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Hamilton M, Ferrer‐González FX, Moran MA. Heterotrophic bacteria trigger transcriptome remodelling in the photosynthetic picoeukaryote Micromonas commoda. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13285. [PMID: 38778545 PMCID: PMC11112143 DOI: 10.1111/1758-2229.13285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Marine biogeochemical cycles are built on interactions between surface ocean microbes, particularly those connecting phytoplankton primary producers to heterotrophic bacteria. Details of these associations are not well understood, especially in the case of direct influences of bacteria on phytoplankton physiology. Here we catalogue how the presence of three marine bacteria (Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14 and Polaribacter dokdonensis MED152) individually and uniquely impact gene expression of the picoeukaryotic alga Micromonas commoda RCC 299. We find a dramatic transcriptomic remodelling by M. commoda after 8 h in co-culture, followed by an increase in cell numbers by 56 h compared with the axenic cultures. Some aspects of the algal transcriptomic response are conserved across all three bacterial co-cultures, including an unexpected reduction in relative expression of photosynthesis and carbon fixation pathways. Expression differences restricted to a single bacterium are also observed, with the Flavobacteriia P. dokdonensis uniquely eliciting changes in relative expression of algal genes involved in biotin biosynthesis and the acquisition and assimilation of nitrogen. This study reveals that M. commoda has rapid and extensive responses to heterotrophic bacteria in ways that are generalizable, as well as in a taxon specific manner, with implications for the diversity of phytoplankton-bacteria interactions ongoing in the surface ocean.
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Affiliation(s)
- Maria Hamilton
- Department of Marine SciencesUniversity of GeorgiaAthensGeorgiaUSA
| | | | - Mary Ann Moran
- Department of Marine SciencesUniversity of GeorgiaAthensGeorgiaUSA
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2
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Kuhlisch C, Shemi A, Barak-Gavish N, Schatz D, Vardi A. Algal blooms in the ocean: hot spots for chemically mediated microbial interactions. Nat Rev Microbiol 2024; 22:138-154. [PMID: 37833328 DOI: 10.1038/s41579-023-00975-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2023] [Indexed: 10/15/2023]
Abstract
The cycling of major nutrients in the ocean is affected by large-scale phytoplankton blooms, which are hot spots of microbial life. Diverse microbial interactions regulate bloom dynamics. At the single-cell level, interactions between microorganisms are mediated by small molecules in the chemical crosstalk that determines the type of interaction, ranging from mutualism to pathogenicity. Algae interact with viruses, bacteria, parasites, grazers and other algae to modulate algal cell fate, and these interactions are dependent on the environmental context. Recent advances in mass spectrometry and single-cell technologies have led to the discovery of a growing number of infochemicals - metabolites that convey information - revealing the ability of algal cells to govern biotic interactions in the ocean. The diversity of infochemicals seems to account for the specificity in cellular response during microbial communication. Given the immense impact of algal blooms on biogeochemical cycles and climate regulation, a major challenge is to elucidate how microscale interactions control the fate of carbon and the recycling of major elements in the ocean. In this Review, we discuss microbial interactions and the role of infochemicals in algal blooms. We further explore factors that can impact microbial interactions and the available tools to decipher them in the natural environment.
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Affiliation(s)
- Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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Branscombe L, Harrison EL, Choong ZYD, Swink C, Keys M, Widdicombe C, Wilson WH, Cunliffe M, Helliwell K. Cryptic bacterial pathogens of diatoms peak during senescence of a winter diatom bloom. THE NEW PHYTOLOGIST 2024; 241:1292-1307. [PMID: 38037269 DOI: 10.1111/nph.19441] [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: 07/12/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023]
Abstract
Diatoms are globally abundant microalgae that form extensive blooms in aquatic ecosystems. Certain bacteria behave antagonistically towards diatoms, killing or inhibiting their growth. Despite their crucial implications to diatom blooms and population health, knowledge of diatom antagonists in the environment is fundamentally lacking. We report systematic characterisation of the diversity and seasonal dynamics of bacterial antagonists of diatoms via plaque assay sampling in the Western English Channel (WEC), where diatoms frequently bloom. Unexpectedly, peaks in detection did not occur during characteristic spring diatom blooms, but coincided with a winter bloom of Coscinodiscus, suggesting that these bacteria likely influence distinct diatom host populations. We isolated multiple bacterial antagonists, spanning 4 classes and 10 bacterial orders. Notably, a diatom attaching Roseobacter Ponticoccus alexandrii was isolated multiple times, indicative of a persistent environmental presence. Moreover, many isolates had no prior reports of antagonistic activity towards diatoms. We verified diatom growth inhibitory effects of eight isolates. In all cases tested, these effects were activated by pre-exposure to diatom organic matter. Discovery of widespread 'cryptic' antagonistic activity indicates that bacterial pathogenicity towards diatoms is more prevalent than previously recognised. Finally, examination of the global biogeography of WEC antagonists revealed co-occurrence patterns with diatom host populations in marine waters globally.
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Affiliation(s)
- Laura Branscombe
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Ellen L Harrison
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Zhi Yi Daniel Choong
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Courtney Swink
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Matthew Keys
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
| | | | - William H Wilson
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Michael Cunliffe
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Katherine Helliwell
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
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Lang-Yona N, Flores JM, Nir-Zadock TS, Nussbaum I, Koren I, Vardi A. Impact of airborne algicidal bacteria on marine phytoplankton blooms. THE ISME JOURNAL 2024; 18:wrae016. [PMID: 38442732 PMCID: PMC10944695 DOI: 10.1093/ismejo/wrae016] [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: 01/09/2024] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 03/07/2024]
Abstract
Ocean microbes are involved in global processes such as nutrient and carbon cycling. Recent studies indicated diverse modes of algal-bacterial interactions, including mutualism and pathogenicity, which have a substantial impact on ecology and oceanic carbon sequestration, and hence, on climate. However, the airborne dispersal and pathogenicity of bacteria in the marine ecosystem remained elusive. Here, we isolated an airborne algicidal bacterium, Roseovarius nubinhibens, emitted to the atmosphere as primary marine aerosol (referred also as sea spray aerosols) and collected above a coccolithophore bloom in the North Atlantic Ocean. The aerosolized bacteria retained infective properties and induced lysis of Gephyrocapsa huxleyi cultures.This suggests that the transport of marine bacteria through the atmosphere can effectively spread infection agents over vast oceanic regions, highlighting its significance in regulating the cell fate in algal blooms.
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Affiliation(s)
- Naama Lang-Yona
- Department of Plant and Environmental Science, Weizmann Institute of Science, Rehovot 7610001, Israel
- Technion - Israel Institute of Technology, Environmental, Water and Agricultural Engineering, Haifa 3200003, Israel
| | - J Michel Flores
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tal Sharon Nir-Zadock
- Department of Plant and Environmental Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Inbal Nussbaum
- Department of Plant and Environmental Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ilan Koren
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Science, Weizmann Institute of Science, Rehovot 7610001, Israel
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Di Costanzo F, Di Dato V, Romano G. Diatom-Bacteria Interactions in the Marine Environment: Complexity, Heterogeneity, and Potential for Biotechnological Applications. Microorganisms 2023; 11:2967. [PMID: 38138111 PMCID: PMC10745847 DOI: 10.3390/microorganisms11122967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/28/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Diatom-bacteria interactions evolved during more than 200 million years of coexistence in the same environment. In this time frame, they established complex and heterogeneous cohorts and consortia, creating networks of multiple cell-to-cell mutualistic or antagonistic interactions for nutrient exchanges, communication, and defence. The most diffused type of interaction between diatoms and bacteria is based on a win-win relationship in which bacteria benefit from the organic matter and nutrients released by diatoms, while these last rely on bacteria for the supply of nutrients they are not able to produce, such as vitamins and nitrogen. Despite the importance of diatom-bacteria interactions in the evolutionary history of diatoms, especially in structuring the marine food web and controlling algal blooms, the molecular mechanisms underlying them remain poorly studied. This review aims to present a comprehensive report on diatom-bacteria interactions, illustrating the different interplays described until now and the chemical cues involved in the communication and exchange between the two groups of organisms. We also discuss the potential biotechnological applications of molecules and processes involved in those fascinating marine microbial networks and provide information on novel approaches to unveiling the molecular mechanisms underlying diatom-bacteria interactions.
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Affiliation(s)
| | - Valeria Di Dato
- Stazione Zoologica Anton Dohrn Napoli, Ecosustainable Marine Biotechnology Department, Via Ammiraglio Ferdinando Acton 55, 80133 Napoli, Italy; (F.D.C.); (G.R.)
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Poulsen N, Kröger N. Thalassiosira pseudonana (Cyclotella nana) (Hustedt) Hasle et Heimdal (Bacillariophyceae): A genetically tractable model organism for studying diatom biology, including biological silica formation. JOURNAL OF PHYCOLOGY 2023; 59:809-817. [PMID: 37424141 DOI: 10.1111/jpy.13362] [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] [Accepted: 06/15/2023] [Indexed: 07/11/2023]
Abstract
In 2004, Thalassiosira pseudonana was the first eukaryotic marine alga to have its genome sequenced. Since then, this species has quickly emerged as a valuable model species for investigating the molecular underpinnings of essentially all aspects of diatom life, particularly bio-morphogenesis of the cell wall. An important prerequisite for the model status of T. pseudonana is the ongoing development of increasingly precise tools to study the function of gene networks and their encoded proteins in vivo. Here, we briefly review the current toolbox for genetic manipulation, highlight specific examples of its application in studying diatom metabolism, and provide a peek into the role of diatoms in the emerging field of silica biotechnology.
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Affiliation(s)
- Nicole Poulsen
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Nils Kröger
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
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Makaranga A, Jutur PP. Dynamic metabolomic crosstalk between Chlorella saccharophila and its new symbiotic bacteria enhances lutein production in microalga without compromising its biomass. Enzyme Microb Technol 2023; 170:110291. [PMID: 37481992 DOI: 10.1016/j.enzmictec.2023.110291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/29/2023] [Accepted: 07/16/2023] [Indexed: 07/25/2023]
Abstract
The microalgae Chlorella saccharophila UTEX247 was co-cultured with its symbiotic indigenous isolated bacterial strain, Exiguobacterium sp., to determine the possible effects of bacteria on microalgae growth and lutein productivity. Under optimal conditions, the lutein productivity of co-culture was 298.97 µg L-1 d-1, which was nearly 1.45-fold higher compared to monocultures i.e., 103.3 µg L-1 d-1. The highest lutein productivities were obtained in co-cultures, accompanied by a significant increase in cell biomass up to 0.84-fold. These conditions were analyzed using an untargeted metabolomics approach to identify metabolites enhancing valuable renewables, i.e., lutein, without compromising growth. Our qualitative metabolomic analysis identified nearly 30 (microalgae alone), 41 (bacteria alone), and 75 (co-cultures) metabolites, respectively. Among these, 46 metabolites were unique in the co-culture alone. The co-culture interactions significantly altered the role of metabolites such as thiamine precursors, reactive sugar anomers like furanose and branched-chain amino acids (BCAA). Nevertheless, the central metabolism cycle upregulation depicted increased availability of carbon skeletons, leading to increased cell biomass and pigments. In conclusion, the co-cultures induce the production of relevant metabolites which regulate growth and lutein simultaneously in C. saccharophila UTEX247, which paves the way for a new perspective in microalgal biorefineries.
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Affiliation(s)
- Abdalah Makaranga
- Omics of Algae Group and DBT-ICGEB Centre for Advanced Bioenergy Research, Industrial Biotechnology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pannaga Pavan Jutur
- Omics of Algae Group and DBT-ICGEB Centre for Advanced Bioenergy Research, Industrial Biotechnology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Zhu J, Tang S, Cheng K, Cai Z, Chen G, Zhou J. Microbial community composition and metabolic potential during a succession of algal blooms from Skeletonema sp. to Phaeocystis sp. Front Microbiol 2023; 14:1147187. [PMID: 37138603 PMCID: PMC10149697 DOI: 10.3389/fmicb.2023.1147187] [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: 01/18/2023] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
Elucidating the interactions between algal and microbial communities is essential for understanding the dynamic mechanisms regulating algal blooms in the marine environment. Shifts in bacterial communities when a single species dominates algal blooms have been extensively investigated. However, bacterioplankton community dynamics during bloom succession when one algal species shift to another is still poorly understood. In this study, we used metagenomic analysis to investigate the bacterial community composition and function during algal bloom succession from Skeletonema sp. to Phaeocystis sp. The results revealed that bacterial community structure and function shifted with bloom succession. The dominant group in the Skeletonema bloom was Alphaproteobacteria, while Bacteroidia and Gammaproteobacteria dominated the Phaeocystis bloom. The most noticeable feature during the successions was the change from Rhodobacteraceae to Flavobacteriaceae in the bacterial communities. The Shannon diversity indices were significantly higher in the transitional phase of the two blooms. Metabolic reconstruction of the metagenome-assembled genomes (MAGs) showed that dominant bacteria exhibited some environmental adaptability in both blooms, capable of metabolizing the main organic compounds, and possibly providing inorganic sulfur to the host algae. Moreover, we identified specific metabolic capabilities of cofactor biosynthesis (e.g., B vitamins) in MAGs in the two algal blooms. In the Skeletonema bloom, Rhodobacteraceae family members might participate in synthesizing vitamin B1 and B12 to the host, whereas in the Phaeocystis bloom, Flavobacteriaceae was the potential contributor for synthesizing vitamin B7 to the host. In addition, signal communication (quorum sensing and indole-3-acetic acid molecules) might have also participated in the bacterial response to bloom succession. Bloom-associated microorganisms showed a noticeable response in composition and function to algal succession. The changes in bacterial community structure and function might be an internal driving factor for the bloom succession.
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Affiliation(s)
- Jianming Zhu
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, Shandong, China
| | - Si Tang
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China
| | - Keke Cheng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, Shandong, China
- *Correspondence: Guofu Chen,
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China
- Jin Zhou,
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