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Schwob G, Cabrol L, Saucède T, Gérard K, Poulin E, Orlando J. Unveiling the co-phylogeny signal between plunderfish Harpagifer spp. and their gut microbiomes across the Southern Ocean. Microbiol Spectr 2024; 12:e0383023. [PMID: 38441978 PMCID: PMC10986581 DOI: 10.1128/spectrum.03830-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
Understanding the factors that sculpt fish gut microbiome is challenging, especially in natural populations characterized by high environmental and host genomic complexity. However, closely related hosts are valuable models for deciphering the contribution of host evolutionary history to microbiome assembly, through the underscoring of phylosymbiosis and co-phylogeny patterns. Here, we propose that the recent diversification of several Harpagifer species across the Southern Ocean would allow the detection of robust phylogenetic congruence between the host and its microbiome. We characterized the gut mucosa microbiome of 77 individuals from four field-collected species of the plunderfish Harpagifer (Teleostei, Notothenioidei), distributed across three biogeographic regions of the Southern Ocean. We found that seawater physicochemical properties, host phylogeny, and geography collectively explained 35% of the variation in bacterial community composition in Harpagifer gut mucosa. The core microbiome of Harpagifer spp. gut mucosa was characterized by a low diversity, mostly driven by selective processes, and dominated by a single Aliivibrio Operational Taxonomic Unit (OTU) detected in more than 80% of the individuals. Nearly half of the core microbiome taxa, including Aliivibrio, harbored co-phylogeny signal at microdiversity resolution with host phylogeny, indicating an intimate symbiotic relationship and a shared evolutionary history with Harpagifer. The clear phylosymbiosis and co-phylogeny signals underscore the relevance of the Harpagifer model in understanding the role of fish evolutionary history in shaping the gut microbiome assembly. We propose that the recent diversification of Harpagifer may have led to the diversification of Aliivibrio, exhibiting patterns that mirror the host phylogeny. IMPORTANCE Although challenging to detect in wild populations, phylogenetic congruence between marine fish and its microbiome is critical, as it highlights intimate associations between hosts and ecologically relevant microbial symbionts. Our study leverages a natural system of closely related fish species in the Southern Ocean to unveil new insights into the contribution of host evolutionary trajectory on gut microbiome assembly, an underappreciated driver of the global marine fish holobiont. Notably, we unveiled striking evidence of co-diversification between Harpagifer and its microbiome, demonstrating both phylosymbiosis of gut bacterial communities and co-phylogeny of some specific bacterial symbionts, mirroring the host diversification patterns. Given Harpagifer's significance as a trophic resource in coastal areas and its vulnerability to climatic and anthropic pressures, understanding the potential evolutionary interdependence between the hosts and its microbiome provides valuable microbial candidates for future monitoring, as they may play a pivotal role in host species acclimatization to a rapidly changing environment.
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Affiliation(s)
- Guillaume Schwob
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
- Institute of Ecology and Biodiversity, Santiago, Chile
| | - Léa Cabrol
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Institute of Ecology and Biodiversity, Santiago, Chile
- Aix Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France, Marseille, France
| | - Thomas Saucède
- UMR 6282 Biogeosciences, University Bourgogne Franche-Comté, CNRS, EPHE, Dijon, France
| | - Karin Gérard
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Laboratory of Antarctic and Subantarctic Marine Ecosystems, Faculty of Sciences, University of Magallanes, Punta Arenas, Chile
- Cape Horn International Center, Puerto Williams, Chile
| | - Elie Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
- Institute of Ecology and Biodiversity, Santiago, Chile
| | - Julieta Orlando
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
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Díaz FP, Dussarrat T, Carrasco-Puga G, Colombié S, Prigent S, Decros G, Bernillon S, Cassan C, Flandin A, Guerrero PC, Gibon Y, Rolin D, Cavieres LA, Pétriacq P, Latorre C, Gutiérrez RA. Ecological and metabolic implications of the nurse effect of Maihueniopsis camachoi in the Atacama Desert. New Phytol 2024; 241:1074-1087. [PMID: 37984856 DOI: 10.1111/nph.19415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023]
Abstract
Plant-plant positive interactions are key drivers of community structure. Yet, the underlying molecular mechanisms of facilitation processes remain unexplored. We investigated the 'nursing' effect of Maihueniopsis camachoi, a cactus that thrives in the Atacama Desert between c. 2800 and 3800 m above sea level. We hypothesised that an important protective factor is thermal amelioration of less cold-tolerant species with a corresponding impact on molecular phenotypes. To test this hypothesis, we compared plant cover and temperatures within the cactus foliage with open areas and modelled the effect of temperatures on plant distribution. We combined eco-metabolomics and machine learning to test the molecular consequences of this association. Multiple species benefited from the interaction with M. camachoi. A conspicuous example was the extended distribution of Atriplex imbricata to colder elevations in association with M. camachoi (400 m higher as compared to plants in open areas). Metabolomics identified 93 biochemical markers predicting the interaction status of A. imbricata with 79% accuracy, independently of year. These findings place M. camachoi as a key species in Atacama plant communities, driving local biodiversity with an impact on molecular phenotypes of nursed species. Our results support the stress-gradient hypothesis and provide pioneer insights into the metabolic consequences of facilitation.
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Affiliation(s)
- Francisca P Díaz
- Instituto de Geografía, Pontificia Universidad Católica de Valparaíso, 2362807, Valparaíso, Chile
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
| | - Thomas Dussarrat
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
| | - Gabriela Carrasco-Puga
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
| | - Sophie Colombié
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Sylvain Prigent
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Guillaume Decros
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
| | - Stéphane Bernillon
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Cédric Cassan
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Amélie Flandin
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Pablo C Guerrero
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 7800003, Concepción, Chile
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos, 8331150, Santiago, Chile
| | - Yves Gibon
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Dominique Rolin
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Lohengrin A Cavieres
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 7800003, Concepción, Chile
| | - Pierre Pétriacq
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Claudio Latorre
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
| | - Rodrigo A Gutiérrez
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
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Echeverría-Alar S, Clerc MG, Bordeu I. Emergence of disordered branching patterns in confined chiral nematic liquid crystals. Proc Natl Acad Sci U S A 2023; 120:e2221000120. [PMID: 37027428 PMCID: PMC10104489 DOI: 10.1073/pnas.2221000120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/06/2023] [Indexed: 04/08/2023] Open
Abstract
Spatial branching processes are ubiquitous in nature, yet the mechanisms that drive their growth may vary significantly from one system to another. In soft matter physics, chiral nematic liquid crystals provide a controlled setting to study the emergence and growth dynamic of disordered branching patterns. Via an appropriate forcing, a cholesteric phase may nucleate in a chiral nematic liquid crystal, which self-organizes into an extended branching pattern. It is known that branching events take place when the rounded tips of cholesteric fingers swell, become unstable, and split into two new cholesteric tips. The origin of this interfacial instability and the mechanisms that drive the large-scale spatial organization of these cholesteric patterns remain unclear. In this work, we investigate experimentally the spatial and temporal organization of thermally driven branching patterns in chiral nematic liquid crystal cells. We describe the observations through a mean-field model and find that chirality is responsible for the creation of fingers, regulates their interactions, and controls the tip-splitting process. Furthermore, we show that the complex dynamics of the cholesteric pattern behaves as a probabilistic process of branching and inhibition of chiral tips that drives the large-scale topological organization. Our theoretical findings are in good agreement with the experimental observations.
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Affiliation(s)
- Sebastián Echeverría-Alar
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, 837.0415Santiago, Chile
- Millennium Institute for Research in Optics, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, 837.0415Santiago, Chile
| | - Marcel G. Clerc
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, 837.0415Santiago, Chile
- Millennium Institute for Research in Optics, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, 837.0415Santiago, Chile
| | - Ignacio Bordeu
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, 837.0415Santiago, Chile
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