the absence of genes linked to antibiotic resistance, is crucial and supports its status as a promising probiotic option.
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Affiliation(s)
- Tariq Aziz
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health Beijing Technology and Business University Haidian District, No. 11 Fucheng Road, Beijing, 100048, China
| | - Hu Hangyu
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health Beijing Technology and Business University Haidian District, No. 11 Fucheng Road, Beijing, 100048, China
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Biological Sciences, Lahore University of Biological & Applied Sciences, Lahore, Punjab, 54800, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Biological Sciences, Lahore University of Biological & Applied Sciences, Lahore, Punjab, 54800, Pakistan
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore , Punjab, 54590, Pakistan
| | - Abid Sarwar
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health Beijing Technology and Business University Haidian District, No. 11 Fucheng Road, Beijing, 100048, China
| | - Jasra Nasbeeb
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health Beijing Technology and Business University Haidian District, No. 11 Fucheng Road, Beijing, 100048, China
| | - Yang Zhennai
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health Beijing Technology and Business University Haidian District, No. 11 Fucheng Road, Beijing, 100048, China.
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
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McKindles KM, Manes M, Neudeck M, McKay RM, Bullerjahn GS. Multi-year molecular quantification and 'omics analysis of Planktothrix-specific cyanophage sequences from Sandusky Bay, Lake Erie. Front Microbiol 2023; 14:1199641. [PMID: 37455749 PMCID: PMC10343443 DOI: 10.3389/fmicb.2023.1199641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Planktothrix agardhii is a microcystin-producing cyanobacterium found in Sandusky Bay, a shallow and turbid embayment of Lake Erie. Previous work in other systems has indicated that cyanophages are an important natural control factor of harmful algal blooms. Currently, there are few cyanophages that are known to infect P. agardhii, with the best-known being PaV-LD, a tail-less cyanophage isolated from Lake Donghu, China. Presented here is a molecular characterization of Planktothrix specific cyanophages in Sandusky Bay. Methods and Results Putative Planktothrix-specific viral sequences from metagenomic data from the bay in 2013, 2018, and 2019 were identified by two approaches: homology to known phage PaV-LD, or through matching CRISPR spacer sequences with Planktothrix host genomes. Several contigs were identified as having viral signatures, either related to PaV-LD or potentially novel sequences. Transcriptomic data from 2015, 2018, and 2019 were also employed for the further identification of cyanophages, as well as gene expression of select viral sequences. Finally, viral quantification was tested using qPCR in 2015-2019 for PaV-LD like cyanophages to identify the relationship between presence and gene expression of these cyanophages. Notably, while PaV-LD like cyanophages were in high abundance over the course of multiple years (qPCR), transcriptomic analysis revealed only low levels of viral gene expression. Discussion This work aims to provide a broader understanding of Planktothrix cyanophage diversity with the goals of teasing apart the role of cyanophages in the control and regulation of harmful algal blooms and designing monitoring methodology for potential toxin-releasing lysis events.
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Affiliation(s)
- Katelyn M. McKindles
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States
| | - Makayla Manes
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Michelle Neudeck
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States
| | - Robert Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States
| | - George S. Bullerjahn
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States
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Aziz T, Naveed M, Shabbir MA, Sarwar A, Ali Khan A, Zhennai Y, Alharbi M, Alsahammari A, Alasmari AF. Comparative genomics of food-derived probiotic Lactiplantibacillus plantarum K25 reveals its hidden potential, compactness, and efficiency. Front Microbiol 2023; 14:1214478. [PMID: 37455721 PMCID: PMC10346846 DOI: 10.3389/fmicb.2023.1214478] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 05/18/2023] [Indexed: 07/18/2023] Open
Abstract
This study aimed to investigate the intricate genetic makeup of the Lactiplantibacillus plantarum K25 strain by conducting a comprehensive analysis of comparative genomics. The results of our study demonstrate that the genome exhibits a high-level efficiency and compactness, comprising a total of 3,199 genes that encode proteins and a GC content of 43.38%. The present study elucidates the evolutionary lineage of Lactiplantibacillus plantarum strains through an analysis of the degree of gene order conservation and synteny across a range of strains, thereby underscoring their closely interrelated evolutionary trajectories. The identification of various genetic components in the K25 strain, such as bacteriocin gene clusters and prophage regions, highlights its potential utility in diverse domains, such as biotechnology and medicine. The distinctive genetic elements possess the potential to unveil innovative therapeutic and biotechnological remedies in future. This study provides a comprehensive analysis of the L. plantarum K25 strain, revealing its remarkable genomic potential and presenting novel prospects for utilizing its unique genetic features in diverse scientific fields. The present study contributes to the existing literature on Lactiplantibacillus plantarum and sets the stage for prospective investigations and practical implementations that leverage the exceptional genetic characteristics of this adap organism.
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Affiliation(s)
- Tariq Aziz
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center for Food Additives, Beijing Technology and Business University, Beijing, China
- Laboratory of Animal Health, Food Hygiene, and Quality, Department of Agriculture, University of Ioannina, Arta, Greece
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Abid Sarwar
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center for Food Additives, Beijing Technology and Business University, Beijing, China
| | - Ayaz Ali Khan
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Yang Zhennai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center for Food Additives, Beijing Technology and Business University, Beijing, China
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alsahammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F. Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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McKindles KM, McKay RML, Bullerjahn GS, Frenken T. Interactions between chytrids cause variable infection strategies on harmful algal bloom forming species. HARMFUL ALGAE 2023; 122:102381. [PMID: 36754455 DOI: 10.1016/j.hal.2023.102381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/25/2022] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
Cyanobacteria have a great diversity of natural enemies, such as herbivores and pathogens, including fungal pathogens within the Chytridiomycota (chytrids). While these pathogens have been previously described on a select number of cyanobacterial hosts and are suspected to play a significant ecological role, little is understood about species interactions and how competition between parasites can affect epidemic development and bloom formation. Here, three Planktothrix agardhii isolates from Sandusky Bay, Lake Erie (OH, USA) were challenged in monoculture and polyculture against infection by three isolates (C1, C2, C10) of their obligate chytrid fungal pathogen, Rhizophydiales sp. The chytrid isolates were inoculated as single isolates or a mixture of up to three different isolates. In monoculture, host isolates were characterized as highly susceptible (P. agardhii 1030), moderately susceptible (P. agardhii 1808) or mostly resistant (P. agardhii 1801). Co-infection of chytrid isolates on the highly susceptible host isolate had an additive effect on chytrid prevalence, leading to a culture crash where 2 or 3 chytrid isolates were present. Co-infection of chytrid isolates on the moderately susceptible and mostly resistant isolates had no effect on chytrid infection outcome or prevalence compared to infection with a single isolate. In polyculture, the effect on host growth was most significant in the single chytrid isolate treatment, which was attenuated with the addition of mixed chytrid treatments. Genetic analysis of the resulting population after the experimental period showed a tendency for the chytrid isolate C1 and P. agardhii 1801 to dominate in mixed population samples. Two different interspecific interactions seem to be in play; varied parasite infection strategies allow for the amplification of infection prevalence due to mixed chytrids in a susceptible monoculture, or competition allows for the dominance of a single chytrid isolate in monoculture and the reduction of infection prevalence in a host polyculture. This work thus highlights how interactions between chytrid infections can change the course of epidemic development and harmful algal bloom formation.
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Affiliation(s)
- Katelyn M McKindles
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109-1085, USA; Great Lakes Institute for Environmental Research (GLIER), University of Windsor, 401 Sunset Ave., Windsor, Ontario, Canada N9B 3P4; Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
| | - R Michael L McKay
- Great Lakes Institute for Environmental Research (GLIER), University of Windsor, 401 Sunset Ave., Windsor, Ontario, Canada N9B 3P4
| | - George S Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Thijs Frenken
- Great Lakes Institute for Environmental Research (GLIER), University of Windsor, 401 Sunset Ave., Windsor, Ontario, Canada N9B 3P4; Cluster Nature & Society, HAS University of Applied Sciences, Onderwijsboulevard 221, 5223 DE, 's-Hertogenbosch, the Netherlands
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Aziz T, Naveed M, Makhdoom SI, Ali U, Mughal MS, Sarwar A, Khan AA, Zhennai Y, Sameeh MY, Dablool AS, Alharbi AA, Shahzad M, Alamri AS, Alhomrani M. Genome Investigation and Functional Annotation of Lactiplantibacillus plantarum YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic Pathogens. Molecules 2023; 28:molecules28020491. [PMID: 36677548 PMCID: PMC9862464 DOI: 10.3390/molecules28020491] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023] Open
Abstract
All nutrient-rich feed and food environments, as well as animal and human mucosae, include lactic acid bacteria known as Lactobacillus plantarum. This study reveals an advanced analysis to study the interaction of probiotics with the gastrointestinal environment, irritable bowel disease, and immune responses along with the analysis of the secondary metabolites’ characteristics of Lp YW11. Whole genome sequencing of Lp YW11 revealed 2297 genes and 1078 functional categories of which 223 relate to carbohydrate metabolism, 21 against stress response, and the remaining 834 are involved in different cellular and metabolic pathways. Moreover, it was found that Lp YW11 consists of carbohydrate-active enzymes, which mainly contribute to 37 glycoside hydrolase and 28 glycosyltransferase enzyme coding genes. The probiotics obtained from the BACTIBASE database (streptin and Ruminococcin-A bacteriocins) were docked with virulent proteins (cdt, spvB, stxB, and ymt) of Salmonella, Shigella, Campylobacter, and Yersinia, respectively. These bacteria are the main pathogenic gut microbes that play a key role in causing various gastrointestinal diseases. The molecular docking, dynamics, and immune simulation analysis in this study predicted streptin and Ruminococcin-A as potent nutritive bacteriocins against gut symbiotic pathogens.
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Affiliation(s)
- Tariq Aziz
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Syeda Izma Makhdoom
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Urooj Ali
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Muhammad Saad Mughal
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Abid Sarwar
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| | - Ayaz Ali Khan
- Department of Biotechnology, University of Malakand, Chakdara 18800, Pakistan
| | - Yang Zhennai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
- Correspondence:
| | - Manal Y. Sameeh
- Chemistry Department, Faculty of Applied Sciences, Al-Leith University College, Umm Al-Qura University, Makkah 24831, Saudi Arabia
| | - Anas S. Dablool
- Department of Public Health, Health Sciences College Al-Leith, Umm Al-Qura University, Makkah al-Mukarramah 24382, Saudi Arabia
| | - Amnah A. Alharbi
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Muhammad Shahzad
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Abdulhakeem S. Alamri
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Taif 21944, Saudi Arabia
| | - Majid Alhomrani
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Taif 21944, Saudi Arabia
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Moreira C, Matos A, Barreiro A, Gomes C, Vasconcelos V, Antunes A. Statistical Inferences Applying Non-Parametric Data on Cyanobacterial Investigations: Contributions to Water Quality and New Trends under Global Changes on Portuguese Freshwater Ecosystems. Toxins (Basel) 2022; 14:toxins14090638. [PMID: 36136576 PMCID: PMC9506200 DOI: 10.3390/toxins14090638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Cyanobacteria are a bloom-forming ancient group of photosynthetic prokaryotes. A rise in temperature is a major contributor to its massive proliferation, namely on freshwater ecosystems, with social and economic impacts. Thus, reliable and cost-effective tools can permit the fast surveillance and assessment of temperature effects on potentially toxic cyanobacteria distribution and impacts. The occurrence of three potentially toxic cyanobacteria species was assessed on seven sampling points across three sampling years. Moreover, the association between the occurrence of those cyanobacteria species with climate change events was addressed. Here, we combined molecular and statistical methods to study the impacts of temperature on the occurrence of three globally occurring cyanotoxin-producing cyanobacteria species—Microcystis aeruginosa (microcystins), Raphidiopsis raciborskii (cylindrospermopsins and saxitoxins) and Planktothrix agardhii (microcystins and saxitoxins). Samples were collected on seven European temperate freshwater systems located on the North and Centre regions of Portugal, across three distinct sampling years with distinct ranges of air temperature. Data support that M. aeruginosa is still a common inhabitant of Portuguese freshwater ecosystems and a new trend was found on R. raciborskii recent invasion and establishment on the colder north ecosystems of Portugal. Additionally, the highest frequency of detection of both cyanobacteria was associated with warmer years. P. agardhii also revealed a new trend, being reported for the first time on North and Centre Regions of Portugal, however with no statistical relation with air temperature, demonstrating a higher ecological fitness. Distinct profiles of the statistical analysis on the three tested cyanobacteria species contribute to deepen the studies on other species as well as of our analyzed species on a global level. This assessment may help to anticipate possible repercussions on water quality and public health due to most probable alterations on cyanotoxins profile given the ecological fitness established among air temperature and PCR detection of potentially toxic cyanobacteria.
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Affiliation(s)
- Cristiana Moreira
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
| | - Ana Matos
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Aldo Barreiro
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
| | - Cidália Gomes
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
| | - Vitor Vasconcelos
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: ; Tel.: +351-223401813
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Aziz T, Naveed M, Sarwar A, Makhdoom SI, Mughal MS, Ali U, Yang Z, Shahzad M, Sameeh MY, Alruways MW, Dablool AS, Almalki AA, Alamri AS, Alhomrani M. Functional Annotation of Lactiplantibacillus plantarum 13-3 as a Potential Starter Probiotic Involved in the Food Safety of Fermented Products. Molecules 2022; 27:molecules27175399. [PMID: 36080167 PMCID: PMC9458025 DOI: 10.3390/molecules27175399] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/16/2022] Open
Abstract
The important role of Lactiplantibacillus plantarum strains in improving the human mucosal and systemic immunity, preventing non-steroidal anti-provocative drug-induced reduction in T-regulatory cells, and as probiotic starter cultures in food processing has motivated in-depth molecular and genomic research of these strains. The current study, building on this research concept, reveals the importance of Lactiplantibacillus plantarum 13-3 as a potential probiotic and bacteriocin-producing strain that helps in improving the condition of the human digestive system and thus enhances the immunity of the living beings via various extracellular proteins and exopolysaccharides. We have assessed the stability and quality of the L. plantarum 13-3 genome through de novo assembly and annotation through FAST-QC and RAST, respectively. The probiotic-producing components, secondary metabolites, phage prediction sites, pathogenicity and carbohydrate-producing enzymes in the genome of L. plantarum 13-3 have also been analyzed computationally. This study reveals that L. plantarum 13-3 is nonpathogenic with 218 subsystems and 32,918 qualities and five classes of sugars with several important functions. Two phage hit sites have been identified in the strain. Cyclic lactone autoinducer, terpenes, T3PKS, and RiPP-like gene clusters have also been identified in the strain evidencing its role in food processing. Combined, the non-pathogenicity and the food-processing ability of this strain have rendered this strain industrially important. The subsystem and qualities characterization provides a starting point to investigate the strain’s healthcare-related applications as well.
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Affiliation(s)
- Tariq Aziz
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 102401, China
- Pak-Austria Fachhochschule—Institute of Applied Sciences and Technology, Mang, Haripur 22621, Pakistan
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Abid Sarwar
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 102401, China
| | - Syeda Izma Makhdoom
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Muhammad Saad Mughal
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Urooj Ali
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Zhennai Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 102401, China
- Correspondence:
| | - Muhammad Shahzad
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25124, Pakistan
| | - Manal Y. Sameeh
- Chemistry Department, Faculty of Applied Sciences, Al-Leith University College, Umm Al-Qura University, Makkah 24831, Saudi Arabia
| | - Mashael W. Alruways
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Shaqra 15273, Saudi Arabia
| | - Anas S. Dablool
- Department of Public Health, Health Sciences College Al-Leith, Umm Al-Qura University, Makkah al-Mukarramah 24382, Saudi Arabia
| | - Abdulraheem Ali Almalki
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Abdulhakeem S. Alamri
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Majid Alhomrani
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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McKindles KM, McKay RM, Bullerjahn GS. Genomic comparison of Planktothrix agardhii isolates from a Lake Erie embayment. PLoS One 2022; 17:e0273454. [PMID: 35998200 PMCID: PMC9398003 DOI: 10.1371/journal.pone.0273454] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/09/2022] [Indexed: 12/04/2022] Open
Abstract
Planktothrix agardhii is a filamentous cyanobacterial species that dominates harmful algal blooms in Sandusky Bay, Lake Erie and other freshwater basins across the world. P. agardhii isolates were obtained from early (June) blooms via single filament isolation; eight have been characterized from 2016, and 12 additional isolates have been characterized from 2018 for a total of 20 new cultures. These novel isolates were processed for genomic sequencing, where reads were used to generate scaffolds and contigs which were annotated with DIAMOND BLAST hit, Pfam, and GO. Analyses include whole genome alignment to generate phylogenetic trees and comparison of genetic rearrangements between isolates. Nitrogen acquisition and metabolism was compared across isolates. Secondary metabolite production was genetically explored including microcystins, two types of aeruginosin clusters, anabaenopeptins, cyanopeptolins, microviridins, and prenylagaramides. Two common and 4 unique CRISPR-cas islands were analyzed for similar sequences across all isolates and against the known Planktothrix-specific cyanophage, PaV-LD. Overall, the uniqueness of each genome from Planktothrix blooms sampled from the same site and at similar times belies the unexplored diversity of this genus.
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Affiliation(s)
- Katelyn M. McKindles
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - R. Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States of America
| | - George S. Bullerjahn
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States of America
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States of America
- * E-mail:
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Aziz T, Sarwar A, Naveed M, Shahzad M, Aqib Shabbir M, Dablool AS, ud Din J, Ali Khan A, Naz S, Cui H, Lin L. Bio-Molecular Analysis of Selected food derivedLactiplantibacillusstrains for CLA Production Reveals possibly a complex mechanism. Food Res Int 2022; 154:111031. [DOI: 10.1016/j.foodres.2022.111031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 11/04/2022]
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McKindles KM, Manes MA, McKay RM, Davis TW, Bullerjahn GS. Environmental factors affecting chytrid (Chytridiomycota) infection rates on Planktothrix agardhii. JOURNAL OF PLANKTON RESEARCH 2021; 43:658-672. [PMID: 34588922 PMCID: PMC8461644 DOI: 10.1093/plankt/fbab058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/17/2021] [Indexed: 05/05/2023]
Abstract
Planktothrix agardhii dominates the cyanobacterial harmful algal bloom biomass in Sandusky Bay, Lake Erie (USA) from May until September. This filamentous cyanobacterium known parasites including the chytrid fungal species Rhizophydium sp. C02, which was previously isolated from this region. The purpose of our work has been to establish how parasitic interactions affect Planktothrix population dynamics during a bloom event. Samples analyzed from the 2015 to 2019 bloom seasons using quantitative PCR investigate the spatial and temporal prevalence of chytrid infections. Abiotic factors examined in lab include manipulating temperature (17-31°C), conductivity (0.226-1.225 mS/cm) and turbulence. Planktothrix-specific chytrids are present throughout the bloom period and are occasionally at high enough densities to exert parasitic pressure on their hosts. Temperatures above 27.1°C in lab can inhibit chytrid infection, indicating the presence of a possible upper thermal refuge for the host. Data suggest that chytrids can survive conductivity spikes in lab at levels three-fold above Sandusky Bay waters if given sufficient time (7-12 days), whereas increased turbulence in lab severely inhibits chytrid infections, perhaps due to disruption of chemical signaling. Overall, these data provide insights into the environmental conditions that inhibit chytrid infections during Planktothrix-dominated blooms in temperate waters.
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Affiliation(s)
- Katelyn M McKindles
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Makayla A Manes
- Department of Biological Sciences, The Ohio State University, Columbus, OH, USA
| | - R Michael McKay
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Timothy W Davis
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
- Great Lakes Center for Fresh Waters and Human Health, Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
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Moreira C, Pimentel A, Vasconcelos V, Antunes A. Preliminary evidence on the presence of cyanobacteria and cyanotoxins from culture enrichments followed by PCR analysis: new perspectives from Africa (Mali) and South Pacific (Fiji) countries. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:31731-31745. [PMID: 33608790 DOI: 10.1007/s11356-021-12662-x] [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: 09/08/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Cyanobacteria are a group of microorganisms that can be found in a diverse range of biogeographical areas and produce potent and damaging cyanotoxins, which reveal importance for continuous studies and surveillance efforts. In this study, we analyzed worldwide two-month culture-enriched water samples collected from 12 distinct countries (Costa Rica, Cuba, Fiji, France, Indonesia, Mali, Portugal, South Africa, Spain, Thailand, USA, Vietnam) including two undisclosed areas (Fiji and Mali). We performed a PCR-based molecular multi-step scheme that consisted in the detection of the main cyanobacterial species, genera, and cyanotoxins biosynthesis genes. Results from this study indicate that Microcystis aeruginosa followed by Planktothrix agardhii were the most prevalent species of all the 12 countries analyzed. Cylindrospermospis raciborskii was detected in Costa Rica, while P. agardhii was detected in Fiji and South Africa. M. aeruginosa was detected in Fiji and Mali. Regarding the main cyanotoxins biosynthesis genes, a cyrC gene fragment (cylindrospermopsins) was amplified in the African continent (South Africa), while anaC (anatoxin-a) was detected in two distinct locations, Mali and Vietnam. Saxitoxins biosynthesis gene was also detected in Fiji and Vietnam. Microcystins biosynthesis gene (mcyA) was co-detected with anatoxin-a biosynthesis gene in Mali and with saxitoxins biosynthesis gene (sxtI) in Portugal. This study therefore constitutes a major contribution to the global biogeography of cyanobacteria and its cyanotoxins and recommends continuous vigilance of toxic cyanobacteria particularly in the more undisclosed areas of the world. The PCR analysis data obtained in our 2-month culture-enriched water samples supports molecular methods as a preliminary tool in the environmental surveillance of cyanobacteria and cyanotoxins in undisclosed locations, particularly since the several positive amplifications detected may indicate that though samples were collected under non-bloom conditions, if environmental conditions change in the ecosystem, there is a risk that bloom-forming species may arose along with their detected cyanotoxicity.
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Affiliation(s)
- Cristiana Moreira
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208, Porto, Portugal
| | - Ana Pimentel
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208, Porto, Portugal
| | - Vitor Vasconcelos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
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12
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Review on Cyanobacterial Studies in Portugal: Current Impacts and Research Needs. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11104355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cyanobacteria have long been associated with harmful effects on humans, animals and aquatic biota. Cyanotoxins are their most toxic metabolite. This review summarizes the current research, impacts and future needs in cyanobacterial studies undertaken in Portugal, the southernmost country of Europe, and with a recent multiplication of cyanotoxicity due to climate change events. Microcystins are still the most prevalent, studied and the only regulated cyanotoxins in Portuguese freshwater systems much like most European countries. With the development of some tools, particularly in molecular studies, the recent discovery of cylindrospermopsins, anatoxins and saxitoxins, both genes and toxins, in North and Center ecosystems of our country highlight current impacts that overall communities are facing with increased risks of exposure and uptake to cyanotoxins. Research needs encompass the expansion of studies at all aspects due to the uprising of these cyanotoxins and reinforces the urgent need of increasing the frequency of surveillance to achieve tangible effects of cyanotoxins in Portugal to ultimately implement regulations on cylindrospermopsins, anatoxins and saxitoxins worldwide.
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13
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Kynshi BL, Sachu M, Syiem MB. Modulation in isocitrate dehydrogenase activity under citrate enrichment affects carbon and nitrogen fixations in the cyanobacterium Nostoc muscorum Meg 1. Biochimie 2021; 186:94-104. [PMID: 33915227 DOI: 10.1016/j.biochi.2021.03.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/05/2021] [Accepted: 03/30/2021] [Indexed: 11/26/2022]
Abstract
The enzyme isocitrate dehydrogenase (IDH) converts isocitrate synthesized from citrate to α-ketoglutarate in the TCA cycle. In cyanobacteria, α-KG has an additional role where it donates its carbon skeleton for ammonium assimilation in the GS-GOGAT pathway thereby linking carbon and nitrogen metabolisms. Looking at this crucial function of IDH that makes α-KG available for both carbon and nitrogen assimilation, changes brought about in its activity under excess availability of citrate in a cyanobacterium was evaluated. Further, how these changes are transmitted downstream affecting carbon and nitrogen metabolisms were also evaluated. A 100 μM citrate supplementation induced IDH activity. Consequently, there was an increase in concentrations of photosynthetic pigments, D1 protein and RuBisCO as well as in PSII activity. Heterocyst differentiation was initiated and an upsurge in the activities of nitrogenase and GS were recorded. An enhancement in the total protein and carbohydrate content reiterated the positive influence of citrate enrichment on carbon and nitrogen fixation. The increase in the mRNA contents of IDH, D1 protein, RuBisCO, nitrogenase and GS indicated their induction at the genetic level. Finally, there was augmentation in total biomass production by ∼28%. Interestingly as citrate concentration was increased to 500 μM, both C- and N- fixations were highly compromised suggesting that even though citrate is an essential metabolite in the cells, it became toxic beyond a certain concentration to the organism. SEM and TEM studies showed no changes in the organism's morphology and ultra-structure in presence of 100 μM citrate while adverse changes were noticed in presence of 500 μM citrate.
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Affiliation(s)
| | - Meguovilie Sachu
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, Meghalaya, India
| | - Mayashree B Syiem
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, Meghalaya, India.
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Yarimizu K, Sildever S, Hamamoto Y, Tazawa S, Oikawa H, Yamaguchi H, Basti L, Mardones JI, Paredes-Mella J, Nagai S. Development of an absolute quantification method for ribosomal RNA gene copy numbers per eukaryotic single cell by digital PCR. HARMFUL ALGAE 2021; 103:102008. [PMID: 33980448 DOI: 10.1016/j.hal.2021.102008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
Recent increase of Harmful Algal Blooms (HAB) causes world-wide ecological, economical, and health issues, and more attention is paid to frequent coastal monitoring for the early detection of HAB species to prevent or reduce such impacts. Use of molecular tools in addition to traditional microscopy-based observation has become one of the promising methodologies for coastal monitoring. However, as ribosomal RNA (rRNA) genes are commonly targeted in molecular studies, variability in the rRNA gene copy number within and between species must be considered to provide quantitative information in quantitative PCR (qPCR), digital PCR (dPCR), and metabarcoding analyses. Currently, this information is only available for a limited number of species. The present study utilized a dPCR technology to quantify copy numbers of rRNA genes per single cell in 16 phytoplankton species, the majority of which are toxin-producers, using a newly developed universal primer set accompanied by a labeled probe with a fluorophore and a double-quencher. In silico PCR using the newly developed primers allowed the detection of taxa from 8 supergroups, demonstrating universality and broad coverage of the primer set. Chelex buffer was found to be suitable for DNA extraction to obtain DNA fragments with suitable size to avoid underestimation of the copy numbers. The study successfully demonstrated the first comparison of absolute quantification of 18S rRNA copy numbers per cell from 16 phytoplankton species by the dPCR technology.
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Affiliation(s)
- Kyoko Yarimizu
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan; Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 22 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
| | - Sirje Sildever
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan; Department of Marine Systems, Tallinn University of Technology, Akadeemia tee 15A, 12618 Tallinn, Estonia
| | - Yoko Hamamoto
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Satoshi Tazawa
- AXIOHELIX Co. Ltd, 12-17 Kandaizumicho, Chiyoda-ku, Tokyo 101-0024, Japan
| | - Hiroshi Oikawa
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Haruo Yamaguchi
- Faculty of Agriculture and Marine Sciences, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Leila Basti
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Minato, Tokyo 108-8477, Japan
| | - Jorge I Mardones
- Instituto de Fomento Pesquero, Centro de Estudios de Algas Nocivas (IFOP-CREAN), Padre Harter 574, Puerto Montt 5501679, Chile; Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Javier Paredes-Mella
- Instituto de Fomento Pesquero, Centro de Estudios de Algas Nocivas (IFOP-CREAN), Padre Harter 574, Puerto Montt 5501679, Chile
| | - Satoshi Nagai
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan.
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Isolation and Characterization of Rhizophydiales sp. (Chytridiomycota), Obligate Parasite of Planktothrix agardhii in a Laurentian Great Lakes Embayment. Appl Environ Microbiol 2021; 87:AEM.02308-20. [PMID: 33310722 PMCID: PMC7851699 DOI: 10.1128/aem.02308-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Planktothrix agardhii dominates the cyanobacterial harmful algal bloom community in Sandusky Bay, Lake Erie (USA) from May through September. This filamentous cyanobacterium is host to a known obligate parasite; the chytrid Rhizophydium sp. During the 2018 bloom season, by utilizing dilution and single filament isolation techniques, 7 chytrid and 12 P. agardhii strains were isolated from Sandusky Bay. These 7 chytrids and a selection of P. agardhii hosts were then characterized with respect to infection rates. Infections by the isolated chytrids were specific to Planktothrix planktonic species and were not found on other filamentous cyanobacterial taxa present in the bay (Aphanizomenon sp. and Cuspidothrix sp.). Even among the potential P. agardhii host strains, individual chytrid isolates had different degrees of infectivity and showed preference for different host isolates, suggesting possible ecological partitioning even within the same sample population. Examining mechanisms of chytrid pathogenesis, the zoospores displayed a swarming pattern to attack and fracture the host filament and create new infection sites at the trichome termini. Infections by these parasitic chytrids also led to a release of intracellular microcystin toxins from the hosts. Additionally, infections were dependent on media type, highlighting the importance of media choice on experimental outcomes. Media in which chytrid swarming was observed closely matched the ionic strength of the natural environment. Understanding pathogenesis by fungal parasites will assist future efforts aimed at determining environmental factors favoring loss mechanisms for Planktothrix agardhii-dominated blooms.IMPORTANCE Whereas many studies have focused on the factors contributing to the establishment and persistence of cyanobacterial harmful algal blooms (cHABs), few studies have examined bloom pathogenesis. Chytrid fungi infect cyanobacteria and stimulate food web interactions through manipulation of previously hard to digest filaments and the release of nutrients to support heterotrophic microbes. Specifically, chytrids infective on filamentous Planktothrix agardhii exhibit a species-specific infection that fragments trichomes into shorter units that can be consumed more easily by grazers. Chytrid zoospores also serve as a high-quality food source for the lower food web. Understanding host-pathogen relationships and mechanisms of pathogenesis on cyanobacteria will be necessary to effectively model the ecology of cHABs.
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16
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Kim Tiam S, Comte K, Dalle C, Duval C, Pancrace C, Gugger M, Marie B, Yéprémian C, Bernard C. Development of a new extraction method based on high-intensity ultra-sonication to study RNA regulation of the filamentous cyanobacteria Planktothrix. PLoS One 2019; 14:e0222029. [PMID: 31490972 PMCID: PMC6730872 DOI: 10.1371/journal.pone.0222029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/20/2019] [Indexed: 11/24/2022] Open
Abstract
Efficient RNA extraction methods are needed to study transcript regulation. Such methods must lyse the cell without degrading the genetic material. For cyanobacteria this can be particularly challenging because of the presence of the cyanobacteria cell envelope. The great breath of cyanobacterial shape and size (unicellular, colonial, or filamentous multicellular) created a variety of cell lysis methods. However, there is still a lack of reliable techniques for nucleic acid extraction for several types of cyanobacteria. Here we designed and tested 15 extraction methods using physical, thermic or chemical stress on the filamentous cyanobacteria Planktothrix agardhii. Techniques based on the use of beads, sonication, and heat shock appeared to be too soft to break the Planktothrix agardhii cell envelope, whereas techniques based on the use of detergents degraded the cell envelope but also the RNA. Two protocols allowed to successfully obtain good-quality RNA. The first protocol consisted to manually crush the frozen cell pellet with a pestle and the second was based on the use of high-intensity ultra-sonication. When comparing these two, the high-intensity ultra-sonication protocol was less laborious, faster and allowed to extract 3.5 times more RNA compared to the liquid nitrogen pestle protocol. The high-intensity ultra-sonication protocol was then tested on five Planktothrix strains, this protocol allowed to obtain >8.5 μg of RNA for approximatively 3.5 × 108 cells. The extracted RNA were characterized by 260/280 and 260/230 ratio > to 2, indicating that the samples were devoid of contaminant, and RNA Quality Number > to 7, meaning that the integrity of RNA was preserved with this extraction method. In conclusion, the method we developed based on high-intensity ultra-sonication proved its efficacy in the extraction of Planktothrix RNA and could be helpful for other types of samples.
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Affiliation(s)
- Sandra Kim Tiam
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes, Muséum National d’Histoire Naturelle, Paris, France
- * E-mail: (SKT); (CB)
| | - Katia Comte
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes, Muséum National d’Histoire Naturelle, Paris, France
| | - Caroline Dalle
- Collection des Cyanobactéries, Institut Pasteur, Paris, France
| | - Charlotte Duval
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes, Muséum National d’Histoire Naturelle, Paris, France
| | - Claire Pancrace
- Collection des Cyanobactéries, Institut Pasteur, Paris, France
| | - Muriel Gugger
- Collection des Cyanobactéries, Institut Pasteur, Paris, France
| | - Benjamin Marie
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes, Muséum National d’Histoire Naturelle, Paris, France
| | - Claude Yéprémian
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes, Muséum National d’Histoire Naturelle, Paris, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes, Muséum National d’Histoire Naturelle, Paris, France
- * E-mail: (SKT); (CB)
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17
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Pollard AT, Okubara PA. Real-time PCR quantification of Fusarium avenaceum in soil and seeds. J Microbiol Methods 2019; 157:21-30. [DOI: 10.1016/j.mimet.2018.12.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/11/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
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18
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Menezes C, Churro C, Dias E. Risk Levels of Toxic Cyanobacteria in Portuguese Recreational Freshwaters. Toxins (Basel) 2017; 9:toxins9100327. [PMID: 29057822 PMCID: PMC5666374 DOI: 10.3390/toxins9100327] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/13/2017] [Accepted: 10/16/2017] [Indexed: 11/16/2022] Open
Abstract
Portuguese freshwater reservoirs are important socio-economic resources, namely for recreational use. National legislation concerning bathing waters does not include mandatory levels or guidelines for cyanobacteria and cyanotoxins. This is an issue of concern since cyanotoxin-based evidence is insufficient to change the law, and the collection of scientific evidence has been hampered by the lack of regulatory levels for cyanotoxins in bathing waters. In this work, we evaluate the profile of cyanobacteria and microcystins (MC) in eight freshwater reservoirs from the center of Portugal, used for bathing/recreation, in order to determine the risk levels concerning toxic cyanobacteria occurrence. Three of the reservoirs did not pose a risk of MC contamination. However, two reservoirs presented a high risk in 7% of the samples according to the World Health Organization (WHO) guidelines for MC in bathing waters (above 20 µg/L). In the remaining three reservoirs, the risk concerning microcystins occurrence was low. However, they exhibited recurrent blooms and persistent contamination with MC up to 4 µg/L. Thus, the risk of exposure to MC and potential acute and/or chronic health outcomes should not be disregarded in these reservoirs. These results contribute to characterize the cyanobacterial blooms profile and to map the risk of toxic cyanobacteria and microcystins occurrence in Portuguese inland waters.
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Affiliation(s)
- Carina Menezes
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisboa, Portugal.
| | - Catarina Churro
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisboa, Portugal.
| | - Elsa Dias
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisboa, Portugal.
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Qiu C, Zhang D, Chi Y, Chen Q, Xu L, Xie Q. Clinical significance of 5-(and 6)-carboxyfluorescein diacetate succinimidyl ester-labeled microspheres for detecting endothelial progenitor cells in human peripheral blood. Exp Ther Med 2017; 14:1659-1664. [PMID: 28810633 DOI: 10.3892/etm.2017.4657] [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: 01/21/2016] [Accepted: 02/14/2017] [Indexed: 11/06/2022] Open
Abstract
The aims of the present study were to establish a single-platform flow cytometry method using 5-(and 6)-carboxyfluorescein diacetate succinimidyl ester (CFSE)-labeled microspheres as the reference for determining endothelial progenitor cell (EPC) number and to evaluate the efficacy of this detection method. Single-platform flow cytometry was used to count cell numbers using CFSE-stained fluorescent microspheres as the internal reference and the EPC numbers in specimens using this novel method were compared with an in vitro clonogenic counting assay. The results of the two counting methods were consistent and compared with the in vitro clonogenic counting assay, the time and cost of the novel method was markedly reduced, as were the corresponding technical requirements. The present findings indicated that single-platform flow cytometry, with CFSE-labeled microspheres as the reference, provides faster and improved detection of EPCs in human peripheral blood specimens, with reduced time and cost, making it more suitable for routine clinical application.
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Affiliation(s)
- Chaolin Qiu
- Clinical Laboratory Department, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai 200135, P.R. China
| | - Denghai Zhang
- Central Laboratory Department, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai 200135, P.R. China
| | - Yongbin Chi
- Clinical Laboratory Department, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai 200135, P.R. China
| | - Qing Chen
- Clinical Laboratory Department, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai 200135, P.R. China
| | - Limin Xu
- Clinical Laboratory Department, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai 200135, P.R. China
| | - Qiuhua Xie
- Clinical Laboratory Department, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai 200135, P.R. China
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Salvador D, Churro C, Valério E. Evaluating the influence of light intensity in mcyA gene expression and microcystin production in toxic strains of Planktothrix agardhii and Microcystis aeruginosa. J Microbiol Methods 2016; 123:4-12. [DOI: 10.1016/j.mimet.2016.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/30/2016] [Accepted: 02/01/2016] [Indexed: 12/30/2022]
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21
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Microfluidics and nanoparticles based amperometric biosensor for the detection of cyanobacteria (Planktothrix agardhii NIVA-CYA 116) DNA. Biosens Bioelectron 2015; 70:426-32. [DOI: 10.1016/j.bios.2015.03.052] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/19/2015] [Accepted: 03/22/2015] [Indexed: 11/20/2022]
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Enhanced survival of human mesenchymal stem cells following co-delivery with glucagon-like peptide-1 analogue in fibrin gel. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2014. [DOI: 10.1007/s40005-014-0156-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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23
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Molecular fingerprinting of cyanobacteria from river biofilms as a water quality monitoring tool. Appl Environ Microbiol 2012; 79:1459-72. [PMID: 23263954 DOI: 10.1128/aem.03351-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Benthic cyanobacterial communities from Guadarrama River (Spain) biofilms were examined using temperature gradient gel electrophoresis (TGGE), comparing the results with microscopic analyses of field-fixed samples and the genetic characterization of cultured isolates from the river. Changes in the structure and composition of cyanobacterial communities and their possible association with eutrophication in the river downstream were studied by examining complex TGGE patterns, band extraction, and subsequent sequencing of 16S rRNA gene fragments. Band profiles differed among sampling sites depending on differences in water quality. The results showed that TGGE band richness decreased in a downstream direction, and there was a clear clustering of phylotypes on the basis of their origins from different locations according to their ecological requirements. Multivariate analyses (cluster analysis and canonical correspondence analysis) corroborated these differences. Results were consistent with those obtained from microscopic observations of field-fixed samples. According to the phylogenetic analysis, morphotypes observed in natural samples were the most common phylotypes in the TGGE sequences. These phylotypes were closely related to Chamaesiphon, Aphanocapsa, Pleurocapsa, Cyanobium, Pseudanabaena, Phormidium, and Leptolyngbya. Differences in the populations in response to environmental variables, principally nutrient concentrations (dissolved inorganic nitrogen and soluble reactive phosphorus), were found. Some phylotypes were associated with low nutrient concentrations and high levels of dissolved oxygen, while other phylotypes were associated with eutrophic-hypertrophic conditions. These results support the view that once a community has been characterized and its genetic fingerprint obtained, this technique could be used for the purpose of monitoring rivers.
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