Jos Kielgast | University of Copenhagen (original) (raw)

Papers by Jos Kielgast

Nature Ecology & Evolution

Animal-associated microbiomes are integral to host health, yet key biotic and abiotic factors tha... more Animal-associated microbiomes are integral to host health, yet key biotic and abiotic factors that shape host-associated microbial communities at the global scale remain poorly understood. We investigated global patterns in amphibian skin bacterial communities, incorporating samples from 2,349 individuals representing 205 amphibian species across a broad biogeographic range. We analyzed how biotic and abiotic factors correlate with skin microbial communities using multiple statistical approaches. Global amphibian skin bacterial richness was consistently correlated with temperature-associated factors. We found more diverse skin microbiomes in environments with colder winters and less stable thermal conditions, compared to environments with warm winters and less annual temperature variation. We used bioinformatically predicted bacterial growth rates, dormancy genes, and antibiotic synthesis genes, as well as inferred bacterial thermal growth optima to propose mechanistic hypotheses that may explain the observed patterns. We conclude that temporal and spatial characteristics of the host's macro-environment mediate microbial diversity.

Molecular ecology, Jan 28, 2017

Organismal traits interact with environmental variation to mediate how species respond to shared ... more Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a shared climatic and geological history. Our species-specific estimates of climatic suitability through time are consistent with temporal and spatial heterogeneity in diversification among the species complexes, indicating that differences in ecological breadth may partly explain these idiosyncratic patterns. Likewise, we demonstrated that fluctuating sea levels periodically exposed a land bridge connecting Bioko Island with the mainlan...

Diseases of Aquatic Organisms, 2017

The ribosomal gene complex is a multi-copy region that is widely used for phylogenetic analyses o... more The ribosomal gene complex is a multi-copy region that is widely used for phylogenetic analyses of organisms from all 3 domains of life. In fungi, the copy number of the internal transcribed spacer (ITS) is used to detect abundance of pathogens causing diseases such as chytridiomycosis in amphibians and white nose syndrome in bats. Chytridiomycosis is caused by the fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), and is responsible for declines and extinctions of amphibians worldwide. Over a decade ago, a qPCR assay was developed to determine Bd prevalence and pathogen load. Here, we demonstrate the effect that ITS copy number variation in Bd strains can have on the estimation of prevalence and pathogen load. We used data sets from different amphibian species to simulate how ITS copy number affects prevalence and pathogen load. In addition, we tested 2 methods (gBlocks ® synthetic standards and digital PCR) to determine ITS copy number in Bd strains. Our results show that assumptions about the ITS copy number can lead to under-or overestimation of Bd prevalence and pathogen load. The use of synthetic standards replicated previously published estimates of ITS copy number, whereas dPCR resulted in estimates that were consistently lower than previously published estimates. Standardizing methods will assist with comparison across studies and produce reliable estimates of prevalence and pathogen load in the wild, while using the same Bd strain for exposure experiments and zoospore standards in qPCR remains the best method for estimating parameters used in epidemiological studies.

Molecular phylogenetics and evolution, Jan 21, 2016

The Mascarene ridged frog, Ptychadena mascareniensis, is a species complex that includes numerous... more The Mascarene ridged frog, Ptychadena mascareniensis, is a species complex that includes numerous lineages occurring mostly in humid savannas and open forests of mainland Africa, Madagascar, the Seychelles, and the Mascarene Islands. Sampling across this broad distribution presents an opportunity to examine the genetic differentiation within this complex and to investigate how the evolution of bioclimatic niches may have shaped current biogeographic patterns. Using model-based phylogenetic methods and molecular-clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the group based on mitochondrial 16S rRNA and cytochrome b (cytb) genes and the nuclear RAG1 gene from 173 individuals. Haplotype networks were reconstructed and species boundaries were investigated using three species-delimitation approaches: Bayesian generalized mixed Yule-coalescent model (bGMYC), the Poisson Tree Process model (PTP) and a cluster algorithm (SpeciesIdentifier). Estimates o...

Biological Conservation, 2015

T he world's second largest continuous tropical rain forest is found in the Congo Basin. It c... more T he world's second largest continuous tropical rain forest is found in the Congo Basin. It comprises a vast river drainage area intriguingly similar to that of the Amazon and includes more than 15 of the global WWF terrestrial ecoregions (Olson et al. 2001; de Wasseige et al. 2009). Fascinatingly, this notable area for tropical biodiversity harbours one of the least known herpetofaunas on our planet (Schiøtz 2006; Andreone et al. 2008). Most of the available knowledge derives from expeditions in the beginning of last century and a few prominent collections during the colonial regimes (e.g. Boulenger 1919; Noble 1924; Ahl 1931; Laurent 1943, 1950, 1972). Comparing the accumulated number of described species through time from the DRC with that of Brazil (The majority of the Congo and Amazon basins respectively) provide an illustration of this (fig. 1). A clearly exponential increase in species numbers since the fifties as observed for Brazil (as well as on global scale) has faile...

T he world's second largest continuous tropical rain forest is found in the Congo Basin. It c... more T he world's second largest continuous tropical rain forest is found in the Congo Basin. It comprises a vast river drainage area intriguingly similar to that of the Amazon and includes more than 15 of the global WWF terrestrial ecoregions (Olson et al. 2001; de Wasseige et al. 2009). Fascinatingly, this notable area for tropical biodiversity harbours one of the least known herpetofaunas on our planet (Schiøtz 2006; Andreone et al. 2008). Most of the available knowledge derives from expeditions in the beginning of last century and a few prominent collections during the colonial regimes (e.g. Boulenger 1919; Noble 1924; Ahl 1931; Laurent 1943, 1950, 1972). Comparing the accumulated number of described species through time from the DRC with that of Brazil (The majority of the Congo and Amazon basins respectively) provide an illustration of this (fig. 1). A clearly exponential increase in species numbers since the fifties as observed for Brazil (as well as on global scale) has faile...

An important driver of amphibian declines is chytridiomy-cosis, a disease caused by the pathogen ... more An important driver of amphibian declines is chytridiomy-cosis, a disease caused by the pathogen Batrachochytrium dendrobatidis (Bd; Berger et al. 1998; Daszak et al. 1999, 2003; Ron and Merino-Viteri 2000; Bosch et al. 2001; Collins and Stor-fer 2003, Ron et al. 2003; La Marca et al. 2005; Wake and Vre-denburg 2008; Walker et al. 2010). Bd is now known to be an emerging pathogen that is rapidly expanding its global range (Fisher et al. 2009) and now has attained a global distribution on all continents that contain amphibians (www.bd-maps.net). Research by Weldon et al. (2004) on the potential origin of Bd suggests that the panzootic originated in South Africa and has perhaps been dispersed by international trade in amphibians, becoming established around the word (Rödder et al. 2009). To date, the rapid and widespread distribution of Bd infection across hundreds of amphibian species is alarming. In Spain, outbreaks of chytridiomycosis and mass mortali-ties has been reported in many...

PLoS ONE, 2014

Pathogenesis is strongly dependent on microbial context, but development of probiotic therapies h... more Pathogenesis is strongly dependent on microbial context, but development of probiotic therapies has neglected the impact of ecological interactions. Dynamics among microbial communities, host immune responses, and environmental conditions may alter the effect of probiotics in human and veterinary medicine, agriculture and aquaculture, and the proposed treatment of emerging wildlife and zoonotic diseases such as those occurring on amphibians or vectored by mosquitoes.

Diseases of Aquatic Organisms, 2009

A survey for the amphibian pathogens ranavirus and Batrachochytrium dendrobatidis (Bd) was conduc... more A survey for the amphibian pathogens ranavirus and Batrachochytrium dendrobatidis (Bd) was conducted in Denmark during August and September 2008. The public was encouraged via the media to register unusual mortalities in a web-based survey. All members of the public that registered cases were interviewed by phone and 10 cases were examined on suspicion of diseaseinduced mortality. All samples were negative for Bd. Ranavirus was isolated from 2 samples of recently dead frogs collected during a mass mortality event in an artificial pond near Slagelse, Denmark. The identity of the virus was confirmed by immunofluorescent antibody test. Sequencing of the major capsid protein gene showed the isolate had more than 97.3% nucleotide homology to 6 other ranaviruses.

Biodiversity Hotspots, 2011

Worldwide amphibian diversity is threatened through the emergence of the disease chytridiomycosis... more Worldwide amphibian diversity is threatened through the emergence of the disease chytridiomycosis, caused by the amphibian chytrid fungus. This pathogen apparently is absent from the amphibian hotspot Madagascar. However, an extinction risk assessment based on environmental niche modelling suggests that a major portion of this island is climatically highly suitable to the fungus. This includes regions of high amphibian species richness. Many species have their entire geographic range in such areas and are at the same time predicted to suffer potentially from chytridiomycosis due to their life history traits. Human-mediated dissemination of the chytrid fungus to Madagascar is considered likely. In particular, there may be a high risk of accidental cointroduction via the animal trade. Severe decline and possibly extinction are expected in a postemergence scenario on Madagascar with more than 270 described and numerous undescribed anuran amphibian species under threat. Effective responses to this potential threat might include (1) an increased attention to 'biosecurity', including the consequent implementation of measures to avoid the introduction of the chytrid fungus, (2) the development of breeding procedures for representatives of all major clades of Madagascan amphibians as a 'pre-emergency prophylaxis' and (3) the development of plans for 'emergency response'.

Biodiversity Hotspots, 2011

Worldwide amphibian diversity is threatened through the emergence of the disease chytridiomycosis... more Worldwide amphibian diversity is threatened through the emergence of the disease chytridiomycosis, caused by the amphibian chytrid fungus. This pathogen apparently is absent from the amphibian hotspot Madagascar. However, an extinction risk assessment based on environmental niche modelling suggests that a major portion of this island is climatically highly suitable to the fungus. This includes regions of high amphibian species richness. Many species have their entire geographic range in such areas and are at the same time predicted to suffer potentially from chytridiomycosis due to their life history traits. Human-mediated dissemination of the chytrid fungus to Madagascar is considered likely. In particular, there may be a high risk of accidental cointroduction via the animal trade. Severe decline and possibly extinction are expected in a postemergence scenario on Madagascar with more than 270 described and numerous undescribed anuran amphibian species under threat. Effective responses to this potential threat might include (1) an increased attention to 'biosecurity', including the consequent implementation of measures to avoid the introduction of the chytrid fungus, (2) the development of breeding procedures for representatives of all major clades of Madagascan amphibians as a 'pre-emergency prophylaxis' and (3) the development of plans for 'emergency response'.

Nature Ecology & Evolution

Animal-associated microbiomes are integral to host health, yet key biotic and abiotic factors tha... more Animal-associated microbiomes are integral to host health, yet key biotic and abiotic factors that shape host-associated microbial communities at the global scale remain poorly understood. We investigated global patterns in amphibian skin bacterial communities, incorporating samples from 2,349 individuals representing 205 amphibian species across a broad biogeographic range. We analyzed how biotic and abiotic factors correlate with skin microbial communities using multiple statistical approaches. Global amphibian skin bacterial richness was consistently correlated with temperature-associated factors. We found more diverse skin microbiomes in environments with colder winters and less stable thermal conditions, compared to environments with warm winters and less annual temperature variation. We used bioinformatically predicted bacterial growth rates, dormancy genes, and antibiotic synthesis genes, as well as inferred bacterial thermal growth optima to propose mechanistic hypotheses that may explain the observed patterns. We conclude that temporal and spatial characteristics of the host's macro-environment mediate microbial diversity.

Molecular ecology, Jan 28, 2017

Organismal traits interact with environmental variation to mediate how species respond to shared ... more Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a shared climatic and geological history. Our species-specific estimates of climatic suitability through time are consistent with temporal and spatial heterogeneity in diversification among the species complexes, indicating that differences in ecological breadth may partly explain these idiosyncratic patterns. Likewise, we demonstrated that fluctuating sea levels periodically exposed a land bridge connecting Bioko Island with the mainlan...

Diseases of Aquatic Organisms, 2017

The ribosomal gene complex is a multi-copy region that is widely used for phylogenetic analyses o... more The ribosomal gene complex is a multi-copy region that is widely used for phylogenetic analyses of organisms from all 3 domains of life. In fungi, the copy number of the internal transcribed spacer (ITS) is used to detect abundance of pathogens causing diseases such as chytridiomycosis in amphibians and white nose syndrome in bats. Chytridiomycosis is caused by the fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), and is responsible for declines and extinctions of amphibians worldwide. Over a decade ago, a qPCR assay was developed to determine Bd prevalence and pathogen load. Here, we demonstrate the effect that ITS copy number variation in Bd strains can have on the estimation of prevalence and pathogen load. We used data sets from different amphibian species to simulate how ITS copy number affects prevalence and pathogen load. In addition, we tested 2 methods (gBlocks ® synthetic standards and digital PCR) to determine ITS copy number in Bd strains. Our results show that assumptions about the ITS copy number can lead to under-or overestimation of Bd prevalence and pathogen load. The use of synthetic standards replicated previously published estimates of ITS copy number, whereas dPCR resulted in estimates that were consistently lower than previously published estimates. Standardizing methods will assist with comparison across studies and produce reliable estimates of prevalence and pathogen load in the wild, while using the same Bd strain for exposure experiments and zoospore standards in qPCR remains the best method for estimating parameters used in epidemiological studies.

Molecular phylogenetics and evolution, Jan 21, 2016

The Mascarene ridged frog, Ptychadena mascareniensis, is a species complex that includes numerous... more The Mascarene ridged frog, Ptychadena mascareniensis, is a species complex that includes numerous lineages occurring mostly in humid savannas and open forests of mainland Africa, Madagascar, the Seychelles, and the Mascarene Islands. Sampling across this broad distribution presents an opportunity to examine the genetic differentiation within this complex and to investigate how the evolution of bioclimatic niches may have shaped current biogeographic patterns. Using model-based phylogenetic methods and molecular-clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the group based on mitochondrial 16S rRNA and cytochrome b (cytb) genes and the nuclear RAG1 gene from 173 individuals. Haplotype networks were reconstructed and species boundaries were investigated using three species-delimitation approaches: Bayesian generalized mixed Yule-coalescent model (bGMYC), the Poisson Tree Process model (PTP) and a cluster algorithm (SpeciesIdentifier). Estimates o...

Biological Conservation, 2015

T he world's second largest continuous tropical rain forest is found in the Congo Basin. It c... more T he world's second largest continuous tropical rain forest is found in the Congo Basin. It comprises a vast river drainage area intriguingly similar to that of the Amazon and includes more than 15 of the global WWF terrestrial ecoregions (Olson et al. 2001; de Wasseige et al. 2009). Fascinatingly, this notable area for tropical biodiversity harbours one of the least known herpetofaunas on our planet (Schiøtz 2006; Andreone et al. 2008). Most of the available knowledge derives from expeditions in the beginning of last century and a few prominent collections during the colonial regimes (e.g. Boulenger 1919; Noble 1924; Ahl 1931; Laurent 1943, 1950, 1972). Comparing the accumulated number of described species through time from the DRC with that of Brazil (The majority of the Congo and Amazon basins respectively) provide an illustration of this (fig. 1). A clearly exponential increase in species numbers since the fifties as observed for Brazil (as well as on global scale) has faile...

T he world's second largest continuous tropical rain forest is found in the Congo Basin. It c... more T he world's second largest continuous tropical rain forest is found in the Congo Basin. It comprises a vast river drainage area intriguingly similar to that of the Amazon and includes more than 15 of the global WWF terrestrial ecoregions (Olson et al. 2001; de Wasseige et al. 2009). Fascinatingly, this notable area for tropical biodiversity harbours one of the least known herpetofaunas on our planet (Schiøtz 2006; Andreone et al. 2008). Most of the available knowledge derives from expeditions in the beginning of last century and a few prominent collections during the colonial regimes (e.g. Boulenger 1919; Noble 1924; Ahl 1931; Laurent 1943, 1950, 1972). Comparing the accumulated number of described species through time from the DRC with that of Brazil (The majority of the Congo and Amazon basins respectively) provide an illustration of this (fig. 1). A clearly exponential increase in species numbers since the fifties as observed for Brazil (as well as on global scale) has faile...

An important driver of amphibian declines is chytridiomy-cosis, a disease caused by the pathogen ... more An important driver of amphibian declines is chytridiomy-cosis, a disease caused by the pathogen Batrachochytrium dendrobatidis (Bd; Berger et al. 1998; Daszak et al. 1999, 2003; Ron and Merino-Viteri 2000; Bosch et al. 2001; Collins and Stor-fer 2003, Ron et al. 2003; La Marca et al. 2005; Wake and Vre-denburg 2008; Walker et al. 2010). Bd is now known to be an emerging pathogen that is rapidly expanding its global range (Fisher et al. 2009) and now has attained a global distribution on all continents that contain amphibians (www.bd-maps.net). Research by Weldon et al. (2004) on the potential origin of Bd suggests that the panzootic originated in South Africa and has perhaps been dispersed by international trade in amphibians, becoming established around the word (Rödder et al. 2009). To date, the rapid and widespread distribution of Bd infection across hundreds of amphibian species is alarming. In Spain, outbreaks of chytridiomycosis and mass mortali-ties has been reported in many...

PLoS ONE, 2014

Pathogenesis is strongly dependent on microbial context, but development of probiotic therapies h... more Pathogenesis is strongly dependent on microbial context, but development of probiotic therapies has neglected the impact of ecological interactions. Dynamics among microbial communities, host immune responses, and environmental conditions may alter the effect of probiotics in human and veterinary medicine, agriculture and aquaculture, and the proposed treatment of emerging wildlife and zoonotic diseases such as those occurring on amphibians or vectored by mosquitoes.

Diseases of Aquatic Organisms, 2009

A survey for the amphibian pathogens ranavirus and Batrachochytrium dendrobatidis (Bd) was conduc... more A survey for the amphibian pathogens ranavirus and Batrachochytrium dendrobatidis (Bd) was conducted in Denmark during August and September 2008. The public was encouraged via the media to register unusual mortalities in a web-based survey. All members of the public that registered cases were interviewed by phone and 10 cases were examined on suspicion of diseaseinduced mortality. All samples were negative for Bd. Ranavirus was isolated from 2 samples of recently dead frogs collected during a mass mortality event in an artificial pond near Slagelse, Denmark. The identity of the virus was confirmed by immunofluorescent antibody test. Sequencing of the major capsid protein gene showed the isolate had more than 97.3% nucleotide homology to 6 other ranaviruses.

Biodiversity Hotspots, 2011

Worldwide amphibian diversity is threatened through the emergence of the disease chytridiomycosis... more Worldwide amphibian diversity is threatened through the emergence of the disease chytridiomycosis, caused by the amphibian chytrid fungus. This pathogen apparently is absent from the amphibian hotspot Madagascar. However, an extinction risk assessment based on environmental niche modelling suggests that a major portion of this island is climatically highly suitable to the fungus. This includes regions of high amphibian species richness. Many species have their entire geographic range in such areas and are at the same time predicted to suffer potentially from chytridiomycosis due to their life history traits. Human-mediated dissemination of the chytrid fungus to Madagascar is considered likely. In particular, there may be a high risk of accidental cointroduction via the animal trade. Severe decline and possibly extinction are expected in a postemergence scenario on Madagascar with more than 270 described and numerous undescribed anuran amphibian species under threat. Effective responses to this potential threat might include (1) an increased attention to 'biosecurity', including the consequent implementation of measures to avoid the introduction of the chytrid fungus, (2) the development of breeding procedures for representatives of all major clades of Madagascan amphibians as a 'pre-emergency prophylaxis' and (3) the development of plans for 'emergency response'.

Biodiversity Hotspots, 2011

Worldwide amphibian diversity is threatened through the emergence of the disease chytridiomycosis... more Worldwide amphibian diversity is threatened through the emergence of the disease chytridiomycosis, caused by the amphibian chytrid fungus. This pathogen apparently is absent from the amphibian hotspot Madagascar. However, an extinction risk assessment based on environmental niche modelling suggests that a major portion of this island is climatically highly suitable to the fungus. This includes regions of high amphibian species richness. Many species have their entire geographic range in such areas and are at the same time predicted to suffer potentially from chytridiomycosis due to their life history traits. Human-mediated dissemination of the chytrid fungus to Madagascar is considered likely. In particular, there may be a high risk of accidental cointroduction via the animal trade. Severe decline and possibly extinction are expected in a postemergence scenario on Madagascar with more than 270 described and numerous undescribed anuran amphibian species under threat. Effective responses to this potential threat might include (1) an increased attention to 'biosecurity', including the consequent implementation of measures to avoid the introduction of the chytrid fungus, (2) the development of breeding procedures for representatives of all major clades of Madagascan amphibians as a 'pre-emergency prophylaxis' and (3) the development of plans for 'emergency response'.