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van der Loos LM, D'hondt S, Engelen AH, Pavia H, Toth GB, Willems A, Weinberger F, De Clerck O, Steinhagen S. Salinity and host drive Ulva-associated bacterial communities across the Atlantic-Baltic Sea gradient. Mol Ecol 2023; 32:6260-6277. [PMID: 35395701 DOI: 10.1111/mec.16462] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/21/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
The green seaweed Ulva is a model system to study seaweed-bacteria interactions, but the impact of environmental drivers on the dynamics of these interactions is little understood. In this study, we investigated the stability and variability of the seaweed-associated bacteria across the Atlantic-Baltic Sea salinity gradient. We characterized the bacterial communities of 15 Ulva sensu lato species along 2,000 km of coastline in a total of 481 samples. Our results demonstrate that the Ulva-associated bacterial composition was strongly structured by both salinity and host species (together explaining between 34% and 91% of the variation in the abundance of the different bacterial genera). The largest shift in the bacterial consortia coincided with the horohalinicum (5-8 PSU, known as the transition zone from freshwater to marine conditions). Low-salinity communities especially contained high relative abundances of Luteolibacter, Cyanobium, Pirellula, Lacihabitans and an uncultured Spirosomaceae, whereas high-salinity communities were predominantly enriched in Litorimonas, Leucothrix, Sulfurovum, Algibacter and Dokdonia. We identified a small taxonomic core community (consisting of Paracoccus, Sulfitobacter and an uncultured Rhodobacteraceae), which together contributed to 14% of the reads per sample, on average. Additional core taxa followed a gradient model, as more core taxa were shared between neighbouring salinity ranges than between ranges at opposite ends of the Atlantic-Baltic Sea gradient. Our results contradict earlier statements that Ulva-associated bacterial communities are taxonomically highly variable across individuals and largely stochastically defined. Characteristic bacterial communities associated with distinct salinity regions may therefore facilitate the host's adaptation across the environmental gradient.
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Affiliation(s)
- Luna M van der Loos
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Sofie D'hondt
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Aschwin H Engelen
- Marine Microbial Ecology & Biotechnology, CCMAR, University of Algarve, Faro, Portugal
| | - Henrik Pavia
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Gunilla B Toth
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Anne Willems
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Sophie Steinhagen
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
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2
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Murúa P, Garvetto A, Egan S, Gachon CMM. The Reemergence of Phycopathology: When Algal Biology Meets Ecology and Biosecurity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:231-255. [PMID: 37253694 DOI: 10.1146/annurev-phyto-020620-120425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Viruses, bacteria, and eukaryotic symbionts interact with algae in a variety of ways to cause disease complexes, often shaping marine and freshwater ecosystems. The advent of phyconomy (a.k.a. seaweed agronomy) represents a need for a greater understanding of algal disease interactions, where underestimated cryptic diversity and lack of phycopathological basis are prospective constraints for algal domestication. Here, we highlight the limited yet increasing knowledge of algal pathogen biodiversity and the ecological interaction with their algal hosts. Finally, we discuss how ecology and cultivation experience contribute to and reinforce aquaculture practice, with the potential to reshape biosecurity policies of seaweed cultivation worldwide.
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Affiliation(s)
- Pedro Murúa
- Instituto de Acuicultura, Universidad Austral de Chile-Sede Puerto Montt, Los Lagos, Chile;
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
| | - Andrea Garvetto
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Tyrol, Austria
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Claire M M Gachon
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
- Muséum National d'Histoire Naturelle, CNRS, Paris, France
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3
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Rowley AF, Coates CJ. Shell disease syndromes of decapod crustaceans. Environ Microbiol 2023; 25:931-947. [PMID: 36708190 PMCID: PMC10946978 DOI: 10.1111/1462-2920.16344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/26/2023] [Indexed: 01/29/2023]
Abstract
The term shell disease subsumes a number of debilitating conditions affecting the outer integument (the carapace) of decapod crustaceans, such as lobsters and crabs. Herein, we seek to find commonality in the aetiology and pathology of such conditions, and those cases that result in the progressive erosion of the cuticle through to the visceral tissues by a cocktail of microbial-derived enzymes including lipases, proteases and chitinases. Aquimarina spp. are involved in shell disease in many different crustaceans across a wide geographical area, but the overall view is that the condition is polymicrobial in nature leading to dysbiosis within the microbial consortium of the damaged cuticle. The role of environment, decapod behaviour and physiology in triggering this disease is also reviewed. Finally, we provide a conceptual model for disease aetiology and suggest several avenues for future research that could improve our understanding of how such factors trigger, or exacerbate, this condition.
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Affiliation(s)
- Andrew F. Rowley
- Department of Biosciences, Faculty of Science and EngineeringSwansea UniversitySwanseaUK
| | - Christopher J. Coates
- Department of Zoology, School of Natural SciencesZoology, Ryan InstituteSchool of Natural Sciences, University of GalwayGalwayIreland
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4
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Liu X, Lyu L, Li J, Sen B, Bai M, Stajich JE, Collier JL, Wang G. Comparative Genomic Analyses of Cellulolytic Machinery Reveal Two Nutritional Strategies of Marine Labyrinthulomycetes Protists. Microbiol Spectr 2023; 11:e0424722. [PMID: 36744882 PMCID: PMC10101102 DOI: 10.1128/spectrum.04247-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/11/2023] [Indexed: 02/07/2023] Open
Abstract
Labyrinthulomycetes are a group of ubiquitous and diverse unicellular Stramenopiles and have long been known for their vital role in ocean carbon cycling. However, their ecological function from the perspective of organic matter degradation remains poorly understood. This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains, namely, Botryochytrium sp. strain S-28 and Oblongichytrium sp. strain S-429, and provides molecular analysis of their ecological functions using comparative genomics and a biochemical assay. Our results suggest that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems because of the significant differences in gene function among different genera. Certain strains could degrade wheat bran independently by secreting cellulase. The key glycoside hydrolase families (GH1, GH5, and GH9) related to cellulase and the functional domains of carbohydrate-active enzymes (CAZymes) were more enriched in their genomes. This group can actively participate in marine biochemical cycles as decomposers. In contrast, other strains that could not produce cellulase may thrive as "leftover scavengers" and act as a source of nutrients to the higher-trophic-level plankton. In addition, our findings emphasize the dual roles of endoglucanase, acting as both exo- and endoglucanases, in the process of cellulose degradation. Using genomic, biochemical, and phylogenetic analyses, our study provides a broader insight into the nutritional patterns and ecological functions of Labyrinthulomycetes. IMPORTANCE Unicellular heterotrophic eukaryotes are an important component of marine ecosystems. However, their ecological functions and modes of nutrition remain largely unknown. Our current understanding of marine microbial ecology is incomplete without integrating these heterotrophic microeukaryotes into the food web models. This study focuses on the unicellular fungus-like protists Labyrinthulomycetes and provides two high-quality genomes of cellulase-producing Labyrinthulomycetes. Our study uncovers the basis of their cellulase production by deciphering the results of genomic, biochemical, and phylogenetic analyses. This study instigates a further investigation of the molecular mechanism of organic matter utilization by Labyrinthulomycetes in the world's oceans.
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Affiliation(s)
- Xiuping Liu
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Lu Lyu
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Jiaqian Li
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Biswarup Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Mohan Bai
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Jason E. Stajich
- Department of Plant Pathology and Microbiology, University of California, Riverside, California, USA
| | - Jackie L. Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
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5
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Schaubeck A, Cao D, Cavaleri V, Mun S, Jeon SJ. Carapace microbiota in American lobsters ( Homarus americanus) associated with epizootic shell disease and the green gland. Front Microbiol 2023; 14:1093312. [PMID: 37089549 PMCID: PMC10113626 DOI: 10.3389/fmicb.2023.1093312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/03/2023] [Indexed: 04/25/2023] Open
Abstract
Epizootic Shell Disease (ESD) has posed a great threat, both ecologically and economically, to the American lobster population of Long Island Sound since its emergence in the late 1990s. Because of the polymicrobial nature of carapace infections, causative agents for ESD remain unclear. In this study, we aimed to identify carapace microbiota associated with ESD and its potential impact on the microbiota of internal organs (green gland, hepatopancreas, intestine, and testis) using high-throughput 16S rRNA gene sequencing. We found that lobsters with ESD harbored specific carapace microbiota characterized by high abundance of Aquimarina, which was significantly different from healthy lobsters. PICRUSt analysis showed that metabolic pathways such as amino acid metabolism were enriched in the carapace microbiota of lobsters with ESD. Aquimarina, Halocynthiibacter, and Tenacibaculum were identified as core carapace bacteria associated with ESD. Particularly, Aquimarina and Halocynthiibacter were detected in the green gland, hepatopancreas, and testis of lobsters with ESD, but were absent from all internal organs tested in healthy lobsters. Hierarchical clustering analysis revealed that the carapace microbiota of lobsters with ESD was closely related to the green gland microbiota, whereas the carapace microbiota of healthy lobsters was more similar to the testis microbiota. Taken together, our findings suggest that ESD is associated with alterations in the structure and function of carapace microbiota, which may facilitate the invasion of bacteria into the green gland.
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Affiliation(s)
- Anna Schaubeck
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY, United States
| | - Dianjun Cao
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY, United States
| | - Vincent Cavaleri
- Division of Marine Resources, New York State Department of Environmental Conservation, East Setauket, NY, United States
| | - Seyoung Mun
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan, Republic of Korea
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, Republic of Korea
| | - Soo Jin Jeon
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY, United States
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6
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Choi A, Cha IT, Lee KE, Son YK, Yu J, Seol D. The Role of Flavobacterium enshiense R6S-5-6 in the Wetland Ecosystem Revealed by Whole-Genome Analysis. Curr Microbiol 2023; 80:83. [PMID: 36680647 PMCID: PMC9867689 DOI: 10.1007/s00284-022-03157-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 11/25/2022] [Indexed: 01/22/2023]
Abstract
The wetland is an important ecosystem for purifying pollutants and circulating nutrients. Numerous microorganisms contribute to maintaining this function. We obtained Flavobacterium enshiense R6S-5-6 which was isolated from Ungok (Ramsar) Wetland and conducted whole-genome sequencing to investigate what contribution R6S-5-6 could make to the wetland community. The complete genome sequence of R6S-5-6 has a size of 3,251,289 bp with 37.68% of GC content. Gene annotation revealed that R6S-5-6 has several pathways to break down pollutants, including denitrification, assimilatory sulfate reduction (ASR), and polyphosphate-accumulating process. Furthermore, R6S-5-6 has genes that can have a positive effect on plants living in wetlands, such as storing essential nutrients, promoting plant growth, and protecting plants against pathogens.
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Affiliation(s)
- Ahhyeon Choi
- eGnome, Inc, 26 Beobwon-ro 9-Gil, Songpa-gu, Seoul, 05836 Republic of Korea
| | - In-Tae Cha
- grid.419519.10000 0004 0400 5474National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 Republic of Korea
| | - Ki-Eun Lee
- grid.419519.10000 0004 0400 5474National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 Republic of Korea
| | - Youn Kyoung Son
- grid.419519.10000 0004 0400 5474National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 Republic of Korea
| | - Jaewoong Yu
- eGnome, Inc, 26 Beobwon-ro 9-Gil, Songpa-gu, Seoul, 05836 Republic of Korea
| | - Donghyeok Seol
- grid.31501.360000 0004 0470 5905Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Republic of Korea ,grid.412480.b0000 0004 0647 3378Present Address: Department of Surgery, Seoul National University Bundang Hospital, 172 Dolma-ro, Bundang-gu, Seongnam, 13605 Republic of Korea
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7
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Hudson J, Egan S. Opportunistic diseases in marine eukaryotes: Could Bacteroidota be the next threat to ocean life? Environ Microbiol 2022; 24:4505-4518. [PMID: 35706128 PMCID: PMC9804302 DOI: 10.1111/1462-2920.16094] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 01/05/2023]
Abstract
Bacteria within the phylum Bacteroidota (Bacteroidetes) are known to cause devastating and widespread disease outbreaks in marine eukaryotic hosts. However, with few pathogens described in detail, their prevalence and virulence strategies remain largely unknown. Here, we systematically reviewed the literature to evaluate the current understanding of Bacteroidota that cause disease in marine hosts. Isolates affiliated with the genera Tenacibaculum and Aquimarina (Flavobacteriaceae) were the most widely reported and characterized pathogens. Although cultured isolates were predominantly Flavobacteriia, culture-independent studies also found classes Bacteroidia, Cytophagia and Sphingobacteriia associated with disease. We found that pathogenic marine Bacteroidota largely conformed to an opportunistic lifestyle but could also act as secondary pathogens or were involved in polymicrobial diseases. Many diseases were also associated with an environmental stressor, especially those affecting coral, macroalgae and fish. Key virulence traits included the production of adhesins and host tissue-degrading enzymes. Overall, the nature of disease involving Bacteroidota pathogens appears to be an outcome of complex host-pathogen-environment interactions; however, our understanding of virulence remains limited by the lack of functional characterization studies. This is concerning as Bacteroidota have the potential to emerge as a serious threat to marine ecosystems and aquaculture industries, driven by global changes in ocean conditions.
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Affiliation(s)
- Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyAustralia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyAustralia
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8
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Hudson J, Deshpande N, Leblanc C, Egan S. Pathogen exposure leads to a transcriptional downregulation of core cellular functions that may dampen the immune response in a macroalga. Mol Ecol 2022; 31:3468-3480. [PMID: 35445473 PMCID: PMC9325437 DOI: 10.1111/mec.16476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/23/2022] [Accepted: 04/11/2022] [Indexed: 11/27/2022]
Abstract
Diseases in marine eukaryotic organisms caused by opportunistic pathogens represent a serious threat to our oceans with potential downstream consequences for ecosystem functioning. Disease outbreaks affecting macroalgae are of particular concern due to their critical role as habitat‐forming organisms. However, there is limited understanding of the molecular strategies used by macroalgae to respond to opportunistic pathogens. In this study, we used mRNA‐sequencing analysis to investigate the early antipathogen response of the model macroalga Delisea pulchra (Rhodophyta) under the environmental conditions that are known to promote the onset of disease. Using de novo assembly methods, 27,586 unique transcripts belonging to D. pulchra were identified that were mostly affiliated with stress response and signal transduction processes. Differential gene expression analysis between a treatment with the known opportunistic pathogen, Aquimarina sp. AD1 (Bacteroidota), and a closely related benign strain (Aquimarina sp. AD10) revealed a downregulation of genes coding for predicted protein metabolism, stress response, energy generation and photosynthesis functions. The rapid repression of genes coding for core cellular processes is likely to interfere with the macroalgal antipathogen response, later leading to infection, tissue damage and bleaching symptoms. Overall, this study provides valuable insight into the genetic features of D. pulchra, highlighting potential antipathogen response mechanisms of macroalgae and contributing to an improved understanding of host–pathogen interactions in a changing environment.
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Affiliation(s)
- Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, Australia
| | - Nandan Deshpande
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Catherine Leblanc
- CNRS, Sorbonne Université, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, Australia
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9
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Bacterial controlled mitigation of dysbiosis in a seaweed disease. THE ISME JOURNAL 2022; 16:378-387. [PMID: 34341505 PMCID: PMC8776837 DOI: 10.1038/s41396-021-01070-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 02/06/2023]
Abstract
Disease in the marine environment is predicted to increase with anthropogenic stressors and already affects major habitat-formers, such as corals and seaweeds. Solutions to address this issue are urgently needed. The seaweed Delisea pulchra is prone to a bleaching disease, which is caused by opportunistic pathogens and involves bacterial dysbiosis. Bacteria that can inhibit these pathogens and/or counteract dysbiosis are therefore hypothesised to reduce disease. This study aimed to identify such disease-protective bacteria and investigate their protective action. One strain, Phaeobacter sp. BS52, isolated from healthy D. pulchra, was antagonistic towards bleaching pathogens and significantly increased the proportion of healthy individuals when applied before the pathogen challenge (pathogen-only vs. BS52 + pathogen: 41-80%), and to a level similar to the control. However, no significant negative correlations between the relative abundances of pathogens and BS52 on D. pulchra were detected. Instead, inoculation of BS52 mitigated pathogen-induced changes in the epibacterial community. These observations suggest that the protective activity of BS52 was due to its ability to prevent dysbiosis, rather than direct pathogen inhibition. This study demonstrates the feasibility of manipulating bacterial communities in seaweeds to reduce disease and that mitigation of dysbiosis can have positive health outcomes.
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10
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Aquimarina algicola sp. nov., isolated from the surface of a marine red alga. Arch Microbiol 2021; 203:5397-5403. [PMID: 34398306 DOI: 10.1007/s00203-021-02524-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 12/29/2022]
Abstract
A bacterial strain, designated M625T, was isolated from the surface of a marine red alga. Phylogenetic trees were reconstructed based on the 16S rRNA gene and RpoB protein sequences, which indicated that the strain belongs to the genus Aquimarina within the family Flavobacteriaceae. Strain M625T showed high sequence similarities to A. aggregata RZW4-3-2 T (95.7%), A. seongsanensis CBA3208T (95.3%) and A. versatilis CBA3207T (95.0%). The AAI and POCP values between strain M625T and A. muelleri DSM 19832 T were 71.8% and 57.9% respectively. The dDDH and ANI values between strain M625T and A. aggregata were 19.5% and 74.6% respectively. The strain was Gram-stain negative, strictly aerobic, non-motile and long rod-shaped, and positive for hydrolysis of starch, cellulose, alginate, DNA and Tween 20. The dominant respiratory quinone was MK-6. The major fatty acids were iso-C15:0, iso-C17:0 3-OH, and iso-C15:1 G, and the polar lipids consisted of phosphatidylethanolamine, one unidentified phospholipid, two unidentified aminolipids, and seven unidentified lipids. Based on the polyphasic comparisons, strain M625T is proposed to represent a novel species within the genus Aquimarina, for which the name Aquimarina algicola sp. nov. (type strain M625T = MCCC 1H00399T = KCTC 72685 T) was proposed.
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11
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A Novel Auxiliary Agarolytic Pathway Expands Metabolic Versatility in the Agar-Degrading Marine Bacterium Colwellia echini A3 T. Appl Environ Microbiol 2021; 87:e0023021. [PMID: 33811026 DOI: 10.1128/aem.00230-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine microorganisms encode a complex repertoire of carbohydrate-active enzymes (CAZymes) for the catabolism of algal cell wall polysaccharides. While the core enzyme cascade for degrading agar is conserved across agarolytic marine bacteria, gain of novel metabolic functions can lead to the evolutionary expansion of the gene repertoire. Here, we describe how two less-abundant GH96 α-agarases harbored in the agar-specific polysaccharide utilization locus (PUL) of Colwellia echini strain A3T facilitate the versatility of the agarolytic pathway. The cellular and molecular functions of the α-agarases examined by genomic, transcriptomic, and biochemical analyses revealed that α-agarases of C. echini A3T create a novel auxiliary pathway. α-Agarases convert even-numbered neoagarooligosaccharides to odd-numbered agaro- and neoagarooligosaccharides, providing an alternative route for the depolymerization process in the agarolytic pathway. Comparative genomic analysis of agarolytic bacteria implied that the agarolytic gene repertoire in marine bacteria has been diversified during evolution, while the essential core agarolytic gene set has been conserved. The expansion of the agarolytic gene repertoire and novel hydrolytic functions, including the elucidated molecular functionality of α-agarase, promote metabolic versatility by channeling agar metabolism through different routes. IMPORTANCE Colwellia echini A3T is an example of how the gain of gene(s) can lead to the evolutionary expansion of agar-specific polysaccharide utilization loci (PUL). C. echini A3T encodes two α-agarases in addition to the core β-agarolytic enzymes in its agarolytic PUL. Among the agar-degrading CAZymes identified so far, only a few α-agarases have been biochemically characterized. The molecular and biological functions of two α-agarases revealed that their unique hydrolytic pattern leads to the emergence of auxiliary agarolytic pathways. Through the combination of transcriptomic, genomic, and biochemical evidence, we elucidate the complete α-agarolytic pathway in C. echini A3T. The addition of α-agarases to the agarolytic enzyme repertoire might allow marine agarolytic bacteria to increase competitive abilities through metabolic versatility.
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Keller-Costa T, Lago-Lestón A, Saraiva JP, Toscan R, Silva SG, Gonçalves J, Cox CJ, Kyrpides N, Nunes da Rocha U, Costa R. Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals. MICROBIOME 2021; 9:72. [PMID: 33766108 PMCID: PMC7993494 DOI: 10.1186/s40168-021-01031-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/08/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella. RESULTS Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host's immune system. CONCLUSIONS This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. Video Abstract.
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Affiliation(s)
- T. Keller-Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
| | - A. Lago-Lestón
- División de Biología Experimental y Aplicada (DBEA), Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carr. Ensenada-Tijuana 3918, Zona Playitas, C.P 22860 Ensenada, Baja California Mexico
| | - J. P. Saraiva
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - R. Toscan
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - S. G. Silva
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
| | - J. Gonçalves
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - C. J. Cox
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - N. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
| | - U. Nunes da Rocha
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - R. Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
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13
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Varasteh T, Tschoeke D, Garcia G, Lima AS, Moreira APB, Thompson C, Thompson F. Insights into the genomic repertoire of Aquimarina litoralis CCMR20, a symbiont of coral Mussismilia braziliensis. Arch Microbiol 2021; 203:2743-2746. [PMID: 33675372 DOI: 10.1007/s00203-021-02194-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/12/2021] [Accepted: 02/04/2021] [Indexed: 11/25/2022]
Abstract
Aquimarina litoralis CCMR20 originated from the coral Mussismilia braziliensis (Sebastião Gomes Reef, Brazil, summer 2010). To gain new insights into the genomic repertoire associated with symbioses, we obtained the genome sequence of this strains using Illumina sequencing. CCMR20 has a genome size of 6.3 Mb, 32.6%GC, and 5513 genes (37 tRNA and 4 rRNA). A more fine-grained examination of the gene repertoire of CCMR20 disclosed genes engaged with symbiosis (heterotrophic carbon metabolism, CAZymes, B-vitamins group, carotenoid pigment and antioxidant molecules production). Genomic evidence further expand the possible relevance of this symbiont in the health of Mussismilia holobiont.Whole Genome Shotgun project has been deposited at DDBJ/ENA/GeneBank under the accession number WEKL00000000.
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Affiliation(s)
- Tooba Varasteh
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Diogo Tschoeke
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Gizele Garcia
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
- Departamento de Ensino de Graduação, Universidade Federal Do Rio de Janeiro, Campus UFRJ, Macae' Professor Aloisio Teixeira, Macae', Rio de Janeiro, RJ, 27930-480, Brazil
| | - Arthur Silva Lima
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Ana Paula B Moreira
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Cristiane Thompson
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Fabiano Thompson
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil.
- SAGE, COPPE, Centro de Gestão Tecnológica-CT2, Rio de Janeiro, RJ, Brazil.
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14
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Varasteh T, Hamerski L, Tschoeke D, Lima AS, Garcia G, Cosenza CAN, Thompson C, Thompson F. Conserved Pigment Profiles in Phylogenetically Diverse Symbiotic Bacteria Associated with the Corals Montastraea cavernosa and Mussismilia braziliensis. MICROBIAL ECOLOGY 2021; 81:267-277. [PMID: 32681284 DOI: 10.1007/s00248-020-01551-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Pigmented bacterial symbionts play major roles in the health of coral holobionts. However, there is scarce knowledge on the diversity of these microbes for several coral species. To gain further insights into holobiont health, pigmented bacterial isolates of Fabibacter pacificus (Bacteroidetes; n = 4), Paracoccus marcusii (Alphaproteobacteria; n = 1), and Pseudoalteromonas shioyasakiensis (Gammaproteobacteria; n = 1) were obtained from the corals Mussismilia braziliensis and Montastraea cavernosa in Abrolhos Bank, Brazil. Cultures of these bacterial symbionts produced strong antioxidant activity (catalase, peroxidase, and oxidase). To explore these bacterial isolates further, we identified their major pigments by HPLC and mass spectrometry. The six phylogenetically diverse symbionts had similar pigment patterns and produced myxol and keto-carotene. In addition, similar carotenoid gene clusters were confirmed in the whole genome sequences of these symbionts, which reinforce their antioxidant potential. This study highlights the possible roles of bacterial symbionts in Montastraea and Mussismilia holobionts.
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Affiliation(s)
- Tooba Varasteh
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Lidilhone Hamerski
- Instituto de Pesquisas de Produtos Naturais, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Diogo Tschoeke
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Arthur Silva Lima
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Gizele Garcia
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
- Departamento de Ensino de Graduação, Universidade Federal do Rio de Janeiro - Campus UFRJ - Macaé Professor Aloisio Teixeira, Macaé, Rio de Janeiro, RJ, 27930-480, Brazil
| | | | - Cristiane Thompson
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Fabiano Thompson
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil.
- SAGE - COPPE, Centro de Gestão Tecnológica - CT2, Rio de Janeiro, RJ, Brazil.
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15
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Ooi MC, Goulden EF, Trotter AJ, Smith GG, Bridle AR. Aquimarina sp. Associated With a Cuticular Disease of Cultured Larval Palinurid and Scyllarid Lobsters. Front Microbiol 2020; 11:573588. [PMID: 33162955 PMCID: PMC7581904 DOI: 10.3389/fmicb.2020.573588] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/07/2020] [Indexed: 11/21/2022] Open
Abstract
Shell (cuticular) disease manifests in various forms and affects many crustaceans, including lobsters. Outbreaks of white leg disease (WLD) with distinct signs of pereiopod tissue whitening and death have been observed in cultured larvae (phyllosomas) of ornate spiny lobster Panulirus ornatus, eastern rock lobster Sagmariasus verreauxi, and slipper lobster Thenus australiensis. This study aimed to characterise and identify the causative agent of WLD through morphological and molecular (16S rRNA gene and whole genome sequencing) analysis, experimental infection of damaged/undamaged P. ornatus and T. australiensis phyllosomas, and bacterial community analysis (16S rRNA gene amplicon sequencing) of P. ornatus phyllosomas presenting with WLD during an outbreak. Bacterial communities of WLD-affected pereiopods showed low bacterial diversity and dominant abundance of Aquimarina spp. compared to healthy pereiopods, which were more diverse and enriched with Sulfitobacter spp. 16S rRNA gene Sanger sequencing of cultures from disease outbreaks identified the dominant bacterial isolate (TRL1) as a Gram-negative, long non-flagellated rod with 100% sequence identity to Aquimarina hainanensis. Aquimarina sp. TRL1 was demonstrated through comparative genome analysis (99.99% OrthoANIu) as the bacterium reisolated from experimentally infected phyllosomas presenting with typical signs of WLD. Pereiopod damage was a major predisposing factor to WLD. Histopathological examination of WLD-affected pereiopods showed masses of internalised bacteria and loss of structural integrity, suggesting that Aquimarina sp. TRL1 could enter the circulatory system and cause death by septicaemia. Aquimarina sp. TRL1 appears to have important genomic traits (e.g., tissue-degrading enzymes, gliding motility, and aggregate-promoting factors) implicated in the pathogenicity of this bacterium. We have shown that Aquimarina sp. TRL1 is the aetiological agent of WLD in cultured Palinurid and Scyllarid phyllosomas and that damaged pereiopods are a predisposing factor to WLD.
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Affiliation(s)
- Mei C Ooi
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Evan F Goulden
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia.,Department of Agriculture and Fisheries, Bribie Island Research Centre, Woorim, QLD, Australia
| | - Andrew J Trotter
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Gregory G Smith
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Andrew R Bridle
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
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16
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Quigley CTC, Capistrant-Fossa KA, Morrison HG, Johnson LE, Morozov A, Hertzberg VS, Brawley SH. Bacterial Communities Show Algal Host ( Fucus spp.)/Zone Differentiation Across the Stress Gradient of the Intertidal Zone. Front Microbiol 2020; 11:563118. [PMID: 33072025 PMCID: PMC7541829 DOI: 10.3389/fmicb.2020.563118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022] Open
Abstract
The intertidal zone often has varying levels of environmental stresses (desiccation, temperature, light) that result in highly stress-tolerant macrobiota occupying the upper zone while less tolerant species occupy the lower zone, but little comparative information is available for intertidal bacteria. Here we describe natural (unmanipulated) bacterial communities of three Fucus congeners (F. spiralis, high zone; F. vesiculosus, mid zone; F. distichus, low zone) as well as those of F. vesiculosus transplanted to the high zone (Dry and Watered treatments) and to the mid zone (Procedural Control) during summer in Maine (United States). We predicted that bacterial communities would be different among the differently zoned natural congeners, and that higher levels of desiccation stress in the high zone would cause bacterial communities of Dry transplants to become similar to F. spiralis, whereas relieving desiccation stress on Watered transplants would maintain the mid-zone F. vesiculosus bacterial community. Bacteria were identified as amplicon sequence variants (ASVs) after sequencing the V4 hypervariable region of the 16S rRNA gene. Microbiome composition and structure were significantly different between the differently zoned congeners at each tissue type (holdfasts, receptacles, vegetative tips). ASVs significantly associated with the mid-zone congener were frequently also present on the high-zone or low-zone congener, whereas overlap in ASVs between the high-zone and low-zone congeners was rare. Only 7 of 6,320 total ASVs were shared among tissues over all congeners and transplant treatments. Holdfast bacterial community composition of Dry transplants was not significantly different from that of F. spiralis, but Watered holdfast communities were significantly different from those of F. spiralis and not significantly different from those of procedural controls. Additional stressor(s) appeared important, because bacterial communities of Dry and Watered transplants were only marginally different from each other (p = 0.059). The relative abundance of Rhodobacteraceae associated with holdfasts generally correlated with environmental stress with highest abundance associated with F. spiralis and the two high-zone transplant treatments. These findings suggest that the abiotic stressors that shape distributional patterns of host species also affect their bacterial communities.
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Affiliation(s)
| | | | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Ladd E Johnson
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - Aleksey Morozov
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Vicki S Hertzberg
- Center for Data Science, Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, United States
| | - Susan H Brawley
- School of Marine Sciences, University of Maine, Orono, ME, United States
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17
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Gavriilidou A, Gutleben J, Versluis D, Forgiarini F, van Passel MWJ, Ingham CJ, Smidt H, Sipkema D. Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis. BMC Genomics 2020; 21:569. [PMID: 32819293 PMCID: PMC7440613 DOI: 10.1186/s12864-020-06971-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/05/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Members of the bacterial family Flavobacteriaceae are widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates. Yet, little is known about the characteristics that drive their ubiquity in diverse ecological niches. Here, we provide an overview of functional traits common to taxonomically diverse members of the family Flavobacteriaceae from different environmental sources, with a focus on the Marine clade. We include seven newly sequenced marine sponge-derived strains that were also tested for gliding motility and antimicrobial activity. RESULTS Comparative genomics revealed that genome similarities appeared to be correlated to 16S rRNA gene- and genome-based phylogeny, while differences were mostly associated with nutrient acquisition, such as carbohydrate metabolism and gliding motility. The high frequency and diversity of genes encoding polymer-degrading enzymes, often arranged in polysaccharide utilization loci (PULs), support the capacity of marine Flavobacteriaceae to utilize diverse carbon sources. Homologs of gliding proteins were widespread among all studied Flavobacteriaceae in contrast to members of other phyla, highlighting the particular presence of this feature within the Bacteroidetes. Notably, not all bacteria predicted to glide formed spreading colonies. Genome mining uncovered a diverse secondary metabolite biosynthesis arsenal of Flavobacteriaceae with high prevalence of gene clusters encoding pathways for the production of antimicrobial, antioxidant and cytotoxic compounds. Antimicrobial activity tests showed, however, that the phenotype differed from the genome-derived predictions for the seven tested strains. CONCLUSIONS Our study elucidates the functional repertoire of marine Flavobacteriaceae and highlights the need to combine genomic and experimental data while using the appropriate stimuli to unlock their uncharted metabolic potential.
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Affiliation(s)
- Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Johanna Gutleben
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dennis Versluis
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Francesca Forgiarini
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Mark W. J. van Passel
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Present address: Ministry of Health, Welfare and Sport, Parnassusplein 5, 2511 VX, The Hague, The Netherlands
| | | | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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18
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Silva SG, Blom J, Keller‐Costa T, Costa R. Comparative genomics reveals complex natural product biosynthesis capacities and carbon metabolism across host‐associated and free‐living
Aquimarina
(
Bacteroidetes, Flavobacteriaceae
) species. Environ Microbiol 2019; 21:4002-4019. [DOI: 10.1111/1462-2920.14747] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 07/12/2019] [Indexed: 01/26/2023]
Affiliation(s)
- Sandra G. Silva
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa Lisbon Portugal
| | - Jochen Blom
- Bioinformatics and Systems Biology Justus‐Liebig‐University Giessen 35392 Giessen Germany
| | - Tina Keller‐Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa Lisbon Portugal
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa Lisbon Portugal
- Centre of Marine Sciences (CCMAR) Algarve University 8005‐139 Faro Portugal
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