The microbiota of frog skin can play an important role in protecting against diseases and parasites. The frog skin microbial community represents a complex mix of microbes that are promoted by the chemical environment of the frog skin and influenced by the animal's immediate past environment. The microbial communities of six species of frogs sampled from the campus of Charles Darwin University (CDU) were more similar within species than between species. The microbiota of the introduced cane toad (Rhinella marina) was most dissimilar among the species. Pairwise comparisons showed that the microbial communities of each species were different, except for the terrestrial Litoria nasuta and the arboreal L. rothii. The microbial communities of the six species were not related to ecological habit (arboreal or terrestrial), and neither was the alpha diversity of the microbes. The core microbes (defined as being on ≥90% of individuals of a species or group) were significantly different among all species, although 89 microbial operational taxonomic units (OTUs) were core microbes for all six species at CDU. Two species, Rhinella marina and Litoria rothii, were sampled at additional sites approximately 10 and 30 km from CDU. The microbial communities and the core OTU composition were different among the sites, but there were nevertheless 194 (R. marina) and 181 (L. rothii) core OTUs present at all three sites. Thus, the core microbiota varied with respect to geographic range and sample size.

Detecting animals by identifying their DNA in water is a valuable tool for locating and monitoring species that are difficult to detect through other survey techniques. We developed a test for detecting the endangered Gouldian finch Erythrura gouldiae, a small bird endemic to northern Australia. Only 1 previous study has reported an environmental DNA (eDNA) test that unequivocally identifies a bird species using the water bodies from which they drink. In controlled aviary trials with a pair of Gouldian finches, first detection in 200 ml of water occurred after as little as 6 h, but the detection rate was higher at 30 h. DNA persisted in water exposed to the sun for <12 h and in the shade for 12 h. In trials with 55 finches, persistence was up to 144 h. The eDNA test for finches and the Gouldian finch-specific test were positive for waterholes where Gouldian and other finch species were observed each morning over 3 d. Importantly, where no Gouldian finches were observed for up to 72 h prior to water sampling, the Gouldian test was negative. Where other species of finch but no Gouldian finch were observed and counted, the finch test was positive, but the Gouldian finch test was negative. This approach could be developed for broadscale monitoring of this endangered species, and potentially applied to a much broader range of terrestrial species that shed DNA into water bodies.

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Nitrogen removal is an important process for wastewater ponds prior to effluent release. Bacteria and archaea can drive nitrogen removal if they possess the genes required to metabolize nitrogen. In the tropical savanna of northern Australia, we identified the previously unresolved microbial communities responsible for nitrogen cycling in a multi-pond wastewater stabilization system by measuring genomic DNA and cDNA for the following: nifH (nitrogen fixation); nosZ (denitrification); hzsA (anammox); archaeal AamoA and bacterial BamoA (ammonia oxidation); nxrB (nitrite oxidation); and nrfA (dissimilatory NO3 reduction to NH3). By collecting 160 DNA and 40 cDNA wastewater samples and measuring nitrogen (N)-cycling genes using a functional gene array, we found that genes from all steps of the N cycle were present and, except for nxrB, were also expressed. As expected, N-cycling communities showed daily, seasonal, and yearly shifts. However, contrary to our prediction, probes from most functional groups, excluding nosZ and AamoA, were different between ponds. Further, different genes that perform the same N-cycling role sometimes had different trends over space and time, resulting in only weak correlations between the different functional communities. Although N-cycling communities were correlated with wastewater nitrogen levels and physico-chemistry, the relationship was not strong enough to reliably predict the presence or diversity of N-cycling microbes. The complex and dynamic response of these genes to other functional groups and the changing physico-chemical environment provides insight into why altering wastewater pond conditions can result an abundance of some gene variants while others are lost.

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