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Jung P, Briegel-Williams L, Werner L, Jost E, Schultz M, Nürnberg DJ, Grube M, Lakatos M. A direct PCR approach with low-biomass insert opens new horizons for molecular sciences on cryptogam communities. Appl Environ Microbiol 2024; 90:e0002424. [PMID: 38349146 PMCID: PMC10952543 DOI: 10.1128/aem.00024-24] [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: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 03/21/2024] Open
Abstract
Molecular sequence data have transformed research on cryptogams (e.g., lichens, microalgae, fungi, and symbionts thereof) but methods are still strongly hampered by the small size and intermingled growth of the target organisms, poor cultivability and detrimental effects of their secondary metabolites. Here, we aim to showcase examples on which a modified direct PCR approach for diverse aspects of molecular work on environmental samples concerning biocrusts, biofilms, and cryptogams gives new options for the research community. Unlike traditional approaches, this methodology only requires biomass equivalent to colonies and fragments of 0.2 mm in diameter, which can be picked directly from the environmental sample, and includes a quick DNA lysis followed by a standardized PCR cycle that allows co-cycling of various organisms/target regions in the same run. We demonstrate that this modified method can (i) amplify the most widely used taxonomic gene regions and those used for applied and environmental sciences from single colonies and filaments of free-living cyanobacteria, bryophytes, fungi, and lichens, including their mycobionts, chlorobionts, and cyanobionts from both isolates and in situ material during co-cycling; (ii) act as a tool to confirm that the dominant lichen photobiont was isolated from the original sample; and (iii) optionally remove inhibitory secondary lichen substances. Our results represent examples which highlight the method's potential for future applications covering mycology, phycology, biocrusts, and lichenology, in particular.IMPORTANCECyanobacteria, green algae, lichens, and other cryptogams play crucial roles in complex microbial systems such as biological soil crusts of arid biomes or biofilms in caves. Molecular investigations on environmental samples or isolates of these microorganisms are often hampered by their dense aggregation, small size, or metabolism products which complicate DNA extraction and subsequent PCRs. Our work presents various examples of how a direct DNA extraction and PCR method relying on low biomass inserts can overcome these common problems and discusses additional applications of the workflow including adaptations.
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Affiliation(s)
- Patrick Jung
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Laura Briegel-Williams
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Lina Werner
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Emily Jost
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Matthias Schultz
- Institute for Plant Science and Microbiology, Herbarium Hamburgense, University of Hamburg, Hamburg, Germany
| | - Dennis J. Nürnberg
- Institute of Experimental Physics, Freie Universität Berlin, Berlin, Germany
- Dahlem Centre for Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Martin Grube
- Institute of Biology, University of Graz, Graz, Austria
| | - Michael Lakatos
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
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Liu F, Zheng B, Zheng N, Alfaiz FA, Ali HE, Al Garalleh H, Assilzadeh H, Xia S. Smart nano generation of transgenic algae expressing white spot syndrome virus in shrimps for inner ear-oral infection treatments using the spotted hyena optimizer (SHO)-Long short-term memory algorithm. ENVIRONMENTAL RESEARCH 2024; 243:117519. [PMID: 37972807 DOI: 10.1016/j.envres.2023.117519] [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: 08/01/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Nanotechnology offers a promising avenue to amplify the effectiveness and precision of using transgenic algae in managing WSSV in shrimp by possibly crafting nano-carriers for targeted therapeutic agent delivery or modifying algae cells at a molecular level. Leveraging the capabilities of nano-scale interventions, this study could explore innovative means to manipulate cellular processes, control biological interactions, and enhance treatment efficacy while minimizing undesirable impacts in aquatic environments. The White Spot Syndrome Virus (WSSV) is a double-stranded DNA virus with a tail and rod form that belongs to theNimaviridaefamily. There is no workable way to manage this illness at the moment. This research proposes a new model based on the Long Short-Term Memory (LSTM) and Spotted Hyena Optimizer (SHO) method to control the inner ear-oral infection, utilizing transgenic algae (Chlamydomonas reinhardtii). It is pretty tricky to modify the weight matrix in LSTM. The output will be more accurate if the weight of the neurons is exact. Histological examinations and nested polymerase chain reaction (PCR) testing were performed on the challenged shrimp every 4 h to assess the degree of white spot disease. The SHO-LSTM has shown the highest accuracy and Roc value (98.12% and 0.93, respectively) and the lowest error values (MSE = 0.182 and MAE = 0.48). The hybrid optimized model improves the overall inner ear-oral linked neurological diseases detection ratio. Additionally, with the slightest technical complexity, it effectively controls the forecast factors required to anticipate the ENT. Algal cells were found to be particularly well-suited for inner ear-oral infections, and shrimps fed a transgenic line had the best survival ratio in WSSV infection studies, with 87% of the shrimp surviving. This shows that using this line would effectively stop the spread of WSSV in shrimp populations.
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Affiliation(s)
- Fanli Liu
- Department of Otolaryngology Head & Neck Surgery, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Bin Zheng
- Department of Rehabilitation Therapeutics, Chongqing Medical University, Chongqing 401120, China
| | - Nan Zheng
- School of Pharmacy, Zhejiang Chinese Medicine University, Hangzhou 310053, China
| | - Faiz Abdulaziz Alfaiz
- Department of Biology, College of Science, Majmaah University, Al-Majmaah, 11952, Saudi Arabia.
| | - H Elhosiny Ali
- Department of Physics, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, Saudi Arabia
| | - Hakim Al Garalleh
- Department of Mathematical Science, College of Engineering, University of Business and Technology, Dahban- Jeddah 21360, Saudi Arabia
| | - Hamid Assilzadeh
- Faculty of Architecture and Urbanism, UTE University, Calle Rumipamba S/N and Bourgeois, Quito, Ecuador; Institute of Research and Development, Duy Tan University, Da Nang, Viet Nam; School of Engineering & Technology, Duy Tan University, Da Nang, Viet Nam; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 600077, India
| | - Siwen Xia
- Department of Otolaryngology Head & Neck Surgery, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China.
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Hept MA, Greene LH. Extracting high-molecular weight DNA from cyanobacteria using Promega's Wizard Ⓡ HMW DNA extraction kit with a modified protocol, METIS. MethodsX 2023; 11:102341. [PMID: 37732290 PMCID: PMC10507432 DOI: 10.1016/j.mex.2023.102341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023] Open
Abstract
Extraction of high molecular weight (HMW) DNA for long read sequencing with little to no fragmentation and high purity is difficult to acquire from cyanobacterial species. Here we describe a modified method of extraction using Promega's WizardⓇ HMW DNA Extraction Kit to acquire high molecular weight DNA from two cyanobacterial species. The protocol used in the kit is the "3.D. Isolating HMW DNA from Gram-Positive and Gram-Negative Bacteria" protocol. During a key step in the protocol, we propose that the lingering remnants of the cellular debris such as the mucilage layer of the cyanobacterial species is removed, preventing it from sticking to the DNA pellet produced. This customized modification is done between steps 11 and 12 and called METIS (maximizing extraction, transfer isopropanol step). This step drastically reduces the remaining mucilage layer, which if kept will stick to the DNA and make the DNA unsuitable for sensitive downstream next generation sequencing, like PacBio Sequencing. This protocol has been used to assemble two genomes from cyanobacteria (Synechococcus sp. and Microcystis aeruginosa) and one from a gram-negative bacterium, Lacibacter. It also allows for HMW DNA to be rapidly extracted without the use of toxic chemicals such as phenol and without extra reagents to be purchased.•Maximizing extraction, transfer isopropanol step (METIS) is the key modification during the step of DNA unraveling•METIS reduces leftover remnants of the mucilage layer in the extraction•High molecular weight DNA is produced with little to no fragmentation, and both a high purity and concentration.
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Affiliation(s)
- Megan A. Hept
- Department of Chemistry and Biochemistry, Old Dominion University, United States
| | - Lesley H. Greene
- Department of Chemistry and Biochemistry, Old Dominion University, United States
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Štenclová L, Wilde SB, Schwark M, Cullen JL, McWhorter SA, Niedermeyer THJ, Henderson WM, Mareš J. Occurrence of aetokthonotoxin producer in natural samples - A PCR protocol for easy detection. HARMFUL ALGAE 2023; 125:102425. [PMID: 37220978 PMCID: PMC10206276 DOI: 10.1016/j.hal.2023.102425] [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: 01/28/2023] [Accepted: 03/17/2023] [Indexed: 05/25/2023]
Abstract
Cyanobacteria are well known producers of bioactive metabolites, including harmful substances. The recently discovered "eagle killer" neurotoxin aetokthonotoxin (AETX) is produced by the epiphytic cyanobacterium Aetokthonos hydrillicola growing on invasive water thyme (Hydrilla verticillata). The biosynthetic gene cluster of AETX was previously identified from an Aetokthonos strain isolated from the J. Strom Thurmond Reservoir, Georgia, USA. Here, a PCR protocol for easy detection of AETX-producers in environmental samples of plant-cyanobacterium consortia was designed and tested. Three different loci of the AETX gene cluster were amplified to confirm the genetic potential for AETX production, along with two variable types of rRNA ITS regions to confirm the homogeneity of the producer´s taxonomic identity. In samples of Hydrilla from three Aetokthonos-positive reservoirs and one Aetokthonos-negative lake, the PCR of all four loci provided results congruent with the Aetokthonos presence/absence detected by light and fluorescence microscopy. The production of AETX in the Aetokthonos-positive samples was confirmed using LC-MS. Intriguingly, in J. Strom Thurmond Reservoir, recently Hydrilla free, an Aetokthonos-like cyanobacterium was found growing on American water-willow (Justicia americana). Those specimens were positive for all three aet markers but contained only minute amounts of AETX. The obtained genetic information (ITS rRNA sequence) and morphology of the novel Aetokthonos distinguished it from all the Hydrilla-hosted A. hydrillicola, likely at the species level. Our results suggest that the toxigenic Aetokthonos spp. can colonize a broader array of aquatic plants, however the level of accumulation of the toxin may be driven by host-specific interactions such as the locally hyper-accumulated bromide in Hydrilla.
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Affiliation(s)
- Lenka Štenclová
- Biology Centre of the CAS, Institute of Hydrobiology, České Budějovice, 370 05 Czechia; University of South Bohemia, Faculty of Science, České Budějovice, 370 05 Czechia
| | - Susan B Wilde
- Daniel B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602 USA
| | - Markus Schwark
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120 Germany
| | - Jeffrey L Cullen
- Daniel B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602 USA
| | - Seth A McWhorter
- Daniel B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602 USA; U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Athens, GA, 30605 USA
| | - Timo H J Niedermeyer
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120 Germany
| | - W Matthew Henderson
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Athens, GA, 30605 USA
| | - Jan Mareš
- Biology Centre of the CAS, Institute of Hydrobiology, České Budějovice, 370 05 Czechia; University of South Bohemia, Faculty of Science, České Budějovice, 370 05 Czechia; Centre Algatech, Institute of Microbiology of the CAS, Třeboň, 379 01 Czechia.
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Saleem F, Jiang JL, Atrache R, Paschos A, Edge TA, Schellhorn HE. Cyanobacterial Algal Bloom Monitoring: Molecular Methods and Technologies for Freshwater Ecosystems. Microorganisms 2023; 11:microorganisms11040851. [PMID: 37110273 PMCID: PMC10144707 DOI: 10.3390/microorganisms11040851] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Cyanobacteria (blue-green algae) can accumulate to form harmful algal blooms (HABs) on the surface of freshwater ecosystems under eutrophic conditions. Extensive HAB events can threaten local wildlife, public health, and the utilization of recreational waters. For the detection/quantification of cyanobacteria and cyanotoxins, both the United States Environmental Protection Agency (USEPA) and Health Canada increasingly indicate that molecular methods can be useful. However, each molecular detection method has specific advantages and limitations for monitoring HABs in recreational water ecosystems. Rapidly developing modern technologies, including satellite imaging, biosensors, and machine learning/artificial intelligence, can be integrated with standard/conventional methods to overcome the limitations associated with traditional cyanobacterial detection methodology. We examine advances in cyanobacterial cell lysis methodology and conventional/modern molecular detection methods, including imaging techniques, polymerase chain reaction (PCR)/DNA sequencing, enzyme-linked immunosorbent assays (ELISA), mass spectrometry, remote sensing, and machine learning/AI-based prediction models. This review focuses specifically on methodologies likely to be employed for recreational water ecosystems, especially in the Great Lakes region of North America.
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Pilgrim EM, Smucker NJ, Wu H, Martinson J, Nietch CT, Molina M, Darling JA, Johnson BR. Developing Indicators of Nutrient Pollution in Streams Using 16S rRNA Gene Metabarcoding of Periphyton-Associated Bacteria. WATER 2022; 14:1-24. [PMID: 36213613 PMCID: PMC9534034 DOI: 10.3390/w14152361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Indicators based on nutrient-biota relationships in streams can inform water quality restoration and protection programs. Bacterial assemblages could be particularly useful indicators of nutrient effects because they are species-rich, important contributors to ecosystem processes in streams, and responsive to rapidly changing conditions. Here, we sampled 25 streams weekly (12-14 times each) and used 16S rRNA gene metabarcoding of periphyton-associated bacteria to quantify the effects of total phosphorus (TP) and total nitrogen (TN). Threshold indicator taxa analysis identified assemblage-level changes and amplicon sequence variants (ASVs) that increased or decreased with increasing TP and TN concentrations (i.e., low P, high P, low N, and high N ASVs). Boosted regression trees confirmed that relative abundances of gene sequence reads for these four indicator groups were associated with nutrient concentrations. Gradient forest analysis complemented these results by using multiple predictors and random forest models for each ASV to identify portions of TP and TN gradients at which the greatest changes in assemblage structure occurred. Synthesized statistical results showed bacterial assemblage structure began changing at 24 μg TP/L with the greatest changes occurring from 110 to 195 μg/L. Changes in the bacterial assemblages associated with TN gradually occurred from 275 to 855 μg/L. Taxonomic and phylogenetic analyses showed that low nutrient ASVs were commonly Firmicutes, Verrucomicrobiota, Flavobacteriales, and Caulobacterales, Pseudomonadales, and Rhodobacterales of Proteobacteria, whereas other groups, such as Chitinophagales of Bacteroidota, and Burkholderiales, Rhizobiales, Sphingomonadales, and Steroidobacterales of Proteobacteria comprised the high nutrient ASVs. Overall, the responses of bacterial ASV indicators in this study highlight the utility of metabarcoding periphyton-associated bacteria for quantifying biotic responses to nutrient inputs in streams.
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Affiliation(s)
- Erik M. Pilgrim
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Nathan J. Smucker
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Huiyun Wu
- School of Public Health & Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - John Martinson
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Christopher T. Nietch
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Marirosa Molina
- United States Environmental Protection Agency, Office of Research and Development, Research Triangle Park, NC 27711, USA
| | - John A. Darling
- United States Environmental Protection Agency, Office of Research and Development, Research Triangle Park, NC 27711, USA
| | - Brent R. Johnson
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
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Gaget V, Almuhtaram H, Kibuye F, Hobson P, Zamyadi A, Wert E, Brookes JD. Benthic cyanobacteria: A utility-centred field study. HARMFUL ALGAE 2022; 113:102185. [PMID: 35287926 DOI: 10.1016/j.hal.2022.102185] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Although there is growing evidence that benthic cyanobacteria represent a significant source of toxins and taste and odour (T&O) compounds in water bodies globally, water utilities rarely monitor for them. Benthic cyanobacteria grow in an array of matrices such as sediments, biofilms, and floating mats, and they can detach and colonize treatment plants. The occurrence of compounds produced by benthic species across matrix and climate types has not been systematically investigated. Consequently, there is a lack of guidance available to utilities to monitor for and mitigate the risk associated with benthic cyanobacteria. To assess toxin and T&O risk across climatic zones and provide guidance to water utilities for the monitoring of benthic mats, two field surveys were conducted across three continents. The surveys examined the occurrence of six secondary metabolites and associated genes, namely, geosmin, 2-methylisoborneol (MIB), anatoxin-a, saxitoxin, microcystin, and cylindrospermopsin, in benthic environmental samples collected across three climates (i.e., temperate, sub-tropical, and tropical) and a range of matrix types. Existing enzyme-linked immunosorbent assays (ELISAs) and qPCR assays and were used to measure compound concentrations and their associated genes in samples. A novel qPCR assay was designed to differentiate the production of MIB by actinobacteria from that of cyanobacteria. MIB occurrence was higher in warmer climates than temperate climates. Cyanobacteria in benthic mats were the major producers of taste and odour compounds. Floating mats contained significantly higher concentrations of geosmin and saxitoxins compared to other matrix types. Samples collected in warmer areas contained significantly more saxitoxin and cylindrospermopsin than samples collected in temperate climates. While these trends were mainly indicative, they can be used to establish monitoring practices. These surveys demonstrate that benthic mats are significant contributors of secondary metabolites in source water and should be monitored accordingly. Benthic cyanobacteria were the sole producers of T&O in up to 17% of the collected samples compared to actinobacteria, which were sole producers in only 1% of the samples. The surveys also provided a platform of choice for the transfer of methodologies and specific knowledge to participating utilities to assist with the establishment of monitoring practices for benthic cyanobacteria and associated secondary metabolites.
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Affiliation(s)
- Virginie Gaget
- University of Adelaide, Water Research Centre, Department of Ecology and Evolutionary Biology, School of Biological Sciences, South Australia, 5005, Australia.
| | - Husein Almuhtaram
- University of Toronto, Department of Civil and Mineral Engineering, Toronto, Ontario, M5S 1A4, Canada
| | - Faith Kibuye
- Department of Research and Development, Southern Nevada Water Authority, Henderson, NV, 89015, USA
| | - Peter Hobson
- Australian Water Quality Centre, South Australia Water Corporation, Adelaide, South Australia, 5000, Australia
| | - Arash Zamyadi
- Water Research Australia Limited, Adelaide, South Australia, 5001, Australia; Department of Chemical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Victoria 3010 Australia
| | - Eric Wert
- Department of Research and Development, Southern Nevada Water Authority, Henderson, NV, 89015, USA
| | - Justin D Brookes
- University of Adelaide, Water Research Centre, Department of Ecology and Evolutionary Biology, School of Biological Sciences, South Australia, 5005, Australia
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Baker D, Basondwah S, Jambi E, Rahimuddin SA, Abuzaid M, Aly M. Molecular Identification, Characterization and Antioxidant Activities of Some Bacteria Associated with Algae in the Red Sea of Jeddah. Pak J Biol Sci 2020; 22:467-476. [PMID: 31930836 DOI: 10.3923/pjbs.2019.467.476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Algae-associated bacteria produce secondary metabolites that have a great biological impact. The aim of this study was isolation, identification and evaluation the antioxidant activities of the associated bacteria of seven algae, Padina pavonica, Dictyota dichotoma, Cystoseira myrica, Halimeda opuntia, Ulva lactuca, Digenea simplex and Jania sp. The bacteria were isolated, characterized and identified. Identification was carried out using 16S rRNA gene sequencing. MATERIALS AND METHODS The identified bacteria were belonging to 6 families, Alteromonadaceae, Bacillaceae, Lactobacillaceae, Pseudomonadaceae, Rhodobacteraceae and Vibrionaceae and 9 genera. The identified bacteria were belonging to genera, Alteromonas, Bacillus, Lysinibacillus Vibrio, Lactobacillus, Paracoccus, Leisingera, Pseudomonas and Pseudovibrio. The antioxidant activities of the bacterial ethyl acetate extracts was examined by scavenging DPPH (2,2-diphenyl-1-picrylhydrazyl) and FRAP (Ferric Reducing Antioxidant Power) methods. RESULTS Out of the 17 isolated bacteria, Lactobacillus plantarum showed 95.7% free radical scavenging with EC50 = 17.7 μg mL-1, which is nearly similar to the positive control (Butylated Hydroxytoluene, BHT). The FRAP value of Lactobacillus extract was 2.00 mM ferric equivalent/mg of the extract. Phytochemical analysis of the bacterial extract revealed the presence of some secondary metabolites such as steroids, saponins, tannins, flavonoids, anthocyanin and betacyanin in all tested extracts. CONCLUSION The Red Sea algal associated bacteria have a great antioxidant potential that can be used in pharmaceutical industries.
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Gaget V, Hobson P, Keulen A, Newton K, Monis P, Humpage AR, Weyrich LS, Brookes JD. Toolbox for the sampling and monitoring of benthic cyanobacteria. WATER RESEARCH 2020; 169:115222. [PMID: 31675609 DOI: 10.1016/j.watres.2019.115222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 10/10/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
Benthic cyanobacteria are a nuisance because they produce highly potent toxins and taste and odour compounds. Despite this, benthic cyanobacteria remain far less studied than their planktonic counterparts. For example, little is known about their growth or the seasonality of their secondary metabolite production. Moreover, sampling and monitoring techniques commonly used for the survey of planktonic species are not necessarily applicable to benthic forms. This study aimed to develop and validate a new sampling device for the routine monitoring of benthic mats. Molecular monitoring techniques were established and validated on environmental samples collected in a South Australian reservoir (SA-L2). A total of eight qPCR assays were applied to samples in order to track seasonal variations in cyanobacteria concentrations and associated secondary metabolite production. Next Generation Sequencing was utilised to conduct a microbial community composition analysis and to select the most appropriate substrate material for the sampling of benthic cyanobacteria. The concentration of the secondary metabolites geosmin and 2-methyl-isoborneol were quantified using High-Performance Liquid Chromatography, and concentrations of key nutrients (N, P) were quantified in water samples. The sampling device designed proved efficient and easy to use in the field. The qPCR assay designed for the amplification of the cyanobacterial MIB synthase had a high efficiency with a minimum limit of quantification of 4 cell-equivalents per reaction and identified a potential source of MIB in SA-L2 Reservoir. The peak season for benthic growth and secondary metabolite production was observed in spring. Proportionally, 35% of the variability in water geosmin concentrations can be explained by benthic actinobacterial and cyanobacterial activity, showing that freshwater benthic mats represent a significant source of taste and odour compounds.
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Affiliation(s)
- Virginie Gaget
- Water Research Centre, Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, South Australia, 5005, Australia.
| | - Peter Hobson
- Australian Water Quality Centre, South Australia Water Corporation, Adelaide, South Australia, 5000, Australia
| | - Angela Keulen
- Water Research Centre, Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, South Australia, 5005, Australia
| | - Kelly Newton
- Australian Water Quality Centre, South Australia Water Corporation, Adelaide, South Australia, 5000, Australia
| | - Paul Monis
- Water Research Centre, Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, South Australia, 5005, Australia; Australian Water Quality Centre, South Australia Water Corporation, Adelaide, South Australia, 5000, Australia
| | - Andrew R Humpage
- Australian Water Quality Centre, South Australia Water Corporation, Adelaide, South Australia, 5000, Australia
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, South Australia, 5005, Australia
| | - Justin D Brookes
- Water Research Centre, Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, South Australia, 5005, Australia
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Pessi IS, Pushkareva E, Lara Y, Borderie F, Wilmotte A, Elster J. Marked Succession of Cyanobacterial Communities Following Glacier Retreat in the High Arctic. MICROBIAL ECOLOGY 2019; 77:136-147. [PMID: 29796758 DOI: 10.1007/s00248-018-1203-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Cyanobacteria are important colonizers of recently deglaciated proglacial soil but an in-depth investigation of cyanobacterial succession following glacier retreat has not yet been carried out. Here, we report on the successional trajectories of cyanobacterial communities in biological soil crusts (BSCs) along a 100-year deglaciation gradient in three glacier forefields in central Svalbard, High Arctic. Distance from the glacier terminus was used as a proxy for soil age (years since deglaciation), and cyanobacterial abundance and community composition were evaluated by epifluorescence microscopy and pyrosequencing of partial 16S rRNA gene sequences, respectively. Succession was characterized by a decrease in phylotype richness and a marked shift in community structure, resulting in a clear separation between early (10-20 years since deglaciation), mid (30-50 years), and late (80-100 years) communities. Changes in cyanobacterial community structure were mainly connected with soil age and associated shifts in soil chemical composition (mainly moisture, SOC, SMN, K, and Na concentrations). Phylotypes associated with early communities were related either to potentially novel lineages (< 97.5% similar to sequences currently available in GenBank) or lineages predominantly restricted to polar and alpine biotopes, suggesting that the initial colonization of proglacial soil is accomplished by cyanobacteria transported from nearby glacial environments. Late communities, on the other hand, included more widely distributed genotypes, which appear to establish only after the microenvironment has been modified by the pioneering taxa.
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Affiliation(s)
- Igor S Pessi
- InBioS - Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium.
- Department of Microbiology, University of Helsinki, P.O. Box 56 (Viikinkaari 9), 00014, Helsinki, Finland.
| | - Ekaterina Pushkareva
- Centre for Polar Ecology, University of South Bohemia, Na Zlaté Stoce 3, 37005, České Budějovice, Czech Republic
| | - Yannick Lara
- InBioS - Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
- UR Geology - Palaeobiogeology-Palaeobotany-Palaeopalynology, University of Liège, Allée du Six Août14, B18, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
| | - Fabien Borderie
- InBioS - Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
- Laboratoire Chrono-environnement, UMR 6249 CNRS Université Bourgogne Franche-Comté UsC INRA, Campus La Bouloie, Route de Gray 16, 25030, Besançon, France
| | - Annick Wilmotte
- InBioS - Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
| | - Josef Elster
- Centre for Polar Ecology, University of South Bohemia, Na Zlaté Stoce 3, 37005, České Budějovice, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, 37982, Třeboň, Czech Republic
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11
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Johnson DB, Beddows PA, Flynn TM, Osburn MR. Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico. GEOBIOLOGY 2018; 16:319-337. [PMID: 29656514 DOI: 10.1111/gbi.12283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
Laguna Bacalar is a sulfate-rich freshwater lake on the Yucatan Peninsula that hosts large microbialites. High sulfate concentrations distinguish Laguna Bacalar from other freshwater microbialite sites such as Pavilion Lake and Alchichica, Mexico, as well as from other aqueous features on the Yucatan Peninsula. While cyanobacterial populations have been described here previously, this study offers a more complete characterization of the microbial populations and corresponding biogeochemical cycling using a three-pronged geobiological approach of microscopy, high-throughput DNA sequencing, and lipid biomarker analyses. We identify and compare diverse microbial communities of Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria that vary with location along a bank-to-bank transect across the lake, within microbialites, and within a neighboring mangrove root agglomeration. In particular, sulfate-reducing bacteria are extremely common and diverse, constituting 7%-19% of phylogenetic diversity within the microbialites, and are hypothesized to significantly influence carbonate precipitation. In contrast, Cyanobacteria account for less than 1% of phylogenetic diversity. The distribution of lipid biomarkers reflects these changes in microbial ecology, providing meaningful biosignatures for the microbes in this system. Polysaturated short-chain fatty acids characteristic of cyanobacteria account for <3% of total abundance in Laguna Bacalar microbialites. By contrast, even short-chain and monounsaturated short-chain fatty acids attributable to both Cyanobacteria and many other organisms including types of Alphaproteobacteria and Gammaproteobacteria constitute 43%-69% and 17%-25%, respectively, of total abundance in microbialites. While cyanobacteria are the largest and most visible microbes within these microbialites and dominate the mangrove root agglomeration, it is clear that their smaller, metabolically diverse associates are responsible for significant biogeochemical cycling in this microbialite system.
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Affiliation(s)
- D B Johnson
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - P A Beddows
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - T M Flynn
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - M R Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
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Pessi IS, Lara Y, Durieu B, Maalouf PDC, Verleyen E, Wilmotte A. Community structure and distribution of benthic cyanobacteria in Antarctic lacustrine microbial mats. FEMS Microbiol Ecol 2018; 94:4935156. [DOI: 10.1093/femsec/fiy042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 03/13/2018] [Indexed: 12/22/2022] Open
Affiliation(s)
- Igor S Pessi
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
| | - Yannick Lara
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
| | - Benoit Durieu
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
| | - Pedro de C Maalouf
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
| | - Elie Verleyen
- Research Group Protistology and Aquatic Ecology, Department of Biology, Ghent University, Campus Sterre, Krijgslaan 281-S8, 9000 Gent, Belgium
| | - Annick Wilmotte
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
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13
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Gaget V, Humpage AR, Huang Q, Monis P, Brookes JD. Benthic cyanobacteria: A source of cylindrospermopsin and microcystin in Australian drinking water reservoirs. WATER RESEARCH 2017; 124:454-464. [PMID: 28787682 DOI: 10.1016/j.watres.2017.07.073] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/21/2017] [Accepted: 07/29/2017] [Indexed: 05/21/2023]
Abstract
Cyanobacteria represent a health hazard worldwide due to their production of a range of highly potent toxins in diverse aquatic environments. While planktonic species have been the subject of many investigations in terms of risk assessment, little is known about benthic forms and their impact on water quality or human and animal health. This study aimed to purify isolates from environmental benthic biofilms sampled from three different drinking water reservoirs and to assess their toxin production by using the following methods: Enzyme-Linked Immunosorbent Assay (ELISA), High-Performance Liquid Chromatography (HPLC), Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) and quantitative PCR (qPCR). Microscopic observation of the isolates allowed the identification of various filamentous cyanobacterial genera: Anabaena (benthic form), Calothrix and Nostoc from the Nostocales and Geitlerinema, Leptolyngbya, Limnothrix, Lyngbya, Oxynema, Phormidium and Pseudanabaena representing non-heterocystous filamentous cyanobacteria. The Phormidium ambiguum strain AWQC-PHO021 was found to produce 739 ng/mg of dry weight (d/w) of cylindrospermopsin and 107 ng/mg (d/w) of deoxy-cylindrospermopsin. The Nostoc linckia strain AWQC-NOS001 produced 400 ng/mg (d/w) of a microcystin analogue. This is the first report of hepatotoxin production by benthic cyanobacteria in temperate Australian drinking water reservoirs. These findings indicate that water quality monitoring programs need to consider benthic cyanobacteria as a potential source of toxins.
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Affiliation(s)
- Virginie Gaget
- Water Research Centre, Ecology and Environmental Sciences, School of Biological Sciences, University of Adelaide, South Australia, 5005, Australia.
| | - Andrew R Humpage
- Australian Water Quality Centre, South Australia Water Corporation, Adelaide, South Australia, 5000, Australia
| | - Qiong Huang
- Australian Water Quality Centre, South Australia Water Corporation, Adelaide, South Australia, 5000, Australia
| | - Paul Monis
- Water Research Centre, Ecology and Environmental Sciences, School of Biological Sciences, University of Adelaide, South Australia, 5005, Australia; Australian Water Quality Centre, South Australia Water Corporation, Adelaide, South Australia, 5000, Australia
| | - Justin D Brookes
- Water Research Centre, Ecology and Environmental Sciences, School of Biological Sciences, University of Adelaide, South Australia, 5005, Australia
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