1
|
Dungan AM, Thomas JL. Fecal bacterial communities of the platypus (Ornithorhynchus anatinus) reflect captivity status-Implications for conservation and management. Integr Zool 2024. [PMID: 39075976 DOI: 10.1111/1749-4877.12865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
The duck-billed platypus (Ornithorhynchus anatinus) is currently listed as near-threatened. A key part of the conservation strategy for this species is its captive maintenance; however, captive animals often have dysbiotic gut bacterial microbiomes. Here, for the first time, we characterize the gut microbiome of wild platypus via fecal samples using high-throughput sequencing of the bacterial 16S rRNA gene and identify microbial biomarkers of captivity in this species. At the phylum level, Firmicutes (50.4%) predominated among all platypuses, followed by Proteobacteria (28.7%), Fusobacteria (13.4%), and Bacteroidota (6.9%), with 21 "core" bacteria identified. Captive individuals did not differ in their microbial α-diversity compared to wild platypus but had significantly different community composition (β-diversity) and exhibited higher abundances of Enterococcus, which are potential pathogenic bacteria. Four taxa were identified as biomarkers of wild platypus, including Rickettsiella, Epulopiscium, Clostridium, and Cetobacterium. This contrast in gut microbiome composition between wild and captive platypus is an essential insight for guiding conservation management, as the rewilding of captive animal microbiomes is a new and emerging tool to improve captive animal health, maximize captive breeding efforts, and give reintroduced or translocated animals the best chance of survival.
Collapse
Affiliation(s)
- Ashley M Dungan
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | | |
Collapse
|
2
|
Soto-Cortés E, Marroquín-Rodríguez M, Basanta MD, Maldonado-López Y, Parra-Olea G, Rebollar EA. Host Species and Environment Shape the Skin Microbiota of Mexican Axolotls. MICROBIAL ECOLOGY 2024; 87:98. [PMID: 39046491 PMCID: PMC11269437 DOI: 10.1007/s00248-024-02411-1] [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: 04/23/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024]
Abstract
Skin microbiomes in amphibians are complex systems that can be influenced by biotic and abiotic factors. In this study, we examined the effect of host species and environmental conditions on the skin bacterial and fungal microbiota of four obligate paedomorphic salamander species, commonly known as axolotls (Ambystoma andersoni, A. dumerilii, A. mexicanum, and A. taylori), all of them endemic to the Trans-Mexican Volcanic Belt. We found that despite their permanent aquatic lifestyle, these species present a host-specific skin microbiota that is distinct from aquatic communities. We identified skin-associated taxa that were unique to each host species and that differentiated axolotl species based on alpha and beta diversity metrics. Moreover, we identified a set of microbial taxa that were shared across hosts with high relative abundances across skin samples. Specifically, bacterial communities were dominated by Burkholderiales and Pseudomonadales bacterial orders and Capnodiales and Pleosporales fungal orders. Host species and environmental variables collectively explained more microbial composition variation in bacteria (R2 = 0.46) in comparison to fungi (R2 = 0.2). Our results contribute to a better understanding of the factors shaping the diversity and composition of skin microbial communities in Ambystoma. Additional studies are needed to disentangle the effects of specific host associated and environmental factors that could influence the skin microbiome of these endangered species.
Collapse
Affiliation(s)
- Enrique Soto-Cortés
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | | | - Maria Delia Basanta
- Department of Biology, University of Nevada Reno, Reno, NV, USA
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, México
| | - Yurixhi Maldonado-López
- Cátedras CONAHCYT - Instituto de Investigaciones Sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Gabriela Parra-Olea
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, México
| | - Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México.
| |
Collapse
|
3
|
Buchanan CE, Galla SJ, Muscarella ME, Forbey JS, Reinking AK, Beck JL. Relating gut microbiome composition and life history metrics for pronghorn (Antilocapra americana) in the Red Desert, Wyoming. PLoS One 2024; 19:e0306722. [PMID: 38985706 PMCID: PMC11236126 DOI: 10.1371/journal.pone.0306722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 06/21/2024] [Indexed: 07/12/2024] Open
Abstract
Host microbial communities (hereafter, the 'microbiome') are recognized as an important aspect of host health and are gaining attention as a useful biomarker to understand the ecology and demographics of wildlife populations. Several studies indicate that the microbiome may contribute to the adaptive capacity of animals to changing environments associated with increasing habitat fragmentation and rapid climate change. To this end, we investigated the gut microbiome of pronghorn (Antilocapra americana), an iconic species in an environment that is undergoing both climatic and anthropogenic change. The bacterial composition of the pronghorn gut microbiome has yet to be described in the literature, and thus our study provides important baseline information about this species. We used 16S rRNA amplicon sequencing of fecal samples to characterize the gut microbiome of pronghorn-a facultative sagebrush (Artemisia spp.) specialist in many regions where they occur in western North America. We collected fecal pellets from 159 captured female pronghorn from four herds in the Red Desert of Wyoming during winters of 2013 and 2014. We found small, but significant differences in diversity of the gut microbiome relative to study area, capture period, and body fat measurements. In addition, we found a difference in gut microbiome composition in pronghorn across two regions separated by Interstate 80. Results indicated that the fecal microbiome may be a potential biomarker for the spatial ecology of free-ranging ungulates. The core gut microbiome of these animals-including bacteria in the phyla Firmicutes (now Bacillota) and Bacteroidota-remained relatively stable across populations and biological metrics. These findings provide a baseline for the gut microbiome of pronghorn that could potentially be used as a target in monitoring health and population structure of pronghorn relative to habitat fragmentation, climate change, and management practices.
Collapse
Affiliation(s)
- Courtney E Buchanan
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming, United States of America
| | - Stephanie J Galla
- Department of Biological Sciences, Boise State University, Boise, Idaho, United States of America
| | - Mario E Muscarella
- Institute of Arctic Biology and Department of Biology & Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Jennifer S Forbey
- Department of Biological Sciences, Boise State University, Boise, Idaho, United States of America
| | - Adele K Reinking
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming, United States of America
- Cooperative Institute for Research in the Atmosphere, Colorado State University, Fort Collins, Colorado, United States of America
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, United States of America
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jeffrey L Beck
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming, United States of America
| |
Collapse
|
4
|
Bacigalupe LD, Solano‐Iguaran JJ, Longo AV, Gaitán‐Espitia JD, Valenzuela‐Sánchez A, Alvarado‐Rybak M, Azat C. Nor climate nor human impact factors: Chytrid infection shapes the skin bacterial communities of an endemic amphibian in a biodiversity hotspot. Ecol Evol 2024; 14:e11249. [PMID: 38590552 PMCID: PMC10999949 DOI: 10.1002/ece3.11249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
The bacterial communities of the amphibian skin (i.e., the bacteriome) are critical to the host's innate immune system. However, it is unclear how different drivers can alter this function by modulating the bacteriome's structure. Our aim was to assess the extent to which different host attributes and extrinsic factors influence the structure of the bacterial communities of the skin. Skin bacterial diversity was examined in 148 individuals of the four-eyed frog (Pleurodema thaul) from 16 localities spanning almost 1800 km in latitude. The richness and beta diversity of bacterial families and the richness and abundance of Bd-inhibitory bacterial genera were used to describe their structure. Predictors associated with the host (developmental stage, genetic lineage, individual Batrachochytrium dendrobatidis [Bd] infection status) and the landscape (current climate, degree of anthropogenic disturbance) were used in the statistical modeling in an information theoretical approach. Bd infection and host developmental stage were the only predictors affecting bacteriome richness, with Bd+ individuals and postmetamorphic stages (adults and juveniles) having higher richness than Bd- ones and tadpoles. High diversity in Bd+ individuals is not driven by bacterial genera with known anti-Bd properties. Beta diversity was not affected by Bd infection and was mainly a consequence of bacterial family turnover rather than nestedness. Finally, for those bacterial genera known to have inhibitory effects on chytrid, Bd+ individuals had a slightly higher diversity than Bd- ones. Our study confirms an association between Bd infection and the host developmental stage with the bacterial communities of the skin of P. thaul. Unexpectedly, macroclimate and human impact factors do not seem to play a role in shaping the amphibian skin microbiome. Our study exemplifies that focusing on a single host-parasite system over a large geographic scale can provide essential insights into the factors driving host-parasite-bacteriome interactions.
Collapse
Affiliation(s)
| | - Jaiber J. Solano‐Iguaran
- Instituto de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
- Departamento de Salud HidrobiológicaInstituto de Fomento PesqueroPuerto MonttChile
| | - Ana V. Longo
- Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
| | - Juan D. Gaitán‐Espitia
- School of Biological Sciences and the SWIRE Institute of Marine ScienceThe University of Hong KongHong KongSARChina
| | | | - Mario Alvarado‐Rybak
- Núcleo de Ciencias Aplicadas en Ciencias Veterinarias y AgronómicasUniversidad de Las AméricasSantiagoChile
| | - Claudio Azat
- Sustainability Research Centre & PhD in Conservation MedicineUniversidad Andres BelloSantiagoChile
| |
Collapse
|
5
|
Hoang KL, Read TD, King KC. Incomplete immunity in a natural animal-microbiota interaction selects for higher pathogen virulence. Curr Biol 2024; 34:1357-1363.e3. [PMID: 38430909 PMCID: PMC10962313 DOI: 10.1016/j.cub.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/18/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024]
Abstract
Incomplete immunity in recovered hosts is predicted to favor more virulent pathogens upon re-infection in the population.1 The microbiota colonizing animals can generate a similarly long-lasting, partial immune response, allowing for infection but dampened disease severity.2 We tracked the evolutionary trajectories of a widespread pathogen (Pseudomonas aeruginosa), experimentally passaged through populations of nematodes immune-primed by a natural microbiota member (P. berkeleyensis). This bacterium can induce genes regulated by a mitogen-activated protein kinase (MAPK) signaling pathway effective at conferring protection against pathogen-induced death despite infection.3 Across host populations, this incomplete immunity selected for pathogens more than twice as likely to kill as those evolved in non-primed (i.e., naive) or immune-compromised (mutants with a knockout of the MAPK ortholog) control populations. Despite the higher virulence, pathogen molecular evolution in immune-primed hosts was slow and constrained. In comparison, evolving pathogens in immune-compromised hosts were characterized by substantial genomic differentiation and attenuated virulence. These findings directly attribute the incomplete host immunity induced from microbiota as a significant force shaping the virulence and evolutionary dynamics of novel infectious diseases.
Collapse
Affiliation(s)
- Kim L Hoang
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA 30322, USA.
| | - Timothy D Read
- Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA 30322, USA
| | - Kayla C King
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology & Immunology, University of British Columbia, 1365 - 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
| |
Collapse
|
6
|
Garcias-Bonet N, Roik A, Tierney B, García FC, Villela HDM, Dungan AM, Quigley KM, Sweet M, Berg G, Gram L, Bourne DG, Ushijima B, Sogin M, Hoj L, Duarte G, Hirt H, Smalla K, Rosado AS, Carvalho S, Thurber RV, Ziegler M, Mason CE, van Oppen MJH, Voolstra CR, Peixoto RS. Horizon scanning the application of probiotics for wildlife. Trends Microbiol 2024; 32:252-269. [PMID: 37758552 DOI: 10.1016/j.tim.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called 'probiotics for wildlife' is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.
Collapse
Affiliation(s)
- Neus Garcias-Bonet
- 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
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), Bremerhaven, Germany
| | - Braden Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Francisca C García
- 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 D M 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
| | - Ashley M Dungan
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kate M Quigley
- Minderoo Foundation, Perth, WA, Australia; James Cook University, Townsville, Australia
| | - Michael Sweet
- Aquatic Research Facility, Nature-based Solutions Research Centre, University of Derby, Derby, UK
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; University of Potsdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Maggie Sogin
- Molecular Cell Biology, University of California, Merced, CA, USA
| | - Lone Hoj
- Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Gustavo 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; IMPG, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heribert Hirt
- Center for Desert Agriculture (CDA), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - 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; 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
| | | | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; WorldQuant Initiative on Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | | | - 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; 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.
| |
Collapse
|
7
|
Buttimer S, Moura-Campos D, Greenspan SE, Neely WJ, Ferrante L, Toledo LF, Becker CG. Skin microbiome disturbance linked to drought-associated amphibian disease. Ecol Lett 2024; 27:e14372. [PMID: 38288868 DOI: 10.1111/ele.14372] [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: 09/11/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
The onset of global climate change has led to abnormal rainfall patterns, disrupting associations between wildlife and their symbiotic microorganisms. We monitored a population of pumpkin toadlets and their skin bacteria in the Brazilian Atlantic Forest during a drought. Given the recognized ability of some amphibian skin bacteria to inhibit the widespread fungal pathogen Batrachochytrium dendrobatidis (Bd), we investigated links between skin microbiome health, susceptibility to Bd and host mortality during a die-off event. We found that rainfall deficit was an indirect predictor of Bd loads through microbiome disruption, while its direct effect on Bd was weak. The microbiome was characterized by fewer putative Bd-inhibitory bacteria following the drought, which points to a one-month lagged effect of drought on the microbiome that may have increased toadlet susceptibility to Bd. Our study underscores the capacity of rainfall variability to disturb complex host-microbiome interactions and alter wildlife disease dynamics.
Collapse
Affiliation(s)
- Shannon Buttimer
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, Center for Infectious Disease Dynamics, Ecology Institute, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Diego Moura-Campos
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Sasha E Greenspan
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Wesley J Neely
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
- Department of Biology, Texas State University, San Marcos, Texas, USA
| | - Lucas Ferrante
- Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Luís Felipe Toledo
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - C Guilherme Becker
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, Center for Infectious Disease Dynamics, Ecology Institute, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| |
Collapse
|
8
|
Alexiev A, Melie T, Martindale R, Delacey C, Quandt CA, McKenzie VJ. Mr. Toad's Wild Fungi: Fungal Isolate Diversity on Colorado Boreal Toads and their Capacity for Pathogen Inhibition. FUNGAL ECOL 2023; 66:101297. [PMID: 38487623 PMCID: PMC10938945 DOI: 10.1016/j.funeco.2023.101297] [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: 03/17/2024]
Abstract
The amphibian skin pathogen Batrachochytrium dendrobatidis (Bd) has caused an ongoing biodiversity crisis, including in the locally endangered Colorado boreal toad (Anaxyrus boreas boreas). Although researchers have investigated the bacteria living on amphibian skin and how they interact with Bd, there is less information about fungal community members. This study describes (1) the diversity of culturable fungi from boreal toad skin, (2) which subset of these isolates is Bd-inhibitory, and (3) how Bd affects these isolates' growth and morphology. Most isolates were from the orders Capnodiales, Helotiales, and Pleosporales. Of 16 isolates tested for Bd-inhibition, two from the genus Neobulgaria and three from Pseudeurotium inhibited Bd. Fungal growth in co-culture with Bd varied with weak statistical support for Neobulgaria sp. (isolate BTF_36) and cf Psychrophila (isolate BTF_60) (p-values = 0.076 and 0.092, respectively). Fungal morphology remained unchanged in co-culture with Bd, however, these results could be attributed to low replication per isolate. Nonetheless, two fungal isolates' growth may have been affected by Bd, implying that fungal growth changes in Bd co-culture could be a variable worth measuring in the future (with higher replication). These findings add to the sparse but growing literature on amphibian-associated fungi and suggest further study may uncover the relevance of fungi to amphibian health and Bd infection.
Collapse
Affiliation(s)
- Alexandra Alexiev
- University of Colorado Boulder, Department of Ecology and Evolutionary Biology
| | - Tina Melie
- University of Colorado Boulder, Department of Ecology and Evolutionary Biology
| | - Rachel Martindale
- University of Colorado Boulder, Department of Ecology and Evolutionary Biology
| | - Cameron Delacey
- University of Colorado Boulder, Department of Ecology and Evolutionary Biology
| | - C. Alisha Quandt
- University of Colorado Boulder, Department of Ecology and Evolutionary Biology
| | - Valerie J. McKenzie
- University of Colorado Boulder, Department of Ecology and Evolutionary Biology
| |
Collapse
|
9
|
Sun D, Herath J, Zhou S, Ellepola G, Meegaskumbura M. Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts. ISME COMMUNICATIONS 2023; 3:123. [PMID: 37993728 PMCID: PMC10665332 DOI: 10.1038/s43705-023-00332-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Amphibian skin harbors microorganisms that are associated with the fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes chytridiomycosis, one of the most significant wildlife diseases known. This pathogen originated in Asia, where diverse Bd lineages exist; hence, native amphibian hosts have co-existed with Bd over long time periods. Determining the nuances of this co-existence is crucial for understanding the prevalence and spread of Bd from a microbial context. However, associations of Bd with the natural skin microbiome remain poorly understood for Asian hosts, especially in relation to skin-associated fungi. We used 16 S rRNA and fungal internal transcribed spacer (ITS) gene sequencing to characterize the skin microbiome of four native Asian amphibian species and examined the relationships between Bd infection and their skin bacterial and fungal communities; we also analyzed the correlates of the putative anti-Bd bacteria. We show that both skin bacterial and fungal community structure and composition had significant associations with infection status (Bd presence/absence) and infection intensity (frequency of Bd sequence reads). We also found that the putative anti-Bd bacterial richness was correlated with Bd infection status and infection intensity, and observed that the relative abundance of anti-Bd bacteria roughly correspond with changes in both Bd prevalence and mean infection intensity in populations. Additionally, the microbial co-occurrence network of infected frogs was significantly different from that of uninfected frogs that were characterized by more keystone nodes (connectors) and larger proportions in correlations between bacteria, suggesting stronger inter-module bacterial interactions. These results indicate that the mutual effects between Bd and skin-associated microbiome, including the interplay between bacteria and fungi, might vary with Bd infection in susceptible amphibian species. This knowledge will help in understanding the dynamics of Bd from a microbial perspective, potentially contributing to mitigate chytridiomycosis in other regions of the world.
Collapse
Affiliation(s)
- Dan Sun
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
| | - Jayampathi Herath
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
- School of Biomedical Sciences, International Institute of Health Sciences (IIHS), No 704 Negombo Rd, Welisara, 71722, Sri Lanka
| | - Shipeng Zhou
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
| | - Gajaba Ellepola
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
- Department of Zoology, Faculty of Science, University of Peradeniya, Peradeniya, KY20400, Sri Lanka
| | - Madhava Meegaskumbura
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Woodhams DC, McCartney J, Walke JB, Whetstone R. The adaptive microbiome hypothesis and immune interactions in amphibian mucus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 145:104690. [PMID: 37001710 PMCID: PMC10249470 DOI: 10.1016/j.dci.2023.104690] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 05/20/2023]
Abstract
The microbiome is known to provide benefits to hosts, including extension of immune function. Amphibians are a powerful immunological model for examining mucosal defenses because of an accessible epithelial mucosome throughout their developmental trajectory, their responsiveness to experimental treatments, and direct interactions with emerging infectious pathogens. We review amphibian skin mucus components and describe the adaptive microbiome as a novel process of disease resilience where competitive microbial interactions couple with host immune responses to select for functions beneficial to the host. We demonstrate microbiome diversity, specificity of function, and mechanisms for memory characteristic of an adaptive immune response. At a time when industrialization has been linked to losses in microbiota important for host health, applications of microbial therapies such as probiotics may contribute to immunotherapeutics and to conservation efforts for species currently threatened by emerging diseases.
Collapse
Affiliation(s)
- Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA.
| | - Julia McCartney
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Jenifer B Walke
- Department of Biology, Eastern Washington University, Cheney, WA, 99004-2440, USA
| | - Ross Whetstone
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| |
Collapse
|
12
|
Miller AJ, Gass J, Jo MC, Bishop L, Petereit J, Woodhams DC, Voyles J. Towards the generation of gnotobiotic larvae as a tool to investigate the influence of the microbiome on the development of the amphibian immune system. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220125. [PMID: 37305911 PMCID: PMC10258664 DOI: 10.1098/rstb.2022.0125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/28/2022] [Indexed: 06/13/2023] Open
Abstract
The immune equilibrium model suggests that exposure to microbes during early life primes immune responses for pathogen exposure later in life. While recent studies using a range of gnotobiotic (germ-free) model organisms offer support for this theory, we currently lack a tractable model system for investigating the influence of the microbiome on immune system development. Here, we used an amphibian species (Xenopus laevis) to investigate the importance of the microbiome in larval development and susceptibility to infectious disease later in life. We found that experimental reductions of the microbiome during embryonic and larval stages effectively reduced microbial richness, diversity and altered community composition in tadpoles prior to metamorphosis. In addition, our antimicrobial treatments resulted in few negative effects on larval development, body condition, or survival to metamorphosis. However, contrary to our predictions, our antimicrobial treatments did not alter susceptibility to the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd) in the adult life stage. While our treatments to reduce the microbiome during early development did not play a critical role in determining susceptibility to disease caused by Bd in X. laevis, they nevertheless indicate that developing a gnotobiotic amphibian model system may be highly useful for future immunological investigations. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.
Collapse
Affiliation(s)
| | - Jordan Gass
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Myung Chul Jo
- Environmental Health and Safety, University of Nevada, Reno, NV 89557, USA
| | - Lucas Bishop
- Nevada Bioinformatics Center, University of Nevada, Reno, NV 89557, USA
| | - Juli Petereit
- Nevada Bioinformatics Center, University of Nevada, Reno, NV 89557, USA
| | | | - Jamie Voyles
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| |
Collapse
|
13
|
Siomko SA, Greenspan SE, Barnett KM, Neely WJ, Chtarbanova S, Woodhams DC, McMahon TA, Becker CG. Selection of an anti-pathogen skin microbiome following prophylaxis treatment in an amphibian model system. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220126. [PMID: 37305917 PMCID: PMC10258671 DOI: 10.1098/rstb.2022.0126] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/03/2022] [Indexed: 06/13/2023] Open
Abstract
With emerging diseases on the rise, there is an urgent need to identify and understand novel mechanisms of prophylactic protection in vertebrate hosts. Inducing resistance against emerging pathogens through prophylaxis is an ideal management strategy that may impact pathogens and their host-associated microbiome. The host microbiome is recognized as a critical component of immunity, but the effects of prophylactic inoculation on the microbiome are unknown. In this study, we investigate the effects of prophylaxis on host microbiome composition, focusing on the selection of anti-pathogenic microbes contributing to host acquired immunity in a model host-fungal disease system, amphibian chytridiomycosis. We inoculated larval Pseudacris regilla against the fungal pathogen Batrachochytrium dendrobatidis (Bd) with a Bd metabolite-based prophylactic. Increased prophylactic concentration and exposure duration were associated with significant increases in proportions of putatively Bd-inhibitory host-associated bacterial taxa, indicating a protective prophylactic-induced shift towards microbiome members that are antagonistic to Bd. Our findings are in accordance with the adaptive microbiome hypothesis, where exposure to a pathogen alters the microbiome to better cope with subsequent pathogen encounters. Our study advances research on the temporal dynamics of microbiome memory and the role of prophylaxis-induced shifts in microbiomes contributing to prophylaxis effectiveness. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.
Collapse
Affiliation(s)
- Samantha A. Siomko
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Sasha E. Greenspan
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - K. M. Barnett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Wesley J. Neely
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | | | - Douglas C. Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Taegan A. McMahon
- Department of Biology, Connecticut College, New London, CT 06320, USA
| | - C. Guilherme Becker
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, One Health Microbiome Center, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
14
|
Gajewski Z, Johnson LR, Medina D, Crainer WW, Nagy CM, Belden LK. Skin bacterial community differences among three species of co-occurring Ranid frogs. PeerJ 2023; 11:e15556. [PMID: 37465150 PMCID: PMC10351513 DOI: 10.7717/peerj.15556] [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: 02/23/2023] [Accepted: 05/23/2023] [Indexed: 07/20/2023] Open
Abstract
Skin microbial communities are an essential part of host health and can play a role in mitigating disease. Host and environmental factors can shape and alter these microbial communities and, therefore, we need to understand to what extent these factors influence microbial communities and how this can impact disease dynamics. Microbial communities have been studied in amphibian systems due to skin microbial communities providing some resistance to the amphibian chytrid fungus, Batrachochytrium dendrobatidis. However, we are only starting to understand how host and environmental factors shape these communities for amphibians. In this study, we examined whether amphibian skin bacterial communities differ among host species, host infection status, host developmental stage, and host habitat. We collected skin swabs from tadpoles and adults of three Ranid frog species (Lithobates spp.) at the Mianus River Gorge Preserve in Bedford, New York, USA, and used 16S rRNA gene amplicon sequencing to determine bacterial community composition. Our analysis suggests amphibian skin bacterial communities change across host developmental stages, as has been documented previously. Additionally, we found that skin bacterial communities differed among Ranid species, with skin communities on the host species captured in streams or bogs differing from the communities of the species captured on land. Thus, habitat use of different species may drive differences in host-associated microbial communities for closely-related host species.
Collapse
Affiliation(s)
- Zachary Gajewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
| | - Leah R. Johnson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
- Department of Statistics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
| | - Daniel Medina
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
| | - William W. Crainer
- Department of Animal Sciences, Cornell University, Ithaca, New York, United States
| | | | - Lisa K. Belden
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
| |
Collapse
|
15
|
Dallas JW, Warne RW. Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation. MICROBIAL ECOLOGY 2023; 85:820-838. [PMID: 35316343 DOI: 10.1007/s00248-022-01991-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/07/2022] [Indexed: 05/04/2023]
Abstract
During the ongoing biodiversity crisis, captive conservation and breeding programs offer a refuge for species to persist and provide source populations for reintroduction efforts. Unfortunately, captive animals are at a higher disease risk and reintroduction efforts remain largely unsuccessful. One potential factor in these outcomes is the host microbiota which includes a large diversity and abundance of bacteria, fungi, and viruses that play an essential role in host physiology. Relative to wild populations, the generalized pattern of gut and skin microbiomes in captivity are reduced alpha diversity and they exhibit a significant shift in community composition and/or structure which often correlates with various physiological maladies. Many conditions of captivity (antibiotic exposure, altered diet composition, homogenous environment, increased stress, and altered intraspecific interactions) likely lead to changes in the host-associated microbiome. To minimize the problems arising from captivity, efforts can be taken to manipulate microbial diversity and composition to be comparable with wild populations through methods such as increasing dietary diversity, exposure to natural environmental reservoirs, or probiotics. For individuals destined for reintroduction, these strategies can prime the microbiota to buffer against novel pathogens and changes in diet and improve reintroduction success. The microbiome is a critical component of animal physiology and its role in species conservation should be expanded and included in the repertoire of future management practices.
Collapse
Affiliation(s)
- Jason W Dallas
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA.
| | - Robin W Warne
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA
| |
Collapse
|
16
|
Schilliger L, Paillusseau C, François C, Bonwitt J. Major Emerging Fungal Diseases of Reptiles and Amphibians. Pathogens 2023; 12:pathogens12030429. [PMID: 36986351 PMCID: PMC10053826 DOI: 10.3390/pathogens12030429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/16/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Emerging infectious diseases (EIDs) are caused by pathogens that have undergone recent changes in terms of geographic spread, increasing incidence, or expanding host range. In this narrative review, we describe three important fungal EIDs with keratin trophism that are relevant to reptile and amphibian conservation and veterinary practice. Nannizziopsis spp. have been mainly described in saurians; infection results in thickened, discolored skin crusting, with eventual progression to deep tissues. Previously only reported in captive populations, it was first described in wild animals in Australia in 2020. Ophidiomyces ophidiicola (formely O. ophiodiicola) is only known to infect snakes; clinical signs include ulcerating lesions in the cranial, ventral, and pericloacal regions. It has been associated with mortality events in wild populations in North America. Batrachochytrium spp. cause ulceration, hyperkeratosis, and erythema in amphibians. They are a major cause of catastrophic amphibian declines worldwide. In general, infection and clinical course are determined by host-related characteristics (e.g., nutritional, metabolic, and immune status), pathogens (e.g., virulence and environmental survival), and environment (e.g., temperature, hygrometry, and water quality). The animal trade is thought to be an important cause of worldwide spread, with global modifications in temperature, hygrometry, and water quality further affecting fungal pathogenicity and host immune response.
Collapse
Affiliation(s)
- Lionel Schilliger
- Argos Veterinary Clinic of Paris Auteuil, 35 Rue Leconte de Lisle, 75016 Paris, France
- SpéNac Referral Center, 100 Boulevard de la Tour Maubourg, 75007 Paris, France
- Correspondence: ; Tel.: +33-188-616-831
| | - Clément Paillusseau
- Argos Veterinary Clinic of Paris Auteuil, 35 Rue Leconte de Lisle, 75016 Paris, France
- SpéNac Referral Center, 100 Boulevard de la Tour Maubourg, 75007 Paris, France
| | - Camille François
- Argos Veterinary Clinic of Paris Auteuil, 35 Rue Leconte de Lisle, 75016 Paris, France
- SpéNac Referral Center, 100 Boulevard de la Tour Maubourg, 75007 Paris, France
| | - Jesse Bonwitt
- Department of Anthropology, Durham University, South Rd., Durham DH1 3LE, UK
| |
Collapse
|
17
|
Alexiev A, Chen MY, Korpita T, Weier AM, McKenzie VJ. Together or Alone: Evaluating the Pathogen Inhibition Potential of Bacterial Cocktails against an Amphibian Pathogen. Microbiol Spectr 2023; 11:e0151822. [PMID: 36719234 PMCID: PMC10100949 DOI: 10.1128/spectrum.01518-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 12/11/2022] [Indexed: 02/01/2023] Open
Abstract
The amphibian fungal skin disease Batrachochytrium dendrobatidis (Bd) has caused major biodiversity losses globally. Several experimental trials have tested the use of Janthinobacterium lividum to reduce mortality due to Bd infections, usually in single-strain amendments. It is well-characterized in terms of its anti-Bd activity mechanisms. However, there are many other microbes that inhibit Bd in vitro, and not all experiments have demonstrated consistent results with J. lividum. We used a series of in vitro assays involving bacterial coculture with Bd lawns, bacterial growth tests in liquid broth, and Bd grown in bacterial cell-free supernatant (CFS) to determine: (i) which skin bacteria isolated from a locally endangered amphibian, namely, the Colorado boreal toad (Anaxyrus boreas boreas), are able to inhibit Bd growth; (ii) whether multistrain combinations are more effective than single-strains; and (iii) the mechanism behind microbe-microbe interactions. Our results indicate that there are some single strain and multistrain probiotics (especially including strains from Pseudomonas, Chryseobacterium, and Microbacterium) that are potentially more Bd-inhibitive than is J. lividum alone and that some combinations may lead to a loss of inhibition, potentially through antagonistic metabolite effects. Additionally, if J. lividum continues being developed as a wild boreal toad probiotic, we should investigate it in combination with Curvibacter CW54D, as they inhibited Bd additively and grew at a higher rate when combined than did either alone. This highlights the fact that combinations of probiotics function in variable and unpredictable ways as well as the importance of considering the potential for interactions among naturally resident host microbiota and probiotic additions. IMPORTANCE Batrachochytrium dendrobatidis (Bd) is a pathogen that infects amphibians globally and is causing a biodiversity crisis. Our research group studies one of the species affected by Bd, namely, the Colorado boreal toad (Anaxyrus boreas boreas). Many researchers focus their studies on one probiotic bacterial isolate called Janthinobacterium lividum, which slows Bd growth in lab cultures and is currently being field tested in Colorado boreal toads. Although promising, J. lividum is not consistently effective across all amphibian individuals or species. For Colorado boreal toads, we addressed whether there are other bacterial strains that also inhibit Bd (potentially better than does J. lividum) and whether we can create two-strain probiotics that function better than do single-strain probiotics. In addition, we evaluate which types of interactions occur between two-strain combinations and what these results mean in the context of adding a probiotic to an existing amphibian skin microbiome.
Collapse
Affiliation(s)
- Alexandra Alexiev
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Melissa Y. Chen
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Timothy Korpita
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Andrew M. Weier
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Valerie J. McKenzie
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| |
Collapse
|
18
|
Fieschi-Méric L, Van Leeuwen P, Hopkins K, Bournonville M, Denoël M, Lesbarrères D. Strong restructuration of skin microbiota during captivity challenges ex-situ conservation of amphibians. Front Microbiol 2023; 14:1111018. [PMID: 36891392 PMCID: PMC9986596 DOI: 10.3389/fmicb.2023.1111018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/31/2023] [Indexed: 02/22/2023] Open
Abstract
In response to the current worldwide amphibian extinction crisis, conservation instances have encouraged the establishment of ex-situ collections for endangered species. The resulting assurance populations are managed under strict biosecure protocols, often involving artificial cycles of temperature and humidity to induce active and overwintering phases, which likely affect the bacterial symbionts living on the amphibian skin. However, the skin microbiota is an important first line of defense against pathogens that can cause amphibian declines, such as the chytrid Batrachochytrium dendrobatidis (Bd). Determining whether current husbandry practices for assurance populations might deplete amphibians from their symbionts is therefore essential to conservation success. Here, we characterize the effect of the transitions from the wild to captivity, and between aquatic and overwintering phases, on the skin microbiota of two newt species. While our results confirm differential selectivity of skin microbiota between species, they underscore that captivity and phase-shifts similarly affect their community structure. More specifically, the translocation ex-situ is associated with rapid impoverishment, decrease in alpha diversity and strong species turnover of bacterial communities. Shifts between active and overwintering phases also cause changes in the diversity and composition of the microbiota, and on the prevalence of Bd-inhibitory phylotypes. Altogether, our results suggest that current husbandry practices strongly restructure the amphibian skin microbiota. Although it remains to be determined whether these changes are reversible or have deleterious effects on their hosts, we discuss methods to limit microbial diversity loss ex-situ and emphasize the importance of integrating bacterial communities to applied amphibian conservation.
Collapse
Affiliation(s)
- Léa Fieschi-Méric
- Laboratory of Ecology and Conservation of Amphibians (LECA), Freshwater and OCeanic science Unit of reSearch (FOCUS), Université de Liège, Liège, Belgium.,Biology Department, Laurentian University, Sudbury, ON, Canada
| | | | - Kevin Hopkins
- Institute of Zoology, Zoological Society of London (ZSL), London, United Kingdom
| | - Marie Bournonville
- Aquarium-Muséum de l'Université de Liège, Freshwater and OCeanic science Unit of reSearch (FOCUS), Liège, Belgium
| | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), Freshwater and OCeanic science Unit of reSearch (FOCUS), Université de Liège, Liège, Belgium
| | - David Lesbarrères
- Biology Department, Laurentian University, Sudbury, ON, Canada.,Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, ON, Canada
| |
Collapse
|
19
|
Goodwin KB, Hutchinson JD, Gompert Z. Spatiotemporal and ontogenetic variation, microbial selection, and predicted Bd-inhibitory function in the skin-associated microbiome of a Rocky Mountain amphibian. Front Microbiol 2022; 13:1020329. [PMID: 36583053 PMCID: PMC9792605 DOI: 10.3389/fmicb.2022.1020329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
Host-associated microbiomes play important roles in host health and pathogen defense. In amphibians, the skin-associated microbiota can contribute to innate immunity with potential implications for disease management. Few studies have examined season-long temporal variation in the amphibian skin-associated microbiome, and the interactions between bacteria and fungi on amphibian skin remain poorly understood. We characterize season-long temporal variation in the skin-associated microbiome of the western tiger salamander (Ambystoma mavortium) for both bacteria and fungi between sites and across salamander life stages. Two hundred seven skin-associated microbiome samples were collected from salamanders at two Rocky Mountain lakes throughout the summer and fall of 2018, and 127 additional microbiome samples were collected from lake water and lake substrate. We used 16S rRNA and ITS amplicon sequencing with Bayesian Dirichlet-multinomial regression to estimate the relative abundances of bacterial and fungal taxa, test for differential abundance, examine microbial selection, and derive alpha diversity. We predicted the ability of bacterial communities to inhibit the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), a cutaneous fungal pathogen, using stochastic character mapping and a database of Bd-inhibitory bacterial isolates. For both bacteria and fungi, we observed variation in community composition through time, between sites, and with salamander age and life stage. We further found that temporal trends in community composition were specific to each combination of salamander age, life stage, and lake. We found salamander skin to be selective for microbes, with many taxa disproportionately represented relative to the environment. Salamander skin appeared to select for predicted Bd-inhibitory bacteria, and we found a negative relationship between the relative abundances of predicted Bd-inhibitory bacteria and Bd. We hope these findings will assist in the conservation of amphibian species threatened by chytridiomycosis and other emerging diseases.
Collapse
Affiliation(s)
- Kenen B. Goodwin
- Department of Watershed Sciences, Utah State University, Logan, UT, United States,Department of Wildland Resources, Utah State University, Logan, UT, United States,*Correspondence: Kenen B. Goodwin,
| | - Jaren D. Hutchinson
- Department of Wildland Resources, Utah State University, Logan, UT, United States
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, UT, United States
| |
Collapse
|
20
|
Martínez-Ugalde E, Ávila-Akerberg V, González Martínez TM, Vázquez Trejo M, Zavala Hernández D, Anaya-Morales SL, Rebollar EA. The skin microbiota of the axolotl Ambystoma altamirani is highly influenced by metamorphosis and seasonality but not by pathogen infection. Anim Microbiome 2022; 4:63. [PMID: 36503640 PMCID: PMC9743558 DOI: 10.1186/s42523-022-00215-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/16/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Microbiomes have been increasingly recognized as major contributors to host health and survival. In amphibians, bacterial members of the skin microbiota protect their hosts by inhibiting the growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). Even though several studies describe the influence of biotic and abiotic factors over the skin microbiota, it remains unclear how these symbiotic bacterial communities vary across time and development. This is particularly relevant for species that undergo metamorphosis as it has been shown that host physiology and ecology drastically influence diversity of the skin microbiome. RESULTS We found that the skin bacterial communities of the axolotl A. altamirani are largely influenced by the metamorphic status of the host and by seasonal variation of abiotic factors such as temperature, pH, dissolved oxygen and conductivity. Despite high Bd prevalence in these samples, the bacterial diversity of the skin microbiota did not differ between infected and non-infected axolotls, although relative abundance of particular bacteria were correlated with Bd infection intensity. CONCLUSIONS Our work shows that metamorphosis is a crucial process that shapes skin bacterial communities and that axolotls under different developmental stages respond differently to environmental seasonal variations. Moreover, this study greatly contributes to a better understanding of the factors that shape amphibian skin microbiota, especially in a largely underexplored group like axolotls (Mexican Ambystoma species).
Collapse
Affiliation(s)
- Emanuel Martínez-Ugalde
- grid.9486.30000 0001 2159 0001Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Víctor Ávila-Akerberg
- grid.412872.a0000 0001 2174 6731Instituto de Ciencias Agropecuarias y Rurales, Universidad Autónoma del Estado de México, Toluca, Mexico
| | - Tanya M. González Martínez
- grid.9486.30000 0001 2159 0001Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Montserrat Vázquez Trejo
- grid.9486.30000 0001 2159 0001Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Dalia Zavala Hernández
- grid.9486.30000 0001 2159 0001Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sara Lucia Anaya-Morales
- grid.9486.30000 0001 2159 0001Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico ,grid.251313.70000 0001 2169 2489 Department of Biology, University of Mississippi, Oxford, MS USA
| | - Eria A. Rebollar
- grid.9486.30000 0001 2159 0001Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| |
Collapse
|
21
|
Case NT, Berman J, Blehert DS, Cramer RA, Cuomo C, Currie CR, Ene IV, Fisher MC, Fritz-Laylin LK, Gerstein AC, Glass NL, Gow NAR, Gurr SJ, Hittinger CT, Hohl TM, Iliev ID, James TY, Jin H, Klein BS, Kronstad JW, Lorch JM, McGovern V, Mitchell AP, Segre JA, Shapiro RS, Sheppard DC, Sil A, Stajich JE, Stukenbrock EE, Taylor JW, Thompson D, Wright GD, Heitman J, Cowen LE. The future of fungi: threats and opportunities. G3 (BETHESDA, MD.) 2022; 12:jkac224. [PMID: 36179219 PMCID: PMC9635647 DOI: 10.1093/g3journal/jkac224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/12/2022] [Indexed: 01/13/2023]
Abstract
The fungal kingdom represents an extraordinary diversity of organisms with profound impacts across animal, plant, and ecosystem health. Fungi simultaneously support life, by forming beneficial symbioses with plants and producing life-saving medicines, and bring death, by causing devastating diseases in humans, plants, and animals. With climate change, increased antimicrobial resistance, global trade, environmental degradation, and novel viruses altering the impact of fungi on health and disease, developing new approaches is now more crucial than ever to combat the threats posed by fungi and to harness their extraordinary potential for applications in human health, food supply, and environmental remediation. To address this aim, the Canadian Institute for Advanced Research (CIFAR) and the Burroughs Wellcome Fund convened a workshop to unite leading experts on fungal biology from academia and industry to strategize innovative solutions to global challenges and fungal threats. This report provides recommendations to accelerate fungal research and highlights the major research advances and ideas discussed at the meeting pertaining to 5 major topics: (1) Connections between fungi and climate change and ways to avert climate catastrophe; (2) Fungal threats to humans and ways to mitigate them; (3) Fungal threats to agriculture and food security and approaches to ensure a robust global food supply; (4) Fungal threats to animals and approaches to avoid species collapse and extinction; and (5) Opportunities presented by the fungal kingdom, including novel medicines and enzymes.
Collapse
Affiliation(s)
- Nicola T Case
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - David S Blehert
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | - Robert A Cramer
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Christina Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Iuliana V Ene
- Department of Mycology, Institut Pasteur, Université de Paris, Paris 75015, France
| | - Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London W2 1PG, UK
| | | | - Aleeza C Gerstein
- Department of Microbiology and Department of Statistics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - N Louise Glass
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA
| | - Neil A R Gow
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Sarah J Gurr
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Chris Todd Hittinger
- Laboratory of Genetics, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Tobias M Hohl
- Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Iliyan D Iliev
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, CA 92507, USA
| | - Bruce S Klein
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Internal Medicine, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - James W Kronstad
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jeffrey M Lorch
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | | | - Aaron P Mitchell
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Donald C Sheppard
- McGill Interdisciplinary Initiative in Infection and Immunology, Departments of Medicine, Microbiology & Immunology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94117, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, CA 92507, USA
| | - Eva E Stukenbrock
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Environmental Genomics, Christian-Albrechts University, Kiel 24118, Germany
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California—Berkeley, Berkeley, CA 94720, USA
| | | | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Medicine, and Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| |
Collapse
|
22
|
Hill AJ, Grisnik M, Walker DM. Bacterial Skin Assemblages of Sympatric Salamanders Are Primarily Shaped by Host Genus. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02127-0. [PMID: 36318280 DOI: 10.1007/s00248-022-02127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Bacterial assemblages on the skins of amphibians are known to influence pathogen resistance and other important physiological functions in the host. Host-specific factors and the environment play significant roles in structuring skin assemblages. This study used high-throughput 16S rRNA sequencing and multivariate analyses to examine differences in skin-bacterial assemblages from 246 salamanders belonging to three genera in the lungless family Plethodontidae along multiple spatial gradients. Composition and α- and β-diversity of bacterial assemblages were defined, indicator species were identified for each host group, and the relative influences of host- versus environment-specific ecological factors were evaluated. At the broadest spatial scale, host genus, host species, and sampling site were predictive of skin assemblage structure, but host genus and species were more influential after controlling for the marginal effects of site, as well as nestedness of site. Furthermore, assemblage similarity within each host genus did not change with increasing geographic distance. At the smallest spatial scale, site-specific climate analyses revealed different relationships to climatic variables for each of the three genera, and these relationships were determined by host ecomode. Variation in bacterial assemblages of terrestrial hosts correlated with landscape-level climatic variability, and this pattern decayed with increasing water dependence of the host. Results from this study highlight host-specific considerations for researchers studying wildlife diseases in co-occurring, yet ecologically divergent, species.
Collapse
Affiliation(s)
- Aubree J Hill
- Department of Biology, Tennessee Technological University, 1100 North Dixie Avenue, Box 5063, Cookeville, TN, 38505, USA.
| | - Matthew Grisnik
- Department of Agricultural and Environmental Sciences, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN, 37209, USA
| | - Donald M Walker
- Department of Biology, Middle Tennessee State University, 1672 Greenland Drive, Murfreesboro, TN, 37132, USA
| |
Collapse
|
23
|
Torres-Sánchez M, Longo AV. Linking pathogen-microbiome-host interactions to explain amphibian population dynamics. Mol Ecol 2022; 31:5784-5794. [PMID: 36130047 DOI: 10.1111/mec.16701] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 01/13/2023]
Abstract
Symbiotic interactions can determine the evolutionary trajectories of host species, influencing genetic variation through selection and changes in demography. In the context of strong selective pressures such as those imposed by infectious diseases, symbionts providing defences could contribute to increase host fitness upon pathogen emergence. Here, we generated genome-wide data of an amphibian species to find evidence of evolutionary pressures driven by two skin symbionts: a batrachochytrid fungal pathogen and an antifungal bacterium. Using demographic modelling, we found evidence of decreased effective population size, probably due to pathogen infections. Additionally, we investigated host genetic associations with infection status, antifungal bacterium abundance and overall microbiome diversity using structural equation models. We uncovered relatively lower nucleotide diversity in infected frogs and potential heterozygote advantage to recruit the candidate beneficial symbiont and fight infections. Our models indicate that environmental conditions have indirect effects on symbiont abundance through both host body traits and microbiome diversity. Likewise, we uncovered a potential offsetting effect among host heterozygosity-fitness correlations, plausibly pointing to different ecological and evolutionary processes among the three species due to dynamic interactions. Our findings revealed that evolutionary pressures not only arise from the pathogen but also from the candidate beneficial symbiont, and both interactions shape the genetics of the host. Our results advance knowledge about multipartite symbiotic relationships and provide a framework to model ecological and evolutionary dynamics in wild populations. Finally, our study approach can be applied to inform conservation actions such as bioaugmentation strategies for other imperilled amphibians affected by infectious diseases.
Collapse
Affiliation(s)
| | - Ana V Longo
- Department of Biology, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
24
|
Ophidiomyces ophidiicola detection and infection: a global review on a potential threat to the world’s snake populations. EUR J WILDLIFE RES 2022. [DOI: 10.1007/s10344-022-01612-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractOphidiomyces ophidiicola (Oo) is one of the most relevant fungal pathogens for snakes. It is the etiological agent of ophidiomycosis, an emerging disease causing dysecdysis, skin abnormalities, crusting cutaneous lesions, and ulcerations. Despite this major tegumentary “tropism”, Oo infection can be systemic and it is capable of inducing visceral lesions. Moreover, ophidiomycosis may lead to abnormalities of reproductive physiology, hunting behavior, and thermoregulation, thus increasing the risks of sublethal effects and predation on affected snakes. Oo seems horizontally transmitted and can induce postnatal mortality. This article reviews published data on Oo detection and infection in all snake species in countries around the world and categorizes these data using new classification parameters. The presence of this fungus has been recorded in 11 states (considering the USA as a whole); however, in four states, the mycosis has only been reported in snakes held in captivity. Detection and/or infection of Oo has been ascertained in 62 snake species, divided into nine families. The taxa have been categorized with diagnostic criteria in order to report, for each species, the highest rank of categorization resulting from all cases. Therefore, 20 species have been included within the class “Ophidiomycosis and Oo shedder”, 11 within “Ophidiomycosis”, 16 in “Apparent ophidiomycosis”, and 15 within “Ophidiomyces ophidiicola present”. We also discuss the significance and limits of case classifications and Oo’s impact on wild populations, and we suggest methods for preliminary surveillance. Standardized methods, interdisciplinary studies, and cooperation between various research institutions may facilitate further Oo screening studies, elucidate the unclear aspects of the disease, and protect ophidiofauna from this emerging threat at the global level.
Collapse
|
25
|
Abstract
Temporal changes and transmission patterns in host-associated microbial communities have important implications for host health. The diversity of amphibian skin microbial communities is associated with disease outcome in amphibians exposed to the fungal pathogen Batrachochytrium dendrobatidis (Bd). To successfully develop conservation strategies against Bd, we need a comprehensive understanding of how skin microbes are maintained and transmitted over time within populations. We used 16S rRNA sequence analysis to compare Epipedobates anthonyi frogs housed with one conspecific to frogs housed singly at four time points over the course of 1 year. We found that both α and β diversity of frog skin bacterial communities changed significantly over the course of the experiment. Specifically, we found that bacterial communities of cohabitating frogs became more similar over time. We also observed that some bacterial taxa were differentially abundant between frogs housed singly and frogs housed with a conspecific. These results suggest that conspecific contact may play a role in mediating amphibian skin microbial diversity and that turnover of skin microbial communities can occur across time. Our findings provide rationale for future studies exploring horizontal transmission as a potential mechanism of host-associated microbial maintenance in amphibians.
Collapse
Affiliation(s)
- Ariel Kruger
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, USA
| | - Spencer Roth
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| |
Collapse
|
26
|
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: 51] [Impact Index Per Article: 25.5] [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.
Collapse
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
| |
Collapse
|
27
|
Estrada A, Medina D, Gratwicke B, Ibáñez R, Belden LK. Body condition, skin bacterial communities and disease status: insights from the first release trial of the limosa harlequin frog,
Atelopus limosus. Proc Biol Sci 2022; 289:20220586. [PMID: 35858072 PMCID: PMC9277274 DOI: 10.1098/rspb.2022.0586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many endangered amphibian species survive in captive breeding facilities, but there have been few attempts to reintroduce captive-born individuals to rebuild wild populations. We conducted a soft-release trial of limosa harlequin frogs,
Atelopus limosus,
which are highly susceptible to the amphibian chytrid fungus
Batrachochytrium dendrobatidis
(Bd), to understand changes associated with the transition from captivity to the wild. Specifically, we assessed changes in body condition, skin-associated bacterial communities and disease status after release. Frogs were housed individually in field mesocosms and monitored for 27 days. Body condition did not significantly change in the mesocosms, and was similar to, or higher than, that of wild conspecifics at day 27. The skin bacteria of captive-born frogs, based on 16S rRNA gene amplicons, became similar to that of wild conspecifics after 27 days in mesocosms. Prevalence of Bd in wild conspecifics was 13–27%, and 15% of the
A. limosus
in mesocosms became infected with Bd, but no mortality of infected frogs was observed. We conclude that mesocosms are suitable for systematically and repeatedly monitoring amphibians during release trials, and that body condition, the skin microbiome, and Bd status can all change within one month of placement of captive-born individuals back into the wild.
Collapse
Affiliation(s)
- Angie Estrada
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0131, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0131, USA
- Smithsonian Tropical Research Institute, Panama City, Panama
- Sistema Nacional de Investigación, SENACYT, Panama
| | - Brian Gratwicke
- Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA 22630, USA
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Panama City, Panama
- Sistema Nacional de Investigación, SENACYT, Panama
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0131, USA
- Smithsonian Tropical Research Institute, Panama City, Panama
| |
Collapse
|
28
|
McKnight DT, Huerlimann R, Bower DS, Schwarzkopf L, Alford RA, Zenger KR. The interplay of fungal and bacterial microbiomes on rainforest frogs following a disease outbreak. Ecosphere 2022. [DOI: 10.1002/ecs2.4037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Donald T. McKnight
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Roger Huerlimann
- College of Science and Engineering James Cook University Townsville Queensland Australia
- Marine Climate Change Unit Okinawa Institute of Science and Technology Onnason Okinawa Japan
| | - Deborah S. Bower
- College of Science and Engineering James Cook University Townsville Queensland Australia
- School of Environmental and Rural Science University of New England Armidale New South Wales Australia
| | - Lin Schwarzkopf
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Ross A. Alford
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Kyall R. Zenger
- College of Science and Engineering James Cook University Townsville Queensland Australia
| |
Collapse
|
29
|
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
| |
Collapse
|
30
|
Forsythe A, Fontaine N, Bissonnette J, Hayashi B, Insuk C, Ghosh S, Kam G, Wong A, Lausen C, Xu J, Cheeptham N. Microbial isolates with Anti-Pseudogymnoascus destructans activities from Western Canadian bat wings. Sci Rep 2022; 12:9895. [PMID: 35701553 PMCID: PMC9198084 DOI: 10.1038/s41598-022-14223-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/02/2022] [Indexed: 11/29/2022] Open
Abstract
Pseudogymnoascus destructans (Pd) is the causative agent of white-nose syndrome, which has resulted in the death of millions of bats in North America (NA) since 2006. Based on mortalities in eastern NA, the westward spread of infections likely poses a significant threat to western NA bats. To help prevent/reduce Pd infections in bats in western NA, we isolated bacteria from the wings of wild bats and screened for inhibitory activity against Pd. In total, we obtained 1,362 bacterial isolates from 265 wild bats of 13 species in western Canada. Among the 1,362 isolates, 96 showed inhibitory activity against Pd based on a coculture assay. The inhibitory activities varied widely among these isolates, ranging from slowing fungal growth to complete inhibition. Interestingly, host bats containing isolates with anti-Pd activities were widely distributed, with no apparent geographic or species-specific pattern. However, characteristics of roosting sites and host demography showed significant associations with the isolation of anti-Pd bacteria. Specifically, anthropogenic roosts and swabs from young males had higher frequencies of anti-Pd bacteria than those from natural roosts and those from other sex and age-groups, respectively. These anti-Pd bacteria could be potentially used to help mitigate the impact of WNS. Field trials using these as well as additional microbes from future screenings are needed in order to determine their effectiveness for the prevention and treatment against WNS.
Collapse
Affiliation(s)
- Adrian Forsythe
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Nick Fontaine
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Julianna Bissonnette
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Brandon Hayashi
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Chadabhorn Insuk
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada.,Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Soumya Ghosh
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada.,Department of Genetics, Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | - Gabrielle Kam
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Aaron Wong
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Cori Lausen
- Wildlife Conservation Society Canada, P.O. Box 606, Kaslo, BC, V0G 1M0, Canada.
| | - Jianping Xu
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada.
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada.
| |
Collapse
|
31
|
Microbial Diversity of the Chinese Tiger Frog (Hoplobatrachus rugulosus) on Healthy versus Ulcerated Skin. Animals (Basel) 2022; 12:ani12101241. [PMID: 35625087 PMCID: PMC9137582 DOI: 10.3390/ani12101241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary As amphibians’ skin is highly sensitive to the environment, skin defects such as ulceration may pose a particular threat to them. Our study has found a stark difference in the microbial communities between healthy and ulcerated Hoplobatrachus rugulosus skin. The proportion and type of bacteria differed between the two groups, and we suggest that ulceration on the skin may lead to changes in skin microbial communities. The functional pathways of skin microbes may be influenced by ulceration on the skin surface of H. rugulosus. We also found that Vogesella is more abundant in healthy H. rugulosus, which may be a potential probiotic candidate for the reduction or removal of pathogens. Abstract The Chinese tiger frog (Hoplobatrachus rugulosus) is extensively farmed in southern China. Due to cramped living conditions, skin diseases are prevalent among unhealthy tiger frogs which thereby affects their welfare. In this study, the differences in microbiota present on healthy versus ulcerated H. rugulosus skin were examined using 16S rRNA sequences. Proteobacteria were the dominant phylum on H. rugulosus skin, but their abundance was greater on the healthy skin than on the ulcerated skin. Rhodocyclaceae and Comamonadaceae were the most dominant families on the healthy skin, whereas Moraxellaceae was the most dominant family on the ulcerated skin. The abundance of these three families was different between the groups. Acidovorax was the most dominant genus on the healthy skin, whereas Acinetobacter was the most dominant genus on the ulcerated skin, and its abundance was greater on the ulcerated skin than on the healthy skin. Moreover, the genes related to the Kyoto Encyclopedia of Genes and Genomes pathways of levels 2–3, especially those genes that are involved in cell motility, flagellar assembly, and bacterial chemotaxis in the skin microbiota, were found to be greater on the healthy skin than on the ulcerated skin, indicating that the function of skin microbiota was affected by ulceration. Overall, the composition, abundance, and function of skin microbial communities differed between the healthy and ulcerated H. rugulosus skin. Our results may assist in developing measures to combat diseases in H. rugulosus.
Collapse
|
32
|
Salazar-Hamm PS, Hathaway JJM, Winter AS, Caimi NA, Buecher DC, Valdez EW, Northup DE. Great diversity of KS α sequences from bat-associated microbiota suggests novel sources of uncharacterized natural products. FEMS MICROBES 2022; 3:xtac012. [PMID: 35573391 PMCID: PMC9097503 DOI: 10.1093/femsmc/xtac012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/10/2022] [Accepted: 04/13/2022] [Indexed: 11/17/2022] Open
Abstract
Polyketide synthases (PKSs) are multidomain enzymes in microorganisms that synthesize complex, bioactive molecules. PKS II systems are iterative, containing only a single representative of each domain: ketosynthase alpha (KS[Formula: see text]), ketosynthase beta and the acyl carrier protein. Any gene encoding for one of these domains is representative of an entire PKS II biosynthetic gene cluster (BGC). Bat skin surfaces represent an extreme environment prolific in Actinobacteria that may constitute a source for bioactive molecule discovery. KS[Formula: see text] sequences were obtained from culturable bacteria from bats in the southwestern United States. From 467 bat bacterial isolates, we detected 215 (46%) had KS[Formula: see text] sequences. Sequencing yielded 210 operational taxonomic units, and phylogenetic placement found 45 (21%) shared <85% homology to characterized metabolites. Additionally, 16 Actinobacteria genomes from the bat microbiome were analyzed for biosynthetic capacity. A range of 69-93% of the BGCs were novel suggesting the bat microbiome may contain valuable uncharacterized natural products. Documenting and characterizing these are important in understanding the susceptibility of bats to emerging infectious diseases, such as white-nose syndrome. Also noteworthy was the relationship between KS [Formula: see text] homology and total BGC novelty within each fully sequenced strain. We propose amplification and detection of KS[Formula: see text] could predict a strain's global biosynthetic capacity.
Collapse
Affiliation(s)
- Paris S Salazar-Hamm
- Department of Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
| | | | - Ara S Winter
- Department of Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
| | - Nicole A Caimi
- Department of Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
| | | | - Ernest W Valdez
- Department of Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
- U.S. Geological Survey, Fort Collins Science Center, Department of Biology, MSC03 2020, University of New Mexico, lbuquerque, NM 87131, USA
| | - Diana E Northup
- Department of Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
| |
Collapse
|
33
|
Jiang H, Luo S, Zhou J, Huang W, Li L, Zhang X, He J, Chen J. Skin Microbiota Was Altered in Crocodile Lizards (Shinisaurus crocodilurus) With Skin Ulcer. Front Vet Sci 2022; 9:817490. [PMID: 35237680 PMCID: PMC8884271 DOI: 10.3389/fvets.2022.817490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/11/2022] [Indexed: 02/02/2023] Open
Abstract
Skin diseases commonly affect reptiles, but their relationships to the closely related skin microbiome are not well-understood. In recent years, both the wild and captive populations of the crocodile lizard, a Class I protected endangered animal in China, have suffered serious skin diseases that hamper the rescue and release projects for their conservation. This study conducted a detailed prevalence investigation of a major dermatosis characterized by foot skin ulcer in crocodile lizards. It should be noticed that skin ulcer has been prevalent in both captive and wild populations. There was positive correlation between skin ulcer and temperature, while no significant relationship between skin ulcer and humidity, sex, and age. We further studied the relationship between skin ulcer and the skin microbiota using meta-taxonomics. Results showed that the skin microbiota of crocodile lizards was significantly different from those of the environmental microbial communities, and that skin microbiota had a significant relationship with skin ulcer despite the impact of environment. Both bacterial and fungal communities on the ulcerated skin were significantly changed, which was characterized by lower community diversity and different dominant microbes. Our findings provide an insight into the relationship between skin microbiota and skin disease in reptile, serving as a reference for dermatological etiology in wildlife conservation.
Collapse
Affiliation(s)
- Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shuyi Luo
- Guangxi Daguishan Crocodile Lizard National Nature Reserve, Hezhou, China
| | - Jiabin Zhou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Wenzhong Huang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jiasong He
- Guangxi Daguishan Crocodile Lizard National Nature Reserve, Hezhou, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
- *Correspondence: Jinping Chen
| |
Collapse
|
34
|
Chen MY, Kueneman JG, González A, Humphrey G, Knight R, McKenzie VJ. Predicting fungal infection rate and severity with skin-associated microbial communities on amphibians. Mol Ecol 2022; 31:2140-2156. [PMID: 35076975 DOI: 10.1111/mec.16372] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 12/16/2021] [Accepted: 01/18/2022] [Indexed: 11/28/2022]
Abstract
Pathogen success (risk and severity) is influenced by host-associated microbiota, but the degree to which variation in microbial community traits predict future infection presence/absence (risk) and load (severity) for the host is unknown. We conducted a time-series experiment by sampling the skin-associated bacterial communities of five amphibian species before and after exposure to the fungal pathogen, Batrachochytrium dendrobaditis (Bd). We ask whether microbial community traits are predictors of, or are affected by, Bd infection risk and intensity. Our results show that richness of putative Bd-inhibitory bacteria strongly predicts infection risk, while the proportion of putative Bd-inhibitory bacteria predicts future infection intensity. Variation in microbial community composition is high across time and individual, and bacterial prevalence is low. Our findings demonstrate how ecological community traits of host-associated microbiota may be used to predict infection risk by pathogenic microbes.
Collapse
Affiliation(s)
- Melissa Y Chen
- Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N-122, UCB 334, Boulder, CO, 80309, USA
| | - Jordan G Kueneman
- Smithsonian Tropical Research Institute, Luis Clement Avenue, Bldg. 401 Tupper, Balboa Ancon, Panama, Republic of Panama
| | - Antonio González
- Department of Pediatrics, Bioengineering and Computer Science and Engineering, and Center for Microbiome Innovation, University of California, Gilman Drive, La Jolla, San Diego, CA, 92093, USA
| | - Greg Humphrey
- Department of Pediatrics, Bioengineering and Computer Science and Engineering, and Center for Microbiome Innovation, University of California, Gilman Drive, La Jolla, San Diego, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, Bioengineering and Computer Science and Engineering, and Center for Microbiome Innovation, University of California, Gilman Drive, La Jolla, San Diego, CA, 92093, USA
| | - Valerie J McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N-122, UCB 334, Boulder, CO, 80309, USA
| |
Collapse
|
35
|
Bacterial biofilm thickness and fungal-inhibitory bacterial richness both prevent establishment of the amphibian fungal pathogen, Batrachochytrium dendrobatidis. Appl Environ Microbiol 2022; 88:e0160421. [PMID: 35044804 DOI: 10.1128/aem.01604-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Host-associated microbial biofilms can provide protection against pathogen establishment. In many host-microbe symbioses (including, but not limited to: humans, plants, insects, and amphibians), there is a correlation between host-associated microbial diversity and pathogen infection risk. Diversity may prevent infection by pathogens through sampling effects and niche complementarity- but an alternative hypothesis may be that microbial biomass is confounded with diversity, and that host-associated biofilms are deterring pathogen establishment through space pre-emption. In this study, we use the amphibian system as a model for host-microbe-pathogen interactions to ask two questions: (1) is bacterial richness confounded with biofilm thickness or cell density, and (2) to what extent does biofilm thickness, cell density, and bacterial richness each deter the establishment of the amphibian fungal pathogen, Batrachochytrium dendrobatidis (Bd)? To answer these questions, we built a custom biofilm microcosm that mimics the host-environment interface by allowing nutrients to diffuse out of a fine-pore biofilm scaffolding. This created a competitive environment in which bacteria and the fungal pathogen compete for colonization space. We then challenged bacterial biofilms ranging in community richness, biofilm thickness, bacterial cell density, and Bd-inhibitory metabolite production with live Bd zoospores to determine how Bd establishment success on membranes vary. We found that biofilm thickness and Bd-inhibitory isolate richness work in complement to reduce Bd establishment success. This work underscores that physical aspects of biofilm communities can play a large role in pathogen inhibition and in many studies, these traits are not studied. IMPORTANCE Our finding highlights the fact that diversity, as measured through 16S rDNA sequencing, may obscure the true mechanisms behind microbe-mediated pathogen defence, and that physical space occupation by biofilm-forming symbionts may significantly contribute to pathogen protection. These findings have implications across a wide range of host-microbe systems, since 16S rDNA sequencing is a standard tool used across many microbial systems. Further, our results are potentially relevant to many host-pathogen systems, since host-associated bacterial biofilms are ubiquitous.
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
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.
Collapse
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.
| |
Collapse
|
39
|
Ellison S, Knapp R, Vredenburg V. Longitudinal patterns in the skin microbiome of wild, individually marked frogs from the Sierra Nevada, California. ISME COMMUNICATIONS 2021; 1:45. [PMID: 37938625 PMCID: PMC9723788 DOI: 10.1038/s43705-021-00047-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 08/04/2021] [Accepted: 08/17/2021] [Indexed: 05/29/2023]
Abstract
The amphibian skin microbiome has been the focus of numerous studies because of the protective effects that some bacteria provide against the pathogenic fungus Batrachochytrium dendrobatidis, which has caused a global panzootic among amphibians. However, the mechanisms driving community structure and function in the amphibian skin microbiome are still poorly understood, and longitudinal analyses of the skin microbiome have not yet been conducted in wild populations. In this study, we investigate longitudinal patterns in the skin microbiome of 19 individually marked adult frogs from two wild populations of the endangered Sierra Nevada yellow-legged frog (Rana sierrae), sampled over the course of 2 years. We found that individuals with low bacterial diversity (dominated by order Burkhorderiales) had significantly more stable bacterial communities than those with higher diversity. Amplicon sequence variants (ASVs) with high relative abundance were significantly less transient than those with low relative abundance, and ASVs with intermediate-level relative abundances experienced the greatest volatility over time. Based on these results, we suggest that efforts to develop probiotic treatments to combat B. dendrobatidis should focus on bacteria that are found at high relative abundances in some members of a population, as these strains are more likely to persist and remain stable in the long term.
Collapse
Affiliation(s)
- Silas Ellison
- Department of Biology, San Francisco State University, San Francisco, California, USA.
| | - Roland Knapp
- Sierra Nevada Aquatic Research Laboratory, University of California, Mammoth Lakes, CA, USA
| | - Vance Vredenburg
- Department of Biology, San Francisco State University, San Francisco, California, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
| |
Collapse
|
40
|
Alvarado-Rybak M, Lepe-Lopez M, Peñafiel-Ricaurte A, Valenzuela-Sánchez A, Valdivia C, Mardones FO, Bacigalupe LD, Puschendorf R, Cunningham AA, Azat C. Bioclimatic and anthropogenic variables shape the occurrence of Batrachochytrium dendrobatidis over a large latitudinal gradient. Sci Rep 2021; 11:17383. [PMID: 34462470 PMCID: PMC8405646 DOI: 10.1038/s41598-021-96535-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 08/05/2021] [Indexed: 02/07/2023] Open
Abstract
Amphibian chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), has caused the greatest known loss of biodiversity due to an infectious disease. We used Bd infection data from quantitative real-time PCR (qPCR) assays of amphibian skin swabs collected across Chile during 2008-2018 to model Bd occurrence with the aim to determine bioclimatic and anthropogenic variables associated with Bd infection. Also, we used Bd presence/absence records to identify geographical Bd high-risk areas and compare Bd prevalence and infection loads between amphibian families, ecoregions, and host ecology. Data comprised 4155 Bd-specific qPCR assays from 162 locations across a latitudinal gradient of 3700 km (18º to 51ºS). Results showed a significant clustering of Bd associated with urban centres and anthropogenically highly disturbed ecosystems in central-south Chile. Both Bd prevalence and Bd infection loads were higher in aquatic than terrestrial amphibian species. Our model indicated positive associations of Bd prevalence with altitude, temperature, precipitation and human-modified landscapes. Also, we found that macroscale drivers, such as land use change and climate, shape the occurrence of Bd at the landscape level. Our study provides with new evidence that can improve the effectiveness of strategies to mitigate biodiversity loss due to amphibian chytridiomycosis.
Collapse
Affiliation(s)
- Mario Alvarado-Rybak
- Sustainability Research Centre & PhD Programme in Conservation Medicine, Life Sciences Faculty, Universidad Andres Bello, Republica 252, Santiago, Chile
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
- Núcleo de Ciencias Aplicadas en Ciencias Veterinarias y Agronómicas, Universidad de las Américas, Echaurren 140, Santiago, Chile
| | - Manuel Lepe-Lopez
- Sustainability Research Centre & PhD Programme in Conservation Medicine, Life Sciences Faculty, Universidad Andres Bello, Republica 252, Santiago, Chile
| | - Alexandra Peñafiel-Ricaurte
- Sustainability Research Centre & PhD Programme in Conservation Medicine, Life Sciences Faculty, Universidad Andres Bello, Republica 252, Santiago, Chile
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Andrés Valenzuela-Sánchez
- Sustainability Research Centre & PhD Programme in Conservation Medicine, Life Sciences Faculty, Universidad Andres Bello, Republica 252, Santiago, Chile
- ONG Ranita de Darwin, Nataniel Cox 152, Santiago, Chile
- Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, 5110566, Valdivia, Chile
| | - Catalina Valdivia
- Sustainability Research Centre & PhD Programme in Conservation Medicine, Life Sciences Faculty, Universidad Andres Bello, Republica 252, Santiago, Chile
| | - Fernando O Mardones
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Leonardo D Bacigalupe
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Robert Puschendorf
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Andrew A Cunningham
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Claudio Azat
- Sustainability Research Centre & PhD Programme in Conservation Medicine, Life Sciences Faculty, Universidad Andres Bello, Republica 252, Santiago, Chile.
| |
Collapse
|
41
|
Identifying fungal-host associations in an amphibian host system. PLoS One 2021; 16:e0256328. [PMID: 34411153 PMCID: PMC8376043 DOI: 10.1371/journal.pone.0256328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 08/04/2021] [Indexed: 02/07/2023] Open
Abstract
Host-associated microbes can interact with macro-organisms in a number of ways that affect host health. Few studies of host-associated microbiomes, however, focus on fungi. In addition, it is difficult to discern whether a fungal organism found in or on an ectotherm host is associating with it in a durable, symbiotic interaction versus a transient one, and to what extent the habitat and host share microbes. We seek to identify these host-microbe interactions on an amphibian, the Colorado boreal toad (Anaxyrus boreas boreas). We sequenced the ITS1 region of the fungal community on the skin of wild toads (n = 124) from four sites in the Colorado Rocky Mountains, across its physiologically dynamic developmental life stages. We also sampled the common habitats used by boreal toads: water from their natal wetland and aquatic pond sediment. We then examined diversity patterns within different life stages, between host and habitat, and identified fungal taxa that could be putatively host-associated with toads by using an indicator species analysis on toad versus environmental samples. Host and habitat were strikingly similar, with the exception of toad eggs. Post-hatching toad life stages were distinct in their various fungal diversity measures. We identified eight fungal taxa that were significantly associated with eggs, but no other fungal taxa were associated with other toad life stages compared with their environmental habitat. This suggests that although pre- and post-metamorphic toad life stages differ from each other, the habitat and host fungal communities are so similar that identifying obligate host symbionts is difficult with the techniques used here. This approach does, however, leverage sequence data from host and habitat samples to predict which microbial taxa are host-associated versus transient microbes, thereby condensing a large set of sequence data into a smaller list of potential targets for further consideration.
Collapse
|
42
|
Fisher MC, Pasmans F, Martel A. Virulence and Pathogenicity of Chytrid Fungi Causing Amphibian Extinctions. Annu Rev Microbiol 2021; 75:673-693. [PMID: 34351790 DOI: 10.1146/annurev-micro-052621-124212] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient enzootic associations between wildlife and their infections allow evolution to innovate mechanisms of pathogenicity that are counterbalanced by host responses. However, erosion of barriers to pathogen dispersal by globalization leads to the infection of hosts that have not evolved effective resistance and the emergence of highly virulent infections. Global amphibian declines driven by the rise of chytrid fungi and chytridiomycosis are emblematic of emerging infections. Here, we review how modern biological methods have been used to understand the adaptations and counteradaptations that these fungi and their amphibian hosts have evolved. We explore the interplay of biotic and abiotic factors that modify the virulence of these infections and dissect the complexity of this disease system. We highlight progress that has led to insights into how we might in the future lessen the impact of these emerging infections. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial School of Public Health, Imperial College London, London W2 1PG, United Kingdom;
| | - Frank Pasmans
- Wildlife Health Ghent, Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - An Martel
- Wildlife Health Ghent, Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| |
Collapse
|
43
|
Olson DH, Ronnenberg KL, Glidden CK, Christiansen KR, Blaustein AR. Global Patterns of the Fungal Pathogen Batrachochytrium dendrobatidis Support Conservation Urgency. Front Vet Sci 2021; 8:685877. [PMID: 34336978 PMCID: PMC8322974 DOI: 10.3389/fvets.2021.685877] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/15/2021] [Indexed: 12/21/2022] Open
Abstract
The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) is a skin pathogen that can cause the emerging infectious disease chytridiomycosis in susceptible species. It has been considered one of the most severe threats to amphibian biodiversity. We aimed to provide an updated compilation of global Bd occurrences by host taxon and geography, and with the larger global Bd dataset we reanalyzed Bd associations with environmental metrics at the world and regional scales. We also compared our Bd data compilation with a recent independent assessment to provide a more comprehensive count of species and countries with Bd occurrences. Bd has been detected in 1,375 of 2,525 (55%) species sampled, more than doubling known species infections since 2013. Bd occurrence is known from 93 of 134 (69%) countries at this writing; this compares to known occurrences in 56 of 82 (68%) countries in 2013. Climate-niche space is highly associated with Bd detection, with different climate metrics emerging as key predictors of Bd occurrence at regional scales; this warrants further assessment relative to climate-change projections. The accretion of Bd occurrence reports points to the common aims of worldwide investigators to understand the conservation concerns for amphibian biodiversity in the face of potential disease threat. Renewed calls for better mitigation of amphibian disease threats resonate across continents with amphibians, especially outside Asia. As Bd appears to be able to infect about half of amphibian taxa and sites, there is considerable room for biosecurity actions to forestall its spread using both bottom-up community-run efforts and top-down national-to-international policies. Conservation safeguards for sensitive species and biodiversity refugia are continuing priorities.
Collapse
Affiliation(s)
- Deanna H Olson
- Pacific Northwest Research Station, United States Department of Agriculture (USDA) Forest Service, Corvallis, OR, United States
| | - Kathryn L Ronnenberg
- Pacific Northwest Research Station, United States Department of Agriculture (USDA) Forest Service, Corvallis, OR, United States
| | | | - Kelly R Christiansen
- Pacific Northwest Research Station, United States Department of Agriculture (USDA) Forest Service, Corvallis, OR, United States
| | - Andrew R Blaustein
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| |
Collapse
|
44
|
Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation †. J Genet 2021. [PMID: 33622992 PMCID: PMC7371965 DOI: 10.1007/s12041-020-01225-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease-mediated extinctions and wildlife epidemics. We then focus on elucidating how host–parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
Collapse
|
45
|
Belasen AM, Riolo MA, Bletz MC, Lyra ML, Toledo LF, James TY. Geography, Host Genetics, and Cross-Domain Microbial Networks Structure the Skin Microbiota of Fragmented Brazilian Atlantic Forest Frog Populations. Ecol Evol 2021; 11:9293-9307. [PMID: 34306622 PMCID: PMC8293785 DOI: 10.1002/ece3.7594] [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: 05/03/2020] [Revised: 08/31/2020] [Accepted: 03/18/2021] [Indexed: 11/09/2022] Open
Abstract
The host-associated microbiome plays a significant role in health. However, the roles of factors such as host genetics and microbial interactions in determining microbiome diversity remain unclear. We examined these factors using amplicon-based sequencing of 175 Thoropa taophora frog skin swabs collected from a naturally fragmented landscape in southeastern Brazil. Specifically, we examined (1) the effects of geography and host genetics on microbiome diversity and structure; (2) the structure of microbial eukaryotic and bacterial co-occurrence networks; and (3) co-occurrence between microeukaryotes with bacterial OTUs known to affect growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). While bacterial alpha diversity varied by both site type and host MHC IIB genotype, microeukaryotic alpha diversity varied only by site type. However, bacteria and microeukaryote composition showed variation according to both site type and host MHC IIB genotype. Our network analysis showed the highest connectivity when both eukaryotes and bacteria were included, implying that ecological interactions may occur among domains. Lastly, anti-Bd bacteria were not broadly negatively co-associated with the fungal microbiome and were positively associated with potential amphibian parasites. Our findings emphasize the importance of considering both domains in microbiome research and suggest that for effective probiotic strategies for amphibian disease management, considering potential interactions among all members of the microbiome is crucial.
Collapse
Affiliation(s)
- Anat M. Belasen
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
| | - Maria A. Riolo
- Center for Complex SystemsUniversity of MichiganAnn ArborMIUSA
| | - Molly C. Bletz
- Department of BiologyUniversity of Massachusetts BostonBostonMAUSA
| | - Mariana L. Lyra
- Instituto de BiociênciasUniversidade Estadual PaulistaRio ClaroBrazil
| | - L. Felipe Toledo
- Laboratório de História Natural de Anfíbios BrasileirosDepartamento de Biologia AnimalInstituto de BiologiaUniversidade Estadual de CampinasCampinasBrazil
| | - Timothy Y. James
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
| |
Collapse
|
46
|
Anslan S, Sachs M, Rancilhac L, Brinkmann H, Petersen J, Künzel S, Schwarz A, Arndt H, Kerney R, Vences M. Diversity and substrate-specificity of green algae and other micro-eukaryotes colonizing amphibian clutches in Germany, revealed by DNA metabarcoding. Naturwissenschaften 2021; 108:29. [PMID: 34181110 PMCID: PMC8238718 DOI: 10.1007/s00114-021-01734-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/20/2021] [Accepted: 05/02/2021] [Indexed: 02/17/2023]
Abstract
Amphibian clutches are colonized by diverse but poorly studied communities of micro-organisms. One of the most noted ones is the unicellular green alga, Oophila amblystomatis, but the occurrence and role of other micro-organisms in the capsular chamber surrounding amphibian clutches have remained largely unstudied. Here, we undertook a multi-marker DNA metabarcoding study to characterize the community of algae and other micro-eukaryotes associated with agile frog (Rana dalmatina) clutches. Samplings were performed at three small ponds in Germany, from four substrates: water, sediment, tree leaves from the bottom of the pond, and R. dalmatina clutches. Sampling substrate strongly determined the community compositions of algae and other micro-eukaryotes. Therefore, as expected, the frog clutch-associated communities formed clearly distinct clusters. Clutch-associated communities in our study were structured by a plethora of not only green algae, but also diatoms and other ochrophytes. The most abundant operational taxonomic units (OTUs) in clutch samples were taxa from Chlamydomonas, Oophila, but also from Nitzschia and other ochrophytes. Sequences of Oophila "Clade B" were found exclusively in clutches. Based on additional phylogenetic analyses of 18S rDNA and of a matrix of 18 nuclear genes derived from transcriptomes, we confirmed in our samples the existence of two distinct clades of green algae assigned to Oophila in past studies. We hypothesize that "Clade B" algae correspond to the true Oophila, whereas "Clade A" algae are a series of Chlorococcum species that, along with other green algae, ochrophytes and protists, colonize amphibian clutches opportunistically and are often cultured from clutch samples due to their robust growth performance. The clutch-associated communities were subject to filtering by sampling location, suggesting that the taxa colonizing amphibian clutches can drastically differ depending on environmental conditions.
Collapse
Affiliation(s)
- Sten Anslan
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
| | - Maria Sachs
- Institute of Zoology, University of Cologne, Zülpicherstr. 47b, 50674, Köln, Germany
| | - Lois Rancilhac
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Henner Brinkmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Anja Schwarz
- Institute of Geosystems and Bioindication, Technische Universität Braunschweig, Braunschweig, Germany
| | - Hartmut Arndt
- Institute of Zoology, University of Cologne, Zülpicherstr. 47b, 50674, Köln, Germany
| | - Ryan Kerney
- Department of Biology, Gettysburg College, Gettysburg, PA, USA
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| |
Collapse
|
47
|
Venesky MD, Laskey CA. Infection with Batrachochytrium dendrobatidis reduces salamander capacity to mount a cell-mediated immune response. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2021; 337:273-281. [PMID: 34102032 DOI: 10.1002/jez.2497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 11/06/2022]
Abstract
The vertebrate immune system is a costly defense system that is responsible for preventing and eliminating parasites and pathogens. Theory predicts that hosts experience tradeoffs associated with immune deployment and other physiological functions. Although empirical evidence for immune-physiology tradeoffs are well documented in the literature, fewer studies have examined tradeoffs within the immune system in wild vertebrates. We explored the topic of concomitant immune challenges in amphibians by exposing salamanders (Plethodon cinereus) to a fungal pathogen Batrachochytrium dendrobatidis (hereafter "Bd") and then to phytohemagglutinin (hereafter "PHA"). We measured Bd infection using quantitative PCR and used measurements of the tail thickness at the PHA injection site as an estimate of skin swelling. We tested whether Bd reduced the salamander's capacity to mount an immune response towards PHA or whether Bd would stimulate immune activity and thereby increase the response towards PHA. Salamanders that were infected with Bd had a reduced skin-swelling when injected with PHA compared to noninfected salamanders, a result that is consistent with the hypothesis that Bd-infected salamanders have lower immunocompetence than noninfected salamanders. We also found that PHA-induced swelling response was negatively associated with Bd infection abundance (i.e., the infection burden of all exposed salamanders, including those that were exposed but not infected), indicating that salamanders with a higher infection abundance had the lowest swelling response to PHA. Our results suggest that individuals of P. cinereus might experience an energetic tradeoff between successfully fighting off Bd and mounting an immune response towards PHA.
Collapse
Affiliation(s)
- Matthew D Venesky
- Department of Biology, Allegheny College, Meadville, Pennsylvania, USA
| | - Corey A Laskey
- Department of Biology, Allegheny College, Meadville, Pennsylvania, USA
| |
Collapse
|
48
|
Gabriel A, Costa S, Henriques I, Lopes I. Effects of Long-Term Exposure to Increased Salinity on the Amphibian Skin Bacterium Erwinia toletana. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 80:779-788. [PMID: 33877369 DOI: 10.1007/s00244-021-00845-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Amphibian's skin bacterial community may help them to cope with several types of environmental perturbations, including osmotic stress caused by increased salinity. This work assessed whether an amphibian skin bacterium could increase its tolerance to NaCl after a long-term exposure to this salt. A strain of Erwinia toletana, isolated from the skin of Pelophylax perezi, was exposed to two salinity scenarios (with 18 g/L of NaCl): (1) long-term exposure (for 46 days; Et-NaCl), and (2) long-term exposure followed by a recovery period (exposure for 30 days to NaCl and then to LB medium for 16 days; Et-R). After exposure, the sensitivity of E. toletana clonal populations to NaCl was assessed by exposing them to 6 NaCl concentrations (LB medium spiked with NaCl) plus a control (LB medium). Genotypic alterations were assessed by PCR-based molecular typing method (BOX-PCR). The results showed that tolerance of E. toletana to NaCl slightly increased after the long-term exposure, EC50 for growth were: 22.5 g/L (8.64-36.4) for Et-LB; 30.3 g/L (23.2-37.4) for Et-NaCl; and 26.1 g/L (19.332.9) for Et-R. Differences in metabolic activity were observed between Et-LB and Et-R and between Et-NaCl and Et-R, suggesting the use of different substrates by this bacterium when exposed to salinized environments. NaCl-induced genotypic alterations were not detected. This work suggests that E. toletana exposed to low levels of salinity, activate different metabolic pathways to cope with osmotic stress. These findings may be further explored to be used in bioaugmentation procedures through the supplementation with this bacterium of the skin microbiome of natural populations of amphibians exposed to salinization.
Collapse
Affiliation(s)
- Antonieta Gabriel
- Department of Biology, CESAM, University of Aveiro, Campus Universitario de Santiago, Aveiro, Portugal.
| | - Sara Costa
- Department of Biology, CESAM, University of Aveiro, Campus Universitario de Santiago, Aveiro, Portugal
| | - Isabel Henriques
- Department of Life Sciences, CESAM, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Isabel Lopes
- Department of Biology, CESAM, University of Aveiro, Campus Universitario de Santiago, Aveiro, Portugal
| |
Collapse
|
49
|
Medina D, Greenspan SE, Carvalho T, Becker CG, Toledo LF. Co-infecting pathogen lineages have additive effects on host bacterial communities. FEMS Microbiol Ecol 2021; 97:6134751. [PMID: 33580951 DOI: 10.1093/femsec/fiab030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/11/2021] [Indexed: 01/08/2023] Open
Abstract
Amphibian skin bacteria may confer protection against the fungus Batrachochytrium dendrobatidis (Bd), but responses of skin bacteria to different Bd lineages are poorly understood. The global panzootic lineage (Bd-GPL) has caused amphibian declines and extinctions globally. However, other lineages are enzootic (Bd-Asia-2/Brazil). Increased contact rates between Bd-GPL and enzootic lineages via globalization pose unknown consequences for host-microbiome-pathogen dynamics. We conducted a laboratory experiment and used 16S rRNA amplicon-sequencing to assess: (i) whether two lineages (Bd-Asia-2/Brazil and Bd-GPL) and their recombinant, in single and mixed infections, differentially affect amphibian skin bacteria; (ii) and the changes associated with the transition to laboratory conditions. We determined no clear differences in bacterial diversity among Bd treatments, despite differences in infection intensity. However, we observed an additive effect of mixed infections on bacterial alpha diversity and a potentially antagonistic interaction between Bd genotypes. Additionally, observed changes in community composition suggest a higher ability of Bd-GPL to alter skin bacteria. Lastly, we observed a drastic reduction in bacterial diversity and a change in community structure in laboratory conditions. We provide evidence for complex interactions between Bd genotypes and amphibian skin bacteria during coinfections, and expand on the implications of experimental conditions in ecological studies.
Collapse
Affiliation(s)
- Daniel Medina
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Instituto de Biologia, Universidade Estadual de Campinas, R. Monteiro Lobato, 255 - CEP 13083-862, Campinas, São Paulo, Brazil.,Sistema Nacional de Investigación, SENACYT, Building 205, City of Knowledge, Clayton, Panama, Republic of Panama
| | - Sasha E Greenspan
- Department of Biological Sciences, The University of Alabama, 1339 Science and Engineering Complex, Tuscaloosa 35487, Alabama, USA
| | - Tamilie Carvalho
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Instituto de Biologia, Universidade Estadual de Campinas, R. Monteiro Lobato, 255 - CEP 13083-862, Campinas, São Paulo, Brazil
| | - C Guilherme Becker
- Department of Biological Sciences, The University of Alabama, 1339 Science and Engineering Complex, Tuscaloosa 35487, Alabama, USA
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Instituto de Biologia, Universidade Estadual de Campinas, R. Monteiro Lobato, 255 - CEP 13083-862, Campinas, São Paulo, Brazil
| |
Collapse
|
50
|
Park H, Park S, Yang YH, Choi KY. Microbial synthesis of violacein pigment and its potential applications. Crit Rev Biotechnol 2021; 41:879-901. [PMID: 33730942 DOI: 10.1080/07388551.2021.1892579] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Violacein is a pigment synthesized by Gram-negative bacteria such as Chromobacterium violaceum. It has garnered significant interest owing to its unique physiological and biological activities along with its synergistic effects with various antibiotics. In addition to C. violaceum, several microorganisms, including: Duganella sp., Pseudoalteromonas sp., Iodobacter sp., and Massilia sp., are known to produce violacein. Along with the identification of violacein-producing strains, the genetic regulation, quorum sensing mechanism, and sequence of the vio-operon involved in the biosynthesis of violacein have been elucidated. From an engineering perspective, the heterologous production of violacein using the genetically engineered Escherichia coli or Citrobacter freundii host has also been attempted. Genetic engineering of host cells involves the heterologous expression of genes involved in the vio operon and the optimization of metabolic pathways and gene regulation. Further, the crystallography of VioD and VioE was revealed, and mass production by enzyme engineering has been accelerated. In this review, we highlight the biologically assisted end-use applications of violacein (such as functional fabric development, nanoparticles, functional polymer composites, and sunscreen ingredients) and violacein activation mechanisms, production strains, and the results of mass production with engineered methods. The prospects for violacein research and engineering applications have also been discussed.
Collapse
Affiliation(s)
- HyunA Park
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea
| | - SeoA Park
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - Kwon-Young Choi
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea.,Department of Environmental and Safety Engineering, College of Engineering, Ajou University, Suwon, South Korea
| |
Collapse
|