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Banchi E, Manna V, Fonti V, Fabbro C, Celussi M. Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:67466-67482. [PMID: 36056283 PMCID: PMC9492620 DOI: 10.1007/s11356-022-22752-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
The Vibrionaceae family groups genetically and metabolically diverse bacteria thriving in all marine environments. Despite often representing a minor fraction of bacterial assemblages, members of this family can exploit a wide variety of nutritional sources, which makes them important players in biogeochemical dynamics. Furthermore, several Vibrionaceae species are well-known pathogens, posing a threat to human and animal health. Here, we applied the phylogenetic placement coupled with a consensus-based approach using 16S rRNA gene amplicon sequencing, aiming to reach a reliable and fine-level Vibrionaceae characterization and identify the dynamics of blooming, ecologically important, and potentially pathogenic species in different sites of the northern Adriatic Sea. Water samples were collected monthly at a Long-Term Ecological Research network site from 2018 to 2021, and in spring and summer of 2019 and 2020 at two sites affected by depurated sewage discharge. The 41 identified Vibrionaceae species represented generally below 1% of the sampled communities; blooms (up to ~ 11%) mainly formed by Vibrio chagasii and Vibrio owensii occurred in summer, linked to increasing temperature and particulate matter concentration. Pathogenic species such as Vibrio anguilllarum, Vibrio tapetis, and Photobacterium damselae were found in low abundance. Depuration plant samples were characterized by a lower abundance and diversity of Vibrionaceae species compared to seawater, highlighting that Vibrionaceae dynamics at sea are unlikely to be related to wastewater inputs. Our work represents a further step to improve the molecular approach based on short reads, toward a shared, updated, and curated phylogeny of the Vibrionaceae family.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy.
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Viviana Fonti
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Cinzia Fabbro
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
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Structure-Function Relationships in Temperature Effects on Bacterial Luciferases: Nothing Is Perfect. Int J Mol Sci 2022; 23:ijms23158119. [PMID: 35897698 PMCID: PMC9332260 DOI: 10.3390/ijms23158119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
The evaluation of temperature effects on the structure and function of enzymes is necessary to understand the mechanisms underlying their adaptation to a constantly changing environment. In the current study, we investigated the influence of temperature variation on the activity, structural dynamics, thermal inactivation and denaturation of Photobacterium leiognathi and Vibrio harveyi luciferases belonging to different subfamilies, as well as the role of sucrose in maintaining the enzymes functioning and stability. We used the stopped-flow technique, differential scanning calorimetry and molecular dynamics to study the activity, inactivation rate, denaturation and structural features of the enzymes under various temperatures. It was found that P. leiognathi luciferase resembles the properties of cold-adapted enzymes with high activity in a narrow temperature range and slightly lower thermal stability than V. harveyi luciferase, which is less active, but more thermostable. Differences in activity at the studied temperatures can be associated with the peculiarities of the mobile loop conformational changes. The presence of sucrose does not provide an advantage in activity but increases the stability of the enzymes. Differential scanning calorimetry experiments showed that luciferases probably follow different denaturation schemes.
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Fuertes-Perez S, Vogel RF, Hilgarth M. Comparative genomics of Photobacterium species from terrestrial and marine habitats. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100087. [PMID: 34950912 PMCID: PMC8671102 DOI: 10.1016/j.crmicr.2021.100087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 11/26/2021] [Indexed: 11/28/2022] Open
Abstract
Photobacterium (P.) is a genus widely studied in regards to its association with and ubiquitous presence in marine environments. However, certain species (P. phosphoreum, P. carnosum, P. iliopiscarium) have been recently described to colonize and spoil raw meats without a marine link. We have studied 27 strains from meat as well as 26 strains from marine environments in order to probe for intraspecies marine/terrestrial subpopulations and identify distinct genomic features acquired by environmental adaptation. We have conducted phylogenetic analysis (MLSA, ANI, fur, codon usage), search of plasmids (plasmidSPADES), phages (PHASTER), CRISPR-cas operons (CRISPR-finder) and secondary metabolites gene clusters (antiSMASH, BAGEL), in addition to a targeted gene search for specific pathways (e.g. TCA cycle, pentose phosphate, respiratory chain) and elements relevant for growth, adaptation and competition (substrate utilization, motility, bioluminescence, sodium and iron transport). P. carnosum appears as a conserved single clade, with one isolate from MAP fish clustering apart that doesn't, however, show distinct features that could indicate different adaptation. The species harbors genes for a wide carbon source utilization (glycogen/starch, maltose, pullulan, fucose) for colonization of diverse niches in its genome. P. phosphoreum is represented by two different clades on the phylogenetic analyses not correlating to their origin or distribution of other features analyzed that can be divided into two novel subspecies based on genome-wide values. A more diverse antimicrobial activity (sactipeptides, microcins), production of secondary metabolites (siderophores and arylpolyenes), stress response and adaptation (bioluminescence, sodium transporters, catalase, high affinity for oxygen cytochrome cbb3 oxidase, DMSO reductase and proton translocating NADH dehydrogenase) is predicted compared to the other species. P. iliopiscarium was divided into two clades based on source of isolation correlating with phylogeny and distribution of several traits. The species shows traits common to the other two species, similar carbon utilization/transport gene conservation as P. carnosum for the meat-isolated strains, and predicted utilization of marine-common DMSO and flagellar cluster for the sea-isolated strains. Results additionally suggest that photobacteria are highly prone to horizontal acquisition/loss of genetic material and genetic transduction, and that it might be a strategy for increasing the frequency of strain- or species-specific features that offers a growth/competition advantage.
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Affiliation(s)
| | - Rudi F. Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Germany
| | - Maik Hilgarth
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Germany
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Acquisition of bioluminescent trait by non-luminous organisms from luminous organisms through various origins. Photochem Photobiol Sci 2021; 20:1547-1562. [PMID: 34714534 DOI: 10.1007/s43630-021-00124-9] [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] [Received: 06/07/2021] [Accepted: 10/20/2021] [Indexed: 12/20/2022]
Abstract
Bioluminescence is a natural light emitting phenomenon that occurs due to a chemical reaction between luciferin and luciferase. It is primarily an innate and inherited trait in most terrestrial luminous organisms. However, most luminous organisms produce light in the ocean by acquiring luminous symbionts, luciferin (substrate), and/or luciferase (enzyme) through various transmission pathways. For instance, coelenterazine, a well-known luciferin, is obtained by cnidarians, crustaceans, and deep-sea fish through multi-level dietary linkages from coelenterazine producers such as ctenophores, decapods, and copepods. In contrast, some non-luminous Vibrio bacteria became bioluminescent by obtaining lux genes from luminous Vibrio species by horizontal gene transfer. Various examples detailed in this review show how non-luminescent organisms became luminescent by acquiring symbionts, dietary luciferins and luciferases, and genes. This review highlights three modes (symbiosis, ingestion, and horizontal gene transfer) that allow organisms lacking genes for autonomous bioluminescent systems to obtain the ability to produce light. In addition to bioluminescence, this manuscript discusses the acquisition of other traits such as pigments, fluorescence, toxins, and others, to infer the potential processes of acquisition.
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Wang ZJ, Chen F, Xu YQ, Huang P, Liu SS. Protein Model and Function Analysis in Quorum-Sensing Pathway of Vibrio qinghaiensis sp.-Q67. BIOLOGY 2021; 10:638. [PMID: 34356493 PMCID: PMC8301110 DOI: 10.3390/biology10070638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 01/08/2023]
Abstract
Bioluminescent bacteria are mainly found in marine habitats. Vibrio qinghaiensis sp.-Q67 (Q67), a nonpathogenic freshwater bacterium, has been a focus due to its wide use in the monitoring of environmental pollution and the assessment of toxicity. However, the lack of available crystal structures limits the elucidation of the structures of the functional proteins of the quorum-sensing (QS) system that regulates bacterial luminescence in Q67. In this study, 19 functional proteins were built through monomer and oligomer modeling based on their coding proteins in the QS system of Q67 using MODELLER. Except for the failure to construct LuxM due to the lack of a suitable template, 18 functional proteins were successfully constructed. Furthermore, the relationships between the function and predicted structures of 19 functional proteins were explored one by one according to the three functional classifications: autoinducer synthases and receptors, signal transmission proteins (phosphotransferases, an RNA chaperone, and a transcriptional regulator), and enzymes involved in bacterial bioluminescence reactions. This is the first analysis of the whole process of bioluminescence regulation from the perspective of nonpathogenic freshwater bacteria at the molecular level. It provides a theoretical basis for the explanation of applications of Q67 in which luminescent inhibition is used as the endpoint.
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Affiliation(s)
- Ze-Jun Wang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; (Z.-J.W.); (Y.-Q.X.)
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China;
| | - Fu Chen
- Department of Environmental Engineering, School of Environmental and Geographical Science, Shanghai Normal University, Shanghai 200234, China;
| | - Ya-Qian Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; (Z.-J.W.); (Y.-Q.X.)
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Peng Huang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China;
- Department of Environmental Engineering, School of Environmental and Geographical Science, Shanghai Normal University, Shanghai 200234, China;
| | - Shu-Shen Liu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; (Z.-J.W.); (Y.-Q.X.)
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China;
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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Burtseva O, Baulina O, Zaytseva A, Fedorenko T, Chekanov K, Lobakova E. In vitro Biofilm Formation by Bioluminescent Bacteria Isolated from the Marine Fish Gut. MICROBIAL ECOLOGY 2021; 81:932-940. [PMID: 33247364 DOI: 10.1007/s00248-020-01652-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
The internal surface of the animal gastrointestinal tract is covered by microbial biofilms. They play an important role in the development and functioning of the host organism and protect it against pathogens. Microbial communities of gastrointestinal biofilms are less elucidated than luminal microbiota. Therefore, the studies of biofilm formation by gastrointestinal microorganisms are a topical issue. For the first time, we report the formation of a biofilm in vitro by the strains of bioluminescent bacteria isolated from the intestines of marine fish. These bacteria exhibit co-aggregation and tend to attach to solid surfaces. The attachment of cells is accompanied by appearance of the pili. Then, we observed the formation of microcolonies and the production of extracellular polymer substances (EPSs) connecting bacterial cells into an integrated system. The presence of acidic polysaccharides is shown in the EPS when using the ruthenium red staining. Acidic polysaccharides in this matrix is a biochemical evidence of microbial biofilms. On the fibers of the polymer matrix, these bacteria form the "mushroom body"-type structures. Matured biofilms exhibit a specific three-dimensional architecture with pores and channels formed by cells and EPS. We also demonstrated the formation of a biofilm by binary culture of the luminous enterobacterium Kosakonia cowanii and a Gram-positive Macrococcus sp. The data obtained help to understand the role of these bacteria in the intestines of fish. They lead to a new study in the field of investigation of the intestinal microbiome of fish.
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Affiliation(s)
- Olga Burtseva
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga Baulina
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna Zaytseva
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Fedorenko
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin Chekanov
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
- National Research Nuclear University MEPhi, Centre for Humanities Research and Technology, Moscow, Russia.
| | - Elena Lobakova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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Chatragadda R, Dufossé L. Ecological and Biotechnological Aspects of Pigmented Microbes: A Way Forward in Development of Food and Pharmaceutical Grade Pigments. Microorganisms 2021; 9:637. [PMID: 33803896 PMCID: PMC8003166 DOI: 10.3390/microorganisms9030637] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/04/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022] Open
Abstract
Microbial pigments play multiple roles in the ecosystem construction, survival, and fitness of all kinds of organisms. Considerably, microbial (bacteria, fungi, yeast, and microalgae) pigments offer a wide array of food, drug, colorants, dyes, and imaging applications. In contrast to the natural pigments from microbes, synthetic colorants are widely used due to high production, high intensity, and low cost. Nevertheless, natural pigments are gaining more demand over synthetic pigments as synthetic pigments have demonstrated side effects on human health. Therefore, research on microbial pigments needs to be extended, explored, and exploited to find potential industrial applications. In this review, the evolutionary aspects, the spatial significance of important pigments, biomedical applications, research gaps, and future perspectives are detailed briefly. The pathogenic nature of some pigmented bacteria is also detailed for awareness and safe handling. In addition, pigments from macro-organisms are also discussed in some sections for comparison with microbes.
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Affiliation(s)
- Ramesh Chatragadda
- Biological Oceanography Division (BOD), Council of Scientific and Industrial Research-National Institute of Oceanography (CSIR-NIO), Dona Paula 403004, Goa, India
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products (CHEMBIOPRO Lab), Ecole Supérieure d’Ingénieurs Réunion Océan Indien (ESIROI), Département Agroalimentaire, Université de La Réunion, F-97744 Saint-Denis, France
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Muneeswaran T, Kalyanaraman N, Vennila T, Rajesh Kannan M, Ramakritinan CM. Rapid assessment of heavy metal toxicity using bioluminescent bacteria Photobacterium leiognathi strain GoMGm1. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:109. [PMID: 33537887 DOI: 10.1007/s10661-021-08860-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Several commercial test kits such as Microtox, LUMIStox, ToxAlert, Aboatox, and ToxScreen have been widely used for toxicity screening. Though this time saving assays offer excellent sensitivity, cost-effectiveness, and accuracy, these commercial assays are limited in terms of real-time monitoring in Indian coastal environment due to warmer temperatures. This necessitates the need to develop a rapid and accurate assay that can be effectively employed for real time monitoring with respect to heavy metals in the Indian coastal waters. With this objective, the present study was conducted by isolating an indigenous luminescent bacterium from the light organs of chordates Gazza minuta which showed higher luminescence in a wide range of temperatures. The isolate could grow well in the temperature of 30 ± 2 °C and withstand temperature up to 35 ± 2 °C. The isolated bacterium was identified as Photobacterium leiognathi GoMGm1 based on 16S rDNA and luxA gene sequences. The suitable growing medium was optimized using central composite rotational design (CCRD) method to obtain optimal growth and luminescence. The optimized medium exemplified the maximal growth and luminescence of P. leiognathi at OD600 nm of 5.78 ± 0.12 and RLU of 12.49 ± 0.43. The isolate was used to assess the toxicity of several heavy metals. The IC50 values of 0.0051, 1.13, 1.37, 3.1, and 6.68 mg L-1 were observed for the Hg, Cr, Cu, Ni, and Zn, respectively, after 15 min of exposure. Results obtained from principal component analysis (PCA) displayed the present assay's compatibility with other luminescent bacterial assay and commercial Microtox™ assay. Thus, it would the right candidate as an early detection system for heavy metals in aquatic bodies in tropical countries. Schematic representation of the present study.
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Affiliation(s)
- Thillaichidambaram Muneeswaran
- Department of Marine and Coastal Studies, School of Energy, Environment and Natural Resources, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Narayanan Kalyanaraman
- Molecular Biology Lab, Meenakshi Mission Hospital and Research Centre (MMHRC), Madurai, Tamil Nadu, 625107, India
| | | | - Murugesan Rajesh Kannan
- Department of Marine and Coastal Studies, School of Energy, Environment and Natural Resources, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Chockalingam Muthiah Ramakritinan
- Department of Marine and Coastal Studies, School of Energy, Environment and Natural Resources, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India.
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Chatragadda R. Terrestrial and marine bioluminescent organisms from the Indian subcontinent: a review. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:747. [PMID: 33150454 DOI: 10.1007/s10661-020-08685-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
The inception of bioluminescence by Harvey (1952) has led to a Nobel Prize to Osamu Shimomura (Chemistry, 2008) in biological research. Consequently, in recent years, bioluminescence-based assays to monitor toxic pollutants as a real-time marker, to study various diseases and their propagation in plants and animals, are developed in many countries. The emission ability of bioluminescence is improved by gene modification, and also, search for novel bioluminescent systems is underway. Over 100 species of organisms belonging to different taxa are known to be luminous in India. However, the diversity and distribution of luminous organisms and their applications are studied scarcely in the Indian scenario. In this context, the present review provides an overview of the current understanding of various bioluminescent organisms, functions, and applications. A detailed checklist of known bioluminescent organisms from India's marine, terrestrial, and freshwater ecosystems is detailed. This review infers that Indian scientists are needed to extend their research on various aspects of luminescent organisms such as biodiversity, genomics, and chemical mechanisms for conservation, ecological, and biomedical applications.
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Affiliation(s)
- Ramesh Chatragadda
- Biological Oceanography Division (BOD), CSIR-National Institute of Oceanography (CSIR-NIO), Dona Paula, Goa, 403004, India.
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10
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Chatragadda R, Raju M. Predominance of Harveyi clade luminous bacteria in coastal waters of South Andaman, India. MARINE POLLUTION BULLETIN 2020; 158:111416. [PMID: 32753200 DOI: 10.1016/j.marpolbul.2020.111416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 06/17/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
The diversity, distribution, and mechanisms of bacterial speciation of Vibrio species belonging to Harveyi clade are an important global research interests due to their pathogenic activity in coastal environments. Luminous bacteria are also known to act as environmental indicators in coastal waters. This study demonstrates that luminous bacteria belonging to harveyi clade are predominant in seawater, sediment, surfaces of marine animals and plants, and light organs of leiognathid fishes. Molecular phylogenies for eighteen morphologically distinct and potentially luminous strains chosen out of 57 isolated luminous bacteria. Sequence analysis of luxA gene as a molecular marker identified luminous bacteria belonging to Harveyi clade, Photobacterium clade, and Anguillarum clade distinctly. Rich biodiversity and distribution of luminous bacterial species (30% to 40%) was found in association with coral reef samples of south Andaman. This study confirms and reveals the evidence on predominant association of Harveyi clade luminous vibrio's in coastal waters of south Andaman.
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Affiliation(s)
- Ramesh Chatragadda
- Department of Ocean Studies and Marine Biology, Pondicherry Central University, Port Blair 744112, Andaman & Nicobar Islands, India.
| | - Mohanraju Raju
- Department of Ocean Studies and Marine Biology, Pondicherry Central University, Port Blair 744112, Andaman & Nicobar Islands, India
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Vannier T, Hingamp P, Turrel F, Tanet L, Lescot M, Timsit Y. Diversity and evolution of bacterial bioluminescence genes in the global ocean. NAR Genom Bioinform 2020; 2:lqaa018. [PMID: 33575578 PMCID: PMC7671414 DOI: 10.1093/nargab/lqaa018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/14/2020] [Accepted: 03/06/2020] [Indexed: 12/19/2022] Open
Abstract
Although bioluminescent bacteria are the most abundant and widely distributed of all light-emitting organisms, the biological role and evolutionary history of bacterial luminescence are still shrouded in mystery. Bioluminescence has so far been observed in the genomes of three families of Gammaproteobacteria in the form of canonical lux operons that adopt the CDAB(F)E(G) gene order. LuxA and luxB encode the two subunits of bacterial luciferase responsible for light-emission. Our deep exploration of public marine environmental databases considerably expands this view by providing a catalog of new lux homolog sequences, including 401 previously unknown luciferase-related genes. It also reveals a broader diversity of the lux operon organization, which we observed in previously undescribed configurations such as CEDA, CAED and AxxCE. This expanded operon diversity provides clues for deciphering lux operon evolution and propagation within the bacterial domain. Leveraging quantitative tracking of marine bacterial genes afforded by planetary scale metagenomic sampling, our study also reveals that the novel lux genes and operons described herein are more abundant in the global ocean than the canonical CDAB(F)E(G) operon.
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Affiliation(s)
- Thomas Vannier
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Pascal Hingamp
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Floriane Turrel
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
| | - Lisa Tanet
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
| | - Magali Lescot
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Youri Timsit
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
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12
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The strains of bioluminescent bacteria isolated from the White Sea finfishes: genera Photobacterium, Aliivibrio, Vibrio, Shewanella, and first luminous Kosakonia. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 208:111895. [PMID: 32447192 DOI: 10.1016/j.jphotobiol.2020.111895] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 11/22/2022]
Abstract
Bioluminescence is a spectacular feature of some prokaryotes. In the present work, we address the distribution of bioluminescence among bacteria isolated from the White Sea finfishes. Luminous bacteria are widely distributed throughout the World Ocean. Many strains have been isolated and described for tropical latitudes, while Nordic seas still remain quite a white spot in studying bioluminescence of bacteria. We describe the strains related to the two main genera of luminous bacteria, Photobacterium and Aliivibrio, as well as Shewanella and Vibrio. They are related to families Vibrionaceae and Shewanellaceae of the Gammaproteobacteria class. Here, we at the first time, report the bioluminescence of the Enterobacteriaceae Kosakonia cowanii. Moreover, we applied the polyphasic approach to identify and describe the isolated microorganisms. The data on sequencing, diversity of cell fine structure, and light emission spectra at room temperature on the solid medium are discussed. The bacteria are characterized by features in their light emission spectra. It may reflect possible molecular mechanisms of bioluminescence as well as features of bacterial composition. The obtained data expands the existing body of knowledge about the bioluminescence spread among the bacteria of Nordic latitudes and provides complex information that is crucial for their precise identification.
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Hayek M, Baraquet C, Lami R, Blache Y, Molmeret M. The Marine Bacterium Shewanella woodyi Produces C 8-HSL to Regulate Bioluminescence. MICROBIAL ECOLOGY 2020; 79:865-881. [PMID: 31741007 DOI: 10.1007/s00248-019-01454-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Quorum sensing (QS), a cell-to-cell communication system involved in the synchronization of bacterial behavior in a cell-density-dependent manner has been shown to control phenotypes such as luminescence, virulence, and biofilm formation. The marine strain, Shewanella woodyi MS32 has been identified as a luminous bacterium. Very little information is known on this bacterium, in particular if its luminescence and biofilm formation are controlled by QS. In this study, we have demonstrated that S. woodyi MS32 emits luminescence in planktonic and sessile conditions. The putative QS regulatory genes homologous to luxI and luxR identified in the S. woodyi MS32 genome, named swoI and swoR, are divergently transcribed and are not genetically linked to the lux operon in contrast with its closest parent Shewanella hanedai and with Aliivibrio fischeri. Interestingly, the phylogenetic analysis based on the SwoI and SwoR sequences shows that a separate horizontal gene transfer (HGT) occurred for the regulatory genes and for the lux operon. Functional analyses demonstrate that the swoI and swoR mutants were non-luminescent. Expression of lux genes was impaired in the QS regulatory mutants. N-octanoyl-L-homoserine lactone (C8-HSL) identified using liquid chromatography mass spectrometry in the wild-type strain (but not in ΔswoI) can induce S. woodyi luminescence. No significant difference has been detected between the wild-type and mutants on adhesion and biofilm formation in the conditions tested. Therefore, we have demonstrated that the luxCDABEG genes of S. woodyi MS32 are involved in luminescence emission and that the swoR/swoI genes, originated from a separate HGT, regulate luminescence through C8-HSL production.
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Affiliation(s)
- Mahmoud Hayek
- Laboratoire MAPIEM, EA4323, Université de Toulon, Avenue de l'université, BP 20132, 83957, La Garde Cedex, France
| | - Claudine Baraquet
- Laboratoire MAPIEM, EA4323, Université de Toulon, Avenue de l'université, BP 20132, 83957, La Garde Cedex, France
| | - Raphaël Lami
- Sorbonne Universités, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Yves Blache
- Laboratoire MAPIEM, EA4323, Université de Toulon, Avenue de l'université, BP 20132, 83957, La Garde Cedex, France
| | - Maëlle Molmeret
- Laboratoire MAPIEM, EA4323, Université de Toulon, Avenue de l'université, BP 20132, 83957, La Garde Cedex, France.
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Bazhenov SV, Khrulnova SA, Konopleva MN, Manukhov IV. Seasonal changes in luminescent intestinal microflora of the fish inhabiting the Bering and Okhotsk seas. FEMS Microbiol Lett 2019; 366:5322163. [PMID: 30772893 DOI: 10.1093/femsle/fnz040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 02/15/2019] [Indexed: 11/14/2022] Open
Abstract
Here, we present a study of luminescent intestinal microflora of the fish inhabiting Bering and Okhotsk seas in summer and winter seasons. Sampling of intestinal luminescent microflora was carried for several years, with all recovered species belonging to psychrophilic bacteria of either Aliivibrio logei or Photobacterium phosphoreum species. A seasonal change in fish intestinal luminescent microflora detected include an increase in prevalence of P. phosphoreum bacteria in summer and an increase in prevalence of A. logei bacteria in winter seasons. In fact, 90% of all luminescent bacteria isolated in winter period (January-March) were A. logei, while 88% of luminescent isolates recovered in summer period (July-September) were that of P. phosphoreum species. Seasonal changes were similar across all six sampling expeditions, three in winter and three in summer seasons, evenly spread through 2010-2018 period.
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Affiliation(s)
- Sergey V Bazhenov
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation.,State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", 1st Dorozhnii pr., 1, Moscow 117545, Russian Federation
| | - Svetlana A Khrulnova
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", 1st Dorozhnii pr., 1, Moscow 117545, Russian Federation
| | - Maria N Konopleva
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
| | - Ilya V Manukhov
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation.,State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", 1st Dorozhnii pr., 1, Moscow 117545, Russian Federation
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15
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Brodl E, Winkler A, Macheroux P. Molecular Mechanisms of Bacterial Bioluminescence. Comput Struct Biotechnol J 2018; 16:551-564. [PMID: 30546856 PMCID: PMC6279958 DOI: 10.1016/j.csbj.2018.11.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/08/2018] [Accepted: 11/10/2018] [Indexed: 02/06/2023] Open
Abstract
Bioluminescence refers to the production of light by living organisms. Bioluminescent bacteria with a variety of bioluminescence emission characteristics have been identified in Vibrionaceae, Shewanellaceae and Enterobacteriaceae. Bioluminescent bacteria are mainly found in marine habitats and they are either free-floating, sessile or have specialized to live in symbiosis with other marine organisms. On the molecular level, bioluminescence is enabled by a cascade of chemical reactions catalyzed by enzymes encoded by the lux operon with the gene order luxCDABEG. The luxA and luxB genes encode the α- and β- subunits, respectively, of the enzyme luciferase producing the light emitting species. LuxC, luxD and luxE constitute the fatty acid reductase complex, responsible for the synthesis of the long-chain aldehyde substrate and luxG encodes a flavin reductase. In bacteria, the heterodimeric luciferase catalyzes the monooxygenation of long-chain aliphatic aldehydes to the corresponding acids utilizing reduced FMN and molecular oxygen. The energy released as a photon results from an excited state flavin-4a-hydroxide, emitting light centered around 490 nm. Advances in the mechanistic understanding of bacterial bioluminescence have been spurred by the structural characterization of protein encoded by the lux operon. However, the number of available crystal structures is limited to LuxAB (Vibrio harveyi), LuxD (Vibrio harveyi) and LuxF (Photobacterium leiognathi). Based on the crystal structure of LuxD and homology models of LuxC and LuxE, we provide a hypothetical model of the overall structure of the LuxCDE fatty acid reductase complex that is in line with biochemical observations.
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Affiliation(s)
| | | | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
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16
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Ongoing Transposon-Mediated Genome Reduction in the Luminous Bacterial Symbionts of Deep-Sea Ceratioid Anglerfishes. mBio 2018; 9:mBio.01033-18. [PMID: 29946051 PMCID: PMC6020299 DOI: 10.1128/mbio.01033-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diverse marine fish and squid form symbiotic associations with extracellular bioluminescent bacteria. These symbionts are typically free-living bacteria with large genomes, but one known lineage of symbionts has undergone genomic reduction and evolution of host dependence. It is not known why distinct evolutionary trajectories have occurred among different luminous symbionts, and not all known lineages previously had genome sequences available. In order to better understand patterns of evolution across diverse bioluminescent symbionts, we de novo sequenced the genomes of bacteria from a poorly studied interaction, the extracellular symbionts from the "lures" of deep-sea ceratioid anglerfishes. Deep-sea anglerfish symbiont genomes are reduced in size by about 50% compared to free-living relatives. They show a striking convergence of genome reduction and loss of metabolic capabilities with a distinct lineage of obligately host-dependent luminous symbionts. These losses include reductions in amino acid synthesis pathways and abilities to utilize diverse sugars. However, the symbiont genomes have retained a number of categories of genes predicted to be useful only outside the host, such as those involved in chemotaxis and motility, suggesting that they may persist in the environment. These genomes contain very high numbers of pseudogenes and show massive expansions of transposable elements, with transposases accounting for 28 and 31% of coding sequences in the symbiont genomes. Transposon expansions appear to have occurred at different times in each symbiont lineage, indicating either independent evolutions of reduction or symbiont replacement. These results suggest ongoing genomic reduction in extracellular luminous symbionts that is facilitated by transposon proliferations.IMPORTANCE Many female deep-sea anglerfishes possess a "lure" containing luminous bacterial symbionts. Here we show that unlike most luminous symbionts, these bacteria are undergoing an evolutionary transition toward small genomes with limited metabolic capabilities. Comparative analyses of the symbiont genomes indicate that this transition is ongoing and facilitated by transposon expansions. This transition may have occurred independently in different symbiont lineages, although it is unclear why. Genomic reduction is common in bacteria that only live within host cells but less common in bacteria that, like anglerfish symbionts, live outside host cells. Since multiple evolutions of genomic reduction have occurred convergently in luminous bacteria, they make a useful system with which to understand patterns of genome evolution in extracellular symbionts. This work demonstrates that ecological factors other than an intracellular lifestyle can lead to dramatic gene loss and evolutionary changes and that transposon expansions may play important roles in this process.
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Xuan G, Xiao Q, Wang J, Lin H, Pavase T. Expression of genes encoding the luciferase from Photobacterium leiognathi in Escherichia coli Rosetta (DE3) and its application in NADH detection. LUMINESCENCE 2018; 33:1010-1018. [PMID: 29920921 DOI: 10.1002/bio.3501] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/22/2018] [Accepted: 04/06/2018] [Indexed: 02/01/2023]
Abstract
Cloning of genes encoding the luciferase from Photobacterium leiognathi YL in Escherichia coli Rosetta (DE3) was performed successfully and the expressed forms of lux AB were purified to homogeneity. Experimental measurements revealed that luciferase from Photobacterium leiognathi YL has good thermal stability and a high residual activity at extreme pH values, which are extremely important for its various ecological, industrial and medical applications. Furthermore, we made a first attempt for quantitative detection of NADH by recombinant E. coli Rosetta (DE3) coupled enzyme system. A good linear relationship between luminescence intensity and NADH with low (1-12 nmol/L) and high (10-500 nmol/L) concentration was observed, whose standard curve was y = 772.97× + 4041.1, R2 = 0.9884 and y = 1710× + 4.99 × 105 , R2 = 0.9727, respectively. Our results demonstrate a high sensitivity of recombinant E. coli coupled enzyme system to NADH on the basis of high soluble expression of recombinant luciferase and continuous and stable expression of some NAD(P)H-dependent flavin mononucleotide (FMN) reductases.
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Affiliation(s)
- Guanhua Xuan
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Qilin Xiao
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Jingxue Wang
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Hong Lin
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Tushar Pavase
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
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18
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Machado H, Gram L. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium. Front Microbiol 2017; 8:1204. [PMID: 28706512 PMCID: PMC5489566 DOI: 10.3389/fmicb.2017.01204] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/13/2017] [Indexed: 11/13/2022] Open
Abstract
Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.
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Affiliation(s)
- Henrique Machado
- Department of Biotechnology and Biomedicine, Technical University of Denmark, MatematiktorvetKgs Lyngby, Denmark.,Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, MatematiktorvetKgs Lyngby, Denmark
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19
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Draft Genome Sequences of Histamine- and Non-Histamine-Producing Photobacterium Strains. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01008-16. [PMID: 27660786 PMCID: PMC5034137 DOI: 10.1128/genomea.01008-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Histamine-producing bacteria (HPBs) have recently been identified from the marine environment. The identification and characterization of HPBs is important to developing effective mitigation strategies for scombrotoxin fish poisoning. We report here the draft genomes of seven histamine-producing and two non-histamine-producing marine Photobacterium strains.
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20
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Abstract
Vibrio vulnificus, carrying a 50% fatality rate, is the most deadly of the foodborne pathogens. It occurs in estuarine and coastal waters and it is found in especially high numbers in oysters and other molluscan shellfish. The biology of V. vulnificus, including its ecology, pathogenesis, and molecular genetics, has been described in numerous reviews. This article provides a brief summary of some of the key aspects of this important human pathogen, including information on biotypes and genotypes, virulence factors, risk factor requirements and the role of iron in disease, association with oysters, geographic distribution, importance of salinity and water temperature, increasing incidence associated with global warming. This article includes some of our findings as presented at the "Vibrios in the Environment 2010" conference held in Biloxi, MS.
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Yang X, Li Y, Zang J, Li Y, Bie P, Lu Y, Wu Q. Analysis of pan-genome to identify the core genes and essential genes of Brucella spp. Mol Genet Genomics 2016; 291:905-12. [DOI: 10.1007/s00438-015-1154-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/01/2015] [Indexed: 01/11/2023]
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Ersoy Omeroglu E. Determination of the Genetic Diversity of Different Bioluminescent Bacteria by Pulsed-Field Gel Electrophoresis (PFGE). Jundishapur J Microbiol 2015; 8:e28378. [PMID: 26421141 PMCID: PMC4584076 DOI: 10.5812/jjm.28378v2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/26/2015] [Accepted: 05/21/2015] [Indexed: 11/16/2022] Open
Abstract
Background: There are 4 different genera (i.e. Vibrio, Aliivibrio, Photobacterium, and Shewanella) in the new classification of bioluminescent bacteria. The mechanism of bioluminescence has yet to be fully elucidated. Therefore, the determination of physiological and genetic characteristics of bioluminescent bacteria isolated from different sources is very important. Pulsed-Field Gel Electrophoresis (PFGE) has the highest discriminatory power among the different molecular typing methods for the investigation of the clonal relationships between bacteria. For the PFGE analysis of bioluminescent bacteria, the NotI-HF™ is the method of choice among the restriction enzymes. Objectives: The present study aimed to determine genetic relatedness via PFGE in 41 bioluminescent bacteria (belonging to 10 different species) isolated and identified from various marine sources. Materials and Methods: Different bioluminescent bacteria (i.e. Vibrio gigantis, V. azureus, V. harveyi, V. lentus, V. crassostreae, V. orientalis, Aliivibrio logei, A. fischeri, Shewanella woodyi, and Photobacterium kishitanii) were analyzed by PFGE using the NotI-HF™ restriction enzyme. The whole DNA of the strains embedded into the agarose plugs was digested with enzyme at 37°C for 30 minutes. CHEF-Mapper PFGE system was used for electrophoresis and band profile of the strains for the NotI-HF™ restriction enzyme were analyzed by Bio-Profil-1D++ software (Vilber Lourmat) at 10% homology coefficient. Results: Although all experiments were performed three times, four of forty-one bioluminescent strains (V. gigantis E-16, H-16 and S3W46 strains and A. fischeri E-4 strain) could not be typed by PFGE technique with NotI-HF™ enzyme. While only two strains (V. crassostreae H-12 and H-19 strains) were exhibiting same band pattern profiles (100% genome homology), thirty-six different PFGE band patterns were obtained. Pattern homologies changed between 66% - 92%, 73% - 83% and 49% - 100% for V. gigantis, V. harveyi and other strains, respectively. Conclusions: The obtained results revealed that there has been a high rate of genetic diversity in bioluminescent strains isolated from Gulf of Izmir and V. lentus and V. crassostreae strains could be also bioluminescent for the first report. At the same time, PFGE analysis of bioluminescent bacteria including four different genera and ten different species were shown for the first time by this study. It is considered that data acquired by this study will contribute evolution and mechanism of bioluminescence to further works to be done.
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Affiliation(s)
- Esra Ersoy Omeroglu
- Biology Department, Faculty of Science, Basic and Industrial Microbiology Section, Ege University, Bornova-Izmir, Turkey
- Corresponding author: Esra Ersoy Omeroglu, Biology Department, Faculty of Science, Basic and Industrial Microbiology Section, Ege University, Bornova-Izmir, Turkey. Tel: +90-2323112811, Fax: +90-2323881036, E-mail:
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Determination of the Genetic Diversity of Different Bioluminescent Bacteria by Pulsed-Field Gel Electrophoresis (PFGE). Jundishapur J Microbiol 2015. [DOI: 10.5812/jjm.28378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Abstract
We report the genome sequence of the environmental Vibrio vulnificus biotype 1_cladeA. This draft genome of the CladeA-yb158 strain, isolated in Israel, represents this newly emerged clonal group that contains both clinical and environmental strains.
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Urbanczyk Y, Ogura Y, Hayashi T, Urbanczyk H. Description of a novel marine bacterium, Vibrio hyugaensis sp. nov., based on genomic and phenotypic characterization. Syst Appl Microbiol 2015; 38:300-4. [PMID: 25952324 DOI: 10.1016/j.syapm.2015.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/06/2015] [Accepted: 04/10/2015] [Indexed: 10/23/2022]
Abstract
Three luminous bacteria strains have been isolated from seawater samples collected in the coastal regions of the Miyazaki prefecture in Japan. Analysis of the 16S rRNA gene sequences identified the three strains as members of the genus Vibrio (Vibrionaceae, Gammaproteobacteria), closely related to bacteria in the so-called 'Harveyi clade.' The genomes of the three strains were estimated to be between 5.49Mbp and 5.95Mbp, with average G+C of 43.91%. The genome sequence data was used to estimate relatedness of the three strains to related Vibrio bacteria, including estimation of frequency of recombination events, calculation of average nucleotide identity (ANI), and a phylogenetic analysis based on concatenated alignment of nucleotide sequences of 135 protein coding genes. Results of these analyses in all cases showed the three strains forming a group clearly separate from previously described Vibrio species. A phenotypic analysis revealed that the three strains have character similar to Vibrio bacteria in the 'Harveyi clade', but can be differentiated from previously described species by testing for hydrolysis of esculin. Based on results of genomic, phylogenetic and phenotypic analyses presented in this study, it can be concluded that the three strains represent a novel species, for which the name Vibrio hyugaensis sp. nov. is proposed. The type strain is 090810a(T) (=LMG 28466(T)=NBRC 110633(T)).
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Affiliation(s)
- Yoshiko Urbanczyk
- Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Gakuen-kibanadai-nishi-1-1, Miyazaki 889-2192, Japan
| | - Yoshitoshi Ogura
- Division of Microbial Genomics, Department of Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan; Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Tetsuya Hayashi
- Division of Microbial Genomics, Department of Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan; Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Henryk Urbanczyk
- Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Gakuen-kibanadai-nishi-1-1, Miyazaki 889-2192, Japan.
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26
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Raz N, Danin-Poleg Y, Hayman RB, Bar-On Y, Linetsky A, Shmoish M, Sanjuán E, Amaro C, Walt DR, Kashi Y. Genome-wide SNP-genotyping array to study the evolution of the human pathogen Vibrio vulnificus biotype 3. PLoS One 2014; 9:e114576. [PMID: 25526263 PMCID: PMC4272304 DOI: 10.1371/journal.pone.0114576] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/11/2014] [Indexed: 12/18/2022] Open
Abstract
Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains of V. vulnificus are classified into three different biotypes. The newly emerged biotype 3 has been found to be clonal and restricted to Israel. In the family Vibrionaceae, horizontal gene transfer is the main mechanism responsible for the emergence of new pathogen groups. To better understand the evolution of the bacterium, and in particular to trace the evolution of biotype 3, we performed genome-wide SNP genotyping of 254 clinical and environmental V. vulnificus isolates with worldwide distribution recovered over a 30-year period, representing all phylogeny groups. A custom single-nucleotide polymorphism (SNP) array implemented on the Illumina GoldenGate platform was developed based on 570 SNPs randomly distributed throughout the genome. In general, the genotyping results divided the V. vulnificus species into three main phylogenetic lineages and an additional subgroup, clade B, consisting of environmental and clinical isolates from Israel. Data analysis suggested that 69% of biotype 3 SNPs are similar to SNPs from clade B, indicating that biotype 3 and clade B have a common ancestor. The rest of the biotype 3 SNPs were scattered along the biotype 3 genome, probably representing multiple chromosomal segments that may have been horizontally inserted into the clade B recipient core genome from other phylogroups or bacterial species sharing the same ecological niche. Results emphasize the continuous evolution of V. vulnificus and support the emergence of new pathogenic groups within this species as a recurrent phenomenon. Our findings contribute to a broader understanding of the evolution of this human pathogen.
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Affiliation(s)
- Nili Raz
- Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Yael Danin-Poleg
- Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Ryan B. Hayman
- Department of Chemistry, Tufts University, Medford, Massachusetts, United States of America
| | - Yudi Bar-On
- Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Alex Linetsky
- Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Michael Shmoish
- Bioinformatics Knowledge Unit, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Eva Sanjuán
- Department of Microbiology, Faculty of Biology, University of Valencia, Valencia, Spain
| | - Carmen Amaro
- Department of Microbiology, Faculty of Biology, University of Valencia, Valencia, Spain
| | - David R. Walt
- Department of Chemistry, Tufts University, Medford, Massachusetts, United States of America
| | - Yechezkel Kashi
- Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
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Chavez-Dozal AA, Gorman C, Lostroh CP, Nishiguchi MK. Gene-swapping mediates host specificity among symbiotic bacteria in a beneficial symbiosis. PLoS One 2014; 9:e101691. [PMID: 25014649 PMCID: PMC4094467 DOI: 10.1371/journal.pone.0101691] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 06/10/2014] [Indexed: 12/12/2022] Open
Abstract
Environmentally acquired beneficial associations are comprised of a wide variety of symbiotic species that vary both genetically and phenotypically, and therefore have differential colonization abilities, even when symbionts are of the same species. Strain variation is common among conspecific hosts, where subtle differences can lead to competitive exclusion between closely related strains. One example where symbiont specificity is observed is in the sepiolid squid-Vibrio mutualism, where competitive dominance exists among V. fischeri isolates due to subtle genetic differences between strains. Although key symbiotic loci are responsible for the establishment of this association, the genetic mechanisms that dictate strain specificity are not fully understood. We examined several symbiotic loci (lux-bioluminescence, pil = pili, and msh-mannose sensitive hemagglutinin) from mutualistic V. fischeri strains isolated from two geographically distinct squid host species (Euprymna tasmanica-Australia and E. scolopes-Hawaii) to determine whether slight genetic differences regulated host specificity. Through colonization studies performed in naïve squid hatchlings from both hosts, we found that all loci examined are important for specificity and host recognition. Complementation of null mutations in non-native V. fischeri with loci from the native V. fischeri caused a gain in fitness, resulting in competitive dominance in the non-native host. The competitive ability of these symbiotic loci depended upon the locus tested and the specific squid species in which colonization was measured. Our results demonstrate that multiple bacterial genetic elements can determine V. fischeri strain specificity between two closely related squid hosts, indicating how important genetic variation is for regulating conspecific beneficial interactions that are acquired from the environment.
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Affiliation(s)
- Alba A. Chavez-Dozal
- New Mexico State University, Department of Biology, Las Cruces, New Mexico, United States of America
| | - Clayton Gorman
- New Mexico State University, Department of Biology, Las Cruces, New Mexico, United States of America
| | - C. Phoebe Lostroh
- Colorado College, Department of Biology, Colorado Springs, Colorado, United States of America
| | - Michele K. Nishiguchi
- New Mexico State University, Department of Biology, Las Cruces, New Mexico, United States of America
- * E-mail:
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Dunlap P. Biochemistry and Genetics of Bacterial Bioluminescence. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 144:37-64. [DOI: 10.1007/978-3-662-43385-0_2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Urbanczyk H, Urbanczyk Y, Hayashi T, Ogura Y. Diversification of two lineages of symbiotic Photobacterium. PLoS One 2013; 8:e82917. [PMID: 24349398 PMCID: PMC3862722 DOI: 10.1371/journal.pone.0082917] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 10/29/2013] [Indexed: 11/19/2022] Open
Abstract
Understanding of processes driving bacterial speciation requires examination of closely related, recently diversified lineages. To gain an insight into diversification of bacteria, we conducted comparative genomic analysis of two lineages of bioluminescent symbionts, Photobacterium leiognathi and 'P. mandapamensis'. The two lineages are evolutionary and ecologically closely related. Based on the methods used in bacterial taxonomy for classification of new species (DNA-DNA hybridization and ANI), genetic relatedness of the two lineages is at a cut-off point for species delineation. In this study, we obtained the whole genome sequence of a representative P. leiognathi strain lrivu.4.1, and compared it to the whole genome sequence of 'P. mandapamensis' svers.1.1. Results of the comparative genomic analysis suggest that P. leiognathi has a more plastic genome and acquired genes horizontally more frequently than 'P. mandapamensis'. We predict that different rates of recombination and gene acquisition contributed to diversification of the two lineages. Analysis of lineage-specific sequences in 25 strains of P. leiognathi and 'P. mandapamensis' found no evidence that bioluminescent symbioses with specific host animals have played a role in diversification of the two lineages.
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Affiliation(s)
- Henryk Urbanczyk
- Interdisciplinary Research Organization, University of Miyazaki, Miyazaki, Japan
| | - Yoshiko Urbanczyk
- Interdisciplinary Research Organization, University of Miyazaki, Miyazaki, Japan
| | - Tetsuya Hayashi
- Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yoshitoshi Ogura
- Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
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Taxonomic revision of Harveyi clade bacteria (family Vibrionaceae) based on analysis of whole genome sequences. Int J Syst Evol Microbiol 2013; 63:2742-2751. [DOI: 10.1099/ijs.0.051110-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Use of inadequate methods for classification of bacteria in the so-called Harveyi clade (family Vibrionaceae, Gammaproteobacteria) has led to incorrect assignment of strains and proliferation of synonymous species. In order to resolve taxonomic ambiguities within the Harveyi clade and to test usefulness of whole genome sequence data for classification of Vibrionaceae, draft genome sequences of 12 strains were determined and analysed. The sequencing included type strains of seven species: Vibrio sagamiensis NBRC 104589T, Vibrio azureus NBRC 104587T, Vibrio harveyi NBRC 15634T, Vibrio rotiferianus LMG 21460T, Vibrio campbellii NBRC 15631T, Vibrio jasicida LMG 25398T, and Vibrio owensii LMG 25443T. Draft genome sequences of strain LMG 25430, previously designated the type strain of [Vibrio communis], and two strains (MWB 21 and 090810c) from the ‘beijerinckii’ lineage were also determined. Whole genomes of two additional strains (ATCC 25919 and 200612B) that previously could not be assigned to any Harveyi clade species were also sequenced. Analysis of the genome sequence data revealed a clear case of synonymy between V. owensii and [V. communis], confirming an earlier proposal to synonymize both species. Both strains from the ‘beijerinckii’ lineage were classified as V. jasicida, while the strains ATCC 25919 and 200612B were classified as V. owensii and V. campbellii, respectively. We also found that two strains, AND4 and Ex25, are closely related to Harveyi clade bacteria, but could not be assigned to any species of the family Vibrionaceae. The use of whole genome sequence data for the taxonomic classification of the Harveyi clade bacteria and other members of the family Vibrionaceae is also discussed.
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Abstract
We report the first genome sequence of the pathogenic Vibrio vulnificus biotype 3. This draft genome sequence of the environmental strain VVyb1(BT3), isolated in Israel, provides a representation of this newly emerged clonal group, which reveals higher similarity to the clinical strains of biotype 1 than to the environmental ones.
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Chiura HX, Uchiyama N, Kogure K. Broad-Host Range Gene Transporter Particles Produced by Aliivibrio fischeri. Microbes Environ 2012; 24:322-9. [PMID: 21566392 DOI: 10.1264/jsme2.me09153] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aliivibrio fischeri NCIMB1281(T) (basonym, Vibrio fischeri) spontaneously started broad-host range vector particle (AfVP) production by budding from the logarithmic phase, and stabilised at around 7.0×10(10)-7.4×10(11) particles mL(-1) without any accompanying change in the host population. AfVPs had a spherical shape and varied in diameter from 18.1 to 159.2 nm [median±SD, 58.4±11.9 nm, n=528], with 95.1% between 30.2 and 84.6 nm in diameter exhibiting a normal distribution. Their buoyant density and DNA content ranged from 1.3607 to 1.3980 g cm(-3), and 17.3 to 95.3 kbp, respectively. Regardless of UV treatment, AfVPs enhanced the efficiency of plating 116-136% at a multiplicity of infection of ca. 140 in Escherichia coli AB1157. Generalised transduction was observed with a frequency of between 10(-4) and 10(-6) cells per AfVP without UV treatment. Upon infection, the particle membrane remained outside the recipient cell, and a string-like structure coated with a fibrous proteinaceous-like material was present. The growth of the E. coli transductant (AfV-E-trans) reached a maximum of ca. 415% that of the parental E. coli recipient. AfV-E-trans acquired the ability to produce budding particles.
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Affiliation(s)
- Hiroshi Xavier Chiura
- Marine Microbiology Laboratory, Department of Marine Ecosystems Dynamics, Ocean Research Institute, University of Tokyo
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Abstract
A pan-genome describes the full complement of genes in species. It is a superset of all the genes in all the individuals of a species, which is composed of a 'core genome' containing genes present in all individuals, and a 'dispensable genome' containing genes present only in some individuals and individual-specific genes. From pan-genome sight, 30 finished genomes from Escherichia coli were employed to analyze their gene and genome compositions and evaluation in this study. The results indicated that the core genes accounted for about 50% of the total number of genes, while about 146 strain-specific genes existed in the each strain tested. The data suggests that the E. coli pan-genome is vast, and unique genes will continue to be identified when more E. coli genomes are sequenced. After analyzing relationships of the gene conservation, GC content and selection pressure in different strains tested, we found that more conserved genes had a nar-row range of GC content, and they also bear more selection pressure. These results will be helpful for better understanding of the evolution profile of E. coli genome, and the dynamic changes of its gene compositions. The E. coli pan-genome pro-vides useful information for prevention and control of the diseases caused by pathogenic E. coli, and also provides a para-digm for the large-scale analysis of pathogenic bacteria genomes.
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Anetzberger C, Schell U, Jung K. Single cell analysis of Vibrio harveyi uncovers functional heterogeneity in response to quorum sensing signals. BMC Microbiol 2012; 12:209. [PMID: 22985329 PMCID: PMC3511230 DOI: 10.1186/1471-2180-12-209] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 09/13/2012] [Indexed: 11/25/2022] Open
Abstract
Background Vibrio harveyi and closely related species are important pathogens in aquaculture. A complex quorum sensing cascade involving three autoinducers controls bioluminescence and several genes encoding virulence factors. Single cell analysis of a V. harveyi population has already indicated intercellular heterogeneity in the production of bioluminescence. This study was undertaken to analyze the expression of various autoinducer-dependent genes in individual cells. Results Here we used reporter strains bearing promoter::gfp fusions to monitor the induction/repression of three autoinducer-regulated genes in wild type conjugates at the single cell level. Two genes involved in pathogenesis - vhp and vscP, which code for an exoprotease and a component of the type III secretion system, respectively, and luxC (the first gene in the lux operon) were chosen for analysis. The lux operon and the exoprotease gene are induced, while vscP is repressed at high cell density. As controls luxS and recA, whose expression is not dependent on autoinducers, were examined. The responses of the promoter::gfp fusions in individual cells from the same culture ranged from no to high induction. Importantly, simultaneous analysis of two autoinducer induced phenotypes, bioluminescence (light detection) and exoproteolytic activity (fluorescence of a promoter::gfp fusion), in single cells provided evidence for functional heterogeneity within a V. harveyi population. Conclusions Autoinducers are not only an indicator for cell density, but play a pivotal role in the coordination of physiological activities within the population.
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Affiliation(s)
- Claudia Anetzberger
- Munich Center for integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität Munich, Großhaderner Str, 2-4, 82152, Martinsried, Germany
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Urbanczyk H, Furukawa T, Yamamoto Y, Dunlap PV. Natural replacement of vertically inherited lux-rib genes of Photobacterium aquimaris by horizontally acquired homologues. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:412-416. [PMID: 23760826 DOI: 10.1111/j.1758-2229.2012.00355.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We report here the first instance of a complete replacement of vertically inherited luminescence genes by horizontally acquired homologues. Different strains of Photobacterium aquimaris contain homologues of the lux-rib genes that have a different evolutionary history. Strain BS1 from the Black Sea contains a vertically inherited lux-rib operon, which presumably arose in the ancestor of this species, whereas the type strain NBRC 104633(T) , from Sagami Bay, lacks the vertically inherited lux-rib operon and instead carries a complete and functional lux-rib operon acquired horizontally from a bacterium related to Photobacterium mandapamensis. The results indicate that the horizontal acquisition of the lux genes expanded the pan-genome of P. aquimaris, but it did not influence the phylogenetic divergence of this species.
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Affiliation(s)
- Henryk Urbanczyk
- Interdisciplinary Research Organization Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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Urbanczyk H, Kiwaki N, Furukawa T, Iwatsuki Y. Limited geographic distribution of certain strains of the bioluminescent symbiont Photobacterium leiognathi. FEMS Microbiol Ecol 2012; 81:355-63. [PMID: 22404110 DOI: 10.1111/j.1574-6941.2012.01353.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 02/08/2012] [Accepted: 02/26/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Henryk Urbanczyk
- Interdisciplinary Research Organization; University of Miyazaki; Miyazaki; Japan
| | - Naomi Kiwaki
- Interdisciplinary Research Organization; University of Miyazaki; Miyazaki; Japan
| | - Takashi Furukawa
- Interdisciplinary Research Organization; University of Miyazaki; Miyazaki; Japan
| | - Yukio Iwatsuki
- Faculty of Agriculture; University of Miyazaki; Miyazaki; Japan
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Wollenberg M, Preheim S, Polz M, Ruby EG. Polyphyly of non-bioluminescent Vibrio fischeri sharing a lux-locus deletion. Environ Microbiol 2012; 14:655-68. [PMID: 21980988 PMCID: PMC3655796 DOI: 10.1111/j.1462-2920.2011.02608.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study reports the first description and molecular characterization of naturally occurring, non-bioluminescent strains of Vibrio fischeri. These 'dark' V. fischeri strains remained non-bioluminescent even after treatment with both autoinducer and aldehyde, substrate additions that typically maximize light production in dim strains of luminous bacteria. Surprisingly, the entire lux locus (eight genes) was absent in over 97% of these dark V. fischeri strains. Although these strains were all collected from a Massachusetts (USA) estuary in 2007, phylogenetic reconstructions allowed us to reject the hypothesis that these newly described non-bioluminescent strains exhibit monophyly within the V. fischeri clade. These dark strains exhibited a competitive disadvantage against native bioluminescent strains when colonizing the light organ of the model V. fischeri host, the Hawaiian bobtail squid Euprymna scolopes. Significantly, we believe that the data collected in this study may suggest the first observation of a functional, parallel locus-deletion event among independent lineages of a non-pathogenic bacterial species.
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Affiliation(s)
- M.S. Wollenberg
- Department of Medical Microbiology and Immunology, University of Wisconsin, 1550 Linden Drive, Room 5245, Madison, WI 53706-1521, USA
| | - S.P. Preheim
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar Street, Bldg 48-417, Cambridge, MA 02139, USA
| | - M.F. Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar Street, Bldg 48-417, Cambridge, MA 02139, USA
| | - E. G. Ruby
- Department of Medical Microbiology and Immunology, University of Wisconsin, 1550 Linden Drive, Room 5245, Madison, WI 53706-1521, USA
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Yoshizawa S, Karatani H, Wada M, Kogure K. Vibrio azureus emits blue-shifted light via an accessory blue fluorescent protein. FEMS Microbiol Lett 2012; 329:61-8. [DOI: 10.1111/j.1574-6968.2012.02507.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 01/08/2012] [Accepted: 01/09/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Susumu Yoshizawa
- Atmosphere and Ocean Research Institute; The University of Tokyo; Kashiwa; Japan
| | - Hajime Karatani
- Department of Biomolecular Engineering; Graduate School of Science and Technology; Kyoto Institute of Technology; Kyoto; Japan
| | - Minoru Wada
- Graduate School of Science and Technology; Nagasaki University; Nagasaki; Japan
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute; The University of Tokyo; Kashiwa; Japan
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Hendry TA, Dunlap PV. The uncultured luminous symbiont of Anomalops katoptron (Beryciformes: Anomalopidae) represents a new bacterial genus. Mol Phylogenet Evol 2011; 61:834-43. [PMID: 21864694 DOI: 10.1016/j.ympev.2011.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 07/30/2011] [Accepted: 08/03/2011] [Indexed: 10/17/2022]
Abstract
Flashlight fishes (Beryciformes: Anomalopidae) harbor luminous symbiotic bacteria in subocular light organs and use the bacterial light for predator avoidance, feeding, and communication. Despite many attempts anomalopid symbionts have not been brought into laboratory culture, which has restricted progress in understanding their phylogenetic relationships with other luminous bacteria, identification of the genes of their luminescence system, as well as the nature of their symbiotic interactions with their fish hosts. To begin addressing these issues, we used culture-independent analysis of the bacteria symbiotic with the anomalopid fish, Anomalops katoptron, to characterize the phylogeny of the bacteria and to identify the genes of their luminescence system including those involved in the regulation of luminescence. Analysis of the 16S rRNA, atpA, gapA, gyrB, pyrH, recA, rpoA, and topA genes resolved the A. katoptron symbionts as a clade nested within and deeply divergent from other members of Vibrionaceae. The bacterial luminescence (lux) genes were identified as a contiguous set (luxCDABEG), as found for the lux operons of other luminous bacteria. Phylogenetic analysis based on the lux genes confirmed the housekeeping gene phylogenetic placement. Furthermore, genes flanking the lux operon in the A. katoptron symbionts differed from those flanking lux operons of other genera of luminous bacteria. We therefore propose the candidate name Candidatus Photodesmus (Greek: photo = light, desmus = servant) katoptron for the species of bacteria symbiotic with A. katoptron. Results of a preliminary genomic analysis for genes regulating luminescence in other bacteria identified only a Vibrio harveyi-type luxR gene. These results suggest that expression of the luminescence system might be continuous in P. katoptron.
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Affiliation(s)
- Tory A Hendry
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, United States.
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Dashtbani-Roozbehani A, Bakhshi B, Katouli M, Pourshafie MR. Comparative sequence analysis of recA gene among Vibrio cholerae isolates from Iran with globally reported sequences. Lett Appl Microbiol 2011; 53:313-23. [PMID: 21707677 DOI: 10.1111/j.1472-765x.2011.03108.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To study the genetic relatedness between V. cholerae isolates from Iran and other countries based on housekeeping gene recA sequence analysis. METHODS AND RESULTS A 995-bp region of the recA gene from 24 V. cholerae isolates obtained from human and surface water origins in Iran over a 5-year period was sequenced and compared with the sequence data from the isolates belonging to other places. Cluster analysis of the constructed dendrogram based on recA sequence divergence for our clinical isolates showed one sequence type (ST), whereas environmental isolates revealed eight STs. Interestingly, one of our environmental isolates was intermixed with clinical isolates in the largest cluster containing the epidemic strains. Our 24 isolates plus 198 global isolates available in the GenBank showed 77 sequence types (STs) with at least one nucleotide difference. CONCLUSIONS Our result suggested that recA sequencing is a reliable analysis method for understanding the relatedness of the local isolates with the isolates obtained elsewhere. SIGNIFICANCE AND IMPACT OF THE STUDY Understanding the genetic relatedness between V. cholerae isolates could give insights into the health care system for better control and prevention of the cholera.
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Genome sequence of Photobacterium mandapamensis strain svers.1.1, the bioluminescent symbiont of the cardinal fish Siphamia versicolor. J Bacteriol 2011; 193:3144-5. [PMID: 21478348 DOI: 10.1128/jb.00370-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Photobacterium mandapamensis is one of three luminous Photobacterium species able to form species-specific bioluminescent symbioses with marine fishes. Here, we present the draft genome sequence of P. mandapamensis strain svers.1.1, the bioluminescent symbiont of the cardinal fish Siphamia versicolor, the first genome of a symbiotic, luminous Photobacterium species to be sequenced. Analysis of the sequence provides insight into differences between P. mandapamensis and other luminous and symbiotic bacteria in genes involved in quorum-sensing regulation of light production and establishment of symbiosis.
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Urbanczyk H, Ast JC, Dunlap PV. Phylogeny, genomics, and symbiosis of Photobacterium. FEMS Microbiol Rev 2010; 35:324-42. [PMID: 20883503 DOI: 10.1111/j.1574-6976.2010.00250.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Photobacterium comprises several species in Vibrionaceae, a large family of Gram-negative, facultatively aerobic, bacteria that commonly associate with marine animals. Members of the genus are widely distributed in the marine environment and occur in seawater, surfaces, and intestines of marine animals, marine sediments and saline lake water, and light organs of fish. Seven Photobacterium species are luminous via the activity of the lux genes, luxCDABEG. Much recent progress has been made on the phylogeny, genomics, and symbiosis of Photobacterium. Phylogenetic analysis demonstrates a robust separation between Photobacterium and its close relatives, Aliivibrio and Vibrio, and reveals the presence of two well-supported clades. Clade 1 contains luminous and symbiotic species and one species with no luminous members, and Clade 2 contains mostly nonluminous species. The genomes of Photobacterium are similar in size, structure, and organization to other members of Vibrionaceae, with two chromosomes of unequal size and multiple rrn operons. Many species of marine fish form bioluminescent symbioses with three Photobacterium species: Photobacterium kishitanii, Photobacterium leiognathi, and Photobacterium mandapamensis. These associations are highly, but not strictly species specific, and they do not exhibit symbiont-host codivergence. Environmental congruence instead of host selection might explain the patterns of symbiont-host affiliation observed from nature.
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Affiliation(s)
- Henryk Urbanczyk
- Interdisciplinary Research Organization, University of Miyazaki, Miyazaki, Japan
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Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins. BMC Genomics 2010; 11:369. [PMID: 20537180 PMCID: PMC2890568 DOI: 10.1186/1471-2164-11-369] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 06/10/2010] [Indexed: 11/17/2022] Open
Abstract
Background Species of the family Vibrionaceae are ubiquitous in marine environments. Several of these species are important pathogens of humans and marine species. Evidence indicates that genetic exchange plays an important role in the emergence of new pathogenic strains within this family. Data from the sequenced genomes of strains in this family could show how the genes encoded by all these strains, known as the pangenome, are distributed. Information about the core, accessory and panproteome of this family can show how, for example, genes encoding virulence-associated proteins are distributed and help us understand how virulence emerges. Results We deduced the complete set of orthologs for eleven strains from this family. The core proteome consists of 1,882 orthologous groups, which is 28% of the 6,629 orthologous groups in this family. There were 4,411 accessory orthologous groups (i.e., proteins that occurred in from 2 to 10 proteomes) and 5,584 unique proteins (encoded once on only one of the eleven genomes). Proteins that have been associated with virulence in V. cholerae were widely distributed across the eleven genomes, but the majority was found only on the genomes of the two V. cholerae strains examined. Conclusions The proteomes are reflective of the differing evolutionary trajectories followed by different strains to similar phenotypes. The composition of the proteomes supports the notion that genetic exchange among species of the Vibrionaceae is widespread and that this exchange aids these species in adapting to their environments.
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Kirkup BC, Chang L, Chang S, Gevers D, Polz MF. Vibrio chromosomes share common history. BMC Microbiol 2010; 10:137. [PMID: 20459749 PMCID: PMC2875227 DOI: 10.1186/1471-2180-10-137] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 05/10/2010] [Indexed: 11/23/2022] Open
Abstract
Background While most gamma proteobacteria have a single circular chromosome, Vibrionales have two circular chromosomes. Horizontal gene transfer is common among Vibrios, and in light of this genetic mobility, it is an open question to what extent the two chromosomes themselves share a common history since their formation. Results Single copy genes from each chromosome (142 genes from chromosome I and 42 genes from chromosome II) were identified from 19 sequenced Vibrionales genomes and their phylogenetic comparison suggests consistent phylogenies for each chromosome. Additionally, study of the gene organization and phylogeny of the respective origins of replication confirmed the shared history. Conclusions Thus, while elements within the chromosomes may have experienced significant genetic mobility, the backbones share a common history. This allows conclusions based on multilocus sequence analysis (MLSA) for one chromosome to be applied equally to both chromosomes.
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Affiliation(s)
- Benjamin C Kirkup
- Dept, of Civil and Environmental Engineering, 15 Vassar Street, Cambridge, MA 02139, USA.
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45
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Yoshizawa S, Wada M, Kita-Tsukamoto K, Yokota A, Kogure K. Photobacterium aquimaris sp. nov., a luminous marine bacterium isolated from seawater. Int J Syst Evol Microbiol 2009; 59:1438-42. [PMID: 19502330 DOI: 10.1099/ijs.0.004309-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two luminous marine bacteria, strains LC2-065(T) and LC2-102, were isolated from seawater at Sagami Bay in Japan. These bacteria were Gram-negative, oxidase-negative, catalase-positive, motile and coccoid-rods. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA) using six loci (ftsZ, gapA, gyrB, mreB, pyrH and topA) and sequence analysis of the alpha subunit of luciferase (luxA) gene revealed that these bacteria were distinct from other species of the genus Photobacterium. These novel strains were most closely related to Photobacterium kishitanii. The DNA-DNA hybridization value between strain LC2-065(T) and Photobacterium kishitanii ATCC BAA-1194(T) was 42.1 %. The major fatty acids were C(12 : 0,) C(14 : 0), C(16 : 0), C(18 : 0) and C(15 : 0) iso 2-OH and/or C(16 : 1)omega7c (summed feature 3). The DNA G+C contents of strains LC2-065(T) and LC2-086 were 42.2 and 42.9 mol%, respectively. The phenotypic features of the novel strains were similar to those of P. kishitanii and P. phosphoreum, but there were sufficient physiological differences for the novel strains to be easily differentiated. On the basis of these results, these new strains represent a novel species, for which the name Photobacterium aquimaris sp. nov. is proposed. The type strain is LC2-065(T) (=NBRC 104633(T)=KCTC 22356(T)).
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Affiliation(s)
- Susumu Yoshizawa
- Ocean Research Institute, The University of Tokyo, 1-15-1, Minamidai, Nakano-Ku, Tokyo 164-8639, Japan.
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Welham PA, Stekel DJ. Mathematical model of the Lux luminescence system in the terrestrial bacterium Photorhabdus luminescens. ACTA ACUST UNITED AC 2009; 5:68-76. [DOI: 10.1039/b812094c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Dunlap PV, Davis KM, Tomiyama S, Fujino M, Fukui A. Developmental and microbiological analysis of the inception of bioluminescent symbiosis in the marine fish Nuchequula nuchalis (Perciformes: Leiognathidae). Appl Environ Microbiol 2008; 74:7471-81. [PMID: 18978090 PMCID: PMC2607158 DOI: 10.1128/aem.01619-08] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Accepted: 10/22/2008] [Indexed: 11/20/2022] Open
Abstract
Many marine fish harbor luminous bacteria as bioluminescent symbionts. Despite the diversity, abundance, and ecological importance of these fish and their apparent dependence on luminous bacteria for survival and reproduction, little is known about developmental and microbiological events surrounding the inception of their symbioses. To gain insight on these issues, we examined wild-caught larvae of the leiognathid fish Nuchequula nuchalis, a species that harbors Photobacterium leiognathi as its symbiont, for the presence, developmental state, and microbiological status of the fish's internal, supraesophageal light organ. Nascent light organs were evident in the smallest specimens obtained, flexion larvae of 6.0 to 6.5 mm in notochord length (NL), a developmental stage at which the stomach had not yet differentiated and the nascent gasbladder had not established an interface with the light organ. Light organs of certain of the specimens in this size range apparently lacked bacteria, whereas light organs of other specimens of 6.5 mm in NL and of all larger specimens harbored large populations of bacteria, representatives of which were identified as P. leiognathi. Bacteria identified as Vibrio harveyi were also present in the light organ of one larval specimen. Light organ populations were composed typically of two or three genetically distinct strain types of P. leiognathi, similar to the situation in adult fish, and the same strain type was only rarely found in light organs of different larval, juvenile, or adult specimens. Light organs of larvae carried a smaller proportion of strains merodiploid for the lux-rib operon, 79 of 249 strains, than those of adults (75 of 91 strains). These results indicate that light organs of N. nuchalis flexion and postflexion larvae of 6.0 to 6.7 mm in NL are at an early stage of development and that inception of the symbiosis apparently occurs in flexion larvae of 6.0 to 6.5 mm in NL. Ontogeny of the light organ therefore apparently precedes acquisition of the symbiotic bacteria. Furthermore, bacterial populations in larval light organs near inception of the symbiosis are genetically diverse, like those of adult fish.
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Affiliation(s)
- Paul V Dunlap
- University of Michigan, Department of Ecology and Evolutionary Biology, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA.
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Diversity and seasonality of bioluminescent Vibrio cholerae populations in Chesapeake Bay. Appl Environ Microbiol 2008; 75:135-46. [PMID: 19011071 DOI: 10.1128/aem.02894-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Association of luminescence with phenotypic and genotypic traits and with environmental parameters was determined for 278 strains of Vibrio cholerae isolated from the Chesapeake Bay during 1998 to 2000. Three clusters of luminescent strains (A, B, and C) and two nonluminescent clusters (X and Y) were identified among 180 clonal types. V. cholerae O1 strains isolated during pandemics and endemic cholera in the Ganges Delta were related to cluster Y. Heat-stable enterotoxin (encoded by stn) and the membrane protein associated with bile resistance (encoded by ompU) were found to be linked to luminescence in strains of cluster A. Succession from nonluminescent to luminescent populations of V. cholerae occurred during spring to midsummer. Occurrence of cluster A strains in water with neutral pH was contrasted with that of cluster Y strains in water with a pH of >8. Cluster A was found to be associated with a specific calanoid population cooccurring with cyclopoids. Cluster B was related to cluster Y, with its maximal prevalence at pH 8. Occurrence of cluster B strains was more frequent with warmer water temperatures and negatively correlated with maturity of the copepod community. It is concluded that each cluster of luminescent V. cholerae strains occupies a distinct ecological niche. Since the dynamics of these niche-specific subpopulations are associated with zooplankton community composition, the ecology of luminescent V. cholerae is concluded to be related to its interaction with copepods and related crustacean species.
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