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Timanikova N, Fletcher K, Han JW, van West P, Woodward S, Kim GH, Küpper FC, Wenzel M. Macroalgal eukaryotic microbiome composition indicates novel phylogenetic diversity and broad host spectrum of oomycete pathogens. Environ Microbiol 2024; 26:e16656. [PMID: 38818657 DOI: 10.1111/1462-2920.16656] [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: 12/01/2023] [Accepted: 05/07/2024] [Indexed: 06/01/2024]
Abstract
Seaweeds are important components of marine ecosystems with emerging potential in aquaculture and as sources of biofuel, food products and pharmacological compounds. However, an increasingly recognised threat to natural and industrial seaweed populations is infection with parasitic single-celled eukaryotes from the relatively understudied oomycete lineage. Here we examine the eukaryomes of diverse brown, red and green marine macroalgae collected from polar (Baffin Island), cold-temperate (Falkland Islands) and tropical (Ascension Island) locations, with a focus on oomycete and closely related diatom taxa. Using 18S rRNA gene amplicon sequencing, we show unexpected genetic and taxonomic diversity of the eukaryomes, a strong broad-brush association between eukaryome composition and geographic location, and some evidence of association between eukaryome structure and macroalgal phylogenetic relationships (phylosymbiosis). However, the oomycete fraction of the eukaryome showed disparate patterns of diversity and structure, highlighting much weaker association with geography and no evidence of phylosymbiosis. We present several novel haplotypes of the most common oomycete Eurychasma dicksonii and report for the first time a cosmopolitan distribution and absence of host specificity of this important pathogen. This indicates rich diversity in macroalgal oomycete pathogens and highlights that these pathogens may be generalist and highly adaptable to diverse environmental conditions.
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Affiliation(s)
| | - Kyle Fletcher
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- Oceanlab, University of Aberdeen, Newburgh, UK
- Aberdeen Oomycete Laboratory, International Centre for Aquaculture Research and Development, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Jon-Wong Han
- Kongju National University, Gongju, South Chungcheong Province, South Korea
| | - Pieter van West
- Aberdeen Oomycete Laboratory, International Centre for Aquaculture Research and Development, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Steve Woodward
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Gwang-Hoon Kim
- Kongju National University, Gongju, South Chungcheong Province, South Korea
| | - Frithjof C Küpper
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- Kongju National University, Gongju, South Chungcheong Province, South Korea
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen, UK
- Department of Chemistry and Biochemistry, San Diego State University, California, San Diego, California, USA
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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Markussen Bjorbaekmo MF, Brodie J, Krabberød AK, Logares R, Fuss J, Fredriksen S, Wold-Dobbe A, Shalchian-Tabrizi K, Bass D. 18S rDNA gene metabarcoding of microeukaryotes and epi-endophytes in the holobiome of seven species of large brown algae. JOURNAL OF PHYCOLOGY 2023; 59:859-878. [PMID: 37726938 DOI: 10.1111/jpy.13377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 09/21/2023]
Abstract
Brown algae (Phaeophyceae) are habitat-forming species in coastal ecosystems and include kelp forests and seaweed beds that support a wide diversity of marine life. Host-associated microbial communities are an integral part of phaeophyte biology, and whereas the bacterial microbial partners have received considerable attention, the microbial eukaryotes associated with brown algae have hardly been studied. Here, we used broadly targeted "pan-eukaryotic" primers (metabarcoding) to investigate brown algal-associated eukaryotes (the eukaryome). Using this approach, we aimed to investigate the eukaryome of seven large brown algae that are important and common species in coastal ecosystems. We also aimed to assess whether these macroalgae harbor novel eukaryotic diversity and to ascribe putative functional roles to the host-associated eukaryome based on taxonomic affiliation and phylogenetic placement. We detected a significant diversity of microeukaryotic and algal lineages associated with the brown algal species investigated. The operational taxonomic units (OTUs) were taxonomically assigned to 10 of the eukaryotic major supergroups, including taxonomic groups known to be associated with seaweeds as epibionts, endobionts, parasites, and commensals. Additionally, we revealed previously unrecorded sequence types, including novel phaeophyte OTUs, particularly in the Fucus spp. samples, that may represent fucoid genomic variants, sequencing artifacts, or undescribed epi-/endophytes. Our results provide baseline data and technical insights that will be useful for more comprehensive seaweed eukaryome studies investigating the evidently lineage-rich and functionally diverse symbionts of brown algae.
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Affiliation(s)
- Marit F Markussen Bjorbaekmo
- Norwegian Institute for Water Research (NIVA), Section for Marine Biology, Oslo, Norway
- Natural History Museum (NHM), Science, London, UK
- Department of Biosciences, Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Integrative Microbial Evolution (CIME), University of Oslo, Oslo, Norway
| | | | - Anders K Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Integrative Microbial Evolution (CIME), University of Oslo, Oslo, Norway
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Janina Fuss
- Department of Biosciences, Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Integrative Microbial Evolution (CIME), University of Oslo, Oslo, Norway
| | - Stein Fredriksen
- Department of Biosciences, Section for Aquatic Biology and Toxicology (AQUA), University of Oslo, Oslo, Norway
| | - Anders Wold-Dobbe
- Department of Biosciences, Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Integrative Microbial Evolution (CIME), University of Oslo, Oslo, Norway
| | - Kamran Shalchian-Tabrizi
- Department of Biosciences, Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Integrative Microbial Evolution (CIME), University of Oslo, Oslo, Norway
| | - David Bass
- Natural History Museum (NHM), Science, London, UK
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Dorset, UK
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
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Murúa P, Müller DG, Etemadi M, van West P, Gachon CMM. Host and pathogen autophagy are central to the inducible local defences and systemic response of the giant kelp Macrocystis pyrifera against the oomycete pathogen Anisolpidium ectocarpii. THE NEW PHYTOLOGIST 2020; 226:1445-1460. [PMID: 31955420 PMCID: PMC7317505 DOI: 10.1111/nph.16438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/08/2020] [Indexed: 05/20/2023]
Abstract
Kelps are key primary producers of cold and temperate marine coastal ecosystems and exhibit systemic defences against pathogens. Yet, the cellular mechanisms underpinning their immunity remain to be elucidated. We investigated the time course of infection of the kelp Macrocystis pyrifera by the oomycete Anisolpidium ectocarpii using TEM, in vivo autophagy markers and autophagy inhibitors. Over several infection cycles, A. ectocarpii undergoes sequential physiological shifts sensitive to autophagy inhibitors. Initially lipid-rich, pathogen thalli become increasingly lipid-depleted; they subsequently tend to become entirely abortive, irrespective of their lipid content. Moreover, infected algal cells mount local defences and can directly eliminate the pathogen by xenophagy. Finally, autophagy-dependent plastid recycling is induced in uninfected host cells. We demonstrate the existence of local, inducible autophagic processes both in the pathogen and infected host cells, which result in the restriction of pathogen propagation. We also show the existence of a systemic algal response mediated by autophagy. We propose a working model accounting for all our observations, whereby the outcome of the algal-pathogen interaction (i.e. completion or not of the pathogen life cycle) is dictated by the induction, and possibly the mutual hijacking, of the host and pathogen autophagy machineries.
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Affiliation(s)
- Pedro Murúa
- Aberdeen Oomycete LaboratoryInternational Centre for Aquaculture Research and DevelopmentUniversity of AberdeenForesterhillAberdeenAB25 2ZDUK
- The Scottish Association for Marine ScienceScottish Marine InstituteObanPA37 1QAUK
| | - Dieter G. Müller
- Fachbereich Biologie der Universität KonstanzD‐78457KonstanzGermany
| | - Mohammad Etemadi
- Institute of MicrobiologyUniversity of InnsbruckA‐6020InnsbruckTyrolAustria
| | - Pieter van West
- Aberdeen Oomycete LaboratoryInternational Centre for Aquaculture Research and DevelopmentUniversity of AberdeenForesterhillAberdeenAB25 2ZDUK
| | - Claire M. M. Gachon
- The Scottish Association for Marine ScienceScottish Marine InstituteObanPA37 1QAUK
- UMR 7245 - Molécules de Communication et Adaptation des Micro-organismesMuséum National d'Histoire NaturelleCP 54, 57 rue Cuvier75005ParisFrance
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Diversity and evolution of chitin synthases in oomycetes (Straminipila: Oomycota). Mol Phylogenet Evol 2019; 139:106558. [PMID: 31288106 DOI: 10.1016/j.ympev.2019.106558] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/05/2019] [Accepted: 07/05/2019] [Indexed: 12/24/2022]
Abstract
The oomycetes are filamentous eukaryotic microorganisms, distinct from true fungi, many of which act as crop or fish pathogens that cause devastating losses in agriculture and aquaculture. Chitin is present in all true fungi, but it occurs in only small amounts in some Saprolegniomycetes and it is absent in Peronosporomycetes. However, the growth of several oomycetes is severely impacted by competitive chitin synthase (CHS) inhibitors. Here, we shed light on the diversity, evolution and function of oomycete CHS proteins. We show by phylogenetic analysis of 93 putative CHSs from 48 highly diverse oomycetes, including the early diverging Eurychasma dicksonii, that all available oomycete genomes contain at least one putative CHS gene. All gene products contain conserved CHS motifs essential for enzymatic activity and form two Peronosporomycete-specific and six Saprolegniale-specific clades. Proteins of all clades, except one, contain an N-terminal microtubule interacting and trafficking (MIT) domain as predicted by protein domain databases or manual analysis, which is supported by homology modelling and comparison of conserved structural features from sequence logos. We identified at least three groups of CHSs conserved among all oomycete lineages and used phylogenetic reconciliation analysis to infer the dynamic evolution of CHSs in oomycetes. The evolutionary aspects of CHS diversity in modern-day oomycetes are discussed. In addition, we observed hyphal tip rupture in Phytophthora infestans upon treatment with the CHS inhibitor nikkomycin Z. Combining data on phylogeny, gene expression, and response to CHS inhibitors, we propose the association of different CHS clades with certain developmental stages.
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Spies CFJ, Grooters AM, Lévesque CA, Rintoul TL, Redhead SA, Glockling SL, Chen CY, de Cock AWAM. Molecular phylogeny and taxonomy of Lagenidium-like oomycetes pathogenic to mammals. Fungal Biol 2016; 120:931-947. [PMID: 27521626 DOI: 10.1016/j.funbio.2016.05.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 05/03/2016] [Accepted: 05/09/2016] [Indexed: 10/21/2022]
Abstract
Over the past twenty years, infections caused by previously unrecognised oomycete pathogens with morphological and molecular similarities to known Lagenidium species have been observed with increasing frequency, primarily in dogs but also in cats and humans. Three of these pathogens were formally described as Lagenidium giganteum forma caninum, Lagenidium deciduum, and Paralagenidium karlingii in advance of published phylogenetic verification. Due to the complex nature of Lagenidium taxonomy alongside recent reports of mammalian pathogenic species, these taxa needed to be verified with due consideration of the available data for Lagenidium and its allied genera. This study does so through morphologic characterisation of the mammalian pathogenic species, and phylogenetic analyses. The six-gene phylogeny generally supports the most recent comprehensive classification of Lagenidium with a well-supported Lagenidium clade that includes the mammalian pathogens L. giganteum f. caninum and L. deciduum, and well-supported clades for which the names Myzocytiopsis and Salilagenidium can be applied. The genus Paralagenidium is phylogenetically unrelated to any of the main clades within the class Peronosporomycetes. Close relationships between pathogens of mammals and those of insects or nematodes were revealed. Further characterisation of Lagenidium-like taxa is needed to establish the risk of mammalian infection by pathogens of insects and nematodes.
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Affiliation(s)
- Christoffel F J Spies
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, K1A 0C6, Ontario, Canada.
| | - Amy M Grooters
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - C André Lévesque
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, K1A 0C6, Ontario, Canada
| | - Tara L Rintoul
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, K1A 0C6, Ontario, Canada
| | - Scott A Redhead
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, K1A 0C6, Ontario, Canada
| | | | - Chi-Yu Chen
- Department of Plant Pathology, National Chung Hsing University, 250 Kuo Kuang Road, Taichung 402, Taiwan
| | - Arthur W A M de Cock
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Strittmatter M, Grenville-Briggs LJ, Breithut L, Van West P, Gachon CMM, Küpper FC. Infection of the brown alga Ectocarpus siliculosus by the oomycete Eurychasma dicksonii induces oxidative stress and halogen metabolism. PLANT, CELL & ENVIRONMENT 2016; 39:259-71. [PMID: 25764246 PMCID: PMC4949667 DOI: 10.1111/pce.12533] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 11/03/2014] [Accepted: 02/07/2015] [Indexed: 05/24/2023]
Abstract
Pathogens are increasingly being recognized as key evolutionary and ecological drivers in marine ecosystems. Defence mechanisms of seaweeds, however, have mostly been investigated by mimicking infection using elicitors. We have established an experimental pathosystem between the genome brown model seaweed Ectocarpus siliculosus and the oomycete Eurychasma dicksonii as a powerful new tool to investigate algal responses to infection. Using proteomics, we identified 21 algal proteins differentially accumulated in response to Eu. dicksonii infection. These include classical algal stress response proteins such as a manganese superoxide dismutase, heat shock proteins 70 and a vanadium bromoperoxidase. Transcriptional profiling by qPCR confirmed the induction of the latter during infection. The accumulation of hydrogen peroxide was observed at different infection stages via histochemical staining. Inhibitor studies confirmed that the main source of hydrogen peroxide is superoxide converted by superoxide dismutase. Our data give an unprecedented global overview of brown algal responses to pathogen infection, and highlight the importance of oxidative stress and halogen metabolism in these interactions. This suggests overlapping defence pathways with herbivores and abiotic stresses. We also identify previously unreported actors, in particular a Rad23 and a plastid-lipid-associated protein, providing novel insights into the infection and defence processes in brown algae.
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Affiliation(s)
- Martina Strittmatter
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, Scotland, PA37 1QA, UK
- Aberdeen Oomycete Laboratory, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK
| | - Laura J Grenville-Briggs
- Aberdeen Oomycete Laboratory, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, 230 53, Sweden
| | - Lisa Breithut
- Fachbereich Biologie, Universität Konstanz, Konstanz, D-78457, Germany
| | - Pieter Van West
- Aberdeen Oomycete Laboratory, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK
| | - Claire M M Gachon
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, Scotland, PA37 1QA, UK
| | - Frithjof C Küpper
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, Scotland, PA37 1QA, UK
- Oceanlab, University of Aberdeen, Main Street, Newburgh, Scotland, AB41 6AA, UK
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Fletcher K, Uljević A, Tsirigoti A, Antolić B, Katsaros C, Nikolić V, van West P, Küpper FC. New record and phylogenetic affinities of the oomycete Olpidiopsis feldmanni infecting Asparagopsis sp. (Rhodophyta). DISEASES OF AQUATIC ORGANISMS 2015; 117:45-57. [PMID: 26575155 DOI: 10.3354/dao02930] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A new geographic record of the oomycete Olpidiopsis feldmanni infecting the tetrasporophytic stage of the red alga Asparagopsis sp. from the Adriatic Sea, confirmed through morphological identification, allowed us to expand previous observations of this organism. Ultrastructural investigations of environmental material showed a large central vacuole and a cell wall thicker than previously reported from other basal oomycete pathogens of algae. Phylogenetic analysis closely associates O. feldmanni to O. bostrychiae concurrent with structural observations. This constitutes the first genetic characterisation of an Olpidiopsis species that was initially described before 1960, adding to the genetic data of 3 other marine Olpidiopsis species established and genetically characterised in the last 2 decades. The paper discusses concurrences of the ultrastructural observations made here and in previous studies of the marine Olpidiopsis species with those made on the freshwater species.
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Affiliation(s)
- Kyle Fletcher
- Oceanlab, University of Aberdeen, Newburgh, AB41 6AA, UK
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Scholz B, Küpper FC, Vyverman W, Karsten U. Eukaryotic pathogens (Chytridiomycota and Oomycota) infecting marine microphytobenthic diatoms - a methodological comparison. JOURNAL OF PHYCOLOGY 2014; 50:1009-1019. [PMID: 26988783 DOI: 10.1111/jpy.12230] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 07/31/2014] [Indexed: 06/05/2023]
Abstract
Using sediment samples from the Solthörn tidal flat (southern North Sea, Germany), collected in bi-weekly intervals from June to July 2012, a range of qualitative and quantitative screening methods for oomycete and chytrid pathogens infecting benthic diatoms were evaluated. Pre-treatment of sediment samples using short ultrasound pulses and gradient centrifugation, in combination with CalcoFluor White, showed the best results in the visualization of both pathogen groups. The highest number of infected benthic diatoms was observed in mid July (5.8% of the total benthic diatom community). Most infections were caused by chytrids and, in a few cases, oomycetes (Lagenisma Drebes (host: Coscinodiscus radiatus Ehrenberg) and Ectrogella Zopf (hosts: Dimeregramma minor in Pritchard and Gyrosigma peisonis). Among the chytrids, sporangium morphology indicated the presence of five different morphotypes, infecting mainly epipelic taxa of the orders Naviculales (e.g., Navicula digitoradiata) and Achnanthales (e.g., Achnanthes brevipes Agardh). The presence of multiple pathogens in several epipelic diatom taxa suggests a significant role for fungal parasitism in affecting microphytobenthic diatom succession.
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Affiliation(s)
- Bettina Scholz
- Institute of Chemistry and Biology of the Marine Environment, University of Oldenburg, Schleusenstrasse 1, Wilhelmshaven, 26382, Germany
| | - Frithjof C Küpper
- Oceanlab, University of Aberdeen, Main Street, Newburgh, AB41 6AA, UK
| | - Wim Vyverman
- Department of Biology, Section of Protistology and Aquatic Ecology, University of Ghent, Krijgslaan 281 S8, Ghent, 9000, Belgium
| | - Ulf Karsten
- Institute of Biological Sciences, Applied Ecology & Phycology, University of Rostock, Albert-Einstein-Strasse 3, Rostock, 18059, Germany
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Mystikou A, Peters AF, Asensi AO, Fletcher KI, Brickle P, van West P, Convey P, Küpper FC. Seaweed biodiversity in the south-western Antarctic Peninsula: surveying macroalgal community composition in the Adelaide Island/Marguerite Bay region over a 35-year time span. Polar Biol 2014. [DOI: 10.1007/s00300-014-1547-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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