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The Woodland Salamander genus Plethodon Tschudi, 1838, consists of terrestrial lungless salamanders, has been cited as an exemplar of a lineage characterized by niche conservatism. This conclusion has contributed to broader hypotheses dealing with the role of niche conservatism in speciation and the maintenance of species diversity. We re-evaluated these salamanders using newly published techniques designed to detect niche conservatism versus niche divergence using computer-based niche modeling and spatial analysis within a phylogenetic framework. We specifically studied parapatric neighbors in the species complex of Plethodon glutinosus (Green, 1818) to determine if there is evidence of a role for niche divergence at speciation or if niche conservatism characterizes the complex as has been reported for the larger genus. We found that new statistical approaches yield different results from earlier work, suggesting that niche divergence has been a much more important player in the speciation process than has heretofore been understood. Although different parts of the overall Plethodon phylogeny may be characterized by different rates of niche evolution, the rapidly burgeoning area of research centered on niche conservatism appears to be in a state of flux with regards to methods that give consistently repeatable results. Key words: speciation, parapatry, Plethodon, ecological niche modeling, SEEVA, salamanders, niche conservatism, niche divergence. Le genre forestier Plethodon Tschudi, 1838, consistant en des salamandres terrestres sans poumons, a ete cite en exemple de lignee caracterise par le conservatisme de niche. Cette conclusion a mene a des hypotheses plus larges sur le role du conservatisme de niche dans la speciation et le maintien de la diversite specifique. Nous avons reevalue ces salamandres a l'aide de techniques recemment publiees visant a departager le conservatisme de niche de la divergence de niche en utilisant la modelisation de niche et l'analyse spatiale par ordinateur dans un cadre phylogenetique. Nous avons etudie plus particulierement des voisins parapatriques au sein du complexe d'especes de Plethodon glutinosus (Green, 1818) afin de determiner si la divergence de niche jouerait un role dans la speciation ou si le conservatisme de niche caracteriserait le complexe, comme cela a ete rapporte pour le genre dans son ensemble. Nous avons constate que les resultats de nouvelles approches statistiques different de ceux de travaux anterieurs et portent a croire que la divergence de niche joue un role beaucoup plus important dans le processus de speciation que ce qu'on en comprenait auparavant. Bien que differentes parties de la phylogenie globale des Plethodon puissent etre caracterisees par differentes vitesses d'evolution des niches, l'etude du conservatisme de niche, un domaine de recherche en pleine croissance, semble evoluer considerablement en ce qui concerne les methodes aptes a donner des resultats uniformement reproductibles. [Traduit par la Redaction] Mots-cles : speciation, parapatrie, Plethodon, modelisation de la niche ecologique, SEEVA, salamandres, conservatisme de niche, divergence de niche., Introduction The influence of natural selection on niche evolution across geographic landscapes is an important consideration in studies of allopatric speciation. There is considerable evidence that divergent selection between different [...]

Batrachochytrium salamandrivorans (Bsal) is an emerging fungal pathogen that affects salamander and newt populations in Asia and Europe. In the Western Hemisphere, Bsal represents a major threat to endemic amphibian populations, which have not evolved resistance to infection, and which could experience local extinction events such as those observed in European fire salamanders (Salamandra salamandra). We report findings of a survey focusing specifically on wild lungless salamanders in the southeastern US, the most biodiverse location for salamander species globally. Between May 2016 and July 2018, we conducted 25 surveys at 10 sites across three ecoregions in Tennessee, US. Using quantitative (q)PCR, we screened water samples and skin swabs from 137 salamanders in five plethodontid genera. Although single replicates of six samples amplified during qPCR cycling, no samples could be confirmed as positive for the presence of Bsal with 28S rRNA PCR and independent laboratory screening. It is probable that we found false positive results, as reported by other researchers using the same assay. We offer recommendations for future monitoring efforts. [ABSTRACT FROM AUTHOR]

Metacommunity ecology represents a framework for identifying linkages between environmental heterogeneity, spatial processes, and local communities of organisms. Despite advancements in metacommunity theory, there remains a need to understand temporal dynamics of multi‐taxa metacommunities in variable ecosystems such as intermittent streams. We present a review of literature, three recent conceptual models, and a case study regarding metacommunity temporal dynamics in intermittent streams. The literature review revealed that the cumulative number of studies addressing temporal dynamics in aquatic metacommunities steadily increased between 2012 and 2020. Intermittent streams were the fourth‐most commonly studied ecosystem and interdisciplinary studies involving multiple taxa were the third‐most common taxonomic focus. The most common analytical method was variation partitioning, and analysis of beta diversity components surpassed both distance decay and elements of metacommunity structure as the second‐most used method from 2018 to 2020. Three recent conceptual models describing metacommunity dynamics in intermittent streams predict: (a) higher local species richness (i.e., alpha diversity) during rewetting and wet hydrologic phases, (b) stronger effects of dispersal over environmental sorting during the rewetting and wet phases, and (c) emergence of primarily nested structures during the wet hydrologic phase. When tested in a case study focused on microbes, aquatic invertebrates, and fishes, each of these predictions were partially, but not completely supported. Our results reveal expanding interest in temporal aspects of aquatic metacommunity structure and highlight how research in intermittent streams is poised to simultaneously advance basic metacommunity ecology and applied conservation biology through continued refinement of new and existing conceptual syntheses. This article is categorized under:Water and Life > Nature of Freshwater EcosystemsWater and Life > Stresses and Pressures on EcosystemsWater and Life > Conservation, Management, and Awareness [ABSTRACT FROM AUTHOR]

The fungal pathogen Ophidiomyces ophiodiicola, the causative agent of snake fungal disease, has been implicated in declines of North American snake populations since 2006 and the geographic range of this pathogen is still not fully known. In Tennessee, US, O. ophiodiicola has been detected since 2012, but large portions of the state have not been surveyed for this pathogen. Our primary objective was to monitor the prevalence of O. ophiodiicola in the Interior Plateau ecoregion of Tennessee by swabbing all snakes that were encountered during road cruising survey efforts in 2017 and 2018. Eleven snakes of four species, copperhead (Agkistrodon contortrix), common water snake (Nerodia sipedon), black kingsnake (Lampropeltis nigra), and smooth earthsnake (Virginia valeriae), tested positive for the presence of O. ophiodiicola. Overall, 9.2% (11/120) of snakes sampled tested positive for the presence of O. ophiodiiola, and we further observed a seasonal trend in detections with summer months having the greatest frequency of detections. Our results extend the known geographic range of O. ophiodiicola in Tennessee by adding four previously unconfirmed O. ophiodiicola-positive counties. Further sampling will need to be conducted across west Tennessee because this is the most data-deficient region of the state. Our results offer additional evidence of the presence of this pathogen in Tennessee and will help researchers further understand the geographic distribution and host range. [ABSTRACT FROM AUTHOR]

Abstract Since 2010, an unknown fungus in the Gnomoniaceae has been found on overwintered leaves and petioles of Styrax obassia (Styracaceae) in Japan. This fungus is characterized by dark brown immersed or partially erumpent ascomata with long necks and fusiform to obovoid asci each with an acute or long tapering stipe. Each ascus bears eight fusiform to filiform ascospores. Our morphological observation and phylogenetic analyses based on the markers LSU, rpb2 , and tef-1α indicated that this is a new monotypic genus in the Gnomoniaceae (Diaporthales), and Tenuignomonia styracis gen. et sp. nov. was descried herein. Members of the Gnomoniaceae are commonly isolated as endophytes, saprobes, and plant pathogens from a broad diversity of herbaceous, shade tree, and agriculturally significant plants. We thus carried out a pathogenicity test to determine if T. styracis is the causative agent of leaf blotch on S. obassia. One week after inoculation, this fungus produced small necrotic spots on the leaves and petioles, and all leaves having necrotic spots were abscised in a short time. We thus confirmed that this fungus has weak pathogenicity on S. obassia. This new species may promote early defoliation of S. obassia during the fall. Highlights • A new monophyletic genus of Tenuignomonia styracis , gen. et sp. nov. was described. • T. styracis has been found on Styrax obassia (Styracaceae) in Japan. • We increase the total number of accepted genera in the Gnomoniaceae to 31. • T. styracis has weak pathogenicity on Styrax obassia. • This new fungus may promote early defoliation of S. obassia during the fall. [ABSTRACT FROM AUTHOR]

The article examines the host range and geographic distribution of Ophidiomyces ophiodiicola, the fungal pathogen responsible for snake fungal disease (SFD), in Tennessee, U.S. It highlights the prevalence of the pathogen among various snake species across different counties and identifies new host species affected by SFD, underscoring the need for comprehensive sampling and standardized detection methods to better understand the pathogen's impact.

Abstract: Extirpated organisms are reintroduced into their former ranges worldwide to combat species declines and biodiversity losses. The growing field of reintroduction biology provides guiding principles for reestablishing populations, though criticisms remain regarding limited integration of initial planning, modeling frameworks, interdisciplinary collaborations, and multispecies approaches. We used an interdisciplinary, multispecies, quantitative framework to plan reintroductions of three fish species into Abrams Creek, Great Smoky Mountains National Park, USA. We first assessed the appropriateness of habitat at reintroduction sites for banded sculpin (Cottus carolinae), greenside darter (Etheostoma blennioides), and mottled sculpin (Cottus bairdii) using species distribution modeling. Next, we evaluated the relative suitability of nine potential source stock sites using population genomics, abundance estimates, and multiple‐criteria decision analysis (MCDA) based on known correlates of reintroduction success. Species distribution modeling identified mottled sculpin as a poor candidate, but banded sculpin and greenside darter as suitable candidates for reintroduction based on species‐habitat relationships and habitats available in Abrams Creek. Genotyping by sequencing revealed acceptable levels of genetic diversity at all candidate source stock sites, identified population clusters, and allowed for estimating the number of fish that should be included in translocations. Finally, MCDA highlighted priorities among candidate source stock sites that were most likely to yield successful reintroductions based on differential weightings of habitat assessment, population genomics, and the number of fish available for translocation. Our integrative approach represents a unification of multiple recent advancements in the field of reintroduction biology and highlights the benefit of shifting away from simply choosing nearby populations for translocation to an information‐based science with strong a priori planning coupled with several suggested posteriori monitoring objectives. Our framework can be applied to optimize reintroduction successes for a multitude of organisms and advances in the science of reintroduction biology by simultaneously addressing a variety of past criticisms of the field. [ABSTRACT FROM AUTHOR]

Ref.: Can. J. Zool. 91(12): 883-892 (2013) dx.doi.org/10.1139/cjz-2013-0097. On p. 886, the text, 'accessed DAY MONTH YEAR' should have been deleted. The phrase should have read as '... natural history [...]

Environmental DNA (eDNA) can be used as an assessment tool to detect populations of threatened species and provide fine-scale data required to make management decisions. The objectives of this project were to use quantitative PCR (qPCR) to: (i) detect spiked salamander DNA in soil, (ii) quantify eDNA degradation over time, (iii) determine detectability of salamander eDNA in a terrestrial environment using soil, faeces, and skin swabs, (iv) detect salamander eDNA in a mesocosm experiment. Salamander eDNA was positively detected in 100% of skin swabs and 66% of faecal samples and concentrations did not differ between the two sources. However, eDNA was not detected in soil samples collected from directly underneath wild-caught living salamanders. Salamander genomic DNA (gDNA) was detected in all qPCR reactions when spiked into soil at 10.0, 5.0, and 1.0 ng/g soil and spike concentration had a significant effect on detected concentrations. Only 33% of samples showed recoverable eDNA when spiked with 0.25 ng/g soil, which was the low end of eDNA detection. To determine the rate of eDNA degradation, gDNA (1 ng/g soil) was spiked into soil and quantified over seven days. Salamander eDNA concentrations decreased across days, but eDNA was still amplifiable at day 7. Salamander eDNA was detected in two of 182 mesocosm soil samples over 12 weeks ( n = 52 control samples; n = 65 presence samples; n = 65 eviction samples). The discrepancy in detection success between experiments indicates the potential challenges for this method to be used as a monitoring technique for small-bodied wild terrestrial salamander populations. [ABSTRACT FROM AUTHOR]

We used the globally widespread genus Ophiognomonia as a model system to investigate climatic niche patterns in fungi, characterizing the climatic profiles of 28 species with seven temperature and seven precipitation variables. Using a novel version of Spatial Evolutionary and Ecological Vicariance Analysis (SEEVA), designed to deal with continuous and correlated variables, we examined well-sampled phyletic splits of a multi-gene phylogeny. We evaluated the degree to which phyletic divergence has been associated with climatic niche divergence between sister lineages, permitting elucidation of climatic associations in evolutionary context. From the 14 inter-correlated climatic variables, we extracted four principal axes, accounting for 93.2% of the climatic variation, with axes broadly labelled as: polarity, tropicality, winter mildness and aridity. We also analysed the two single variables maximum monthly temperature and precipitation. We detected climatic associations that were compatible with both niche conservatism and niche divergence within the phylogeny, and different cladistic bifurcations associated with different climatic splits. As might have been anticipated, geographic separation (or lack thereof) of phylogenetic splits was correlated with climate niche divergence (or conservation). This elaborated SEEVA method provides a visual and statistically solid basis for characterizing climatic niche divergence that should prove useful for elucidation of many other taxonomic groups. [ABSTRACT FROM AUTHOR]

The article focuses on developing a standardized protocol for washing environmental microbes from amphibian skin. It provides information about the skin morphology of different amphibian species and the increasing understanding of amphibian microbial communities in relation to wildlife disease. It also discusses the use of plethodontid salamanders in conducting identical protocols.

The flow of energy within an ecosystem can be considered either top-down, where predators influence consumers, or bottom-up, where producers influence consumers. Plethodon cinereus (Red-backed Salamander) is a terrestrial keystone predator who feeds on invertebrates within the ecosystem. We investigated the impact of the removal of P. cinereus on the detritivore food web in an upland deciduous forest in northwest Ohio, U.S.A. A total of eight aluminum enclosures, each containing a single P. cinereus under a small log, were constructed in the deciduous forest. On Day 1 of the experiment, four salamanders were evicted from four of the eight enclosures. Organic matter and soil were collected from the center of each enclosure at Day 1 and Day 21. From each sample, DNA was extracted, fungal-specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU). Changes in overall fungal community composition or species diversity were not statistically significant between treatments. Statistically significant shifts in the most abundant taxonomic groups of fungi were documented in presence but not absence enclosures. We concluded that P. cinereus does not affect the overall composition or diversity of fungal communities, but does have an impact on specific groups of fungi. This study used a metagenomics-based approach to investigate a missing link among a keystone predator, P. cinereus, invertebrates, and fungal communities, all of which are critical in the detritivore food web. [ABSTRACT FROM AUTHOR]

In this study evolutionary host plant patterns at ranks from order to species were analysed using spatial evolutionary and ecological vicariance analysis ( SEEVA), based on a multigene phylogeny of 45 ascomycete fungal species . The objective was to understand speciation events and host associations in Ophiognomonia ( Gnomoniaceae). Species of this genus are perithecial fungi that occur as endophytes, pathogens, and latent saprobes on plants in the families of Betulaceae, Fagaceae, Juglandaceae, Lauraceae, Malvaceae, Platanaceae, Rosaceae, Salicaceae, and Sapindaceae. A second objective was to determine whether speciation events are influenced by host conservatism, host specialization, or host switching at different taxonomic host ranks. Host differences between sister clades were interpreted using the divergence index ( D) from the SEEVA analysis, ranging from 0 for no divergence to 1 for maximum possible divergence. Several fungal subclades showed clear patterns of host order/family conservatism ( D = 1.00) for hosts in Betulaceae, Fagaceae, Juglandaceae, and Rosaceae. Clear trends of host specialization at host genus and species ranks ( D = 1.00) were suggested within these host families. Independent host jumps were observed for two species at the family rank and three at the order rank. As a result of this study, host specificity and specialization is hypothesized as a mechanism that can strongly contribute to speciation patterns in fungal pathogens. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 1-16. [ABSTRACT FROM AUTHOR]

Abstract: Although significant progress has been made resolving deep branches of the fungal tree of life, many fungal systematists are interested in species-level questions to both define species and assess fungal biodiversity. Fungal genome sequences are a useful resource to systematic biologists for developing new phylogenetic markers that better represent the whole genome. Here we report primers for two newly identified single-copy protein-coding genes, FG1093 and MS204, for use with ascomycetes. Although fungi were the focus of this study, this methodological approach could be easily applied to marker development for studies of other organisms. The tests used here to assess phylogenetic informativeness are computationally rapid, require only rudimentary datasets to evaluate existing or newly developed markers, and can be applied to other non-model organisms to assist in experimental design of phylogenetic studies. Phylogenetic utility of the markers was tested in two genera, Gnomoniopsis and Ophiognomonia (Gnomoniaceae, Diaporthales). The phylogenetic performance of β-tubulin, ITS, and tef-1α was compared with FG1093 and MS204. Phylogenies inferred from FG1093 and MS204 were largely in agreement with β-tubulin, ITS, and tef-1α although some topological conflict was observed. Resolution and support for branches differed based on the combination of markers used for each genus. Based on two independent tests of phylogenetic performance, FG1093 and MS204 were determined to be equal to or better than β-tubulin, ITS, and tef-1α in resolving species relationships. Differences were found in site-specific rate of evolution in all five markers. In addition, isolates from 15 orders and 22 families of Ascomycota were screened using primers for FG1093 and MS204 to demonstrate primer utility across a wide diversity of ascomycetes. The primer sets for the newly identified genes FG1093 and MS204 and methods used to develop them are useful additions to the ascomycete systematists’ toolbox. [Copyright &y& Elsevier]

The article focuses on a report of amphibian decline, including Midland Painted Turtles, or Chrysemys picta marginata, and Wood Frogs, or Lithobates sylvaticus, attributed to ranaviruses in Ohio. It provides details about DNA extraction from whole dead or moribund frogs as well as the collection of skin swab samples.

Snake Fungal Disease (SFD) negatively impacts wild snake populations in the eastern United States and Europe. Ophidiomyces ophidiicola causes SFD and manifests clinically by the formation of heterophilic granulomas around the mouth and eyes, weight loss, impaired vision, and sometimes death. Field observations have documented early seasonal basking behaviors in severely infected snakes, potentially suggesting induction of a behavioral febrile response to combat the mycosis. This study tested the hypothesis that snakes inoculated with Ophidiomyces ophidiicola would seek elevated basking temperatures to control body temperature and behaviorally induce a febrile response. Eastern ribbon snakes (Thamnophis saurita, n = 29) were experimentally or sham inoculated with O. ophidiicola. Seven days after inoculation, snakes were tested on a thermal gradient and the internal body temperature and substrate temperature of each snake was recorded over time. Quantitative PCR was used when snakes arrived, during pre-inoculation, and post-inoculation to test snakes for the presence of O. ophidiicola. Some snakes arrived with O. ophidiicola and were subsequently inoculated, allowing for an assessment of secondary exposure effects. Snake thermoregulatory behavior was compared between 1) O. ophidiicola inoculated vs. sham inoculated treatments, 2) infected vs. disease negative groups, and 3) disease naïve vs. pre-exposed immune response categories. Neither internal nor substrate temperatures differed among initially prescribed, and qPCR recovered disease states, although infected snakes tended to reach a preferred body temperature faster than disease negative snakes. Snakes experiencing their first exposure (disease naïve) sought higher substrate temperatures than snakes experiencing their second exposure (pre-exposed). Here, we recover no evidence for behaviorally induced fever in snakes with SFD but do elucidate a febrile immune response associated with secondary exposure. • Snakes inoculated with Ophidiomyces ophidiicola do not exhibit a behavioral febrile response. • Snakes naïve to Ophidiomyces ophidiicola sought higher substrate temperatures than those previously exposed. • Generalized Additive Models are a valuable analysis for experimental thermal data across time. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The soil decomposer community is a primary driver of carbon cycling in forest ecosystems. Understanding the processes that structure this community is critical to our understanding of the global carbon cycle. In North American forests, soil fungal communities are regulated by grazing soil invertebrates, which are in turn controlled by the predatory red-backed salamander (Plethodon cinereus). The presence of these soil invertebrate taxa is known to exert direct top-down control via selective grazing on saprotrophic fungi, with direct consequences for biogeochemical cycling in soil. We investigated whether the removal of P. cinereus would relieve top-down control on decomposer fungal communities in a tri-trophic mesocosm study. Fungal communities were characterized using metabarcoding and high-throughput DNA sequencing. The β-diversity of fungal communities differed between salamander presence and absence treatments with a strong effect on saprotrophic fungal communities. We concluded that P. cinereus, a mesopredator in the detritivore food chain, exerts a prominent control on the composition and functional diversity of fungal communities in soil through a multi-trophic top-down process. Given their capacity to govern the compositions of soil invertebrates, the activity of these amphibians may be important for regulating ecosystem function and nutrient cycling in temperate forest systems. [ABSTRACT FROM AUTHOR]

A correction to the article "Re-evaluating niche conservatism versus divergence in the Woodland Salamander genus Plethodon: a case study of the parapatric members of the Plethodon glutinosus species complex" that was published in a 2013 issue is presented.

Emerging infectious diseases are increasingly recognized as a significant threat to global biodiversity conservation. Elucidating the relationship between pathogens and the host microbiome could lead to novel approaches for mitigating disease impacts. Pathogens can alter the host microbiome by inducing dysbiosis, an ecological state characterized by a reduction in bacterial alpha diversity, an increase in pathobionts, or a shift in beta diversity. We used the snake fungal disease (SFD; ophidiomycosis), system to examine how an emerging pathogen may induce dysbiosis across two experimental scales. We used quantitative polymerase chain reaction, bacterial amplicon sequencing, and a deep learning neural network to characterize the skin microbiome of free-ranging snakes across a broad phylogenetic and spatial extent. Habitat suitability models were used to find variables associated with fungal presence on the landscape. We also conducted a laboratory study of northern watersnakes to examine temporal changes in the skin microbiome following inoculation with Ophidiomyces ophidiicola. Patterns characteristic of dysbiosis were found at both scales, as were nonlinear changes in alpha and alterations in beta diversity, although structural-level and dispersion changes differed between field and laboratory contexts. The neural network was far more accurate (99.8% positive predictive value [PPV]) in predicting disease state than other analytic techniques (36.4% PPV). The genus Pseudomonas was characteristic of disease-negative microbiomes, whereas, positive snakes were characterized by the pathobionts Chryseobacterium, Paracoccus, and Sphingobacterium. Geographic regions suitable for O. ophidiicola had high pathogen loads (>0.66 maximum sensitivity + specificity). We found that pathogen-induced dysbiosis of the microbiome followed predictable trends, that disease state could be classified with neural network analyses, and that habitat suitability models predicted habitat for the SFD pathogen., (© 2024 The Author(s). Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

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., Competing Interests: The authors declare no conflict of interest.

The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric-artificially joined-DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353., (Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US.)