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Kim EJ, Doh H, Yang J, Eyun SI. The occurrence of positive selection on BicA transporter of Microcystis aeruginosa. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116795. [PMID: 39083868 DOI: 10.1016/j.ecoenv.2024.116795] [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: 03/19/2024] [Revised: 07/10/2024] [Accepted: 07/24/2024] [Indexed: 08/02/2024]
Abstract
The rapid growth of cyanobacteria, particularly Microcystis aeruginosa, poses a significant threat to global water security. The proliferation of toxic Microcystis aeruginosa raises concerns due to its potential harm to human health and socioeconomic impacts. Dense blooms contribute to spatiotemporal inorganic carbon depletion, promoting interest in the roles of carbon-concentrating mechanisms (CCMs) for competitive carbon uptake. Despite the importance of HCO3- transporters, genetic evaluations and functional predictions in M. aeruginosa remain insufficient. In this study, we explored the diversity of HCO3- transporters in the genomes of 46 strains of M. aeruginosa, assessing positive selection for each. Intriguingly, although the Microcystis BicA transporter became a partial gene in 23 out of 46 genomic strains, we observed significant positive sites. Structural analyses, including predicted 2D and 3D models, confirmed the structural conservation of the Microcystis BicA transporter. Our findings suggest that the Microcystis BicA transport likely plays a crucial role in competitive carbon uptake, emphasizing its ecological significance. The ecological function of the Microcystis BicA transport in competitive growth during cyanobacterial blooms raises important questions. Future studies require experimental confirmation to better understand the role of the Microcysits BicA transporter in cyanobacterial blooms dynamics.
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Affiliation(s)
- Eun-Jeong Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Huijeong Doh
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Jihye Yang
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea.
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2
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Zhang X, Xiao L, Liu J, Tian Q, Xie J. Trade-off in genome turnover events leading to adaptive evolution of Microcystis aeruginosa species complex. BMC Genomics 2023; 24:462. [PMID: 37592233 PMCID: PMC10433662 DOI: 10.1186/s12864-023-09555-3] [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: 03/21/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Numerous studies in the past have expanded our understanding of the genetic differences of global distributed cyanobacteria that originated around billions of years ago, however, unraveling how gene gain and loss drive the genetic evolution of cyanobacterial species, and the trade-off of these evolutionary forces are still the central but poorly understood issues. RESULTS To delineate the contribution of gene flow in mediating the hereditary differentiation and shaping the microbial evolution, a global genome-wide study of bloom-forming cyanobacterium, Microcystis aeruginosa species complex, provided robust evidence for genetic diversity, reflected by enormous variation in gene repertoire among various strains. Mathematical extrapolation showed an 'open' microbial pan-genome of M. aeruginosa species, since novel genes were predicted to be introduced after new genomes were sequenced. Identification of numerous horizontal gene transfer's signatures in genome regions of interest suggested that genome expansion via transformation and phage-mediated transduction across bacterial lineage as an evolutionary route may contribute to the differentiation of Microcystis functions (e.g., carbohydrate metabolism, amino acid metabolism, and energy metabolism). Meanwhile, the selective loss of some dispensable genes at the cost of metabolic versatility is as a mean of adaptive evolution that has the potential to increase the biological fitness. CONCLUSIONS Now that the recruitment of novel genes was accompanied by a parallel loss of some other ones, a trade-off in gene content may drive the divergent differentiation of M. aeruginosa genomes. Our study provides a genetic framework for the evolution of M. aeruginosa species and illustrates their possible evolutionary patterns.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China.
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Central South University, Changsha, China.
| | - Lijun Xiao
- Guangdong Corps Hospital of Chinese People's Armed Police Forces, Guangzhou, China
| | - Jiahui Liu
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Qibai Tian
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Jiaqi Xie
- Hunan Food and Drug Vocational College, Changsha, China
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3
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Cai H, McLimans CJ, Beyer JE, Krumholz LR, Hambright KD. Microcystis pangenome reveals cryptic diversity within and across morphospecies. SCIENCE ADVANCES 2023; 9:eadd3783. [PMID: 36638170 PMCID: PMC9839332 DOI: 10.1126/sciadv.add3783] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Microcystis, a common harmful algal bloom (HAB) taxon, threatens water supplies and human health, yet species delimitation is contentious in this taxon, leading to challenges in research and management of this threat. Historical and common morphology-based classifications recognize multiple morphospecies, most with variable and diverse ecologies, while DNA sequence-based classifications indicate a single species with multiple ecotypes. To better delimit Microcystis species, we conducted a pangenome analysis of 122 genomes. Core- and non-core gene phylogenetic analyses placed 113 genomes into 23 monophyletic clusters containing at least two genomes. Overall, genome-related indices revealed that Microcystis contains at least 16 putative genospecies. Fifteen genospecies included at least one Microcystis aeruginosa morphospecies, and 10 genospecies included two or more morphospecies. This classification system will enable consistent taxonomic identification of Microcystis and thereby aid in resolving some of the complexities and controversies that have long characterized eco-evolutionary research and management of this important HAB taxon.
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Affiliation(s)
- Haiyuan Cai
- Plankton Ecology and Limnology Laboratory, Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Christopher J. McLimans
- Plankton Ecology and Limnology Laboratory, Department of Biology, University of Oklahoma, Norman, OK, USA
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Jessica E. Beyer
- Plankton Ecology and Limnology Laboratory, Department of Biology, University of Oklahoma, Norman, OK, USA
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Lee R. Krumholz
- Department of Microbiology and Plant Biology and Institute for Energy and the Environment, University of Oklahoma, Norman, OK, USA
| | - K. David Hambright
- Plankton Ecology and Limnology Laboratory, Department of Biology, University of Oklahoma, Norman, OK, USA
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, USA
- Geographical Ecology, Department of Biology, University of Oklahoma, Norman, OK, USA
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4
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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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5
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Cao H, Xu D, Zhang T, Ren Q, Xiang L, Ning C, Zhang Y, Gao R. Comprehensive and functional analyses reveal the genomic diversity and potential toxicity of Microcystis. HARMFUL ALGAE 2022; 113:102186. [PMID: 35287927 DOI: 10.1016/j.hal.2022.102186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Microcystis is a cyanobacteria that is widely distributed across the world. It has attracted great attention because it produces the hepatotoxin microcystin (MC) that can inhibit eukaryotic protein phosphatases and pose a great risk to animal and human health. Due to the high diversity of morphospecies and genomes, it is still difficult to classify Microcystis species. In this study, we investigated the pangenome of 23 Microcystis strains to detect the genetic diversity and evolutionary dynamics. Microcystis revealed an open pangenome containing 22,009 gene families and exhibited different functional constraints. The core-genome phylogenetic analysis accurately differentiated the toxic and nontoxic strains and could be used as a taxonomic standard at the genetic level. We also investigated the functions of HGT events, of which were mostly conferred from cyanobacteria and closely related species. In order to detect the potential toxicity of Microcystis, we searched and characterized MC biosynthetic gene clusters and other secondary metabolite gene clusters. Our work provides insights into the genetic diversity, evolutionary dynamics, and potential toxicity of Microcystis, which could benefit the species classification and development of new methods for drinking water quality control and management of bloom formation in the future.
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Affiliation(s)
- Hengchun Cao
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Da Xu
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Tiantian Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Qiufang Ren
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Li Xiang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Chunhui Ning
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Yusen Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China.
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan 250061, Shandong, China.
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6
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Feist SM, Lance RF. Genetic detection of freshwater harmful algal blooms: A review focused on the use of environmental DNA (eDNA) in Microcystis aeruginosa and Prymnesium parvum. HARMFUL ALGAE 2021; 110:102124. [PMID: 34887004 DOI: 10.1016/j.hal.2021.102124] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Recurrence and severity of harmful algal blooms (HABs) are increasing due to a number of factors, including human practices and climate change. Sensitive and robust methods that allow for early and expedited HAB detection across large landscape scales are needed. Among the suite of HAB detection tools available, a powerful option exists in genetics-based approaches utilizing environmental sampling, also termed environmental DNA (eDNA). Here we provide a detailed methodological review of three HAB eDNA approaches (quantitative PCR, high throughput sequencing, and isothermal amplification). We then summarize and synthesize recently published eDNA applications covering a variety of HAB surveillance and research objectives, all with a specific emphasis in the detection of two widely problematic freshwater species, Microcystis aeruginosa and Prymnesium parvum. In our summary and conclusion we build on this literature by discussing ways in which eDNA methods could be advanced to improve HAB detection. We also discuss ways in which eDNA data could be used to potentially provide novel insight into the ecology, mitigation, and prediction of HABs.
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Affiliation(s)
- Sheena M Feist
- Environmental Lab, United States Army Corps of Engineers Research and Development Center, Vicksburg, MS, 39180, United States.
| | - Richard F Lance
- Environmental Lab, United States Army Corps of Engineers Research and Development Center, Vicksburg, MS, 39180, United States
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7
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Huo D, Gan N, Geng R, Cao Q, Song L, Yu G, Li R. Cyanobacterial blooms in China: diversity, distribution, and cyanotoxins. HARMFUL ALGAE 2021; 109:102106. [PMID: 34815019 DOI: 10.1016/j.hal.2021.102106] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Cyanobacterial blooms, which refer to the massive growth of harmful cyanobacteria, have altered the global freshwater ecosystems during the past decades. China has the largest population in the world, and it is suffering from the harmful effect of water eutrophication and cyanobacterial blooms along with rapid development of the economy and society. Research on cyanobacterial blooms and cyanotoxins in China have been overwhelmingly enhanced and emphasized during the past decades. In the present review, the research on cyanobacterial blooms in China is generally introduced, including the history of cyanobacterial bloom studies, the diversity of the bloom-forming cyanobacteria species (BFCS), and cyanotoxin studies in China. Most studies have focused on Microcystis, its blooms, and microcystins. Newly emerging blooms with the dominance of non-Microcystis BFCS have been gradually expanding to wide regions in China. Understanding the basic features of these non-Microcystis BFCS and their blooms, including their diversity, occurrence, physio-ecology, and harmful metabolites, will provide direction on future studies of cyanobacterial blooms in China.
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Affiliation(s)
- Da Huo
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Nanqin Gan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Ruozhen Geng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 400049, PR China
| | - Qi Cao
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Lirong Song
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Gongliang Yu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Renhui Li
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325000, PR China.
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8
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Bouma-Gregson K, Crits-Christoph A, Olm MR, Power ME, Banfield JF. Microcoleus (Cyanobacteria) form watershed-wide populations without strong gradients in population structure. Mol Ecol 2021; 31:86-103. [PMID: 34608694 PMCID: PMC9298114 DOI: 10.1111/mec.16208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 11/28/2022]
Abstract
The relative importance of separation by distance and by environment to population genetic diversity can be conveniently tested in river networks, where these two drivers are often independently distributed over space. To evaluate the importance of dispersal and environmental conditions in shaping microbial population structures, we performed genome‐resolved metagenomic analyses of benthic Microcoleus‐dominated cyanobacterial mats collected in the Eel and Russian River networks (California, USA). The 64 Microcoleus genomes were clustered into three species that shared >96.5% average nucleotide identity (ANI). Most mats were dominated by one strain, but minor alleles within mats were often shared, even over large spatial distances (>300 km). Within the most common Microcoleus species, the ANI between the dominant strains within mats decreased with increasing spatial separation. However, over shorter spatial distances (tens of kilometres), mats from different subwatersheds had lower ANI than mats from the same subwatershed, suggesting that at shorter spatial distances environmental differences between subwatersheds in factors like canopy cover, conductivity, and mean annual temperature decreases ANI. Since mats in smaller creeks had similar levels of nucleotide diversity (π) as mats in larger downstream subwatersheds, within‐mat genetic diversity does not appear to depend on the downstream accumulation of upstream‐derived strains. The four‐gamete test and sequence length bias suggest recombination occurs between almost all strains within each species, even between populations separated by large distances or living in different habitats. Overall, our results show that, despite some isolation by distance and environmental conditions, sufficient gene‐flow occurs among cyanobacterial strains to prevent either driver from producing distinctive population structures across the watershed.
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Affiliation(s)
- Keith Bouma-Gregson
- Office of Information Management and Analysis, State Water Resources Control Board, Sacramento, California, USA.,Earth and Planetary Science Department, University of California, Berkeley, California, USA
| | | | - Mathew R Olm
- Plant and Microbial Ecology Department, University of California, Berkeley, California, USA
| | - Mary E Power
- Integrative Biology Department, University of California, Berkeley, California, USA
| | - Jillian F Banfield
- Earth and Planetary Science Department, University of California, Berkeley, California, USA.,Plant and Microbial Ecology Department, University of California, Berkeley, California, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
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9
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Cyanobacteria and Cyanotoxins in a Changing Environment: Concepts, Controversies, Challenges. WATER 2021. [DOI: 10.3390/w13182463] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Concern is widely being published that the occurrence of toxic cyanobacteria is increasing in consequence of climate change and eutrophication, substantially threatening human health. Here, we review evidence and pertinent publications to explore in which types of waterbodies climate change is likely to exacerbate cyanobacterial blooms; whether controlling blooms and toxin concentrations requires a balanced approach of reducing not only the concentrations of phosphorus (P) but also those of nitrogen (N); how trophic and climatic changes affect health risks caused by toxic cyanobacteria. We propose the following for further discussion: (i) Climate change is likely to promote blooms in some waterbodies—not in those with low concentrations of P or N stringently limiting biomass, and more so in shallow than in stratified waterbodies. Particularly in the latter, it can work both ways—rendering conditions for cyanobacterial proliferation more favourable or less favourable. (ii) While N emissions to the environment need to be reduced for a number of reasons, controlling blooms can definitely be successful by reducing only P, provided concentrations of P can be brought down to levels sufficiently low to stringently limit biomass. Not the N:P ratio, but the absolute concentration of the limiting nutrient determines the maximum possible biomass of phytoplankton and thus of cyanobacteria. The absolute concentrations of N or P show which of the two nutrients is currently limiting biomass. N can be the nutrient of choice to reduce if achieving sufficiently low concentrations has chances of success. (iii) Where trophic and climate change cause longer, stronger and more frequent blooms, they increase risks of exposure, and health risks depend on the amount by which concentrations exceed those of current WHO cyanotoxin guideline values for the respective exposure situation. Where trophic change reduces phytoplankton biomass in the epilimnion, thus increasing transparency, cyanobacterial species composition may shift to those that reside on benthic surfaces or in the metalimnion, changing risks of exposure. We conclude that studying how environmental changes affect the genotype composition of cyanobacterial populations is a relatively new and exciting research field, holding promises for understanding the biological function of the wide range of metabolites found in cyanobacteria, of which only a small fraction is toxic to humans. Overall, management needs case-by-case assessments focusing on the impacts of environmental change on the respective waterbody, rather than generalisations.
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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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11
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Draft Genome Sequences of Four Microcystis aeruginosa Strains (NIES-3787, NIES-3804, NIES-3806, and NIES-3807) Isolated from Lake Kasumigaura, Japan. Microbiol Resour Announc 2020; 9:9/14/e00052-20. [PMID: 32241856 PMCID: PMC7118182 DOI: 10.1128/mra.00052-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microcystis aeruginosa is a bloom-forming cyanobacterium found in freshwater environments. The draft genomes of the M. aeruginosa strains NIES-3787, NIES-3804, NIES-3806, and NIES-3807, which were isolated from Lake Kasumigaura, Japan, were sequenced. The genome sizes of NIES-3787, NIES-3804, NIES-3806, and NIES-3807 were 4,524,637, 4,522,701, 4,370,004, and 4,378,226 bp, respectively. Microcystis aeruginosa is a bloom-forming cyanobacterium found in freshwater environments. The draft genomes of the M. aeruginosa strains NIES-3787, NIES-3804, NIES-3806, and NIES-3807, which were isolated from Lake Kasumigaura, Japan, were sequenced. The genome sizes of NIES-3787, NIES-3804, NIES-3806, and NIES-3807 were 4,524,637, 4,522,701, 4,370,004, and 4,378,226 bp, respectively.
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12
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Yamaguchi H, Suzuki S, Osana Y, Kawachi M. Genomic Characteristics of the Toxic Bloom-Forming Cyanobacterium Microcystis aeruginosa NIES-102. J Genomics 2020; 8:1-6. [PMID: 31892993 PMCID: PMC6930136 DOI: 10.7150/jgen.40978] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/20/2019] [Indexed: 01/10/2023] Open
Abstract
Microcystis aeruginosa, a bloom-forming cyanobacterium distributed mainly in freshwater environments, can be divided into at least 12 groups (A-K and X) based on multi-locus phylogenetic analyses. In this study, we characterized the genome of microcystin-producing M. aeruginosa NIES-102, assigned to group A, isolated from Lake Kasumigaura, Japan. The complete genome sequence of M. aeruginosa NIES-102 comprised a 5.87-Mbp circular chromosome containing 5,330 coding sequences. The genome was the largest among all sequenced genomes for the species. In a comparison with the genome of M. aeruginosa NIES-843, which belongs to the same group, the microcystin biosynthetic gene cluster and CRISPR-Cas locus were highly similar. A synteny analysis revealed small-scale rearrangements between the two genomes. Genes encoding transposases were more abundant in these two genomes than in other Microcystis genomes. Our results improve our understanding of structural genomic changes and adaptation to a changing environment in the species.
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Affiliation(s)
- Haruyo Yamaguchi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Shigekatsu Suzuki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Yasunori Osana
- Department of Electrical and Electronics Engineering, University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa 903-0213, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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Ikehara T, Kuniyoshi K, Yamaguchi H, Tanabe Y, Sano T, Yoshimoto M, Oshiro N, Nakashima S, Yasumoto-Hirose M. First Report of Microcystis Strains Producing MC-FR and -WR Toxins in Japan. Toxins (Basel) 2019; 11:toxins11090521. [PMID: 31505765 PMCID: PMC6784158 DOI: 10.3390/toxins11090521] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/06/2019] [Accepted: 09/06/2019] [Indexed: 11/16/2022] Open
Abstract
Microcystins (MCs) are a group of cyclic heptapeptide hepatotoxins produced by Microcystis and several other genera of cyanobacteria. Many structural variants have been characterized using various methods such as liquid chromatography-mass spectrometry (LC-MS) analysis, enzyme-linked immunosorbent assay (ELISA) and protein phosphatase 2A (PP2A) inhibition assay. The representative MC, MC-LR, and related cyanobacterial toxins strongly inhibit PP2A activity and can therefore be assayed by measuring the extent of PP2A inhibition. However, these methods require reference toxin standards for the quantification and identification of known MCs. To obtain various MC-producing cyanobacterial strains, we surveyed and collected MC-producing cyanobacteria from environmental sources of water in Okinawa, Japan. Using a dual assay (LC-MS analysis and PP2A inhibition assay), we identified and isolated Microcystis strains producing five MC variants (MC-LR, -RR, -LA, -FR and -WR). Approximately 4 mg of MC-WR and -FR toxins were purified from the laboratory culture of the Microcystis isolate NIES-4344. Pure MC-WR and -FR variants were prepared for future use as toxin standards in LC-MS analysis. Phylogenetic analysis based on ftsZ revealed that the NIES-4344 strain belongs to the identified groups in Microcystis aeruginosa. This is the first report of Microcystis strains producing mainly MC-WR and -FR toxins in Japan.
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Affiliation(s)
- Tsuyoshi Ikehara
- Department of Food Science and Technology, National Fisheries University, 2-7-1 Nagata-honmachi, Shimonoseki, Yamaguchi 759-6595, Japan.
| | - Kyoko Kuniyoshi
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan.
| | - Haruyo Yamaguchi
- National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan.
| | - Yuuhiko Tanabe
- National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan.
| | - Tomoharu Sano
- National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan.
| | - Masahiro Yoshimoto
- Okinawa Institute for the Conservation of the Environment Co. Ltd., 7-11 Suzaki, Uruma, Okinawa 904-2234, Japan.
| | - Naomasa Oshiro
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan.
| | - Shihoko Nakashima
- Faculty of Sports and Health Science, Fukuoka University, Fukuoka 814-0180, Japan.
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Tanabe Y, Yamaguchi H, Sano T, Kawachi M. A novel salt-tolerant genotype illuminates the sucrose gene evolution in freshwater bloom-forming cyanobacterium Microcystis aeruginosa. FEMS Microbiol Lett 2019; 366:5561441. [PMID: 31504438 DOI: 10.1093/femsle/fnz190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/02/2019] [Indexed: 12/13/2022] Open
Abstract
Microcystis aeruginosa is a water bloom-forming cyanobacterium found in fresh and brackish water ecosystems worldwide. Previously, we showed that several instances of M. aeruginosa bloom in brackish water can be explained by the proliferation of salt-tolerant M. aeruginosa strains harboring genes for a compatible solute sucrose. However, evolutionary history of sucrose genes in M. aeruginosa remains unclear because salt-tolerant strains have been poorly described. Here, we characterized a novel salt-tolerant strain of M. aeruginosa (NIES-4325) isolated from the brackish water of Lake Abashiri, Japan. A whole-genome analysis of M. aeruginosa NIES-4325 identified genes for sucrose synthesis (sppA, spsA and susA). Quantitative sucrose and gene expression analyses suggested that sucrose is implicated in acclimation to high salt in NIES-4325. Notably, the sucrose genes of M. aeruginosa are monophyletic, yet sucrose genes of NIES-4325 are highly divergent from those of other salt-tolerant M. aeruginosa strains. This suggests an early sucrose gene import into M. aeruginosa from other cyanobacteria, followed by multiple losses during intraspecific diversification. One of a few survivors of salt-tolerant strains is a likely donor of recent horizontal spreads of sucrose genes across M. aeruginosa lineages.
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Affiliation(s)
- Yuuhiko Tanabe
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Haruyo Yamaguchi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Tomoharu Sano
- Center for Environmental Measurement and Analysis, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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15
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Pérez-Carrascal OM, Terrat Y, Giani A, Fortin N, Greer CW, Tromas N, Shapiro BJ. Coherence of Microcystis species revealed through population genomics. ISME JOURNAL 2019; 13:2887-2900. [PMID: 31363173 DOI: 10.1038/s41396-019-0481-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/05/2019] [Accepted: 07/05/2019] [Indexed: 11/09/2022]
Abstract
Microcystis is a genus of freshwater cyanobacteria, which causes harmful blooms in ecosystems worldwide. Some Microcystis strains produce harmful toxins such as microcystin, impacting drinking water quality. Microcystis colony morphology, rather than genetic similarity, is often used to classify Microcystis into morphospecies. Yet colony morphology is a plastic trait, which can change depending on environmental and laboratory culture conditions, and is thus an inadequate criterion for species delineation. Furthermore, Microcystis populations are thought to disperse globally and constitute a homogeneous gene pool. However, this assertion is based on relatively incomplete characterization of Microcystis genomic diversity. To better understand these issues, we performed a population genomic analysis of 33 newly sequenced genomes mainly from Canada and Brazil. We identified 17 Microcystis clusters of genomic similarity, five of which correspond to monophyletic clades containing at least three newly sequenced genomes. Four out of these five clades match to named morphospecies. Notably, M. aeruginosa is paraphyletic, distributed across 12 genomic clusters, suggesting it is not a coherent species. A few clades of closely related isolates are specific to a unique geographic location, suggesting biogeographic structure over relatively short evolutionary time scales. Higher homologous recombination rates within than between clades further suggest that monophyletic groups might adhere to a Biological Species-like concept, in which barriers to gene flow maintain species distinctness. However, certain genes-including some involved in microcystin and micropeptin biosynthesis-are recombined between monophyletic groups in the same geographic location, suggesting local adaptation.
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Affiliation(s)
| | - Yves Terrat
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
| | - Alessandra Giani
- Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | - Nicolas Tromas
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada.
| | - B Jesse Shapiro
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
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16
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Martins MD, Machado-de-Lima NM, Branco LHZ. Polyphasic approach using multilocus analyses supports the establishment of the new aerophytic cyanobacterial genus Pycnacronema (Coleofasciculaceae, Oscillatoriales). JOURNAL OF PHYCOLOGY 2019; 55:146-159. [PMID: 30362579 DOI: 10.1111/jpy.12805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
A new Phormidium-like genus was found during an investigation of Oscillatoriales diversity in Brazil. Eight aerophytic populations from south and southeastern regions were isolated in monospecific cultures and submitted to polyphasic evaluation. The populations presented homogeneous morphology with straight trichomes, not attenuated, and apical cell with thickened cell wall. Phylogenetic analyses based on 16S rRNA gene sequences showed that these populations, plus the Brazilian strain Phomidium sp. B-Tom from GenBank, formed a highly supported and distinctive clade, which corresponds to the new genus Pycnacronema, comprising six new species: P. brasiliensis (type species), P. arboriculum, P. conicum, P. marmoreum, P. rubrum, and P. savannensis. These results were confirmed and supported by rpoC1 and rbcL genes evaluated independently and by the concatenated analysis of 16S rRNA, rpoC1 and rbcL genes (for all species but P. savannensis). Secondary structures of the D1-D1', box-B, and V3 regions of the internal transcribed spacer were informative at specific level, being conserved in P. brasiliensis and variable among the other strains, also confirming the phylogenetic analyses. The generic name and specific epithets of the new taxa are proposed under the provisions of the International Code of Nomenclature of algae, fungi, and plants.
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Affiliation(s)
- Mariéllen Dornelles Martins
- Zoology and Botany Department, São José do Rio Preto campus (IBILCE), São Paulo State University (UNESP), R. Cristóvão Colombo, 2265 - BR15054-000, S. J. Rio Preto (SP), Brazil
| | - Náthali Maria Machado-de-Lima
- Microbiology Graduate Program (IBILCE/UNESP), Zoology and Botany Department, São José do Rio Preto campus (IBILCE), São Paulo State University (UNESP), R. Cristóvão Colombo, 2265 - BR15054-000, S. J. Rio Preto (SP), Brazil
| | - Luis Henrique Zanini Branco
- Zoology and Botany Department, São José do Rio Preto campus (IBILCE), São Paulo State University (UNESP), R. Cristóvão Colombo, 2265 - BR15054-000, S. J. Rio Preto (SP), Brazil
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17
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LANDRIEL SOLEDADCAMINATA, CASTILLO JULIETAD, TABOGA OSCARA, FERRAROTTI SUSANAA, GOTTLIEB ALEXANDRAM, COSTA HERNÁN. Molecular identification of a cyclodextrin glycosyltransferase-producing microorganism and phylogenetic assessment of enzymatic activities. AN ACAD BRAS CIENC 2019; 91:e20180568. [DOI: 10.1590/0001-3765201920180568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 01/10/2019] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | - OSCAR A. TABOGA
- Instituto Nacional de Tecnología Agropecuaria (IABIMO-INTA-CONICET), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas/CONICET, Argentina
| | | | - ALEXANDRA M. GOTTLIEB
- Universidad de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas/CONICET, Argentina
| | - HERNÁN COSTA
- Universidad Nacional de Luján, Argentina; Universidad Nacional de Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas/CONICET, Argentina
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18
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Tanabe Y, Hodoki Y, Sano T, Tada K, Watanabe MM. Adaptation of the Freshwater Bloom-Forming Cyanobacterium Microcystis aeruginosa to Brackish Water Is Driven by Recent Horizontal Transfer of Sucrose Genes. Front Microbiol 2018; 9:1150. [PMID: 29922255 PMCID: PMC5996124 DOI: 10.3389/fmicb.2018.01150] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022] Open
Abstract
Microcystis aeruginosa is a bloom-forming cyanobacterium found in eutrophic water bodies worldwide. M. aeruginosa blooms usually occur in freshwater; however, they have also been reported to occur in brackish water. Because M. aeruginosa often produces the cyanotoxin microcystin, they are a major concern to public health and environment. Despite this, the ecology, genomic basis, and evolutionary process underlying the M. aeruginosa bloom invasion from fresh to brackish water have been poorly investigated. Hence, in the present study, we have sequenced and characterized genomes of two newly discovered salt-tolerant M. aeruginosa strains obtained from Japanese brackish water lakes (Lakes Shinji and Tofutsu). Both genomes contain a set of genes for the synthesis of osmolyte sucrose (sppA, spsA, and susA), hitherto identified in only one strain (PCC 7806) of M. aeruginosa. Chemical and gene expression analyses confirmed sucrose accumulation induced by salt. A comprehensive genetic survey of >200 strains indicated that sucrose genes are extremely rare in M. aeruginosa. Most surprisingly, comparative genome analyses of the three strains indicated extremely low genetic diversity in the sucrose genes compared with other core genome genes, suggesting very recent acquisitions via horizontal transfer. Invasion of M. aeruginosa blooms into brackish water may be a recent event triggered by anthropogenic eutrophication of brackish water.
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Affiliation(s)
- Yuuhiko Tanabe
- Algae Biomass and Energy System R&D Center, University of Tsukuba, Tsukuba, Japan
| | | | - Tomoharu Sano
- Center for Environmental Measurement and Analysis, National Institute for Environmental Studies, Tsukuba, Japan
| | - Kiyoshi Tada
- Algae Biomass and Energy System R&D Center, University of Tsukuba, Tsukuba, Japan
| | - Makoto M Watanabe
- Algae Biomass and Energy System R&D Center, University of Tsukuba, Tsukuba, Japan
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19
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Yamaguchi H, Suzuki S, Osana Y, Kawachi M. Complete Genome Sequence of Microcystis aeruginosa NIES-2481 and Common Genomic Features of Group G M. aeruginosa. J Genomics 2018; 6:30-33. [PMID: 29576807 PMCID: PMC5865083 DOI: 10.7150/jgen.24935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 02/21/2018] [Indexed: 11/05/2022] Open
Abstract
Microcystis aeruginosa is a freshwater bloom-forming cyanobacterium that is distributed worldwide. M. aeruginosa can be divided into at least 8 phylogenetic groups (A-G and X) at the intraspecific level. Here, we report the complete genome sequence of M. aeruginosa NIES-2481, which was isolated from Lake Kasumigaura, Japan, and is assigned to group G. The complete genome sequence of M. aeruginosa NIES-2481 comprises a 4.29-Mbp circular chromosome and a 147,539-bp plasmid; the circular chromosome and the plasmid contain 4,332 and 167 protein-coding genes, respectively. Comparative analysis with the complete genome of M. aeruginosa NIES-2549, which belongs to the same group with NIES-2481, showed that the genome size is the smallest level in previously sequenced M. aeruginosa strains, and the genomes do not contain a microcystin biosynthetic gene cluster in common. Synteny analysis revealed only small-scale rearrangements between the two genomes.
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Affiliation(s)
- Haruyo Yamaguchi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Shigekatsu Suzuki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Yasunori Osana
- Department of Electrical and Electronics Engineering, University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa 903-0213, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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20
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Hoetzinger M, Hahn MW. Genomic divergence and cohesion in a species of pelagic freshwater bacteria. BMC Genomics 2017; 18:794. [PMID: 29037158 PMCID: PMC5644125 DOI: 10.1186/s12864-017-4199-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 10/08/2017] [Indexed: 11/15/2022] Open
Abstract
Background In many prokaryotic genera a clustered phylogeny is observed, akin to the occurrence of species in sexually reproducing organisms. For some taxa, homologous recombination has been invoked as the underlying mechanism providing genomic cohesion among conspecific individuals. Whether this mechanism is applicable to prokaryotes in freshwaters with low habitat connectivity – i.e. elevated geographic barriers to gene flow – is unclear. To investigate further we studied genomic trends within the globally abundant PnecC cluster (genus Polynucleobacter, Betaproteobacteria) and analyzed homologous recombination within the affiliated species P. asymbioticus. Results Comparisons among 20 PnecC genomes revealed a clearly discontinuous distribution of nucleotide sequence similarities. Among the nine conspecific individuals (P. asymbioticus) all average nucleotide identity (ANI) values were greater than 97%, whereas all other comparisons exhibited ANI values lower than 85%. The reconstruction of recombination and mutation events for the P. asymbioticus core genomes yielded an r/m ratio of 7.4, which is clearly above estimated thresholds for recombination to act as a cohesive force. Hotspots of recombination were found to be located in the flanking regions of genomic islands. Even between geographically separated habitats a high flux of recombination was evident. While a biogeographic population structure was suggested from MLST data targeting rather conserved loci, such a structure was barely visible when whole genome data was considered. However, both MLST and whole genome data showed evidence of differentiation between two lineages of P. asymbioticus. The ratios of non-synonymous to synonymous substitution rates as well as growth rates in transplantation experiments suggested that this divergence was not selectively neutral. Conclusions The high extent of homologous recombination among P. asymbioticus bacteria can act as a cohesive force that effectively counteracts genetic divergence. At least on a regional scale, homologous recombination can act across geographically separated ecosystems and therefore plays an important role in the evolution and consistency of bacterial freshwater species. A species model akin to the biological species concept may be applicable for P. asymbioticus. Nonetheless, two genetically distinct lineages have emerged and further research may clarify if their divergence has been initiated by reinforced geographical barriers or has been evolving in sympatry. Electronic supplementary material The online version of this article (10.1186/s12864-017-4199-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthias Hoetzinger
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310, Mondsee, Austria.
| | - Martin W Hahn
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310, Mondsee, Austria
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21
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Meyer KA, Davis TW, Watson SB, Denef VJ, Berry MA, Dick GJ. Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms. PLoS One 2017; 12:e0183859. [PMID: 29020009 PMCID: PMC5647855 DOI: 10.1371/journal.pone.0183859] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 08/11/2017] [Indexed: 12/15/2022] Open
Abstract
Blooms of the potentially toxic cyanobacterium Microcystis are increasing worldwide. In the Laurentian Great Lakes they pose major socioeconomic, ecological, and human health threats, particularly in western Lake Erie. However, the interpretation of "omics" data is constrained by the highly variable genome of Microcystis and the small number of reference genome sequences from strains isolated from the Great Lakes. To address this, we sequenced two Microcystis isolates from Lake Erie (Microcystis aeruginosa LE3 and M. wesenbergii LE013-01) and one from upstream Lake St. Clair (M. cf aeruginosa LSC13-02), and compared these data to the genomes of seventeen Microcystis spp. from across the globe as well as one metagenome and seven metatranscriptomes from a 2014 Lake Erie Microcystis bloom. For the publically available strains analyzed, the core genome is ~1900 genes, representing ~11% of total genes in the pan-genome and ~45% of each strain's genome. The flexible genome content was related to Microcystis subclades defined by phylogenetic analysis of both housekeeping genes and total core genes. To our knowledge this is the first evidence that the flexible genome is linked to the core genome of the Microcystis species complex. The majority of strain-specific genes were present and expressed in bloom communities in Lake Erie. Roughly 8% of these genes from the lower Great Lakes are involved in genome plasticity (rapid gain, loss, or rearrangement of genes) and resistance to foreign genetic elements (such as CRISPR-Cas systems). Intriguingly, strain-specific genes from Microcystis cultured from around the world were also present and expressed in the Lake Erie blooms, suggesting that the Microcystis pangenome is truly global. The presence and expression of flexible genes, including strain-specific genes, suggests that strain-level genomic diversity may be important in maintaining Microcystis abundance during bloom events.
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Affiliation(s)
- Kevin Anthony Meyer
- Cooperative Institute for Great Lakes Research (CIGLR), University of
Michigan, Ann Arbor, MI, United States of America
- Department of Earth and Environmental Sciences, University of Michigan,
Ann Arbor, MI, United States of America
| | - Timothy W. Davis
- NOAA Great Lakes Environmental Research Laboratory, Ann Arbor, MI, United
States of America
| | - Susan B. Watson
- Environment and Climate Change Canada, Burlington, ON,
Canada
| | - Vincent J. Denef
- Department of Ecology and Evolutionary Biology, University of Michigan,
Ann Arbor, MI, United States of America
| | - Michelle A. Berry
- Department of Ecology and Evolutionary Biology, University of Michigan,
Ann Arbor, MI, United States of America
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan,
Ann Arbor, MI, United States of America
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22
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Shirani S, Hellweger FL. Neutral Evolution and Dispersal Limitation Produce Biogeographic Patterns in Microcystis aeruginosa Populations of Lake Systems. MICROBIAL ECOLOGY 2017; 74:416-426. [PMID: 28303312 DOI: 10.1007/s00248-017-0963-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/02/2017] [Indexed: 06/06/2023]
Abstract
Molecular observations reveal substantial biogeographic patterns of cyanobacteria within systems of connected lakes. An important question is the relative role of environmental selection and neutral processes in the biogeography of these systems. Here, we quantify the effect of genetic drift and dispersal limitation by simulating individual cyanobacteria cells using an agent-based model (ABM). In the model, cells grow (divide), die, and migrate between lakes. Each cell has a full genome that is subject to neutral mutation (i.e., the growth rate is independent of the genome). The model is verified by simulating simplified lake systems, for which theoretical solutions are available. Then, it is used to simulate the biogeography of the cyanobacterium Microcystis aeruginosa in a number of real systems, including the Great Lakes, Klamath River, Yahara River, and Chattahoochee River. Model output is analyzed using standard bioinformatics tools (BLAST, MAFFT). The emergent patterns of nucleotide divergence between lakes are dynamic, including gradual increases due to accumulation of mutations and abrupt changes due to population takeovers by migrant cells (coalescence events). The model predicted nucleotide divergence is heterogeneous within systems, and for weakly connected lakes, it can be substantial. For example, Lakes Superior and Michigan are predicted to have an average genomic nucleotide divergence of 8200 bp or 0.14%. The divergence between more strongly connected lakes is much lower. Our results provide a quantitative baseline for future biogeography studies. They show that dispersal limitation can be an important factor in microbe biogeography, which is contrary to the common belief, and could affect how a system responds to environmental change.
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Affiliation(s)
- Sahar Shirani
- Department of Civil & Environmental Engineering, Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
| | - Ferdi L Hellweger
- Department of Civil & Environmental Engineering, Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA.
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23
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Liyanage HM, Magana Arachchi DN, Chandrasekaran NV. Genetic divergence among toxic and non-toxic cyanobacteria of the dry zone of Sri Lanka. SPRINGERPLUS 2016; 5:2026. [PMID: 27995003 PMCID: PMC5125326 DOI: 10.1186/s40064-016-3680-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/11/2016] [Indexed: 12/20/2022]
Abstract
Sri Lanka has rich cyanobacterial diversity, however, only few studies have been conducted to identify the potential toxin producers in water bodies used for human consumption. As the detection of cyanotoxin is vital in water quality management, a study was done by employing 16S rRNA gene to explore the genetic divergence, phylogenetic relationships and potential toxin producing cyanobacteria in reservoirs and well waters in the dry zone of Sri Lanka. Forty five, 16S rRNA gene sequences were assayed and phylogenetic tree was constructed. Among 45 isolates, 20 isolates were classified as unidentified cyanobacteria and considered as novel cyanobacterial genera. Of 25 identified isolates, seven isolates were identified up to species level. With 16S rRNA phylogeny, 20 unidentified cyanobacterial isolates were able to place on their taxonomic positions up to order level. Results revealed that water samples understudy had vast cyanobacterial diversity with potential microcystin (MC) and cylindrospermopsin (CYN) producers and eleven clusters clearly demonstrated five cyanobacterial orders with more than 90% similarity irrespective to their toxicity which showed the suitability of 16S rRNA gene for taxonomic differentiation. Sixteen isolates had the potential to produce MC and two isolates to produce CYN. Findings of the study confirm the rich cyanobacterial diversity and the divergence among the potential cyanotoxin producers in the dry zone water bodies of Sri Lanka.
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Affiliation(s)
- Harshini M Liyanage
- National Institute of Fundamental Studies (NIFS), Hantana Road, Kandy, 20000 Sri Lanka
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24
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Genetic characterization of Microcystis aeruginosa isolates from Portuguese freshwater systems. World J Microbiol Biotechnol 2016; 32:118. [PMID: 27263013 DOI: 10.1007/s11274-016-2063-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/31/2016] [Indexed: 10/21/2022]
Abstract
Cyanobacteria are microorganisms that pose a serious threat to the aquatic waterways through the production of dense blooms under eutrophic conditions and the release of toxic secondary metabolites-cyanotoxins. Within cyanobacteria, the colonial planktonic Microcystis aeruginosa is widely distributed in both fresh and brackish aquatic environments throughout the world being frequently observed in the Portuguese water systems. Apart from the well-established distribution of M. aeruginosa in Portugal, knowledge of its genetic diversity and population structure is unknown. Therefore, in this study twenty-seven strains were obtained from the North, Centre and South regions of Portugal and were subjected to extensive phylogenetic analyses using simultaneously four distinct genetic markers (16S rRNA, 16S-23S ITS, DNA gyrase subunit ß and cell division protein (ftsZ)) encompassing in total 2834 bp. With this work we characterized the phylogenetic relationship among the Portuguese strains, with the southern strains showing higher genetic structure relatively to the North and Centre strains. A total of fifteen genotypes were determined for M. aeruginosa in Portuguese water systems revealing a high genetic diversity. This is also the first study to report geographic variation on the population structure of the Portuguese M. aeruginosa.
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Sun LW, Jiang WJ, Sato H, Kawachi M, Lu XW. Rapid Classification and Identification of Microcystis aeruginosa Strains Using MALDI-TOF MS and Polygenetic Analysis. PLoS One 2016; 11:e0156275. [PMID: 27227555 PMCID: PMC4881969 DOI: 10.1371/journal.pone.0156275] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/11/2016] [Indexed: 11/18/2022] Open
Abstract
Matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry (MALDI-TOF MS) was used to establish a rapid, simple, and accurate method to differentiate among strains of Microcystis aeruginosa, one of the most prevalent types of bloom-forming cyanobacteria. M. aeruginosa NIES-843, for which a complete genome has been sequenced, was used to characterize ribosomal proteins as biomarkers and to optimize conditions for observing ribosomal proteins as major peaks in a given mass spectrum. Thirty-one of 52 ribosomal subunit proteins were detected and identified along the mass spectrum. Fifty-five strains of M. aeruginosa from different habitats were analyzed using MALDI-TOF MS; among these samples, different ribosomal protein types were observed. A polygenetic analysis was performed using an unweighted pair-group method with arithmetic means and different ribosomal protein types to classify the strains into five major clades. Two clades primarily contained toxic strains, and the other three clades contained exclusively non-toxic strains. This is the first study to differentiate cyanobacterial strains using MALDI-TOF MS.
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Affiliation(s)
- Li-Wei Sun
- School of Energy & Environment, Southeast University, Nanjing, Jiangsu, China
- * E-mail: (LWS); (HS)
| | - Wen-Jing Jiang
- School of Energy & Environment, Southeast University, Nanjing, Jiangsu, China
| | - Hiroaki Sato
- Environmental Measurement Technology Group, Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
- * E-mail: (LWS); (HS)
| | - Masanobu Kawachi
- Biodiversity Resource Conservation Section, Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Xi-Wu Lu
- School of Energy & Environment, Southeast University, Nanjing, Jiangsu, China
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Bao Q, Song Y, Xu H, Yu J, Zhang W, Menghe B, Zhang H, Sun Z. Multilocus sequence typing of Lactobacillus casei isolates from naturally fermented foods in China and Mongolia. J Dairy Sci 2016; 99:5202-5213. [PMID: 27179867 DOI: 10.3168/jds.2016-10857] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/28/2016] [Indexed: 11/19/2022]
Abstract
Lactobacillus casei is a lactic acid bacterium used in manufacturing of many fermented food products. To investigate the genetic diversity and population biology of this food-related bacterium, 224 Lb. casei isolates and 5 reference isolates were examined by multilocus sequence typing (MLST). Among them, 224 Lb. casei isolates were isolated from homemade fermented foods, including naturally fermented dairy products, acidic gruel, and Sichuan pickles from 38 different regions in China and Mongolia. The MLST scheme was developed based on the analysis of 10 selected housekeeping genes (carB, clpX, dnaA, groEL, murE, pyrG, pheS, recA, rpoC, and uvrC). All 229 isolates could be allocated to 171 unique sequence types, including 25 clonal complexes and 71 singletons. The high index of association value (1.3524) and standardized index of association value (0.1503) indicate the formation of an underlying clonal population by all the isolates. However, split-decomposition, relative frequency of occurrence of recombination and mutation, and relative effect of recombination and mutation in the diversification values confirm that recombination may have occurred, and were more frequent than mutation during the evolution of Lb. casei. Results from Structure analyses (version 2.3; http://pritch.bsd.uchicago.edu/structure.html) demonstrated that there were 5 lineages in the Lb. casei isolates, and the overall relatedness built by minimum spanning tree showed no clear relationship between the clonal complexes with either the isolation sources or sampling locations of the isolates. Our newly developed MLST scheme of Lb. casei was an easy and valuable tool that, together with the construction of an MLST database, will contribute to further detailed studies on the evolution and population genetics of Lb. casei from various niches.
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Affiliation(s)
- Qiuhua Bao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Yuqin Song
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Bilige Menghe
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China.
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Bosmans L, Álvarez-Pérez S, Moerkens R, Wittemans L, Van Calenberge B, Kerckhove SV, Paeleman A, De Mot R, Rediers H, Lievens B. Assessment of the genetic and phenotypic diversity among rhizogenic Agrobacterium biovar 1 strains infecting solanaceous and cucurbit crops. FEMS Microbiol Ecol 2015; 91:fiv081. [PMID: 26187479 DOI: 10.1093/femsec/fiv081] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2015] [Indexed: 01/14/2023] Open
Abstract
Rhizogenic Agrobacterium biovar 1 strains have been found to cause extensive root proliferation on hydroponically grown Cucurbitaceae and Solanaceae crops, resulting in substantial economic losses. As these agrobacteria live under similar ecological conditions, infecting a limited number of crops, it may be hypothesized that genetic and phenotypic variation among such strains is relatively low. In this study we assessed the phenotypic diversity as well as the phylogenetic and evolutionary relationships of several rhizogenic Agrobacterium biovar 1 strains from cucurbit and solanaceous crops. A collection of 41 isolates was subjected to a number of phenotypic assays and characterized by MLSA targeting four housekeeping genes (16S rRNA gene, recA, rpoB and trpE) and two loci from the root-inducing Ri-plasmid (part of rolB and virD2). Besides phenotypic variation, remarkable genotypic diversity was observed, especially for some chromosomal loci such as trpE. In contrast, genetic diversity was lower for the plasmid-borne loci, indicating that the studied chromosomal housekeeping genes and Ri-plasmid-borne loci might not exhibit the same evolutionary history. Furthermore, phylogenetic and network analyses and several recombination tests suggested that recombination could be contributing in some extent to the evolutionary dynamics of rhizogenic Agrobacterium populations. Finally, a genomospecies-level identification analysis revealed that at least four genomospecies may occur on cucurbit and tomato crops (G1, G3, G8 and G9). Together, this study gives a first glimpse at the genetic and phenotypic diversity within this economically important plant pathogenic bacterium.
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Affiliation(s)
- Lien Bosmans
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Sergio Álvarez-Pérez
- Department of Animal Health, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Rob Moerkens
- Research Centre Hoogstraten vzw, B-2328 Meerle, Belgium
| | - Lieve Wittemans
- Research Station for Vegetable Production vzw, B-2860 Sint-Katelijne-Waver, Belgium
| | - Bart Van Calenberge
- Research Station for Vegetable Production vzw, B-2860 Sint-Katelijne-Waver, Belgium
| | | | | | - René De Mot
- Centre of Microbial and Plant Genetics, MS, KU Leuven, B-3001 Leuven, Belgium
| | - Hans Rediers
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
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28
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Gaget V, Welker M, Rippka R, de Marsac NT. A polyphasic approach leading to the revision of the genus Planktothrix (Cyanobacteria) and its type species, P. agardhii, and proposal for integrating the emended valid botanical taxa, as well as three new species, Planktothrix paucivesiculata sp. nov.ICNP, Planktothrix tepida sp. nov.ICNP, and Planktothrix serta sp. nov.ICNP, as genus and species names with nomenclatural standing under the ICNP. Syst Appl Microbiol 2015; 38:141-58. [PMID: 25757799 DOI: 10.1016/j.syapm.2015.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 02/10/2015] [Accepted: 02/13/2015] [Indexed: 10/23/2022]
Abstract
Twenty strains of Planktothrix and five of 'Oscillatoria' were characterized by a polyphasic approach, for clarification of their taxonomic relationships. Emphasis was given to the strains (17) of the Pasteur Culture Collection of Cyanobacteria (PCC). Phenotypic characters analyzed comprised morphology, phycobiliprotein composition, temperature and salinity tolerance. The gvpA gas vesicle gene was detected by PCR in all strains, and transmission electron microscopy confirmed gas vesicle formation in the strains of 'Oscillatoria'. MALDI-TOF mass spectrometry revealed 13 chemotypes, nine of which produce microcystins. A multi-locus sequence typing (MLST) analysis was conducted using individual and concatenated nucleotide sequences of the 16S rDNA, internal transcribed spacer (ITS), gyrB, rpoC1 and rpoB. The results highlighted an unexpected diversity within the genus Planktothrix, showing that the five strains of 'Oscillatoria' need to be included in this taxon. Consequently, the genus consists of seven phylogenetic clusters, three of which represent new species, named Planktothrix paucivesiculata sp. nov.ICNP (type strain: PCC 8926T), Planktothrix tepida sp. nov.ICNP (type strain: PCC 9214T) and Planktothrix serta sp. nov.ICNP (type strain: PCC 8927T). These, together with the emended genus Planktothrix and its type species P. agardhii, valid taxa under the ICN, are described/re-described for gaining nomenclatural standing under the ICNP.
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MESH Headings
- Cluster Analysis
- Cyanobacteria/classification
- Cyanobacteria/cytology
- Cyanobacteria/genetics
- Cyanobacteria/physiology
- Cytoplasmic Vesicles/ultrastructure
- DNA Gyrase/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- DNA-Directed RNA Polymerases/genetics
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Multilocus Sequence Typing
- Phycobiliproteins/analysis
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Salinity
- Sequence Analysis, DNA
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Temperature
- Terminology as Topic
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Affiliation(s)
- Virginie Gaget
- Institut Pasteur, Unité des Cyanobactéries, Centre National de la Recherche Scientifique (CNRS) Unité de Recherche Associée (URA) 2172, 75724 Paris Cedex 15, France; Centre d'Analyse Environnementales, Bât. Dufy, 1 place de Turenne, 94417 Saint-Maurice Cedex, France.
| | - Martin Welker
- AnagnosTec GmbH, Am Mühlenberg 11, 14476 Potsdam-Golm, Germany
| | - Rosmarie Rippka
- Institut Pasteur, Unité des Cyanobactéries, Centre National de la Recherche Scientifique (CNRS) Unité de Recherche Associée (URA) 2172, 75724 Paris Cedex 15, France
| | - Nicole Tandeau de Marsac
- Institut Pasteur, Unité des Cyanobactéries, Centre National de la Recherche Scientifique (CNRS) Unité de Recherche Associée (URA) 2172, 75724 Paris Cedex 15, France
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OKANO K, SUZUKI E, OHTA S, MIYATA N, TANI Y, OZAKI Y. Seasonal Changes in Cyanotoxin Microcystin and Toxic Cyanobacteria in Lake Hachiro. ACTA ACUST UNITED AC 2015. [DOI: 10.2965/jswe.38.23] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Kunihiro OKANO
- Department of Biological Environment, Akita Prefectural University
| | - Eiji SUZUKI
- Department of Biological Production, Akita Prefectural University
| | - Shiori OHTA
- Graduate School of Bioresource Sciences, Akita Prefectural University
| | - Naoyuki MIYATA
- Department of Biological Environment, Akita Prefectural University
| | - Yukinori TANI
- Department of Environmental and Life Sciences, University of Shizuoka
| | - Yasuo OZAKI
- Department of Biological Environment, Akita Prefectural University
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30
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Penn K, Wang J, Fernando SC, Thompson JR. Secondary metabolite gene expression and interplay of bacterial functions in a tropical freshwater cyanobacterial bloom. THE ISME JOURNAL 2014; 8:1866-78. [PMID: 24646695 PMCID: PMC4139720 DOI: 10.1038/ismej.2014.27] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/08/2014] [Accepted: 01/17/2014] [Indexed: 11/09/2022]
Abstract
Cyanobacterial harmful algal blooms (cyanoHABs) appear to be increasing in frequency on a global scale. The Cyanobacteria in blooms can produce toxic secondary metabolites that make freshwater dangerous for drinking and recreation. To characterize microbial activities in a cyanoHAB, transcripts from a eutrophic freshwater reservoir in Singapore were sequenced for six samples collected over one day-night period. Transcripts from the Cyanobacterium Microcystis dominated all samples and were accompanied by at least 533 genera primarily from the Cyanobacteria, Proteobacteria, Bacteroidetes and Actinobacteria. Within the Microcystis population, abundant transcripts were from genes for buoyancy, photosynthesis and synthesis of the toxin microviridin, suggesting that these are necessary for competitive dominance in the Reservoir. During the day, Microcystis transcripts were enriched in photosynthesis and energy metabolism while at night enriched pathways included DNA replication and repair and toxin biosynthesis. Microcystis was the dominant source of transcripts from polyketide and non-ribosomal peptide synthase (PKS and NRPS, respectively) gene clusters. Unexpectedly, expression of all PKS/NRPS gene clusters, including for the toxins microcystin and aeruginosin, occurred throughout the day-night cycle. The most highly expressed PKS/NRPS gene cluster from Microcystis is not associated with any known product. The four most abundant phyla in the reservoir were enriched in different functions, including photosynthesis (Cyanobacteria), breakdown of complex organic molecules (Proteobacteria), glycan metabolism (Bacteroidetes) and breakdown of plant carbohydrates, such as cellobiose (Actinobacteria). These results provide the first estimate of secondary metabolite gene expression, functional partitioning and functional interplay in a freshwater cyanoHAB.
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Affiliation(s)
- Kevin Penn
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jia Wang
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Samodha C Fernando
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Janelle R Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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Moreira C, Spillane C, Fathalli A, Vasconcelos V, Antunes A. African origin and europe-mediated global dispersal of the cyanobacterium Microcystis aeruginosa. Curr Microbiol 2014; 69:628-33. [PMID: 24952206 DOI: 10.1007/s00284-014-0628-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/30/2014] [Indexed: 10/25/2022]
Abstract
Microcystis aeruginosa is a bloom-forming cyanobacteria, which currently has a cosmopolitan distribution. Since M. aeruginosa can produce toxic compounds across all continents that it inhabits, it is of major public health relevance to assess its origin and dispersal. Thus, we conducted a worldwide study using 29 isolates representative of all the main continents, and used a concatenated genetic system for phylogenetic analyses consisting of four genetic markers (spanning ca. 3,485 bp). Our results support an early origin of M. aeruginosa in the African continent, with a subsequent dispersal to establish a second genetic pool in the European continent, from where M. aeruginosa then colonized the remaining continental regions. Our findings indicate that the European population has a cosmopolitan distribution, and is genetically closer to populations from Africa and North America. Our study also highlights the utility of using a concatenated dataset for phylogenetic inferences in cyanobacteria.
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Affiliation(s)
- Cristiana Moreira
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123, Porto, Portugal
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32
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D'Alelio D, Salmaso N, Gandolfi A. Frequent recombination shapes the epidemic population structure of Planktothrix (Cyanoprokaryota) in Italian subalpine lakes. JOURNAL OF PHYCOLOGY 2013; 49:1107-1117. [PMID: 27007631 DOI: 10.1111/jpy.12116] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 07/22/2013] [Indexed: 06/05/2023]
Abstract
The planktonic genus Planktothrix, as other cyanobacteria, shows signals of both homologous and nonhomologous recombination. However, the frequency of recombination and its effect on Planktothrix population structuring is unknown. We isolated 290 Planktothrix strains from seven neighboring lakes in the subalpine Italian region and analyzed these using multilocus sequence typing. Four of six loci analyzed were polymorphic, resulting in 20 distinct multilocus genotypes. Association indices among alleles at different loci were suggestive of an "epidemic population structure," resulting from an explosive (and temporary) dominance of one genotype against a panmictic background. ClonalFrame analyses supported this view by detecting: (i) three major clades affected by three distinct recombination events, (ii) a recombination rate about equal to the mutation rate, and (iii) the fact that recombination had an impact on introducing molecular diversity more than double the mutation rate. Furthermore, analysis of molecular variance over an annual cycle in three of seven lakes revealed that both local clonal expansion and recombination processes affected among-lake diversity. Our observations suggest that recombination affects microevolution of Planktothrix and that an epidemic structure can emerge in populations of this genus.
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Affiliation(s)
- Domenico D'Alelio
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige (TN), I-38010, Italy
| | - Nico Salmaso
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige (TN), I-38010, Italy
| | - Andrea Gandolfi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige (TN), I-38010, Italy
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Moreira C, Vasconcelos V, Antunes A. Phylogeny and biogeography of cyanobacteria and their produced toxins. Mar Drugs 2013; 11:4350-69. [PMID: 24189276 PMCID: PMC3853732 DOI: 10.3390/md11114350] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/29/2013] [Accepted: 10/09/2013] [Indexed: 11/17/2022] Open
Abstract
Phylogeny is an evolutionary reconstruction of the past relationships of DNA or protein sequences and it can further be used as a tool to assess population structuring, genetic diversity and biogeographic patterns. In the microbial world, the concept that everything is everywhere is widely accepted. However, it is much debated whether microbes are easily dispersed globally or whether they, like many macro-organisms, have historical biogeographies. Biogeography can be defined as the science that documents the spatial and temporal distribution of a given taxa in the environment at local, regional and continental scales. Speciation, extinction and dispersal are proposed to explain the generation of biogeographic patterns. Cyanobacteria are a diverse group of microorganisms that inhabit a wide range of ecological niches and are well known for their toxic secondary metabolite production. Knowledge of the evolution and dispersal of these microorganisms is still limited, and further research to understand such topics is imperative. Here, we provide a compilation of the most relevant information regarding these issues to better understand the present state of the art as a platform for future studies, and we highlight examples of both phylogenetic and biogeographic studies in non-symbiotic cyanobacteria and cyanotoxins.
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Affiliation(s)
- Cristiana Moreira
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 289, Porto 4050-123, Portugal; E-Mails: (C.M.); (V.V.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto 4169-007, Portugal
| | - Vitor Vasconcelos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 289, Porto 4050-123, Portugal; E-Mails: (C.M.); (V.V.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto 4169-007, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 289, Porto 4050-123, Portugal; E-Mails: (C.M.); (V.V.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto 4169-007, Portugal
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A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa. PLoS One 2013; 8:e70747. [PMID: 23950996 PMCID: PMC3741299 DOI: 10.1371/journal.pone.0070747] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 06/28/2013] [Indexed: 11/28/2022] Open
Abstract
Microcystis aeruginosa is one of the most common bloom-forming cyanobacteria in freshwater ecosystems worldwide. This species produces numerous secondary metabolites, including microcystins, which are harmful to human health. We sequenced the genomes of ten strains of M. aeruginosa in order to explore the genomic basis of their ability to occupy varied environments and proliferate. Our findings show that M. aeruginosa genomes are characterized by having a large open pangenome, and that each genome contains similar proportions of core and flexible genes. By comparing the GC content of each gene to the mean value of the whole genome, we estimated that in each genome, around 11% of the genes seem to result from recent horizontal gene transfer events. Moreover, several large gene clusters resulting from HGT (up to 19 kb) have been found, illustrating the ability of this species to integrate such large DNA molecules. It appeared also that all M. aeruginosa displays a large genomic plasticity, which is characterized by a high proportion of repeat sequences and by low synteny values between the strains. Finally, we identified 13 secondary metabolite gene clusters, including three new putative clusters. When comparing the genomes of Microcystis and Prochlorococcus, one of the dominant picocyanobacteria living in marine ecosystems, our findings show that they are characterized by having almost opposite evolutionary strategies, both of which have led to ecological success in their respective environments.
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35
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Ohbayashi K, Hodoki Y, Kobayashi Y, Okuda N, Nakano SI. Genotypic composition and the relationship between genotypic composition and geographical proximity of the cyanobacterium Microcystis aeruginosa in western Japan. Can J Microbiol 2013; 59:266-72. [PMID: 23586751 DOI: 10.1139/cjm-2012-0724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microcystis aeruginosa is one of the bloom-forming harmful algae in freshwater ecosystems. We genetically characterized Microcystis populations during bloom-forming periods in various reservoirs, lakes, and ponds in Japan during 2009. Using phylogenetic analysis, we evaluated the relationship between current genotype expansions and geographic location within western Japan and intraspecific variation. Microcystis aeruginosa colonies were isolated at 15 sites and were analyzed by sequencing the 16S-23S internal transcribed spacer (ITS) region of the ribosomal operon, and the potential to produce toxins was assessed by PCR-based detection of the microcystin synthetase gene mcyG. In total, 171 colonies were separated into 41 genotypes. The highest genotypic composition was detected in the south basin of Lake Biwa and the lowest in Lagoon Iba. Cluster analysis indicated no obvious association between genotypic composition and geographic distance. Thus, clear genetic differentiation accompanied by geographic origins was not found in western Japan. The resulting neighbor-joining tree revealed 3 clusters, 2 of which contained strains that showed both nonamplification and amplification of the mcyG gene.
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Affiliation(s)
- Kako Ohbayashi
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga 520-2113 Japan
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36
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Garcia A, Goñi P, Cieloszyk J, Fernandez MT, Calvo-Beguería L, Rubio E, Fillat MF, Peleato ML, Clavel A. Identification of free-living amoebae and amoeba-associated bacteria from reservoirs and water treatment plants by molecular techniques. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:3132-3140. [PMID: 23444840 DOI: 10.1021/es400160k] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The occurrence of free-living amoebae (FLA) was investigated in 83 water samples from reservoirs and water treatment plants, with culture positive in 64 of them (77.1%). Polymerase chain reaction (PCR) of partial 18S rRNA gene and ITS region was performed in order to identify amoeba isolates, and the presence of Legionella pneumophila , Mycobacterium spp., Pseudomonas spp., and Microcystis aeruginosa was investigated in 43 isolates of amoebae by multiplex PCR. Of the isolated amoebae, 31 were Acanthamoeba spp., 21 were Hartmannella vermiformis, 13 were Naegleria spp., and one was Vanella spp. T2, T4, and T5 genotypes of Acanthamoeba have been identified, and T4 isolates were grouped into five subgenotypes and graphically represented with a Weblog application. Inside amoebae, L. pneumophila was detected in 13.9% (6/43) of the isolates, and Pseudomonas spp. and Mycobacterium spp. were detected in 32.6% (14/43) and 41.9% (18/43), respectively. No statistical correlation was demonstrated between FLA isolation and seasonality, but the presence of intracellular bacteria was associated with warm water temperatures, and also the intracellular presence of Mycobacterium spp. and Pseudomonas spp. were associated. These results highlight the importance of amoebae in natural waters as reservoirs of potential pathogens and its possible role in the spread of bacterial genera with interest in public and environmental health.
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Affiliation(s)
- Alicia Garcia
- Area of Parasitology and §Area of Biomedicine and Public Health Biostatistics, Department of Microbiology, Preventive Medicine and Public Health, Faculty of Medicine, University of Zaragoza, 50009 Zaragoza, Spain
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Ng KW, Pointing SB, Dvornyk V. Patterns of nucleotide diversity of the ldpA circadian gene in closely related species of cyanobacteria from extreme cold deserts. Appl Environ Microbiol 2013; 79:1516-22. [PMID: 23263969 PMCID: PMC3591978 DOI: 10.1128/aem.03439-12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 12/14/2012] [Indexed: 11/20/2022] Open
Abstract
In the circadian system of cyanobacteria, the ldpA gene is a component of the input to the clock. We comparatively analyzed nucleotide polymorphism of this gene in populations of two closely related species of cyanobacteria (denoted as Synechococcus species S1 and S2, respectively) from extreme cold deserts in Antarctica, the Canadian Arctic, and Tibet. Although both species manifested similarly high haplotype diversities (0.990 and 0.809, respectively), the nucleotide diversity differed significantly (0.0091 in S1 and 0.0037 in S2). The populations of species S2 were more differentiated (F(ST) = 0.2242) compared to those of species S1 (F(ST) between 0.0296 and 0.1188). An analysis of positive selection with several tests yielded highly significant values (P < 0.01) for both species. On the other hand, these results may be somewhat compromised by fluctuating population sizes of the species. The apparent selection pressure coupled with the pronounced demographic factors, such as population expansion, small effective population size, and genetic drift, may thus result in the observed significant interpopulation differentiation and subsequent speciation of cyanobacteria.
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Affiliation(s)
- Ka Wai Ng
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
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D'Alelio D, Gandolfi A. Recombination Signals In The rpoC1 Gene Indicate Gene-Flow Between Planktothrix (Cyanoprokaryota) Species. JOURNAL OF PHYCOLOGY 2012; 48:1424-1432. [PMID: 27009993 DOI: 10.1111/j.1529-8817.2012.01225.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 05/07/2012] [Indexed: 06/05/2023]
Abstract
The delineation of species boundaries in the potentially harmful cyanobacterium Planktothrix Anagnostidis et Komárek 1988 is particularly tangled. Genetic recombination has been invoked to explain the occurrence of overlapping biological traits among recognized species. Although horizontal gene transfer is shown as a driver of diversification in this genus, clear evidence for homologous recombination at the single gene level is still lacking. Several Planktothrix strains (n = 244) sampled in eight fresh water lakes in north Italy were characterized by sequencing the rpoC1 gene, a molecular marker previously proposed to discriminate between species. Six haplotypes were detected, four of which are newly described. A relevant number of rpoC1 sequences (n = 54) showed evidence of homologous recombination. By comparing the sequences produced in the work presented here to those available on GenBank for the genus, multiple recombination events were tracked between haplotypes associated to P. rubescens, P. suspensa and P. agardhii, the latter being a species not found in our survey. Recombination signals were in form of (i) a vast mosaic structure present in the alignment of rpoC1 haplotypes, (ii) multiple and statistically significant paths in the split decomposition network connecting these haplotypes and (iii) many individual crossing-over events detected by means of recombination detection tests. Data suggest that the molecular evolution of the rpoC1 gene in the genus Planktothrix appears as strongly influenced by homologous recombination. In addition, rpoC1 diversity effectively tracks recombinational processes among species in the complex made up by P. rubescens, P. agardhii and P. suspensa, which are not isolated in terms of gene-flow.
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Affiliation(s)
- Domenico D'Alelio
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige, TN, I-38010, Italy
| | - Andrea Gandolfi
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige, TN, I-38010, Italy
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Moreira C, Vasconcelos V, Antunes A. Phylogeny of Microcystins: Evidence of a Biogeographical Trend? Curr Microbiol 2012; 66:214-21. [DOI: 10.1007/s00284-012-0258-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 10/03/2012] [Indexed: 01/22/2023]
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Gene flow, recombination, and selection in cyanobacteria: population structure of geographically related Planktothrix freshwater strains. Appl Environ Microbiol 2012; 79:508-15. [PMID: 23124237 DOI: 10.1128/aem.02417-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several Planktothrix strains, each producing a distinct oligopeptide profile, have been shown to coexist within Lake Steinsfjorden (Norway). Using nonribosomal peptide synthetase (NRPS) genes as markers, it has been shown that the Planktothrix community comprises distinct genetic variants displaying differences in bloom dynamics, suggesting a Planktothrix subpopulation structure. Here, we investigate the Planktothrix variants inhabiting four lakes in southeast of Norway utilizing both NRPS and non-NRPS genes. Phylogenetic analyses showed similar topologies for both NRPS and non-NRPS genes, and the lakes appear to have similar structuring of Planktothrix genetic variants. The structure of distinct variants was also supported by very low genetic diversity within variants compared to the between-variant diversity. Incongruent topologies and split decomposition revealed recombination events between Planktothrix variants. In several strains the gene variants seem to be a result of recombination. Both NRPS and non-NRPS genes are dominated by purifying selection; however, sites subjected to positive selection were also detected. The presence of similar and well-separated Planktothrix variants with low internal genetic diversity indicates gene flow within Planktothrix populations. Further, the low genetic diversity found between lakes (similar range as within lakes) indicates gene flow also between Planktothrix populations and suggests recent, or recurrent, dispersals. Our data also indicate that recombination has resulted in new genetic variants. Stability within variants and the development of new variants are likely to be influenced by selection patterns and within-variant homologous recombination.
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Hargreaves KR, Anderson NJ, Clokie MRJ. Recovery of viable cyanophages from the sediments of a eutrophic lake at decadal timescales. FEMS Microbiol Ecol 2012; 83:450-6. [PMID: 22963199 DOI: 10.1111/1574-6941.12005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 08/22/2012] [Accepted: 09/03/2012] [Indexed: 12/01/2022] Open
Abstract
Cyanobacteria and their associated viruses (cyanophages) are abundant throughout the world in both marine and freshwater environments. The predator-prey relationship influences population dynamics within these ecosystems and facilitates the co-evolution of both organisms. Evidence of the close-linked interactions between cyanobacteria and viruses has been found extensively throughout marine biomes, but freshwater systems are less well studied. Eutrophic lake sediments potentially allow the preservation of cyanophages. If historic cyanophages could be isolated, they could provide insights into the evolution, biology and population dynamics over defined timescales. To determine whether viable phages are present in this environment, sectioned sediment cores (~ 50 cm in length) were taken from a eutrophic, stratifying lake (Rostherne Mere, Cheshire, UK). They were examined under the transmission electron microscope, and phages were isolated on two Microcystis strains PCC 7820 and BC 84/1. Viable phages were recovered from ~ 33- and ~ 50-year-old sediments. This is the first known study to investigate the viability of freshwater cyanophages recovered from dated lake sediments.
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Affiliation(s)
- Kate R Hargreaves
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
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Yoshida-Takashima Y, Yoshida M, Ogata H, Nagasaki K, Hiroishi S, Yoshida T. Cyanophage infection in the bloom-forming cyanobacteria Microcystis aeruginosa in surface freshwater. Microbes Environ 2012; 27:350-5. [PMID: 23047146 PMCID: PMC4103541 DOI: 10.1264/jsme2.me12037] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Host-like genes are often found in viral genomes. To date, multiple host-like genes involved in photosynthesis and the pentose phosphate pathway have been found in phages of marine cyanobacteria Synechococcus and Prochlorococcus. These gene products are predicted to redirect host metabolism to deoxynucleotide biosynthesis for phage replication while maintaining photosynthesis. A cyanophage, Ma-LMM01, infecting the toxic cyanobacterium Microcystis aeruginosa, was isolated from a eutrophic freshwater lake and assigned as a member of a new lineage of the Myoviridae family. The genome encodes a host-like NblA. Cyanobacterial NblA is known to be involved in the degradation of the major light harvesting complex, the phycobilisomes. Ma-LMM01 nblA gene showed an early expression pattern and was highly transcribed during phage infection. We speculate that the co-option of nblA into Microcystis phages provides a significant fitness advantage to phages by preventing photoinhibition during infection and possibly represents an important part of the co-evolutionary interactions between cyanobacteria and their phages.
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Affiliation(s)
- Yukari Yoshida-Takashima
- Subsurface Geobiology Advanced Research Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
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Dvornyk V, Jahan AS. Extreme conservation and non-neutral evolution of the cpmA Circadian locus in a globally distributed Chroococcidiopsis sp. from naturally stressful habitats. Mol Biol Evol 2012; 29:3899-907. [PMID: 22844070 DOI: 10.1093/molbev/mss191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Cyanobacteria are among the most ancient organisms known to have circadian rhythms. The cpmA gene is involved in controlling the circadian output signal. We studied polymorphism and divergence of this gene in six populations of a stress-tolerant cyanobacterium, Chroococcidiopsis sp., sampled in extreme habitats across the globe. Despite high haplotype diversity (0.774), nucleotide diversity of cpmA is very low (π = 0.0034): the gene appears to be even more conserved than housekeeping genes. Even though the populations were sampled thousands kilometers apart, they manifested virtually no genetic differentiation at this locus (F(ST) = 0.0228). Using various tests for neutrality, we determined that evolution of cpmA significantly departures from the neutral model and is governed by episodic positive selection.
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Affiliation(s)
- Volodymyr Dvornyk
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
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Intricate interactions between the bloom-forming cyanobacterium Microcystis aeruginosa and foreign genetic elements, revealed by diversified clustered regularly interspaced short palindromic repeat (CRISPR) signatures. Appl Environ Microbiol 2012; 78:5353-60. [PMID: 22636003 DOI: 10.1128/aem.00626-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) confer sequence-dependent, adaptive resistance in prokaryotes against viruses and plasmids via incorporation of short sequences, called spacers, derived from foreign genetic elements. CRISPR loci are thus considered to provide records of past infections. To describe the host-parasite (i.e., cyanophages and plasmids) interactions involving the bloom-forming freshwater cyanobacterium Microcystis aeruginosa, we investigated CRISPR in four M. aeruginosa strains and in two previously sequenced genomes. The number of spacers in each locus was larger than the average among prokaryotes. All spacers were strain specific, except for a string of 11 spacers shared in two closely related strains, suggesting diversification of the loci. Using CRISPR repeat-based PCR, 24 CRISPR genotypes were identified in a natural cyanobacterial community. Among 995 unique spacers obtained, only 10 sequences showed similarity to M. aeruginosa phage Ma-LMM01. Of these, six spacers showed only silent or conservative nucleotide mutations compared to Ma-LMM01 sequences, suggesting a strategy by the cyanophage to avert CRISPR immunity dependent on nucleotide identity. These results imply that host-phage interactions can be divided into M. aeruginosa-cyanophage combinations rather than pandemics of population-wide infectious cyanophages. Spacer similarity also showed frequent exposure of M. aeruginosa to small cryptic plasmids that were observed only in a few strains. Thus, the diversification of CRISPR implies that M. aeruginosa has been challenged by diverse communities (almost entirely uncharacterized) of cyanophages and plasmids.
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Kuno S, Yoshida T, Kamikawa R, Hosoda N, Sako Y. The distribution of a phage-related insertion sequence element in the cyanobacterium, Microcystis aeruginosa. Microbes Environ 2011; 25:295-301. [PMID: 21576885 DOI: 10.1264/jsme2.me10125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The cyanophage Ma-LMM01, specifically-infecting Microcystis aeruginosa, has an insertion sequence (IS) element that we named IS607-cp showing high nucleotide similarity to a counterpart in the genome of the cyanobacterium Cyanothece sp. We tested 21 strains of M. aeruginosa for the presence of IS607-cp using PCR and detected the element in strains NIES90, NIES112, NIES604, and RM6. Thermal asymmetric interlaced PCR (TAIL-PCR) revealed each of these strains has multiple copies of IS607-cp. Some of the ISs were classified into three types based on their inserted positions; IS607-cp-1 is common in strains NIES90, NIES112 and NIES604, whereas IS607-cp-2 and IS607-cp-3 are specific to strains NIES90 and RM6, respectively. This multiplicity may reflect the replicative transposition of IS607-cp. The sequence of IS607-cp in Ma-LMM01 showed robust affinity to those found in M. aeruginosa and Cyanothece spp. in a phylogenetic tree inferred from counterparts of various bacteria. This suggests the transfer of IS607-cp between the cyanobacterium and its cyanophage. We discuss the potential role of Ma-LMM01-related phages as donors of IS elements that may mediate the transfer of IS607-cp; and thereby partially contribute to the genome plasticity of M. aeruginosa.
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Affiliation(s)
- Sotaro Kuno
- Department of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606–8502, Japan
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van Gremberghe I, Leliaert F, Mergeay J, Vanormelingen P, Van der Gucht K, Debeer AE, Lacerot G, De Meester L, Vyverman W. Lack of phylogeographic structure in the freshwater cyanobacterium Microcystis aeruginosa suggests global dispersal. PLoS One 2011; 6:e19561. [PMID: 21573169 PMCID: PMC3088681 DOI: 10.1371/journal.pone.0019561] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 04/11/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Free-living microorganisms have long been assumed to have ubiquitous distributions with little biogeographic signature because they typically exhibit high dispersal potential and large population sizes. However, molecular data provide contrasting results and it is far from clear to what extent dispersal limitation determines geographic structuring of microbial populations. We aimed to determine biogeographical patterns of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa. Being widely distributed on a global scale but patchily on a regional scale, this prokaryote is an ideal model organism to study microbial dispersal and biogeography. METHODOLOGY/PRINCIPAL FINDINGS The phylogeography of M. aeruginosa was studied based on a dataset of 311 rDNA internal transcribed spacer (ITS) sequences sampled from six continents. Richness of ITS sequences was high (239 ITS types were detected). Genetic divergence among ITS types averaged 4% (maximum pairwise divergence was 13%). Preliminary analyses revealed nearly completely unresolved phylogenetic relationships and a lack of genetic structure among all sequences due to extensive homoplasy at multiple hypervariable sites. After correcting for this, still no clear phylogeographic structure was detected, and no pattern of isolation by distance was found on a global scale. Concomitantly, genetic differentiation among continents was marginal, whereas variation within continents was high and was mostly shared with all other continents. Similarly, no genetic structure across climate zones was detected. CONCLUSIONS/SIGNIFICANCE The high overall diversity and wide global distribution of common ITS types in combination with the lack of phylogeographic structure suggest that intercontinental dispersal of M. aeruginosa ITS types is not rare, and that this species might have a truly cosmopolitan distribution.
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Affiliation(s)
- Ineke van Gremberghe
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Ghent, Belgium
| | | | - Joachim Mergeay
- Laboratory of Aquatic Ecology and Evolutionary Biology, Katholieke Universiteit Leuven, Leuven, Belgium
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Pieter Vanormelingen
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Ghent, Belgium
| | | | - Ann-Eline Debeer
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Gissell Lacerot
- Department of Aquatic Ecology and Water Quality Management, Wageningen University, Wageningen, The Netherlands
- Facultad de Ciencias, Sección Limnología, Universidad de la República, Montevideo, Uruguay
| | - Luc De Meester
- Laboratory of Aquatic Ecology and Evolutionary Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Ghent, Belgium
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Tanabe Y, Watanabe MM. Local expansion of a panmictic lineage of water bloom-forming cyanobacterium Microcystis aeruginosa. PLoS One 2011; 6:e17085. [PMID: 21390221 PMCID: PMC3044731 DOI: 10.1371/journal.pone.0017085] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 01/17/2011] [Indexed: 11/18/2022] Open
Abstract
In previous studies, we have demonstrated that the population structure of the bloom-forming cyanobacterium Microcystis aeruginosa is clonal. Expanded multilocus sequence typing analysis of M. aeruginosa using 412 isolates identified five intraspecific lineages suggested to be panmictic while maintaining overall clonal structure probably due to a reduced recombination rate between lineages. Interestingly, since 2005 most strains belonging to one of these panmictic clusters (group G) have been found in a particular locality (Lake Kasumigaura Basin) in Japan. In this locality, multiple, similar but distinct genotypes of this lineage predominated in the bloom, a pattern that is unprecedented for M. aeruginosa. The population structure underlying blooms associated with this lineage is comparable to epidemics of pathogens. Our results may reveal an expansion of the possible adaptive lineage in a localized aquatic environment, providing us with a unique opportunity to investigate its ecological and biogeographical consequences.
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Affiliation(s)
- Yuuhiko Tanabe
- Graduate School of Life & Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
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Kurmayer R, Schober E, Tonk L, Visser PM, Christiansen G. Spatial divergence in the proportions of genes encoding toxic peptide synthesis among populations of the cyanobacterium Planktothrix in European lakes. FEMS Microbiol Lett 2011; 317:127-37. [PMID: 21251055 PMCID: PMC3118798 DOI: 10.1111/j.1574-6968.2011.02222.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
It has been frequently reported that seasonal changes in toxin production by cyanobacteria are due to changes in the proportion of toxic/nontoxic genotypes in parallel to increases or decreases in population density during the seasonal cycle of bloom formation. In order to find out whether there is a relationship between the proportion of genes encoding toxic peptide synthesis and population density of Planktothrix spp. we compared the proportion of three gene regions that are indicative of the synthesis of the toxic heptapeptide microcystin (mcyB), and the bioactive peptides aeruginoside (aerB) and anabaenopeptin (apnC) in samples from 23 lakes of five European countries (n=153). The mcyB, aerB, and apnC genes occurred in 99%, 99%, and 97% of the samples, respectively, and on average comprised 60 ± 3%, 22 ± 2%, and 54 ± 4% of the total population, respectively. Although the populations differed widely in abundance (10−3–103 mm3 L−1) no dependence of the proportion of the mcyB, aerB, and apnC genes on the density of the total population was found. In contrast populations differed significantly in their average mcyB, aerB, and apnC gene proportions, with no change between prebloom and bloom conditions. These results emphasize stable population-specific differences in mcyB, aerB, and apnC proportions that are independent from seasonal influences.
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Affiliation(s)
- Rainer Kurmayer
- Austrian Academy of Sciences, Institute for Limnology, Mondsee, Austria.
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Characterization of epidemiologically unrelated Acinetobacter baumannii isolates from four continents by use of multilocus sequence typing, pulsed-field gel electrophoresis, and sequence-based typing of bla(OXA-51-like) genes. J Clin Microbiol 2010; 48:2476-83. [PMID: 20421437 DOI: 10.1128/jcm.02431-09] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study used a diverse collection of epidemiologically unrelated Acinetobacter baumannii isolates to compare the robustness of a multilocus sequence typing (MLST) scheme, based on conserved regions of seven housekeeping genes, gltA, gdhB, recA, cpn60, rpoD, gyrB, and gpi, with that of sequence-based typing of bla(OXA-51-like) genes (SBT-bla(OXA-51-like) genes). The data obtained by analysis of MLST and SBT-bla(OXA-51-like) genes were compared to the data generated by pulsed-field gel electrophoresis (PFGE). The topologies of the phylogenetic trees generated for the gyrB and gpi genes showed evidence of recombination and were inconsistent with those of the trees generated for the other five genes. MLST identified 24 sequence types (STs), of which 19 were novel, and 5 novel alleles. Clonality was demonstrated by eBURST analysis and standardized index of association values of >1 (P < 0.001). MLST data revealed that all isolates harboring the major bla(OXA-51-like) alleles OXA-66, OXA-69, and OXA-71 fell within the three major European clonal lineages. However, the MLST data were not always in concordance with the PFGE data, and some isolates containing the same bla(OXA-51-like) allele demonstrated <50% relatedness by PFGE. It was concluded that the gyrB and gpi genes are not good candidates for use in MLST analysis and that a SBT-bla(OXA-51-like) gene scheme produced results comparable to those produced by MLST for the identification of the major epidemic lineages, with the advantage of having a significantly reduced sequencing cost and time. It is proposed that studies of A. baumannii epidemiology could involve initial screening of bla(OXA-51-like) alleles to identify isolates belonging to major epidemic lineages, followed by MLST analysis to categorize isolates from common lineages, with PFGE being reserved for fine-scale typing.
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Gaget V, Gribaldo S, Tandeau de Marsac N. An rpoB signature sequence provides unique resolution for the molecular typing of cyanobacteria. Int J Syst Evol Microbiol 2010; 61:170-183. [PMID: 20190018 DOI: 10.1099/ijs.0.019018-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The use of morphological characters for the classification of cyanobacteria has often led to ambiguous strain assignment. In the past two decades, the availability of sequences, such as those of the 16S rRNA, nif, cpc and rpoC1 genes, and the use of metagenomics, has steadily increased and has made the reconstruction of evolutionary relationships of some cyanobacterial groups possible in addition to improving strain assignment. Conserved indels (insertions/deletions) are present in all cyanobacterial RpoB (β subunit of RNA polymerase) sequences presently available in public databases. These indels are located in the Rpb2_6 domain of RpoB, which is involved in DNA binding and DNA-directed RNA polymerase activity. They are variable in length (6-44 aa) and sequence, and form part of what appears to be a longer signature sequence (43-81 aa). Indeed, a number of these sequences turn out to be distinctive among several strains of a given genus and even among strains of a given species. These signature sequences can thus be used to identify cyanobacteria at a subgenus level and can be useful molecular markers to establish the taxonomic positions of cyanobacterial isolates in laboratory cultures, and/or to assess cyanobacterial biodiversity in space and time in natural ecosystems.
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Affiliation(s)
- Virginie Gaget
- Institut Pasteur, Unité des Cyanobactéries; URA CNRS 2172, 75015 Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Unité de Biologie Moléculaire du Gène Chez les Extrêmophiles; 75015, Paris, France
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