1
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Gould AL, Henderson JB. Comparative genomics of symbiotic Photobacterium using highly contiguous genome assemblies from long read sequences. Microb Genom 2023; 9:001161. [PMID: 38112751 PMCID: PMC10763503 DOI: 10.1099/mgen.0.001161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
This study presents the assembly and comparative genomic analysis of luminous Photobacterium strains isolated from the light organs of 12 fish species using Oxford Nanopore Technologies (ONT) sequencing. The majority of assemblies achieved chromosome-level continuity, consisting of one large (>3 Mbp) and one small (~1.5 Mbp) contig, with near complete BUSCO scores along with varying plasmid sequences. Leveraging this dataset, this study significantly expanded the available genomes for P. leiognathi and its subspecies P. 'mandapamensis', enabling a comparative genomic analysis between the two lineages. An analysis of the large and small chromosomes unveiled distinct patterns of core and accessory genes, with a larger fraction of the core genes residing on the large chromosome, supporting the hypothesis of secondary chromosome evolution from megaplasmids in Vibrionaceae. In addition, we discovered a proposed new species, Photobacterium acropomis sp. nov., isolated from an acropomatid host, with an average nucleotide identify (ANI) of 93 % compared to the P. leiognathi and P. 'mandapamensis' strains. A comparison of the P. leiognathi and P. 'mandapamensis' lineages revealed minimal differences in gene content, yet highlighted the former's larger genome size and potential for horizontal gene transfer. An investigation of the lux-rib operon, responsible for light production, indicated congruence between the presence of luxF and host family, challenging its role in differentiating P. 'mandapamensis' from P. leiognathi. Further insights were derived from the identification of metabolic differences, such as the presence of the NADH:quinone oxidoreductase respiratory complex I in P. leiognathi as well as variations in the type II secretion system (T2S) genes between the lineages, potentially impacting protein secretion and symbiosis. In summary, this study advances our understanding of Photobacterium genome evolution, highlighting subtle differences between closely related lineages, specifically P. leiognathi and P. 'mandapamensis'. These findings highlight the benefit of long read sequencing for bacterial genome assembly and pangenome analysis and provide a foundation for exploring early bacterial speciation processes of these facultative light organ symbionts.
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Affiliation(s)
- Alison L. Gould
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr. San Francisco, CA 94118, California, USA
| | - James B. Henderson
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr. San Francisco, CA 94118, California, USA
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2
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Kim HJ, Kim KE, Kim YJ, Kang H, Shin JW, Kim S, Lee SH, Jung SW, Lee TK. Marine Bacterioplankton Community Dynamics and Potentially Pathogenic Bacteria in Seawater around Jeju Island, South Korea, via Metabarcoding. Int J Mol Sci 2023; 24:13561. [PMID: 37686367 PMCID: PMC10487856 DOI: 10.3390/ijms241713561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Understanding marine bacterioplankton composition and distribution is necessary for improving predictions of ecosystem responses to environmental change. Here, we used 16S rRNA metabarcoding to investigate marine bacterioplankton diversity and identify potential pathogenic bacteria in seawater samples collected in March, May, September, and December 2013 from two sites near Jeju Island, South Korea. We identified 1343 operational taxonomic units (OTUs) and observed that community diversity varied between months. Alpha- and Gamma-proteobacteria were the most abundant classes, and in all months, the predominant genera were Candidatus Pelagibacter, Leisingera, and Citromicrobium. The highest number of OTUs was observed in September, and Vibrio (7.80%), Pseudoalteromonas (6.53%), and Citromicrobium (6.16%) showed higher relative abundances or were detected only in this month. Water temperature and salinity significantly affected bacterial distribution, and these conditions, characteristic of September, were adverse for Aestuariibacter but favored Citromicrobium. Potentially pathogenic bacteria, among which Vibrio (28 OTUs) and Pseudoalteromonas (six OTUs) were the most abundant in September, were detected in 49 OTUs, and their abundances were significantly correlated with water temperature, increasing rapidly in September, the warmest month. These findings suggest that monthly temperature and salinity variations affect marine bacterioplankton diversity and potential pathogen abundance.
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Affiliation(s)
- Hyun-Jung Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Oceanography and Marine Research Institute, Pusan National University, Busan 46241, Republic of Korea;
| | - Kang Eun Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Yu Jin Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Hangoo Kang
- Vessel Operation & Observation Team, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea;
| | - Ji Woo Shin
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
| | - Soohyun Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
| | - Sang Heon Lee
- Department of Oceanography and Marine Research Institute, Pusan National University, Busan 46241, Republic of Korea;
| | - Seung Won Jung
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Taek-Kyun Lee
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
- Ecological Risk Research Department, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
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3
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Gould AL, Henderson JB, Lam AW. Chromosome-Level Genome Assembly of the Bioluminescent Cardinalfish Siphamia tubifer: An Emerging Model for Symbiosis Research. Genome Biol Evol 2022; 14:evac044. [PMID: 35349687 PMCID: PMC9035438 DOI: 10.1093/gbe/evac044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 11/15/2022] Open
Abstract
The bioluminescent symbiosis involving the sea urchin cardinalfish Siphamia tubifer and the luminous bacterium Photobacterium mandapamensis is an emerging vertebrate model for the study of microbial symbiosis. However, little genetic data are available for the host, limiting the scope of research that can be implemented with this association. We present a chromosome-level genome assembly for S. tubifer using a combination of PacBio HiFi sequencing and Hi-C technologies. The final assembly was 1.2 Gb distributed on 23 chromosomes and contained 32,365 protein coding genes with a BUSCO score of 99%. A comparison of the S. tubifer genome to that of another nonluminous species of cardinalfish revealed a high degree of synteny, whereas a comparison to a more distant relative in the sister order Gobiiformes revealed the fusion of two chromosomes in the cardinalfish genomes. The complete mitogenome of S. tubifer was also assembled, and an inversion in the vertebrate WANCY tRNA genes as well as heteroplasmy in the length of the control region were discovered. A phylogenetic analysis based on whole the mitochondrial genome indicated that S. tubifer is divergent from the rest of the cardinalfish family, highlighting the potential role of the bioluminescent symbiosis in the initial divergence of Siphamia. This high-quality reference genome will provide novel opportunities for the bioluminescent S. tubifer-P. mandapamensis association to be used as a model for symbiosis research.
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Affiliation(s)
- A. L. Gould
- Ichthyology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, California 94118, USA
| | - J. B. Henderson
- Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, California 94118, USA
| | - A. W. Lam
- Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, California 94118, USA
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4
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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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Gould AL, Fritts-Penniman A, Gaisiner A. Museum Genomics Illuminate the High Specificity of a Bioluminescent Symbiosis for a Genus of Reef Fish. Front Ecol Evol 2021; 9:630207. [PMID: 34485316 PMCID: PMC8412414 DOI: 10.3389/fevo.2021.630207] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Symbiotic relationships between bioluminescent bacteria and fishes have evolved multiple times across hundreds of fish taxa, but relatively little is known about the specificity of these associations and how stable they are over host generations. This study describes the degree of specificity of a bioluminescent symbiosis between cardinalfishes in the genus Siphamia and luminous bacteria in the Vibrio family. Primarily using museum specimens, we investigated the codivergence of host and symbiont and test for patterns of divergence that correlate with both biogeography and time. Contrary to expectations, we determined that the light organ symbionts of all 14 Siphamia species examined belong to one genetic clade of Photobacterium mandapamensis (Clade II), indicating that the association is highly specific and conserved throughout the host genus. Thus, we did not find evidence of codivergence among hosts and symbionts. We did observe that symbionts hosted by individuals sampled from colder water regions were more divergent, containing more than three times as many single nucleotide polymorphisms than the rest of the symbionts examined. Overall, our findings indicate that the symbiosis between Siphamia fishes and P. mandapamensis Clade II has been highly conserved across host taxa and over a broad geographic range despite the facultative nature of the bacterial symbiont. We also present a new approach to simultaneously recover genetic information from a bacterial symbiont and its vertebrate host from formalin-fixed specimens, enhancing the utility of museum collections.
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Affiliation(s)
- Alison L. Gould
- California Academy of Sciences, San Francisco, CA, United States
| | | | - Ana Gaisiner
- California Academy of Sciences, San Francisco, CA, United States
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Gould AL, Dunlap PV. Shedding Light on Specificity: Population Genomic Structure of a Symbiosis Between a Coral Reef Fish and Luminous Bacterium. Front Microbiol 2019; 10:2670. [PMID: 31824455 PMCID: PMC6879551 DOI: 10.3389/fmicb.2019.02670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/01/2019] [Indexed: 11/13/2022] Open
Abstract
All organisms depend on symbiotic associations with bacteria for their success, yet how these interspecific interactions influence the population structure, ecology, and evolution of microbial symbionts is not well understood. Additionally, patterns of genetic variation in interacting species can reveal ecological traits that are important to gene flow and co-evolution. In this study, we define patterns of spatial and temporal genetic variation of a coral reef fish, Siphamia tubifer, and its luminous bacterial symbiont, Photobacterium mandapamensis in the Okinawa Islands, Japan. Using restriction site-associated sequencing (RAD-Seq) methods, we show that populations of the facultative light organ symbiont of S. tubifer exhibit genetic structure at fine spatial scales of tens of kilometers despite the absence of physical barriers to dispersal and in contrast to populations of the host fish. These results suggest that the host’s behavioral ecology and environmental interactions between host and symbiont help to structure symbiont populations in the region, consequently fostering the specificity of the association between host generations. Our approach also revealed several symbiont genes that were divergent between host populations, including hfq and a homolog of varS, both of which play a role in host association in Vibrio cholerae. Overall, this study highlights the important role that a host animal can play in structuring the distribution of its bacterial symbiont, particularly in highly connected marine environments, thereby promoting specificity of the symbiosis between host generations.
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Affiliation(s)
- Alison L Gould
- Department of Ichthyology, California Academy of Sciences, San Francisco, CA, United States.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Paul V Dunlap
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
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7
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Baker LJ, Freed LL, Easson CG, Lopez JV, Fenolio D, Sutton TT, Nyholm SV, Hendry TA. Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment. eLife 2019; 8:47606. [PMID: 31571583 PMCID: PMC6773444 DOI: 10.7554/elife.47606] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/21/2019] [Indexed: 11/13/2022] Open
Abstract
Deep-sea anglerfishes are relatively abundant and diverse, but their luminescent bacterial symbionts remain enigmatic. The genomes of two symbiont species have qualities common to vertically transmitted, host-dependent bacteria. However, a number of traits suggest that these symbionts may be environmentally acquired. To determine how anglerfish symbionts are transmitted, we analyzed bacteria-host codivergence across six diverse anglerfish genera. Most of the anglerfish species surveyed shared a common species of symbiont. Only one other symbiont species was found, which had a specific relationship with one anglerfish species, Cryptopsaras couesii. Host and symbiont phylogenies lacked congruence, and there was no statistical support for codivergence broadly. We also recovered symbiont-specific gene sequences from water collected near hosts, suggesting environmental persistence of symbionts. Based on these results we conclude that diverse anglerfishes share symbionts that are acquired from the environment, and that these bacteria have undergone extreme genome reduction although they are not vertically transmitted. The deep sea is home to many different species of anglerfish, a group of animals in which females often display a dangling lure on the top of their heads. This organ shelters bacteria that make light, a partnership (known as symbiosis) that benefits both parties. The bacteria get a safe environment in which to grow, while the animal may use the light to confuse predators as well as attract prey and mates. The genetic information of these bacteria has changed since they became associated with their host. Their genomes have become smaller and more specialized, limiting their ability to survive outside of the fish. This phenomenon is also observed in other symbiotic bacteria, but mostly in microorganisms that are directly transmitted from parent to offspring, never having to live on their own. Yet, some evidence suggests that the bacteria in the lure of anglerfish may be spending time in the water until they find a new host, crossing thousands of meters of ocean in the process. To explore this paradox, Baker et al. looked into the type of bacteria carried by different groups of anglerfish. If each type of fish has its own kind of bacteria, this would suggest that the microorganisms are passed from one generation to the next, and are evolving with their hosts. On the other hand, if the same sort of bacteria can be found in different anglerfish species, this would imply that the bacteria pass from host to host and evolve independently from the fish. Genetic data analysis showed that amongst six groups of anglerfishes, one species of bacteria is shared across five groups while another is specific to one type of fish. The analyses also revealed that anglerfish and their bacteria are most likely not evolving together. This means that the bacteria must make the difficult journey from host to host by persisting in the deep sea, which was confirmed by finding the genetic information of these bacteria in the water near the fish. Anglerfish and the bacteria that light up their lure are hard to study, as they live so deep in the ocean. In fact, many symbiotic relationships are equally difficult to investigate. Examining genetic information can help to give an insight into how hosts and bacteria interact across the tree of life.
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Affiliation(s)
- Lydia J Baker
- Department of Microbiology, Cornell University, New York, United States
| | - Lindsay L Freed
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States
| | - Cole G Easson
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States.,Department of Biology, Middle Tennessee State University, Murfreesboro, United States
| | - Jose V Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States
| | - Danté Fenolio
- Center for Conservation and Research, San Antonio Zoo, San Antonio, United States
| | - Tracey T Sutton
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States
| | - Spencer V Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States
| | - Tory A Hendry
- Department of Microbiology, Cornell University, New York, United States
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8
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Abstract
Phylogenetic relationships between species in the genus Photobacterium have been poorly studied despite pathogenic and ecological relevance of some of its members. This is the first phylogenetic study that includes new species of Photobacterium (validated or not) that have not been included in any of the previously described clades, using 16S rRNA sequences and multilocus sequence analysis (MLSA) in concatenated sequences of gyrB, gapA, topA, ftsZ and mreB housekeeping genes. Sequence analysis has been implemented using Maximum-parsimony (MP), Neighbour-joining (NJ) and Maximum likelihood (ML) treeing methods and the predicted evolutionary relationship between the Photobacterium clades was established on the basis of bootstrap values of >75% for 16S rRNA sequences and MLSA. We have grouped 22 species of the genus Photobacterium into the following 5 clades: Phosphoreum (comprises P. aquimaris, “P. carnosum,” P. iliopiscarium, P. kishitanii, P. phosphoreum, “P. piscicola” and “P. toruni”); clade Profundum (composed of P. aestuarii, P. alginatilyticum, P. frigidiphilum, P. indicum, P. jeanii, P. lipolyticum, “P. marinum,” and P. profundum); clade Damselae (two subspecies of P. damselae, damselae and piscicida); and two new clades: clade Ganghwense (includes P. aphoticum, P. aquae, P. galatheae, P. ganghwense, P. halotolerans, P. panuliri and P. proteolyticum); and clade Leiognathi (composed by P. angustum, P. leiognathi subsp. leiognathi and “P. leiognathi subsp. mandapamensis”). Two additional clades, Rosenbergii and Swingsii, were formed using a phylogenetic method based on 16S rRNA gene, although they are not confirmed by any MLSA methods. Only P. aplysiae could not be included in none of the established clade, constituting an orphan clade.
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Affiliation(s)
- Alejandro M Labella
- Department of Microbiology, Faculty of Sciences, Universidad de Malaga, 29071 Malaga, Spain.
| | - M Dolores Castro
- Department of Microbiology, Faculty of Sciences, Universidad de Malaga, 29071 Malaga, Spain.
| | - Manuel Manchado
- Puerto de Santa María, Junta de Andalucía, IFAPA Centro El Toruño, 11500 Cadiz, Spain.
| | - Juan J Borrego
- Department of Microbiology, Faculty of Sciences, Universidad de Malaga, 29071 Malaga, Spain.
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Gould AL, Dunlap PV. Genomic analysis of a cardinalfish with larval homing potential reveals genetic admixture in the Okinawa Islands. Mol Ecol 2017; 26:3870-3882. [DOI: 10.1111/mec.14169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 04/05/2017] [Accepted: 04/25/2017] [Indexed: 01/12/2023]
Affiliation(s)
- A. L. Gould
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI USA
| | - P. V. Dunlap
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI USA
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10
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Moi IM, Roslan NN, Leow ATC, Ali MSM, Rahman RNZRA, Rahimpour A, Sabri S. The biology and the importance of Photobacterium species. Appl Microbiol Biotechnol 2017; 101:4371-4385. [PMID: 28497204 DOI: 10.1007/s00253-017-8300-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 10/19/2022]
Abstract
Photobacterium species are Gram-negative coccobacilli which are distributed in marine habitats worldwide. Some species are unique because of their capability to produce luminescence. Taxonomically, about 23 species and 2 subspecies are validated to date. Genomes from a few Photobacterium spp. have been sequenced and studied. They are considered a special group of bacteria because some species are capable of producing essential polyunsaturated fatty acids, antibacterial compounds, lipases, esterases and asparaginases. They are also used as biosensors in food and environmental monitoring and detectors of drown victim, as well as an important symbiont.
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Affiliation(s)
- Ibrahim Musa Moi
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Bauchi State University Gadau, P.M.B. O65, Bauchi, Bauchi State, Nigeria
| | - Noordiyanah Nadhirah Roslan
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Azam Rahimpour
- Department of Tissue Engineering and Regenerative Medicine, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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11
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Zhang SD, Santini CL, Zhang WJ, Barbe V, Mangenot S, Guyomar C, Garel M, Chen HT, Li XG, Yin QJ, Zhao Y, Armengaud J, Gaillard JC, Martini S, Pradel N, Vidaud C, Alberto F, Médigue C, Tamburini C, Wu LF. Genomic and physiological analysis reveals versatile metabolic capacity of deep-sea Photobacterium phosphoreum ANT-2200. Extremophiles 2016; 20:301-10. [PMID: 27039108 DOI: 10.1007/s00792-016-0822-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/01/2016] [Indexed: 10/22/2022]
Abstract
Bacteria of the genus Photobacterium thrive worldwide in oceans and show substantial eco-physiological diversity including free-living, symbiotic and piezophilic life styles. Genomic characteristics underlying this variability across species are poorly understood. Here we carried out genomic and physiological analysis of Photobacterium phosphoreum strain ANT-2200, the first deep-sea luminous bacterium of which the genome has been sequenced. Using optical mapping we updated the genomic data and reassembled it into two chromosomes and a large plasmid. Genomic analysis revealed a versatile energy metabolic potential and physiological analysis confirmed its growth capacity by deriving energy from fermentation of glucose or maltose, by respiration with formate as electron donor and trimethlyamine N-oxide (TMAO), nitrate or fumarate as electron acceptors, or by chemo-organo-heterotrophic growth in rich media. Despite that it was isolated at a site with saturated dissolved oxygen, the ANT-2200 strain possesses four gene clusters coding for typical anaerobic enzymes, the TMAO reductases. Elevated hydrostatic pressure enhances the TMAO reductase activity, mainly due to the increase of isoenzyme TorA1. The high copy number of the TMAO reductase isoenzymes and pressure-enhanced activity might imply a strategy developed by bacteria to adapt to deep-sea habitats where the instant TMAO availability may increase with depth.
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Affiliation(s)
- Sheng-Da Zhang
- Deep-Sea Microbial Cell Biology, Department of Deep Sea Sciences, Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China
| | - Claire-Lise Santini
- LCB UMR 7257, Aix-Marseille Université, CNRS, IMM, 31, Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.,France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China
| | - Wei-Jia Zhang
- Deep-Sea Microbial Cell Biology, Department of Deep Sea Sciences, Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China
| | | | | | - Charlotte Guyomar
- LCB UMR 7257, Aix-Marseille Université, CNRS, IMM, 31, Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.,France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China
| | - Marc Garel
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM110, 13288, Marseille, France
| | - Hai-Tao Chen
- Deep-Sea Microbial Cell Biology, Department of Deep Sea Sciences, Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China
| | - Xue-Gong Li
- Deep-Sea Microbial Cell Biology, Department of Deep Sea Sciences, Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China
| | - Qun-Jian Yin
- Deep-Sea Microbial Cell Biology, Department of Deep Sea Sciences, Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China
| | - Yuan Zhao
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | | | - Séverine Martini
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM110, 13288, Marseille, France
| | - Nathalie Pradel
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM110, 13288, Marseille, France
| | | | - François Alberto
- LCB UMR 7257, Aix-Marseille Université, CNRS, IMM, 31, Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.,France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China
| | - Claudine Médigue
- Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, CEA/DSV/IG/Genoscope and CNRS-UMR 8030 and Univ. Evry Val d'Esssone, Evry, France
| | - Christian Tamburini
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM110, 13288, Marseille, France
| | - Long-Fei Wu
- LCB UMR 7257, Aix-Marseille Université, CNRS, IMM, 31, Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France. .,France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China.
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12
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Dunn AK, Rader BA, Stabb EV, Mandel MJ. Regulation of Bioluminescence in Photobacterium leiognathi Strain KNH6. J Bacteriol 2015; 197:3676-85. [PMID: 26350139 PMCID: PMC4626902 DOI: 10.1128/jb.00524-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/03/2015] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED Bacterial bioluminescence is taxonomically restricted to certain proteobacteria, many of which belong to the Vibrionaceae. In the most well-studied cases, pheromone signaling plays a key role in regulation of light production. However, previous reports have indicated that certain Photobacterium strains do not use this regulatory method for controlling luminescence. In this study, we combined genome sequencing with genetic approaches to characterize the regulation of luminescence in Photobacterium leiognathi strain KNH6, an extremely bright isolate. Using transposon mutagenesis and screening for decreased luminescence, we identified insertions in genes encoding components necessary for the luciferase reaction (lux, lum, and rib operons) as well as in nine other loci. These additional loci encode gene products predicted to be involved in the tricarboxylic acid (TCA) cycle, DNA and RNA metabolism, transcriptional regulation, and the synthesis of cytochrome c, peptidoglycan, and fatty acids. The mutagenesis screen did not identify any mutants with disruptions of predicted pheromone-related loci. Using targeted gene insertional disruptions, we demonstrate that under the growth conditions tested, luminescence levels do not appear to be controlled through canonical pheromone signaling systems in this strain. IMPORTANCE Despite the long-standing interest in luminous bacteria, outside a few model organisms, little is known about the regulation and function of luminescence. Light-producing marine bacteria are widely distributed and have diverse lifestyles, suggesting that the control and significance of luminescence may be similarly diverse. In this study, we apply genetic tools to the study of regulation of light production in the extremely bright isolate Photobacterium leiognathi KNH6. Our results suggest an unusual lack of canonical pheromone-mediated control of luminescence and contribute to a better understanding of alternative strategies for regulation of a key bacterial behavior. These experiments lay the groundwork for further study of the regulation and role of bioluminescence in P. leiognathi.
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Affiliation(s)
- Anne K Dunn
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Bethany A Rader
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Eric V Stabb
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Mark J Mandel
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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13
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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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14
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Theodore CM, Lorig-Roach N, Still PC, Johnson TA, Drašković M, Schwochert JA, Naphen CN, Crews MS, Barker SA, Valeriote FA, Lokey RS, Crews P. Biosynthetic products from a nearshore-derived gram-negative bacterium enable reassessment of the kailuin depsipeptides. JOURNAL OF NATURAL PRODUCTS 2015; 78:441-52. [PMID: 25699470 PMCID: PMC4699550 DOI: 10.1021/np500840n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Sampling of California nearshore sediments resulted in the isolation of a Gram-negative bacterium, Photobacterium halotolerans, capable of producing unusual biosynthetic products. Liquid culture in artificial seawater-based media provided cyclic depsipeptides including four known compounds, kailuins B-E (2-5), and two new analogues, kailuins G and H (7 and 8). The structures of the new and known compounds were confirmed through extensive spectroscopic and Marfey's analyses. During the course of these studies, a correction was made to the previously reported double-bond geometry of kailuin D (4). Additionally, through the application of a combination of derivatization with Mosher's reagent and extensive (13)C NMR shift analysis, the previously unassigned chiral center at position C-3 of the β-acyloxy group of all compounds was determined. To evaluate bioactivity and structure-activity relationships, the kailuin core (13) and kailuin lactam (14) were prepared by chiral synthesis using an Fmoc solid-phase peptide strategy followed by solution-phase cyclization. All isolated compounds and synthetic cores were assayed for solid tumor cell cytotoxicity and showed only minimal activity, contrary to other published reports. Additional phenotypic screenings were done on 4 and 5, with little evidence of activity.
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Affiliation(s)
- Christine M. Theodore
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Nicholas Lorig-Roach
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Patrick C. Still
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Tyler A. Johnson
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Marija Drašković
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Joshua A. Schwochert
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Cassandra N. Naphen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Mitchell S. Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Simone A. Barker
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Frederick A. Valeriote
- Josephine Ford Cancer Center, Henry Ford Health System, Detroit, Michigan 48202, United States
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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15
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Amaral GRS, Campeão ME, Swings J, Thompson FL, Thompson CC. Finding diagnostic phenotypic features of Photobacterium in the genome sequences. Antonie van Leeuwenhoek 2015; 107:1351-8. [PMID: 25724129 DOI: 10.1007/s10482-015-0414-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 02/23/2015] [Indexed: 01/14/2023]
Abstract
Photobacterium species are ubiquitous in the aquatic environment and can be found in association with animal hosts including pathogenic and mutualistic associations. The traditional phenotypic characterization of Photobacterium is expensive, time-consuming and restricted to a limited number of features. An alternative is to infer phenotypic information directly from whole genome sequences. The present study evaluates the usefulness of whole genome sequences as a source of phenotypic information and compares diagnostic phenotypes of the Photobacterium species from the literature with the predicted phenotypes obtained from whole genome sequences. All genes coding for the specific proteins involved in metabolic pathways responsible for positive phenotypes of the seventeen diagnostic features were found in the majority of the Photobacterium genomes. In the Photobacterium species that were negative for a given phenotype, at least one or several genes involved in the respective biochemical pathways were absent.
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Affiliation(s)
- Gilda Rose S Amaral
- Laboratory for Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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16
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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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17
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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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18
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Hendry TA, de Wet JR, Dunlap PV. Genomic signatures of obligate host dependence in the luminous bacterial symbiont of a vertebrate. Environ Microbiol 2013; 16:2611-22. [DOI: 10.1111/1462-2920.12302] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 10/01/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Tory A. Hendry
- Department of Ecology and Evolutionary Biology; University of Michigan; 830 North University Ave. Ann Arbor MI 48109-1048 USA
| | - Jeffrey R. de Wet
- Department of Computational Medicine and Bioinformatics; University of Michigan Medical School; 100 Washtenaw Ave. Ann Arbor MI 48109-2218 USA
| | - Paul V. Dunlap
- Department of Ecology and Evolutionary Biology; University of Michigan; 830 North University Ave. Ann Arbor MI 48109-1048 USA
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19
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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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20
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Dunlap PV, Gould AL, Wittenrich ML, Nakamura M. Symbiosis initiation in the bacterially luminous sea urchin cardinalfish Siphamia versicolor. JOURNAL OF FISH BIOLOGY 2012; 81:1340-1356. [PMID: 22957874 DOI: 10.1111/j.1095-8649.2012.03415.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
To determine how each new generation of the sea urchin cardinalfish Siphamia versicolor acquires the symbiotic luminous bacterium Photobacterium mandapamensis, and when in its development the S. versicolor initiates the symbiosis, procedures were established for rearing S. versicolor larvae in an aposymbiotic state. Under the conditions provided, larvae survived and developed for 28 days after their release from the mouths of males. Notochord flexion began at 8 days post release (dpr). By 28 dpr, squamation was evident and the caudal complex was complete. The light organ remained free of bacteria but increased in size and complexity during development of the larvae. Thus, aposymbiotic larvae of the fish can survive and develop for extended periods, major components of the luminescence system develop in the absence of the bacteria and the bacteria are not acquired directly from a parent, via the egg or during mouth brooding. Presentation of the symbiotic bacteria to aposymbiotic larvae at 8-10 dpr, but not earlier, led to initiation of the symbiosis. Upon colonization of the light organ, the bacterial population increased rapidly and cells forming the light-organ chambers exhibited a differentiated appearance. Therefore, the light organ apparently first becomes receptive to colonization after 1 week post-release development, the symbiosis is initiated by bacteria acquired from the environment and bacterial colonization induces morphological changes in the nascent light organ. The abilities to culture larvae of S. versicolor for extended periods and to initiate the symbiosis in aposymbiotic larvae are key steps in establishing the experimental tractability of this highly specific vertebrate and microbe mutualism.
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Affiliation(s)
- P V Dunlap
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA.
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21
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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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22
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Nelson OW, Garrity GM. Genome sequences published outside of Standards in Genomic Sciences, January – June 2011. Stand Genomic Sci 2011. [DOI: 10.4056/sigs.2044675] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
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