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Zhang J, Zhang F, Dong Z, Zhang W, Sun T, Chen L. Response and acclimation of cyanobacteria to acidification: A comprehensive review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173978. [PMID: 38897479 DOI: 10.1016/j.scitotenv.2024.173978] [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: 04/17/2024] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
Cyanobacteria, as vital components of aquatic ecosystems, face increasing challenges due to acidification driven by various anthropogenic and natural factors. Understanding how cyanobacteria adapt and respond to acidification is crucial for predicting their ecological dynamics and potential impacts on ecosystem health. This comprehensive review synthesizes current knowledge on the acclimation mechanisms and responses of cyanobacteria to acidification stress. Detailly, ecological roles of cyanobacteria were firstly briefly concluded, followed by the effects of acidification on aquatic ecosystems and cyanobacteria. Then the review focuses on the physiological, biochemical, and molecular strategies employed by cyanobacteria to cope with acidification stress, highlighting key adaptive mechanisms and their ecological implications. Finally, a summary of strategies to enhance acid resistance in cyanobacteria and future directions was discussed. Utilizing omics data and machine learning technology to build a cyanobacterial acid regulatory network allows for predicting the impact of acidification on cyanobacteria and inferring its broader effects on ecosystems. Additionally, acquiring acid-tolerant chassis cells of cyanobacteria through innovative techniques facilitates the advancement of environmentally friendly production of acidic chemicals. By synthesizing empirical evidence and theoretical frameworks, this review aims to elucidate the complex interplay between cyanobacteria and acidification stressors, providing insights for future research directions and ecosystem management strategies.
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Affiliation(s)
- Jie Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China
| | - Fenfang Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China
| | - Zhengxin Dong
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, PR China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, PR China..
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China.
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Chen Y, Jiang Y, He Z, Gao J, Li R, Yu G. First report of PST-producing Microseira wollei from China reveals its novel toxin profile. HARMFUL ALGAE 2024; 137:102655. [PMID: 39003021 DOI: 10.1016/j.hal.2024.102655] [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: 01/16/2024] [Revised: 04/26/2024] [Accepted: 05/21/2024] [Indexed: 07/15/2024]
Abstract
Microseira wollei, a globally distributed freshwater bloom-forming benthic cyanobacterium, is known for its production of cyanotoxins and taste and odor (T&O). While CYN (Cylindrospermopsin)-producing populations of M. wollei are confined to Australia, PST (Paralytic shellfish toxins)-producing populations have been exclusively documented in North America. In this study, four benthic cyanobacterial strains, isolated from West Lake in China, were identified as M. wollei based on morphological and phylogenetic analyses. Detection of sxtA gene and UPLC-MS/MS analysis conclusively confirmed the PST-producing capability of M. wollei CHAB5998. In the phylogenetic tree of 16S rDNA, M. wollei strains formed a monophyletic group with two subclades. Notably, non-PST-producing Chinese strains clustered with Australian strains in Clade II, while all other strains, including PST-producing ones, clustered in Clade I. Additionally, CHAB5998 contains ten PST variants, of which STX, NEO, GTX2, GTX3, GTX5 and C1 were identified for the first time in M. wollei. Sequence analysis of PST biosynthetic gene cluster (sxt) genes indicated potential base variations, gene rearrangements, insertions, and deletions in the strain CHAB5998. Also, sxt gene has a longer evolutionary history in M. wollei than that in cyanobacteria from Nostocales. Multiple recombination breakpoints detected in sxt genes and the inconsistency in the topology of the phylogenetic trees between sxt and 16S rDNA suggested that multiple horizontal gene transfers (HGT) have occurred. Overall, the present study marks the first documented occurrence of PST-producing M. wollei outside of North America and identifies it as the first toxic freshwater benthic cyanobacterium in China. This revelation implies that benthic cyanobacteria may pose a higher environmental risk in China than previously acknowledged.
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Affiliation(s)
- Youxin Chen
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yongguang Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, 430074, China
| | - Zhongshi He
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, 21202, USA
| | - Jin Gao
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Renhui Li
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China; National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Wenzhou, Zhejiang, 325035, China
| | - Gongliang Yu
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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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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4
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Liu X, Tang K, Hu J. Application of Cyanobacteria as Chassis Cells in Synthetic Biology. Microorganisms 2024; 12:1375. [PMID: 39065143 PMCID: PMC11278661 DOI: 10.3390/microorganisms12071375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Synthetic biology is an exciting new area of research that combines science and engineering to design and build new biological functions and systems. Predictably, with the development of synthetic biology, more efficient and economical photosynthetic microalgae chassis will be successfully constructed, making it possible to break through laboratory research into large-scale industrial applications. The synthesis of a range of biochemicals has been demonstrated in cyanobacteria; however, low product titers are the biggest barrier to the commercialization of cyanobacterial biotechnology. This review summarizes the applied improvement strategies from the perspectives of cyanobacteria chassis cells and synthetic biology. The harvest advantages of cyanobacterial products and the latest progress in improving production strategies are discussed according to the product status. As cyanobacteria synthetic biology is still in its infancy, apart from the achievements made, the difficulties and challenges in the application and development of cyanobacteria genetic tool kits in biochemical synthesis, environmental monitoring, and remediation were assessed.
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Affiliation(s)
| | | | - Jinlu Hu
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China; (X.L.); (K.T.)
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Li H, Li R, Kang J, Hii KS, Mohamed HF, Xu X, Luo Z. Okeanomitos corallinicola gen. and sp. nov. (Nostocales, Cyanobacteria), a new toxic marine heterocyte-forming Cyanobacterium from a coral reef. JOURNAL OF PHYCOLOGY 2024. [PMID: 38943258 DOI: 10.1111/jpy.13473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/05/2024] [Accepted: 05/11/2024] [Indexed: 07/01/2024]
Abstract
Cyanobacterial mats supplanting coral and spreading coral diseases in tropical reefs, intensified by environmental shifts caused by human-induced pressures, nutrient enrichment, and global climate change, pose grave risks to the survival of coral ecosystems. In this study, we characterized Okeanomitos corallinicola gen. and sp. nov., a newly discovered toxic marine heterocyte-forming cyanobacterium isolated from a coral reef ecosystem of the South China Sea. Phylogenetic analysis, based on the 16S rRNA gene and the secondary structure of the 16S-23S rRNA intergenic region, placed this species in a clade distinct from closely related genera, that is, Sphaerospermopsis stricto sensu, Raphidiopsis, and Amphiheterocytum. The O. corallinicola is a marine benthic species lacking gas vesicles, distinguishing it from other members of the Aphanizomenonaceae family. The genome of O. corallinicola is large and exhibits diverse functional capabilities, potentially contributing to the resilience and adaptability of coral reef ecosystems. In vitro assays revealed that O. corallinicola demonstrates notable cytotoxic activity against various cancer cell lines, suggesting its potential as a source of novel anticancer compounds. Furthermore, the identification of residual saxitoxin biosynthesis function in the genome of O. corallinicola, a marine cyanobacteria, supports the theory that saxitoxin genes in cyanobacteria and dinoflagellates may have been horizontally transferred between them or may have originated from a shared ancestor. Overall, the identification and characterization of O. corallinicola provides valuable contributions to cyanobacterial taxonomy, offering novel perspectives on complex interactions within coral reef ecosystems.
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Affiliation(s)
- Haiyan Li
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Institute of Marine Drugs/Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Renhui Li
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, China
| | - Jianhua Kang
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Kieng Soon Hii
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, Bachok, Kelantan, Malaysia
| | - Hala F Mohamed
- Botany & Microbiology Department, Faculty of Science, Al-Azhar University (Girls Branch), Cairo, Egypt
| | - Xinya Xu
- Institute of Marine Drugs/Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Zhaohe Luo
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, China
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Lyons TW, Tino CJ, Fournier GP, Anderson RE, Leavitt WD, Konhauser KO, Stüeken EE. Co-evolution of early Earth environments and microbial life. Nat Rev Microbiol 2024:10.1038/s41579-024-01044-y. [PMID: 38811839 DOI: 10.1038/s41579-024-01044-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/31/2024]
Abstract
Two records of Earth history capture the evolution of life and its co-evolving ecosystems with interpretable fidelity: the geobiological and geochemical traces preserved in rocks and the evolutionary histories captured within genomes. The earliest vestiges of life are recognized mostly in isotopic fingerprints of specific microbial metabolisms, whereas fossils and organic biomarkers become important later. Molecular biology provides lineages that can be overlayed on geologic and geochemical records of evolving life. All these data lie within a framework of biospheric evolution that is primarily characterized by the transition from an oxygen-poor to an oxygen-rich world. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, fundamental transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and their links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. The evolution of microbial life and its ecological impacts directly mirror the Earth's chemical and physical evolution through cause-and-effect relationships.
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Affiliation(s)
- Timothy W Lyons
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA.
| | - Christopher J Tino
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
| | - Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rika E Anderson
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- Biology Department, Carleton College, Northfield, MN, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, USA
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Eva E Stüeken
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews, UK
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Pawar S, Pingale P, Garkal A, Osmani RAM, Gajbhiye K, Kulkarni M, Pardeshi K, Mehta T, Rajput A. Unlocking the potential of nanocarrier-mediated mRNA delivery across diverse biomedical frontiers: A comprehensive review. Int J Biol Macromol 2024; 267:131139. [PMID: 38615863 DOI: 10.1016/j.ijbiomac.2024.131139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/23/2024] [Accepted: 03/23/2024] [Indexed: 04/16/2024]
Abstract
Messenger RNA (mRNA) has gained marvelous attention for managing and preventing various conditions like cancer, Alzheimer's, infectious diseases, etc. Due to the quick development and success of the COVID-19 mRNA-based vaccines, mRNA has recently grown in prominence. A lot of products are in clinical trials and some are already FDA-approved. However, still improvements in line of optimizing stability and delivery, reducing immunogenicity, increasing efficiency, expanding therapeutic applications, scalability and manufacturing, and long-term safety monitoring are needed. The delivery of mRNA via a nanocarrier system gives a synergistic outcome for managing chronic and complicated conditions. The modified nanocarrier-loaded mRNA has excellent potential as a therapeutic strategy. This emerging platform covers a wide range of diseases, recently, several clinical studies are ongoing and numerous publications are coming out every year. Still, many unexplained physical, biological, and technical problems of mRNA for safer human consumption. These complications were addressed with various nanocarrier formulations. This review systematically summarizes the solved problems and applications of nanocarrier-based mRNA delivery. The modified nanocarrier mRNA meaningfully improved mRNA stability and abridged its immunogenicity issues. Furthermore, several strategies were discussed that can be an effective solution in the future for managing complicated diseases.
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Affiliation(s)
- Smita Pawar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, N.P. Marg, Matunga (E), Mumbai 400019, Maharashtra, India
| | - Prashant Pingale
- Department of Pharmaceutics, GES's Sir Dr. M. S. Gosavi College of Pharmaceutical Education and Research, Nashik 422005, Maharashtra, India
| | - Atul Garkal
- Department of Pharmaceutics, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujarat, India; Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Riyaz Ali M Osmani
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
| | - Kavita Gajbhiye
- Department of Pharmaceutics, Bharti Vidyapeeth Deemed University, Poona College of Pharmacy, Erandwane, Pune 411038, Maharashtra, India
| | - Madhur Kulkarni
- SCES's Indira College of Pharmacy, New Pune Mumbai Highway, Tathwade 411033, Pune, Maharashtra, India
| | - Krutika Pardeshi
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Sandip University, Nashik 422213, Maharashtra, India
| | - Tejal Mehta
- Department of Pharmaceutics, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujarat, India
| | - Amarjitsing Rajput
- Department of Pharmaceutics, Bharti Vidyapeeth Deemed University, Poona College of Pharmacy, Erandwane, Pune 411038, Maharashtra, India.
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Liu Y, Guo W, Wei C, Huang H, Nan F, Liu X, Liu Q, Lv J, Feng J, Xie S. Rainfall-induced changes in aquatic microbial communities and stability of dissolved organic matter: Insight from a Fen river analysis. ENVIRONMENTAL RESEARCH 2024; 246:118107. [PMID: 38181848 DOI: 10.1016/j.envres.2024.118107] [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: 11/12/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]
Abstract
Microbial communities are pivotal in aquatic ecosystems, as they affect water quality, energy dynamics, nutrient cycling, and hydrological stability. This study explored the effects of rainfall on hydrological and photosynthetic parameters, microbial composition, and functional gene profiles in the Fen River. Our results demonstrated that rainfall-induced decreases in stream temperature, dissolved oxygen, pH, total phosphorus, chemical oxygen demand, and dissolved organic carbon concentrations. In contrast, rainfall increased total dissolved solids, salinity, and ammonia-nitrogen concentrations. A detailed microbial community structure analysis revealed that Cyanobacteria was the dominant microbial taxon in the Fen River, accounting for approximately 75% and 25% of the microalgal and bacterial communities, respectively. The abundance of Chlorophyta and Bacillariophyta increased by 47.66% and 29.92%, respectively, whereas the relative abundance of Bacteroidetes decreased by 37.55% under rainfall conditions. Stochastic processes predominantly affected the assembly of the bacterial community on rainy days. Functional gene analysis revealed variations in bacterial functions between sunny (Sun) and rainy (Rain) conditions, particularly in genes associated with the carbon cycle. The 3-oxoacyl-[acyl-carrier-protein] reductase gene was more abundant in the Fen River bacterial community. Particular genes involved in metabolism and environmental information processing, including the acetyl-CoA C-acetyltransferase (atoB), enoyl-CoA hydratase (paaF), and branched-chain amino acid transport system gene (livK), which are integral to environmental information processing, were more abundant in Sun than the Rain conditions. In contrast, the phosphate transport system gene, the galactose metabolic gene, and the pyruvate metabolic gene were more abundant in Rain. The excitation-emission matrix analysis with parallel factor analysis identified four fluorescence components (C1-C4) in the river, which were predominantly protein- (C1) and humic-like (C2-C4) substances. Rainfall affected organic matter production and transport, leading to changes in the degradation and stability of dissolved organic matter. Overall, this study offers insight into how rainfall affects aquatic ecosystems.
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Affiliation(s)
- Yang Liu
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Weinan Guo
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Caihua Wei
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Hanjie Huang
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Fangru Nan
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Xudong Liu
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Qi Liu
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Junping Lv
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Jia Feng
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Shulian Xie
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China.
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Baunach M, Guljamow A, Miguel-Gordo M, Dittmann E. Harnessing the potential: advances in cyanobacterial natural product research and biotechnology. Nat Prod Rep 2024; 41:347-369. [PMID: 38088806 DOI: 10.1039/d3np00045a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Covering: 2000 to 2023Cyanobacteria produce a variety of bioactive natural products that can pose a threat to humans and animals as environmental toxins, but also have potential for or inspire pharmaceutical use. As oxygenic phototrophs, cyanobacteria furthermore hold great promise for sustainable biotechnology. Yet, the necessary tools for exploiting their biotechnological potential have so far been established only for a few model strains of cyanobacteria, while large untapped biosynthetic resources are hidden in slow-growing cyanobacterial genera that are difficult to access by genetic techniques. In recent years, several approaches have been developed to circumvent the bottlenecks in cyanobacterial natural product research. Here, we summarize current progress that has been made in unlocking or characterizing cryptic metabolic pathways using integrated omics techniques, orphan gene cluster activation, use of genetic approaches in original producers, heterologous expression and chemo-enzymatic techniques. We are mainly highlighting genomic mining concepts and strategies towards high-titer production of cyanobacterial natural products from the last 10 years and discuss the need for further research developments in this field.
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Affiliation(s)
- Martin Baunach
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
- University of Bonn, Institute of Pharmaceutical Biology, Nußallee 6, 53115 Bonn, Germany
| | - Arthur Guljamow
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - María Miguel-Gordo
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - Elke Dittmann
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
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10
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Kim M, Kim W, Park Y, Jung J, Park W. Lineage-specific evolution of Aquibium, a close relative of Mesorhizobium, during habitat adaptation. Appl Environ Microbiol 2024; 90:e0209123. [PMID: 38412007 PMCID: PMC10952388 DOI: 10.1128/aem.02091-23] [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: 11/17/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
The novel genus Aquibium that lacks nitrogenase was recently reclassified from the Mesorhizobium genus. The genomes of Aquibium species isolated from water were smaller and had higher GC contents than those of Mesorhizobium species. Six Mesorhizobium species lacking nitrogenase were found to exhibit low similarity in the average nucleotide identity values to the other 24 Mesorhizobium species. Therefore, they were classified as the non-N2-fixing Mesorhizobium lineage (N-ML), an evolutionary intermediate species. The results of our phylogenomic analyses and the loss of Rhizobiales-specific fur/mur indicated that Mesorhizobium species may have evolved from Aquibium species through an ecological transition. Halotolerant and alkali-resistant Aquibium and Mesorhizobium microcysteis belonging to N-ML possessed many tripartite ATP-independent periplasmic transporter and sodium/proton antiporter subunits composed of seven genes (mrpABCDEFG). These genes were not present in the N2-fixing Mesorhizobium lineage (ML), suggesting that genes acquired for adaptation to highly saline and alkaline environments were lost during the evolution of ML as the habitat changed to soil. Land-to-water habitat changes in Aquibium species, close relatives of Mesorhizobium species, could have influenced their genomic evolution by the gain and loss of genes. Our study indicated that lineage-specific evolution could have played a significant role in shaping their genome architecture and conferring their ability to thrive in different habitats.IMPORTANCEPhylogenetic analyses revealed that the Aquibium lineage (AL) and non-N2-fixing Mesorhizobium lineage (N-ML) were monophyletically grouped into distinct clusters separate from the N2-fixing Mesorhizobium lineage (ML). The N-ML, an evolutionary intermediate species having characteristics of both ancestral and descendant species, could provide a genomic snapshot of the genetic changes that occur during adaptation. Genomic analyses of AL, N-ML, and ML revealed that changes in the levels of genes related to transporters, chemotaxis, and nitrogen fixation likely reflect adaptations to different environmental conditions. Our study sheds light on the complex and dynamic nature of the evolution of rhizobia in response to changes in their environment and highlights the crucial role of genomic analysis in understanding these processes.
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Affiliation(s)
- Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Yerim Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Jaejoon Jung
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
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Shu HY, Zhao L, Jia Y, Liu FF, Chen J, Chang CM, Jin T, Yang J, Shu WS. CyanoStrainChip: A Novel DNA Microarray Tool for High-Throughput Detection of Environmental Cyanobacteria at the Strain Level. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:5024-5034. [PMID: 38454313 PMCID: PMC10956431 DOI: 10.1021/acs.est.3c11096] [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: 12/30/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/09/2024]
Abstract
Detecting cyanobacteria in environments is an important concern due to their crucial roles in ecosystems, and they can form blooms with the potential to harm humans and nonhuman entities. However, the most widely used methods for high-throughput detection of environmental cyanobacteria, such as 16S rRNA sequencing, typically provide above-species-level resolution, thereby disregarding intraspecific variation. To address this, we developed a novel DNA microarray tool, termed the CyanoStrainChip, that enables strain-level comprehensive profiling of environmental cyanobacteria. The CyanoStrainChip was designed to target 1277 strains; nearly all major groups of cyanobacteria are included by implementing 43,666 genome-wide, strain-specific probes. It demonstrated strong specificity by in vitro mock community experiments. The high correlation (Pearson's R > 0.97) between probe fluorescence intensities and the corresponding DNA amounts (ranging from 1-100 ng) indicated excellent quantitative capability. Consistent cyanobacterial profiles of field samples were observed by both the CyanoStrainChip and next-generation sequencing methods. Furthermore, CyanoStrainChip analysis of surface water samples in Lake Chaohu uncovered a high intraspecific variation of abundance change within the genus Microcystis between different severity levels of cyanobacterial blooms, highlighting two toxic Microcystis strains that are of critical concern for Lake Chaohu harmful blooms suppression. Overall, these results suggest a potential for CyanoStrainChip as a valuable tool for cyanobacterial ecological research and harmful bloom monitoring to supplement existing techniques.
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Affiliation(s)
- Hao-Yue Shu
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
- School
of Food and Drug, Shenzhen Polytechnic, Shenzhen 518081, PR China
| | - Liang Zhao
- Institute
of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity
and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology
for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510006, PR China
| | - Yanyan Jia
- School
of Ecology, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Fei-Fei Liu
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
| | - Jiang Chen
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
| | - Chih-Min Chang
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
| | - Tao Jin
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
- One
Health Biotechnology (Suzhou) Co., Ltd., Suzhou 215009, PR China
| | - Jian Yang
- School
of Food and Drug, Shenzhen Polytechnic, Shenzhen 518081, PR China
| | - Wen-Sheng Shu
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
- Institute
of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity
and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology
for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510006, PR China
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12
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Rockwell NC, Lagarias JC. Cyanobacteriochromes from Gloeobacterales Provide New Insight into the Diversification of Cyanobacterial Photoreceptors. J Mol Biol 2024; 436:168313. [PMID: 37839679 PMCID: PMC11218821 DOI: 10.1016/j.jmb.2023.168313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/15/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
The phytochrome superfamily comprises three groups of photoreceptors sharing a conserved GAF (cGMP-specific phosphodiesterases, cyanobacterial adenylate cyclases, and formate hydrogen lyase transcription activator FhlA) domain that uses a covalently attached linear tetrapyrrole (bilin) chromophore to sense light. Knotted red/far-red phytochromes are widespread in both bacteria and eukaryotes, but cyanobacteria also contain knotless red/far-red phytochromes and cyanobacteriochromes (CBCRs). Unlike typical phytochromes, CBCRs require only the GAF domain for bilin binding, chromophore ligation, and full, reversible photoconversion. CBCRs can sense a wide range of wavelengths (ca. 330-750 nm) and can regulate phototaxis, second messenger metabolism, and optimization of the cyanobacterial light-harvesting apparatus. However, the origins of CBCRs are not well understood: we do not know when or why CBCRs evolved, or what selective advantages led to retention of early CBCRs in cyanobacterial genomes. In the current work, we use the increasing availability of genomes and metagenome-assembled-genomes from early-branching cyanobacteria to explore the origins of CBCRs. We reaffirm the earliest branches in CBCR evolution. We also show that early-branching cyanobacteria contain late-branching CBCRs, implicating early appearance of CBCRs during cyanobacterial evolution. Moreover, we show that early-branching CBCRs behave as integrators of light and pH, providing a potential unique function for early CBCRs that led to their retention and subsequent diversification. Our results thus provide new insight into the origins of these diverse cyanobacterial photoreceptors.
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Affiliation(s)
- Nathan C Rockwell
- 31 Briggs Hall, Department of Molecular and Cell Biology, One Shields Avenue, University of California at Davis, Davis, CA 95616, USA.
| | - J Clark Lagarias
- 31 Briggs Hall, Department of Molecular and Cell Biology, One Shields Avenue, University of California at Davis, Davis, CA 95616, USA.
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13
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Bustos-Diaz ED, Cruz-Perez A, Garfias-Gallegos D, D'Agostino PM, Gehringer MM, Cibrian-Jaramillo A, Barona-Gomez F. Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals. Microb Genom 2024; 10:001207. [PMID: 38451250 PMCID: PMC10999742 DOI: 10.1099/mgen.0.001207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/09/2024] [Indexed: 03/08/2024] Open
Abstract
Cycads are known to host symbiotic cyanobacteria, including Nostocales species, as well as other sympatric bacterial taxa within their specialized coralloid roots. Yet, it is unknown if these bacteria share a phylogenetic origin and/or common genomic functions that allow them to engage in facultative symbiosis with cycad roots. To address this, we obtained metagenomic sequences from 39 coralloid roots sampled from diverse cycad species and origins in Australia and Mexico. Culture-independent shotgun metagenomic sequencing was used to validate sub-community co-cultures as an efficient approach for functional and taxonomic analysis. Our metanalysis shows a host-independent microbiome core consisting of seven bacterial orders with high species diversity within the identified taxa. Moreover, we recovered 43 cyanobacterial metagenome-assembled genomes, and in addition to Nostoc spp., symbiotic cyanobacteria of the genus Aulosira were identified for the first time. Using this robust dataset, we used phylometagenomic analysis to reveal three monophyletic cyanobiont clades, two host-generalist and one cycad-specific that includes Aulosira spp. Although the symbiotic clades have independently arisen, they are enriched in certain functional genes, such as those related to secondary metabolism. Furthermore, the taxonomic composition of associated sympatric bacterial taxa remained constant. Our research quadruples the number of cycad cyanobiont genomes and provides a robust framework to decipher cyanobacterial symbioses, with the potential of improving our understanding of symbiotic communities. This study lays a solid foundation to harness cyanobionts for agriculture and bioprospection, and assist in conservation of critically endangered cycads.
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Affiliation(s)
- Edder D. Bustos-Diaz
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
- Institute of Biology, Leiden University, Netherlands, 2333 BE, Leiden
| | - Arely Cruz-Perez
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
| | - Diego Garfias-Gallegos
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
| | - Paul M. D'Agostino
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069 Dresden, Germany
| | - Michelle M. Gehringer
- Department of Microbiology, University of Kaiserslautern-Landau (RPTU), 67663 Kaiserslautern, Germany
| | - Angelica Cibrian-Jaramillo
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
- Naturalis Biodiversity Center, Leiden 2333 CR, Netherlands
| | - Francisco Barona-Gomez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
- Institute of Biology, Leiden University, Netherlands, 2333 BE, Leiden
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14
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Li C, Liao H, Xu L, Wang C, Yao M, Wang J, Li X. Comparative genomics reveals the adaptation of ammonia-oxidising Thaumarchaeota to arid soils. Environ Microbiol 2024; 26:e16601. [PMID: 38454574 DOI: 10.1111/1462-2920.16601] [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: 06/08/2023] [Accepted: 02/09/2024] [Indexed: 03/09/2024]
Abstract
Thaumarchaeota are predominant in oligotrophic habitats such as deserts and arid soils, but their adaptations to these arid conditions are not well understood. In this study, we assembled 23 Thaumarchaeota genomes from arid and semi-arid soils collected from the Inner Mongolia Steppe and the Qinghai-Tibet Plateau. Using a comparative genomics approach, integrated with 614 Thaumarchaeota genomes from public databases, we identified the traits and evolutionary forces that contribute to their adaptations to aridity. Our results showed that the newly assembled genomes represent an early diverging group within the lineage of ammonia-oxidising Thaumarchaeota. While the genomic functions previously identified in arid soil lineages were conserved across terrestrial, shallow-ocean and deep-ocean lineages, several traits likely contribute to Thaumarchaeota's adaptation to aridity. These include chlorite dismutase, arsenate reductase, V-type ATPase and genes dealing with oxidative stresses. The acquisition and loss of traits at the last common ancestor of arid soil lineages may have facilitated the specialisation of Thaumarchaeota in arid soils. Additionally, the acquisition of unique adaptive traits, such as a urea transporter, Ca2+ :H+ antiporter, mannosyl-3-phosphoglycerate synthase and phosphatase, DNA end-binding protein Ku and phage shock protein A, further distinguishes arid soil Thaumarchaeota. This study provides evidence for the adaptations of Thaumarchaeota to arid soil, enhancing our understanding of the nitrogen and carbon cycling driven by Thaumarchaeota in drylands.
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Affiliation(s)
- Chaonan Li
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Haijun Liao
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Normal University of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Lin Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Changting Wang
- Institute of Qinghai-Tibet Plateau, Southwest Minzu University, Chengdu, China
| | - Minjie Yao
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junming Wang
- Section of Climate Science, Illinois State Water Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Xiangzhen Li
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
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15
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Zuo J, Xiao P, Heino J, Tan F, Soininen J, Chen H, Yang J. Eutrophication increases the similarity of cyanobacterial community features in lakes and reservoirs. WATER RESEARCH 2024; 250:120977. [PMID: 38128306 DOI: 10.1016/j.watres.2023.120977] [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: 06/14/2023] [Revised: 11/05/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Eutrophication of inland waters is a mostly anthropogenic phenomenon impacting aquatic biodiversity worldwide, and might change biotic community structure and ecosystem functions. However, little is known about the patterns of cyanobacterial community variations and changes both on alpha and beta diversity levels in response to eutrophication. Here, we investigated cyanobacterial communities sampled at 140 sites from 59 lakes and reservoirs along a strong eutrophication gradient in eastern China through using CPC-IGS and 16S rRNA gene amplicon sequencing. We found that taxonomic diversity increased, but phylogenetic diversity decreased significantly along the eutrophication gradient. Both niche width and niche overlap of cyanobacteria significantly decreased from low- to high-nutrient waterbodies. Cyanobacterial community distance-decay relationship became weaker from mesotrophic to hypereutrophic waterbodies, while ecological uniqueness (i.e., local contributions to beta diversity) tended to increase in high-nutrient waterbodies. Latitude and longitude were more important in shaping cyanobacterial community structure than other environmental variables. These findings suggest that eutrophication affects alpha and beta diversity of cyanobacterial communities, leading to increasingly similar community structures in lakes and reservoirs with a higher level of eutrophication. Our work highlights how cyanobacterial communities respond to anthropogenic eutrophication and calls for an urgent need to develop conservation and management strategies to control lake eutrophication and protect freshwater biodiversity.
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Affiliation(s)
- Jun Zuo
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Lab for Water Environment and Marine Biological Resources Protection, Institute for Eco-Environmental Research of Sanyang Wetland, Wenzhou University, Wenzhou 325035, China
| | - Peng Xiao
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Lab for Water Environment and Marine Biological Resources Protection, Institute for Eco-Environmental Research of Sanyang Wetland, Wenzhou University, Wenzhou 325035, China
| | - Jani Heino
- Geography Research Unit, University of Oulu, P.O. Box 8000, Oulu FI-90014, Finland
| | - Fengjiao Tan
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Janne Soininen
- Department of Geosciences and Geography, University of Helsinki, P.O. Box 64, Helsinki FI-00014, Finland
| | - Huihuang Chen
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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16
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Tang J, Hu Z, Zhang J, Daroch M. Genome-scale identification and comparative analysis of transcription factors in thermophilic cyanobacteria. BMC Genomics 2024; 25:44. [PMID: 38195395 PMCID: PMC10775510 DOI: 10.1186/s12864-024-09969-7] [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: 01/03/2024] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND The transcription factors (TFs) in thermophilic cyanobacteria might represent a uniquely evolved gene repertoire in light of the strong selective pressure caused by hostile habitats. Understanding the molecular composition of the TF genes in thermophilic cyanobacteria will facilitate further studies regarding verifying their exact biochemical functions and genetic engineering. However, limited information is available on the TFs of thermophilic cyanobacteria. Herein, a thorough investigation and comparative analysis were performed to gain insights into the molecular composition of the TFs in 22 thermophilic cyanobacteria. RESULTS The results suggested a fascinating diversity of the TFs among these thermophiles. The abundance and type of TF genes were diversified in these genomes. The identified TFs are speculated to play various roles in biological regulations. Further comparative and evolutionary genomic analyses revealed that HGT may be associated with the genomic plasticity of TF genes in Thermostichus and Thermosynechococcus strains. Comparative analyses also indicated different pattern of TF composition between thermophiles and corresponding mesophilic reference cyanobacteria. Moreover, the identified unique TFs of thermophiles are putatively involved in various biological regulations, mainly as responses to ambient changes, may facilitating the thermophiles to survive in hot springs. CONCLUSION The findings herein shed light on the TFs of thermophilic cyanobacteria and fundamental knowledge for further research regarding thermophilic cyanobacteria with a broad potential for transcription regulations in responses to environmental fluctuations.
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Affiliation(s)
- Jie Tang
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106, China
| | - Zhe Hu
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106, China
| | - Jing Zhang
- Food Safety Detection Key Laboratory of Sichuan, Technical Center of Chengdu Customs, Chengdu, 610041, China.
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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17
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Xiong L, Li Y, Zeng K, Wei Y, Li H, Ji X. Revealing viral diversity in the Napahai plateau wetland based on metagenomics. Antonie Van Leeuwenhoek 2023; 117:3. [PMID: 38153618 DOI: 10.1007/s10482-023-01912-2] [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: 08/30/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
We focused on exploring the diversity of viruses in the Napahai plateau wetland, a unique ecosystem located in Yunnan, China. While viruses in marine environments have been extensively studied for their influence on microbial metabolism and biogeochemical cycles, little is known about their composition and function in plateau wetlands. Metagenomic analysis was employed to investigate the viral diversity and biogeochemical impacts in the Napahai wetland. It revealed that the Caudoviricetes and Malgrandaviricetes class level was the most abundant viral category based on phylogenetic analysis. Additionally, a gene-sharing network highlighted the presence of numerous unexplored viruses and demonstrated their unique characteristics and significant variation within the viral community of the Napahai wetland. Furthermore, the study identified the auxiliary metabolic genes (AMGs). AMGs provide phages with additional functions, such as protection against host degradation and involvement in metabolic pathways, such as the pentose phosphate pathway and DNA biosynthesis. The viruses in the Napahai wetland were found to influence carbon, nitrogen, sulfur, and amino acid metabolism, indirectly contributing to biogeochemical cycling through these AMGs. Overall, the research sheds light on the diverse and unique viral communities in the Napahai plateau wetland and emphasizes the significant roles of viruses in microbial ecology. The findings contribute to a deeper understanding of the characteristics and ecological functions of viral communities in plateau wetland ecosystems.
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Affiliation(s)
- Lingling Xiong
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yanmei Li
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Kun Zeng
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yunlin Wei
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Xiuling Ji
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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18
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Feng X, Xing P. Genomics of Yoonia sp. Isolates (Family Roseobacteraceae) from Lake Zhangnai on the Tibetan Plateau. Microorganisms 2023; 11:2817. [PMID: 38004828 PMCID: PMC10673129 DOI: 10.3390/microorganisms11112817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/18/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023] Open
Abstract
Understanding the genomic differentiation between marine and non-marine aquatic microbes remains a compelling question in ecology. While previous research has identified several lacustrine lineages within the predominantly marine Roseobacteraceae family, limited genomic data have constrained our understanding of their ecological adaptation mechanisms. In this study, we isolated four novel Yoonia strains from a brackish lake on the Tibetan Plateau. These strains have diverged from their marine counterparts within the same genus, indicating a recent habitat transition event from marine to non-marine environments. Metabolic comparisons and ancestral genomic reconstructions in a phylogenetic framework reveal metabolic shifts in salinity adaptation, compound transport, aromatics degradation, DNA repair, and restriction systems. These findings not only corroborate the metabolic changes commonly observed in other non-marine Roseobacters but also unveil unique adaptations, likely reflecting the localized metabolic changes in responses to Tibetan Plateau environments. Collectively, our study expands the known genomic diversity of non-marine Roseobacteraceae lineages and enhances our understanding of microbial adaptations to lacustrine ecosystems.
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Affiliation(s)
- Xiaoyuan Feng
- Shenzhen Research Institute, Chinese University of Hong Kong, Shenzhen 518000, China;
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
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19
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Gisriel CJ, Bryant DA, Brudvig GW, Cardona T. Molecular diversity and evolution of far-red light-acclimated photosystem I. FRONTIERS IN PLANT SCIENCE 2023; 14:1289199. [PMID: 38053766 PMCID: PMC10694217 DOI: 10.3389/fpls.2023.1289199] [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: 09/05/2023] [Accepted: 10/31/2023] [Indexed: 12/07/2023]
Abstract
The need to acclimate to different environmental conditions is central to the evolution of cyanobacteria. Far-red light (FRL) photoacclimation, or FaRLiP, is an acclimation mechanism that enables certain cyanobacteria to use FRL to drive photosynthesis. During this process, a well-defined gene cluster is upregulated, resulting in changes to the photosystems that allow them to absorb FRL to perform photochemistry. Because FaRLiP is widespread, and because it exemplifies cyanobacterial adaptation mechanisms in nature, it is of interest to understand its molecular evolution. Here, we performed a phylogenetic analysis of the photosystem I subunits encoded in the FaRLiP gene cluster and analyzed the available structural data to predict ancestral characteristics of FRL-absorbing photosystem I. The analysis suggests that FRL-specific photosystem I subunits arose relatively late during the evolution of cyanobacteria when compared with some of the FRL-specific subunits of photosystem II, and that the order Nodosilineales, which include strains like Halomicronema hongdechloris and Synechococcus sp. PCC 7335, could have obtained FaRLiP via horizontal gene transfer. We show that the ancestral form of FRL-absorbing photosystem I contained three chlorophyll f-binding sites in the PsaB2 subunit, and a rotated chlorophyll a molecule in the A0B site of the electron transfer chain. Along with our previous study of photosystem II expressed during FaRLiP, these studies describe the molecular evolution of the photosystem complexes encoded by the FaRLiP gene cluster.
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Affiliation(s)
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Gary W. Brudvig
- Department of Chemistry, Yale University, New Haven, CT, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Tanai Cardona
- Department of Life Sciences, Imperial College London, London, United Kingdom
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
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20
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Sheridan PO, Meng Y, Williams TA, Gubry-Rangin C. Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae. Nat Commun 2023; 14:7305. [PMID: 37951938 PMCID: PMC10640624 DOI: 10.1038/s41467-023-43196-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023] Open
Abstract
Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota. Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary divergence between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also did not support the previous hypothesis of a thermophilic last common ancestor of the ammonia-oxidising archaea. Ultimately, this study provides a good model for studying mechanisms driving niche partitioning between spatially related ecosystems.
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Affiliation(s)
- Paul O Sheridan
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Yiyu Meng
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
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21
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Fang GY, Liu XQ, Mu XJ, Huang BW, Jiang YJ. Distinct increase in antimicrobial resistance genes among Vibrio parahaemolyticus in recent decades worldwide. CHEMOSPHERE 2023; 340:139905. [PMID: 37611759 DOI: 10.1016/j.chemosphere.2023.139905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/18/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023]
Abstract
Vibrio parahaemolyticus is a common pathogen, and has emerged with multiple antimicrobial resistance (AMR). However, few studies have conducted large-scale investigations of AMR and virulence trends of V. parahaemolyticus worldwide. This study longitudinally monitored antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) trends of 1540 V. parahaemolyticus isolates isolated from 1951 to 2021. The number of ARGs in V. parahaemolyticus isolates distinctly increased over the years (P = 5.9e-10), while the number of VFGs decreased significantly (P < 2.2e-16). However, the number of VFGs of isolates isolated from humans has not changed significantly over the years (R = 0.013, P = 0.74), suggesting that the pathogenic risk to humans has not been reduced. Besides, mobile genetic elements are important contributors to ARGs in V. parahaemolyticus (R = 0.34, P < 2.2e-16), but have no promoting effect on VFGs (P = 0.50). The structural equation model illustrated that the human development index promoted the consumption of antibiotics, thereby indirectly promoting an increase in the AMR of the V. parahaemolyticus isolates. Finally, the random forest was performed to predict the ARG and VFG risks of global terrestrial V. parahaemolyticus isolates, and successfully map these threats with over 80% accuracy. This study aimed to evaluate the global risks posed by AMR and virulence, which helps to develop methods specifically targeting V. parahaemolyticus to mitigate these threats.
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Affiliation(s)
- Guan-Yu Fang
- College of Food and Health, Zhejiang A&F University, Hangzhou, 311300, PR China.
| | - Xing-Quan Liu
- College of Food and Health, Zhejiang A&F University, Hangzhou, 311300, PR China
| | - Xiao-Jing Mu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, PR China; Suzhou Precision Biotechco., Ltd, Suzhou, 215000, PR China
| | - Bing-Wen Huang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, PR China
| | - Yu-Jian Jiang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, PR China
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22
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Timms VJ, Hassan KA, Pearson LA, Neilan BA. Cyanobacteria as a critical reservoir of the environmental antimicrobial resistome. Environ Microbiol 2023; 25:2266-2276. [PMID: 37365851 DOI: 10.1111/1462-2920.16453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/04/2023] [Indexed: 06/28/2023]
Abstract
Antimicrobial resistance (AMR) is predicted to cause a worldwide annual toll of 10 million deaths by 2050. This looming public health threat has been linked to antibiotic overuse and pollution, which places selective pressures on AMR maintenance and transfer in and between microbial populations. We examined the distribution, diversity and potential mobility of AMR genes in cyanobacteria. While cyanobacteria are not pathogenic, we hypothesised that they could be a major environmental reservoir for AMR genes. Genes encoding AMR to seven antimicrobial drug classes were found in 10% of cyanobacterial genomes. AMR genes were found in 13% of freshwater, 19% of terrestrial, 34% of symbiotic, 2% of thermal spring, and 3% of marine genomes. AMR genes were found in five cyanobacterial orders with 23% of Nostocales and 8% of Oscillatoriales strains containing AMR genes. The most frequently observed alleles were ansamycin resistance genes, which were present in 7% of strains. AMR genes responsible for resistance to broad-spectrum β-lactams, chloramphenicols, tetracyclines, macrolides, and aminoglycosides were associated with mobile genetic elements or plasmid replicons or both. These results suggest that cyanobacteria are an extensive reservoir, and potential vector, for AMR genes in diverse terrestrial and aquatic habitats.
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Affiliation(s)
- V J Timms
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - K A Hassan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - L A Pearson
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - B A Neilan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
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23
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Ben Moussa H, Pédron J, Hugouvieux-Cotte-Pattat N, Barny MA. Two species with a peculiar evolution within the genus Pectobacterium suggest adaptation to a new environmental niche. Environ Microbiol 2023; 25:2465-2480. [PMID: 37550252 DOI: 10.1111/1462-2920.16479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023]
Abstract
Historically, research on Soft Rot Pectobacteriacea (SRP) has focused on economically important crops and ornamentals and knowledge of these bacteria outside the plant context remains poorly investigated. Recently, two closely related species Pectobacterium aquaticum and Pectobacterium quasiaquaticum were isolated from water and have not been isolated from any plant yet. To identify the distinctive characteristics of these two species, we performed a comparative genomic analysis of 80 genomes representing 19 Pectobacterium species and performed an evolutionary reconstruction. Both water species underwent a reduction in genome size associated with a high pseudogene content. A high gene loss was predicted at the emergence of both species. Among the 199 gene families missing from both P. aquaticum and P. quasiaquaticum genomes but present in at least 80% of other Pectobacterium genomes, COG analysis identified many genes involved in nutrient transport systems. In addition, many type II secreted proteins were also missing in both species. Phenotypic analysis revealed that both species had reduced pectinolytic activity, a biofilm formation defect, were highly motile and had reduced virulence on several plants. These genomic and phenotypic data suggest that the ecological niche of P. aquaticum and P. quasiaquaticum may differ from that of other Pectobacterium species.
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Affiliation(s)
- Hajar Ben Moussa
- Sorbonne Université, INRAE, IRD, CNRS, UPEC, UMR 7618 Institut d'Écologie et des Sciences de l'Environnement de Paris, Paris, France
| | - Jacques Pédron
- Sorbonne Université, INRAE, IRD, CNRS, UPEC, UMR 7618 Institut d'Écologie et des Sciences de l'Environnement de Paris, Paris, France
| | | | - Marie-Anne Barny
- Sorbonne Université, INRAE, IRD, CNRS, UPEC, UMR 7618 Institut d'Écologie et des Sciences de l'Environnement de Paris, Paris, France
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24
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Roberts WR, Ruck EC, Downey KM, Pinseel E, Alverson AJ. Resolving Marine-Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance. Syst Biol 2023; 72:984-997. [PMID: 37335140 DOI: 10.1093/sysbio/syad038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 06/02/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023] Open
Abstract
Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats worldwide. We generated a phylogenomic data set of genomes and transcriptomes for 59 diatom taxa to resolve freshwater transitions in one lineage, the Thalassiosirales. Although most parts of the species tree were consistently resolved with strong support, we had difficulties resolving a Paleocene radiation, which affected the placement of one freshwater lineage. This and other parts of the tree were characterized by high levels of gene tree discordance caused by incomplete lineage sorting and low phylogenetic signal. Despite differences in species trees inferred from concatenation versus summary methods and codons versus amino acids, traditional methods of ancestral state reconstruction supported six transitions into freshwaters, two of which led to subsequent species diversification. Evidence from gene trees, protein alignments, and diatom life history together suggest that habitat transitions were largely the product of homoplasy rather than hemiplasy, a condition where transitions occur on branches in gene trees not shared with the species tree. Nevertheless, we identified a set of putatively hemiplasious genes, many of which have been associated with shifts to low salinity, indicating that hemiplasy played a small but potentially important role in freshwater adaptation. Accounting for differences in evolutionary outcomes, in which some taxa became locked into freshwaters while others were able to return to the ocean or become salinity generalists, might help further distinguish different sources of adaptive mutation in freshwater diatoms.
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Affiliation(s)
- Wade R Roberts
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Elizabeth C Ruck
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Kala M Downey
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Eveline Pinseel
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
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25
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Xi H, Nie X, Gao F, Liang X, Li H, Zhou H, Cai Y, Yang C. A bacterial spermidine biosynthetic pathway via carboxyaminopropylagmatine. SCIENCE ADVANCES 2023; 9:eadj9075. [PMID: 37878710 PMCID: PMC10599626 DOI: 10.1126/sciadv.adj9075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/22/2023] [Indexed: 10/27/2023]
Abstract
Spermidine, a ubiquitous polyamine, is known to be required for critical physiological functions in bacteria. Two principal pathways are known for spermidine biosynthesis, both of which involve aminopropylation of putrescine. Here, we identified a spermidine biosynthetic pathway via a previously unknown metabolite, carboxyaminopropylagmatine (CAPA), in a model cyanobacterium Synechocystis sp. PCC 6803 through an approach combining 13C and 15N tracers, metabolomics, and genetic and biochemical characterization. The CAPA pathway starts with reductive condensation of agmatine and l-aspartate-β-semialdehyde into CAPA by a previously unknown CAPA dehydrogenase, followed by decarboxylation of CAPA to form aminopropylagmatine, and ends with conversion of aminopropylagmatine to spermidine by an aminopropylagmatine ureohydrolase. Thus, the pathway does not involve putrescine and depends on l-aspartate-β-semialdehyde as the aminopropyl group donor. Genomic, biochemical, and metagenomic analyses showed that the CAPA-pathway genes are widespread in 15 different phyla of bacteria distributed in marine, freshwater, and other ecosystems.
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Affiliation(s)
- Huachao Xi
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoqun Nie
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Fang Gao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xinxin Liang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Hu Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haiyan Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Chen Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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26
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Antonaru LA, Selinger VM, Jung P, Di Stefano G, Sanderson ND, Barker L, Wilson DJ, Büdel B, Canniffe DP, Billi D, Nürnberg DJ. Common loss of far-red light photoacclimation in cyanobacteria from hot and cold deserts: a case study in the Chroococcidiopsidales. ISME COMMUNICATIONS 2023; 3:113. [PMID: 37857858 PMCID: PMC10587186 DOI: 10.1038/s43705-023-00319-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/29/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023]
Abstract
Deserts represent an extreme challenge for photosynthetic life. Despite their aridity, they are often inhabited by diverse microscopic communities of cyanobacteria. These organisms are commonly found in lithic habitats, where they are partially sheltered from extremes of temperature and UV radiation. However, living under the rock surface imposes additional constraints, such as limited light availability, and enrichment of longer wavelengths than are typically usable for oxygenic photosynthesis. Some cyanobacteria from the genus Chroococcidiopsis can use this light to photosynthesize, in a process known as far-red light photoacclimation, or FaRLiP. This genus has commonly been reported from both hot and cold deserts. However, not all Chroococcidiopsis strains carry FaRLiP genes, thus motivating our study into the interplay between FaRLiP and extreme lithic environments. The abundance of sequence data and strains provided the necessary material for an in-depth phylogenetic study, involving spectroscopy, microscopy, and determination of pigment composition, as well as gene and genome analyses. Pigment analyses revealed the presence of red-shifted chlorophylls d and f in all FaRLiP strains tested. In addition, eight genus-level taxa were defined within the encompassing Chroococcidiopsidales, clarifying the phylogeny of this long-standing polyphyletic order. FaRLiP is near universally present in a generalist genus identified in a wide variety of environments, Chroococcidiopsis sensu stricto, while it is rare or absent in closely related, extremophile taxa, including those preferentially inhabiting deserts. This likely reflects the evolutionary process of gene loss in specialist lineages.
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Affiliation(s)
- Laura A Antonaru
- Institute for Experimental Physics, Freie Universität Berlin, Berlin, Germany.
- Department of Life Sciences, Imperial College London, London, UK.
| | - Vera M Selinger
- Institute for Experimental Physics, Freie Universität Berlin, Berlin, Germany
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Patrick Jung
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Giorgia Di Stefano
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- PhD Program in Cellular and Molecular Biology, Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Nicholas D Sanderson
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel J Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Burkhard Büdel
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Daniel P Canniffe
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daniela Billi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Dennis J Nürnberg
- Institute for Experimental Physics, Freie Universität Berlin, Berlin, Germany.
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany.
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27
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Thawabteh AM, Naseef HA, Karaman D, Bufo SA, Scrano L, Karaman R. Understanding the Risks of Diffusion of Cyanobacteria Toxins in Rivers, Lakes, and Potable Water. Toxins (Basel) 2023; 15:582. [PMID: 37756009 PMCID: PMC10535532 DOI: 10.3390/toxins15090582] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/10/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023] Open
Abstract
Blue-green algae, or cyanobacteria, may be prevalent in our rivers and tap water. These minuscule bacteria can grow swiftly and form blooms in warm, nutrient-rich water. Toxins produced by cyanobacteria can pollute rivers and streams and harm the liver and nervous system in humans. This review highlights the properties of 25 toxin types produced by 12 different cyanobacteria genera. The review also covered strategies for reducing and controlling cyanobacteria issues. These include using physical or chemical treatments, cutting back on fertilizer input, algal lawn scrubbers, and antagonistic microorganisms for biocontrol. Micro-, nano- and ultrafiltration techniques could be used for the removal of internal and extracellular cyanotoxins, in addition to powdered or granular activated carbon, ozonation, sedimentation, ultraviolet radiation, potassium permanganate, free chlorine, and pre-treatment oxidation techniques. The efficiency of treatment techniques for removing intracellular and extracellular cyanotoxins is also demonstrated. These approaches aim to lessen the risks of cyanobacterial blooms and associated toxins. Effective management of cyanobacteria in water systems depends on early detection and quick action. Cyanobacteria cells and their toxins can be detected using microscopy, molecular methods, chromatography, and spectroscopy. Understanding the causes of blooms and the many ways for their detection and elimination will help the management of this crucial environmental issue.
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Affiliation(s)
- Amin Mahmood Thawabteh
- Faculty of Pharmacy, Nursing and Health Professions, Birzeit University, Ramallah 00972, Palestine
- General Safety Section, General Services Department, Birzeit University, Bir Zeit 71939, Palestine
| | - Hani A Naseef
- Faculty of Pharmacy, Nursing and Health Professions, Birzeit University, Ramallah 00972, Palestine
| | - Donia Karaman
- Faculty of Pharmacy, Al-Quds University, Jerusalem 20002, Palestine
| | - Sabino A Bufo
- Department of Sciences, University of Basilicata, Via dell'Ateneo Lucano 10, 85100 Potenza, Italy
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg 2092, South Africa
| | - Laura Scrano
- Department of European and Mediterranean Cultures, University of Basilicata, Via Lanera 20, 75100 Matera, Italy
| | - Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, Jerusalem 20002, Palestine
- Department of Sciences, University of Basilicata, Via dell'Ateneo Lucano 10, 85100 Potenza, Italy
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28
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Arsın S, Delbaje E, Jokela J, Wahlsten M, Farrar ZM, Permi P, Fewer D. A Plastic Biosynthetic Pathway for the Production of Structurally Distinct Microbial Sunscreens. ACS Chem Biol 2023; 18:1959-1967. [PMID: 37603862 PMCID: PMC10510106 DOI: 10.1021/acschembio.3c00112] [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: 02/20/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
Mycosporine-like amino acids (MAAs) are small, colorless, and water-soluble secondary metabolites. They have high molar extinction coefficients and a unique UV radiation absorption mechanism that make them effective sunscreens. Here we report the discovery of two structurally distinct MAAs from the lichen symbiont strain Nostoc sp. UHCC 0926. We identified these MAAs as aplysiapalythine E (C23H38N2O15) and tricore B (C34H53N4O15) using a combination of high-resolution liquid chromatography-mass spectrometry (HR-LCMS) analysis and nuclear magnetic resonance (NMR) spectroscopy. We obtained a 8.3 Mb complete genome sequence of Nostoc sp. UHCC 0926 to gain insights into the genetic basis for the biosynthesis of these two structural distinct MAAs. We identified MAA biosynthetic genes encoded in three separate locations of the genome. The organization of biosynthetic enzymes in Nostoc sp. UHCC 0926 necessitates a branched biosynthetic pathway to produce two structurally distinct MAAs. We detected the presence of such discontiguous MAA biosynthetic gene clusters in 12% of the publicly available complete cyanobacterial genomes. Bioinformatic analysis of public MAA biosynthetic gene clusters suggests that they are subject to rapid evolutionary processes resulting in highly plastic biosynthetic pathways that are responsible for the chemical diversity in this family of microbial sunscreens.
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Affiliation(s)
- Sıla Arsın
- University
of Helsinki, Department of Microbiology,
Faculty of Agriculture and Forestry, 00014 Helsinki, Finland
| | - Endrews Delbaje
- University
of São Paulo, Center for Nuclear
Energy in Agriculture, Avenida Centenário 303, 13400-970 Piracicaba, São Paulo, Brazil
| | - Jouni Jokela
- University
of Helsinki, Department of Microbiology,
Faculty of Agriculture and Forestry, 00014 Helsinki, Finland
| | - Matti Wahlsten
- University
of Helsinki, Department of Microbiology,
Faculty of Agriculture and Forestry, 00014 Helsinki, Finland
| | - Zoë M. Farrar
- University
of Helsinki, Department of Microbiology,
Faculty of Agriculture and Forestry, 00014 Helsinki, Finland
| | - Perttu Permi
- Department
of Chemistry, University of Jyväskylä, 40014 Jyväskylä, Finland
- Department
of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - David Fewer
- University
of Helsinki, Department of Microbiology,
Faculty of Agriculture and Forestry, 00014 Helsinki, Finland
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29
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González D, Morales-Olavarria M, Vidal-Veuthey B, Cárdenas JP. Insights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut. Front Microbiol 2023; 14:1238580. [PMID: 37779688 PMCID: PMC10540074 DOI: 10.3389/fmicb.2023.1238580] [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: 06/12/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
Akkermansia, a relevant mucin degrader from the vertebrate gut microbiota, is a member of the deeply branched Verrucomicrobiota, as well as the only known member of this phylum to be described as inhabitants of the gut. Only a few Akkermansia species have been officially described so far, although there is genomic evidence addressing the existence of more species-level variants for this genus. This niche specialization makes Akkermansia an interesting model for studying the evolution of microorganisms to their adaptation to the gastrointestinal tract environment, including which kind of functions were gained when the Akkermansia genus originated or how the evolutionary pressure functions over those genes. In order to gain more insight into Akkermansia adaptations to the gastrointestinal tract niche, we performed a phylogenomic analysis of 367 high-quality Akkermansia isolates and metagenome-assembled genomes, in addition to other members of Verrucomicrobiota. This work was focused on three aspects: the definition of Akkermansia genomic species clusters and the calculation and functional characterization of the pangenome for the most represented species; the evolutionary relationship between Akkermansia and their closest relatives from Verrucomicrobiota, defining the gene families which were gained or lost during the emergence of the last Akkermansia common ancestor (LAkkCA) and; the evaluation of the evolutionary pressure metrics for each relevant gene family of main Akkermansia species. This analysis found 25 Akkermansia genomic species clusters distributed in two main clades, divergent from their non-Akkermansia relatives. Pangenome analyses suggest that Akkermansia species have open pangenomes, and the gene gain/loss model indicates that genes associated with mucin degradation (both glycoside hydrolases and peptidases), (micro)aerobic metabolism, surface interaction, and adhesion were part of LAkkCA. Specifically, mucin degradation is a very ancestral innovation involved in the origin of Akkermansia. Horizontal gene transfer detection suggests that Akkermansia could receive genes mostly from unknown sources or from other Gram-negative gut bacteria. Evolutionary metrics suggest that Akkemansia species evolved differently, and even some conserved genes suffered different evolutionary pressures among clades. These results suggest a complex evolutionary landscape of the genus and indicate that mucin degradation could be an essential feature in Akkermansia evolution as a symbiotic species.
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Affiliation(s)
- Dámariz González
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Mauricio Morales-Olavarria
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Boris Vidal-Veuthey
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Juan P. Cárdenas
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
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30
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Zhang X, Xiao L, Liu J, Tian Q, Xie J. Trade-off in genome turnover events leading to adaptive evolution of Microcystis aeruginosa species complex. BMC Genomics 2023; 24:462. [PMID: 37592233 PMCID: PMC10433662 DOI: 10.1186/s12864-023-09555-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Numerous studies in the past have expanded our understanding of the genetic differences of global distributed cyanobacteria that originated around billions of years ago, however, unraveling how gene gain and loss drive the genetic evolution of cyanobacterial species, and the trade-off of these evolutionary forces are still the central but poorly understood issues. RESULTS To delineate the contribution of gene flow in mediating the hereditary differentiation and shaping the microbial evolution, a global genome-wide study of bloom-forming cyanobacterium, Microcystis aeruginosa species complex, provided robust evidence for genetic diversity, reflected by enormous variation in gene repertoire among various strains. Mathematical extrapolation showed an 'open' microbial pan-genome of M. aeruginosa species, since novel genes were predicted to be introduced after new genomes were sequenced. Identification of numerous horizontal gene transfer's signatures in genome regions of interest suggested that genome expansion via transformation and phage-mediated transduction across bacterial lineage as an evolutionary route may contribute to the differentiation of Microcystis functions (e.g., carbohydrate metabolism, amino acid metabolism, and energy metabolism). Meanwhile, the selective loss of some dispensable genes at the cost of metabolic versatility is as a mean of adaptive evolution that has the potential to increase the biological fitness. CONCLUSIONS Now that the recruitment of novel genes was accompanied by a parallel loss of some other ones, a trade-off in gene content may drive the divergent differentiation of M. aeruginosa genomes. Our study provides a genetic framework for the evolution of M. aeruginosa species and illustrates their possible evolutionary patterns.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China.
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Central South University, Changsha, China.
| | - Lijun Xiao
- Guangdong Corps Hospital of Chinese People's Armed Police Forces, Guangzhou, China
| | - Jiahui Liu
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Qibai Tian
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Jiaqi Xie
- Hunan Food and Drug Vocational College, Changsha, China
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31
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Jiang Y, Tang J, Liu X, Daroch M. Polyphasic characterization of a novel hot-spring cyanobacterium Thermocoleostomius sinensis gen et sp. nov. and genomic insights into its carbon concentration mechanism. Front Microbiol 2023; 14:1176500. [PMID: 37564287 PMCID: PMC10410155 DOI: 10.3389/fmicb.2023.1176500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/06/2023] [Indexed: 08/12/2023] Open
Abstract
Thermophilic cyanobacteria play a crucial role as primary producers in hot spring ecosystems, yet their microbiological, taxonomic, and ecological characteristics are not extensively studied. This study aimed to characterize a novel strain of thermophilic cyanobacteria, PKUAC-SCTA174 (A174), using a combination of traditional polyphasic methods and modern genomic-based approaches. The study included 16S rRNA-based phylogeny, ITS secondary structure prediction, morphological and habitat analyses, as well as high-quality genome sequencing with corresponding phylogenomic analyses. The results of the 16S rRNA, 16S-23S ITS secondary structure, morphology, and habitat analyses supported the classification of the strain as a member of a novel genus within the family Oculatellaceae, closely related to Albertania and Trichotorquatus. Genomic analysis revealed the presence of a sophisticated carbon-concentrating mechanism (CCM) in the strain, involving two CO2 uptake systems NDH-I3, and NDH-I4, three types of bicarbonate transporters (BCT1, bicA, sbtA,) and two distinct putative carboxysomal carbonic anhydrases (ccaA1 and ccaA2). The expression of CCM genes was investigated with a CO2 shift experiment, indicating varying transcript abundance among different carbon uptake systems. Based on the comprehensive characterization, the strain was delineated as Thermocoleostomius sinensis, based on the botanical code. The study of the complete genome of strain A174 contributes valuable insights into the genetic characteristics of the genus Thermocoleostomius and related organisms and provides a systematic understanding of thermophilic cyanobacteria. The findings presented here offer valuable data that can be utilized for future research in taxogenomics, ecogenomics, and geogenomics.
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Affiliation(s)
- Ying Jiang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Jie Tang
- School of Food and Bioengineering, Chengdu University, Chengdu, Sichuan, China
| | - Xiangjian Liu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
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Pessi IS, Popin RV, Durieu B, Lara Y, Tytgat B, Savaglia V, Roncero-Ramos B, Hultman J, Verleyen E, Vyverman W, Wilmotte A. Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics. Microb Genom 2023; 9:mgen001056. [PMID: 37417735 PMCID: PMC10438808 DOI: 10.1099/mgen.0.001056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided important insights into the diversity of polar Cyanobacteria, only a handful of genomes have been sequenced to date. Here, we applied a genome-resolved metagenomics approach to data obtained from Arctic, sub-Antarctic and Antarctic microbial mats. We recovered 37 metagenome-assembled genomes (MAGs) of Cyanobacteria representing 17 distinct species, most of which are only distantly related to genomes that have been sequenced so far. These include (i) lineages that are common in polar microbial mats such as the filamentous taxa Pseudanabaena, Leptolyngbya, Microcoleus/Tychonema and Phormidium; (ii) the less common taxa Crinalium and Chamaesiphon; (iii) an enigmatic Chroococcales lineage only distantly related to Microcystis; and (iv) an early branching lineage in the order Gloeobacterales that is distributed across the cold biosphere, for which we propose the name Candidatus Sivonenia alaskensis. Our results show that genome-resolved metagenomics is a powerful tool for expanding our understanding of the diversity of Cyanobacteria, especially in understudied remote and extreme environments.
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Affiliation(s)
- Igor S. Pessi
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland
| | - Rafael V. Popin
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Benoit Durieu
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Yannick Lara
- Early Life Traces & Evolution-Astrobiology, UR-Astrobiology, University of Liège, Liège, Belgium
| | - Bjorn Tytgat
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Valentina Savaglia
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Beatriz Roncero-Ramos
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
- Department of Plant Biology and Ecology, University of Sevilla, Sevilla, Spain
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland
- Natural Resources Institute Finland (LUKE), Helsinki, Finland
| | - Elie Verleyen
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Annick Wilmotte
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
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Zhao L, Lin LZ, Zeng Y, Teng WK, Chen MY, Brand JJ, Zheng LL, Gan NQ, Gong YH, Li XY, Lv J, Chen T, Han BP, Song LR, Shu WS. The facilitating role of phycospheric heterotrophic bacteria in cyanobacterial phosphonate availability and Microcystis bloom maintenance. MICROBIOME 2023; 11:142. [PMID: 37365664 DOI: 10.1186/s40168-023-01582-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/23/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Phosphonates are the main components in the global phosphorus redox cycle. Little is known about phosphonate metabolism in freshwater ecosystems, although rapid consumption of phosphonates has been observed frequently. Cyanobacteria are often the dominant primary producers in freshwaters; yet, only a few strains of cyanobacteria encode phosphonate-degrading (C-P lyase) gene clusters. The phycosphere is defined as the microenvironment in which extensive phytoplankton and heterotrophic bacteria interactions occur. It has been demonstrated that phytoplankton may recruit phycospheric bacteria based on their own needs. Therefore, the establishment of a phycospheric community rich in phosphonate-degrading-bacteria likely facilitates cyanobacterial proliferation, especially in waters with scarce phosphorus. We characterized the distribution of heterotrophic phosphonate-degrading bacteria in field Microcystis bloom samples and in laboratory cyanobacteria "phycospheres" by qPCR and metagenomic analyses. The role of phosphonate-degrading phycospheric bacteria in cyanobacterial proliferation was determined through coculturing of heterotrophic bacteria with an axenic Microcystis aeruginosa strain and by metatranscriptomic analysis using field Microcystis aggregate samples. RESULTS Abundant bacteria that carry C-P lyase clusters were identified in plankton samples from freshwater Lakes Dianchi and Taihu during Microcystis bloom periods. Metagenomic analysis of 162 non-axenic laboratory strains of cyanobacteria (consortia cultures containing heterotrophic bacteria) showed that 20% (128/647) of high-quality bins from eighty of these consortia encode intact C-P lyase clusters, with an abundance ranging up to nearly 13%. Phycospheric bacterial phosphonate catabolism genes were expressed continually across bloom seasons, as demonstrated through metatranscriptomic analysis using sixteen field Microcystis aggregate samples. Coculturing experiments revealed that although Microcystis cultures did not catabolize methylphosphonate when axenic, they demonstrated sustained growth when cocultured with phosphonate-utilizing phycospheric bacteria in medium containing methylphosphonate as the sole source of phosphorus. CONCLUSIONS The recruitment of heterotrophic phosphonate-degrading phycospheric bacteria by cyanobacteria is a hedge against phosphorus scarcity by facilitating phosphonate availability. Cyanobacterial consortia are likely primary contributors to aquatic phosphonate mineralization, thereby facilitating sustained cyanobacterial growth, and even bloom maintenance, in phosphate-deficient waters. Video Abstract.
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Affiliation(s)
- Liang Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
| | - Li-Zhou Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Ying Zeng
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Wen-Kai Teng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Meng-Yun Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jerry J Brand
- Department of Molecular Biosciences and the Culture Collection of Algae, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ling-Ling Zheng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
- National Aquatic Biological Resource Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Nan-Qin Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
| | - Yong-Hui Gong
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Xin-Yi Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jin Lv
- Analysis and Testing Center, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Ting Chen
- Institute for Artificial Intelligence and Department of Computer Science and Technology, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, 510632, People's Republic of China.
| | - Li-Rong Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China.
- National Aquatic Biological Resource Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.
| | - Wen-Sheng Shu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China.
- Guangdong Magigene Biotechnology Co., Ltd., Shenzhen, 518081, People's Republic of China.
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do Amaral SC, Xavier LP, Vasconcelos V, Santos AV. Cyanobacteria: A Promising Source of Antifungal Metabolites. Mar Drugs 2023; 21:359. [PMID: 37367684 DOI: 10.3390/md21060359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/28/2023] Open
Abstract
Cyanobacteria are a rich source of secondary metabolites, and they have received a great deal of attention due to their applicability in different industrial sectors. Some of these substances are known for their notorious ability to inhibit fungal growth. Such metabolites are very chemically and biologically diverse. They can belong to different chemical classes, including peptides, fatty acids, alkaloids, polyketides, and macrolides. Moreover, they can also target different cell components. Filamentous cyanobacteria have been the main source of these compounds. This review aims to identify the key features of these antifungal agents, as well as the sources from which they are obtained, their major targets, and the environmental factors involved when they are being produced. For the preparation of this work, a total of 642 documents dating from 1980 to 2022 were consulted, including patents, original research, review articles, and theses.
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Affiliation(s)
- Samuel Cavalcante do Amaral
- Laboratory of Biotechnology of Enzymes and Biotransformation, Biological Sciences Institute, Federal University of Pará, Belém 66075-110, Brazil
| | - Luciana Pereira Xavier
- Laboratory of Biotechnology of Enzymes and Biotransformation, Biological Sciences Institute, Federal University of Pará, Belém 66075-110, Brazil
| | - Vítor Vasconcelos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, 4450-208 Matosinhos, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Agenor Valadares Santos
- Laboratory of Biotechnology of Enzymes and Biotransformation, Biological Sciences Institute, Federal University of Pará, Belém 66075-110, Brazil
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Deng A, Wang T, Wang J, Li L, Wang X, Liu L, Wen T. Adaptive mechanisms of Bacillus to near space extreme environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 886:163952. [PMID: 37164076 DOI: 10.1016/j.scitotenv.2023.163952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 05/12/2023]
Abstract
Earth's near space is an extreme atmosphere environment with high levels of radiation, low atmospheric pressure and dramatic temperature fluctuations. The region is above the flight altitude of aircraft but below the orbit of satellites, which has special and Mars-like conditions for investigating the survival and evolution of life. Technical limitations including flight devices, payloads and technologies/methodologies hinder microbiological research in near space. In this study, we investigated microbial survival and adaptive strategies in near space using a scientific balloon fight mission and multi-omics analyses. Methods for sample preparation, storage, protector and vessel were optimized to prepare the exposed microbial samples. After 3 h 17 min of exposure at a float altitude of ~32 km, only Bacillus strains were alive with survival efficiencies of 0-10-6. Diverse mutants with significantly altered metabolites were generated, firstly proving that Earth's near space could be used as a new powerful microbial breeding platform. Multi-omics analyses of mutants revealed cascade changes at the genome, transcriptome and proteome levels. In response to environmental stresses, two mutants had similar proteome changes caused by different genomic mutations and mRNA expression levels. Metabolic network analysis combined with proteins' expression levels revealed that metabolic fluxes of EMP, PPP and purine synthesis-related pathways were significantly altered to increase/decrease inosine production. Further analysis showed that proteins related to translation, molecular chaperones, cell wall/membrane, sporulation, DNA replication/repair and anti-oxidation were significantly upregulated, enabling cells to efficiently repair DNA/protein damages and improve viability against environmental stress. Overall, these results revealed genetic and metabolic responses of Bacillus to the harsh conditions in near space, providing a research basis for bacterial adaptive mechanisms in extreme environments.
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Affiliation(s)
- Aihua Deng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Tiantian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junyue Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lai Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueliang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Liu
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Tingyi Wen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid medical school, University of Chinese Academy of Sciences, Beijing 100049, China; China Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing, China.
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36
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Rockwell NC, Lagarias JC. GUN4 appeared early in cyanobacterial evolution. PNAS NEXUS 2023; 2:pgad131. [PMID: 37152672 PMCID: PMC10156173 DOI: 10.1093/pnasnexus/pgad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/15/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023]
Abstract
Photosynthesis relies on chlorophylls, which are synthesized via a common tetrapyrrole trunk pathway also leading to heme, vitamin B12, and other pigmented cofactors. The first committed step for chlorophyll biosynthesis is insertion of magnesium into protoporphyrin IX by magnesium chelatase. Magnesium chelatase is composed of H-, I-, and D-subunits, with the tetrapyrrole substrate binding to the H-subunit. This subunit is rapidly inactivated in the presence of substrate, light, and oxygen, so oxygenic photosynthetic organisms require mechanisms to protect magnesium chelatase from similar loss of function. An additional protein, GUN4, binds to the H-subunit and to tetrapyrroles. GUN4 has been proposed to serve this protective role via its ability to bind linear tetrapyrroles (bilins). In the current work, we probe the origins of bilin binding by GUN4 via comparative phylogenetic analysis and biochemical validation of a conserved bilin-binding motif. Based on our results, we propose that bilin-binding GUN4 proteins arose early in cyanobacterial evolution and that this early acquisition represents an ancient adaptation for maintaining chlorophyll biosynthesis in the presence of light and oxygen.
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37
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Sun J, Lu F, Luo Y, Bie L, Xu L, Wang Y. OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res 2023:7146343. [PMID: 37114999 DOI: 10.1093/nar/gkad313] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Advancements in comparative genomics research have led to a growing interest in studying species evolution and genetic diversity. To facilitate this research, OrthoVenn3 has been developed as a powerful, web-based tool that enables users to efficiently identify and annotate orthologous clusters and infer phylogenetic relationships across a range of species. The latest upgrade of OrthoVenn includes several important new features, including enhanced orthologous cluster identification accuracy, improved visualization capabilities for numerous sets of data, and wrapped phylogenetic analysis. Furthermore, OrthoVenn3 now provides gene family contraction and expansion analysis to support researchers better understanding the evolutionary history of gene families, as well as collinearity analysis to detect conserved and variable genomic structures. With its intuitive user interface and robust functionality, OrthoVenn3 is a valuable resource for comparative genomics research. The tool is freely accessible at https://orthovenn3.bioinfotoolkits.net.
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Affiliation(s)
- Jiahe Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Fang Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Yongjiang Luo
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Lingzi Bie
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Ling Xu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yi Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
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38
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Cheng W, Hwang S, Guo Q, Qian L, Liu W, Yu Y, Liu L, Tao Y, Cao H. The Special and General Mechanism of Cyanobacterial Harmful Algal Blooms. Microorganisms 2023; 11:microorganisms11040987. [PMID: 37110410 PMCID: PMC10144548 DOI: 10.3390/microorganisms11040987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
Cyanobacterial harmful algal blooms (CyanoHABs) are longstanding aquatic hazards worldwide, of which the mechanism is not yet fully understood, i.e., the process in which cyanobacteria establish dominance over coexisting algae in the same eutrophic waters. The dominance of CyanoHABs represents a deviation from their low abundance under conventional evolution in the oligotrophic state, which has been the case since the origin of cyanobacteria on early Earth. To piece together a comprehensive mechanism of CyanoHABs, we revisit the origin and adaptive radiation of cyanobacteria in oligotrophic Earth, demonstrating ubiquitous adaptive radiation enabled by corresponding biological functions under various oligotrophic conditions. Next, we summarize the biological functions (ecophysiology) which drive CyanoHABs and ecological evidence to synthesize a working mechanism at the population level (the special mechanism) for CyanoHABs: CyanoHABs are the consequence of the synergistic interaction between superior cyanobacterial ecophysiology and elevated nutrients. Interestingly, these biological functions are not a result of positive selection by water eutrophication, but an adaptation to a longstanding oligotrophic state as all the genes in cyanobacteria are under strong negative selection. Last, to address the relative dominance of cyanobacteria over coexisting algae, we postulate a "general" mechanism of CyanoHABs at the community level from an energy and matter perspective: cyanobacteria are simpler life forms and thus have lower per capita nutrient demand for growth than coexisting eukaryotic algae. We prove this by comparing cyanobacteria and eukaryotic algae in cell size and structure, genome size, size of genome-scale metabolic networks, cell content, and finally the golden standard-field studies with nutrient supplementation in the same waters. To sum up, the comprehensive mechanism of CyanoHABs comprises a necessary condition, which is the general mechanism, and a sufficient condition, which is the special mechanism. One prominent prediction based on this tentative comprehensive mechanism is that eukaryotic algal blooms will coexist with or replace CyanoHABs if eutrophication continues and goes over the threshold nutrient levels for eukaryotic algae. This two-fold comprehensive mechanism awaits further theoretic and experimental testing and provides an important guide to control blooms of all algal species.
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Affiliation(s)
- Wenduo Cheng
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Somin Hwang
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Qisen Guo
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Leyuan Qian
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Weile Liu
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Yang Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Li Liu
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Yi Tao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Huansheng Cao
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
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D'Angelo T, Goordial J, Lindsay MR, McGonigle J, Booker A, Moser D, Stepanauskus R, Orcutt BN. Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota. THE ISME JOURNAL 2023; 17:891-902. [PMID: 37012337 DOI: 10.1038/s41396-023-01397-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023]
Abstract
The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms important to biogeochemical and industrial processes. These phyla are common inhabitants of marine and terrestrial subsurface environments and contain members capable of diverse physiologies in addition to nitrite oxidation and complete ammonia oxidation. Here, we use phylogenomics and gene-based analysis with ancestral state reconstruction and gene-tree-species-tree reconciliation methods to investigate the life histories of these two phyla. We find that basal clades of both phyla primarily inhabit marine and terrestrial subsurface environments. The genomes of basal clades in both phyla appear smaller and more densely coded than the later-branching clades. The extant basal clades of both phyla share many traits inferred to be present in their respective common ancestors, including hydrogen, one-carbon, and sulfur-based metabolisms. Later-branching groups, namely the more frequently studied classes Nitrospiria and Nitrospinia, are both characterized by genome expansions driven by either de novo origination or laterally transferred genes that encode functions expanding their metabolic repertoire. These expansions include gene clusters that perform the unique nitrogen metabolisms that both phyla are most well known for. Our analyses support replicated evolutionary histories of these two bacterial phyla, with modern subsurface environments representing a genomic repository for the coding potential of ancestral metabolic traits.
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Affiliation(s)
- Timothy D'Angelo
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - Jacqueline Goordial
- University of Guelph, School of Environmental Sciences, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Melody R Lindsay
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - Julia McGonigle
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
- Basepaws Pet Genetics, 1820 W. Carson Street, Suite 202-351, Torrance, CA, 90501, USA
| | - Anne Booker
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - Duane Moser
- Desert Research Institute, 755 East Flamingo Road, Las Vegas, NV, 89119, USA
| | - Ramunas Stepanauskus
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA.
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40
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Fang GY, Mu XJ, Huang BW, Jiang YJ. Monitoring Longitudinal Trends and Assessment of the Health Risk of Shigella flexneri Antimicrobial Resistance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4971-4983. [PMID: 36929874 DOI: 10.1021/acs.est.2c08766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Shigella flexneri infection is the main cause of diarrhea in humans worldwide. The emergence of antimicrobial resistance (AMR) of S. flexneri is a growing public health threat worldwide, while large-scale studies monitoring the longitudinal AMR trends of isolates remain scarce. Here, the AMR gene (ARG) profiles of 717 S. flexneri isolates from 1920 to 2020 worldwide were determined. The results showed that the average number of ARGs in isolates has increased significantly, from 19.2 ± 2.4 before 1970 to 29.6 ± 5.3 after 2010. In addition, mobile genetic elements were important contributors to ARGs in S. flexneri isolates. The results of the structural equation model showed that the human development index drove the consumption of antibiotics and indirectly promoted the antibiotic resistance. Finally, a machine learning algorithm was used to predict the antibiotic resistance risk of global terrestrial S. flexneri isolates and successfully map the antibiotic resistance threats in global land habitats with over 80% accuracy. Collectively, this study monitored the longitudinal AMR trends, quantitatively surveilled the health risk of S. flexneri AMR, and provided a theoretical basis for mitigating the threat of antibiotic resistance.
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Affiliation(s)
- Guan-Yu Fang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
| | - Xiao-Jing Mu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
- Suzhou Precision Biotech Co., Ltd, Suzhou 215000, P. R. China
| | - Bing-Wen Huang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
| | - Yu-Jian Jiang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
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41
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Rodríguez-Gijón A, Buck M, Andersson AF, Izabel-Shen D, Nascimento FJA, Garcia SL. Linking prokaryotic genome size variation to metabolic potential and environment. ISME COMMUNICATIONS 2023; 3:25. [PMID: 36973336 PMCID: PMC10042847 DOI: 10.1038/s43705-023-00231-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023]
Abstract
While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.
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Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, Stockholm, Sweden
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
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Li F, Hou W, Wang S, Zhang Y, He Q, Zhang W, Dong H. Effects of Mineral on Taxonomic and Functional Structures of Microbial Community in Tengchong Hot Springs via in-situ cultivation. ENVIRONMENTAL MICROBIOME 2023; 18:22. [PMID: 36949539 PMCID: PMC10035157 DOI: 10.1186/s40793-023-00481-1] [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: 12/13/2022] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
Diverse mineralogical compositions occur in hot spring sediments, but the impact of minerals on the diversity and structure of microbial communities remains poorly elucidated. In this study, different mineral particles with various chemistries (i.e., hematite, biotite, K-feldspar, quartz, muscovite, aragonite, serpentine, olivine, barite, apatite, and pyrite) were incubated for ten days in two Tengchong hot springs, one alkaline (pH ~ 8.34) with a high temperature (~ 82.8 °C) (Gumingquan, short as GMQ) and one acidic (pH ~ 3.63) with a relatively low temperature (~ 43.3 °C) (Wenguangting, short as WGT), to determine the impacts of minerals on the microbial communities taxonomic and functional diversities. Results showed that the mineral-associated bacterial taxa differed from those of the bulk sediment samples in the two hot springs. The relative abundance of Proteobacteria, Euryarchaeota, and Acidobacteria increased in all minerals, indicating that these microorganisms are apt to colonize on solid surfaces. The α-diversity indices of the microbial communities on the mineral surfaces in the WGT were higher than those from the bulk sediment samples (p < 0.05), which may be caused by the stochastically adhering process on the mineral surface during 10-day incubation, different from the microbial community in sediment which has experienced long-term environmental and ecological screening. Chemoheterotrophy increased with minerals incubation, which was high in most cultured minerals (the relative contents were 5.8 - 21.4%). Most notably, the sulfate respiration bacteria (mainly related to Desulfobulbaceae and Syntrophaceae) associated with aragonite in the acidic hot spring significantly differed from other minerals, possibly due to the pH buffering effect of aragonite providing more favorable conditions for their survival and proliferation. By comparison, aragonite cultured in the alkaline hot spring highly enriched denitrifying bacteria and may have promoted the nitrogen cycle within the system. Collectively, we speculated that diverse microbes stochastically adhered on the surface of minerals in the water flows, and the physicochemical properties of minerals drove the enrichment of certain microbial communities and functional groups during the short-term incubation. Taken together, these findings thereby provide novel insights into mechanisms of community assembly and element cycling in the terrestrial hydrothermal system associated with hot springs.
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Affiliation(s)
- Fangru Li
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Weiguo Hou
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Yidi Zhang
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Qing He
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Wenhui Zhang
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
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Chiriac MC, Haber M, Salcher MM. Adaptive genetic traits in pelagic freshwater microbes. Environ Microbiol 2023; 25:606-641. [PMID: 36513610 DOI: 10.1111/1462-2920.16313] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.
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Affiliation(s)
| | - Markus Haber
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
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Tang J, Yao D, Zhou H, Wang M, Daroch M. Distinct Molecular Patterns of Two-Component Signal Transduction Systems in Thermophilic Cyanobacteria as Revealed by Genomic Identification. BIOLOGY 2023; 12:biology12020271. [PMID: 36829548 PMCID: PMC9953108 DOI: 10.3390/biology12020271] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
Two-component systems (TCSs) play crucial roles in sensing and responding to environmental signals, facilitating the acclimation of cyanobacteria to hostile niches. To date, there is limited information on the TCSs of thermophilic cyanobacteria. Here, genome-based approaches were used to gain insights into the structure and architecture of the TCS in 17 well-described thermophilic cyanobacteria, namely strains from the genus Leptodesmis, Leptolyngbya, Leptothermofonsia, Thermoleptolyngbya, Thermostichus, and Thermosynechococcus. The results revealed a fascinating complexity and diversity of the TCSs. A distinct composition of TCS genes existed among these thermophilic cyanobacteria. A majority of TCS genes were classified as orphan, followed by the paired and complex cluster. A high proportion of histidine kinases (HKs) were predicted to be cytosolic subcellular localizations. Further analyses suggested diversified domain architectures of HK and response regulators (RRs), putatively in association with various functions. Comparative and evolutionary genomic analyses indicated that the horizontal gene transfer, as well as duplications events, might be involved in the evolutionary history of TCS genes in Thermostichus and Thermosynechococcus strains. A comparative analysis between thermophilic and mesophilic cyanobacteria indicated that one HK cluster and one RR cluster were uniquely shared by all the thermophilic cyanobacteria studied, while two HK clusters and one RR cluster were common to all the filamentous thermophilic cyanobacteria. These results suggested that these thermophile-unique clusters may be related to thermal characters and morphology. Collectively, this study shed light on the TCSs of thermophilic cyanobacteria, which may confer the necessary regulatory flexibility; these findings highlight that the genomes of thermophilic cyanobacteria have a broad potential for acclimations to environmental fluctuations.
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Affiliation(s)
- Jie Tang
- School of Food and Bioengineering, Chengdu University, Chengdu 610106, China
| | - Dan Yao
- School of Food and Bioengineering, Chengdu University, Chengdu 610106, China
| | - Huizhen Zhou
- School of Food and Bioengineering, Chengdu University, Chengdu 610106, China
| | - Mingcheng Wang
- School of Food and Bioengineering, Chengdu University, Chengdu 610106, China
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, 2199 Lishui Road, Shenzhen 518055, China
- Correspondence: ; Tel.: +86-0755-2603-2184
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Kokate PP, Bales E, Joyner D, Hazen TC, Techtmann SM. Biogeographic patterns in populations of marine Pseudoalteromonas atlantica isolates. FEMS Microbiol Lett 2023; 370:fnad081. [PMID: 37573136 DOI: 10.1093/femsle/fnad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/14/2023] [Accepted: 08/11/2023] [Indexed: 08/14/2023] Open
Abstract
Intra-specific genomic diversity is well documented in microbes. The question, however, remains whether natural selection or neutral evolution is the major contributor to this diversity. We undertook this study to estimate genomic diversity in Pseudoalteromonas atlantica populations and whether the diversity, if present, could be attributed to environmental factors or distance effects. We isolated and sequenced twenty-three strains of P. atlantica from three geographically distant deep marine basins and performed comparative genomic analyses to study the genomic diversity of populations among these basins. Average nucleotide identity followed a strictly geographical pattern. In two out of three locations, the strains within the location exhibited >99.5% identity, whereas, among locations, the strains showed <98.11% identity. Phylogenetic and pan-genome analysis also reflected the biogeographical separation of the strains. Strains from the same location shared many accessory genes and clustered closely on the phylogenetic tree. Phenotypic diversity between populations was studied in ten out of twenty-three strains testing carbon and nitrogen source utilization and osmotolerance. A genetic basis for phenotypic diversity could be established in most cases but was apparently not influenced by local environmental conditions. Our study suggests that neutral evolution may have a substantial role in the biodiversity of P. atlantica.
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Affiliation(s)
- Prajakta P Kokate
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, United States
| | - Erika Bales
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN 37996, United States
| | - Dominique Joyner
- Department of Civil and Environmental Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, United States
| | - Terry C Hazen
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, United States
| | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, United States
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Tang J, Zhou H, Jiang Y, Yao D, Waleron KF, Du LM, Daroch M. Characterization of a novel thermophilic cyanobacterium within Trichocoleusaceae, Trichothermofontia sichuanensis gen. et sp. nov., and its CO 2-concentrating mechanism. Front Microbiol 2023; 14:1111809. [PMID: 37180226 PMCID: PMC10172474 DOI: 10.3389/fmicb.2023.1111809] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
Thermophiles from extreme thermal environments have shown tremendous potential regarding ecological and biotechnological applications. Nevertheless, thermophilic cyanobacteria remain largely untapped and are rarely characterized. Herein, a polyphasic approach was used to characterize a thermophilic strain, PKUAC-SCTB231 (hereafter B231), isolated from a hot spring (pH 6.62, 55.5°C) in Zhonggu village, China. The analyses of 16S rRNA phylogeny, secondary structures of 16S-23S ITS and morphology strongly supported strain B231 as a novel genus within Trichocoleusaceae. Phylogenomic inference and three genome-based indices further verified the genus delineation. Based on the botanical code, the isolate is herein delineated as Trichothermofontia sichuanensis gen. et sp. nov., a genus closely related to a validly described genus Trichocoleus. In addition, our results suggest that Pinocchia currently classified to belong to the family Leptolyngbyaceae may require revision and assignment to the family Trichocoleusaceae. Furthermore, the complete genome of Trichothermofontia B231 facilitated the elucidation of the genetic basis regarding genes related to its carbon-concentrating mechanism (CCM). The strain belongs to β-cyanobacteria according to its β-carboxysome shell protein and 1B form of Ribulose bisphosphate Carboxylase-Oxygenase (RubisCO). Compared to other thermophilic strains, strain B231contains a relatively low diversity of bicarbonate transporters (only BicA for HCO3- transport) but a higher abundance of different types of carbonic anhydrase (CA), β-CA (ccaA) and γ-CA (ccmM). The BCT1 transporter consistently possessed by freshwater cyanobacteria was absent in strain B231. Similar situation was occasionally observed in freshwater thermal Thermoleptolyngbya and Thermosynechococcus strains. Moreover, strain B231 shows a similar composition of carboxysome shell proteins (ccmK1-4, ccmL, -M, -N, -O, and -P) to mesophilic cyanobacteria, the diversity of which was higher than many thermophilic strains lacking at least one of the four ccmK genes. The genomic distribution of CCM-related genes suggests that the expression of some components is regulated as an operon and others in an independently controlled satellite locus. The current study also offers fundamental information for future taxogenomics, ecogenomics and geogenomic studies on distribution and significance of thermophilic cyanobacteria in the global ecosystem.
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Affiliation(s)
- Jie Tang
- School of Food and Bioengineering, Chengdu University, Chengdu, Sichuan, China
| | - Huizhen Zhou
- School of Food and Bioengineering, Chengdu University, Chengdu, Sichuan, China
| | - Ying Jiang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Dan Yao
- School of Food and Bioengineering, Chengdu University, Chengdu, Sichuan, China
| | - Krzysztof F. Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy Medical University of Gdańsk, Gdańsk, Poland
| | - Lian-Ming Du
- School of Food and Bioengineering, Chengdu University, Chengdu, Sichuan, China
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
- *Correspondence: Maurycy Daroch,
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Quantification of Marine Picocyanobacteria on Water Column Particles and in Sediments Using Real-Time PCR Reveals Their Role in Carbon Export. mSphere 2022; 7:e0049922. [PMID: 36472446 PMCID: PMC9769826 DOI: 10.1128/msphere.00499-22] [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] [Indexed: 12/12/2022] Open
Abstract
Picocyanobacteria are the most abundant primary producers in the ocean and play a fundamental role in marine carbon cycling. Quantification of picocyanobacteria on sinking particles and in sediments is essential to understanding their contribution to the biological carbon pump. We designed a primer set targeting the 16S-23S rRNA internal transcribed spacer (ITS) sequence of cyanobacteria and established a quantitative PCR (qPCR) method for quantifying the ITS sequence abundance. High-throughput sequencing confirmed that this primer set can cover broad diversities of marine picocyanobacteria and avoid amplification of other marine cyanobacteria such as Trichodesmium and Crocosphaera. Amplification efficiencies were slightly different when seven marine Synechococcus and Prochlorococcus strains were assayed. The qPCR results were comparable with flow cytometry for water samples. Using this method, we found that, in the dark ocean, picocyanobacterial ITS sequence abundances were 10 to 100 copies/mL in the size fraction of 0.2 to 3 μm, which were 1 to 3 orders of magnitude more abundant than on the >3-μm particles. We also found that picocyanobacterial ITS abundance in sediment ranged from 105 to 107 copies/g along two nearshore-to-offshore transects in the northern South China Sea. These results further explain the important role of picocyanobacteria in carbon export. Collectively, we provide a qPCR method quantifying the total abundance of marine picocyanobacteria on water column particles and in sediments. Moreover, this newly designed primer set can be also applied to investigate the community of picocyanobacteria via high-throughput sequencing. IMPORTANCE Picocyanobacteria are the most abundant primary producers in the ocean. However, quantification of picocyanobacteria on the sinking particles and in sediments remains challenging using flow cytometry or epifluorescence microscopy. Here, we developed a real-time PCR method to quantify picocyanobacteria using a newly designed primer set specifically targeting the 16S-23S rRNA ITS sequence of cyanobacteria. We showed that in the dark ocean, picocyanobacteria are 1 to 3 orders of magnitude more abundant in small particles (0.2 to 3 μm) than in larger particles (>3 μm). This result supports the important role of direct sinking free-living picocyanobacteria cells in the carbon export to deep ocean. We also found that the picocyanobacterial ITS sequence abundance were 105 to 107 copies per gram in sediments, suggesting significant accumulation of sinking picocyanobacteria in the benthic ecosystem. This qPCR method can be used to quantify the contribution of picocyanobacteria to the biological carbon pump.
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Cyanobacterial Blooms Are Not a Result of Positive Selection by Freshwater Eutrophication. Microbiol Spectr 2022; 10:e0319422. [PMID: 36445094 PMCID: PMC9769789 DOI: 10.1128/spectrum.03194-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Long-standing cyanobacterial harmful algal blooms (CyanoHABs) are known to result from synergistic interaction between elevated nutrients and superior ecophysiology of cyanobacteria. However, it remains to be determined whether CyanoHABs are a result of positive selection by eutrophic waters. To address this, we conducted molecular evolutionary analyses on the genomes of 9 bloom-forming cyanobacteria, combined with pangenomics and metatranscriptomics. The results showed no positive selection by water eutrophication. Instead, all homologous genes in the species are under strong purifying selection based on the ratio of divergence at nonsynonymous and synonymous sites (dN/dS) and phylogeny. The dN/dS < 0.85 (median = 0.3) for all homologous genes are similar between the genes in the pathways driving CyanoHABs and housekeeping functions. Phylogenetic support for non-positive selection comes from the mixed clustering of strains: strains of the same species from diverse geographic origins form the same clusters, while strains from the same origins form different clusters. Further support lies in the codon adaptation index (CAI) and single nucleotide polymorphism (SNP). The CAI ranged from 0.42 to 0.9 (mean = 0.75), which indicates high-level codon usage bias; the pathways for CyanoHABs and housekeeping functions showed a similar CAI. Interestingly, CAI was negatively correlated with gene expression in 3 metatranscriptomes. The numbers of SNPs were concentrated around 5 to 50. As the SNP number increases, the gene expression level decreases. These negative correlations agree with the population-level dN/dS and phylogeny in supporting purifying selection in bloom-forming cyanobacteria. In summary, superior ecophysiology appears to be acquired prior to water eutrophication. IMPORTANCE CyanoHABs are global environmental hazards, and their mechanisms of action are being intensively investigated. On an ecological scale, CyanoHABs are consequences of synergistic interactions between biological functions and elevated nutrients in eutrophic waters. On an evolutionary scale, one important question is how bloom-forming cyanobacteria acquire these superior biological functions. There are several possibilities, including adaptive evolution and horizontal gene transfer. Here, we explored the possibility of positive selection. We reasoned that there are two possible periods for cyanobacteria to acquire these functions: before the onset of water eutrophication or during water eutrophication. Either way, there should be molecular signatures in protein sequences for positive selection. Interestingly, we found no positive selection by water eutrophication, but strong purifying selection instead on nearly all the genes, suggesting these superior functions aiding CyanoHABs are acquired prior to water eutrophication.
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Saati-Santamaría Z, Baroncelli R, Rivas R, García-Fraile P. Comparative Genomics of the Genus Pseudomonas Reveals Host- and Environment-Specific Evolution. Microbiol Spectr 2022; 10:e0237022. [PMID: 36354324 PMCID: PMC9769992 DOI: 10.1128/spectrum.02370-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
Each Earth ecosystem has unique microbial communities. Pseudomonas bacteria have evolved to occupy a plethora of different ecological niches, including living hosts, such as animals and plants. Many genes necessary for the Pseudomonas-niche interaction and their encoded functions remain unknown. Here, we describe a comparative genomic study of 3,274 genomes with 19,056,667 protein-coding sequences from Pseudomonas strains isolated from diverse environments. We detected functional divergence of Pseudomonas that depends on the niche. Each group of strains from a certain environment harbored a distinctive set of metabolic pathways or functions. The horizontal transfer of genes, which mainly proceeded between closely related taxa, was dependent on the isolation source. Finally, we detected thousands of undescribed proteins and functions associated with each Pseudomonas lifestyle. This research represents an effort to reveal the mechanisms underlying the ecology, pathogenicity, and evolution of Pseudomonas, and it will enable clinical, ecological, and biotechnological advances. IMPORTANCE Microbes play important roles in the health of living beings and in the environment. The knowledge of these functions may be useful for the development of new clinical and biotechnological applications and the restoration and preservation of natural ecosystems. However, most mechanisms implicated in the interaction of microbes with the environment remain poorly understood; thus, this field of research is very important. Here, we try to understand the mechanisms that facilitate the differential adaptation of Pseudomonas-a large and ubiquitous bacterial genus-to the environment. We analyzed more than 3,000 Pseudomonas genomes and searched for genetic patterns that can be related with their coevolution with different hosts (animals, plants, or fungi) and environments. Our results revealed that thousands of genes and genetic features are associated with each niche. Our data may be useful to develop new technical and theoretical advances in the fields of ecology, health, and industry.
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Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
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50
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Kim J, Cha IT, Lee KE, Son YK, Yu J, Seol D. Characteristics and adaptability of Flavobacterium panici BSSL-CR3 in tidal flat revealed by comparative genomic and enzymatic analysis. Arch Microbiol 2022; 205:22. [PMID: 36495352 DOI: 10.1007/s00203-022-03359-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/22/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
Tidal flat microbes play an important ecological role by removing organic pollutants and providing an energy source. However, bacteria isolated from tidal flats and their genomes have been scarcely reported, making it difficult to elucidate which genes and pathways are potentially involved in the above roles. In this study, strain BSSL-CR3, the third reported species among the tidal flat Flavobacterium was analyzed using whole-genome sequencing to investigate its adaptability and functionality in tidal flats. BSSL-CR3 is comprised of a circular chromosome of 5,972,859 bp with a GC content of 33.84%. Genome annotation and API ZYM results showed that BSSL-CR3 has a variety of secondary metabolic gene clusters and enzyme activities including α-galactosidase. BSSL-CR3 had more proteins with a low isoelectric point (pI) than terrestrial Flavobacterium strains, and several genes related to osmotic regulation were found in the genomic island (GI). Comparative genomic analysis with other tidal flat bacteria also revealed that BSSL-CR3 had the largest number of genes encoding Carbohydrate Active EnZymes (CAZymes) which are related to algae degradation. This study will provide insight into the adaptability of BSSL-CR3 to the tidal flats and contribute to facilitating future comparative analysis of bacteria in tidal flats.
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Affiliation(s)
- Jina Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
| | - In-Tae Cha
- Microorganism Resources Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Youn Kyoung Son
- Microorganism Resources Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Jaewoong Yu
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea.
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea.
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