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Van Le V, Kang M, Ko SR, Park CY, Lee JJ, Choi IC, Oh HM, Ahn CY. Response of particle-attached and free-living bacterial communities to Microcystis blooms. Appl Microbiol Biotechnol 2024; 108:42. [PMID: 38183480 DOI: 10.1007/s00253-023-12828-2] [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: 03/24/2023] [Revised: 07/29/2023] [Accepted: 11/13/2023] [Indexed: 01/08/2024]
Abstract
The massive proliferation of Microcystis threatens freshwater ecosystems and degrades water quality globally. Understanding the mechanisms that contribute to Microcystis growth is crucial for managing Microcystis blooms. The lifestyles of bacteria can be classified generally into two groups: particle-attached (PA; > 3 µm) and free-living (FL; 0.2-3.0 µm). However, little is known about the response of PA and FL bacteria to Microcystis blooms. Using 16S rRNA gene high-throughput sequencing, we investigated the stability, assembly process, and co-occurrence patterns of PA and FL bacterial communities during distinct bloom stages. PA bacteria were phylogenetically different from their FL counterparts. Microcystis blooms substantially influenced bacterial communities. The time decay relationship model revealed that Microcystis blooms might increase the stability of both PA and FL bacterial communities. A contrasting community assembly mechanism was observed between the PA and FL bacterial communities. Throughout Microcystis blooms, homogeneous selection was the major assembly process that impacted the PA bacterial community, whereas drift explained much of the turnover of the FL bacterial community. Both PA and FL bacterial communities could be separated into modules related to different phases of Microcystis blooms. Microcystis blooms altered the assembly process of PA and FL bacterial communities. PA bacterial community appeared to be more responsive to Microcystis blooms than FL bacteria. Decomposition of Microcystis blooms may enhance cooperation among bacteria. Our findings highlight the importance of studying bacterial lifestyles to understand their functions in regulating Microcystis blooms. KEY POINTS: • Microcystis blooms alter the assembly process of PA and FL bacterial communities • Microcystis blooms increase the stability of both PA and FL bacterial communities • PA bacteria seem to be more responsive to Microcystis blooms than FL bacteria.
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Affiliation(s)
- Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Mingyeong Kang
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
| | - Chan-Yeong Park
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jay Jung Lee
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk, 29027, Republic of Korea
| | - In-Chan Choi
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk, 29027, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea.
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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Ji W, Ma J, Zheng Z, Al-Herrawy AZ, Xie B, Wu D. Algae blooms with resistance in fresh water: Potential interplay between Microcystis and antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 940:173528. [PMID: 38802023 DOI: 10.1016/j.scitotenv.2024.173528] [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: 02/26/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Microcystis, a type of cyanobacteria known for producing microcystins (MCs), is experiencing a global increase in blooms. They have been recently recognized as potential contributors to the widespread of antibiotic resistance genes (ARGs). By reviewing approximately 150 pieces of recent studies, a hypothesis has been formulated suggesting that significant fluctuations in MCs concentrations and microbial community structure during Microcystis blooms could influence the dynamics of waterborne ARGs. Among all MCs, microcystin-LR (MC-LR) is the most widely distributed worldwide, notably abundant in reservoirs during summer. MCs inhibit protein phosphatases or increase reactive oxygen species (ROS), inducing oxidative stresses, enhancing membrane permeability, and causing DNA damage. This further enhances selective pressures and horizontal gene transfer (HGT) chances of ARGs. The mechanisms by which Microcystis regulates ARG dissemination have been systematically organized for the first time, focusing on the secretion of MCs and the alterations of bacterial community structure. However, several knowledge gaps remain, particularly concerning how MCs interfere with the electron transport chain and how Microcystis facilitates HGT of ARGs. Concurrently, the predominance of Microcystis forming the algal microbial aggregates is considered a hotspot for preserving and transferring ARGs. Yet, Microcystis can deplete the nutrients from other taxa within these aggregates, thereby reducing the density of ARG-carrying bacteria. Therefore, further studies are needed to explore the 'symbiotic - competitive' relationships between Microcystis and ARG-hosting bacteria under varied nutrient conditions. Addressing these knowledge gaps is crucial to understand the impacts of the algal aggregates on dynamics of waterborne antibiotic resistome, and underscores the need for effective control of Microcystis to curb the spread of antibiotic resistance. Constructed wetlands and photocatalysis represent advantageous strategies for halting the spread of ARGs from the perspective of Microcystis blooms, as they can effectively control Microcystis and MCs while maintaining the stability of aquatic ecosystem.
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Affiliation(s)
- Wenhui Ji
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, China
| | - Jingkai Ma
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, China
| | - Zhipeng Zheng
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, China
| | - Ahmad Z Al-Herrawy
- Water Pollution Research Department, National Research Centre, Giza, Egypt
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, China.
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Krausfeldt LE, Shmakova E, Lee HW, Mazzei V, Loftin KA, Smith RP, Karwacki E, Fortman PE, Rosen BH, Urakawa H, Dadlani M, Colwell RR, Lopez JV. Microbial diversity, genomics, and phage-host interactions of cyanobacterial harmful algal blooms. mSystems 2024; 9:e0070923. [PMID: 38856205 PMCID: PMC11265339 DOI: 10.1128/msystems.00709-23] [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: 07/13/2023] [Accepted: 11/13/2023] [Indexed: 06/11/2024] Open
Abstract
The occurrence of cyanobacterial harmful algal blooms (cyanoHABs) is related to their physical and chemical environment. However, less is known about their associated microbial interactions and processes. In this study, cyanoHABs were analyzed as a microbial ecosystem, using 1 year of 16S rRNA sequencing and 70 metagenomes collected during the bloom season from Lake Okeechobee (Florida, USA). Biogeographical patterns observed in microbial community composition and function reflected ecological zones distinct in their physical and chemical parameters that resulted in bloom "hotspots" near major lake inflows. Changes in relative abundances of taxa within multiple phyla followed increasing bloom severity. Functional pathways that correlated with increasing bloom severity encoded organic nitrogen and phosphorus utilization, storage of nutrients, exchange of genetic material, phage defense, and protection against oxidative stress, suggesting that microbial interactions may promote cyanoHAB resilience. Cyanobacterial communities were highly diverse, with picocyanobacteria ubiquitous and oftentimes most abundant, especially in the absence of blooms. The identification of novel bloom-forming cyanobacteria and genomic comparisons indicated a functionally diverse cyanobacterial community with differences in its capability to store nitrogen using cyanophycin and to defend against phage using CRISPR and restriction-modification systems. Considering blooms in the context of a microbial ecosystem and their interactions in nature, physiologies and interactions supporting the proliferation and stability of cyanoHABs are proposed, including a role for phage infection of picocyanobacteria. This study displayed the power of "-omics" to reveal important biological processes that could support the effective management and prediction of cyanoHABs. IMPORTANCE Cyanobacterial harmful algal blooms pose a significant threat to aquatic ecosystems and human health. Although physical and chemical conditions in aquatic systems that facilitate bloom development are well studied, there are fundamental gaps in the biological understanding of the microbial ecosystem that makes a cyanobacterial bloom. High-throughput sequencing was used to determine the drivers of cyanobacteria blooms in nature. Multiple functions and interactions important to consider in cyanobacterial bloom ecology were identified. The microbial biodiversity of blooms revealed microbial functions, genomic characteristics, and interactions between cyanobacterial populations that could be involved in bloom stability and more coherently define cyanobacteria blooms. Our results highlight the importance of considering cyanobacterial blooms as a microbial ecosystem to predict, prevent, and mitigate them.
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Affiliation(s)
- Lauren E. Krausfeldt
- Department of Biological Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, Florida, USA
| | - Elizaveta Shmakova
- Department of Biological Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, Florida, USA
| | - Hyo Won Lee
- Department of Biological Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, Florida, USA
| | - Viviana Mazzei
- U.S. Geological Survey, Caribbean–Florida Water Science Center, Orlando, Florida, USA
| | - Keith A. Loftin
- U.S. Geological Survey, Kansas Water Science Center, Lawrence, Kansas, USA
| | - Robert P. Smith
- Department of Biological Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, Florida, USA
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, USA
| | - Emily Karwacki
- U.S. Geological Survey, Caribbean–Florida Water Science Center, Orlando, Florida, USA
| | - P. Eric Fortman
- Department of Biological Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, Florida, USA
| | - Barry H. Rosen
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, Florida, USA
| | | | - Rita R. Colwell
- Institute for Advanced Computer Studies, University of Maryland College Park, College Park, Maryland, USA
| | - Jose V. Lopez
- Department of Biological Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, Florida, USA
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Le VV, Tran QG, Ko SR, Oh HM, Ahn CY. Insights into cyanobacterial blooms through the lens of omics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173028. [PMID: 38723963 DOI: 10.1016/j.scitotenv.2024.173028] [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: 12/26/2023] [Revised: 05/04/2024] [Accepted: 05/04/2024] [Indexed: 05/20/2024]
Abstract
Cyanobacteria are oxygen-producing photosynthetic bacteria that convert carbon dioxide into biomass upon exposure to sunlight. However, favorable conditions cause harmful cyanobacterial blooms (HCBs), which are the dense accumulation of biomass at the water surface or subsurface, posing threats to freshwater ecosystems and human health. Understanding the mechanisms underlying cyanobacterial bloom formation is crucial for effective management. In this regard, recent advancements in omics technologies have provided valuable insights into HCBs, which have raised expectations to develop more effective control methods in the near future. This literature review aims to present the genomic architecture, adaptive mechanisms, microbial interactions, and ecological impacts of HCBs through the lens of omics. Genomic analysis indicates that the genome plasticity of cyanobacteria has enabled their resilience and effective adaptation to environmental changes. Transcriptomic investigations have revealed that cyanobacteria use various strategies for adapting to environmental stress. Additionally, metagenomic and metatranscriptomic analyses have emphasized the significant role of the microbial community in regulating HCBs. Finally, we offer perspectives on potential opportunities for further research in this field.
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Affiliation(s)
- Ve Van Le
- Cell factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | | | - So-Ra Ko
- Cell factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hee-Mock Oh
- Cell factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea.
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Mohan R, Pillai SS, Purushothaman A, Thomas LC, Padmakumar KB. Phylogenic diversity of bacteria associated with potentially toxic cyanobacteria Microcystis aeruginosa: a synthesis on its bloom dynamics. Folia Microbiol (Praha) 2024; 69:677-691. [PMID: 37991690 DOI: 10.1007/s12223-023-01108-1] [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: 06/04/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
The occurrence of toxic bloom-forming cyanobacteria, Microcystis aeruginosa, has been frequently reported worldwide. These colony forming toxic cyanobacteria harbour a wide range of heterotrophic bacterial communities. The present study has attempted to understand the bloom dynamics of M. aeruginosa along with isolating their colony-associated culturable heterotrophic bacteria from two freshwater ponds in south India with a persisting cyanobacterial bloom. The monthly monitoring of these study areas revealed the conducive role of warm, stagnant waters with high nutrients in forming M. aeruginosa bloom. The peak values of temperature, nitrate, and phosphate at station 1 reached up to 30.5 °C, 4.48 mg/L, 1.64 mg/L, and at station 2, 31 °C, 3.45 mg/L, and 0.62 mg/L, respectively. Twenty-eight bacterial isolates belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, and Firmicutes were obtained during the study. Among these 28 isolates, Firmicutes was dominant with the M. aeruginosa bloom from both the study areas.
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Affiliation(s)
- Renju Mohan
- Department of Marine Biology, Microbiology & Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi-16, Kerala, India
| | - Sreya S Pillai
- Department of Marine Biology, Microbiology & Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi-16, Kerala, India
| | - Aishwarya Purushothaman
- Department of Marine Biology, Microbiology & Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi-16, Kerala, India
| | - Lathika Cicily Thomas
- Department of Marine Biology, Microbiology & Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi-16, Kerala, India
| | - K B Padmakumar
- Department of Marine Biology, Microbiology & Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi-16, Kerala, India.
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Cai H, McLimans CJ, Jiang H, Chen F, Krumholz LR, Hambright KD. Aerobic anoxygenic phototrophs play important roles in nutrient cycling within cyanobacterial Microcystis bloom microbiomes. MICROBIOME 2024; 12:88. [PMID: 38741135 PMCID: PMC11089705 DOI: 10.1186/s40168-024-01801-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/25/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND During the bloom season, the colonial cyanobacterium Microcystis forms complex aggregates which include a diverse microbiome within an exopolymer matrix. Early research postulated a simple mutualism existing with bacteria benefitting from the rich source of fixed carbon and Microcystis receiving recycled nutrients. Researchers have since hypothesized that Microcystis aggregates represent a community of synergistic and interacting species, an interactome, each with unique metabolic capabilities that are critical to the growth, maintenance, and demise of Microcystis blooms. Research has also shown that aggregate-associated bacteria are taxonomically different from free-living bacteria in the surrounding water. Moreover, research has identified little overlap in functional potential between Microcystis and members of its microbiome, further supporting the interactome concept. However, we still lack verification of general interaction and know little about the taxa and metabolic pathways supporting nutrient and metabolite cycling within Microcystis aggregates. RESULTS During a 7-month study of bacterial communities comparing free-living and aggregate-associated bacteria in Lake Taihu, China, we found that aerobic anoxygenic phototrophic (AAP) bacteria were significantly more abundant within Microcystis aggregates than in free-living samples, suggesting a possible functional role for AAP bacteria in overall aggregate community function. We then analyzed gene composition in 102 high-quality metagenome-assembled genomes (MAGs) of bloom-microbiome bacteria from 10 lakes spanning four continents, compared with 12 complete Microcystis genomes which revealed that microbiome bacteria and Microcystis possessed complementary biochemical pathways that could serve in C, N, S, and P cycling. Mapping published transcripts from Microcystis blooms onto a comprehensive AAP and non-AAP bacteria MAG database (226 MAGs) indicated that observed high levels of expression of genes involved in nutrient cycling pathways were in AAP bacteria. CONCLUSIONS Our results provide strong corroboration of the hypothesized Microcystis interactome and the first evidence that AAP bacteria may play an important role in nutrient cycling within Microcystis aggregate microbiomes. Video Abstract.
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Affiliation(s)
- Haiyuan Cai
- School of Biological Sciences, University of Oklahoma, Norman, USA
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | | | - Helong Jiang
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, USA
| | - Lee R Krumholz
- School of Biological Sciences, University of Oklahoma, Norman, USA
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Kim W, Park Y, Kim M, Cha Y, Jung J, Jeon CO, Park W. Sustainable control of Microcystis aeruginosa, a harmful cyanobacterium, using Selaginella tamariscina extracts. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 277:116375. [PMID: 38677071 DOI: 10.1016/j.ecoenv.2024.116375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/02/2024] [Accepted: 04/20/2024] [Indexed: 04/29/2024]
Abstract
Eco-friendly reagents derived from plants represent a promising strategy to mitigate the occurrence of toxic cyanobacterial blooms. The use of an amentoflavone-containing Selaginella tamariscina extract (STE) markedly decreased the number of Microcystis aeruginosa cells, thus demonstrating significant anti-cyanobacterial activity. In particular, the Microcystis-killing fraction obtained from pulverized S. tamariscina using hot-water-based extraction at temperatures of 40 °C induced cell disruption in both axenic and xenic M. aeruginosa. Liquid chromatographic analysis was also conducted to measure the concentration of amentoflavone in the STE, thus supporting the potential M. aeruginosa-specific killing effects of STE. Bacterial community analysis revealed that STE treatment led to a reduction in the relative abundance of Microcystis species while also increasing the 16S rRNA gene copy number in both xenic M. aeruginosa NIBR18 and cyanobacterial bloom samples isolated from a freshwater environment. Subsequent testing on bacteria, cyanobacteria, and algae isolated from freshwater revealed that STE was not toxic for other taxa. Furthermore, ecotoxicology assessment involving Aliivibrio fischeri, Daphnia magna, and Danio rerio found that high STE doses immobilized D. magna but did not impact the other organisms, while there was no change in the water quality. Overall, due to its effective Microcystis-killing capability and low ecotoxicity, aqueous STE represents a promising practical alternative for the management of Microcystis blooms.
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Affiliation(s)
- Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, South Korea
| | - Yerim Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, South Korea
| | - Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, South Korea
| | - Yeji Cha
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, South Korea
| | - Jaejoon Jung
- Department of Life Science, Chung-Ang University, Seoul 02841, South Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 02841, South Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, South Korea.
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Wang X, Xiao Y, Deng Y, Sang X, Deng QL, Wang L, Yang YW, Zhang BH, Zhang YQ. Sphingomonas lacusdianchii sp. nov., an attached bacterium inhibited by metabolites from its symbiotic cyanobacterium. Appl Microbiol Biotechnol 2024; 108:309. [PMID: 38661971 PMCID: PMC11045571 DOI: 10.1007/s00253-024-13081-x] [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: 07/24/2023] [Revised: 02/12/2024] [Accepted: 02/20/2024] [Indexed: 04/26/2024]
Abstract
An alpha-proteobacterial strain JXJ CY 53 T was isolated from the cyanosphere of Microcystis sp. FACHB-905 (MF-905) collected from Lake Dianchi, China. JXJ CY 53 T was observed to be an aerobic, Gram-stain-negative, oval shaped, and mucus-secreting bacterium. It had C18:1ω7c and C16:0 as the major cellular fatty acids, Q-10 as the predominant ubiquinone, and sphingoglycolipid, diphosphatidylglycerol, phosphatidylcholine, and phosphatidylmethylethanolamine as the polar lipids. The G + C content of DNA was 65.85%. The bacterium had 16S rRNA gene sequence identities of 98.9% and 98.7% with Sphingomonas panni DSM 15761 T and Sphingomonas hankookensis KCTC 22579 T, respectively, while less than 97.4% identities with other members of the genus. Further taxonomic analysis indicated that JXJ CY 53 T represented a new member of Sphingomonas, and the species epithet was proposed as Sphingomonas lacusdianchii sp. nov. (type strain JXJ CY 53 T = KCTC 72813 T = CGMCC 1.17657 T). JXJ CY 53 T promoted the growth of MF-905 by providing bio-available phosphorus and nitrogen, plant hormones, vitamins, and carotenoids. It could modulate the relative abundances of nonculturable bacteria associated with MF-905 and influence the interactions of MF-905 and other bacteria isolated from the cyanobacterium, in addition to microcystin production characteristics. Meanwhile, MF-905 could provide JXJ CY 53 T dissolved organic carbon for growth, and control the growth of JXJ CY 53 T by secreting specific chemicals other than microcystins. Overall, these results suggest that the interactions between Microcystis and its attached bacteria are complex and dynamic, and may influence the growth characteristics of the cyanobacterium. This study provided new ideas to understand the interactions between Microcystis and its attached bacteria. KEY POINTS: • A novel bacterium (JXJCY 53 T) was isolated from the cyanosphere of Microcystis sp. FACHB-905 (MF-905) • JXJCY 53 T modulated the growth and microcystin production of MF-905 • MF-905 could control the attached bacteria by specific chemicals other than microcystins (MCs).
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Affiliation(s)
- Xin Wang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Yao Xiao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Yang Deng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Xue Sang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Qing-Lin Deng
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Le Wang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Yi-Wen Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Bing-Huo Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China.
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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Reignier O, Bormans M, Hervé F, Robert E, Savar V, Tanniou S, Amzil Z, Noël C, Briand E. Spatio-temporal connectivity of a toxic cyanobacterial community and its associated microbiome along a freshwater-marine continuum. HARMFUL ALGAE 2024; 134:102627. [PMID: 38705620 DOI: 10.1016/j.hal.2024.102627] [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: 01/26/2024] [Revised: 03/22/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
Due to climate changes and eutrophication, blooms of predominantly toxic freshwater cyanobacteria are intensifying and are likely to colonize estuaries, thus impacting benthic organisms and shellfish farming representing a major ecological, health and economic risk. In the natural environment, Microcystis form large mucilaginous colonies that influence the development of both cyanobacterial and embedded bacterial communities. However, little is known about the fate of natural colonies of Microcystis by salinity increase. In this study, we monitored the fate of a Microcystis dominated bloom and its microbiome along a French freshwater-marine gradient at different phases of a bloom. We demonstrated changes in the cyanobacterial genotypic composition, in the production of specific metabolites (toxins and compatible solutes) and in the heterotrophic bacteria structure in response to the salinity increase. In particular M. aeruginosa and M. wesenbergii survived salinities up to 20. Based on microcystin gene abundance, the cyanobacteria became more toxic during their estuarine transfer but with no selection of specific microcystin variants. An increase in compatible solutes occurred along the continuum with extensive trehalose and betaine accumulations. Salinity structured most the heterotrophic bacteria community, with an increased in the richness and diversity along the continuum. A core microbiome in the mucilage-associated attached fraction was highly abundant suggesting a strong interaction between Microcystis and its microbiome and a likely protecting role of the mucilage against an osmotic shock. These results underline the need to better determine the interactions between the Microcystis colonies and their microbiome as a likely key to their widespread success and adaptation to various environmental conditions.
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Affiliation(s)
| | - Myriam Bormans
- UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes F-35042, France
| | - Fabienne Hervé
- IFREMER, PHYTOX, Laboratoire METALG, Nantes F-44000, France
| | - Elise Robert
- IFREMER, PHYTOX, Laboratoire GENALG, Nantes F-44000, France
| | | | - Simon Tanniou
- IFREMER, PHYTOX, Laboratoire METALG, Nantes F-44000, France
| | - Zouher Amzil
- IFREMER, PHYTOX, Laboratoire METALG, Nantes F-44000, France
| | - Cyril Noël
- IFREMER, IRSI - Service de Bioinformatique (SeBiMER), Plouzané, France
| | - Enora Briand
- IFREMER, PHYTOX, Laboratoire GENALG, Nantes F-44000, France.
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10
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Wang L, Xiao Y, Lai W, Jia R, Deng Q, Wang X, Shi H, Yang Y, Zhang B. Micrococcus lacusdianchii sp. nov., an attached bacterium inhibited by metabolites from its symbiotic algae. J Antibiot (Tokyo) 2024; 77:163-169. [PMID: 38148391 DOI: 10.1038/s41429-023-00690-3] [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: 08/21/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 12/28/2023]
Abstract
A novel actinobacterial strain, designated as JXJ CY 30 T, was isolated from the phycosphere of Microcystis aeruginosa FACHB-905 (Maf) collected from Lake Dianchi, China. The strain was a Gram-stain-positive, aerobic and coccus-shaped actinobacterium. It had alanine, glutamic acid, aspartic acid, and lysine in the peptidoglycan, and mannose, ribose and arabinose in its cell wall sugars, anteiso-C15:0 and iso-C15:0 as the main cellular fatty acids, MK-7 and MK-8 as the major respiratory quinones, and phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, glycolipid, and an unidentified phospholipid as the polar lipids. The DNA G + C content was 73.08%. Its 16 S rRNA gene sequence shared 99.14%, and 98.75% similarities with Micrococcus flavus DSM 19079 T and M. porci KD337-16T, respectively, and ≤98.41% similarities with other type strains of the genus Micrococcus. It formed independent clade with M. flavus DSM 19079 T on the phylogenetic trees. The digital DNA-DNA hybridization and average nucleotide identity values between strain JXJ CY 30 T and M. flavus DSM 19079 T and M. porci KD337-16T were 48.0% and 92.1%, 25.5% and 83.2%, respectively. These data above indicated that strain JXJ CY 30 T represented a new species of the genus Micrococcus, and the species epithet is proposed as Micrococcus lacusdianchii sp. nov. (type strain JXJ CY 30 T = KCTC 49378 T = CGMCC 1.17508 T). Strain JXJ CY 30 T can potentially provide Maf with various nutrients such as available phosphorus and nitrogen, plant hormones, various vitamins and carotenoids for growth, while it was inhibited by metabolites from its symbiotic algae Maf.
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Affiliation(s)
- Le Wang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Yao Xiao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Wenxin Lai
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Ru Jia
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Qinglin Deng
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Xin Wang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Hongqiu Shi
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Yiwen Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China.
| | - Binghuo Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China.
- Jiujiang Key Laboratory for the Development and Utilization of Traditional Chinese Medicine resources in Northwest Jiangxi, Jiujiang, China.
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11
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Xiao Y, Du M, Deng Y, Deng Q, Wang X, Yang Y, Zhang B, Zhang YQ. Modulation of growth, microcystin production, and algal-bacterial interactions of the bloom-forming algae Microcystis aeruginosa by a novel bacterium recovered from its phycosphere. Front Microbiol 2024; 15:1295696. [PMID: 38495512 PMCID: PMC10940515 DOI: 10.3389/fmicb.2024.1295696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/21/2024] [Indexed: 03/19/2024] Open
Abstract
Harmful algal blooms (HABs) in natural waters are of escalating global concern due to their detrimental impact on environmental health. Emerging evidence indicates that algae-bacteria symbionts can affect HAB features, though much about this interplay remains largely unexplored. The current study isolated a new species of Mucilaginibacter (type strain JXJ CY 39T) from culture biomass of the bloom-causing Microcystis aeruginosa FACHB-905 (Maf) from Lake Dianchi, China. Strain JXJ CY 39T was an aerobic, Gram-stain-negative rod bacterium that grew at 5-38°C, pH 4.0-11.0, and 0-3.0% NaCl. Taxonomic evaluation proposed a new species, with Mucilaginibacter lacusdianchii sp. nov., as the species epithet. Experimental results revealed that strain JXJ CY 39T spurred the growth of Maf by supplying soluble phosphorus and nitrogen during cultivation, despite the unavailability of soluble phosphorus and nitrogen. Additionally, by producing the plant hormone indole-3-acetate, strain JXJ CY 39T possibly impacted Maf's functionality. Results from co-culture experiments with other strains from Maf biomass showed possible effects of strain JXJ CY 39T on the relationship between Maf and other cohabiting bacteria, as well as microcystin toxin production characteristics. Although Maf could foster the growth of strain JXJ CY 39T by supplying organic carbon, the strain's growth could be regulated via specific chemical compounds based on antibiotic assays. Community composition analysis disclosed that this Mucilaginibacter strain positively affected Maf's growth and modified densities and types of bacteria linked to Maf. Overall, these results suggest that the interactions between important HAB-causing organisms and their attached bacteria are complex, dynamic, and may influence the growth characteristics of algae.
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Affiliation(s)
- Yao Xiao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mijia Du
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Yang Deng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qinglin Deng
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xin Wang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Yiwen Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Binghuo Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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12
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Kim W, Park Y, Jung J, Jeon CO, Toyofuku M, Lee J, Park W. Biological and Chemical Approaches for Controlling Harmful Microcystis Blooms. J Microbiol 2024; 62:249-260. [PMID: 38587591 DOI: 10.1007/s12275-024-00115-2] [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: 12/26/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 04/09/2024]
Abstract
The proliferation of harmful cyanobacterial blooms dominated by Microcystis aeruginosa has become an increasingly serious problem in freshwater ecosystems due to climate change and eutrophication. Microcystis-blooms in freshwater generate compounds with unpleasant odors, reduce the levels of dissolved O2, and excrete microcystins into aquatic ecosystems, potentially harming various organisms, including humans. Various chemical and biological approaches have thus been developed to mitigate the impact of the blooms, though issues such as secondary pollution and high economic costs have not been adequately addressed. Red clays and H2O2 are conventional treatment methods that have been employed worldwide for the mitigation of the blooms, while novel approaches, such as the use of plant or microbial metabolites and antagonistic bacteria, have also recently been proposed. Many of these methods rely on the generation of reactive oxygen species, the inhibition of photosynthesis, and/or the disruption of cellular membranes as their mechanisms of action, which may also negatively impact other freshwater microbiota. Nevertheless, the underlying molecular mechanisms of anticyanobacterial chemicals and antagonistic bacteria remain unclear. This review thus discusses both conventional and innovative approaches for the management of M. aeruginosa in freshwater bodies.
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Affiliation(s)
- Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Yerim Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Jaejoon Jung
- Department of Life Science, Chung-Ang University, Seoul, 02841, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 02841, Republic of Korea
| | - Masanori Toyofuku
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-0006, Japan
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, 43210, USA
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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13
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Baker D, Godwin CM, Khanam M, Burtner AM, Dick GJ, Denef VJ. Variation in resource competition traits among Microcystis strains is affected by their microbiomes. MLIFE 2023; 2:401-415. [PMID: 38818269 PMCID: PMC10989160 DOI: 10.1002/mlf2.12094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 06/01/2024]
Abstract
Freshwater harmful algal blooms are often dominated by Microcystis, a phylogenetically cohesive group of cyanobacteria marked by extensive genetic and physiological diversity. We have previously shown that this genetic diversity and the presence of a microbiome of heterotrophic bacteria influences competitive interactions with eukaryotic phytoplankton. In this study, we sought to explain these observations by characterizing Monod equation parameters for resource usage (maximum growth rate μ max, half-saturation value for growth K s, and quota) as a function of N and P levels for four strains (NIES-843, PCC 9701, PCC 7806 [WT], and PCC 7806 ΔmcyB) in presence and absence of a microbiome derived from Microcystis isolated from Lake Erie. Results indicated limited differences in maximum growth rates but more pronounced differences in half-saturation values among Microcystis strains. The largest impact of the microbiome was reducing the minimal nitrogen concentration sustaining growth and reducing half saturation values, with variable results depending on the Microcystis strain. Microcystis strains also differed from each other in their N and P quotas and the extent to which microbiome presence affected them. Our data highlight the importance of the microbiome in altering Microcystis-intrinsic traits, strain competitive hierarchies, and thus bloom dynamics. As quota, μ max, and K s are commonly used in models for harmful algal blooms, our data suggest that model improvement may be possible by incorporating genotype dependencies of resource-use parameters.
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Affiliation(s)
- Dylan Baker
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichiganUSA
| | - Casey M. Godwin
- Cooperative Institute for Great Lakes Research, School for Environment and SustainabilityUniversity of MichiganAnn ArborMichiganUSA
| | - Muhtamim Khanam
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichiganUSA
| | - Ashley M. Burtner
- Cooperative Institute for Great Lakes Research, School for Environment and SustainabilityUniversity of MichiganAnn ArborMichiganUSA
| | - Gregory J. Dick
- Cooperative Institute for Great Lakes Research, School for Environment and SustainabilityUniversity of MichiganAnn ArborMichiganUSA
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMichiganUSA
| | - Vincent J. Denef
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichiganUSA
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14
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Laux M, Piroupo CM, Setubal JC, Giani A. The Raphidiopsis (= Cylindrospermopsis) raciborskii pangenome updated: Two new metagenome-assembled genomes from the South American clade. HARMFUL ALGAE 2023; 129:102518. [PMID: 37951618 DOI: 10.1016/j.hal.2023.102518] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 11/14/2023]
Abstract
Two Raphidiopsis (=Cylindrospermopsis) raciborskii metagenome-assembled genomes (MAGs) were recovered from two freshwater metagenomic datasets sampled in 2011 and 2012 in Pampulha Lake, a hypereutrophic, artificial, shallow reservoir, located in the city of Belo Horizonte (MG), Brazil. Since the late 1970s, the lake has undergone increasing eutrophication pressure, due to wastewater input, leading to the occurrence of frequent cyanobacterial blooms. The major difference observed between PAMP2011 and PAMP2012 MAGs was the lack of the saxitoxin gene cluster in PAMP2012, which also presented a smaller genome, while PAMP2011 presented the complete sxt cluster and all essential proteins and clusters. The pangenome analysis was performed with all Raphidiopsis/Cylindrospermopsis genomes available at NCBI to date, with the addition of PAMP2011 and PAMP2012 MAGs (All33 subset), but also without the South American strains (noSA subset), and only among the South American strains (SA10 and SA8 subsets). We observed a substantial increase in the core genome size for the 'noSA' subset, in comparison to 'All33' subset, and since the core genome reflects the closeness among the pangenome members, the results strongly suggest that the conservation level of the essential gene repertoire seems to be affected by the geographic origin of the strains being analyzed, supporting the existence of a distinct SA clade. The Raphidiopsis pangenome comprised a total of 7943 orthologous protein clusters, and the two new MAGs increased the pangenome size by 11%. The pangenome based phylogenetic relationships among the 33 analyzed genomes showed that the SA genomes clustered together with 99% bootstrap support, reinforcing the metabolic particularity of the Raphidiopsis South American clade, related to its saxitoxin producing unique ability, while also indicating a different evolutionary history due to its geographic isolation.
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Affiliation(s)
- Marcele Laux
- Department of Botany, Phycology Laboratory, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil
| | - Carlos Morais Piroupo
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | - João Carlos Setubal
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | - Alessandra Giani
- Department of Botany, Phycology Laboratory, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil.
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15
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Potvin M, Gauthier J, Langevin C, Mohit V, da Costa NB, Deschênes T, Pomerleau M, Kukavica-Ibrulj I, Verreault D, Comte J, Levesque RC. Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencing. Front Microbiol 2023; 14:1267652. [PMID: 38029199 PMCID: PMC10646836 DOI: 10.3389/fmicb.2023.1267652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
With the increasing occurrence and severity of cyanobacterial harmful algal blooms (cHAB) at the global scale, there is an urgent need for rapid, accurate, accessible, and cost-effective detection tools. Here, we detail the RosHAB workflow, an innovative, in-the-field applicable genomics approach for real-time, early detection of cHAB outbreaks. We present how the proposed workflow offers consistent taxonomic identification of water samples in comparison to traditional microscopic analyses in a few hours and discuss how the generated data can be used to deepen our understanding on cyanobacteria ecology and forecast HABs events. In parallel, processed water samples will be used to iteratively build the International cyanobacterial toxin database (ICYATOX; http://icyatox.ibis.ulaval.ca) containing the analysis of novel cyanobacterial genomes, including phenomics and genomics metadata. Ultimately, RosHAB will (1) improve the accuracy of on-site rapid diagnostics, (2) standardize genomic procedures in the field, (3) facilitate these genomics procedures for non-scientific personnel, and (4) identify prognostic markers for evidence-based decisions in HABs surveillance.
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Affiliation(s)
- Marianne Potvin
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Jeff Gauthier
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Christophe Langevin
- Centre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, Canada
- Groupe de recherche interuniversitaire en limnologie (GRIL), Montréal, QC, Canada
| | - Vani Mohit
- Direction générale de la coordination scientifique et du Centre d’expertise en analyse environnementale du Québec (CEAEQ), Ministère de l’Environnement et de la Lutte contre les changements climatiques, de la Faune et des Parcs (MELCCFP), Québec, QC, Canada
| | - Naíla Barbosa da Costa
- Centre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, Canada
- Groupe de recherche interuniversitaire en limnologie (GRIL), Montréal, QC, Canada
| | - Thomas Deschênes
- Centre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, Canada
| | - Maude Pomerleau
- Centre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, Canada
| | - Irena Kukavica-Ibrulj
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Daniel Verreault
- Direction générale de la coordination scientifique et du Centre d’expertise en analyse environnementale du Québec (CEAEQ), Ministère de l’Environnement et de la Lutte contre les changements climatiques, de la Faune et des Parcs (MELCCFP), Québec, QC, Canada
| | - Jérôme Comte
- Centre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, Canada
- Groupe de recherche interuniversitaire en limnologie (GRIL), Montréal, QC, Canada
| | - Roger C. Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
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16
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Wang L, Ding R, He S, Wang Q, Zhou Y. A Pipeline for Constructing Reference Genomes for Large Cohort-Specific Metagenome Compression. Microorganisms 2023; 11:2560. [PMID: 37894218 PMCID: PMC10609127 DOI: 10.3390/microorganisms11102560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
Metagenomic data compression is very important as metagenomic projects are facing the challenges of larger data volumes per sample and more samples nowadays. Reference-based compression is a promising method to obtain a high compression ratio. However, existing microbial reference genome databases are not suitable to be directly used as references for compression due to their large size and redundancy, and different metagenomic cohorts often have various microbial compositions. We present a novel pipeline that generated simplified and tailored reference genomes for large metagenomic cohorts, enabling the reference-based compression of metagenomic data. We constructed customized reference genomes, ranging from 2.4 to 3.9 GB, for 29 real metagenomic datasets and evaluated their compression performance. Reference-based compression achieved an impressive compression ratio of over 20 for human whole-genome data and up to 33.8 for all samples, demonstrating a remarkable 4.5 times improvement than the standard Gzip compression. Our method provides new insights into reference-based metagenomic data compression and has a broad application potential for faster and cheaper data transfer, storage, and analysis.
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Affiliation(s)
- Linqi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.W.); (Q.W.)
| | - Renpeng Ding
- MGI Tech, Shenzhen 518083, China; (R.D.); (S.H.)
| | - Shixu He
- MGI Tech, Shenzhen 518083, China; (R.D.); (S.H.)
| | - Qinyu Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.W.); (Q.W.)
| | - Yan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.W.); (Q.W.)
- MGI Tech, Shenzhen 518083, China; (R.D.); (S.H.)
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17
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Xue X, Su X, Zhou L, Ji J, Qin Z, Liu J, Li K, Wang H, Wang Z. Antibiotic-Induced Recruitment of Specific Algae-Associated Microbiome Enhances the Adaptability of Chlorella vulgaris to Antibiotic Stress and Incidence of Antibiotic Resistance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13336-13345. [PMID: 37642958 DOI: 10.1021/acs.est.3c02801] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Insights into the symbiotic relation between eukaryotic hosts and their microbiome lift the curtain on the crucial roles of microbes in host fitness, behavior, and ecology. However, it remains unclear whether and how abiotic stress shapes the microbiome and further affects host adaptability. This study first investigated the effect of antibiotic exposure on behavior across varying algae taxa at the community level. Chlorophyta, in particular Chlorella vulgaris, exhibited remarkable adaptability to antibiotic stress, leading to their dominance in phytoplankton communities. Accordingly, we isolated C. vulgaris strains and compared the growth of axenic and nonaxenic ones under antibiotic conditions. The positive roles of antibiotics in algal growth were apparent only in the presence of bacteria. Results of 16S rRNA sequencing further revealed that antibiotic challenges resulted in the recruitment of specific bacterial consortia in the phycosphere, whose functions were tightly linked to the host growth promotion and adaptability enhancement. In addition, the algal phycosphere was characterized with 47-fold higher enrichment capability of antibiotic resistance genes (ARGs) than the surrounding water. Under antibiotic stress, specific ARG profiles were recruited in C. vulgaris phycosphere, presumably driven by the specific assembly of bacterial consortia and mobile genetic elements induced by antibiotics. Moreover, the antibiotics even enhanced the dissemination potential of the bacteria carrying ARGs from the algal phycosphere to broader environmental niches. Overall, this study provides an in-depth understanding into the potential functional significance of antibiotic-mediated recruitment of specific algae-associated bacteria for algae adaptability and ARG proliferation in antibiotic-polluted waters.
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Affiliation(s)
- Xue Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoyue Su
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linjun Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiaqi Ji
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ziwei Qin
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jialin Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kaiqi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - He Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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18
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Vos M. Accessory microbiomes. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37167086 DOI: 10.1099/mic.0.001332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In microbiome research, considerable effort has been invested in finding core microbiomes, which have been hypothesized to contain the species most important for host function. Much less attention has been paid to microbiome members that are present in only a subset of hosts. Such accessory microbiomes must in large part consist of species that have no effect on fitness, but some will have deleterious effects on fitness (pathogens), and it is also possible that some accessory microbiome members benefit an ecologically distinct subset of hosts. This short paper discusses what we know about accessory microbiomes, specifically by comparing it with the concept of accessory genomes.
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Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, Environment and Sustainability Institute, University of Exeter, Penryn Campus, TR10 9FE, Penryn, UK
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19
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El-Baky NA, Rezk NMF, Amara AA. Arthrospira platensis Variants: A Comparative Study Based on C-phycocyanin Gene and Protein, Habitat, and Growth Conditions. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2023; 11:663. [DOI: 10.3390/jmse11030663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
This study aimed to map the differences between Arthrospira sp. and Arthrospira platensis strains and variants from the order Oscillatoriales at the gene and protein levels of C-phycocyanin alpha chain via multiple alignment, phylogenetic trees of species, and analysis of the nucleotide and amino acid composition of the studied sequences. The links between gene/protein and environmental features of the habitat or source of isolation were also investigated. Phycocyanin was extracted from three A. platensis strains: an Egyptian isolate cultivated in the laboratory under static conditions in a highly saline medium and two commercial products. The French commercial strain showed the highest extraction yield but the lowest C-phycocyanin purity, and the color intensity of the extracted pigment from the Egyptian isolate was significantly weaker than those of the two commercial strains. All the analyzed species and strains had GC content of more than 54.5% in C-phycocyanin alpha chain gene and showed high abundance of alanine, an amino acid encoded exclusively by GC-biased codons, in their protein. The frequencies of the acidic amino acids aspartic acid and glutamic acid were 5.2% and 5.0% on average, respectively, which were slightly higher than those of the basic residues (4.3% arginine, 0.6% histidine, and 5.0% lysine). Data relating to the isolation source of most of the analyzed species revealed harsh conditions, such as high alkalinity, salinity, CO2 saturation, and/or temperature. These findings may link the gene/protein of C-phycocyanin, which is one of the most important bioactive proteins of A. platensis, to the adaptation of this organism to harsh environmental conditions and associate the color of the pigment to cultivation conditions and/or isolation source.
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Affiliation(s)
- Nawal Abd El-Baky
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
| | - Neama Mahmoud Fattouh Rezk
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
| | - Amro A. Amara
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
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20
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Determinants of Total and Active Microbial Communities Associated with Cyanobacterial Aggregates in a Eutrophic Lake. mSystems 2023; 8:e0099222. [PMID: 36927063 PMCID: PMC10134853 DOI: 10.1128/msystems.00992-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Cyanobacterial aggregates (CAs) comprised of photosynthetic and phycospheric microorganisms are often the cause of cyanobacterial blooms in eutrophic freshwater lakes. Although phylogenetic diversity in CAs has been extensively studied, much less was understood about the activity status of microorganisms inside CAs and determinants of their activities. In this study, the 16S rRNA gene (rDNA)-based total communities within CAs in Lake Taihu of China were analyzed over a period of 6 months during the bloom season; the 16S rRNA-based active communities during daytime, nighttime, and under anoxic conditions were also profiled. Synchronous turnover of both cyanobacterial and phycospheric communities was observed, suggesting the presence of close interactions. The rRNA/rDNA ratio-based relative activities of individual taxa were predominantly determined by their rDNA-based relative abundances. In particular, high-abundance taxa demonstrated comparatively lower activities, whereas low-abundance taxa were generally more active. In comparison, hydrophysicochemical factors as well as diurnal and redox conditions showed much less impact on relative activities of microbial taxa within CAs. Nonetheless, total and active communities exhibited differences in community assembly processes, the former of which were almost exclusively controlled by homogeneous selection during daytime and under anoxia. Taken together, the results from this study provide novel insights into the relationships among microbial activities, community structure, and environmental conditions and highlight the importance of further exploring the regulatory mechanisms of microbial activities at the community level. IMPORTANCE Cyanobacterial aggregates are important mediators of biogeochemical cycles in eutrophic lakes during cyanobacterial blooms, yet regulators of microbial activities within them are not well understood. This study revealed rDNA-based abundances strongly affected the relative activities of microbial taxa within Microcystis aggregates, as well as trade-off effects between microbial abundances and activities. Environmental conditions further improved the levels of relative activities and affected community assembly mechanisms in phycospheric communities. The relationships among microbial activities, abundances, and environmental conditions improve our understanding of the regulatory mechanisms of microbial activities in cyanobacterial aggregates and also provide a novel clue for studying determinants of microbial activities in other ecosystems.
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Tanabe Y, Yamaguchi H, Yoshida M, Kai A, Okazaki Y. Characterization of a bloom-associated alphaproteobacterial lineage, 'Candidatus Phycosocius': insights into freshwater algal-bacterial interactions. ISME COMMUNICATIONS 2023; 3:20. [PMID: 36906708 PMCID: PMC10008586 DOI: 10.1038/s43705-023-00228-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/13/2023]
Abstract
Marine bacterial lineages associated with algal blooms, such as the Roseobacter clade, have been well characterized in ecological and genomic contexts, yet such lineages have rarely been explored in freshwater blooms. This study performed phenotypic and genomic analyses of an alphaproteobacterial lineage 'Candidatus Phycosocius' (denoted the CaP clade), one of the few lineages ubiquitously associated with freshwater algal blooms, and described a novel species: 'Ca. Phycosocius spiralis.' Phylogenomic analyses indicated that the CaP clade is a deeply branching lineage in the Caulobacterales. Pangenome analyses revealed characteristic features of the CaP clade: aerobic anoxygenic photosynthesis and essential vitamin B auxotrophy. Genome size varies widely among members of the CaP clade (2.5-3.7 Mb), likely a result of independent genome reductions at each lineage. This includes a loss of tight adherence pilus genes (tad) in 'Ca. P. spiralis' that may reflect its adoption of a unique spiral cell shape and corkscrew-like burrowing activity at the algal surface. Notably, quorum sensing (QS) proteins showed incongruent phylogenies, suggesting that horizontal transfers of QS genes and QS-involved interactions with specific algal partners might drive CaP clade diversification. This study elucidates the ecophysiology and evolution of proteobacteria associated with freshwater algal blooms.
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Affiliation(s)
- Yuuhiko Tanabe
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki, 305-8506, Japan.
- Algae Biomass and Energy System R&D Center, University of Tsukuba, Ibaraki, 305-8572, Japan.
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki, 305-8506, Japan
| | - Masaki Yoshida
- Algae Biomass and Energy System R&D Center, University of Tsukuba, Ibaraki, 305-8572, Japan
| | - Atsushi Kai
- Algae Biomass and Energy System R&D Center, University of Tsukuba, Ibaraki, 305-8572, Japan
| | - Yusuke Okazaki
- Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan
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Cyanobacterial Harmful Bloom Lipopolysaccharides Induce Pro-Inflammatory Effects in Immune and Intestinal Epithelial Cells In Vitro. Toxins (Basel) 2023; 15:toxins15030169. [PMID: 36977060 PMCID: PMC10058507 DOI: 10.3390/toxins15030169] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/02/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Freshwater cyanobacterial harmful blooms (CyanoHABs) produce a variety of toxic and bioactive compounds including lipopolysaccharides (LPSs). The gastrointestinal tract can be exposed to them via contaminated water even during recreational activities. However, there is no evidence of an effect of CyanoHAB LPSs on intestinal cells. We isolated LPSs of four CyanoHABs dominated by different cyanobacterial species and LPSs of four laboratory cultures representing the respective dominant cyanobacterial genera. Two intestinal and one macrophage cell lines were used to detect in vitro pro-inflammatory activity of the LPS. All LPSs isolated from CyanoHABs and laboratory cultures induced cytokines production in at least one in vitro model, except for LPSs from the Microcystis PCC7806 culture. LPSs isolated from cyanobacteria showed unique migration patterns in SDS-PAGE that were qualitatively distinct from those of endotoxins from Gram-negative bacteria. There was no clear relationship between the biological activity of the LPS and the share of genomic DNA of Gram-negative bacteria in the respective biomass. Thus, the total share of Gram-negative bacteria, or the presence of Escherichia coli-like LPSs, did not explain the observed pro-inflammatory activities. The pro-inflammatory properties of environmental mixtures of LPSs from CyanoHABs indicate their human health hazards, and further attention should be given to their assessment and monitoring.
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Lang-Yona N, Alster A, Cummings D, Freiman Z, Kaplan-Levy R, Lupu A, Malinsky-Rushansky N, Ninio S, Sukenik A, Viner-Mozzini Y, Zohary T. Gloeotrichia pisum in Lake Kinneret: A successful epiphytic cyanobacterium. JOURNAL OF PHYCOLOGY 2023; 59:97-110. [PMID: 36371652 DOI: 10.1111/jpy.13301] [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: 04/19/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
With climate change and re-oligotrophication of lakes due to restoration efforts, the relative importance of benthic cyanobacteria is increasing, but they are much less studied than their planktonic counterparts. Following a major water level rise event that inundated massive reed stands in Lake Kinneret, Israel, we discovered the appearance of a vast abundance of Gloeotrichia pisum (cyanobacteria). This provided an opportunity to investigate the biology and ecology of a benthic epiphytic colonial cyanobacterium, proliferating under altered environmental conditions, with possible toxin production potential and as a model for an invasive epiphyte. The species was identified by its typical morphology, and by sequencing its 16S rRNA gene and the intragenic space. We report on the abundance and spatial distribution of the detected colonies, their morphological characteristics, and pigment composition. High phycoerythrin content provides a brownish color and supports growth at low light levels. Genomic community composition analysis revealed that G. pisum colonies host a diverse microbial community of microalgae, cyanobacteria, bacteria, and archaea with a conserved and characteristic taxonomic composition. The Synechococcales order showed high relative abundance in the colony, as well as other prokaryotes producing secondary metabolites, such as the rhodopsin producer Pseudorhodobacter. The microbial consortium in the colonies performed nitrogen fixation. The diazotroph's phylogenetic relations were demonstrated. Tests for the presence of cyanotoxins (microcystin and cylindrospermopsin) proved negative. This study is the first documentation of this genus in Israel, providing insights into the invasive nature of G. pisum and the ecological implications of its appearance in a lake ecosystem.
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Affiliation(s)
- Naama Lang-Yona
- Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, 14950, Israel
| | - Alla Alster
- Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, 14950, Israel
| | - David Cummings
- Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, 14950, Israel
| | - Zohar Freiman
- Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, 14950, Israel
| | - Ruth Kaplan-Levy
- Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, 14950, Israel
| | - Achsa Lupu
- Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, 14950, Israel
| | | | - Shira Ninio
- Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, 14950, Israel
| | - Assaf Sukenik
- Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, 14950, Israel
| | - Yehudith Viner-Mozzini
- Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, 14950, Israel
| | - Tamar Zohary
- Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, 14950, Israel
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Te SH, Kok JWK, Luo R, You L, Sukarji NH, Goh KC, Sim ZY, Zhang D, He Y, Gin KYH. Coexistence of Synechococcus and Microcystis Blooms in a Tropical Urban Reservoir and Their Links with Microbiomes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1613-1624. [PMID: 36653016 PMCID: PMC9894078 DOI: 10.1021/acs.est.2c04943] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Bacteria play a crucial role in driving ecological processes in aquatic ecosystems. Studies have shown that bacteria-cyanobacteria interactions contributed significantly to phytoplankton dynamics. However, information on the contribution of bacterial communities to blooms remains scarce. Here, we tracked changes in the bacterial community during the development of a cyanobacterial bloom in an equatorial estuarine reservoir. Two forms of blooms were observed simultaneously corresponding to the lotic and lentic characteristics of the sampling sites where significant spatial variabilities in physicochemical water quality, cyanobacterial biomass, secondary metabolites, and cyanobacterial/bacterial compositions were detected. Microcystis dominated the upstream sites during peak periods and were succeeded by Synechococcus when the bloom subsided. For the main body of the reservoir, a mixed bloom featuring coccoid and filamentous cyanobacteria (Microcystis, Synechococcus, Planktothricoides, Nodosilinea, Raphidiopsis, and Prochlorothrix) was observed. Concentrations of the picocyanobacteria Synechococcus remained high throughout the study, and their positive correlations with cylindrospermopsin and anatoxin-a suggested that they could produce cyanotoxins, which pose more damaging impacts than previously supposed. Succession of different cyanobacteria (Synechococcus and Microcystis) following changes in nutrient composition and ionic strength was demonstrated. The microbiomes associated with blooms were unique to the dominant cyanobacteria. Generic and specialized bloom biomarkers for the Microcystis and downstream mixed blooms were also identified. Microscillaceae, Chthoniobacteraceae, and Roseomonas were the major heterotrophic bacteria associated with Microcystis bloom, whereas Phycisphaeraceae and Methylacidiphilaceae were the most prominent groups for the Synechococcus bloom. Collectively, bacterial community can be greatly deviated by the geological condition, monsoon season, cyanobacterial density, and dominant cyanobacteria.
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Affiliation(s)
- Shu Harn Te
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Jerome Wai Kit Kok
- Department
of Civil and Environmental Engineering, National University of Singapore, Blk E1A-07-03, 1 Engineering Drive 2, 117576 Singapore
| | - Rong Luo
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Luhua You
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Nur Hanisah Sukarji
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Kwan Chien Goh
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Zhi Yang Sim
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Dong Zhang
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Yiliang He
- School
of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Karina Yew-Hoong Gin
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
- Department
of Civil and Environmental Engineering, National University of Singapore, Blk E1A-07-03, 1 Engineering Drive 2, 117576 Singapore
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Zhu J, Yang F, Du K, Wei ZL, Wu QF, Chen Y, Li WF, Li Q, Zhou CZ. Phylogenomics of five Pseudanabaena cyanophages and evolutionary traces of horizontal gene transfer. ENVIRONMENTAL MICROBIOME 2023; 18:3. [PMID: 36639816 PMCID: PMC9837993 DOI: 10.1186/s40793-023-00461-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanobacterial bloom. Systematic isolation and characterization of freshwater cyanophages might provide a biological solution to control the awful blooms. However, genomic sequences and related investigations on the freshwater cyanophages remain very limited to date. RESULTS Following our recently reported five cyanophages Pam1~Pam5 from Lake Chaohu in China, here we isolated another five cyanophages, termed Pan1~Pan5, which infect the cyanobacterium Pseudanabaena sp. Chao 1811. Whole-genome sequencing showed that they all contain a double-stranded DNA genome of 37.2 to 72.0 kb in length, with less than half of the putative open reading frames annotated with known functions. Remarkably, the siphophage Pan1 encodes an auxiliary metabolic gene phoH and constitutes, together with the host, a complete queuosine modification pathway. Proteomic analyses revealed that although Pan1~Pan5 are distinct from each other in evolution, Pan1 and Pan3 are somewhat similar to our previously identified cyanophages Pam3 and Pam1 at the genomic level, respectively. Moreover, phylogenetic analyses suggested that Pan1 resembles the α-proteobacterial phage vB_DshS-R5C, revealing direct evidence for phage-mediated horizontal gene transfer between cyanobacteria and α-proteobacteria. CONCLUSION In addition to the previous reports of Pam1~Pam5, the present findings on Pan1~Pan5 largely enrich the library of reference freshwater cyanophages. The abundant genomic information provides a pool to identify novel genes and proteins of unknown function. Moreover, we found for the first time the evolutionary traces in the cyanophage that horizontal gene transfer might occur at the level of not only inter-species, but even inter-phylum. It indicates that the bacteriophage or cyanophage could be developed as a powerful tool for gene manipulation among various species or phyla.
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Affiliation(s)
- Jie Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Feng Yang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Kang Du
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Zi-Lu Wei
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Qing-Fa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Yuxing Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Wei-Fang Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Qiong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Cong-Zhao Zhou
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
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Halary S, Duperron S, Demay J, Duval C, Hamlaoui S, Piquet B, Reinhardt A, Bernard C, Marie B. Metagenome-Based Exploration of Bacterial Communities Associated with Cyanobacteria Strains Isolated from Thermal Muds. Microorganisms 2022; 10:microorganisms10122337. [PMID: 36557590 PMCID: PMC9785279 DOI: 10.3390/microorganisms10122337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
Cyanobacteria constitute a pioneer colonizer of specific environments for whom settlement in new biotopes precedes the establishment of composite microbial consortia. Some heterotrophic bacteria constitute cyanobacterial partners that are considered as their cyanosphere, being potentially involved in mutualistic relationships through the exchange and recycling of key nutrients and the sharing of common goods. Several non-axenic cyanobacterial strains have been recently isolated, along with their associated cyanospheres, from the thermal mud of Balaruc-les-Bains (France) and the biofilms of the retention basin where they develop. The community structure and relationships among the members of the isolated cyanobacterial strains were characterized using a metagenomic approach combined with taxonomic and microscopic descriptions of the microbial consortia. The results provided insights into the potential role and metabolic capabilities of the microorganisms of thermal mud-associated cyanobacterial biofilms. Thus, the physical proximity, host-specificity, and genetic potential functions advocate for their complementarity between cyanobacteria and their associated microbiota. Besides these findings, our results also highlighted the great influence of the reference protein database chosen for performing functional annotation of the metagenomes from organisms of the cyanosphere and the difficulty of selecting one unique database that appropriately covers both autotroph and heterotroph metabolic specificities.
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Affiliation(s)
- Sébastien Halary
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Sébastien Duperron
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Justine Demay
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
- Thermes de Balaruc-Les-Bains, 1 rue du Mont Saint-Clair BP 45, 34540 Balaruc-Les-Bains, France
| | - Charlotte Duval
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Sahima Hamlaoui
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Bérénice Piquet
- Electron Microscopy Platform, Muséum National d’Histoire Naturelle, CP 39, 12 rue Buffon, CEDEX 05, 75231 Paris, France
| | - Anita Reinhardt
- Thermes de Balaruc-Les-Bains, 1 rue du Mont Saint-Clair BP 45, 34540 Balaruc-Les-Bains, France
| | - Cécile Bernard
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Benjamin Marie
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
- Correspondence:
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Le VV, Srivastava A, Ko SR, Ahn CY, Oh HM. Microcystis colony formation: Extracellular polymeric substance, associated microorganisms, and its application. BIORESOURCE TECHNOLOGY 2022; 360:127610. [PMID: 35840029 DOI: 10.1016/j.biortech.2022.127610] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Microcystis sp., amongst the most prevalent bloom-forming cyanobacteria, is typically found as a colonial form with multiple microorganisms embedded in the mucilage known as extracellular polymeric substance. The colony-forming ability of Microcystis has been thoroughly investigated, as has the connection between Microcystis and other microorganisms, which is crucial for colony development. The following are the key subjects to comprehend Microcystis bloom in depth: 1) key issues related to the Microcystis bloom, 2) features and functions of extracellular polymeric substance, as well as diversity of associated microorganisms, and 3) applications of Microcystis-microorganisms interaction including bloom control, polluted water bioremediation, and bioactive compound production. Future research possibilities and recommendations regarding Microcystis-microorganism interactions and their significance in Microcystis colony formation are also explored. More information on such interactions, as well as the mechanism of Microcystis colony formation, can bring new insights into cyanobacterial bloom regulation and a better understanding of the aquatic ecosystem.
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Affiliation(s)
- Ve Van Le
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Ankita Srivastava
- Department of Botany, Siddharth University, Kapilvastu, Siddharth Nagar 272202, Uttar Pradesh, India
| | - So-Ra Ko
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34141, Republic of Korea.
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Uptake of Phytoplankton-Derived Carbon and Cobalamins by Novel Acidobacteria Genera in Microcystis Blooms Inferred from Metagenomic and Metatranscriptomic Evidence. Appl Environ Microbiol 2022; 88:e0180321. [PMID: 35862730 PMCID: PMC9317899 DOI: 10.1128/aem.01803-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Interactions between bacteria and phytoplankton can influence primary production, community composition, and algal bloom development. However, these interactions are poorly described for many consortia, particularly for freshwater bloom-forming cyanobacteria. Here, we assessed the gene content and expression of two uncultivated Acidobacteria from Lake Erie Microcystis blooms. These organisms were targeted because they were previously identified as important catalase producers in Microcystis blooms, suggesting that they protect Microcystis from H2O2. Metatranscriptomics revealed that both Acidobacteria transcribed genes for uptake of organic compounds that are known cyanobacterial products and exudates, including lactate, glycolate, amino acids, peptides, and cobalamins. Expressed genes for amino acid metabolism and peptide transport and degradation suggest that use of amino acids and peptides by Acidobacteria may regenerate nitrogen for cyanobacteria and other organisms. The Acidobacteria genomes lacked genes for biosynthesis of cobalamins but expressed genes for its transport and remodeling. This indicates that the Acidobacteria obtained cobalamins externally, potentially from Microcystis, which has a complete gene repertoire for pseudocobalamin biosynthesis; expressed them in field samples; and produced pseudocobalamin in axenic culture. Both Acidobacteria were detected in Microcystis blooms worldwide. Together, the data support the hypotheses that uncultured and previously unidentified Acidobacteria taxa exchange metabolites with phytoplankton during harmful cyanobacterial blooms and influence nitrogen available to phytoplankton. Thus, novel Acidobacteria may play a role in cyanobacterial physiology and bloom development. IMPORTANCE Interactions between heterotrophic bacteria and phytoplankton influence competition and successions between phytoplankton taxa, thereby influencing ecosystem-wide processes such as carbon cycling and algal bloom development. The cyanobacterium Microcystis forms harmful blooms in freshwaters worldwide and grows in buoyant colonies that harbor other bacteria in their phycospheres. Bacteria in the phycosphere and in the surrounding community likely influence Microcystis physiology and ecology and thus the development of freshwater harmful cyanobacterial blooms. However, the impacts and mechanisms of interaction between bacteria and Microcystis are not fully understood. This study explores the mechanisms of interaction between Microcystis and uncultured members of its phycosphere in situ with population genome resolution to investigate the cooccurrence of Microcystis and freshwater Acidobacteria in blooms worldwide.
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