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Impact of Phaeobacter Inhibens on Marine Eukaryote-Associated Microbial Communities Downloaded from orbit.dtu.dk on: Oct 05, 2021 Impact of Phaeobacter inhibens on marine eukaryote-associated microbial communities Dittmann, Karen K.; Sonnenschein, Eva C.; Egan, Suhelen; Gram, Lone; Bentzon-Tilia, Mikkel Published in: Environmental Microbiology Reports Link to article, DOI: 10.1111/1758-2229.12698 Publication date: 2019 Document Version Peer reviewed version Link back to DTU Orbit Citation (APA): Dittmann, K. K., Sonnenschein, E. C., Egan, S., Gram, L., & Bentzon-Tilia, M. (2019). Impact of Phaeobacter inhibens on marine eukaryote-associated microbial communities. Environmental Microbiology Reports, 11(3), 401-413. https://doi.org/10.1111/1758-2229.12698 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Impact of Phaeobacter inhibens on marine eukaryote-associated microbial communities Karen K. Dittmann1, Eva C. Sonnenschein1, Suhelen Egan2, Lone Gram1, Mikkel Bentzon-Tilia1* 1Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark. 2School of Biological, Earth and Environmental Sciences, The University of New South Wales, BiologicalArticle Sciences Building D26-link-wing, Randwick NSW 2052, Australia. * Address correspondence to Mikkel Bentzon-Tilia: [email protected] Tel.: (+45) 45 25 25 18 Running title: Impact of P. inhibens on marine microbiomes Accepted Keywords: Microbial community analysis, Microbiome, Emiliania huxleyi, oyster, Ostrea edulis, Phaeobacter, roseobacters, secondary metabolites, tropodithietic acid Thi s article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this 1 article as doi: 10.1111/1758-2229.12698 This article is protected by copyright. All rights reserved. Originality-Significance Statement: This study demonstrates that the marine, host-associated and conspicuous secondary metabolite producer Phaeobacter inhibens can shape the microbiomes of eukaryotic host organisms. It also offers insight into how the abundance of specific members, such as vibrios, of the microbial communities of the coccolithophorid microalga Emiliania huxleyi and the European flat oyster Ostrea edulis is affected by increasing abundance of P. inhibens. Summary Bacteria-host interactions are universal in nature and have significant effects on host functionality. Bacterial secondary metabolites are believed to play key roles in such interactions as well as in interactionsArticle within the host-associated microbial community. Hence, prominent secondary metabolite-producing bacteria may be strong drivers of microbial community composition in natural host-associated microbiomes. This has however not been rigorously tested, and the purpose of this study was to investigate how the secondary metabolite producer Phaeobacter inhibens affects the diversity and composition of microbiomes associated with the microalga Emiliania huxleyi and the European flat oyster, Ostrea edulis. Roseobacters were indigenous to both communities exhibiting relative abundances between 2.8 % and 7.0 %. Addition of P. inhibens caused substantial changes in the overall structure of the low-complexity microbiome of E. huxleyi, but did not shape microbial community structure to the same degree in the more complex oyster microbiomes. Species-specific interactions occurred in both microbiomes and specifically the abundances of other putative secondary metabolite-producers such as vibrios and Accepted pseudoalteromonads were reduced. Thus, the impact of a bioactive strain like P. inhibens on host- associated microbiomes depends on the complexity and composition of the existing microbiome. 2 This article is protected by copyright. All rights reserved. Introduction In nature, microorganisms live and interact as part of complex multispecies communities. These interspecies interactions may be of a synergistic, amensal, or commensal nature and can be facilitated by the exchange of metabolites in syntrophic cooperation, or by the production of bioactive secondary metabolites (Cole, 1982). In parallel to the use of secondary metabolites as defense against microbial infections by plants (Pusztahelyi et al., 2015), bacterial secondary metabolites with antimicrobial properties are currently believed to facilitate the success of the compound-producer by killing competitors. Not all bacteria are equally proficient in secondary metabolite production, and whereas some groups appear to produce few or no metabolites, others such as filamentous soil bacteria and marine vibrios, roseobacters, and Pseudoalteromonas spp. produceArticle an array of different bioactive compounds (Brinkhoff et al., 2004; Murphy et al., 2012; Rasmussen et al., 2014; Maansson et al., 2016; Sonnenschein, Stierhof, et al., 2017). Hence, if the role of these compounds is to eliminate competing microorganisms, proficient secondary metabolite producers should be strong drivers of microbial community composition in natural environments. The Roseobacter group represents one of the most abundant groups of marine bacteria, constituting on average 3 – 5 % of microbial communities in the upper mixed layer (Wietz et al., 2010). On a global scale, the group exhibits a positive abundance-chlorophyll a correlation (Wietz et al., 2010) and may exhibit relative abundances of up to 20 – 30 % during algal blooms (González and Moran, 1997; González et al., 2000; Zubkov et al., 2001; West et al., 2008), suggesting association with microalgae. The paraphyletic Roseobacter group comprises multiple deeply branching clades (NewtonAccepted et al., 2010; Simon et al., 2017), of which especially clade 1 includes prominent producers of bioactive secondary metabolites, such as the antimicrobial compounds tropodithietic acid (TDA) (Brinkhoff et al., 2004; Bruhn et al., 2005; Sonnenschein, Nielsen, et al., 2017), indigoidine (Cude 3 This article is protected by copyright. All rights reserved. et al., 2012; Gromek et al., 2016), and likely multiple other small molecules (Machado et al., 2015; Bentzon-Tilia and Gram, 2017; Sonnenschein et al., 2018). One conspicuous genus of Roseobacter clade 1 is Phaeobacter, which is often found in microbial communities associated with a wide variety of marine eukaryotes including micro- and macroalgae (Rao et al., 2005; Segev, Wyche, et al., 2016), mesozooplankton (Freese et al., 2017), and larger animals such as bivalve molluscs (Ruiz-Ponte et al., 1998; Prado et al., 2009; Wegner et al., 2013). Recently, it was shown that the species Phaeobacter inhibens produces small bioactive molecules, e.g. indole-3-acetic acid, which affect the metabolism of the coccolithophorid microalga Emiliania huxleyi (Segev, Castañeda, et al., 2016; Segev, Wyche, et al., 2016). It has been proposed that the interaction between E. huxleyi and P. inhibens exhibits a biphasic pattern where a mutualistic symbiosisArticle gives way for a parasitic interaction where the bacteria accelerates algal lysis in response to algal break-down products (Seyedsayamdost et al., 2011). Mutualistic mechanisms have also been suggested for the symbiosis between bioactive Roseobacter clade 1 organisms living in association with the Hawaiian bobtail squid (Euprymna scolopes), specifically on the outer surface of the eggs and in the accessory nidamental gland (Collins et al., 2012; Gromek et al., 2016), where they supposedly ward off potential pathogens through the production of antimicrobials. Hence, proficient secondary metabolite-producing species, such as members of the Phaeobacter genus might be strong modulators of both the behavior and the microbiome composition of their eukaryotic hosts. For P. inhibens, TDA is the most studied secondary metabolite and its antimicrobial property is likelyAccepted a result of the ability of TDA to act as a proton antiporter at the cytoplasmic membrane (Wilson et al., 2016). Hence, TDA is a broad-spectrum antibiotic affecting a wide range of both Gram-positive and Gram-negative bacteria (Porsby et al., 2011). Despite the fact that resistance towards TDA does not arise easily (Porsby et al., 2011; Rasmussen et al., 2016), a large fraction of 4 This article is protected by copyright. All rights reserved. bacterial isolates from eukaryote-associated microbiomes similar to those harboring TDA-producers are tolerant towards TDA (Harrington et al., 2014). Such microbiomes may hence be resilient to perturbations caused by compounds such as TDA. Recently, Geng et al. (2016) showed that additions of the pure TDA compound had pronounced dose-dependent effects on community structure and composition of the microalgal Nannochloropsis salina microbiome at relatively low concentrations (31 – 500 nM). At these concentrations,
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