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Pérez-Ferrer PA, Ashraf M, Rodrigues M, Troncoso J, Nishiguchi MK. Genetic Variation in the Atlantic Bobtail Squid-Vibrio Symbiosis From the Galician Rías. Mol Ecol 2025; 34:e17596. [PMID: 39625066 DOI: 10.1111/mec.17596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 09/25/2024] [Accepted: 10/10/2024] [Indexed: 12/24/2024]
Abstract
Symbiotic marine bacteria that are transmitted through the environment are susceptible to abiotic factors (salinity, temperature, physical barriers) that can influence their ability to colonize their specific hosts. Given that many symbioses are driven by host specificity, environmentally transmitted symbionts are more susceptible to extrinsic factors depending on conditions over space and time. In order to determine whether the population structure of environmentally transmitted symbionts reflects host specificity or biogeography, we analysed the genetic structure of Sepiola atlantica (Cephalopoda: Sepiolidae) and their Vibrio symbionts (V. fischeri and V. logei) in four Galician Rías (Spain). This geographical location is characterized by a jagged coastline with a deep-sea entrance into the land, ideal for testing whether such population barriers exist due to genetic isolation. We used haplotype estimates combined with nested clade analysis to determine the genetic relatedness for both S. atlantica and Vibrio bacteria. Analyses of molecular variance (AMOVA) were used to estimate variation within and between populations for both host and symbiont genetic data. Our analyses reveal a low percentage of variation among and between host populations, suggesting that these populations are panmictic. In contrast, Vibrio symbiont populations show certain degree of genetic structure, demonstrating that the hydrology of the rías is driving bacterial distribution (and not host specificity). Thus, for environmentally transmitted symbioses such as the sepiolid squid-Vibrio association, abiotic factors can be a major selective force for determining population structure for one of the partners.
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Affiliation(s)
- P A Pérez-Ferrer
- Department of Molecular and Cell Biology, Quantitative Systems Biology, University of California Merced, Merced, California, USA
| | - M Ashraf
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
| | - M Rodrigues
- Brookes Bell LLP, Liverpool, UK
- Universidad de Vigo, Vigo, Spain
| | | | - M K Nishiguchi
- Department of Molecular and Cell Biology, Quantitative Systems Biology, University of California Merced, Merced, California, USA
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
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2
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Brockhurst MA, Cameron DD, Beckerman AP. Fitness trade-offs and the origins of endosymbiosis. PLoS Biol 2024; 22:e3002580. [PMID: 38607979 PMCID: PMC11014431 DOI: 10.1371/journal.pbio.3002580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024] Open
Abstract
Endosymbiosis drives evolutionary innovation and underpins the function of diverse ecosystems. The mechanistic origins of symbioses, however, remain unclear, in part because early evolutionary events are obscured by subsequent evolution and genetic drift. This Essay highlights how experimental studies of facultative, host-switched, and synthetic symbioses are revealing the important role of fitness trade-offs between within-host and free-living niches during the early-stage evolution of new symbiotic associations. The mutational targets underpinning such trade-offs are commonly regulatory genes, such that single mutations have major phenotypic effects on multiple traits, thus enabling and reinforcing the transition to a symbiotic lifestyle.
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Affiliation(s)
- Michael A. Brockhurst
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Duncan D. Cameron
- Department of Environmental and Earth Sciences, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
| | - Andrew P. Beckerman
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, United Kingdom
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3
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Baden T, Briseño J, Coffing G, Cohen-Bodénès S, Courtney A, Dickerson D, Dölen G, Fiorito G, Gestal C, Gustafson T, Heath-Heckman E, Hua Q, Imperadore P, Kimbara R, Król M, Lajbner Z, Lichilín N, Macchi F, McCoy MJ, Nishiguchi MK, Nyholm SV, Otjacques E, Pérez-Ferrer PA, Ponte G, Pungor JR, Rogers TF, Rosenthal JJC, Rouressol L, Rubas N, Sanchez G, Santos CP, Schultz DT, Seuntjens E, Songco-Casey JO, Stewart IE, Styfhals R, Tuanapaya S, Vijayan N, Weissenbacher A, Zifcakova L, Schulz G, Weertman W, Simakov O, Albertin CB. Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology. Integr Comp Biol 2023; 63:1226-1239. [PMID: 37370232 PMCID: PMC10755191 DOI: 10.1093/icb/icad087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Few animal groups can claim the level of wonder that cephalopods instill in the minds of researchers and the general public. Much of cephalopod biology, however, remains unexplored: the largest invertebrate brain, difficult husbandry conditions, and complex (meta-)genomes, among many other things, have hindered progress in addressing key questions. However, recent technological advancements in sequencing, imaging, and genetic manipulation have opened new avenues for exploring the biology of these extraordinary animals. The cephalopod molecular biology community is thus experiencing a large influx of researchers, emerging from different fields, accelerating the pace of research in this clade. In the first post-pandemic event at the Cephalopod International Advisory Council (CIAC) conference in April 2022, over 40 participants from all over the world met and discussed key challenges and perspectives for current cephalopod molecular biology and evolution. Our particular focus was on the fields of comparative and regulatory genomics, gene manipulation, single-cell transcriptomics, metagenomics, and microbial interactions. This article is a result of this joint effort, summarizing the latest insights from these emerging fields, their bottlenecks, and potential solutions. The article highlights the interdisciplinary nature of the cephalopod-omics community and provides an emphasis on continuous consolidation of efforts and collaboration in this rapidly evolving field.
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Affiliation(s)
- Tom Baden
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - John Briseño
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Gabrielle Coffing
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Sophie Cohen-Bodénès
- Laboratoire des Systèmes Perceptifs, Département d'Etudes Cognitives, Ecole Normale Supérieure, PSL University, CNRS, 75005 Paris, France
| | - Amy Courtney
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Dominick Dickerson
- Friday Harbor Laboratory, University of Washington, Seattle, WA 98250, USA
| | - Gül Dölen
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Camino Gestal
- Laboratory of Marine Molecular Pathobiology, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo 36208, Spain
| | | | - Elizabeth Heath-Heckman
- Departments of Integrative Biology and Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Qiaz Hua
- Department of Ecology and Evolution, University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Ryosuke Kimbara
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Kanagawa 238-0225, Japan
| | - Mirela Król
- Adam Mickiewicz University in Poznań, Poznań 61-712, Poland
| | - Zdeněk Lajbner
- Physics and Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan
| | - Nicolás Lichilín
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Filippo Macchi
- Program in Biology, New York University Abu Dhabi, P.O. Box 129188 Abu Dhabi, United Arab Emirates
| | - Matthew J McCoy
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Michele K Nishiguchi
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 N. Lake Blvd., Merced, CA 95343, USA
| | - Spencer V Nyholm
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Eve Otjacques
- MARE—Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal
- Division of Biosphere Sciences and Engineering, Carnegie Institution for Science, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Pedro Antonio Pérez-Ferrer
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 N. Lake Blvd., Merced, CA 95343, USA
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Judit R Pungor
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Thea F Rogers
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Joshua J C Rosenthal
- Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA 02543-1015, USA
| | - Lisa Rouressol
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Noelle Rubas
- Department of Molecular Biosciences and Bioengineering, University of Hawaii Manoa, Honolulu, HI 96822, USA
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Catarina Pereira Santos
- MARE—Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal
| | - Darrin T Schultz
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Jeremea O Songco-Casey
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Ian Erik Stewart
- Neural Circuits and Behaviour Lab, Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin 13125, Germany
| | - Ruth Styfhals
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Surangkana Tuanapaya
- Laboratory of genetics and applied breeding of molluscs, Fisheries College, Ocean University of China, Qingdao 266100, China
| | - Nidhi Vijayan
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | | | - Lucia Zifcakova
- Physics and Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan
| | | | - Willem Weertman
- Friday Harbor Laboratory, University of Washington, Seattle, WA 98250, USA
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Caroline B Albertin
- Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA 02543-1015, USA
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4
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Soto W. Emerging Research Topics in the Vibrionaceae and the Squid- Vibrio Symbiosis. Microorganisms 2022; 10:microorganisms10101946. [PMID: 36296224 PMCID: PMC9607633 DOI: 10.3390/microorganisms10101946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022] Open
Abstract
The Vibrionaceae encompasses a cosmopolitan group that is mostly aquatic and possesses tremendous metabolic and genetic diversity. Given the importance of this taxon, it deserves continued and deeper research in a multitude of areas. This review outlines emerging topics of interest within the Vibrionaceae. Moreover, previously understudied research areas are highlighted that merit further exploration, including affiliations with marine plants (seagrasses), microbial predators, intracellular niches, and resistance to heavy metal toxicity. Agarases, phototrophy, phage shock protein response, and microbial experimental evolution are also fields discussed. The squid-Vibrio symbiosis is a stellar model system, which can be a useful guiding light on deeper expeditions and voyages traversing these "seas of interest". Where appropriate, the squid-Vibrio mutualism is mentioned in how it has or could facilitate the illumination of these various subjects. Additional research is warranted on the topics specified herein, since they have critical relevance for biomedical science, pharmaceuticals, and health care. There are also practical applications in agriculture, zymology, food science, and culinary use. The tractability of microbial experimental evolution is explained. Examples are given of how microbial selection studies can be used to examine the roles of chance, contingency, and determinism (natural selection) in shaping Earth's natural history.
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Affiliation(s)
- William Soto
- Integrated Science Center Rm 3035, Department of Biology, College of William & Mary, 540 Landrum Dr., Williamsburg, VA 23185, USA
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5
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A lasting symbiosis: how Vibrio fischeri finds a squid partner and persists within its natural host. Nat Rev Microbiol 2021; 19:654-665. [PMID: 34089008 DOI: 10.1038/s41579-021-00557-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2021] [Indexed: 01/10/2023]
Abstract
As our understanding of the human microbiome progresses, so does the need for natural experimental animal models that promote a mechanistic understanding of beneficial microorganism-host interactions. Years of research into the exclusive symbiosis between the Hawaiian bobtail squid, Euprymna scolopes, and the bioluminescent bacterium Vibrio fischeri have permitted a detailed understanding of those bacterial genes underlying signal exchange and rhythmic activities that result in a persistent, beneficial association, as well as glimpses into the evolution of symbiotic competence. Migrating from the ambient seawater to regions deep inside the light-emitting organ of the squid, V. fischeri experiences, recognizes and adjusts to the changing environmental conditions. Here, we review key advances over the past 15 years that are deepening our understanding of these events.
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6
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Obeng N, Bansept F, Sieber M, Traulsen A, Schulenburg H. Evolution of Microbiota-Host Associations: The Microbe's Perspective. Trends Microbiol 2021; 29:779-787. [PMID: 33674142 DOI: 10.1016/j.tim.2021.02.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
Microbiota-host associations are ubiquitous in nature. They are often studied using a host-centered view, while microbes are assumed to have coevolved with hosts or colonize hosts as nonadapted entities. Both assumptions are often incorrect. Instead, many host-associated microbes are adapted to a biphasic life cycle in which they alternate between noncoadapted hosts and a free-living phase. Full appreciation of microbiota-host symbiosis thus needs to consider how microbes optimize fitness across this life cycle. Here, we evaluate the key stages of the biphasic life cycle and propose a new conceptual framework for microbiota-host interactions which includes an integrative measure of microbial fitness, related to the parasite fitness parameter R0, and which will help in-depth assessment of the evolution of these widespread associations.
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Affiliation(s)
- Nancy Obeng
- Department of Evolutionary Ecology and Genetics, University of Kiel, Am Botanischen Garten 1- 9, 24118 Kiel, Germany
| | - Florence Bansept
- Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Ploen, Germany
| | - Michael Sieber
- Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Ploen, Germany
| | - Arne Traulsen
- Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Ploen, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, University of Kiel, Am Botanischen Garten 1- 9, 24118 Kiel, Germany; Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Ploen, Germany.
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7
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Nourabadi N, Nishiguchi MK. pH Adaptation Drives Diverse Phenotypes in a Beneficial Bacterium-Host Mutualism. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.611411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abiotic variation can influence the evolution of specific phenotypes that contribute to the diversity of bacterial strains observed in the natural environment. Environmentally transmitted symbiotic bacteria are particularly vulnerable to abiotic fluctuations, given that they must accommodate the transition between the free-living state and the host's internal environment. This type of life history strategy can strongly influence the success of a symbiont, and whether adapting to changes outside the host will allow a greater capacity to survive in symbiosis with the host partner. One example of how environmental breadth is advantageous to the symbiosis is the beneficial association between Vibrio fischeri and sepiolid squids (Cephalopoda: Sepiolidae). Since Vibrio bacteria are environmentally transmitted, they are subject to a wide variety of abiotic variables prior to infecting juvenile squids and must be poised to survive in the host light organ. In order to better understand how a changing abiotic factor (e.g., pH) influences the diversification of symbionts and their eventual symbiotic competence, we used an experimental evolution approach to ascertain how pH adaptation affects symbiont fitness. Results show that low pH adapted Vibrio strains have more efficient colonization rates compared to their ancestral strains. In addition, growth rates had significant differences compared to ancestral strains (pH 6.5–6.8, and 7.2). Bioluminescence production (a marker for symbiont competence) of pH evolved strains also improved at pH 6.5–7.2. Results imply that the evolution and diversification of Vibrio strains adapted to low pH outside the squid improves fitness inside the squid by allowing a higher success rate for host colonization and symbiotic competence.
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8
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Identification of a Transcriptomic Network Underlying the Wrinkly and Smooth Phenotypes of Vibrio fischeri. J Bacteriol 2021; 203:JB.00259-20. [PMID: 33199286 PMCID: PMC7811199 DOI: 10.1128/jb.00259-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/04/2020] [Indexed: 01/27/2023] Open
Abstract
Vibrio fischeri is a cosmopolitan marine bacterium that oftentimes displays different colony morphologies, switching from a smooth to a wrinkly phenotype in order to adapt to changes in the environment. This wrinkly phenotype has also been associated with increased biofilm formation, an essential characteristic for V. fischeri to adhere to substrates, to suspended debris, and within the light organs of sepiolid squids. Elevated levels of biofilm formation are correlated with increased microbial survival of exposure to environmental stressors and the ability to expand niche breadth. Since V. fischeri has a biphasic life history strategy between its free-living and symbiotic states, we were interested in whether the wrinkly morphotype demonstrated differences in its expression profile in comparison to the naturally occurring and more common smooth variant. We show that genes involved in major biochemical cascades, including those involved in protein sorting, oxidative stress, and membrane transport, play a role in the wrinkly phenotype. Interestingly, only a few unique genes are specifically involved in macromolecule biosynthesis in the wrinkly phenotype, which underlies the importance of other pathways utilized for adaptation under the conditions in which Vibrio bacteria are producing this change in phenotype. These results provide the first comprehensive analysis of the complex form of genetic activation that underlies the diversity in morphologies of V. fischeri when switching between two different colony morphotypes, each representing a unique biofilm ecotype.IMPORTANCE The wrinkly bacterial colony phenotype has been associated with increased squid host colonization in V. fischeri The significance of our research is in identifying the genetic mechanisms that are responsible for heightened biofilm formation in V. fischeri This report also advances our understanding of gene regulation in V. fischeri and brings to the forefront a number of previously overlooked genetic networks. Several loci that were identified in this study were not previously known to be associated with biofilm formation in V. fischeri.
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Cohen ML, Mashanova EV, Jagannathan SV, Soto W. Adaptation to pH stress by Vibrio fischeri can affect its symbiosis with the Hawaiian bobtail squid ( Euprymna scolopes). MICROBIOLOGY-SGM 2020; 166:262-277. [PMID: 31967537 PMCID: PMC7376262 DOI: 10.1099/mic.0.000884] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many microorganisms engaged in host-microbe interactions pendulate between a free-living phase and a host-affiliated stage. How adaptation to stress during the free-living phase affects host-microbe associations is unclear and understudied. To explore this topic, the symbiosis between Hawaiian bobtail squid (Euprymna scolopes) and the luminous bacterium Vibrio fischeri was leveraged for a microbial experimental evolution study. V. fischeri experienced adaptation to extreme pH while apart from the squid host. V. fischeri was serially passaged for 2000 generations to the lower and upper pH growth limits for this microorganism, which were pH 6.0 and 10.0, respectively. V. fischeri was also serially passaged for 2000 generations to vacillating pH 6.0 and 10.0. Evolution to pH stress both facilitated and impaired symbiosis. Microbial evolution to acid stress promoted squid colonization and increased bioluminescence for V. fischeri, while symbiont adaptation to alkaline stress diminished these two traits. Oscillatory selection to acid and alkaline stress also improved symbiosis for V. fischeri, but the facilitating effects were less than that provided by microbial adaptation to acid stress. In summary, microbial adaptation to harsh environments amid the free-living phase may impact the evolution of host-microbe interactions in ways that were not formerly considered.
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Affiliation(s)
- Meagan Leah Cohen
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Ekaterina Vadimovna Mashanova
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Sveta Vivian Jagannathan
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - William Soto
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
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Hewson I. Technical pitfalls that bias comparative microbial community analyses of aquatic disease Ian Hewson. DISEASES OF AQUATIC ORGANISMS 2019; 137:109-124. [PMID: 31854329 DOI: 10.3354/dao03432] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The accessibility of high-throughput DNA sequencing technologies has attracted the application of comparative microbial analyses to study diseases. These studies present a window into host microbiome diversity and composition that can be used to address ecological theory in the context of host biology and behavior. Recently, comparative microbiome studies have been used to study non-vertebrate aquatic diseases to elucidate microorganisms potentially involved in disease processes or in disease prevention. These investigations suffer from many well-described biases, especially prior to sequence analyses, that could lead to misleading conclusions. Microbiome-focused studies of aquatic metazoan diseases provide valuable documentation of microbial ecology, although, they are only a starting point for establishing disease etiology, which demands quantitative validation through targeted approaches. The microbiome approach to understanding disease is most useful after laboratory diagnostics guided by pathology have failed to identify a causative agent. This opinion piece presents several technical pitfalls which may affect wider interpretation of microbe-host interactions through comparative microbial community analyses and provides recommendations, based on studies in non-aquatic systems, for incorporation into future aquatic disease research.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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11
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Cohen ML, Mashanova EV, Rosen NM, Soto W. Adaptation to temperature stress by Vibrio fischeri facilitates this microbe's symbiosis with the Hawaiian bobtail squid (Euprymna scolopes). Evolution 2019; 73:1885-1897. [PMID: 31397886 DOI: 10.1111/evo.13819] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 08/02/2019] [Accepted: 08/03/2019] [Indexed: 11/29/2022]
Abstract
For microorganisms cycling between free-living and host-associated stages, where reproduction occurs in both of these lifestyles, an interesting inquiry is whether adaptation to stress during the free-living stage can impact microbial fitness in the host. To address this topic, the mutualism between the Hawaiian bobtail squid (Euprymna scolopes) and the marine bioluminescent bacterium Vibrio fischeri was utilized. Using microbial experimental evolution, V. fischeri was selected to low (8°C), high (34°C), and fluctuating temperature stress (8°C/34°C) for 2000 generations. The temperatures 8°C and 34°C were the lower and upper growth limits, respectively. V. fischeri was also selected to benign temperatures (21°C and 28°C) for 2000 generations, which served as controls. V. fischeri demonstrated significant adaptation to low, high, and fluctuating temperature stress. V. fischeri did not display significant adaptation to the benign temperatures. Adaptation to stressful temperatures facilitated V. fischeri's ability to colonize the squid host relative to the ancestral lines. Bioluminescence levels also increased. Evolution to benign temperatures did not manifest these results. In summary, microbial adaptation to stress during the free-living stage can promote coevolution between hosts and microorganisms.
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Affiliation(s)
- Meagan Leah Cohen
- Department of Biology, College of William & Mary, Williamsburg, Virginia, 23185
| | | | | | - William Soto
- Department of Biology, College of William & Mary, Williamsburg, Virginia, 23185
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12
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Soto W, Travisano M, Tolleson AR, Nishiguchi MK. Symbiont evolution during the free-living phase can improve host colonization. MICROBIOLOGY-SGM 2019; 165:174-187. [PMID: 30648935 PMCID: PMC7003651 DOI: 10.1099/mic.0.000756] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
For micro-organisms cycling between free-living and host-associated stages, where reproduction occurs in both of these lifestyles, an interesting inquiry is whether evolution during the free-living stage can be positively pleiotropic to microbial fitness in a host environment. To address this topic, the squid host Euprymna tasmanica and the marine bioluminescent bacterium Vibrio fischeri were utilized. Microbial ecological diversification in static liquid microcosms was used to simulate symbiont evolution during the free-living stage. Thirteen genetically distinct V. fischeri strains from a broad diversity of ecological sources (e.g. squid light organs, fish light organs and seawater) were examined to see if the results were reproducible in many different genetic settings. Genetic backgrounds that are closely related can be predisposed to considerable differences in how they respond to similar selection pressures. For all strains examined, new mutations with striking and facilitating effects on host colonization arose quickly during microbial evolution in the free-living stage, regardless of the ecological context under consideration for a strain’s genetic background. Microbial evolution outside a host environment promoted host range expansion, improved host colonization for a micro-organism, and diminished the negative correlation between biofilm formation and motility.
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Affiliation(s)
- William Soto
- 1College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr Williamsburg, VA 23185, USA
| | - Michael Travisano
- 2Department of Ecology, Evolution, and Behavior, University of Minnesota-Twin Cities, 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, MN 55108, USA.,3BioTechnology Institute, University of Minnesota-Twin Cities, 140 Gortner Labs, 1479 Gortner Avenue, St Paul, MN 55108, USA
| | - Alexandra Rose Tolleson
- 1College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr Williamsburg, VA 23185, USA
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Pankey MS, Foxall RL, Ster IM, Perry LA, Schuster BM, Donner RA, Coyle M, Cooper VS, Whistler CA. Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria. eLife 2017; 6:e24414. [PMID: 28447935 PMCID: PMC5466423 DOI: 10.7554/elife.24414] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/23/2017] [Indexed: 01/14/2023] Open
Abstract
Host immune and physical barriers protect against pathogens but also impede the establishment of essential symbiotic partnerships. To reveal mechanisms by which beneficial organisms adapt to circumvent host defenses, we experimentally evolved ecologically distinct bioluminescent Vibrio fischeri by colonization and growth within the light organs of the squid Euprymna scolopes. Serial squid passaging of bacteria produced eight distinct mutations in the binK sensor kinase gene, which conferred an exceptional selective advantage that could be demonstrated through both empirical and theoretical analysis. Squid-adaptive binK alleles promoted colonization and immune evasion that were mediated by cell-associated matrices including symbiotic polysaccharide (Syp) and cellulose. binK variation also altered quorum sensing, raising the threshold for luminescence induction. Preexisting coordinated regulation of symbiosis traits by BinK presented an efficient solution where altered BinK function was the key to unlock multiple colonization barriers. These results identify a genetic basis for microbial adaptability and underscore the importance of hosts as selective agents that shape emergent symbiont populations.
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Affiliation(s)
- M Sabrina Pankey
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
| | - Randi L Foxall
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
| | - Ian M Ster
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
- Graduate Program in Biochemistry, University of New Hampshire, Durham, United States
| | - Lauren A Perry
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Graduate Program in Microbiology, University of New Hampshire, Durham, United States
| | - Brian M Schuster
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Rachel A Donner
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Matthew Coyle
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Graduate Program in Microbiology, University of New Hampshire, Durham, United States
| | - Vaughn S Cooper
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
| | - Cheryl A Whistler
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
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Dillon MM, Sung W, Sebra R, Lynch M, Cooper VS. Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations in Vibrio cholerae and Vibrio fischeri. Mol Biol Evol 2016; 34:93-109. [PMID: 27744412 PMCID: PMC5854121 DOI: 10.1093/molbev/msw224] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The vast diversity in nucleotide composition and architecture among bacterial genomes may be partly explained by inherent biases in the rates and spectra of spontaneous mutations. Bacterial genomes with multiple chromosomes are relatively unusual but some are relevant to human health, none more so than the causative agent of cholera, Vibrio cholerae Here, we present the genome-wide mutation spectra in wild-type and mismatch repair (MMR) defective backgrounds of two Vibrio species, the low-%GC squid symbiont V. fischeri and the pathogen V. cholerae, collected under conditions that greatly minimize the efficiency of natural selection. In apparent contrast to their high diversity in nature, both wild-type V. fischeri and V. cholerae have among the lowest rates for base-substitution mutations (bpsms) and insertion-deletion mutations (indels) that have been measured, below 10-3/genome/generation. Vibrio fischeri and V. cholerae have distinct mutation spectra, but both are AT-biased and produce a surprising number of multi-nucleotide indels. Furthermore, the loss of a functional MMR system caused the mutation spectra of these species to converge, implying that the MMR system itself contributes to species-specific mutation patterns. Bpsm and indel rates varied among genome regions, but do not explain the more rapid evolutionary rates of genes on chromosome 2, which likely result from weaker purifying selection. More generally, the very low mutation rates of Vibrio species correlate inversely with their immense population sizes and suggest that selection may not only have maximized replication fidelity but also optimized other polygenic traits relative to the constraints of genetic drift.
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Affiliation(s)
- Marcus M Dillon
- Microbiology Graduate Program, University of New Hampshire, Durham, NH
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, Charlotte, NC.,Department of Biology, Indiana University, Bloomington, IN
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN
| | - Vaughn S Cooper
- Microbiology Graduate Program, University of New Hampshire, Durham, NH .,Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA
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Soto W, Nishiguchi MK. Microbial experimental evolution as a novel research approach in the Vibrionaceae and squid-Vibrio symbiosis. Front Microbiol 2014; 5:593. [PMID: 25538686 PMCID: PMC4260504 DOI: 10.3389/fmicb.2014.00593] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/20/2014] [Indexed: 12/21/2022] Open
Abstract
The Vibrionaceae are a genetically and metabolically diverse family living in aquatic habitats with a great propensity toward developing interactions with eukaryotic microbial and multicellular hosts (as either commensals, pathogens, and mutualists). The Vibrionaceae frequently possess a life history cycle where bacteria are attached to a host in one phase and then another where they are free from their host as either part of the bacterioplankton or adhered to solid substrates such as marine sediment, riverbeds, lakebeds, or floating particulate debris. These two stages in their life history exert quite distinct and separate selection pressures. When bound to solid substrates or to host cells, the Vibrionaceae can also exist as complex biofilms. The association between bioluminescent Vibrio spp. and sepiolid squids (Cephalopoda: Sepiolidae) is an experimentally tractable model to study bacteria and animal host interactions, since the symbionts and squid hosts can be maintained in the laboratory independently of one another. The bacteria can be grown in pure culture and the squid hosts raised gnotobiotically with sterile light organs. The partnership between free-living Vibrio symbionts and axenic squid hatchlings emerging from eggs must be renewed every generation of the cephalopod host. Thus, symbiotic bacteria and animal host can each be studied alone and together in union. Despite virtues provided by the Vibrionaceae and sepiolid squid-Vibrio symbiosis, these assets to evolutionary biology have yet to be fully utilized for microbial experimental evolution. Experimental evolution studies already completed are reviewed, along with exploratory topics for future study.
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Affiliation(s)
- William Soto
- BEACON Center for the Study of Evolution in Action, Michigan State UniversityEast Lansing, MI, USA
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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: 0.6] [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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