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Svendsen PB, Henriksen NNSE, Jarmusch SA, Andersen AJC, Smith K, Selsmark MW, Zhang SD, Schostag MD, Gram L. Co-existence of two antibiotic-producing marine bacteria: Pseudoalteromonas piscicida reduce gene expression and production of the antibacterial compound, tropodithietic acid, in Phaeobacter sp. Appl Environ Microbiol 2024; 90:e0058824. [PMID: 39136490 PMCID: PMC11409694 DOI: 10.1128/aem.00588-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/16/2024] [Indexed: 09/19/2024] Open
Abstract
Many bacteria co-exist and produce antibiotics, yet we know little about how they cope and occupy the same niche. The purpose of the present study was to determine if and how two potent antibiotic-producing marine bacteria influence the secondary metabolome of each other. We established an agar- and broth-based system allowing co-existence of a Phaeobacter species and Pseudoalteromonas piscicida that, respectively, produce tropodithietic acid (TDA) and bromoalterochromides (BACs). Co-culturing of Phaeobacter sp. strain A36a-5a on Marine Agar with P. piscicida strain B39bio caused a reduction of TDA production in the Phaeobacter colony. We constructed a transcriptional gene reporter fusion in the tdaC gene in the TDA biosynthetic pathway in Phaeobacter and demonstrated that the reduction of TDA by P. piscicida was due to the suppression of the TDA biosynthesis. A stable liquid co-cultivation system was developed, and the expression of tdaC in Phaeobacter was reduced eightfold lower (per cell) in the co-culture compared to the monoculture. Mass spectrometry imaging of co-cultured colonies revealed a reduction of TDA and indicated that BACs diffused into the Phaeobacter colony. BACs were purified from Pseudoalteromonas; however, when added as pure compounds or a mixture they did not influence TDA production. In co-culture, the metabolome was dominated by Pseudoalteromonas features indicating that production of other Phaeobacter compounds besides TDA was reduced. In conclusion, co-existence of two antibiotic-producing bacteria may be allowed by one causing reduction in the antagonistic potential of the other. The reduction (here of TDA) was not caused by degradation but by a yet uncharacterized mechanism allowing Pseudoalteromonas to reduce expression of the TDA biosynthetic pathway.IMPORTANCEThe drug potential of antimicrobial secondary metabolites has been the main driver of research into these compounds. However, in recent years, their natural role in microbial systems and microbiomes has become important to determine the assembly and development of microbiomes. Herein, we demonstrate that two potent antibiotic-producing bacteria can co-exist, and one mechanism allowing the co-existence is the specific reduction of antibiotic production in one bacterium by the other. Understanding the molecular mechanisms in complex interactions provides insights for applied uses, such as when developing TDA-producing bacteria for use as biocontrol in aquaculture.
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Affiliation(s)
- Peter Bing Svendsen
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nathalie N. S. E. Henriksen
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Scott A. Jarmusch
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Aaron J. C. Andersen
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kirsty Smith
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Chemistry, University of Aberdeen, King’s College, Aberdeen, United Kingdom
| | - Marcus Weichel Selsmark
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Morten D. Schostag
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
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Alghamdi AK, Parween S, Hirt H, Saad MM. Unraveling the genomic secrets of Tritonibacter mobilis AK171: a plant growth-promoting bacterium isolated from Avicennia marina. BMC Genomics 2024; 25:672. [PMID: 38969999 PMCID: PMC11225332 DOI: 10.1186/s12864-024-10555-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
The scarcity of freshwater resources resulting in a significant yield loss presents a pressing challenge in agriculture. To address this issue, utilizing abundantly available saline water could offer a smart solution. In this study, we demonstrate that the genome sequence rhizosphere bacterium Tritonibacter mobilis AK171, a halophilic marine bacterium recognized for its ability to thrive in saline and waterlogged environments, isolated from mangroves, has the remarkable ability to enable plant growth using saline irrigation. AK171 is characterized as rod-shaped cells, displays agile movement in free-living conditions, and adopts a rosette arrangement in static media. Moreover, The qualitative evaluation of PGP traits showed that AK171 could produce siderophores and IAA but could not solubilize phosphate nor produce hydrolytic enzymes it exhibits a remarkable tolerance to high temperatures and salinity. In this study, we conducted a comprehensive genome sequence analysis of T. mobilis AK171 to unravel the genetic mechanisms underlying its plant growth-promoting abilities in such challenging conditions. Our analysis revealed diverse genes and pathways involved in the bacterium's adaptation to salinity and waterlogging stress. Notably, T. mobilis AK171 exhibited a high level of tolerance to salinity and waterlogging through the activation of stress-responsive genes and the production of specific enzymes and metabolites. Additionally, we identified genes associated with biofilm formation, indicating its potential role in establishing symbiotic relationships with host plants. Furthermore, our analysis unveiled the presence of genes responsible for synthesizing antimicrobial compounds, including tropodithietic acid (TDA), which can effectively control phytopathogens. This genomic insight into T. mobilis AK171 provides valuable information for understanding the molecular basis of plant-microbial interactions in saline and waterlogged environments. It offers potential applications for sustainable agriculture in challenging conditions.
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Affiliation(s)
- Amal Khalaf Alghamdi
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Sabiha Parween
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Max Perutz Laboratories, University of Vienna, Vienna, Austria.
| | - Maged M Saad
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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Droumpali A, Liu Y, Ferrer-Florensa X, Sternberg C, Dimaki M, Andersen AJC, Strube ML, Kempen PJ, Gram L, Taboryski R. Biosynthesis enhancement of tropodithietic acid (TDA) antibacterial compound through biofilm formation by marine bacteria Phaeobacter inhibens on micro-structured polymer surfaces. RSC Adv 2023; 13:33159-33166. [PMID: 37964901 PMCID: PMC10641763 DOI: 10.1039/d3ra05407a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/29/2023] [Indexed: 11/16/2023] Open
Abstract
Although aquaculture is a major player in current and future food production, the routine use of antibiotics provides ample ground for development of antibiotic resistance. An alternative route to disease control is the use of probiotic bacteria such as the marine bacteria Phaeobacter inhibens which produces tropodithietic acid (TDA) that inhibit pathogens without affecting the fish. Improving conditions for the formation of biofilm and TDA-synthesis is a promising avenue for biocontrol in aquaculture. In this study, the biosynthesis of TDA by Phaeobacter inhibens grown on micro-structured polymeric surfaces in micro-fluidic flow-cells is investigated. The formation of biofilms on three surface topographies; hexagonal micro-pit-arrays, hexagonal micro-pillar-arrays, and planar references is investigated. The biomass on these surfaces is measured by a non-invasive confocal microscopy 3D imaging technique, and the corresponding TDA production is monitored by liquid chromatography mass spectrometry (LC-MS) in samples collected from the outlets of the microfluidic channels. Although all surfaces support growth of P. inhibens, biomass appears to be decoupled from total TDA biosynthesis as the micro-pit-arrays generate the largest biomass while the micro-pillar-arrays produce significantly higher amounts of TDA. The findings highlight the potential for optimized micro-structured surfaces to maintain biofilms of probiotic bacteria for sustainable aquacultures.
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Affiliation(s)
- Ariadni Droumpali
- DTU Nanolab, National Centre for Nano Fabrication and Characterization, Technical University of Denmark Ørsteds Plads, Building 347 DK-2800 Kgs. Lyngby Denmark
| | - Yuyan Liu
- DTU Nanolab, National Centre for Nano Fabrication and Characterization, Technical University of Denmark Ørsteds Plads, Building 347 DK-2800 Kgs. Lyngby Denmark
| | - Xavier Ferrer-Florensa
- DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 221 DK-2800 Kgs. Lyngby Denmark
| | - Claus Sternberg
- DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 221 DK-2800 Kgs. Lyngby Denmark
| | - Maria Dimaki
- DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 221 DK-2800 Kgs. Lyngby Denmark
| | - Aaron J C Andersen
- DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 221 DK-2800 Kgs. Lyngby Denmark
| | - Mikael L Strube
- DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 221 DK-2800 Kgs. Lyngby Denmark
| | - Paul J Kempen
- DTU Nanolab, National Centre for Nano Fabrication and Characterization, Technical University of Denmark Ørsteds Plads, Building 347 DK-2800 Kgs. Lyngby Denmark
| | - Lone Gram
- DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 221 DK-2800 Kgs. Lyngby Denmark
| | - Rafael Taboryski
- DTU Nanolab, National Centre for Nano Fabrication and Characterization, Technical University of Denmark Ørsteds Plads, Building 347 DK-2800 Kgs. Lyngby Denmark
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Bech PK, Zhang SD, Henriksen NNSE, Bentzon-Tilia M, Strube ML, Gram L. The potential to produce tropodithietic acid by Phaeobacter inhibens affects the assembly of microbial biofilm communities in natural seawater. NPJ Biofilms Microbiomes 2023; 9:12. [PMID: 36959215 PMCID: PMC10036634 DOI: 10.1038/s41522-023-00379-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 03/10/2023] [Indexed: 03/25/2023] Open
Abstract
Microbial secondary metabolites play important roles in biotic interactions in microbial communities and yet, we do not understand how these compounds impact the assembly and development of microbial communities. To address the implications of microbial secondary metabolite production on biotic interactions in the assembly of natural seawater microbiomes, we constructed a model system where the assembly of a natural seawater biofilm community was influenced by the addition of the marine biofilm forming Phaeobacter inhibens that can produce the antibiotic secondary metabolite tropodithietic acid (TDA), or a mutant incapable of TDA production. Because of the broad antibiotic activity of TDA, we hypothesized that the potential of P. inhibens to produce TDA would strongly affect both biofilm and planktonic community assembly patterns. We show that 1.9 % of the microbial composition variance across both environments could be attributed to the presence of WT P. inhibens, and especially genera of the Bacteriodetes were increased by the presence of the TDA producer. Moreover, network analysis with inferred putative microbial interactions revealed that P. inhibens mainly displayed strong positive associations with genera of the Flavobacteriaceae and Alteromonadaceae, and that P. inhibens acts as a keystone OTU in the biofilm exclusively due to its potential to produce TDA. Our results demonstrate the potential impact of microbial secondary metabolites on microbial interactions and assembly dynamics of complex microbial communities.
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Affiliation(s)
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
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Tropodithietic Acid, a Multifunctional Antimicrobial, Facilitates Adaption and Colonization of the Producer, Phaeobacter piscinae. mSphere 2023; 8:e0051722. [PMID: 36622251 PMCID: PMC9942592 DOI: 10.1128/msphere.00517-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In the marine environment, surface-associated bacteria often produce an array of antimicrobial secondary metabolites, which have predominantly been perceived as competition molecules. However, they may also affect other hallmarks of surface-associated living, such as motility and biofilm formation. Here, we investigate the ecological significance of an antibiotic secondary metabolite, tropodithietic acid (TDA), in the producing bacterium, Phaeobacter piscinae S26. We constructed a markerless in-frame deletion mutant deficient in TDA biosynthesis, S26ΔtdaB. Molecular networking demonstrated that other chemical sulfur-containing features, likely related to TDA, were also altered in the secondary metabolome. We found several changes in the physiology of the TDA-deficient mutant, ΔtdaB, compared to the wild type. Growth of the two strains was similar; however, ΔtdaB cells were shorter and more motile. Transcriptome and proteome profiling revealed an increase in gene expression and protein abundance related to a type IV secretion system, and to a prophage, and a gene transfer agent in ΔtdaB. All these systems may contribute to horizontal gene transfer (HGT), which may facilitate adaptation to novel niches. We speculate that once a TDA-producing population has been established in a new niche, the accumulation of TDA acts as a signal of successful colonization, prompting a switch to a sessile lifestyle. This would lead to a decrease in motility and the rate of HGT, while filamentous cells could form the base of a biofilm. In addition, the antibiotic properties of TDA may inhibit invading competing microorganisms. This points to a role of TDA in coordinating colonization and adaptation. IMPORTANCE Despite the broad clinical usage of microbial secondary metabolites with antibiotic activity, little is known about their role in natural microbiomes. Here, we studied the effect of production of the antibiotic tropodithietic acid (TDA) on the producing strain, Phaeobacter piscinae S26, a member of the Roseobacter group. We show that TDA affects several phenotypes of the producing strain, including motility, cell morphology, metal metabolism, and three horizontal gene transfer systems: a prophage, a type IV secretion system, and a gene transfer agent. Together, this indicates that TDA participates in coordinating the colonization process of the producer. TDA is thus an example of a multifunctional secondary metabolite that can mediate complex interactions in microbial communities. This work broadens our understanding of the ecological role that secondary metabolites have in microbial community dynamics.
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Henriksen NNSE, Lindqvist LL, Wibowo M, Sonnenschein EC, Bentzon-Tilia M, Gram L. Role is in the eye of the beholder-the multiple functions of the antibacterial compound tropodithietic acid produced by marine Rhodobacteraceae. FEMS Microbiol Rev 2022; 46:fuac007. [PMID: 35099011 PMCID: PMC9075582 DOI: 10.1093/femsre/fuac007] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Many microbial secondary metabolites have been studied for decades primarily because of their antimicrobial properties. However, several of these metabolites also possess nonantimicrobial functions, both influencing the physiology of the producer and their ecological neighbors. An example of a versatile bacterial secondary metabolite with multiple functions is the tropone derivative tropodithietic acid (TDA). TDA is a broad-spectrum antimicrobial compound produced by several members of the Rhodobacteraceae family, a major marine bacterial lineage, within the genera Phaeobacter, Tritonibacter, and Pseudovibrio. The production of TDA is governed by the mode of growth and influenced by the availability of nutrient sources. The antibacterial effect of TDA is caused by disruption of the proton motive force of target microorganisms and, potentially, by its iron-chelating properties. TDA also acts as a signaling molecule, affecting gene expression in other bacteria, and altering phenotypic traits such as motility, biofilm formation, and antibiotic production in the producer. In microbial communities, TDA-producing bacteria cause a reduction of the relative abundance of closely related species and some fast-growing heterotrophic bacteria. Here, we summarize the current understanding of the chemical ecology of TDA, including the environmental niches of TDA-producing bacteria, and the molecular mechanisms governing the function and regulation of TDA.
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Affiliation(s)
- Nathalie N S E Henriksen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Laura L Lindqvist
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Mario Wibowo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
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Roseobacter group probiotics exhibit differential killing of fish pathogenic Tenacibaculum species. Appl Environ Microbiol 2022; 88:e0241821. [PMID: 35080904 DOI: 10.1128/aem.02418-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fish pathogenic bacteria of the Tenacibaculum genus are a serious emerging concern in modern aquaculture, causing tenacibaculosis in a broad selection of cultured finfish. Data describing their virulence mechanisms are scarce and few means, antibiotic treatment aside, are available to control their proliferation in aquaculture systems. We genome sequenced a collection of 19 putative Tenacibaculum isolates from outbreaks at two aquaculture facilities and tested their susceptibility to treatment with tropodithietic acid (TDA)-producing Roseobacter group probiotics. We found that local outbreaks of Tenacibaculum can involve heterogeneous assemblages of species and strains with the capacity to produce multiple different virulence factors related to host invasion and infection. The probiotic Phaeobacter piscinae S26 proved efficient in killing pathogenic Tenacibaculum species such as T. maritimum, T. soleae, and some T. discolor strains. However, the T. mesophilum and T. gallaicum species exhibit natural tolerance towards TDA and are hence not likely to be easily killed by TDA-producing probiotics. Tolerance towards TDA in Tenacibaculum is likely involving multiple inherent physiological features pertaining to electron and proton transport, iron sequestration, and potentially also drug efflux mechanisms, as genetic determinants encoding such features were significantly associated with TDA tolerance. Collectively, our results support the use of TDA-producers to prevent tenacibaculosis, however, their efficacy is likely limited to some Tenacibaculum species. Importance A productive and sustainable aquaculture sector is needed to meet the UN sustainable development goals (SDGs) and supply the growing world population with high-protein food sources. A sustainable way to prevent disease outbreaks in the industry is the application of probiotic bacteria that can antagonize fish pathogens in the aquaculture systems. TDA-producing Roseobacter group probiotics have proven efficient in killing important vibrio pathogens and protecting fish larvae against infection, yet their efficacy against different fish pathogenic species of the Tenacibaculum genus has not been explored. Therefore, we tested the efficacy of such potential probiotics against a collection of different Tenacibaculum isolates and found the probiotic to efficiently kill a subset of relevant strains and species, supporting their use as sustainable disease control measure in aquaculture.
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The Roseobacter-Group Bacterium Phaeobacter as a Safe Probiotic Solution for Aquaculture. Appl Environ Microbiol 2021; 87:e0258120. [PMID: 33310713 DOI: 10.1128/aem.02581-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phaeobacter inhibens has been assessed as a probiotic bacterium for application in aquaculture. Studies addressing the efficacy and safety indicate that P. inhibens maintains its antagonistic activity against pathogenic vibrios in aquaculture live cultures (live feed and fish egg/larvae) while having no or a positive effect on the host organisms and a minor impact on the host microbiomes. While P. inhibens produces antibacterial and algicidal compounds, no study has so far found a virulent phenotype of P. inhibens cells against higher organisms. Additionally, an in silico search for antibiotic resistance genes using published genomes of representative strains did not raise concerns regarding the risk for antimicrobial resistance. P. inhibens occurs naturally in aquaculture systems, supporting its safe usage in this environment. In conclusion, at the current state of knowledge, P. inhibens is a "safe-to-use" organism.
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Duan Y, Petzold M, Saleem‐Batcha R, Teufel R. Bacterial Tropone Natural Products and Derivatives: Overview of their Biosynthesis, Bioactivities, Ecological Role and Biotechnological Potential. Chembiochem 2020; 21:2384-2407. [PMID: 32239689 PMCID: PMC7497051 DOI: 10.1002/cbic.201900786] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/02/2020] [Indexed: 12/05/2022]
Abstract
Tropone natural products are non-benzene aromatic compounds of significant ecological and pharmaceutical interest. Herein, we highlight current knowledge on bacterial tropones and their derivatives such as tropolones, tropodithietic acid, and roseobacticides. Their unusual biosynthesis depends on a universal CoA-bound precursor featuring a seven-membered carbon ring as backbone, which is generated by a side reaction of the phenylacetic acid catabolic pathway. Enzymes encoded by separate gene clusters then further modify this key intermediate by oxidation, CoA-release, or incorporation of sulfur among other reactions. Tropones play important roles in the terrestrial and marine environment where they act as antibiotics, algaecides, or quorum sensing signals, while their bacterial producers are often involved in symbiotic interactions with plants and marine invertebrates (e. g., algae, corals, sponges, or mollusks). Because of their potent bioactivities and of slowly developing bacterial resistance, tropones and their derivatives hold great promise for biomedical or biotechnological applications, for instance as antibiotics in (shell)fish aquaculture.
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Affiliation(s)
- Ying Duan
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | - Melanie Petzold
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | | | - Robin Teufel
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
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Amino Acid and Sugar Catabolism in the Marine Bacterium Phaeobacter inhibens DSM 17395 from an Energetic Viewpoint. Appl Environ Microbiol 2019; 85:AEM.02095-19. [PMID: 31604772 DOI: 10.1128/aem.02095-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 11/20/2022] Open
Abstract
Growth energetics and metabolic efficiency contribute to the lifestyle and habitat imprint of microorganisms. Roseobacters constitute one of the most abundant and successful marine bacterioplankton groups. Here, we reflect on the energetics and metabolic efficiency of Phaeobacter inhibens DSM 17395, a versatile heterotrophic roseobacter. Fourteen different substrates (five sugars and nine amino acids) and their degradation pathways were assessed for energetic efficiencies based on catabolic ATP yields, calculated from net formed ATP and reducing equivalents. The latter were converted into ATP by employing the most divergent coupling ratios (i.e., ions per ATP) currently known for F1Fo ATP synthases in heterotrophic bacteria. The catabolic ATP yields of the pathways studied in P. inhibens differed ∼3-fold. The actual free energy costs for ATP synthesis were estimated at 81.6 kJ per mol ATP (3.3 ions per ATP) or 104.2 kJ per mol ATP (4.3 ions per ATP), yielding an average thermodynamic efficiency of ∼37.7% or ∼29.5%, respectively. Growth performance (rates, yields) and carbon assimilation efficiency were determined for P. inhibens growing in process-controlled bioreactors with 10 different single substrates (Glc, Man, N-acetylglucosamine [Nag], Phe, Trp, His, Lys, Thr, Val, or Leu) and with 2 defined substrate mixtures. The efficiencies of carbon assimilation into biomass ranged from ∼28% to 61%, with His/Trp and Thr/Leu yielding the lowest and highest levels. These efficiencies correlated with catabolic and ATP yields only to some extent. Substrate-specific metabolic demands and/or functions, as well as the compositions of the substrate mixtures, apparently affected the energetic costs of growth. These include energetic burdens associated with, e.g., slow growth, stress, and/or the production of tropodithietic acid.IMPORTANCE Heterotrophic members of the bacterioplankton serve the marine ecosystem by transforming organic matter, an activity that is governed by the bacterial growth efficiencies (BGEs) obtained under given environmental conditions. In marine ecology, the concept of BGE refers to the carbon assimilation efficiency within natural communities. The marine bacterium studied here, Phaeobacter inhibens DSM 17395, is a copiotrophic representative of the globally abundant Roseobacter group, and the 15 catabolic pathways investigated are widespread among these marine heterotrophs. Combining pathway-specific catabolic ATP yields with in-depth quantitative physiological data could (i) provide a new baseline for the study of growth energetics and efficiency in further Roseobacter group members and other copiotrophic marine bacteria in productive coastal ecosystems and (ii) contribute to a better understanding of the factors controlling BGE (including the additional energetic burden arising from widespread secondary-metabolite formation) based on laboratory studies with pure cultures.
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Dittmann KK, Porsby CH, Goncalves P, Mateiu RV, Sonnenschein EC, Bentzon-Tilia M, Egan S, Gram L. Tropodithietic acid induces oxidative stress response, cell envelope biogenesis and iron uptake in Vibrio vulnificus. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:581-588. [PMID: 31102321 DOI: 10.1111/1758-2229.12771] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 06/09/2023]
Abstract
The Roseobacter group is a widespread marine bacterial group, of which some species produce the broad-spectrum antibiotic tropodithietic acid (TDA). A mode of action for TDA has previously been proposed in Escherichia coli, but little is known about its effect on non-producing marine bacteria at in situ concentrations. The purpose of this study was to investigate how a sub-lethal level of TDA affects Vibrio vulnificus at different time points (30 and 60 min) using a transcriptomic approach. Exposure to TDA for as little as 30 min resulted in the differential expression of genes associated with cell regeneration, including the up-regulation of those involved in biogenesis of the cell envelope. Defence mechanisms including oxidative stress defence proteins and iron uptake systems were also up-regulated in response to TDA, while motility-related genes were down-regulated. Gene expression data and scanning electron microscopy imaging revealed a switch to a biofilm phenotype in the presence of TDA. Our study shows that a low concentration of this antibiotic triggers a defence response to reactive oxygen species and iron depletion in V. vulnificus, which indicates that the mode of action of TDA is likely more complex in this bacterium than what is known for E. coli.
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Affiliation(s)
- Karen K Dittmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Randwick, NSW, 2052, Australia
| | - Cisse H Porsby
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Priscila Goncalves
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Randwick, NSW, 2052, Australia
| | - Ramona Valentina Mateiu
- Center for Electron Nanoscopy, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Suhelen Egan
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Randwick, NSW, 2052, Australia
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
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12
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Muthukrishnan T, Al Khaburi M, Abed RMM. Fouling Microbial Communities on Plastics Compared with Wood and Steel: Are They Substrate- or Location-Specific? MICROBIAL ECOLOGY 2019; 78:361-374. [PMID: 30535914 DOI: 10.1007/s00248-018-1303-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/27/2018] [Indexed: 05/20/2023]
Abstract
Although marine biofouling has been widely studied on different substrates, information on biofouling on plastics in the Arabian Gulf is limited. Substrate- and location-specific effects were investigated by comparing the microbial communities developed on polyethylene terephthalate (PET) and polyethylene (PE) with those on steel and wood, at two locations in the Sea of Oman. Total biomass was lower on PET and PE than on steel and wood. PET had the highest bacterial abundance at both locations, whereas chlorophyll a concentrations did not vary between substrates. MiSeq 16S ribosomal RNA sequencing revealed comparable operational taxonomic unit (OTU) richness on all substrates at one location but lower numbers on PET and PE at the other location. Non-metric multidimensional scaling (NMDS) showed distinct clusters of the bacterial communities based on substrate (analysis of similarity (ANOSIM), R = 0.45-0.97, p < 0.03) and location (ANOSIM, R = 0.56, p < 0.0001). The bacterial genera Microcystis and Hydrogenophaga and the diatoms Licmophora and Mastogloia were specifically detected on plastics. Desulfovibrio and Pseudomonas spp. exhibited their highest abundance on steel and Corynebacterium spp. on wood. Scanning electron microscopy (SEM) revealed fissure formation on PET and PE, indicating physical degradation. The presence of free radicals on PET and carbonyl bonds (C=O) on PE, as revealed by Fourier transform infrared (FTIR) spectroscopy, indicated abiotic degradation while hydroxyl groups and spectral peaks for proteins and polysaccharides on PE indicated biotic degradation. We conclude that fouling microbial communities are not only substrate-specific but also location-specific and microbes developing on plastics could potentially contribute to their degradation in the marine environment.
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Affiliation(s)
- Thirumahal Muthukrishnan
- Biology Department, College of Science, Sultan Qaboos University, P. O. Box 36, PC, 123, Al Khoud, Sultanate of Oman
| | - Maryam Al Khaburi
- Biology Department, College of Science, Sultan Qaboos University, P. O. Box 36, PC, 123, Al Khoud, Sultanate of Oman
| | - Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, P. O. Box 36, PC, 123, Al Khoud, Sultanate of Oman.
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13
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Phippen CBW, Jørgensen CM, Bentzon-Tilia M, Gotfredsen CH, Larsen TO, Gram L, Sonnenschein EC. Isolation of Methyl Troposulfenin from Phaeobacter inhibens. JOURNAL OF NATURAL PRODUCTS 2019; 82:1387-1390. [PMID: 30978024 DOI: 10.1021/acs.jnatprod.8b01097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
An S-methylated analogue of tropodithietic acid (TDA, 1), methyl troposulfenin (2), was isolated from the marine alphaproteobacterium Phaeobacter inhibens. The structure was elucidated by NMR and HRMS. Its inhibitory effect against the fish pathogen Vibrio anguillarum was 4-fold to 100-fold lower than that of the known antibacterial compound TDA. Methyl troposulfenin lacks the acidic proton of TDA, indicating that the methylation turns the potent antibacterial TDA into an inactive compound, and thereby, this analysis supports the proposed mode of action of TDA.
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Affiliation(s)
- Christopher B W Phippen
- Department of Biotechnology and Biomedicine , Technical University of Denmark , Søltofts Plads 221 , Kongens Lyngby , 2800 , Denmark
| | - Cecilie M Jørgensen
- Department of Biotechnology and Biomedicine , Technical University of Denmark , Søltofts Plads 221 , Kongens Lyngby , 2800 , Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine , Technical University of Denmark , Søltofts Plads 221 , Kongens Lyngby , 2800 , Denmark
| | - Charlotte Held Gotfredsen
- Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , Kongens Lyngby , 2800 , Denmark
| | - Thomas O Larsen
- Department of Biotechnology and Biomedicine , Technical University of Denmark , Søltofts Plads 221 , Kongens Lyngby , 2800 , Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine , Technical University of Denmark , Søltofts Plads 221 , Kongens Lyngby , 2800 , Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine , Technical University of Denmark , Søltofts Plads 221 , Kongens Lyngby , 2800 , Denmark
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14
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Rasmussen BB, Erner KE, Bentzon‐Tilia M, Gram L. Effect of TDA-producing Phaeobacter inhibens on the fish pathogen Vibrio anguillarum in non-axenic algae and copepod systems. Microb Biotechnol 2018; 11:1070-1079. [PMID: 29732685 PMCID: PMC6196398 DOI: 10.1111/1751-7915.13275] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/27/2018] [Accepted: 04/08/2018] [Indexed: 12/15/2022] Open
Abstract
The expanding aquaculture industry plays an important role in feeding the growing human population and with the expansion, sustainable bacterial disease control, such as probiotics, becomes increasingly important. Tropodithietic acid (TDA)-producing Phaeobacter spp. can protect live feed, for example rotifers and Artemia as well as larvae of turbot and cod against pathogenic vibrios. Here, we show that the emerging live feed, copepods, is unaffected by colonization of the fish pathogen Vibrio anguillarum, making them potential infection vectors. However, TDA-producing Phaeobacter inhibens was able to significantly inhibit V. anguillarum in non-axenic cultures of copepod Acartia tonsa and the copepod feed Rhodomonas salina. Vibrio grew to 106 CFU ml-1 and 107 CFU ml-1 in copepod and R. salina cultures, respectively. However, vibrio counts remained at the inoculum level (104 CFU ml-1 ) when P. inhibens was also added. We further developed a semi-strain-specific qPCR for V. anguillarum to detect and quantify the pathogen in non-axenic systems. In conclusion, P. inhibens efficiently inhibits the fish larval pathogen V. anguillarum in the emerging live feed, copepods, supporting its use as a probiotic in aquaculture. Furthermore, qPCR provides an effective method for detecting vibrio pathogens in complex non-axenic live feed systems.
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Affiliation(s)
- Bastian Barker Rasmussen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkAnker Engelundsvej bldg. 301DK‐2800Kgs. LyngbyDenmark
| | - Katrine Ege Erner
- Department of Biotechnology and BiomedicineTechnical University of DenmarkAnker Engelundsvej bldg. 301DK‐2800Kgs. LyngbyDenmark
| | - Mikkel Bentzon‐Tilia
- Department of Biotechnology and BiomedicineTechnical University of DenmarkAnker Engelundsvej bldg. 301DK‐2800Kgs. LyngbyDenmark
| | - Lone Gram
- Department of Biotechnology and BiomedicineTechnical University of DenmarkAnker Engelundsvej bldg. 301DK‐2800Kgs. LyngbyDenmark
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15
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Trautwein K, Hensler M, Wiegmann K, Skorubskaya E, Wöhlbrand L, Wünsch D, Hinrichs C, Feenders C, Müller C, Schell K, Ruppersberg H, Vagts J, Koßmehl S, Steinbüchel A, Schmidt-Kopplin P, Wilkes H, Hillebrand H, Blasius B, Schomburg D, Rabus R. The marine bacterium Phaeobacter inhibens secures external ammonium by rapid buildup of intracellular nitrogen stocks. FEMS Microbiol Ecol 2018; 94:5074353. [PMID: 30124819 PMCID: PMC6122490 DOI: 10.1093/femsec/fiy154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 08/13/2018] [Indexed: 11/27/2022] Open
Abstract
Reduced nitrogen species are key nutrients for biological productivity in the oceans. Ammonium is often present in low and growth-limiting concentrations, albeit peaks occur during collapse of algal blooms or via input from deep sea upwelling and riverine inflow. Autotrophic phytoplankton exploit ammonium peaks by storing nitrogen intracellularly. In contrast, the strategy of heterotrophic bacterioplankton to acquire ammonium is less well understood. This study revealed the marine bacterium Phaeobacter inhibens DSM 17395, a Roseobacter group member, to have already depleted the external ammonium when only ∼⅓ of the ultimately attained biomass is formed. This was paralleled by a three-fold increase in cellular nitrogen levels and rapid buildup of various nitrogen-containing intracellular metabolites (and enzymes for their biosynthesis) and biopolymers (DNA, RNA and proteins). Moreover, nitrogen-rich cells secreted potential RTX proteins and the antibiotic tropodithietic acid, perhaps to competitively secure pulses of external ammonium and to protect themselves from predation. This complex response may ensure growing cells and their descendants exclusive provision with internal nitrogen stocks. This nutritional strategy appears prevalent also in other roseobacters from distant geographical provenances and could provide a new perspective on the distribution of reduced nitrogen in marine environments, i.e. temporary accumulation in bacterioplankton cells.
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Affiliation(s)
- Kathleen Trautwein
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Michael Hensler
- Bioinformatics and Biochemistry, Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Rebenring 56, Braunschweig 38106, Germany
| | - Katharina Wiegmann
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Ekaterina Skorubskaya
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Daniel Wünsch
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Christina Hinrichs
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Christoph Feenders
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Constanze Müller
- Analytical BioGeoChemistry, HelmholtzZentrum München, German Research Centre for Environmental Health, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Kristina Schell
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Hanna Ruppersberg
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Jannes Vagts
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Sebastian Koßmehl
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Alexander Steinbüchel
- Institute for Molecular Microbiology and Biotechnology, WWU Münster, Corrensstr. 3, Münster 48149, Germany
| | - Philippe Schmidt-Kopplin
- Analytical BioGeoChemistry, HelmholtzZentrum München, German Research Centre for Environmental Health, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Heinz Wilkes
- Organic Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Helmut Hillebrand
- Planktology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstr. 231, Oldenburg 23129, Germany
| | - Bernd Blasius
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Dietmar Schomburg
- Bioinformatics and Biochemistry, Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Rebenring 56, Braunschweig 38106, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
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16
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Sonnenschein EC, Phippen CBW, Bentzon-Tilia M, Rasmussen SA, Nielsen KF, Gram L. Phylogenetic distribution of roseobacticides in the Roseobacter group and their effect on microalgae. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:383-393. [PMID: 29624899 DOI: 10.1111/1758-2229.12649] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 03/21/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
The Roseobacter-group species Phaeobacter inhibens produces the antibacterial tropodithietic acid (TDA) and the algaecidal roseobacticides with both compound classes sharing part of the same biosynthetic pathway. The purpose of this study was to investigate the production of roseobacticides more broadly in TDA-producing roseobacters and to compare the effect of producers and non-producers on microalgae. Of 33 roseobacters analyzed, roseobacticide production was a unique feature of TDA-producing P. inhibens, P. gallaeciensis and P. piscinae strains. One TDA-producing Phaeobacter, 27-4, did not produce roseobacticides, possibly due to a transposable element. TDA-producing Ruegeria and Pseudovibrio did not produce roseobacticides. Addition of roseobacticide-containing bacterial extracts affected the growth of the microalgae Rhodomonas salina, Thalassiosira pseudonana and Emiliania huxleyi, while growth of Tetraselmis suecica was unaffected. During co-cultivation, growth of E. huxleyi was initially stimulated by the roseobacticide producer DSM 17395, while the subsequent decline in algal cell numbers during senescence was enhanced. Strain 27-4 that does not produce roseobacticides had no effect on algal growth. Both bacterial strains, DSM 17395 and 27-4, grew during co-cultivation presumably utilizing algal exudates. Furthermore, TDA-producing roseobacters have potential as probiotics in marine larviculture and it is promising that the live feed Tetraselmis was unaffected by roseobacticides-containing extracts.
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Affiliation(s)
- Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
| | | | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
| | - Silas Anselm Rasmussen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
| | - Kristian Fog Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
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17
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Will SE, Neumann-Schaal M, Heydorn RL, Bartling P, Petersen J, Schomburg D. The limits to growth - energetic burden of the endogenous antibiotic tropodithietic acid in Phaeobacter inhibens DSM 17395. PLoS One 2017; 12:e0177295. [PMID: 28481933 PMCID: PMC5421792 DOI: 10.1371/journal.pone.0177295] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/25/2017] [Indexed: 12/01/2022] Open
Abstract
Phaeobacter inhibens DSM 17395, a model organism for marine Roseobacter group, was studied for its response to its own antimicrobial compound tropodithietic acid (TDA). TDA biosynthesis is encoded on the largest extrachromosomal element of P. inhibens, the 262 kb plasmid, whose curation leads to an increased growth and biomass yield. In this study, the plasmid-cured strain was compared to the wild-type strain and to transposon mutants lacking single genes of the TDA biosynthesis. The data show that the growth inhibition of the wild-type strain can be mainly attributed to the TDA produced by P. inhibens itself. Oxygen uptake rates remained constant in all strains but the growth rate dropped in the wild-type which supports the recently proposed mode of TDA action. Metabolome analysis showed no metabolic alterations that could be attributed directly to TDA. Taken together, the growth of P. inhibens is limited by its own antibacterial compound due to a partial destruction of the proton gradient which leads to a higher energetic demand. The universal presence of TDA biosynthesis in genome-sequenced isolates of the genus Phaeobacter shows that there must be a high benefit of TDA for P. inhibens in its ecological niche despite the drawback on its metabolism.
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Affiliation(s)
- Sabine Eva Will
- Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry and Braunschweig Integrated Center of Systems Biology (BRICS), Braunschweig, Germany
| | - Meina Neumann-Schaal
- Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry and Braunschweig Integrated Center of Systems Biology (BRICS), Braunschweig, Germany
| | - Raymond Leopold Heydorn
- Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry and Braunschweig Integrated Center of Systems Biology (BRICS), Braunschweig, Germany
| | - Pascal Bartling
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörn Petersen
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dietmar Schomburg
- Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry and Braunschweig Integrated Center of Systems Biology (BRICS), Braunschweig, Germany
- * E-mail:
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18
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Trautwein K, Feenders C, Hulsch R, Ruppersberg HS, Strijkstra A, Kant M, Vagts J, Wünsch D, Michalke B, Maczka M, Schulz S, Hillebrand H, Blasius B, Rabus R. Non-Redfield, nutrient synergy and flexible internal elemental stoichiometry in a marine bacterium. FEMS Microbiol Ecol 2017; 93:3806670. [PMID: 28486660 PMCID: PMC5458051 DOI: 10.1093/femsec/fix059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/04/2017] [Indexed: 01/01/2023] Open
Abstract
The stoichiometric constraints of algal growth are well understood, whereas there is less knowledge for heterotrophic bacterioplankton. Growth of the marine bacterium Phaeobacter inhibens DSM 17395, belonging to the globally distributed Roseobacter group, was studied across a wide concentration range of NH4+ and PO43-. The unique dataset covers 415 different concentration pairs, corresponding to 207 different molar N:P ratios (from 10-2 to 105). Maximal growth (by growth rate and biomass yield) was observed within a restricted concentration range at N:P ratios (∼50-120) markedly above Redfield. Experimentally determined growth parameters deviated to a large part from model predictions based on Liebig's law of the minimum, thus implicating synergistic co-limitation due to biochemical dependence of resources. Internal elemental ratios of P. inhibens varied with external nutrient supply within physiological constraints, thus adding to the growing evidence that aquatic bacteria can be flexible in their internal elemental composition. Taken together, the findings reported here revealed that P. inhibens is well adapted to fluctuating availability of inorganic N and P, expected to occur in its natural habitat (e.g. colonized algae, coastal areas). Moreover, this study suggests that elemental variability in bacterioplankton needs to be considered in the ecological stoichiometry of the oceans.
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Affiliation(s)
- Kathleen Trautwein
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Oldenburg 26111, Germany
| | - Christoph Feenders
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Oldenburg 26111, Germany
| | - Reiner Hulsch
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Oldenburg 26111, Germany
| | - Hanna S. Ruppersberg
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Oldenburg 26111, Germany
| | - Annemieke Strijkstra
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Oldenburg 26111, Germany
| | - Mirjam Kant
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Oldenburg 26111, Germany
| | - Jannes Vagts
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Oldenburg 26111, Germany
| | - Daniel Wünsch
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Oldenburg 26111, Germany
| | - Bernhard Michalke
- Research Unit Analytical Biogeochemistry, HelmholtzZentrum München, Neuherberg 85764, Germany
| | - Michael Maczka
- Institute for Organic Chemistry, Technische Universität Carolo-Wilhelmina, Braunschweig 38106, Germany
| | - Stefan Schulz
- Institute for Organic Chemistry, Technische Universität Carolo-Wilhelmina, Braunschweig 38106, Germany
| | - Helmut Hillebrand
- Department of Planktology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg 26111, Germany
| | - Bernd Blasius
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Oldenburg 26111, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Oldenburg 26111, Germany
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19
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Romano S, Bondarev V, Kölling M, Dittmar T, Schulz-Vogt HN. Phosphate Limitation Triggers the Dissolution of Precipitated Iron by the Marine Bacterium Pseudovibrio sp. FO-BEG1. Front Microbiol 2017; 8:364. [PMID: 28352252 PMCID: PMC5348524 DOI: 10.3389/fmicb.2017.00364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/21/2017] [Indexed: 12/12/2022] Open
Abstract
Phosphorus is an essential nutrient for all living organisms. In bacteria, the preferential phosphorus source is phosphate, which is often a limiting macronutrient in many areas of the ocean. The geochemical cycle of phosphorus is strongly interconnected with the cycles of other elements and especially iron, because phosphate tends to adsorb onto iron minerals, such as iron oxide formed in oxic marine environments. Although the response to either iron or phosphate limitation has been investigated in several bacterial species, the metabolic interplay between these two nutrients has rarely been considered. In this study we evaluated the impact of phosphate limitation on the iron metabolism of the marine bacterium Pseudovibrio sp. FO-BEG1. We observed that phosphate limitation led to an initial decrease of soluble iron in the culture up to three times higher than under phosphate surplus conditions. Similarly, a decrease in soluble cobalt was more pronounced under phosphate limitation. These data point toward physiological changes induced by phosphate limitation that affect either the cellular surface and therefore the metal adsorption onto it or the cellular metal uptake. We discovered that under phosphate limitation strain FO-BEG1, as well as selected strains of the Roseobacter clade, secreted iron-chelating molecules. This leads to the hypothesis that these bacteria might release such molecules to dissolve iron minerals, such as iron-oxyhydroxide, in order to access the adsorbed phosphate. As the adsorption of phosphate onto iron minerals can significantly decrease phosphate concentrations in the environment, the observed release of iron-chelators might represent an as yet unrecognized link between the biogeochemical cycle of phosphorus and iron, and it suggests another biological function of iron-chelating molecules in addition to metal-scavenging.
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Affiliation(s)
- Stefano Romano
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Martin Kölling
- Marum Center for Marine Environmental Sciences, Bremen, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Heide N Schulz-Vogt
- Biological Oceanography, Leibniz Institut für Ostseeforschung, Warnemünde, Germany
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20
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Sonnenschein EC, Nielsen KF, D'Alvise P, Porsby CH, Melchiorsen J, Heilmann J, Kalatzis PG, López-Pérez M, Bunk B, Spröer C, Middelboe M, Gram L. Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis. THE ISME JOURNAL 2017; 11:569-583. [PMID: 27552638 PMCID: PMC5270555 DOI: 10.1038/ismej.2016.111] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 06/12/2016] [Accepted: 07/03/2016] [Indexed: 11/08/2022]
Abstract
Tropodithietic acid (TDA)-producing Ruegeria mobilis strains of the Roseobacter clade have primarily been isolated from marine aquaculture and have probiotic potential due to inhibition of fish pathogens. We hypothesized that TDA producers with additional novel features are present in the oceanic environment. We isolated 42 TDA-producing R. mobilis strains during a global marine research cruise. While highly similar on the 16S ribosomal RNA gene level (99-100% identity), the strains separated into four sub-clusters in a multilocus sequence analysis. They were further differentiated to the strain level by average nucleotide identity using pairwise genome comparison. The four sub-clusters could not be associated with a specific environmental niche, however, correlated with the pattern of sub-typing using co-isolated phages, the number of prophages in the genomes and the distribution in ocean provinces. Major genomic differences within the sub-clusters include prophages and toxin-antitoxin systems. In general, the genome of R. mobilis revealed adaptation to a particle-associated life style and querying TARA ocean data confirmed that R. mobilis is more abundant in the particle-associated fraction than in the free-living fraction occurring in 40% and 6% of the samples, respectively. Our data and the TARA data, although lacking sufficient data from the polar regions, demonstrate that R. mobilis is a globally distributed marine bacterial species found primarily in the upper open oceans. It has preserved key phenotypic behaviors such as the production of TDA, but contains diverse sub-clusters, which could provide new capabilities for utilization in aquaculture.
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Affiliation(s)
- Eva C Sonnenschein
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kristian F Nielsen
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Paul D'Alvise
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Cisse H Porsby
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
- Biogen Manufacturing, Biogen Idec Allé 1, Hillerød, Denmark
| | - Jette Melchiorsen
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jens Heilmann
- Technical University of Denmark, National Institute for Aquatic Resources, Charlottenlund, Denmark
| | - Panos G Kalatzis
- Hellenic Centre for Marine Research, Institute of Aquaculture, Heraklion, Greece
- Section for Marine Biology, University of Copenhagen, Helsingør, Denmark
| | - Mario López-Pérez
- División de Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan, Alicante, Spain
| | - Boyke Bunk
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Cathrin Spröer
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mathias Middelboe
- Section for Marine Biology, University of Copenhagen, Helsingør, Denmark
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
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21
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Trautwein K, Will SE, Hulsch R, Maschmann U, Wiegmann K, Hensler M, Michael V, Ruppersberg H, Wünsch D, Feenders C, Neumann-Schaal M, Kaltenhäuser S, Ulbrich M, Schmidt-Hohagen K, Blasius B, Petersen J, Schomburg D, Rabus R. Native plasmids restrict growth of Phaeobacter inhibens DSM 17395: Energetic costs of plasmids assessed by quantitative physiological analyses. Environ Microbiol 2016; 18:4817-4829. [PMID: 27233797 DOI: 10.1111/1462-2920.13381] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Plasmid carriage is associated with energetic costs, and thus only those plasmids providing fitness benefits are stably maintained in the host lineage. Marine bacteria of the Roseobacter clade harbor up to 11 extrachromosomal replicons, adding lifestyle-relevant and possibly habitat success-promoting functions to their genomic repertoire. Phaeobacter inhibens DSM 17395 is a nutritionally versatile representative, carrying three stable and functionally distinct plasmids (65, 78, and 262 kb). The present study investigates the physiological and energetic consequences of plasmid carriage in P. inhibens DSM 17395, employing mutants cured from all native plasmids in every possible combination (seven different). Cultivation in process-controlled bioreactors with casamino acids as organic substrate revealed a complex physiological response, suggesting existence of functional interconnections between the replicons. Deletion of the 262 kb plasmid boosted growth rate (>3-fold) and growth efficiency (yields for carbon, O2 and CO2 ), which was not observed for the 65 or 78 kb plasmid. Carriage of the 262 kb plasmid was most costly for the wild type, i.e. contributing ∼50% to its energetic (dissimilatory) expenditures. Cost-benefit analysis of plasmid carriage reflects the high value of plasmids for niche specialization of P. inhibens DSM 17395 and most likely also for related Phaeobacter species.
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Affiliation(s)
- Kathleen Trautwein
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Sabine Eva Will
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Carolo-Wilhelmina Braunschweig, Braunschweig, Germany
| | - Reiner Hulsch
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Uwe Maschmann
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Katharina Wiegmann
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Michael Hensler
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Carolo-Wilhelmina Braunschweig, Braunschweig, Germany
| | - Victoria Michael
- Department Microbial Ecology and Diversity Projects, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hanna Ruppersberg
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Daniel Wünsch
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Christoph Feenders
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Meina Neumann-Schaal
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Carolo-Wilhelmina Braunschweig, Braunschweig, Germany
| | - Sabine Kaltenhäuser
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Carolo-Wilhelmina Braunschweig, Braunschweig, Germany
| | - Marcus Ulbrich
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Carolo-Wilhelmina Braunschweig, Braunschweig, Germany
| | - Kerstin Schmidt-Hohagen
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Carolo-Wilhelmina Braunschweig, Braunschweig, Germany
| | - Bernd Blasius
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Jörn Petersen
- Department Microbial Ecology and Diversity Projects, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dietmar Schomburg
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Carolo-Wilhelmina Braunschweig, Braunschweig, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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22
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Bentzon-Tilia M, Sonnenschein EC, Gram L. Monitoring and managing microbes in aquaculture - Towards a sustainable industry. Microb Biotechnol 2016; 9:576-84. [PMID: 27452663 PMCID: PMC4993175 DOI: 10.1111/1751-7915.12392] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 07/10/2016] [Indexed: 11/29/2022] Open
Abstract
Microorganisms are of great importance to aquaculture where they occur naturally, and can be added artificially, fulfilling different roles. They recycle nutrients, degrade organic matter and, occasionally, they infect and kill the fish, their larvae or the live feed. Also, some microorganisms may protect fish and larvae against disease. Hence, monitoring and manipulating the microbial communities in aquaculture environments hold great potential; both in terms of assessing and improving water quality, but also in terms of controlling the development of microbial infections. Using microbial communities to monitor water quality and to efficiently carry out ecosystem services within the aquaculture systems may only be a few years away. Initially, however, we need to thoroughly understand the microbiomes of both healthy and diseased aquaculture systems, and we need to determine how to successfully manipulate and engineer these microbiomes. Similarly, we can reduce the need to apply antibiotics in aquaculture through manipulation of the microbiome, i.e. by the use of probiotic bacteria. Recent studies have demonstrated that fish pathogenic bacteria in live feed can be controlled by probiotics and that mortality of infected fish larvae can be reduced significantly by probiotic bacteria. However, the successful management of the aquaculture microbiota is currently hampered by our lack of knowledge of relevant microbial interactions and the overall ecology of these systems.
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Affiliation(s)
- Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Matematiktorvet Bldg. 301, DK-2800, Kgs. Lyngby, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Matematiktorvet Bldg. 301, DK-2800, Kgs. Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Matematiktorvet Bldg. 301, DK-2800, Kgs. Lyngby, Denmark
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