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Johnston LH, Huang Y, Bermarija TD, Rafuse C, Zamlynny L, Bruce MR, Graham C, Comeau AM, Valadez-Cano C, Lawrence JE, Beach DG, Jamieson RC. Proliferation and anatoxin production of benthic cyanobacteria associated with canine mortalities along a stream-lake continuum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170476. [PMID: 38290679 DOI: 10.1016/j.scitotenv.2024.170476] [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: 10/16/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/01/2024]
Abstract
Proliferations of benthic cyanobacteria are increasingly in the public eye, with rising animal deaths associated with benthic rather than planktonic blooms. In early June 2021, two dogs died after consuming material on the shore of Shubenacadie Grand Lake, Nova Scotia. Preliminary investigations indicated anatoxins produced by benthic cyanobacterial mats were responsible for the deaths. In this study, we monitored the growth of a toxic benthic cyanobacterial species (Microcoleus sp.) along a stream-lake continuum where the canine poisonings occurred. We found that the species was able to proliferate in both lentic and lotic environments, but temporal growth dynamics and the predominant sub-species were influenced by habitat type, and differed with hydrodynamic setting, nutrient and sunlight availability. Toxin concentration was greatest in cyanobacterial mats growing in the oligotrophic lakeshore environment (maximum measured total anatoxins (ATXs) >20 mg·kg-1 wet weight). This corresponded with a shift in the profile of ATX analogues, which also indicated changing sub-species dominance along the stream-lake transition.
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Affiliation(s)
- Lindsay H Johnston
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, NS, Canada
| | - Yannan Huang
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, NS, Canada
| | - Tessa D Bermarija
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, NS, Canada
| | - Cheryl Rafuse
- Biotoxin Metrology, National Research Council Canada, 1411 Oxford St, Halifax, NS, Canada
| | - Lydia Zamlynny
- Biotoxin Metrology, National Research Council Canada, 1411 Oxford St, Halifax, NS, Canada
| | - Meghann R Bruce
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, P.O. Box 4400, Fredericton, NB, Canada
| | - Catherine Graham
- Nova Scotia Department of Agriculture, Animal Health Laboratory, 65 River Rd, Bible Hill, NS, Canada
| | - André M Comeau
- Integrated Microbiome Resource (IMR), Dalhousie University, Halifax, Canada
| | - Cecilio Valadez-Cano
- Biology Department, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Janice E Lawrence
- Biology Department, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Daniel G Beach
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, NS, Canada; Biotoxin Metrology, National Research Council Canada, 1411 Oxford St, Halifax, NS, Canada
| | - Rob C Jamieson
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, NS, Canada.
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2
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Stanojković A, Skoupý S, Johannesson H, Dvořák P. The global speciation continuum of the cyanobacterium Microcoleus. Nat Commun 2024; 15:2122. [PMID: 38459017 PMCID: PMC10923798 DOI: 10.1038/s41467-024-46459-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/27/2024] [Indexed: 03/10/2024] Open
Abstract
Speciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacterium Microcoleus. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found that Microcoleus represents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.
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Affiliation(s)
- Aleksandar Stanojković
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic
| | - Svatopluk Skoupý
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic
| | - Hanna Johannesson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Petr Dvořák
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic.
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3
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Doré H, Eisenberg AR, Junkins EN, Leventhal GE, Ganesh A, Cordero OX, Paul BG, Valentine DL, O’Malley MA, Wilbanks EG. Targeted hypermutation of putative antigen sensors in multicellular bacteria. Proc Natl Acad Sci U S A 2024; 121:e2316469121. [PMID: 38354254 PMCID: PMC10907252 DOI: 10.1073/pnas.2316469121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024] Open
Abstract
Diversity-generating retroelements (DGRs) are used by bacteria, archaea, and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these targeted genes. However, the function and benefits of DGR-diversified proteins in cellular hosts remain elusive. We find that 82% of DGRs from one of the major monophyletic lineages of DGR reverse transcriptases are encoded by multicellular bacteria, which often have two or more DGR loci in their genomes. Using the multicellular purple sulfur bacterium Thiohalocapsa sp. PB-PSB1 as an example, we characterized nine distinct DGR loci capable of generating 10282 different combinations of target proteins. With environmental metagenomes from individual Thiohalocapsa aggregates, we show that most of PB-PSB1's DGR target genes are diversified across its biogeographic range, with spatial heterogeneity in the diversity of each locus. In Thiohalocapsa PB-PSB1 and other bacteria hosting this lineage of cellular DGRs, the diversified target genes are associated with NACHT-domain anti-phage defenses and putative ternary conflict systems previously shown to be enriched in multicellular bacteria. We propose that these DGR-diversified targets act as antigen sensors that confer a form of adaptive immunity to their multicellular consortia, though this remains to be experimentally tested. These findings could have implications for understanding the evolution of multicellularity, as the NACHT-domain anti-phage systems and ternary systems share both domain homology and conceptual similarities with the innate immune and programmed cell death pathways of plants and metazoans.
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Affiliation(s)
- H. Doré
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93106
| | - A. R. Eisenberg
- Department of Chemical Engineering, University of California, Santa Barbara, CA93106
| | - E. N. Junkins
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93106
| | - G. E. Leventhal
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Anakha Ganesh
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA02543
| | - O. X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - B. G. Paul
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA02543
| | - D. L. Valentine
- Department of Earth Science, University of California, Santa Barbara, CA93106
- Marine Science Institute, University of California, Santa Barbara, CA93106
| | - M. A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA93106
- Department of Bioengineering, University of California, Santa Barbara, CA93106
| | - E. G. Wilbanks
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93106
- Department of Bioengineering, University of California, Santa Barbara, CA93106
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Valadez-Cano C, Reyes-Prieto A, Lawrence J. Novel virulent and temperate cyanophages predicted to infect Microcoleus associated with anatoxin-producing benthic mats. Environ Microbiol 2023; 25:3319-3332. [PMID: 37849433 DOI: 10.1111/1462-2920.16527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023]
Abstract
Cyanophages are crucial for regulating cyanobacterial populations, but their influence on anatoxin-producing Microcoleus mat dynamics remains unexplored. Here, we use metagenomics to explore phage presence in benthic mats from the Wolastoq|Saint John River (New Brunswick, Canada) and the Eel River (California, USA). We recovered multiple viral-like sequences associated with different putative bacterial hosts, including two cyanophage genomes with apparently different replication strategies. A temperate cyanophage was found integrated in the genomes of Microcoleus sp. 3 recovered from the Eel River and is phylogenetically related to Phormidium phages. We also recovered novel virulent cyanophage genomes from Wolastoq and Eel River mats that were dominated by anatoxin-producing Microcoleus species predicted to be the host. Despite the geographical distance, these genomes have similar sizes (circa 239 kbp) and share numerous orthologous genes with high sequence identity. A considerable reduction of the anatoxin-producing Microcoleus species in Wolastoq mats following the emergence of the virulent phage suggests that phage infections have an important role in limiting the abundance of this toxigenic cyanobacterium and releasing anatoxins into the surrounding water. Our results constitute the first report of cyanophages predicted to infect mat-forming Microcoleus species associated with anatoxin production.
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Affiliation(s)
- Cecilio Valadez-Cano
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Janice Lawrence
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
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Roussel T, Halary S, Duval C, Piquet B, Cadoret JP, Vernès L, Bernard C, Marie B. Monospecific renaming within the cyanobacterial genus Limnospira (Spirulina) and consequences for food authorization. J Appl Microbiol 2023; 134:lxad159. [PMID: 37558396 DOI: 10.1093/jambio/lxad159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 06/27/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023]
Abstract
AIMS The cyanobacterial genus, Limnospira (anc. Arthrospira Stizenberger ex Gomont 1892), commonly called "Spirulina", is widely used for commercial purposes because of its high protein content and beneficial probiotic metabolites. Thus, the taxonomy of this genus is important because of its consequences for food applications. METHODS AND RESULTS We constructed a database with formation on all Limnospira strains plus new ones from 72 new French isolates. We used a polyphasic approach (phylogenetic, phylogenomic, presence or absence of coding DNA sequences, morphological, and ultrastructure analyses) to confirm that the species A. platensis belonged to the genus Limnospira (L. platensis Gomont comb. nov. Basionym. Arthrospira platensis Gomont 1892) and that the genus Limnospira was monospecific, only represented by L. platensis. CONCLUSIONS This study highlighted the large intra-specific diversity of L. platensis, independent of the affiliations of the phylogenetic clades or geographical location of the habitats and the subsequent physiological and metabolic plasticity.
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Affiliation(s)
- Théotime Roussel
- UMR7245 MCAM MNHN-CNRS, Muséum National d'Histoire Naturelle, CP 39, 12 rue Buffon, F-75231 Paris Cedex 05, France
- Algama, 81 rue Réaumur, 75002 Paris, France
| | - Sébastien Halary
- UMR7245 MCAM MNHN-CNRS, Muséum National d'Histoire Naturelle, CP 39, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | - Charlotte Duval
- UMR7245 MCAM MNHN-CNRS, Muséum National d'Histoire Naturelle, CP 39, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | - Bérénice Piquet
- Electron Microscopy Platform, Muséum National d'Histoire Naturelle, CP 39, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | | | - Léa Vernès
- Algama, 81 rue Réaumur, 75002 Paris, France
| | - Cécile Bernard
- UMR7245 MCAM MNHN-CNRS, Muséum National d'Histoire Naturelle, CP 39, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | - Benjamin Marie
- UMR7245 MCAM MNHN-CNRS, Muséum National d'Histoire Naturelle, CP 39, 12 rue Buffon, F-75231 Paris Cedex 05, France
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Jang K, Otim O. Harmful algae blooms: an analysis of recent spatiotemporal trends on California's inland waterbodies. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2023. [PMID: 37183787 DOI: 10.1039/d3em00115f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Harmful algae blooms (HABs) are unwelcome annual events on waterbodies in California (USA). The unseemly sights of lifeless fish drifting ashore and the mammalian illnesses resulting from close contacts with HABs once in ahile are telltale signs of their presence. California as such tracks HABs closely for immediate public warnings. That said, a lack of statewide monitoring standards for producing comparable and high-quality data, however, hinders a deeper insight into HABs on California's inland waterbodies. In their absence, the current study demonstrates the utility of empirical dataset in advancing an understanding of spatiotemporal distribution of HABs on inland waterbodies. With a 2016-2021 mostly observational data, the questions asked are whether HABs incidences are expanding in California with time, whether there are localities more prone to HABs than others, and whether bivariate relationships exist between HABs reports and population density, or waterbody size, land area and geographical location. Overall, the frequency with which HABs are observed is found to increase statewide, an increase not correlated with population density, but with land area and inland waterbody size. Results also show that North Coast, Central Valley, and San Diego are the most affected regions of California. Also revealed by this mostly observational data were recent HABs spikes in the January months (California winter) which, if proven, may be signaling an emerging year-round problem that California will have to contend with.
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Affiliation(s)
- Kate Jang
- Crossroads School for Arts and Sciences, Santa Monica, CA 90404, USA
- TEAMS Research Institute, National Youth Community Center, Los Angeles, CA 90010, USA
| | - Ochan Otim
- TEAMS Research Institute, National Youth Community Center, Los Angeles, CA 90010, USA
- Environmental Monitoring Division, City of Los Angeles, Playa Del Rey, CA 90293, USA.
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7
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Dong X, Peng Y, Wang M, Woods L, Wu W, Wang Y, Xiao X, Li J, Jia K, Greening C, Shao Z, Hubert CRJ. Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps. Nat Commun 2023; 14:1127. [PMID: 36854684 PMCID: PMC9974965 DOI: 10.1038/s41467-023-36877-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
Deep sea cold seep sediments host abundant and diverse microbial populations that significantly influence biogeochemical cycles. While numerous studies have revealed their community structure and functional capabilities, little is known about genetic heterogeneity within species. Here, we examine intraspecies diversity patterns of 39 abundant species identified in sediment layers down to 430 cm below the sea floor across six cold seep sites. These populations are grouped as aerobic methane-oxidizing bacteria, anaerobic methanotrophic archaea and sulfate-reducing bacteria. Different evolutionary trajectories are observed at the genomic level among these physiologically and phylogenetically diverse populations, with generally low rates of homologous recombination and strong purifying selection. Functional genes related to methane (pmoA and mcrA) and sulfate (dsrA) metabolisms are under strong purifying selection in most species investigated. These genes differ in evolutionary trajectories across phylogenetic clades but are functionally conserved across sites. Intrapopulation diversification of genomes and their mcrA and dsrA genes is depth-dependent and subject to different selection pressure throughout the sediment column redox zones at different sites. These results highlight the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep extreme environments, shedding light on microbial adaptation in the subseafloor biosphere.
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Affiliation(s)
- Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Muhua Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Laura Woods
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Wenxue Wu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Yong Wang
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Xi Xiao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, 510075, China
| | - Jiwei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Kuntong Jia
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
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Abstract
The subseafloor is a vast habitat that supports microorganisms that have a global scale impact on geochemical cycles. Many of the endemic microbial communities inhabiting the subseafloor consist of small populations under growth-limited conditions. For small populations, stochastic evolutionary events can have large impacts on intraspecific population dynamics and allele frequencies. These conditions are fundamentally different from those experienced by most microorganisms in surface environments, and it is unknown how small population sizes and growth-limiting conditions influence evolution and population structure in the subsurface. Using a 2-year, high-resolution environmental time series, we examine the dynamics of microbial populations from cold, oxic crustal fluids collected from the subseafloor site North Pond, located near the mid-Atlantic ridge. Our results reveal rapid shifts in overall abundance, allele frequency, and strain abundance across the time points observed, with evidence for homologous recombination between coexisting lineages. We show that the subseafloor aquifer is a dynamic habitat that hosts microbial metapopulations that disperse frequently through the crustal fluids, enabling gene flow and recombination between microbial populations. The dynamism and stochasticity of microbial population dynamics in North Pond suggest that these forces are important drivers in the evolution of microbial populations in the vast subseafloor habitat.
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