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Kise H, Eduarda Alves Santos M, Julie Loïs Fourreau C, Iguchi A, Goto R, Davis Reimer J. Evolutionary patterns of host switching, lifestyle mode, and the diversification history in symbiotic zoantharians. Mol Phylogenet Evol 2023; 182:107732. [PMID: 36781031 DOI: 10.1016/j.ympev.2023.107732] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/26/2023] [Accepted: 02/09/2023] [Indexed: 02/13/2023]
Abstract
Symbioses play important roles in forming the structural and distributional patterns of marine diversity. Understanding how interspecies interactions through symbioses contribute to biodiversity is an essential topic. Host switching has been considered as one of the main drivers of diversification in symbiotic systems. However, its process and patterns remain poorly investigated in the marine realm. Hexacoral species of the order Zoantharia (=zoantharians) are often epizoic on other marine invertebrates and generally use specific taxa as hosts. The present study investigates the patterns of host switching and the diversification history of zoantharians based on the most comprehensive molecular phylogenetic analyses to date, using sequences from three mitochondrial and three nuclear markers from representatives of 27 of 29 genera. Our results indicate that symbiotic zoantharians, in particular those within suborder Macrocnemina, diversified through repeated host switching. In addition, colonization of new host taxa appears to have driven morphological and ecological specialization in zoantharians. These findings have important implications for understanding the role of symbioses in the morphological and ecological evolution of marine invertebrates.
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Affiliation(s)
- Hiroki Kise
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan; Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan.
| | - Maria Eduarda Alves Santos
- Okinawa Institute of Science and Technology Graduate University, Evolution, Cell Biology, and Symbiosis Unit, Okinawa 904-0495, Japan
| | - Chloé Julie Loïs Fourreau
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan; Research Laboratory on Environmentally-conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan
| | - Ryutaro Goto
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, 459 Shirahama, Nishimuro, Wakayama 649-2211, Japan
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan; Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
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Manthey JD, Girón JC, Hruska JP. Impact of host demography and evolutionary history on endosymbiont molecular evolution: A test in carpenter ants (genus Camponotus) and their Blochmannia endosymbionts. Ecol Evol 2022; 12:e9026. [PMID: 35795355 PMCID: PMC9251289 DOI: 10.1002/ece3.9026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 11/28/2022] Open
Abstract
Obligate endosymbioses are tight associations between symbionts and the hosts they live inside. Hosts and their associated obligate endosymbionts generally exhibit codiversification, which has been documented in taxonomically diverse insect lineages. Host demography (e.g., effective population sizes) may impact the demography of endosymbionts, which may lead to an association between host demography and the patterns and processes of endosymbiont molecular evolution. Here, we used whole-genome sequencing data for carpenter ants (Genus Camponotus; subgenera Camponotus and Tanaemyrmex) and their Blochmannia endosymbionts as our study system to address whether Camponotus demography shapes Blochmannia molecular evolution. Using whole-genome phylogenomics, we confirmed previous work identifying codiversification between carpenter ants and their Blochmannia endosymbionts. We found that Blochmannia genes have evolved at a pace ~30× faster than that of their hosts' molecular evolution and that these rates are positively associated with host rates of molecular evolution. Using multiple tests for selection in Blochmannia genes, we found signatures of positive selection and shifts in selection strength across the phylogeny. Host demography was associated with Blochmannia shifts toward increased selection strengths, but not associated with Blochmannia selection relaxation, positive selection, genetic drift rates, or genome size evolution. Mixed support for relationships between host effective population sizes and Blochmannia molecular evolution suggests weak or uncoupled relationships between host demography and Blochmannia population genomic processes. Finally, we found that Blochmannia genome size evolution was associated with genome-wide estimates of genetic drift and number of genes with relaxed selection pressures.
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Affiliation(s)
- Joseph D. Manthey
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
| | - Jennifer C. Girón
- Department of EntomologyPurdue UniversityWest LafayetteIndianaUSA
- Natural Science Research LaboratoryMuseum of Texas Tech UniversityLubbockTexasUSA
| | - Jack P. Hruska
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
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Matos A, Antunes A. Symbiotic Associations in Ascidians: Relevance for Functional Innovation and Bioactive Potential. Mar Drugs 2021; 19:370. [PMID: 34206769 PMCID: PMC8303170 DOI: 10.3390/md19070370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 12/22/2022] Open
Abstract
Associations between different organisms have been extensively described in terrestrial and marine environments. These associations are involved in roles as diverse as nutrient exchanges, shelter or adaptation to adverse conditions. Ascidians are widely dispersed marine invertebrates associated to invasive behaviours. Studying their microbiomes has interested the scientific community, mainly due to its potential for bioactive compounds production-e.g., ET-73 (trabectedin, Yondelis), an anticancer drug. However, these symbiotic interactions embrace several environmental and biological functions with high ecological relevance, inspiring diverse biotechnological applications. We thoroughly reviewed microbiome studies (microscopic to metagenomic approaches) of around 171 hosts, worldwide dispersed, occurring at different domains of life (Archaea, Bacteria, Eukarya), to illuminate the functions and bioactive potential of associated organisms in ascidians. Associations with Bacteria are the most prevalent, namely with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria and Planctomycetes phyla. The microbiomes of ascidians belonging to Aplousobranchia order have been the most studied. The integration of worldwide studies characterizing ascidians' microbiome composition revealed several functions including UV protection, bioaccumulation of heavy metals and defense against fouling or predators through production of natural products, chemical signals or competition. The critical assessment and characterization of these communities is extremely valuable to comprehend their biological/ecological role and biotechnological potential.
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Affiliation(s)
- Ana Matos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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The Bacterial Enhancer Binding Protein VasH Promotes Expression of a Type VI Secretion System in Vibrio fischeri during Symbiosis. J Bacteriol 2020; 202:JB.00777-19. [PMID: 31964698 DOI: 10.1128/jb.00777-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/13/2020] [Indexed: 11/20/2022] Open
Abstract
Vibrio fischeri is a bacterial symbiont that colonizes the light organ of the Hawaiian bobtail squid, Euprymna scolopes Certain strains of V. fischeri express a type VI secretion system (T6SS), which delivers effectors into neighboring cells that result in their death. Strains that are susceptible to the T6SS fail to establish symbiosis with a T6SS-positive strain within the same location of the squid light organ, which is a phenomenon termed strain incompatibility. This study investigates the regulation of the T6SS in V. fischeri strain FQ-A001. Here, we report that the expression of Hcp, a necessary structural component of the T6SS, depends on the alternative sigma factor σ54 and the bacterial enhancer binding protein VasH. VasH is necessary for FQ-A001 to kill other strains, suggesting that VasH-dependent regulation is essential for the T6SS of V. fischeri to affect intercellular interactions. In addition, this study demonstrates VasH-dependent transcription of hcp within host-associated populations of FQ-A001, suggesting that the T6SS is expressed within the host environment. Together, these findings establish a model for transcriptional control of hcp in V. fischeri within the squid light organ, thereby increasing understanding of how the T6SS is regulated during symbiosis.IMPORTANCE Animals harbor bacterial symbionts with specific traits that promote host fitness. Mechanisms that facilitate intercellular interactions among bacterial symbionts impact which bacterial lineages ultimately establish symbiosis with the host. How these mechanisms are regulated is poorly characterized in nonhuman bacterial symbionts. This study establishes a model for the transcriptional regulation of a contact-dependent killing machine, thereby increasing understanding of mechanisms by which different strains compete while establishing symbiosis.
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Forte FP, Schmid J, Dijkwel PP, Nagy I, Hume DE, Johnson RD, Simpson WR, Monk SM, Zhang N, Sehrish T, Asp T. Fungal Endophyte Colonization Patterns Alter Over Time in the Novel Association Between Lolium perenne and Epichloë Endophyte AR37. FRONTIERS IN PLANT SCIENCE 2020; 11:570026. [PMID: 33193501 PMCID: PMC7658011 DOI: 10.3389/fpls.2020.570026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/22/2020] [Indexed: 05/16/2023]
Abstract
Infection of the pasture grass Lolium perenne with the seed-transmitted fungal endophyte Epichloë festucae enhances its resilience to biotic and abiotic stress. Agricultural benefits of endophyte infection can be increased by generating novel symbiotic associations through inoculating L. perenne with selected Epichloë strains. Natural symbioses have coevolved over long periods. Thus, artificial symbioses will probably not have static properties, but symbionts will coadapt over time improving the fitness of the association. Here we report for the first time on temporal changes in a novel association of Epichloë strain AR37 and the L. perenne cultivar Grasslands Samson. Over nine generations, a seed maintenance program had increased the endophyte seed transmission rates to > 95% (from an initial 76%). We observed an approximately fivefold decline in endophyte biomass concentration in vegetative tissues over time (between generations 2 and 9). This indicates strong selection pressure toward reducing endophyte-related fitness costs by reducing endophyte biomass, without compromising the frequency of endophyte transmission to seed. We observed no obvious changes in tillering and only minor transcriptomic changes in infected plants over time. Functional analysis of 40 plant genes, showing continuously decreasing expression over time, suggests that adaptation of host metabolism and defense mechanisms are important for increasing the fitness of this association, and possibly fitness of such symbioses in general. Our results indicate that fitness of novel associations is likely to improve over time and that monitoring changes in novel associations can assist in identifying key features of endophyte-mediated enhancement of host fitness.
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Affiliation(s)
- Flavia Pilar Forte
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- *Correspondence: Flavia Pilar Forte,
| | - Jan Schmid
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Ferguson Street Laboratories, Palmerston North, New Zealand
| | - Paul P. Dijkwel
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
| | - David E. Hume
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Wayne R. Simpson
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Ningxin Zhang
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Tina Sehrish
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
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Ibarra-Juarez LA, Desgarennes D, Vázquez-Rosas-Landa M, Villafan E, Alonso-Sánchez A, Ferrera-Rodríguez O, Moya A, Carrillo D, Cruz L, Carrión G, López-Buenfil A, García-Avila C, Ibarra-Laclette E, Lamelas A. Impact of Rearing Conditions on the Ambrosia Beetle's Microbiome. Life (Basel) 2018; 8:E63. [PMID: 30551580 PMCID: PMC6316638 DOI: 10.3390/life8040063] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 02/07/2023] Open
Abstract
Ambrosia beetles, along with termites and leafcutter ants, are the only fungus-farming lineages within the tree of life. Bacteria harbored by ambrosia beetles may play an essential role in the nutritional symbiotic interactions with their associated fungi; however, little is known about the impact of rearing conditions on the microbiota of ambrosia beetles. We have used culture-independent methods to explore the effect of rearing conditions on the microbiome associated with Xyleborus affinis, Xyleborus bispinatus, and Xyleborus volvulus, evaluating different media in laboratory-controlled conditions and comparing wild and laboratory conditions. Our results revealed that rearing conditions affected the fungal and bacterial microbiome structure and had a strong influence on bacterial metabolic capacities. We propose that the rearing conditions influence the ambrosia-associated fungal and bacterial communities. Furthermore, bacterial microbiome flexibility may help beetles adapt to different substrates.
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Affiliation(s)
- Luis Arturo Ibarra-Juarez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa C.P. 91070, Mexico.
- Cátedras CONACyT. Instituto de Ecología, A. C., Carretera Antigua a Coatepec 351, Xalapa C.P. 91070, Mexico.
| | - Damaris Desgarennes
- Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa C.P. 91070, Mexico.
| | | | - Emanuel Villafan
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa C.P. 91070, Mexico.
| | | | | | - Andrés Moya
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO), 46010 Valencia, Spain.
- Institute for Integrative System Biology, University of Valencia-CSIC, 46010 Valencia, Spain.
| | - Daniel Carrillo
- Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA.
| | - Luisa Cruz
- Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA.
| | - Gloria Carrión
- Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa C.P. 91070, Mexico.
| | - Abel López-Buenfil
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Unidad Integral de Diagnóstico, Servicios y Constatación, Tecámac, Estado de Mexico 55740, Mexico.
| | - Clemente García-Avila
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Unidad Integral de Diagnóstico, Servicios y Constatación, Tecámac, Estado de Mexico 55740, Mexico.
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa C.P. 91070, Mexico.
| | - Araceli Lamelas
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa C.P. 91070, Mexico.
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In Memoriam. Proc (Bayl Univ Med Cent) 2017. [DOI: 10.1080/08998280.2017.11929632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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The role of symbiosis in the transition of some eukaryotes from aquatic to terrestrial environments. Symbiosis 2015. [DOI: 10.1007/s13199-015-0321-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Focal point theory models for dissecting dynamic duality problems of microbial infections. J Biomed Biotechnol 2008; 2008:856314. [PMID: 18350122 PMCID: PMC2266975 DOI: 10.1155/2008/856314] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Accepted: 12/19/2007] [Indexed: 12/13/2022] Open
Abstract
Extending along the dynamic continuum from conflict to cooperation, microbial infections always involve symbiosis (Sym) and pathogenesis (Pat). There exists a dynamic Sym-Pat duality (DSPD) in microbial infection that is the most fundamental problem in infectomics. DSPD is encoded by the genomes of both the microbes and their hosts. Three focal point (FP) theory-based game models (pure cooperative, dilemma, and pure conflict) are proposed for resolving those problems. Our health is associated with the dynamic interactions of three microbial communities (nonpathogenic microbiota (NP) (Cooperation), conditional pathogens (CP) (Dilemma), and unconditional pathogens (UP) (Conflict)) with the hosts at different health statuses. Sym and Pat can be quantitated by measuring symbiotic index (SI), which is quantitative fitness for the symbiotic partnership, and pathogenic index (PI), which is quantitative damage to the symbiotic partnership, respectively. Symbiotic point (SP), which bears analogy to FP, is a function of SI and PI. SP-converting and specific pathogen-targeting strategies can be used for the rational control of microbial infections.
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