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Sun QW, Chen JZ, Liao XF, Huang XL, Liu JM. Identification of keystone taxa in rhizosphere microbial communities using different methods and their effects on compounds of the host Cinnamomum migao. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171952. [PMID: 38537823 DOI: 10.1016/j.scitotenv.2024.171952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
Exploring keystone taxa affecting microbial community stability and host function is crucial for understanding ecosystem functions. However, identifying keystone taxa from humongous microbial communities remains challenging. We collected 344 rhizosphere and bulk soil samples from the endangered plant C. migao for 2 years consecutively. Used high-throughput sequencing 16S rDNA and ITS to obtain the composition of bacterial and fungal communities. We explored keystone taxa and the applicability and limitations of five methods (SPEC-OCCU, Zi-Pi, Subnetwork, Betweenness, and Module), as well as the impact of microbial community domain, time series, and rhizosphere boundary on the identification of keystone taxa in the communities. Our results showed that the five methods, identified abundant keystone taxa in rhizosphere and bulk soil microbial communities. However, the keystone taxa shared by the rhizosphere and bulk soil microbial communities over time decreased rapidly decrease in the five methods. Among five methods on the identification of keystone taxa in the rhizosphere community, Module identified 113 taxa, SPEC-OCCU identified 17 taxa, Betweenness identified 3 taxa, Subnetwork identified 3 taxa, and Zi-Pi identified 4 taxa. The keystone taxa are mainly conditionally rare taxa, and their ecological functions include chemoheterotrophy, aerobic chemoheterotrophy, nitrate reduction, and anaerobic photoautotrophy. The results of the random forest model and structural equation model predict that keystone taxa Mortierella and Ellin6513 may have an effects on the accumulation of 1, 4, 7, - Cycloundecatriene, 1, 5, 9, 9-tetramethyl-, Z, Z, Z-, beta-copaene, bicyclogermacrene, 1,8-Cineole in C. migao fruits, but their effects still need further evidence. Our study evidence an unstable microbial community in the bulk soil, and the definition of microbial boundary and ecologically functional affected the identification of keystone taxa in the community. Subnetwork and Module are more in line with the definition of keystone taxa in microbial ecosystems in terms of maintaining community stability and hosting function.
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Affiliation(s)
- Qing-Wen Sun
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; Guizhou Province Key Laboratory of Chinese Pharmacology and Pharmacognosy, 550025, China
| | - Jing-Zhong Chen
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; Guizhou Province Key Laboratory of Chinese Pharmacology and Pharmacognosy, 550025, China.
| | | | | | - Ji-Ming Liu
- College of Forestry, Guizhou University, Guiyang 550025, China
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Cortazar-Chinarro M, Richter-Boix A, Rödin-Mörch P, Halvarsson P, Logue JB, Laurila A, Höglund J. Association between the skin microbiome and MHC class II diversity in an amphibian. Mol Ecol 2024; 33:e17198. [PMID: 37933583 DOI: 10.1111/mec.17198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023]
Abstract
Microbiomes play an important role in determining the ecology and behaviour of their hosts. However, questions remain pertaining to how host genetics shape microbiomes, and how microbiome composition influences host fitness. We explored the effects of geography, evolutionary history and host genetics on the skin microbiome diversity and structure in a widespread amphibian. More specifically, we examined the association between bacterial diversity and composition and the major histocompatibility complex class II exon 2 diversity in 12 moor frog (Rana arvalis) populations belonging to two geographical clusters that show signatures of past and ongoing differential selection. We found that while bacterial alpha diversity did not differ between the two clusters, MHC alleles/supertypes and genetic diversity varied considerably depending on geography and evolutionary history. Bacterial alpha diversity was positively correlated with expected MHC heterozygosity and negatively with MHC nucleotide diversity. Furthermore, bacterial community composition showed significant variation between the two geographical clusters and between specific MHC alleles/supertypes. Our findings emphasize the importance of historical demographic events on hologenomic variation and provide new insights into how immunogenetic host variability and microbial diversity may jointly influence host fitness with consequences for disease susceptibility and population persistence.
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Affiliation(s)
- M Cortazar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- MEMEG/Department of Biology, Lund University, Lund, Sweden
- Department of Earth Ocean and Atmospheric Sciences, Faculty of Science 2020-2207, University of British Columbia, Vancouver, British Columbia, Canada
| | - A Richter-Boix
- Department of Political and Social Science, Pompeu Fabra University, Barcelona, Spain
| | - P Rödin-Mörch
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - P Halvarsson
- Parasitology/Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - J B Logue
- Aquatic Ecology/Department of Biology, Lund University, Lund, Sweden
- SLU University Library, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - A Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - J Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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Ramírez-Barahona S, González-Serrano FM, Martínez-Ugalde E, Soto-Pozos A, Parra-Olea G, Rebollar EA. Host phylogeny and environment shape the diversity of salamander skin bacterial communities. Anim Microbiome 2023; 5:52. [PMID: 37828573 PMCID: PMC10571319 DOI: 10.1186/s42523-023-00271-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023] Open
Abstract
The composition and diversity of animal-associated microbial communities are shaped by multiple ecological and evolutionary processes acting at different spatial and temporal scales. Skin microbiomes are thought to be strongly influenced by the environment due to the direct interaction of the host's skin with the external media. As expected, the diversity of amphibian skin microbiomes is shaped by climate and host sampling habitats, whereas phylogenetic effects appear to be weak. However, the relative strength of phylogenetic and environmental effects on salamander skin microbiomes remains poorly understood. Here, we analysed sequence data from 1164 adult salamanders of 44 species to characterise and compare the diversity and composition of skin bacteria. We assessed the relative contribution of climate, host sampling habitat, and host phylogeny to the observed patterns of bacterial diversity. We found that bacterial alpha diversity was mainly associated with host sampling habitat and climate, but that bacterial beta diversity was more strongly associated with host taxonomy and phylogeny. This phylogenetic effect predominantly occurred at intermediate levels of host divergence (0-50 Mya). Our results support the importance of environmental factors shaping the diversity of salamander skin microbiota, but also support host phylogenetic history as a major factor shaping these bacterial communities.
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Affiliation(s)
- S Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - F M González-Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - E Martínez-Ugalde
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - A Soto-Pozos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - G Parra-Olea
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - E A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
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Weitzman CL, Kaestli M, Rose A, Hudson CM, Gibb K, Brown GP, Shine R, Christian K. Geographic variation in bacterial assemblages on cane toad skin is influenced more by local environments than by evolved changes in host traits. Biol Open 2023; 12:286922. [PMID: 36745034 PMCID: PMC9932784 DOI: 10.1242/bio.059641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
Bacterial assemblages on amphibian skin may play an important role in protecting hosts against infection. In hosts that occur over a range of environments, geographic variation in composition of bacterial assemblages might be due to direct effects of local factors and/or to evolved characteristics of the host. Invasive cane toads (Rhinella marina) are an ideal candidate to evaluate environmental and genetic mechanisms, because toads have evolved major shifts in physiology, morphology, and behavior during their brief history in Australia. We used samples from free-ranging toads to quantify site-level differences in bacterial assemblages and a common-garden experiment to see if those differences disappeared when toads were raised under standardised conditions at one site. The large differences in bacterial communities on toads from different regions were not seen in offspring raised in a common environment. Relaxing bacterial clustering to operational taxonomic units in place of amplicon sequence variants likewise revealed high similarity among bacterial assemblages on toads in the common-garden study, and with free-ranging toads captured nearby. Thus, the marked geographic divergence in bacterial assemblages on wild-caught cane toads across their Australian invasion appears to result primarily from local environmental effects rather than evolved shifts in the host.
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Affiliation(s)
- Chava L. Weitzman
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0909, Australia,Author for correspondence ()
| | - Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0909, Australia
| | - Alea Rose
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0909, Australia
| | - Cameron M. Hudson
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0909, Australia
| | - Gregory P. Brown
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Richard Shine
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Keith Christian
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0909, Australia
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Worsley SF, Davies CS, Mannarelli ME, Komdeur J, Dugdale HL, Richardson DS. Assessing the causes and consequences of gut mycobiome variation in a wild population of the Seychelles warbler. MICROBIOME 2022; 10:242. [PMID: 36575553 PMCID: PMC9795730 DOI: 10.1186/s40168-022-01432-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Considerable research has focussed on the importance of bacterial communities within the vertebrate gut microbiome (GM). However, studies investigating the significance of other microbial kingdoms, such as fungi, are notably lacking, despite their potential to influence host processes. Here, we characterise the fungal GM of individuals living in a natural population of Seychelles warblers (Acrocephalus sechellensis). We evaluate the extent to which fungal GM structure is shaped by environment and host factors, including genome-wide heterozygosity and variation at key immune genes (major histocompatibility complex (MHC) and Toll-like receptor (TLR)). Importantly, we also explore the relationship between fungal GM differences and subsequent host survival. To our knowledge, this is the first time that the genetic drivers and fitness consequences of fungal GM variation have been characterised for a wild vertebrate population. RESULTS Environmental factors, including season and territory quality, explain the largest proportion of variance in the fungal GM. In contrast, neither host age, sex, genome-wide heterozygosity, nor TLR3 genotype was associated with fungal GM differences in Seychelles warblers. However, the presence of four MHC-I alleles and one MHC-II allele was associated with changes in fungal GM alpha diversity. Changes in fungal richness ranged from between 1 and 10 sequencing variants lost or gained; in some cases, this accounted for 20% of the fungal variants carried by an individual. In addition to this, overall MHC-I allelic diversity was associated with small, but potentially important, changes in fungal GM composition. This is evidenced by the fact that fungal GM composition differed between individuals that survived or died within 7 months of being sampled. CONCLUSIONS Our results suggest that environmental factors play a primary role in shaping the fungal GM, but that components of the host immune system-specifically the MHC-may also contribute to the variation in fungal communities across individuals within wild populations. Furthermore, variation in the fungal GM can be associated with differential survival in the wild. Further work is needed to establish the causality of such relationships and, thus, the extent to which components of the GM may impact host evolution. Video Abstract.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
| | - Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Maria-Elena Mannarelli
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
- Nature Seychelles, Roche Caiman, Mahé, Republic of Seychelles.
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Goodwin KB, Hutchinson JD, Gompert Z. Spatiotemporal and ontogenetic variation, microbial selection, and predicted Bd-inhibitory function in the skin-associated microbiome of a Rocky Mountain amphibian. Front Microbiol 2022; 13:1020329. [PMID: 36583053 PMCID: PMC9792605 DOI: 10.3389/fmicb.2022.1020329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
Host-associated microbiomes play important roles in host health and pathogen defense. In amphibians, the skin-associated microbiota can contribute to innate immunity with potential implications for disease management. Few studies have examined season-long temporal variation in the amphibian skin-associated microbiome, and the interactions between bacteria and fungi on amphibian skin remain poorly understood. We characterize season-long temporal variation in the skin-associated microbiome of the western tiger salamander (Ambystoma mavortium) for both bacteria and fungi between sites and across salamander life stages. Two hundred seven skin-associated microbiome samples were collected from salamanders at two Rocky Mountain lakes throughout the summer and fall of 2018, and 127 additional microbiome samples were collected from lake water and lake substrate. We used 16S rRNA and ITS amplicon sequencing with Bayesian Dirichlet-multinomial regression to estimate the relative abundances of bacterial and fungal taxa, test for differential abundance, examine microbial selection, and derive alpha diversity. We predicted the ability of bacterial communities to inhibit the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), a cutaneous fungal pathogen, using stochastic character mapping and a database of Bd-inhibitory bacterial isolates. For both bacteria and fungi, we observed variation in community composition through time, between sites, and with salamander age and life stage. We further found that temporal trends in community composition were specific to each combination of salamander age, life stage, and lake. We found salamander skin to be selective for microbes, with many taxa disproportionately represented relative to the environment. Salamander skin appeared to select for predicted Bd-inhibitory bacteria, and we found a negative relationship between the relative abundances of predicted Bd-inhibitory bacteria and Bd. We hope these findings will assist in the conservation of amphibian species threatened by chytridiomycosis and other emerging diseases.
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Affiliation(s)
- Kenen B. Goodwin
- Department of Watershed Sciences, Utah State University, Logan, UT, United States,Department of Wildland Resources, Utah State University, Logan, UT, United States,*Correspondence: Kenen B. Goodwin,
| | - Jaren D. Hutchinson
- Department of Wildland Resources, Utah State University, Logan, UT, United States
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, UT, United States
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Martínez-Ugalde E, Ávila-Akerberg V, González Martínez TM, Vázquez Trejo M, Zavala Hernández D, Anaya-Morales SL, Rebollar EA. The skin microbiota of the axolotl Ambystoma altamirani is highly influenced by metamorphosis and seasonality but not by pathogen infection. Anim Microbiome 2022; 4:63. [PMID: 36503640 PMCID: PMC9743558 DOI: 10.1186/s42523-022-00215-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/16/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Microbiomes have been increasingly recognized as major contributors to host health and survival. In amphibians, bacterial members of the skin microbiota protect their hosts by inhibiting the growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). Even though several studies describe the influence of biotic and abiotic factors over the skin microbiota, it remains unclear how these symbiotic bacterial communities vary across time and development. This is particularly relevant for species that undergo metamorphosis as it has been shown that host physiology and ecology drastically influence diversity of the skin microbiome. RESULTS We found that the skin bacterial communities of the axolotl A. altamirani are largely influenced by the metamorphic status of the host and by seasonal variation of abiotic factors such as temperature, pH, dissolved oxygen and conductivity. Despite high Bd prevalence in these samples, the bacterial diversity of the skin microbiota did not differ between infected and non-infected axolotls, although relative abundance of particular bacteria were correlated with Bd infection intensity. CONCLUSIONS Our work shows that metamorphosis is a crucial process that shapes skin bacterial communities and that axolotls under different developmental stages respond differently to environmental seasonal variations. Moreover, this study greatly contributes to a better understanding of the factors that shape amphibian skin microbiota, especially in a largely underexplored group like axolotls (Mexican Ambystoma species).
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Affiliation(s)
- Emanuel Martínez-Ugalde
- grid.9486.30000 0001 2159 0001Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Víctor Ávila-Akerberg
- grid.412872.a0000 0001 2174 6731Instituto de Ciencias Agropecuarias y Rurales, Universidad Autónoma del Estado de México, Toluca, Mexico
| | - Tanya M. González Martínez
- grid.9486.30000 0001 2159 0001Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Montserrat Vázquez Trejo
- grid.9486.30000 0001 2159 0001Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Dalia Zavala Hernández
- grid.9486.30000 0001 2159 0001Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sara Lucia Anaya-Morales
- grid.9486.30000 0001 2159 0001Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico ,grid.251313.70000 0001 2169 2489 Department of Biology, University of Mississippi, Oxford, MS USA
| | - Eria A. Rebollar
- grid.9486.30000 0001 2159 0001Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Martins RA, Greenspan SE, Medina D, Buttimer S, Marshall VM, Neely WJ, Siomko S, Lyra ML, Haddad CFB, São-Pedro V, Becker CG. Signatures of functional bacteriome structure in a tropical direct-developing amphibian species. Anim Microbiome 2022; 4:40. [PMID: 35672870 PMCID: PMC9172097 DOI: 10.1186/s42523-022-00188-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Host microbiomes may differ under the same environmental conditions and these differences may influence susceptibility to infection. Amphibians are ideal for comparing microbiomes in the context of disease defense because hundreds of species face infection with the skin-invading microbe Batrachochytrium dendrobatidis (Bd), and species richness of host communities, including their skin bacteria (bacteriome), may be exceptionally high. We conducted a landscape-scale Bd survey of six co-occurring amphibian species in Brazil’s Atlantic Forest. To test the bacteriome as a driver of differential Bd prevalence, we compared bacteriome composition and co-occurrence network structure among the six focal host species.
Results
Intensive sampling yielded divergent Bd prevalence in two ecologically similar terrestrial-breeding species, a group with historically low Bd resistance. Specifically, we detected the highest Bd prevalence in Ischnocnema henselii but no Bd detections in Haddadus binotatus. Haddadus binotatus carried the highest bacteriome alpha and common core diversity, and a modular network partitioned by negative co-occurrences, characteristics associated with community stability and competitive interactions that could inhibit Bd colonization.
Conclusions
Our findings suggest that community structure of the bacteriome might drive Bd resistance in H. binotatus, which could guide microbiome manipulation as a conservation strategy to protect diverse radiations of direct-developing species from Bd-induced population collapses.
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Longo AV. Metabarcoding approaches in amphibian disease ecology: Disentangling the functional contributions of skin bacteria on disease outcome. Integr Comp Biol 2022; 62:252-261. [PMID: 35640913 DOI: 10.1093/icb/icac062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/10/2022] [Accepted: 05/25/2022] [Indexed: 01/09/2023] Open
Abstract
Molecular technologies have revolutionized the field of wildlife disease ecology, allowing the detection of outbreaks, novel pathogens, and invasive strains. In particular, metabarcoding approaches, defined here as tools used to amplify and sequence universal barcodes from a single sample (e.g., 16S rRNA for bacteria, ITS for fungi, 18S rRNA for eukaryotes), are expanding our traditional view of host-pathogen dynamics by integrating microbial interactions that modulate disease outcome. Here, I provide an analysis from the perspective of the field of amphibian disease ecology, where the emergence of multi-host pathogens has caused global declines and species extinctions. I re-analyzed an experimental mesocosm dataset to infer the functional profiles of the skin microbiomes of coqui frogs (Eleutherodactylus coqui), an amphibian species that is consistently found infected with the fungal pathogen Batrachochytrium dendrobatidis and has high turnover of skin bacteria driven by seasonal shifts. I found that the metabolic activities of microbiomes operate at different capacities depending on the season. Global enrichment of predicted functions was more prominent during the warm-wet season, indicating that microbiomes during the cool-dry season were either depauperate, resistant to new bacterial colonization, or that their functional space was more saturated. These findings suggest important avenues to investigate how microbes regulate population growth and contribute to host physiological processes. Overall, this study highlights the current challenges and future opportunities in the application of metabarcoding to investigate the causes and consequences of disease in wild systems.
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Affiliation(s)
- Ana V Longo
- University of Florida, Department of Biology, PO Box 118525, Gainesville, FL
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