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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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2
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Viegas C, Gomes B, Cervantes R, Moreira S, Dias M, Pena P, Carolino E, Twarużek M, Kosicki R, Soszczyńska E, Caetano LA, Cañas L, Pozdniakova S, Borràs S, Viegas S. Microbial contamination in grocery stores from Portugal and Spain - The neglected indoor environment to be tackled in the scope of the One Health approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162602. [PMID: 36878289 DOI: 10.1016/j.scitotenv.2023.162602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Microbial contamination in grocery shops (GS) should be evaluated since food commodities are commonly handled by workers and customers increasing the risk of food contamination and disease transmission. The aim of this study was to evaluate the microbial contamination in Portuguese and Spanish GS with a multi-approach protocol using passive (electrostatic dust cloths and surface swabs) sampling methods. The molecular detection of Aspergillus sections, mycotoxin analysis, screening of azole resistance as well as cytotoxicity measurement were conducted to better estimate the potential health risks of exposure and to identify possible relations between the risk factors studied. Fruits/vegetables sampling location was the one identified has being the most contaminated (bacteria and fungi) area in GS from both countries. Aspergillus section Fumigati and Fusarium species were observed in samples from Portuguese groceries with reduced susceptibilities to azoles commonly used in the clinical treatment of fungal infections. Fumonisin B2 was detected in Portuguese GS possible unveiling this emergent threat concerning occupational exposure and food safety. Overall, the results obtained raise concerns regarding human health and food safety and must be surveilled applying a One Health approach.
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Affiliation(s)
- Carla Viegas
- H&TRC - Health & Technology Research Center, ESTeSL - Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal; NOVA National School of Public Health, Public Health Research Centre, Comprehensive Health Research Center, CHRC, NOVA University Lisbon, Lisbon, Portugal.
| | - Bianca Gomes
- H&TRC - Health & Technology Research Center, ESTeSL - Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Renata Cervantes
- H&TRC - Health & Technology Research Center, ESTeSL - Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Sílvia Moreira
- H&TRC - Health & Technology Research Center, ESTeSL - Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Marta Dias
- H&TRC - Health & Technology Research Center, ESTeSL - Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal; NOVA National School of Public Health, Public Health Research Centre, Comprehensive Health Research Center, CHRC, NOVA University Lisbon, Lisbon, Portugal
| | - Pedro Pena
- H&TRC - Health & Technology Research Center, ESTeSL - Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Elisabete Carolino
- H&TRC - Health & Technology Research Center, ESTeSL - Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Magdalena Twarużek
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Robert Kosicki
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Ewelina Soszczyńska
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Liliana Aranha Caetano
- H&TRC - Health & Technology Research Center, ESTeSL - Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal; Kazimierz Wielki University, Faculty of Biological Sciences, Department of Physiology and Toxicology, Chodkiewicza 30, 85-064 Bydgoszcz, Poland
| | - Lídia Cañas
- AIRLAB, Climate and Health Program, Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Sofya Pozdniakova
- AIRLAB, Climate and Health Program, Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Sílvia Borràs
- AIRLAB, Climate and Health Program, Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Susana Viegas
- H&TRC - Health & Technology Research Center, ESTeSL - Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal; NOVA National School of Public Health, Public Health Research Centre, Comprehensive Health Research Center, CHRC, NOVA University Lisbon, Lisbon, Portugal
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3
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El Samak M, Zakeer S, Hanora A, Solyman SM. Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community. Mar Genomics 2023; 70:101032. [PMID: 37084583 DOI: 10.1016/j.margen.2023.101032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 04/23/2023]
Abstract
Marine sponges associated microorganisms are considered to be prolific source of bioactive natural products. Omics-based techniques such as metagenomics and metatranscriptomics have been used as effective tools to discover natural products. In this study, we used integrated metagenomic and metatranscriptomic analysis of three samples of the Egyptian Red Sea sponge Theonella sp. microbiome to obtain a complete picture of its biosynthetic activity to produce bioactive compounds. Our data revealed high biodiversity of the Egyptian sponge microbiota represented by 38 bacterial phyla with Candidate Phylum Poribacteria as the most abundant phyla with an average of 27.5% of the microbial community. The analysis also revealed high biosynthetic activity of the sponge microbiome through detecting different types of biosynthetic gene clusters (BGCs) with predicted antibacterial, cytotoxic and inhibitory bioactivity and the majority of these clusters were found to be actively transcribed. The complete BGCs of the cytotoxic theonellamide and misakinolide were detected and found to be actively transcribed. The majority of the detected BGCs were predicted to be novel as they did not show any similarity with any known cluster in the MIBiG database.
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Affiliation(s)
- Manar El Samak
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt
| | - Samira Zakeer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt
| | - Amro Hanora
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt.
| | - Samar M Solyman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt; Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University- Elkantara branch, Egypt
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4
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Limited Metabolomic Overlap between Commensal Bacteria and Marine Sponge Holobionts Revealed by Large Scale Culturing and Mass Spectrometry-Based Metabolomics: An Undergraduate Laboratory Pedagogical Effort at Georgia Tech. Mar Drugs 2023; 21:md21010053. [PMID: 36662226 PMCID: PMC9862627 DOI: 10.3390/md21010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Sponges are the richest source of bioactive organic small molecules, referred to as natural products, in the marine environment. It is well established that laboratory culturing-resistant symbiotic bacteria residing within the eukaryotic sponge host matrix often synthesize the natural products that are detected in the sponge tissue extracts. However, the contributions of the culturing-amenable commensal bacteria that are also associated with the sponge host to the overall metabolome of the sponge holobiont are not well defined. In this study, we cultured a large library of bacteria from three marine sponges commonly found in the Florida Keys. Metabolomes of isolated bacterial strains and that of the sponge holobiont were compared using mass spectrometry to reveal minimal metabolomic overlap between commensal bacteria and the sponge hosts. We also find that the phylogenetic overlap between cultured commensal bacteria and that of the sponge microbiome is minimal. Despite these observations, the commensal bacteria were found to be a rich resource for novel natural product discovery. Mass spectrometry-based metabolomics provided structural insights into these cryptic natural products. Pedagogic innovation in the form of laboratory curricula development is described which provided undergraduate students with hands-on instruction in microbiology and natural product discovery using metabolomic data mining strategies.
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5
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Abbas S, Mahmoud H. Identification of Sponge-Associated Bacteria From the Coast of Kuwait and Their Potential Biotechnological Applications. Front Microbiol 2022; 13:896718. [PMID: 35859748 PMCID: PMC9289682 DOI: 10.3389/fmicb.2022.896718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/07/2022] [Indexed: 11/19/2022] Open
Abstract
Sponges are among the most ancient animals harboring complex microbial communities with potential applications in biotechnology. The Arabian Gulf is a thermally stressed enclosed body of water located in an arid region where sponges and their halobionts are understudied. This study combined 16S rRNA next-generation gene amplicon sequencing and cultivation techniques to explore the abundance and diversity of sponge-associated bacteria. Culture-independent techniques showed the associations of more than 25 bacterial phyla with Amphimedon sp., Chondrilla australiensis, Haliclona sp., and Niphates spp. Regarding cultivable bacteria, 315 bacterial isolates associated with the sponge Haliclona sp. were cultivated; these isolates were affiliated with the phyla Proteobacteria and Firmicutes and were distributed among six bacterial genera. Selected strains of Bacillus, Ferrimonas, Pseudovibrio, Shewanella, Spongiobacter, and Vibrio were tested for antimicrobial activity against indicator microorganisms and protease enzyme production. Seven Bacillus strains exhibited weak to moderate growth inhibition against Bacillus subtilis, Staphylococcus aureus, and Candida albicans. Furthermore, 29 different strains of Bacillus, Ferrimonas, Shewanella, and Vibrio exhibited different degrees of positive protease activity. In addition, cultivated strains of Bacillus, Shewanella, Pseudovibrio, and Vibrio were tested for their biomineralization abilities. Herein we report for the first time the isolation of biomineralizing bacteria from sponge tissue where eleven bacterial isolates produced different shapes of calcium carbonate crystals on agar. Our observations shed light on the diversity and biotechnological potentials of sponges-associated bacteria inhabiting one of the world’s hottest seas.
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6
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Clark CM, Hernandez A, Mullowney MW, Fitz-Henley J, Li E, Romanowski SB, Pronzato R, Manconi R, Sanchez LM, Murphy BT. Relationship between bacterial phylotype and specialized metabolite production in the culturable microbiome of two freshwater sponges. ISME COMMUNICATIONS 2022; 2:22. [PMID: 37938725 PMCID: PMC9723699 DOI: 10.1038/s43705-022-00105-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/09/2023]
Abstract
Microbial drug discovery programs rely heavily on accessing bacterial diversity from the environment to acquire new specialized metabolite (SM) lead compounds for the therapeutic pipeline. Therefore, knowledge of how commonly culturable bacterial taxa are distributed in nature, in addition to the degree of variation of SM production within those taxa, is critical to informing these front-end discovery efforts and making the overall sample collection and bacterial library creation process more efficient. In the current study, we employed MALDI-TOF mass spectrometry and the bioinformatics pipeline IDBac to analyze diversity within phylotype groupings and SM profiles of hundreds of bacterial isolates from two Eunapius fragilis freshwater sponges, collected 1.5 km apart. We demonstrated that within two sponge samples of the same species, the culturable bacterial populations contained significant overlap in approximate genus-level phylotypes but mostly nonoverlapping populations of isolates when grouped lower than the level of genus. Further, correlations between bacterial phylotype and SM production varied at the species level and below, suggesting SM distribution within bacterial taxa must be analyzed on a case-by-case basis. Our results suggest that two E. fragilis freshwater sponges collected in similar environments can exhibit large culturable diversity on a species-level scale, thus researchers should scrutinize the isolates with analyses that take both phylogeny and SM production into account to optimize the chemical space entering into a downstream bacterial library.
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Affiliation(s)
- Chase M Clark
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Antonio Hernandez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Michael W Mullowney
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Jhewelle Fitz-Henley
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Emma Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Sean B Romanowski
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Roberto Pronzato
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università di Genova, Genova, Italy
| | - Renata Manconi
- Dipartimento Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Brian T Murphy
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA.
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7
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Kogawa M, Miyaoka R, Hemmerling F, Ando M, Yura K, Ide K, Nishikawa Y, Hosokawa M, Ise Y, Cahn JKB, Takada K, Matsunaga S, Mori T, Piel J, Takeyama H. Single-cell metabolite detection and genomics reveals uncultivated talented producer. PNAS NEXUS 2022; 1:pgab007. [PMID: 36712793 PMCID: PMC9802089 DOI: 10.1093/pnasnexus/pgab007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 10/24/2021] [Accepted: 01/03/2022] [Indexed: 02/01/2023]
Abstract
The production of bioactive metabolites is increasingly recognized as an important function of host-associated bacteria. An example is defensive symbiosis that might account for much of the chemical richness of marine invertebrates including sponges (Porifera), 1 of the oldest metazoans. However, most bacterial members of sponge microbiomes have not been cultivated or sequenced, and therefore, remain unrecognized. Unequivocally linking metabolic functions to a cellular source in sponge microbiomes is, therefore, a challenge. Here, we report an analysis pipeline of microfluidic encapsulation, Raman microscopy, and integrated digital genomics (MERMAID) for an efficient identification of uncultivated producers. We applied this method to the chemically rich bacteriosponge (sponge that hosts a rich bacterial community) Theonella swinhoei, previously shown to contain 'Entotheonella' symbionts that produce most of the bioactive substances isolated from the sponge. As an exception, the antifungal aurantosides had remained unassigned to a source. Raman-guided single-bacterial analysis and sequencing revealed a cryptic, distinct multiproducer, 'Candidatus Poriflexus aureus' from a new Chloroflexi lineage as the aurantoside producer. Its exceptionally large genome contains numerous biosynthetic loci and suggested an even higher chemical richness of this sponge than previously appreciated. This study highlights the importance of complementary technologies to uncover microbiome functions, reveals remarkable parallels between distantly related symbionts of the same host, and adds functional support for diverse chemically prolific lineages being present in microbial dark matter.
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Affiliation(s)
| | | | | | - Masahiro Ando
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162–0041, Japan
| | - Kei Yura
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162–8480, Japan,Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162–0041, Japan,Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Keigo Ide
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162–8480, Japan,Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169–0072, Japan
| | - Yohei Nishikawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162–8480, Japan,Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169–0072, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162–8480, Japan,Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162–0041, Japan
| | - Yuji Ise
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Kunigami, Okinawa 905-0227, Japan
| | - Jackson K B Cahn
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Kentaro Takada
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Tetsushi Mori
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Jörn Piel
- To whom correspondence should be addressed: (JP)
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8
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Koch MJ, Hesketh-Best PJ, Smerdon G, Warburton PJ, Howell K, Upton M. Impact of growth media and pressure on the diversity and antimicrobial activity of isolates from two species of hexactinellid sponge. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34898418 PMCID: PMC8744994 DOI: 10.1099/mic.0.001123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Access to deep-sea sponges brings with it the potential to discover novel antimicrobial candidates, as well as novel cold- and pressure-adapted bacteria with further potential clinical or industrial applications. In this study, we implemented a combination of different growth media, increased pressure and high-throughput techniques to optimize recovery of isolates from two deep-sea hexactinellid sponges, Pheronema carpenteri and Hertwigia sp., in the first culture-based microbial analysis of these two sponges. Using 16S rRNA gene sequencing for isolate identification, we found a similar number of cultivable taxa from each sponge species, as well as improved recovery of morphotypes from P. carpenteri at 22-25 °C compared to other temperatures, which allows a greater potential for screening for novel antimicrobial compounds. Bacteria recovered under conditions of increased pressure were from the phyla Proteobacteria, Actinobacteria and Firmicutes, except at 4 %O2/5 bar, when the phylum Firmicutes was not observed. Cultured isolates from both sponge species displayed antimicrobial activity against Micrococcus luteus, Staphylococcus aureus and Escherichia coli.
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Affiliation(s)
- Matthew J Koch
- School of Biomedical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Poppy J Hesketh-Best
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Gary Smerdon
- Diving Diseases Research Centre Healthcare, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK
| | - Philip J Warburton
- School of Biomedical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Kerry Howell
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Mathew Upton
- School of Biomedical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
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9
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Dat TTH, Steinert G, Cuc NTK, Smidt H, Sipkema D. Bacteria Cultivated From Sponges and Bacteria Not Yet Cultivated From Sponges-A Review. Front Microbiol 2021; 12:737925. [PMID: 34867854 PMCID: PMC8634882 DOI: 10.3389/fmicb.2021.737925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022] Open
Abstract
The application of high-throughput microbial community profiling as well as "omics" approaches unveiled high diversity and host-specificity of bacteria associated with marine sponges, which are renowned for their wide range of bioactive natural products. However, exploration and exploitation of bioactive compounds from sponge-associated bacteria have been limited because the majority of the bacteria remains recalcitrant to cultivation. In this review, we (i) discuss recent/novel cultivation techniques that have been used to isolate sponge-associated bacteria, (ii) provide an overview of bacteria isolated from sponges until 2017 and the associated culture conditions and identify the bacteria not yet cultured from sponges, and (iii) outline promising cultivation strategies for cultivating the uncultivated majority of bacteria from sponges in the future. Despite intensive cultivation attempts, the diversity of bacteria obtained through cultivation remains much lower than that seen through cultivation-independent methods, which is particularly noticeable for those taxa that were previously marked as "sponge-specific" and "sponge-enriched." This poses an urgent need for more efficient cultivation methods. Refining cultivation media and conditions based on information obtained from metagenomic datasets and cultivation under simulated natural conditions are the most promising strategies to isolate the most wanted sponge-associated bacteria.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Nguyen Thi Kim Cuc
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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10
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Goldberg SR, Haltli BA, Correa H, Kerr RG. Curvivirga aplysinae gen. nov., sp. nov., a marine bacterium isolated from the sea sponge Aplysina fistularis. Int J Syst Evol Microbiol 2021; 71. [PMID: 34228608 DOI: 10.1099/ijsem.0.004873] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, motile bacterium, designated strain RKSG073T, was isolated from the sea sponge Aplysina fistularis, collected off the west coast of San Salvador, The Bahamas. Cells were curved-to-spiral rods with single, bipolar (amphitrichous) flagella, oxidase- and catalase-positive, non-nitrate-reducing and required salt for growth. RKSG073T grew optimally at 30-37 °C, pH 6-7, and with 2-3 % (w/v) NaCl. The predominant fatty acids of RKSG073T were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0. Major isoprenoid quinones were identified as Q-10 and Q-9. Phylogenetic analyses of nearly complete 16S rRNA genes and genome sequences positioned strain RKSG073T in a clade with its closest relative Aestuariispira insulae AH-MY2T (92.1 % 16S rRNA gene sequence similarity), which subsequently clustered with Hwanghaeella grinnelliae Gri0909T, Marivibrio halodurans ZC80T and type species of the genera Kiloniella, Thalassospira and Terasakiella. The DNA G+C content calculated from the genome of RKSG073T was 42.2 mol%. On the basis of phylogenetic distinctiveness and polyphasic analysis, here we propose that RKSG073T (culture deposit numbers: ATCC collection = TSD-74T, BCCM collection = LMG 29869T) represents the type strain of a novel genus and species within the family Kiloniellaceae, order Rhodospirillales and class Alphaproteobacteria, for which the name Curvivirga aplysinae gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Stacey R Goldberg
- Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Brad A Haltli
- Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada.,Nautilus Biosciences Croda, Duffy Research Center, Charlottetown, Prince Edward Island, Canada
| | - Hebelin Correa
- Nautilus Biosciences Croda, Duffy Research Center, Charlottetown, Prince Edward Island, Canada
| | - Russell G Kerr
- Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada.,Nautilus Biosciences Croda, Duffy Research Center, Charlottetown, Prince Edward Island, Canada.,Department of Chemistry, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
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11
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Dat TTH, Cuc NTK, Cuong PV, Smidt H, Sipkema D. Diversity and Antimicrobial Activity of Vietnamese Sponge-Associated Bacteria. Mar Drugs 2021; 19:md19070353. [PMID: 34206202 PMCID: PMC8307940 DOI: 10.3390/md19070353] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022] Open
Abstract
This study aimed to assess the diversity and antimicrobial activity of cultivable bacteria associated with Vietnamese sponges. In total, 460 bacterial isolates were obtained from 18 marine sponges. Of these, 58.3% belonged to Proteobacteria, 16.5% to Actinobacteria, 18.0% to Firmicutes, and 7.2% to Bacteroidetes. At the genus level, isolated strains belonged to 55 genera, of which several genera, such as Bacillus, Pseudovibrio, Ruegeria, Vibrio, and Streptomyces, were the most predominant. Culture media influenced the cultivable bacterial composition, whereas, from different sponge species, similar cultivable bacteria were recovered. Interestingly, there was little overlap of bacterial composition associated with sponges when the taxa isolated were compared to cultivation-independent data. Subsequent antimicrobial assays showed that 90 isolated strains exhibited antimicrobial activity against at least one of seven indicator microorganisms. From the culture broth of the isolated strain with the strongest activity (Bacillus sp. M1_CRV_171), four secondary metabolites were isolated and identified, including cyclo(L-Pro-L-Tyr) (1), macrolactin A (2), macrolactin H (3), and 15,17-epoxy-16-hydroxy macrolactin A (4). Of these, compounds 2-4 exhibited antimicrobial activity against a broad spectrum of reference microorganisms.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
- Correspondence: (T.T.H.D.); (D.S.); Tel.: +84-94-949-2778 (T.T.H.D.); +31-317-483-113 (D.S.)
| | - Nguyen Thi Kim Cuc
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
| | - Pham Viet Cuong
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
- Correspondence: (T.T.H.D.); (D.S.); Tel.: +84-94-949-2778 (T.T.H.D.); +31-317-483-113 (D.S.)
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12
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Robbins SJ, Song W, Engelberts JP, Glasl B, Slaby BM, Boyd J, Marangon E, Botté ES, Laffy P, Thomas T, Webster NS. A genomic view of the microbiome of coral reef demosponges. THE ISME JOURNAL 2021; 15:1641-1654. [PMID: 33469166 PMCID: PMC8163846 DOI: 10.1038/s41396-020-00876-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/23/2020] [Accepted: 12/07/2020] [Indexed: 01/30/2023]
Abstract
Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution.
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Affiliation(s)
- S J Robbins
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia
| | - W Song
- Centre for Marine Science & Innovation, University of New South Wales, Kensington, NSW, 2052, Australia
| | - J P Engelberts
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia
| | - B Glasl
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - B M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - J Boyd
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia
| | - E Marangon
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
- College of Science and Engineering, James Cook University, Townsville, QLD, 4810, Australia
| | - E S Botté
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - P Laffy
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - T Thomas
- Centre for Marine Science & Innovation, University of New South Wales, Kensington, NSW, 2052, Australia
| | - N S Webster
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia.
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia.
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13
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Baum L, Nguyen MTHD, Jia Y, Biazik J, Thomas T. Characterization of a novel roseophage and the morphological and transcriptional response of the sponge symbiont Ruegeria AU67 to infection. Environ Microbiol 2021; 23:2532-2549. [PMID: 33754443 DOI: 10.1111/1462-2920.15474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/18/2021] [Indexed: 12/31/2022]
Abstract
Sponges have recently been recognized to contain complex communities of bacteriophages; however, little is known about how they interact with their bacterial hosts. Here, we isolated a novel phage, called Ruegeria phage Tedan, and characterized its impact on the bacterial sponge symbiont Ruegeria AU67 on a morphological and molecular level. Phage Tedan was structurally, genomically and phylogenetically characterized to be affiliated with the genus Xiamenvirus of the family Siphoviridae. Through microscopic observations and transcriptomic analysis, we show that phage Tedan upon infection induces a process leading to metabolic and morphological changes in its host. These changes would render Ruegeria AU67 better adapted to inhabit the sponge holobiont due to an improved utilization of ecologically relevant energy and carbon sources as well as a potential impediment of phagocytosis by the sponge through cellular enlargement. An increased survival or better growth of the bacterium in the sponge environment will likely benefit the phage reproduction. Our results point towards the possibility that phages from host-associated environments require, and have thus evolved, different strategies to interact with their host when compared to those phages from free-living or planktonic environments.
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Affiliation(s)
- Lisa Baum
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Mary T H D Nguyen
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Yunke Jia
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Joanna Biazik
- Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
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14
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Bibi F, Azhar EI. Analysis of bacterial communities in sponges and coral inhabiting Red Sea, using barcoded 454 pyrosequencing. Saudi J Biol Sci 2020; 28:847-854. [PMID: 33424375 PMCID: PMC7783839 DOI: 10.1016/j.sjbs.2020.11.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 11/18/2022] Open
Abstract
Microbial communities are linked with marine sponge are diverse in their structure and function. Our understanding of the sponge-associated microbial diversity is limited especially from Red Sea in Saudi Arabia where few species of sponges have been studied. Here we used pyrosequencing to study two marine sponges and coral species sampled from Obhur region from Red sea in Jeddah. A total of 168 operational taxonomic units (OTUs) were identified from Haliclona caerulea, Stylissa carteri and Rhytisma fulvum. Taxonomic identification of tag sequences of 16S ribosomal RNA revealed 6 different bacterial phyla and 9 different classes. A proportion of unclassified reads were was also observed in sponges and coral sample. We found diverse bacterial communities associated with two sponges and a coral sample. Diversity and richness estimates based on OUTs revealed that sponge H. caerulea had significantly high bacterial diversity. The identified OTUs showed unique clustering in three sponge samples as revealed by Principal coordinate analysis (PCoA). Proteobacteria (88-95%) was dominant phyla alonwith Bacteroidetes, Planctomycetes, Cyanobacteria, Firmicutes and Nitrospirae. Seventeen different genera were identified where genus Pseudoalteromonas was dominant in all three samples. This is first study to assess bacterial communities of sponge and coral sample that have never been studied before to unravel their microbial communities using 454-pyrosequencing method.
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Affiliation(s)
- Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
- Corresponding author at: Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
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15
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Cleary DFR, Polónia ARM, Reijnen BT, Berumen ML, de Voogd NJ. Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea. MICROBIAL ECOLOGY 2020; 80:103-119. [PMID: 31932882 DOI: 10.1007/s00248-019-01465-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.
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Affiliation(s)
- D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - A R M Polónia
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - B T Reijnen
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - M L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - N J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Environmental Sciences, Environmental Biology Department, Leiden University, Leiden, The Netherlands
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16
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Viegas C, Caetano LA, Cox J, Korkalainen M, Haines SR, Dannemiller KC, Viegas S, Reponen T. The effects of waste sorting in environmental microbiome, THP-1 cell viability and inflammatory responses. ENVIRONMENTAL RESEARCH 2020; 185:109450. [PMID: 32244107 DOI: 10.1016/j.envres.2020.109450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/28/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Workers in the waste sorting industry are exposed to diverse bioaerosols. Characterization of these bioaerosols is necessary to more accurately assess the health risks of exposure. The use of high-throughput DNA sequencing for improved analysis of microbial composition of bioaerosols, in combination with their in vitro study in relevant cell cultures, represents an important opportunity to find answers on the biological effects of bioaerosols. This study aimed to characterize by high-throughput sequencing the biodiversity present in complex aerosol mixtures retained in forklift air conditioning filters of a waste-sorting industry and its effects on cytotoxicity and secretion of proinflammatory cytokines in vitro using human macrophages derived from monocytic THP-1 cells. Seventeen filters from the filtration system from forklifts operating in one waste sorting facility and one control filter (similar filter without prior use) were analyzed using high-throughput sequencing and toxicological tests in vitro. A trend of positive correlation was seen between the number of bacterial and fungal OTUs (r = 0.47, p = 0.06). Seven filters (39%) exhibited low or moderate cytotoxicity (p < 0.05). The highest cytotoxic responses had a reduction in cell viability between 17 and 22%. Filter samples evoked proinflammatory responses, especially the production of TNFα. No significant correlation was found between fungal richness and inflammatory responses in vitro. The data obtained stress the need of thorough exposure assessment in waste-sorting industry and to take immunomodulatory properties into consideration for bioaerosols hazard characterization. The broad spectrum of microbial contamination detected in this study demonstrates that adequate monitoring of bioaerosol exposure is necessary to evaluate and minimize risks. The combined techniques can support the implementation of effective environmental monitoring programs of public and occupational health importance.
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Affiliation(s)
- C Viegas
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Portugal; NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal; Comprehensive Health Research Center (CHRC), Portugal.
| | - L A Caetano
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Portugal; Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 649-003, Lisbon, Portugal
| | - J Cox
- Department of Environmental Health, University of Cincinnati, P.O. Box 670056, Cincinnati, OH, 45242, USA
| | - M Korkalainen
- Finnish Institute for Health and Welfare (THL), Environmental Health, P.O. Box 95, FIN-70701, Kuopio, Finland
| | - S R Haines
- Department of Civil, Environmental, and Geodetic Engineering, College of Engineering, The Ohio State University, Columbus, OH, USA; Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Science Graduate Program, The Ohio State University, Columbus, OH, USA
| | - K C Dannemiller
- Department of Civil, Environmental, and Geodetic Engineering, College of Engineering, The Ohio State University, Columbus, OH, USA; Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - S Viegas
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Portugal; NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal; Comprehensive Health Research Center (CHRC), Portugal
| | - T Reponen
- Department of Environmental Health, University of Cincinnati, P.O. Box 670056, Cincinnati, OH, 45242, USA
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17
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Goldberg SR, Correa H, Haltli BA, Kerr RG. Fulvivirga aurantia sp. nov. and Xanthovirga aplysinae gen. nov., sp. nov., marine bacteria isolated from the sponge Aplysina fistularis, and emended description of the genus Fulvivirga. Int J Syst Evol Microbiol 2020; 70:2766-2781. [PMID: 32238229 DOI: 10.1099/ijsem.0.004108] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, strictly aerobic, marine bacteria, designated as strains RKSG066T and RKSG123T, were isolated from a sponge Aplysina fistularis collected at a depth of 15 m off the west coast of San Salvador, The Bahamas. Investigation of nearly full-length 16S rRNA gene and whole genome-based phylogenies revealed that both strains belong to the order Cytophagales within the class Cytophagia and phylum Bacteroidetes. Strain RKSG066T formed a monophyletic clade with described members of the genus Fulvivirga, while strain RKSG123T formed a well-supported paraphyletic branch apart from this and other related genera within the family Flammeovirgaceae. For both RKSG066T and RKSG123T, optimal growth parameters were 30-37 °C, pH 7-8 and 2-3 % (w/v) NaCl; cells were catalase- and oxidase-positive, and flexirubin-type pigments were absent. The predominant fatty acids were iso-C15 : 0, C16 : 0, C18 : 0, iso-C17 : 0 3-OH, C16 : 1 ω5c, iso-C15 : 0 3-OH, C18 : 1 ω9c and iso-C15 : 1 G for RKSG066T, and iso-C17 : 0 3-OH, C16 : 1 ω5c, iso-C15 : 0, C16 : 0 3-OH and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) for RKSG123T. Menaquinone-7 was the major respiratory quinone for both strains. The DNA G+C contents of RKSG066T and RKSG123T were 39.5 and 36.7 mol%, respectively. On the basis of phylogenetic distinctiveness and polyphasic analysis, the type strain RKSG066T (=TSD-73T=LMG 29870T) is proposed to represent a novel species of the genus Fulvivirga, for which the name Fulvivirga aurantia sp. nov. is proposed. The type strain RKSG123T (=TSD-75T=LMG 30075T) is proposed to represent the type species of a novel genus and species with the proposed name Xanthovirga aplysinae gen. nov., sp. nov. Additionally, the genus Fulvivirga is emended to include strains of orange-pigmented colonies that contain the predominant cellular fatty acids C16 : 0, C18 : 0, C16 : 1 ω5c and C18 : 1 ω9c.
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Affiliation(s)
- Stacey R Goldberg
- Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Hebelin Correa
- Nautilus Biosciences, Croda, Duffy Research Center, Charlottetown, Prince Edward Island, Canada
| | - Brad A Haltli
- Nautilus Biosciences, Croda, Duffy Research Center, Charlottetown, Prince Edward Island, Canada.,Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Russell G Kerr
- Department of Chemistry, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada.,Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada.,Nautilus Biosciences, Croda, Duffy Research Center, Charlottetown, Prince Edward Island, Canada
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18
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Gutleben J, Loureiro C, Ramírez Romero LA, Shetty S, Wijffels RH, Smidt H, Sipkema D. Cultivation of Bacteria From Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients. Front Microbiol 2020; 11:175. [PMID: 32140143 PMCID: PMC7042410 DOI: 10.3389/fmicb.2020.00175] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/24/2020] [Indexed: 12/22/2022] Open
Abstract
Sponge-associated bacteria possess biotechnologically interesting properties but as yet have largely evaded cultivation. Thus, "omics"-based information on the ecology and functional potential of sponge symbionts is awaiting its integration into the design of innovative cultivation approaches. To cultivate bacteria derived from the marine sponge Aplysina aerophoba, nine novel media formulations were created based on the predicted genomic potential of the prevalent sponge symbiont lineage Poribacteria. In addition, to maintain potential microbial metabolic interactions in vitro, a Liquid-Solid cultivation approach and a Winogradsky-column approach were applied. The vast majority of microorganisms in the inoculum appeared viable after cryopreservation of sponge specimen as determined by selective propidium monoazide DNA modification of membrane-compromised cells, however, only 2% of the initial prokaryotic diversity could be recovered through cultivation. In total, 256 OTUs encompassing seven prokaryotic phyla were cultivated. The diversity of the cultivated community was influenced by the addition of the antibiotic aeroplysinin-1 as well as by medium dilution, rather than carbon source. Furthermore, the Winogradsky-column approach reproducibly enriched distinct communities at different column depths, amongst which were numerous Clostridia and OTUs that could not be assigned to a known phylum. While some bacterial taxa such as Pseudovibrio and Ruegeria were recovered from nearly all applied cultivation conditions, others such as Bacteroidetes were specific to certain medium types. Predominant sponge-associated prokaryotic taxa remained uncultured, nonetheless, alternative cultivation approaches applied here enriched for previously uncultivated microbes.
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Affiliation(s)
- Johanna Gutleben
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Catarina Loureiro
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | | | - Sudarshan Shetty
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - René H. Wijffels
- Bioprocess Engineering, AlgaePARC, Wageningen University, Wageningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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19
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Laport MS, Pinheiro U, Rachid CTCDC. Freshwater Sponge Tubella variabilis Presents Richer Microbiota Than Marine Sponge Species. Front Microbiol 2019; 10:2799. [PMID: 31849922 PMCID: PMC6902092 DOI: 10.3389/fmicb.2019.02799] [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: 07/25/2019] [Accepted: 11/18/2019] [Indexed: 02/02/2023] Open
Abstract
Sponges can host diverse and abundant communities of microorganisms, which constitute an interesting source of bioactive compounds. Thus, to broaden our knowledge about the diversity of the microbiota that is found in freshwater sponges, the microbial community of Tubella variabilis was analyzed using culture-independent and culture-dependent approaches. Additionally, sponge-associated bacteria were compared with those living in the surrounding waters. Bacteria were also tested for antimicrobial production. Overall, the microbial composition identified comprises at least 44 phyla belonging mainly to Proteobacteria and low percentages of Bacteroidetes, Acidobacteria, and Verrucomicrobia. Alphaproteobacteria was the dominant class in T. variabilis while Betaproteobacteria was dominant in freshwater. Our data also revealed a high richness of bacteria in comparison to another freshwater sponge and 32 marine sponges. A global comparison of the structure of microbiota of different sponges showed that the main structuring factor may be the sponge environment, with T. variabilis and all freshwater sponges clustering together, and far away from the marine sponges. Bacterial strains from sponges and from freshwater were isolated and 163 morphotypes were phylogenetically identified. These belong to 26 genera, of which 12 were exclusively found in sponge samples and three only in freshwater. Inhibitory activities were also detected among 20–25% of the isolates from sponges and freshwater, respectively. This study presents new information on the composition of the microbial community found in freshwater sponges, which is diverse, abundant and distinct from some marine sponges. Moreover, the antimicrobial activity observed from the bacterial strains might play an important role in shaping microbial communities of the environment.
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Affiliation(s)
- Marinella Silva Laport
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ulisses Pinheiro
- Department of Zoology, Federal University of Pernambuco, Recife, Brazil
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20
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Cultivation of Sponge-Associated Bacteria from Agelas sventres and Xestospongia muta Collected from Different Depths. Mar Drugs 2019; 17:md17100578. [PMID: 31614540 PMCID: PMC6836257 DOI: 10.3390/md17100578] [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: 07/22/2019] [Revised: 09/23/2019] [Accepted: 10/05/2019] [Indexed: 01/15/2023] Open
Abstract
Sponge-associated bacteria have been mostly cultured from shallow water (≤30 m) sponges, whereas only few studies targeted specimens from below 30 m. This study assessed the cultivability of bacteria from two marine sponges Xestospongia muta and Agelas sventres collected from shallow (<30 m), upper mesophotic (30–60 m), and lower mesophotic (60–90 m) reefs. Sponge-associated bacteria were cultivated on six different media, and replicate plates were used to pick individual colonies or to recover the entire biomass. Prokaryotic community analysis was conducted using Illumina MiSeq sequencing of 16S rRNA gene amplicons. A total of 144 bacterial isolates were picked following a colony morphology coding scheme and subsequently identified by 16S rRNA gene sequence analysis. Sponge individuals at each depth-range harboured specific cultivable bacteria that were not retrieved from specimens collected at other depths. However, there were substantial differences in the number of colonies obtained for replicate sponges of the same species. In addition, source of inoculum and cultivation medium had more impact on the cultured prokaryotic community than sample collection depth. This suggests that the “plate count anomaly” is larger than differences in sponge-associated prokaryotic community composition related to depth.
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21
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Swierts T, Cleary DFR, de Voogd NJ. Prokaryotic communities of Indo-Pacific giant barrel sponges are more strongly influenced by geography than host phylogeny. FEMS Microbiol Ecol 2019; 94:5115559. [PMID: 30289448 PMCID: PMC6196991 DOI: 10.1093/femsec/fiy194] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/04/2018] [Indexed: 12/19/2022] Open
Abstract
Sponges harbor complex communities of microorganisms that carry out essential roles for the functioning and survival of their hosts. In some cases, genetically related sponges from different geographic regions share microbes, while in other cases microbial communities are more similar in unrelated sponges collected from the same location. To better understand how geography and host phylogeny cause variation in the prokaryotic community of sponges, we compared the prokaryotic community of 44 giant barrel sponges (Xestospongia spp.). These sponges belonged to six reproductively isolated genetic groups from eight areas throughout the Indo-Pacific region. Using Illumina sequencing, we obtained 440 000 sequences of the 16S rRNA gene V3V4 variable region that were assigned to 3795 operational taxonomic units (OTUs). The prokaryotic community of giant barrel sponges was characterized by 71 core OTUs (i.e. OTUs present in each specimen) that represented 57.5% of the total number of sequences. The relative abundance of these core OTUs varied significantly among samples, and this variation was predominantly related to the geographic origin of the sample. These results show that in giant barrel sponges, the variation in the prokaryotic community is primarily associated with geography as opposed to phylogenetic relatedness.
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Affiliation(s)
- T Swierts
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.,Institute of Environmental Sciences, Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands
| | - D F R Cleary
- Departamento de Biologia CESAM, Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
| | - N J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.,Institute of Environmental Sciences, Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands
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22
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Ngangbam AK, Mouatt P, Smith J, Waters DLE, Benkendorff K. Bromoperoxidase Producing Bacillus spp. Isolated from the Hypobranchial Glands of a Muricid Mollusc Are Capable of Tyrian Purple Precursor Biogenesis. Mar Drugs 2019; 17:md17050264. [PMID: 31058830 PMCID: PMC6562550 DOI: 10.3390/md17050264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 11/16/2022] Open
Abstract
The secondary metabolite Tyrian purple, also known as shellfish purple and royal purple, is a dye with historical importance for humans. The biosynthetic origin of Tyrian purple in Muricidae molluscs is not currently known. A possible role for symbiotic bacteria in the production of tyrindoxyl sulphate, the precursor to Tyrian purple stored in the Australian species, Dicathais orbita, has been proposed. This study aimed to culture bacterial symbionts from the purple producing hypobranchial gland, and screen the isolates for bromoperoxidase genes using molecular methods. The ability of bromoperoxidase positive isolates to produce the brominated indole precursor to Tyrian purple was then established by extraction of the culture, and analysis by liquid chromatography-mass spectrometry (LC-MS). In total, 32 bacterial isolates were cultured from D. orbita hypobranchial glands, using marine agar, marine agar with hypobranchial gland aqueous extracts, blood agar, thiosulphate citrate bile salts sucrose agar, and cetrimide agar at pH 7.2. These included 26 Vibrio spp., two Bacillus spp., one Phaeobacter sp., one Shewanella sp., one Halobacillus sp. and one Pseudoalteromonas sp. The two Bacillus species were the only isolates found to have coding sequences for bromoperoxidase enzymes. LC-MS analysis of the supernatant and cell pellets from the bromoperoxidase producing Bacillus spp. cultured in tryptone broth, supplemented with KBr, confirmed their ability to produce the brominated precursor to Tyrian purple, tyrindoxyl sulphate. This study supports a potential role for symbiotic Bacillus spp. in the biosynthesis of Tyrian purple.
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Affiliation(s)
- Ajit Kumar Ngangbam
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia.
| | - Peter Mouatt
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia.
| | - Joshua Smith
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia.
| | - Daniel L E Waters
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia.
- ARC Industrial Transformation Training Centre for Functional Grains, Charles Sturt University, Wagga, NSW 2650, Australia.
| | - Kirsten Benkendorff
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia.
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Yang Q, Franco CMM, Zhang W. Uncovering the hidden marine sponge microbiome by applying a multi-primer approach. Sci Rep 2019; 9:6214. [PMID: 30996336 PMCID: PMC6470215 DOI: 10.1038/s41598-019-42694-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/05/2019] [Indexed: 02/07/2023] Open
Abstract
Marine sponges (phylum Porifera) are hosts to microorganisms that make up to 40–60% of the mesohyl volume. The challenge is to characterise this microbial diversity more comprehensively. To accomplish this, a new method was for the first time proposed to obtain sequence coverage of all the variable regions of the 16S rRNA gene to analyze the amplicon-based microbiomes of four representative sponge species belonging to different orders. The five primer sets targeting nine variable regions of the 16S rRNA gene revealed a significant increase in microbiome coverage of 29.5% of phylum level OTUs and 35.5% class level OTUs compared to the community revealed by the commonly used V4 region-specific primer set alone. Among the resulting OTUs, 52.6% and 61.3% were unaffiliated, including candidate OTUs, at the phylum and class levels, respectively, which demonstrated a substantially superior performance in uncovering taxonomic ‘blind spots’. Overall, a more complete sponge microbiome profile was achieved by this multi-primer approach, given the significant improvement of microbial taxonomic coverage and the enhanced capacity to uncover novel microbial taxa. This multi-primer approach represents a fundamental and practical change from the conventional single primer set amplicon-based microbiome approach, and can be broadly applicable to other microbiome studies.
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Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, 5042, Australia.,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, 5042, Australia
| | - Wei Zhang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, 5042, Australia. .,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
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24
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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: 34] [Impact Index Per Article: 6.8] [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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25
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Kuo J, Yang YT, Lu MC, Wong TY, Sung PJ, Huang YS. Antimicrobial activity and diversity of bacteria associated with Taiwanese marine sponge Theonella swinhoei. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-018-1414-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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26
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Najafi A, Moradinasab M, Seyedabadi M, Haghighi MA, Nabipour I. First Molecular Identification of Symbiotic Archaea in a Sponge Collected from the Persian Gulf, Iran. Open Microbiol J 2018; 12:323-332. [PMID: 30450139 PMCID: PMC6198412 DOI: 10.2174/1874285801812010323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/21/2018] [Accepted: 09/23/2018] [Indexed: 11/22/2022] Open
Abstract
Background Marine sponges are associated with numerically vast and phylogenetically diverse microbial communities at different geographical locations. However, little is known about the archaeal diversity of sponges in the Persian Gulf. The present study was aimed to identify the symbiotic archaea with a sponge species gathered from the Persian Gulf, Iran. Methods Sponge sample was collected from a depth of 3 m offshore Bushehr, Persian Gulf, Iran. Metagenomic DNA was extracted using a hexadecyl trimethyl ammonium bromide (CTAB) method. The COI mtDNA marker was used for molecular taxonomy identification of sponge sample. Also, symbiotic archaea were identified using the culture-independent analysis of the 16S rRNA gene and PCR- cloning. Results In this study, analysis of multilocus DNA marker and morphological characteristics revealed that the sponge species belonged to Chondrilla australiensis isolate PG_BU4. PCR cloning and sequencing showed that all of the sequences of archaeal 16S rRNA gene libraries clustered into the uncultured archaeal group. Conclusion The present study is the first report of the presence of the genus of Chondrilla in the Persian Gulf. Traditional taxonomy methods, when used along with molecular techniques, could play a significant role in the accurate taxonomy of sponges. Also, the uncultured archaea may promise a potential source for bioactive compounds. Further functional studies are needed to explore the role of the sponge-associated uncultured archaea as a part of the marine symbiosis.
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Affiliation(s)
- Akram Najafi
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Maryam Moradinasab
- The Persian Gulf Tropical Medicine Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohammad Seyedabadi
- Department of Pharmacology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohammad A Haghighi
- Department of Microbiology and Parasitology, Faculty of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
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27
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Batista D, Costa R, Carvalho AP, Batista WR, Rua CPJ, de Oliveira L, Leomil L, Fróes AM, Thompson FL, Coutinho R, Dobretsov S. Environmental conditions affect activity and associated microorganisms of marine sponges. MARINE ENVIRONMENTAL RESEARCH 2018; 142:59-68. [PMID: 30274716 DOI: 10.1016/j.marenvres.2018.09.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/09/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
Changes in environmental conditions can influence sponges and their holobionts. The present study investigated the effect of upwelling and anthropogenic pollution on the bioactivity of marine sponges, microbial communities and functional genes, and composition of their chemical compounds. The species Dysidea etheria, Darwinella sp., Hymeniacidon heliophila and Tedania ignis were collected from areas with distinct influence of upwelling and low anthropogenic impact and from areas without influence of upwelling but affected by sewage and the port. In most cases, the same sponge species collected from areas with distinct environmental conditions had a different chemical composition, antifouling activity, composition and diversity of associated microorganisms. Antimicrobial, quorum sensing inhibitory and anti-larval activities of sponge extracts were more pronounced in the area without upwelling showing higher level of anthropogenic pollution. This study suggests that upwelling and anthropogenic pollution affect the chemical activity and holobiome composition of sponges.
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Affiliation(s)
- Daniela Batista
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil.
| | - Rafaela Costa
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - Ana Polycarpa Carvalho
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - William Romão Batista
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - Cintia P J Rua
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Louisi de Oliveira
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Luciana Leomil
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Adriana M Fróes
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Ricardo Coutinho
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - Sergey Dobretsov
- Marine Science and Fisheries Department, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123. PO Box 34, Muscat, Oman; Center of Excellence in Marine Biotechnology, Sultan Qaboos University, Al-Khoud 123. PO Box 50, Muscat, Oman.
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Najafi A, Moradinasab M, Nabipour I. First Record of Microbiomes of Sponges Collected From the Persian Gulf, Using Tag Pyrosequencing. Front Microbiol 2018; 9:1500. [PMID: 30034382 PMCID: PMC6043863 DOI: 10.3389/fmicb.2018.01500] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
The Persian Gulf is a special habitat of marine sponges whose bacterial communities are under-investigated. Recently, next-generation sequencing technology has comprehensively improved the knowledge of marine sponge-associated bacteria. For the first time, this study aimed to evaluate the diversity of the Persian Gulf sponge-associated bacteria using tag pyrosequencing in Iran. In this study, 10 sponge samples from 6 different taxonomic orders were collected from the Persian Gulf using SCUBA diving. The diversity of the bacteria associated with the marine sponges was investigated using the 16S rRNA gene PCR-tagged pyrosequencing method. A total of 68,628 high-quality sequences were obtained and clustered at a 97% similarity into 724 unique operational taxonomic units (OTUs), representing 17 bacterial phyla. Cyanobacteria was the most abundant phylum in the sponges, followed by Proteobacteria, Chloroflexi, Acidobacteria, and Actinobacteria. Other phyla were detected as minor groups of bacteria. Bacterial community richness, Shannon, and Simpson indices revealed the highest diversity in sponge S11 (Dictyoceratida sp.) compared to other sponges. This study showed a diverse structure of bacterial communities associated with the Persian Gulf sponges. The dominance of Cyanobacteria may suggest an ecological importance of this phylum in the Persian Gulf sponges.
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Affiliation(s)
- Akram Najafi
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Maryam Moradinasab
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
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29
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Ecology and Biotechnological Potential of Bacteria Belonging to the Genus Pseudovibrio. Appl Environ Microbiol 2018; 84:AEM.02516-17. [PMID: 29453252 DOI: 10.1128/aem.02516-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Members of the genus Pseudovibrio have been isolated worldwide from a great variety of marine sources as both free-living and host-associated bacteria. So far, the available data depict a group of alphaproteobacteria characterized by a versatile metabolism, which allows them to use a variety of substrates to meet their carbon, nitrogen, sulfur, and phosphorous requirements. Additionally, Pseudovibrio-related bacteria have been shown to proliferate under extreme oligotrophic conditions, tolerate high heavy-metal concentrations, and metabolize potentially toxic compounds. Considering this versatility, it is not surprising that they have been detected from temperate to tropical regions and are often the most abundant isolates obtained from marine invertebrates. Such an association is particularly recurrent with marine sponges and corals, animals that play a key role in benthic marine systems. The data so far available indicate that these bacteria are mainly beneficial to the host, and besides being involved in major nutrient cycles, they could provide the host with both vitamins/cofactors and protection from potential pathogens via the synthesis of antimicrobial secondary metabolites. In fact, the biosynthetic abilities of Pseudovibrio spp. have been emerging in recent years, and both genomic and analytic studies have underlined how these organisms promise novel natural products of biotechnological value.
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30
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Versluis D, McPherson K, van Passel MWJ, Smidt H, Sipkema D. Recovery of Previously Uncultured Bacterial Genera from Three Mediterranean Sponges. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:454-468. [PMID: 28695385 PMCID: PMC5599449 DOI: 10.1007/s10126-017-9766-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/14/2017] [Indexed: 06/07/2023]
Abstract
Sponges often harbour a dense and diverse microbial community. Presently, a large discrepancy exists between the cultivable bacterial fraction from sponges and the community in its natural environment. Here, we aimed to acquire additional insights into cultivability of (previously uncultured) bacteria from three sponge species, namely Aplysina aerophoba, Corticium candelabrum and Petrosia ficiformis, by studying bacterial growth on five media in the form of 60 communities scraped from plates without antibiotics, as well as in the form of individual isolates that were grown on these media supplemented with antibiotics. We applied (double-)barcoded 16S ribosomal RNA (rRNA) gene amplicon sequencing for species identification. We show that previously uncultured bacteria can be cultivated using conventional plating and that application of antibiotics in the media can serve to capture a greater bacterial diversity. Moreover, we present criteria to address an important caveat of the plate scraping method whereby bacteria may be detected that did not actually grow. Fourteen out of 27 cultivated novel taxa (<95% identity of the 16S rRNA gene amplicon to reported species) belong to Actinobacteria, which indicates the presence of a large untapped reservoir of bioactive compounds. Three Flavobacteriaceae spp. were isolated that potentially constitute two new genera and one new species.
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Affiliation(s)
- Dennis Versluis
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Kyle McPherson
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Mark W J van Passel
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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Culturable bacterial communities associated to Brazilian Oscarella species (Porifera: Homoscleromorpha) and their antagonistic interactions. Antonie van Leeuwenhoek 2016; 110:489-499. [DOI: 10.1007/s10482-016-0818-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 12/08/2016] [Indexed: 01/08/2023]
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32
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Zhao F, Liu H, Zhang Z, Xiao L, Sun X, Xie J, Pan Y, Zhao Y. Reducing bias in complex microbial community analysis in shrimp based on propidium monoazide combined with PCR-DGGE. Food Control 2016. [DOI: 10.1016/j.foodcont.2016.03.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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33
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Kumar V, Zozaya-Valdes E, Kjelleberg S, Thomas T, Egan S. Multiple opportunistic pathogens can cause a bleaching disease in the red seaweed Delisea pulchra. Environ Microbiol 2016; 18:3962-3975. [PMID: 27337296 DOI: 10.1111/1462-2920.13403] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While macroalgae (or seaweeds) are increasingly recognized to suffer from disease, in most cases the causative agents are unknown. The model macroalga Delisea pulchra is susceptible to a bleaching disease and previous work has identified two epiphytic bacteria, belonging to the Roseobacter clade, that cause bleaching under laboratory conditions. However, recent environmental surveys have shown that these in vitro pathogens are not abundant in naturally bleached D. pulchra, suggesting the presence of other pathogens capable of causing this algal disease. To test this hypothesis, we cultured bacteria that were abundant on bleached tissue across multiple disease events and assessed their ability to cause bleaching disease. We identified the new pathogens Alteromonas sp. BL110, Aquimarina sp. AD1 and BL5 and Agarivorans sp BL7 that are phylogenetically diverse, distinct from the previous two pathogens and can also be found in low abundance in healthy individuals. Moreover, we found that bacterial communities of diseased individuals that were infected with these pathogens were less diverse and more divergent from each other than those of healthy algae. This study demonstrates that multiple and opportunistic pathogens can cause the same disease outcome for D. pulchra and we postulate that such pathogens are more common in marine systems than previously anticipated.
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Affiliation(s)
- Vipra Kumar
- Centre for Marine Bio-Innovation & School of Biological, Earth and Environmental Sciences. The University of New South Wales Sydney, NSW, 2052, Australia
| | - Enrique Zozaya-Valdes
- Centre for Marine Bio-Innovation & School of Biological, Earth and Environmental Sciences. The University of New South Wales Sydney, NSW, 2052, Australia
| | - Staffan Kjelleberg
- Centre for Marine Bio-Innovation & School of Biological, Earth and Environmental Sciences. The University of New South Wales Sydney, NSW, 2052, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Torsten Thomas
- Centre for Marine Bio-Innovation & School of Biological, Earth and Environmental Sciences. The University of New South Wales Sydney, NSW, 2052, Australia
| | - Suhelen Egan
- Centre for Marine Bio-Innovation & School of Biological, Earth and Environmental Sciences. The University of New South Wales Sydney, NSW, 2052, Australia
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de Bakker DM, Meesters EHWG, van Bleijswijk JDL, Luttikhuizen PC, Breeuwer HJAJ, Becking LE. Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta. PLoS One 2016; 11:e0155969. [PMID: 27223808 PMCID: PMC4880336 DOI: 10.1371/journal.pone.0155969] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 05/07/2016] [Indexed: 12/11/2022] Open
Abstract
Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp) and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp) on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s–1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (π = 0.055) and X. muta (π = 0.0010) was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12–0.52) were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02–0.32) were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples) as well as overgrowth (48.1%), predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5%) showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to replenish genetic diversity or as a storehouse of diversity that can be utilized if needed for restoration practices.
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Affiliation(s)
- Didier M. de Bakker
- Institute for Marine Resources and Ecosystem Studies (IMARES), Wageningen UR, P.O. Box 57, 1780 AB, Den Helder, The Netherlands
- Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, the Netherlands, and Utrecht University, Utrecht, The Netherlands
- * E-mail: (DdB); (LEB)
| | - Erik H. W. G. Meesters
- Institute for Marine Resources and Ecosystem Studies (IMARES), Wageningen UR, P.O. Box 57, 1780 AB, Den Helder, The Netherlands
| | - Judith D. L. van Bleijswijk
- Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, the Netherlands, and Utrecht University, Utrecht, The Netherlands
| | - Pieternella C. Luttikhuizen
- Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, the Netherlands, and Utrecht University, Utrecht, The Netherlands
| | - Hans J. A. J. Breeuwer
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94248, 1090 GE, Amsterdam, The Netherlands
| | - Leontine E. Becking
- Institute for Marine Resources and Ecosystem Studies (IMARES), Wageningen UR, P.O. Box 57, 1780 AB, Den Helder, The Netherlands
- Marine Animal Ecology, Wageningen UR, PO Box 338, 6700 AH, Wageningen, The Netherlands
- Naturalis Biodiversity Center, Darwinweg 2, 2300 RA, Leiden, The Netherlands
- * E-mail: (DdB); (LEB)
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Esteves AIS, Amer N, Nguyen M, Thomas T. Sample Processing Impacts the Viability and Cultivability of the Sponge Microbiome. Front Microbiol 2016; 7:499. [PMID: 27242673 PMCID: PMC4876369 DOI: 10.3389/fmicb.2016.00499] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/28/2016] [Indexed: 12/17/2022] Open
Abstract
Sponges host complex microbial communities of recognized ecological and biotechnological importance. Extensive cultivation efforts have been made to isolate sponge bacteria, but most still elude cultivation. To identify the bottlenecks of sponge bacterial cultivation, we combined high-throughput 16S rRNA gene sequencing with a variety of cultivation media and incubation conditions. We aimed to determine the extent to which sample processing and cultivation conditions can impact bacterial viability and recovery in culture. We isolated 325 sponge bacteria from six specimens of Cymbastela concentrica and three specimens of Scopalina sp. These isolates were distributed over 37 different genera and 47 operational taxonomic units (defined at 97% 16S rRNA gene sequence identity). The cultivable bacterial community was highly specific to its sponge host and different media compositions yielded distinct microbial isolates. Around 97% of the isolates could be detected in the original sponge and represented a large but highly variable proportion (0.5–92% total abundance, depending on sponge species) of viable bacteria obtained after sample processing, as determined by propidium monoazide selective DNA modification of compromised cells. Our results show that the most abundant viable bacteria are also the most predominant groups found in cultivation, reflecting, to some extent, the relative abundances of the viable bacterial community, rather than the overall community estimated by direct molecular approaches. Cultivation is therefore shaped not only by the growth conditions provided, but also by the different cell viabilities of the bacteria that constitute the cultivation inoculum. These observations highlight the need to perform experiments to assess each method of sample processing for its accurate representation of the actual in situ bacterial community and its yield of viable cells.
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Affiliation(s)
- Ana I S Esteves
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales Kensington, NSW, Australia
| | - Nimra Amer
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales Kensington, NSW, Australia
| | - Mary Nguyen
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales Kensington, NSW, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales Kensington, NSW, Australia
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Yang Q, Franco CMM, Zhang W. Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification. Appl Microbiol Biotechnol 2015; 99:8731-40. [PMID: 26245685 DOI: 10.1007/s00253-015-6875-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/16/2015] [Accepted: 07/21/2015] [Indexed: 11/26/2022]
Abstract
Experiments were designed to validate the two common DNA extraction protocols (CTAB-based method and DNeasy Blood & Tissue Kit) used to effectively recover actinobacterial DNA from sponge samples in order to study the sponge-associated actinobacterial diversity. This was done by artificially spiking sponge samples with actinobacteria (spores, mycelia and a combination of the two). Our results demonstrated that both DNA extraction methods were effective in obtaining DNA from the sponge samples as well as the sponge samples spiked with different amounts of actinobacteria. However, it was noted that in the presence of the sponge, the bacterial 16S rRNA gene could not be amplified unless the combined DNA template was diluted. To test the hypothesis that the extracted sponge DNA contained inhibitors, dilutions of the DNA extracts were tested for six sponge species representing five orders. The results suggested that the inhibitors were co-extracted with the sponge DNA, and a high dilution of this DNA was required for the successful PCR amplification for most of the samples. The optimized PCR conditions, including primer selection, PCR reaction system and program optimization, further improved the PCR performance. However, no single PCR condition was found to be suitable for the diverse sponge samples using various primer sets. These results highlight for the first time that the DNA extraction methods used are effective in obtaining actinobacterial DNA and that the presence of inhibitors in the sponge DNA requires high dilution coupled with fine tuning of the PCR conditions to achieve success in the study of sponge-associated actinobacterial diversity.
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Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia.
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia.
| | - Wei Zhang
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia.
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia.
- Centre for Marine Drugs, Renji Hospital, Shanghai Jiaotong University, Shanghai, 200240, China.
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Fiore CL, Labrie M, Jarett JK, Lesser MP. Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange. Front Microbiol 2015; 6:364. [PMID: 25972851 PMCID: PMC4412061 DOI: 10.3389/fmicb.2015.00364] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/10/2015] [Indexed: 11/13/2022] Open
Abstract
Compared to our understanding of the taxonomic composition of the symbiotic microbes in marine sponges, the functional diversity of these symbionts is largely unknown. Furthermore, the application of genomic, transcriptomic, and proteomic techniques to functional questions on sponge host-symbiont interactions is in its infancy. In this study, we generated a transcriptome for the host and a metatranscriptome of its microbial symbionts for the giant barrel sponge, Xestospongia muta, from the Caribbean. In combination with a gene-specific approach, our goals were to (1) characterize genetic evidence for nitrogen cycling in X. muta, an important limiting nutrient on coral reefs (2) identify which prokaryotic symbiont lineages are metabolically active and, (3) characterize the metabolic potential of the prokaryotic community. Xestospongia muta expresses genes from multiple nitrogen transformation pathways that when combined with the abundance of this sponge, and previous data on dissolved inorganic nitrogen fluxes, shows that this sponge is an important contributor to nitrogen cycling biogeochemistry on coral reefs. Additionally, we observed significant differences in gene expression of the archaeal amoA gene, which is involved in ammonia oxidation, between coral reef locations consistent with differences in the fluxes of dissolved inorganic nitrogen previously reported. In regards to symbiont metabolic potential, the genes in the biosynthetic pathways of several amino acids were present in the prokaryotic metatranscriptome dataset but in the host-derived transcripts only the catabolic reactions for these amino acids were present. A similar pattern was observed for the B vitamins (riboflavin, biotin, thiamin, cobalamin). These results expand our understanding of biogeochemical cycling in sponges, and the metabolic interchange highlighted here advances the field of symbiont physiology by elucidating specific metabolic pathways where there is high potential for host-prokaryote interactions.
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Affiliation(s)
- Cara L. Fiore
- Department of Molecular, Cellular and Biomedical Sciences, University of New HampshireDurham, NH, USA
| | - Micheline Labrie
- Department of Molecular, Cellular and Biomedical Sciences, University of New HampshireDurham, NH, USA
| | - Jessica K. Jarett
- Department of Molecular, Cellular and Biomedical Sciences, University of New HampshireDurham, NH, USA
| | - Michael P. Lesser
- School of Marine Science and Ocean Engineering, University of New HampshireDurham, NH, USA
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Sharp KH, Sneed JM, Ritchie KB, Mcdaniel L, Paul VJ. Induction of Larval Settlement in the Reef Coral Porites astreoides by a Cultivated Marine Roseobacter Strain. THE BIOLOGICAL BULLETIN 2015; 228:98-107. [PMID: 25920713 DOI: 10.1086/bblv228n2p98] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Successful larval settlement and recruitment by corals is critical for the survival of coral reef ecosystems. Several closely related strains of γ-proteobacteria have been identified as cues for coral larval settlement, but the inductive properties of other bacterial taxa naturally occurring in reef ecosystems have not yet been explored. In this study, we assayed bacterial strains representing taxonomic groups consistently detected in corals for their ability to influence larval settlement in the coral Porites astreoides. We identified one α-proteobacterial strain, Roseivivax sp. 46E8, which significantly increased larval settlement in P. astreoides. Logarithmic growth phase (log phase) cell cultures of Roseivivax sp. 46E8 and filtrates (0.22μm) from log phase Roseivivax sp. 46E8 cultures significantly increased settlement, suggesting that an extracellular settlement factor is produced during active growth phase. Filtrates from log phase cultures of two other bacterial isolates, Marinobacter sp. 46E3, and Cytophaga sp. 46B6, also significantly increased settlement, but the cell cultures themselves did not. Monospecific biofilms of the three strains did not result in significant increases in larval settlement. Organic and aqueous/methanol extracts of Roseivivax sp. 46E8 cultures did not affect larval settlement. Examination of filtrates from cell cultures showed that Roseivivax sp. 46E8 spontaneously generated virus-like particles in log and stationary phase growth. Though the mechanism of settlement enhancement by Roseivivax sp. 46E8 is not yet elucidated, our findings point to a new aspect of coral-Roseobacter interactions that should be further investigated, especially in naturally occurring, complex microbial biofilms on reef surfaces.
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Affiliation(s)
- K H Sharp
- Eckerd College, 4200 54th Avenue South, St. Petersburg, Florida 33711;
| | - J M Sneed
- Smithsonian Marine Station, 701 Seaway Drive, Fort Pierce, Florida 34949
| | - K B Ritchie
- Mote Marine Laboratory, 1600 Ken Thompson Pkwy, Sarasota, Florida 34236; and
| | - L Mcdaniel
- University of South Florida College of Marine Science, 140 7th Avenue S., St. Petersburg, Florida 33701
| | - V J Paul
- Smithsonian Marine Station, 701 Seaway Drive, Fort Pierce, Florida 34949
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Bauvais C, Zirah S, Piette L, Chaspoul F, Domart-Coulon I, Chapon V, Gallice P, Rebuffat S, Pérez T, Bourguet-Kondracki ML. Sponging up metals: bacteria associated with the marine sponge Spongia officinalis. MARINE ENVIRONMENTAL RESEARCH 2015; 104:20-30. [PMID: 25575352 DOI: 10.1016/j.marenvres.2014.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 12/22/2014] [Accepted: 12/24/2014] [Indexed: 06/04/2023]
Abstract
The present study explored the bacteria of the sponge Spongia officinalis in a metal-polluted environment, using PCR-DGGE fingerprinting, culture-dependent approaches and in situ hybridization. The sponge samples collected over three consecutive years in the Western Mediterranean Sea contained high concentrations of zinc, nickel, lead and copper determined by ICP-MS. DGGE signatures indicated a sponge specific bacterial association and suggested spatial and temporal variations. The bacterial culturable fraction associated with S. officinalis and tolerant to heavy metals was isolated using metal-enriched microbiological media. The obtained 63 aerobic strains were phylogenetically affiliated to the phyla Proteobacteria, Actinobacteria, and Firmicutes. All isolates showed high tolerances to the selected heavy metals. The predominant genus Pseudovibrio was localized via CARD-FISH in the sponge surface tissue and validated as a sponge-associated epibiont. This study is the first step in understanding the potential involvement of the associated bacteria in sponge's tolerance to heavy metals.
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Affiliation(s)
- Cléa Bauvais
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes, CNRS/MNHN UMR 7245, Muséum National d'Histoire Naturelle, 57 rue Cuvier (CP 54), 75005 Paris, France; Université Pierre et Marie Curie, 75005 Paris, France
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes, CNRS/MNHN UMR 7245, Muséum National d'Histoire Naturelle, 57 rue Cuvier (CP 54), 75005 Paris, France
| | - Laurie Piette
- Laboratoire des Interactions Protéines Métal, CEA, DSV, IBEB, SBVME, Bât 185, CEA de Cadarache, 13108 Saint-Paul-Lez-Durance, France; CNRS, UMR 7265, Bât 185, CEA de Cadarache, 13108 Saint-Paul-Lez-Durance, France; Université d'Aix-Marseille, Bât 185, CEA de Cadarache, 13108 Saint-Paul-Lez-Durance, France
| | - Florence Chaspoul
- Laboratoire de Physique Chimie Prévention des risques, Faculté de Pharmacie, 13385 Marseille Cedex 5, France; Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Aix-Marseille Université, UMR CNRS 7263, IRD 237, 13385 Marseille Cedex 5, France
| | - Isabelle Domart-Coulon
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes, CNRS/MNHN UMR 7245, Muséum National d'Histoire Naturelle, 57 rue Cuvier (CP 54), 75005 Paris, France
| | - Virginie Chapon
- Laboratoire des Interactions Protéines Métal, CEA, DSV, IBEB, SBVME, Bât 185, CEA de Cadarache, 13108 Saint-Paul-Lez-Durance, France; CNRS, UMR 7265, Bât 185, CEA de Cadarache, 13108 Saint-Paul-Lez-Durance, France; Université d'Aix-Marseille, Bât 185, CEA de Cadarache, 13108 Saint-Paul-Lez-Durance, France
| | - Philippe Gallice
- Laboratoire de Physique Chimie Prévention des risques, Faculté de Pharmacie, 13385 Marseille Cedex 5, France; Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Aix-Marseille Université, UMR CNRS 7263, IRD 237, 13385 Marseille Cedex 5, France
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes, CNRS/MNHN UMR 7245, Muséum National d'Histoire Naturelle, 57 rue Cuvier (CP 54), 75005 Paris, France
| | - Thierry Pérez
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Aix-Marseille Université, UMR 7263 CNRS 7263, IRD 237, Station Marine d'Endoume, Rue de la Batterie des Lions, 13007 Marseille, France
| | - Marie-Lise Bourguet-Kondracki
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes, CNRS/MNHN UMR 7245, Muséum National d'Histoire Naturelle, 57 rue Cuvier (CP 54), 75005 Paris, France.
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de Voogd NJ, Cleary DFR, Polónia ARM, Gomes NCM. Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand islands reef complex, West Java, Indonesia. FEMS Microbiol Ecol 2015; 91:fiv019. [PMID: 25764467 DOI: 10.1093/femsec/fiv019] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2015] [Indexed: 11/12/2022] Open
Abstract
In the present study, we assessed the composition of Bacteria in four biotopes namely sediment, seawater and two sponge species (Stylissa massa and Xestospongia testudinaria) at four different reef sites in a coral reef ecosystem in West Java, Indonesia. In addition to this, we used a predictive metagenomic approach to estimate to what extent nitrogen metabolic pathways differed among bacterial communities from different biotopes. We observed marked differences in bacterial composition of the most abundant bacterial phyla, classes and orders among sponge species, water and sediment. Proteobacteria were by far the most abundant phylum in terms of both sequences and Operational Taxonomic Units (OTUs). Predicted counts for genes associated with the nitrogen metabolism suggested that several genes involved in the nitrogen cycle were enriched in sponge samples, including nosZ, nifD, nirK, norB and nrfA genes. Our data show that a combined barcoded pyrosequencing and predictive metagenomic approach can provide novel insights into the potential ecological functions of the microbial communities. Not only is this approach useful for our understanding of the vast microbial diversity found in sponges but also to understand the potential response of microbial communities to environmental change.
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Affiliation(s)
- Nicole J de Voogd
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands Institute for Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, the Netherlands
| | - Daniel F R Cleary
- Departamento de Biologia, CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Ana R M Polónia
- Departamento de Biologia, CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Newton C M Gomes
- Departamento de Biologia, CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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Singh AK, Sun X, Bai X, Kim H, Abdalhaseib MU, Bae E, Bhunia AK. Label-free, non-invasive light scattering sensor for rapid screening of Bacillus colonies. J Microbiol Methods 2015; 109:56-66. [DOI: 10.1016/j.mimet.2014.12.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 11/26/2022]
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O'Connor-Sánchez A, Rivera-Domínguez AJ, Santos-Briones CDL, López-Aguiar LK, Peña-Ramírez YJ, Prieto-Davo A. Acidobacteria appear to dominate the microbiome of two sympatric Caribbean Sponges and one Zoanthid. Biol Res 2014; 47:67. [PMID: 25723107 PMCID: PMC4335776 DOI: 10.1186/0717-6287-47-67] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 11/27/2014] [Indexed: 11/10/2022] Open
Abstract
Background Marine invertebrate-associated microbial communities are interesting examples of complex symbiotic systems and are a potential source of biotechnological products. Results In this work, pyrosequencing-based assessment from bacterial community structures of sediments, two sponges, and one zoanthid collected in the Mexican Caribbean was performed. The results suggest that the bacterial diversity at the species level is higher in the sediments than in the animal samples. Analysis of bacterial communities’ structure showed that about two thirds of the bacterial diversity in all the samples belongs to the phyla Acidobacteria and Proteobacteria. The genus Acidobacterium appears to dominate the bacterial community in all the samples, reaching almost 80% in the sponge Hyrtios. Conclusions Our evidence suggests that the sympatric location of these benthonic species may lead to common bacterial structure features among their bacterial communities. The results may serve as a first insight to formulate hypotheses that lead to more extensive studies of sessile marine organisms’ microbiomes from the Mexican Caribbean. Electronic supplementary material The online version of this article (doi:10.1186/0717-6287-47-67) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aileen O'Connor-Sánchez
- Unidad de Biotecnología. Centro de Investigación Científica de Yucatán A.C, Calle 43 # 130, Chuburná de Hidalgo, 97200, Mérida, Yucatán, México.
| | - Adán J Rivera-Domínguez
- Unidad de Biotecnología. Centro de Investigación Científica de Yucatán A.C, Calle 43 # 130, Chuburná de Hidalgo, 97200, Mérida, Yucatán, México.
| | - César de los Santos-Briones
- Unidad de Biotecnología. Centro de Investigación Científica de Yucatán A.C, Calle 43 # 130, Chuburná de Hidalgo, 97200, Mérida, Yucatán, México.
| | - Lluvia K López-Aguiar
- Facultad de Química - Unidad Académica Sisal, Universidad Nacional Autónoma de México, Puerto de abrigo s/n, Municipio de Hunucmá, 97356, Sisal, Yucatán, México.
| | - Yuri J Peña-Ramírez
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur - Unidad Campeche, Campeche, México.
| | - Alejandra Prieto-Davo
- Facultad de Química - Unidad Académica Sisal, Universidad Nacional Autónoma de México, Puerto de abrigo s/n, Municipio de Hunucmá, 97356, Sisal, Yucatán, México.
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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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Cuvelier ML, Blake E, Mulheron R, McCarthy PJ, Blackwelder P, Thurber RLV, Lopez JV. Two distinct microbial communities revealed in the sponge Cinachyrella. Front Microbiol 2014; 5:581. [PMID: 25408689 PMCID: PMC4219487 DOI: 10.3389/fmicb.2014.00581] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/15/2014] [Indexed: 11/25/2022] Open
Abstract
Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes), which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rRNA gene tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the same South Florida reef at two different times of year. In total, 639 OTUs (12 archaeal and 627 bacterial) belonging to 2 archaeal and 21 bacterial phyla were detected in the sponges. Based on their microbiomes, the six sponge samples formed two distinct groups, namely sponge group 1 (SG1) with lower diversity (Shannon-Weiner index: 3.73 ± 0.22) and SG2 with higher diversity (Shannon-Weiner index: 5.95 ± 0.25). Hosts' 28S rRNA gene sequences further confirmed that the sponge specimens were composed of two taxa closely related to Cinachyrella kuekenthalli. Both sponge groups were dominated by Proteobacteria, but Alphaproteobacteria were significantly more abundant in SG1. SG2 harbored many bacterial phyla (>1% of sequences) present in low abundance or below detection limits (<0.07%) in SG1 including: Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, PAUC34f, Poribacteria, and Verrucomicrobia. Furthermore, SG1 and SG2 only had 95 OTUs in common, representing 30.5 and 22.4% of SG1 and SG2's total OTUs, respectively. These results suggest that the sponge host may exert a pivotal influence on the nature and structure of the microbial community and may only be marginally affected by external environment parameters.
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Affiliation(s)
- Marie L. Cuvelier
- Biological Sciences Department, Florida International UniversityMiami, FL, USA
| | - Emily Blake
- Oceanographic Center, Nova Southeastern UniversityDania Beach, FL, USA
| | - Rebecca Mulheron
- Oceanographic Center, Nova Southeastern UniversityDania Beach, FL, USA
| | - Peter J. McCarthy
- Marine Biomedical and Biotechnology Research, Harbor Branch Oceanographic Institute, Florida Atlantic UniversityFort Pierce, FL, USA
| | - Patricia Blackwelder
- Oceanographic Center, Nova Southeastern UniversityDania Beach, FL, USA
- Marine Geosciences, Rosenstiel School of Marine and Atmospheric Science, University of MiamiMiami, FL, USA
| | | | - Jose V. Lopez
- Oceanographic Center, Nova Southeastern UniversityDania Beach, FL, USA
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Abstract
Nucleic acid-based analytical methods, ranging from species-targeted PCRs to metagenomics, have greatly expanded our understanding of microbiological diversity in natural samples. However, these methods provide only limited information on the activities and physiological states of microorganisms in samples. Even the most fundamental physiological state, viability, cannot be assessed cross-sectionally by standard DNA-targeted methods such as PCR. New PCR-based strategies, collectively called molecular viability analyses, have been developed that differentiate nucleic acids associated with viable cells from those associated with inactivated cells. In order to maximize the utility of these methods and to correctly interpret results, it is necessary to consider the physiological diversity of life and death in the microbial world. This article reviews molecular viability analysis in that context and discusses future opportunities for these strategies in genetic, metagenomic, and single-cell microbiology.
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