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Macdonald JFH, Pérez-García P, Schneider YKH, Blümke P, Indenbirken D, Andersen JH, Krohn I, Streit WR. Community dynamics and metagenomic analyses reveal Bacteroidota's role in widespread enzymatic Fucus vesiculosus cell wall degradation. Sci Rep 2024; 14:10237. [PMID: 38702505 PMCID: PMC11068906 DOI: 10.1038/s41598-024-60978-8] [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: 11/13/2023] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
Enzymatic degradation of algae cell wall carbohydrates by microorganisms is under increasing investigation as marine organic matter gains more value as a sustainable resource. The fate of carbon in the marine ecosystem is in part driven by these degradation processes. In this study, we observe the microbiome dynamics of the macroalga Fucus vesiculosus in 25-day-enrichment cultures resulting in partial degradation of the brown algae. Microbial community analyses revealed the phylum Pseudomonadota as the main bacterial fraction dominated by the genera Marinomonas and Vibrio. More importantly, a metagenome-based Hidden Markov model for specific glycosyl hydrolyses and sulphatases identified Bacteroidota as the phylum with the highest potential for cell wall degradation, contrary to their low abundance. For experimental verification, we cloned, expressed, and biochemically characterised two α-L-fucosidases, FUJM18 and FUJM20. While protein structure predictions suggest the highest similarity to a Bacillota origin, protein-protein blasts solely showed weak similarities to defined Bacteroidota proteins. Both enzymes were remarkably active at elevated temperatures and are the basis for a potential synthetic enzyme cocktail for large-scale algal destruction.
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Affiliation(s)
- Jascha F H Macdonald
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Pablo Pérez-García
- Institute for General Microbiology, Molecular Microbiology, Kiel University, Kiel, Germany
| | - Yannik K-H Schneider
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Patrick Blümke
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Hamburg, Germany
| | - Daniela Indenbirken
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Hamburg, Germany
| | - Jeanette H Andersen
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Ines Krohn
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany.
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
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Oppong-Danquah E, Blümel M, Tasdemir D. Metabolomics and Microbiomics Insights into Differential Surface Fouling of Three Macroalgal Species of Fucus (Fucales, Phaeophyceae) That Co-Exist in the German Baltic Sea. Mar Drugs 2023; 21:595. [PMID: 37999420 PMCID: PMC10672516 DOI: 10.3390/md21110595] [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] [Received: 10/20/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023] Open
Abstract
The brown algal genus Fucus provides essential ecosystem services crucial for marine environments. Macroalgae (seaweeds) release dissolved organic matter, hence, are under strong settlement pressure from micro- and macrofoulers. Seaweeds are able to control surface epibionts directly by releasing antimicrobial compounds onto their surfaces, and indirectly by recruiting beneficial microorganisms that produce antimicrobial/antifouling metabolites. In the Kiel Fjord, in the German Baltic Sea, three distinct Fucus species coexist: F. vesiculosus, F. serratus, and F. distichus subsp. evanescens. Despite sharing the same habitat, they show varying fouling levels; F. distichus subsp. evanescens is the least fouled, while F. vesiculosus is the most fouled. The present study explored the surface metabolomes and epiphytic microbiota of these three Fucus spp., aiming to uncover the factors that contribute to the differences in the fouling intensity on their surfaces. Towards this aim, algal surface metabolomes were analyzed using comparative untargeted LC-MS/MS-based metabolomics, to identify the marker metabolites influencing surface fouling. Their epiphytic microbial communities were also comparatively characterized using high-throughput amplicon sequencing, to pinpoint the differences in the surface microbiomes of the algae. Our results show that the surface of the least fouling species, F. distichus subsp. evanescens, is enriched with bioactive compounds, such as betaine lipids MGTA, 4-pyridoxic acid, and ulvaline, which are absent from the other species. Additionally, it exhibits a high abundance of the fungal genera Mucor and Alternaria, along with the bacterial genus Yoonia-Loktanella. These taxa are known for producing antimicrobial/antifouling compounds, suggesting their potential role in the observed fouling resistance on the surface of the F. distichus subsp. evanescens compared to F. serratus and F. vesiculosus. These findings provide valuable clues on the differential surface fouling intensity of Fucus spp., and their importance in marine chemical defense and fouling dynamics.
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Affiliation(s)
- Ernest Oppong-Danquah
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse 1–3, 24148 Kiel, Germany; (E.O.-D.); (M.B.)
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse 1–3, 24148 Kiel, Germany; (E.O.-D.); (M.B.)
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse 1–3, 24148 Kiel, Germany; (E.O.-D.); (M.B.)
- Faculty of Mathematics and Natural Science, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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Kuba GM, Spalding HL, Hill-Spanik KM, Williams TM, Paiano MO, Sherwood AR, Hauk BB, Kosaki RK, Fullerton H. Characterization of macroalgal-associated microbial communities from shallow to mesophotic depths at Manawai, Papahānaumokuākea Marine National Monument, Hawai'i. PeerJ 2023; 11:e16114. [PMID: 37842050 PMCID: PMC10569167 DOI: 10.7717/peerj.16114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/27/2023] [Indexed: 10/17/2023] Open
Abstract
The Papahānaumokuākea Marine National Monument, Hawai'i, is one of the most isolated and protected archipelagos in the world, making it a natural laboratory to examine macroalgal-microbial diversity because of limited direct anthropogenic impacts. We collected the most abundant macroalgae from nine sites ranging from shallow subtidal (1.5 m) to mesophotic (75 m) depths around Manawai (Pearl and Hermes Atoll). We characterized the macroalgal bacterial communities via high-throughput amplicon sequencing and compared the influence of host phylum, species, site, and depth on these relationships at a single atoll. Ochrophyta species had the lowest bacterial diversity compared to Chlorophyta and Rhodophyta. Site and/or depth may influence the microbial community structure associated with Microdictyon setchellianum, indicating a possible disconnect of these microbial communities among habitats. Chondria tumulosa, a cryptogenic species with invasive traits, differed in associated microbiota compared to the native Laurencia galtsoffii, an alga from the same family collected at the same site and depth. While there was overlap of bacterial communities across sites for some algal species, the majority had minimal macroalgal-microbial community connectivity across Manawai. This mesophotic system, therefore, did not appear to be refugia for shallow water coral reefs at microscopic scales. Additional studies are required to identify other significant influences on microbial community variation.
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Affiliation(s)
- Gabrielle M. Kuba
- Department of Biology, College of Charleston, Charleston, SC, United States
| | | | - Kristina M. Hill-Spanik
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, SC, United States
| | - Taylor M. Williams
- Department of Biology, College of Charleston, Charleston, SC, United States
| | - Monica O. Paiano
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, HI, United States
| | - Alison R. Sherwood
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, HI, United States
| | - Brian B. Hauk
- Cooperative Institute for Marine and Atmospheric Research, University of Hawai‘i at Mānoa, Honolulu, HI, United States
- Papahānaumokuākea Marine National Monument, National Oceanic and Atmospheric Administration, Honolulu, HI, United States
| | - Randall K. Kosaki
- Papahānaumokuākea Marine National Monument, National Oceanic and Atmospheric Administration, Honolulu, HI, United States
- Center for the Exploration of Coral Reef Ecosystems (XCoRE), Bishop Museum, Honolulu, HI, United States
| | - Heather Fullerton
- Department of Biology, College of Charleston, Charleston, SC, United States
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Mancuso FP, Morrissey KL, De Clerck O, Airoldi L. Warming and nutrient enrichment can trigger seaweed loss by dysregulation of the microbiome structure and predicted function. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:162919. [PMID: 36958561 DOI: 10.1016/j.scitotenv.2023.162919] [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: 12/09/2022] [Revised: 03/05/2023] [Accepted: 03/13/2023] [Indexed: 05/17/2023]
Abstract
Warming and nutrient enrichment are key pervasive drivers of ecological shifts in both aquatic and terrestrial ecosystems, impairing the physiology and survival of a wide range of foundation species. But the underlying mechanisms often remain unclear, and experiments have overlooked the potential effects mediated by changes in the microbial communities. We experimentally tested in the field orthogonal stress combinations from simulated air warming and nutrient enrichment on the intertidal foundation seaweed Cystoseira compressa, and its associated bacterial communities. A total of 523 Amplicon Sequence Variance (ASVs) formed the bacterial community on C. compressa, with 222 ASVs assigned to 69 taxa at the genus level. Most bacteria taxa experienced changes in abundance as a result of additive (65 %) and antagonistic (30 %) interactions between the two stressors, with synergies (5 %) occurring less frequently. The analysis of the predicted bacterial functional profile identified 160 metabolic pathways, and showed that these were mostly affected by additive interactions (74 %) between air warming and nutrient enrichment, while antagonisms (20 %) and synergisms (6 %) were less frequent. Overall, the two stressors combined increased functions associated with seaweed disease or degradation of major cell-wall polymers and other algicidal processes, and decreased functions associated with Quorum Quenching and photosynthetic response. We conclude that warming and nutrient enrichment can dysregulate the microbiome of seaweeds, providing a plausible mechanism for their ongoing loss, and encourage more research into the effects of human impacts on crucial but yet largely unstudied host-microbiome relationships in different aquatic and terrestrial species.
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Affiliation(s)
- Francesco Paolo Mancuso
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, viale delle Scienze Ed. 16, 90128 Palermo, Italy; Department of Biological, Geological, and Environmental Sciences, University of Bologna, Ravenna, Italy; NBFC, National Biodiversity Future Center, Palermo 90133, Italy.
| | - Kathryn Lee Morrissey
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Laura Airoldi
- NBFC, National Biodiversity Future Center, Palermo 90133, Italy; Chioggia Hydrobiological Station "Umberto D'Ancona", Department of Biology, UO CoNISMa, University of Padova, Chioggia, Italy.
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Delva S, De Baets B, Baetens JM, De Clerck O, Stock W. No bacterial-mediated alleviation of thermal stress in a brown seaweed suggests the absence of ecological bacterial rescue effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162532. [PMID: 36870499 DOI: 10.1016/j.scitotenv.2023.162532] [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: 10/21/2022] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
While microbiome alterations are increasingly proposed as a rapid mechanism to buffer organisms under changing environmental conditions, studies of these processes in the marine realm are lagging far behind their terrestrial counterparts. Here, we used a controlled laboratory experiment to examine whether the thermal tolerance of the brown seaweed Dictyota dichotoma, a common species in European coastal ecosystems, could be enhanced by the repeated addition of bacteria from its natural environment. Juvenile algae from three genotypes were subjected for two weeks to a temperature gradient, spanning almost the entire thermal range that can be tolerated by the species (11-30 °C). At the start of the experiment and again in the middle of the experiment, the algae were inoculated with bacteria from their natural environment or left untouched as a control. Relative growth rate was measured over the two-week period, and we assessed bacterial community composition prior to and at the end of the experiment. Since the growth of D. dichotoma over the full thermal gradient was not affected by supplementing bacteria, our results indicate no scope for bacterial-mediated stress alleviation. The minimal changes in the bacterial communities linked to bacterial addition, particularly at temperatures above the thermal optimum (22-23 °C), suggest the existence of a barrier to bacterial recruitment. These findings indicate that ecological bacterial rescue is unlikely to play a role in mitigating the effects of ocean warming on this brown seaweed.
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Affiliation(s)
- Soria Delva
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium; Research Unit Knowledge-Based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Bernard De Baets
- Research Unit Knowledge-Based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Jan M Baetens
- Research Unit Knowledge-Based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium.
| | - Willem Stock
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium.
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Li H, Li JJ, Gao TH, Bi YX, Liu ZY. The Influence of Host Specificity and Temperature on Bacterial Communities Associated with Sargassum (Phaeophyceae) Species. JOURNAL OF PHYCOLOGY 2022; 58:815-828. [PMID: 36308470 DOI: 10.1111/jpy.13293] [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: 05/22/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Host-related microbiota are critically important for the adaptation/acclimation of hosts to changing environments, but how environmental factors and host characteristics shape the microbial communities remains largely unknown. We investigated the effects of temperature on habitat-forming macroalgae and their associated bacterial communities. Three Sargassum species (S. horneri, S. fusiforme, and S. thunbergii) and seawater samples were sampled in Gouqi Island, China, and these macroalgal samples were incubated at different temperatures (10, 20, and 27°C) for 7 d. Bacterial communities were identified from the 16S rRNA gene V3-V4 regions. The algae-associated bacterial communities of the field samples were significantly different from seawater, implying host specificity. During laboratory incubation, decreased physiological status (photosynthetic rate and oxidative stress response) was detected for all the species at 10°C, especially with regard to S. horneri and S. fusiforme. For each host, associated bacterial communities at 20 and 27°C clustered closely, and these were separated from samples at 10°C based on constrained PCoA analyses. Permutational multivariate analysis of variance revealed that algae-associated bacterial communities were more affected by host species (23.3%) than by temperature (2.48%) during laboratory incubation. The changes in bacterial community composition may be influenced by algae metabolites, which should be tested in a future study. These results further contribute to our understanding of algal microbiome changes in response to environmental changes.
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Affiliation(s)
- Huan Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing, 210024, China
- College of Oceanography, Hohai University, Nanjing, 210024, China
| | - Jing-Jing Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing, 210024, China
- College of Oceanography, Hohai University, Nanjing, 210024, China
| | - Tian-Heng Gao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing, 210024, China
- College of Oceanography, Hohai University, Nanjing, 210024, China
| | - Yuan-Xin Bi
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Marine Fisheries Research Institute of Zhejiang Province, Zhoushan, 316021, China
| | - Zheng-Yi Liu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chunhui Road, Yantai, 264003, China
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Sun T, Yang Z, Chen J, Li Y, Wang J, Wang X, Tang X, Xiao H. Effects of Water Loss Stress under Tidal Effects on the Epiphytic Bacterial Community of Sargassum thunbergii in the Intertidal Zone. mSphere 2022; 7:e0030722. [PMID: 36173121 PMCID: PMC9599519 DOI: 10.1128/msphere.00307-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/14/2022] [Indexed: 11/20/2022] Open
Abstract
Intertidal macroalgae face periodic water loss and rehydration caused by daily tidal changes. However, the effect of water loss stress on algal epiphytic bacteria has not yet been reported. In this study, the effects of water loss stress on the epiphytic bacteria community of Sargassum thunbergii were analyzed, and the different responses of epiphytic bacteria to water loss stress were compared between male and female algae. The results showed that after water loss stress, the diversity of the epiphytic bacterial community of S. thunbergii first decreased and then increased. Among the dominant taxa, the abundance of Cyanobacteria decreased significantly, whereas the abundance of Portibacter and Aquimarina first increased and then decreased. Additionally, the indicator species and the abundance of predicted functional genes related to carbon, nitrogen, and sulfur metabolism both changed significantly. More importantly, when the epiphytic bacteria were analyzed separately according to the algal sex, the changes in algal epiphytic bacterial community structure and indicator species were more significant, and there were sexual differences. Therefore, it was concluded that water loss stress has a significant effect on the community structure and function of the epiphytic bacteria on S. thunbergii. Meanwhile, the epiphytic bacteria community of two sexes of S. thunbergii differed in the response to water loss stress. IMPORTANCE Periodic water loss caused by the tide is an important environmental factor that is faced by intertidal macroalgae, but the impact of periodic water loss on the epiphytic bacterial communities associated with macroalgae is still unknown. Through this study, we found that the diversity, the relative abundance of dominant taxa, the indicator species, and the abundance of the predicted functional genes in the epiphytic bacteria on S. thunbergii changed with the time of water loss. Moreover, male and female S. thunbergii exhibited different responses to water loss stress. This study not only paves the way for the delineation of the interactions between S. thunbergii and its epiphytic bacteria but also provides new insights for the mechanisms of the adaptation and evolution of macroalgae in the intertidal zone.
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Affiliation(s)
- Tao Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhibo Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yang Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiya Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hui Xiao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Alterations in Epiphytic Bacterial Communities during the Occurrence of Green Rot Disease in Saccharina japonica Seedlings. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacteria are one of the causes of green rot disease (GRD) in Saccharina japonica mariculture, which may lead to complete failure of seedling production. However, the association between bacterial community and host disease severity remains largely unknown. Therefore, in this study, the bacterial communities associated with GRD-infected seedlings with naturally varying disease severity from two seedling hatcheries in Northern China were analyzed to investigate the interactions between bacterial communities and GRD. The results indicated incorrect nutrient supply in both sites. Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes were prevalent in all samples. Significant structural alterations were detected for epibacterial communities, which were further evidenced by differently abundant bacterial taxa associated with seedlings with varying disease severity. The predicted pathways of bacterial adhesion and antimicrobial compounds biosynthesis were significantly enriched in less severely diseased seedlings, whereas glutathione metabolism and lipopolysaccharide biosynthesis were significantly increased in more severely diseased seedlings. The predicted categories of a two-component system, flagellar assembly, bacterial chemotaxis, and biofilm formation were significantly enriched in the bacterioplankton in more severely infected seawater. The differential bacterial community compositions and predicted functions provide new clues to elucidate the mechanism underlying the interaction between GRD occurrence and bacterial communities.
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Ramírez-Puebla ST, Weigel BL, Jack L, Schlundt C, Pfister CA, Mark Welch JL. Spatial organization of the kelp microbiome at micron scales. MICROBIOME 2022; 10:52. [PMID: 35331334 PMCID: PMC8944128 DOI: 10.1186/s40168-022-01235-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/21/2022] [Indexed: 05/15/2023]
Abstract
BACKGROUND Elucidating the spatial structure of host-associated microbial communities is essential for understanding taxon-taxon interactions within the microbiota and between microbiota and host. Macroalgae are colonized by complex microbial communities, suggesting intimate symbioses that likely play key roles in both macroalgal and bacterial biology, yet little is known about the spatial organization of microbes associated with macroalgae. Canopy-forming kelp are ecologically significant, fixing teragrams of carbon per year in coastal kelp forest ecosystems. We characterized the micron-scale spatial organization of bacterial communities on blades of the kelp Nereocystis luetkeana using fluorescence in situ hybridization and spectral imaging with a probe set combining phylum-, class-, and genus-level probes to localize and identify > 90% of the microbial community. RESULTS We show that kelp blades host a dense microbial biofilm composed of disparate microbial taxa in close contact with one another. The biofilm is spatially differentiated, with clustered cells of the dominant symbiont Granulosicoccus sp. (Gammaproteobacteria) close to the kelp surface and filamentous Bacteroidetes and Alphaproteobacteria relatively more abundant near the biofilm-seawater interface. A community rich in Bacteroidetes colonized the interior of kelp tissues. Microbial cell density increased markedly along the length of the kelp blade, from sparse microbial colonization of newly produced tissues at the meristematic base of the blade to an abundant microbial biofilm on older tissues at the blade tip. Kelp from a declining population hosted fewer microbial cells compared to kelp from a stable population. CONCLUSIONS Imaging revealed close association, at micrometer scales, of different microbial taxa with one another and with the host. This spatial organization creates the conditions necessary for metabolic exchange among microbes and between host and microbiota, such as provisioning of organic carbon to the microbiota and impacts of microbial nitrogen metabolisms on host kelp. The biofilm coating the surface of the kelp blade is well-positioned to mediate interactions between the host and surrounding organisms and to modulate the chemistry of the surrounding water column. The high density of microbial cells on kelp blades (105-107 cells/cm2), combined with the immense surface area of kelp forests, indicates that biogeochemical functions of the kelp microbiome may play an important role in coastal ecosystems. Video abstract.
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Affiliation(s)
- S. Tabita Ramírez-Puebla
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
- Present Address: The Forsyth Institute, Cambridge, MA USA
| | - Brooke L. Weigel
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL USA
- Present Address: Friday Harbor Laboratories, University of Washington, Friday Harbor, WA USA
| | - Loretha Jack
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
- Present Address: Wisconsin’s Green Fire, Rhinelander, WI USA
| | - Cathleen Schlundt
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
- Present Address: GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
| | | | - Jessica L. Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
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Florez JZ, Camus C, Hengst MB, Buschmann AH. A mesocosm study on bacteria-kelp interactions: Importance of nitrogen availability and kelp genetics. JOURNAL OF PHYCOLOGY 2021; 57:1777-1791. [PMID: 34570392 DOI: 10.1111/jpy.13213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 06/12/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
Macroalgal holobiont studies involve understanding interactions between the host, its microbiota, and the environment. We analyzed the effect of bacteria-kelp interactions on phenotypic responses of two genetically distinct populations of giant kelp, Macrocystis pyrifera (north and south), exposed to different nitrogen (N) concentrations. In co-culture experiments with different N concentration treatments, we evaluated kelp growth responses and changes in three specific molecular markers associated with the N cycle, both in epiphytic bacteria (relative abundance of nrfA-gene: cytochrome c nitrite reductase) and macroalgae (expression of NR-gene: nitrate reductase; GluSyn-gene: glutamate synthase). Both kelp populations responded differently to N limitation, with M. pyrifera-south sporophytes having a lower specific growth rate (SGR) under N-limiting conditions than the northern population; M. pyrifera-north sporophytes showed no significant differences in SGR when exposed to low-N and high-N concentrations. This corresponded to a higher GluSyn-gene expression in the M. pyrifera-north sporophytes and the co-occurrence of specific nrfA bacterial taxa. These bacteria may increase ammonium availability under low-N concentrations, allowing M. pyrifera-north to optimize nutrient assimilation by increasing the expression of GluSyn. We conclude that bacteria-kelp interactions are important in enhancing kelp growth rates under low N availability, although this effect may be regulated by the genetic background of kelp populations.
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Affiliation(s)
- July Z Florez
- Programa de Doctorado en Ciencias mención Conservación y Manejo de Recursos Naturales, Universidad de Los Lagos, Puerto Montt, Chile
- Centro i˜mar and CeBiB, Universidad de Los Lagos, Puerto Montt, Chile
- Departamento de Ciencias Farmacéuticas, Universidad Católica del Norte, Antofagasta, Chile
| | - Carolina Camus
- Centro i˜mar and CeBiB, Universidad de Los Lagos, Puerto Montt, Chile
| | - Martha B Hengst
- Departamento de Ciencias Farmacéuticas, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Biotecnología y Bioingeniería (CeBiB), Santiago, Chile
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Paix B, Potin P, Schires G, Le Poupon C, Misson B, Leblanc C, Culioli G, Briand JF. Synergistic effects of temperature and light affect the relationship between Taonia atomaria and its epibacterial community: a controlled conditions study. Environ Microbiol 2021; 23:6777-6797. [PMID: 34490980 DOI: 10.1111/1462-2920.15758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 11/29/2022]
Abstract
In the context of global warming, this study aimed to assess the effect of temperature and irradiance on the macroalgal Taonia atomaria holobiont dynamics. We developed an experimental set-up using aquaria supplied by natural seawater with three temperatures combined with three irradiances. The holobiont response was monitored over 14 days using a multi-omics approach coupling algal surface metabolomics and metabarcoding. Both temperature and irradiance appeared to shape the microbiota and the surface metabolome, but with a distinct temporality. Epibacterial community first changed according to temperature, and later in relation to irradiance, while the opposite occurred for the surface metabolome. An increased temperature revealed a decreasing richness of the epiphytic community together with an increase of several bacterial taxa. Irradiance changes appeared to quickly impact surface metabolites production linked with the algal host photosynthesis (e.g. mannitol, fucoxanthin, dimethylsulfoniopropionate), which was hypothesized to explain modifications of the structure of the epiphytic community. Algal host may also directly adapt its surface metabolome to changing temperature with time (e.g. lipids content) and also in response to changing microbiota (e.g. chemical defences). Finally, this study brought new insights highlighting complex direct and indirect responses of seaweeds and their associated microbiota under changing environments.
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Affiliation(s)
- Benoit Paix
- Université de Toulon, Laboratoire MAPIEM, La Garde, EA 4323, France
| | - Philippe Potin
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), UMR 8227, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Gaëtan Schires
- Sorbonne Université, CNRS, Center for Biological Marine Resources (CRBM), FR 2424, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Christophe Le Poupon
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM110, La Garde, France
| | - Benjamin Misson
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM110, La Garde, France
| | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), UMR 8227, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Gérald Culioli
- Université de Toulon, Laboratoire MAPIEM, La Garde, EA 4323, France
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12
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Paix B, Layglon N, Le Poupon C, D'Onofrio S, Misson B, Garnier C, Culioli G, Briand JF. Integration of spatio-temporal variations of surface metabolomes and epibacterial communities highlights the importance of copper stress as a major factor shaping host-microbiota interactions within a Mediterranean seaweed holobiont. MICROBIOME 2021; 9:201. [PMID: 34641951 PMCID: PMC8507236 DOI: 10.1186/s40168-021-01124-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Although considered as holobionts, macroalgae and their surface microbiota share intimate interactions that are still poorly understood. Little is known on the effect of environmental parameters on the close relationships between the host and its surface-associated microbiota, and even more in a context of coastal pollutions. Therefore, the main objective of this study was to decipher the impact of local environmental parameters, especially trace metal concentrations, on an algal holobiont dynamics using the Phaeophyta Taonia atomaria as a model. Through a multidisciplinary multi-omics approach combining metabarcoding and untargeted LC-MS-based metabolomics, the epibacterial communities and the surface metabolome of T. atomaria were monitored along a spatio-temporal gradient in the bay of Toulon (Northwestern Mediterranean coast) and its surrounding. Indeed, this geographical area displays a well-described trace metal gradient particularly relevant to investigate the effect of such pollutants on marine organisms. RESULTS Epibacterial communities of T. atomaria exhibited a high specificity whatever the five environmentally contrasted collecting sites investigated on the NW Mediterranean coast. By integrating metabarcoding and metabolomics analyses, the holobiont dynamics varied as a whole. During the occurrence period of T. atomaria, epibacterial densities and α-diversity increased while the relative proportion of core communities decreased. Pioneer bacterial colonizers constituted a large part of the specific and core taxa, and their decrease might be linked to biofilm maturation through time. Then, the temporal increase of the Roseobacter was proposed to result from the higher temperature conditions, but also the increased production of dimethylsulfoniopropionate (DMSP) at the algal surface which could constitute of the source of carbon and sulfur for the catabolism pathways of these taxa. Finally, as a major result of this study, copper concentration constituted a key factor shaping the holobiont system. Thus, the higher expression of carotenoids suggested an oxidative stress which might result from an adaptation of the algal surface metabolome to high copper levels. In turn, this change in the surface metabolome composition could result in the selection of particular epibacterial taxa. CONCLUSION We showed that associated epibacterial communities were highly specific to the algal host and that the holobiont dynamics varied as a whole. While temperature increase was confirmed to be one of the main parameters associated to Taonia dynamics, the originality of this study was highlighting copper-stress as a major driver of seaweed-epibacterial interactions. In a context of global change, this study brought new insights on the dynamics of a Mediterranean algal holobiont submitted to heavy anthropic pressures. Video abstract.
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Affiliation(s)
- Benoît Paix
- Université de Toulon, Laboratoire MAPIEM, EA, 4323, Toulon, France
- Present adress: Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Nicolas Layglon
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM, 110, Toulon, France
| | - Christophe Le Poupon
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM, 110, Toulon, France
| | - Sébastien D'Onofrio
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM, 110, Toulon, France
| | - Benjamin Misson
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM, 110, Toulon, France
| | - Cédric Garnier
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM, 110, Toulon, France
| | - Gérald Culioli
- Université de Toulon, Laboratoire MAPIEM, EA, 4323, Toulon, France.
- Present address: Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), UMR CNRS-IRD-Avignon Université-Aix-Marseille Université, Avignon, France.
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13
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Korlević M, Markovski M, Zhao Z, Herndl GJ, Najdek M. Seasonal Dynamics of Epiphytic Microbial Communities on Marine Macrophyte Surfaces. Front Microbiol 2021; 12:671342. [PMID: 34603223 PMCID: PMC8482799 DOI: 10.3389/fmicb.2021.671342] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/10/2021] [Indexed: 11/13/2022] Open
Abstract
Surfaces of marine macrophytes are inhabited by diverse microbial communities. Most studies focusing on epiphytic communities of macrophytes did not take into account temporal changes or applied low sampling frequency approaches. The seasonal dynamics of epiphytic microbial communities was determined in a meadow of Cymodocea nodosa invaded by Caulerpa cylindracea and in a monospecific settlement of C. cylindracea at monthly intervals. For comparison the ambient prokaryotic picoplankton community was also characterized. At the OTU level, the microbial community composition differed between the ambient water and the epiphytic communities exhibiting host-specificity. Also, successional changes were observed connected to the macrophyte growth cycle. Taxonomic analysis, however, showed similar high rank taxa (phyla and classes) in the ambient water and the epiphytic communities, with the exception of Desulfobacterota, which were only found on C. cylindracea. Cyanobacteria showed seasonal changes while other high rank taxa were present throughout the year. In months of high Cyanobacteria presence the majority of cyanobacterial sequences were classified as Pleurocapsa. Phylogenetic groups present throughout the year (e.g., Saprospiraceae, Rhodobacteraceae, members without known relatives within Gammaproteobacteria, Desulfatitalea, and members without known relatives within Desulfocapsaceae) constituted most of the sequences, while less abundant taxa showed seasonal patterns connected to the macrophyte growth cycle. Taken together, epiphytic microbial communities of the seagrass C. nodosa and the macroalga C. cylindracea appear to be host-specific and contain taxa that undergo successional changes.
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Affiliation(s)
- Marino Korlević
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Marsej Markovski
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, Netherlands
| | - Mirjana Najdek
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
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Davis KM, Mazel F, Parfrey LW. The microbiota of intertidal macroalgae Fucus distichus is site-specific and resistant to change following transplant. Environ Microbiol 2021; 23:2617-2631. [PMID: 33817918 DOI: 10.1111/1462-2920.15496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023]
Abstract
It is unclear how host-associated microbial communities will be affected by future environmental change. Characterizing how microbiota differ across sites with varying environmental conditions and assessing the stability of the microbiota in response to abiotic variation are critical steps towards predicting outcomes of environmental change. Intertidal organisms are valuable study systems because they experience extreme variation in environmental conditions on tractable timescales such as tide cycles and across small spatial gradients in the intertidal zone. Here we show a widespread intertidal macroalgae, Fucus distichus, hosts site-specific microbiota over small (meters to kilometres) spatial scales. We demonstrate stability of site-specific microbial associations by manipulating the host environment and microbial species pool with common garden and reciprocal transplant experiments. We hypothesized that F. distichus microbiota would readily shift to reflect the contemporary environment due to selective filtering by abiotic conditions and/or colonization by microbes from the new environment or nearby hosts. Instead, F. distichus microbiota was stable for days after transplantation in both the laboratory and field. Our findings expand the current understanding of microbiota dynamics on an intertidal foundation species. These results may also point to adaptations for withstanding short-term environmental variation, in hosts and/or microbes, facilitating stable host-microbial associations.
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Affiliation(s)
- Katherine M Davis
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Hakai Institute, PO Box 309, Heriot Bay, BC, V0P 1H0, Canada
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15
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Environmental factors shape the epiphytic bacterial communities of Gracilariopsis lemaneiformis. Sci Rep 2021; 11:8671. [PMID: 33883606 PMCID: PMC8060329 DOI: 10.1038/s41598-021-87977-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/06/2021] [Indexed: 02/02/2023] Open
Abstract
Macroalgae host various symbionts on their surface, which play a critical role in their growth and development processes. However, there is still incomplete understanding of this epiphytic bacteria-host algae interactions. This study comprehensively analysed variation of the epiphytic bacterial communities (EBC) composition of red macroalga Gracilariopsis lemaneiformis at different geographic locations and environmental factors (i.e., nitrogen and phosphorus), which shape the EBC composition of G. lemaneiformis. The composition and structure of EBC were characterized using high throughput sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. The results revealed that epiphytic bacteria varied significantly among three different geographic locations in China, i.e., Nan'ao Island (NA), Lianjiang County (LJ), and Nanri Island (NR). Redundancy analysis (RDA) showed that the relative abundance of Bacteroidetes, Firmicutes, Verrucomicrobia, and Epsilonbacteraeota at NR were strongly positively correlated with total nitrogen (TN), total phosphorus (TP), nitrate nitrogen (NO3-N), and dissolved inorganic nitrogen (DIN), but negatively correlated with nitrite nitrogen (NO2-N). The relative abundance of Cyanobacteria at NA and LJ were strongly positively correlated with NO2-N, but negatively correlated with TN, TP, NO3-N, and DIN. Besides, the Mantel test results indicated that the EBC composition was significantly correlated with these environmental factors, which was also confirmed by Spearman correlation analysis. Thus, environmental factors such as NO3-N and DIN play a key role in the community composition of epiphytic bacteria on G. lemaneiformis. This study provides important baseline knowledge on the community composition of epiphytic bacteria on G. lemaneiformis and shows correlation between different epiphytic bacteria and their surrounding environmental factors.
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16
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Weigel BL, Pfister CA. Oxygen metabolism shapes microbial settlement on photosynthetic kelp blades compared to artificial kelp substrates. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:176-184. [PMID: 33372322 DOI: 10.1111/1758-2229.12923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
We examined factors shaping community assembly of the bull kelp (Nereocystis luetkeana) microbiome by comparing microbial biofilm formation on photosynthetic kelp blade tissues and artificial kelp substrates ('agar substrates') deployed into a kelp forest. New kelp blade tissues were colonized by markedly distinct microbial taxa relative to agar substrates during the same time interval, even when agar substrates were infused with N. luetkeana blades, suggesting that microbial settlement onto kelp surfaces is more than just attraction to a polysaccharide-rich surface. Further, common seawater taxa such as Colwellia sp. and Psychromonas sp. became abundant on agar substrates but avoided new kelp blade tissues, indicating that host-specific factors may deter certain surface-associated marine microbial taxa. Over two-thirds of the bacterial taxa in the kelp microbiome were associated with strictly aerobic metabolisms; thus, photosynthetic production of O2 may favour aerobic microbial metabolisms. While living kelp blades primarily recruited aerobic microbes, including the obligate aerobe Granulosicoccus sp., microbes that colonized agar substrates were predominantly facultative anaerobes. We also found that infusion of kelp tissues into agar substrates altered microbial community composition and lowered taxonomic diversity relative to control agar substrates, suggesting that non-living components of the kelp blade also impact microbial community assembly.
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Affiliation(s)
- Brooke L Weigel
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA
| | - Catherine A Pfister
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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17
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Brunet M, de Bettignies F, Le Duff N, Tanguy G, Davoult D, Leblanc C, Gobet A, Thomas F. Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities. Environ Microbiol 2021; 23:1638-1655. [PMID: 33400326 PMCID: PMC8248336 DOI: 10.1111/1462-2920.15389] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/14/2020] [Accepted: 01/02/2021] [Indexed: 12/30/2022]
Abstract
Kelps are dominant primary producers in temperate coastal ecosystems. Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota. Here, we investigated the bacterial community associated with the kelp Laminaria hyperborea during its accumulation and degradation on the seafloor. Kelp tissue, seawater and sediment were sampled during a 6-month in situ experiment simulating kelp detritus accumulation. Evaluation of the epiphytic bacterial community abundance, structure, taxonomic composition and predicted functional profiles evidenced a biphasic succession. Initially, dominant genera (Hellea, Litorimonas, Granulosicoccus) showed a rapid and drastic decrease in sequence abundance, probably outcompeted by algal polysaccharide-degraders such as Bacteroidia members which responded within 4 weeks. Acidimicrobiia, especially members of the Sva0996 marine group, colonized the degrading kelp biomass after 11 weeks. These secondary colonizers could act as opportunistic scavenger bacteria assimilating substrates exposed by early degraders. In parallel, kelp accumulation modified bacterial communities in the underlying sediment, notably favouring anaerobic taxa potentially involved in the sulfur and nitrogen cycles. Overall, this study provides insights into the bacterial degradation of algal biomass in situ, an important link in coastal trophic chains.
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Affiliation(s)
- Maéva Brunet
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Florian de Bettignies
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Nolwen Le Duff
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Gwenn Tanguy
- Sorbonne Université, CNRS, FR2424, Genomer, Station Biologique de RoscoffRoscoff29680France
| | - Dominique Davoult
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Angélique Gobet
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRDSèteFrance
| | - François Thomas
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
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Jung J, Gillevet PM, Sikaroodi M, Andrews J, Song B, Shields JD. Comparative study of the hemolymph microbiome between live and recently dead American lobsters Homarus americanus. DISEASES OF AQUATIC ORGANISMS 2021; 143:147-158. [PMID: 33629659 DOI: 10.3354/dao03568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lobsters and other crustaceans do not have sterile hemolymph. Despite this, little is known about the microbiome in the hemolymph of the lobster Homarus americanus. The purpose of this study was to characterize the hemolymph microbiome in lobsters. The lobsters were part of a larger study on the effect of temperature on epizootic shell disease, and several died during the course of the study, providing an opportunity to examine differences in the microbiomes between live and recently dead (1-24 h) animals. The hemolymph microbiomes of live lobsters was different from those in dead animals and both were different from the tank microbiome in which the animals had been held. The microbiomes of live lobsters were more diverse and had a different suite of bacteria than those from dead animals. The dominant taxa in live lobsters belonged to Flavobacteriaceae and Rhodobacteraceae, whereas Vibrionaceae and Enterobacteriaceae were predominant in the dead lobsters. Although aquarium microbiomes overlapped with the hemolymph microbiomes, there was less overlap and lower abundance of taxa in comparison with hemolymph from live lobsters. Previous studies reporting bacteria in the digestive tract of lobsters suggested that Vibrionaceae and Enterobacteriaceae had invaded the hemolymph via the gut. Our study suggests that hemolymph bacteria abundant in live lobsters do not originate from the tank milieu and comprise a rich, natural, or native background of bacterial constituents.
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Affiliation(s)
- Jibom Jung
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, Republic of Korea
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Wolter LA, Wietz M, Ziesche L, Breider S, Leinberger J, Poehlein A, Daniel R, Schulz S, Brinkhoff T. Pseudooceanicola algae sp. nov., isolated from the marine macroalga Fucus spiralis, shows genomic and physiological adaptations for an algae-associated lifestyle. Syst Appl Microbiol 2021; 44:126166. [PMID: 33310406 DOI: 10.1016/j.syapm.2020.126166] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/23/2022]
Abstract
The genus Pseudooceanicola from the alphaproteobacterial Roseobacter group currently includes ten validated species. We herein describe strain Lw-13eT, the first Pseudooceanicola species from marine macroalgae, isolated from the brown alga Fucus spiralis abundant at European and North American coasts. Physiological and pangenome analyses of Lw-13eT showed corresponding adaptive features. Adaptations to the tidal environment include a broad salinity tolerance, degradation of macroalgae-derived substrates (mannitol, mannose, proline), and resistance to several antibiotics and heavy metals. Notably, Lw-13eT can degrade oligomeric alginate via PL15 alginate lyase encoded in a polysaccharide utilization locus (PUL), rarely described for roseobacters to date. Plasmid localization of the PUL strengthens the importance of mobile genetic elements for evolutionary adaptations within the Roseobacter group. PL15 homologs were primarily detected in marine plant-associated metagenomes from coastal environments but not in the open ocean, corroborating its adaptive role in algae-rich habitats. Exceptional is the tolerance of Lw-13eT against the broad-spectrum antibiotic tropodithietic acid, produced by Phaeobacter spp. co-occurring in coastal habitats. Furthermore, Lw-13eT exhibits features resembling terrestrial plant-bacteria associations, i.e. biosynthesis of siderophores, terpenes and volatiles, which may contribute to mutual bacteria-algae interactions. Closest described relative of Lw-13eT is Pseudopuniceibacterium sediminis CY03T with 98.4% 16S rRNA gene sequence similarity. However, protein sequence-based core genome phylogeny and average nucleotide identity indicate affiliation of Lw-13eT with the genus Pseudooceanicola. Based on phylogenetic, physiological and (chemo)taxonomic distinctions, we propose strain Lw-13eT (=DSM 29013T=LMG 30557T) as a novel species with the name Pseudooceanicola algae.
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Affiliation(s)
- Laura A Wolter
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany; JST ERATO Nomura Project, Faculty of Life and Environmental Sciences, Tsukuba, Japan.
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Lisa Ziesche
- Institute of Organic Chemistry, Technische Universität Braunschweig, Germany
| | - Sven Breider
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Janina Leinberger
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Anja Poehlein
- Institute of Microbiology and Genetics, Genomic and Applied Microbiology, and Göttingen Genomics Laboratory, Germany
| | - Rolf Daniel
- Institute of Microbiology and Genetics, Genomic and Applied Microbiology, and Göttingen Genomics Laboratory, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany.
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20
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Quigley CTC, Capistrant-Fossa KA, Morrison HG, Johnson LE, Morozov A, Hertzberg VS, Brawley SH. Bacterial Communities Show Algal Host ( Fucus spp.)/Zone Differentiation Across the Stress Gradient of the Intertidal Zone. Front Microbiol 2020; 11:563118. [PMID: 33072025 PMCID: PMC7541829 DOI: 10.3389/fmicb.2020.563118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022] Open
Abstract
The intertidal zone often has varying levels of environmental stresses (desiccation, temperature, light) that result in highly stress-tolerant macrobiota occupying the upper zone while less tolerant species occupy the lower zone, but little comparative information is available for intertidal bacteria. Here we describe natural (unmanipulated) bacterial communities of three Fucus congeners (F. spiralis, high zone; F. vesiculosus, mid zone; F. distichus, low zone) as well as those of F. vesiculosus transplanted to the high zone (Dry and Watered treatments) and to the mid zone (Procedural Control) during summer in Maine (United States). We predicted that bacterial communities would be different among the differently zoned natural congeners, and that higher levels of desiccation stress in the high zone would cause bacterial communities of Dry transplants to become similar to F. spiralis, whereas relieving desiccation stress on Watered transplants would maintain the mid-zone F. vesiculosus bacterial community. Bacteria were identified as amplicon sequence variants (ASVs) after sequencing the V4 hypervariable region of the 16S rRNA gene. Microbiome composition and structure were significantly different between the differently zoned congeners at each tissue type (holdfasts, receptacles, vegetative tips). ASVs significantly associated with the mid-zone congener were frequently also present on the high-zone or low-zone congener, whereas overlap in ASVs between the high-zone and low-zone congeners was rare. Only 7 of 6,320 total ASVs were shared among tissues over all congeners and transplant treatments. Holdfast bacterial community composition of Dry transplants was not significantly different from that of F. spiralis, but Watered holdfast communities were significantly different from those of F. spiralis and not significantly different from those of procedural controls. Additional stressor(s) appeared important, because bacterial communities of Dry and Watered transplants were only marginally different from each other (p = 0.059). The relative abundance of Rhodobacteraceae associated with holdfasts generally correlated with environmental stress with highest abundance associated with F. spiralis and the two high-zone transplant treatments. These findings suggest that the abiotic stressors that shape distributional patterns of host species also affect their bacterial communities.
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Affiliation(s)
| | | | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Ladd E Johnson
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - Aleksey Morozov
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Vicki S Hertzberg
- Center for Data Science, Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, United States
| | - Susan H Brawley
- School of Marine Sciences, University of Maine, Orono, ME, United States
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Mensch B, Neulinger SC, Künzel S, Wahl M, Schmitz RA. Warming, but Not Acidification, Restructures Epibacterial Communities of the Baltic Macroalga Fucus vesiculosus With Seasonal Variability. Front Microbiol 2020; 11:1471. [PMID: 32676070 PMCID: PMC7333354 DOI: 10.3389/fmicb.2020.01471] [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: 12/18/2019] [Accepted: 06/05/2020] [Indexed: 11/13/2022] Open
Abstract
Due to ocean acidification and global warming, surface seawater of the western Baltic Sea is expected to reach an average of ∼1100 μatm pCO2 and an increase of ∼5°C by the year 2100. In four consecutive experiments (spanning 10-11 weeks each) in all seasons within 1 year, the abiotic factors temperature (+5°C above in situ) and pCO2 (adjusted to ∼1100 μatm) were tested for their single and combined effects on epibacterial communities of the brown macroalga Fucus vesiculosus and on bacteria present in the surrounding seawater. The experiments were set up in three biological replicates using the Kiel Outdoor Benthocosm facility (Kiel, Germany). Phylogenetic analyses of the respective microbiota were performed by bacterial 16S (V1-V2) rDNA Illumina MiSeq amplicon sequencing after 0, 4, 8, and 10/11 weeks per season. The results demonstrate (I) that the bacterial community composition varied in time and (II) that relationships between operational taxonomic units (OTUs) within an OTU association network were mainly governed by the habitat. (III) Neither single pCO2 nor pCO2:Temperature interaction effects were statistically significant. However, significant impact of ocean warming was detected varying among seasons. (IV) An indicator OTU (iOTU) analysis identified several iOTUs that were strongly influenced by temperature in spring, summer, and winter. In the warming treatments of these three seasons, we observed decreasing numbers of bacteria that are commonly associated with a healthy marine microbial community and-particularly during spring and summer-an increase in potentially pathogenic and bacteria related to intensified microfouling. This might lead to severe consequences for the F. vesiculosus holobiont finally affecting the marine ecosystem.
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Affiliation(s)
- Birte Mensch
- Department of Biology, Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Sven C. Neulinger
- Department of Biology, Institute of General Microbiology, Kiel University, Kiel, Germany
- omics2view.consulting GbR, Kiel, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Martin Wahl
- Marine Ecology Division, Research Unit Experimental Ecology, Benthic Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Ruth A. Schmitz
- Department of Biology, Institute of General Microbiology, Kiel University, Kiel, Germany
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22
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Paix B, Carriot N, Barry-Martinet R, Greff S, Misson B, Briand JF, Culioli G. A Multi-Omics Analysis Suggests Links Between the Differentiated Surface Metabolome and Epiphytic Microbiota Along the Thallus of a Mediterranean Seaweed Holobiont. Front Microbiol 2020; 11:494. [PMID: 32269559 PMCID: PMC7111306 DOI: 10.3389/fmicb.2020.00494] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/06/2020] [Indexed: 11/13/2022] Open
Abstract
Marine macroalgae constitute an important living resource in marine ecosystems and complex ecological interactions occur at their surfaces with microbial communities. In this context, the present study aimed to investigate how the surface metabolome of the algal holobiont Taonia atomaria could drive epiphytic microbiota variations at the thallus scale. First, a clear discrimination was observed between algal surface, planktonic and rocky prokaryotic communities. These data strengthened the hypothesis of an active role of the algal host in the selection of epiphytic communities. Moreover, significant higher epibacterial density and α-diversity were found at the basal algal parts compared to the apical ones, suggesting a maturation gradient of the community along the thallus. In parallel, a multiplatform mass spectrometry-based metabolomics study, using molecular networking to annotate relevant metabolites, highlighted a clear chemical differentiation at the algal surface along the thallus with similar clustering as for microbial communities. In that respect, higher amounts of sesquiterpenes, phosphatidylcholines (PCs), and diacylglycerylhydroxymethyl-N,N,N-trimethyl-β-alanines (DGTAs) were observed at the apical regions while dimethylsulfoniopropionate (DMSP) and carotenoids were predominantly found at the basal parts of the thalli. A weighted UniFrac distance-based redundancy analysis linking the metabolomics and metabarcoding datasets indicated that these surface compounds, presumably of algal origin, may drive the zonal variability of the epibacterial communities. As only few studies were focused on microbiota and metabolome variation along a single algal thallus, these results improved our understanding about seaweed holobionts. Through this multi-omics approach at the thallus scale, we suggested a plausible scenario where the chemical production at the surface of T. atomaria, mainly induced by the algal physiology, could explain the specificity and the variations of the surface microbiota along the thallus.
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Affiliation(s)
- Benoît Paix
- EA 4323, Matériaux Polymères Interfaces Environnement Marin, Université de Toulon, Toulon, France
| | - Nathan Carriot
- EA 4323, Matériaux Polymères Interfaces Environnement Marin, Université de Toulon, Toulon, France
| | - Raphaëlle Barry-Martinet
- EA 4323, Matériaux Polymères Interfaces Environnement Marin, Université de Toulon, Toulon, France
| | - Stéphane Greff
- UMR 7263, Aix Marseille Université, CNRS, IRD, Avignon Université, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, Station Marine d'Endoume, Marseille, France
| | - Benjamin Misson
- UMR 7294, Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, Marseille, France
| | - Jean-François Briand
- EA 4323, Matériaux Polymères Interfaces Environnement Marin, Université de Toulon, Toulon, France
| | - Gérald Culioli
- EA 4323, Matériaux Polymères Interfaces Environnement Marin, Université de Toulon, Toulon, France
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23
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Tarquinio F, Hyndes GA, Laverock B, Koenders A, Säwström C. The seagrass holobiont: understanding seagrass-bacteria interactions and their role in seagrass ecosystem functioning. FEMS Microbiol Lett 2020; 366:5382495. [PMID: 30883643 DOI: 10.1093/femsle/fnz057] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 03/16/2019] [Indexed: 12/27/2022] Open
Abstract
This review shows that the presence of seagrass microbial community is critical for the development of seagrasses; from seed germination, through to phytohormone production and enhanced nutrient availability, and defence against pathogens and saprophytes. The tight seagrass-bacterial relationship highlighted in this review supports the existence of a seagrass holobiont and adds to the growing evidence for the importance of marine eukaryotic microorganisms in sustaining vital ecosystems. Incorporating a micro-scale view on seagrass ecosystems substantially expands our understanding of ecosystem functioning and may have significant implications for future seagrass management and mitigation against human disturbance.
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Affiliation(s)
- Flavia Tarquinio
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, Western Australia, Australia.,Commonwealth Scientific and Industrial Research Organization, Crawley, 6009, Western Australia, Australia
| | - Glenn A Hyndes
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Bonnie Laverock
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, 2007, Australia.,School of Science, Auckland University of Technology, Auckland, 1010, New Zealand
| | - Annette Koenders
- Centre for Ecosystem Management, Edith Cowan University, Joondalup, 6027, Western Australia, Australia
| | - Christin Säwström
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, Western Australia, Australia
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24
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Thomas F, Dittami SM, Brunet M, Le Duff N, Tanguy G, Leblanc C, Gobet A. Evaluation of a new primer combination to minimize plastid contamination in 16S rDNA metabarcoding analyses of alga-associated bacterial communities. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:30-37. [PMID: 31692275 DOI: 10.1111/1758-2229.12806] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 05/21/2023]
Abstract
Plant- and alga-associated bacterial communities are generally described via 16S rDNA metabarcoding using universal primers. As plastid genomes encode 16S rDNA related to cyanobacteria, these data sets frequently contain >90% plastidial sequences, and the bacterial diversity may be under-sampled. To overcome this limitation we evaluated in silico the taxonomic coverage for four primer combinations targeting the 16S rDNA V3-V4 region. They included a forward primer universal to Bacteria (S-D-Bact-0341-b-S-17) and four reverse primers designed to avoid plastid DNA amplification. The best primer combination (NOCHL) was compared to the universal primer set in the wet lab using a synthetic community and samples from three macroalgal species. The proportion of plastid sequences was reduced by 99%-100% with the NOCHL primers compared to the universal primers, irrespective of algal hosts, sample collection and extraction protocols. Additionally, the NOCHL primers yielded a higher richness while maintaining the community structure. As Planctomycetes, Verrucomicrobia and Cyanobacteria were underrepresented (70%-90%) compared to universal primers, combining the NOCHL set with taxon-specific primers may be useful for a complete description of the alga-associated bacterial diversity. The NOCHL primers represent an innovation to study algal holobionts without amplifying host plastid sequences and may further be applied to other photosynthetic hosts.
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Affiliation(s)
- François Thomas
- Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), 29680, Roscoff, France
| | - Simon M Dittami
- Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), 29680, Roscoff, France
| | - Maéva Brunet
- Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), 29680, Roscoff, France
| | - Nolwen Le Duff
- Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), 29680, Roscoff, France
| | - Gwenn Tanguy
- Station Biologique de Roscoff, CNRS, Sorbonne Université, FR2424, Genomer, 29680, Roscoff, France
| | - Catherine Leblanc
- Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), 29680, Roscoff, France
| | - Angélique Gobet
- Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), 29680, Roscoff, France
- MARBEC, Ifremer, IRD, Université de Montpellier, CNRS, 34203, Sète, France
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25
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Saha M, Ferguson RMW, Dove S, Künzel S, Meichssner R, Neulinger SC, Petersen FO, Weinberger F. Salinity and Time Can Alter Epibacterial Communities of an Invasive Seaweed. Front Microbiol 2020; 10:2870. [PMID: 32010064 PMCID: PMC6974479 DOI: 10.3389/fmicb.2019.02870] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/28/2019] [Indexed: 11/13/2022] Open
Abstract
The establishment of epibacterial communities is fundamental to seaweed health and fitness, in modulating ecological interactions and may also facilitate adaptation to new environments. Abiotic factors like salinity can determine bacterial abundance, growth and community composition. However, influence of salinity as a driver of epibacterial community composition (until species level) has not been investigated for seaweeds and especially under long time scales. We also do not know how abiotic stressors may influence the 'core' bacterial species of seaweeds. Following an initial (immediately after field collection) sampling of epibacterial community of an invasive red seaweed Agarophyton vermicullophylum, we conducted a long term mesocosm experiment for 5 months, to examine the influence of three different salinities (low, medium and high) at two different time points (3 months after start of experiment and 5 months, i.e., at the end of experiment) on the epibacterial community richness and composition of Agarophyton. Metagenomic sequencing showed that epibacterial communities changed significantly according to salinity and time points sampled. Epibacterial richness was significantly different between low and high salinities at both time points. Epibacterial richness also varied significantly between 3 months (after start of experiment) and 5 months (end of experiment) within low, medium and high salinity level. Irrespective of salinity levels and time points sampled 727 taxa consistently appeared in all Agarophyton samples hinting at the presence of core bacterial species on the surface of the alga. Our results indicate that both salinity and time can be major driving forces in structuring epibacterial communities of seaweeds with respect to richness and β-diversity. We highlight the necessity of conducting long term experiments allowing us to detect and understand epibacterial succession over time on seaweeds.
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Affiliation(s)
- Mahasweta Saha
- Benthic Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.,The School of Life Sciences, University of Essex, Colchester, United Kingdom.,Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Plymouth, United Kingdom
| | - Robert M W Ferguson
- The School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Shawn Dove
- Centre for Biodiversity and Environment Research, University College London, London, United Kingdom.,Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Rafael Meichssner
- Department of Biology, Botanical Institute, Christian-Albrechts-University, Kiel, Germany.,Coastal Research & Management, Kiel, Germany
| | | | - Finn Ole Petersen
- Department of Biology, Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Florian Weinberger
- Benthic Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
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26
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Florez JZ, Camus C, Hengst MB, Marchant F, Buschmann AH. Structure of the epiphytic bacterial communities of Macrocystis pyrifera in localities with contrasting nitrogen concentrations and temperature. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101706] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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27
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Fischer MA, Ulbricht A, Neulinger SC, Refai S, Waßmann K, Künzel S, Schmitz RA. Immediate Effects of Ammonia Shock on Transcription and Composition of a Biogas Reactor Microbiome. Front Microbiol 2019; 10:2064. [PMID: 31555248 PMCID: PMC6742706 DOI: 10.3389/fmicb.2019.02064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/21/2019] [Indexed: 12/22/2022] Open
Abstract
The biotechnological process of biogas production from organic material is carried out by a diverse microbial community under anaerobic conditions. However, the complex and sensitive microbial network present in anaerobic degradation of organic material can be disturbed by increased ammonia concentration introduced into the system by protein-rich substrates and imbalanced feeding. Here, we report on a simulated increase of ammonia concentration in a fed batch lab-scale biogas reactor experiment. Two treatment conditions were used simulating total ammonia nitrogen concentrations of 4.9 and 8.0 g/L with four replicate reactors. Each reactor was monitored concerning methane generation and microbial composition using 16S rRNA gene amplicon sequencing, while the transcriptional activity of the overall process was investigated by metatranscriptomic analysis. This allowed investigating the response of the microbial community in terms of species composition and transcriptional activity to a rapid upshift to high ammonia conditions. Clostridia and Methanomicrobiales dominated the microbial community throughout the entire experiment under both experimental conditions, while Methanosarcinales were only present in minor abundance. Transcription analysis demonstrated clostridial dominance with respect to genes encoding for enzymes of the hydrolysis step (cellulase, EC 3.2.1.4) as well as dominance of key genes for enzymes of the methanogenic pathway (methyl-CoM reductase, EC 2.8.4.1; heterodisulfide reductase, EC 1.8.98.1). Upon ammonia shock, the selected marker genes showed significant changes in transcriptional activity. Cellulose hydrolysis as well as methanogenesis were significantly reduced at high ammonia concentrations as indicated by reduced transcription levels of the corresponding genes. Based on these experiments we concluded that, apart from the methanogenic archaea, hydrolytic cellulose-degrading microorganisms are negatively affected by high ammonia concentrations. Further, Acholeplasma and Erysipelotrichia showed lower abundance under increased ammonia concentrations and thus might serve as indicator species for an earlier detection in order to counteract against ammonia crises.
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Affiliation(s)
- Martin A Fischer
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Andrea Ulbricht
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Sven C Neulinger
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Sarah Refai
- Department of Biology, Institut für Mikrobiologie und Biotechnologie, University Bonn, Bonn, Germany
| | - Kati Waßmann
- Department of Biology, Institut für Mikrobiologie und Biotechnologie, University Bonn, Bonn, Germany
| | - Sven Künzel
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - Ruth A Schmitz
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
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28
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Paix B, Othmani A, Debroas D, Culioli G, Briand JF. Temporal covariation of epibacterial community and surface metabolome in the Mediterranean seaweed holobiont Taonia atomaria. Environ Microbiol 2019; 21:3346-3363. [PMID: 30945796 DOI: 10.1111/1462-2920.14617] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/31/2019] [Indexed: 11/30/2022]
Abstract
An integrative multi-omics approach allowed monthly variations for a year of the surface metabolome and the epibacterial community of the Mediterranean Phaeophyceae Taonia atomaria to be investigated. The LC-MS-based metabolomics and 16S rDNA metabarcoding data sets were integrated in a multivariate meta-omics analysis (multi-block PLS-DA from the MixOmic DIABLO analysis) showing a strong seasonal covariation (Mantel test: p < 0.01). A network based on positive and negative correlations between the two data sets revealed two clusters of variables, one relative to the 'spring period' and a second to the 'summer period'. The 'spring period' cluster was mainly characterized by dipeptides positively correlated with a single bacterial taxon of the Alteromonadaceae family (BD1-7 clade). Moreover, 'summer' dominant epibacterial taxa from the second cluster (including Erythrobacteraceae, Rhodospirillaceae, Oceanospirillaceae and Flammeovirgaceae) showed positive correlations with few metabolites known as macroalgal antifouling defences [e.g. dimethylsulphoniopropionate (DMSP) and proline] which exhibited a key role within the correlation network. Despite a core community that represents a significant part of the total epibacteria, changes in the microbiota structure associated with surface metabolome variations suggested that both environment and algal host shape the bacterial surface microbiota.
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Affiliation(s)
- Benoît Paix
- Université de Toulon, Laboratoire MAPIEM, EA 4323, Toulon, France
| | - Ahlem Othmani
- Université de Toulon, Laboratoire MAPIEM, EA 4323, Toulon, France
| | - Didier Debroas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, UMR 6023, Clermont-Ferrand, France
| | - Gérald Culioli
- Université de Toulon, Laboratoire MAPIEM, EA 4323, Toulon, France
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29
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Haemolymph microbiome of the cultured spiny lobster Panulirus ornatus at different temperatures. Sci Rep 2019; 9:1677. [PMID: 30737466 PMCID: PMC6368590 DOI: 10.1038/s41598-019-39149-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 01/18/2019] [Indexed: 02/02/2023] Open
Abstract
Lobsters have an open circulatory system with haemolymph that contains microorganisms even in the healthy individuals. Understanding the role of these microorganisms becomes increasingly important particularly for the diagnosis of disease as the closed life-cycle aquaculture of the spiny lobster Panulirus ornatus nears commercial reality. This study aimed to characterise haemolymph responses of healthy cultured P. ornatus juveniles at control (28 °C) and elevated (34 °C) temperatures. This was assessed by measuring immune parameters (total granulocyte counts, total haemocyte counts, clotting times), and culture-independent (pyrosequencing of haemolymph DNA) and culture-dependent (isolation using nonselective growth medium) techniques to analyse bacterial communities from lobster haemolymph sampled on days 0, 4 and 6 post-exposure to the temperature regimes. Elevated temperature (34 °C) affected lobster survival, total granulocyte counts, and diversity, load and functional potential of the haemolymph bacterial community. Pyrosequencing analyses showed that the core haemolymph microbiome consisted of phyla Proteobacteria and Bacteriodetes. Overall, culture-independent methods captured a higher bacterial diversity and load when compared to culture-dependent methods, however members of the Rhodobacteraceae were strongly represented in both analyses. This is the first comprehensive study providing comparisons of haemolymph bacterial communities from healthy and thermally stressed cultured juvenile P. ornatus and has the potential to be used in health monitoring programs.
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30
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Parrot D, Blümel M, Utermann C, Chianese G, Krause S, Kovalev A, Gorb SN, Tasdemir D. Mapping the Surface Microbiome and Metabolome of Brown Seaweed Fucus vesiculosus by Amplicon Sequencing, Integrated Metabolomics and Imaging Techniques. Sci Rep 2019; 9:1061. [PMID: 30705420 PMCID: PMC6355876 DOI: 10.1038/s41598-018-37914-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/17/2018] [Indexed: 02/05/2023] Open
Abstract
The brown alga Fucus vesiculosus is a keystone marine species, which is subject to heavy surface colonisation. This study was designed to analyse the surface epibiome of F. vesiculosus in conjunction with the composition and spatial distribution of its surface metabolome. The amplicon sequencing, SEM and CARD-FISH imaging studies showed Alphaproteobacteria to predominate the epibiotic bacteria. Fungi of the class Eurotiomycetes were visualised for the first time on an algal surface. An untargeted metabolomics approach using molecular networks, in silico prediction and manual dereplication showed the differential metabolome of the surface and the whole tissue extracts. In total, 50 compounds were putatively dereplicated by UPLC-MS/MS, 37 of which were previously reported from both seaweeds and microorganisms. Untargeted spatial metabolomics by DESI-Imaging MS identified the specific localisation and distribution of various primary and secondary metabolites on surface imprints and in algal cross sections. The UPLC-MS, DESI-IMS and NMR analyses failed to confirm the presence of any surface-associated metabolite, except for mannitol, which were previously reported from F. vesiculosus. This is the first study analysing the seaweed surface microbiome in conjunction with untargeted surface metabolomics and spatial metabolomics approaches.
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Affiliation(s)
- Delphine Parrot
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, Kiel, 24106, Germany
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, Kiel, 24106, Germany
| | - Caroline Utermann
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, Kiel, 24106, Germany
| | - Giuseppina Chianese
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, Kiel, 24106, Germany
| | - Stefan Krause
- Research Unit Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse 1-3, Kiel, 24148, Germany
| | - Alexander Kovalev
- Department of Functional Morphology and Biomechanics, Institute of Zoology, Kiel University, Am Botanischen Garten 9, Kiel, 24118, Germany
| | - Stanislav N Gorb
- Department of Functional Morphology and Biomechanics, Institute of Zoology, Kiel University, Am Botanischen Garten 9, Kiel, 24118, Germany
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, Kiel, 24106, Germany.
- Kiel University, Christian-Albrechts-Platz 4, Kiel, 24118, Germany.
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31
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Serebryakova A, Aires T, Viard F, Serrão EA, Engelen AH. Summer shifts of bacterial communities associated with the invasive brown seaweed Sargassum muticum are location and tissue dependent. PLoS One 2018; 13:e0206734. [PMID: 30517113 PMCID: PMC6281184 DOI: 10.1371/journal.pone.0206734] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 10/18/2018] [Indexed: 02/05/2023] Open
Abstract
Seaweed-associated microbiota experience spatial and temporal shifts in response to changing environmental conditions and seaweed physiology. These shifts may result in structural, functional and behavioral changes in the host with potential consequences for its fitness. They, thus, may help the host to adapt to changing environmental conditions. The current knowledge of seasonal variation of seaweed-associated microbiota is however still limited. In this study, we explored temporal and spatial variation of microbial communities associated with the invasive brown seaweed S. muticum. We sampled in northern and southern Portugal, in September, March and July-August (summer). In addition, as (pseudo-)perennial seaweeds display seasonal reproductive phenology, we sampled various parts of the individuals to disentangle the effect of temporal changes from those due to structural development variations. The diversity and structure of associated microbial communities were determined using next generation sequencing of the variable regions V5-7 of the 16S rDNA. We expected to find differentiation in associated microbial communities between regions and sampling months, but with differences depending on the seaweed structure examined. As expected, the study revealed substantial temporal shifts in S. muticum microbiome, for instance with large abundance of Rhodobacteraceae and Loktanella in September-March but prevalence of Pirellulales during the summer months. Variations between regions and tissues were also observed: in northern Portugal and on basal structures, bacterial diversity was higher as compared to the South and apical parts. All examined seaweed structures showed temporal differences in associated microbial community structure over time, except for holdfasts between September and March. Bacteria contributing to these changes varied spatially. Conversely to all other structures, the holdfast also did not show differences in associated community structure between southern and northern regions. Our study highlights the importance of structural microscale differentiations within seaweeds hosts with regard to their associated microbial communities and their importance across temporal and spatial dimensions.
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Affiliation(s)
- Alexandra Serebryakova
- Center for Marine Sciences (CCMAR), F.C.T. University of Algarve, Faro, Portugal
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, UPMC Univ Paris, Roscoff, France
| | - Tania Aires
- Center for Marine Sciences (CCMAR), F.C.T. University of Algarve, Faro, Portugal
| | - Frédérique Viard
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, UPMC Univ Paris, Roscoff, France
| | - Ester A. Serrão
- Center for Marine Sciences (CCMAR), F.C.T. University of Algarve, Faro, Portugal
| | - Aschwin H. Engelen
- Center for Marine Sciences (CCMAR), F.C.T. University of Algarve, Faro, Portugal
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32
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Mathai PP, Dunn HM, Magnone P, Brown CM, Chun CL, Sadowsky MJ. Spatial and temporal characterization of epiphytic microbial communities associated with Eurasian watermilfoil: a highly invasive macrophyte in North America. FEMS Microbiol Ecol 2018; 94:5089967. [DOI: 10.1093/femsec/fiy178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/01/2018] [Indexed: 01/19/2023] Open
Affiliation(s)
- Prince P Mathai
- BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave, St. Paul, MN 55108, USA
| | - Hannah M Dunn
- BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave, St. Paul, MN 55108, USA
| | - Paolo Magnone
- BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave, St. Paul, MN 55108, USA
| | - Clairessa M Brown
- BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave, St. Paul, MN 55108, USA
| | - Chan Lan Chun
- Department of Civil Engineering, University of Minnesota, 1405 University Drive, Duluth, MN 55812, USA
- National Resources Research Institute, University of Minnesota, 5013 Miller Trunk Highway, Duluth, MN 55811, USA
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave, St. Paul, MN 55108, USA
- Department of Soil, Water, and Climate, University of Minnesota, 439 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
- Department of Plant and Microbial Biology, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave, St. Paul, MN 55108, USA
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33
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Alvarado P, Huang Y, Wang J, Garrido I, Leiva S. Phylogeny and bioactivity of epiphytic Gram-positive bacteria isolated from three co-occurring antarctic macroalgae. Antonie Van Leeuwenhoek 2018; 111:1543-1555. [PMID: 29460205 DOI: 10.1007/s10482-018-1044-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 02/07/2018] [Indexed: 12/25/2022]
Abstract
Marine macroalgae are emerging as an untapped source of novel microbial diversity and, therefore, of new bioactive secondary metabolites. This study was aimed at assessing the diversity and antimicrobial activity of the culturable Gram-positive bacteria associated with the surface of three co-occurring Antarctic macroalgae. Specimens of Adenocystis utricularis (brown alga), Iridaea cordata (red alga) and Monostroma hariotii (green alga) were collected from the intertidal zone of King George Island, Antarctica. Gram-positive bacteria were investigated by cultivation-based methods and 16S rRNA gene sequencing, and screened for antimicrobial activity against a panel of pathogenic microorganisms. Isolates were found to belong to 12 families, with a dominance of Microbacteriaceae and Micrococcaceae. Seventeen genera of Actinobacteria and 2 of Firmicutes were cultured from the three macroalgae, containing 29 phylotypes. Three phylotypes within Actinobacteria were regarded as potentially novel species. Sixteen isolates belonging to the genera Agrococcus, Arthrobacter, Micrococcus, Pseudarthrobacter, Pseudonocardia, Sanguibacter, Staphylococcus, Streptomyces and Tessaracoccus exhibited antibiotic activity against at least one of the indicator strains. The bacterial phylotype composition was distinct among the three macroalgae species, suggesting that these macroalgae host species-specific Gram-positive associates. The results highlight the importance of Antarctic macroalgae as a rich source of Gram-positive bacterial diversity and potentially novel species, and a reservoir of bacteria producing biologically active compounds with pharmacological potential.
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Affiliation(s)
- Pamela Alvarado
- Universidad Tecnológica de Chile INACAP, Avenida René Soriano 2382, Osorno, Chile
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ignacio Garrido
- Département de Biologie et Québec-Océan, Université Laval, Pavillon Alexandre-Vachon 1045, Avenue de la Médecine, Québec, QC, G1V 0A6, Canada
- Centro FONDAP de Investigaciones en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Sergio Leiva
- Instituto de Bioquímica & Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.
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Roth‐Schulze AJ, Pintado J, Zozaya‐Valdés E, Cremades J, Ruiz P, Kjelleberg S, Thomas T. Functional biogeography and host specificity of bacterial communities associated with the Marine Green Alga
Ulva
spp. Mol Ecol 2018; 27:1952-1965. [DOI: 10.1111/mec.14529] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 01/30/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Alexandra J. Roth‐Schulze
- Centre for Marine Bio‐Innovation School of Biological, Earth and Environmental Sciences The University of New South Wales Sydney NSW Australia
| | - José Pintado
- Centre for Marine Bio‐Innovation School of Biological, Earth and Environmental Sciences The University of New South Wales Sydney NSW Australia
- Instituto de Investigacións Mariñas (IIM ‐ CSIC) Vigo Spain
| | - Enrique Zozaya‐Valdés
- Centre for Marine Bio‐Innovation School of Biological, Earth and Environmental Sciences The University of New South Wales Sydney NSW Australia
| | - Javier Cremades
- BIOCOST Centro de Investigaciones Científicas Avanzadas (CICA) Universidade da Coruña A Coruña Spain
| | - Patricia Ruiz
- Instituto de Investigacións Mariñas (IIM ‐ CSIC) Vigo Spain
| | - Staffan Kjelleberg
- Centre for Marine Bio‐Innovation School of Biological, Earth and Environmental Sciences The University of New South Wales Sydney NSW Australia
| | - Torsten Thomas
- Centre for Marine Bio‐Innovation School of Biological, Earth and Environmental Sciences The University of New South Wales Sydney NSW Australia
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35
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Smale DA, Taylor JD, Coombs SH, Moore G, Cunliffe M. Community responses to seawater warming are conserved across diverse biological groupings and taxonomic resolutions. Proc Biol Sci 2018; 284:rspb.2017.0534. [PMID: 28878056 PMCID: PMC5597821 DOI: 10.1098/rspb.2017.0534] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/28/2017] [Indexed: 02/01/2023] Open
Abstract
Temperature variability is a major driver of ecological pattern, with recent changes in average and extreme temperatures having significant impacts on populations, communities and ecosystems. In the marine realm, very few experiments have manipulated temperature in situ, and current understanding of temperature effects on community dynamics is limited. We developed new technology for precise seawater temperature control to examine warming effects on communities of bacteria, microbial eukaryotes (protists) and metazoans. Despite highly contrasting phylogenies, size spectra and diversity levels, the three community types responded similarly to seawater warming treatments of +3°C and +5°C, highlighting the critical and overarching importance of temperature in structuring communities. Temperature effects were detectable at coarse taxonomic resolutions and many taxa responded positively to warming, leading to increased abundances at the community-level. Novel field-based experimental approaches are essential to improve mechanistic understanding of how ocean warming will alter the structure and functioning of diverse marine communities.
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Affiliation(s)
- Dan A Smale
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Joe D Taylor
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.,Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Steve H Coombs
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | | | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.,Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK
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36
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Zimmermann A, Knecht H, Häsler R, Zissel G, Gaede KI, Hofmann S, Nebel A, Müller-Quernheim J, Schreiber S, Fischer A. Atopobium and Fusobacterium as novel candidates for sarcoidosis-associated microbiota. Eur Respir J 2017; 50:50/6/1600746. [PMID: 29242257 DOI: 10.1183/13993003.00746-2016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/28/2017] [Indexed: 01/20/2023]
Abstract
Sarcoidosis is a granulomatous disease that mainly affects the lung. A role of microbial factors in disease pathogenesis is assumed, but has not been investigated systematically in a large cohort.This cross-sectional study compared the lung microbiota of 71 patients with sarcoidosis, 15 patients with idiopathic pulmonary fibrosis (non-infectious controls) and 10 healthy controls (HCs). Next-generation sequencing of 16S DNA was used on bronchoalveolar lavage samples to characterise the microbial composition, which was analysed for diversity and indicator species. Host genotypes for 13 known sarcoidosis risk variants were determined and correlated with microbial parameters.The microbial composition differed significantly between sarcoidosis and HC samples (redundancy analysis ANOVA, p=0.025) and between radiographic Scadding types. Atopobium spp. was detected in 68% of sarcoidosis samples, but not in HC samples. Fusobacterium spp. was significantly more abundant in sarcoidosis samples compared with those from HCs. Mycobacteria were found in two of 71 sarcoidosis samples. Host-genotype analysis revealed an association of the rs2076530 (BTNL2) risk allele with a decrease in bacterial burden (p=0.002).Our results indicate Scadding type-dependent microbiota in sarcoidosis BAL samples. Atopobium spp. and Fusobacterium spp. were identified as sarcoidosis-associated bacteria, which may enable new insights into the pathogenesis and treatment of the disease.
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Affiliation(s)
- Alexandra Zimmermann
- Institute of Clinical Molecular Biology, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Henrik Knecht
- Institute of Clinical Molecular Biology, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gernot Zissel
- Dept of Pneumology, University of Freiburg, Freiburg, Germany
| | - Karoline I Gaede
- BioMaterialBank Nord, Dept of Medicine, Research Center Borstel, Leibniz Center for Medicine and Biosciences, Borstel, Germany.,Airway Research Center North, Member of the German Center for Lung Research
| | - Sylvia Hofmann
- Dept of Conservation Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany.,Clinic of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Annegret Fischer
- Institute of Clinical Molecular Biology, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
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37
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Dogs M, Wemheuer B, Wolter L, Bergen N, Daniel R, Simon M, Brinkhoff T. Rhodobacteraceae on the marine brown alga Fucus spiralis are abundant and show physiological adaptation to an epiphytic lifestyle. Syst Appl Microbiol 2017; 40:370-382. [PMID: 28641923 DOI: 10.1016/j.syapm.2017.05.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/05/2017] [Accepted: 05/12/2017] [Indexed: 12/01/2022]
Abstract
Macroalgae harbour specific microbial communities on their surface that have functions related to host health and defence. In this study, the bacterial biofilm of the marine brown alga Fucus spiralis was investigated using 16S rRNA gene amplicon-based analysis and isolation of bacteria. Rhodobacteraceae (Alphaproteobacteria) were the predominant family constituting 23% of the epibacterial community. At the genus level, Sulfitobacter, Loktanella, Octadecabacter and a previously undescribed cluster were most abundant, and together they comprised 89% of the Rhodobacteraceae. Supported by a specific PCR approach, 23 different Rhodobacteraceae-affiliated strains were isolated from the surface of F. spiralis, which belonged to 12 established and three new genera. For seven strains, closely related sequences were detected in the 16S rRNA gene dataset. Growth experiments with substrates known to be produced by Fucus spp. showed that all of them were consumed by at least three strains, and vitamin B12 was produced by 70% of the isolates. Since growth of F. spiralis depends on B12 supplementation, bacteria may provide the alga with this vitamin. Most strains produced siderophores, which can enhance algal growth under iron-deficient conditions. Inhibiting properties against other bacteria were only observed when F. spiralis material was present in the medium. Thus, the physiological properties of the isolates indicated adaption to an epiphytic lifestyle.
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Affiliation(s)
- Marco Dogs
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bernd Wemheuer
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Laura Wolter
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Nils Bergen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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38
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Rickert E, Wahl M, Link H, Richter H, Pohnert G. Seasonal Variations in Surface Metabolite Composition of Fucus vesiculosus and Fucus serratus from the Baltic Sea. PLoS One 2016; 11:e0168196. [PMID: 27959901 PMCID: PMC5154555 DOI: 10.1371/journal.pone.0168196] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/28/2016] [Indexed: 11/18/2022] Open
Abstract
Perennial macroalgae within the genus Fucus are known to exude metabolites through their outer thallus surface. Some of these metabolites have pro- and/or antifouling properties. Seasonal fluctuations of natural fouling pressure and chemical fouling control strength against micro- and macrofoulers have previously been observed in Fucus, suggesting that control strength varies with threat. To date, a study on the seasonal composition of surface associated metabolites, responsible for much of the fouling control, has not been done. We sampled individuals of the two co-occurring species F. vesiculosus and F. serratus at monthly intervals (six per species and month) during a one-year field study. We analysed the chemical composition of surface associated metabolites of both Fucus species by means of gas chromatography-mass spectrometry (GC-MS) to describe temporal patterns in chemical surface composition. Additionally, we correlated abiotic and biotic parameters recorded monthly within the sampled habitat with the variation in the chemical surface landscape of Fucus. Our study revealed that the chemical surface composition of both Fucus species exhibits substantial seasonal differences between spring/summer and autumn/winter months. Light and temperature explained most of the seasonal variability in surface metabolite composition of both Fucus species. A strong summerly up-regulation of eighteen saccharides and two hydroxy acids in F. vesiculosus as well as of four fatty acids and two saccharides in F. serratus was observed. We discuss how these up-regulated molecules may have a complex effect on associated microfoulers, both promoting or decreasing fouling depending on metabolite and bacterial identity. These seasonal shifts in the surface metabolome seem to exert a compound control of density and composition of the Fucus associated biofilm.
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Affiliation(s)
- Esther Rickert
- Department of Marine Ecology, Division of Benthic Ecology, Helmholtz Centre for Ocean Research Kiel GEOMAR, Kiel, Germany
| | - Martin Wahl
- Department of Marine Ecology, Division of Benthic Ecology, Helmholtz Centre for Ocean Research Kiel GEOMAR, Kiel, Germany
| | - Heike Link
- Institute for Ecosystem Research, Kiel University, Kiel, Germany
| | - Hannes Richter
- Institute for Inorganic and Analytical Chemistry, Department for Bioorganic Analytics, Friedrich Schiller University Jena, Jena, Germany
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Department for Bioorganic Analytics, Friedrich Schiller University Jena, Jena, Germany
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39
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Roik A, Röthig T, Roder C, Ziegler M, Kremb SG, Voolstra CR. Year-Long Monitoring of Physico-Chemical and Biological Variables Provide a Comparative Baseline of Coral Reef Functioning in the Central Red Sea. PLoS One 2016; 11:e0163939. [PMID: 27828965 PMCID: PMC5102394 DOI: 10.1371/journal.pone.0163939] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 09/16/2016] [Indexed: 11/26/2022] Open
Abstract
Coral reefs in the central Red Sea are sparsely studied and in situ data on physico-chemical and key biotic variables that provide an important comparative baseline are missing. To address this gap, we simultaneously monitored three reefs along a cross-shelf gradient for an entire year over four seasons, collecting data on currents, temperature, salinity, dissolved oxygen (DO), chlorophyll-a, turbidity, inorganic nutrients, sedimentation, bacterial communities of reef water, and bacterial and algal composition of epilithic biofilms. Summer temperature (29–33°C) and salinity (39 PSU) exceeded average global maxima for coral reefs, whereas DO concentration was low (2–4 mg L-1). While temperature and salinity differences were most pronounced between seasons, DO, chlorophyll-a, turbidity, and sedimentation varied most between reefs. Similarly, biotic communities were highly dynamic between reefs and seasons. Differences in bacterial biofilms were driven by four abundant families: Rhodobacteraceae, Flavobacteriaceae, Flammeovirgaceae, and Pseudanabaenaceae. In algal biofilms, green crusts, brown crusts, and crustose coralline algae were most abundant and accounted for most of the variability of the communities. Higher bacterial diversity of biofilms coincided with increased algal cover during spring and summer. By employing multivariate matching, we identified temperature, salinity, DO, and chlorophyll-a as the main contributing physico-chemical drivers of biotic community structures. These parameters are forecast to change most with the progression of ocean warming and increased nutrient input, which suggests an effect on the recruitment of Red Sea benthic communities as a result of climate change and anthropogenic influence. In conclusion, our study provides insight into coral reef functioning in the Red Sea and a comparative baseline to support coral reef studies in the region.
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Affiliation(s)
- Anna Roik
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Saudi Arabia
| | - Till Röthig
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Saudi Arabia
| | - Cornelia Roder
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Saudi Arabia
| | - Maren Ziegler
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Saudi Arabia
| | - Stephan G. Kremb
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Saudi Arabia
| | - Christian R. Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Saudi Arabia
- * E-mail:
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40
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Säwström C, Hyndes GA, Eyre BD, Huggett MJ, Fraser MW, Lavery PS, Thomson PG, Tarquinio F, Steinberg PD, Laverock B. Coastal connectivity and spatial subsidy from a microbial perspective. Ecol Evol 2016; 6:6662-6671. [PMID: 27777738 PMCID: PMC5058536 DOI: 10.1002/ece3.2408] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 08/06/2016] [Indexed: 01/04/2023] Open
Abstract
The transfer of organic material from one coastal environment to another can increase production in recipient habitats in a process known as spatial subsidy. Microorganisms drive the generation, transformation, and uptake of organic material in shallow coastal environments, but their significance in connecting coastal habitats through spatial subsidies has received limited attention. We address this by presenting a conceptual model of coastal connectivity that focuses on the flow of microbially mediated organic material in key coastal habitats. Our model suggests that it is not the difference in generation rates of organic material between coastal habitats but the amount of organic material assimilated into microbial biomass and respiration that determines the amount of material that can be exported from one coastal environment to another. Further, the flow of organic material across coastal habitats is sensitive to environmental change as this can alter microbial remineralization and respiration rates. Our model highlights microorganisms as an integral part of coastal connectivity and emphasizes the importance of including a microbial perspective in coastal connectivity studies.
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Affiliation(s)
- Christin Säwström
- School of Science Centre for Marine Ecosystems Research Edith Cowan University Joondalup WA Australia
| | - Glenn A Hyndes
- School of Science Centre for Marine Ecosystems Research Edith Cowan University Joondalup WA Australia
| | - Bradley D Eyre
- School of Environment Science and Engineering Centre for Coastal Biogeochemistry Research Southern Cross University Lismore NSW Australia
| | - Megan J Huggett
- School of Science Centre for Marine Ecosystems Research Edith Cowan University Joondalup WA Australia
| | - Matthew W Fraser
- The UWA Oceans Institute and the School of Plant Biology The University of Western Australia Crawley WA Australia
| | - Paul S Lavery
- School of Science Centre for Marine Ecosystems Research Edith Cowan University Joondalup WA Australia
| | - Paul G Thomson
- The School of Civil, Environmental and Mining Engineering and The UWA Oceans Institute The University of Western Australia Crawley WA Australia
| | - Flavia Tarquinio
- School of Science Centre for Marine Ecosystems Research Edith Cowan University Joondalup WA Australia
| | - Peter D Steinberg
- Sydney Institute of Marine Science Mosman NSW Australia; Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
| | - Bonnie Laverock
- The UWA Oceans Institute and the School of Plant Biology The University of Western Australia Crawley WA Australia; Plant Functional Biology and Climate Change Cluster University of Technology Sydney Sydney NSW Australia
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41
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Egan S, Gardiner M. Microbial Dysbiosis: Rethinking Disease in Marine Ecosystems. Front Microbiol 2016; 7:991. [PMID: 27446031 PMCID: PMC4914501 DOI: 10.3389/fmicb.2016.00991] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/09/2016] [Indexed: 11/16/2022] Open
Abstract
With growing environmental pressures placed on our marine habitats there is concern that the prevalence and severity of diseases affecting marine organisms will increase. Yet relative to terrestrial systems, we know little about the underlying causes of many of these diseases. Moreover, factors such as saprophytic colonizers and a lack of baseline data on healthy individuals make it difficult to accurately assess the role of specific microbial pathogens in disease states. Emerging evidence in the field of medicine suggests that a growing number of human diseases result from a microbiome imbalance (or dysbiosis), questioning the traditional view of a singular pathogenic agent. Here we discuss the possibility that many diseases seen in marine systems are, similarly, the result of microbial dysbiosis and the rise of opportunistic or polymicrobial infections. Thus, understanding and managing disease in the future will require us to also rethink definitions of disease and pathogenesis for marine systems. We suggest that a targeted, multidisciplinary approach that addresses the questions of microbial symbiosis in both healthy and diseased states, and at that the level of the holobiont, will be key to progress in this area.
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Affiliation(s)
- Suhelen Egan
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, SydneyNSW, Australia
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42
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Roth-Schulze AJ, Zozaya-Valdés E, Steinberg PD, Thomas T. Partitioning of functional and taxonomic diversity in surface-associated microbial communities. Environ Microbiol 2016; 18:4391-4402. [PMID: 27062175 DOI: 10.1111/1462-2920.13325] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 03/29/2016] [Accepted: 03/31/2016] [Indexed: 12/14/2022]
Abstract
Surfaces, including those submerged in the marine environment, are subjected to constant interactions and colonisation by surrounding microorganisms. The principles that determine the assembly of those epibiotic communities are however poorly understood. In this study, we employed a hierarchical design to assess the functionality and diversity of microbial communities on different types of host surfaces (e.g. macroalgae, seagrasses). We found that taxonomic diversity was unique to each type of host, but that the majority of functions (> 95%) could be found in any given surface community, suggesting a high degree of functional redundancy. However, some community functions were enriched on certain surfaces and were related to host-specific properties (e.g. the degradation of specific polysaccharides). Together these observations support a model, whereby communities on surfaces are assembled from guilds of microorganisms with a functionality that is partitioned into general properties for a surface-associated life-style, but also specific features that mediate host-specificity.
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Affiliation(s)
- Alexandra J Roth-Schulze
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Enrique Zozaya-Valdés
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Peter D Steinberg
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia.,Sydney Institute of Marine Science, 2 Chowder Bay Rd., Mosman, NSW, 2088, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
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43
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Mancuso FP, D'Hondt S, Willems A, Airoldi L, De Clerck O. Diversity and Temporal Dynamics of the Epiphytic Bacterial Communities Associated with the Canopy-Forming Seaweed Cystoseira compressa (Esper) Gerloff and Nizamuddin. Front Microbiol 2016; 7:476. [PMID: 27092130 PMCID: PMC4824759 DOI: 10.3389/fmicb.2016.00476] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 03/22/2016] [Indexed: 02/01/2023] Open
Abstract
Canopy-forming seaweed species of the genus Cystoseira form diverse and productive habitats along temperate rocky coasts of the Mediterranean Sea. Despite numerous studies on the rich macrofauna and flora associated with Cystoseira spp., there is little knowledge about the epiphytic bacteria. We analyzed bacterial populations associated with canopies of Cystoseira compressa, over an annual vegetative cycle (May-October), and their relationships with the bacterial populations in the surrounding seawater, at intertidal rocky shores in Vasto (Chieti—Italy). The bacterial diversity was assessed using Illumina Miseq sequences of V1-V3 hypervariable regions of 16S rRNA gene. C. compressa bacterial community was dominated by sequences of Proteobacteria and Bacteroidetes, Verrucomicrobia, Actinobacteria, and Cyanobacteria especially of the Rhodobacteriaceae, Flavobacteriaceae, Sapropiraceae, Verrucomicrobiaceae, and Phyllobacteriaceae families. Seawater libraries were also dominated by Proteobacteria and Bacteroidetes sequences, especially of the Candidatus Pelagibacter (SAR11) and Rhodobacteriaceae families, but were shown to be clearly distinct from C. compressa libraries with only few species in common between the two habitats. We observed a clear successional pattern in the epiphytic bacteria of C. compressa over time. These variations were characterized by gradual addition of OTUs (Verrucomicrobia, Actinobacteria and SR1) to the community over a growing season, indicative of a temporal gradient, rather than a radical reorganization of the bacterial community. Moreover, we also found an increase in abundance over time of Rhodobacteraceae, comprising six potential pathogenic genera, Ruegeria, Nautella, Aquimarina, Loktanella, Saprospira, and Phaeobacter which seemed to be associated to aged thalli of C. compressa. These bacteria could have the potential to affect the health and ecology of the algae, suggesting the hypothesis of a possible, but still unexplored, role of the microbial communities in contributing to the extensive ongoing declines of populations of Cystoseira spp. in the Mediterranean Sea.
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Affiliation(s)
- Francesco P Mancuso
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, Centro Interdipartimentale di Ricerca per le Scienze Ambientali, UO CoNISMa, University of BolognaRavenna, Italy; Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent UniversityGhent, Belgium
| | - Sofie D'Hondt
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University Ghent, Belgium
| | - Anne Willems
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Laura Airoldi
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, Centro Interdipartimentale di Ricerca per le Scienze Ambientali, UO CoNISMa, University of Bologna Ravenna, Italy
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University Ghent, Belgium
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Mensch B, Neulinger SC, Graiff A, Pansch A, Künzel S, Fischer MA, Schmitz RA. Restructuring of Epibacterial Communities on Fucus vesiculosus forma mytili in Response to Elevated pCO2 and Increased Temperature Levels. Front Microbiol 2016; 7:434. [PMID: 27065988 PMCID: PMC4814934 DOI: 10.3389/fmicb.2016.00434] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/17/2016] [Indexed: 12/31/2022] Open
Abstract
Marine multicellular organisms in composition with their associated microbiota-representing metaorganisms-are confronted with constantly changing environmental conditions. In 2110, the seawater temperature is predicted to be increased by ~5°C, and the atmospheric carbon dioxide partial pressure (pCO2) is expected to reach approximately 1000 ppm. In order to assess the response of marine metaorganisms to global changes, e.g., by effects on host-microbe interactions, we evaluated the response of epibacterial communities associated with Fucus vesiculosus forma mytili (F. mytili) to future climate conditions. During an 11-week lasting mesocosm experiment on the island of Sylt (Germany) in spring 2014, North Sea F. mytili individuals were exposed to elevated pCO2 (1000 ppm) and increased temperature levels (Δ+5°C). Both abiotic factors were tested for single and combined effects on the epibacterial community composition over time, with three replicates per treatment. The respective community structures of bacterial consortia associated to the surface of F. mytili were analyzed by Illumina MiSeq 16S rDNA amplicon sequencing after 0, 4, 8, and 11 weeks of treatment (in total 96 samples). The results demonstrated that the epibacterial community structure was strongly affected by temperature, but only weakly by elevated pCO2. No interaction effect of both factors was observed in the combined treatment. We identified several indicator operational taxonomic units (iOTUs) that were strongly influenced by the respective experimental factors. An OTU association network analysis revealed that relationships between OTUs were mainly governed by habitat. Overall, this study contributes to a better understanding of how epibacterial communities associated with F. mytili may adapt to future changes in seawater acidity and temperature, ultimately with potential consequences for host-microbe interactions.
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Affiliation(s)
- Birte Mensch
- Department of Biology, Institute for General Microbiology, Christian-Albrechts University Kiel Kiel, Germany
| | - Sven C Neulinger
- Department of Biology, Institute for General Microbiology, Christian-Albrechts University Kiel Kiel, Germany
| | - Angelika Graiff
- Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock Rostock, Germany
| | - Andreas Pansch
- Coastal Ecology, Alfred Wegener Institute List on the island of Sylt, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology Plön, Germany
| | - Martin A Fischer
- Department of Biology, Institute for General Microbiology, Christian-Albrechts University Kiel Kiel, Germany
| | - Ruth A Schmitz
- Department of Biology, Institute for General Microbiology, Christian-Albrechts University Kiel Kiel, Germany
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Vieira C, Engelen AH, Guentas L, Aires T, Houlbreque F, Gaubert J, Serrão EA, De Clerck O, Payri CE. Species Specificity of Bacteria Associated to the Brown Seaweeds Lobophora (Dictyotales, Phaeophyceae) and Their Potential for Induction of Rapid Coral Bleaching in Acropora muricata. Front Microbiol 2016; 7:316. [PMID: 27047453 PMCID: PMC4800410 DOI: 10.3389/fmicb.2016.00316] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/29/2016] [Indexed: 11/13/2022] Open
Abstract
While reef degradation is occurring worldwide, it is not uncommon to see phase shifts from coral to macroalgal dominated reefs. Numerous studies have addressed the mechanisms by which macroalgae may outcompete corals and a few recent studies highlighted the putative role of bacteria at the interface between macroalgae and corals. Some studies suggest that macroalgae may act as vectors and/or foster proliferation of microorganisms pathogenic for corals. Using a combination of high throughput sequencing, bacterial culturing, and in situ bioassays we question if the adversity of macroalgal-associated bacteria to corals is mediated by specific bacterial taxa. Using Illumina sequencing, we characterized and compared the bacterial community from two Lobophora (Dictyotales, Phaeophyceae) species. The two species presented distinctive bacterial communities. Both species shared approximately half of their OTUs, mainly the most abundant bacteria. Species-specific OTUs belong to Planctomycetes, Proteobacteria, and Bacteroidetes. In total, 16 culturable bacterial strain were isolated and identified from the Lobophora surface, consisting of 10 genera (from nine families, four classes, and three phyla), some of which are not known as, but are related to pathogens involved in coral diseases, and others are naturally associated to corals. When patches of marine agar with 24 h cultures of each of these bacteria were placed in direct contact with the branches of the scleractinian coral Acropora muricata, they caused severe bleaching after 24 h exposure. Results suggest that regardless of taxonomic affinities, increase in density of these bacteria can be adverse to corals. Nevertheless, the microbial community associated to macroalgal surface may not represent a threat to corals, because the specific bacterial screening and control exerted by the alga preventing specific bacterial proliferation.
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Affiliation(s)
- Christophe Vieira
- IFD, Sorbonne Universités, UPMC Univ Paris 06Paris, France; UMR ENTROPIE (UR, IRD, Centre National de la Recherche Scientifique), Institut de Recherche pour le DéveloppementNouméa, New Caledonia; Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent UniversityGhent, Belgium
| | | | - Linda Guentas
- Laboratoire MAPIEM EA 4323, Université de ToulonLa Garde, France; Laboratoire LIVE, Université de Nouvelle-CalédonieNouméa, New Caledonia
| | - Tânia Aires
- Centre of Marine Sciences, University of the Algarve Portugal
| | - Fanny Houlbreque
- UMR ENTROPIE (UR, IRD, Centre National de la Recherche Scientifique), Institut de Recherche pour le Développement Nouméa, New Caledonia
| | - Julie Gaubert
- UMR ENTROPIE (UR, IRD, Centre National de la Recherche Scientifique), Institut de Recherche pour le Développement Nouméa, New Caledonia
| | - Ester A Serrão
- Centre of Marine Sciences, University of the Algarve Portugal
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University Ghent, Belgium
| | - Claude E Payri
- UMR ENTROPIE (UR, IRD, Centre National de la Recherche Scientifique), Institut de Recherche pour le Développement Nouméa, New Caledonia
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Martin M, Barbeyron T, Martin R, Portetelle D, Michel G, Vandenbol M. The Cultivable Surface Microbiota of the Brown Alga Ascophyllum nodosum is Enriched in Macroalgal-Polysaccharide-Degrading Bacteria. Front Microbiol 2015; 6:1487. [PMID: 26734000 PMCID: PMC4690005 DOI: 10.3389/fmicb.2015.01487] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/10/2015] [Indexed: 11/30/2022] Open
Abstract
Bacteria degrading algal polysaccharides are key players in the global carbon cycle and in algal biomass recycling. Yet the water column, which has been studied largely by metagenomic approaches, is poor in such bacteria and their algal-polysaccharide-degrading enzymes. Even more surprisingly, the few published studies on seaweed-associated microbiomes have revealed low abundances of such bacteria and their specific enzymes. However, as macroalgal cell-wall polysaccharides do not accumulate in nature, these bacteria and their unique polysaccharidases must not be that uncommon. We, therefore, looked at the polysaccharide-degrading activity of the cultivable bacterial subpopulation associated with Ascophyllum nodosum. From A. nodosum triplicates, 324 bacteria were isolated and taxonomically identified. Out of these isolates, 78 (~25%) were found to act on at least one tested algal polysaccharide (agar, ι- or κ-carrageenan, or alginate). The isolates “active” on algal-polysaccharides belong to 11 genera: Cellulophaga, Maribacter, Algibacter, and Zobellia in the class Flavobacteriia (41) and Pseudoalteromonas, Vibrio, Cobetia, Shewanella, Colwellia, Marinomonas, and Paraglaceciola in the class Gammaproteobacteria (37). A major part represents likely novel species. Different proportions of bacterial phyla and classes were observed between the isolated cultivable subpopulation and the total microbial community previously identified on other brown algae. Here, Bacteroidetes and Gammaproteobacteria were found to be the most abundant and some phyla (as Planctomycetes and Cyanobacteria) frequently encountered on brown algae weren't identified. At a lower taxonomic level, twelve genera, well-known to be associated with algae (with the exception for Colwellia), were consistently found on all three A. nosodum samples. Even more interesting, 9 of the 11 above mentioned genera containing polysaccharolytic isolates were predominant in this common core. The cultivable fraction of the bacterial community associated with A. nodosum is, thus, significantly enriched in macroalgal-polysaccharide-degrading bacteria and these bacteria seem important for the seaweed holobiont even though they are under-represented in alga-associated microbiome studies.
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Affiliation(s)
- Marjolaine Martin
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
| | - Tristan Barbeyron
- Sorbonne Université, UPMC, Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models Roscoff, France
| | - Renee Martin
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
| | - Daniel Portetelle
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
| | - Gurvan Michel
- Sorbonne Université, UPMC, Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models Roscoff, France
| | - Micheline Vandenbol
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
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Graham LE, Wilcox LW, Knack JJ. Why we need more algal metagenomes(1). JOURNAL OF PHYCOLOGY 2015; 51:1029-1036. [PMID: 26986998 DOI: 10.1111/jpy.12344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/14/2015] [Indexed: 06/05/2023]
Abstract
A recent perspective article ably argued that fully sequencing more algal genomes would enable progress in diverse areas of fundamental and applied studies. More algal genomes would add resources needed to build well-supported phylogenies, improve our understanding of how horizontal gene transfer has influenced the evolution of algal genomes, provide useful ecological insights, and generate information essential to manipulating the genomes of industrially useful algae (J. Phycol. 51:1). We agree that more algal genomes would be quite beneficial, and also propose that more algal metagenomes would enable progress in both predictable and unforeseen directions.
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Affiliation(s)
- Linda E Graham
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Lee W Wilcox
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Jennifer J Knack
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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48
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Zimmermann A, Zissel G, Müller-Quernheim J, Hofmann S, Schreiber S, Fischer A. Are bronchoalveolar lavages a good source for microbial profiling? Differences between throat and bronchoalveolar lavage microbiomes. J Med Microbiol 2015; 64:948-951. [PMID: 26271248 DOI: 10.1099/jmm.0.000112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Gernot Zissel
- Department of Pneumology, Center for Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Joachim Müller-Quernheim
- Department of Pneumology, Center for Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Sylvia Hofmann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Annegret Fischer
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
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49
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Heinsen FA, Knecht H, Neulinger SC, Schmitz RA, Knecht C, Kühbacher T, Rosenstiel PC, Schreiber S, Friedrichs AK, Ott SJ. Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin. Gut Microbes 2015; 6:243-54. [PMID: 26178862 PMCID: PMC4615565 DOI: 10.1080/19490976.2015.1062959] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Gut microbiota play a key role in the host's health system. Broad antibiotic therapy is known to disrupt the microbial balance affecting pathogenic as well as host-associated microbes. The aim of the present study was to investigate the influence of antibiotic paromomycin on the luminal and mucosa-associated microbiota at the DNA (abundance) and RNA (potential activity) level as well as to identify possible differences. The influence of antibiotic treatment on intestinal microbiota was investigated in 5 healthy individuals (age range: 20-22 years). All participants received the antibiotic paromomycin for 3 d. Fecal samples as well as sigmoidal biopsies were collected before and immediately after cessation of antibiotic treatment as well as after a recovery phase of 42 d. Compartment- and treatment status-specific indicator operational taxonomic units (OTUs) as well as abundance- and activity-specific patterns were identified by 16S rRNA and 16S rRNA gene amplicon libraries and high-throughput pyrosequencing. Microbial composition of lumen and mucosa were significantly different at the DNA compared to the RNA level. Antibiotic treatment resulted in changes of the microbiota, affecting the luminal and mucosal bacteria in a similar way. Several OTUs were identified as compartment- and/or treatment status-specific. Abundance and activity patterns of some indicator OTUs differed considerably. The study shows fundamental changes in composition of gut microbiota under antibiotic therapy at both the potential activity and the abundance level at different treatment status. It may help to understand the complex processes of gut microbiota changes involved in resilience mechanisms and on development of antibiotic-associated clinical diseases.
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Affiliation(s)
- Femke-Anouska Heinsen
- Institute of Clinical Molecular Biology (ICMB); Christian-Albrechts-University (CAU) Kiel; Kiel, Germany
| | - Henrik Knecht
- Institute of Clinical Molecular Biology (ICMB); Christian-Albrechts-University (CAU) Kiel; Kiel, Germany
| | - Sven C Neulinger
- Institute for General Microbiology (IFAM); CAU Kiel; Kiel, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology (IFAM); CAU Kiel; Kiel, Germany
| | - Carolin Knecht
- Institute of Medical Informatics and Statistics (IMIS); CAU Kiel; Kiel, Germany
| | - Tanja Kühbacher
- Institute of Clinical Molecular Biology (ICMB); Christian-Albrechts-University (CAU) Kiel; Kiel, Germany,Department of Internal Medicine I; University Hospital Schleswig-Holstein (UKSH); Campus Kiel; Kiel, Germany
| | - Philip C Rosenstiel
- Institute of Clinical Molecular Biology (ICMB); Christian-Albrechts-University (CAU) Kiel; Kiel, Germany,Department of Internal Medicine I; University Hospital Schleswig-Holstein (UKSH); Campus Kiel; Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology (ICMB); Christian-Albrechts-University (CAU) Kiel; Kiel, Germany,Department of Internal Medicine I; University Hospital Schleswig-Holstein (UKSH); Campus Kiel; Kiel, Germany
| | - Anette K Friedrichs
- Institute of Clinical Molecular Biology (ICMB); Christian-Albrechts-University (CAU) Kiel; Kiel, Germany,Department of Internal Medicine I; University Hospital Schleswig-Holstein (UKSH); Campus Kiel; Kiel, Germany
| | - Stephan J Ott
- Institute of Clinical Molecular Biology (ICMB); Christian-Albrechts-University (CAU) Kiel; Kiel, Germany,Department of Internal Medicine I; University Hospital Schleswig-Holstein (UKSH); Campus Kiel; Kiel, Germany,Corresponding author: Stephan J Ott; E-mail:
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50
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Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population. Appl Environ Microbiol 2015; 81:6038-52. [PMID: 26116680 DOI: 10.1128/aem.01601-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/19/2015] [Indexed: 01/25/2023] Open
Abstract
The scyphozoan Aurelia aurita is recognized as a key player in marine ecosystems and a driver of ecosystem change. It is thus intensely studied to address ecological questions, although its associations with microorganisms remain so far undescribed. In the present study, the microbiota associated with A. aurita was visualized with fluorescence in situ hybridization (FISH) analysis, and community structure was analyzed with respect to different life stages, compartments, and populations of A. aurita by 16S rRNA gene amplicon sequencing. We demonstrate that the composition of the A. aurita microbiota is generally highly distinct from the composition of communities present in ambient water. Comparison of microbial communities from different developmental stages reveals evidence for life stage-specific community patterns. Significant restructuring of the microbiota during strobilation from benthic polyp to planktonic life stages is present, arguing for a restructuring during the course of metamorphosis. Furthermore, the microbiota present in different compartments of the adult medusa (exumbrella mucus and gastric cavity) display significant differences, indicating body part-specific colonization. A novel Mycoplasma strain was identified in both compartment-specific microbiota and is most likely present inside the epithelium as indicated by FISH analysis of polyps, indicating potential endosymbiosis. Finally, comparison of polyps of different populations kept under the same controlled laboratory conditions in the same ambient water showed population-specific community patterns, most likely due the genetic background of the host. In conclusion, the presented data indicate that the associated microbiota of A. aurita may play important functional roles, e.g., during the life cycle.
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