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Cahyani NKD, Kasanah N, Kurnia DS, Hamann MT. Profiling Prokaryotic Communities and Aaptamines of Sponge Aaptos suberitoides from Tulamben, Bali. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:1158-1175. [PMID: 38008858 PMCID: PMC11329227 DOI: 10.1007/s10126-023-10268-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 11/04/2023] [Indexed: 11/28/2023]
Abstract
Sponges (Porifera) harbor a diversity of microorganisms that contribute largely to the production a vast array of bioactive compounds. The microorganisms associated with sponge have an important impact on the chemical diversity of the natural products. Herein, our study focuses on an Aaptos suberitoides commonly found in Indonesia. The objective of this study was to investigate the profile of prokaryotic community and the presence of aaptamine metabolites in sponge Aaptos suberitoides. Sponges were collected from two site locations (Liberty Wreck and Drop Off) in Tulamben, Bali. The sponges were identified by barcoding DNA cytochrome oxidase subunit I (COI) gene. The profile of prokaryotic composition was investigated by amplifying the 16S rRNA gene using primers 515f and 806r to target the V4 region. The metabolites were analyzed using LC-MS, and dereplication was done to identify the aaptamines and its derivates. The barcoding DNA of the sponges confirmed the identity of samples as Aaptos suberitoides. The prokaryotic communities of samples A. suberitoides were enriched and dominated by taxa Proteobacteria, Chloroflexi, Actinobacteria, and Acidobacteria. The chemical analysis showed that all sponges produce aaptamine and isoaaptamine except A. suberitoides S2421 produce analog of aaptamines. This is the first report on the profile of prokaryotic community and the aaptamine of tropical marine sponges, A. suberitoides, from Tulamben, Bali.
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Affiliation(s)
- Ni Kadek Dita Cahyani
- Biology Department, Faculty of Science and Mathematics, Diponegoro University, Semarang, Central Java, Indonesia
| | - Noer Kasanah
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Dewi Sri Kurnia
- Department of Biotechnology, Graduate School, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mark T Hamann
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, SC, USA
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2
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Iskandar M, Ruiz-Houston KM, Bracco SD, Sharkasi SR, Calabi Villarroel CL, Desai MN, Gerges AG, Ortiz Lopez NA, Xiao Barbero M, German AA, Moluguri VS, Walker SM, Silva Higashi J, Palma JM, Medina DZ, Patel M, Patel P, Valentin M, Diaz AC, Karthaka JP, Santiago AD, Skiles RB, Romero Umana LA, Ungrey MD, Wojtkowiak A, Howard DV, Nurge R, Woods KG, Nanjundan M. Deep-Sea Sponges and Corals off the Western Coast of Florida-Intracellular Mechanisms of Action of Bioactive Compounds and Technological Advances Supporting the Drug Discovery Pipeline. Mar Drugs 2023; 21:615. [PMID: 38132936 PMCID: PMC10744787 DOI: 10.3390/md21120615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
The majority of natural products utilized to treat a diverse array of human conditions and diseases are derived from terrestrial sources. In recent years, marine ecosystems have proven to be a valuable resource of diverse natural products that are generated to defend and support their growth. Such marine sources offer a large opportunity for the identification of novel compounds that may guide the future development of new drugs and therapies. Using the National Oceanic and Atmospheric Administration (NOAA) portal, we explore deep-sea coral and sponge species inhabiting a segment of the U.S. Exclusive Economic Zone, specifically off the western coast of Florida. This area spans ~100,000 km2, containing coral and sponge species at sea depths up to 3000 m. Utilizing PubMed, we uncovered current knowledge on and gaps across a subset of these sessile organisms with regards to their natural products and mechanisms of altering cytoskeleton, protein trafficking, and signaling pathways. Since the exploitation of such marine organisms could disrupt the marine ecosystem leading to supply issues that would limit the quantities of bioactive compounds, we surveyed methods and technological advances that are necessary for sustaining the drug discovery pipeline including in vitro aquaculture systems and preserving our natural ecological community in the future. Collectively, our efforts establish the foundation for supporting future research on the identification of marine-based natural products and their mechanism of action to develop novel drugs and therapies for improving treatment regimens of human conditions and diseases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Meera Nanjundan
- Department of Molecular Biosciences, University of South Florida, 4202 East Fowler Avenue, ISA2015, Tampa, FL 33620, USA; (M.I.); (K.M.R.-H.); (S.D.B.); (S.R.S.); (C.L.C.V.); (M.N.D.); (A.G.G.); (N.A.O.L.); (M.X.B.); (A.A.G.); (V.S.M.); (S.M.W.); (J.S.H.); (J.M.P.); (D.Z.M.); (M.P.); (P.P.); (M.V.); (A.C.D.); (J.P.K.); (A.D.S.); (R.B.S.); (L.A.R.U.); (M.D.U.); (A.W.); (D.V.H.); (R.N.); (K.G.W.)
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3
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The Marine Sponge Petrosia ficiformis Harbors Different Cyanobacteria Strains with Potential Biotechnological Application. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2020. [DOI: 10.3390/jmse8090638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Marine cyanobacteria are a source of bioactive natural compounds, with a wide range of biotechnological applications. However, information on sponge-associated cyanobacteria are relatively scarce to date. In this paper, we carried out the morphological and molecular characterization of eight cyanobacterial strains, previously isolated from the Mediterranean sponge Petrosia ficiformis, and evaluated their biological activities on epithelial- and neuron-like cultured cells of human and murine origin. The new analysis allowed maintaining the assignment of three strains (Cyanobium sp., Leptolyngbya ectocarpi, and Synechococcus sp.), while two strains previously identified as Synechococcus sp. and Leptolyngbya sp. were assigned to Pseudanabaena spp. One strain, i.e., ITAC104, and the ITAC101 strain corresponding to Halomicronema metazoicum, shared extremely high sequence identity, practically representing two clones of the same species. Finally, for only one strain, i.e., ITAC105, assignment to a specific genus was not possible. Concerning bioactivity analyses, incubation of cyanobacterial aqueous cell supernatants induced variable responses in cultured cells, depending on cell type, with some of them showing toxic activity on human epithelial-like cells and no toxic effects on human and rat neuron-like cells. Future investigations will allow to better define the bioactive properties of these cyanobacteria strains and to understand if they can be useful for (a) therapeutic purpose(s).
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Knobloch S, Jóhannsson R, Marteinsson V. Co-cultivation of the marine sponge Halichondria panicea and its associated microorganisms. Sci Rep 2019; 9:10403. [PMID: 31320673 PMCID: PMC6639338 DOI: 10.1038/s41598-019-46904-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/03/2019] [Indexed: 12/29/2022] Open
Abstract
Marine sponges host bacterial symbionts with biotechnological potential, yet isolation of true sponge symbionts remains difficult due to their host dependency. Moreover, attempts to grow sponges for their pharmacologically-active compounds outside of their habitat often results in a shift of their microbial community. In this study we evaluate suitable sponge cultivation methods that allow maintenance of both the marine sponge Halichondria panicea and its associated bacteria in an ex situ environment. In addition, we present a method for co-cultivation of sponge explants and microbes separated by a membrane in a multi-chamber device. Tests on ex situ cultivation of H. panicea under different controlled conditions showed that only high water exchange rates in the aquarium enabled maintenance of its dominant symbiont “Candidatus Halichondribacter symbioticus” at a high relative abundance in the sponge body, a prerequisite for co-cultivation. The bacterial enrichment retrieved from co-cultivation contained bacteria from nine different classes in addition to sequences corresponding to “Ca. H. symbioticus”. This represents an increase of the cultivable bacterial classes from H. panicea compared to standard isolation techniques on solid media plates. The current study provides insights into sponge-microbe maintenance under ex situ conditions and proposes a new method for the isolation of sponge-associated bacteria.
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Affiliation(s)
- Stephen Knobloch
- Microbiology Group, Department of Research and Innovation, Matís ohf., 113, Reykjavik, Iceland. .,Faculty of Life and Environmental Sciences, University of Iceland, 101, Reykjavík, Iceland.
| | - Ragnar Jóhannsson
- Marine and Freshwater Research Institute, Hafrannsóknastofnun, 101, Reykjavik, Iceland
| | - Viggó Marteinsson
- Microbiology Group, Department of Research and Innovation, Matís ohf., 113, Reykjavik, Iceland.,Faculty of Food Science and Nutrition, University of Iceland, 101, Reykjavik, Iceland
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Sacristán‐Soriano O, Winkler M, Erwin P, Weisz J, Harriott O, Heussler G, Bauer E, West Marsden B, Hill A, Hill M. Ontogeny of symbiont community structure in two carotenoid-rich, viviparous marine sponges: comparison of microbiomes and analysis of culturable pigmented heterotrophic bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:249-261. [PMID: 30761773 PMCID: PMC6850349 DOI: 10.1111/1758-2229.12739] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/31/2019] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
Marine sponges harbour diverse communities of microbes. Mechanisms used to establish microbial symbioses in sponges are poorly understood, and the relative contributions of horizontal and vertical transmission are unknown for most species. We examined microbial communities in adults and larvae of carotenoid-rich Clathria prolifera and Halichondria bowerbanki from the mid-Atlantic region of the eastern United States. We sequenced microbiomes from larvae and their mothers and seawater (16S rRNA gene sequencing), and compared microbial community characteristics between species and ambient seawater. The microbial communities in sponges were significantly different than those found in seawater, and each species harboured a distinctive microbiome. Larval microbiomes exhibited significantly lower richness compared with adults, with both sponges appearing to transfer to larvae a particular subset of the adult microbiome. We also surveyed culturable bacteria isolated from larvae of both species. Due to conspicuous coloration of adults and larvae, we focused on pigmented heterotrophic bacteria. We found that the densities of bacteria, in terms of colony-forming units and pigmented heterotrophic bacteria, were higher in larvae than in seawater. We identified a common mode of transmission (vertical and horizontal) of microbes in both sponges that might differ between species.
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Affiliation(s)
- Oriol Sacristán‐Soriano
- Department of BiologyUniversity of RichmondRichmondVAUSA
- Marine Ecology DepartmentCentro de Estudios Avanzados de Blanes (CEAB, CSIC)BlanesSpain
| | - Marina Winkler
- Department of BiologyUniversity of RichmondRichmondVAUSA
| | - Patrick Erwin
- Department of Biology and Marine Biology, Center for Marine ScienceUniversity of North CarolinaWilmingtonNCUSA
| | - Jeremy Weisz
- Department of BiologyLinfield CollegeMcMinnvilleORUSA
| | | | - Gary Heussler
- Department of BiologyFairfield UniversityFairfieldCTUSA
| | - Emily Bauer
- Department of BiologyUniversity of RichmondRichmondVAUSA
| | | | - April Hill
- Department of BiologyUniversity of RichmondRichmondVAUSA
| | - Malcolm Hill
- Department of BiologyUniversity of RichmondRichmondVAUSA
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Sponges-Cyanobacteria associations: Global diversity overview and new data from the Eastern Mediterranean. PLoS One 2018; 13:e0195001. [PMID: 29596453 PMCID: PMC5875796 DOI: 10.1371/journal.pone.0195001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/14/2018] [Indexed: 11/19/2022] Open
Abstract
Sponge-cyanobacteria associations have attracted research interest from an ecological, evolutionary and biotechnological perspective. Current knowledge is, in its majority, “hidden” in metagenomics research studying the entire microbial communities of sponges, while knowledge on these associations is totally missing for certain geographic areas. In this study, we (a) investigated the occurrence of cyanobacteria in 18 sponge species, several of which are studied for the first time for their cyanobionts, from a previously unexplored eastern Mediterranean ecoregion, the Aegean Sea, (b) isolated sponge-associated cyanobacteria, and characterized them based on a polyphasic (morphological-morphometric and molecular phylogenetic analysis) approach, and (c) conducted a meta-analysis on the global diversity of sponge species hosting cyanobacteria, as well as the diversity of cyanobacterial symbionts. Our research provided new records for nine sponge species, previously unknown for this association, while the isolated cyanobacteria were found to form novel clades within Synechococcus, Leptolyngbyaceae, Pseudanabaenaceae, and Schizotrichaceae, whose taxonomic status requires further investigation; this is the first report of a Schizotrichaceae cyanobacterium associated with sponges. The extensive evaluation of the literature along with the new data from the Aegean Sea raised the number of sponge species known for hosting cyanobacteria to 320 and showed that the cyanobacterial diversity reported from sponges is yet underestimated.
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7
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Two new pyrrolo-2-aminoimidazoles from a Myanmarese marine sponge, Clathria prolifera. J Nat Med 2018; 72:803-807. [PMID: 29569222 DOI: 10.1007/s11418-018-1205-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
Abstract
Marine organisms such as marine sponges and soft corals are valuable sources of pharmacologically active secondary metabolites. In our ongoing research on the discovery of new secondary metabolites from marine organisms, two new pyrrolo-2-aminoimidazoles, clathriroles A (1) and B (2), were isolated from the water-soluble portion prepared from the methanol and acetone (2:1) extract of the marine sponge, Clathria prolifera, collected in Myanmar. The chemical structures of the isolated compounds were determined using extensive spectroscopic techniques, including NMR, HRESIMS, IR, and optical rotation, and comparisons with the reported literature. The spectroscopic analyses of 1 and 2 suggested that 1 is an enantiomer of antifungal N-methylmanzacidin C isolated from the marine sponge Axinella brevistyla, whereas 2 is a diastereomer of manzacidin D at C-11 isolated from the marine sponge Astrosclera willeyana. To the best of our knowledge, this is the first report of the isolation of the pyrrolo-2-aminoimidazole compounds from C. prolifera. Furthermore, in contrast to the potency of N-methylmanzacidin C against Saccharomyces cerevisiae, the antifungal assay revealed that 1 and 2 lack any activity against this strain. Thus, these observations may suggest that the absolute configurations at both C-9 and C-11 play an important role in controlling the antifungal activity of this type of compound.
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8
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Flechas SV, Blasco-Zúñiga A, Merino-Viteri A, Ramírez-Castañeda V, Rivera M, Amézquita A. The effect of captivity on the skin microbial symbionts in three Atelopus species from the lowlands of Colombia and Ecuador. PeerJ 2017; 5:e3594. [PMID: 28785515 PMCID: PMC5541920 DOI: 10.7717/peerj.3594] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/29/2017] [Indexed: 12/19/2022] Open
Abstract
Many amphibian species are at risk of extinction in their natural habitats due to the presence of the fungal pathogen Batrachochytrium dendrobatidis (Bd). For the most highly endangered species, captive assurance colonies have been established as an emergency measure to avoid extinction. Experimental research has suggested that symbiotic microorganisms in the skin of amphibians play a key role against Bd. While previous studies have addressed the effects of captivity on the cutaneous bacterial community, it remains poorly studied whether and how captive conditions affect the proportion of beneficial bacteria or their anti-Bd performance on amphibian hosts. In this study we sampled three amphibian species of the highly threatened genus, Atelopus, that remain in the wild but are also part of ex situ breeding programs in Colombia and Ecuador. Our goals were to (1) estimate the diversity of culturable bacterial assemblages in these three species of Atelopus, (2) describe the effect of captivity on the composition of skin microbiota, and (3) examine how captivity affects the bacterial ability to inhibit Bd growth. Using challenge assays we tested each bacterial isolate against Bd, and through sequencing of the 16S rRNA gene, we identified species from thirteen genera of bacteria that inhibited Bd growth. Surprisingly, we did not detect a reduction in skin bacteria diversity in captive frogs. Moreover, we found that frogs in captivity still harbor bacteria with anti-Bd activity. Although the scope of our study is limited to a few species and to the culturable portion of the bacterial community, our results indicate that captive programs do not necessarily change bacterial communities of the toad skins in a way that impedes the control of Bd in case of an eventual reintroduction.
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Affiliation(s)
- Sandra V Flechas
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Ailin Blasco-Zúñiga
- Laboratorio de Investigación en Citogenética y Biomoléculas de Anfibios (LICBA), Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Andrés Merino-Viteri
- Museo de Zoología (QCAZ), Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | | | - Miryan Rivera
- Laboratorio de Investigación en Citogenética y Biomoléculas de Anfibios (LICBA), Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Adolfo Amézquita
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
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Wan X, Ruan R, McLaughlin RW, Hao Y, Zheng J, Wang D. Fecal Bacterial Composition of the Endangered Yangtze Finless Porpoises Living Under Captive and Semi-natural Conditions. Curr Microbiol 2015; 72:306-14. [PMID: 26620537 DOI: 10.1007/s00284-015-0954-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/22/2015] [Indexed: 11/25/2022]
Abstract
Intestinal microbiota is essential to the health and physiology of host animals. We undertook the first microbiological study of the fecal bacterial composition from critically endangered (CR) Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis; YFPs) living under captive and semi-natural conditions using both high-throughput sequencing method and 16S rRNA gene clone library method. As determined by high-throughput sequencing of V3-V4 regions of the 16S rRNA gene, semi-natural samples harbored 30 and 36 operational taxonomic units (OTUs), which was more than the 22 and 27 OTUs detected from YFPs living in captivity. In captive YFPs Firmicutes was the predominant phylum, whereas this was Proteobacteria for YFPs living in semi-nature conditions. This suggests habitat-specific fecal bacterial composition of YFPs. Plesiomonas spp. and Aeromonas spp., which are potentially pathogenic, were identified in all the feces. Bacterial diversity from one porpoise living in captivity was also determined by constructing a 16S rRNA gene clone library and only 1 phylum was identified. High-throughput sequencing was more effective at determining the bacterial diversity compared to the 16S rRNA gene clone library. This study provides important information for the management and conservation of the CR YFPs.
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Affiliation(s)
- Xiaoling Wan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Rui Ruan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Richard William McLaughlin
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuhan, 430072, China.,Biology Department, Saint Mary's University of Minnesota, 700 Terrace, Winona, MN, 55987-1399, USA
| | - Yujiang Hao
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuhan, 430072, China
| | - Jinsong Zheng
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuhan, 430072, China.
| | - Ding Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuhan, 430072, China.
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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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11
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Leal MC, Sheridan C, Osinga R, Dionísio G, Rocha RJM, Silva B, Rosa R, Calado R. Marine microorganism-invertebrate assemblages: perspectives to solve the "supply problem" in the initial steps of drug discovery. Mar Drugs 2014; 12:3929-52. [PMID: 24983638 PMCID: PMC4113807 DOI: 10.3390/md12073929] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/04/2014] [Accepted: 06/06/2014] [Indexed: 01/11/2023] Open
Abstract
The chemical diversity associated with marine natural products (MNP) is unanimously acknowledged as the "blue gold" in the urgent quest for new drugs. Consequently, a significant increase in the discovery of MNP published in the literature has been observed in the past decades, particularly from marine invertebrates. However, it remains unclear whether target metabolites originate from the marine invertebrates themselves or from their microbial symbionts. This issue underlines critical challenges associated with the lack of biomass required to supply the early stages of the drug discovery pipeline. The present review discusses potential solutions for such challenges, with particular emphasis on innovative approaches to culture invertebrate holobionts (microorganism-invertebrate assemblages) through in toto aquaculture, together with methods for the discovery and initial production of bioactive compounds from these microbial symbionts.
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Affiliation(s)
- Miguel Costa Leal
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal.
| | - Christopher Sheridan
- Biology of Marine Organisms and Biomimetics Laboratory, Research Institute for Biosciences, University of Mons, Pentagone 2B, 6 Avenue du Champ de Mars, Mons 7000, Belgium.
| | - Ronald Osinga
- Department of Aquaculture and Fisheries, Wageningen University, P.O. Box 338, 6700 AH Wageningen, The Netherlands.
| | - Gisela Dionísio
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal.
| | - Rui Jorge Miranda Rocha
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal.
| | - Bruna Silva
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal.
| | - Rui Rosa
- Laboratório Marítimo da Guia, Centro de Oceanografia, Faculdade de Ciências da Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, Cascais 2750-374, Portugal.
| | - Ricardo Calado
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal.
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12
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Jeong IH, Kim KH, Lee HS, Park JS. Analysis of bacterial diversity in sponges collected from Chuuk and Kosrae Islands in Micronesia. J Microbiol 2014; 52:20-6. [PMID: 24390834 DOI: 10.1007/s12275-014-3619-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 12/13/2013] [Accepted: 12/16/2013] [Indexed: 10/25/2022]
Abstract
The bacteria resident in sponges collected from Chuuk Lagoon and Kosrae Island of Micronesia were investigated using the 16S rRNA gene PCR-tagged pyrosequencing method. These sponges were clustered into 5 groups based on their bacterial composition. Diversity indexes and cumulative rank abundance curves showed the different compositions of bacterial communities in the various groups of sponges. Reads related to the phylum Chloroflexi were observed predominantly (9.7-68.2%) in 9 sponges of 3 groups and unobserved in the other 2 groups. The Chloroflexi-containing group had similar bacterial patterns at the phylum and lower taxonomic levels, for example, significant proportions of Acidobacteria, Gemmatimonadetes, SBR1093, and PAUC34f were observed in most members of this group. The three groups in the Chloroflexi-containing group, however, showed some minor differences in the composition and diversity. The other two groups contained high proportions of Proteobacteria (>87%) or Bacteroidetes (>61%) and different composition and diversity compared to the Chloroflexi-containing group and each other. Four pairs of specimens with the same species showed similar bacterial profiles, but, the bacteria in sponges were highly specific at the individual level.
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Affiliation(s)
- In-Hye Jeong
- Department of Biological Science and Biotechnology, Hannam University, Daejeon, 305-811, Republic of Korea
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13
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Analysis of bacterial diversity in sponges collected off Chujado, an Island in Korea, using barcoded 454 pyrosequencing: Analysis of a distinctive sponge group containing Chloroflexi. J Microbiol 2013; 51:570-7. [DOI: 10.1007/s12275-013-3426-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 10/04/2013] [Indexed: 01/10/2023]
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14
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Depuration of tetrodotoxin and changes in bacterial communities in Pleurobranchea maculata adults and egg masses maintained in captivity. J Chem Ecol 2012; 38:1342-50. [PMID: 23151964 DOI: 10.1007/s10886-012-0212-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 09/17/2012] [Accepted: 10/22/2012] [Indexed: 10/27/2022]
Abstract
Depuration of tetrodotoxin (TTX) was investigated in adult grey side-gilled sea slugs, Pleurobranchaea maculata, maintained in captivity on a TTX-free diet. Three adults were harvested every 21 days for 126 days, and TTX concentrations were measured in organs/tissues and egg masses. Automated rRNA intergenic spacer analysis (ARISA) was used to investigate bacterial community structure in selected samples. Linear modeling of adult data demonstrated a decline (P<0.001) in average total TTX concentrations over time. Temporal data obtained from a wild population showed similar depuration rates, indicating that once adults reach a certain size, or sexual maturity, TTX is no longer produced or acquired substantially. Depuration rates differed among organs, with concentrations in the heart declining the fastest. The gonads had the slowest and least significant depuration rate indicating, at most, weak depuration of this tissue. There was a strong correlation (R(2)=0.66) between TTX concentrations in the first-laid egg masses and total TTX in the corresponding adult. These data suggest that adult P. maculata transfer TTX to their offspring, and presumably that functions as a chemical defense. ARISA data showed a shift in bacterial community structure within 3 weeks of introduction to captivity. Based on the combined data, the exact origin of TTX in P. maculata is unclear, with evidence both in favor and against a dietary source, and endogenous or bacterial production.
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15
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Diversity and biosynthetic potential of culturable actinomycetes associated with marine sponges in the China Seas. Int J Mol Sci 2012; 13:5917-5932. [PMID: 22754340 PMCID: PMC3382808 DOI: 10.3390/ijms13055917] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 04/27/2012] [Accepted: 05/07/2012] [Indexed: 11/23/2022] Open
Abstract
The diversity and secondary metabolite potential of culturable actinomycetes associated with eight different marine sponges collected from the South China Sea and the Yellow sea were investigated. A total of 327 strains were isolated and 108 representative isolates were selected for phylogenetic analysis. Ten families and 13 genera of Actinomycetales were detected, among which five genera represent first records isolated from marine sponges. Oligotrophic medium M5 (water agar) proved to be efficient for selective isolation, and “Micromonospora–Streptomyces” was proposed as the major distribution group of sponge-associated actinomycetes from the China Seas. Ten isolates are likely to represent novel species. Sponge Hymeniacidon perleve was found to contain the highest genus diversity (seven genera) of actinomycetes. Housekeeping gene phylogenetic analyses of the isolates indicated one ubiquitous Micromonospora species, one unique Streptomyces species and one unique Verrucosispora phylogroup. Of the isolates, 27.5% displayed antimicrobial activity, and 91% contained polyketide synthase and/or nonribosomal peptide synthetase genes, indicating that these isolates had a high potential to produce secondary metabolites. The isolates from sponge Axinella sp. contained the highest presence of both antimicrobial activity and NRPS genes, while those from isolation medium DNBA showed the highest presence of antimicrobial activity and PKS I genes.
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16
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Richardson C, Hill M, Marks C, Runyen-Janecky L, Hill A. Experimental manipulation of sponge/bacterial symbiont community composition with antibiotics: sponge cell aggregates as a unique tool to study animal/microorganism symbiosis. FEMS Microbiol Ecol 2012; 81:407-18. [DOI: 10.1111/j.1574-6941.2012.01365.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 02/24/2012] [Accepted: 03/07/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
| | - Malcolm Hill
- Department of Biology; University of Richmond; Richmond; VA; USA
| | - Carolyn Marks
- Department of Biology; University of Richmond; Richmond; VA; USA
| | | | - April Hill
- Department of Biology; University of Richmond; Richmond; VA; USA
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17
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Quinn GA, Maloy AP, McClean S, Carney B, Slater JW. Lipopeptide biosurfactants from Paenibacillus polymyxa inhibit single and mixed species biofilms. BIOFOULING 2012; 28:1151-1166. [PMID: 23113815 DOI: 10.1080/08927014.2012.738292] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Although biofilms are recognised as important in microbial colonisation, solutions to their inhibition are predominantly based on planktonic assays. These solutions have limited efficacy against biofilms. Here, a series of biofilm-orientated tests were used to identify anti-biofilm compounds from marine micro-flora. This led to the isolation of a complex of anti-biofilm compounds from an extract of Paenibacillus polymyxa (PPE). A combination of rpHPLC and mass spectrometry identified the principle components of PPE as fusaricidin B (LI-FO4b) and polymyxin D1, with minor contributions from surfactins. This complex (PPE) reduced the biofilm biomass of Bacillus subtilis, Micrococcus luteus, Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus bovis. In contrast, ampicillin was only effective against S. aureus. PPE also inhibited a self-assembling marine biofilm (SAMB) in co-incubation assays by 99.3% ± 1.9 and disrupted established SAMB by 72.4% ± 4.4, while ampicillin showed no significant reduction. The effectiveness of this complex of lipopeptides against single and multispecies biofilms suggests a future role in biofilm prevention strategies.
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Affiliation(s)
- Gerry A Quinn
- Centre of Applied Marine Biotechnology, Letterkenny Institute of Technology, Letterkenny, County Donegal, Republic of Ireland.
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Thacker RW, Freeman CJ. Sponge-microbe symbioses: recent advances and new directions. ADVANCES IN MARINE BIOLOGY 2012; 62:57-111. [PMID: 22664121 DOI: 10.1016/b978-0-12-394283-8.00002-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Sponges can host abundant and diverse communities of symbiotic microorganisms. In this chapter, we review recent work in the area of sponge-microbe symbioses, focusing on (1) the diversity of these associations, (2) host specificity, (3) modes of symbiont transmission, and (4) the positive and negative impacts of symbionts on their hosts. Over the past 4 years, numerous studies have catalogued the diversity of sponge-microbe symbioses, challenging previous hypotheses of a uniform, vertically transmitted microbial community and supporting a mixed model of symbiont community transmission. We emphasize the need for experimental manipulations of sponge-symbiont interactions coupled with advanced laboratory techniques to determine the identity of metabolically active microbial symbionts, to investigate the physiological processes underlying these interactions, and to elucidate whether symbionts act as mutualists, commensals, or parasites. The amazing diversity of these complex associations continues to offer critical insights into the evolution of symbiosis and the impacts of symbiotic microbes on nutrient cycling and other ecosystem functions.
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Schippers KJ, Sipkema D, Osinga R, Smidt H, Pomponi SA, Martens DE, Wijffels RH. Cultivation of sponges, sponge cells and symbionts: achievements and future prospects. ADVANCES IN MARINE BIOLOGY 2012; 62:273-337. [PMID: 22664125 DOI: 10.1016/b978-0-12-394283-8.00006-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Marine sponges are a rich source of bioactive compounds with pharmaceutical potential. Since biological production is one option to supply materials for early drug development, the main challenge is to establish generic techniques for small-scale production of marine organisms. We analysed the state of the art for cultivation of whole sponges, sponge cells and sponge symbionts. To date, cultivation of whole sponges has been most successful in situ; however, optimal conditions are species specific. The establishment of sponge cell lines has been limited by the inability to obtain an axenic inoculum as well as the lack of knowledge on nutritional requirements in vitro. Approaches to overcome these bottlenecks, including transformation of sponge cells and using media based on yolk, are elaborated. Although a number of bioactive metabolite-producing microorganisms have been isolated from sponges, and it has been suggested that the source of most sponge-derived bioactive compounds is microbial symbionts, cultivation of sponge-specific microorganisms has had limited success. The current genomics revolution provides novel approaches to cultivate these microorganisms.
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Affiliation(s)
- Klaske J Schippers
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands
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20
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Bergman O, Mayzel B, Anderson MA, Shpigel M, Hill RT, Ilan M. Examination of marine-based cultivation of three demosponges for acquiring bioactive marine natural products. Mar Drugs 2011; 9:2201-2219. [PMID: 22163182 PMCID: PMC3229231 DOI: 10.3390/md9112201] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 10/08/2011] [Accepted: 10/21/2011] [Indexed: 11/16/2022] Open
Abstract
Marine sponges are an extremely rich and important source of natural products. Mariculture is one solution to the so-called "supply problem" that often hampers further studies and development of novel compounds from sponges. We report the extended culture (767 days) at sea in depths of 10 and 20 m of three sponge species: Negombata magnifica, Amphimedon chloros and Theonella swinhoei that produce latrunculin-B, halitoxin and swinholide-A, respectively. Since sponge-associated microorganisms may be the true producers of many of the natural products found in sponges and also be linked to the health of the sponges, we examined the stability of the bacterial communities in cultured versus wild sponges. Growth rate of the sponges (ranging from 308 to 61 and -19 (%)(year(-1)) in N. magnifica, A. chloros and T. swinhoei, respectively) differed significantly between species but not between the two depths at which the species were cultivated. Survivorship varied from 96% to 57%. During culture all species maintained the content of the desired natural product. Denaturing gradient gel electrophoresis analysis of the sponge-associated bacterial consortia revealed that differences existed between cultured and wild sponges in T. swinhoei and A. chloros but the communities remained quite stable in N. magnifica. The cultivation technique for production of natural products was found to be most appropriate for N. magnifica, while for T. swinhoei and A. chloros it was less successful, because of poorer growth and survival rates and shifts in their bacterial consortia.
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Affiliation(s)
- Oded Bergman
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; E-Mails: (O.B.); (B.M.)
| | - Boaz Mayzel
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; E-Mails: (O.B.); (B.M.)
| | - Matthew A. Anderson
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, Suite 236, 701 East Pratt Street, Baltimore, MD 21202, USA; E-Mails: (M.A.A.); (R.T.H.)
| | - Muki Shpigel
- National Center for Mariculture, IOLR, P.O. Box 1212, Eilat 88212, Israel; E-Mail:
| | - Russell T. Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, Suite 236, 701 East Pratt Street, Baltimore, MD 21202, USA; E-Mails: (M.A.A.); (R.T.H.)
| | - Micha Ilan
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; E-Mails: (O.B.); (B.M.)
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Webster NS, Cobb RE, Soo R, Anthony SL, Battershill CN, Whalan S, Evans-Illidge E. Bacterial community dynamics in the marine sponge Rhopaloeides odorabile under in situ and ex situ cultivation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:296-304. [PMID: 20544249 DOI: 10.1007/s10126-010-9300-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 05/25/2010] [Indexed: 05/29/2023]
Abstract
Cultivation of sponges is being explored to supply biomaterial for the pharmaceutical and cosmetics industries. This study assesses the impact of various cultivation methods on the microbial community within the sponge Rhopaloeides odorabile during: (1) in situ cultivation under natural environmental conditions, (2) ex situ cultivation in small flow-through aquaria and (3) ex situ cultivation in large mesocosm systems. Principal components analysis of denaturing gradient gel electrophoresis profiles indicated a stable microbial community in sponges cultured in situ (grown in the wild) and in sponges cultured ex situ in small flow-through aquaria over 12 weeks. In contrast, a shift in the microbial community was detected in sponges cultivated ex situ in large mesocosm aquaria for 12 months. This shift included (1) a loss of some stable microbial inhabitants, including members of the Poribacteria, Chloroflexi and Acidobacteria and (2) the addition of new microbes not detected in the wild sponges. Many of these acquired bacteria had highest similarity to known sponge-associated microbes, indicating that the sponge may be capable of actively selecting its microbial community. Alternatively, long-term ex situ cultivation may cause a shift in the dominant microbes that facilitates the growth of the more rare species. The microbial community composition varied between sponges cultivated in mesocosm aquaria with different nutrient concentrations and seawater chemistry, suggesting that these variables play a role in structuring the sponge-associated microbes. The high growth and symbiont stability in R. odorabile cultured in situ confirm that this is the preferred method of aquaculture for this species at this time.
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Affiliation(s)
- Nicole S Webster
- Australian Institute of Marine Science, PMB 3, Townsville Mail Centre, 4810, Townsville, Qld, Australia.
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Webster NS, Taylor MW. Marine sponges and their microbial symbionts: love and other relationships. Environ Microbiol 2011; 14:335-46. [PMID: 21443739 DOI: 10.1111/j.1462-2920.2011.02460.x] [Citation(s) in RCA: 322] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Many marine sponges harbour dense and diverse microbial communities of considerable ecological and biotechnological importance. While the past decade has seen tremendous advances in our understanding of the phylogenetic diversity of sponge-associated microorganisms (more than 25 bacterial phyla have now been reported from sponges), it is only in the past 3-4 years that the in situ activity and function of these microbes has become a major research focus. Already the rewards of this new emphasis are evident, with genomics and experimental approaches yielding novel insights into symbiont function. Key steps in the nitrogen cycle [denitrification, anaerobic ammonium oxidation (Anammox)] have recently been demonstrated in sponges for the first time, with diverse bacteria - including the sponge-associated candidate phylum 'Poribacteria'- being implicated in these processes. In this minireview we examine recent major developments in the microbiology of sponges, and identify several research areas (e.g. biology of viruses in sponges, effects of environmental stress) that we believe are deserving of increased attention.
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Affiliation(s)
- Nicole S Webster
- Australian Institute of Marine Science, PMB 3, Townsville Mail Centre, Qld 4810, Australia
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Phylogenetic diversity of bacteria associated with the endemic freshwater sponge Lubomirskia baicalensis. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0654-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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New phylogenetic lineages of the Spirochaetes phylum associated with Clathrina species (Porifera). J Microbiol 2010; 48:411-8. [DOI: 10.1007/s12275-010-0017-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 03/25/2010] [Indexed: 11/27/2022]
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