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Henriksen NNSE, Lindqvist LL, Wibowo M, Sonnenschein EC, Bentzon-Tilia M, Gram L. Role is in the eye of the beholder-the multiple functions of the antibacterial compound tropodithietic acid produced by marine Rhodobacteraceae. FEMS Microbiol Rev 2022; 46:fuac007. [PMID: 35099011 PMCID: PMC9075582 DOI: 10.1093/femsre/fuac007] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Many microbial secondary metabolites have been studied for decades primarily because of their antimicrobial properties. However, several of these metabolites also possess nonantimicrobial functions, both influencing the physiology of the producer and their ecological neighbors. An example of a versatile bacterial secondary metabolite with multiple functions is the tropone derivative tropodithietic acid (TDA). TDA is a broad-spectrum antimicrobial compound produced by several members of the Rhodobacteraceae family, a major marine bacterial lineage, within the genera Phaeobacter, Tritonibacter, and Pseudovibrio. The production of TDA is governed by the mode of growth and influenced by the availability of nutrient sources. The antibacterial effect of TDA is caused by disruption of the proton motive force of target microorganisms and, potentially, by its iron-chelating properties. TDA also acts as a signaling molecule, affecting gene expression in other bacteria, and altering phenotypic traits such as motility, biofilm formation, and antibiotic production in the producer. In microbial communities, TDA-producing bacteria cause a reduction of the relative abundance of closely related species and some fast-growing heterotrophic bacteria. Here, we summarize the current understanding of the chemical ecology of TDA, including the environmental niches of TDA-producing bacteria, and the molecular mechanisms governing the function and regulation of TDA.
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Affiliation(s)
- Nathalie N S E Henriksen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Laura L Lindqvist
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Mario Wibowo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
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2
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Matos A, Antunes A. Symbiotic Associations in Ascidians: Relevance for Functional Innovation and Bioactive Potential. Mar Drugs 2021; 19:370. [PMID: 34206769 PMCID: PMC8303170 DOI: 10.3390/md19070370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 12/22/2022] Open
Abstract
Associations between different organisms have been extensively described in terrestrial and marine environments. These associations are involved in roles as diverse as nutrient exchanges, shelter or adaptation to adverse conditions. Ascidians are widely dispersed marine invertebrates associated to invasive behaviours. Studying their microbiomes has interested the scientific community, mainly due to its potential for bioactive compounds production-e.g., ET-73 (trabectedin, Yondelis), an anticancer drug. However, these symbiotic interactions embrace several environmental and biological functions with high ecological relevance, inspiring diverse biotechnological applications. We thoroughly reviewed microbiome studies (microscopic to metagenomic approaches) of around 171 hosts, worldwide dispersed, occurring at different domains of life (Archaea, Bacteria, Eukarya), to illuminate the functions and bioactive potential of associated organisms in ascidians. Associations with Bacteria are the most prevalent, namely with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria and Planctomycetes phyla. The microbiomes of ascidians belonging to Aplousobranchia order have been the most studied. The integration of worldwide studies characterizing ascidians' microbiome composition revealed several functions including UV protection, bioaccumulation of heavy metals and defense against fouling or predators through production of natural products, chemical signals or competition. The critical assessment and characterization of these communities is extremely valuable to comprehend their biological/ecological role and biotechnological potential.
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Affiliation(s)
- Ana Matos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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3
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An Analysis of Biosynthesis Gene Clusters and Bioactivity of Marine Bacterial Symbionts. Curr Microbiol 2021; 78:2522-2533. [PMID: 34041587 DOI: 10.1007/s00284-021-02535-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 05/05/2021] [Indexed: 01/28/2023]
Abstract
Symbiotic marine bacteria have a pivotal role in drug discovery due to the synthesis of diverse biologically potential compounds. The marine bacterial phyla proteobacteria, actinobacteria and firmicutes are commonly associated with marine macro organisms and frequently reported as dominant bioactive compound producers. They can produce biologically active compounds that possess antimicrobial, antiviral, antitumor, antibiofilm and antifouling properties. Synthesis of these bioactive compounds is controlled by a set of genes of their genomes that is known as biosynthesis gene clusters (BGCs). The development in the field of biotechnology and bioinformatics has uncovered the potential BGCs of the bacterial genome and its functions. Now-a-days researchers have focused their attention on the identification of potential BGCs for the discovery of novel bioactive compounds using advanced technology. This review highlights the marine bacterial symbionts and their BGCs which are responsible for the synthesis of bioactive compounds.
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4
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Duan Y, Petzold M, Saleem‐Batcha R, Teufel R. Bacterial Tropone Natural Products and Derivatives: Overview of their Biosynthesis, Bioactivities, Ecological Role and Biotechnological Potential. Chembiochem 2020; 21:2384-2407. [PMID: 32239689 PMCID: PMC7497051 DOI: 10.1002/cbic.201900786] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/02/2020] [Indexed: 12/05/2022]
Abstract
Tropone natural products are non-benzene aromatic compounds of significant ecological and pharmaceutical interest. Herein, we highlight current knowledge on bacterial tropones and their derivatives such as tropolones, tropodithietic acid, and roseobacticides. Their unusual biosynthesis depends on a universal CoA-bound precursor featuring a seven-membered carbon ring as backbone, which is generated by a side reaction of the phenylacetic acid catabolic pathway. Enzymes encoded by separate gene clusters then further modify this key intermediate by oxidation, CoA-release, or incorporation of sulfur among other reactions. Tropones play important roles in the terrestrial and marine environment where they act as antibiotics, algaecides, or quorum sensing signals, while their bacterial producers are often involved in symbiotic interactions with plants and marine invertebrates (e. g., algae, corals, sponges, or mollusks). Because of their potent bioactivities and of slowly developing bacterial resistance, tropones and their derivatives hold great promise for biomedical or biotechnological applications, for instance as antibiotics in (shell)fish aquaculture.
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Affiliation(s)
- Ying Duan
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | - Melanie Petzold
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | | | - Robin Teufel
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
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5
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Phylogenomic Analyses of Members of the Widespread Marine Heterotrophic Genus Pseudovibrio Suggest Distinct Evolutionary Trajectories and a Novel Genus, Polycladidibacter gen. nov. Appl Environ Microbiol 2020; 86:AEM.02395-19. [PMID: 31811036 PMCID: PMC6997731 DOI: 10.1128/aem.02395-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 12/04/2019] [Indexed: 12/16/2022] Open
Abstract
Bacteria belonging to the Pseudovibrio genus are widespread, metabolically versatile, and able to thrive as both free-living and host-associated organisms. Although more than 50 genomes are available, a comprehensive comparative genomics study to resolve taxonomic inconsistencies is currently missing. We analyzed all available genomes and used 552 core genes to perform a robust phylogenomic reconstruction. This in-depth analysis revealed the divergence of two monophyletic basal lineages of strains isolated from polyclad flatworm hosts, namely, Pseudovibrio hongkongensis and Pseudovibrio stylochi These strains have reduced genomes and lack sulfur-related metabolisms and major biosynthetic gene clusters, and their environmental distribution appears to be tightly associated with invertebrate hosts. We showed experimentally that the divergent strains are unable to utilize various sulfur compounds that, in contrast, can be utilized by the type strain Pseudovibrio denitrificans Our analyses suggest that the lineage leading to these two strains has been subject to relaxed purifying selection resulting in great gene loss. Overall genome relatedness indices (OGRI) indicate substantial differences between the divergent strains and the rest of the genus. While 16S rRNA gene analyses do not support the establishment of a different genus for the divergent strains, their substantial genomic, phylogenomic, and physiological differences strongly suggest a divergent evolutionary trajectory and the need for their reclassification. Therefore, we propose the novel genus Polycladidibacter gen. nov.IMPORTANCE The genus Pseudovibrio is commonly associated with marine invertebrates, which are essential for ocean health and marine nutrient cycling. Traditionally, the phylogeny of the genus has been based on 16S rRNA gene analysis. The use of the 16S rRNA gene or any other single marker gene for robust phylogenetic placement has recently been questioned. We used a large set of marker genes from all available Pseudovibrio genomes for in-depth phylogenomic analyses. We identified divergent monophyletic basal lineages within the Pseudovibrio genus, including two strains isolated from polyclad flatworms. These strains showed reduced sulfur metabolism and biosynthesis capacities. The phylogenomic analyses revealed distinct evolutionary trajectories and ecological adaptations that differentiate the divergent strains from the other Pseudovibrio members and suggest that they fall into a novel genus. Our data show the importance of widening the use of phylogenomics for better understanding bacterial physiology, phylogeny, and evolution.
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Cirri E, De Decker S, Bilcke G, Werner M, Osuna-Cruz CM, De Veylder L, Vandepoele K, Werz O, Vyverman W, Pohnert G. Associated Bacteria Affect Sexual Reproduction by Altering Gene Expression and Metabolic Processes in a Biofilm Inhabiting Diatom. Front Microbiol 2019; 10:1790. [PMID: 31428077 PMCID: PMC6688387 DOI: 10.3389/fmicb.2019.01790] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/19/2019] [Indexed: 01/23/2023] Open
Abstract
Diatoms are unicellular algae with a fundamental role in global biogeochemical cycles as major primary producers at the base of aquatic food webs. In recent years, chemical communication between diatoms and associated bacteria has emerged as a key factor in diatom ecology, spurred by conceptual and technological advancements to study the mechanisms underlying these interactions. Here, we use a combination of physiological, transcriptomic, and metabolomic approaches to study the influence of naturally co-existing bacteria, Maribacter sp. and Roseovarius sp., on the sexual reproduction of the biofilm inhabiting marine pennate diatom Seminavis robusta. While Maribacter sp. severely reduces the reproductive success of S. robusta cultures, Roseovarius sp. slightly enhances it. Contrary to our expectation, we demonstrate that the effect of the bacterial exudates is not caused by altered cell-cycle regulation prior to the switch to meiosis. Instead, Maribacter sp. exudates cause a reduced production of diproline, the sexual attraction pheromone of S. robusta. Transcriptomic analyses show that this is likely an indirect consequence of altered intracellular metabolic fluxes in the diatom, especially those related to amino acid biosynthesis, oxidative stress response, and biosynthesis of defense molecules. This study provides the first insights into the influence of bacteria on diatom sexual reproduction and adds a new dimension to the complexity of a still understudied phenomenon in natural diatom populations.
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Affiliation(s)
- Emilio Cirri
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Sam De Decker
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Gust Bilcke
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Markus Werner
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Jena, Germany
| | - Cristina Maria Osuna-Cruz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Jena, Germany
| | - Wim Vyverman
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
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7
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Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria. Sci Rep 2019; 9:1999. [PMID: 30760820 PMCID: PMC6374434 DOI: 10.1038/s41598-019-38737-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/09/2019] [Indexed: 02/07/2023] Open
Abstract
Marine sponges are early-branching, filter-feeding metazoans that usually host complex microbiomes comprised of several, currently uncultivatable symbiotic lineages. Here, we use a low-carbon based strategy to cultivate low-abundance bacteria from Spongia officinalis. This approach favoured the growth of Alphaproteobacteria strains in the genera Anderseniella, Erythrobacter, Labrenzia, Loktanella, Ruegeria, Sphingorhabdus, Tateyamaria and Pseudovibrio, besides two likely new genera in the Rhodobacteraceae family. Mapping of complete genomes against the metagenomes of S. officinalis, seawater, and sediments confirmed the rare status of all the above-mentioned lineages in the marine realm. Remarkably, this community of low-abundance Alphaproteobacteria possesses several genomic attributes common to dominant, presently uncultivatable sponge symbionts, potentially contributing to host fitness through detoxification mechanisms (e.g. heavy metal and metabolic waste removal, degradation of aromatic compounds), provision of essential vitamins (e.g. B6 and B12 biosynthesis), nutritional exchange (especially regarding the processing of organic sulphur and nitrogen) and chemical defence (e.g. polyketide and terpenoid biosynthesis). None of the studied taxa displayed signs of genome reduction, indicative of obligate mutualism. Instead, versatile nutrient metabolisms along with motility, chemotaxis, and tight-adherence capacities - also known to confer environmental hardiness – were inferred, underlying dual host-associated and free-living life strategies adopted by these diverse sponge-associated Alphaproteobacteria.
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8
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Versluis D, Nijsse B, Naim MA, Koehorst JJ, Wiese J, Imhoff JF, Schaap PJ, van Passel MWJ, Smidt H, Sipkema D. Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio. Genome Biol Evol 2018; 10:125-142. [PMID: 29319806 PMCID: PMC5765558 DOI: 10.1093/gbe/evx271] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2017] [Indexed: 12/19/2022] Open
Abstract
Pseudovibrio is a marine bacterial genus members of which are predominantly isolated from sessile marine animals, and particularly sponges. It has been hypothesized that Pseudovibrio spp. form mutualistic relationships with their hosts. Here, we studied Pseudovibrio phylogeny and genetic adaptations that may play a role in host colonization by comparative genomics of 31 Pseudovibrio strains, including 25 sponge isolates. All genomes were highly similar in terms of encoded core metabolic pathways, albeit with substantial differences in overall gene content. Based on gene composition, Pseudovibrio spp. clustered by geographic region, indicating geographic speciation. Furthermore, the fact that isolates from the Mediterranean Sea clustered by sponge species suggested host-specific adaptation or colonization. Genome analyses suggest that Pseudovibrio hongkongensis UST20140214-015BT is only distantly related to other Pseudovibrio spp., thereby challenging its status as typical Pseudovibrio member. All Pseudovibrio genomes were found to encode numerous proteins with SEL1 and tetratricopeptide repeats, which have been suggested to play a role in host colonization. For evasion of the host immune system, Pseudovibrio spp. may depend on type III, IV, and VI secretion systems that can inject effector molecules into eukaryotic cells. Furthermore, Pseudovibrio genomes carry on average seven secondary metabolite biosynthesis clusters, reinforcing the role of Pseudovibrio spp. as potential producers of novel bioactive compounds. Tropodithietic acid, bacteriocin, and terpene biosynthesis clusters were highly conserved within the genus, suggesting an essential role in survival, for example through growth inhibition of bacterial competitors. Taken together, these results support the hypothesis that Pseudovibrio spp. have mutualistic relations with sponges.
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Affiliation(s)
- Dennis Versluis
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands
| | - Bart Nijsse
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands.,Laboratory of Systems and Synthetic Biology, Wageningen University & Research, The Netherlands
| | - Mohd Azrul Naim
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, The Netherlands
| | - Jutta Wiese
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Johannes F Imhoff
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, The Netherlands
| | - Mark W J van Passel
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands.,National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands
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9
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Choudhary A, Naughton LM, Dobson ADW, Rai DK. High-performance liquid chromatography/electrospray ionisation mass spectrometric characterisation of metabolites produced by Pseudovibrio sp. W64, a marine sponge derived bacterium isolated from Irish waters. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1737-1745. [PMID: 29971859 DOI: 10.1002/rcm.8226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE In recent years, metabolites produced by Pseudovibrio species have gained scientific attention due to their potent antimicrobial activity. Recently, we also have assessed the antibacterial activities of Pseudovibrio sp. W64 isolates against Staphylococcus aureus, where only the dominant tropodithietic acid (TDA) was identified. However, characterisation of other metabolites is necessary as these metabolites may also serve as potent antimicrobial agents. METHODS Liquid chromatography/tandem mass spectrometry (LC/MS/MS), aided by accurate mass measurements, was employed to screen and characterise a range of metabolites produced by Pseudovibrio sp. W64 via assessment of ethyl acetate fractions generated from bacterial cultures. RESULTS Thirteen metabolites unique to the bacterial culture were detected and their chemical structures were assigned by MS/MS and accurate mass measurements. Among the thirteen metabolites, a methyl ester of TDA, a number of cholic acid derivatives, and amino diols and triols were characterised. CONCLUSIONS Pseudovibrio sp. W64 produces methylated TDA in addition to TDA, and metabolises lipids and amino acids in the cell-culture medium. To the best of our knowledge, this is the first report of methylated TDA, cholic acid and its various analogs, and sphinganine being detected in this Pseudovibrio strain. The data generated may help to better understand the biochemical processes and metabolism of bacterial strains towards discovery of antimicrobial agents from marine sources.
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Affiliation(s)
- Alka Choudhary
- Department of Food Biosciences, Teagasc Food Research Centre Ashtown, Dublin, D15 KN3K, Ireland
| | - Lynn M Naughton
- School of Microbiology, University College Cork, Western Road, Cork, T12 YN60, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Western Road, Cork, T12 YN60, Ireland
- Environmental Research Institute, University College Cork, Lee Road, Cork, T23 XE10, Ireland
| | - Dilip K Rai
- Department of Food Biosciences, Teagasc Food Research Centre Ashtown, Dublin, D15 KN3K, Ireland
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Alex A, Antunes A. Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts. PLoS One 2018; 13:e0194368. [PMID: 29775460 PMCID: PMC5959193 DOI: 10.1371/journal.pone.0194368] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 03/01/2018] [Indexed: 11/18/2022] Open
Abstract
Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater. The analyses revealed a certain degree of commonality among the majority of sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tunicates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flatworm-associated bacteria and the sponge-associated bacterium P. axinellae AD2, through the loss of major secretion systems (type III/VI) and virulence/symbioses factors such as proteins involved in adhesion and attachment to the host. Our study also unraveled the presence of a CRISPR-Cas system in P. stylochi UST20140214-052 a flatworm-associated bacterium possibly suggesting the role of CRISPR-based adaptive immune system against the invading virus particles. Detection of mobile elements and genomic islands (GIs) in all bacterial members highlighted the role of horizontal gene transfer for the acquisition of novel genetic features, likely enhancing the bacterial ecological fitness. These findings are insightful to understand the role of genome diversity in Pseudovibrio as an evolutionary strategy to increase their colonizing success across a wide range of marine eukaryotic hosts.
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Affiliation(s)
- Anoop Alex
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- * E-mail: (AA); (AA)
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- * E-mail: (AA); (AA)
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11
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Pérez-Bonilla M, Oves-Costales D, de la Cruz M, Kokkini M, Martín J, Vicente F, Genilloud O, Reyes F. Phocoenamicins B and C, New Antibacterial Spirotetronates Isolated from a Marine Micromonospora sp. Mar Drugs 2018; 16:md16030095. [PMID: 29547589 PMCID: PMC5867639 DOI: 10.3390/md16030095] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 11/16/2022] Open
Abstract
Phocoenamicins B and C (1 and 2), together with the known spirotetronate phocoenamicin (3), were isolated from cultures of Micromonospora sp. The acetone extract from a culture of this strain, isolated from marine sediments collected in the Canary Islands, displayed activity against methicillin-resistant Staphylococcus aureus (MRSA), Mycobacterium tuberculosis H37Ra and Mycobacterium bovis. Bioassay-guided fractionation of this extract using SP207ss column chromatography and preparative reversed-phased HPLC led to the isolation of the new compounds 1 and 2 belonging to the spirotetronate class of polyketides. Their structures were determined using a combination of HRMS, 1D and 2D NMR experiments and comparison with the spectra reported for phocoenamicin. Antibacterial activity tests of the pure compounds against these pathogens revealed minimal inhibitory concentration (MIC) values ranging from 4 to 64 µg/mL for MRSA, and 16 to 32 µg/mL for M. tuberculosis H37Ra, with no significant activity found against M. bovis and vancomycin-resistant Enterococcus faecium (VRE) at concentrations below 128 µg/mL, and weak activity detected against Bacillus subtilis grown on agar plates.
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Affiliation(s)
- Mercedes Pérez-Bonilla
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain.
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain.
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain.
| | - Maria Kokkini
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain.
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain.
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain.
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain.
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain.
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12
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An Overview on Marine Sponge-Symbiotic Bacteria as Unexhausted Sources for Natural Product Discovery. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040040] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Microbial symbiotic communities of marine macro-organisms carry functional metabolic profiles different to the ones found terrestrially and within surrounding marine environments. These symbiotic bacteria have increasingly been a focus of microbiologists working in marine environments due to a wide array of reported bioactive compounds of therapeutic importance resulting in various patent registrations. Revelations of symbiont-directed host specific functions and the true nature of host-symbiont interactions, combined with metagenomic advances detecting functional gene clusters, will inevitably open new avenues for identification and discovery of novel bioactive compounds of biotechnological value from marine resources. This review article provides an overview on bioactive marine symbiotic organisms with specific emphasis placed on the sponge-associated ones and invites the international scientific community to contribute towards establishment of in-depth information of the environmental parameters defining selection and acquisition of true symbionts by the host organisms.
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Diversity and Bioactivity of Marine Bacteria Associated with the Sponges Candidaspongia flabellata and Rhopaloeides odorabile from the Great Barrier Reef in Australia. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9030039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Naughton LM, Romano S, O'Gara F, Dobson ADW. Identification of Secondary Metabolite Gene Clusters in the Pseudovibrio Genus Reveals Encouraging Biosynthetic Potential toward the Production of Novel Bioactive Compounds. Front Microbiol 2017; 8:1494. [PMID: 28868049 PMCID: PMC5563371 DOI: 10.3389/fmicb.2017.01494] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/25/2017] [Indexed: 11/18/2022] Open
Abstract
Increased incidences of antimicrobial resistance and the emergence of pan-resistant ‘superbugs’ have provoked an extreme sense of urgency amongst researchers focusing on the discovery of potentially novel antimicrobial compounds. A strategic shift in focus from the terrestrial to the marine environment has resulted in the discovery of a wide variety of structurally and functionally diverse bioactive compounds from numerous marine sources, including sponges. Bacteria found in close association with sponges and other marine invertebrates have recently gained much attention as potential sources of many of these novel bioactive compounds. Members of the genus Pseudovibrio are one such group of organisms. In this study, we interrogate the genomes of 21 Pseudovibrio strains isolated from a variety of marine sources, for the presence, diversity and distribution of biosynthetic gene clusters (BGCs). We expand on results obtained from antiSMASH analysis to demonstrate the similarity between the Pseudovibrio-related BGCs and those characterized in other bacteria and corroborate our findings with phylogenetic analysis. We assess how domain organization of the most abundant type of BGCs present among the isolates (Non-ribosomal peptide synthetases and Polyketide synthases) may influence the diversity of compounds produced by these organisms and highlight for the first time the potential for novel compound production from this genus of bacteria, using a genome guided approach.
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Affiliation(s)
- Lynn M Naughton
- School of Microbiology, University College Cork, National University of IrelandCork, Ireland
| | - Stefano Romano
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
| | - Fergal O'Gara
- School of Biomedical Sciences, Curtin University, PerthWA, Australia.,BIOMERIT Research Centre, School of Microbiology, University College Cork, National University of IrelandCork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, National University of IrelandCork, Ireland
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Nicacio KJ, Ióca LP, Fróes AM, Leomil L, Appolinario LR, Thompson CC, Thompson FL, Ferreira AG, Williams DE, Andersen RJ, Eustaquio AS, Berlinck RGS. Cultures of the Marine Bacterium Pseudovibrio denitrificans Ab134 Produce Bromotyrosine-Derived Alkaloids Previously Only Isolated from Marine Sponges. JOURNAL OF NATURAL PRODUCTS 2017; 80:235-240. [PMID: 28191971 DOI: 10.1021/acs.jnatprod.6b00838] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Herein we report the isolation and spectroscopic identification of fistularin-3 (1), 11-hydroxyaerothionin (2), and verongidoic acid (3), as well as the UPLC-HRMS detection of aerothionin (4), homopurpuroceratic acid B (5), purealidin L (6), and aplysinamisine II (7), from cultures of the marine bacterium Pseudovibrio denitrificans Ab134, isolated from tissues of the marine sponge Arenosclera brasiliensis. These results unambiguously demonstrate for the first time that bromotyrosine-derived alkaloids that were previously isolated only from Verongida sponges can be biosynthesized by a marine bacterium.
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Affiliation(s)
- Karen J Nicacio
- Instituto de Química de São Carlos, Universidade de São Paulo , CP 780, CEP 13560-970, São Carlos, SP, Brazil
| | - Laura P Ióca
- Instituto de Química de São Carlos, Universidade de São Paulo , CP 780, CEP 13560-970, São Carlos, SP, Brazil
| | - Adriana M Fróes
- Instituto de Biologia, Centro de Ciência da Saúde, Universidade Federal do Rio de Janeiro , Avenida Carlos Chagas Fo. 373, Bloco A, Anexo A3, Sl. 302, Cidade Universitária, CEP 21941-599, Rio de Janeiro, RJ, Brazil
| | - Luciana Leomil
- Instituto de Biologia, Centro de Ciência da Saúde, Universidade Federal do Rio de Janeiro , Avenida Carlos Chagas Fo. 373, Bloco A, Anexo A3, Sl. 302, Cidade Universitária, CEP 21941-599, Rio de Janeiro, RJ, Brazil
| | - Luciana R Appolinario
- Instituto de Biologia, Centro de Ciência da Saúde, Universidade Federal do Rio de Janeiro , Avenida Carlos Chagas Fo. 373, Bloco A, Anexo A3, Sl. 302, Cidade Universitária, CEP 21941-599, Rio de Janeiro, RJ, Brazil
| | - Christiane C Thompson
- Instituto de Biologia, Centro de Ciência da Saúde, Universidade Federal do Rio de Janeiro , Avenida Carlos Chagas Fo. 373, Bloco A, Anexo A3, Sl. 302, Cidade Universitária, CEP 21941-599, Rio de Janeiro, RJ, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia, Centro de Ciência da Saúde, Universidade Federal do Rio de Janeiro , Avenida Carlos Chagas Fo. 373, Bloco A, Anexo A3, Sl. 302, Cidade Universitária, CEP 21941-599, Rio de Janeiro, RJ, Brazil
| | - Antonio G Ferreira
- Departamento de Química, Universidade Federal de São Carlos , CEP 13565-905, São Carlos, SP, Brazil
| | - David E Williams
- Departments of Chemistry and Earth, Ocean & Atmospheric Sciences, University of British Columbia , Vancouver, BC V6T 1Z1, Canada
| | - Raymond J Andersen
- Departments of Chemistry and Earth, Ocean & Atmospheric Sciences, University of British Columbia , Vancouver, BC V6T 1Z1, Canada
| | - Alessandra S Eustaquio
- College of Pharmacy, Department of Medicinal Chemistry and Pharmacognosy, Center for Biomolecular Sciences, University of Illinois at Chicago , 900 S. Ashland Avenue, Chicago, Illinois 60607, United States
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo , CP 780, CEP 13560-970, São Carlos, SP, Brazil
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Saurav K, Bar-Shalom R, Haber M, Burgsdorf I, Oliviero G, Costantino V, Morgenstern D, Steindler L. In Search of Alternative Antibiotic Drugs: Quorum-Quenching Activity in Sponges and their Bacterial Isolates. Front Microbiol 2016; 7:416. [PMID: 27092109 PMCID: PMC4821063 DOI: 10.3389/fmicb.2016.00416] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/14/2016] [Indexed: 02/01/2023] Open
Abstract
Owing to the extensive development of drug resistance in pathogens against the available antibiotic arsenal, antimicrobial resistance is now an emerging major threat to public healthcare. Anti-virulence drugs are a new type of therapeutic agent aiming at virulence factors rather than killing the pathogen, thus providing less selective pressure for evolution of resistance. One promising example of this therapeutic concept targets bacterial quorum sensing (QS), because QS controls many virulence factors responsible for bacterial infections. Marine sponges and their associated bacteria are considered a still untapped source for unique chemical leads with a wide range of biological activities. In the present study, we screened extracts of 14 sponge species collected from the Red and Mediterranean Sea for their quorum-quenching (QQ) potential. Half of the species showed QQ activity in at least 2 out of 3 replicates. Six out of the 14 species were selected for bacteria isolation, to test for QQ activity also in isolates, which, once cultured, represent an unlimited source of compounds. We show that ≈20% of the isolates showed QQ activity based on a Chromobacterium violaceum CV026 screen, and that the presence or absence of QQ activity in a sponge extract did not correlate with the abundance of isolates with the same activity from the same sponge species. This can be explained by the unknown source of QQ compounds in sponge-holobionts (host or symbionts), and further by the possible non-symbiotic nature of bacteria isolated from sponges. The potential symbiotic nature of the isolates showing QQ activity was tested according to the distribution and abundance of taxonomically close bacterial Operational Taxonomic Units (OTUs) in a dataset including 97 sponge species and 178 environmental samples (i.e., seawater, freshwater, and marine sediments). Most isolates were found not to be enriched in sponges and may simply have been trapped in the filtration channels of the sponge at the time of collection. Our results highlight potential for QQ-bioactive lead molecules for anti-virulence therapy both from sponges and the bacteria isolated thereof, independently on the symbiotic nature of the latter.
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Affiliation(s)
- Kumar Saurav
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
| | - Rinat Bar-Shalom
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
| | - Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
| | - Giorgia Oliviero
- The Blue Chemistry Lab Group, Department of Pharmacy, Università degli Studi di Napoli Federico II Napoli, Italy
| | - Valeria Costantino
- The Blue Chemistry Lab Group, Department of Pharmacy, Università degli Studi di Napoli Federico II Napoli, Italy
| | | | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
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Alex A, Antunes A. Whole Genome Sequencing of the Symbiont Pseudovibrio sp. from the Intertidal Marine Sponge Polymastia penicillus Revealed a Gene Repertoire for Host-Switching Permissive Lifestyle. Genome Biol Evol 2015; 7:3022-32. [PMID: 26519859 PMCID: PMC5635592 DOI: 10.1093/gbe/evv199] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Sponges harbor a complex consortium of microbial communities living in symbiotic relationship benefiting each other through the integration of metabolites. The mechanisms influencing a successful microbial association with a sponge partner are yet to be fully understood. Here, we sequenced the genome of Pseudovibrio sp. POLY-S9 strain isolated from the intertidal marine sponge Polymastia penicillus sampled from the Atlantic coast of Portugal to identify the genomic features favoring the symbiotic relationship. The draft genome revealed an exceptionally large genome size of 6.6 Mbp compared with the previously reported genomes of the genus Pseudovibrio isolated from a coral and a sponge larva. Our genomic study detected the presence of several biosynthetic gene clusters—polyketide synthase, nonribosomal peptide synthetase and siderophore—affirming the potential ability of the genus Pseudovibrio to produce a wide variety of metabolic compounds. Moreover, we identified a repertoire of genes encoding adaptive symbioses factors (eukaryotic-like proteins), such as the ankyrin repeats, tetratrico peptide repeats, and Sel1 repeats that improve the attachment to the eukaryotic hosts and the avoidance of the host’s immune response. The genome also harbored a large number of mobile elements (∼5%) and gene transfer agents, which explains the massive genome expansion and suggests a possible mechanism of horizontal gene transfer. In conclusion, the genome of POLY-S9 exhibited an increase in size, number of mobile DNA, multiple metabolite gene clusters, and secretion systems, likely to influence the genome diversification and the evolvability.
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Affiliation(s)
- Anoop Alex
- CIMAR/CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Agostinho Antunes
- CIMAR/CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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