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Hill LJ, Messias CSMDA, Vilela CLS, Garritano AN, Villela HDM, do Carmo FL, Thomas T, Peixoto RS. Bacteria associated with the in hospite Symbiodiniaceae's phycosphere. iScience 2024; 27:109531. [PMID: 38585661 PMCID: PMC10995889 DOI: 10.1016/j.isci.2024.109531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/23/2023] [Accepted: 03/16/2024] [Indexed: 04/09/2024] Open
Abstract
Symbiotic interactions between Symbiodiniaceae and bacteria are still poorly explored, especially those in hospite. Here, we adapted a technique that allows for the enrichment of intact and metabolically active in hospite Symbiodiniaceae cells (ihSC) and their associated bacteria from the tissue of the model coral Pocillopora damicornis, using a discontinuous gradient of solution of isotonic Percoll (SIP). The ihSC were concentrated in the 50% SIP fraction, as determined by microscopy. The presence of bacteria associated with ihSC was confirmed by fluorescence in situ hybridization, while microbiome analysis indicated that bacteria of the families Halieaceae, Flavobacteriaceae, and Alcanivoraceae are significantly associated with ihSC. Extracellular vesicles that could be exuding molecules were detected on the symbiosome membranes. Our technique and data contribute to elucidate ihSC-bacteria interactions.
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Affiliation(s)
- Lilian Jorge Hill
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | | | - Caren Leite Spindola Vilela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Alessandro N Garritano
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Helena Dias Muller Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - Flavia Lima do Carmo
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Raquel S. Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
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2
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Delgadillo-Ordoñez N, Garcias-Bonet N, Raimundo I, García FC, Villela H, Osman EO, Santoro EP, Curdia J, Rosado JGD, Cardoso P, Alsaggaf A, Barno A, Antony CP, Bocanegra C, Berumen ML, Voolstra CR, Benzoni F, Carvalho S, Peixoto RS. Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment. Commun Biol 2024; 7:434. [PMID: 38594357 PMCID: PMC11004148 DOI: 10.1038/s42003-024-06135-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
Beneficial microorganisms for corals (BMCs), or probiotics, can enhance coral resilience against stressors in laboratory trials. However, the ability of probiotics to restructure the coral microbiome in situ is yet to be determined. As a first step to elucidate this, we inoculated putative probiotic bacteria (pBMCs) on healthy colonies of Pocillopora verrucosa in situ in the Red Sea, three times per week, during 3 months. pBMCs significantly influenced the coral microbiome, while bacteria of the surrounding seawater and sediment remained unchanged. The inoculated genera Halomonas, Pseudoalteromonas, and Bacillus were significantly enriched in probiotic-treated corals. Furthermore, the probiotic treatment also correlated with an increase in other beneficial groups (e.g., Ruegeria and Limosilactobacillus), and a decrease in potential coral pathogens, such as Vibrio. As all corals (treated and non-treated) remained healthy throughout the experiment, we could not track health improvements or protection against stress. Our data indicate that healthy, and therefore stable, coral microbiomes can be restructured in situ, although repeated and continuous inoculations may be required in these cases. Further, our study provides supporting evidence that, at the studied scale, pBMCs have no detectable off-target effects on the surrounding microbiomes of seawater and sediment near inoculated corals.
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Affiliation(s)
- Nathalia Delgadillo-Ordoñez
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Neus Garcias-Bonet
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Inês Raimundo
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Francisca C García
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Helena Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Eslam O Osman
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Erika P Santoro
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Joao Curdia
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Joao G D Rosado
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Pedro Cardoso
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ahmed Alsaggaf
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Adam Barno
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Chakkiath Paul Antony
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carolina Bocanegra
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael L Berumen
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Francesca Benzoni
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Raquel S Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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3
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Voolstra CR, Raina JB, Dörr M, Cárdenas A, Pogoreutz C, Silveira CB, Mohamed AR, Bourne DG, Luo H, Amin SA, Peixoto RS. The coral microbiome in sickness, in health and in a changing world. Nat Rev Microbiol 2024:10.1038/s41579-024-01015-3. [PMID: 38438489 DOI: 10.1038/s41579-024-01015-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 03/06/2024]
Abstract
Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.
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Affiliation(s)
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia.
| | - Melanie Dörr
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Anny Cárdenas
- Department of Biology, American University, Washington, DC, USA
| | - Claudia Pogoreutz
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | | | - Amin R Mohamed
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Haiwei Luo
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, State Key Laboratory of Agrobiotechnology and Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shady A Amin
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Raquel S Peixoto
- Red Sea Research Center (RSRC) and Computational Biology Research Center (CBRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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4
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Garcias-Bonet N, Roik A, Tierney B, García FC, Villela HDM, Dungan AM, Quigley KM, Sweet M, Berg G, Gram L, Bourne DG, Ushijima B, Sogin M, Hoj L, Duarte G, Hirt H, Smalla K, Rosado AS, Carvalho S, Thurber RV, Ziegler M, Mason CE, van Oppen MJH, Voolstra CR, Peixoto RS. Horizon scanning the application of probiotics for wildlife. Trends Microbiol 2024; 32:252-269. [PMID: 37758552 DOI: 10.1016/j.tim.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called 'probiotics for wildlife' is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.
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Affiliation(s)
- Neus Garcias-Bonet
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), Bremerhaven, Germany
| | - Braden Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Francisca C García
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena D M Villela
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ashley M Dungan
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kate M Quigley
- Minderoo Foundation, Perth, WA, Australia; James Cook University, Townsville, Australia
| | - Michael Sweet
- Aquatic Research Facility, Nature-based Solutions Research Centre, University of Derby, Derby, UK
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; University of Potsdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Maggie Sogin
- Molecular Cell Biology, University of California, Merced, CA, USA
| | - Lone Hoj
- Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Gustavo Duarte
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; IMPG, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heribert Hirt
- Center for Desert Agriculture (CDA), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Alexandre S Rosado
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; WorldQuant Initiative on Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | | | - Raquel S Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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5
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Staab S, Cardénas A, Peixoto RS, Schreiber F, Voolstra CR. Coracle-a machine learning framework to identify bacteria associated with continuous variables. Bioinformatics 2024; 40:btad749. [PMID: 38123508 PMCID: PMC10766586 DOI: 10.1093/bioinformatics/btad749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/06/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023] Open
Abstract
SUMMARY We present Coracle, an artificial intelligence (AI) framework that can identify associations between bacterial communities and continuous variables. Coracle uses an ensemble approach of prominent feature selection methods and machine learning (ML) models to identify features, i.e. bacteria, associated with a continuous variable, e.g. host thermal tolerance. The results are aggregated into a score that incorporates the performances of the different ML models and the respective feature importance, while also considering the robustness of feature selection. Additionally, regression coefficients provide first insights into the direction of the association. We show the utility of Coracle by analyzing associations between bacterial composition data (i.e. 16S rRNA Amplicon Sequence Variants, ASVs) and coral thermal tolerance (i.e. standardized short-term heat stress-derived diagnostics). This analysis identified high-scoring bacterial taxa that were previously found associated with coral thermal tolerance. Coracle scales with feature number and performs well with hundreds to thousands of features, corresponding to the typical size of current datasets. Coracle performs best if run at a higher taxonomic level first (e.g. order or family) to identify groups of interest that can subsequently be run at the ASV level. AVAILABILITY AND IMPLEMENTATION Coracle can be accessed via a dedicated web server that allows free and simple access: http://www.micportal.org/coracle/index. The underlying code is open-source and available via GitHub https://github.com/SebastianStaab/coracle.git.
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Affiliation(s)
- Sebastian Staab
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Anny Cardénas
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
- Department of Biology, American University, Washington, DC, 20016, USA
| | - Raquel S Peixoto
- Computational Biology Research Center (CBRC) and Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz 78457, Germany
- Faculty of Information Technology, Monash University, 3168, Australia
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Carvalho S, Shchepanik H, Aylagas E, Berumen ML, Costa FO, Costello MJ, Duarte S, Ferrario J, Floerl O, Heinle M, Katsanevakis S, Marchini A, Olenin S, Pearman JK, Peixoto RS, Rabaoui LJ, Ruiz G, Srėbalienė G, Therriault TW, Vieira PE, Zaiko A. Hurdles and opportunities in implementing marine biosecurity systems in data-poor regions. Bioscience 2023; 73:494-512. [PMID: 37560322 PMCID: PMC10408360 DOI: 10.1093/biosci/biad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 08/11/2023] Open
Abstract
Managing marine nonindigenous species (mNIS) is challenging, because marine environments are highly connected, allowing the dispersal of species across large spatial scales, including geopolitical borders. Cross-border inconsistencies in biosecurity management can promote the spread of mNIS across geopolitical borders, and incursions often go unnoticed or unreported. Collaborative surveillance programs can enhance the early detection of mNIS, when response may still be possible, and can foster capacity building around a common threat. Regional or international databases curated for mNIS can inform local monitoring programs and can foster real-time information exchange on mNIS of concern. When combined, local species reference libraries, publicly available mNIS databases, and predictive modeling can facilitate the development of biosecurity programs in regions lacking baseline data. Biosecurity programs should be practical, feasible, cost-effective, mainly focused on prevention and early detection, and be built on the collaboration and coordination of government, nongovernment organizations, stakeholders, and local citizens for a rapid response.
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Affiliation(s)
- Susana Carvalho
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
| | - Hailey Shchepanik
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
| | - Eva Aylagas
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
- Red Sea Global, Riyadh 12382-6726, Saudi Arabia
| | - Michael L Berumen
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA) and Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | | | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Jasmine Ferrario
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | | | - Moritz Heinle
- Applied Research Center for Environment & Marine Studies, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
- International Centre for Water Resources and Global Change, Federal Institute of Hydrology, Koblenz, Germany
| | | | - Agnese Marchini
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Sergej Olenin
- Marine Research Institute, Klaipeda University, Lithuania
| | | | - Raquel S Peixoto
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
| | - Lotfi J Rabaoui
- Applied Research Center for Environment & Marine Studies, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
- National Center for Wildlife, Riyadh, Saudi Arabia
| | - Greg Ruiz
- Smithsonian Environmental Research Center, Edgewater, Maryland
| | | | | | - Pedro E Vieira
- Centre of Molecular and Environmental Biology (CBMA) and Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Anastasija Zaiko
- Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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7
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Voolstra CR, Peixoto RS, Ferrier-Pagès C. Mitigating the ecological collapse of coral reef ecosystems: Effective strategies to preserve coral reef ecosystems: Effective strategies to preserve coral reef ecosystems. EMBO Rep 2023; 24:e56826. [PMID: 36862379 PMCID: PMC10074092 DOI: 10.15252/embr.202356826] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/25/2023] [Accepted: 02/09/2023] [Indexed: 03/03/2023] Open
Abstract
Global warming is decimating coral reefs. We need to implement mitigation and restoration strategies now to prevent coral reefs from disappearing altogether.
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Affiliation(s)
| | - Raquel S Peixoto
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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8
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Pinheiro Y, Faria da Mota F, Peixoto RS, van Elsas JD, Lins U, Mazza Rodrigues JL, Rosado AS. A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environments. Commun Biol 2023; 6:230. [PMID: 36859706 PMCID: PMC9977764 DOI: 10.1038/s42003-023-04617-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
A thermophilic, chemolithoautotrophic, and aerobic microbial consortium (termed carbonitroflex) growing in a nutrient-poor medium and an atmosphere containing N2, O2, CO2, and CO is investigated as a model to expand our understanding of extreme biological systems. Here we show that the consortium is dominated by Carbonactinospora thermoautotrophica (strain StC), followed by Sphaerobacter thermophilus, Chelatococcus spp., and Geobacillus spp. Metagenomic analysis of the consortium reveals a mutual relationship among bacteria, with C. thermoautotrophica StC exhibiting carboxydotrophy and carbon-dioxide storage capacity. C. thermoautotrophica StC, Chelatococcus spp., and S. thermophilus harbor genes encoding CO dehydrogenase and formate oxidase. No pure cultures were obtained under the original growth conditions, indicating that a tightly regulated interactive metabolism might be required for group survival and growth in this extreme oligotrophic system. The breadwinner hypothesis is proposed to explain the metabolic flux model and highlight the vital role of C. thermoautotrophica StC (the sole keystone species and primary carbon producer) in the survival of all consortium members. Our data may contribute to the investigation of complex interactions in extreme environments, exemplifying the interconnections and dependency within microbial communities.
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Affiliation(s)
- Yuri Pinheiro
- Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabio Faria da Mota
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Raquel S Peixoto
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | | | - Ulysses Lins
- Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jorge L Mazza Rodrigues
- Department of Land, Air, and Water Resources, University of California Davis, Davis, CA, USA
| | - Alexandre Soares Rosado
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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9
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Rachid CTCC, Balieiro FC, Peixoto RS, Fonseca ES, Jesus HE, Novotny EH, Chaer GM, Santos FM, Tiedje JM, Rosado AS. Mycobiome structure does not affect field litter decomposition in Eucalyptus and Acacia plantations. Front Microbiol 2023; 14:1106422. [PMID: 36925466 PMCID: PMC10011713 DOI: 10.3389/fmicb.2023.1106422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/01/2023] [Indexed: 03/08/2023] Open
Abstract
Mixed tree plantations have been studied because of their potential to improve biomass production, ecosystem diversity, and soil quality. One example is a mixture of Eucalyptus and Acacia trees, which is a promising strategy to improve microbial diversity and nutrient cycling in soil. We examined how a mixture of these species may influence the biochemical attributes and fungal community associated with leaf litter, and the effects on litter decomposition. We studied the litter from pure and mixed plantations, evaluating the effects of plant material and incubation site on the mycobiome and decomposition rate using litterbags incubated in situ. Our central hypothesis was litter fungal community would change according to incubation site, and it would interfere in litter decomposition rate. Both the plant material and the incubation locale significantly affected the litter decomposition. The origin of the litter was the main modulator of the mycobiome, with distinct communities from one plant species to another. The community changed with the incubation time but the incubation site did not influence the mycobiome community. Our data showed that litter and soil did not share the main elements of the community. Contrary to our hypothesis, the microbial community structure and diversity lacked any association with the decomposition rate. The differences in the decomposition pattern are explained basically as a function of the exchange of nitrogen compounds between the litter.
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Affiliation(s)
- Caio T C C Rachid
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Raquel S Peixoto
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Eduardo S Fonseca
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Hugo E Jesus
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Felipe M Santos
- Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil.,Rede ILPF, Brasília, Brazil
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
| | - Alexandre S Rosado
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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10
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Davies SW, Gamache MH, Howe-Kerr LI, Kriefall NG, Baker AC, Banaszak AT, Bay LK, Bellantuono AJ, Bhattacharya D, Chan CX, Claar DC, Coffroth MA, Cunning R, Davy SK, del Campo J, Díaz-Almeyda EM, Frommlet JC, Fuess LE, González-Pech RA, Goulet TL, Hoadley KD, Howells EJ, Hume BCC, Kemp DW, Kenkel CD, Kitchen SA, LaJeunesse TC, Lin S, McIlroy SE, McMinds R, Nitschke MR, Oakley CA, Peixoto RS, Prada C, Putnam HM, Quigley K, Reich HG, Reimer JD, Rodriguez-Lanetty M, Rosales SM, Saad OS, Sampayo EM, Santos SR, Shoguchi E, Smith EG, Stat M, Stephens TG, Strader ME, Suggett DJ, Swain TD, Tran C, Traylor-Knowles N, Voolstra CR, Warner ME, Weis VM, Wright RM, Xiang T, Yamashita H, Ziegler M, Correa AMS, Parkinson JE. Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. PeerJ 2023; 11:e15023. [PMID: 37151292 PMCID: PMC10162043 DOI: 10.7717/peerj.15023] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/17/2023] [Indexed: 05/09/2023] Open
Abstract
Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
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Affiliation(s)
- Sarah W. Davies
- Department of Biology, Boston University, Boston, MA, United States
| | - Matthew H. Gamache
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
| | | | | | - Andrew C. Baker
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | - Anastazia T. Banaszak
- Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Line Kolind Bay
- Australian Institute of Marine Science, Townsville, Australia
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Danielle C. Claar
- Nearshore Habitat Program, Washington State Department of Natural Resources, Olympia, WA, USA
| | | | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL, United States
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Javier del Campo
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | | | - Jörg C. Frommlet
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Lauren E. Fuess
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Raúl A. González-Pech
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
- Department of Biology, Pennsylvania State University, State College, PA, United States
| | - Tamar L. Goulet
- Department of Biology, University of Mississippi, University, MS, United States
| | - Kenneth D. Hoadley
- Department of Biological Sciences, University of Alabama—Tuscaloosa, Tuscaloosa, AL, United States
| | - Emily J. Howells
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | | | - Dustin W. Kemp
- Department of Biology, University of Alabama—Birmingham, Birmingham, Al, United States
| | - Carly D. Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sheila A. Kitchen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Todd C. LaJeunesse
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Mansfield, CT, United States
| | - Shelby E. McIlroy
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ryan McMinds
- Center for Global Health and Infectious Disease Research, University of South Florida, Tampa, FL, United States
| | | | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Raquel S. Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | | | - Hannah G. Reich
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - James Davis Reimer
- Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | - Stephanie M. Rosales
- The Cooperative Institute For Marine and Atmospheric Studies, Miami, FL, United States
| | - Osama S. Saad
- Department of Biological Oceanography, Red Sea University, Port-Sudan, Sudan
| | - Eugenia M. Sampayo
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Scott R. Santos
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Edward G. Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Michael Stat
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Timothy G. Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Marie E. Strader
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - David J. Suggett
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy D. Swain
- Department of Marine and Environmental Science, Nova Southeastern University, Dania Beach, FL, United States
| | - Cawa Tran
- Department of Biology, University of San Diego, San Diego, CA, United States
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | | | - Mark E. Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Rachel M. Wright
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, United States
| | - Tingting Xiang
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen (Germany), Giessen, Germany
| | | | - John Everett Parkinson
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
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11
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Delgadillo-Ordoñez N, Raimundo I, Barno AR, Osman EO, Villela H, Bennett-Smith M, Voolstra CR, Benzoni F, Peixoto RS. Red Sea Atlas of Coral-Associated Bacteria Highlights Common Microbiome Members and Their Distribution across Environmental Gradients-A Systematic Review. Microorganisms 2022; 10:microorganisms10122340. [PMID: 36557593 PMCID: PMC9787610 DOI: 10.3390/microorganisms10122340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/12/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
The Red Sea is a suitable model for studying coral reefs under climate change due to its strong environmental gradient that provides a window into future global warming scenarios. For instance, corals in the southern Red Sea thrive at temperatures predicted to occur at the end of the century in other biogeographic regions. Corals in the Red Sea thrive under contrasting thermal and environmental regimes along their latitudinal gradient. Because microbial communities associated with corals contribute to host physiology, we conducted a systematic review of the known diversity of Red Sea coral-associated bacteria, considering geographic location and host species. Our assessment comprises 54 studies of 67 coral host species employing cultivation-dependent and cultivation-independent techniques. Most studies have been conducted in the central and northern Red Sea, while the southern and western regions remain largely unexplored. Our data also show that, despite the high diversity of corals in the Red Sea, the most studied corals were Pocillopora verrucosa, Dipsastraea spp., Pleuractis granulosa, and Stylophora pistillata. Microbial diversity was dominated by bacteria from the class Gammaproteobacteria, while the most frequently occurring bacterial families included Rhodobacteraceae and Vibrionaceae. We also identified bacterial families exclusively associated with each of the studied coral orders: Scleractinia (n = 125), Alcyonacea (n = 7), and Capitata (n = 2). This review encompasses 20 years of research in the Red Sea, providing a baseline compendium for coral-associated bacterial diversity.
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Affiliation(s)
- Nathalia Delgadillo-Ordoñez
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Inês Raimundo
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Adam R. Barno
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Eslam O. Osman
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Helena Villela
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Morgan Bennett-Smith
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Christian R. Voolstra
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Francesca Benzoni
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Raquel S. Peixoto
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Correspondence:
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12
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Peixoto RS, Voolstra CR, Sweet M, Duarte CM, Carvalho S, Villela H, Lunshof JE, Gram L, Woodhams DC, Walter J, Roik A, Hentschel U, Thurber RV, Daisley B, Ushijima B, Daffonchio D, Costa R, Keller-Costa T, Bowman JS, Rosado AS, Reid G, Mason CE, Walke JB, Thomas T, Berg G. Harnessing the microbiome to prevent global biodiversity loss. Nat Microbiol 2022; 7:1726-1735. [PMID: 35864220 DOI: 10.1038/s41564-022-01173-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/14/2022] [Indexed: 01/21/2023]
Abstract
Global biodiversity loss and mass extinction of species are two of the most critical environmental issues the world is currently facing, resulting in the disruption of various ecosystems central to environmental functions and human health. Microbiome-targeted interventions, such as probiotics and microbiome transplants, are emerging as potential options to reverse deterioration of biodiversity and increase the resilience of wildlife and ecosystems. However, the implementation of these interventions is urgently needed. We summarize the current concepts, bottlenecks and ethical aspects encompassing the careful and responsible management of ecosystem resources using the microbiome (termed microbiome stewardship) to rehabilitate organisms and ecosystem functions. We propose a real-world application framework to guide environmental and wildlife probiotic applications. This framework details steps that must be taken in the upscaling process while weighing risks against the high toll of inaction. In doing so, we draw parallels with other aspects of contemporary science moving swiftly in the face of urgent global challenges.
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Affiliation(s)
- Raquel S Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Christian R Voolstra
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena Villela
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jeantine E Lunshof
- Department of Global Health and Social Medicine, Center for Bioethics, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jens Walter
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Ute Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Brendan Daisley
- Lawson Health Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Jeff S Bowman
- Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
| | - Alexandre S Rosado
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gregor Reid
- Lawson Health Research Institute, University of Western Ontario, London, Ontario, Canada
| | | | - Jenifer B Walke
- Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Torsten Thomas
- Centre for Marine Science and Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.,University of Postdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
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13
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Cardoso PM, Alsaggaf AA, Villela HM, Peixoto RS. Inducing Polyp Bail-out in Coral Colonies to Obtain Individualized Micropropagates for Laboratory Experimental Use. J Vis Exp 2022. [DOI: 10.3791/63840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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14
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Barno AR, Villela HDM, Aranda M, Thomas T, Peixoto RS. Correction referring to: Host under epigenetic control: A novel perspective on the interaction between microorganisms and corals. Bioessays 2021; 43:e2170086. [PMID: 34510509 DOI: 10.1002/bies.202170086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Barno AR, Villela HDM, Aranda M, Thomas T, Peixoto RS. Host under epigenetic control: A novel perspective on the interaction between microorganisms and corals. Bioessays 2021; 43:e2100068. [PMID: 34463364 DOI: 10.1002/bies.202100068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022]
Abstract
Coral reefs have been challenged by the current rate and severity of environmental change that might outpace their ability to adapt and survive. Current research focuses on understanding how microbial communities and epigenetic changes separately affect phenotypes and gene expression of corals. Here, we provide the hypothesis that coral-associated microorganisms may directly or indirectly affect the coral's phenotypic response through the modulation of its epigenome. Homologs of ankyrin-repeat protein A and internalin B, which indirectly cause histone modifications in humans, as well as Rv1988 histone methyltransferase, and the DNA methyltransferases Rv2966c, Mhy1, Mhy2, and Mhy3 found in coral-associated bacteria indicate that there are potential host epigenome-modifying proteins in the coral microbiome. With the ideas presented here, we suggest that microbiome manipulation may be a means to alter a coral's epigenome, which could aid the current efforts to protect coral reefs. Also see the video abstract here: https://youtu.be/CW9GbChjKM4.
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Affiliation(s)
- Adam R Barno
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia
| | - Helena D M Villela
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia
| | - Manuel Aranda
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Australia
| | - Raquel S Peixoto
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia.,Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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16
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Santoro EP, Borges RM, Espinoza JL, Freire M, Messias CSMA, Villela HDM, Pereira LM, Vilela CLS, Rosado JG, Cardoso PM, Rosado PM, Assis JM, Duarte GAS, Perna G, Rosado AS, Macrae A, Dupont CL, Nelson KE, Sweet MJ, Voolstra CR, Peixoto RS. Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality. Sci Adv 2021; 7:7/33/eabg3088. [PMID: 34389536 PMCID: PMC8363143 DOI: 10.1126/sciadv.abg3088] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/24/2021] [Indexed: 05/03/2023]
Abstract
Beneficial microorganisms for corals (BMCs) ameliorate environmental stress, but whether they can prevent mortality and the underlying host response mechanisms remains elusive. Here, we conducted omics analyses on the coral Mussismilia hispida exposed to bleaching conditions in a long-term mesocosm experiment and inoculated with a selected BMC consortium or a saline solution placebo. All corals were affected by heat stress, but the observed "post-heat stress disorder" was mitigated by BMCs, signified by patterns of dimethylsulfoniopropionate degradation, lipid maintenance, and coral host transcriptional reprogramming of cellular restructuration, repair, stress protection, and immune genes, concomitant with a 40% survival rate increase and stable photosynthetic performance by the endosymbiotic algae. This study provides insights into the responses that underlie probiotic host manipulation. We demonstrate that BMCs trigger a dynamic microbiome restructuring process that instigates genetic and metabolic alterations in the coral host that eventually mitigate coral bleaching and mortality.
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Affiliation(s)
- Erika P Santoro
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ricardo M Borges
- Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Josh L Espinoza
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA
- Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Marcelo Freire
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Infectious Diseases and Global Health, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Camila S M A Messias
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Helena D M Villela
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Leandro M Pereira
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Caren L S Vilela
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - João G Rosado
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Pedro M Cardoso
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Phillipe M Rosado
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Juliana M Assis
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gustavo A S Duarte
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gabriela Perna
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Alexandre S Rosado
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Andrew Macrae
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Christopher L Dupont
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA
| | - Karen E Nelson
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA
| | - Michael J Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Christian R Voolstra
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Raquel S Peixoto
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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17
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Silva DP, Villela HDM, Santos HF, Duarte GAS, Ribeiro JR, Ghizelini AM, Vilela CLS, Rosado PM, Fazolato CS, Santoro EP, Carmo FL, Ximenes DS, Soriano AU, Rachid CTCC, Vega Thurber RL, Peixoto RS. Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites. Microbiome 2021; 9:118. [PMID: 34020712 PMCID: PMC8138999 DOI: 10.1186/s40168-021-01041-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/22/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Beginning in the last century, coral reefs have suffered the consequences of anthropogenic activities, including oil contamination. Chemical remediation methods, such as dispersants, can cause substantial harm to corals and reduce their resilience to stressors. To evaluate the impacts of oil contamination and find potential alternative solutions to chemical dispersants, we conducted a mesocosm experiment with the fire coral Millepora alcicornis, which is sensitive to environmental changes. We exposed M. alcicornis to a realistic oil-spill scenario in which we applied an innovative multi-domain bioremediator consortium (bacteria, filamentous fungi, and yeast) and a chemical dispersant (Corexit® 9500, one of the most widely used dispersants), to assess the effects on host health and host-associated microbial communities. RESULTS The selected multi-domain microbial consortium helped to mitigate the impacts of the oil, substantially degrading the polycyclic aromatic and n-alkane fractions and maintaining the physiological integrity of the corals. Exposure to Corexit 9500 negatively impacted the host physiology and altered the coral-associated microbial community. After exposure, the abundances of certain bacterial genera such as Rugeria and Roseovarius increased, as previously reported in stressed or diseased corals. We also identified several bioindicators of Corexit 9500 in the microbiome. The impact of Corexit 9500 on the coral health and microbial community was far greater than oil alone, killing corals after only 4 days of exposure in the flow-through system. In the treatments with Corexit 9500, the action of the bioremediator consortium could not be observed directly because of the extreme toxicity of the dispersant to M. alcicornis and its associated microbiome. CONCLUSIONS Our results emphasize the importance of investigating the host-associated microbiome in order to detect and mitigate the effects of oil contamination on corals and the potential role of microbial mitigation and bioindicators as conservation tools. Chemical dispersants were far more damaging to corals and their associated microbiome than oil, and should not be used close to coral reefs. This study can aid in decision-making to minimize the negative effects of oil and dispersants on coral reefs. Video abstract.
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Affiliation(s)
- Denise P Silva
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Helena D M Villela
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Henrique F Santos
- Department of Marine Biology, Fluminense Federal University (UFF), Niterói, Brazil
| | - Gustavo A S Duarte
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - José Roberto Ribeiro
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Angela M Ghizelini
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Caren L S Vilela
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Phillipe M Rosado
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Carolline S Fazolato
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Erika P Santoro
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Flavia L Carmo
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Dalton S Ximenes
- Processes Laboratory, Leopoldo Américo Miguez de Mello Research Center (CENPES), Petrobras, Rio de Janeiro, Brazil
| | - Adriana U Soriano
- Environmental Treatments, Wastes and Water Resources, Leopoldo Américo Miguez de Mello Research Center (CENPES), Petrobras, Rio de Janeiro, Brazil
| | - Caio T C C Rachid
- LABEM, Paulo de Góes Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Rebecca L Vega Thurber
- Department of Microbiology, Oregon State University, Nash Hall 226, OSU, Corvallis, OR, 97331, USA.
| | - Raquel S Peixoto
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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18
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Vilela CLS, Villela HDM, Duarte GAS, Santoro EP, Rachid CTCC, Peixoto RS. Estrogen induces shift in abundances of specific groups of the coral microbiome. Sci Rep 2021; 11:2767. [PMID: 33531587 PMCID: PMC7854615 DOI: 10.1038/s41598-021-82387-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
Synthetic estrogens such as ethinylestradiol (EE2) are persistent micropollutants that are not effectively removed from wastewater by conventional treatments. These contaminants are released into waterbodies, where they disrupt endocrine systems of organisms and cause harmful effects such as feminization, infertility, reproduction problems and genital malformations. The consequences of this pollution for key marine ecosystems such as coral reefs and their associated microbiomes are underexplored. We evaluated the effects of EE2 concentrations of 100 ng L-1 and 100 µg L-1 on the coral metaorganism Mussismilia harttii. The results indicated no effects on visible bleaching or Fv/Fm ratios in the corals during a 17-day microcosm experiment. However, next-generation sequencing of 16S rDNA revealed a statistically significant effect of high EE2 concentrations on OTU richness, and shifts in specific microbial groups after treatments with or without EE2. These groups might be bioindicators of early shifts in the metaorganism composition caused by EE2 contamination.
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Affiliation(s)
- Caren L S Vilela
- Department of General Microbiology, Paulo de Goes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Helena D M Villela
- Department of General Microbiology, Paulo de Goes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gustavo A S Duarte
- Department of General Microbiology, Paulo de Goes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Erika P Santoro
- Department of General Microbiology, Paulo de Goes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Caio T C C Rachid
- Department of General Microbiology, Paulo de Goes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel S Peixoto
- Department of General Microbiology, Paulo de Goes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuval, Saudi Arabia.
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19
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Assis JM, Abreu F, Villela HMD, Barno A, Valle RF, Vieira R, Taveira I, Duarte G, Bourne DG, Høj L, Peixoto RS. Delivering Beneficial Microorganisms for Corals: Rotifers as Carriers of Probiotic Bacteria. Front Microbiol 2021; 11:608506. [PMID: 33384676 PMCID: PMC7769773 DOI: 10.3389/fmicb.2020.608506] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/25/2020] [Indexed: 01/10/2023] Open
Abstract
The use of Beneficial Microorganisms for Corals (BMCs) to increase the resistance of corals to environmental stress has proven to be effective in laboratory trials. Because direct inoculation of BMCs in larger tanks or in the field can be challenging, a delivery mechanism is needed for efficient transmission of the BMC consortium. Packaged delivery mechanisms have been successfully used to transmit probiotics to other organisms, including humans, lobsters, and fish. Here, we tested a method for utilizing rotifers of the species Brachionus plicatilis for delivery of BMCs to corals of the species Pocillopora damicornis. Epifluorescence microscopy combined with a live/dead cell staining assay was used to evaluate the viability of the BMCs and monitor their in vivo uptake by the rotifers. The rotifers efficiently ingested BMCs, which accumulated in the digestive system and on the body surface after 10 min of interaction. Scanning electron microscopy confirmed the adherence of BMCs to the rotifer surfaces. BMC-enriched rotifers were actively ingested by P. damicornis corals, indicating that this is a promising technique for administering coral probiotics in situ. Studies to track the delivery of probiotics through carriers such as B. plicatilis, and the provision or establishment of beneficial traits in corals are the next proof-of-concept research priorities.
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Affiliation(s)
- Juliana M Assis
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda Abreu
- Laboratory of Cellular Biology and Magnetotaxis, Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Helena M D Villela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adam Barno
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael F Valle
- IMAM-AquaRio - Rio de Janeiro Aquarium Research Center, Rio de Janeiro, Brazil
| | - Rayssa Vieira
- IMAM-AquaRio - Rio de Janeiro Aquarium Research Center, Rio de Janeiro, Brazil
| | - Igor Taveira
- Laboratory of Cellular Biology and Magnetotaxis, Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gustavo Duarte
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,IMAM-AquaRio - Rio de Janeiro Aquarium Research Center, Rio de Janeiro, Brazil
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, WA, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Lone Høj
- Australian Institute of Marine Science, Townsville, WA, Australia
| | - Raquel S Peixoto
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,IMAM-AquaRio - Rio de Janeiro Aquarium Research Center, Rio de Janeiro, Brazil
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20
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Abstract
The use of Beneficial Microorganisms for Corals (BMCs) has been proposed recently as a tool for the improvement of coral health, with knowledge in this research topic advancing rapidly. BMCs are defined as consortia of microorganisms that contribute to coral health through mechanisms that include (a) promoting coral nutrition and growth, (b) mitigating stress and impacts of toxic compounds, (c) deterring pathogens, and (d) benefiting early life-stage development. Here, we review the current proposed BMC approach and outline the studies that have proven its potential to increase coral resilience to stress. We revisit and expand the list of putative beneficial microorganisms associated with corals and their proposed mechanismsthat facilitate improved host performance. Further, we discuss the caveats and bottlenecks affecting the efficacy of BMCs and close by focusing on the next steps to facilitate application at larger scales that can improve outcomes for corals and reefs globally.
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Affiliation(s)
- Raquel S Peixoto
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; .,IMAM-AquaRio, Rio de Janeiro Aquarium Research Center, Rio de Janeiro, 20220-360, Brazil.,Current affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, United Kingdom
| | - Helena D M Villela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil;
| | - Pedro Cardoso
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil;
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Christian R Voolstra
- Department of Biology, University of Konstanz, Konstanz 78457, Germany.,Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Lone Høj
- Australian Institute of Marine Science, Townsville, Queensland 4810, Australia
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Queensland 4810, Australia.,College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
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21
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Abstract
Host-associated microbiomes contribute in many ways to the homeostasis of the metaorganism. The microbiome's contributions range from helping to provide nutrition and aiding growth, development, and behavior to protecting against pathogens and toxic compounds. Here we summarize the current knowledge of the diversity and importance of the microbiome to animals, using representative examples of wild and domesticated species. We demonstrate how the beneficial ecological roles of animal-associated microbiomes can be generally grouped into well-defined main categories and how microbe-based alternative treatments can be applied to mitigate problems for both economic and conservation purposes and to provide crucial knowledge about host-microbiota symbiotic interactions. We suggest a Customized Combination of Microbial-Based Therapies to promote animal health and contribute to the practice of sustainable husbandry. We also discuss the ecological connections and threats associated with animal biodiversity loss, microorganism extinction, and emerging diseases, such as the COVID-19 pandemic.
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Affiliation(s)
- Raquel S Peixoto
- Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; .,Current affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudia Arabia;
| | - Derek M Harkins
- J. Craig Venter Institute, Rockville, Maryland 20850, USA; ,
| | - Karen E Nelson
- J. Craig Venter Institute, Rockville, Maryland 20850, USA; ,
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22
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Modolon F, Barno AR, Villela HDM, Peixoto RS. Ecological and biotechnological importance of secondary metabolites produced by coral-associated bacteria. J Appl Microbiol 2020; 129:1441-1457. [PMID: 32627318 DOI: 10.1111/jam.14766] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/20/2020] [Accepted: 06/28/2020] [Indexed: 12/16/2022]
Abstract
Symbiotic relationships between corals and their associated micro-organisms are essential to maintain host homeostasis. Coral-associated bacteria (CAB) can have different beneficial roles in the coral metaorganism, such as metabolizing essential nutrients for the coral host and protecting the coral from pathogens. Many CAB exert these functions via secondary metabolites, which include antibacterial, antifouling, antitumour, antiparasitic and antiviral compounds. This review describes how analysis of CAB has led to the discovery of secondary metabolites with potential biotechnological applications. The most commonly found types of secondary metabolites, antimicrobial and antibiofilm compounds, are emphasized and described. Recently developed methods that can be applied to enhance the culturing of CAB from shallow-water reefs and the less-studied deep-sea coral reefs are also discussed. Last, we suggest how the combined use of meta-omics and innovative growth-diffusion techniques can vastly improve the discovery of novel compounds in coral environments.
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Affiliation(s)
- F Modolon
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil
| | - A R Barno
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil
| | - H D M Villela
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil
| | - R S Peixoto
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil.,IMAM-AquaRio - Rio de Janeiro Aquarium Research Center, Rio de Janeiro, RJ, Brazil
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23
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Lopez JV, Peixoto RS, Rosado AS. Inevitable future: space colonization beyond Earth with microbes first. FEMS Microbiol Ecol 2020; 95:5553461. [PMID: 31437273 PMCID: PMC6748721 DOI: 10.1093/femsec/fiz127] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022] Open
Abstract
Based on modern microbiology, we propose a major revision in current space exploration philosophy and planetary protection policy, especially regarding microorganisms in space. Mainly, microbial introduction should not be considered accidental but inevitable. We hypothesize the near impossibility of exploring new planets without carrying and/or delivering any microbial travelers. In addition, although we highlight the importance of controlling and tracking such contaminations-to explore the existence of extraterrestrial microorganisms-we also believe that we must discuss the role of microbes as primary colonists and assets, rather than serendipitous accidents, for future plans of extraterrestrial colonization. This paradigm shift stems partly from the overwhelming evidence of microorganisms' diverse roles in sustaining life on Earth, such as symbioses and ecosystem services (decomposition, atmosphere effects, nitrogen fixation, etc.). Therefore, we propose a framework for new discussion based on the scientific implications of future colonization and terraforming: (i) focus on methods to track and avoid accidental delivery of Earth's harmful microorganisms and genes to extraterrestrial areas; (ii) begin a rigorous program to develop and explore 'Proactive Inoculation Protocols'. We outline a rationale and solicit feedback to drive a public and private research agenda that optimizes diverse organisms for potential space colonization.
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Affiliation(s)
- Jose V Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL 33004, USA
| | - Raquel S Peixoto
- Institute of Microbiology, Federal University of Rio de Janeiro-UFRJ, Av. Carlos Chagas Filho, 373. CCS, Bloco E, Ilha do Fundão, CEP: 21941-902 Rio de Janeiro, Brazil.,University of California Davis, Davis, CA 95616, USA
| | - Alexandre S Rosado
- Institute of Microbiology, Federal University of Rio de Janeiro-UFRJ, Av. Carlos Chagas Filho, 373. CCS, Bloco E, Ilha do Fundão, CEP: 21941-902 Rio de Janeiro, Brazil.,University of California Davis, Davis, CA 95616, USA
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24
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Villela HDM, Vilela CLS, Assis JM, Varona N, Burke C, Coil DA, Eisen JA, Peixoto RS. Prospecting Microbial Strains for Bioremediation and Probiotics Development for Metaorganism Research and Preservation. J Vis Exp 2019. [PMID: 31736494 DOI: 10.3791/60238] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Pollution affects all biomes. Marine environments have been particularly impacted, especially coral reefs, one of the most sensitive ecosystems on Earth. Globally, 4.5 billion people are economically dependent on the sea, where most of their livelihood is provided by coral reefs. Corals are of great importance and therefore their extinction leads to catastrophic consequences. There are several possible solutions to remediate marine pollutants and local contamination, including bioremediation. Bioremediation is the capacity of organisms to degrade contaminants. The approach presents several advantages, such as sustainability, relatively low cost, and the fact that it can be applied in different ecosystems, causing minimal impacts to the environment. As an extra advantage, the manipulation of endogenous microbiomes, including putative beneficial microorganisms for corals (pBMCs), may have probiotic effects for marine animals. In this context, the use of the two approaches, bioremediation and pBMC inoculation combined, could be promising. This strategy would promote the degradation of specific pollutants that can be harmful to corals and other metaorganisms while also increasing host resistance and resilience to deal with pollution and other threats. This method focuses on the selection of pBMCs to degrade two contaminants: the synthetic estrogen 17a-ethinylestradiol (EE2) and crude oil. Both have been reported to negatively impact marine animals, including corals, and humans. The protocol describes how to isolate and test bacteria capable of degrading the specific contaminants, followed by a description of how to detect some putative beneficial characteristics of these associated microbes to their coral host. The methodologies described here are relatively cheap, easy to perform, and highly adaptable. Almost any kind of soluble target compound can be used instead of EE2 and oil.
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Affiliation(s)
- Helena D M Villela
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ)
| | - Caren L S Vilela
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ)
| | - Juliana M Assis
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ)
| | | | | | | | | | - Raquel S Peixoto
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ); Genome Center, University of California, Davis; IMAM-AquaRio - Rio de Janeiro Aquarium Research Center;
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25
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Villela HDM, Peixoto RS, Soriano AU, Carmo FL. Microbial bioremediation of oil contaminated seawater: A survey of patent deposits and the characterization of the top genera applied. Sci Total Environ 2019; 666:743-758. [PMID: 30812008 DOI: 10.1016/j.scitotenv.2019.02.153] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 02/09/2019] [Accepted: 02/10/2019] [Indexed: 05/20/2023]
Abstract
Petroleum has been the world's major source of energy since the middle of the twentieth century, leading to positive changes but also social, political, and environmental problems worldwide. Oil contamination affects all ecosystems, and the remediation of polluted sites using environmentally friendly strategies is crucial. Here, we report an analysis of the patent documents of potential petroleum bioremediation techniques that use microbes to clean seawater. The patent search was performed using Orbit Intelligence®, SciFinder® and the Derwent World Patents Index®. A group of 500 patent documents were validated according to the search objective and carefully studied. Increases in patent deposits coincide with periods following widely reported oil spills, suggesting a relationship between media disclosure and stimulation of innovation activities. China leads the list of countries with patent applications in bioremediation with 152 deposits, followed by Russia with 133 and the US with 48. These three countries have completely different temporal deposit profiles, influenced by their historical, political, and economic scenarios. A total of 368 patents described degradation of the oil compounds exclusively by bacteria, 24 by fungi and yeasts, 1 by Archaea, 1 using a microalgal strain, and 32 by mixed consortia. The leading microbial genera found in the patents are Pseudomonas (114 patents), Bacillus (75), and Rhodococcus (60). In the top-10 list of microbial strains mostly cited/claimed, no genera are obligate hydrocarbonoclastic bacteria. This fact, together with the broad pattern found in the main International Patent Classification (IPC) codes, suggest that most of the documents are general bioremediation approaches and not focused on oil-polluted seawater. This work highlights the importance of stimulating the development of innovative environmentally friendly strategies focused on the degradation of oil hydrocarbons in marine ecosystems.
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Affiliation(s)
- Helena D M Villela
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS, Bl E, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil.
| | - Raquel S Peixoto
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS, Bl E, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil; IMAM-AquaRio - Rio Marine Aquarium Research Center, Praça Muhammad Ali, Gambôa, Rio de Janeiro, RJ 20220-360, Brazil
| | - Adriana U Soriano
- Leopoldo A. Miguez de Mello Research and Development Center, CENPES, PETROBRAS - Petroleo Brasileiro S. A, CENPES, Cidade Universitária, Rio de Janeiro, RJ, 21941-598, Brazil
| | - Flavia L Carmo
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS, Bl E, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil; Innovation Agency UFRJ, Federal University of Rio de Janeiro. R. Hélio de Almeida, s/n - Incubadora de Empresas - Prédio 2 (salas 25 a 29), Cidade Universitária, Rio de Janeiro, RJ 21941-614, Brazil
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26
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Silva DP, Duarte G, Villela HD, Santos HF, Rosado PM, Rosado JG, Rosado AS, Ferreira EM, Soriano AU, Peixoto RS. Adaptable mesocosm facility to study oil spill impacts on corals. Ecol Evol 2019; 9:5172-5185. [PMID: 31110670 PMCID: PMC6509398 DOI: 10.1002/ece3.5095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/13/2019] [Accepted: 03/01/2019] [Indexed: 11/05/2022] Open
Abstract
Although numerous studies have been carried out on the impacts of oil spills on coral physiology, most have relied on laboratory assays. This scarcity is partly explained by the difficulty of reproducing realistic conditions in a laboratory setting or of performing experiments with toxic compounds in the field. Mesocosm systems provide the opportunity to carry out such studies with safe handling of contaminants while reproducing natural conditions required by living organisms. The mesocosm design is crucial and can lead to the development of innovative technologies to mitigate environmental impacts. Therefore, this study aimed to develop a mesocosm system for studies simulating oil spills with several key advantages, including true replication and the use of gravity to control flow-through that reduces reliance on pumps that can clog thereby decreasing errors and costs. This adaptable system can be configured to (a) have continuous flow-through; (b) operate as an open or closed system; (c) be fed by gravity; (d) have separate mesocosm sections that can be used for individual and simultaneous experiments; and (e) simulate the migration of oil from ocean oil spills to the nearby reefs. The mesocosm performance was assessed with two experiments using the hydrocoral Millepora alcicornis and different configurations to simulate two magnitudes of oil spills. With few exceptions, physical and chemical parameters remained stable within replicates and within treatments throughout the experiments. Physical and chemical parameters that expressed change during the experiment were still within the range of natural conditions observed in Brazilian marine environments. The photosynthetic potential (Fv/Fm ) of the algae associated with M. alcicornis decreased in response to an 1% crude-oil contamination, suggesting a successful delivery of the toxic contaminant to the targeted replicates. This mesocosm is customizable and adjustable for several types of experiments and proved to be effective for studies of oil spills.
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Affiliation(s)
- Denise P. Silva
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de GóesFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
| | - Gustavo Duarte
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de GóesFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
- IMAM‐AquaRio – Rio de Janeiro Aquarium Research CenterRio de JaneiroBrazil
| | - Helena D.M. Villela
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de GóesFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
| | - Henrique F. Santos
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de GóesFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
- Present address:
Department of Marine BiologyFluminense Federal UniversityRio de JaneiroBrazil
| | - Phillipe M. Rosado
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de GóesFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
| | - João Gabriel Rosado
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de GóesFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
| | - Alexandre S. Rosado
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de GóesFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
| | - Edir M. Ferreira
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de GóesFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
| | - Adriana U. Soriano
- Biotechnology Section, Leopoldo Américo Miguez de Mello Research & Development Center – CENPESPETROBRASRio de JaneiroBrazil
| | - Raquel S. Peixoto
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de GóesFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
- IMAM‐AquaRio – Rio de Janeiro Aquarium Research CenterRio de JaneiroBrazil
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Leite DCA, Salles JF, Calderon EN, Castro CB, Bianchini A, Marques JA, van Elsas JD, Peixoto RS. Coral Bacterial-Core Abundance and Network Complexity as Proxies for Anthropogenic Pollution. Front Microbiol 2018; 9:833. [PMID: 29755445 PMCID: PMC5934943 DOI: 10.3389/fmicb.2018.00833] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 04/12/2018] [Indexed: 02/01/2023] Open
Abstract
Acclimatization via changes in the stable (core) or the variable microbial diversity and/or abundance is an important element in the adaptation of coral species to environmental changes. Here, we explored the spatial-temporal dynamics, diversity and interactions of variable and core bacterial populations associated with the coral Mussismilia hispida and the surrounding water. This survey was performed on five reefs along a transect from the coast (Reef 1) to offshore (Reef 5), representing a gradient of influence of the river mouth, for almost 12 months (4 sampling times), in the dry and rainy seasons. A clear increasing gradient of organic-pollution proxies (nitrogen content and fecal coliforms) was observed from Reef 1 to Reef 5, during both seasons, and was highest at the Buranhém River mouth (Reef 1). Conversely, a clear inverse gradient of the network analysis of the whole bacterial communities also revealed more-complex network relationships at Reef 5. Our data also indicated a higher relative abundance of members of the bacterial core, dominated by Acinetobacter sp., at Reef 5, and higher diversity of site-stable bacterial populations, likely related to the higher abundance of total coliforms and N content (proxies of sewage or organic pollution) at Reef 1, during the rainy season. Thus, the less “polluted” areas may show a more-complex network and a high relative abundance of members of the bacterial core (almost 97% in some cases), resulting in a more-homogeneous and well-established bacteriome among sites/samples, when the influence of the river is stronger (rainy seasons).
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Affiliation(s)
- Deborah C A Leite
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joana F Salles
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Emiliano N Calderon
- Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Coral Vivo, Santa Cruz Cabrália, Brazil
| | - Clovis B Castro
- Instituto Coral Vivo, Santa Cruz Cabrália, Brazil.,Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adalto Bianchini
- Instituto Coral Vivo, Santa Cruz Cabrália, Brazil.,Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Joseane A Marques
- Programa de Pós-Graduação em Oceanografia Biológica, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Jan Dirk van Elsas
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Raquel S Peixoto
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Museu Aquário Marinho do Rio de Janeiro-AquaRio - Rio de Janeiro Marine Aquarium Research Center, Rio de Janeiro, Brazil
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Leite DCA, Salles JF, Calderon EN, van Elsas JD, Peixoto RS. Specific plasmid patterns and high rates of bacterial co-occurrence within the coral holobiont. Ecol Evol 2018; 8:1818-1832. [PMID: 29435256 PMCID: PMC5792611 DOI: 10.1002/ece3.3717] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 12/24/2022] Open
Abstract
Despite the importance of coral microbiomes for holobiont persistence, the interactions among these are not well understood. In particular, knowledge of the co-occurrence and taxonomic importance of specific members of the microbial core, as well as patterns of specific mobile genetic elements (MGEs), is lacking. We used seawater and mucus samples collected from Mussismilia hispida colonies on two reefs located in Bahia, Brazil, to disentangle their associated bacterial communities, intertaxa correlations, and plasmid patterns. Proxies for two broad-host-range (BHR) plasmid groups, IncP-1β and PromA, were screened. Both groups were significantly (up to 252 and 100%, respectively) more abundant in coral mucus than in seawater. Notably, the PromA plasmid group was detected only in coral mucus samples. The core bacteriome of M. hispida mucus was composed primarily of members of the Proteobacteria, followed by those of Firmicutes. Significant host specificity and co-occurrences among different groups of the dominant phyla (e.g., Bacillaceae and Pseudoalteromonadaceae and the genera Pseudomonas, Bacillus, and Vibrio) were detected. These relationships were observed for both the most abundant phyla and the bacteriome core, in which most of the operational taxonomic units showed intertaxa correlations. The observed evidence of host-specific bacteriome and co-occurrence (and potential symbioses or niche space co-dominance) among the most dominant members indicates a taxonomic selection of members of the stable bacterial community. In parallel, host-specific plasmid patterns could also be, independently, related to the assembly of members of the coral microbiome.
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Affiliation(s)
- Deborah C. A. Leite
- Institute of MicrobiologyFederal University of Rio de JaneiroRio de JaneiroBrazil
| | - Joana F. Salles
- Genomics Research in Ecology and Evolution in Nature ‐ Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Emiliano N. Calderon
- NUPEM/MacaéFederal University of Rio de JaneiroRio de JaneiroBrazil
- Instituto Coral VivoSanta Cruz CabráliaBrazil
| | - Jan D. van Elsas
- Genomics Research in Ecology and Evolution in Nature ‐ Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Raquel S. Peixoto
- Institute of MicrobiologyFederal University of Rio de JaneiroRio de JaneiroBrazil
- IMAM‐AquaRio – Rio Marine Aquarium Research CenterRio de JaneiroBrazil
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Peixoto RS, Rosado PM, Leite DCDA, Rosado AS, Bourne DG. Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience. Front Microbiol 2017; 8:341. [PMID: 28326066 PMCID: PMC5339234 DOI: 10.3389/fmicb.2017.00341] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/17/2017] [Indexed: 12/21/2022] Open
Abstract
The symbiotic association between the coral animal and its endosymbiotic dinoflagellate partner Symbiodinium is central to the success of corals. However, an array of other microorganisms associated with coral (i.e., Bacteria, Archaea, Fungi, and viruses) have a complex and intricate role in maintaining homeostasis between corals and Symbiodinium. Corals are sensitive to shifts in the surrounding environmental conditions. One of the most widely reported responses of coral to stressful environmental conditions is bleaching. During this event, corals expel Symbiodinium cells from their gastrodermal tissues upon experiencing extended seawater temperatures above their thermal threshold. An array of other environmental stressors can also destabilize the coral microbiome, resulting in compromised health of the host, which may include disease and mortality in the worst scenario. However, the exact mechanisms by which the coral microbiome supports coral health and increases resilience are poorly understood. Earlier studies of coral microbiology proposed a coral probiotic hypothesis, wherein a dynamic relationship exists between corals and their symbiotic microorganisms, selecting for the coral holobiont that is best suited for the prevailing environmental conditions. Here, we discuss the microbial-host relationships within the coral holobiont, along with their potential roles in maintaining coral health. We propose the term BMC (Beneficial Microorganisms for Corals) to define (specific) symbionts that promote coral health. This term and concept are analogous to the term Plant Growth Promoting Rhizosphere (PGPR), which has been widely explored and manipulated in the agricultural industry for microorganisms that inhabit the rhizosphere and directly or indirectly promote plant growth and development through the production of regulatory signals, antibiotics and nutrients. Additionally, we propose and discuss the potential mechanisms of the effects of BMC on corals, suggesting strategies for the use of this knowledge to manipulate the microbiome, reversing dysbiosis to restore and protect coral reefs. This may include developing and using BMC consortia as environmental "probiotics" to improve coral resistance after bleaching events and/or the use of BMC with other strategies such as human-assisted acclimation/adaption to shifting environmental conditions.
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Affiliation(s)
- Raquel S. Peixoto
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
- Instituto Museu Aquário Marinho do Rio de Janeiro-AquaRio (IMAM/AquaRio) – Rio de Janeiro Marine Aquarium Research CenterRio de Janeiro, Brazil
| | - Phillipe M. Rosado
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
- Instituto Museu Aquário Marinho do Rio de Janeiro-AquaRio (IMAM/AquaRio) – Rio de Janeiro Marine Aquarium Research CenterRio de Janeiro, Brazil
| | | | - Alexandre S. Rosado
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
- Instituto Museu Aquário Marinho do Rio de Janeiro-AquaRio (IMAM/AquaRio) – Rio de Janeiro Marine Aquarium Research CenterRio de Janeiro, Brazil
| | - David G. Bourne
- College of Science and Engineering, James Cook University, TownsvilleQLD, Australia
- Australian Institute of Marine Science, TownsvilleQLD, Australia
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Leite DCA, Leão P, Garrido AG, Lins U, Santos HF, Pires DO, Castro CB, van Elsas JD, Zilberberg C, Rosado AS, Peixoto RS. Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core. Front Microbiol 2017; 8:176. [PMID: 28223979 PMCID: PMC5293827 DOI: 10.3389/fmicb.2017.00176] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/24/2017] [Indexed: 02/01/2023] Open
Abstract
The hologenome theory of evolution (HTE), which is under fierce debate, presupposes that parts of the microbiome are transmitted from one generation to the next [vertical transmission (VT)], which may also influence the evolution of the holobiont. Even though bacteria have previously been described in early life stages of corals, these early life stages (larvae) could have been inoculated in the water and not inside the parental colony (through gametes) carrying the parental microbiome. How Symbiodinium is transmitted to offspring is also not clear, as only one study has described this mechanism in spawners. All other studies refer to incubators. To explore the VT hypothesis and the key components being transferred, colonies of the broadcast spawner species Mussismilia hispida were kept in nurseries until spawning. Gamete bundles, larvae and adult corals were analyzed to identify their associated microbiota with respect to composition and location. Symbiodinium and bacteria were detected by sequencing in gametes and coral planula larvae. However, no cells were detected using microscopy at the gamete stage, which could be related to the absence of those cells inside the oocytes/dispersed in the mucus or to a low resolution of our approach. A preliminary survey of Symbiodinium diversity indicated that parental colonies harbored Symbiodinium clades B, C and G, whereas only clade B was found in oocytes and planula larvae [5 days after fertilization (a.f.)]. The core bacterial populations found in the bundles, planula larvae and parental colonies were identified as members of the genera Burkholderia, Pseudomonas, Acinetobacter, Ralstonia, Inquilinus and Bacillus, suggesting that these populations could be vertically transferred through the mucus. The collective data suggest that spawner corals, such as M. hispida, can transmit Symbiodinium cells and the bacterial core to their offspring by a coral gamete (and that this gamete, with its bacterial load, is released into the water), supporting the HTE. However, more data are required to indicate the stability of the transmitted populations to indicate whether the holobiont can be considered a unit of natural selection or a symbiotic assemblage of independently evolving organisms.
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Affiliation(s)
- Deborah C A Leite
- Institute of Microbiology, Federal University of Rio de Janeiro Rio de Janeiro, Brazil
| | - Pedro Leão
- Institute of Microbiology, Federal University of Rio de Janeiro Rio de Janeiro, Brazil
| | - Amana G Garrido
- Institute of Biology, Federal University of Rio de Janeiro Rio de Janeiro, Brazil
| | - Ulysses Lins
- Institute of Microbiology, Federal University of Rio de Janeiro Rio de Janeiro, Brazil
| | - Henrique F Santos
- Institute of Microbiology, Federal University of Rio de JaneiroRio de Janeiro, Brazil; Instituto Coral VivoSanta Cruz Cabrália, Brazil
| | - Débora O Pires
- Instituto Coral VivoSanta Cruz Cabrália, Brazil; National Museum, Federal University of Rio de JaneiroRio de Janeiro, Brazil
| | - Clovis B Castro
- Instituto Coral VivoSanta Cruz Cabrália, Brazil; National Museum, Federal University of Rio de JaneiroRio de Janeiro, Brazil
| | - Jan D van Elsas
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen Groningen, Netherlands
| | - Carla Zilberberg
- Institute of Biology, Federal University of Rio de JaneiroRio de Janeiro, Brazil; Instituto Coral VivoSanta Cruz Cabrália, Brazil
| | - Alexandre S Rosado
- Institute of Microbiology, Federal University of Rio de JaneiroRio de Janeiro, Brazil; Instituto Coral VivoSanta Cruz Cabrália, Brazil
| | - Raquel S Peixoto
- Institute of Microbiology, Federal University of Rio de JaneiroRio de Janeiro, Brazil; Instituto Coral VivoSanta Cruz Cabrália, Brazil
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Santos HF, Carmo FL, Martirez N, Duarte GAS, Calderon EN, Castro CB, Pires DO, Rosado AS, Peixoto RS. Cyanobacterial and microeukaryotic profiles of healthy, diseased, and dead Millepora alcicornis from the South Atlantic. Dis Aquat Organ 2016; 119:163-172. [PMID: 27137074 DOI: 10.3354/dao02972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Coral reefs are at risk due to events associated with human activities, which have resulted in the increasing occurrence of coral diseases. Corals live in symbiotic relationships with different microorganisms, such as cyanobacteria, a very important group. Members of the phylum Cyanobacteria are found in great abundance in the marine environment and may play an essential role in keeping corals healthy but may also be pathogenic. Furthermore, some studies are showing a rise in cyanobacterial abundance in coral reefs as a result of climate change. The current study aimed to improve our understanding of the relationship between cyanobacteria and coral health. Our results revealed that the cyanobacterial genus GPI (Anabaena) is a possible opportunistic pathogen of the coral species Millepora alcicornis in the South Atlantic Ocean. Furthermore, the bacterial and microeukaryotic profile of healthy, diseased, and post-disease (skeletal) regions of affected coral indicated that a microbial consortium composed of Anabaena sp., Prosthecochloris sp., and microeukaryotes could be involved in this pathogenicity or could be taking advantage of the diseased state.
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Affiliation(s)
- Henrique F Santos
- LEMM - Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, RJ, Brazil
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Rachid CTCC, Pires CA, Leite DCA, Coutinho HLC, Peixoto RS, Rosado AS, Salton J, Zanatta JA, Mercante FM, Angelini GAR, Balieiro FDC. Sugarcane trash levels in soil affects the fungi but not bacteria in a short-term field experiment. Braz J Microbiol 2016; 47:322-6. [PMID: 26991293 PMCID: PMC4874680 DOI: 10.1016/j.bjm.2016.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/10/2015] [Indexed: 11/29/2022] Open
Abstract
The sugarcane in Brazil is passing through a management transition that is leading to the abolition of pre-harvest burning. Without burning, large amounts of sugarcane trash is generated, and there is a discussion regarding the utilization of this biomass in the industry versus keeping it in the field to improve soil quality. To study the effects of the trash removal on soil quality, we established an experimental sugarcane plantation with different levels of trash over the soil (0%, 50% and 100% of the original trash deposition) and analyzed the structure of the bacterial and fungal community as the bioindicators of impacts. The soil DNA was extracted, and the microbial community was screened by denaturing gradient gel electrophoresis in two different seasons. Our results suggest that there are no effects from the different levels of trash on the soil chemistry and soil bacterial community. However, the fungal community was significantly impacted, and after twelve months, the community presented different structures among the treatments.
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Affiliation(s)
- C T C C Rachid
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - C A Pires
- Embrapa Solos, Rio de Janeiro, Brazil; Federal Rural University of Rio de Janeiro, Seropédica, Brazil
| | - D C A Leite
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - R S Peixoto
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A S Rosado
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - J Salton
- Embrapa Agropecuária Oeste, Dourados, Brazil
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Duarte G, Calderon EN, Pereira CM, Marangoni LFB, Santos HF, Peixoto RS, Bianchini A, Castro CB. A novel marine mesocosm facility to study global warming, water quality, and ocean acidification. Ecol Evol 2015; 5:4555-66. [PMID: 26668722 PMCID: PMC4670062 DOI: 10.1002/ece3.1670] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 06/18/2015] [Accepted: 07/09/2015] [Indexed: 11/12/2022] Open
Abstract
We describe a completely randomizable flow‐through outdoor mesocosm for climate change and ecotoxicology studies that was built with inexpensive materials. The 16 raceway tanks allow up to 6× water renewal per hour, avoiding changes in natural abiotic seawater conditions. We use an open‐source hardware board (Arduino) that was adapted to control heaters and an innovative CO2 injection system. This system reduced seawater pH up to −0.9 units and increased temperature up to +6°C in three treatments and a control. Treatments can be continuously compared with the control and vary according to diel fluctuations, thus following the diel range observed in the sea. The mesocosm facility also includes an integrated secondary system of 48 aquaria for ecotoxicology studies. We validated the reproducibility and relevance of our experimental system by analyzing the variation of the total DNA of the microbial community extracted from corals in three elevated temperature scenarios during a 40‐day experiment. We also present data from temperature, acidification, and copper contamination trials, which allowed continuous, reliable, and consistent treatment manipulations.
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Affiliation(s)
- Gustavo Duarte
- Instituto Coral Vivo Rio de Janeiro Brazil ; Museu Nacional Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | | | | | - Laura F B Marangoni
- Instituto Coral Vivo Rio de Janeiro Brazil ; Pós-Graduação em Oceanografia Biológica Instituto de Oceanografia Universidade Federal do Rio Grande Rio Grande Brazil
| | - Henrique F Santos
- Instituto Coral Vivo Rio de Janeiro Brazil ; Instituto de Microbiologia Paulo de Góes UFRJ Rio de Janeiro Brazil
| | - Raquel S Peixoto
- Instituto Coral Vivo Rio de Janeiro Brazil ; Instituto de Microbiologia Paulo de Góes UFRJ Rio de Janeiro Brazil
| | - Adalto Bianchini
- Instituto Coral Vivo Rio de Janeiro Brazil ; Instituto de Ciências Biológicas Universidade Federal do Rio Grande Rio Grande Brazil
| | - Clovis B Castro
- Instituto Coral Vivo Rio de Janeiro Brazil ; Museu Nacional Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
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Leite AMO, Miguel MAL, Peixoto RS, Ruas-Madiedo P, Paschoalin VMF, Mayo B, Delgado S. Probiotic potential of selected lactic acid bacteria strains isolated from Brazilian kefir grains. J Dairy Sci 2015; 98:3622-32. [PMID: 25841972 DOI: 10.3168/jds.2014-9265] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/16/2015] [Indexed: 12/26/2022]
Abstract
A total of 34 lactic acid bacteria isolates from 4 different Brazilian kefir grains were identified and characterized among a group of 150 isolates, using the ability to tolerate acidic pH and resistance to bile salts as restrictive criteria for probiotic potential. All isolates were identified by amplified ribosomal DNA restriction analysis and 16S rDNA sequencing of representative amplicons. Eighteen isolates belonged to the species Leuconostoc mesenteroides, 11 to Lactococcus lactis (of which 8 belonged to subspecies cremoris and 3 to subspecies lactis), and 5 to Lactobacillus paracasei. To exclude replicates, a molecular typing analysis was performed by combining repetitive extragenic palindromic-PCR and random amplification of polymorphic DNA techniques. Considering a threshold of 90% similarity, 32 different strains were considered. All strains showed some antagonistic activity against 4 model food pathogens. In addition, 3 Lc. lactis strains and 1 Lb. paracasei produced bacteriocin-like inhibitory substances against at least 2 indicator organisms. Moreover, 1 Lc. lactis and 2 Lb. paracasei presented good total antioxidative activity. None of these strains showed undesirable enzymatic or hemolytic activities, while proving susceptible or intrinsically resistant to a series of clinically relevant antibiotics. The Lb. paracasei strain MRS59 showed a level of adhesion to human Caco-2 epithelial cells comparable with that observed for Lactobacillus rhamnosus GG. Taken together, these properties allow the MRS59 strain to be considered a promising probiotic candidate.
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Affiliation(s)
- A M O Leite
- Curso Farmácia, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, RJ, Brazil 27930-560; Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain 33300; Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil 21941-904
| | - M A L Miguel
- Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil 21941-904
| | - R S Peixoto
- Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil 21941-904
| | - P Ruas-Madiedo
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain 33300
| | - V M F Paschoalin
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil 21941-904.
| | - B Mayo
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain 33300
| | - S Delgado
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain 33300
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Bezerra TM, Ferreira DC, Carmo FL, Pinheiro R, Leite DCA, Cavalcante FS, Belinho RA, Peixoto RS, Rosado AS, dos Santos KRN, Castro GFBA. Herpesvirus in the oral cavity of children with leukaemia and its impact on the oral bacterial community profile. J Clin Pathol 2015; 68:222-8. [DOI: 10.1136/jclinpath-2014-202668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Mayo B, Rachid CTCC, Alegría A, Leite AMO, Peixoto RS, Delgado S. Impact of next generation sequencing techniques in food microbiology. Curr Genomics 2014; 15:293-309. [PMID: 25132799 PMCID: PMC4133952 DOI: 10.2174/1389202915666140616233211] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 06/04/2014] [Accepted: 06/13/2014] [Indexed: 02/07/2023] Open
Abstract
Understanding the Maxam-Gilbert and Sanger sequencing as the first generation, in recent years there has been an explosion of newly-developed sequencing strategies, which are usually referred to as next generation sequencing (NGS) techniques. NGS techniques have high-throughputs and produce thousands or even millions of sequences at the same time. These sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and those present in small numbers. In specific applications, NGS provides a complete inventory of all microbial operons and genes present or being expressed under different study conditions. NGS techniques are revolutionizing the field of microbial ecology and have recently been used to examine several food ecosystems. After a short introduction to the most common NGS systems and platforms, this review addresses how NGS techniques have been employed in the study of food microbiota and food fermentations, and discusses their limits and perspectives. The most important findings are reviewed, including those made in the study of the microbiota of milk, fermented dairy products, and plant-, meat- and fish-derived fermented foods. The knowledge that can be gained on microbial diversity, population structure and population dynamics via the use of these technologies could be vital in improving the monitoring and manipulation of foods and fermented food products. They should also improve their safety.
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Affiliation(s)
- Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
| | - Caio T C C Rachid
- Instituto de Microbiologia, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, 21941904-Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Angel Alegría
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
| | - Analy M O Leite
- Instituto de Microbiologia, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, 21941904-Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Raquel S Peixoto
- Instituto de Microbiologia, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, 21941904-Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Susana Delgado
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
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Carmo FL, Santos HF, Peixoto RS, Rosado AS, Araujo FV. Tank bromeliad water: similar or distinct environments for research of bacterial bioactives? Braz J Microbiol 2014; 45:185-92. [PMID: 24948929 PMCID: PMC4059294 DOI: 10.1590/s1517-83822014000100024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/01/2013] [Indexed: 11/24/2022] Open
Abstract
The Atlantic Rainforest does not have a uniform physiognomy, its relief determines different environmental conditions that define the composition of its flora and fauna. Within this ecosystem, bromeliads that form tanks with their leaves hold water reservoirs throughout the year, maintaining complex food chains, based mainly on autotrophic and heterotrophic bacteria. Some works concluded that the water held by tank bromeliads concentrate the microbial diversity of their ecosystem. To investigate the bacterial diversity and the potential biotechnology of these ecosystems, tank bromeliads of the Neoregelia cruenta species from the Atlantic Rainforest in Brazil were used as models for this research. Bacteria isolated from these models were tested for production of bioactive compounds. DGGE of the water held by tank bromeliads was performed in different seasons, locations and sun exposure to verify whether these environmental factors affect bacterial communities. The DGGE bands profile showed no grouping of bacterial community by the environmental factors tested. Most of the isolates demonstrated promising activities in the tests performed. Collectively, these results suggest that tank bromeliads of the N. cruenta species provide important habitats for a diverse microbial community, suggesting that each tank forms a distinct micro-habitat. These tanks can be considered excellent sources for the search for new enzymes and/or new bioactive composites of microbial origin.
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Affiliation(s)
- F L Carmo
- Departamento de Microbiologia Geral Instituto de Microbiologia Professor Paulo de Góes Universidade Federal do Rio de Janeiro Rio de JaneiroRJ Brazil ; Programa de Pós-Graduação em Biotecnologia Vegetal Universidade Federal do Rio de Janeiro Rio de JaneiroRJ Brazil
| | - H F Santos
- Departamento de Microbiologia Geral Instituto de Microbiologia Professor Paulo de Góes Universidade Federal do Rio de Janeiro Rio de JaneiroRJ Brazil
| | - R S Peixoto
- Departamento de Microbiologia Geral Instituto de Microbiologia Professor Paulo de Góes Universidade Federal do Rio de Janeiro Rio de JaneiroRJ Brazil
| | - A S Rosado
- Departamento de Microbiologia Geral Instituto de Microbiologia Professor Paulo de Góes Universidade Federal do Rio de Janeiro Rio de JaneiroRJ Brazil
| | - F V Araujo
- Departamento de Ciências Faculdade de Formação de Professores Universidade do Estado do Rio de Janeiro Rio de JaneiroRJ Brazil
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Leite DCA, Balieiro FC, Pires CA, Madari BE, Rosado AS, Coutinho HLC, Peixoto RS. Comparison of DNA extraction protocols for microbial communities from soil treated with biochar. Braz J Microbiol 2014; 45:175-83. [PMID: 24948928 PMCID: PMC4059293 DOI: 10.1590/s1517-83822014000100023] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 04/01/2013] [Indexed: 11/22/2022] Open
Abstract
Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.
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Affiliation(s)
- D C A Leite
- Laboratório de Ecologia Microbiana Molecular Instituto de Microbiologia Prof. Paulo de Góes Universidade Federal do Rio de Janeiro Rio de JaneiroRJ Brazil
| | - F C Balieiro
- Empresa Brasileira de Pesquisa Agropecuária Solos Rio de JaneiroRJ Brazil
| | - C A Pires
- Empresa Brasileira de Pesquisa Agropecuária Solos Rio de JaneiroRJ Brazil
| | - B E Madari
- Empresa Brasileira de Pesquisa Agropecuária Arroz e Feijão GoiásGO Brazil
| | - A S Rosado
- Laboratório de Ecologia Microbiana Molecular Instituto de Microbiologia Prof. Paulo de Góes Universidade Federal do Rio de Janeiro Rio de JaneiroRJ Brazil
| | - H L C Coutinho
- Empresa Brasileira de Pesquisa Agropecuária Solos Rio de JaneiroRJ Brazil
| | - R S Peixoto
- Laboratório de Ecologia Microbiana Molecular Instituto de Microbiologia Prof. Paulo de Góes Universidade Federal do Rio de Janeiro Rio de JaneiroRJ Brazil
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Teixeira LCRS, Yeargeau E, Balieiro FC, Piccolo MC, Peixoto RS, Greer CW, Rosado AS. Plant and bird presence strongly influences the microbial communities in soils of Admiralty Bay, Maritime Antarctica. PLoS One 2013; 8:e66109. [PMID: 23840411 PMCID: PMC3688718 DOI: 10.1371/journal.pone.0066109] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 05/06/2013] [Indexed: 11/19/2022] Open
Abstract
Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing relatively large changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific.
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Affiliation(s)
- Lia C. R. S. Teixeira
- Laboratório de Ecologia Microbiana Molecular, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Etienne Yeargeau
- Biotechnology Research Institute, National Research Council of Canada, Montréal, QC, Canada
| | - Fabiano C. Balieiro
- Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) solos, Rio de Janeiro, RJ, Brasil
| | - Marisa C. Piccolo
- Laboratório de Ciclagem de Nutrientes, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, SP, Brasil
| | - Raquel S. Peixoto
- Laboratório de Ecologia Microbiana Molecular, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Charles W. Greer
- Biotechnology Research Institute, National Research Council of Canada, Montréal, QC, Canada
| | - Alexandre S. Rosado
- Laboratório de Ecologia Microbiana Molecular, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
- * E-mail:
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Hardoim CCP, Cox CJ, Peixoto RS, Rosado AS, Costa R, van Elsas JD. Diversity of the candidate phylum Poribacteria in the marine sponge Aplysina fulva. Braz J Microbiol 2013; 44:329-34. [PMID: 24159324 PMCID: PMC3804218 DOI: 10.1590/s1517-83822013000100048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 07/02/2012] [Indexed: 11/22/2022] Open
Abstract
Poribacterial clone libraries constructed for Aplysina fulva sponge specimens were analysed with respect to diversity and phylogeny. Results imply the coexistence of several, prevalently “intra-specific” poribacterial genotypes in a single sponge host, and suggest quantitative analysis as a desirable approach in studies of the diversity and distribution of poribacterial cohorts in marine sponges.
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Affiliation(s)
- C C P Hardoim
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve, Gambelas, Faro, Portugal
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Delgado S, Rachid CTCC, Fernández E, Rychlik T, Alegría A, Peixoto RS, Mayo B. Diversity of thermophilic bacteria in raw, pasteurized and selectively-cultured milk, as assessed by culturing, PCR-DGGE and pyrosequencing. Food Microbiol 2013; 36:103-11. [PMID: 23764225 DOI: 10.1016/j.fm.2013.04.015] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 04/18/2013] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
Abstract
Thermophilic lactic acid bacteria (LAB) species, such as Streptococcus thermophilus, Lactobacillus delbrueckii and Lactobacillus helveticus, enjoy worldwide economic importance as dairy starters. To assess the diversity of thermophilic bacteria in milk, milk samples were enriched in thermophilic organisms through a stepwise procedure which included pasteurization of milk at 63 °C for 30 min (PM samples) and pasteurization followed by incubation at 42 °C for 24 h (IPM samples). The microbial composition of these samples was analyzed by culture-dependent (at 42 °C) and culture-independent (PCR-DGGE and pyrosequencing of 16S rRNA gene amplicons) microbial techniques. The results were then compared to those obtained for their corresponding starting raw milk counterparts (RM samples). Twenty different species were scored by culturing among 352 isolates purified from the counting plates and identified by molecular methods. Mesophilic LAB species (Lactococcus lactis, Lactococcus garvieae) were dominant (87% of the isolates) among the RM samples. However, S. thermophilus and Lb. delbrueckii were found to be the dominant recoverable organisms in both PM and IPM samples. The DGGE profiles of RM and PM samples were found to be very similar; the most prominent bands belonging to Lactococcus, Leuconostoc and Streptococcus species. In contrast, just three DGGE bands were obtained for IPM samples, two of which were assigned to S. thermophilus. The pyrosequencing results scored 95 operational taxonomic units (OTUs) at 3% sequence divergence in an RM sample, while only 13 were encountered in two IPM samples. This technique identified Leuconostoc citreum as the dominant microorganism in the RM sample, while S. thermophilus constituted more than 98% of the reads in the IPM samples. The procedure followed in this study allowed to estimate the bacterial diversity in milk and afford a suitable strategy for the isolation of new thermophilic LAB strains, among which adequate starters might be selected.
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Affiliation(s)
- Susana Delgado
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias-IPLA-CSIC, Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
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Leite AMO, Leite DCA, Del Aguila EM, Alvares TS, Peixoto RS, Miguel MAL, Silva JT, Paschoalin VMF. Microbiological and chemical characteristics of Brazilian kefir during fermentation and storage processes. J Dairy Sci 2013; 96:4149-59. [PMID: 23628252 DOI: 10.3168/jds.2012-6263] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 03/08/2013] [Indexed: 11/19/2022]
Abstract
The microbial community composition and chemical characteristics of a Brazilian milk kefir sample produced during its manufacturing and refrigerated storage were investigated by culture-dependent and -independent methods and HPLC. Lactococcus lactis ssp. cremoris and ssp. lactis, Leuconostoc mesenteroides, Acetobacter lovaniensis, and Saccharomyces cerevisiae were isolated, whereas the detected bands on denaturing gel gradient electrophoresis corresponded to Lactobacillus kefiranofaciens, Lactobacillus kefiri, Lactobacillus parakefiri, and S. cerevisiae. After fermentation, lactic acid bacteria were present at levels of 10 log units, whereas acetic acid bacteria and yeast were present at levels of 7.8 and 6 log units, respectively. The lactic acid bacteria and yeast counts remained constant, whereas acetic acid bacteria counts decreased to 7.2 log units during storage. From fermentation to final storage, the pH, lactose content and citric acid of the kefir beverage decreased, followed by an increase in the concentrations of glucose, galactose, ethanol, and lactic, acetic, butyric, and propionic acids. These microbiological and chemical characteristics contribute to the unique taste and aroma of kefir. This research may serve as a basis for the future industrial production of this beverage in Brazil.
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Affiliation(s)
- A M O Leite
- Departamento de Bioquímica, Instituto de Química, Brazil.
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Rachid CTCC, Santos AL, Piccolo MC, Balieiro FC, Coutinho HLC, Peixoto RS, Tiedje JM, Rosado AS. Effect of sugarcane burning or green harvest methods on the Brazilian Cerrado soil bacterial community structure. PLoS One 2013; 8:e59342. [PMID: 23533619 PMCID: PMC3606482 DOI: 10.1371/journal.pone.0059342] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 02/13/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The Brazilian Cerrado is one of the most important biodiversity reservoirs in the world. The sugarcane cultivation is expanding in this biome and necessitates the study of how it may impact the soil properties of the Cerrado. There is a lack of information especially about the impacts of different sugarcane management on the native bacterial communities of Cerrado soil. Therefore, our objective was to evaluate and compare the soil bacterial community structure of the Cerrado vegetation with two sugarcane systems. METHODS We evaluated samples under native vegetation and the impact of the two most commonly used management strategies for sugarcane cultivation (burnt cane and green cane) on this diversity using pyrosequencing and quantitative PCR of the rrs gene (16S rRNA). RESULTS AND CONCLUSIONS Nineteen different phyla were identified, with Acidobacteria (≈35%), Proteobacteria (≈24%) and Actinobacteria (≈21%) being the most abundant. Many of the sequences were represented by few operational taxonomic units (OTUs, 3% of dissimilarity), which were found in all treatments. In contrast, there were very strong patterns of local selection, with many OTUs occurring only in one sample. Our results reveal a complex bacterial diversity, with a large fraction of microorganisms not yet described, reinforcing the importance of this biome. As possible sign of threat, the qPCR detected a reduction of the bacterial population in agricultural soils compared with native Cerrado soil communities. We conclude that sugarcane cultivation promoted significant structural changes in the soil bacterial community, with Firmicutes phylum and Acidobacteria classes being the groups most affected.
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Affiliation(s)
- Caio T. C. C. Rachid
- Center for Nuclear Energy in Agriculture, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adriana L. Santos
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marisa C. Piccolo
- Center for Nuclear Energy in Agriculture, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | | | | | - Raquel S. Peixoto
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | - Alexandre S. Rosado
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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Gomes DLR, Peixoto RS, Barbosa EAB, Napoleão F, Sabbadini PS, Dos Santos KRN, Mattos-Guaraldi AL, Hirata R. SubMICs of penicillin and erythromycin enhance biofilm formation and hydrophobicity of Corynebacterium diphtheriae strains. J Med Microbiol 2013; 62:754-760. [PMID: 23449875 DOI: 10.1099/jmm.0.052373-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Subinhibitory concentrations (subMICs) of antibiotics may alter bacterial surface properties and change microbial physiology. This study aimed to investigate the effect of a subMIC (⅛ MIC) of penicillin (PEN) and erythromycin (ERY) on bacterial morphology, haemagglutinating activity, cell-surface hydrophobicity (CSH) and biofilm formation on glass and polystyrene surfaces, as well as the distribution of cell-surface acidic anionic residues of Corynebacterium diphtheriae strains (HC01 tox(-) strain; CDC-E8392 and 241 tox(+) strains). All micro-organisms tested were susceptible to PEN and ERY. Growth in the presence of PEN induced bacterial filamentation, whereas subMIC of ERY caused cell-size reduction of strains 241 and CDC-E8392. Adherence to human erythrocytes was reduced after growth in the presence of ERY, while CSH was increased by a subMIC of both antibiotics in bacterial adherence to n-hexadecane assays. Conversely, antibiotic inhibition of biofilm formation was not observed. All strains enhanced biofilm formation on glass after treatment with ERY, while only strain 241 increased glass adherence after cultivation in the presence of PEN. Biofilm production on polystyrene surfaces was improved by ⅛ MIC of ERY. After growth in the presence of both antimicrobial agents, strains 241 and CDC-E8392 exhibited anionic surface charges with focal distribution. In conclusion, subMICs of PEN and ERY modified bacterial surface properties and enhanced not only biofilm formation but also cell-surface hydrophobicity. Antibiotic-induced biofilm formation may contribute to the inconsistent success of antimicrobial therapy for C. diphtheriae infections.
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Affiliation(s)
- D L R Gomes
- Faculty of Pharmacy, Federal Institute of Education, Science and Technology of Rio de Janeiro, IFRJ, Rio de Janeiro RJ, Brazil
- Laboratory of Diphtheria and Corynebacteria of Medical Relevance, Faculty of Medical Sciences, Rio de Janeiro State University, UERJ, Rio de Janeiro RJ, Brazil
| | - R S Peixoto
- Department of Medical Microbiology, Institute of Microbiology, Rio de Janeiro Federal University, UFRJ, Rio de Janeiro RJ, Brazil
- Laboratory of Diphtheria and Corynebacteria of Medical Relevance, Faculty of Medical Sciences, Rio de Janeiro State University, UERJ, Rio de Janeiro RJ, Brazil
| | - E A B Barbosa
- Faculty of Pharmacy, Federal Institute of Education, Science and Technology of Rio de Janeiro, IFRJ, Rio de Janeiro RJ, Brazil
| | - F Napoleão
- Laboratory of Diphtheria and Corynebacteria of Medical Relevance, Faculty of Medical Sciences, Rio de Janeiro State University, UERJ, Rio de Janeiro RJ, Brazil
| | - P S Sabbadini
- Laboratory of Diphtheria and Corynebacteria of Medical Relevance, Faculty of Medical Sciences, Rio de Janeiro State University, UERJ, Rio de Janeiro RJ, Brazil
| | - K R N Dos Santos
- Department of Medical Microbiology, Institute of Microbiology, Rio de Janeiro Federal University, UFRJ, Rio de Janeiro RJ, Brazil
| | - A L Mattos-Guaraldi
- Laboratory of Diphtheria and Corynebacteria of Medical Relevance, Faculty of Medical Sciences, Rio de Janeiro State University, UERJ, Rio de Janeiro RJ, Brazil
| | - R Hirata
- Laboratory of Diphtheria and Corynebacteria of Medical Relevance, Faculty of Medical Sciences, Rio de Janeiro State University, UERJ, Rio de Janeiro RJ, Brazil
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Sodré V, Caetano VS, Rocha RM, Carmo FL, Medici LO, Peixoto RS, Rosado AS, Reinert F. Physiological aspects of mangrove (Laguncularia racemosa) grown in microcosms with oil-degrading bacteria and oil contaminated sediment. Environ Pollut 2013; 172:243-249. [PMID: 23064202 DOI: 10.1016/j.envpol.2012.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 08/23/2012] [Accepted: 09/08/2012] [Indexed: 06/01/2023]
Abstract
To assess the severity of oil spills on mangroves, diagnosis of the vegetation health is crucial. Some aspects of photosynthesis such as photochemical efficiency and leaf pigment composition together with the level of oxidative stress may constitute reliable indicators for vegetation health. To test this approach 14 month old Laguncularia racemosa were contaminated with 5 L m(-2) of the marine fuel oil MF-380 and treated with an oil degrading bacterial consortium in microcosms. Contamination resulted in a 20% decrease in shoot dry weight after 128 days. Photochemical efficiency, pigment content, catalase and ascorbate peroxidase remained unchanged. Multivariate ordination of DGGE microbial community fingerprints revealed a pronounced separation between the oil contaminated and the non-contaminated samples. Further studies are necessary before physiological parameters can be recommended as indicators for plant's health in oil polluted mangroves.
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Affiliation(s)
- Vanessa Sodré
- Laboratório de Ecofisiologia Vegetal, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Brazil
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Andrade LL, Leite DCA, Ferreira EM, Ferreira LQ, Paula GR, Maguire MJ, Hubert CRJ, Peixoto RS, Domingues RMCP, Rosado AS. Microbial diversity and anaerobic hydrocarbon degradation potential in an oil-contaminated mangrove sediment. BMC Microbiol 2012; 12:186. [PMID: 22935169 PMCID: PMC3579730 DOI: 10.1186/1471-2180-12-186] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 08/23/2012] [Indexed: 12/04/2022] Open
Abstract
Background Mangrove forests are coastal wetlands that provide vital ecosystem services and serve as barriers against natural disasters like tsunamis, hurricanes and tropical storms. Mangroves harbour a large diversity of organisms, including microorganisms with important roles in nutrient cycling and availability. Due to tidal influence, mangroves are sites where crude oil from spills farther away can accumulate. The relationship between mangrove bacterial diversity and oil degradation in mangrove sediments remains poorly understood. Results Mangrove sediment was sampled from 0–5, 15–20 and 35–40 cm depth intervals from the Suruí River mangrove (Rio de Janeiro, Brazil), which has a history of oil contamination. DGGE fingerprinting for bamA, dsr and 16S rRNA encoding fragment genes, and qPCR analysis using dsr and 16S rRNA gene fragment revealed differences with sediment depth. Conclusions Analysis of bacterial 16S rRNA gene diversity revealed changes with depth. DGGE for bamA and dsr genes shows that the anaerobic hydrocarbon-degrading community profile also changed between 5 and 15 cm depth, and is similar in the two deeper sediments, indicating that below 15 cm the anaerobic hydrocarbon-degrading community appears to be well established and homogeneous in this mangrove sediment. qPCR analysis revealed differences with sediment depth, with general bacterial abundance in the top layer (0–5 cm) being greater than in both deeper sediment layers (15–20 and 35–40 cm), which were similar to each other.
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Affiliation(s)
- Luiza L Andrade
- Laboratório de Ecologia Molecular Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Rachid CTCC, Piccolo MC, Leite DCA, Balieiro FC, Coutinho HLC, van Elsas JD, Peixoto RS, Rosado AS. Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems. BMC Microbiol 2012; 12:170. [PMID: 22873209 PMCID: PMC3438109 DOI: 10.1186/1471-2180-12-170] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 07/19/2012] [Indexed: 11/23/2022] Open
Abstract
Background Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under the common burnt cane management. The green cane soil also presented different profiles compared to the control soil, but to at a lesser degree.
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Affiliation(s)
- Caio T C C Rachid
- Center for Nuclear Energy in Agriculture, Universidade de São Paulo, Piracicaba, Brazil.
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Santos HF, Carmo FL, Leite DCA, Jesus HE, Maalouf PDC, Almeida C, Soriano AU, Altomari D, Suhett L, Vólaro V, Valoni E, Francisco M, Vieira J, Rocha R, Sardinha BL, Mendes LB, João RR, Lacava B, Jesus RF, Sebastian GV, Pessoa A, van Elsas JD, Rezende RP, Pires DO, Duarte G, Castro CB, Rosado AS, Peixoto RS. Comparison of different protocols for the extraction of microbial DNA from reef corals. Braz J Microbiol 2012; 43:517-27. [PMID: 24031859 PMCID: PMC3768815 DOI: 10.1590/s1517-83822012000200012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Accepted: 06/07/2012] [Indexed: 02/03/2023] Open
Abstract
This study aimed to test different protocols for the extraction of microbial DNA from the coral Mussismilia harttii. Four different commercial kits were tested, three of them based on methods for DNA extraction from soil (FastDNA SPIN Kit for soil, MP Bio, PowerSoil DNA Isolation Kit, MoBio, and ZR Soil Microbe DNA Kit, Zymo Research) and one kit for DNA extraction from plants (UltraClean Plant DNA Isolation Kit, MoBio). Five polyps of the same colony of M. harttii were macerated and aliquots were submitted to DNA extraction by the different kits. After extraction, the DNA was quantified and PCR-DGGE was used to study the molecular fingerprint of Bacteria and Eukarya. Among the four kits tested, the ZR Soil Microbe DNA Kit was the most efficient with respect to the amount of DNA extracted, yielding about three times more DNA than the other kits. Also, we observed a higher number and intensities of DGGE bands for both Bacteria and Eukarya with the same kit. Considering these results, we suggested that the ZR Soil Microbe DNA Kit is the best adapted for the study of the microbial communities of corals.
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Affiliation(s)
- H F Santos
- Laboratório de Ecologia Molecular Microbiana, Universidade Federal do Rio de Janeiro , Rio de Janeiro, RJ , Brasil
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Castro ALMD, Vollú RE, Peixoto RS, Grigorevski-Lima AL, Coelho RRR, Bon EPS, Rosado AS, Seldin L. Cellulolytic potential of a novel strain of Paenibacillus sp. isolated from the armored catfish Parotocinclus maculicauda gut. Braz J Microbiol 2011. [DOI: 10.1590/s1517-83822011000400048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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