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Ma C, Xu C, Zhang T, Mu Q, Lv J, Xing Q, Yang Z, Xu Z, Guan Y, Chen C, Ni K, Dai X, Ding W, Hu J, Bao Z, Wang S, Liu P. Tracking the hologenome dynamics in aquatic invertebrates by the holo-2bRAD approach. Commun Biol 2024; 7:827. [PMID: 38972908 PMCID: PMC11228047 DOI: 10.1038/s42003-024-06509-7] [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: 12/21/2023] [Accepted: 06/26/2024] [Indexed: 07/09/2024] Open
Abstract
The "hologenome" concept is an increasingly popular way of thinking about microbiome-host for marine organisms. However, it is challenging to track hologenome dynamics because of the large amount of material, with tracking itself usually resulting in damage or death of the research object. Here we show the simple and efficient holo-2bRAD approach for the tracking of hologenome dynamics in marine invertebrates (i.e., scallop and shrimp) from one holo-2bRAD library. The stable performance of our approach was shown with high genotyping accuracy of 99.91% and a high correlation of r > 0.99 for the species-level profiling of microorganisms. To explore the host-microbe association underlying mass mortality events of bivalve larvae, core microbial species changed with the stages were found, and two potentially associated host SNPs were identified. Overall, our research provides a powerful tool with various advantages (e.g., cost-effective, simple, and applicable for challenging samples) in genetic, ecological, and evolutionary studies.
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Affiliation(s)
- Cen Ma
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, China
| | - Chang Xu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Tianqi Zhang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qianqian Mu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Jia Lv
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Qiang Xing
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, China
| | - Zhihui Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Zhenyuan Xu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Yalin Guan
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chengqin Chen
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Kuo Ni
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Dai
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Institute of Gerontology, Geriatrics Center, University of Michigan, Ann Arbor, MI, USA
| | - Wei Ding
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jingjie Hu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Zhenmin Bao
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Shi Wang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Pingping Liu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
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2
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Stuij TM, Cleary DFR, Rocha RJM, Polónia ARM, Silva DAM, Louvado A, de Voogd NJ, Gomes NCM. Impacts of humic substances, elevated temperature, and UVB radiation on bacterial communities of the marine sponge Chondrilla sp. FEMS Microbiol Ecol 2024; 100:fiae022. [PMID: 38366951 PMCID: PMC10939426 DOI: 10.1093/femsec/fiae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Sponges are abundant components of coral reefs known for their filtration capabilities and intricate interactions with microbes. They play a crucial role in maintaining the ecological balance of coral reefs. Humic substances (HS) affect bacterial communities across terrestrial, freshwater, and marine ecosystems. However, the specific effects of HS on sponge-associated microbial symbionts have largely been neglected. Here, we used a randomized-controlled microcosm setup to investigate the independent and interactive effects of HS, elevated temperature, and UVB radiation on bacterial communities associated with the sponge Chondrilla sp. Our results indicated the presence of a core bacterial community consisting of relatively abundant members, apparently resilient to the tested environmental perturbations, alongside a variable bacterial community. Elevated temperature positively affected the relative abundances of ASVs related to Planctomycetales and members of the families Pseudohongiellaceae and Hyphomonadaceae. HS increased the relative abundances of several ASVs potentially involved in recalcitrant organic matter degradation (e.g., the BD2-11 terrestrial group, Saccharimonadales, and SAR202 clade). There was no significant independent effect of UVB and there were no significant interactive effects of HS, heat, and UVB on bacterial diversity and composition. The significant, independent impact of HS on the composition of sponge bacterial communities suggests that alterations to HS inputs may have cascading effects on adjacent marine ecosystems.
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Affiliation(s)
- Tamara M Stuij
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Daniel F R Cleary
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Rui J M Rocha
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Ana R M Polónia
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Davide A M Silva
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Antonio Louvado
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, the Netherlands
- Institute of Biology (IBL), Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Newton C M Gomes
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
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3
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Luter HM, Laffy P, Flores F, Brinkman DL, Fisher R, Negri AP. Molecular responses of sponge larvae exposed to partially weathered condensate oil. MARINE POLLUTION BULLETIN 2024; 199:115928. [PMID: 38141581 DOI: 10.1016/j.marpolbul.2023.115928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 12/25/2023]
Abstract
Anthropogenic inputs of petroleum hydrocarbons into the marine environment can have long lasting impacts on benthic communities. Sponges form an abundant and diverse component of benthic habitats, contributing a variety of important functional roles; however, their responses to petroleum hydrocarbons are largely unknown. This study combined a traditional ecotoxicological experimental design and endpoint with global gene expression profiling and microbial indicator species analysis to examine the effects of a water accommodated fraction (WAF) of condensate oil on a common Indo-Pacific sponge, Phyllospongia foliascens. A no significant effect concentration (N(S)EC) of 2.1 % WAF was obtained for larval settlement, while gene-specific (N(S)EC) thresholds ranged from 3.4 % to 8.8 % WAF. Significant shifts in global gene expression were identified at WAF treatments ≥20 %, with larvae exposed to 100 % WAF most responsive. Results from this study provide an example on the incorporation of non-conventional molecular and microbiological responses into ecotoxicological studies on petroleum hydrocarbons.
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Affiliation(s)
- Heidi M Luter
- Australian Institute of Marine Science, Townsville 4810, QLD, Australia; AIMS@JCU, Division of Research & Innovation, James Cook University, Townsville 4811, QLD, Australia.
| | - Patrick Laffy
- Australian Institute of Marine Science, Townsville 4810, QLD, Australia; AIMS@JCU, Division of Research & Innovation, James Cook University, Townsville 4811, QLD, Australia
| | - Florita Flores
- Australian Institute of Marine Science, Townsville 4810, QLD, Australia
| | - Diane L Brinkman
- Australian Institute of Marine Science, Townsville 4810, QLD, Australia
| | - Rebecca Fisher
- Australian Institute of Marine Science, Crawley 6009, WA, Australia
| | - Andrew P Negri
- Australian Institute of Marine Science, Townsville 4810, QLD, Australia; AIMS@JCU, Division of Research & Innovation, James Cook University, Townsville 4811, QLD, Australia
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4
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Nguyen VH, Wemheuer B, Song W, Bennett H, Palladino G, Burgsdorf I, Sizikov S, Steindler L, Webster NS, Thomas T. Functional characterization and taxonomic classification of novel gammaproteobacterial diversity in sponges. Syst Appl Microbiol 2023; 46:126401. [PMID: 36774720 DOI: 10.1016/j.syapm.2023.126401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 01/18/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023]
Abstract
Sponges harbour exceptionally diverse microbial communities, whose members are largely uncultured. The class Gammaproteobacteria often dominates the microbial communities of various sponge species, but most of its diversity remains functional and taxonomically uncharacterised. Here we reconstructed and characterised 32 metagenome-assembled genomes (MAGs) derived from three sponge species. These MAGs represent ten novel species and belong to seven orders, of which one is new. We propose nomenclature for all these taxa. These new species comprise sponge-specific bacteria with varying levels of host specificity. Functional gene profiling highlights significant differences in metabolic capabilities across the ten species, though each also often exhibited a large degree of metabolic diversity involving various nitrogen- and sulfur-based compounds. The genomic features of the ten species suggest they have evolved to form symbiotic interaction with their hosts or are well-adapted to survive within the sponge environment. These Gammaproteobacteria are proposed to scavenge substrates from the host environment, including metabolites or cellular components of the sponge. Their diverse metabolic capabilities may allow for efficient cycling of organic matter in the sponge environment, potentially to the benefit of the host and other symbionts.
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Affiliation(s)
- Viet Hung Nguyen
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Holly Bennett
- Australian Institute of Marine Science, Townsville, Queensland, Australia; Cawthron Institute, Nelson, New Zealand
| | - Giorgia Palladino
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia; Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | | | | | | | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia; Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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5
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Bulleri F, Pretti C, Bertolino M, Magri M, Pittaluga GB, Sicurelli D, Tardelli F, Manzini C, Vannini C, Verani M, Federigi I, Zampieri G, De Marchi L. Adding functions to marine infrastructure: Pollutant accumulation, physiological and microbiome changes in sponges attached to floating pontoons inside marinas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157773. [PMID: 35926598 DOI: 10.1016/j.scitotenv.2022.157773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
The rate of introduction of man-made habitats in coastal environments is growing at an unprecedented pace, as a consequence of the expansion of urban areas. Floating installations, due to their unique hydrodynamic features, are able to provide great opportunities for enhancing water detoxification through the use of sessile, filtering organisms. We assessed whether the application of sponges to floating pontoons could function as a tool for biomonitoring organic and inorganic pollutants and for improving water quality inside a moderately contaminated marina in the NW Mediterranean. Fragments of two common Mediterranean sponges (Petrosia (Petrosia) ficiformis and Ircinia oros) were fixed to either suspended natural fibre nets beneath a floating pontoon or to metal frames deployed on the sea bottom. We assessed the accumulation of organic and inorganic contaminants in sponge fragments and, in order to provide an insight into their health status, we examined changes in their metabolic and oxidative stress responses and associated microbiomes. Fragments of both sponge species filtered out pollutants from seawater on both support types, but generally showed a better physiological and metabolic status when fixed to nets underneath the pontoon than to bottom frames. P. (P) ficiformis maintained a more efficient metabolism and exhibited a lower physiological stress levels and higher stability of the associated microbiome in comparison with I. oros. Our study suggests that the application of sponges to floating pontoon represents a promising nature-based solution to improve the ecological value of urban environments.
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Affiliation(s)
- Fabio Bulleri
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Carlo Pretti
- Department of Veterinary Sciences, University of Pisa, Pisa, Italy; Consorzio per il Centro Interuniversitario di Biologia Marina ed Ecologia Applicata "G. Bacci" (CIBM), Livorno, Italy
| | - Marco Bertolino
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Genova, Italy
| | | | - Gianluca Bontà Pittaluga
- Consorzio per il Centro Interuniversitario di Biologia Marina ed Ecologia Applicata "G. Bacci" (CIBM), Livorno, Italy
| | | | - Federica Tardelli
- Consorzio per il Centro Interuniversitario di Biologia Marina ed Ecologia Applicata "G. Bacci" (CIBM), Livorno, Italy
| | - Chiara Manzini
- Consorzio per il Centro Interuniversitario di Biologia Marina ed Ecologia Applicata "G. Bacci" (CIBM), Livorno, Italy
| | | | - Marco Verani
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | | | | | - Lucia De Marchi
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy; Consorzio per il Centro Interuniversitario di Biologia Marina ed Ecologia Applicata "G. Bacci" (CIBM), Livorno, Italy.
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6
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Bibi F, Azhar EI. Analysis of bacterial communities in sponges and coral inhabiting Red Sea, using barcoded 454 pyrosequencing. Saudi J Biol Sci 2020; 28:847-854. [PMID: 33424375 PMCID: PMC7783839 DOI: 10.1016/j.sjbs.2020.11.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 11/18/2022] Open
Abstract
Microbial communities are linked with marine sponge are diverse in their structure and function. Our understanding of the sponge-associated microbial diversity is limited especially from Red Sea in Saudi Arabia where few species of sponges have been studied. Here we used pyrosequencing to study two marine sponges and coral species sampled from Obhur region from Red sea in Jeddah. A total of 168 operational taxonomic units (OTUs) were identified from Haliclona caerulea, Stylissa carteri and Rhytisma fulvum. Taxonomic identification of tag sequences of 16S ribosomal RNA revealed 6 different bacterial phyla and 9 different classes. A proportion of unclassified reads were was also observed in sponges and coral sample. We found diverse bacterial communities associated with two sponges and a coral sample. Diversity and richness estimates based on OUTs revealed that sponge H. caerulea had significantly high bacterial diversity. The identified OTUs showed unique clustering in three sponge samples as revealed by Principal coordinate analysis (PCoA). Proteobacteria (88-95%) was dominant phyla alonwith Bacteroidetes, Planctomycetes, Cyanobacteria, Firmicutes and Nitrospirae. Seventeen different genera were identified where genus Pseudoalteromonas was dominant in all three samples. This is first study to assess bacterial communities of sponge and coral sample that have never been studied before to unravel their microbial communities using 454-pyrosequencing method.
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Affiliation(s)
- Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
- Corresponding author at: Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
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7
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Luter HM, Andersen M, Versteegen E, Laffy P, Uthicke S, Bell JJ, Webster NS. Cross-generational effects of climate change on the microbiome of a photosynthetic sponge. Environ Microbiol 2020; 22:4732-4744. [PMID: 32869905 DOI: 10.1111/1462-2920.15222] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/13/2020] [Accepted: 08/27/2020] [Indexed: 01/04/2023]
Abstract
Coral reefs are facing increasing pressure from rising seawater temperatures and ocean acidification. Sponges have been proposed as possible winners in the face of climate change; however, little is known about the mechanisms underpinning their predicted tolerance. Here we assessed whether microbiome-mediated cross-generational acclimatization could enable the photosynthetic sponge Carteriospongia foliascens to survive under future climate scenarios. To achieve this, we first established the potential for vertical (cross-generational) transmission of symbionts. Sixty-four amplicon sequence variants accounting for >90% of the total C. foliascens microbial community were present across adult, larval and juvenile life stages, showing that a large proportion of the microbiome is vertically acquired and maintained. When C. foliascens were exposed to climate scenarios projected for 2050 and 2100, the host remained visibly unaffected (i.e. no necrosis/bleaching) and the overall microbiome was not significantly different amongst treatments in adult tissue, the respective larvae or recruits transplanted amongst climate treatments. However, indicator species analysis revealed that parental exposure to future climate scenarios altered the presence and abundance of a small suite of microbial taxa in the recruits, thereby revealing the potential for microbiome-mediated cross-generational acclimatization through both symbiont shuffling and symbiont switching within a vertically acquired microbiome.
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Affiliation(s)
- Heidi M Luter
- Australian Institute of Marine Science, QLD, Townsville, Australia.,School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Maria Andersen
- Australian Institute of Marine Science, QLD, Townsville, Australia.,AIMS@JCU, QLD, Townsville, Australia
| | - Elien Versteegen
- Australian Institute of Marine Science, QLD, Townsville, Australia.,AIMS@JCU, QLD, Townsville, Australia
| | - Patrick Laffy
- Australian Institute of Marine Science, QLD, Townsville, Australia
| | - Sven Uthicke
- Australian Institute of Marine Science, QLD, Townsville, Australia
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Nicole S Webster
- Australian Institute of Marine Science, QLD, Townsville, Australia.,Australian Centre for Ecogenomics, University of Queensland, QLD, Brisbane, Australia
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Kohn T, Wiegand S, Boedeker C, Rast P, Heuer A, Jetten MSM, Schüler M, Becker S, Rohde C, Müller RW, Brümmer F, Rohde M, Engelhardt H, Jogler M, Jogler C. Planctopirus ephydatiae, a novel Planctomycete isolated from a freshwater sponge. Syst Appl Microbiol 2019; 43:126022. [PMID: 31785948 DOI: 10.1016/j.syapm.2019.126022] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 01/28/2023]
Abstract
The microbiome of freshwater sponges is rarely studied, and not a single novel bacterial species has been isolated and subsequently characterized from a freshwater sponge to date. A previous study showed that 14.4% of the microbiome from Ephydatia fluviatilis belong to the phylum Planctomycetes. Therefore, we sampled an Ephydatia sponge from a freshwater lake and employed enrichment techniques targeting bacteria from the phylum Planctomycetes. The obtained strain spb1T was subject to genomic and phenomic characterization and found to represent a novel planctomycetal species proposed as Planctopirus ephydatiae sp. nov. (DSM 106606 = CECT 9866). In the process of differentiating spb1T from its next relative Planctopirus limnophila DSM 3776T, we identified and characterized the first phage - Planctopirus phage vB_PlimS_J1 - infecting planctomycetes that was only mentioned anecdotally before. Interestingly, classical chemotaxonomic methods would have failed to distinguish Planctopirus ephydatiae strain spb1T from Planctopirus limnophila DSM 3776T. Our findings demonstrate and underpin the need for whole genome-based taxonomy to detect and differentiate planctomycetal species.
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Affiliation(s)
- T Kohn
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - S Wiegand
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - C Boedeker
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - P Rast
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - A Heuer
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - M S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - M Schüler
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - S Becker
- University of Veterinary Medicine Hannover, Germany
| | - C Rohde
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - R-W Müller
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Germany
| | - F Brümmer
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Germany
| | - M Rohde
- Central Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), Braunschweig, Germany
| | - H Engelhardt
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - M Jogler
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - C Jogler
- Department of Microbiology, Radboud University, Nijmegen, Netherlands; Department of Microbial Interactions, Friedrich Schiller Universität Jena, Germany.
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9
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Turon M, Cáliz J, Triadó-Margarit X, Casamayor EO, Uriz MJ. Sponges and Their Microbiomes Show Similar Community Metrics Across Impacted and Well-Preserved Reefs. Front Microbiol 2019; 10:1961. [PMID: 31507568 PMCID: PMC6713927 DOI: 10.3389/fmicb.2019.01961] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/09/2019] [Indexed: 11/13/2022] Open
Abstract
Sponge diversity has been reported to decrease from well-preserved to polluted environments, but whether diversity and intra-species variation of their associated microbiomes also change as function of environmental quality remains unknown. Our study aimed to assess whether microbiome composition and structure are related to the proliferation of some sponges and not others under degraded conditions. We characterized the most frequent sponges and their associated bacteria in two close areas (impacted and well-preserved) of Nha Trang Bay (Indo-Pacific). Sponge assemblages were richer and more diverse in the well-preserved reefs, but more abundant (individuals/m. transect) in the impacted environments, where two species (Clathria reinwardti and Amphimedon paraviridis) dominated. Sponge microbiomes from the polluted zones had, in general, lower bacterial diversity and core size and consequently, higher intra-species dispersion than microbiomes of sponges from the well-preserved environments. Microbial communities reflect the reduction of diversity and richness shown by their host sponges. In this sense, sponges with less complex and more variable microbiomes proliferate under degraded environmental conditions, following the ecological paradigm that negatively correlates community diversity and environmental degradation. Thereby, the diversity and structure of sponge microbiomes might indirectly determine the presence and proliferation of sponge species in certain habitats.
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Affiliation(s)
| | | | | | | | - Maria J. Uriz
- Centre d’Estudis Avançats de Blanes, CEAB-CSIC, Girona, Spain
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10
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Feng G, Zhang F, Banakar S, Karlep L, Li Z. Analysis of functional gene transcripts suggests active CO2 assimilation and CO oxidation by diverse bacteria in marine sponges. FEMS Microbiol Ecol 2019; 95:5513993. [DOI: 10.1093/femsec/fiz087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/08/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Guofang Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai 200240, China
| | - Fengli Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai 200240, China
| | - Shivakumar Banakar
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai 200240, China
| | - Liisi Karlep
- Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Ehitajate 5, Tallinn 19086, Estonia
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai 200240, China
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11
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Yang Q, Franco CMM, Zhang W. Uncovering the hidden marine sponge microbiome by applying a multi-primer approach. Sci Rep 2019; 9:6214. [PMID: 30996336 PMCID: PMC6470215 DOI: 10.1038/s41598-019-42694-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/05/2019] [Indexed: 02/07/2023] Open
Abstract
Marine sponges (phylum Porifera) are hosts to microorganisms that make up to 40–60% of the mesohyl volume. The challenge is to characterise this microbial diversity more comprehensively. To accomplish this, a new method was for the first time proposed to obtain sequence coverage of all the variable regions of the 16S rRNA gene to analyze the amplicon-based microbiomes of four representative sponge species belonging to different orders. The five primer sets targeting nine variable regions of the 16S rRNA gene revealed a significant increase in microbiome coverage of 29.5% of phylum level OTUs and 35.5% class level OTUs compared to the community revealed by the commonly used V4 region-specific primer set alone. Among the resulting OTUs, 52.6% and 61.3% were unaffiliated, including candidate OTUs, at the phylum and class levels, respectively, which demonstrated a substantially superior performance in uncovering taxonomic ‘blind spots’. Overall, a more complete sponge microbiome profile was achieved by this multi-primer approach, given the significant improvement of microbial taxonomic coverage and the enhanced capacity to uncover novel microbial taxa. This multi-primer approach represents a fundamental and practical change from the conventional single primer set amplicon-based microbiome approach, and can be broadly applicable to other microbiome studies.
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Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, 5042, Australia.,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, 5042, Australia
| | - Wei Zhang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, 5042, Australia. .,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
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12
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Wooster MK, Voigt O, Erpenbeck D, Wörheide G, Berumen ML. Sponges of the Red Sea. CORAL REEFS OF THE RED SEA 2019. [DOI: 10.1007/978-3-030-05802-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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13
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Najafi A, Moradinasab M, Seyedabadi M, Haghighi MA, Nabipour I. First Molecular Identification of Symbiotic Archaea in a Sponge Collected from the Persian Gulf, Iran. Open Microbiol J 2018; 12:323-332. [PMID: 30450139 PMCID: PMC6198412 DOI: 10.2174/1874285801812010323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/21/2018] [Accepted: 09/23/2018] [Indexed: 11/22/2022] Open
Abstract
Background Marine sponges are associated with numerically vast and phylogenetically diverse microbial communities at different geographical locations. However, little is known about the archaeal diversity of sponges in the Persian Gulf. The present study was aimed to identify the symbiotic archaea with a sponge species gathered from the Persian Gulf, Iran. Methods Sponge sample was collected from a depth of 3 m offshore Bushehr, Persian Gulf, Iran. Metagenomic DNA was extracted using a hexadecyl trimethyl ammonium bromide (CTAB) method. The COI mtDNA marker was used for molecular taxonomy identification of sponge sample. Also, symbiotic archaea were identified using the culture-independent analysis of the 16S rRNA gene and PCR- cloning. Results In this study, analysis of multilocus DNA marker and morphological characteristics revealed that the sponge species belonged to Chondrilla australiensis isolate PG_BU4. PCR cloning and sequencing showed that all of the sequences of archaeal 16S rRNA gene libraries clustered into the uncultured archaeal group. Conclusion The present study is the first report of the presence of the genus of Chondrilla in the Persian Gulf. Traditional taxonomy methods, when used along with molecular techniques, could play a significant role in the accurate taxonomy of sponges. Also, the uncultured archaea may promise a potential source for bioactive compounds. Further functional studies are needed to explore the role of the sponge-associated uncultured archaea as a part of the marine symbiosis.
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Affiliation(s)
- Akram Najafi
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Maryam Moradinasab
- The Persian Gulf Tropical Medicine Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohammad Seyedabadi
- Department of Pharmacology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohammad A Haghighi
- Department of Microbiology and Parasitology, Faculty of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
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14
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Wiegand S, Jogler M, Jogler C. On the maverick Planctomycetes. FEMS Microbiol Rev 2018; 42:739-760. [DOI: 10.1093/femsre/fuy029] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/22/2018] [Indexed: 01/01/2023] Open
Affiliation(s)
- Sandra Wiegand
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Mareike Jogler
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
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15
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Najafi A, Moradinasab M, Nabipour I. First Record of Microbiomes of Sponges Collected From the Persian Gulf, Using Tag Pyrosequencing. Front Microbiol 2018; 9:1500. [PMID: 30034382 PMCID: PMC6043863 DOI: 10.3389/fmicb.2018.01500] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
The Persian Gulf is a special habitat of marine sponges whose bacterial communities are under-investigated. Recently, next-generation sequencing technology has comprehensively improved the knowledge of marine sponge-associated bacteria. For the first time, this study aimed to evaluate the diversity of the Persian Gulf sponge-associated bacteria using tag pyrosequencing in Iran. In this study, 10 sponge samples from 6 different taxonomic orders were collected from the Persian Gulf using SCUBA diving. The diversity of the bacteria associated with the marine sponges was investigated using the 16S rRNA gene PCR-tagged pyrosequencing method. A total of 68,628 high-quality sequences were obtained and clustered at a 97% similarity into 724 unique operational taxonomic units (OTUs), representing 17 bacterial phyla. Cyanobacteria was the most abundant phylum in the sponges, followed by Proteobacteria, Chloroflexi, Acidobacteria, and Actinobacteria. Other phyla were detected as minor groups of bacteria. Bacterial community richness, Shannon, and Simpson indices revealed the highest diversity in sponge S11 (Dictyoceratida sp.) compared to other sponges. This study showed a diverse structure of bacterial communities associated with the Persian Gulf sponges. The dominance of Cyanobacteria may suggest an ecological importance of this phylum in the Persian Gulf sponges.
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Affiliation(s)
- Akram Najafi
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Maryam Moradinasab
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
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16
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Ramsby BD, Hoogenboom MO, Whalan S, Webster NS. Elevated seawater temperature disrupts the microbiome of an ecologically important bioeroding sponge. Mol Ecol 2018; 27:2124-2137. [PMID: 29473977 DOI: 10.1111/mec.14544] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 01/08/2023]
Abstract
Bioeroding sponges break down calcium carbonate substratum, including coral skeleton, and their capacity for reef erosion is expected to increase in warmer and more acidic oceans. However, elevated temperature can disrupt the functionally important microbial symbionts of some sponge species, often with adverse consequences for host health. Here, we provide the first detailed description of the microbial community of the bioeroding sponge Cliona orientalis and assess how the community responds to seawater temperatures incrementally increasing from 23°C to 32°C. The microbiome, identified using 16S rRNA gene sequencing, was dominated by Alphaproteobacteria, including a single operational taxonomic unit (OTU; Rhodothalassium sp.) that represented 21% of all sequences. The "core" microbial community (taxa present in >80% of samples) included putative nitrogen fixers and ammonia oxidizers, suggesting that symbiotic nitrogen metabolism may be a key function of the C. orientalis holobiont. The C. orientalis microbiome was generally stable at temperatures up to 27°C; however, a community shift occurred at 29°C, including changes in the relative abundance and turnover of microbial OTUs. Notably, this microbial shift occurred at a lower temperature than the 32°C threshold that induced sponge bleaching, indicating that changes in the microbiome may play a role in the destabilization of the C. orientalis holobiont. C. orientalis failed to regain Symbiodinium or restore its baseline microbial community following bleaching, suggesting that the sponge has limited ability to recover from extreme thermal exposure, at least under aquarium conditions.
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Affiliation(s)
- Blake D Ramsby
- College of Science and Engineering and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Qld, Australia
| | - Mia O Hoogenboom
- College of Science and Engineering and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia
| | - Steve Whalan
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Qld, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld, Australia
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17
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Gao ZM, Zhou GW, Huang H, Wang Y. The Cyanobacteria-Dominated Sponge Dactylospongia elegans in the South China Sea: Prokaryotic Community and Metagenomic Insights. Front Microbiol 2017; 8:1387. [PMID: 28790992 PMCID: PMC5524777 DOI: 10.3389/fmicb.2017.01387] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/10/2017] [Indexed: 11/25/2022] Open
Abstract
The South China Sea is a special reservoir of sponges of which prokaryotic communities are less studied. Here, a new record of the sponge Dactylospongia elegans is reported near the coast of Jinqing Island in the South China Sea, and its prokaryotic community is comprehensively investigated. Sponge specimens displayed lower microbial diversity compared with surrounding seawater. At the phylum level, prokaryotic communities were consistently dominated by Proteobacteria, followed by Cyanobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Gemmatimonadetes, Thaumarchaeota, and Poribacteria. Operational taxonomic unit (OTU) analysis alternatively showed that the most abundant symbiont was the sponge-specific cyanobacterial species “Candidatus Synechococcus spongiarum,” followed by OTUs belonging to the unidentified Chloroflexi and Acidobacteria. Phylogenetic tree based on 16S-23S internal transcribed spacer regions indicated that the dominated cyanobacterial OTU represented a new clade of “Ca. Synechococcus spongiarum.” More reliable metagenomic data further revealed that poribacterial symbionts were highly abundant and only secondary to the cyanobacterial symbiont. One draft genome for each of the Cyanobacteria, Chloroflexi and Acidobacteria and three poribacterial genomes were extracted from the metagenomes. Among them, genomes affiliated with the Chloroflexi and Acidobacteria were reported for the first time in sponge symbionts. Eukaryotic-like domains were found in all the binned genomes, indicating their potential symbiotic roles with the sponge host. The high quality of the six recovered genomes of sponge symbionts from the sponge D. elegans makes it possible to understand their symbiotic roles and interactions with the sponge host as well as among one another.
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Affiliation(s)
- Zhao-Ming Gao
- Institute of Deep Sea Science and Engineering, Chinese Academy of SciencesSanya, China
| | - Guo-Wei Zhou
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhou, China
| | - Hui Huang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhou, China
| | - Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of SciencesSanya, China
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18
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Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform. PLoS One 2017; 12:e0176716. [PMID: 28453559 PMCID: PMC5409056 DOI: 10.1371/journal.pone.0176716] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/15/2017] [Indexed: 12/12/2022] Open
Abstract
Illumina’s MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1–3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and with caution. For example, including technical replicates, removing spurious sequences and unrepresentative OTUs, using a clustering method with a high stringency for OTU generation, estimating treatment effects at higher taxonomic levels, and adapting the unique molecular identifier (UMI) and other newly developed methods to lower PCR and sequencing error and to identify true low abundance rare species all can increase reproducibility.
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19
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Blanquer A, Uriz MJ, Cebrian E, Galand PE. Snapshot of a Bacterial Microbiome Shift during the Early Symptoms of a Massive Sponge Die-Off in the Western Mediterranean. Front Microbiol 2016; 7:752. [PMID: 27242765 PMCID: PMC4871885 DOI: 10.3389/fmicb.2016.00752] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 05/03/2016] [Indexed: 02/01/2023] Open
Abstract
Ocean warming is affecting marine benthic ecosystems through mass mortality events that involve marine invertebrates, in particular bivalves, corals, and sponges. Among these events, extensive die-offs of Ircinia fasciculata sponges have been recurrently reported in western Mediterranean. The goal of our study was to test whether the temperature-related mass sponge die-offs were associated with or preceded by an early unbalanced bacterial microbiome in the sponge tissues. We took advantage of the early detection of disease and compared the microbiomes of healthy vs. early diseased I. fasciculata tissues. Our results showed a microbiome shift in early diseased tissues. The abundance of Gammaproteobacteria and Acidobacteria increased and that of Deltaproteobacteria decreased in diseased vs. healthy tissues. The change in community composition was also noticeable at the operational taxonomic unit (OTU) level. Diseased tissues contained more bacterial sequences previously identified in injured or stressed sponges and corals than healthy tissues. Bacterial diversity increased significantly in diseased tissues, which contained a higher number of low abundance OTUs. Our results do not support the hypothesis of one particular pathogen, whether a Vibrio or any other bacteria, triggering the Northwestern Mediterranean mass mortalities of I. fasciculata. Our data rather suggest an early disruption of the bacterial microbiome balance in healthy sponges through a shift in OTU abundances, and the purported consequent decline of the sponge fitness and resistance to infections. Opportunistic bacteria could colonize the sponge tissues, taking benefit of the sponge weakness, before one or more virulent pathogens might proliferate ending in the mass sponge die-off.
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Affiliation(s)
- Andrea Blanquer
- Centre d'Estudis Avançats de Blanes, Consejo Superior de Investigaciones Científicas Girona, Spain
| | - Maria J Uriz
- Centre d'Estudis Avançats de Blanes, Consejo Superior de Investigaciones Científicas Girona, Spain
| | - Emma Cebrian
- Centre d'Estudis Avançats de Blanes, Consejo Superior de Investigaciones CientíficasGirona, Spain; Departament de Ciències Ambientals, Facultat de Ciències, Universitat de GironaGirona, Spain
| | - Pierre E Galand
- Laboratoire d'Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls, Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, Centre National de la Recherche Scientifique Paris, France
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20
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Abstract
The Planctomycetes genus Gemmata is represented by both uncultured organisms and cultured Gemmata obscuriglobus and 'Gemmata massiliana' organisms. Their plasmidless 9.2 Mb genomes encode a complex cell plan, cell signaling capacities, antibiotic and trace metal resistance and multidrug resistance efflux pumps. As they lack iron metabolism pathways, they are fastidious. Gemmata spp. are mainly found in aquatic and soil environments but have also been found in hospital water networks in close proximity to patients, in animals, on human skin, the gut microbiota and in the blood of aplastic leukemic patients. Due to their panoply of attack and defense mechanisms and their recently demonstrated association with humans, the potential of Gemmata organisms to behave as opportunistic pathogens should be more widely recognized.
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Affiliation(s)
- Rita Aghnatios
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. Faculté de Médecine, Marseille 13005, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. Faculté de Médecine, Marseille 13005, France
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21
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Luter HM, Widder S, Botté ES, Abdul Wahab M, Whalan S, Moitinho-Silva L, Thomas T, Webster NS. Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens. PeerJ 2015; 3:e1435. [PMID: 26713229 PMCID: PMC4690404 DOI: 10.7717/peerj.1435] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/03/2015] [Indexed: 01/07/2023] Open
Abstract
Sponges are well known for hosting dense and diverse microbial communities, but how these associations vary with biogeography and environment is less clear. Here we compared the microbiome of an ecologically important sponge species, Carteriospongia foliascens, over a large geographic area and identified environmental factors likely responsible for driving microbial community differences between inshore and offshore locations using co-occurrence networks (NWs). The microbiome of C. foliascens exhibited exceptionally high microbial richness, with more than 9,000 OTUs identified at 97% sequence similarity. A large biogeographic signal was evident at the OTU level despite similar phyla level diversity being observed across all geographic locations. The C. foliascens bacterial community was primarily comprised of Gammaproteobacteria (34.2% ± 3.4%) and Cyanobacteria (32.2% ± 3.5%), with lower abundances of Alphaproteobacteria, Bacteroidetes, unidentified Proteobacteria, Actinobacteria, Acidobacteria and Deltaproteobacteria. Co-occurrence NWs revealed a consistent increase in the proportion of Cyanobacteria over Bacteroidetes between turbid inshore and oligotrophic offshore locations, suggesting that the specialist microbiome of C. foliascens is driven by environmental factors.
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Affiliation(s)
- Heidi M Luter
- NAMRA and the Research Institute for the Environment & Livelihoods, Charles Darwin University , Darwin, Northern Territory , Australia
| | - Stefanie Widder
- CUBE, Department of Microbiology and Ecosystem Science, University of Vienna , Vienna , Austria
| | - Emmanuelle S Botté
- Australian Institute of Marine Science , Townsville, Queensland , Australia
| | | | - Stephen Whalan
- Marine Ecology Research Centre, School of Environment, Science and Engineering,Southern Cross University , Lismore, New South Wales , Australia
| | - Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences,University of New South Wales , Sydney, New South Wales , Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences,University of New South Wales , Sydney, New South Wales , Australia
| | - Nicole S Webster
- Australian Institute of Marine Science , Townsville, Queensland , Australia
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22
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Alex A, Antunes A. Whole Genome Sequencing of the Symbiont Pseudovibrio sp. from the Intertidal Marine Sponge Polymastia penicillus Revealed a Gene Repertoire for Host-Switching Permissive Lifestyle. Genome Biol Evol 2015; 7:3022-32. [PMID: 26519859 PMCID: PMC5635592 DOI: 10.1093/gbe/evv199] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Sponges harbor a complex consortium of microbial communities living in symbiotic relationship benefiting each other through the integration of metabolites. The mechanisms influencing a successful microbial association with a sponge partner are yet to be fully understood. Here, we sequenced the genome of Pseudovibrio sp. POLY-S9 strain isolated from the intertidal marine sponge Polymastia penicillus sampled from the Atlantic coast of Portugal to identify the genomic features favoring the symbiotic relationship. The draft genome revealed an exceptionally large genome size of 6.6 Mbp compared with the previously reported genomes of the genus Pseudovibrio isolated from a coral and a sponge larva. Our genomic study detected the presence of several biosynthetic gene clusters—polyketide synthase, nonribosomal peptide synthetase and siderophore—affirming the potential ability of the genus Pseudovibrio to produce a wide variety of metabolic compounds. Moreover, we identified a repertoire of genes encoding adaptive symbioses factors (eukaryotic-like proteins), such as the ankyrin repeats, tetratrico peptide repeats, and Sel1 repeats that improve the attachment to the eukaryotic hosts and the avoidance of the host’s immune response. The genome also harbored a large number of mobile elements (∼5%) and gene transfer agents, which explains the massive genome expansion and suggests a possible mechanism of horizontal gene transfer. In conclusion, the genome of POLY-S9 exhibited an increase in size, number of mobile DNA, multiple metabolite gene clusters, and secretion systems, likely to influence the genome diversification and the evolvability.
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Affiliation(s)
- Anoop Alex
- CIMAR/CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Agostinho Antunes
- CIMAR/CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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23
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Abstract
Metagenomics has significantly advanced the field of marine microbial ecology, revealing the vast diversity of previously unknown microbial life forms in different marine niches. The tremendous amount of data generated has enabled identification of a large number of microbial genes (metagenomes), their community interactions, adaptation mechanisms, and their potential applications in pharmaceutical and biotechnology-based industries. Comparative metagenomics reveals that microbial diversity is a function of the local environment, meaning that unique or unusual environments typically harbor novel microbial species with unique genes and metabolic pathways. The Red Sea has an abundance of unique characteristics; however, its microbiota is one of the least studied among marine environments. The Red Sea harbors approximately 25 hot anoxic brine pools, plus a vibrant coral reef ecosystem. Physiochemical studies describe the Red Sea as an oligotrophic environment that contains one of the warmest and saltiest waters in the world with year-round high UV radiations. These characteristics are believed to have shaped the evolution of microbial communities in the Red Sea. Over-representation of genes involved in DNA repair, high-intensity light responses, and osmoregulation were found in the Red Sea metagenomic databases suggesting acquisition of specific environmental adaptation by the Red Sea microbiota. The Red Sea brine pools harbor a diverse range of halophilic and thermophilic bacterial and archaeal communities, which are potential sources of enzymes for pharmaceutical and biotechnology-based application. Understanding the mechanisms of these adaptations and their function within the larger ecosystem could also prove useful in light of predicted global warming scenarios where global ocean temperatures are expected to rise by 1-3°C in the next few decades. In this review, we provide an overview of the published metagenomic studies that were conducted in the Red Sea, and the bio-prospecting potential of the Red Sea microbiota. Furthermore, we discuss the limitations of the previous studies and the need for generating a large and representative metagenomic database of the Red Sea to help establish a dynamic model of the Red Sea microbiota.
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Affiliation(s)
- Hayedeh Behzad
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal 23955-6900, Saudi Arabia
| | - Martin Augusto Ibarra
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal 23955-6900, Saudi Arabia
| | - Katsuhiko Mineta
- King Abdullah University of Science and Technology, Computer, Electrical, and Mathematical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal 23955-6900, Saudi Arabia; King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.
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24
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Yang Q, Franco CMM, Zhang W. Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification. Appl Microbiol Biotechnol 2015; 99:8731-40. [PMID: 26245685 DOI: 10.1007/s00253-015-6875-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/16/2015] [Accepted: 07/21/2015] [Indexed: 11/26/2022]
Abstract
Experiments were designed to validate the two common DNA extraction protocols (CTAB-based method and DNeasy Blood & Tissue Kit) used to effectively recover actinobacterial DNA from sponge samples in order to study the sponge-associated actinobacterial diversity. This was done by artificially spiking sponge samples with actinobacteria (spores, mycelia and a combination of the two). Our results demonstrated that both DNA extraction methods were effective in obtaining DNA from the sponge samples as well as the sponge samples spiked with different amounts of actinobacteria. However, it was noted that in the presence of the sponge, the bacterial 16S rRNA gene could not be amplified unless the combined DNA template was diluted. To test the hypothesis that the extracted sponge DNA contained inhibitors, dilutions of the DNA extracts were tested for six sponge species representing five orders. The results suggested that the inhibitors were co-extracted with the sponge DNA, and a high dilution of this DNA was required for the successful PCR amplification for most of the samples. The optimized PCR conditions, including primer selection, PCR reaction system and program optimization, further improved the PCR performance. However, no single PCR condition was found to be suitable for the diverse sponge samples using various primer sets. These results highlight for the first time that the DNA extraction methods used are effective in obtaining actinobacterial DNA and that the presence of inhibitors in the sponge DNA requires high dilution coupled with fine tuning of the PCR conditions to achieve success in the study of sponge-associated actinobacterial diversity.
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Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia.
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia.
| | - Wei Zhang
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia.
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia.
- Centre for Marine Drugs, Renji Hospital, Shanghai Jiaotong University, Shanghai, 200240, China.
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Gao ZM, Wang Y, Tian RM, Lee OO, Wong YH, Batang ZB, Al-Suwailem A, Lafi FF, Bajic VB, Qian PY. Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora. PeerJ 2015; 3:e890. [PMID: 26082867 PMCID: PMC4465955 DOI: 10.7717/peerj.890] [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: 11/30/2014] [Accepted: 03/23/2015] [Indexed: 11/20/2022] Open
Abstract
Sponge diseases have been widely reported, yet the causal factors and major pathogenic microbes remain elusive. In this study, two individuals of the sponge Crella cyathophora in total that showed similar disease-like characteristics were collected from two different locations along the Red Sea coast separated by more than 30 kilometers. The disease-like parts of the two individuals were both covered by green surfaces, and the body size was much smaller compared with adjacent healthy regions. Here, using high-throughput pyrosequencing technology, we investigated the prokaryotic communities in healthy and disease-like sponge tissues as well as adjacent seawater. Microbes in healthy tissues belonged mainly to the Proteobacteria, Cyanobacteria and Bacteroidetes, and were much more diverse at the phylum level than reported previously. Interestingly, the disease-like tissues from the two sponge individuals underwent shifts of prokaryotic communities and were both enriched with a novel clade affiliated with the phylum Verrucomicrobia, implying its intimate connection with the disease-like Red Sea sponge C. cyathophora. Enrichment of the phylum Verrucomicrobia was also considered to be correlated with the presence of algae assemblages forming the green surface of the disease-like sponge tissues. This finding represents an interesting case of sponge disease and is valuable for further study.
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Affiliation(s)
- Zhao-Ming Gao
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, PR China
- Sanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, PR China
| | - Yong Wang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, PR China
- Sanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, PR China
| | - Ren-Mao Tian
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, PR China
| | - On On Lee
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, PR China
| | - Yue Him Wong
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, PR China
| | - Zenon B. Batang
- Coastal and Marine Resources Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdulaziz Al-Suwailem
- Coastal and Marine Resources Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Feras F. Lafi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Vladimir B. Bajic
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Pei-Yuan Qian
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, PR China
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