https://pubs.rsc.org/en/content/articlepdf/2015/np/c5np00010f

Defensive symbioses of animals with prokaryotic and eukaryotic microorganisms

The central aim of conservation biology is to understand and mitigate the effects of human activities on biodiversity. To successfully achieve this objective, researchers must take an interdiscipli...

https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2018.2448

Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices

Environmental temperature and gut microbial communities can both have profound impacts on the digestive performance of ectothermic vertebrates. Additionally, the diversity, composition and function of gut microbial communities themselves are influenced by temperature. It is typically assumed that the temperature-dependent nature of ectotherm digestive performance is due to factors such as host physiological changes and adaptation to local climatic conditions. However, it is also possible that temperature-induced alterations to gut microbiota may influence the relationship between temperature and digestion. To explore the connections between these three factors, we compared digestive performance and gut microbial community diversity and composition in red-backed salamanders housed at three experimental temperatures: 10, 15 and 20°C. We also investigated associations between specific bacterial taxa and temperature or salamander digestive performance. We found that salamander digestive performance was greatest at 15°C, while gut microbial diversity was reduced at 20°C. Further, gut microbial community composition differed among the three temperature treatments. The relative abundance of 25 bacterial genera was dependent on temperature, with high temperatures being associated with reductions in the relative abundance of disease-resistant bacteria and increases in pathogenic taxa. The relative abundance of four bacterial genera was correlated with salamander energy assimilation, two of which are known to digest chitin, a main component of the red-backed salamander diet. These findings suggest that gut microbiota may mediate the relationship between temperature and digestion in ectotherms. We discuss how global climate change may impact ectotherms by altering host–microbe interactions.

/pdf/environmental-temperature-alters-the-digestive-performance-34jn8gwoc8.pdf

Environmental temperature alters the digestive performance and gut microbiota of a terrestrial amphibian.

Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called “omics,” are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the Kolmogorov–Smirnov Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics, or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species.

/pdf/using-omics-and-integrated-multi-omics-approaches-to-guide-2qo8msprm7.pdf

Using “omics” and integrated multi-omics approaches to guide probiotic selection to mitigate chytridiomycosis and other emerging infectious diseases

Agricultural activities inevitably result in anthropogenic interference with natural habitats. The diet and the gut microbiota of farmland wildlife can be altered due to the changes in food webs within agricultural ecosystems. In this work, we compared the diet and intestinal microbiota of the frog Fejervarya limnocharis in natural and farmland habitats in order to understand how custom farming affects the health of in vivo microbial ecosystems. The occurrence, abundance, and the numbers of prey categories of stomach content were significantly different between the frogs inhabiting natural and farmland habitats. In addition, differences in the abundance, species richness, and alpha-diversity of intestinal microbial communities were also statistically significant. The microbial composition, and particularly the composition of dominant microbes living in intestines, indicated that the land use practices might be one of factors affecting the gut microbial community composition. Although the first three dominant microbial phyla Bacteroidetes, Firmicutes, and Proteobacteria found in the intestines of frogs were classified as generalists among habitats, the most dominant gut bacterial phylum Bacteroidetes in natural environments was replaced by the microbial phylum Firmicutes in farmland frogs. Increased intestinal microbial richness of the farmland frogs, which is mostly contributed by numerous microbial species of Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes, not only reflects the possible shifts in microbial community composition through the alteration of external ecosystem, but also indicates the higher risk of invasion by disease-related microbes. This study indicates that anthropogenic activities, such as the custom farming, have not only affected the food resources of frogs, but also influenced the health and in vivo microbial ecosystem of wildlife.

/pdf/changes-of-diet-and-dominant-intestinal-microbes-in-farmland-15g1anaddy.pdf

Changes of diet and dominant intestinal microbes in farmland frogs.

Janthinobacterium lividum, a bacterium that inhibits the growth of the lethal amphibian pathogen Batrachochytrium dendrobatidis, has been found in myriad environments, including the skins of amphibians that resist the fungus. We present evidence that the gastrointestinal tract of Plethodon cinereus, the Eastern Red-backed Salamander, can serve as a reservoir for J. lividum. Two of six individuals collected from a natural environment harbored J. lividum in the gut tube. Violacein, whose intense violet color allows for rapid visual detection and chemical analysis, served as a first indicator for the presence of J. lividum. This secondary metabolite of J. lividum was confirmed through reverse-phase high performance liquid chromatography, UV-Vis analysis, and high-resolution mass spectrometry. The identity of J. lividum was confirmed by PCR amplification with J. lividum-specific primers of DNA extracted from the isolated bacteria. Because J. lividum survives in the digestive tract, it will likely be inoculated onto skin around the cloaca and into the soil and indirectly onto salamander skins. Thus, the gut may act as an important reservoir for this antifungal bacterium.

Gut of Red-backed Salamanders (Plethodon cinereus) May Serve as a Reservoir for an Antifungal Cutaneous Bacterium

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Gut of Red-backed Salamanders (Plethodon cinereus) May Serve as a Reservoir for an Antifungal Cutaneous Bacterium