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Wan B, Chen G, Poon ESK, Fung HS, Lau A, Sin SYW. Environmental factors and host sex influence the skin microbiota structure of Hong Kong newt (Paramesotriton hongkongensis) in a coldspot of chytridiomycosis in subtropical East Asia. Integr Zool 2024. [PMID: 38872359 DOI: 10.1111/1749-4877.12855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Chytridiomycosis, an infectious skin disease caused by the chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans, poses a significant threat to amphibian biodiversity worldwide. Antifungal bacteria found on the skin of chytrid-resistant amphibians could potentially provide defense against chytridiomycosis and lower mortality rates among resistant individuals. The Hong Kong newt (Paramesotriton hongkongensis) is native to East Asia, a region suspected to be the origin of chytrids, and has exhibited asymptomatic infection, suggesting a long-term coexistence with the chytrids. Therefore, the skin microbiota of this resistant species warrant investigation, along with other factors that can affect the microbiota. Among the 149 newts sampled in their natural habitats in Hong Kong, China, putative antifungal bacteria were found in all individuals. There were 314 amplicon sequence variants distributed over 25 genera of putative antifungal bacteria; abundant ones included Acinetobacter, Flavobacterium, and Novosphingobium spp. The skin microbiota compositions were strongly influenced by the inter-site geographical distances. Despite inter-site differences, we identified some core skin microbes across sites that could be vital to P. hongkongensis. The dominant cores included the family Comamonadaceae, family Chitinophagaceae, and class Betaproteobacteria. Moreover, habitat elevation and host sex also exhibited significant effects on skin microbiota compositions. The antifungal bacteria found on these newts offer an important resource for conservation against chytridiomycosis, such as developing probiotic treatments for susceptible species.
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Affiliation(s)
- Bowen Wan
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Guoling Chen
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Emily Shui Kei Poon
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Hon Shing Fung
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Anthony Lau
- Science Unit, Lingnan University, Hong Kong, China
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
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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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3
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Robak MJ, Saenz V, de Cortie E, Richards-Zawacki CL. Effects of temperature on the interaction between amphibian skin bacteria and Batrachochytrium dendrobatidis. Front Microbiol 2023; 14:1253482. [PMID: 37942072 PMCID: PMC10628663 DOI: 10.3389/fmicb.2023.1253482] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023] Open
Abstract
Symbiotic relationships between animals and microbes are important for a range of functions, from digestion to protection from pathogens. However, the impact of temperature variation on these animal-microbe interactions remains poorly understood. Amphibians have experienced population declines and even extinctions on a global scale due to chytridiomycosis, a disease caused by chytrid fungi in the genus Batrachochytrium. Variation in susceptibility to this disease exists within and among host species. While the mechanisms generating differences in host susceptibility remain elusive, differences in immune system components, as well as variation in host and environmental temperatures, have been associated with this variation. The symbiotic cutaneous bacteria of amphibians are another potential cause for variation in susceptibility to chytridiomycosis, with some bacterial species producing antifungal metabolites that prevent the growth of Bd. The growth of both Bd and bacteria are affected by temperature, and thus we hypothesized that amphibian skin bacteria may be more effective at preventing Bd growth at certain temperatures. To test this, we collected bacteria from the skins of frogs, harvested the metabolites they produced when grown at three different temperatures, and then grew Bd in the presence of those metabolites under those same three temperatures in a three-by-three fully crossed design. We found that both the temperature at which cutaneous bacteria were grown (and metabolites produced) as well as the temperature at which Bd is grown can impact the ability of cutaneous bacteria to inhibit the growth of Bd. While some bacterial isolates showed the ability to inhibit Bd growth across multiple temperature treatments, no isolate was found to be inhibitive across all combinations of bacterial incubation or Bd challenge temperatures, suggesting that temperature affects both the metabolites produced and the effectiveness of those metabolites against the Bd pathogen. These findings move us closer to a mechanistic understanding of why chytridiomycosis outbreaks and related amphibian declines are often limited to certain climates and seasons.
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Affiliation(s)
- Matthew J. Robak
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, United States
| | - Veronica Saenz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biology, The Pennsylvania State University, State College, PA, United States
| | - Esmee de Cortie
- Falk School of Sustainability and Environment, Chatham University, Pittsburgh, PA, United States
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4
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Ujszegi J, Boros Z, Fodor A, Vajna B, Hettyey A. Metabolites of Xenorhabdus bacteria are potent candidates for mitigating amphibian chytridiomycosis. AMB Express 2023; 13:88. [PMID: 37615904 PMCID: PMC10449739 DOI: 10.1186/s13568-023-01585-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/20/2023] [Indexed: 08/25/2023] Open
Abstract
Chytridiomycosis, caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), has caused extreme losses in amphibian biodiversity. Finding bacteria that produce metabolites with antifungal properties may turn out to be invaluable in the fight against this devastating disease. The entomopathogenic bacteria, Xenorhabdus szentirmaii and X. budapestensis produce secondary metabolites that are effective against a wide range of fungal plant pathogens. To assess whether they may also be effective against Bd, we extracted cell-free culture media (CFCM) from liquid cultures of X. szentirmaii and X. budapestensis and tested their ability to inhibit Bd growth in vitro. As a second step, using juvenile common toads (Bufo bufo) experimentally infected with Bd we also tested the in vivo antifungal efficacy of X. szentirmaii CFCM diluted to 2 and 10% (v/v), while also assessing possible malign side effects on amphibians. Results of the in vitro experiment documented highly effective growth inhibition by CFCMs of both Xenorhabdus species. The in vivo experiment showed that treatment with CFCM of X. szentirmaii applied at a dilution of 10% resulted in infection intensities reduced by ca. 73% compared to controls and to juvenile toads treated with CFCM applied at a dilution of 2%. At the same time, we detected no negative side effects of treatment with CFCM on toad survival and development. Our results clearly support the idea that metabolites of X. szentirmaii, and perhaps of several other Xenorhabdus species as well, may prove highly useful for the treatment of Bd infected amphibians.
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Affiliation(s)
- János Ujszegi
- Department of Evolutionary Ecology, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Budapest, Hungary.
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, Hungary.
| | - Zsófia Boros
- Department of Evolutionary Ecology, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - András Fodor
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Balázs Vajna
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Attila Hettyey
- Department of Evolutionary Ecology, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, Hungary
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5
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Jones KR, Hughey MC, Belden LK. Colonization order of bacterial isolates on treefrog embryos impacts microbiome structure in tadpoles. Proc Biol Sci 2023; 290:20230308. [PMID: 36946107 PMCID: PMC10031419 DOI: 10.1098/rspb.2023.0308] [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: 02/06/2022] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Priority effects, or impacts of colonization order, may have lasting influence on ecological community composition. The embryonic microbiome is subject to stochasticity in colonization order of bacteria. Stochasticity may be especially impactful for embryos developing in bacteria-rich environments, such as the embryos of many amphibians. To determine if priority effects experienced as embryos impacted bacterial community composition in newly hatched tadpoles, we selectively inoculated the embryos of laboratory-raised hourglass treefrogs, Dendropsophus ebraccatus, with bacteria initially isolated from the skin of wild D. ebraccatus adults over 2 days. First, embryos were inoculated with two bacteria in alternating sequences. Next, we evaluated the outcomes of priority effects in an in vitro co-culture assay absent of host factors. We then performed a second embryo experiment, inoculating embryos with one of three bacteria on the first day and a community of five target bacteria on the second. Through 16S rRNA gene amplicon sequencing, we observed relative abundance shifts in tadpole bacteria communities due to priority effects. Our results suggest that the initial bacterial source pools of embryos shape bacterial communities at later life stages; however, the magnitude of those changes is dependent on the host environment and the identity of bacterial colonists.
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Affiliation(s)
- Korin Rex Jones
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0131, USA
| | - Myra C. Hughey
- Department of Biology, Vassar College, Poughkeepsie, NY 12604, USA
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0131, USA
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6
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Weitzman CL, Kaestli M, Rose A, Hudson CM, Gibb K, Brown GP, Shine R, Christian K. Geographic variation in bacterial assemblages on cane toad skin is influenced more by local environments than by evolved changes in host traits. Biol Open 2023; 12:286922. [PMID: 36745034 PMCID: PMC9932784 DOI: 10.1242/bio.059641] [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: 09/20/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
Bacterial assemblages on amphibian skin may play an important role in protecting hosts against infection. In hosts that occur over a range of environments, geographic variation in composition of bacterial assemblages might be due to direct effects of local factors and/or to evolved characteristics of the host. Invasive cane toads (Rhinella marina) are an ideal candidate to evaluate environmental and genetic mechanisms, because toads have evolved major shifts in physiology, morphology, and behavior during their brief history in Australia. We used samples from free-ranging toads to quantify site-level differences in bacterial assemblages and a common-garden experiment to see if those differences disappeared when toads were raised under standardised conditions at one site. The large differences in bacterial communities on toads from different regions were not seen in offspring raised in a common environment. Relaxing bacterial clustering to operational taxonomic units in place of amplicon sequence variants likewise revealed high similarity among bacterial assemblages on toads in the common-garden study, and with free-ranging toads captured nearby. Thus, the marked geographic divergence in bacterial assemblages on wild-caught cane toads across their Australian invasion appears to result primarily from local environmental effects rather than evolved shifts in the host.
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Affiliation(s)
- Chava L. Weitzman
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0909, Australia,Author for correspondence ()
| | - Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0909, Australia
| | - Alea Rose
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0909, Australia
| | - Cameron M. Hudson
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0909, Australia
| | - Gregory P. Brown
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Richard Shine
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Keith Christian
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0909, Australia
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7
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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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8
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Peixoto RS, Voolstra CR, Sweet M, Duarte CM, Carvalho S, Villela H, Lunshof JE, Gram L, Woodhams DC, Walter J, Roik A, Hentschel U, Thurber RV, Daisley B, Ushijima B, Daffonchio D, Costa R, Keller-Costa T, Bowman JS, Rosado AS, Reid G, Mason CE, Walke JB, Thomas T, Berg G. Harnessing the microbiome to prevent global biodiversity loss. Nat Microbiol 2022; 7:1726-1735. [PMID: 35864220 DOI: 10.1038/s41564-022-01173-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/14/2022] [Indexed: 01/21/2023]
Abstract
Global biodiversity loss and mass extinction of species are two of the most critical environmental issues the world is currently facing, resulting in the disruption of various ecosystems central to environmental functions and human health. Microbiome-targeted interventions, such as probiotics and microbiome transplants, are emerging as potential options to reverse deterioration of biodiversity and increase the resilience of wildlife and ecosystems. However, the implementation of these interventions is urgently needed. We summarize the current concepts, bottlenecks and ethical aspects encompassing the careful and responsible management of ecosystem resources using the microbiome (termed microbiome stewardship) to rehabilitate organisms and ecosystem functions. We propose a real-world application framework to guide environmental and wildlife probiotic applications. This framework details steps that must be taken in the upscaling process while weighing risks against the high toll of inaction. In doing so, we draw parallels with other aspects of contemporary science moving swiftly in the face of urgent global challenges.
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Affiliation(s)
- Raquel S Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Christian R Voolstra
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena Villela
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jeantine E Lunshof
- Department of Global Health and Social Medicine, Center for Bioethics, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jens Walter
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Ute Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Brendan Daisley
- Lawson Health Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Jeff S Bowman
- Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
| | - Alexandre S Rosado
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gregor Reid
- Lawson Health Research Institute, University of Western Ontario, London, Ontario, Canada
| | | | - Jenifer B Walke
- Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Torsten Thomas
- Centre for Marine Science and Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.,University of Postdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
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9
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Besedin D, Turner BJ, Deo P, Lopes MDB, Williams CR. Effect of captivity and water salinity on culture-dependent frog skin microbiota and Batrachochytrium dendrobatidis ( Bd) infection. T ROY SOC SOUTH AUST 2022. [DOI: 10.1080/03721426.2022.2086358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Darislav Besedin
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Brandon J. Turner
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Permal Deo
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- Health and Biomedical Innovation, UniSA Clinical and Health Science, University of South Australia, Adelaide, South Australia, Australia
| | - Miguel De Barros Lopes
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- Health and Biomedical Innovation, UniSA Clinical and Health Science, University of South Australia, Adelaide, South Australia, Australia
| | - Craig R. Williams
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
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10
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Zhu W, Zhao C, Feng J, Chang J, Zhu W, Chang L, Liu J, Xie F, Li C, Jiang J, Zhao T. Effects of Habitat River Microbiome on the Symbiotic Microbiota and Multi-Organ Gene Expression of Captive-Bred Chinese Giant Salamander. Front Microbiol 2022; 13:884880. [PMID: 35770173 PMCID: PMC9234736 DOI: 10.3389/fmicb.2022.884880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/11/2022] [Indexed: 11/21/2022] Open
Abstract
The reintroduction of captive-bred individuals is a primary approach to rebuild the wild populations of the Chinese giant salamander (Andrias davidianus), the largest extant amphibian species. However, the complexity of the wild habitat (e.g., diverse microorganisms and potential pathogens) potentially threatens the survival of reintroduced individuals. In this study, fresh (i.e., containing environmental microbiota) or sterilized river sediments (120°C sterilized treatment) were added to the artificial habitats to treat the larvae of the Chinese giant salamander (control group—Cnt: 20 individuals, treatment group 1 with fresh river sediments—T1: 20 individuals, and treatment group 2 with sterilized river sediments—T2: 20 individuals). The main objective of this study was to test whether this procedure could provoke their wild adaptability from the perspective of commensal microbiotas (skin, oral cavity, stomach, and gut) and larvae transcriptomes (skin, spleen, liver, and brain). Our results indicated that the presence of habitat sediments (whether fresh or sterilized) reshaped the oral bacterial community composition. Specifically, Firmicutes decreased dramatically from ~70% to ~20–25% (mainly contributed by Lactobacillaceae), while Proteobacteria increased from ~6% to ~31–36% (mainly contributed by Gammaproteobacteria). Consequently, the proportion of antifungal operational taxonomic units (OTUs) increased, and the function of oral microbiota likely shifted from growth-promoting to pathogen defense. Interestingly, the skin microbiota, rather than the colonization of habitat microbiota, was the major source of the pre-treated oral microbiota. From the host perspective, the transcriptomes of all four organs were changed for treated individuals. Specifically, the proteolysis and apoptosis in the skin were promoted, and the transcription of immune genes was activated in the skin, spleen, and liver. Importantly, more robust immune activation was detected in individuals treated with sterilized sediments. These results suggested that the pathogen defense of captive-bred individuals was improved after being treated, which may benefit their survival in the wild. Taken together, our results suggested that the pre-exposure of captive-bred Chinese giant salamander individuals to habitat sediments could be considered and added into the reintroduction processes to help them better adapt to wild conditions.
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Affiliation(s)
- Wei Zhu
- Chinese Academy of Sciences (CAS) Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chengdu, China
| | - Chunlin Zhao
- Chinese Academy of Sciences (CAS) Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chengdu, China
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianyi Feng
- Chinese Academy of Sciences (CAS) Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chengdu, China
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Wenbo Zhu
- Chinese Academy of Sciences (CAS) Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chengdu, China
| | - Liming Chang
- Chinese Academy of Sciences (CAS) Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chengdu, China
| | - Jiongyu Liu
- Chinese Academy of Sciences (CAS) Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chengdu, China
| | - Feng Xie
- Chinese Academy of Sciences (CAS) Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chengdu, China
| | - Cheng Li
- Chinese Academy of Sciences (CAS) Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chengdu, China
| | - Jianping Jiang
- Chinese Academy of Sciences (CAS) Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chengdu, China
- *Correspondence: Jianping Jiang
| | - Tian Zhao
- Chinese Academy of Sciences (CAS) Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chengdu, China
- Tian Zhao
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11
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Knapp RA, Joseph MB, Smith TC, Hegeman EE, Vredenburg VT, Erdman Jr JE, Boiano DM, Jani AJ, Briggs CJ. Effectiveness of antifungal treatments during chytridiomycosis epizootics in populations of an endangered frog. PeerJ 2022; 10:e12712. [PMID: 35036095 PMCID: PMC8742549 DOI: 10.7717/peerj.12712] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023] Open
Abstract
The recently-emerged amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has had an unprecedented impact on global amphibian populations, and highlights the urgent need to develop effective mitigation strategies. We conducted in-situ antifungal treatment experiments in wild populations of the endangered mountain yellow-legged frog during or immediately after Bd-caused mass die-off events. The objective of treatments was to reduce Bd infection intensity ("load") and in doing so alter frog-Bd dynamics and increase the probability of frog population persistence despite ongoing Bd infection. Experiments included treatment of early life stages (tadpoles and subadults) with the antifungal drug itraconazole, treatment of adults with itraconazole, and augmentation of the skin microbiome of subadults with Janthinobacterium lividum, a commensal bacterium with antifungal properties. All itraconazole treatments caused immediate reductions in Bd load, and produced longer-term effects that differed between life stages. In experiments focused on early life stages, Bd load was reduced in the 2 months immediately following treatment and was associated with increased survival of subadults. However, Bd load and frog survival returned to pre-treatment levels in less than 1 year, and treatment had no effect on population persistence. In adults, treatment reduced Bd load and increased frog survival over the entire 3-year post-treatment period, consistent with frogs having developed an effective adaptive immune response against Bd. Despite this protracted period of reduced impacts of Bd on adults, recruitment into the adult population was limited and the population eventually declined to near-extirpation. In the microbiome augmentation experiment, exposure of subadults to a solution of J. lividum increased concentrations of this potentially protective bacterium on frogs. However, concentrations declined to baseline levels within 1 month and did not have a protective effect against Bd infection. Collectively, these results indicate that our mitigation efforts were ineffective in causing long-term changes in frog-Bd dynamics and increasing population persistence, due largely to the inability of early life stages to mount an effective immune response against Bd. This results in repeated recruitment failure and a low probability of population persistence in the face of ongoing Bd infection.
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Affiliation(s)
- Roland A. Knapp
- Sierra Nevada Aquatic Research Laboratory, University of California, Mammoth Lakes, California, United States
- Earth Research Institute, University of California, Santa Barbara, California, United States
| | | | - Thomas C. Smith
- Sierra Nevada Aquatic Research Laboratory, University of California, Mammoth Lakes, California, United States
- Earth Research Institute, University of California, Santa Barbara, California, United States
| | - Ericka E. Hegeman
- Sierra Nevada Aquatic Research Laboratory, University of California, Mammoth Lakes, California, United States
- Earth Research Institute, University of California, Santa Barbara, California, United States
| | - Vance T. Vredenburg
- Department of Biology, San Francisco State University, San Francisco, California, United States
| | - James E. Erdman Jr
- California Department of Fish and Wildlife, Bishop, California, United States
| | - Daniel M. Boiano
- Sequoia and Kings Canyon National Parks, National Park Service, Three Rivers, California, United States
| | - Andrea J. Jani
- Pacific Biosciences Research Center, University of Hawai’i at Mànoa, Honolulu, Hawai’i, United States
| | - Cheryl J. Briggs
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California, United States
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12
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McGrath-Blaser S, Steffen M, Grafe TU, Torres-Sánchez M, McLeod DS, Muletz-Wolz CR. Early life skin microbial trajectory as a function of vertical and environmental transmission in Bornean foam-nesting frogs. Anim Microbiome 2021; 3:83. [PMID: 34930504 PMCID: PMC8686334 DOI: 10.1186/s42523-021-00147-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The amphibian skin microbiome is an important mediator of host health and serves as a potential source of undiscovered scientifically significant compounds. However, the underlying modalities of how amphibian hosts obtain their initial skin-associated microbiome remains unclear. Here, we explore microbial transmission patterns in foam-nest breeding tree frogs from Southeast Asia (Genus: Polypedates) whose specialized breeding strategy allows for better delineation between vertically and environmentally derived microbes. To facilitate this, we analyzed samples associated with adult frog pairs taken after mating-including adults of each sex, their foam nests, environments, and tadpoles before and after environmental interaction-for the bacterial communities using DNA metabarcoding data (16S rRNA). Samples were collected from frogs in-situ in Brunei, Borneo, a previously unsampled region for amphibian-related microbial diversity. RESULTS Adult frogs differed in skin bacterial communities among species, but tadpoles did not differ among species. Foam nests had varying bacterial community composition, most notably in the nests' moist interior. Nest interior bacterial communities were discrete for each nest and overall displayed a narrower diversity compared to the nest exteriors. Tadpoles sampled directly from the foam nest displayed a bacterial composition less like the nest interior and more similar to that of the adults and nest exterior. After one week of pond water interaction the tadpole skin microbiome shifted towards the tadpole skin and pond water microbial communities being more tightly coupled than between tadpoles and the internal nest environment, but not to the extent that the skin microbiome mirrored the pond bacterial community. CONCLUSIONS Both vertical influence and environmental interaction play a role in shaping the tadpole cutaneous microbiome. Interestingly, the interior of the foam nest had a distinct bacterial community from the tadpoles suggesting a limited environmental effect on tadpole cutaneous bacterial selection at initial stages of life. The shift in the tadpole microbiome after environmental interaction indicates an interplay between underlying host and ecological mechanisms that drive community formation. This survey serves as a baseline for further research into the ecology of microbial transmission in aquatic animals.
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Affiliation(s)
- Sarah McGrath-Blaser
- Department of Biology, University of Florida, 421 Carr Hall, Gainesville, FL 32611 USA
| | - Morgan Steffen
- Department of Biology, James Madison University, 951 Carrier Dr, Harrisonburg, VA 22807 USA
| | - T. Ulmar Grafe
- Universiti Brunei Darussalam, Tungku Link, Gadong, BE 1410 Brunei
| | - María Torres-Sánchez
- Department of Biology, University of Florida, 421 Carr Hall, Gainesville, FL 32611 USA
| | - David S. McLeod
- Department of Biology, James Madison University, 951 Carrier Dr, Harrisonburg, VA 22807 USA
- North Carolina Museum of Natural Sciences, 11 West Jones Street, Raleigh, NC 27601 USA
| | - Carly R. Muletz-Wolz
- Smithsonian National Zoo and Conservation Biology Institute, Center for Conservation Genomics, 3001 Connecticut Ave., Washington, DC 20008 USA
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13
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Buttimer S, Hernández-Gómez O, Rosenblum EB. Skin bacterial metacommunities of San Francisco Bay Area salamanders are structured by host genus and habitat quality. FEMS Microbiol Ecol 2021; 97:6464136. [PMID: 34918086 DOI: 10.1093/femsec/fiab162] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/14/2021] [Indexed: 11/13/2022] Open
Abstract
Host-associated microbial communities can influence physiological processes of macroorganisms, including contributing to infectious disease resistance. For instance, some bacteria that live on amphibian skin produce antifungal compounds that inhibit two lethal fungal pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal). Therefore, differences in microbiome composition among host species or populations within a species can contribute to variation in susceptibility to Bd/Bsal. This study applies 16S rRNA sequencing to characterize the skin bacterial microbiomes of three widespread terrestrial salamander genera native to the western United States. Using a metacommunity structure analysis, we identified dispersal barriers for these influential bacteria between salamander families and localities. We also analyzed the effects of habitat characteristics such as percent natural cover and temperature seasonality on the microbiome. We found that certain environmental variables may influence the skin microbial communities of some salamander genera more strongly than others. Each salamander family had a somewhat distinct community of putative anti-Bd skin bacteria, suggesting that salamanders may select for a functional assembly of cutaneous symbionts that could differ in its ability to protect these amphibians from disease. Our observations raise the need to consider host identity and environmental heterogeneity during the selection of probiotics to treat wildlife diseases.
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Affiliation(s)
- Shannon Buttimer
- Department of Environmental Science, Policy, and Management - The University of California, Berkeley, Berkeley, CA, U.S.A.,Department of Biological Sciences - The University of Alabama, Tuscaloosa, AL, U.S.A
| | - Obed Hernández-Gómez
- Department of Environmental Science, Policy, and Management - The University of California, Berkeley, Berkeley, CA, U.S.A.,School of Health and Natural Sciences - Dominican University of California, San Rafael, CA, U.S.A
| | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, and Management - The University of California, Berkeley, Berkeley, CA, U.S.A
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14
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Becker MH, Brophy JAN, Barrett K, Bronikowski E, Evans M, Glassey E, Kaganer AW, Klocke B, Lassiter E, Meyer AJ, Muletz-Wolz CR, Fleischer RC, Voigt CA, Gratwicke B. Genetically modifying skin microbe to produce violacein and augmenting microbiome did not defend Panamanian golden frogs from disease. ISME COMMUNICATIONS 2021; 1:57. [PMID: 37938636 PMCID: PMC9723765 DOI: 10.1038/s43705-021-00044-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 04/21/2023]
Abstract
We designed two probiotic treatments to control chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd) on infected Panamanian golden frogs (Atelopus zeteki), a species that is thought to be extinct in the wild due to Bd. The first approach disrupted the existing skin microbe community with antibiotics then exposed the frogs to a core golden frog skin microbe (Diaphorobacter sp.) that we genetically modified to produce high titers of violacein, a known antifungal compound. One day following probiotic treatment, the engineered Diaphorobacter and the violacein-producing pathway could be detected on the frogs but the treatment failed to improve frog survival when exposed to Bd. The second approach exposed frogs to the genetically modified bacterium mixed into a consortium with six other known anti-Bd bacteria isolated from captive A. zeteki, with no preliminary antibiotic treatment. The consortium treatment increased the frequency and abundance of three probiotic isolates (Janthinobacterium, Chryseobacterium, and Stenotrophomonas) and these persisted on the skin 4 weeks after probiotic treatment. There was a temporary increase in the frequency and abundance of three other probiotics isolates (Masillia, Serratia, and Pseudomonas) and the engineered Diaphorobacter isolate, but they subsequently disappeared from the skin. This treatment also failed to reduce frog mortality upon exposure.
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Affiliation(s)
- Matthew H Becker
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA, USA
- Liberty University Department of Biology and Chemistry, Lynchburg, VA, USA
| | - Jennifer A N Brophy
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Ed Bronikowski
- Smithsonian's National Zoo and Conservation Biology Institute Reptile Discovery Center, Washington, DC, USA
| | - Matthew Evans
- Smithsonian's National Zoo and Conservation Biology Institute Reptile Discovery Center, Washington, DC, USA
| | - Emerson Glassey
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alyssa W Kaganer
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA, USA
| | - Blake Klocke
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA, USA
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Elliot Lassiter
- Smithsonian's National Zoo and Conservation Biology Institute Reptile Discovery Center, Washington, DC, USA
| | - Adam J Meyer
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carly R Muletz-Wolz
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Conservation Genetics, Washington, DC, 20001, USA
| | - Robert C Fleischer
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Conservation Genetics, Washington, DC, 20001, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian Gratwicke
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA, USA.
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15
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Abstract
Animals live in symbiosis with numerous microbe species. While some can protect hosts from infection and benefit host health, components of the microbiota or changes to the microbial landscape have the potential to facilitate infections and worsen disease severity. Pathogens and pathobionts can exploit microbiota metabolites, or can take advantage of a depletion in host defences and changing conditions within a host, to cause opportunistic infection. The microbiota might also favour a more virulent evolutionary trajectory for invading pathogens. In this review, we consider the ways in which a host microbiota contributes to infectious disease throughout the host's life and potentially across evolutionary time. We further discuss the implications of these negative outcomes for microbiota manipulation and engineering in disease management.
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Affiliation(s)
- Emily J. Stevens
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kieran A. Bates
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kayla C. King
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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16
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The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance. ISME JOURNAL 2021; 15:1628-1640. [PMID: 33564111 PMCID: PMC8163836 DOI: 10.1038/s41396-020-00875-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/24/2020] [Accepted: 12/07/2020] [Indexed: 12/29/2022]
Abstract
Infectious pathogens can disrupt the microbiome in addition to directly affecting the host. Impacts of disease may be dependent on the ability of the microbiome to recover from such disturbance, yet remarkably little is known about microbiome recovery after disease, particularly in nonhuman animals. We assessed the resilience of the amphibian skin microbial community after disturbance by the pathogen, Batrachochytrium dendrobatidis (Bd). Skin microbial communities of laboratory-reared mountain yellow-legged frogs were tracked through three experimental phases: prior to Bd infection, after Bd infection (disturbance), and after clearing Bd infection (recovery period). Bd infection disturbed microbiome composition and altered the relative abundances of several dominant bacterial taxa. After Bd infection, frogs were treated with an antifungal drug that cleared Bd infection, but this did not lead to recovery of microbiome composition (measured as Unifrac distance) or relative abundances of dominant bacterial groups. These results indicate that Bd infection can lead to an alternate stable state in the microbiome of sensitive amphibians, or that microbiome recovery is extremely slow—in either case resilience is low. Furthermore, antifungal treatment and clearance of Bd infection had the additional effect of reducing microbial community variability, which we hypothesize results from similarity across frogs in the taxa that colonize community vacancies resulting from the removal of Bd. Our results indicate that the skin microbiota of mountain yellow-legged frogs has low resilience following Bd-induced disturbance and is further altered by the process of clearing Bd infection, which may have implications for the conservation of this endangered amphibian.
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17
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Le Sage EH, LaBumbard BC, Reinert LK, Miller BT, Richards-Zawacki CL, Woodhams DC, Rollins-Smith LA. Preparatory immunity: Seasonality of mucosal skin defences and Batrachochytrium infections in Southern leopard frogs. J Anim Ecol 2020; 90:542-554. [PMID: 33179786 DOI: 10.1111/1365-2656.13386] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/28/2020] [Indexed: 12/14/2022]
Abstract
Accurately predicting the impacts of climate change on wildlife health requires a deeper understanding of seasonal rhythms in host-pathogen interactions. The amphibian pathogen, Batrachochytrium dendrobatidis (Bd), exhibits seasonality in incidence; however, the role that biological rhythms in host defences play in defining this pattern remains largely unknown. The aim of this study was to examine whether host immune and microbiome defences against Bd correspond with infection risk and seasonal fluctuations in temperature and humidity. Over the course of a year, five populations of Southern leopard frogs (Rana [Lithobates] sphenocephala) in Tennessee, United States, were surveyed for host immunity, microbiome and pathogen dynamics. Frogs were swabbed for pathogen load and skin bacterial diversity and stimulated to release stored antimicrobial peptides (AMPs). Secretions were analysed to estimate total hydrophobic peptide concentrations, presence of known AMPs and effectiveness of Bd growth inhibition in vitro. The diversity and proportion of bacterial reads with a 99% match to sequences of isolates known to inhibit Bd growth in vitro were used as an estimate of predicted anti-Bd function of the skin microbiome. Batrachochytrium dendrobatidis dynamics followed the expected seasonal fluctuations-peaks in cooler months-which coincided with when host mucosal defences were most potent against Bd. Specifically, the concentration and expression of stored AMPs cycled synchronously with Bd dynamics. Although microbiome changes followed more linear trends over time, the proportion of bacteria that can function to inhibit Bd growth was greatest when risk of Bd infection was highest. We interpret the increase in peptide storage in the fall and the shift to a more anti-Bd microbiome over winter as a preparatory response for subsequent infection risk during the colder periods when AMP synthesis and bacterial growth is slow and pathogen pressure from this cool-adapted fungus is high. Given that a decrease in stored AMP concentrations as temperatures warm in spring likely means greater secretion rates, the subsequent decrease in prevalence suggests seasonality of Bd in this host may be in part regulated by annual immune rhythms, and dominated by the effects of temperature.
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Affiliation(s)
- Emily H Le Sage
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Laura K Reinert
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Brian T Miller
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | | | - Doug C Woodhams
- Department of Biology, University of Massachusetts, Boston, MA, USA
| | - Louise A Rollins-Smith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA
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18
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Martin H. C, Ibáñez R, Nothias LF, Caraballo-Rodríguez AM, Dorrestein PC, Gutiérrez M. Metabolites from Microbes Isolated from the Skin of the Panamanian Rocket Frog Colostethus panamansis (Anura: Dendrobatidae). Metabolites 2020; 10:E406. [PMID: 33065987 PMCID: PMC7601193 DOI: 10.3390/metabo10100406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 01/02/2023] Open
Abstract
The Panamanian rocket frog Colostethus panamansis (family Dendrobatidae) has been affected by chytridiomycosis, a deadly disease caused by the fungus Batrachochytrium dendrobatidis (Bd). While there are still uninfected frogs, we set out to isolate microbes from anatomically distinct regions in an effort to create a cultivable resource within Panama for potential drug/agricultural/ecological applications that perhaps could also be used as part of a strategy to protect frogs from infections. To understand if there are specific anatomies that should be explored in future applications of this resource, we mapped skin-associated bacteria of C. panamansis and their metabolite production potential by mass spectrometry on a 3D model. Our results indicate that five bacterial families (Enterobacteriaceae, Comamonadaceae, Aeromonadaceae, Staphylococcaceae and Pseudomonadaceae) dominate the cultivable microbes from the skin of C. panamansis. The combination of microbial classification and molecular analysis in relation to the anti-Bd inhibitory databases reveals the resource has future potential for amphibian conservation.
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Affiliation(s)
- Christian Martin H.
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, Panama 0843-01103, Panama;
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522510, India
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama 0843-03092, Panama;
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; (L.-F.N.); (A.M.C.-R.); (P.C.D.)
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; (L.-F.N.); (A.M.C.-R.); (P.C.D.)
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; (L.-F.N.); (A.M.C.-R.); (P.C.D.)
| | - Marcelino Gutiérrez
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, Panama 0843-01103, Panama;
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19
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Tong Q, Cui LY, Du XP, Hu ZF, Bie J, Xiao JH, Wang HB, Zhang JT. Comparison of Gut Microbiota Diversity and Predicted Functions Between Healthy and Diseased Captive Rana dybowskii. Front Microbiol 2020; 11:2096. [PMID: 32983063 PMCID: PMC7490342 DOI: 10.3389/fmicb.2020.02096] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 08/10/2020] [Indexed: 01/26/2023] Open
Abstract
The gut microbiota plays a key role in host health, and disruptions to gut bacterial homeostasis can cause disease. However, the effect of disease on gut microbiota assembly remains unclear and gut microbiota-based predictions of health status is a promising yet poorly established field. Using Illumina high-throughput sequencing technology, we compared the gut microbiota between healthy (HA and HB) and diarrhoeic (DS) Rana dybowskii groups and analyzed the functional profiles through a phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis. In addition, we estimated the correlation between gut microbiota structures and predicted the functional compositions. The results showed significant differences in the phylogenetic diversity (Pd), Shannon, and observed richness (Sobs) indices between the DS and HB groups, with significant differences observed in the gut microbiota composition between the DS group and the HA and HB groups. Linear discriminant analysis (LDA) effect size (LEfSe) results revealed that Proteobacteria were significantly enriched in the DS group; Bacteroidetes were significantly enriched in the HA and HB groups; and Aeromonas, Citrobacter, Enterococcus, Hafnia-Obesumbacterium, Morganella, Lactococcus, Providencia, Vagococcus, and Staphylococcus were significantly enriched in the DS group. Venn diagrams revealed that there were many more unique genera in the DS group than the HA and HB groups. Among 102 sensitive species selected using the indicator method, 33 indicated a healthy status and 69 (e.g., Acinetobacter, Aeromonas, Legionella, Morganella, Proteus, Providencia, Staphylococcus, and Vagococcus) indicated a diseased status. There was a significant and positive association between the composition and functional composition of the gut microbiota, thus indicating low functional redundancy of the frog gut bacterial community. Rana dybowskii disease was associated with changes in the gut microbiota, which subsequently disrupted bacterial-mediated functions. The results of this study can aid in revealing the effect of the R. dybowskii gut microbiota on host health and provide a basis for elucidating the mechanism of the occurrence of R. dybowskii disease.
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Affiliation(s)
- Qing Tong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Jiamusi Branch of Heilongjiang Academy of Forestry Sciences, Jiamusi, China
| | - Li-Yong Cui
- Jiamusi Branch of Heilongjiang Academy of Forestry Sciences, Jiamusi, China
| | - Xiao-Peng Du
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Zong-Fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jia Bie
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jian-Hua Xiao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Hong-Bin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jian-Tao Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
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20
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Loudon AH, Kurtz A, Esposito E, Umile TP, Minbiole KPC, Parfrey LW, Sheafor BA. Columbia spotted frogs (Rana luteiventris) have characteristic skin microbiota that may be shaped by cutaneous skin peptides and the environment. FEMS Microbiol Ecol 2020; 96:5894915. [DOI: 10.1093/femsec/fiaa168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/13/2020] [Indexed: 01/20/2023] Open
Abstract
ABSTRACT
Global amphibian declines due to the fungal pathogen Batrachochytrium dendrobatidis (Bd) have led to questions about how amphibians defend themselves against skin diseases. A total of two amphibian defense mechanisms are antimicrobial peptides (AMPs), a component of amphibian innate immune defense and symbiotic skin bacteria, which can act in synergy. We characterized components of these factors in four populations of Columbia spotted frogs (Rana luteiventris) to investigate their role in disease defense. We surveyed the ability of their AMPs to inhibit Bd, skin bacterial community composition, skin metabolite profiles and presence and intensity of Bd infection. We found that AMPs from R. luteiventris inhibited Bd in bioassays, but inhibition did not correlate with Bd intensity on frogs. R. luteiventris had two prevalent and abundant core bacteria: Rhizobacter and Chryseobacterium. Rhizobacter relative abundance was negatively correlated with AMP's ability to inhibit Bd, but was not associated with Bd status itself. There was no relationship between metabolites and Bd. Bacterial communities and Bd differ by location, which suggests a strong environmental influence. R. luteiventris are dominated by consistent core bacteria, but also house transient bacteria that are site specific. Our emergent hypothesis is that host control and environmental factors shape the microbiota on R. luteiventris.
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Affiliation(s)
- A H Loudon
- Department of Zoology and Biodiversity Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, CA
| | - A Kurtz
- Biology Department, Carroll College, Helena, Montana, 59625-0002, USA
| | - E Esposito
- Biology Department, Carroll College, Helena, Montana, 59625-0002, USA
| | - T P Umile
- Department of Chemistry, Villanova University, Villanova, Pennsylvania, 19085-1603, USA
| | - K P C Minbiole
- Department of Chemistry, Villanova University, Villanova, Pennsylvania, 19085-1603, USA
| | - L W Parfrey
- Department of Zoology and Biodiversity Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, CA
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, CA
| | - B A Sheafor
- Biology Department, Carroll College, Helena, Montana, 59625-0002, USA
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21
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Rebollar EA, Martínez-Ugalde E, Orta AH. The Amphibian Skin Microbiome and Its Protective Role Against Chytridiomycosis. HERPETOLOGICA 2020. [DOI: 10.1655/0018-0831-76.2.167] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Emanuel Martínez-Ugalde
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Alberto H. Orta
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
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22
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Tong Q, Hu ZF, Du XP, Bie J, Wang HB. Effects of Seasonal Hibernation on the Similarities Between the Skin Microbiota and Gut Microbiota of an Amphibian (Rana dybowskii). MICROBIAL ECOLOGY 2020; 79:898-909. [PMID: 31820074 DOI: 10.1007/s00248-019-01466-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Both the gut and skin microbiotas have important functions for amphibians. The gut microbiota plays an important role in both the health and evolution of the host species, whereas the role of skin microbiota in disease resistance is particularly important for amphibians. Many studies have examined the effects of environmental factors on the skin and gut microbiotas, but no study has yet explored the similarities between the skin and gut microbiotas. In this study, the gut and skin microbiotas of Rana dybowskii in summer and winter were investigated via high-throughput Illumina sequencing. The results showed that the alpha diversity of gut and skin microbiotas decreased significantly from summer to winter. In both seasons, the microbial composition and structure differed significantly between the gut and skin, and the similarities between these microbiotas differed between seasons. The pairwise distances between the gut and skin microbiotas were greater in winter than in summer. The ratio of core OTUs and shared OTUs to the sum of the OTUs in the gut and skin microbiotas in summer was significantly higher than that in winter. The similarities between the gut and skin microbiotas are important for understanding amphibian ecology and life history.
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Affiliation(s)
- Qing Tong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, People's Republic of China
- Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, Harbin, 150030, China
| | - Zong-Fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Xiao-Peng Du
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Jia Bie
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Hong-Bin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
- Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, Harbin, 150030, China.
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23
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Kruger A. Functional Redundancy of Batrachochytrium dendrobatidis Inhibition in Bacterial Communities Isolated from Lithobates clamitans Skin. MICROBIAL ECOLOGY 2020; 79:231-240. [PMID: 31165187 DOI: 10.1007/s00248-019-01387-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/29/2019] [Indexed: 06/09/2023]
Abstract
The cutaneous microbial community can influence the health of amphibians exposed to Batrachochytrium dendrobatidis (Bd), a fungal pathogen that has contributed to recent amphibian declines. Resistance to Bd in amphibian populations is correlated with the presence of anti-Bd cutaneous microbes, which confer disease resistance by inhibiting Bd growth. I aimed to determine if green frogs (Lithobates clamitans), an abundant and widely distributed species in New Jersey, harbored bacteria that inhibit Bd and whether the presence and identity of these microbes varied among sites. I used in vitro challenge assays to determine if bacteria isolated from green frog skin could inhibit or enhance the growth of Bd. I found that green frogs at all sites harbored anti-Bd bacteria. However, there were differences in Bd inhibition capabilities among bacterial isolates identified as the same operational taxonomic unit (OTU), lending support to the idea that phylogenetic relatedness does not always predict Bd inhibition status. Additionally, anti-Bd bacterial richness did not vary by site, but the composition of anti-Bd bacterial taxa was distinct at each site. This suggests that there is functional redundancy of Bd inhibition across unique communities of anti-Bd symbionts found on frogs at different sites. These findings highlight the need to better elucidate the structure-function relationship of microbiomes and their role in disease resistance.
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Affiliation(s)
- Ariel Kruger
- Graduate Program in Ecology and Evolution, Department of Ecology, Evolution, and Natural Resources, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, 08901, USA.
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24
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Niederle MV, Bosch J, Ale CE, Nader-Macías ME, Aristimuño Ficoseco C, Toledo LF, Valenzuela-Sánchez A, Soto-Azat C, Pasteris SE. Skin-associated lactic acid bacteria from North American bullfrogs as potential control agents of Batrachochytrium dendrobatidis. PLoS One 2019; 14:e0223020. [PMID: 31560707 PMCID: PMC6764794 DOI: 10.1371/journal.pone.0223020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/11/2019] [Indexed: 11/18/2022] Open
Abstract
The fungal pathogen Batrachochytrium dendrobatidis (Bd) is the causative agent of chytridiomycosis and has been a key driver in the catastrophic decline of amphibians globally. While many strategies have been proposed to mitigate Bd outbreaks, few have been successful. In recent years, the use of probiotic formulations that protect an amphibian host by killing or inhibiting Bd have shown promise as an effective chytridiomycosis control strategy. The North American bullfrog (Lithobates catesbeianus) is a common carrier of Bd and harbours a diverse skin microbiota that includes lactic acid bacteria (LAB), a microbial group containing species classified as safe and conferring host benefits. We investigated beneficial/probiotic properties: anti-Bd activity, and adhesion and colonisation characteristics (hydrophobicity, biofilm formation and exopolysaccharide-EPS production) in two confirmed LAB (cLAB-Enterococcus gallinarum CRL 1826, Lactococcus garvieae CRL 1828) and 60 presumptive LAB (pLAB) [together named as LABs] isolated from bullfrog skin.We challenged LABs against eight genetically diverse Bd isolates and found that 32% of the LABs inhibited at least one Bd isolate with varying rates of inhibition. Thus, we established a score of sensitivity from highest (BdGPL AVS7) to lowest (BdGPL C2A) for the studied Bd isolates. We further reveal key factors underlying host adhesion and colonisation of LABs. Specifically, 90.3% of LABs exhibited hydrophilic properties that may promote adhesion to the cutaneous mucus, with the remaining isolates (9.7%) being hydrophobic in nature with a surface polarity compatible with colonisation of acidic, basic or both substrate types. We also found that 59.7% of LABs showed EPS synthesis and 66.1% produced biofilm at different levels: 21% weak, 29% moderate, and 16.1% strong. Together all these properties enhance colonisation of the host surface (mucus or epithelial cells) and may confer protective benefits against Bd through competitive exclusion. Correspondence analysis indicated that biofilm synthesis was LABs specific with high aggregating bacteria correlating with strong biofilm producers, and EPS producers being correlated to negative biofilm producing LABs. We performed Random Amplified Polymorphic DNA (RAPD)-PCR analysis and demonstrated a higher degree of genetic diversity among rod-shaped pLAB than cocci. Based on the LAB genetic analysis and specific probiotic selection criteria that involve beneficial properties, we sequenced 16 pLAB which were identified as Pediococcus pentosaceus, Enterococcus thailandicus, Lactobacillus pentosus/L. plantarum, L. brevis, and L. curvatus. Compatibility assays performed with cLAB and the 16 species described above indicate that all tested LAB can be included in a mixed probiotic formula. Based on our analyses, we suggest that E. gallinarum CRL 1826, L. garvieae CRL 1828, and P. pentosaceus 15 and 18B represent optimal probiotic candidates for Bd control and mitigation.
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Affiliation(s)
- M. V. Niederle
- Instituto Superior de Investigaciones Biológicas (INSIBIO), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Instituto de Biología “Dr. Francisco D. Barbieri”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT), San Miguel de Tucumán, Argentina
| | - J. Bosch
- Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
- Research Unit of Biodiversity (CSIC, UO, PA), Oviedo University—Campus Mieres, Spain
| | - C. E. Ale
- Instituto Superior de Investigaciones Biológicas (INSIBIO), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Instituto de Biología “Dr. Francisco D. Barbieri”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT), San Miguel de Tucumán, Argentina
| | - M. E. Nader-Macías
- Centro de Referencia para Lactobacilos (CERELA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Miguel de Tucumán, Argentina
| | - C. Aristimuño Ficoseco
- Centro de Referencia para Lactobacilos (CERELA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Miguel de Tucumán, Argentina
| | - L. F. Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - A. Valenzuela-Sánchez
- Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Organización No Gubernamental (ONG) Ranita de Darwin, Santiago, Chile
- Organización No Gubernamental (ONG) Ranita de Darwin, Valdivia, Chile
| | - C. Soto-Azat
- Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - S. E. Pasteris
- Instituto Superior de Investigaciones Biológicas (INSIBIO), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Instituto de Biología “Dr. Francisco D. Barbieri”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT), San Miguel de Tucumán, Argentina
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25
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Medina D, Ibáñez R, Lips KR, Crawford AJ. Amphibian diversity in Serranía de Majé, an isolated mountain range in eastern Panamá. Zookeys 2019; 859:117-130. [PMID: 31327925 PMCID: PMC6616096 DOI: 10.3897/zookeys.859.32869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/29/2019] [Indexed: 11/12/2022] Open
Abstract
Eastern Panamá is within the Mesoamerican biodiversity hotspot and supports an understudied amphibian fauna. Here we characterize the amphibian diversity across an elevational gradient in one of the least studied mountain ranges in eastern Panamá, Serranía de Majé. A total of 38 species were found, which represent 17% of all species reported for Panamá. Based on expected richness function and individual-based rarefaction curves, it is estimated that this is an underestimate and that at least 44 amphibian species occur in this area. Members of all three amphibian orders were encountered, represented by ten families and 22 genera, including five species endemic to Central America. Estimated species richness decreased with elevation, and the mid-elevation site supported both lowland and highland species. Our study provides a baseline for understanding the distribution pattern of amphibians in Panamá, for conservation efforts, and for determining disease-induced changes in amphibian communities.
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Affiliation(s)
- Daniel Medina
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, SP 13083-862, Brazil Smithsonian Tropical Research Institute Panamá Panama.,Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, República de Panamá Universidade Estadual de Campinas Campinas Brazil
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, República de Panamá Universidade Estadual de Campinas Campinas Brazil.,Círculo Herpetológico de Panamá, Estafeta Universitaria, Apartado Postal 10762, Panamá, República de Panamá Estafeta Universitaria Panamá Panama.,Departamento de Zoología, Universidad de Panamá, Panamá, República de Panamá Universidad de Panamá Panamá Panama.,Sistema Nacional de Investigación, Panamá, República de Panamá Sistema Nacional de Investigación Panamá Panama
| | - Karen R Lips
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, República de Panamá Universidade Estadual de Campinas Campinas Brazil.,Department of Biology, University of Maryland, College Park, MD 20742, USA University of Maryland College Park United States of America
| | - Andrew J Crawford
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, República de Panamá Universidade Estadual de Campinas Campinas Brazil.,Círculo Herpetológico de Panamá, Estafeta Universitaria, Apartado Postal 10762, Panamá, República de Panamá Estafeta Universitaria Panamá Panama.,Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, 111711, Colombia Universidad de los Andes Bogotá Colombia
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26
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Muletz-Wolz CR, Fleischer RC, Lips KR. Fungal disease and temperature alter skin microbiome structure in an experimental salamander system. Mol Ecol 2019; 28:2917-2931. [PMID: 31066947 DOI: 10.1111/mec.15122] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/27/2019] [Accepted: 04/25/2019] [Indexed: 12/29/2022]
Abstract
Pathogens compete with host microbiomes for space and resources. Their shared environment impacts pathogen-microbiome-host interactions, which can lead to variation in disease outcome. The skin microbiome of red-backed salamanders (Plethodon cinereus) can reduce infection by the pathogen Batrachochytrium dendrobatidis (Bd) at moderate infection loads, with high species richness and high abundance of competitors as putative mechanisms. However, it is unclear if the skin microbiome can reduce epizootic Bd loads across temperatures. We conducted a laboratory experiment to quantify skin microbiome and host responses (P. cinereus: n = 87) to Bd at mimicked epizootic loads across temperatures (13, 17 and 21°C). We quantified skin microbiomes using 16S rRNA gene metabarcoding and identified operational taxonomic units (OTUs) taxonomically similar to culturable bacteria known to kill Bd (anti-Bd OTUs). Prior to pathogen exposure, temperature changed the microbiome (OTU richness decreased by 12% and the abundance of anti-Bd OTUs increased by 18% per degree increase in temperature), but these changes were not predictive of disease outcome. After exposure, Bd changed the microbiome (OTU richness decreased by 0.1% and the abundance of anti-Bd OTUs increased by 0.2% per 1% increase in Bd load) and caused high host mortality across temperatures (35/45: 78%). Temperature indirectly impacted microbiome change and mortality through its direct effect on pathogen load. We did not find support for the microbiome impacting Bd load or host survival. Our research reveals complex host, pathogen, microbiome and environmental interactions to demonstrate that during epizootic events the microbiome will be unlikely to reduce pathogen invasion, even for putatively Bd-resistant species.
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Affiliation(s)
- Carly R Muletz-Wolz
- Department of Biology, University of Maryland, College Park, Maryland.,Center for Conservation Genomics, Smithsonian National Zoological Park and Conservation Biology Institute, Washington, District of Columbia
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian National Zoological Park and Conservation Biology Institute, Washington, District of Columbia
| | - Karen R Lips
- Department of Biology, University of Maryland, College Park, Maryland
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27
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Frenken T, Agha R, Schmeller DS, van West P, Wolinska J. Biological Concepts for the Control of Aquatic Zoosporic Diseases. Trends Parasitol 2019; 35:571-582. [PMID: 31076352 DOI: 10.1016/j.pt.2019.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/04/2019] [Accepted: 04/06/2019] [Indexed: 12/26/2022]
Abstract
Aquatic zoosporic diseases are threatening global biodiversity and ecosystem services, as well as economic activities. Current means of controlling zoosporic diseases are restricted primarily to chemical treatments, which are usually harmful or likely to be ineffective in the long term. Furthermore, some of these chemicals have been banned due to adverse effects. As a result, there is a need for alternative methods with minimal side-effects on the ecosystem or environment. Here, we integrate existing knowledge of three poorly interconnected areas of disease research - amphibian conservation, aquaculture, and plankton ecology - and arrange it into seven biological concepts to control zoosporic diseases. These strategies may be less harmful and more sustainable than chemical approaches. However, more research is needed before safe application is possible.
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Affiliation(s)
- Thijs Frenken
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.
| | - Ramsy Agha
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Dirk S Schmeller
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Pieter van West
- Aberdeen Oomycete Laboratory, College of Life Sciences and Medicine, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Justyna Wolinska
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institute of Biology, Freie Universität Berlin, Berlin, Germany
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28
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Hernández-Gómez O, Briggler JT, Williams RN. Captivity-Induced Changes in the Skin Microbial Communities of Hellbenders (Cryptobranchus alleganiensis). MICROBIAL ECOLOGY 2019; 77:782-793. [PMID: 30209587 DOI: 10.1007/s00248-018-1258-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/30/2018] [Indexed: 05/20/2023]
Abstract
Variation in environmental conditions can result in disparate associations between hosts and microbial symbionts. As such, it is imperative to evaluate how environmental variables (e.g., habitat quality) can influence host-associated microbiome composition. Within wildlife conservation programs, captive conditions can negatively influence the establishment and maintenance of "wild-type" microbiotas within a host. Alternative microbial communities can result in the proliferation of disease among captive stock or upon reintroduction. Hellbenders (Cryptobranchus alleganiensis) are a threatened salamander for which extensive captive management is currently employed. Using metabarcoding, we characterized the skin microbiota of wild and captive hellbenders from two subspecies in the state of Missouri, the eastern (C. a. alleganiensis) and the Ozark hellbender (C. a. bishopi). Both subspecies in our study included wild adults and captive juveniles that were collected from the wild as eggs. Our objectives were to investigate differences in the skin microbial communities' richness/diversity, composition, and functional profiles of microbes between wild and captive individuals. Captive eastern hellbenders possessed richer communities than wild cohorts, whereas the opposite pattern was observed within the Ozark subspecies. We found significant microbial community structure between wild and captive populations of both subspecies. Microbiota structure translated into differences in the predicted metagenome of wild and captive individuals as well. As such, we can expect captive hellbenders to experience alternative microbial structure and function upon reintroduction into the wild. Our study provides a baseline for the effect of captivity on the skin microbial communities of hellbenders, and highlights the need to incorporate microbiota management in current captive-rearing programs.
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Affiliation(s)
- Obed Hernández-Gómez
- Department of Environmental Science, Policy, and Management, University of California-Berkeley, 147 Hilgard Hall, Berkeley, CA, 94720, USA.
| | - Jeffrey T Briggler
- Missouri Department of Conservation, 2901 W. Truman Blvd, Jefferson City, MO, 65109, USA
| | - Rod N Williams
- Department of Forestry and Natural Resources, Purdue University, 715 W. State St, West Lafayette, IN, 47907, USA
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29
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Jin Song S, Woodhams DC, Martino C, Allaband C, Mu A, Javorschi-Miller-Montgomery S, Suchodolski JS, Knight R. Engineering the microbiome for animal health and conservation. Exp Biol Med (Maywood) 2019; 244:494-504. [PMID: 30776908 PMCID: PMC6547002 DOI: 10.1177/1535370219830075] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
IMPACT STATEMENT Considering the clear effects of microbiota on important aspects of animal biology and development (including in humans), this topic is timely and broadly appealing, as it compels us to consider the possibilities of altering the microbiome (without antibiotics) to positively affect animal health. In this review, we highlight three general approaches to manipulating the microbiome that have demonstrated success and promise for use in animal health. We also point out knowledge gaps where further inquiry would most benefit the field. Our paper not only provides a short and digestible overview of the current state of application, but also calls for further exploration of the microbial diversity at hand to expand our toolkit, while also leveraging the diversity and flexibility of animal systems to better understand mechanisms of efficacy.
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Affiliation(s)
- Se Jin Song
- Department of Pediatrics, University of California, San Diego, CA 92093, USA
| | - Douglas C Woodhams
- Biology Department, University of Massachusetts Boston, Boston, MA 02125, USA
- Smithsonian Tropical Research Institute, Panama city 0843-03092, Panama
| | - Cameron Martino
- Bioinformatics and Systems Biology Program, University of California, San Diego, CA 92093, USA
| | - Celeste Allaband
- Biomedical Sciences Graduate Program, University of California, San Diego, CA 92093, USA
| | - Andre Mu
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville 3010, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Parkville 3010, Australia
| | - Sandrine Javorschi-Miller-Montgomery
- Department of Bioengineering, University of California, San Diego, CA 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, CA 92093, USA
| | - Jan S Suchodolski
- Gastrointestinal Laboratory, Texas A&M University, College Station, TX 77843, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, CA 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, CA 92093, USA
- Department of Computer Science and Engineering, University of California, San Diego, CA 92093, USA
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30
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31
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Christian K, Weitzman C, Rose A, Kaestli M, Gibb K. Ecological patterns in the skin microbiota of frogs from tropical Australia. Ecol Evol 2018; 8:10510-10519. [PMID: 30464823 PMCID: PMC6238143 DOI: 10.1002/ece3.4518] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/14/2018] [Accepted: 08/17/2018] [Indexed: 12/20/2022] Open
Abstract
The microbiota of frog skin can play an important role in protecting against diseases and parasites. The frog skin microbial community represents a complex mix of microbes that are promoted by the chemical environment of the frog skin and influenced by the animal's immediate past environment. The microbial communities of six species of frogs sampled from the campus of Charles Darwin University (CDU) were more similar within species than between species. The microbiota of the introduced cane toad (Rhinella marina) was most dissimilar among the species. Pairwise comparisons showed that the microbial communities of each species were different, except for the terrestrial Litoria nasuta and the arboreal L. rothii. The microbial communities of the six species were not related to ecological habit (arboreal or terrestrial), and neither was the alpha diversity of the microbes. The core microbes (defined as being on ≥90% of individuals of a species or group) were significantly different among all species, although 89 microbial operational taxonomic units (OTUs) were core microbes for all six species at CDU. Two species, Rhinella marina and Litoria rothii, were sampled at additional sites approximately 10 and 30 km from CDU. The microbial communities and the core OTU composition were different among the sites, but there were nevertheless 194 (R. marina) and 181 (L. rothii) core OTUs present at all three sites. Thus, the core microbiota varied with respect to geographic range and sample size.
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Affiliation(s)
- Keith Christian
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | | | - Alea Rose
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Mirjam Kaestli
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Karen Gibb
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
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32
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Comparing the bacterial communities of wild and captive golden mantella frogs: Implications for amphibian conservation. PLoS One 2018; 13:e0205652. [PMID: 30379861 PMCID: PMC6209184 DOI: 10.1371/journal.pone.0205652] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 09/28/2018] [Indexed: 01/09/2023] Open
Abstract
Bacterial communities are frequently found in symbiotic associations with most animal species. The characteristically moist amphibian skin provides a good environment for the growth of some species of bacteria; among these a few can act as a first line defense mechanism against infections. Amphibians in the wild have relatively high exposure to bacteria through environmental transmission and through interactions with different conspecifics, whilst in captivity animals interact with fewer individuals, as well as experiencing a less complex environment through which to obtain their bacterial community. Here we compared the skin microbiota of captive and wild Mantella aurantiaca to investigate whether the captive environment was affecting individuals' skin associated bacteria. This could have survivorship implications if captive animals had a different skin microbial community in comparison to wild counterparts and they were to be used in a reintroduction program. The microbial community were characterized through 16S rRNA amplicon sequencing methodology. Analyses showed that captive individuals had significantly lower diversity of bacterial species and lower relative abundant microbiota when compared to wild populations; this could result in captive frogs released back to the wild probably has greater susceptibility to infections due to inadequate skin microbiota.
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33
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DeCandia AL, Dobson AP, vonHoldt BM. Toward an integrative molecular approach to wildlife disease. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2018; 32:798-807. [PMID: 29380417 PMCID: PMC7162296 DOI: 10.1111/cobi.13083] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/12/2017] [Accepted: 01/19/2018] [Indexed: 05/03/2023]
Abstract
Pathogens pose serious threats to human health, agricultural investment, and biodiversity conservation through the emergence of zoonoses, spillover to domestic livestock, and epizootic outbreaks. As such, wildlife managers are often tasked with mitigating the negative effects of disease. Yet, parasites form a major component of biodiversity that often persist. This is due to logistical challenges of implementing management strategies and to insufficient understanding of host-parasite dynamics. We advocate for an inclusive understanding of molecular diversity in driving parasite infection and variable host disease states in wildlife systems. More specifically, we examine the roles of genetic, epigenetic, and commensal microbial variation in disease pathogenesis. These include mechanisms underlying parasite virulence and host resistance and tolerance, and the development, regulation, and parasite subversion of immune pathways, among other processes. Case studies of devil facial tumor disease in Tasmanian devils (Sarcophilus harrisii) and chytridiomycosis in globally distributed amphibians exemplify the broad range of questions that can be addressed by examining different facets of molecular diversity. For particularly complex systems, integrative molecular analyses present a promising frontier that can provide critical insights necessary to elucidate disease dynamics operating across scales. These insights enable more accurate risk assessment, reconstruction of transmission pathways, discernment of optimal intervention strategies, and development of more effective and ecologically sound treatments that minimize damage to the host population and environment. Such measures are crucial when mitigating threats posed by wildlife disease to humans, domestic animals, and species of conservation concern.
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Affiliation(s)
- Alexandra L. DeCandia
- Department of Ecology and Evolutionary BiologyPrinceton University106A Guyot HallPrincetonNJ 08544U.S.A.
| | - Andrew P. Dobson
- Department of Ecology and Evolutionary BiologyPrinceton University106A Guyot HallPrincetonNJ 08544U.S.A.
| | - Bridgett M. vonHoldt
- Department of Ecology and Evolutionary BiologyPrinceton University106A Guyot HallPrincetonNJ 08544U.S.A.
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Bell SC, Garland S, Alford RA. Increased Numbers of Culturable Inhibitory Bacterial Taxa May Mitigate the Effects of Batrachochytrium dendrobatidis in Australian Wet Tropics Frogs. Front Microbiol 2018; 9:1604. [PMID: 30072970 PMCID: PMC6058028 DOI: 10.3389/fmicb.2018.01604] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 06/27/2018] [Indexed: 11/20/2022] Open
Abstract
Symbiotic bacterial communities resident on amphibian skin can benefit their hosts. For example, antibiotic production by community members can control the pathogen Batrachochytrium dendrobatidis (Bd) and it is possible for these community members to be used as probiotics to reduce infection levels. In the early 1990s, the emergence of Bd caused declines and disappearances of frogs in the Australian Wet Tropics; the severity of its effects varied among species and sites. Some species have since recolonized despite enzootic Bd within their populations. This variation in history among species and sites provided an opportunity to investigate the role of anti-fungal cutaneous bacteria in protecting frogs against Bd infection. We collected cutaneous swab samples from three species of frogs at two upland and two lowland sites in the Wet Tropics, and used in vitro challenge assays to identify culturable Bd-inhibitory bacterial isolates for further analysis. We sequenced DNA from cultured inhibitory isolates to identify taxa, resulting in the classification of 16 Bd-inhibitory OTUs, and determined whether inhibitory taxa were associated with frog species, site, or intensity of infection. We present preliminary results showing that the upper limit of Bd infection intensity was negatively correlated with number of inhibitory OTUs present per frog indicating that increased numbers of Bd-inhibiting taxa may play a role in reducing the intensity of Bd infections, facilitating frog coexistence with enzootic Bd. One upland site had a significantly lower prevalence of Bd infection, a significantly higher proportion of frogs with one or more culturable Bd-inhibitory OTUs, a greater number of inhibitory bacterial genera present per frog, and statistically significant clustering of individual frogs with similar Bd-inhibitory signatures when compared to all other sites. This suggests that Bd-inhibitory taxa are likely to be particularly important to frogs at this site and may have played a role in their ability to recolonize following population declines. Our findings suggest that the use of multi-taxon Bd-inhibitory probiotics to support at-risk amphibian populations may be more effective than single-taxon alternatives.
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Affiliation(s)
- Sara C. Bell
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Stephen Garland
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Ross A. Alford
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
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Kearns PJ, Fischer S, Fernández-Beaskoetxea S, Gabor CR, Bosch J, Bowen JL, Tlusty MF, Woodhams DC. Fight Fungi with Fungi: Antifungal Properties of the Amphibian Mycobiome. Front Microbiol 2017; 8:2494. [PMID: 29312201 PMCID: PMC5735112 DOI: 10.3389/fmicb.2017.02494] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/30/2017] [Indexed: 12/11/2022] Open
Abstract
Emerging infectious diseases caused by fungal taxa are increasing and are placing a substantial burden on economies and ecosystems worldwide. Of the emerging fungal diseases, chytridomycosis caused by the fungus Batrachochytrium dendrobatidis (hereafter Bd) is linked to global amphibian declines. Amphibians have innate immunity, as well as additional resistance through cutaneous microbial communities. Despite the targeting of bacteria as potential probiotics, the role of fungi in the protection against Bd infection in unknown. We used a four-part approach, including high-throughput sequencing of bacterial and fungal communities, cultivation of fungi, Bd challenge assays, and experimental additions of probiotic to Midwife Toads (Altyes obstetricans), to examine the overlapping roles of bacterial and fungal microbiota in pathogen defense in captive bred poison arrow frogs (Dendrobates sp.). Our results revealed that cutaneous fungal taxa differed from environmental microbiota across three species and a subspecies of Dendrobates spp. frogs. Cultivation of host-associated and environmental fungi realved numerous taxa with the ability to inhibit or facilitate the growth of Bd. The abundance of cutaneous fungi contributed more to Bd defense (~45% of the fungal community), than did bacteria (~10%) and frog species harbored distinct inhibitory communities that were distinct from the environment. Further, we demonstrated that a fungal probiotic therapy did not induce an endocrine-immune reaction, in contrast to bacterial probiotics that stressed amphibian hosts and suppressed antimicrobial peptide responses, limiting their long-term colonization potential. Our results suggest that probiotic strategies against amphibian fungal pathogens should, in addition to bacterial probiotics, focus on host-associated and environmental fungi such as Penicillium and members of the families Chaetomiaceae and Lasiosphaeriaceae.
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Affiliation(s)
- Patrick J Kearns
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA, United States
| | - Sarah Fischer
- Department of Biology, University of Massachusetts Boston, Boston, MA, United States
| | | | - Caitlin R Gabor
- Department of Biology, Population and Conservation Biology Program, Texas State University, San Marcos, TX, United States
| | - Jaime Bosch
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA, United States
| | - Michael F Tlusty
- Anderson Cabot Center for Ocean Life, New England Aquarium, Boston, MA, United States.,School for the Environment, University of Massachusetts Boston, Boston, MA, United States
| | - Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, United States
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Barnhart K, Forman ME, Umile TP, Kueneman J, McKenzie V, Salinas I, Minbiole KPC, Woodhams DC. Identification of Bufadienolides from the Boreal Toad, Anaxyrus boreas, Active Against a Fungal Pathogen. MICROBIAL ECOLOGY 2017; 74:990-1000. [PMID: 28631214 DOI: 10.1007/s00248-017-0997-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/12/2017] [Indexed: 05/25/2023]
Abstract
Amphibian granular glands provide a wide range of compounds on the skin that defend against pathogens and predators. We identified three bufadienolides-the steroid-like compounds arenobufagin, gamabufotalin, and telocinobufagin-from the boreal toad, Anaxyrus boreas, through liquid chromatography mass spectrometry (LC/MS). Compounds were detected both after inducing skin gland secretions and in constitutive mucosal rinses from toads. We described the antimicrobial properties of each bufadienolide against Batrachochytrium dendrobatidis (Bd), an amphibian fungal pathogen linked with boreal toad population declines. All three bufadienolides were found to inhibit Bd growth at similar levels. The maximum Bd inhibition produced by arenobufagin, gamabufotalin, and telocinobufagin were approximately 50%, in contrast to the complete Bd inhibition shown by antimicrobial skin peptides produced by some amphibian species. In addition, skin mucus samples significantly reduced Bd viability, and bufadienolides were detected in 15 of 62 samples. Bufadienolides also appeared to enhance growth of the anti-Bd bacterium Janthinobacterium lividum, and thus may be involved in regulation of the skin microbiome. Here, we localized skin bacteria within the mucus layer and granular glands of toads with fluorescent in situ hybridization. Overall, our results suggest that bufadienolides can function in antifungal defense on amphibian skin and their production is a potentially convergent trait similar to antimicrobial peptide defenses found on the skin of other species. Further studies investigating bufadienolide expression across toad populations, their regulation, and interactions with other components of the skin mucosome will contribute to understanding the complexities of amphibian immune defense.
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Affiliation(s)
- Kelly Barnhart
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Megan E Forman
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
| | - Thomas P Umile
- Division of Natural and Computational Science, Gwynedd Mercy University, Gwynedd Valley, PA, 19437, USA
| | - Jordan Kueneman
- Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N122, UCB 334, Boulder, CO, 80309, USA
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N122, UCB 334, Boulder, CO, 80309, USA
| | - Irene Salinas
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131-0001, USA
| | - Kevin P C Minbiole
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.
| | - Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA.
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Prado-Irwin SR, Bird AK, Zink AG, Vredenburg VT. Intraspecific Variation in the Skin-Associated Microbiome of a Terrestrial Salamander. MICROBIAL ECOLOGY 2017; 74:745-756. [PMID: 28466089 PMCID: PMC5909955 DOI: 10.1007/s00248-017-0986-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 04/18/2017] [Indexed: 05/28/2023]
Abstract
Resident microbial communities living on amphibian skin can have significant effects on host health, yet the basic ecology of the host-microbiome relationship of many amphibian taxa is poorly understood. We characterized intraspecific variation in the skin microbiome of the salamander Ensatina eschscholtzii xanthoptica, a subspecies composed of four genetically distinct populations distributed throughout the San Francisco Bay Area and the Sierra Nevada mountains in California, USA. We found that salamanders from four geographically and genetically isolated populations harbor similar skin microbial communities, which are dominated by a common core set of bacterial taxa. Additionally, within a population, the skin microbiome does not appear to differ significantly between salamanders of different ages or sexes. In all cases, the salamander skin microbiomes were significantly different from those of the surrounding terrestrial environment. These results suggest that the relationship between E. e. xanthoptica salamanders and their resident skin microbiomes is conserved, possibly indicating a stable mutualism between the host and microbiome.
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Affiliation(s)
- Sofia R Prado-Irwin
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA.
| | - Alicia K Bird
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Andrew G Zink
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA, 94132, USA
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA, 94132, USA
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38
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Rodeo™ Herbicide Negatively Affects Blanchard's Cricket Frogs (Acris blanchardi) Survival and Alters the Skin-Associated Bacterial Community. J HERPETOL 2017. [DOI: 10.1670/16-092] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Muletz Wolz CR, Yarwood SA, Campbell Grant EH, Fleischer RC, Lips KR. Effects of host species and environment on the skin microbiome of Plethodontid salamanders. J Anim Ecol 2017; 87:341-353. [DOI: 10.1111/1365-2656.12726] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/08/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Carly R. Muletz Wolz
- Department of Biology; University of Maryland; College Park MD USA
- Center for Conservation Genomics; Smithsonian Conservation Biology Institute; National Zoological Park; Washington DC USA
| | - Stephanie A. Yarwood
- Department of Environmental Science & Technology; University of Maryland; College Park MD USA
| | - Evan H. Campbell Grant
- S.O. Conte Anadromous Fish Research Laboratory; United States Geological Survey Patuxent Wildlife Research Center; Turners Falls MA USA
| | - Robert C. Fleischer
- Center for Conservation Genomics; Smithsonian Conservation Biology Institute; National Zoological Park; Washington DC USA
| | - Karen R. Lips
- Department of Biology; University of Maryland; College Park MD USA
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40
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Sabino‐Pinto J, Galán P, Rodríguez S, Bletz MC, Bhuju S, Geffers R, Jarek M, Vences M. Temporal changes in cutaneous bacterial communities of terrestrial‐ and aquatic‐phase newts (Amphibia). Environ Microbiol 2017; 19:3025-3038. [DOI: 10.1111/1462-2920.13762] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 04/05/2017] [Accepted: 04/08/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Joana Sabino‐Pinto
- Zoological InstituteBraunschweig University of TechnologyBraunschweig38106 Germany
| | - Pedro Galán
- Departamento de Bioloxía, Facultade de CienciasUniversidade da Coruña, Grupo de Investigación en Biología Evolutiva (GIBE)A Coruña15071 Spain
| | - Silvia Rodríguez
- Departamento de Bioloxía, Facultade de CienciasUniversidade da Coruña, Grupo de Investigación en Biología Evolutiva (GIBE)A Coruña15071 Spain
| | - Molly C. Bletz
- Zoological InstituteBraunschweig University of TechnologyBraunschweig38106 Germany
| | - Sabin Bhuju
- Department of Genome AnalyticsHelmholtz Centre for Infection ResearchBraunschweig38124 Germany
| | - Robert Geffers
- Department of Genome AnalyticsHelmholtz Centre for Infection ResearchBraunschweig38124 Germany
| | - Michael Jarek
- Department of Genome AnalyticsHelmholtz Centre for Infection ResearchBraunschweig38124 Germany
| | - Miguel Vences
- Zoological InstituteBraunschweig University of TechnologyBraunschweig38106 Germany
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41
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Antifungal Bacteria on Woodland Salamander Skin Exhibit High Taxonomic Diversity and Geographic Variability. Appl Environ Microbiol 2017; 83:AEM.00186-17. [PMID: 28213545 DOI: 10.1128/aem.00186-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/10/2017] [Indexed: 12/31/2022] Open
Abstract
Diverse bacteria inhabit amphibian skin; some of those bacteria inhibit growth of the fungal pathogen Batrachochytrium dendrobatidis Yet there has been no systematic survey of anti-B. dendrobatidis bacteria across localities, species, and elevations. This is important given geographic and taxonomic variations in amphibian susceptibility to B. dendrobatidis Our collection sites were at locations within the Appalachian Mountains where previous sampling had indicated low B. dendrobatidis prevalence. We determined the numbers and identities of anti-B. dendrobatidis bacteria on 61 Plethodon salamanders (37 P. cinereus, 15 P. glutinosus, 9 P. cylindraceus) via culturing methods and 16S rRNA gene sequencing. We sampled co-occurring species at three localities and sampled P. cinereus along an elevational gradient (700 to 1,000 meters above sea level [masl]) at one locality. We identified 50 anti-B. dendrobatidis bacterial operational taxonomic units (OTUs) and found that the degree of B. dendrobatidis inhibition was not correlated with relatedness. Five anti-B. dendrobatidis bacterial strains occurred on multiple amphibian species at multiple localities, but none were shared among all species and localities. The prevalence of anti-B. dendrobatidis bacteria was higher at Shenandoah National Park (NP), VA, with 96% (25/26) of salamanders hosting at least one anti-B. dendrobatidis bacterial species compared to 50% (7/14) at Catoctin Mountain Park (MP), MD, and 38% (8/21) at Mt. Rogers National Recreation Area (NRA), VA. At the individual level, salamanders at Shenandoah NP had more anti-B. dendrobatidis bacteria per individual (μ = 3.3) than those at Catoctin MP (μ = 0.8) and at Mt. Rogers NRA (μ = 0.4). All salamanders tested negative for B. dendrobatidis Anti-B. dendrobatidis bacterial species are diverse in central Appalachian Plethodon salamanders, and their distribution varied geographically. The antifungal bacterial species that we identified may play a protective role for these salamanders.IMPORTANCE Amphibians harbor skin bacteria that can kill an amphibian fungal pathogen, Batrachochytrium dendrobatidis Some amphibians die from B. dendrobatidis infection, whereas others do not. The bacteria that can kill B. dendrobatidis, called anti-B. dendrobatidis bacteria, are thought to influence the B. dendrobatidis infection outcome for the amphibian. Yet how anti-B. dendrobatidis bacterial species vary among amphibian species and populations is unknown. We determined the distribution of anti-B. dendrobatidis bacterial species among three salamander species (n = 61) sampled at three localities. We identified 50 unique anti-B. dendrobatidis bacterial species and found that all of the tested salamanders were negative for B. dendrobatidis Five anti-B. dendrobatidis bacterial species were commonly detected, suggesting a stable, functional association with these salamanders. The number of anti-B. dendrobatidis bacteria per individual varied among localities but not among co-occurring salamander species, demonstrating that environment is more influential than host factors in structuring the anti-B. dendrobatidis bacterial community. These anti-B. dendrobatidis bacteria may serve a protective function for their salamander hosts.
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Bletz MC, Perl RGB, Bobowski BT, Japke LM, Tebbe CC, Dohrmann AB, Bhuju S, Geffers R, Jarek M, Vences M. Amphibian skin microbiota exhibits temporal variation in community structure but stability of predicted Bd-inhibitory function. ISME JOURNAL 2017; 11:1521-1534. [PMID: 28387770 DOI: 10.1038/ismej.2017.41] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 02/07/2017] [Accepted: 02/09/2017] [Indexed: 12/22/2022]
Abstract
Host-associated microbiomes are increasingly recognized to contribute to host disease resistance; the temporal dynamics of their community structure and function, however, are poorly understood. We investigated the cutaneous bacterial communities of three newt species, Ichthyosaura alpestris, Lissotriton vulgaris and Triturus cristatus, at approximately weekly intervals for 3 months using 16S ribosomal RNA amplicon sequencing. We hypothesized cutaneous microbiota would vary across time, and that such variation would be linked to changes in predicted fungal-inhibitory function. We observed significant temporal variation within the aquatic phase, and also between aquatic and terrestrial phase newts. By keeping T. cristatus in mesocosms, we demonstrated that structural changes occurred similarly across individuals, highlighting the non-stochastic nature of the bacterial community succession. Temporal changes were mainly associated with fluctuations in relative abundance rather than full turnover of bacterial operational taxonomic units (OTUs). Newt skin microbe fluctuations were not correlated with that of pond microbiota; however, a portion of community variation was explained by environmental temperature. Using a database of amphibian skin bacteria that inhibit the pathogen Batrachochytrium dendrobatidis (Bd), we found that the proportion of reads associated with 'potentially' Bd-inhibitory OTUs did not vary temporally for two of three newt species, suggesting that protective function may be maintained despite temporal variation in community structure.
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Affiliation(s)
- Molly C Bletz
- Zoologisches Institut, Technische Universität Braunschweig, Braunschweig, Germany
| | - R G Bina Perl
- Zoologisches Institut, Technische Universität Braunschweig, Braunschweig, Germany
| | - Bianca Tc Bobowski
- Zoologisches Institut, Technische Universität Braunschweig, Braunschweig, Germany
| | - Laura M Japke
- Zoologisches Institut, Technische Universität Braunschweig, Braunschweig, Germany
| | - Christoph C Tebbe
- Institut für Biodiversität, Thünen Institut für Ländliche Räume, Wald und Fischerei, Braunschweig, Germany
| | - Anja B Dohrmann
- Institut für Biodiversität, Thünen Institut für Ländliche Räume, Wald und Fischerei, Braunschweig, Germany
| | - Sabin Bhuju
- Genomanalytik, Helmholtz Zentrum für Infektionsforschung, Braunschweig, Germany
| | - Robert Geffers
- Genomanalytik, Helmholtz Zentrum für Infektionsforschung, Braunschweig, Germany
| | - Michael Jarek
- Genomanalytik, Helmholtz Zentrum für Infektionsforschung, Braunschweig, Germany
| | - Miguel Vences
- Zoologisches Institut, Technische Universität Braunschweig, Braunschweig, Germany
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Weng FCH, Shaw GTW, Weng CY, Yang YJ, Wang D. Inferring Microbial Interactions in the Gut of the Hong Kong Whipping Frog ( Polypedates megacephalus) and a Validation Using Probiotics. Front Microbiol 2017; 8:525. [PMID: 28424669 PMCID: PMC5371668 DOI: 10.3389/fmicb.2017.00525] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 03/13/2017] [Indexed: 12/20/2022] Open
Abstract
The concerted activity of intestinal microbes is crucial to the health and development of their host organisms. Investigation of microbial interactions in the gut should deepen our understanding of how these micro-ecosystems function. Due to advances in Next Generation Sequencing (NGS) technologies, various bioinformatic strategies have been proposed to investigate these microbial interactions. However, due to the complexity of the intestinal microbial community and difficulties in monitoring their interactions, at present there is a gap between the theory and biological application. In order to construct and validate microbial relationships, we first induce a community shift from simple to complex by manipulating artificial hibernation (AH) in the treefrog Polypedates megacephalus. To monitor community growth and microbial interactions, we further performed a time-course screen using a 16S rRNA amplicon approach and a Lotka-Volterra model. Lotka-Volterra models, also known as predator–prey equations, predict the dynamics of microbial communities and how communities are structured and sustained. An interaction network of gut microbiota at the genus level in the treefrog was constructed using Metagenomic Microbial Interaction Simulator (MetaMIS) package. The interaction network obtained had 1,568 commensal, 1,737 amensal, 3,777 mutual, and 3,232 competitive relationships, e.g., Lactococcus garvieae has a commensal relationship with Corynebacterium variabile. To validate the interacting relationships, the gut microbe composition was analyzed after probiotic trials using single strain (L. garvieae, C. variabile, and Bacillus coagulans, respectively) and a combination of L. garvieae, C. variabile, and B. coagulans, because of the cooperative relationship among their respective genera identified in the interaction network. After a 2 week trial, we found via 16S rRNA amplicon analysis that the combination of cooperative microbes yielded significantly higher probiotic concentrations than single strains, and the immune response (interleukin-10 expression) also significantly changed in a manner consistent with improved probiotic effects. By taking advantage of microbial community shift from simple to complex, we thus constructed a reliable microbial interaction network, and validated it using probiotic strains as a test system.
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Affiliation(s)
- Francis Cheng-Hsuan Weng
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan.,Department of Life Science, National Taiwan Normal UniversityTaipei, Taiwan.,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal UniversityTaipei, Taiwan
| | | | - Chieh-Yin Weng
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan
| | - Yi-Ju Yang
- Department of Natural Resources and Environmental Studies, National Dong Hwa UniversityHualien, Taiwan
| | - Daryi Wang
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan
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44
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Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions. Nat Commun 2016; 7:13699. [PMID: 27976718 PMCID: PMC5171763 DOI: 10.1038/ncomms13699] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/26/2016] [Indexed: 02/06/2023] Open
Abstract
Complex microbial communities inhabit vertebrate digestive systems but thorough understanding of the ecological dynamics and functions of host-associated microbiota within natural habitats is limited. We investigate the role of environmental conditions in shaping gut and skin microbiota under natural conditions by performing a field survey and reciprocal transfer experiments with salamander larvae inhabiting two distinct habitats (ponds and streams). We show that gut and skin microbiota are habitat-specific, demonstrating environmental factors mediate community structure. Reciprocal transfer reveals that gut microbiota, but not skin microbiota, responds differentially to environmental change. Stream-to-pond larvae shift their gut microbiota to that of pond-to-pond larvae, whereas pond-to-stream larvae change to a community structure distinct from both habitat controls. Predicted functions, however, match that of larvae from the destination habitats in both cases. Thus, microbial function can be matched without taxonomic coherence and gut microbiota appears to exhibit metagenomic plasticity.
Host-associated microbial communities can shift in structure or function when hosts change locations. Bletz et al. reciprocally transfer salamander larvae between pond and stream habitats to show that gut microbiomes shift in function, but not necessarily taxonomic identities, when hosts encounter a new environment.
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45
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Woodhams DC, Bletz M, Kueneman J, McKenzie V. Managing Amphibian Disease with Skin Microbiota. Trends Microbiol 2016; 24:161-4. [PMID: 26916805 DOI: 10.1016/j.tim.2015.12.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/27/2015] [Accepted: 12/28/2015] [Indexed: 10/22/2022]
Abstract
The contribution of emerging amphibian diseases to the sixth mass extinction is driving innovative wildlife management strategies, including the use of probiotics. Bioaugmentation of the skin mucosome, a dynamic environment including host and microbial components, may not provide a generalized solution. Multi-omics technologies and ecological context underlie effective implementation.
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Affiliation(s)
- Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.
| | - Molly Bletz
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jordan Kueneman
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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Short-Term Exposure to Coal Combustion Waste Has Little Impact on the Skin Microbiome of Adult Spring Peepers (Pseudacris crucifer). Appl Environ Microbiol 2016; 82:3493-3502. [PMID: 27037118 DOI: 10.1128/aem.00045-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/29/2016] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED Disruptions to the microbiome can impact host health as can exposure to environmental contaminants. However, few studies have addressed how environmental contaminants impact the microbiome. We explored this question for frogs that breed in wetlands contaminated with fly ash, a by-product of coal combustion that is enriched in trace elements. We found differences in the bacterial communities among a fly ash-contaminated site and several reference wetlands. We then experimentally assessed the impacts of fly ash on the skin microbiome of adult spring peepers (Pseudacris crucifer). Frogs were exposed to fly ash in the laboratory for 12 h, the duration of a typical breeding event, and the skin microbiome was assessed after 5 days (experiment 1) or after 5 and 15 days (experiment 2). We examined bacterial community structure using 16S rRNA gene amplicon sequencing and metabolite profiles using high-pressure liquid chromatography-mass spectrometry (HPLC-MS). We found little impact as the result of acute exposure to fly ash on the bacterial communities or metabolite profiles in either experiment, suggesting that the bacterial symbiont communities of adults may be relatively resistant to brief contaminant exposure. However, housing frogs in the laboratory altered bacterial community structure in the two experiments, which supports prior research suggesting that environmental source pools are important for maintaining the amphibian skin microbiome. Therefore, for contaminants like fly ash that may alter the potential source pool of symbionts, we think it may be important to explore how contaminants affect the initial assembly of the amphibian skin microbiome in larval amphibians that develop within contaminated sites. IMPORTANCE Animals are hosts to many symbiotic microorganisms, collectively called the microbiome, that play critical roles in host health. Therefore, environmental contaminants that alter the microbiome may impact hosts. Some of the most widespread contaminants, produced worldwide, are derived from the mining, storage, and combustion of coal for energy. Fly ash, for example, is a by-product of coal combustion. It contains compounds such as arsenic, selenium, cadmium, and strontium and is a recognized source of ground and surface water contamination. Here, we experimentally investigated the impacts of short-term fly ash exposure on the skin microbiome of spring peepers, one of many species of amphibian that sometimes breed in open fly ash disposal ponds. This research provides a look into the potential impacts of fly ash on an animal's microbiome and suggests important future directions for research on the effects of environmental contaminants on the microbiome.
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Rodríguez-Brenes S, Rodriguez D, Ibáñez R, Ryan MJ. Spread of Amphibian Chytrid Fungus across Lowland Populations of Túngara Frogs in Panamá. PLoS One 2016; 11:e0155745. [PMID: 27176629 PMCID: PMC4866759 DOI: 10.1371/journal.pone.0155745] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 05/03/2016] [Indexed: 01/08/2023] Open
Abstract
Chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), is an emergent infectious disease partially responsible for worldwide amphibian population declines. The spread of Bd along highland habitats (> 500 meters above sea level, m a.s.l.) of Costa Rica and Panamá is well documented and has been linked to amphibian population collapses. In contrast, data are scarce on the prevalence and dispersal of Bd in lowland habitats where amphibians may be infected but asymptomatic. Here we describe the spread (2009 to 2014) of Bd across lowland habitats east of the Panamá Canal (< 500 m a.s.l.) with a focus on the Túngara frog (Physalaemus [Engystomops] pustulosus), one of the most common and abundant frog species in this region. Highland populations in western Panamá were already infected with Bd at the start of the study, which was consistent with previous studies indicating that Bd is enzootic in this region. In central Panamá, we collected the first positive samples in 2010, and by 2014, we detected Bd from remote sites in eastern Panamá (Darién National Park). We discuss the importance of studying Bd in lowland species, which may serve as potential reservoirs and agents of dispersal of Bd to highland species that are more susceptible to chytridiomycosis.
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Affiliation(s)
- Sofía Rodríguez-Brenes
- Department of Integrative Biology, University of Texas, Austin, Texas, United States of America
- * E-mail:
| | - David Rodriguez
- Department of Biology, Texas State University, San Marcos, Texas, United States of America
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Balboa, Panamá
- Departamento de Zoología, Universidad de Panamá, Panamá, Panamá
| | - Michael J. Ryan
- Department of Integrative Biology, University of Texas, Austin, Texas, United States of America
- Smithsonian Tropical Research Institute, Balboa, Panamá
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Direct and Indirect Horizontal Transmission of the Antifungal Probiotic Bacterium Janthinobacterium lividum on Green Frog (Lithobates clamitans) Tadpoles. Appl Environ Microbiol 2016; 82:2457-2466. [PMID: 26873311 DOI: 10.1128/aem.04147-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/09/2016] [Indexed: 01/11/2023] Open
Abstract
Amphibian populations worldwide are being threatened by the disease chytridiomycosis, which is caused by Batrachochytrium dendrobatidis To mitigate the effects of B. dendrobatidis, bioaugmentation of antifungal bacteria has been shown to be a promising strategy. One way to implement bioaugmentation is through indirect horizontal transmission, defined as the transfer of bacteria from a host to the environment and to another host. In addition, direct horizontal transmission among individuals can facilitate the spread of a probiotic in a population. In this study, we tested whether the antifungal bacterium Janthinobacterium lividum could be horizontally transferred, directly or indirectly, in a laboratory experiment using Lithobates clamitans tadpoles. We evaluated the ability of J. lividumto colonize the tadpoles' skin and to persist through time using culture-dependent and culture-independent techniques. We also tested whether the addition of J. lividum affected the skin community in L. clamitans tadpoles. We found that transmission occurred rapidly by direct and indirect horizontal transmission, but indirect transmission that included a potential substrate was more effective. Even though J. lividum colonized the skin, its relative abundance on the tadpole skin decreased over time. The inoculation of J. lividum did not significantly alter the skin bacterial diversity of L. clamitans tadpoles, which was dominated by Pseudomonas Our results show that indirect horizontal transmission can be an effective bioaugmentation method. Future research is needed to determine the best conditions, including the presence of substrates, under which a probiotic can persist on the skin so that bioaugmentation becomes a successful strategy to mitigate chytridiomycosis.
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Rebollar EA, Antwis RE, Becker MH, Belden LK, Bletz MC, Brucker RM, Harrison XA, Hughey MC, Kueneman JG, Loudon AH, McKenzie V, Medina D, Minbiole KPC, Rollins-Smith LA, Walke JB, Weiss S, Woodhams DC, Harris RN. Using "Omics" and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases. Front Microbiol 2016; 7:68. [PMID: 26870025 PMCID: PMC4735675 DOI: 10.3389/fmicb.2016.00068] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 01/14/2016] [Indexed: 12/20/2022] Open
Abstract
Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called "omics," are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the Kolmogorov-Smirnov Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics, or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species.
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Affiliation(s)
- Eria A. Rebollar
- Department of Biology, James Madison UniversityHarrisonburg, VA, USA
| | - Rachael E. Antwis
- Unit for Environmental Sciences and Management, North-West UniversityPotchefstroom, South Africa
- Institute of Zoology, Zoological Society of LondonLondon, UK
- School of Environment and Life Sciences, University of SalfordSalford, UK
| | - Matthew H. Becker
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological ParkWashington, DC, USA
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Molly C. Bletz
- Zoological Institute, Technische Universität BraunschweigBraunschweig, Germany
| | | | | | - Myra C. Hughey
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Jordan G. Kueneman
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Andrew H. Loudon
- Department of Zoology, Biodiversity Research Centre, University of British ColumbiaVancouver, BC, Canada
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | | | - Louise A. Rollins-Smith
- Department of Pathology, Microbiology and Immunology and Department of Pediatrics, Vanderbilt University School of Medicine, Department of Biological Sciences, Vanderbilt UniversityNashville, TN, USA
| | - Jenifer B. Walke
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado at BoulderBoulder, CO, USA
| | | | - Reid N. Harris
- Department of Biology, James Madison UniversityHarrisonburg, VA, USA
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Rebollar EA, Hughey MC, Medina D, Harris RN, Ibáñez R, Belden LK. Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis. ISME JOURNAL 2016; 10:1682-95. [PMID: 26744810 DOI: 10.1038/ismej.2015.234] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/29/2015] [Accepted: 11/06/2015] [Indexed: 01/06/2023]
Abstract
Symbiotic bacteria on amphibian skin can inhibit growth of the fungus Batrachochytrium dendrobatidis (Bd) that has caused dramatic population declines and extinctions of amphibians in the Neotropics. It remains unclear how the amphibians' skin microbiota is influenced by environmental bacterial reservoirs, host-associated factors such as susceptibility to pathogens, and pathogen presence in tropical amphibians. We sampled skin bacteria from five co-occurring frog species that differ in Bd susceptibility at one Bd-naive site, and sampled one of the non-susceptible species from Bd-endemic and Bd-naive sites in Panama. We hypothesized that skin bacterial communities (1) would be distinct from the surrounding environment regardless of the host habitat, (2) would differ between Bd susceptible and non-susceptible species and (3) would differ on hosts in Bd-naive and Bd-endemic sites. We found that skin bacterial communities were enriched in bacterial taxa that had low relative abundances in the environment. Non-susceptible species had very similar skin bacterial communities that were enriched in particular taxa such as the genera Pseudomonas and Acinetobacter. Bacterial communities of Craugastor fitzingeri in Bd-endemic sites were less diverse than in the naive site, and differences in community structure across sites were explained by changes in relative abundance of specific bacterial taxa. Our results indicate that skin microbial structure was associated with host susceptibility to Bd and might be associated to the history of Bd presence at different sites.
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Affiliation(s)
- Eria A Rebollar
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Myra C Hughey
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
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