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Cheng L, Mu H, Zhang X, Jiang P, Liu L, Li J. Deinococcus arenicola sp. nov., a novel radiation-resistant bacterium isolated from sandy soil in Antarctica. Int J Syst Evol Microbiol 2024; 74. [PMID: 38787370 DOI: 10.1099/ijsem.0.006397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024] Open
Abstract
A Gram-stain-positive, aerobic, non-mobile and spherical strain, designated ZS9-10T, belonging to the genus Deinococcus was isolated from soil sampled at the Chinese Zhong Shan Station, Antarctica. Growth was observed in the presence of 0-4 % (w/v) NaCl, at pH 7.0-8.0 and at 4-25 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZS9-10T formed a lineage in the genus Deinococcus. It exhibited highest sequence similarity (97.4 %) to Deinococcus marmoris DSM 12784T. The major phospholipids of ZS9-10T were unidentified phosphoglycolipid, unidentified glycolipids and unidentified lipids. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C16 : 1 ω7c. MK-8 was the predominant respiratory quinone. The digital DNA-DNA hybridization and average nucleotide identity values between strain ZS9-10T and its close relative D. marmoris DSM 12784T were 27.4 and 83.9 %, respectively. Based on phenotypic, phylogenetic and genotypic data, a novel species, named Deinococcus arenicola sp. nov., is proposed. The type strain iis ZS9-10T (=CCTCC AB 2019392T=KCTC43192T).
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Affiliation(s)
- Li Cheng
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Hongmei Mu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Xinyu Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Peiqiang Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Lukuan Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Jing Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
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Girão M, Alexandrino DAM, Cao W, Costa I, Jia Z, Carvalho MF. Unveiling the culturable and non-culturable actinobacterial diversity in two macroalgae species from the northern Portuguese coast. Environ Microbiol 2024; 26:e16620. [PMID: 38627038 DOI: 10.1111/1462-2920.16620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/16/2024] [Indexed: 04/19/2024]
Abstract
Actinomycetota, associated with macroalgae, remains one of the least explored marine niches. The secondary metabolism of Actinomycetota, the primary microbial source of compounds relevant to biotechnology, continues to drive research into the distribution, dynamics, and metabolome of these microorganisms. In this study, we employed a combination of traditional cultivation and metagenomic analysis to investigate the diversity of Actinomycetota in two native macroalgae species from the Portuguese coast. We obtained and taxonomically identified a collection of 380 strains, which were distributed across 12 orders, 15 families, and 25 genera affiliated with the Actinomycetia class, with Streptomyces making up approximately 60% of the composition. Metagenomic results revealed the presence of Actinomycetota in both Chondrus crispus and Codium tomentosum datasets, with relative abundances of 11% and 2%, respectively. This approach identified 12 orders, 16 families, and 17 genera affiliated with Actinomycetota, with minimal overlap with the cultivation results. Acidimicrobiales emerged as the dominant actinobacterial order in both macroalgae, although no strain affiliated with this taxonomic group was successfully isolated. Our findings suggest that macroalgae represent a hotspot for Actinomycetota. The synergistic use of both culture-dependent and independent approaches proved beneficial, enabling the identification and recovery of not only abundant but also rare taxonomic members.
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Affiliation(s)
- Mariana Girão
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Diogo A M Alexandrino
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Environmental Health, School of Health, Porto, Portugal
| | - Weiwei Cao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Isabel Costa
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Maria F Carvalho
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
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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: 3] [Impact Index Per Article: 1.5] [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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Liu Z, Jiang P, Niu G, Wang W, Li J. Lysobacter antarcticus sp. nov., an SUF-system-containing bacterium from Antarctic coastal sediment. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005250] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A Gram-stain-negative, heterotrophic, aerobic, non-motile, rod-shaped bacterial strain (GW1-59T) belonging to the genus
Lysobacter
was isolated from coastal sediment collected from the Chinese Great Wall Station, Antarctica. The strain was identified using a polyphasic taxonomic approach. The strain grew well on Reasoner's 2A media and could grow in the presence of 0–4 % (w/v) NaCl (optimum, 1 %), at pH 9.0–11.0 and at 15–37 °C (optimum, 30 °C). Strain GW1-59T possessed ubiquinone-8 as the sole respiratory quinone. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1
ω9c), iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, C16 : 0 and iso-C11 : 0 3-OH. DNA–DNA relatedness with
Lysobacter concretionis
Ko07T, the nearest phylogenetic relative (98.5 % 16S rRNA gene sequence similarity) was 23.4 % (21.1–25.9 %). The average nucleotide identity value between strain GW1-59T and
L. concretionis
Ko07T was 80.1 %. The physiological and biochemical results and low level of DNA–DNA relatedness suggested the phenotypic and genotypic differentiation of strain GW1-59T from other
Lysobacter
species. On the basis of phenotypic, phylogenetic and genotypic data, a novel species, Lysobacter antarcticus sp. nov., is proposed. The type strain is GW1-59T (=CCTCC AB 2019390T=KCTC 72831T).
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Affiliation(s)
- Zuoyang Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Peiqiang Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Guojiang Niu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Wenjing Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
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Anteneh YS, Yang Q, Brown MH, Franco CMM. Factors affecting the isolation and diversity of marine sponge-associated bacteria. Appl Microbiol Biotechnol 2022; 106:1729-1744. [PMID: 35103809 PMCID: PMC8882111 DOI: 10.1007/s00253-022-11791-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/24/2022]
Abstract
Marine sponges are an ideal source for isolating as yet undiscovered microorganisms with some sponges having about 50% of their biomass composed of microbial symbionts. This study used a variety of approaches to investigate the culturable diversity of the sponge-associated bacterial community from samples collected from the South Australian marine environment. Twelve sponge samples were selected from two sites and their bacterial population cultivated using seven different agar media at two temperatures and three oxygen levels over 3 months. These isolates were identified using microscopic, macroscopic, and 16S rRNA gene analysis. A total of 1234 bacterial colonies were isolated which consisted of four phyla: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes, containing 21 genera. The diversity of the bacterial population was demonstrated to be influenced by the type of isolation medium, length of the incubation period and temperature, sponge type, and oxygen level. The findings of this study showed that marine sponges of South Australia can yield considerable bacterial culturable diversity if a comprehensive isolation strategy is implemented. Two sponges, with the highest and the lowest diversity of culturable isolates, were examined using next-generation sequencing to better profile the bacterial population. A marked difference in terms of phyla and genera was observed using culture-based and culture-independent approaches. This observed variation displays the importance of utilizing both methods to reflect a more complete picture of the microbial population of marine sponges. KEY POINTS: Improved bacterial diversity due to long incubations, 2 temperatures, and 3 oxygen levels. Isolates identified by morphology, restriction digests, and 16S rRNA gene sequencing. At least 70% of culturable genera were not revealed by NGS methods.
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Affiliation(s)
- Yitayal S Anteneh
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
- Department of Medical Microbiology, College of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
| | - Qi Yang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
- Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Melissa H Brown
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Christopher M M Franco
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.
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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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7
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Chen RW, He YQ, Cui LQ, Li C, Shi SB, Long LJ, Tian XP. Diversity and Distribution of Uncultured and Cultured Gaiellales and Rubrobacterales in South China Sea Sediments. Front Microbiol 2021; 12:657072. [PMID: 34220745 PMCID: PMC8248818 DOI: 10.3389/fmicb.2021.657072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/23/2021] [Indexed: 02/01/2023] Open
Abstract
Actinobacteria are ubiquitous in marine ecosystems, and they are regarded as an important, underexplored, potential pharmaceutical resource. The orders Gaiellales and Rubrobacterales are deep taxonomic lineages of the phylum Actinobacteria, both are represented by a single genus and contain only a few species. Although they have been detected frequently by high-throughput sequencing, their functions and characteristics in marine habitats remain unknown due to the lack of indigenous phenotypes. Here, we investigated the status of the orders in South China Sea (SCS) sediments using culture-independent and culture-dependent methods. Gaiellales is the second-most abundant order of Actinobacteria and was widely distributed in SCS sediments at water depths of 42-4,280 m, and four novel marine representatives in this group were successfully cultured. Rubrobacterales was present at low abundance in energy-limited marine habitats. An isolation strategy for Rubrobacterales from marine samples was proposed, and a total of 138 mesophilic Rubrobacterales strains were isolated under conditions of light and culture time combined with high-salinity or low-nutrient media. Marine representatives recovered in this study formed branches with a complex evolutionary history in the phylogenetic tree. Overall, the data indicate that both Gaiellales and Rubrobacterales can adapt to and survive in extreme deep-sea environments. This study lays the groundwork for further analysis of the distribution and diversity of the orders Gaiellales and Rubrobacterales in the ocean and provides a specific culture strategy for each group. The results open a window for further research on the ecological roles of the two orders in marine ecosystems.
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Affiliation(s)
- Rou-Wen Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuan-Qiu He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lin-Qing Cui
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cun Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Song-Biao Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Li-Juan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xin-Peng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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Ruocco N, Esposito R, Bertolino M, Zazo G, Sonnessa M, Andreani F, Coppola D, Giordano D, Nuzzo G, Lauritano C, Fontana A, Ianora A, Verde C, Costantini M. A Metataxonomic Approach Reveals Diversified Bacterial Communities in Antarctic Sponges. Mar Drugs 2021; 19:173. [PMID: 33810171 PMCID: PMC8004616 DOI: 10.3390/md19030173] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 02/06/2023] Open
Abstract
Marine sponges commonly host a repertoire of bacterial-associated organisms, which significantly contribute to their health and survival by producing several anti-predatory molecules. Many of these compounds are produced by sponge-associated bacteria and represent an incredible source of novel bioactive metabolites with biotechnological relevance. Although most investigations are focused on tropical and temperate species, to date, few studies have described the composition of microbiota hosted by Antarctic sponges and the secondary metabolites that they produce. The investigation was conducted on four sponges collected from two different sites in the framework of the XXXIV Italian National Antarctic Research Program (PNRA) in November-December 2018. Collected species were characterized as Mycale (Oxymycale) acerata, Haliclona (Rhizoniera) dancoi, Hemigellius pilosus and Microxina sarai by morphological analysis of spicules and amplification of four molecular markers. Metataxonomic analysis of these four Antarctic sponges revealed a considerable abundance of Amplicon Sequence Variants (ASVs) belonging to the phyla Proteobacteria, Bacteroidetes, Actinobacteria and Verrucomicrobia. In particular, M. (Oxymycale) acerata, displayed several genera of great interest, such as Endozoicomonas, Rubritalea, Ulvibacter, Fulvivirga and Colwellia. On the other hand, the sponges H. pilosus and H. (Rhizoniera) dancoi hosted bacteria belonging to the genera Pseudhongella, Roseobacter and Bdellovibrio, whereas M. sarai was the sole species showing some strains affiliated to the genus Polaribacter. Considering that most of the bacteria identified in the present study are known to produce valuable secondary metabolites, the four Antarctic sponges could be proposed as potential tools for the discovery of novel pharmacologically active compounds.
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Affiliation(s)
- Nadia Ruocco
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
| | - Roberta Esposito
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cinthia 21, 80126 Napoli, Italy
| | - Marco Bertolino
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, Corso Europa 26, 16132 Genova, Italy;
| | - Gianluca Zazo
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| | - Michele Sonnessa
- Bio-Fab Research srl, Via Mario Beltrami, 5, 00135 Roma, Italy; (M.S.); (F.A.)
| | - Federico Andreani
- Bio-Fab Research srl, Via Mario Beltrami, 5, 00135 Roma, Italy; (M.S.); (F.A.)
| | - Daniela Coppola
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Daniela Giordano
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Genoveffa Nuzzo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica Biomolecolare, Via Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy; (G.N.); (A.F.)
| | - Chiara Lauritano
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
| | - Angelo Fontana
- Consiglio Nazionale delle Ricerche, Istituto di Chimica Biomolecolare, Via Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy; (G.N.); (A.F.)
| | - Adrianna Ianora
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
| | - Cinzia Verde
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Maria Costantini
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
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Davidovich N, Morick D, Carella F. Mycobacteriosis in Aquatic Invertebrates: A Review of Its Emergence. Microorganisms 2020; 8:E1249. [PMID: 32824567 PMCID: PMC7464023 DOI: 10.3390/microorganisms8081249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/05/2020] [Accepted: 08/14/2020] [Indexed: 12/30/2022] Open
Abstract
Mycobacteriosis is a chronic bacterial disease reported in aquatic and terrestrial animals, including humans. The disease affects a wide range of cultured and wild organisms worldwide. Mycobacteriosis is well-known in aquatic vertebrates (e.g., finfish, marine mammals), while in the last few years, reports of its presence in aquatic invertebrates have been on the rise, for both freshwater and marine species. The number of cases is likely to increase as a result of increased awareness, surveillance and availability of diagnostic methods. Domestication of wild aquatic species and the intensification of modern aquaculture are also leading to an increase in the number of reported cases. Moreover, climate changes are affecting fresh and marine aquatic ecosystems. The increasing reports of mycobacteriosis in aquatic invertebrates may also be influenced by global climate warming, which could contribute to the microbes' development and survival rates, pathogen transmission and host susceptibility. Several species of the genus Mycobacterium have been diagnosed in aquatic invertebrates; a few of them are significant due to their wide host spectrum, economic impact in aquaculture, and zoonotic potential. The impact of mycobacteriosis in aquatic invertebrates is probably underestimated, and there is currently no effective treatment other than facility disinfection. In this review, we provide an overview of the diversity of mycobacterial infections reported in molluscs, crustaceans, cnidarians, echinoderms and sponges. We highlight important issues relating to its pathological manifestation, diagnosis and zoonotic considerations.
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Affiliation(s)
| | - Danny Morick
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel;
- Morris Kahn Marine Research Station, University of Haifa, Haifa 3498838, Israel
- Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong, China
| | - Francesca Carella
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia, Ed. 7, 80136 Naples, Italy;
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10
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Zhang B, Wu X, Tai X, Sun L, Wu M, Zhang W, Chen X, Zhang G, Chen T, Liu G, Dyson P. Variation in Actinobacterial Community Composition and Potential Function in Different Soil Ecosystems Belonging to the Arid Heihe River Basin of Northwest China. Front Microbiol 2019; 10:2209. [PMID: 31608036 PMCID: PMC6769177 DOI: 10.3389/fmicb.2019.02209] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/09/2019] [Indexed: 12/18/2022] Open
Abstract
Actinobacteria are known for their metabolic potential of producing diverse secondary metabolites such as antibiotics. Actinobacteria also playimportant roles in biogeochemical cycling and how soils develop. However, little is known about the effect of the vegetation type on the actinobacterial community structures in soils from arid regions. For these reasons, we have analyzed the actinobacterial communities of five types of ecosystem (tree grove, shrub, meadow, desert, and farm) in the Heihe river basin. Using 16S rRNA high-throughput sequencing, we found 11 classes of Actinobacteria, with dominant classes of Actinobacteria (36.2%), Thermoleophilia (28.3%), Acidimicrobiia (19.4%). Five classes, 15 orders, 20 families and 36 genera were present in all samples. The dominant generalist genera were Gaiella, Solirubrobacter, Nocardioides, Mycobacterium, and Pseudonocardia. The actinobacterial community structures were significantly affected by the environment and vegetation type. The diversity of the actinobacterial community in the desert ecosystem was high, and this ecosystem harbored the highest proportion of unclassified sequences, representing rare Actinobacteria. Functional metagenomic prediction, using PICRUSt, indicated that Actinobacteria play an important role in nitrogen cycling in both desert and cultivated farm ecosystems.
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Affiliation(s)
- Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xiukun Wu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xisheng Tai
- College of Geography and Environmental Engineering, Lanzhou City University, Lanzhou, China
| | - Likun Sun
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Minghui Wu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Ximing Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Paul Dyson
- Institute of Life Science, Swansea University Medical School, Swansea, United Kingdom
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11
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Abraham J, Gajendiran A. Biodegradation of fipronil and its metabolite fipronil sulfone by Streptomyces rochei strain AJAG7 and its use in bioremediation of contaminated soil. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 155:90-100. [PMID: 30857632 DOI: 10.1016/j.pestbp.2019.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/05/2019] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Fipronil is a most widely used insecticide. It has been found to be highly toxic to insects with alarming decline in honey bees' population. It has shown to cause severe contamination of soil and water. The present study was undertaken to understand the degradation of fipronil and its metabolite fipronil sulfone using actinomycetes. Fipronil degrading actinomycetes strain AJAG7 was isolated from fipronil contaminated agricultural field by enrichment method. Molecular identification by 16S rRNA gene sequencing identified strain AJAG7 as Streptomyces rochei. The biodegradation of fipronil and its metabolite fipronil sulfone by strain AJAG7 was examined by HPLC. Biodegradation pathway of fipronil by strain AJAG7 was deduced with GC-MS analysis. Scanning electron microscopy was used to investigate the surface morphological changes of strain AJAG7 upon fipronil degradation. Apart from fipronil degradation, low cost powder formulation of strain AJAG7 was prepared using agricultural waste to remediate the fipronil contaminated agricultural field. Results of the present study suggest that strain AJAG7 qualifies as an ideal candidate for biodegradation of fipronil contaminated environment.
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Affiliation(s)
- Jayanthi Abraham
- Microbial Biotechnology Laboratory, School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India.
| | - Anudurga Gajendiran
- Microbial Biotechnology Laboratory, School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
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12
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Illumina-Based Sequencing Analysis Directed Selection for Actinobacterial Probiotic Candidates for Banana Plants. Probiotics Antimicrob Proteins 2019; 10:284-292. [PMID: 28560514 DOI: 10.1007/s12602-017-9293-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
As potential probiotic candidates, plant vertically transmitted actinobacteria are beneficial to growth and health of host plants. New methods to isolate the actinobacterial taxa with low growth rates should be developed. Based on the actinobacterial population information, the probiotic actinobacterial taxa could be directly isolated from healthy banana shoot tips. However, actinobacterial DNAs with high GC contents could bias estimates of actinobacteria by PCR. In the study, two amplicon sequencing strategies were adopted to elucidate the endophytic actinobacterial community of banana plants. More than 92.5% bacterial OTUs were affiliated with actinobacteria by these two strategies, and total 14,289 actinobacterial OTUs with above 97% similarity were detected in banana shoot tips. Although the libraries generated by the two strategies differed in the abundance of some genera, Mycobacterium and Nocardia dominated both libraries and most actinobacterial taxa were overlapped. Higher phylogenetic resolution actinobacteriome of banana plants was successfully established. Based on the endophytic actinobacterial community information, the streptomycetes were isolated from shoot tips. Pot experiments illustrated that the strain could promote banana plantlet growth and elevate resistance to Fusarium oxysporum f. sp. cubense (FOC) under FOC infested soils. The results suggested that the selection for probiotic agents based on actinobacteriome analysis is reliable and feasible compared with present greenhouse selection.
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13
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Selective isolation and characterisation of novel members of the family Nocardiopsaceae and other actinobacteria from a marine sediment of Tioman Island. Antonie van Leeuwenhoek 2018; 111:727-742. [DOI: 10.1007/s10482-018-1042-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 02/06/2018] [Indexed: 11/26/2022]
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14
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Sowani H, Kulkarni M, Zinjarde S. An insight into the ecology, diversity and adaptations of Gordonia species. Crit Rev Microbiol 2017; 44:393-413. [PMID: 29276839 DOI: 10.1080/1040841x.2017.1418286] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The bacterial genus Gordonia encompasses a variety of versatile species that have been isolated from a multitude of environments. Gordonia was described as a genus about 20 years ago, and to date, 39 different species have been identified. Gordonia is recognized for symbiotic associations with multiple hosts, including aquatic (marine and fresh water) biological forms and terrestrial invertebrates. Some Gordonia species isolated from clinical specimens are known to be opportunistic human pathogens causing secondary infections in immunocompromised and immunosuppressive individuals. They are also predominant in mangrove ecosystems and terrestrial sites. Members of the genus Gordonia are ecologically adaptable and show marked variations in their properties and products. They generate diverse bioactive compounds and produce a variety of extracellular enzymes. In addition, production of surface active compounds and carotenoid pigments allows this group of microorganisms to grow under different conditions. Several isolates from water and soil have been implicated in bioremediation of different environments and plant associated species have been explored for agricultural applications. This review highlights the prevalence of the members of this versatile genus in diverse environments, details its associations with living forms, summarizes the biotechnologically relevant products that can be obtained and discusses the salient genomic features that allow this Actinomycete to survive in different ecological niches.
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Affiliation(s)
- Harshada Sowani
- a Department of Chemistry , Biochemistry Division Savitribai Phule Pune University , Pune , India
| | - Mohan Kulkarni
- a Department of Chemistry , Biochemistry Division Savitribai Phule Pune University , Pune , India
| | - Smita Zinjarde
- b Institute of Bioinformatics and Biotechnology , Savitribai Phule Pune University , Pune , India.,c Department of Microbiology , Savitribai Phule Pune University , Pune , India
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15
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Dholakiya RN, Kumar R, Mishra A, Mody KH, Jha B. Antibacterial and Antioxidant Activities of Novel Actinobacteria Strain Isolated from Gulf of Khambhat, Gujarat. Front Microbiol 2017; 8:2420. [PMID: 29270160 PMCID: PMC5725476 DOI: 10.3389/fmicb.2017.02420] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/22/2017] [Indexed: 02/02/2023] Open
Abstract
Bacterial secondary metabolites possess a wide range of biologically active compounds including antibacterial and antioxidants. In this study, a Gram-positive novel marine Actinobacteria was isolated from sea sediment which showed 84% 16S rRNA gene sequence (KT588655) similarity with Streptomyces variabilis (EU841661) and designated as Streptomyces variabilis RD-5. The genus Streptomyces is considered as a promising source of bioactive secondary metabolites. The isolated novel bacterial strain was characterized by antibacterial characteristics and antioxidant activities. The BIOLOG based analysis suggested that S. variabilis RD-5 utilized a wide range of substrates compared to the reference strain. The result is further supported by statistical analysis such as AWCD (average well color development), heat-map and PCA (principal component analysis). The whole cell fatty acid profiling showed the dominance of iso/anteiso branched C15–C17 long chain fatty acids. The identified strain S. variabilis RD-5 exhibited a broad spectrum of antibacterial activities for the Gram-negative bacteria (Escherichia coli NCIM 2065, Shigella boydii NCIM, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas sp. NCIM 2200 and Salmonella enteritidis NCIM), and Gram-positive bacteria (Bacillus subtilis NCIM 2920 and Staphylococcus aureus MTCC 96). Extract of S. variabilis strain RD-5 showed 82.86 and 89% of 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging and metal chelating activity, respectively, at 5.0 mg/mL. While H2O2 scavenging activity was 74.5% at 0.05 mg/mL concentration. Furthermore, polyketide synthases (PKSs types I and II), an enzyme complex that produces polyketides, the encoding gene(s) detected in the strain RD-5 which may probably involve for the synthesis of antibacterial compound(s). In conclusion, a novel bacterial strain of Actinobacteria, isolated from the unexplored sea sediment of Alang, Gulf of Khambhat (Gujarat), India showed promising antibacterial activities. However, fractionation and further characterization of active compounds from S. variabilis RD-5 are needed for their optimum utilization toward antibacterial purposes.
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Affiliation(s)
- Riddhi N Dholakiya
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Raghawendra Kumar
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Avinash Mishra
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Kalpana H Mody
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Bhavanath Jha
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
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16
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Eliwa EM, Abdel-Razek AS, Frese M, Wibberg D, Halawa AH, El-Agrody AM, Bedair AH, Kalinowski J, Sewald N, Shaaban M. New bioactive compounds from the marine-derived actinomycete Nocardiopsis lucentensis sp. ASMR2. ACTA ACUST UNITED AC 2017. [DOI: 10.1515/znb-2016-0250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
In the search for new bioactive compounds from extremophilic actinomycetes, a new marine actinomycete strain, Nocardiopsis lucentensis sp. ASMR2 has been isolated and taxonomically identified from marine plants collected in the Red Sea at Hurghada coasts. A large-scale fermentation of the strain on modified rice solid medium was performed, followed by work-up and purification of the obtained extract using a series of chromatographic purifications, delivering the novel butenolide system 3′-hydroxy-N-(2-oxo-2,5-dihydrofuran-4-yl)propionamide (1a) along with the naturally new 4-methoxy-2H-isoquinolin-1-one (2). Furthermore, eight known bioactive compounds are also reported, namely, indole-3-carboxylic acid, indole-3-acetic acid, indole-3-acetic acid methyl ester, furan-2,5-dimethanol, tyrosol, glycerol linoleate, cyclo-(Tyr, Pro), and adenosine. The chemical structures of the new compounds (1a, 2) were confirmed by extensive one- and two-dimensional (1D and 2D) nuclear magnetic resonance (NMR) spectroscopy, electron ionization high resolution (EI-HR) mass spectrometry, and by comparison with literature data. The antimicrobial activity of the strain extract, as well as of compounds 1a and 2, were studied using a panel of pathogenic microorganisms. The in vitro cytotoxicity of the bacterial extract and compounds 1a and 2 were studied against the human cervix carcinoma cell line (KB-3-1) and its multidrug-resistant subclone (KB-V1).
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Affiliation(s)
- Essam M. Eliwa
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City-Cairo 11884, Egypt
| | - Ahmed S. Abdel-Razek
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
- Microbial Chemistry Department, Division of Genetic Engineering and Biotechnology Research, National Research Centre, El-Behoos St. 33, Dokki-Cairo 12622, Egypt
| | - Marcel Frese
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
| | - Daniel Wibberg
- Centrum für Biotechnologie (CeBiTec), Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Ahmed H. Halawa
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City-Cairo 11884, Egypt
| | - Ahmed M. El-Agrody
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City-Cairo 11884, Egypt
| | - Ahmed H. Bedair
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City-Cairo 11884, Egypt
| | - Jörn Kalinowski
- Centrum für Biotechnologie (CeBiTec), Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
| | - Mohamed Shaaban
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
- Chemistry of Natural Compounds Department, Division of Pharmaceutical Industries, National Research Centre, El-Behoos St. 33, Dokki, Cairo 12622, Egypt , Tel.: +202-270-1728/int-2609. Fax: +202-333-70931
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17
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Matobole RM, van Zyl LJ, Parker-Nance S, Davies-Coleman MT, Trindade M. Antibacterial Activities of Bacteria Isolated from the Marine Sponges Isodictya compressa and Higginsia bidentifera Collected from Algoa Bay, South Africa. Mar Drugs 2017; 15:E47. [PMID: 28218694 PMCID: PMC5334627 DOI: 10.3390/md15020047] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/30/2017] [Indexed: 11/16/2022] Open
Abstract
Due to the rise in multi-drug resistant pathogens and other diseases, there is renewed interest in marine sponge endosymbionts as a rich source of natural products (NPs). The South African marine environment is rich in marine biota that remains largely unexplored and may represent an important source for the discovery of novel NPs. We first investigated the bacterial diversity associated with five South African marine sponges, whose microbial populations had not previously been investigated, and select the two sponges (Isodictya compressa and Higginsia bidentifera) with highest species richness to culture bacteria. By employing 33 different growth conditions 415 sponge-associated bacterial isolates were cultured and screened for antibacterial activity. Thirty-five isolates showed antibacterial activity, twelve of which exhibited activity against the multi-drug resistant Escherichia coli 1699, implying that some of the bioactive compounds could be novel. Genome sequencing of two of these isolates confirmed that they harbour uncharacterized biosynthetic pathways that may encode novel chemical structures.
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Affiliation(s)
- Relebohile Matthew Matobole
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, Cape Town, South Africa.
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, Cape Town, South Africa.
| | - Shirley Parker-Nance
- Department of Zoology, Nelson Mandela Metropolitan University, University Way, Port Elizabeth 6031, South Africa.
- South African Institute for Aquatic Biodiversity (SAIAB), Somerset Street, Grahamstown 6139, South Africa.
| | - Michael T Davies-Coleman
- Department of Chemistry, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, Cape Town, South Africa.
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, Cape Town, South Africa.
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18
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Phenazine-1-carboxylic acid-induced programmed cell death in human prostate cancer cells is mediated by reactive oxygen species generation and mitochondrial-related apoptotic pathway. J Appl Biomed 2016. [DOI: 10.1016/j.jab.2016.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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19
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Ettoumi B, Chouchane H, Guesmi A, Mahjoubi M, Brusetti L, Neifar M, Borin S, Daffonchio D, Cherif A. Diversity, ecological distribution and biotechnological potential of Actinobacteria inhabiting seamounts and non-seamounts in the Tyrrhenian Sea. Microbiol Res 2016; 186-187:71-80. [DOI: 10.1016/j.micres.2016.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/16/2016] [Accepted: 03/31/2016] [Indexed: 11/26/2022]
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20
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Diversity of actinobacteria associated with Nostoc commune Vaucher ex Bornet & Flahault macrocolonies. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1063-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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21
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Kuang W, Li J, Zhang S, Long L. Diversity and distribution of Actinobacteria associated with reef coral Porites lutea. Front Microbiol 2015; 6:1094. [PMID: 26539166 PMCID: PMC4612714 DOI: 10.3389/fmicb.2015.01094] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/22/2015] [Indexed: 12/22/2022] Open
Abstract
Actinobacteria is a ubiquitous major group in coral holobiont. The diversity and spatial and temporal distribution of actinobacteria have been rarely documented. In this study, diversity of actinobacteria associated with mucus, tissue and skeleton of Porites lutea and in the surrounding seawater were examined every 3 months for 1 year on Luhuitou fringing reef. The population structures of the P. lutea-associated actinobacteria were analyzed using phylogenetic analysis of 16S rRNA gene clone libraries, which demonstrated highly diverse actinobacteria profiles in P. lutea. A total of 25 described families and 10 unnamed families were determined in the populations, and 12 genera were firstly detected in corals. The Actinobacteria diversity was significantly different between the P. lutea and the surrounding seawater. Only 10 OTUs were shared by the seawater and coral samples. Redundancy and hierarchical cluster analyses were performed to analyze the correlation between the variations of actinobacteria population within the divergent compartments of P. lutea, seasonal changes, and environmental factors. The actinobacteria communities in the same coral compartment tended to cluster together. Even so, an extremely small fraction of OTUs was common in all three P. lutea compartments. Analysis of the relationship between actinobacteria assemblages and the environmental parameters showed that several genera were closely related to specific environmental factors. This study highlights that coral-associated actinobacteria populations are highly diverse, and spatially structured within P. lutea, and they are distinct from which in the ambient seawater.
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Affiliation(s)
- Weiqi Kuang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China ; College of Earth Science, University of Chinese Academy of Sciences Beijing, China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China
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22
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Sun W, Zhang F, He L, Karthik L, Li Z. Actinomycetes from the South China Sea sponges: isolation, diversity, and potential for aromatic polyketides discovery. Front Microbiol 2015; 6:1048. [PMID: 26483773 PMCID: PMC4589764 DOI: 10.3389/fmicb.2015.01048] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/14/2015] [Indexed: 12/21/2022] Open
Abstract
Marine sponges often harbor dense and diverse microbial communities including actinobacteria. To date no comprehensive investigation has been performed on the culturable diversity of the actinomycetes associated with South China Sea sponges. Structurally novel aromatic polyketides were recently discovered from marine sponge-derived Streptomyces and Saccharopolyspora strains, suggesting that sponge-associated actinomycetes can serve as a new source of aromatic polyketides. In this study, a total of 77 actinomycete strains were isolated from 15 South China Sea sponge species. Phylogenetic characterization of the isolates based on 16S rRNA gene sequencing supported their assignment to 12 families and 20 genera, among which three rare genera (Marihabitans, Polymorphospora, and Streptomonospora) were isolated from marine sponges for the first time. Subsequently, β-ketoacyl synthase (KSα) gene was used as marker for evaluating the potential of the actinomycete strains to produce aromatic polyketides. As a result, KSα gene was detected in 35 isolates related to seven genera (Kocuria, Micromonospora, Nocardia, Nocardiopsis, Saccharopolyspora, Salinispora, and Streptomyces). Finally, 10 strains were selected for small-scale fermentation, and one angucycline compound was detected from the culture extract of Streptomyces anulatus strain S71. This study advanced our knowledge of the sponge-associated actinomycetes regarding their diversity and potential in producing aromatic polyketides.
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Affiliation(s)
- Wei Sun
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Fengli Zhang
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Liming He
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Loganathan Karthik
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
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23
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Steinert G, Taylor MW, Schupp PJ. Diversity of Actinobacteria Associated with the Marine Ascidian Eudistoma toealensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:377-385. [PMID: 25678260 DOI: 10.1007/s10126-015-9622-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/20/2015] [Indexed: 06/04/2023]
Abstract
Ascidians have yielded a wide variety of bioactive natural products. The colonial ascidian Eudistoma toealensis from Micronesia has been identified as the source of a series of staurosporine derivatives, though the exact origin of these derivatives is still unknown. To identify known staurosporine-producing microbes associated with E. toealensis, we analyzed with 16S rRNA gene tag pyrosequencing the overall bacterial community and focused on potential symbiotic bacteria already known from other ascidians or other marine hosts, such as sponges. The described microbiota was one of very high diversity, comprising 43 phyla: two from archaea, 34 described bacterial phyla, and seven candidate bacterial phyla. Many bacteria, which are renowned community members of other ascidians and marine holobionts, such as sponges and corals, were also part of the E. toealensis microbial community. Furthermore, two known producers of indolocarbazoles, Salinispora and Verrucosispora, were found with high abundance exclusively in the ascidian tissue, suggesting that microbial symbionts and not the organism itself may be the true producers of the staurosporines in E. toealensis.
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Affiliation(s)
- Georg Steinert
- Institute for the Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany,
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24
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Functional gene-based discovery of phenazines from the actinobacteria associated with marine sponges in the South China Sea. Appl Microbiol Biotechnol 2015; 99:5939-50. [PMID: 25820602 DOI: 10.1007/s00253-015-6547-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/05/2015] [Accepted: 03/15/2015] [Indexed: 10/23/2022]
Abstract
Phenazines represent a large group of nitrogen-containing heterocyclic compounds produced by the diverse group of bacteria including actinobacteria. In this study, a total of 197 actinobacterial strains were isolated from seven different marine sponge species in the South China Sea using five different culture media. Eighty-seven morphologically different actinobacterial strains were selected and grouped into 13 genera, including Actinoalloteichus, Kocuria, Micrococcus, Micromonospora, Mycobacterium, Nocardiopsis, Prauserella, Rhodococcus, Saccharopolyspora, Salinispora, Serinicoccus, and Streptomyces by the phylogenetic analysis of 16S rRNA gene. Based on the screening of phzE genes, ten strains, including five Streptomyces, two Nocardiopsis, one Salinispora, one Micrococcus, and one Serinicoccus were found to be potential for phenazine production. The level of phzE gene expression was highly expressed in Nocardiopsis sp. 13-33-15, 13-12-13, and Serinicoccus sp. 13-12-4 on the fifth day of fermentation. Finally, 1,6-dihydroxy phenazine (1) from Nocardiopsis sp. 13-33-15 and 13-12-13, and 1,6-dimethoxy phenazine (2) from Nocardiopsis sp. 13-33-15 were isolated and identified successfully based on ESI-MS and NMR analysis. The compounds 1 and 2 showed antibacterial activity against Bacillus mycoides SJ14, Staphylococcus aureus SJ51, Escherichia coli SJ42, and Micrococcus luteus SJ47. This study suggests that the integrated approach of gene screening and chemical analysis is an effective strategy to find the target compounds and lays the basis for the production of phenazine from the sponge-associated actinobacteria.
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Valliappan K, Sun W, Li Z. Marine actinobacteria associated with marine organisms and their potentials in producing pharmaceutical natural products. Appl Microbiol Biotechnol 2014; 98:7365-77. [PMID: 25064352 DOI: 10.1007/s00253-014-5954-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/10/2014] [Accepted: 07/11/2014] [Indexed: 01/09/2023]
Abstract
Actinobacteria are ubiquitous in the marine environment, playing an important ecological role in the recycling of refractory biomaterials and producing novel natural products with pharmic applications. Actinobacteria have been detected or isolated from the marine creatures such as sponges, corals, mollusks, ascidians, seaweeds, and seagrass. Marine organism-associated actinobacterial 16S rRNA gene sequences, i.e., 3,003 sequences, deposited in the NCBI database clearly revealed enormous numbers of actinobacteria associated with marine organisms. For example, RDP classification of these sequences showed that 112 and 62 actinobacterial genera were associated with the sponges and corals, respectively. In most cases, it is expected that these actinobacteria protect the host against pathogens by producing bioactive compounds. Natural products investigation and functional gene screening of the actinobacteria associated with the marine organisms revealed that they can synthesize numerous natural products including polyketides, isoprenoids, phenazines, peptides, indolocarbazoles, sterols, and others. These compounds showed anticancer, antimicrobial, antiparasitic, neurological, antioxidant, and anti-HIV activities. Therefore, marine organism-associated actinobacteria represent an important resource for marine drugs. It is an upcoming field of research to search for novel actinobacteria and pharmaceutical natural products from actinobacteria associated with the marine organisms. In this review, we attempt to summarize the present knowledge on the diversity and natural products production of actinobacteria associated with the marine organisms, based on the publications from 1991 to 2013.
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Affiliation(s)
- Karuppiah Valliappan
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240, Shanghai, China
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Rua CPJ, Trindade-Silva AE, Appolinario LR, Venas TM, Garcia GD, Carvalho LS, Lima A, Kruger R, Pereira RC, Berlinck RGS, Valle RAB, Thompson CC, Thompson F. Diversity and antimicrobial potential of culturable heterotrophic bacteria associated with the endemic marine sponge Arenosclera brasiliensis. PeerJ 2014; 2:e419. [PMID: 25024903 PMCID: PMC4081303 DOI: 10.7717/peerj.419] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/18/2014] [Indexed: 01/13/2023] Open
Abstract
Marine sponges are the oldest Metazoa, very often presenting a complex microbial consortium. Such is the case of the marine sponge Arenosclera brasiliensis, endemic to Rio de Janeiro State, Brazil. In this investigation we characterized the diversity of some of the culturable heterotrophic bacteria living in association with A. brasiliensis and determined their antimicrobial activity. The genera Endozoicomonas (N = 32), Bacillus (N = 26), Shewanella (N = 17), Pseudovibrio (N = 12), and Ruegeria (N = 8) were dominant among the recovered isolates, corresponding to 97% of all isolates. Approximately one third of the isolates living in association with A. brasiliensis produced antibiotics that inhibited the growth of Bacillus subtilis, suggesting that bacteria associated with this sponge play a role in its health.
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Affiliation(s)
- Cintia P J Rua
- Instituto de Biologia, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | | | - Luciana R Appolinario
- Instituto de Biologia, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | - Tainá M Venas
- Instituto de Biologia, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | - Gizele D Garcia
- Instituto de Biologia, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | - Lucas S Carvalho
- Departamento de Biologia Celular, Universidade de Brasília , Brasília, DF , Brazil
| | - Alinne Lima
- Departamento de Biologia Celular, Universidade de Brasília , Brasília, DF , Brazil
| | - Ricardo Kruger
- Departamento de Biologia Celular, Universidade de Brasília , Brasília, DF , Brazil
| | - Renato C Pereira
- Instituto de Biologia, Universidade Federal Fluminense , Niterói, RJ , Brazil
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo , São Carlos, SP , Brazil
| | - Rogério A B Valle
- SAGE-COPPE Centro de Gestão Tecnológica, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | - Fabiano Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil ; SAGE-COPPE Centro de Gestão Tecnológica, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
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Abdelmohsen UR, Yang C, Horn H, Hajjar D, Ravasi T, Hentschel U. Actinomycetes from Red Sea sponges: sources for chemical and phylogenetic diversity. Mar Drugs 2014; 12:2771-89. [PMID: 24824024 PMCID: PMC4052315 DOI: 10.3390/md12052771] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 04/10/2014] [Accepted: 04/14/2014] [Indexed: 02/01/2023] Open
Abstract
The diversity of actinomycetes associated with marine sponges collected off Fsar Reef (Saudi Arabia) was investigated in the present study. Forty-seven actinomycetes were cultivated and phylogenetically identified based on 16S rRNA gene sequencing and were assigned to 10 different actinomycete genera. Eight putatively novel species belonging to genera Kocuria, Mycobacterium, Nocardia, and Rhodococcus were identified based on sequence similarity values below 98.2% to other 16S rRNA gene sequences available in the NCBI database. PCR-based screening for biosynthetic genes including type I and type II polyketide synthases (PKS-I, PKS-II) as well as nonribosomal peptide synthetases (NRPS) showed that 20 actinomycete isolates encoded each at least one type of biosynthetic gene. The organic extracts of nine isolates displayed bioactivity against at least one of the test pathogens, which were Gram-positive and Gram-negative bacteria, fungi, human parasites, as well as in a West Nile Virus protease enzymatic assay. These results emphasize that marine sponges are a prolific resource for novel bioactive actinomycetes with potential for drug discovery.
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Affiliation(s)
- Usama Ramadan Abdelmohsen
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, Würzburg D-97082, Germany.
| | - Chen Yang
- Division of Chemical & Life Sciences and Engineering and Division of Applied Mathematics and Computer Science, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Hannes Horn
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, Würzburg D-97082, Germany.
| | - Dina Hajjar
- Division of Chemical & Life Sciences and Engineering and Division of Applied Mathematics and Computer Science, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Timothy Ravasi
- Division of Chemical & Life Sciences and Engineering and Division of Applied Mathematics and Computer Science, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, Würzburg D-97082, Germany.
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Sun W, Zhang F, He L, Li Z. Pyrosequencing reveals diverse microbial community associated with the zoanthid Palythoa australiae from the South China Sea. MICROBIAL ECOLOGY 2014; 67:942-950. [PMID: 24682342 DOI: 10.1007/s00248-014-0395-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
Diverse sessile organisms inhabit the coral reef ecosystems, including corals, sponges, and sea anemones. In the past decades, scleractinian corals (Cnidaria, Anthozoa, Scleractinia) and their associated microorganisms have attracted much attention. Zoanthids (Cnidaria, Anthozoa, Zoanthidea) are commonly found in coral reefs. However, little is known about the community structure of zoanthid-associated microbiota. In this study, the microbial community associated with the zoanthid Palythoa australiae in the South China Sea was investigated by 454 pyrosequencing. As a result, 2,353 bacterial, 583 archaeal, and 36 eukaryotic microbial ribotypes were detected, respectively. A total of 22 bacterial phyla (16 formally described phyla and six candidate phyla) were recovered. Proteobacteria was the most abundant group, followed by Chloroflexi and Actinobacteria. High-abundance Rhizobiales and diverse Chloroflexi were observed in the bacterial community. The archaeal population was composed of Crenarchaeota and Euryarchaeota, with Marine Group I as the dominant lineage. In particular, Candidatus Nitrosopumilus dominated the archaeal community. Besides bacteria and archaea, the zoanthid harbored eukaryotic microorganisms including fungi and algae though their diversity was very low. This study provided the first insights into the microbial community associated with P. australiae by 454 pyrosequencing, consequently laid a basis for the understanding of the association of P. australiae-microbes symbioses.
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Affiliation(s)
- Wei Sun
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
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Diversity and novelty of actinobacteria in Arctic marine sediments. Antonie van Leeuwenhoek 2014; 105:743-54. [PMID: 24519808 DOI: 10.1007/s10482-014-0130-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/29/2014] [Indexed: 01/17/2023]
Abstract
The actinobacterial diversity of Arctic marine sediments was investigated using culture-dependent and culture-independent approaches. A total of 152 strains were isolated from seven different media; 18 isolates were selected for phylogenetic analysis on the basis of their 16S rRNA gene sequences. Results showed that the 18 isolates belonged to a potential novel genus and 10 known genera including Actinotalea, Arthrobacter, Brachybacterium, Brevibacterium, Kocuria, Kytococcus, Microbacterium, Micrococcus, Mycobacterium, and Pseudonocardia. Subsequently, 172 rDNA clones were selected by restriction fragment length polymorphism analysis from 692 positive clones within four actinobacteria-specific 16S rDNA libraries of Arctic marine sediments, and then these 172 clones were sequenced. In total, 67 phylotypes were clustered in 11 known genera of actinobacteria including Agrococcus, Cellulomonas, Demequina, Iamia, Ilumatobacter, Janibacter, Kocuria, Microbacterium, Phycicoccus, Propionibacterium, and Pseudonocardia, along with other, unidentified actinobacterial clones. Based on the detection of a substantial number of uncultured phylotypes showing low BLAST identities (<95 %), this study confirms that Arctic marine environments harbour highly diverse actinobacterial communities, many of which appear to be novel, uncultured species.
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Abdelmohsen UR, Bayer K, Hentschel U. Diversity, abundance and natural products of marine sponge-associated actinomycetes. Nat Prod Rep 2014; 31:381-99. [DOI: 10.1039/c3np70111e] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review discusses the diversity, abundance and natural products repertoire of actinomycetes associated with marine sponges. Comprehensive phylogenetic analysis was carried out and qPCR data on actinomycete abundances in sponge ecosystems are presented.
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Affiliation(s)
- Usama Ramadan Abdelmohsen
- Department of Botany II
- Julius-von-Sachs-Institute for Biological Sciences
- University of Würzburg
- 97082 Würzburg, Germany
- Department of Pharmacognosy
| | - Kristina Bayer
- Department of Botany II
- Julius-von-Sachs-Institute for Biological Sciences
- University of Würzburg
- 97082 Würzburg, Germany
| | - Ute Hentschel
- Department of Botany II
- Julius-von-Sachs-Institute for Biological Sciences
- University of Würzburg
- 97082 Würzburg, Germany
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Öner Ö, Ekiz G, Hameş EE, Demir V, Gübe Ö, Özkaya FC, Yokeş MB, Uzel A, Bedir E. Cultivable Sponge-Associated Actinobacteria from Coastal Area of Eastern Mediterranean Sea. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/aim.2014.46037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Jose PA, Jebakumar SRD. Non-streptomycete actinomycetes nourish the current microbial antibiotic drug discovery. Front Microbiol 2013; 4:240. [PMID: 23970883 PMCID: PMC3747354 DOI: 10.3389/fmicb.2013.00240] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 07/31/2013] [Indexed: 11/17/2022] Open
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Yang S, Sun W, Tang C, Jin L, Zhang F, Li Z. Phylogenetic diversity of actinobacteria associated with soft coral Alcyonium gracllimum and stony coral Tubastraea coccinea in the East China Sea. MICROBIAL ECOLOGY 2013; 66:189-199. [PMID: 23503990 DOI: 10.1007/s00248-013-0205-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 02/21/2013] [Indexed: 06/01/2023]
Abstract
Actinobacteria are widely distributed in the marine environment. To date, few studies have been performed to explore the coral-associated Actinobacteria, and little is known about the diversity of coral-associated Actinobacteria. In this study, the actinobacterial diversity associated with one soft coral Alcyonium gracllimum and one stony coral Tubastraea coccinea collected from the East China Sea was investigated using both culture-independent and culture-dependent approaches. A total of 19 actinobacterial genera were detected in these two corals, among which nine genera (Corynebacterium, Dietzia, Gordonia, Kocuria, Microbacterium, Micrococcus, Mycobacterium, Streptomyces, and Candidatus Microthrix) were common, three genera (Cellulomonas, Dermatophilus, and Janibacter) were unique to the soft coral, and seven genera (Brevibacterium, Dermacoccus, Leucobacter, Micromonospora, Nocardioides, Rhodococcus, and Serinicoccus) were unique to the stony coral. This finding suggested that highly diverse Actinobacteria were associated with different types of corals. In particular, five actinobacterial genera (Cellulomonas, Dermacoccus, Gordonia, Serinicoccus, and Candidatus Microthrix) were recovered from corals for the first time, extending the known diversity of coral-associated Actinobacteria. This study shows that soft and stony corals host diverse Actinobacteria and can serve as a new source of marine actinomycetes.
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Affiliation(s)
- Shan Yang
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
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Prieto-Davó A, Villarreal-Gómez LJ, Forschner-Dancause S, Bull AT, Stach JEM, Smith DC, Rowley DC, Jensen PR. Targeted search for actinomycetes from nearshore and deep-sea marine sediments. FEMS Microbiol Ecol 2013; 84:510-8. [PMID: 23360553 DOI: 10.1111/1574-6941.12082] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 01/16/2013] [Accepted: 01/21/2013] [Indexed: 11/27/2022] Open
Abstract
Sediment samples collected off the coast of San Diego were analyzed for actinomycete diversity using culture-independent techniques. Eight new operational taxonomic units (OTUs) in the Streptomycetaceae were identified as well as new diversity within previously cultured marine OTUs. Sequences belonging to the marine actinomycete genus Salinispora were also detected, despite the fact that this genus has only been reported from more tropical environments. Independent analyses of marine sediments from the Canary Basin (3814 m) and the South Pacific Gyre (5126 and 5699 m) also revealed Salinispora sequences providing further support for the occurrence of this genus in deep-sea sediments. Efforts to culture Salinispora spp. from these samples have yet to be successful. This is the first report of Salinispora spp. from marine sediments > 1100 m and suggests that the distribution of this genus is broader than previously believed.
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Affiliation(s)
- Alejandra Prieto-Davó
- Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA.
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RETRACTED: Marine actinobacterial metabolites: current status and future perspectives. Microbiol Res 2013; 168:311-332. [PMID: 23480961 DOI: 10.1016/j.micres.2013.02.002] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 01/25/2013] [Accepted: 02/06/2013] [Indexed: 11/24/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal).
This article has been retracted at the request of the Editor. Authors and Editor agreed to retract this article because substantial parts of the text were copied from the following sources without proper attribution: Lam, K.S. (2006), Discovery of novel metabolites from marine actinomycetes. Current Opinion in Microbiology 9(3), pp. 245–251; Subramani, R., Aalbersberg, W. (2012), Marine actinomycetes: An ongoing source of novel bioactive metabolites. Microbiological Research 167(10), pp. 571–580; Dharmaraj, S. (2010), Marine Streptomyces as a novel source of bioactive substances. World Journal of Microbiology and Biotechnology 26(12), pp. 2123–2139. The authors apologize for this oversight and any inconvenience caused.
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Qin S, Chen HH, Zhao GZ, Li J, Zhu WY, Xu LH, Jiang JH, Li WJ. Abundant and diverse endophytic actinobacteria associated with medicinal plant Maytenus austroyunnanensis in Xishuangbanna tropical rainforest revealed by culture-dependent and culture-independent methods. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:522-531. [PMID: 23760897 DOI: 10.1111/j.1758-2229.2012.00357.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Endophytes are now considered as an important component of biodiversity. However, the diversity of endophytic actinobacteria associated with tropical rainforest native medicinal plants is essentially unknown. In this study, the diversity of endophytic actinobacteria residing in root, stem and leaf tissues of medicinal plant Maytenus austroyunnanensis collected from tropical rainforest in Xishuangbanna, China was investigated with a combination of cultivation and culture-independent analysis on the basis of 16S rRNA gene sequencing. By using different selective isolation media and methods, a total of 312 actinobacteria were obtained, and they were affiliated with the order Actinomycetales (distributed into 21 genera). Based on a protocol for endophytes enrichment, three 16S rRNA gene clone libraries were constructed and 84 distinct operational taxonomic units were identified and they distributed among the orders Actinomycetales and Acidimicrobiales, including eight suborders and at least 38 genera with a number of rare actinobacteria genera. Phylogenetic analysis showed that 32% of the clones in the libraries had lower than 97% similarities with related type strains. Interestingly, six genera from the order Actinomycetales and uncultured clones from Acidimicrobiales have not, to our knowledge, been previously reported as endophytes. Our study confirms abundant endophytic actinobacterial consortium in tropical rainforest native plant and suggests that this special habitat represents an underexplored reservoir of diverse and novel actinobacteria of potential interest for bioactive compounds discovery.
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Affiliation(s)
- Sheng Qin
- The Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, Yunnan, China
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Abstract
A renewed interest in the development of new antimicrobial agents is urgently needed to combat the increasing number of antibiotic-resistant strains of pathogenic microorganisms. Actinomycetes continue to be the mainstream supplier of antibiotics used in industry. The likelihood of discovering a new compound with novel chemical structure can be increased with intensive efforts in isolating and screening of rare genera of microorganisms to include in natural-product-screening collections. An unexpected variety of rare actinomycetes is now being isolated worldwide from previously uninvestigated diverse natural habitats, using different selective isolation methods. These isolation efforts include methods to enhance growth (enrichment) of rare actinomycetes, and eliminate unwanted microorganisms (pretreatment). To speed up the strain isolation process, knowledge about the distribution of such unexploited groups of microorganisms must also be augmented. This is a summary of using these microorganisms as new potential biological resources, and a review of almost all of the selective isolation methods, including pretreatment and enrichment techniques that have been developed to date for the isolation of rare actinomycetes.
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Affiliation(s)
- Kavita Tiwari
- School of Biotechnology, Guru Gobind Singh Indraprastha University, Delhi, India
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Subramani R, Aalbersberg W. Marine actinomycetes: an ongoing source of novel bioactive metabolites. Microbiol Res 2012; 167:571-80. [PMID: 22796410 DOI: 10.1016/j.micres.2012.06.005] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 05/15/2012] [Accepted: 06/23/2012] [Indexed: 11/16/2022]
Abstract
Actinomycetes are virtually unlimited sources of novel compounds with many therapeutic applications and hold a prominent position due to their diversity and proven ability to produce novel bioactive compounds. There are more than 22,000 known microbial secondary metabolites, 70% of which are produced by actinomycetes, 20% from fungi, 7% from Bacillus spp. and 1-2% by other bacteria. Among the actinomycetes, streptomycetes group are considered economically important because out of the approximately more than 10,000 known antibiotics, 50-55% are produced by this genus. The ecological role of actinomycetes in the marine ecosystem is largely neglected and various assumptions meant there was little incentive to isolate marine strains for search and discovery of new drugs. The search for and discovery of rare and new actinomycetes is of significant interest to drug discovery due to a growing need for the development of new and potent therapeutic agents. Modern molecular technologies are adding strength to the target-directed search for detection and isolation of bioactive actinomycetes, and continued development of improved cultivation methods and molecular technologies for accessing the marine environment promises to provide access to this significant new source of chemical diversity with novel/rare actinomycetes including new species of previously reported actinomycetes.
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Affiliation(s)
- Ramesh Subramani
- Centre for Drug Discovery and Conservation, Institute of Applied Sciences, The University of the South Pacific, Laucala Campus, Suva, Fiji.
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39
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Seipke RF, Kaltenpoth M, Hutchings MI. Streptomycesas symbionts: an emerging and widespread theme? FEMS Microbiol Rev 2012; 36:862-76. [DOI: 10.1111/j.1574-6976.2011.00313.x] [Citation(s) in RCA: 277] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 10/20/2011] [Indexed: 12/24/2022] Open
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Jackson SA, Kennedy J, Morrissey JP, O'Gara F, Dobson ADW. Pyrosequencing reveals diverse and distinct sponge-specific microbial communities in sponges from a single geographical location in Irish waters. MICROBIAL ECOLOGY 2012; 64:105-116. [PMID: 22281804 DOI: 10.1007/s00248-011-0002-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 12/22/2011] [Indexed: 05/31/2023]
Abstract
Marine sponges are host to numerically vast and phylogenetically diverse bacterial communities, with 26 major phyla to date having been found in close association with sponge species worldwide. Analyses of these microbial communities have revealed many sponge-specific novel genera and species. These endosymbiotic microbes are believed to play significant roles in sponge physiology including the production of an array of bioactive secondary metabolites. Here, we report on the use of culture-based and culture-independent (pyrosequencing) techniques to elucidate the bacterial community profiles associated with the marine sponges Raspailia ramosa and Stelligera stuposa sampled from a single geographical location in Irish waters and with ambient seawater. To date, little is known about the microbial ecology of sponges of these genera. Culture isolation grossly underestimated sponge-associated bacterial diversity. Four bacterial phyla (Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria) were represented amongst ~200 isolates, compared with ten phyla found using pyrosequencing. Long average read lengths of ~430 bp (V1-V3 region of 16S rRNA gene) allowed for robust resolution of sequences to genus level. Bacterial OTUs (2,109 total), at 95% sequence similarity, from ten bacterial phyla were recovered from R. ramosa, 349 OTUs were identified in S. stuposa representing eight phyla, while 533 OTUs from six phyla were found in surrounding seawater. Bacterial communities differed significantly between sponge species and the seawater. Analysis of the data for sponge-specific taxa revealed that 2.8% of classified reads from the sponge R. ramosa can be defined as sponge-specific, while 26% of S. stuposa sequences represent sponge-specific bacteria. Novel sponge-specific clusters were identified, whereas the majority of previously reported sponge-specific clusters (e.g. Poribacteria) were absent from these sponge species. This deep and robust analysis provides further evidence that the microbial communities associated with marine sponge species are highly diverse and divergent from one another and appear to be host-selected through as yet unknown processes.
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Affiliation(s)
- Stephen A Jackson
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
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Diversity and biosynthetic potential of culturable actinomycetes associated with marine sponges in the China Seas. Int J Mol Sci 2012; 13:5917-5932. [PMID: 22754340 PMCID: PMC3382808 DOI: 10.3390/ijms13055917] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 04/27/2012] [Accepted: 05/07/2012] [Indexed: 11/23/2022] Open
Abstract
The diversity and secondary metabolite potential of culturable actinomycetes associated with eight different marine sponges collected from the South China Sea and the Yellow sea were investigated. A total of 327 strains were isolated and 108 representative isolates were selected for phylogenetic analysis. Ten families and 13 genera of Actinomycetales were detected, among which five genera represent first records isolated from marine sponges. Oligotrophic medium M5 (water agar) proved to be efficient for selective isolation, and “Micromonospora–Streptomyces” was proposed as the major distribution group of sponge-associated actinomycetes from the China Seas. Ten isolates are likely to represent novel species. Sponge Hymeniacidon perleve was found to contain the highest genus diversity (seven genera) of actinomycetes. Housekeeping gene phylogenetic analyses of the isolates indicated one ubiquitous Micromonospora species, one unique Streptomyces species and one unique Verrucosispora phylogroup. Of the isolates, 27.5% displayed antimicrobial activity, and 91% contained polyketide synthase and/or nonribosomal peptide synthetase genes, indicating that these isolates had a high potential to produce secondary metabolites. The isolates from sponge Axinella sp. contained the highest presence of both antimicrobial activity and NRPS genes, while those from isolation medium DNBA showed the highest presence of antimicrobial activity and PKS I genes.
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Schippers KJ, Sipkema D, Osinga R, Smidt H, Pomponi SA, Martens DE, Wijffels RH. Cultivation of sponges, sponge cells and symbionts: achievements and future prospects. ADVANCES IN MARINE BIOLOGY 2012; 62:273-337. [PMID: 22664125 DOI: 10.1016/b978-0-12-394283-8.00006-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Marine sponges are a rich source of bioactive compounds with pharmaceutical potential. Since biological production is one option to supply materials for early drug development, the main challenge is to establish generic techniques for small-scale production of marine organisms. We analysed the state of the art for cultivation of whole sponges, sponge cells and sponge symbionts. To date, cultivation of whole sponges has been most successful in situ; however, optimal conditions are species specific. The establishment of sponge cell lines has been limited by the inability to obtain an axenic inoculum as well as the lack of knowledge on nutritional requirements in vitro. Approaches to overcome these bottlenecks, including transformation of sponge cells and using media based on yolk, are elaborated. Although a number of bioactive metabolite-producing microorganisms have been isolated from sponges, and it has been suggested that the source of most sponge-derived bioactive compounds is microbial symbionts, cultivation of sponge-specific microorganisms has had limited success. The current genomics revolution provides novel approaches to cultivate these microorganisms.
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Affiliation(s)
- Klaske J Schippers
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands
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Tabares P, Pimentel-Elardo SM, Schirmeister T, Hünig T, Hentschel U. Anti-protease and immunomodulatory activities of bacteria associated with Caribbean sponges. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:883-892. [PMID: 21222136 PMCID: PMC7088305 DOI: 10.1007/s10126-010-9349-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 12/20/2010] [Indexed: 05/30/2023]
Abstract
Marine sponges and their associated bacteria have been proven to be a rich source of novel secondary metabolites with therapeutic usefulness in cancer, infection, and autoimmunity. In this study, 79 strains belonging to 20 genera of the order Actinomycetales and seven strains belonging to two genera of the order Sphingomonadales were cultivated from 18 different Caribbean sponges and identified by 16S rRNA gene sequencing. Seven of these strains are likely to represent novel species. Crude extracts from selected strains were found to exhibit protease inhibition against cathepsins B and L, rhodesain, and falcipain-2 as well as immunomodulatory activities such as induction of cytokine release by human peripheral blood mononuclear cells. These results highlight the significance of marine sponge-associated bacteria to produce bioactive secondary metabolites with therapeutic potential in the treatment of infectious diseases and disorders of the immune system.
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Affiliation(s)
- Paula Tabares
- Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
| | - Sheila M. Pimentel-Elardo
- Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
| | - Tanja Schirmeister
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Thomas Hünig
- Institute for Virology and Immunobiology, University of Würzburg, Versbacherstr. 7, 97078 Würzburg, Germany
| | - Ute Hentschel
- Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
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Kim BY, Kshetrimayum JD, Goodfellow M. Detection, selective isolation and characterisation of Dactylosporangium strains from diverse environmental samples. Syst Appl Microbiol 2011; 34:606-16. [PMID: 21596505 DOI: 10.1016/j.syapm.2011.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/25/2011] [Accepted: 03/28/2011] [Indexed: 10/18/2022]
Abstract
A culture-independent, nested PCR procedure based on genus-specific oligonucleotide primers detected the presence of members of the genus Dactylosporangium in 14 out of 21 diverse environmental samples. Clones generated from the 14 positive environmental samples formed distinct phyletic lines in the dactylosporangial 16S rRNA gene tree. Presumptive dactylosporangiae were isolated from 7 of these samples using a medium designed to be selective for members of the genus Dactylosporangium, namely Streptomyces Isolation Medium supplemented with gentamicin and antifungal antibiotics. One hundred and two out of 219 representative presumptive dactylosporangiae were considered as authentic members of the genus Dactylosporangium as they gave PCR amplification products using the genus-specific primers and had chemical features typical of dactylosporangiae. Representative of the Dactylosporangium isolates formed distinctive phyletic lines in the dactylosporangial 16S rRNA gene tree, contained the non-ribosomal peptide and type-I polyketide synthase genes and inhibited the growth of Bacillus subtilis, Kocuria rhizophila and Staphylococcus aureus strains. It is evident from these results that the genus Dactylosporangium is underspeciated, widely distributed in natural habitats and is a potentially rich source of novel secondary metabolites.
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Affiliation(s)
- Byung-Yong Kim
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Ouyang Y, Wu H, Xie L, Wang G, Dai S, Chen M, Yang K, Li X. A method to type the potential angucycline producers in actinomycetes isolated from marine sponges. Antonie van Leeuwenhoek 2011; 99:807-15. [PMID: 21287404 DOI: 10.1007/s10482-011-9554-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 01/12/2011] [Indexed: 11/25/2022]
Abstract
Angucyclines are aromatic polyketides with antimicrobial, antitumor, antiviral and enzyme inhibition activities. In this study, a new pair of degenerate primers targeting the cyclase genes that are involved in the aromatization of the first and/or second ring of angucycline, were designed and evaluated in a PCR protocol targeting the jadomycin cyclase gene of Streptomyces venezuelae ISP5230. The identity of the target amplicon was confirmed by sequencing. After validation, the primers were used to screen 49 actinomycete isolates from three different marine sponges to identify putative angucycline producers. Seven isolates were positively identified using this method. Sequence analysis of the positive amplicons confirmed their identity as putative angucycline cyclases with sequence highly similar to known angucycline cyclases. Phylogenetic analysis clustered these positives into the angucycline group of cyclases. Furthermore, amplifications of the seven isolates using ketosynthase-specific primers were positive, backing the results using the cyclase primers. Together these results provided strong support for the presence of angucycline biosynthetic genes in these isolates. The specific primer set targeting the cyclase can be used to identify putative angucycline producers among marine actinobacteria, and aid in the discovery of novel angucyclines.
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Affiliation(s)
- Yongchang Ouyang
- Key Laboratory of Marine Bio-resources Sustainable Utilization (LMB-CAS), Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
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Huang J, Xin Y, Cao X, Zhang W. Phylogenetic diversity and characterization of 2-haloacid degrading bacteria from the marine sponge Hymeniacidon perlevis. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-010-0636-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gaidos E, Rusch A, Ilardo M. Ribosomal tag pyrosequencing of DNA and RNA from benthic coral reef microbiota: community spatial structure, rare members and nitrogen-cycling guilds. Environ Microbiol 2010; 13:1138-52. [DOI: 10.1111/j.1462-2920.2010.02392.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Izumi H, Gauthier MEA, Degnan BM, Ng YK, Hewavitharana AK, Shaw PN, Fuerst JA. Diversity of Mycobacterium species from marine sponges and their sensitivity to antagonism by sponge-derived rifamycin-synthesizing actinobacterium in the genus Salinispora. FEMS Microbiol Lett 2010; 313:33-40. [PMID: 20883497 DOI: 10.1111/j.1574-6968.2010.02118.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Eleven isolates of Mycobacterium species as well as an antimycobacterial Salinispora arenicola strain were cultured from the sponge Amphimedon queenslandica. The 16S rRNA, rpoB, and hsp65 genes from these Mycobacterium isolates were sequenced, and phylogenetic analysis of a concatenated alignment showed the formation of a large clade with Mycobacterium poriferae isolated previously from another sponge species. The separation of these Mycobacterium isolates into three species-level groups was evident from sequence similarity and phylogenetic analyses. In addition, an isolate that is phylogenetically related to Mycobacterium tuberculosis was recovered from the sponge Fascaplysinopsis sp. Several different mycobacteria thus appear to co-occur in the same sponge. An actinobacterium closely related to S. arenicola, a known producer of the antimycobacterial rifamycins, was coisolated from the same A. queenslandica specimen from which mycobacteria had been isolated. This Salinispora isolate was confirmed to synthesize rifamycin and displayed inhibitory effects against representatives from two of three Mycobacterium phylotype groups. Evidence for antagonism of sponge-derived Salinispora against sponge-derived Mycobacterium strains from the same sponge specimen and the production of antimycobacterial antibiotics by this Salinispora strain suggest that the synthesis of such antibiotics may have functions in competition between sponge microbial community members.
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Affiliation(s)
- Hiroshi Izumi
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia
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