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Cordeiro IF, Lemes CGDC, Sanchez AB, da Silva AK, de Paula CH, de Matos RC, Ribeiro DF, de Matos JP, Garcia CCM, Beirão M, Becker CG, Pires MRS, Moreira LM. Amphibian tolerance to arsenic: microbiome-mediated insights. Sci Rep 2024; 14:10193. [PMID: 38702361 PMCID: PMC11068734 DOI: 10.1038/s41598-024-60879-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
Amphibians are often recognized as bioindicators of healthy ecosystems. The persistence of amphibian populations in heavily contaminated environments provides an excellent opportunity to investigate rapid vertebrate adaptations to harmful contaminants. Using a combination of culture-based challenge assays and a skin permeability assay, we tested whether the skin-associated microbiota may confer adaptive tolerance to tropical amphibians in regions heavily contaminated with arsenic, thus supporting the adaptive microbiome principle and immune interactions of the amphibian mucus. At lower arsenic concentrations (1 and 5 mM As3+), we found a significantly higher number of bacterial isolates tolerant to arsenic from amphibians sampled at an arsenic contaminated region (TES) than from amphibians sampled at an arsenic free region (JN). Strikingly, none of the bacterial isolates from our arsenic free region tolerated high concentrations of arsenic. In our skin permeability experiment, where we tested whether a subset of arsenic-tolerant bacterial isolates could reduce skin permeability to arsenic, we found that isolates known to tolerate high concentrations of arsenic significantly reduced amphibian skin permeability to this metalloid. This pattern did not hold true for bacterial isolates with low arsenic tolerance. Our results describe a pattern of environmental selection of arsenic-tolerant skin bacteria capable of protecting amphibians from intoxication, which helps explain the persistence of amphibian populations in water bodies heavily contaminated with arsenic.
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Affiliation(s)
- Isabella Ferreira Cordeiro
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | | | - Angélica Bianchini Sanchez
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Ana Karla da Silva
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Camila Henriques de Paula
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Rosilene Cristina de Matos
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Dilson Fagundes Ribeiro
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Jéssica Pereira de Matos
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Camila Carrião Machado Garcia
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
- Laboratório de Genômica e Interação Bactérias-Ambiente, Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Marina Beirão
- Departamento de Biodiversidade Evolução e Meio Ambiente, Instituto de Ciências Biológicas, Universidade Federal de Ouro Preto, Belo Horizonte, MG, 31270-901, Brazil
| | - C Guilherme Becker
- Department of Biology, One Health Microbiome Center, Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Maria Rita Silvério Pires
- Departamento de Biodiversidade Evolução e Meio Ambiente, Instituto de Ciências Biológicas, Universidade Federal de Ouro Preto, Belo Horizonte, MG, 31270-901, Brazil
| | - Leandro Marcio Moreira
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil.
- Laboratório de Genômica e Interação Bactérias-Ambiente, Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil.
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2
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Romero-Contreras YJ, González-Serrano F, Bello-López E, Formey D, Aragón W, Cevallos MÁ, Rebollar EA, Serrano M. Bacteria from the skin of amphibians promote growth of Arabidopsis thaliana and Solanum lycopersicum by modifying hormone-related transcriptome response. PLANT MOLECULAR BIOLOGY 2024; 114:39. [PMID: 38615069 PMCID: PMC11016013 DOI: 10.1007/s11103-024-01444-x] [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: 10/20/2023] [Accepted: 03/11/2024] [Indexed: 04/15/2024]
Abstract
Plants and microorganisms establish beneficial associations that can improve their development and growth. Recently, it has been demonstrated that bacteria isolated from the skin of amphibians can contribute to plant growth and defense. However, the molecular mechanisms involved in the beneficial effect for the host are still unclear. In this work, we explored whether bacteria isolated from three tropical frogs species can contribute to plant growth. After a wide screening, we identified three bacterial strains with high biostimulant potential, capable of modifying the root structure of Arabidopsis thaliana plants. In addition, applying individual bacterial cultures to Solanum lycopersicum plants induced an increase in their growth. To understand the effect that these microorganisms have over the host plant, we analysed the transcriptomic profile of A. thaliana during the interaction with the C32I bacterium, demonstrating that the presence of the bacteria elicits a transcriptional response associated to plant hormone biosynthesis. Our results show that amphibian skin bacteria can function as biostimulants to improve agricultural crops growth and development by modifying the plant transcriptomic responses.
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Affiliation(s)
- Yordan J Romero-Contreras
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
- Programa de Doctorado en Ciencias Biomédicas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
| | | | - Elena Bello-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Wendy Aragón
- Instituto de Biociencias, Universidad Autónoma de Chiapas, Blvd. Príncipe Akishino s/n, 30798, Tapachula, Chiapas, Mexico
| | - Miguel Ángel Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
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3
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Romero-Contreras YJ, Gonzalez-Serrano F, Formey D, Aragón W, Chacón FI, Torres M, Cevallos MÁ, Dib JR, Rebollar EA, Serrano M. Amphibian skin bacteria display antifungal activity and induce plant defense mechanisms against Botrytis cinerea. FRONTIERS IN PLANT SCIENCE 2024; 15:1392637. [PMID: 38654899 PMCID: PMC11035788 DOI: 10.3389/fpls.2024.1392637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Botrytis cinerea is the causal agent of gray mold, which affects a wide variety of plant species. Chemical agents have been used to prevent the disease caused by this pathogenic fungus. However, their toxicity and reduced efficacy have encouraged the development of new biological control alternatives. Recent studies have shown that bacteria isolated from amphibian skin display antifungal activity against plant pathogens. However, the mechanisms by which these bacteria act to reduce the effects of B. cinerea are still unclear. From a diverse collection of amphibian skin bacteria, three proved effective in inhibiting the development of B. cinerea under in vitro conditions. Additionally, the individual application of each bacterium on the model plant Arabidopsis thaliana, Solanum lycopersicum and post-harvest blueberries significantly reduced the disease caused by B. cinerea. To understand the effect of bacteria on the host plant, we analyzed the transcriptomic profile of A. thaliana in the presence of the bacterium C32I and the fungus B. cinerea, revealing transcriptional regulation of defense-related hormonal pathways. Our study shows that bacteria from the amphibian skin can counteract the activity of B. cinerea by regulating the plant transcriptional responses.
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Affiliation(s)
- Yordan J. Romero-Contreras
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Francisco Gonzalez-Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Wendy Aragón
- Instituto de Biociencias, Universidad Autónoma de Chiapas, Tapachula, Chiapas, Mexico
| | - Florencia Isabel Chacón
- Planta Piloto de Procesos Industriales Microbiológicos (PROIM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Tucumán, Argentina
| | - Martha Torres
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Miguel Ángel Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Julian Rafael Dib
- Planta Piloto de Procesos Industriales Microbiológicos (PROIM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Tucumán, Argentina
- Instituto de Microbiología, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Vargas-Gastélum L, Romer AS, Ghotbi M, Dallas JW, Alexander NR, Moe KC, McPhail KL, Neuhaus GF, Shadmani L, Spatafora JW, Stajich JE, Tabima JF, Walker DM. Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria. mSphere 2024; 9:e0047523. [PMID: 38349154 PMCID: PMC10964425 DOI: 10.1128/msphere.00475-23] [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: 08/22/2023] [Accepted: 01/10/2024] [Indexed: 03/27/2024] Open
Abstract
Reptiles and amphibians (herptiles) are some of the most endangered and threatened species on the planet and numerous conservation strategies are being implemented with the goal of ensuring species recovery. Little is known, however, about the gut microbiome of wild herptiles and how it relates to the health of these populations. Here, we report results from the gut microbiome characterization of both a broad survey of herptiles, and the correlation between the fungus Basidiobolus, and the bacterial community supported by a deeper, more intensive sampling of Plethodon glutinosus, known as slimy salamanders. We demonstrate that bacterial communities sampled from frogs, lizards, and salamanders are structured by the host taxonomy and that Basidiobolus is a common and natural component of these wild gut microbiomes. Intensive sampling of multiple hosts across the ecoregions of Tennessee revealed that geography and host:geography interactions are strong predictors of distinct Basidiobolus operational taxonomic units present within a given host. Co-occurrence analyses of Basidiobolus and bacterial community diversity support a correlation and interaction between Basidiobolus and bacteria, suggesting that Basidiobolus may play a role in structuring the bacterial community. We further the hypothesis that this interaction is advanced by unique specialized metabolism originating from horizontal gene transfer from bacteria to Basidiobolus and demonstrate that Basidiobolus is capable of producing a diversity of specialized metabolites including small cyclic peptides.IMPORTANCEThis work significantly advances our understanding of biodiversity and microbial interactions in herptile microbiomes, the role that fungi play as a structural and functional members of herptile gut microbiomes, and the chemical functions that structure microbiome phenotypes. We also provide an important observational system of how the gut microbiome represents a unique environment that selects for novel metabolic functions through horizontal gene transfer between fungi and bacteria. Such studies are needed to better understand the complexity of gut microbiomes in nature and will inform conservation strategies for threatened species of herpetofauna.
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Affiliation(s)
- Lluvia Vargas-Gastélum
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Alexander S. Romer
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Marjan Ghotbi
- Research Division 3, Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jason W. Dallas
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - N. Reed Alexander
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Kylie C. Moe
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - George F. Neuhaus
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Leila Shadmani
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Javier F. Tabima
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | - Donald M. Walker
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
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5
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Schuck LK, Neely WJ, Buttimer SM, Moser CF, Barth PC, Liskoski PE, Caberlon CDA, Valiati VH, Tozetti AM, Becker CG. Effects of grassland controlled burning on symbiotic skin microbes in Neotropical amphibians. Sci Rep 2024; 14:959. [PMID: 38200064 PMCID: PMC10781984 DOI: 10.1038/s41598-023-50394-9] [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: 08/11/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Climate change has led to an alarming increase in the frequency and severity of wildfires worldwide. While it is known that amphibians have physiological characteristics that make them highly susceptible to fire, the specific impacts of wildfires on their symbiotic skin bacterial communities (i.e., bacteriomes) and infection by the deadly chytrid fungus, Batrachochytrium dendrobatidis, remain poorly understood. Here, we address this research gap by evaluating the effects of fire on the amphibian skin bacteriome and the subsequent risk of chytridiomycosis. We sampled the skin bacteriome of the Neotropical species Scinax squalirostris and Boana leptolineata in fire and control plots before and after experimental burnings. Fire was linked with a marked increase in bacteriome beta dispersion, a proxy for skin microbial dysbiosis, alongside a trend of increased pathogen loads. By shedding light on the effects of fire on amphibian skin bacteriomes, this study contributes to our broader understanding of the impacts of wildfires on vulnerable vertebrate species.
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Affiliation(s)
- Laura K Schuck
- Programa de Pós-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022-750, Brazil.
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Wesley J Neely
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
- Department of Biology, Texas State University, San Marcos, TX, 78666, USA
| | - Shannon M Buttimer
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Infectious Disease Dynamics and One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Camila F Moser
- Programa de Pos-Graduacão em Zoologia, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Priscila C Barth
- Programa de Pós-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022-750, Brazil
| | - Paulo E Liskoski
- Programa de Pós-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022-750, Brazil
| | - Carolina de A Caberlon
- Programa de Pós-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022-750, Brazil
| | - Victor Hugo Valiati
- Programa de Pós-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022-750, Brazil
| | - Alexandro M Tozetti
- Programa de Pós-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022-750, Brazil.
| | - C Guilherme Becker
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Center for Infectious Disease Dynamics and One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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6
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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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López-García P, Gutiérrez-Preciado A, Krupovic M, Ciobanu M, Deschamps P, Jardillier L, López-Pérez M, Rodríguez-Valera F, Moreira D. Metagenome-derived virus-microbe ratios across ecosystems. THE ISME JOURNAL 2023; 17:1552-1563. [PMID: 37169871 PMCID: PMC10504350 DOI: 10.1038/s41396-023-01431-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/20/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023]
Abstract
It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa-200 µm size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by ~13 fold and in plankton from marine and saline waters by ~2-4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.
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Affiliation(s)
- Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
| | - Ana Gutiérrez-Preciado
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Maria Ciobanu
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Philippe Deschamps
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Ludwig Jardillier
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Mario López-Pérez
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | | | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
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8
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Wax N, Walke JB, Haak DC, Belden LK. Comparative genomics of bacteria from amphibian skin associated with inhibition of an amphibian fungal pathogen, Batrachochytrium dendrobatidis. PeerJ 2023; 11:e15714. [PMID: 37637170 PMCID: PMC10452622 DOI: 10.7717/peerj.15714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/16/2023] [Indexed: 08/29/2023] Open
Abstract
Chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), is a skin disease associated with worldwide amphibian declines. Symbiotic microbes living on amphibian skin interact with Bd and may alter infection outcomes. We completed whole genome sequencing of 40 bacterial isolates cultured from the skin of four amphibian species in the Eastern US. Each isolate was tested in vitro for the ability to inhibit Bd growth. The aim of this study was to identify genomic differences among the isolates and generate hypotheses about the genomic underpinnings of Bd growth inhibition. We identified sixty-five gene families that were present in all 40 isolates. Screening for common biosynthetic gene clusters revealed that this set of isolates contained a wide variety of clusters; the two most abundant clusters with potential antifungal activity were siderophores (N=17 isolates) and Type III polyketide synthases (N=22 isolates). We then examined various subsets of the 22 isolates in the phylum Proteobacteria for genes encoding specific compounds that may inhibit fungal growth, including chitinase and violacein. We identified differences in Agrobacterium and Sphingomonas isolates in the chitinase genes that showed some association with anti-Bd activity, as well as variation in the violacein genes in the Janthinobacterium isolates. Using a comparative genomics approach, we generated several testable hypotheses about differences among bacterial isolates from amphibian skin communities that could contribute to variation in the ability to inhibit Bd growth. Further work is necessary to explore and uncover the various mechanisms utilized by amphibian skin bacterial isolates to inhibit Bd.
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Affiliation(s)
- Noah Wax
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Jenifer B. Walke
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
- Department of Biology, Eastern Washington University, Cheney, WA, United States of America
| | - David C. Haak
- School of Plant and Environmental 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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9
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Schilliger L, Paillusseau C, François C, Bonwitt J. Major Emerging Fungal Diseases of Reptiles and Amphibians. Pathogens 2023; 12:pathogens12030429. [PMID: 36986351 PMCID: PMC10053826 DOI: 10.3390/pathogens12030429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/16/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Emerging infectious diseases (EIDs) are caused by pathogens that have undergone recent changes in terms of geographic spread, increasing incidence, or expanding host range. In this narrative review, we describe three important fungal EIDs with keratin trophism that are relevant to reptile and amphibian conservation and veterinary practice. Nannizziopsis spp. have been mainly described in saurians; infection results in thickened, discolored skin crusting, with eventual progression to deep tissues. Previously only reported in captive populations, it was first described in wild animals in Australia in 2020. Ophidiomyces ophidiicola (formely O. ophiodiicola) is only known to infect snakes; clinical signs include ulcerating lesions in the cranial, ventral, and pericloacal regions. It has been associated with mortality events in wild populations in North America. Batrachochytrium spp. cause ulceration, hyperkeratosis, and erythema in amphibians. They are a major cause of catastrophic amphibian declines worldwide. In general, infection and clinical course are determined by host-related characteristics (e.g., nutritional, metabolic, and immune status), pathogens (e.g., virulence and environmental survival), and environment (e.g., temperature, hygrometry, and water quality). The animal trade is thought to be an important cause of worldwide spread, with global modifications in temperature, hygrometry, and water quality further affecting fungal pathogenicity and host immune response.
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Affiliation(s)
- Lionel Schilliger
- Argos Veterinary Clinic of Paris Auteuil, 35 Rue Leconte de Lisle, 75016 Paris, France
- SpéNac Referral Center, 100 Boulevard de la Tour Maubourg, 75007 Paris, France
- Correspondence: ; Tel.: +33-188-616-831
| | - Clément Paillusseau
- Argos Veterinary Clinic of Paris Auteuil, 35 Rue Leconte de Lisle, 75016 Paris, France
- SpéNac Referral Center, 100 Boulevard de la Tour Maubourg, 75007 Paris, France
| | - Camille François
- Argos Veterinary Clinic of Paris Auteuil, 35 Rue Leconte de Lisle, 75016 Paris, France
- SpéNac Referral Center, 100 Boulevard de la Tour Maubourg, 75007 Paris, France
| | - Jesse Bonwitt
- Department of Anthropology, Durham University, South Rd., Durham DH1 3LE, UK
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10
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Martínez-Ugalde E, Ávila-Akerberg V, González Martínez TM, Vázquez Trejo M, Zavala Hernández D, Anaya-Morales SL, Rebollar EA. The skin microbiota of the axolotl Ambystoma altamirani is highly influenced by metamorphosis and seasonality but not by pathogen infection. Anim Microbiome 2022; 4:63. [PMID: 36503640 PMCID: PMC9743558 DOI: 10.1186/s42523-022-00215-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/16/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Microbiomes have been increasingly recognized as major contributors to host health and survival. In amphibians, bacterial members of the skin microbiota protect their hosts by inhibiting the growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). Even though several studies describe the influence of biotic and abiotic factors over the skin microbiota, it remains unclear how these symbiotic bacterial communities vary across time and development. This is particularly relevant for species that undergo metamorphosis as it has been shown that host physiology and ecology drastically influence diversity of the skin microbiome. RESULTS We found that the skin bacterial communities of the axolotl A. altamirani are largely influenced by the metamorphic status of the host and by seasonal variation of abiotic factors such as temperature, pH, dissolved oxygen and conductivity. Despite high Bd prevalence in these samples, the bacterial diversity of the skin microbiota did not differ between infected and non-infected axolotls, although relative abundance of particular bacteria were correlated with Bd infection intensity. CONCLUSIONS Our work shows that metamorphosis is a crucial process that shapes skin bacterial communities and that axolotls under different developmental stages respond differently to environmental seasonal variations. Moreover, this study greatly contributes to a better understanding of the factors that shape amphibian skin microbiota, especially in a largely underexplored group like axolotls (Mexican Ambystoma species).
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Affiliation(s)
| | - Víctor Ávila-Akerberg
- Instituto de Ciencias Agropecuarias y Rurales, Universidad Autónoma del Estado de México, Toluca, Mexico
| | | | | | | | - Sara Lucia Anaya-Morales
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
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11
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Cevallos MA, Basanta MD, Bello-López E, Escobedo-Muñoz AS, González-Serrano FM, Nemec A, Romero-Contreras YJ, Serrano M, Rebollar EA. Genomic characterization of antifungal Acinetobacter bacteria isolated from the skin of the frogs Agalychnis callidryas and Craugastor fitzingeri. FEMS Microbiol Ecol 2022; 98:6775075. [PMID: 36288213 DOI: 10.1093/femsec/fiac126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/09/2022] [Accepted: 10/24/2022] [Indexed: 01/21/2023] Open
Abstract
Chytridiomycosis, a lethal fungal disease caused by Batrachochytrium dendrobatidis (Bd), is responsible for population declines and extinctions of amphibians worldwide. However, not all amphibian species are equally susceptible to the disease; some species persist in Bd enzootic regions with no population reductions. Recently, it has been shown that the amphibian skin microbiome plays a crucial role in the defense against Bd. Numerous bacterial isolates with the capacity to inhibit the growth of Batrachochytrium fungi have been isolated from the skin of amphibians. Here, we characterized eight Acinetobacter bacteria isolated from the frogs Agalychnis callidryas and Craugastor fitzingeri at the genomic level. A total of five isolates belonged to Acinetobacter pittii,Acinetobacter radioresistens, or Acinetobactermodestus, and three were not identified as any of the known species, suggesting they are members of new species. We showed that seven isolates inhibited the growth of Bd and that all eight isolates inhibited the growth of the phytopathogen fungus Botrytis cinerea. Finally, we identified the biosynthetic gene clusters that could be involved in the antifungal activity of these isolates. Our results suggest that the frog skin microbiome includes Acinetobacter isolates that are new to science and have broad antifungal functions, perhaps driven by distinct genetic mechanisms.
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Affiliation(s)
- M A Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - M D Basanta
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México.,Department of Biology, University of Nevada Reno, 1664 N Virgina St, Reno, NV 89557, United States
| | - E Bello-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - A S Escobedo-Muñoz
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - F M González-Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - A Nemec
- Laboratory of Bacterial Genetics, Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, 100 00 Prague 10, Czechia.,Department of Medical Microbiology, Second Faculty of Medicine, Charles University, and Motol University Hospital, V Úvalu 84, 150 06 Prague 5, Czechia
| | - Y J Romero-Contreras
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - M Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - E A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
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12
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Grisnik M, Grinath JB, Munafo JP, Walker DM. Functional Redundancy in Bat Microbial Assemblage in the Presence of the White Nose Pathogen. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02098-2. [PMID: 35953677 DOI: 10.1007/s00248-022-02098-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Understanding how host-associated microbial assemblages respond to pathogen invasion has implications for host health. Until recently, most investigations have focused on understanding the taxonomic composition of these assemblages. However, recent studies have suggested that microbial assemblage taxonomic composition is decoupled from its function, with assemblages being taxonomically varied but functionally constrained. The objective of this investigation was to understand how the Tri-colored bat, Perimyotis subflavus cutaneous microbial assemblage responds to fungal pathogen invasion within a functional context. We hypothesized that at a broad scale (e.g., KEGG pathways), there will be no difference in the functional assemblages between the white nose pathogen, Pseudogymnoascus destructans, positive and negative bats; and this pattern will be driven by the functional redundancy of bacterial taxa. At finer scales (e.g., gene models), we postulate differences in function attributed to interactions between bacteria and P. destructans, resulting in the production of antifungal metabolites. To test this, we used a combination of shotgun metagenomic and amplicon sequencing to characterize the bat cutaneous microbial assemblage in the presence/absence of P. destructans. Results showed that while there was a shift in taxonomic assemblage composition between P. destructans positive and negative bats, there was little overall difference in microbial function. Functional redundancy across bacterial taxa was clear at a broad-scale; however, both redundancy and variation in bacterial capability related to defense against pathogens was evident at finer scales. While functionality of the microbial assemblage was largely conserved in relation to P. destructans, the roles of particular functional pathways in resistance to fungal pathogens require further attention.
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Affiliation(s)
- Matthew Grisnik
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
| | - Joshua B Grinath
- Department of Biological Sciences, Idaho State University, Pocatello, ID, 83209, USA
| | - John P Munafo
- Department of Food Science, University of Tennessee Knoxville, Knoxville, TN, 37996, USA
| | - Donald M Walker
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
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13
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Li Z, Li A, Dai W, Leng H, Liu S, Jin L, Sun K, Feng J. Skin Microbiota Variation Among Bat Species in China and Their Potential Defense Against Pathogens. Front Microbiol 2022; 13:808788. [PMID: 35432245 PMCID: PMC9009094 DOI: 10.3389/fmicb.2022.808788] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Host-associated skin bacteria are essential for resisting pathogen infections and maintaining health. However, we have little understanding of how chiropteran skin microbiota are distributed among bat species and their habitats, or of their putative roles in defending against Pseudogymnoascus destructans in China. In this study, we characterized the skin microbiomes of four bat species at five localities using 16S rRNA gene amplicon sequencing to understand their skin microbial composition, structure, and putative relationship with disease. The alpha- and beta-diversities of skin microbiota differed significantly among the bat species, and the differences were affected by environmental temperature, sampling sites, and host body condition. The chiropteran skin microbial communities were enriched in bacterial taxa that had low relative abundances in the environment. Most of the potential functions of skin microbiota in bat species were associated with metabolism. Focusing on their functions of defense against pathogens, we found that skin microbiota could metabolize a variety of active substances that could be potentially used to fight P. destructans. The skin microbial communities of bats in China are related to the environment and the bat host, and may be involved in the host's defense against pathogens.
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Affiliation(s)
- Zhongle Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Sen Liu
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
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14
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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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15
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Chimetto Tonon LA, Rua C, Crnkovic CM, Bernardi DI, Pires Junior OR, Haddad CFB, Pedrosa CSG, Souza LRQ, Rehen SK, de Azevedo GPR, Thompson CC, Thompson FL, Berlinck RGS. Microbiome associated with the tetrodotoxin-bearing anuran Brachycephalus pitanga. Toxicon 2021; 203:139-146. [PMID: 34653444 DOI: 10.1016/j.toxicon.2021.10.002] [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: 03/11/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 11/15/2022]
Abstract
The genus Brachycephalus includes small species of aposematic anurans known as microendemic, occurring in the mountains of the Atlantic Forest. Brachycephalus ephippium, B. nodoterga and B. pernix have been reported to contain the neurotoxin tetrodotoxin in skin and viscera. The biological conservation of several Brachycephalus species is currently threatened by climate change, deforestation, and the pandemic caused by the fungus Batrachochytrium dendrobatidis (Bd). Despite the well-known importance of amphibians' associated bacteria in the defensive role against pathogens, there is still a poor understanding of amphibian microbiome composition. The present study investigated the composition of B. pitanga microbial community and the presence of TTX in the host and in cultures of bacterial isolates, using a combination of metagenomics, bacterial culture isolation, mass spectrometry and metabolomic analyses. Results of culture-dependent and -independent analyses characterized the microbial communities associated with the skin and viscera of B. pitanga. Mass spectrometry analysis indicated the presence of TTX in host tissues, while bacterial production of TTX was not observed under the experimental conditions used in this investigation. This is the first report confirming the occurrence of TTX in B. pitanga.
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Affiliation(s)
- Luciane A Chimetto Tonon
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil; Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil.
| | - Cintia Rua
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil; Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Camila M Crnkovic
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil; Departamento de Tecnologia Bioquímico-Farmacêutica (FBT), Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Darlon I Bernardi
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil
| | - Osmindo R Pires Junior
- Laboratório de Toxinologia, Instituto de Biologia, Universidade de Brasília, Brasília, DF, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | | | | | - Stevens K Rehen
- Instituto D'Or de Pesquisa e Ensino (IDOR), RJ, Brazil; Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Gustavo P R de Azevedo
- Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil.
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
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16
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Whole-Genome Sequencing Analysis to Identify Infection with Multiple Species of Nontuberculous Mycobacteria. Pathogens 2021; 10:pathogens10070879. [PMID: 34358029 PMCID: PMC8308675 DOI: 10.3390/pathogens10070879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/30/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
Mixed infection with multiple species of nontuberculous mycobacteria (NTM) is difficult to identify and to treat. Current conventional molecular-based methods for identifying mixed infections are limited due to low specificity. Here, we evaluated the utility of whole-genome sequencing (WGS) analysis to detect and identify mixed NTM infections. Analytical tools used included PubMLST, MetaPhlAn3, Kraken2, Mykrobe-Predictor and analysis of heterozygous SNP frequencies. The ability of each to identify mixed infections of NTM species was compared. Sensitivity was tested using 101 samples (sequence sets) including 100 in-silico simulated mixed samples with various proportions of known NTM species and one sample of known mixed NTM species from a public database. Single-species NTM control samples (155 WGS samples from public databases and 15 samples from simulated reads) were tested for specificity. Kraken2 exhibited 100% sensitivity and 98.23% specificity for detection and identification of mixed NTM species with accurate estimation of relative abundance of each species in the mixture. PubMLST (99% and 96.47%) and MetaPhlAn3 (95.04% and 83.52%) had slightly lower sensitivity and specificity. Mykrobe-Predictor had the lowest sensitivity (57.42%). Analysis of read frequencies supporting single nucleotide polymorphisms (SNPs) could not detect mixed NTM samples. Clinical NTM samples (n = 16), suspected on the basis of a 16S-23S rRNA gene sequence-based line-probe assay (LPA) to contain more than one NTM species, were investigated using WGS-analysis tools. This identified only a small proportion (37.5%, 6/16 samples) of the samples as mixed infections and exhibited only partial agreement with LPA results. LPAs seem to be inadequate for detecting mixed NTM species infection. This study demonstrated that WGS-analysis tools can be used for diagnosis of mixed infections with different species of NTM.
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17
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Zeitler EF, Cecala KK, McGrath DA. Carryover effects minimized the positive effects of treated wastewater on anuran development. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 289:112571. [PMID: 33866133 DOI: 10.1016/j.jenvman.2021.112571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 03/26/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Constructed wetlands (CWs) are a potential solution for wastewater treatment due to their capacity to support native species and provide tertiary wastewater treatment. However, CWs can expose wildlife communities to excess nutrients and harmful contaminants, affecting their development, morphology, and behavior. To examine how wastewater CWs may affect wildlife, we raised Southern leopard frogs, Lithobates sphenocephalus, in wastewater from conventional secondary lagoon and tertiary CW treatments for comparison with pondwater along with the presence and absence of a common plant invader to these systems - common duckweed (Lemna minor) - and monitored their juvenile development for potential carryover effects into the terrestrial environment. The tertiary CW treatment did not change demographic or morphological outcomes relative to conventional wastewater treatment in our study. Individuals emerging from both wastewater treatments demonstrated lower terrestrial survival rates than those emerging from pondwater throughout the experiment though experiment-wide survival rates were equivalent among treatments. Individuals from wastewater treatments transformed at larger sizes relative to those in pondwater, but this advantage was minimized in the terrestrial environment. Individuals that developed with duckweed had consistent but marginally better performance in both environments. Our results suggest a potential trade-off between short-term benefits of development in treated effluent and long-term consequences on overall fitness. Overall, we demonstrate that CWs for the purpose of wastewater treatment may not be suitable replicates for wildlife habitat and could have consequences for local population dynamics.
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Affiliation(s)
- Emma F Zeitler
- Department of Biology, University of the South, Sewanee, TN, 37383, USA
| | - Kristen K Cecala
- Department of Biology, University of the South, Sewanee, TN, 37383, USA.
| | - Deborah A McGrath
- Department of Biology, University of the South, Sewanee, TN, 37383, USA
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18
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Smith SN, Colston TJ, Siler CD. Venomous Snakes Reveal Ecological and Phylogenetic Factors Influencing Variation in Gut and Oral Microbiomes. Front Microbiol 2021; 12:657754. [PMID: 33841384 PMCID: PMC8032887 DOI: 10.3389/fmicb.2021.657754] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 02/28/2021] [Indexed: 11/16/2022] Open
Abstract
The gastrointestinal tract (GIT) of vertebrates contains a series of organs beginning with the mouth and ending with the anus or cloacal opening. Each organ represents a unique environment for resident microorganisms. Due to their simple digestive anatomy, snakes are good models for studying microbiome variation along the GIT. Cloacal sampling captures the majority of the microbial diversity found in the GIT of snakes—yet little is known about the oral microbiota of snakes. Most research on the snake mouth and gut microbiota are limited to studies of a single species or captive-bred individuals. It therefore remains unclear how a host’s life history, diet, or evolutionary history correlate with differences in the microbial composition within the mouths and guts of wild snakes. We sampled the mouth and gut microbial communities from three species of Asian venomous snakes and utilized 16S rRNA microbial inventories to test if host phylogenetic and ecological differences correlate with distinct microbial compositions within the two body sites. These species occupy three disparate habitat types: marine, semi-arboreal, and arboreal, our results suggest that the diversity of snake mouth and gut microbial communities correlate with differences in both host ecology and phylogeny.
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Affiliation(s)
- Sierra N Smith
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, United States
| | - Timothy J Colston
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Cameron D Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, United States
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19
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Romero-Zambrano GL, Bermúdez-Puga SA, Sánchez-Yumbo AF, Yánez-Galarza JK, Ortega-Andrade HM, Naranjo-Briceño L. Amphibian chytridiomycosis, a lethal pandemic disease caused by the killer fungus Batrachochytrium dendrobatidis: New approaches to host defense mechanisms and techniques for detection and monitoring. BIONATURA 2021. [DOI: 10.21931/rb/2021.06.01.28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Chytridiomycosis is a catastrophic disease currently decimating worldwide amphibian populations, caused by the panzootic chytrid fungus Batrachochytrium dendrobatidis. Massive species decline to extinction catalyzes radical changes in ecosystems globally, including the largest continuous rainforest ecosystem on Earth, the Amazon rainforest. Innovative research that aims to propose feasible mechanisms of mitigation and the origins of the disease is vital, including studies addressing climatic effects on the expansion of chytridiomycosis. Thus, this publication aims to provide a comprehensive review of: i) the current technologies used for B. dendrobatidis detection and monitoring, and ii) the known Neotropical amphibian's skin microbiota with anti-fungal properties against B. dendrobatidis. Several immunologic and DNA-based methods are discussed to understand the emerging fungal pathogens and their effects on the biosphere, which can help to mitigate the devastating ecological impacts of mass amphibian morbidity. The establishment of rapid and highly accurate B. dendrobatidis detection techniques and methods for monitoring amphibian's cutaneous microbiome is crucial in the fight against chytridiomycosis.
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Affiliation(s)
- Génesis L. Romero-Zambrano
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
| | - Stalin A. Bermúdez-Puga
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
| | - Alex F. Sánchez-Yumbo
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
| | - Jomira K. Yánez-Galarza
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
| | - H. Mauricio Ortega-Andrade
- 2Biogeography and Spatial Ecology Research Group, Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150 3Herpetology Division, Instituto Nacional de Biodiversidad (INABIO), calle Rumipamba 341 y Av. de los Shyris, Quito, Ecuador
| | - Leopoldo Naranjo-Briceño
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
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20
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The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance. ISME JOURNAL 2021; 15:1628-1640. [PMID: 33564111 PMCID: PMC8163836 DOI: 10.1038/s41396-020-00875-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/24/2020] [Accepted: 12/07/2020] [Indexed: 12/29/2022]
Abstract
Infectious pathogens can disrupt the microbiome in addition to directly affecting the host. Impacts of disease may be dependent on the ability of the microbiome to recover from such disturbance, yet remarkably little is known about microbiome recovery after disease, particularly in nonhuman animals. We assessed the resilience of the amphibian skin microbial community after disturbance by the pathogen, Batrachochytrium dendrobatidis (Bd). Skin microbial communities of laboratory-reared mountain yellow-legged frogs were tracked through three experimental phases: prior to Bd infection, after Bd infection (disturbance), and after clearing Bd infection (recovery period). Bd infection disturbed microbiome composition and altered the relative abundances of several dominant bacterial taxa. After Bd infection, frogs were treated with an antifungal drug that cleared Bd infection, but this did not lead to recovery of microbiome composition (measured as Unifrac distance) or relative abundances of dominant bacterial groups. These results indicate that Bd infection can lead to an alternate stable state in the microbiome of sensitive amphibians, or that microbiome recovery is extremely slow—in either case resilience is low. Furthermore, antifungal treatment and clearance of Bd infection had the additional effect of reducing microbial community variability, which we hypothesize results from similarity across frogs in the taxa that colonize community vacancies resulting from the removal of Bd. Our results indicate that the skin microbiota of mountain yellow-legged frogs has low resilience following Bd-induced disturbance and is further altered by the process of clearing Bd infection, which may have implications for the conservation of this endangered amphibian.
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21
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Piccinni MZ, Watts JEM, Fourny M, Guille M, Robson SC. The skin microbiome of Xenopus laevis and the effects of husbandry conditions. Anim Microbiome 2021; 3:17. [PMID: 33546771 PMCID: PMC7866774 DOI: 10.1186/s42523-021-00080-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Historically the main source of laboratory Xenopus laevis was the environment. The increase in genetically altered animals and evolving governmental constraints around using wild-caught animals for research has led to the establishment of resource centres that supply animals and reagents worldwide, such as the European Xenopus Resource Centre. In the last decade, centres were encouraged to keep animals in a "low microbial load" or "clean" state, where embryos are surface sterilized before entering the housing system; instead of the conventional, "standard" conditions where frogs and embryos are kept without prior surface treatment. Despite Xenopus laevis having been kept in captivity for almost a century, surprisingly little is known about the frogs as a holobiont and how changing the microbiome may affect resistance to disease. This study examines how the different treatment conditions, "clean" and "standard" husbandry in recirculating housing, affects the skin microbiome of tadpoles and female adults. This is particularly important when considering the potential for poor welfare caused by a change in husbandry method as animals move from resource centres to smaller research colonies. RESULTS We found strong evidence for developmental control of the surface microbiome on Xenopus laevis; adults had extremely similar microbial communities independent of their housing, while both tadpole and environmental microbiome communities were less resilient and showed greater diversity. CONCLUSIONS Our findings suggest that the adult Xenopus laevis microbiome is controlled and selected by the host. This indicates that the surface microbiome of adult Xenopus laevis is stable and defined independently of the environment in which it is housed, suggesting that the use of clean husbandry conditions poses little risk to the skin microbiome when transferring adult frogs to research laboratories. This will have important implications for frog health applicable to Xenopus laevis research centres throughout the world.
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Affiliation(s)
- Maya Z. Piccinni
- grid.4701.20000 0001 0728 6636School of Biological Sciences, University of Portsmouth, Portsmouth, UK
- grid.4701.20000 0001 0728 6636European Xenopus Resource Centre, University of Portsmouth, Portsmouth, UK
| | - Joy E. M. Watts
- grid.4701.20000 0001 0728 6636School of Biological Sciences, University of Portsmouth, Portsmouth, UK
- grid.4701.20000 0001 0728 6636Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK
| | - Marie Fourny
- grid.10400.350000 0001 2108 3034University of Rouen-Normandy, Rouen, France
| | - Matt Guille
- grid.4701.20000 0001 0728 6636School of Biological Sciences, University of Portsmouth, Portsmouth, UK
- grid.4701.20000 0001 0728 6636European Xenopus Resource Centre, University of Portsmouth, Portsmouth, UK
| | - Samuel C. Robson
- grid.4701.20000 0001 0728 6636Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK
- grid.4701.20000 0001 0728 6636School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
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22
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Douglas AJ, Hug LA, Katzenback BA. Composition of the North American Wood Frog (Rana sylvatica) Bacterial Skin Microbiome and Seasonal Variation in Community Structure. MICROBIAL ECOLOGY 2021; 81:78-92. [PMID: 32613267 DOI: 10.1007/s00248-020-01550-5] [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: 01/28/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
While a number of amphibian skin microbiomes have been characterized, it is unclear how these communities might vary in response to seasonal changes in the environment and the corresponding behaviors that many amphibians exhibit. Given recent studies demonstrating the importance of the skin microbiome in frog innate immune defense against pathogens, investigating how changes in the environment impact the microbial species present will provide a better understanding of conditions that may alter host susceptibility to pathogens in their environment. We sampled the bacterial skin microbiome of North American wood frogs (Rana sylvatica) from two breeding ponds in the spring, along with the bacterial community present in their vernal breeding pools, and frogs from the nearby forest floor in the summer and fall to determine whether community composition differs by sex, vernal pond site, or temporally across season (spring, summer, fall). Taxon relative abundance data reveals a profile of bacterial phyla similar to those previously described on anuran skin, with Proteobacteria, Bacteroidetes, and Actinobacteria dominating the wood frog skin microbiome. Our results indicate that sex had no significant effect on skin microbiota diversity; however, this may be due to our limited female frog sample size. Vernal pool site had a small but significant effect on skin microbiota, but skin-associated communities were more similar to each other than to the communities observed in the frogs' respective pond water. Across seasons, diversity analyses suggest that there are significant differences between the bacterial skin microbiome of frogs from spring and summer/fall groups while the average α-diversity per frog remained consistent. These results illustrate seasonal variation in wood frog skin microbiome structure and highlight the importance of considering temporal trends in an amphibian microbiome, particularly for species whose life history requires recurrent shifts in habitat and behavior.
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Affiliation(s)
- Alexander J Douglas
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Barbara A Katzenback
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
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23
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Grisnik M, Bowers O, Moore AJ, Jones BF, Campbell JR, Walker DM. The cutaneous microbiota of bats has in vitro antifungal activity against the white nose pathogen. FEMS Microbiol Ecol 2020; 96:5710932. [PMID: 31960913 DOI: 10.1093/femsec/fiz193] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 01/20/2020] [Indexed: 01/31/2023] Open
Abstract
Since its introduction into the USA, Pseudogymnoascus destructans (Pd), the fungal pathogen of white-nose syndrome, has killed millions of bats. Recently, bacteria capable of inhibiting the growth of Pd have been identified within bat microbial assemblages, leading to increased interest in elucidating bacterial assemblage-pathogen interactions. Our objectives were to determine if bat cutaneous bacteria have antifungal activity against Pd, and correlate differences in the bat cutaneous microbiota with the presence/absence of Pd. We hypothesized that the cutaneous microbiota of bats is enriched with antifungal bacteria, and that the skin assemblage will correlate with Pd status. To test this, we sampled bat microbiota, adjacent roost surfaces and soil from Pd positive caves to infer possible overlap of antifungal taxa, we tested these bacteria for bioactivity in vitro, and lastly compared bacterial assemblages using both amplicon and shotgun high-throughput DNA sequencing. Results suggest that the presence of Pd has an inconsistent influence on the bat cutaneous microbial assemblage across sites. Operational taxonomic units (OTUs) that corresponded with cultured antifungal bacteria were present within all sample types but were significantly more abundant on bat skin relative to the environment. Additionally, the microbial assemblage of Pd negative bats was found to have more OTUs that corresponded to antifungal taxa than positive bats, suggesting an interaction between the fungal pathogen and cutaneous microbial assemblage.
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Affiliation(s)
- Matthew Grisnik
- Middle Tennessee State University, Toxicology and Disease Group, Biology Department, 1672 Greenland Drive, Murfreesboro, Tennessee 37132, USA
| | - Olivia Bowers
- Middle Tennessee State University, Toxicology and Disease Group, Biology Department, 1672 Greenland Drive, Murfreesboro, Tennessee 37132, USA
| | - Andrew J Moore
- Tennessee Technological University, Department of Biological Sciences, 1100 N. Dixie Ave, Cookeville, Tennessee 38505, USA
| | - Benjamin F Jones
- Tennessee Technological University, Department of Biological Sciences, 1100 N. Dixie Ave, Cookeville, Tennessee 38505, USA
| | - Joshua R Campbell
- Tennessee Wildlife Resources Agency, 5105 Edmondson Pike, Nashville, Tennessee 37211, USA
| | - Donald M Walker
- Middle Tennessee State University, Toxicology and Disease Group, Biology Department, 1672 Greenland Drive, Murfreesboro, Tennessee 37132, USA
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24
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Bernardo-Cravo AP, Schmeller DS, Chatzinotas A, Vredenburg VT, Loyau A. Environmental Factors and Host Microbiomes Shape Host-Pathogen Dynamics. Trends Parasitol 2020; 36:616-633. [PMID: 32402837 DOI: 10.1016/j.pt.2020.04.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 04/11/2020] [Accepted: 04/11/2020] [Indexed: 12/18/2022]
Abstract
Microorganisms are increasingly recognized as ecosystem-relevant components because they affect the population dynamics of hosts. Functioning at the interface of the host and pathogen, skin and gut microbiomes are vital components of immunity. Recent work reveals a strong influence of biotic and abiotic environmental factors (including the environmental microbiome) on disease dynamics, yet the importance of the host-host microbiome-pathogen-environment interaction has been poorly reflected in theory. We use amphibians and the disease chytridiomycosis caused by the fungal pathogen Batrachochytrium dendrobatidis to show how interactions between host, host microbiome, pathogen, and the environment all affect disease outcome. Our review provides new perspectives that improve our understanding of disease dynamics and ecology by incorporating environmental factors and microbiomes into disease theory.
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Affiliation(s)
- Adriana P Bernardo-Cravo
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France; Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Dirk S Schmeller
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France.
| | - Antonis Chatzinotas
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstrasse 15, 04318, Leipzig, Germany; Leipzig University, Institute of Biology, Johannisallee 21-23, 04103 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | - Adeline Loyau
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France; Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhütte 2, Stechlin, D-16775, Germany
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25
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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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26
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Campbell LJ, Pawlik AH, Harrison XA. Amphibian ranaviruses in Europe: important directions for future research. Facets (Ott) 2020. [DOI: 10.1139/facets-2020-0007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Ranaviruses are an emerging group of pathogens capable of infecting all cold-blooded vertebrates. In Europe, ranaviruses pose a particularly potent threat to wild amphibian populations. Since the 1980s research on amphibian-infecting ranaviruses in Europe has been growing. The wide distribution of amphibian populations in Europe, the ease with which many are monitored, and the tractable nature of counterpart ex situ experimental systems have provided researchers with a unique opportunity to study many aspects of host–ranavirus interactions in the wild. These characteristics of European amphibian populations will also enable researchers to lead the way as the field of host–ranavirus interactions progresses. In this review, we provide a summary of the current key knowledge regarding amphibian infecting ranaviruses throughout Europe. We then outline important areas of further research and suggest practical ways each could be pursued. We address the study of potential interactions between the amphibian microbiome and ranaviruses, how pollution may exacerbate ranaviral disease either as direct stressors of amphibians or indirect modification of the amphibian microbiome. Finally, we discuss the need for continued surveillance of ranaviral emergence in the face of climate change.
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Affiliation(s)
- Lewis J. Campbell
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Alice H. Pawlik
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Xavier A. Harrison
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall TR10 9FE, UK
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27
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Tierney BT, Yang Z, Luber JM, Beaudin M, Wibowo MC, Baek C, Mehlenbacher E, Patel CJ, Kostic AD. The Landscape of Genetic Content in the Gut and Oral Human Microbiome. Cell Host Microbe 2019; 26:283-295.e8. [PMID: 31415755 PMCID: PMC6716383 DOI: 10.1016/j.chom.2019.07.008] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/01/2019] [Accepted: 06/19/2019] [Indexed: 02/06/2023]
Abstract
Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were "singletons," or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.
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Affiliation(s)
- Braden T Tierney
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Zhen Yang
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario, Canada
| | - Jacob M Luber
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marc Beaudin
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Marsha C Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Christina Baek
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Aleksandar D Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
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28
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Albecker MA, Belden LK, McCoy MW. Comparative Analysis of Anuran Amphibian Skin Microbiomes Across Inland and Coastal Wetlands. MICROBIAL ECOLOGY 2019; 78:348-360. [PMID: 30535916 DOI: 10.1007/s00248-018-1295-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/15/2018] [Indexed: 05/16/2023]
Abstract
Amphibians host a community of microbes on their skin that helps resist infectious disease via the dual influence of anti-pathogenic microbial species and emergent community dynamics. Many frogs rely on freshwater habitats, but salinization is rapidly increasing saltwater concentrations in wetlands around the globe, increasing the likelihood that frogs will come into contact with salt-contaminated habitats. Currently, we know little about how increased salt exposure will affect the symbiotic relationship between the skin microbes and frog hosts. To better understand how salt exposure in a natural context affects the frog skin microbiome, we use Hyla cinerea, a North American treefrog species that can inhabit brackish wetlands, to explore three questions. First, we determine the extent that microbial communities in the environment and on frog skin are similar across populations. Second, we assess the microbial species richness and relative abundance on frogs from habitats with different salinity levels to determine how salinity affects the microbiome. Third, we test whether the relative abundances of putatively pathogen-resistant bacterial species differ between frogs from inland and coastal environments. We found that the frog microbiome is more similar among frogs than to the microbial communities found in surface water and soil, but there is overlap between frog skin and the environmental samples. Skin microbial community richness did not differ among populations, but the relative abundances of microbes were different across populations and salinities. We found no differences in the relative abundances of the anti-fungal bacteria Janthinobacterium lividum, the genus Pseudomonas, and Serratia marcescens, suggesting that environmental exposure to saltwater has a limited influence on these putatively beneficial bacterial taxa.
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Affiliation(s)
- Molly A Albecker
- Department of Biology, East Carolina University, Greenville, NC, USA.
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Michael W McCoy
- Department of Biology, East Carolina University, Greenville, NC, USA
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29
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Rebollar EA, Bridges T, Hughey MC, Medina D, Belden LK, Harris RN. Integrating the role of antifungal bacteria into skin symbiotic communities of three Neotropical frog species. ISME JOURNAL 2019; 13:1763-1775. [PMID: 30867545 DOI: 10.1038/s41396-019-0388-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/16/2019] [Accepted: 02/28/2019] [Indexed: 01/10/2023]
Abstract
Chytridiomycosis, caused by the pathogen Batrachochytrium dendrobatidis (Bd), has led to population declines and extinctions of frog species around the world. While it is known that symbiotic skin bacteria can play a protective role against pathogens, it is not known how these defensive bacteria are integrated into the bacterial community on amphibian skin. In this study, we used 16S rRNA gene amplicon sequencing, culturing and Bd inhibition bioassays to characterize the communities of skin bacteria on three Neotropical frog species that persist in a Bd-infected area in Panama and determined the abundance and integration of anti-Bd bacteria into the community. We found that the two treefrog species had a similar bacterial community structure, which differed from the more diverse community found on the terrestrial frog. Co-occurrence networks also revealed differences between frog species such that the treefrogs had a significantly higher number of culturable Bd-inhibitory OTUs with high centrality scores compared with the terrestrial frog. We found that culture-dependent OTUs captured between 21 and 39% of the total relative abundance revealed in culture-independent communities. Our results suggest different ecological strategies occurring within skin antifungal communities on host species that have not succumbed to Bd infections in the wild.
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Affiliation(s)
- Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
| | - Tiffany Bridges
- Lake Erie College of Osteopathic Medicine, Bradenton, FL, USA
| | - Myra C Hughey
- Department of Biology, Vassar College, Poughkeepsie, NY, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Reid N Harris
- Department of Biology, James Madison University, MSC 7801, Harrisonburg, VA, USA.,Amphibian Survival Alliance, London, UK
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30
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Urbina J, Galeano SP, Bacigalupe LD, Flechas SV. Disease Ecology: Past and Present for a Better FutureXI Latin American Congress of Herpetology, Quito, Ecuador, July 24–28 2017. COPEIA 2019. [DOI: 10.1643/ch-18-053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Jenny Urbina
- Department of Fisheries and Wildlife, Oregon State University, 2820 SW Campus way, Corvallis, Oregon 97331; . Send reprint requests to this address
| | - Sandra P. Galeano
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Calle 28A 15-09, Bogotá, Colombia 111311
| | - Leonardo D. Bacigalupe
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, Valdivia, Chile
| | - Sandra V. Flechas
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Calle 28A 15-09, Bogotá, Colombia 111311
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31
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Abarca JG, Vargas G, Zuniga I, Whitfield SM, Woodhams DC, Kerby J, McKenzie VJ, Murillo-Cruz C, Pinto-Tomás AA. Assessment of Bacterial Communities Associated With the Skin of Costa Rican Amphibians at La Selva Biological Station. Front Microbiol 2018; 9:2001. [PMID: 30233511 PMCID: PMC6129598 DOI: 10.3389/fmicb.2018.02001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 08/08/2018] [Indexed: 12/15/2022] Open
Abstract
Amphibian skin is a suitable environment for rich communities of microorganisms, both beneficial and detrimental to the host. The amphibian cutaneous microbiota has been hypothesized to play an important role as symbionts, protecting their hosts against disease. Costa Rica has one of the most diverse assemblages of amphibians in the world and we know very little about the microbiota of these tropical animals. For comparison with other studies, we explore the diversity of the skin bacterial communities employing16S rRNA amplicon sequencing of swab samples from twelve species of frogs at La Selva Biological Station in Sarapiquí, Heredia province. The predominant phylum detected in our studies was Proteobacteria, followed by Bacteroidetes and Actinobacteria, with these three phyla representing 89.9% of the total bacterial taxa. At the family level, Sphingobacteriaceae and Comamonadaceae were highly represented among samples. Our results suggest that host species and host family are significant predictors of the variation in microbiota composition. This study helps set the foundation for future research about microbiota composition and resilience to unfavorable conditions, leading to improvement in managing strategies for endangered amphibian species.
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Affiliation(s)
- Juan G. Abarca
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Gabriel Vargas
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Ibrahim Zuniga
- Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Steven M. Whitfield
- Department of Conservation and Research, Zoo Miami, Miami, FL, United States
| | - Douglas C. Woodhams
- Department of Biology, University of Massachusetts, Boston, MA, United States
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jacob Kerby
- Department of Biology, University of South Dakota, Vermillion, SD, United States
| | - Valerie J. McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Adrián A. Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro, Costa Rica
- Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro, Costa Rica
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