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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. New Phytol 2024; 241:1292-1307. [PMID: 38037269 DOI: 10.1111/nph.19441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Mayali X, Samo TJ, Kimbrel JA, Morris MM, Rolison K, Swink C, Ramon C, Kim YM, Munoz-Munoz N, Nicora C, Purvine S, Lipton M, Stuart RK, Weber PK. Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum. Nat Commun 2023; 14:5642. [PMID: 37704622 PMCID: PMC10499878 DOI: 10.1038/s41467-023-41179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
Bacterial remineralization of algal organic matter fuels algal growth but is rarely quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others. Here, we quantified bacterial incorporation of algal-derived complex dissolved organic carbon and nitrogen and algal incorporation of remineralized carbon and nitrogen in fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum at the single-cell level using isotope tracing and nanoSIMS. We found unexpected strain-to-strain and cell-to-cell variability in net carbon and nitrogen incorporation, including non-ubiquitous complex organic nitrogen utilization and remineralization. We used these data to identify three distinct functional guilds of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional guilds were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics, highlighting the need for direct activity-based measurements in ecological studies of microbial metabolic interactions.
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Affiliation(s)
- Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Ty J Samo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jeff A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Megan M Morris
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kristina Rolison
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Courtney Swink
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Christina Ramon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Nathalie Munoz-Munoz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Carrie Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Sam Purvine
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Mary Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Rhona K Stuart
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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Brisson V, Swink C, Kimbrel J, Mayali X, Samo T, Kosina SM, Thelen M, Northen TR, Stuart RK. Dynamic Phaeodactylum tricornutum exometabolites shape surrounding bacterial communities. New Phytol 2023. [PMID: 37301990 DOI: 10.1111/nph.19051] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/10/2023] [Indexed: 06/12/2023]
Abstract
Roles of different ecological classes of algal exometabolites in regulating microbial community composition are not well understood. Here, we identify exometabolites from the model diatom Phaeodactylum tricornutum and demonstrate their potential to influence bacterial abundances. We profiled exometabolites across a time course of axenic algal growth using liquid chromatography-tandem mass spectrometry. We then investigated growth of 12 bacterial isolates on individual-identified exometabolites. Lastly, we compared responses of a P. tricornutum-adapted enrichment community to additions of two contrasting metabolites: selective growth substrate 4-hydroxybenzoic acid and putative signaling/facilitator molecule lumichrome. We identified 50 P. tricornutum metabolites and found distinct temporal accumulation patterns. Two exometabolites (of 12 tested) supported growth of distinct subsets of bacterial isolates. While algal exudates and algal presence drove similar changes in community composition compared with controls, exogenous 4-hydroxybenzoic acid addition promoted increased abundances of taxa that utilized it in isolation, and also revealed the importance of factors relating to algal presence in regulating community composition. This work demonstrates that secretion of selective bacterial growth substrates represents one mechanism by which algal exometabolites can influence bacterial community composition and illustrates how the algal exometabolome has the potential to modulate bacterial communities as a function of algal growth.
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Affiliation(s)
- Vanessa Brisson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Courtney Swink
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Jeffrey Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Ty Samo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Michael Thelen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Rhona K Stuart
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
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