scholarly journals Skin bacterial microbiome of a generalist Puerto Rican frog varies along elevation and land use gradients

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3688 ◽  
Author(s):  
Myra C. Hughey ◽  
Janelle A. Pena ◽  
Roberto Reyes ◽  
Daniel Medina ◽  
Lisa K. Belden ◽  
...  
Keyword(s):  
Land Use ◽  
Environmental Conditions ◽  
Batrachochytrium Dendrobatidis ◽  
Environmental Changes ◽  
Environmental Gradients ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Skin Microbiome ◽  
Amphibian Skin ◽  
Microbiome Diversity

Host-associated microbial communities are ubiquitous among animals, and serve important functions. For example, the bacterial skin microbiome of amphibians can play a role in preventing or reducing infection by the amphibian chytrid fungus, Batrachochytrium dendrobatidis. Evidence suggests that environmental bacteria likely serve as a source pool for at least some of the members of the amphibian skin bacterial community, underscoring the potential for local environmental changes to disrupt microbial community source pools that could be critical to the health of host organisms. However, few studies have assessed variation in the amphibian skin microbiome along clear environmental gradients, and so we know relatively little about how local environmental conditions influence microbiome diversity. We sampled the skin bacterial communities of Coqui frogs, Eleutherodactylus coqui (N = 77), along an elevational gradient in eastern Puerto Rico (0–875 m), with transects in two land use types: intact forest (N = 4 sites) and disturbed (N = 3 sites) forest. We found that alpha diversity (as assessed by Shannon, Simpson, and Phylogenetic Diversity indices) varied across sites, but this variation was not correlated with elevation or land use. Beta diversity (community structure), on the other hand, varied with site, elevation and land use, primarily due to changes in the relative abundance of certain bacterial OTUs (∼species) within these communities. Importantly, although microbiome diversity varied, E. coqui maintained a common core microbiota across all sites. Thus, our findings suggest that environmental conditions can influence the composition of the skin microbiome of terrestrial amphibians, but that some aspects of the microbiome remain consistent despite environmental variation.

scholarly journals The Fungicide Chlorothalonil Changes the Amphibian Skin Microbiome: A Potential Factor Disrupting a Host Disease-Protective Trait

2021 ◽  
Vol 1 (1) ◽  
pp. 26-37
Author(s):  
Randall R. Jiménez ◽  
Gilbert Alvarado ◽  
Clemens Ruepert ◽  
Erick Ballestero ◽  
Simone Sommer
Keyword(s):  
Batrachochytrium Dendrobatidis ◽  
Bacterial Community Composition ◽  
Model Organism ◽  
Amplicon Sequencing ◽  
Anthropogenic Factors ◽  
Skin Microbiome ◽  
Amphibian Skin ◽  
16S Rrna Amplicon Sequencing ◽  
Potential Factor ◽  
Inhibitory Bacteria

The skin microbiome is an important part of amphibian immune defenses and protects against pathogens such as the chytrid fungus Batrachochytrium dendrobatidis (Bd), which causes the skin disease chytridiomycosis. Alteration of the microbiome by anthropogenic factors, like pesticides, can impact this protective trait, disrupting its functionality. Chlorothalonil is a widely used fungicide that has been recognized as having an impact on amphibians, but so far, no studies have investigated its effects on amphibian microbial communities. In the present study, we used the amphibian Lithobates vibicarius from the montane forest of Costa Rica, which now appears to persist despite ongoing Bd-exposure, as an experimental model organism. We used 16S rRNA amplicon sequencing to investigate the effect of chlorothalonil on tadpoles’ skin microbiome. We found that exposure to chlorothalonil changes bacterial community composition, with more significant changes at a higher concentration. We also found that a larger number of bacteria were reduced on tadpoles’ skin when exposed to the higher concentration of chlorothalonil. We detected four presumed Bd-inhibitory bacteria being suppressed on tadpoles exposed to the fungicide. Our results suggest that exposure to a widely used fungicide could be impacting host-associated bacterial communities, potentially disrupting an amphibian protective trait against pathogens.

scholarly journals Assembly of the amphibian microbiome is influenced by the effects of land-use change on environmental reservoirs

2020 ◽  
Author(s):  
Elle M. Barnes ◽  
Steve Kutos ◽  
Nina Naghshineh ◽  
Marissa Mesko ◽  
Qing You ◽  
...  
Keyword(s):  
New York ◽  
Land Use ◽  
Microbial Community ◽  
Community Composition ◽  
Batrachochytrium Dendrobatidis ◽  
Pathogenic Fungus ◽  
Microbial Community Composition ◽  
Canopy Cover ◽  
Amphibian Skin ◽  
Regional Species Pool

0AbstractA growing focus in microbial ecology is understanding of how beneficial microbiome function is created and maintained through both stochastic and deterministic assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species pools in the soil and local communities of an amphibian host. To address this, we compared the microbiomes of over 200 Plethodon cinereus salamanders along a 65km land-use gradient in the greater New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that if soil functions as the main regional species pool to amphibian skin, variation in skin microbial community composition would correlate with changes seen in soil. We found that salamanders share many microbial taxa with their soil environment but that these two microbiomes exhibit key differences, especially in the relative abundances of the bacteria phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varied with changes in land-use associated factors such as canopy cover, impervious surface, and concentrations of the soil elements Al, Ni, and Hg, creating site-specific compositions. In addition, high dissimilarity among individual amphibian microbiomes across and within sites suggest that both stochastic and deterministic mechanisms guide assembly of microbes onto amphibian skin, with likely consequences in disease preventative function.

scholarly journals Modelled land use and land cover change emissions – A spatio-temporal comparison of different approaches

2021 ◽  
Author(s):  
Wolfgang A. Obermeier ◽  
Julia E. M. S. Nabel ◽  
Tammas Loughran ◽  
Kerstin Hartung ◽  
Ana Bastos ◽  
...  
Keyword(s):  
Land Use ◽  
Land Cover ◽  
Environmental Conditions ◽  
Agricultural Land ◽  
Environmental Changes ◽  
Land Cover Changes ◽  
Legacy Effects ◽  
Spatio Temporal ◽  
The Impact ◽  
Global Carbon

Abstract. Quantifying the net carbon flux from land use and land cover changes (fLULCC) is critical for understanding the global carbon cycle, and hence, to support climate change mitigation. However, large-scale fLULCC is not directly measurable, but has to be inferred from models instead, such as semi-empirical bookkeeping models, and process-based dynamic global vegetation models (DGVMs). By definition, fLULCC estimates are not directly comparable between these two different model types. As an example, DGVM-based fLULCC in the annual global carbon budgets is estimated under transient environmental forcing and includes the so-called Loss of Additional Sink Capacity (LASC). The LASC accounts for the impact of environmental changes on land carbon storage potential of managed land compared to potential vegetation which is not represented in bookkeeping models. In addition, fLULCC from transient DGVM simulations differs depending on the arbitrary chosen simulation time period and the historical timing of land use and land cover changes (including different accumulation periods for legacy effects). An approximation of fLULCC by DGVMs that is independent of the timing of land use and land cover changes and their legacy effects requires simulations assuming constant pre-industrial or present-day environmental forcings. Here, we analyze three DGVM-derived fLULCC estimations for twelve models within 18 regions and quantify their differences as well as climate- and CO2-induced components. The three estimations stem from the commonly performed simulation with transiently changing environmental conditions and two simulations that keep environmental conditions fixed, at pre-industrial and present-day conditions. Averaged across the models, we find a global fLULCC (under transient conditions) of 2.0 ± 0.6 PgC yr-1 for 2009–2018, of which ∼40 % are attributable to the LASC (0.8 ± 0.3 PgC yr-1). From 1850 onward, fLULCC accumulated to 189 ± 56 PgC with 40 ± 15 PgC from the LASC. Regional hotspots of high cumulative and annual LASC values are found in the USA, China, Brazil, Equatorial Africa and Southeast Asia, mainly due to deforestation for cropland. Distinct negative LASC estimates, in Europe (early reforestation) and from 2000 onward in the Ukraine (recultivation of post-Soviet abandoned agricultural land), indicate that fLULCC estimates in these regions are lower in transient DGVM- compared to bookkeeping-approaches. By unraveling spatio-temporal variability in three alternative DGVM-derived fLULCC estimates, our results call for a harmonized attribution of model-derived fLULCC. We propose an approach that bridges bookkeeping and DGVM approaches for fLULCC estimation by adopting a mean DGVM-ensemble LASC for a defined reference period.

scholarly journals Habitat disturbance Linked with Host Microbiome Dispersion and Bd Dynamics in Temperate Amphibians

2021 ◽  
Author(s):  
Wesley James Neely ◽  
Sasha E Greenspan ◽  
Leigha M Stahl ◽  
Sam D Heraghty ◽  
Vanessa M Marshall ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Population Health ◽  
Batrachochytrium Dendrobatidis ◽  
Habitat Disturbance ◽  
Skin Microbiome ◽  
Amphibian Skin ◽  
Community Interactions ◽  
Microbiome Composition ◽  
Habitat Disturbances ◽  
Anthropogenic Habitat

Abstract Anthropogenic habitat disturbances can dramatically alter ecological community interactions, including host-pathogen dynamics. Recent work has highlighted the potential for habitat disturbances to alter host-associated microbial communities, but the associations between anthropogenic disturbance, host microbiomes, and pathogens are unresolved. Amphibian skin microbial communities are particularly responsive to factors like temperature, physiochemistry, pathogen infection, and environmental microbial reservoirs. Through a field survey on wild populations of Acris crepitans (Hylidae) and Lithobates catesbeianus (Ranidae), we assessed effects of habitat disturbance on environmental bacterial resevoirs, Batrachochytrium dendrobatidis (Bd) infection, and skin microbiome composition. We found higher measures of microbiome dispersion (a measure of community stability) in A. crepitans from more disturbed ponds, supporting the hypothesis that disturbance increases stochasticity in biological communties. We also found that habitat disturbance limited microbiome similarity between locations for both species, suggesting less bacterial exchange in more disturbed areas. Higher disturbance was associated with lower Bd prevalence for A. crepitans, which could signify suboptimal microclimates for Bd in disturbed habitats. In this system we use microbiome dispersion as a metric of population health. Combined, our findings show that reduced microbiome stability stemming from habitat disturbance could compromise population health, even in the absence of pathogenic infection.

scholarly journals Modelled land use and land cover change emissions – a spatio-temporal comparison of different approaches

2021 ◽  
Vol 12 (2) ◽  
pp. 635-670
Author(s):  
Wolfgang A. Obermeier ◽  
Julia E. M. S. Nabel ◽  
Tammas Loughran ◽  
Kerstin Hartung ◽  
Ana Bastos ◽  
...  
Keyword(s):  
Land Use ◽  
Land Cover ◽  
Land Cover Change ◽  
Environmental Conditions ◽  
Agricultural Land ◽  
Environmental Changes ◽  
Land Cover Changes ◽  
Environmental Forcing ◽  
The Impact ◽  
Global Carbon

Abstract. Quantifying the net carbon flux from land use and land cover changes (fLULCC) is critical for understanding the global carbon cycle and, hence, to support climate change mitigation. However, large-scale fLULCC is not directly measurable and has to be inferred from models instead, such as semi-empirical bookkeeping models and process-based dynamic global vegetation models (DGVMs). By definition, fLULCC estimates are not directly comparable between these two different model types. As an important example, DGVM-based fLULCC in the annual global carbon budgets is estimated under transient environmental forcing and includes the so-called loss of additional sink capacity (LASC). The LASC results from the impact of environmental changes on land carbon storage potential of managed land compared to potential vegetation and accumulates over time, which is not captured in bookkeeping models. The fLULCC from transient DGVM simulations, thus, strongly depends on the timing of land use and land cover changes mainly because LASC accumulation is cut off at the end of the simulated period. To estimate the LASC, the fLULCC from pre-industrial DGVM simulations, which is independent of changing environmental conditions, can be used. Additionally, DGVMs using constant present-day environmental forcing enable an approximation of bookkeeping estimates. Here, we analyse these three DGVM-derived fLULCC estimations (under transient, pre-industrial, and present-day forcing) for 12 models within 18 regions and quantify their differences as well as climate- and CO2-induced components and compare them to bookkeeping estimates. Averaged across the models, we find a global fLULCC (under transient conditions) of 2.0±0.6 PgC yr−1 for 2009–2018, of which ∼40 % are attributable to the LASC (0.8±0.3 PgC yr−1). From 1850 onward, the fLULCC accumulated to 189±56 PgC with 40±15 PgC from the LASC. Around 1960, the accumulating nature of the LASC causes global transient fLULCC estimates to exceed estimates under present-day conditions, despite generally increased carbon stocks in the latter. Regional hotspots of high cumulative and annual LASC values are found in the USA, China, Brazil, equatorial Africa, and Southeast Asia, mainly due to deforestation for cropland. Distinct negative LASC estimates in Europe (early reforestation) and from 2000 onward in the Ukraine (recultivation of post-Soviet abandoned agricultural land), indicate that fLULCC estimates in these regions are lower in transient DGVM compared to bookkeeping approaches. Our study unravels the strong dependence of fLULCC estimates on the time a certain land use and land cover change event happened to occur and on the chosen time period for the forcing of environmental conditions in the underlying simulations. We argue for an approach that provides an accounting of the fLULCC that is more robust against these choices, for example by estimating a mean DGVM ensemble fLULCC and LASC for a defined reference period and homogeneous environmental changes (CO2 only).

scholarly journals Evaluation of Amphotericin B and Chloramphenicol as Alternative Drugs for Treatment of Chytridiomycosis and Their Impacts on Innate Skin Defenses

2014 ◽  
Vol 80 (13) ◽  
pp. 4034-4041 ◽  
Author(s):  
Whitney M. Holden ◽  
Alexander R. Ebert ◽  
Peter F. Canning ◽  
Louise A. Rollins-Smith
Keyword(s):  
Amphotericin B ◽  
Batrachochytrium Dendrobatidis ◽  
Amphibian Declines ◽  
Antifungal Drugs ◽  
Skin Microbiome ◽  
Amphibian Skin ◽  
Content Type ◽  
Practical Applications ◽  
Leopard Frogs

ABSTRACTChytridiomycosis, an amphibian skin disease caused by the emerging fungal pathogenBatrachochytrium dendrobatidis, has been implicated in catastrophic global amphibian declines. The result is an alarming decrease in amphibian diversity that is a great concern for the scientific community. Clinical trials testing potential antifungal drugs are needed to identify alternative treatments for amphibians infected with this pathogen. In this study, we quantified the MICs of chloramphenicol (800 μg/ml), amphotericin B (0.8 to 1.6 μg/ml), and itraconazole (Sporanox) (20 ng/ml) againstB. dendrobatidis. Both chloramphenicol and amphotericin B significantly reducedB. dendrobatidisinfection in naturally infected southern leopard frogs (Rana[Lithobates]sphenocephala), although neither drug was capable of complete fungal clearance. Long-term exposure ofR. sphenocephalato these drugs did not inhibit antimicrobial peptide (AMP) synthesis, indicating that neither drug is detrimental to this important innate skin defense. However, we observed that chloramphenicol, but not amphotericin B or itraconazole, inhibited the growth of multipleR. sphenocephalaskin bacterial isolatesin vitroat concentrations below the MIC againstB. dendrobatidis. These results indicate that treatment with chloramphenicol might dramatically alter the protective natural skin microbiome when used as an antifungal agent. This study represents the first examination of the effects of alternative antifungal drug treatments on amphibian innate skin defenses, a crucial step to validating these treatments for practical applications.

Co-infecting pathogen lineages have additive effects on host bacterial communities

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Daniel Medina ◽  
Sasha E Greenspan ◽  
Tamilie Carvalho ◽  
C Guilherme Becker ◽  
Luís Felipe Toledo
Keyword(s):  
Bacterial Diversity ◽  
Batrachochytrium Dendrobatidis ◽  
Infection Intensity ◽  
Alpha Diversity ◽  
Amphibian Declines ◽  
Mixed Infections ◽  
Amphibian Skin ◽  
Experimental Conditions ◽  
Laboratory Conditions ◽  
Skin Bacteria

ABSTRACT Amphibian skin bacteria may confer protection against the fungus Batrachochytrium dendrobatidis (Bd), but responses of skin bacteria to different Bd lineages are poorly understood. The global panzootic lineage (Bd-GPL) has caused amphibian declines and extinctions globally. However, other lineages are enzootic (Bd-Asia-2/Brazil). Increased contact rates between Bd-GPL and enzootic lineages via globalization pose unknown consequences for host-microbiome-pathogen dynamics. We conducted a laboratory experiment and used 16S rRNA amplicon-sequencing to assess: (i) whether two lineages (Bd-Asia-2/Brazil and Bd-GPL) and their recombinant, in single and mixed infections, differentially affect amphibian skin bacteria; (ii) and the changes associated with the transition to laboratory conditions. We determined no clear differences in bacterial diversity among Bd treatments, despite differences in infection intensity. However, we observed an additive effect of mixed infections on bacterial alpha diversity and a potentially antagonistic interaction between Bd genotypes. Additionally, observed changes in community composition suggest a higher ability of Bd-GPL to alter skin bacteria. Lastly, we observed a drastic reduction in bacterial diversity and a change in community structure in laboratory conditions. We provide evidence for complex interactions between Bd genotypes and amphibian skin bacteria during coinfections, and expand on the implications of experimental conditions in ecological studies.

scholarly journals A research framework for projecting ecosystem change in highly diverse tropical mountain ecosystems

Oecologia ◽  
2021 ◽  
Author(s):  
Jörg Bendix ◽  
Nicolay Aguire ◽  
Erwin Beck ◽  
Achim Bräuning ◽  
Roland Brandl ◽  
...  
Keyword(s):  
Land Use ◽  
Functional Traits ◽  
Biomass Production ◽  
Environmental Changes ◽  
Ecosystem Functions ◽  
Ecosystem Change ◽  
Mountain Ecosystems ◽  
Abiotic Conditions ◽  
Research Framework ◽  
Tropical Mountain

AbstractTropical mountain ecosystems are threatened by climate and land-use changes. Their diversity and complexity make projections how they respond to environmental changes challenging. A suitable way are trait-based approaches, by distinguishing between response traits that determine the resistance of species to environmental changes and effect traits that are relevant for species' interactions, biotic processes, and ecosystem functions. The combination of those approaches with land surface models (LSM) linking the functional community composition to ecosystem functions provides new ways to project the response of ecosystems to environmental changes. With the interdisciplinary project RESPECT, we propose a research framework that uses a trait-based response-effect-framework (REF) to quantify relationships between abiotic conditions, the diversity of functional traits in communities, and associated biotic processes, informing a biodiversity-LSM. We apply the framework to a megadiverse tropical mountain forest. We use a plot design along an elevation and a land-use gradient to collect data on abiotic drivers, functional traits, and biotic processes. We integrate these data to build the biodiversity-LSM and illustrate how to test the model. REF results show that aboveground biomass production is not directly related to changing climatic conditions, but indirectly through associated changes in functional traits. Herbivory is directly related to changing abiotic conditions. The biodiversity-LSM informed by local functional trait and soil data improved the simulation of biomass production substantially. We conclude that local data, also derived from previous projects (platform Ecuador), are key elements of the research framework. We specify essential datasets to apply this framework to other mountain ecosystems.

scholarly journals Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hua Zha ◽  
Fengping Liu ◽  
Zongxin Ling ◽  
Kevin Chang ◽  
Jiezuan Yang ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Vital Role ◽  
Rrna Gene ◽  
Beta Glucosidase

AbstractType 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.

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