51
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Crowley SP, O'Gara F, O'Sullivan O, Cotter PD, Dobson ADW. Marine Pseudovibrio sp. as a novel source of antimicrobials. Mar Drugs 2014; 12:5916-29. [PMID: 25501794 PMCID: PMC4278209 DOI: 10.3390/md12125916] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 11/16/2022] Open
Abstract
Antibiotic resistance among pathogenic microorganisms is becoming ever more common. Unfortunately, the development of new antibiotics which may combat resistance has decreased. Recently, however the oceans and the marine animals that reside there have received increased attention as a potential source for natural product discovery. Many marine eukaryotes interact and form close associations with microorganisms that inhabit their surfaces, many of which can inhibit the attachment, growth or survival of competitor species. It is the bioactive compounds responsible for the inhibition that is of interest to researchers on the hunt for novel bioactives. The genus Pseudovibrio has been repeatedly identified from the bacterial communities isolated from marine surfaces. In addition, antimicrobial activity assays have demonstrated significant antimicrobial producing capabilities throughout the genus. This review will describe the potency, spectrum and possible novelty of the compounds produced by these bacteria, while highlighting the capacity for this genus to produce natural antimicrobial compounds which could be employed to control undesirable bacteria in the healthcare and food production sectors.
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Affiliation(s)
- Susan P Crowley
- Teagasc, Moorepark Food Research Centre, Fermoy Co. Cork, Ireland.
| | - Fergal O'Gara
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.
| | - Orla O'Sullivan
- Teagasc, Moorepark Food Research Centre, Fermoy Co. Cork, Ireland.
| | - Paul D Cotter
- Teagasc, Moorepark Food Research Centre, Fermoy Co. Cork, Ireland.
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.
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52
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Hardoim CCP, Cardinale M, Cúcio ACB, Esteves AIS, Berg G, Xavier JR, Cox CJ, Costa R. Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges. Front Microbiol 2014; 5:611. [PMID: 25477868 PMCID: PMC4235377 DOI: 10.3389/fmicb.2014.00611] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 10/27/2014] [Indexed: 11/16/2022] Open
Abstract
Complex and distinct bacterial communities inhabit marine sponges and are believed to be essential to host survival, but our present-day inability to domesticate sponge symbionts in the laboratory hinders our access to the full metabolic breadth of these microbial consortia. We address bacterial cultivation bias in marine sponges using a procedure that enables direct comparison between cultivated and uncultivated symbiont community structures. Bacterial community profiling of the sympatric keratose species Sarcotragus spinosulus and Ircinia variabilis (Dictyoceratida, Irciniidae) was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and 454-pyrosequecing of 16S rRNA gene fragments. Whereas cultivation-independent methods revealed species-specific bacterial community structures in these hosts, cultivation-dependent methods resulted in equivalent community assemblages from both species. Between 15 and 18 bacterial phyla were found in S. spinosulus and I. variabilis using cultivation-independent methods. However, Alphaproteobacteria and Gammaproteobacteria dominated the cultivation-dependent bacterial community. While cultivation-independent methods revealed about 200 and 220 operational taxonomic units (OTUs, 97% gene similarity) in S. spinosulus and I. variabilis, respectively, only 33 and 39 OTUs were found in these species via culturing. Nevertheless, around 50% of all cultured OTUs escaped detection by cultivation-independent methods, indicating that standard cultivation makes otherwise host-specific bacterial communities similar by selectively enriching for rarer and generalist symbionts. This study sheds new light on the diversity spectrum encompassed by cultivated and uncultivated sponge-associated bacteria. Moreover, it highlights the need to develop alternative culturing technologies to capture the dominant sponge symbiont fraction that currently remains recalcitrant to laboratory manipulation.
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Affiliation(s)
- Cristiane C P Hardoim
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve Faro, Portugal
| | | | - Ana C B Cúcio
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve Faro, Portugal ; Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, Netherlands
| | - Ana I S Esteves
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve Faro, Portugal
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology Graz, Austria
| | - Joana R Xavier
- Department of Biology, Centre for Geobiology, University of Bergen Bergen, Norway
| | - Cymon J Cox
- Plant Systematics and Bioinformatics, Centre of Marine Sciences, University of Algarve Faro, Portugal
| | - Rodrigo Costa
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve Faro, Portugal
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53
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Microbial communities and bioactive compounds in marine sponges of the family irciniidae-a review. Mar Drugs 2014; 12:5089-122. [PMID: 25272328 PMCID: PMC4210886 DOI: 10.3390/md12105089] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/12/2014] [Accepted: 09/16/2014] [Indexed: 11/16/2022] Open
Abstract
Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species—the vast majority of which are difficult to cultivate—and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed.
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54
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Rua CPJ, Trindade-Silva AE, Appolinario LR, Venas TM, Garcia GD, Carvalho LS, Lima A, Kruger R, Pereira RC, Berlinck RGS, Valle RAB, Thompson CC, Thompson F. Diversity and antimicrobial potential of culturable heterotrophic bacteria associated with the endemic marine sponge Arenosclera brasiliensis. PeerJ 2014; 2:e419. [PMID: 25024903 PMCID: PMC4081303 DOI: 10.7717/peerj.419] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/18/2014] [Indexed: 01/13/2023] Open
Abstract
Marine sponges are the oldest Metazoa, very often presenting a complex microbial consortium. Such is the case of the marine sponge Arenosclera brasiliensis, endemic to Rio de Janeiro State, Brazil. In this investigation we characterized the diversity of some of the culturable heterotrophic bacteria living in association with A. brasiliensis and determined their antimicrobial activity. The genera Endozoicomonas (N = 32), Bacillus (N = 26), Shewanella (N = 17), Pseudovibrio (N = 12), and Ruegeria (N = 8) were dominant among the recovered isolates, corresponding to 97% of all isolates. Approximately one third of the isolates living in association with A. brasiliensis produced antibiotics that inhibited the growth of Bacillus subtilis, suggesting that bacteria associated with this sponge play a role in its health.
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Affiliation(s)
- Cintia P J Rua
- Instituto de Biologia, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | | | - Luciana R Appolinario
- Instituto de Biologia, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | - Tainá M Venas
- Instituto de Biologia, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | - Gizele D Garcia
- Instituto de Biologia, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | - Lucas S Carvalho
- Departamento de Biologia Celular, Universidade de Brasília , Brasília, DF , Brazil
| | - Alinne Lima
- Departamento de Biologia Celular, Universidade de Brasília , Brasília, DF , Brazil
| | - Ricardo Kruger
- Departamento de Biologia Celular, Universidade de Brasília , Brasília, DF , Brazil
| | - Renato C Pereira
- Instituto de Biologia, Universidade Federal Fluminense , Niterói, RJ , Brazil
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo , São Carlos, SP , Brazil
| | - Rogério A B Valle
- SAGE-COPPE Centro de Gestão Tecnológica, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | - Fabiano Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil ; SAGE-COPPE Centro de Gestão Tecnológica, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
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55
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Hardoim CCP, Costa R. Temporal dynamics of prokaryotic communities in the marine spongeSarcotragus spinosulus. Mol Ecol 2014; 23:3097-112. [DOI: 10.1111/mec.12789] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/30/2014] [Accepted: 05/05/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Cristiane C. P. Hardoim
- Microbial Ecology and Evolution Research Group; Centre of Marine Sciences (CCMar); University of Algarve (UAlg); Gambelas 8005-139 Faro Portugal
| | - Rodrigo Costa
- Microbial Ecology and Evolution Research Group; Centre of Marine Sciences (CCMar); University of Algarve (UAlg); Gambelas 8005-139 Faro Portugal
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56
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Zuppa A, Costantini S, Costantini M. Comparative sequence analysis of bacterial symbionts from the marine sponges Geodia cydonium and Ircinia muscarum. Bioinformation 2014; 10:196-200. [PMID: 24966520 PMCID: PMC4070049 DOI: 10.6026/97320630010196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 02/24/2014] [Indexed: 11/23/2022] Open
Abstract
Marine sponges (Porifera) live in a symbiotic relationship with microorganisms, primarily bacteria. Recently, several studies indicated that sponges are the most prolific source of biologically-active compounds produced by symbiotic microorganisms rather than by the sponges themselves. In the present study we characterized the bacterial symbionts from two Demospongiae, Ircinia muscarum and Geodia cydonium. We amplified 16S rRNA by PCR, using specific bacterial-primers. The phylogenetic analysis revealed the presence of nine bacterial clones from I. muscarum and ten from G. cydonium. In particular, I. muscarum resulted enriched in Bacillus species and G. cydonium in Proteobacterium species. Since these bacteria were able to produce secondary metabolites with potential biotechnological and biopharmaceutical applications, we hypothesized that I. muscarum and G. cydonium could be a considered as a "gold mine" of natural products.
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Affiliation(s)
- Antonio Zuppa
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Susan Costantini
- Istituto Nazionale per lo Studio e la Cura dei Tumori ‘Fondazione Giovanni Pascale’, IRCCS, Napoli, Italia
| | - Maria Costantini
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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57
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Montalvo NF, Davis J, Vicente J, Pittiglio R, Ravel J, Hill RT. Integration of culture-based and molecular analysis of a complex sponge-associated bacterial community. PLoS One 2014; 9:e90517. [PMID: 24618773 PMCID: PMC3949686 DOI: 10.1371/journal.pone.0090517] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 02/02/2014] [Indexed: 12/25/2022] Open
Abstract
The bacterial communities of sponges have been studied using molecular techniques as well as culture-based techniques, but the communities described by these two methods are remarkably distinct. Culture-based methods describe communities dominated by Proteobacteria, and Actinomycetes while molecular methods describe communities dominated by predominantly uncultivated groups such as the Chloroflexi, Acidobacteria, and Acidimicrobidae. In this study, we used a wide range of culture media to increase the diversity of cultivable bacteria from the closely related giant barrel sponges, Xestospongia muta collected from the Florida Keys, Atlantic Ocean and Xestospongia testudinaria, collected from Indonesia, Pacific Ocean. Over 400 pure cultures were isolated and identified from X. muta and X. testudinaria and over 90 bacterial species were represented. Over 16,000 pyrosequences were analyzed and assigned to 976 OTUs. We employed both cultured-based methods and pyrosequencing to look for patterns of overlap between the culturable and molecular communities. Only one OTU was found in both the molecular and culturable communities, revealing limitations inherent in both approaches.
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Affiliation(s)
- Naomi F. Montalvo
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Jeanette Davis
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Jan Vicente
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Raquel Pittiglio
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Russell T. Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
- * E-mail:
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58
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Graça AP, Bondoso J, Gaspar H, Xavier JR, Monteiro MC, de la Cruz M, Oves-Costales D, Vicente F, Lage OM. Antimicrobial activity of heterotrophic bacterial communities from the marine sponge Erylus discophorus (Astrophorida, Geodiidae). PLoS One 2013; 8:e78992. [PMID: 24236081 PMCID: PMC3827338 DOI: 10.1371/journal.pone.0078992] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/25/2013] [Indexed: 12/17/2022] Open
Abstract
Heterotrophic bacteria associated with two specimens of the marine sponge Erylus discophorus were screened for their capacity to produce bioactive compounds against a panel of human pathogens (Staphylococcus aureus wild type and methicillin-resistant S. aureus (MRSA), Bacillus subtilis, Pseudomonas aeruginosa, Acinetobacter baumanii, Candida albicans and Aspergillus fumigatus), fish pathogen (Aliivibrio fischeri) and environmentally relevant bacteria (Vibrio harveyi). The sponges were collected in Berlengas Islands, Portugal. Of the 212 isolated heterotrophic bacteria belonging to Alpha- and Gammaproteobacteria, Actinobacteria and Firmicutes, 31% produced antimicrobial metabolites. Bioactivity was found against both Gram positive and Gram negative and clinically and environmentally relevant target microorganisms. Bioactivity was found mainly against B. subtilis and some bioactivity against S. aureus MRSA, V. harveyi and A. fisheri. No antifungal activity was detected. The three most bioactive genera were Pseudovibrio (47.0%), Vibrio (22.7%) and Bacillus (7.6%). Other less bioactive genera were Labrenzia, Acinetobacter, Microbulbifer, Pseudomonas, Gordonia, Microbacterium, Micrococcus and Mycobacterium, Paenibacillus and Staphylococcus. The search of polyketide I synthases (PKS-I) and nonribosomal peptide synthetases (NRPSs) genes in 59 of the bioactive bacteria suggested the presence of PKS-I in 12 strains, NRPS in 3 strains and both genes in 3 strains. Our results show the potential of the bacterial community associated with Erylus discophorus sponges as producers of bioactive compounds.
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Affiliation(s)
- Ana Patrícia Graça
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIMAR/CIIMAR), Porto, Portugal
| | - Joana Bondoso
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIMAR/CIIMAR), Porto, Portugal
| | - Helena Gaspar
- Centro de Química e Bioquímica e Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa Campo Grande, Lisboa, Portugal
| | - Joana R. Xavier
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores – Departamento de Biologia da Universidade dos Açores, Ponta Delgada, Portugal
- CEAB, Centre d'Estudis Avançats de Blanes, (CSIC), Blanes (Girona), Spain
| | - Maria Cândida Monteiro
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Armilla, Granada, Spain
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Armilla, Granada, Spain
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Armilla, Granada, Spain
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Armilla, Granada, Spain
| | - Olga Maria Lage
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIMAR/CIIMAR), Porto, Portugal
- * E-mail:
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