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Kiledal EA, Reitz LA, Kuiper EQ, Evans J, Siddiqui R, Denef VJ, Dick GJ. Comparative genomic analysis of Microcystis strain diversity using conserved marker genes. HARMFUL ALGAE 2024; 132:102580. [PMID: 38331539 DOI: 10.1016/j.hal.2024.102580] [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: 04/25/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/10/2024]
Abstract
Microcystis-dominated cyanobacterial harmful algal blooms (cyanoHABs) have a global impact on freshwater environments, affecting both wildlife and human health. Microcystis diversity and function in field samples and laboratory cultures can be determined by sequencing whole genomes of cultured isolates or natural populations, but these methods remain computationally and financially expensive. Amplicon sequencing of marker genes is a lower cost and higher throughput alternative to characterize strain composition and diversity in mixed samples. However, the selection of appropriate marker gene region(s) and primers requires prior understanding of the relationship between single gene genotype, whole genome content, and phenotype. To identify phylogenetic markers of Microcystis strain diversity, we compared phylogenetic trees built from each of 2,351 individual core genes to an established phylogeny and assessed the ability of these core genes to predict whole genome content and bioactive compound genotypes. We identified single-copy core genes better able to resolve Microcystis phylogenies than previously identified marker genes. We developed primers suitable for current Illumina-based amplicon sequencing with near-complete coverage of available Microcystis genomes and demonstrate that they outperform existing options for assessing Microcystis strain composition. Results showed that genetic markers can be used to infer Microcystis gene content and phenotypes such as potential production of bioactive compounds , although marker performance varies by bioactive compound gene and sequence similarity. Finally, we demonstrate that these markers can be used to characterize the Microcystis strain composition of laboratory or field samples like those collected for surveillance and modeling of Microcystis-dominated cyanobacterial harmful algal blooms.
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Affiliation(s)
- E Anders Kiledal
- Department of Earth and Environmental Sciences, University of Michigan, 2534 North University Building, 1100 North University Avenue Ave, Rm. 2004, Ann Arbor, MI 48109-1005, USA.
| | - Laura A Reitz
- Department of Earth and Environmental Sciences, University of Michigan, 2534 North University Building, 1100 North University Avenue Ave, Rm. 2004, Ann Arbor, MI 48109-1005, USA
| | - Esmée Q Kuiper
- Department of Earth and Environmental Sciences, University of Michigan, 2534 North University Building, 1100 North University Avenue Ave, Rm. 2004, Ann Arbor, MI 48109-1005, USA
| | - Jacob Evans
- Department of Ecology and Evolutionary Biology, University of Michigan, 2220 Biological Sciences Building, 1105 North University Avenue, Ann Arbor, MI 48109-1005, USA
| | - Ruqaiya Siddiqui
- Microbiome Core, University of Michigan, 1500 MSRB 1, 1150W Medical Center Drive, Ann Arbor, MI 48109-5666, USA
| | - Vincent J Denef
- Department of Ecology and Evolutionary Biology, University of Michigan, 2220 Biological Sciences Building, 1105 North University Avenue, Ann Arbor, MI 48109-1005, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, 2534 North University Building, 1100 North University Avenue Ave, Rm. 2004, Ann Arbor, MI 48109-1005, USA; Cooperative Institute for Great Lakes Research, University of Michigan, 4040 Dana Building, 440 Church Street, Ann Arbor, MI 48109-1041, USA
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Yancey CE, Kiledal EA, Chaganti SR, Denef VJ, Errera RM, Evans JT, Hart LN, Isailovic D, James WS, Kharbush JJ, Kimbrel JA, Li W, Mayali X, Nitschky H, Polik CA, Powers MA, Premathilaka SH, Rappuhn NA, Reitz LA, Rivera SR, Zwiers CC, Dick GJ. The Western Lake Erie culture collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome. HARMFUL ALGAE 2023; 126:102440. [PMID: 37290887 DOI: 10.1016/j.hal.2023.102440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 06/10/2023]
Abstract
Cyanobacterial harmful algal blooms (cyanoHABs) dominated by Microcystis spp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 primarily unialgal Microcystis cultures collected from western Lake Erie between 2017 and 2019. While some cultures isolated in different years have a high degree of genetic similarity (genomic Average Nucleotide Identity >99%), genomic data show that these cultures also represent much of the breadth of known Microcystis diversity in natural populations. Only five isolates contained all the genes required for microcystin biosynthesis while two isolates contained a previously described partial mcy operon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 μg L⁻¹) in cultures with complete mcy operons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated with Microcystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity among Microcystis strains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. This culture collection significantly increases the availability of environmentally relevant Microcystis strains from temperate North America.
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Affiliation(s)
- Colleen E Yancey
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - E Anders Kiledal
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, 4840 S State Road, Ann Arbor, MI 48108, United States of America
| | - Vincent J Denef
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Reagan M Errera
- National Oceanic and Atmospheric Administration (NOAA), Great Lakes Environmental Research Laboratory (GLERL), 4840 S State Road, Ann Arbor, MI 48108, United States of America
| | - Jacob T Evans
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Lauren N Hart
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, United States of America; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Dragan Isailovic
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States of America
| | - William S James
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Jenan J Kharbush
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Wei Li
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Helena Nitschky
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Catherine A Polik
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - McKenzie A Powers
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Sanduni H Premathilaka
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States of America
| | - Nicole A Rappuhn
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Laura A Reitz
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Sara R Rivera
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Claire C Zwiers
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Gregory J Dick
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America; Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, 4840 S State Road, Ann Arbor, MI 48108, United States of America.
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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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