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Neely WJ, Souza KMC, Martins RA, Marshall VM, Buttimer SM, Brito de Assis A, Medina D, Whetstone RD, Lyra ML, Ribeiro JW, Greenspan SE, Haddad CFB, Alves dos Anjos L, Becker CG. Host-associated helminth diversity and microbiome composition contribute to anti-pathogen defences in tropical frogs impacted by forest fragmentation. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240530. [PMID: 39100162 PMCID: PMC11296196 DOI: 10.1098/rsos.240530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/23/2024] [Indexed: 08/06/2024]
Abstract
Habitat fragmentation can negatively impact wildlife populations by simplification of ecological interactions, but little is known about how these impacts extend to host-associated symbiotic communities. The symbiotic communities of amphibians play important roles in anti-pathogen defences, particularly against the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). In this study, we analyse the role of macroparasitic helminth communities in concert with microbial communities in defending the host against Bd infection within the context of forest fragmentation. We found that skin microbial and helminth communities are disrupted at fragmented habitats, while gut microbiomes appear more resilient to environmental change. We also detected potential protective roles of helminth diversity and anti-pathogen microbial function in limiting Bd infection. Microbial network analysis revealed strong patterns of structure in both skin and gut communities, with helminths playing central roles in these networks. We reveal consistent roles of microbial and helminth diversity in driving host-pathogen interactions and the potential implications of fragmentation on host fitness.
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Affiliation(s)
- Wesley J. Neely
- Department of Biology, The University of Alabama, Tuscaloosa, AL35487, USA
- Department of Biology, Texas State University, San Marcos, TX78666, USA
| | - Kassia M. C. Souza
- Departamento de Biologia e Zootecnia, Universidade Estadual Paulista, Ilha Solteira, São Paulo 15385-000, Brazil
| | - Renato A. Martins
- Department of Biology, The Pennsylvania State University, University Park, PA16803, USA
| | | | - Shannon M. Buttimer
- Department of Biology, The Pennsylvania State University, University Park, PA16803, USA
| | - Ananda Brito de Assis
- Department of Biodiversity and Aquaculture Center, Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900, Brazil
| | - Daniel Medina
- Department of Biology, The Pennsylvania State University, University Park, PA16803, USA
- Sistema Nacional de Investigación, SENACYT, City of Knowledge, Clayton, Panama, Republic of Panama
| | - Ross D. Whetstone
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Mariana L. Lyra
- Department of Biodiversity and Aquaculture Center, Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900, Brazil
- New York University Abu Dhabi, Abu Dhabi, UAE
| | - José Wagner Ribeiro
- Department of Biodiversity and Aquaculture Center, Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900, Brazil
| | - Sasha E. Greenspan
- Department of Biology, The University of Alabama, Tuscaloosa, AL35487, USA
| | - Célio F. B. Haddad
- Department of Biodiversity and Aquaculture Center, Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900, Brazil
| | - Luciano Alves dos Anjos
- Departamento de Biologia e Zootecnia, Universidade Estadual Paulista, Ilha Solteira, São Paulo 15385-000, Brazil
| | - C. Guilherme Becker
- Department of Biology, The Pennsylvania State University, University Park, PA16803, USA
- One Health Microbiome Center, Center for Infectious Disease Dynamics, Ecology Institute, Huch Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA16803, USA
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Martínez-Ugalde E, Ávila-Akerberg V, González Martínez TM, Rebollar EA. Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent. Microb Genom 2024; 10:001181. [PMID: 38240649 PMCID: PMC10868611 DOI: 10.1099/mgen.0.001181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the A. altamirani skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of A. altamirani skin microbiome differed between B. dendrobatidis infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the A. altamirani skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of A. altamirani to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.
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Affiliation(s)
| | - Víctor Ávila-Akerberg
- Instituto de Ciencias Agropecuarias y Rurales, Universidad Autónoma del Estado de México, Toluca, Mexico
| | | | - Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Neely WJ, Martins RA, Mendonça da Silva CM, Ferreira da Silva T, Fleck LE, Whetstone RD, Woodhams DC, Cook WH, Prist PR, Valiati VH, Greenspan SE, Tozetti AM, Earley RL, Becker CG. Linking microbiome and stress hormone responses in wild tropical treefrogs across continuous and fragmented forests. Commun Biol 2023; 6:1261. [PMID: 38087051 PMCID: PMC10716138 DOI: 10.1038/s42003-023-05600-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
The amphibian skin microbiome is an important component of anti-pathogen defense, but the impact of environmental change on the link between microbiome composition and host stress remains unclear. In this study, we used radiotelemetry and host translocation to track microbiome composition and function, pathogen infection, and host stress over time across natural movement paths for the forest-associated treefrog, Boana faber. We found a negative correlation between cortisol levels and putative microbiome function for frogs translocated to forest fragments, indicating strong integration of host stress response and anti-pathogen potential of the microbiome. Additionally, we observed a capacity for resilience (resistance to structural change and functional loss) in the amphibian skin microbiome, with maintenance of putative pathogen-inhibitory function despite major temporal shifts in microbiome composition. Although microbiome community composition did not return to baseline during the study period, the rate of microbiome change indicated that forest fragmentation had more pronounced effects on microbiome composition than translocation alone. Our findings reveal associations between stress hormones and host microbiome defenses, with implications for resilience of amphibians and their associated microbes facing accelerated tropical deforestation.
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Affiliation(s)
- Wesley J Neely
- Department of Biology, The University of Alabama, Tuscaloosa, AL, 35487, USA.
- Department of Biology, Texas State University, San Marcos, TX, 78666, USA.
| | - Renato A Martins
- Department of Biology, and Center for Infectious Disease Dynamics, One Health Microbiome Center, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Camila M Mendonça da Silva
- Programa de Pos‑Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022‑750, Brazil
| | - Tainá Ferreira da Silva
- Programa de Pos‑Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022‑750, Brazil
| | - Lucas E Fleck
- Programa de Pos‑Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022‑750, Brazil
| | - Ross D Whetstone
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - W Harrison Cook
- Department of Biology, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Paula R Prist
- EcoHealth Alliance, 520 Eight Avenue, Suite 1200, New York, NY, 10018, USA
| | - Victor H Valiati
- Programa de Pos‑Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022‑750, Brazil
| | - Sasha E Greenspan
- Department of Biology, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Alexandro M Tozetti
- Programa de Pos‑Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022‑750, Brazil
| | - Ryan L Earley
- Department of Biology, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - C Guilherme Becker
- Department of Biology, and Center for Infectious Disease Dynamics, One Health Microbiome Center, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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Siomko SA, Greenspan SE, Barnett KM, Neely WJ, Chtarbanova S, Woodhams DC, McMahon TA, Becker CG. Selection of an anti-pathogen skin microbiome following prophylaxis treatment in an amphibian model system. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220126. [PMID: 37305917 PMCID: PMC10258671 DOI: 10.1098/rstb.2022.0126] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/03/2022] [Indexed: 06/13/2023] Open
Abstract
With emerging diseases on the rise, there is an urgent need to identify and understand novel mechanisms of prophylactic protection in vertebrate hosts. Inducing resistance against emerging pathogens through prophylaxis is an ideal management strategy that may impact pathogens and their host-associated microbiome. The host microbiome is recognized as a critical component of immunity, but the effects of prophylactic inoculation on the microbiome are unknown. In this study, we investigate the effects of prophylaxis on host microbiome composition, focusing on the selection of anti-pathogenic microbes contributing to host acquired immunity in a model host-fungal disease system, amphibian chytridiomycosis. We inoculated larval Pseudacris regilla against the fungal pathogen Batrachochytrium dendrobatidis (Bd) with a Bd metabolite-based prophylactic. Increased prophylactic concentration and exposure duration were associated with significant increases in proportions of putatively Bd-inhibitory host-associated bacterial taxa, indicating a protective prophylactic-induced shift towards microbiome members that are antagonistic to Bd. Our findings are in accordance with the adaptive microbiome hypothesis, where exposure to a pathogen alters the microbiome to better cope with subsequent pathogen encounters. Our study advances research on the temporal dynamics of microbiome memory and the role of prophylaxis-induced shifts in microbiomes contributing to prophylaxis effectiveness. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.
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Affiliation(s)
- Samantha A. Siomko
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Sasha E. Greenspan
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - K. M. Barnett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Wesley J. Neely
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | | | - Douglas C. Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Taegan A. McMahon
- Department of Biology, Connecticut College, New London, CT 06320, USA
| | - C. Guilherme Becker
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, One Health Microbiome Center, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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Assis VR, Robert J, Titon SCM. Introduction to the special issue Amphibian immunity: stress, disease and ecoimmunology. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220117. [PMID: 37305915 PMCID: PMC10258669 DOI: 10.1098/rstb.2022.0117] [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: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Amphibian populations have been declining worldwide, with global climate changes and infectious diseases being among the primary causes of this scenario. Infectious diseases are among the primary drivers of amphibian declines, including ranavirosis and chytridiomycosis, which have gained more attention lately. While some amphibian populations are led to extinction, others are disease-resistant. Although the host's immune system plays a major role in disease resistance, little is known about the immune mechanisms underlying amphibian disease resistance and host-pathogen interactions. As ectotherms, amphibians are directly subjected to changes in temperature and rainfall, which modulate stress-related physiology, including immunity and pathogen physiology associated with diseases. In this sense, the contexts of stress, disease and ecoimmunology are essential for a better understanding of amphibian immunity. This issue brings details about the ontogeny of the amphibian immune system, including crucial aspects of innate and adaptive immunity and how ontogeny can influence amphibian disease resistance. In addition, the papers in the issue demonstrate an integrated view of the amphibian immune system associated with the influence of stress on immune-endocrine interactions. The collective body of research presented herein can provide valuable insights into the mechanisms underlying disease outcomes in natural populations, particularly in the context of changing environmental conditions. These findings may ultimately enhance our ability to forecast effective conservation strategies for amphibian populations. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.
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Affiliation(s)
- Vania Regina Assis
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, 05508-900 São Paulo, Brazil
- College of Public Health, University of South Florida, Tampa, FL 33612-9415, USA
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA
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