1
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McGrath-Blaser SE, McGathey N, Pardon A, Hartmann AM, Longo AV. Invasibility of a North American soil ecosystem to amphibian-killing fungal pathogens. Proc Biol Sci 2024; 291:20232658. [PMID: 38628130 PMCID: PMC11021929 DOI: 10.1098/rspb.2023.2658] [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: 12/07/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
North American salamanders are threatened by intercontinental spread of chytridiomycosis, a deadly disease caused by the fungal pathogen Batrachochytrium salamandrivorans (Bsal). To predict potential dispersal of Bsal spores to salamander habitats, we evaluated the capacity of soil microbial communities to resist invasion. We determined the degree of habitat invasibility using soils from five locations throughout the Great Smoky Mountains National Park, a region with a high abundance of susceptible hosts. Our experimental design consisted of replicate soil microcosms exposed to different propagule pressures of the non-native pathogen, Bsal, and an introduced but endemic pathogen, B. dendrobatidis (Bd). To compare growth and competitive interactions, we used quantitative PCR, live/dead cell viability assays, and full-length 16S rRNA sequencing. We found that soil microcosms with intact bacterial communities inhibited both Bsal and Bd growth, but inhibitory capacity diminished with increased propagule pressure. Bsal showed greater persistence than Bd. Linear discriminant analysis (LDA) identified the family Burkolderiaceae as increasing in relative abundance with the decline of both pathogens. Although our findings provide evidence of environmental filtering in soils, such barriers weakened in response to pathogen type and propagule pressure, showing that habitats vary their invasibility based on properties of their local microbial communities.
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Affiliation(s)
| | - Natalie McGathey
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Allison Pardon
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Arik M. Hartmann
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Ana V. Longo
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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2
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Bornbusch SL, Power ML, Schulkin J, Drea CM, Maslanka MT, Muletz-Wolz CR. Integrating microbiome science and evolutionary medicine into animal health and conservation. Biol Rev Camb Philos Soc 2024; 99:458-477. [PMID: 37956701 DOI: 10.1111/brv.13030] [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: 04/03/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
Microbiome science has provided groundbreaking insights into human and animal health. Similarly, evolutionary medicine - the incorporation of eco-evolutionary concepts into primarily human medical theory and practice - is increasingly recognised for its novel perspectives on modern diseases. Studies of host-microbe relationships have been expanded beyond humans to include a wide range of animal taxa, adding new facets to our understanding of animal ecology, evolution, behaviour, and health. In this review, we propose that a broader application of evolutionary medicine, combined with microbiome science, can provide valuable and innovative perspectives on animal care and conservation. First, we draw on classic ecological principles, such as alternative stable states, to propose an eco-evolutionary framework for understanding variation in animal microbiomes and their role in animal health and wellbeing. With a focus on mammalian gut microbiomes, we apply this framework to populations of animals under human care, with particular relevance to the many animal species that suffer diseases linked to gut microbial dysfunction (e.g. gut distress and infection, autoimmune disorders, obesity). We discuss diet and microbial landscapes (i.e. the microbes in the animal's external environment), as two factors that are (i) proposed to represent evolutionary mismatches for captive animals, (ii) linked to gut microbiome structure and function, and (iii) potentially best understood from an evolutionary medicine perspective. Keeping within our evolutionary framework, we highlight the potential benefits - and pitfalls - of modern microbial therapies, such as pre- and probiotics, faecal microbiota transplants, and microbial rewilding. We discuss the limited, yet growing, empirical evidence for the use of microbial therapies to modulate animal gut microbiomes beneficially. Interspersed throughout, we propose 12 actionable steps, grounded in evolutionary medicine, that can be applied to practical animal care and management. We encourage that these actionable steps be paired with integration of eco-evolutionary perspectives into our definitions of appropriate animal care standards. The evolutionary perspectives proposed herein may be best appreciated when applied to the broad diversity of species under human care, rather than when solely focused on humans. We urge animal care professionals, veterinarians, nutritionists, scientists, and others to collaborate on these efforts, allowing for simultaneous care of animal patients and the generation of valuable empirical data.
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Affiliation(s)
- Sally L Bornbusch
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Michael L Power
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Jay Schulkin
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, 1959 NE Pacific St., Box 356460, Seattle, WA, 98195, USA
| | - Christine M Drea
- Department of Evolutionary Anthropology, Duke University, 104 Biological Sciences, Campus Box 90383, Durham, NC, 27708, USA
| | - Michael T Maslanka
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
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3
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Osborne OG, Jiménez RR, Byrne AQ, Gratwicke B, Ellison A, Muletz-Wolz CR. Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders. THE ISME JOURNAL 2024; 18:wrae104. [PMID: 38861457 PMCID: PMC11195472 DOI: 10.1093/ismejo/wrae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/09/2024] [Accepted: 06/10/2024] [Indexed: 06/13/2024]
Abstract
Phylosymbiosis is an association between host-associated microbiome composition and host phylogeny. This pattern can arise via the evolution of host traits, habitat preferences, diets, and the co-diversification of hosts and microbes. Understanding the drivers of phylosymbiosis is vital for modelling disease-microbiome interactions and manipulating microbiomes in multi-host systems. This study quantifies phylosymbiosis in Appalachian salamander skin in the context of infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd), while accounting for environmental microbiome exposure. We sampled ten salamander species representing >150M years of divergence, assessed their Bd infection status, and analysed their skin and environmental microbiomes. Our results reveal a significant signal of phylosymbiosis, whereas the local environmental pool of microbes, climate, geography, and Bd infection load had a smaller impact. Host-microbe co-speciation was not evident, indicating that the effect stems from the evolution of host traits influencing microbiome assembly. Bd infection is correlated with host phylogeny and the abundance of Bd-inhibitory bacterial strains, suggesting that the long-term evolutionary dynamics between salamander hosts and their skin microbiomes affect the present-day distribution of the pathogen, along with habitat-linked exposure risk. Five Bd-inhibitory bacterial strains showed unusual generalism: occurring in most host species and habitats. These generalist strains may enhance the likelihood of probiotic manipulations colonising and persisting on hosts. Our results underscore the substantial influence of host-microbiome eco-evolutionary dynamics on environmental health and disease outcomes.
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Affiliation(s)
- Owen G Osborne
- School of Environmental and Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2DG, United Kingdom
| | - Randall R Jiménez
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, United States
- International Union for Conservation of Nature, C. 39, Los Yoses, San Jose, 146-2150, Costa Rica
| | - Allison Q Byrne
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720-3114, United States
| | - Brian Gratwicke
- Center for Species Survival, Smithsonian’s National Zoological Park and Conservation Biology Institute, Front Royal, VA 22630, United States
| | - Amy Ellison
- School of Environmental and Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2DG, United Kingdom
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, United States
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4
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Belasen AM, Peek RA, Adams AJ, Russell ID, De León ME, Adams MJ, Bettaso J, Breedveld KGH, Catenazzi A, Dillingham CP, Grear DA, Halstead BJ, Johnson PG, Kleeman PM, Koo MS, Koppl CW, Lauder JD, Padgett-Flohr G, Piovia-Scott J, Pope KL, Vredenburg V, Westphal M, Wiseman K, Kupferberg SJ. Chytrid infections exhibit historical spread and contemporary seasonality in a declining stream-breeding frog. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231270. [PMID: 38298390 PMCID: PMC10827429 DOI: 10.1098/rsos.231270] [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: 08/26/2023] [Accepted: 12/18/2023] [Indexed: 02/02/2024]
Abstract
Species with extensive geographical ranges pose special challenges to assessing drivers of wildlife disease, necessitating collaborative and large-scale analyses. The imperilled foothill yellow-legged frog (Rana boylii) inhabits a wide geographical range and variable conditions in rivers of California and Oregon (USA), and is considered threatened by the pathogen Batrachochytrium dendrobatidis (Bd). To assess drivers of Bd infections over time and space, we compiled over 2000 datapoints from R. boylii museum specimens (collected 1897-2005) and field samples (2005-2021) spanning 9° of latitude. We observed a south-to-north spread of Bd detections beginning in the 1940s and increase in prevalence from the 1940s to 1970s, coinciding with extirpation from southern latitudes. We detected eight high-prevalence geographical clusters through time that span the species' geographical range. Field-sampled male R. boylii exhibited the highest prevalence, and juveniles sampled in autumn exhibited the highest loads. Bd infection risk was highest in lower elevation rain-dominated watersheds, and with cool temperatures and low stream-flow conditions at the end of the dry season. Through a holistic assessment of relationships between infection risk, geographical context and time, we identify the locations and time periods where Bd mitigation and monitoring will be critical for conservation of this imperilled species.
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Affiliation(s)
- A. M. Belasen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - R. A. Peek
- California Department of Fish and Wildlife, West Sacramento, CA, USA
| | - A. J. Adams
- Earth Research Institute, University of California, Santa Barbara, CA, USA
| | - I. D. Russell
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, USA
| | - M. E. De León
- Genome Center, University of California, Davis, CA, USA
| | - M. J. Adams
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Corvallis, OR, USA
| | - J. Bettaso
- Six Rivers National Forest, Lower Trinity Ranger District, USDA Forest Service, P.O. Box 68, Willow Creek, CA, USA
| | | | - A. Catenazzi
- Department of Biological Sciences, Florida International University, Miami, FL, USA
| | | | - D. A. Grear
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI, USA
| | - B. J. Halstead
- Point Reyes Field Station, U.S. Geological Survey, Western Ecological Research Center, Point Reyes Station, CA, USA
| | - P. G. Johnson
- Pinnacles National Park, National Park Service, Paicines, CA, USA
| | - P. M. Kleeman
- Point Reyes Field Station, U.S. Geological Survey, Western Ecological Research Center, Point Reyes Station, CA, USA
| | - M. S. Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, CA
| | - C. W. Koppl
- Plumas National Forest, USDA Forest Service, Quincy, CA, USA
| | | | | | - J. Piovia-Scott
- School of Biological Sciences, Washington State University, Vancouver, WA, USA
| | - K. L. Pope
- Pacific Southwest Research Station, USDA Forest Service, Arcata, CA, USA
| | - V. Vredenburg
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - M. Westphal
- Central Coast Field Office, United States Bureau of Land Management, Marina, CA, USA
| | - K. Wiseman
- Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
| | - S. J. Kupferberg
- Department of Integrative Biology, University of California, Berkeley, CA, USA
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5
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Webb RJ, Rush C, Berger L, Skerratt LF, Roberts AA. Glutathione is required for growth and cadmium tolerance in the amphibian chytrid fungus, Batrachochytrium dendrobatidis. Biochimie 2023; 220:22-30. [PMID: 38104714 DOI: 10.1016/j.biochi.2023.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 11/24/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
Batrachochytrium dendrobatidis (Bd) is a lethal amphibian pathogen, partly due to its ability to evade the immune system of susceptible frog species. In many pathogenic fungi, the antioxidant glutathione is a virulence factor that helps neutralise oxidative stressors generated from host immune cells, as well as other environmental stressors such as heavy metals. The role of glutathione in stress tolerance in Bd has not been investigated. Here, we examine the changes in the glutathione pool after stress exposure and quantify the effect of glutathione depletion on cell growth and stress tolerance. Depletion of glutathione repressed growth and release of zoospores, suggesting that glutathione is essential for life cycle completion in Bd. Supplementation with <2 mM exogenous glutathione accelerated zoospore development, but concentrations >2 mM were strongly inhibitory to Bd cells. While hydrogen peroxide exposure lowered the total cellular glutathione levels by 42 %, glutathione depletion did not increase the sensitivity to hydrogen peroxide. Exposure to cadmium increased total cellular glutathione levels by 93 %. Glutathione-depleted cells were more sensitive to cadmium, and this effect was attenuated by glutathione supplementation, suggesting that glutathione plays an important role in cadmium tolerance. The effects of heat and salt were exacerbated by the addition of exogenous glutathione. The impact of glutathione levels on Bd stress sensitivity may help explain differences in host susceptibility to chytridiomycosis and may provide opportunities for synergistic therapeutics.
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Affiliation(s)
- Rebecca J Webb
- James Cook University, Townsville, QLD, 4811, Australia; Melbourne Veterinary School, University of Melbourne, Werribee, VIC, 3030, Australia.
| | | | - Lee Berger
- Melbourne Veterinary School, University of Melbourne, Werribee, VIC, 3030, Australia
| | - Lee F Skerratt
- Melbourne Veterinary School, University of Melbourne, Werribee, VIC, 3030, Australia
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6
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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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7
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Sun D, Herath J, Zhou S, Ellepola G, Meegaskumbura M. Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts. ISME COMMUNICATIONS 2023; 3:123. [PMID: 37993728 PMCID: PMC10665332 DOI: 10.1038/s43705-023-00332-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Amphibian skin harbors microorganisms that are associated with the fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes chytridiomycosis, one of the most significant wildlife diseases known. This pathogen originated in Asia, where diverse Bd lineages exist; hence, native amphibian hosts have co-existed with Bd over long time periods. Determining the nuances of this co-existence is crucial for understanding the prevalence and spread of Bd from a microbial context. However, associations of Bd with the natural skin microbiome remain poorly understood for Asian hosts, especially in relation to skin-associated fungi. We used 16 S rRNA and fungal internal transcribed spacer (ITS) gene sequencing to characterize the skin microbiome of four native Asian amphibian species and examined the relationships between Bd infection and their skin bacterial and fungal communities; we also analyzed the correlates of the putative anti-Bd bacteria. We show that both skin bacterial and fungal community structure and composition had significant associations with infection status (Bd presence/absence) and infection intensity (frequency of Bd sequence reads). We also found that the putative anti-Bd bacterial richness was correlated with Bd infection status and infection intensity, and observed that the relative abundance of anti-Bd bacteria roughly correspond with changes in both Bd prevalence and mean infection intensity in populations. Additionally, the microbial co-occurrence network of infected frogs was significantly different from that of uninfected frogs that were characterized by more keystone nodes (connectors) and larger proportions in correlations between bacteria, suggesting stronger inter-module bacterial interactions. These results indicate that the mutual effects between Bd and skin-associated microbiome, including the interplay between bacteria and fungi, might vary with Bd infection in susceptible amphibian species. This knowledge will help in understanding the dynamics of Bd from a microbial perspective, potentially contributing to mitigate chytridiomycosis in other regions of the world.
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Affiliation(s)
- Dan Sun
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
| | - Jayampathi Herath
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
- School of Biomedical Sciences, International Institute of Health Sciences (IIHS), No 704 Negombo Rd, Welisara, 71722, Sri Lanka
| | - Shipeng Zhou
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
| | - Gajaba Ellepola
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
- Department of Zoology, Faculty of Science, University of Peradeniya, Peradeniya, KY20400, Sri Lanka
| | - Madhava Meegaskumbura
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China.
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8
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White A, Giannetto M, Mulla L, Del Rosario A, Lim T, Culver E, Timmer M, Bushell J, Lambert MR, Hernández-Gómez O. Bacterial communities of the threatened Western Pond Turtle may be impacted by land use. FEMS Microbiol Ecol 2023; 99:fiad143. [PMID: 37950563 DOI: 10.1093/femsec/fiad143] [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: 03/30/2023] [Revised: 11/05/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023] Open
Abstract
As semi-aquatic species that use both terrestrial and aquatic habitats, freshwater turtles and their microbial communities are especially sensitive to the impacts of habitat disturbance. In this study, we use 16S rRNA amplicon sequencing to characterize the shell and cloacal bacterial communities of turtles in the San Francisco Bay Area. We captured western pond turtles (Actinemys/Emys marmorata) across eight sites located in urban and rural environments, along with invasive red-eared sliders (Trachemys scripta elegans). We assessed differences in western pond turtle bacterial communities diversity/composition between shell and cloacal samples and evaluated how alpha/beta diversity metrics were influenced by habitat quality. We found phylum-level bacterial taxonomic turnover in the bacterial communities of western pond turtles relative to the host tissue substrate samples. Our findings indicate that location identity elicits a high degree of lower-level (i.e. species/genus) bacterial taxonomic turnover. Further, we found that samples originating from good quality habitat had poorer shell bacterial communities but more diverse cloacal ones. The shell bacterial communities of red-eared sliders overlapped with those western pond turtles suggesting the existence of microbial dispersal between these two species. Our results add to our current understanding of turtle symbiont microbial ecology by establishing patterns of bacterial symbiont variation in an urban to rural gradient.
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Affiliation(s)
- Alison White
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Madison Giannetto
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Lubna Mulla
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Amber Del Rosario
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Tammy Lim
- East Bay Regional Parks, Oakland, CA 94605, United States
| | - Edward Culver
- East Bay Regional Parks, Oakland, CA 94605, United States
| | - Matthew Timmer
- Land Trust of Santa Cruz County, Santa Cruz, CA 95060, United States
| | - Jessie Bushell
- San Francisco Zoo and Gardens, San Francisco, CA 94132, United States
| | - Max R Lambert
- Washington Department of Fish and Wildlife, Olympia, WA 98501, United States
| | - Obed Hernández-Gómez
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA 94901, United States
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9
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Ramírez-Barahona S, González-Serrano FM, Martínez-Ugalde E, Soto-Pozos A, Parra-Olea G, Rebollar EA. Host phylogeny and environment shape the diversity of salamander skin bacterial communities. Anim Microbiome 2023; 5:52. [PMID: 37828573 PMCID: PMC10571319 DOI: 10.1186/s42523-023-00271-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023] Open
Abstract
The composition and diversity of animal-associated microbial communities are shaped by multiple ecological and evolutionary processes acting at different spatial and temporal scales. Skin microbiomes are thought to be strongly influenced by the environment due to the direct interaction of the host's skin with the external media. As expected, the diversity of amphibian skin microbiomes is shaped by climate and host sampling habitats, whereas phylogenetic effects appear to be weak. However, the relative strength of phylogenetic and environmental effects on salamander skin microbiomes remains poorly understood. Here, we analysed sequence data from 1164 adult salamanders of 44 species to characterise and compare the diversity and composition of skin bacteria. We assessed the relative contribution of climate, host sampling habitat, and host phylogeny to the observed patterns of bacterial diversity. We found that bacterial alpha diversity was mainly associated with host sampling habitat and climate, but that bacterial beta diversity was more strongly associated with host taxonomy and phylogeny. This phylogenetic effect predominantly occurred at intermediate levels of host divergence (0-50 Mya). Our results support the importance of environmental factors shaping the diversity of salamander skin microbiota, but also support host phylogenetic history as a major factor shaping these bacterial communities.
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Affiliation(s)
- S Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - F M González-Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - E Martínez-Ugalde
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - A Soto-Pozos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - G Parra-Olea
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - E A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
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10
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Woodhams DC, McCartney J, Walke JB, Whetstone R. The adaptive microbiome hypothesis and immune interactions in amphibian mucus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 145:104690. [PMID: 37001710 DOI: 10.1016/j.dci.2023.104690] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 05/20/2023]
Abstract
The microbiome is known to provide benefits to hosts, including extension of immune function. Amphibians are a powerful immunological model for examining mucosal defenses because of an accessible epithelial mucosome throughout their developmental trajectory, their responsiveness to experimental treatments, and direct interactions with emerging infectious pathogens. We review amphibian skin mucus components and describe the adaptive microbiome as a novel process of disease resilience where competitive microbial interactions couple with host immune responses to select for functions beneficial to the host. We demonstrate microbiome diversity, specificity of function, and mechanisms for memory characteristic of an adaptive immune response. At a time when industrialization has been linked to losses in microbiota important for host health, applications of microbial therapies such as probiotics may contribute to immunotherapeutics and to conservation efforts for species currently threatened by emerging diseases.
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Affiliation(s)
- Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA.
| | - Julia McCartney
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Jenifer B Walke
- Department of Biology, Eastern Washington University, Cheney, WA, 99004-2440, USA
| | - Ross Whetstone
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
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11
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Schilliger L, Paillusseau C, François C, Bonwitt J. Major Emerging Fungal Diseases of Reptiles and Amphibians. Pathogens 2023; 12:pathogens12030429. [PMID: 36986351 PMCID: PMC10053826 DOI: 10.3390/pathogens12030429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/16/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Emerging infectious diseases (EIDs) are caused by pathogens that have undergone recent changes in terms of geographic spread, increasing incidence, or expanding host range. In this narrative review, we describe three important fungal EIDs with keratin trophism that are relevant to reptile and amphibian conservation and veterinary practice. Nannizziopsis spp. have been mainly described in saurians; infection results in thickened, discolored skin crusting, with eventual progression to deep tissues. Previously only reported in captive populations, it was first described in wild animals in Australia in 2020. Ophidiomyces ophidiicola (formely O. ophiodiicola) is only known to infect snakes; clinical signs include ulcerating lesions in the cranial, ventral, and pericloacal regions. It has been associated with mortality events in wild populations in North America. Batrachochytrium spp. cause ulceration, hyperkeratosis, and erythema in amphibians. They are a major cause of catastrophic amphibian declines worldwide. In general, infection and clinical course are determined by host-related characteristics (e.g., nutritional, metabolic, and immune status), pathogens (e.g., virulence and environmental survival), and environment (e.g., temperature, hygrometry, and water quality). The animal trade is thought to be an important cause of worldwide spread, with global modifications in temperature, hygrometry, and water quality further affecting fungal pathogenicity and host immune response.
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Affiliation(s)
- Lionel Schilliger
- Argos Veterinary Clinic of Paris Auteuil, 35 Rue Leconte de Lisle, 75016 Paris, France
- SpéNac Referral Center, 100 Boulevard de la Tour Maubourg, 75007 Paris, France
- Correspondence: ; Tel.: +33-188-616-831
| | - Clément Paillusseau
- Argos Veterinary Clinic of Paris Auteuil, 35 Rue Leconte de Lisle, 75016 Paris, France
- SpéNac Referral Center, 100 Boulevard de la Tour Maubourg, 75007 Paris, France
| | - Camille François
- Argos Veterinary Clinic of Paris Auteuil, 35 Rue Leconte de Lisle, 75016 Paris, France
- SpéNac Referral Center, 100 Boulevard de la Tour Maubourg, 75007 Paris, France
| | - Jesse Bonwitt
- Department of Anthropology, Durham University, South Rd., Durham DH1 3LE, UK
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12
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Kaganer AW, Ossiboff RJ, Keith NI, Schuler KL, Comizzoli P, Hare MP, Fleischer RC, Gratwicke B, Bunting EM. Immune priming prior to pathogen exposure sheds light on the relationship between host, microbiome and pathogen in disease. ROYAL SOCIETY OPEN SCIENCE 2023; 10:220810. [PMID: 36756057 PMCID: PMC9890126 DOI: 10.1098/rsos.220810] [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: 08/11/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Dynamic interactions between host, pathogen and host-associated microbiome dictate infection outcomes. Pathogens including Batrachochytrium dendrobatidis (Bd) threaten global biodiversity, but conservation efforts are hindered by limited understanding of amphibian host, Bd and microbiome interactions. We conducted a vaccination and infection experiment using Eastern hellbender salamanders (Cryptobranchus alleganiensis alleganiensis) challenged with Bd to observe infection, skin microbial communities and gene expression of host skin, pathogen and microbiome throughout the experiment. Most animals survived high Bd loads regardless of their vaccination status and vaccination did not affect pathogen load, but host gene expression differed based on vaccination. Oral vaccination (exposure to killed Bd) stimulated immune gene upregulation while topically and sham-vaccinated animals did not significantly upregulate immune genes. In early infection, topically vaccinated animals upregulated immune genes but orally and sham-vaccinated animals downregulated immune genes. Bd increased pathogenicity-associated gene expression in late infection when Bd loads were highest. The microbiome was altered by Bd, but there was no correlation between anti-Bd microbe abundance or richness and pathogen burden. Our observations suggest that hellbenders initially generate a vigorous immune response to Bd, which is ineffective at controlling disease and is subsequently modulated. Interactions with antifungal skin microbiota did not influence disease progression.
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Affiliation(s)
- Alyssa W. Kaganer
- Department of Natural Resources and the Environment, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
| | - Robert J. Ossiboff
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Nicole I. Keith
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Biology Department, Hamilton College, Clinton, NY, 13323, USA
| | - Krysten L. Schuler
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Pierre Comizzoli
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Matthew P. Hare
- Department of Natural Resources and the Environment, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Robert C. Fleischer
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Brian Gratwicke
- Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA
| | - Elizabeth M. Bunting
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
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13
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Goodwin KB, Hutchinson JD, Gompert Z. Spatiotemporal and ontogenetic variation, microbial selection, and predicted Bd-inhibitory function in the skin-associated microbiome of a Rocky Mountain amphibian. Front Microbiol 2022; 13:1020329. [PMID: 36583053 PMCID: PMC9792605 DOI: 10.3389/fmicb.2022.1020329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
Host-associated microbiomes play important roles in host health and pathogen defense. In amphibians, the skin-associated microbiota can contribute to innate immunity with potential implications for disease management. Few studies have examined season-long temporal variation in the amphibian skin-associated microbiome, and the interactions between bacteria and fungi on amphibian skin remain poorly understood. We characterize season-long temporal variation in the skin-associated microbiome of the western tiger salamander (Ambystoma mavortium) for both bacteria and fungi between sites and across salamander life stages. Two hundred seven skin-associated microbiome samples were collected from salamanders at two Rocky Mountain lakes throughout the summer and fall of 2018, and 127 additional microbiome samples were collected from lake water and lake substrate. We used 16S rRNA and ITS amplicon sequencing with Bayesian Dirichlet-multinomial regression to estimate the relative abundances of bacterial and fungal taxa, test for differential abundance, examine microbial selection, and derive alpha diversity. We predicted the ability of bacterial communities to inhibit the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), a cutaneous fungal pathogen, using stochastic character mapping and a database of Bd-inhibitory bacterial isolates. For both bacteria and fungi, we observed variation in community composition through time, between sites, and with salamander age and life stage. We further found that temporal trends in community composition were specific to each combination of salamander age, life stage, and lake. We found salamander skin to be selective for microbes, with many taxa disproportionately represented relative to the environment. Salamander skin appeared to select for predicted Bd-inhibitory bacteria, and we found a negative relationship between the relative abundances of predicted Bd-inhibitory bacteria and Bd. We hope these findings will assist in the conservation of amphibian species threatened by chytridiomycosis and other emerging diseases.
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Affiliation(s)
- Kenen B. Goodwin
- Department of Watershed Sciences, Utah State University, Logan, UT, United States,Department of Wildland Resources, Utah State University, Logan, UT, United States,*Correspondence: Kenen B. Goodwin,
| | - Jaren D. Hutchinson
- Department of Wildland Resources, Utah State University, Logan, UT, United States
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, UT, United States
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14
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Martínez-Ugalde E, Ávila-Akerberg V, González Martínez TM, Vázquez Trejo M, Zavala Hernández D, Anaya-Morales SL, Rebollar EA. The skin microbiota of the axolotl Ambystoma altamirani is highly influenced by metamorphosis and seasonality but not by pathogen infection. Anim Microbiome 2022; 4:63. [PMID: 36503640 PMCID: PMC9743558 DOI: 10.1186/s42523-022-00215-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/16/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Microbiomes have been increasingly recognized as major contributors to host health and survival. In amphibians, bacterial members of the skin microbiota protect their hosts by inhibiting the growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). Even though several studies describe the influence of biotic and abiotic factors over the skin microbiota, it remains unclear how these symbiotic bacterial communities vary across time and development. This is particularly relevant for species that undergo metamorphosis as it has been shown that host physiology and ecology drastically influence diversity of the skin microbiome. RESULTS We found that the skin bacterial communities of the axolotl A. altamirani are largely influenced by the metamorphic status of the host and by seasonal variation of abiotic factors such as temperature, pH, dissolved oxygen and conductivity. Despite high Bd prevalence in these samples, the bacterial diversity of the skin microbiota did not differ between infected and non-infected axolotls, although relative abundance of particular bacteria were correlated with Bd infection intensity. CONCLUSIONS Our work shows that metamorphosis is a crucial process that shapes skin bacterial communities and that axolotls under different developmental stages respond differently to environmental seasonal variations. Moreover, this study greatly contributes to a better understanding of the factors that shape amphibian skin microbiota, especially in a largely underexplored group like axolotls (Mexican Ambystoma species).
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Affiliation(s)
- Emanuel Martínez-Ugalde
- grid.9486.30000 0001 2159 0001Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Víctor Ávila-Akerberg
- grid.412872.a0000 0001 2174 6731Instituto de Ciencias Agropecuarias y Rurales, Universidad Autónoma del Estado de México, Toluca, Mexico
| | - Tanya M. González Martínez
- grid.9486.30000 0001 2159 0001Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Montserrat Vázquez Trejo
- grid.9486.30000 0001 2159 0001Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Dalia Zavala Hernández
- grid.9486.30000 0001 2159 0001Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sara Lucia Anaya-Morales
- grid.9486.30000 0001 2159 0001Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico ,grid.251313.70000 0001 2169 2489 Department of Biology, University of Mississippi, Oxford, MS USA
| | - Eria A. Rebollar
- grid.9486.30000 0001 2159 0001Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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15
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Hill AJ, Grisnik M, Walker DM. Bacterial Skin Assemblages of Sympatric Salamanders Are Primarily Shaped by Host Genus. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02127-0. [PMID: 36318280 DOI: 10.1007/s00248-022-02127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Bacterial assemblages on the skins of amphibians are known to influence pathogen resistance and other important physiological functions in the host. Host-specific factors and the environment play significant roles in structuring skin assemblages. This study used high-throughput 16S rRNA sequencing and multivariate analyses to examine differences in skin-bacterial assemblages from 246 salamanders belonging to three genera in the lungless family Plethodontidae along multiple spatial gradients. Composition and α- and β-diversity of bacterial assemblages were defined, indicator species were identified for each host group, and the relative influences of host- versus environment-specific ecological factors were evaluated. At the broadest spatial scale, host genus, host species, and sampling site were predictive of skin assemblage structure, but host genus and species were more influential after controlling for the marginal effects of site, as well as nestedness of site. Furthermore, assemblage similarity within each host genus did not change with increasing geographic distance. At the smallest spatial scale, site-specific climate analyses revealed different relationships to climatic variables for each of the three genera, and these relationships were determined by host ecomode. Variation in bacterial assemblages of terrestrial hosts correlated with landscape-level climatic variability, and this pattern decayed with increasing water dependence of the host. Results from this study highlight host-specific considerations for researchers studying wildlife diseases in co-occurring, yet ecologically divergent, species.
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Affiliation(s)
- Aubree J Hill
- Department of Biology, Tennessee Technological University, 1100 North Dixie Avenue, Box 5063, Cookeville, TN, 38505, USA.
| | - Matthew Grisnik
- Department of Agricultural and Environmental Sciences, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN, 37209, USA
| | - Donald M Walker
- Department of Biology, Middle Tennessee State University, 1672 Greenland Drive, Murfreesboro, TN, 37132, USA
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