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Osborne OG, Jiménez RR, Byrne AQ, Gratwicke B, Ellison A, Muletz-Wolz CR. Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders. THE ISME JOURNAL 2024; 18:wrae104. [PMID: 38861457 PMCID: PMC11195472 DOI: 10.1093/ismejo/wrae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/09/2024] [Accepted: 06/10/2024] [Indexed: 06/13/2024]
Abstract
Phylosymbiosis is an association between host-associated microbiome composition and host phylogeny. This pattern can arise via the evolution of host traits, habitat preferences, diets, and the co-diversification of hosts and microbes. Understanding the drivers of phylosymbiosis is vital for modelling disease-microbiome interactions and manipulating microbiomes in multi-host systems. This study quantifies phylosymbiosis in Appalachian salamander skin in the context of infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd), while accounting for environmental microbiome exposure. We sampled ten salamander species representing >150M years of divergence, assessed their Bd infection status, and analysed their skin and environmental microbiomes. Our results reveal a significant signal of phylosymbiosis, whereas the local environmental pool of microbes, climate, geography, and Bd infection load had a smaller impact. Host-microbe co-speciation was not evident, indicating that the effect stems from the evolution of host traits influencing microbiome assembly. Bd infection is correlated with host phylogeny and the abundance of Bd-inhibitory bacterial strains, suggesting that the long-term evolutionary dynamics between salamander hosts and their skin microbiomes affect the present-day distribution of the pathogen, along with habitat-linked exposure risk. Five Bd-inhibitory bacterial strains showed unusual generalism: occurring in most host species and habitats. These generalist strains may enhance the likelihood of probiotic manipulations colonising and persisting on hosts. Our results underscore the substantial influence of host-microbiome eco-evolutionary dynamics on environmental health and disease outcomes.
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Affiliation(s)
- Owen G Osborne
- School of Environmental and Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2DG, United Kingdom
| | - Randall R Jiménez
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, United States
- International Union for Conservation of Nature, C. 39, Los Yoses, San Jose, 146-2150, Costa Rica
| | - Allison Q Byrne
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720-3114, United States
| | - Brian Gratwicke
- Center for Species Survival, Smithsonian’s National Zoological Park and Conservation Biology Institute, Front Royal, VA 22630, United States
| | - Amy Ellison
- School of Environmental and Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2DG, United Kingdom
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, United States
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2
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Martínez-Ugalde E, Ávila-Akerberg V, González Martínez TM, Rebollar EA. Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent. Microb Genom 2024; 10:001181. [PMID: 38240649 PMCID: PMC10868611 DOI: 10.1099/mgen.0.001181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the A. altamirani skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of A. altamirani skin microbiome differed between B. dendrobatidis infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the A. altamirani skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of A. altamirani to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.
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Affiliation(s)
| | - Víctor Ávila-Akerberg
- Instituto de Ciencias Agropecuarias y Rurales, Universidad Autónoma del Estado de México, Toluca, Mexico
| | | | - Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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3
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Sun D, Herath J, Zhou S, Ellepola G, Meegaskumbura M. Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts. ISME COMMUNICATIONS 2023; 3:123. [PMID: 37993728 PMCID: PMC10665332 DOI: 10.1038/s43705-023-00332-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Amphibian skin harbors microorganisms that are associated with the fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes chytridiomycosis, one of the most significant wildlife diseases known. This pathogen originated in Asia, where diverse Bd lineages exist; hence, native amphibian hosts have co-existed with Bd over long time periods. Determining the nuances of this co-existence is crucial for understanding the prevalence and spread of Bd from a microbial context. However, associations of Bd with the natural skin microbiome remain poorly understood for Asian hosts, especially in relation to skin-associated fungi. We used 16 S rRNA and fungal internal transcribed spacer (ITS) gene sequencing to characterize the skin microbiome of four native Asian amphibian species and examined the relationships between Bd infection and their skin bacterial and fungal communities; we also analyzed the correlates of the putative anti-Bd bacteria. We show that both skin bacterial and fungal community structure and composition had significant associations with infection status (Bd presence/absence) and infection intensity (frequency of Bd sequence reads). We also found that the putative anti-Bd bacterial richness was correlated with Bd infection status and infection intensity, and observed that the relative abundance of anti-Bd bacteria roughly correspond with changes in both Bd prevalence and mean infection intensity in populations. Additionally, the microbial co-occurrence network of infected frogs was significantly different from that of uninfected frogs that were characterized by more keystone nodes (connectors) and larger proportions in correlations between bacteria, suggesting stronger inter-module bacterial interactions. These results indicate that the mutual effects between Bd and skin-associated microbiome, including the interplay between bacteria and fungi, might vary with Bd infection in susceptible amphibian species. This knowledge will help in understanding the dynamics of Bd from a microbial perspective, potentially contributing to mitigate chytridiomycosis in other regions of the world.
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Affiliation(s)
- Dan Sun
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
| | - Jayampathi Herath
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
- School of Biomedical Sciences, International Institute of Health Sciences (IIHS), No 704 Negombo Rd, Welisara, 71722, Sri Lanka
| | - Shipeng Zhou
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
| | - Gajaba Ellepola
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
- Department of Zoology, Faculty of Science, University of Peradeniya, Peradeniya, KY20400, Sri Lanka
| | - Madhava Meegaskumbura
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China.
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4
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Vickers E, Kerney R. Screening Salamanders for Symbionts. Methods Mol Biol 2023; 2562:425-442. [PMID: 36272092 DOI: 10.1007/978-1-0716-2659-7_28] [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] [Indexed: 06/16/2023]
Abstract
Microbial symbionts are broadly categorized by their impacts on host fitness: commensals, pathogens, and mutualists. However, recent investigations into the physiological basis of these impacts have revealed nuanced microbial influences on a wide range of host developmental, immunological, and physiological processes, including regeneration. Exploring these impacts begins with knowing which microbes are present. This methodological pipeline contains both targeted assays using PCR and culturing, as well as culture-independent approaches, to survey host salamander tissues for common and unknown microbial symbionts.
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Affiliation(s)
- Elli Vickers
- Gettysburg College, Department of Biology, Gettysburg, PA, USA
| | - Ryan Kerney
- Gettysburg College, Department of Biology, Gettysburg, PA, USA.
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5
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Hill AJ, Grisnik M, Walker DM. Bacterial Skin Assemblages of Sympatric Salamanders Are Primarily Shaped by Host Genus. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02127-0. [PMID: 36318280 DOI: 10.1007/s00248-022-02127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Bacterial assemblages on the skins of amphibians are known to influence pathogen resistance and other important physiological functions in the host. Host-specific factors and the environment play significant roles in structuring skin assemblages. This study used high-throughput 16S rRNA sequencing and multivariate analyses to examine differences in skin-bacterial assemblages from 246 salamanders belonging to three genera in the lungless family Plethodontidae along multiple spatial gradients. Composition and α- and β-diversity of bacterial assemblages were defined, indicator species were identified for each host group, and the relative influences of host- versus environment-specific ecological factors were evaluated. At the broadest spatial scale, host genus, host species, and sampling site were predictive of skin assemblage structure, but host genus and species were more influential after controlling for the marginal effects of site, as well as nestedness of site. Furthermore, assemblage similarity within each host genus did not change with increasing geographic distance. At the smallest spatial scale, site-specific climate analyses revealed different relationships to climatic variables for each of the three genera, and these relationships were determined by host ecomode. Variation in bacterial assemblages of terrestrial hosts correlated with landscape-level climatic variability, and this pattern decayed with increasing water dependence of the host. Results from this study highlight host-specific considerations for researchers studying wildlife diseases in co-occurring, yet ecologically divergent, species.
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Affiliation(s)
- Aubree J Hill
- Department of Biology, Tennessee Technological University, 1100 North Dixie Avenue, Box 5063, Cookeville, TN, 38505, USA.
| | - Matthew Grisnik
- Department of Agricultural and Environmental Sciences, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN, 37209, USA
| | - Donald M Walker
- Department of Biology, Middle Tennessee State University, 1672 Greenland Drive, Murfreesboro, TN, 37132, USA
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6
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Inhibitory Bacterial Diversity and Mucosome Function Differentiate Susceptibility of Appalachian Salamanders to Chytrid Fungal Infection. Appl Environ Microbiol 2022; 88:e0181821. [PMID: 35348389 PMCID: PMC9040618 DOI: 10.1128/aem.01818-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Mucosal defenses are crucial in animals for protection against pathogens and predators. Host defense peptides (antimicrobial peptides, AMPs) as well as skin-associated microbes are key components of mucosal immunity, particularly in amphibians. We integrate microbiology, molecular biology, network-thinking, and proteomics to understand how host and microbially derived products on amphibian skin (referred to as the mucosome) serve as pathogen defenses. We studied defense mechanisms against chytrid pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), in four salamander species with different Batrachochytrium susceptibilities. Bd infection was quantified using qPCR, mucosome function (i.e., ability to kill Bd or Bsal zoospores in vitro), skin bacterial communities using 16S rRNA gene amplicon sequencing, and the role of Bd-inhibitory bacteria in microbial networks across all species. We explored the presence of candidate-AMPs in eastern newts and red-backed salamanders. Eastern newts had the highest Bd prevalence and mucosome function, while red-back salamanders had the lowest Bd prevalence and mucosome function, and two-lined salamanders and seal salamanders were intermediates. Salamanders with highest Bd infection intensity showed greater mucosome function. Bd infection prevalence significantly decreased as putative Bd-inhibitory bacterial richness and relative abundance increased on hosts. In co-occurrence networks, some putative Bd-inhibitory bacteria were found as hub-taxa, with red-backs having the highest proportion of protective hubs and positive associations related to putative Bd-inhibitory hub bacteria. We found more AMP candidates on salamanders with lower Bd susceptibility. These findings suggest that salamanders possess distinct innate mechanisms that affect chytrid fungi. IMPORTANCE How host mucosal defenses interact, and influence disease outcome is critical in understanding host defenses against pathogens. A more detailed understanding is needed of the interactions between the host and the functioning of its mucosal defenses in pathogen defense. This study investigates the variability of chytrid susceptibility in salamanders and the innate defenses each species possesses to mediate pathogens, thus advancing the knowledge toward a deeper understanding of the microbial ecology of skin-associated bacteria and contributing to the development of bioaugmentation strategies to mediate pathogen infection and disease. This study improves the understanding of complex immune defense mechanisms in salamanders and highlights the potential role of the mucosome to reduce the probability of Bd disease development and that putative protective bacteria may reduce likelihood of Bd infecting skin.
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7
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Hughey MC, Rebollar EA, Harris RN, Ibáñez R, Loftus SC, House LL, Minbiole KPC, Bletz MC, Medina D, Shoemaker WR, Swartwout MC, Belden LK. An experimental test of disease resistance function in the skin-associated bacterial communities of three tropical amphibian species. FEMS Microbiol Ecol 2022; 98:6536914. [PMID: 35212765 DOI: 10.1093/femsec/fiac023] [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: 08/06/2021] [Revised: 02/10/2022] [Accepted: 02/23/2022] [Indexed: 11/14/2022] Open
Abstract
Variation in the structure of host-associated microbial communities has been correlated with the occurrence and severity of disease in diverse host taxa, suggesting a key role of the microbiome in pathogen defense. However, whether these correlations are typically a cause or consequence of pathogen exposure remains an open question, and requires experimental approaches to disentangle. In amphibians, infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd) alters the skin microbial community in some host species, whereas in other species, the skin microbial community appears to mediate infection dynamics. In this study, we completed experimental Bd exposures in three species of tropical frogs (Agalychnis callidryas, Dendropsophus ebraccatus, Craugastor fitzingeri) that were sympatric with Bd at the time of the study. For all three species, we identified key taxa within the skin bacterial communities that were linked to Bd infection dynamics. We also measured higher Bd infection intensities in D. ebraccatus and C. fitzingeri that were associated with higher mortality in C. fitzingeri. Our findings indicate that microbially-mediated pathogen resistance is a complex trait that can vary within and across host species, and suggest that symbiont communities that have experienced prior selection for defensive microbes may be less likely to be disturbed by pathogen exposure.
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Affiliation(s)
- Myra C Hughey
- Biology Department; Vassar College; 124 Raymond Avenue; Poughkeepsie, NY 12604; USA
| | - Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, México
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Panamá, Republic of Panama. Sistema Nacional de Investigación, SENACYT, Panamá, Republic of Panama
| | | | | | | | - Molly C Bletz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | | | - William R Shoemaker
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | | | - Lisa K Belden
- Department of Biological Sciences, VA Tech, Blacksburg, VA, USA
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8
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Nava-González B, Suazo-Ortuño I, López PB, Maldonado-López Y, Lopez-Toledo L, Raggi L, Parra-Olea G, Alvarado-Díaz J, Gómez-Gil B. Inhibition of Batrachochytrium dendrobatidis Infection by Skin Bacterial Communities in Wild Amphibian Populations. MICROBIAL ECOLOGY 2021; 82:666-676. [PMID: 33598748 DOI: 10.1007/s00248-021-01706-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
Skin-associated bacteria are known to inhibit infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd) in amphibians. It has also been postulated that skin-associated bacterial community is related to Bd infection intensity. However, our understanding of host microbial dynamics and their importance in regulating Bd intensity is limited. We analyzed Bd infection and skin-associated bacteria from two amphibian species, the salamander Ambystoma rivulare and the frog Lithobates spectabilis that co-occurred in a tropical high-altitude site in central Mexico. Sixty-three percent of sampled salamander individuals and 80% of frog individuals tested positive for Bd. Overall, we registered 622 skin-associated bacterial genera, from which 73 are known to have Bd inhibitory effects. These inhibitory taxa represented a relative abundance of 50% in relation to total relative bacterial abundance. Our results indicated that, although sharing some bacterial taxa, bacterial community from the skin of both species was different in taxonomic composition and in relative abundance. Pseudomonas spp. and Stenotrophomonas spp. were among the five most abundant bacterial taxa of both species. Both bacterial taxa inhibit Bd infection. We detected that bacterial richness and relative abundance of inhibitory Bd bacteria were negatively related to intensity of Bd infection independent of species and seasons. Despite the high Bd prevalence in both host species, no dead or sick individuals were registered during field surveys. The relatively low levels of Bd load apparently do not compromise survival of host species. Therefore, our results suggested that individuals analyzed were able to survive and thrive under a dynamic relation with enzootic infections of Bd and their microbiota.
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Affiliation(s)
- Bisbrian Nava-González
- Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Avenida Juanito Itzícuaro SN, Nueva Esperanza, 58330, Morelia, Michoacán, México
| | - Ireri Suazo-Ortuño
- Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Avenida Juanito Itzícuaro SN, Nueva Esperanza, 58330, Morelia, Michoacán, México.
| | - Perla Bibian López
- Universidad Tecnológica de Morelia, Avenida Vicepresidente Pino Suárez 750, Cd. Industrial, 58200, Morelia, Michoacán, México
| | - Yurixhi Maldonado-López
- CONACyT-Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Avenida Juanito Itzícuaro SN, Nueva Esperanza, 58330, Morelia, Michoacán, México
| | - Leonel Lopez-Toledo
- Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Avenida Juanito Itzícuaro SN, Nueva Esperanza, 58330, Morelia, Michoacán, México
| | - Luciana Raggi
- CONACYT-Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Avenida Juanito Itzícuaro SN, Nueva Esperanza, 58330, Morelia, Michoacán, México
| | - Gabriela Parra-Olea
- Instituto de Biología, Universidad Nacional Autónoma de México, Cd de México, México
| | - Javier Alvarado-Díaz
- Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Avenida Juanito Itzícuaro SN, Nueva Esperanza, 58330, Morelia, Michoacán, México
| | - Bruno Gómez-Gil
- CIAD A.C., Mazatlán Unit for Aquaculture, AP 711, Mazatlán, 82000, Sinaloa, México
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9
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Mutnale MC, Reddy GS, Vasudevan K. Bacterial Community in the Skin Microbiome of Frogs in a Coldspot of Chytridiomycosis Infection. MICROBIAL ECOLOGY 2021; 82:554-558. [PMID: 33442763 PMCID: PMC8384794 DOI: 10.1007/s00248-020-01669-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Chytridiomycosis is a fungal disease caused by the pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), which has caused declines in amphibian populations worldwide. Asia is considered as a coldspot of infection, since adult frogs are less susceptible to Bd-induced mortality or morbidity. Using the next-generation sequencing approach, we assessed the cutaneous bacterial community composition and presence of anti-Bd bacteria in six frog species from India using DNA isolated from skin swabs. All the six frog species sampled were tested using nested PCR and found Bd negative. We found a total of 551 OTUs on frog skin, of which the bacterial phyla such as Proteobacteria (56.15% average relative abundance) was dominated followed by Actinobacteria (21.98% average relative abundance) and Firmicutes (13.7% average relative abundance). The contribution of Proteobacteria in the anti-Bd community was highest and represented by 175 OTUs. Overall, the anti-Bd bacterial community dominated (51.7% anti-Bd OTUs) the skin microbiome of the frogs. The study highlights the putative role of frog skin microbiome in affording resistance to Bd infections in coldspots of infection.
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Affiliation(s)
- Milind C Mutnale
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Gundlapally S Reddy
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Karthikeyan Vasudevan
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India.
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10
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Walke JB, Becker MH, Krinos A, Chang EAB, Santiago C, Umile TP, Minbiole KPC, Belden LK. Seasonal changes and the unexpected impact of environmental disturbance on skin bacteria of individual amphibians in a natural habitat. FEMS Microbiol Ecol 2021; 97:6024676. [PMID: 33278302 DOI: 10.1093/femsec/fiaa248] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/02/2020] [Indexed: 01/16/2023] Open
Abstract
Amphibians host diverse skin bacteria that have a role in pathogen defense, but these skin communities could change over time and impact this function. Here, we monitored individual Eastern red-spotted newts (Notophthalmus viridescens; N = 17) for 2 years in a field pond enclosure and assessed the effects of season and disturbance on skin bacterial community dynamics. We created disturbances by adding additional pond substrate to the enclosure at two timepoints. We planned to sample the skin bacterial community and metabolite profiles of each newt every 6 weeks; we ultimately sampled eight individuals at least six times. We used 16S rRNA gene amplicon sequencing to characterize the bacterial communities and HPLC-MS for metabolite profiling. We found that disturbance had a dramatic effect on skin bacterial communities and metabolite profiles, while season had an effect only using select metrics. There were seven core bacterial taxa (97% OTUs) that were found on all newts in all seasons, pre- and post-disturbance. Lastly, there was a correlation between bacterial and metabolite profiles post-disturbance, which was not observed pre-disturbance. This longitudinal study suggests that environmental disturbances can have lasting effects on skin bacterial communities that overwhelm seasonal changes, although the core bacteria remain relatively consistent over time.
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Affiliation(s)
- Jenifer B Walke
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Matthew H Becker
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Arianna Krinos
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Celina Santiago
- Department of Chemistry, Villanova University, Villanova, PA 19085, USA
| | - Thomas P Umile
- Department of Chemistry, Villanova University, Villanova, PA 19085, USA
| | | | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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11
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Bhattarai K, Bhattarai K, Kabir ME, Bastola R, Baral B. Fungal natural products galaxy: Biochemistry and molecular genetics toward blockbuster drugs discovery. ADVANCES IN GENETICS 2021; 107:193-284. [PMID: 33641747 DOI: 10.1016/bs.adgen.2020.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Secondary metabolites synthesized by fungi have become a precious source of inspiration for the design of novel drugs. Indeed, fungi are prolific producers of fascinating, diverse, structurally complex, and low-molecular-mass natural products with high therapeutic leads, such as novel antimicrobial compounds, anticancer compounds, immunosuppressive agents, among others. Given that these microorganisms possess the extraordinary capacity to secrete diverse chemical scaffolds, they have been highly exploited by the giant pharma companies to generate small molecules. This has been made possible because the isolation of metabolites from fungal natural sources is feasible and surpasses the organic synthesis of compounds, which otherwise remains a significant bottleneck in the drug discovery process. Here in this comprehensive review, we have discussed recent studies on different fungi (pathogenic, non-pathogenic, commensal, and endophytic/symbiotic) from different habitats (terrestrial and marines), the specialized metabolites they biosynthesize, and the drugs derived from these specialized metabolites. Moreover, we have unveiled the logic behind the biosynthesis of vital chemical scaffolds, such as NRPS, PKS, PKS-NRPS hybrid, RiPPS, terpenoids, indole alkaloids, and their genetic mechanisms. Besides, we have provided a glimpse of the concept behind mycotoxins, virulence factor, and host immune response based on fungal infections.
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Affiliation(s)
- Keshab Bhattarai
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany
| | - Keshab Bhattarai
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Md Ehsanul Kabir
- Animal Health Research Division, Bangladesh Livestock Research Institute, Savar, Dhaka, Bangladesh
| | - Rina Bastola
- Spinal Cord Injury Association-Nepal (SCIAN), Pokhara, Nepal
| | - Bikash Baral
- Department of Biochemistry, University of Turku, Turku, Finland.
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12
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Muletz‐Wolz CR, Wilson Rankin E, McGrath‐Blaser S, Venkatraman M, Maldonado JE, Gruner DS, Fleischer RC. Identification of novel bacterial biomarkers to detect bird scavenging by invasive rats. Ecol Evol 2021; 11:1814-1828. [PMID: 33614005 PMCID: PMC7882976 DOI: 10.1002/ece3.7171] [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: 07/31/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 01/04/2023] Open
Abstract
Rapid advances in genomic tools for use in ecological contexts and non-model systems allow unprecedented insight into interactions that occur beyond direct observation. We developed an approach that couples microbial forensics with molecular dietary analysis to identify species interactions and scavenging by invasive rats on native and introduced birds in Hawaii. First, we characterized bacterial signatures of bird carcass decay by conducting 16S rRNA high-throughput sequencing on chicken (Gallus gallus domesticus) tissues collected over an 11-day decomposition study in natural Hawaiian habitats. Second, we determined if field-collected invasive black rats (Rattus rattus; n = 51, stomach and fecal samples) had consumed birds using molecular diet analysis with two independent PCR assays (mitochondrial Cytochrome Oxidase I and Cytochrome b genes) and Sanger sequencing. Third, we characterized the gut microbiome of the same rats using 16S rRNA high-throughput sequencing and identified 15 bacterial taxa that were (a) detected only in rats that consumed birds (n = 20/51) and (b) were indicative of decaying tissue in the chicken decomposition experiment. We found that 18% of rats (n = 9/51) likely consumed birds as carrion by the presence of bacterial biomarkers of decayed tissue in their gut microbiome. One species of native bird (Myadestes obscurus) and three introduced bird species (Lophura leucomelanos, Meleagris gallopavo, Zosterops japonicus) were detected in the rats' diets, with individuals from these species (except L. nycthemera) likely consumed through scavenging. Bacterial biomarkers of bird carcass decay can persist through rat digestion and may serve as biomarkers of scavenging. Our approach can be used to reveal trophic interactions that are challenging to measure through direct observation.
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Affiliation(s)
- Carly R. Muletz‐Wolz
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Erin Wilson Rankin
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
- Department of EntomologyUniversity of MarylandCollege ParkMDUSA
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Sarah McGrath‐Blaser
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Madhvi Venkatraman
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
- Department of EntomologyUniversity of MarylandCollege ParkMDUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | | | - Robert C. Fleischer
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
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13
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Nocera FP, De Filippis A, Piscopo N, Esposito L, De Martino L. Similarities between skin culturable bacterial species of pool frogs (Pelophylax lessonae) and their habitat. BULGARIAN JOURNAL OF VETERINARY MEDICINE 2021. [DOI: 10.15547/bjvm.2019-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The aim of the present study was to investigate the culturable microflora of pool frogs (Pelophylax lessonae) and their belonging aquatic environment. A total of 60 samples (56 frog cutaneous swabs, 4 water samples) were inoculated onto different selective and differential agar plates to isolate Gram-positive and Gram-negative bacteria or yeasts. Microbial investigation of the water hosting frogs was also performed. Isolates were identified by API system and their antibiotic resistance profiles were evaluated by disk diffusion method on Mueller Hinton agar plates. Aeromonas hydrophila and Enterococcus durans were detected in almost all collected samples. Many of the bacterial isolates showed multidrug-resistant profiles. Importantly, this study highlights that skin frog microbiota is correlated to the belonging environment, and, moreover, some isolated bacterial strains resulted to be of interest in animal and public health, since the park was frequented by visitors of all ages.
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14
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Friday B, Holzheuser C, Lips KR, Longo AV. Preparing for invasion: Assessing risk of infection by chytrid fungi in southeastern plethodontid salamanders. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2020; 333:829-840. [PMID: 33174393 DOI: 10.1002/jez.2427] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/30/2020] [Accepted: 10/23/2020] [Indexed: 12/31/2022]
Abstract
Understanding the responses of naïve communities to the invasion of multihost pathogens requires accurate estimates of susceptibility across taxa. In the Americas, the likely emergence of a second amphibian pathogenic fungus (Batrachochytrium salamandrivorans, Bsal) calls for new ways of prioritizing disease mitigation among species due to the high diversity of naïve hosts with prior B. dendrobatidis (Bd) infections. Here, we applied the concept of pathogenic potential to quantify the virulence of chytrid fungi on naïve amphibians and evaluate species for conservation efforts in the event of an outbreak. The benefit of this measure is that it combines and summarizes the variation in disease effects into a single numerical index, allowing for comparisons across species, populations or groups of individuals that may inherently exhibit differences in susceptibility. As a proof of concept, we obtained standardized responses of disease severity by performing experimental infections with Bsal on five plethodontid salamanders from southeastern United States. Four out of five species carried natural infections of Bd at the start of the experiments. We showed that Bsal exhibited its highest value of pathogenic potential in a species that is already declining (Desmognathus auriculatus). We find that this index provides additional information beyond the standard measures of disease prevalence, intensity, and mortality, because it leveraged these disease parameters within each categorical group. Scientists and practitioners could use this measure to justify research, funding, trade, or conservation measures.
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Affiliation(s)
- Brenna Friday
- Department of Biology, University of Maryland, College Park, Maryland, USA.,Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Chace Holzheuser
- Department of Biology, University of Maryland, College Park, Maryland, USA.,Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Karen R Lips
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Ana V Longo
- Department of Biology, University of Florida, Gainesville, Florida, USA
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15
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Jiménez RR, Alvarado G, Sandoval J, Sommer S. Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog. BMC Microbiol 2020; 20:292. [PMID: 32962670 PMCID: PMC7509932 DOI: 10.1186/s12866-020-01979-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The skin microbiome serves as a first line defense against pathogens in vertebrates. In amphibians, it has the potential to protect against the chytrid fungus Batrachochytrium dendrobatis (Bd), a likely agent of amphibian declines. Alteration of the microbiome associated with unfavorable environmental changes produced by anthropogenic activities may make the host more susceptible to pathogens. Some amphibian species that were thought to be "extinct" have been rediscovered years after population declines in the late 1980s probably due to evolved Bd-resistance and are now threatened by anthropogenic land-use changes. Understanding the effects of habitat disturbance on the host skin microbiome is relevant for understanding the health of these species, along with its susceptibility to pathogens such as Bd. Here, we investigate the influence of habitat alteration on the skin bacterial communities as well as specifically the putative Bd-inhibitory bacterial communities of the montane frog Lithobates vibicarius. This species, after years of not being observed, was rediscovered in small populations inhabiting undisturbed and disturbed landscapes, and with continuous presence of Bd. RESULTS We found that cutaneous bacterial communities of tadpoles and adults differed between undisturbed and disturbed habitats. The adults from disturbed habitats exhibited greater community dispersion than those from undisturbed habitats. We observed a higher richness of putative Bd-inhibitory bacterial strains in adults from disturbed habitats than in those from undisturbed habitats, as well as a greater number of these potential protective bacteria with a high relative abundance. CONCLUSIONS Our findings support the microbial "Anna Karenina principle", in which disturbance is hypothesized to cause greater microbial dispersion in communities, a so-called dysbiosis, which is a response of animal microbiomes to stress factors that decrease the ability of the host or its microbiome to regulate community composition. On the positive side, the high richness and relative abundance of putative Bd-inhibitory bacteria may indicate the development of a defense mechanism that enhances Bd-protection, attributed to a co-occurrence of more than 30-years of host and pathogen in these disturbed habitats. Our results provide important insight into the influence of human-modified landscapes on the skin microbiome and health implications of Bd-survivor species.
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Affiliation(s)
- Randall R Jiménez
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89069, Ulm, Germany.
| | - Gilbert Alvarado
- Laboratory of Comparative Wildlife Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, Av. Orlando Marques de Paiva 87, São Paulo, Brazil
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - José Sandoval
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89069, Ulm, Germany
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16
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Kruger A. Frog Skin Microbiota Vary With Host Species and Environment but Not Chytrid Infection. Front Microbiol 2020; 11:1330. [PMID: 32670233 PMCID: PMC7328345 DOI: 10.3389/fmicb.2020.01330] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/25/2020] [Indexed: 01/15/2023] Open
Abstract
Describing the structure and function of the amphibian cutaneous microbiome has gained importance with the spread of Batrachochytrium dendrobatidis (Bd), the fungal pathogen that can cause the skin disease chytridiomycosis. Sampling amphibian skin microbiota is needed to characterize current infection status and to help predict future susceptibility to Bd based on microbial composition since some skin microbes have antifungal capabilities that may confer disease resistance. Here, I use 16S rRNA sequencing to describe the composition and structure of the cutaneous microbiota of six species of amphibians. Frog skin samples were also tested for Bd, and I found 11.8% Bd prevalence among all individuals sampled (n = 76). Frog skin microbiota varied by host species and sampling site, but did not differ among Bd-positive and Bd-negative individuals. These results suggest that bacterial composition reflects host species and the environment, but does not reflect Bd infection among the species sampled here. Of the bacterial OTUs identified using an indicator species analysis as strongly associated with amphibians, significantly more indicator OTUs were putative anti-Bd taxa than would be expected based on the proportion of anti-Bd OTUs among all frog OTUs, suggesting strong associations between host species and anti-Bd OTUs. This relationship may partially explain why some of these frogs are asymptomatic carriers of Bd, but more work is needed to determine the other factors that contribute to interspecific variation in Bd susceptibility. This work provides important insights on inter- and intra-specific variation in microbial community composition, putative function, and disease dynamics in populations of amphibians that appear to be coexisting with Bd.
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Affiliation(s)
- Ariel Kruger
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, United States
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17
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Walker DM, Hill AJ, Albecker MA, McCoy MW, Grisnik M, Romer A, Grajal-Puche A, Camp C, Kelehear C, Wooten J, Rheubert J, Graham SP. Variation in the Slimy Salamander (Plethodon spp.) Skin and Gut-Microbial Assemblages Is Explained by Geographic Distance and Host Affinity. MICROBIAL ECOLOGY 2020; 79:985-997. [PMID: 31802185 DOI: 10.1007/s00248-019-01456-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
A multicellular host and its microbial communities are recognized as a metaorganism-a composite unit of evolution. Microbial communities have a variety of positive and negative effects on the host life history, ecology, and evolution. This study used high-throughput amplicon sequencing to characterize the complete skin and gut microbial communities, including both bacteria and fungi, of a terrestrial salamander, Plethodon glutinosus (Family Plethodontidae). We assessed salamander populations, representing nine mitochondrial haplotypes ('clades'), for differences in microbial assemblages across 13 geographic locations in the Southeastern United States. We hypothesized that microbial assemblages were structured by both host factors and geographic distance. We found a strong correlation between all microbial assemblages at close geographic distances, whereas, as spatial distance increases, the patterns became increasingly discriminate. Network analyses revealed that gut-bacterial communities have the highest degree of connectedness across geographic space. Host salamander clade was explanatory of skin-bacterial and gut-fungal assemblages but not gut-bacterial assemblages, unless the latter were analyzed within a phylogenetic context. We also inferred the function of gut-fungal assemblages to understand how an understudied component of the gut microbiome may influence salamander life history. We concluded that dispersal limitation may in part describe patterns in microbial assemblages across space and also that the salamander host may select for skin and gut communities that are maintained over time in closely related salamander populations.
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Affiliation(s)
- Donald M Walker
- Department of Biology, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, 37132, USA.
| | - Aubree J Hill
- Department of Biology, Tennessee Technological University, 1100 N. Dixie Ave, Cookeville, TN, 38505, USA
| | - Molly A Albecker
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Michael W McCoy
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Matthew Grisnik
- Department of Biology, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, 37132, USA
| | - Alexander Romer
- Department of Biology, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, 37132, USA
| | - Alejandro Grajal-Puche
- Department of Biology, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, 37132, USA
| | - Carlos Camp
- Department of Biology, Piedmont College, 1021 Central Avenue, Demorest, GA, 30535, USA
| | - Crystal Kelehear
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Ancon, Panama, Republic of Panama
- Department of Biology, Geology and Physical Sciences, Sul Ross State University, Alpine, TX, 79832, USA
| | - Jessica Wooten
- Department of Biology, Piedmont College, 1021 Central Avenue, Demorest, GA, 30535, USA
| | - Justin Rheubert
- Department of Natural Sciences, The University of Findlay, 1000 N. Main St, Findlay, OH, 45840, USA
| | - Sean P Graham
- Department of Biology, Geology and Physical Sciences, Sul Ross State University, Alpine, TX, 79832, USA
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18
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Kruger A. Functional Redundancy of Batrachochytrium dendrobatidis Inhibition in Bacterial Communities Isolated from Lithobates clamitans Skin. MICROBIAL ECOLOGY 2020; 79:231-240. [PMID: 31165187 DOI: 10.1007/s00248-019-01387-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/29/2019] [Indexed: 06/09/2023]
Abstract
The cutaneous microbial community can influence the health of amphibians exposed to Batrachochytrium dendrobatidis (Bd), a fungal pathogen that has contributed to recent amphibian declines. Resistance to Bd in amphibian populations is correlated with the presence of anti-Bd cutaneous microbes, which confer disease resistance by inhibiting Bd growth. I aimed to determine if green frogs (Lithobates clamitans), an abundant and widely distributed species in New Jersey, harbored bacteria that inhibit Bd and whether the presence and identity of these microbes varied among sites. I used in vitro challenge assays to determine if bacteria isolated from green frog skin could inhibit or enhance the growth of Bd. I found that green frogs at all sites harbored anti-Bd bacteria. However, there were differences in Bd inhibition capabilities among bacterial isolates identified as the same operational taxonomic unit (OTU), lending support to the idea that phylogenetic relatedness does not always predict Bd inhibition status. Additionally, anti-Bd bacterial richness did not vary by site, but the composition of anti-Bd bacterial taxa was distinct at each site. This suggests that there is functional redundancy of Bd inhibition across unique communities of anti-Bd symbionts found on frogs at different sites. These findings highlight the need to better elucidate the structure-function relationship of microbiomes and their role in disease resistance.
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Affiliation(s)
- Ariel Kruger
- Graduate Program in Ecology and Evolution, Department of Ecology, Evolution, and Natural Resources, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, 08901, USA.
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19
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Niederle MV, Bosch J, Ale CE, Nader-Macías ME, Aristimuño Ficoseco C, Toledo LF, Valenzuela-Sánchez A, Soto-Azat C, Pasteris SE. Skin-associated lactic acid bacteria from North American bullfrogs as potential control agents of Batrachochytrium dendrobatidis. PLoS One 2019; 14:e0223020. [PMID: 31560707 PMCID: PMC6764794 DOI: 10.1371/journal.pone.0223020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/11/2019] [Indexed: 11/18/2022] Open
Abstract
The fungal pathogen Batrachochytrium dendrobatidis (Bd) is the causative agent of chytridiomycosis and has been a key driver in the catastrophic decline of amphibians globally. While many strategies have been proposed to mitigate Bd outbreaks, few have been successful. In recent years, the use of probiotic formulations that protect an amphibian host by killing or inhibiting Bd have shown promise as an effective chytridiomycosis control strategy. The North American bullfrog (Lithobates catesbeianus) is a common carrier of Bd and harbours a diverse skin microbiota that includes lactic acid bacteria (LAB), a microbial group containing species classified as safe and conferring host benefits. We investigated beneficial/probiotic properties: anti-Bd activity, and adhesion and colonisation characteristics (hydrophobicity, biofilm formation and exopolysaccharide-EPS production) in two confirmed LAB (cLAB-Enterococcus gallinarum CRL 1826, Lactococcus garvieae CRL 1828) and 60 presumptive LAB (pLAB) [together named as LABs] isolated from bullfrog skin.We challenged LABs against eight genetically diverse Bd isolates and found that 32% of the LABs inhibited at least one Bd isolate with varying rates of inhibition. Thus, we established a score of sensitivity from highest (BdGPL AVS7) to lowest (BdGPL C2A) for the studied Bd isolates. We further reveal key factors underlying host adhesion and colonisation of LABs. Specifically, 90.3% of LABs exhibited hydrophilic properties that may promote adhesion to the cutaneous mucus, with the remaining isolates (9.7%) being hydrophobic in nature with a surface polarity compatible with colonisation of acidic, basic or both substrate types. We also found that 59.7% of LABs showed EPS synthesis and 66.1% produced biofilm at different levels: 21% weak, 29% moderate, and 16.1% strong. Together all these properties enhance colonisation of the host surface (mucus or epithelial cells) and may confer protective benefits against Bd through competitive exclusion. Correspondence analysis indicated that biofilm synthesis was LABs specific with high aggregating bacteria correlating with strong biofilm producers, and EPS producers being correlated to negative biofilm producing LABs. We performed Random Amplified Polymorphic DNA (RAPD)-PCR analysis and demonstrated a higher degree of genetic diversity among rod-shaped pLAB than cocci. Based on the LAB genetic analysis and specific probiotic selection criteria that involve beneficial properties, we sequenced 16 pLAB which were identified as Pediococcus pentosaceus, Enterococcus thailandicus, Lactobacillus pentosus/L. plantarum, L. brevis, and L. curvatus. Compatibility assays performed with cLAB and the 16 species described above indicate that all tested LAB can be included in a mixed probiotic formula. Based on our analyses, we suggest that E. gallinarum CRL 1826, L. garvieae CRL 1828, and P. pentosaceus 15 and 18B represent optimal probiotic candidates for Bd control and mitigation.
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Affiliation(s)
- M. V. Niederle
- Instituto Superior de Investigaciones Biológicas (INSIBIO), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Instituto de Biología “Dr. Francisco D. Barbieri”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT), San Miguel de Tucumán, Argentina
| | - J. Bosch
- Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
- Research Unit of Biodiversity (CSIC, UO, PA), Oviedo University—Campus Mieres, Spain
| | - C. E. Ale
- Instituto Superior de Investigaciones Biológicas (INSIBIO), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Instituto de Biología “Dr. Francisco D. Barbieri”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT), San Miguel de Tucumán, Argentina
| | - M. E. Nader-Macías
- Centro de Referencia para Lactobacilos (CERELA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Miguel de Tucumán, Argentina
| | - C. Aristimuño Ficoseco
- Centro de Referencia para Lactobacilos (CERELA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Miguel de Tucumán, Argentina
| | - L. F. Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - A. Valenzuela-Sánchez
- Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Organización No Gubernamental (ONG) Ranita de Darwin, Santiago, Chile
- Organización No Gubernamental (ONG) Ranita de Darwin, Valdivia, Chile
| | - C. Soto-Azat
- Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - S. E. Pasteris
- Instituto Superior de Investigaciones Biológicas (INSIBIO), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Instituto de Biología “Dr. Francisco D. Barbieri”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT), San Miguel de Tucumán, Argentina
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20
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Jiménez RR, Alvarado G, Estrella J, Sommer S. Moving Beyond the Host: Unraveling the Skin Microbiome of Endangered Costa Rican Amphibians. Front Microbiol 2019; 10:2060. [PMID: 31572313 PMCID: PMC6751270 DOI: 10.3389/fmicb.2019.02060] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/21/2019] [Indexed: 01/12/2023] Open
Abstract
Some neotropical amphibians, including a few species in Costa Rica, were presumed to be "extinct" after dramatic population declines in the late 1980s but have been rediscovered in isolated populations. Such populations seem to have evolved a resistance/tolerance to Batrachochytrium dendrobatidis (Bd), a fungal pathogen that causes a deadly skin disease and is considered one of the main drivers of worldwide amphibian declines. The skin microbiome is an important component of the host's innate immune system and is associated with Bd-resistance. However, the way that the bacterial diversity of the skin microbiome confers protection against Bd in surviving species remains unclear. We studied variation in the skin microbiome and the prevalence of putatively anti-Bd bacterial taxa in four co-habiting species in the highlands of the Juan Castro Blanco National Park in Costa Rica using 16S rRNA amplicon sequencing. Lithobates vibicarius, Craugastor escoces, and Isthmohyla rivularis have recently been rediscovered, whereas Isthmohyla pseudopuma has suffered population fluctuations but has never disappeared. To investigate the life stage at which the protective skin microbiome is shaped and when shifts occur in the diversity of putatively anti-Bd bacteria, we studied the skin microbiome of tadpoles, juveniles and adults of L. vibicarius. We show that the skin bacterial composition of sympatric species and hosts with distinct Bd-infection statuses differs at the phyla, family, and genus level. We detected 94 amplicon sequence variants (ASVs) with putative anti-Bd activity pertaining to distinct bacterial taxa, e.g., Pseudomonas spp., Acinetobacter johnsonii, and Stenotrophomonas maltophilia. Bd-uninfected L. vibicarius harbored 79% more putatively anti-Bd ASVs than Bd-infected individuals. Although microbiome composition and structure differed across life stages, the diversity of putative anti-Bd bacteria was similar between pre- and post-metamorphic stages of L. vibicarius. Despite low sample size, our results support the idea that the skin microbiome is dynamic and protects against ongoing Bd presence in endangered species persisting after their presumed extinction. Our study serves as a baseline to understand the microbial patterns in species of high conservation value. Identification of microbial signatures linked to variation in disease susceptibility might, therefore, inform mitigation strategies for combating the global decline of amphibians.
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Affiliation(s)
- Randall R. Jiménez
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Gilbert Alvarado
- Laboratory of Comparative Wildlife Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - Josimar Estrella
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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21
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Becker CG, Bletz MC, Greenspan SE, Rodriguez D, Lambertini C, Jenkinson TS, Guimarães PR, Assis APA, Geffers R, Jarek M, Toledo LF, Vences M, Haddad CFB. Low-load pathogen spillover predicts shifts in skin microbiome and survival of a terrestrial-breeding amphibian. Proc Biol Sci 2019; 286:20191114. [PMID: 31409249 DOI: 10.1098/rspb.2019.1114] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Wildlife disease dynamics are strongly influenced by the structure of host communities and their symbiotic microbiota. Conspicuous amphibian declines associated with the waterborne fungal pathogen Batrachochytrium dendrobatidis (Bd) have been observed in aquatic-breeding frogs globally. However, less attention has been given to cryptic terrestrial-breeding amphibians that have also been declining in tropical regions. By experimentally manipulating multiple tropical amphibian assemblages harbouring natural microbial communities, we tested whether Bd spillover from naturally infected aquatic-breeding frogs could lead to Bd amplification and mortality in our focal terrestrial-breeding host: the pumpkin toadlet Brachycephalus pitanga. We also tested whether the strength of spillover could vary depending on skin bacterial transmission within host assemblages. Terrestrial-breeding toadlets acquired lethal spillover infections from neighbouring aquatic hosts and experienced dramatic but generally non-protective shifts in skin bacterial composition primarily attributable to their Bd infections. By contrast, aquatic-breeding amphibians maintained mild Bd infections and higher survival, with shifts in bacterial microbiomes that were unrelated to Bd infections. Our results indicate that Bd spillover from even mildly infected aquatic-breeding hosts may lead to dysbiosis and mortality in terrestrial-breeding species, underscoring the need to further investigate recent population declines of terrestrial-breeding amphibians in the tropics.
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Affiliation(s)
- C Guilherme Becker
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35847, USA
| | - Molly C Bletz
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Sasha E Greenspan
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35847, USA
| | - David Rodriguez
- Department of Biology, Texas State University, San Marcos, TX 78666, USA
| | - Carolina Lambertini
- Department of Animal Biology, Universidade Estadual de Campinas, Campinas, SP 13083-865, Brazil
| | - Thomas S Jenkinson
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA 94720, USA
| | - Paulo R Guimarães
- Departamento de Ecologia, Universidade de Sao Paulo, Sao Paulo, SP 05508-090, Brazil
| | - Ana Paula A Assis
- Departamento de Ecologia, Universidade de Sao Paulo, Sao Paulo, SP 05508-090, Brazil
| | - Robert Geffers
- Department of Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, LS 38124, Germany
| | - Michael Jarek
- Department of Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, LS 38124, Germany
| | - Luís Felipe Toledo
- Department of Animal Biology, Universidade Estadual de Campinas, Campinas, SP 13083-865, Brazil
| | - Miguel Vences
- Division of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, Braunschweig, LS 38106, Germany
| | - Célio F B Haddad
- Department of Zoology and Aquaculture Center (CAUNESP), Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
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22
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Muletz-Wolz CR, Fleischer RC, Lips KR. Fungal disease and temperature alter skin microbiome structure in an experimental salamander system. Mol Ecol 2019; 28:2917-2931. [PMID: 31066947 DOI: 10.1111/mec.15122] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/27/2019] [Accepted: 04/25/2019] [Indexed: 12/29/2022]
Abstract
Pathogens compete with host microbiomes for space and resources. Their shared environment impacts pathogen-microbiome-host interactions, which can lead to variation in disease outcome. The skin microbiome of red-backed salamanders (Plethodon cinereus) can reduce infection by the pathogen Batrachochytrium dendrobatidis (Bd) at moderate infection loads, with high species richness and high abundance of competitors as putative mechanisms. However, it is unclear if the skin microbiome can reduce epizootic Bd loads across temperatures. We conducted a laboratory experiment to quantify skin microbiome and host responses (P. cinereus: n = 87) to Bd at mimicked epizootic loads across temperatures (13, 17 and 21°C). We quantified skin microbiomes using 16S rRNA gene metabarcoding and identified operational taxonomic units (OTUs) taxonomically similar to culturable bacteria known to kill Bd (anti-Bd OTUs). Prior to pathogen exposure, temperature changed the microbiome (OTU richness decreased by 12% and the abundance of anti-Bd OTUs increased by 18% per degree increase in temperature), but these changes were not predictive of disease outcome. After exposure, Bd changed the microbiome (OTU richness decreased by 0.1% and the abundance of anti-Bd OTUs increased by 0.2% per 1% increase in Bd load) and caused high host mortality across temperatures (35/45: 78%). Temperature indirectly impacted microbiome change and mortality through its direct effect on pathogen load. We did not find support for the microbiome impacting Bd load or host survival. Our research reveals complex host, pathogen, microbiome and environmental interactions to demonstrate that during epizootic events the microbiome will be unlikely to reduce pathogen invasion, even for putatively Bd-resistant species.
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Affiliation(s)
- Carly R Muletz-Wolz
- Department of Biology, University of Maryland, College Park, Maryland.,Center for Conservation Genomics, Smithsonian National Zoological Park and Conservation Biology Institute, Washington, District of Columbia
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian National Zoological Park and Conservation Biology Institute, Washington, District of Columbia
| | - Karen R Lips
- Department of Biology, University of Maryland, College Park, Maryland
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23
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Woodhams DC, LaBumbard BC, Barnhart KL, Becker MH, Bletz MC, Escobar LA, Flechas SV, Forman ME, Iannetta AA, Joyce MD, Rabemananjara F, Gratwicke B, Vences M, Minbiole KPC. Prodigiosin, Violacein, and Volatile Organic Compounds Produced by Widespread Cutaneous Bacteria of Amphibians Can Inhibit Two Batrachochytrium Fungal Pathogens. MICROBIAL ECOLOGY 2018; 75:1049-1062. [PMID: 29119317 DOI: 10.1007/s00248-017-1095-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 10/19/2017] [Indexed: 06/07/2023]
Abstract
Symbiotic bacteria can produce secondary metabolites and volatile compounds that contribute to amphibian skin defense. Some of these symbionts have been used as probiotics to treat or prevent the emerging disease chytridiomycosis. We examined 20 amphibian cutaneous bacteria for the production of prodigiosin or violacein, brightly colored defense compounds that pigment the bacteria and have characteristic spectroscopic properties making them readily detectable, and evaluated the antifungal activity of these compounds. We detected violacein from all six isolates of Janthinobacterium lividum on frogs from the USA, Switzerland, and on captive frogs originally from Panama. We detected prodigiosin from five isolates of Serratia plymuthica or S. marcescens, but not from four isolates of S. fonticola or S. liquefaciens. All J. lividum isolates produced violacein when visibly purple, while prodigiosin was only detected on visibly red Serratia isolates. When applied to cultures of chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), prodigiosin caused significant growth inhibition, with minimal inhibitory concentrations (MIC) of 10 and 50 μM, respectively. Violacein showed a MIC of 15 μM against both fungi and was slightly more active against Bsal than Bd at lower concentrations. Although neither violacein nor prodigiosin showed aerosol activity and is not considered a volatile organic compound (VOC), J. lividum and several Serratia isolates did produce antifungal VOCs. White Serratia isolates with undetectable prodigiosin levels could still inhibit Bd growth indicating additional antifungal compounds in their chemical arsenals. Similarly, J. lividum can produce antifungal compounds such as indole-3-carboxaldehyde in addition to violacein, and isolates are not always purple, or turn purple under certain growth conditions. When Serratia isolates were grown in the presence of cell-free supernatant (CFS) from the fungi, CFS from Bd inhibited growth of the prodigiosin-producing isolates, perhaps indicative of an evolutionary arms race; Bsal CFS did not inhibit bacterial growth. In contrast, growth of one J. lividum isolate was facilitated by CFS from both fungi. Isolates that grow and continue to produce antifungal compounds in the presence of pathogens may represent promising probiotics for amphibians infected or at risk of chytridiomycosis. In a global analysis, 89% of tested Serratia isolates and 82% of J. lividum isolates were capable of inhibiting Bd and these have been reported from anurans and caudates from five continents, indicating their widespread distribution and potential for host benefit.
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Affiliation(s)
- Douglas C Woodhams
- Biology Department, University of Massachusetts Boston, Boston, MA, 02125, USA.
| | - Brandon C LaBumbard
- Biology Department, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Kelly L Barnhart
- Biology Department, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Matthew H Becker
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
- Department of Biology and Chemistry, Liberty University, Lynchburg, VA, USA
| | - Molly C Bletz
- Biology Department, University of Massachusetts Boston, Boston, MA, 02125, USA
- Zoological Institute, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Laura A Escobar
- School of Sciences, Pontificia Universidad Javeriana, Bogotá, AA 56710, Colombia
| | - Sandra V Flechas
- Department of Biological Sciences, Universidad de los Andes, Bogotá, AA 4976, Colombia
| | - Megan E Forman
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
| | - Anthony A Iannetta
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Maureen D Joyce
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
| | | | - Brian Gratwicke
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Kevin P C Minbiole
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.
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24
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Catenazzi A, Flechas SV, Burkart D, Hooven ND, Townsend J, Vredenburg VT. Widespread Elevational Occurrence of Antifungal Bacteria in Andean Amphibians Decimated by Disease: A Complex Role for Skin Symbionts in Defense Against Chytridiomycosis. Front Microbiol 2018; 9:465. [PMID: 29593698 PMCID: PMC5861192 DOI: 10.3389/fmicb.2018.00465] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 02/28/2018] [Indexed: 12/23/2022] Open
Abstract
Emerging infectious disease is a growing threat to global health, and recent discoveries reveal that the microbiota dwelling on and within hosts can play an important role in health and disease. To understand the capacity of skin bacteria to protect amphibian hosts from the fungal disease chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd), we isolated 192 bacterial morphotypes from the skin of 28 host species of frogs (families Bufonidae, Centrolenidae, Hemiphractidae, Hylidae, Leptodactylidae, Strabomantidae, and Telmatobiidae) collected from the eastern slopes of the Peruvian Andes (540-3,865 m a.s.l.) in the Kosñipata Valley near Manu National Park, a site where we previously documented the collapse of montane frog communities following chytridiomycosis epizootics. We obtained isolates through agar culture from skin swabs of wild frogs, and identified bacterial isolates by comparing 16S rRNA sequences against the GenBank database using BLAST. We identified 178 bacterial strains of 38 genera, including 59 bacterial species not previously reported from any amphibian host. The most common bacterial isolates were species of Pseudomonas, Paenibacillus, Chryseobacterium, Comamonas, Sphingobacterium, and Stenotrophomonas. We assayed the anti-fungal abilities of 133 bacterial isolates from 26 frog species. To test whether cutaneous bacteria might inhibit growth of the fungal pathogen, we used a local Bd strain isolated from the mouthparts of stream-dwelling tadpoles (Hypsiboas gladiator, Hylidae). We quantified Bd-inhibition in vitro with co-culture assays. We found 20 bacterial isolates that inhibited Bd growth, including three isolates not previously known for such inhibitory abilities. Anti-Bd isolates occurred on aquatic and terrestrial breeding frogs across a wide range of elevations (560-3,695 m a.s.l.). The inhibitory ability of anti-Bd isolates varied considerably. The proportion of anti-Bd isolates was lowest at mid-elevations (6%), where amphibian declines have been steepest, and among hosts that are highly susceptible to chytridiomycosis (0-14%). Among non-susceptible species, two had the highest proportion of anti-Bd isolates (40 and 45%), but one common and non-susceptible species had a low proportion (13%). In conclusion, we show that anti-Bd bacteria are widely distributed elevationally and phylogenetically across frog species that have persisted in a region where chytridiomycosis emerged, caused a devastating epizootic and continues to infect amphibians.
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Affiliation(s)
- Alessandro Catenazzi
- Department of Biological Sciences, Florida International University, Miami, FL, United States.,Department of Zoology, Southern Illinois University, Carbondale, IL, United States
| | - Sandra V Flechas
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - David Burkart
- Department of Zoology, Southern Illinois University, Carbondale, IL, United States
| | - Nathan D Hooven
- Department of Zoology, Southern Illinois University, Carbondale, IL, United States
| | - Joseph Townsend
- Department of Zoology, Southern Illinois University, Carbondale, IL, United States
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, San Francisco, CA, United States
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25
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Becker CG, Longo AV, Haddad CFB, Zamudio KR. Land cover and forest connectivity alter the interactions among host, pathogen and skin microbiome. Proc Biol Sci 2018; 284:rspb.2017.0582. [PMID: 28835551 DOI: 10.1098/rspb.2017.0582] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/14/2017] [Indexed: 12/11/2022] Open
Abstract
Deforestation has detrimental consequences on biodiversity, affecting species interactions at multiple scales. The associations among vertebrates, pathogens and their commensal/symbiotic microbial communities (i.e. microbiomes) have important downstream effects for biodiversity conservation, yet we know little about how deforestation contributes to changes in host microbial diversity and pathogen abundance. Here, we tested the effects of landcover, forest connectivity and infection by the chytrid fungus Batrachochytrium dendrobatidis (Bd) on amphibian skin bacterial diversity along deforestation gradients in Brazilian landscapes. If disturbance to natural habitat alters skin microbiomes as it does in vertebrate host communities, then we would expect higher host bacterial diversity in natural forest habitats. Bd infection loads are also often higher in these closed-canopy forests, which may in turn impact skin-associated bacterial communities. We found that forest corridors shaped composition of host skin microbiomes; high forest connectivity predicted greater similarity of skin bacterial communities among host populations. In addition, we found that host skin bacterial diversity and Bd loads increased towards natural vegetation. Because symbiotic bacteria can potentially buffer hosts from Bd infection, we also evaluated the bi-directional microbiome-Bd link but failed to find a significant effect of skin bacterial diversity reducing Bd infections. Although weak, we found support for Bd increasing bacterial diversity and/or for core bacteria dominance reducing Bd loads. Our research incorporates a critical element in the study of host microbiomes by linking environmental heterogeneity of landscapes to the host-pathogen-microbiome triangle.
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Affiliation(s)
- C G Becker
- Universidade Estadual Paulista, Instituto de Biociências, Departamento de Zoologia and Centro de Aquicultura (CAUNESP), 13506-900 Rio Claro, SP, Brazil
| | - A V Longo
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - C F B Haddad
- Universidade Estadual Paulista, Instituto de Biociências, Departamento de Zoologia and Centro de Aquicultura (CAUNESP), 13506-900 Rio Claro, SP, Brazil
| | - K R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
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26
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Hughey MC, Pena JA, Reyes R, Medina D, Belden LK, Burrowes PA. Skin bacterial microbiome of a generalist Puerto Rican frog varies along elevation and land use gradients. PeerJ 2017; 5:e3688. [PMID: 28875068 PMCID: PMC5580383 DOI: 10.7717/peerj.3688] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 07/24/2017] [Indexed: 02/01/2023] Open
Abstract
Host-associated microbial communities are ubiquitous among animals, and serve important functions. For example, the bacterial skin microbiome of amphibians can play a role in preventing or reducing infection by the amphibian chytrid fungus, Batrachochytrium dendrobatidis. Evidence suggests that environmental bacteria likely serve as a source pool for at least some of the members of the amphibian skin bacterial community, underscoring the potential for local environmental changes to disrupt microbial community source pools that could be critical to the health of host organisms. However, few studies have assessed variation in the amphibian skin microbiome along clear environmental gradients, and so we know relatively little about how local environmental conditions influence microbiome diversity. We sampled the skin bacterial communities of Coqui frogs, Eleutherodactylus coqui (N = 77), along an elevational gradient in eastern Puerto Rico (0-875 m), with transects in two land use types: intact forest (N = 4 sites) and disturbed (N = 3 sites) forest. We found that alpha diversity (as assessed by Shannon, Simpson, and Phylogenetic Diversity indices) varied across sites, but this variation was not correlated with elevation or land use. Beta diversity (community structure), on the other hand, varied with site, elevation and land use, primarily due to changes in the relative abundance of certain bacterial OTUs (∼species) within these communities. Importantly, although microbiome diversity varied, E. coqui maintained a common core microbiota across all sites. Thus, our findings suggest that environmental conditions can influence the composition of the skin microbiome of terrestrial amphibians, but that some aspects of the microbiome remain consistent despite environmental variation.
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Affiliation(s)
- Myra C Hughey
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Janelle A Pena
- Department of Biology, Universidad de Puerto Rico, San Juan, Puerto Rico
| | - Roberto Reyes
- Department of Biology, Universidad de Puerto Rico, San Juan, Puerto Rico
| | - Daniel Medina
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
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27
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Muletz-Wolz CR, Almario JG, Barnett SE, DiRenzo GV, Martel A, Pasmans F, Zamudio KR, Toledo LF, Lips KR. Inhibition of Fungal Pathogens across Genotypes and Temperatures by Amphibian Skin Bacteria. Front Microbiol 2017; 8:1551. [PMID: 28871241 PMCID: PMC5566582 DOI: 10.3389/fmicb.2017.01551] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/31/2017] [Indexed: 01/20/2023] Open
Abstract
Symbiotic bacteria may dampen the impacts of infectious diseases on hosts by inhibiting pathogen growth. However, our understanding of the generality of pathogen inhibition by different bacterial taxa across pathogen genotypes and environmental conditions is limited. Bacterial inhibitory properties are of particular interest for the amphibian-killing fungal pathogens (Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans), for which probiotic applications as conservation strategies have been proposed. We quantified the inhibition strength of five putatively B. dendrobatidis-inhibitory bacteria isolated from woodland salamander skin against six Batrachochytrium genotypes at two temperatures (12 and 18°C). We selected six genotypes from across the Batrachochytrium phylogeny: B. salamandrivorans, B. dendrobatidis-Brazil and four genotypes of the B. dendrobatidis Global Panzootic Lineage (GPL1: JEL647, JEL404; GPL2: SRS810, JEL423). We performed 96-well plate challenge assays in a full factorial design. We detected a Batrachochytrium genotype by temperature interaction on bacterial inhibition score for all bacteria, indicating that bacteria vary in ability to inhibit Batrachochytrium depending on pathogen genotype and temperature. Acinetobacter rhizosphaerae moderately inhibited B. salamandrivorans at both temperatures (μ = 46–53%), but not any B. dendrobatidis genotypes. Chryseobacterium sp. inhibited three Batrachochytrium genotypes at both temperatures (μ = 5–71%). Pseudomonas sp. strain 1 inhibited all Batrachochytrium genotypes at 12°C and four Batrachochytrium genotypes at 18°C (μ = 5–100%). Pseudomonas sp. strain 2 and Stenotrophomonas sp. moderately to strongly inhibited all six Batrachochytrium genotypes at both temperatures (μ = 57–100%). All bacteria consistently inhibited B. salamandrivorans. Using cluster analysis of inhibition scores, we found that more closely related Batrachochytrium genotypes grouped together, suggesting that bacterial inhibition strength may be predictable based on Batrachochytrium relatedness. We conclude that bacterial inhibition capabilities change among bacterial strains, Batrachochytrium genotypes and temperatures. A comprehensive understanding of bacterial inhibitory function, across pathogen genotypes and temperatures, is needed to better predict the role of bacterial symbionts in amphibian disease ecology. For targeted conservation applications, we recommend using bacterial strains identified as strongly inhibitory as they are most likely to produce broad-spectrum antimicrobial agents at a range of temperatures.
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Affiliation(s)
- Carly R Muletz-Wolz
- Department of Biology, University of Maryland, College ParkMD, United States.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, WashingtonDC, United States
| | - Jose G Almario
- Department of Biology, University of Maryland, College ParkMD, United States
| | - Samuel E Barnett
- Department of Biology, University of Maryland, College ParkMD, United States.,Department of Microbiology, Cornell University, IthacaNY, United States
| | - Graziella V DiRenzo
- Department of Biology, University of Maryland, College ParkMD, United States.,Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa BarbaraCA, United States
| | - An Martel
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent UniversityGhent, Belgium
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent UniversityGhent, Belgium
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, IthacaNY, United States
| | - Luís Felipe Toledo
- Department of Animal Biology, State University of CampinasCampinas, Brazil
| | - Karen R Lips
- Department of Biology, University of Maryland, College ParkMD, United States
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28
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Muletz Wolz CR, Yarwood SA, Campbell Grant EH, Fleischer RC, Lips KR. Effects of host species and environment on the skin microbiome of Plethodontid salamanders. J Anim Ecol 2017; 87:341-353. [DOI: 10.1111/1365-2656.12726] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/08/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Carly R. Muletz Wolz
- Department of Biology; University of Maryland; College Park MD USA
- Center for Conservation Genomics; Smithsonian Conservation Biology Institute; National Zoological Park; Washington DC USA
| | - Stephanie A. Yarwood
- Department of Environmental Science & Technology; University of Maryland; College Park MD USA
| | - Evan H. Campbell Grant
- S.O. Conte Anadromous Fish Research Laboratory; United States Geological Survey Patuxent Wildlife Research Center; Turners Falls MA USA
| | - Robert C. Fleischer
- Center for Conservation Genomics; Smithsonian Conservation Biology Institute; National Zoological Park; Washington DC USA
| | - Karen R. Lips
- Department of Biology; University of Maryland; College Park MD USA
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