In the last decades fungal pathogens are causing devastating population declines across a broad range of taxa. A newly emerging fungal disease, sea turtle egg fusariosis, caused by members of the Fusarium solani species complex (FSSC), has been reported to be responsible for hatching failure in sea turtles around the world. However, this has not been reported in other non-marine turtle species. Herein we report high hatching failure from eggs symptomatic of fusariosis in the yellow-spotted Amazon river turtle ( Podocnemis unifilis), inhabiting a pristine environment in the Ecuadorian Amazon. We assessed hatching success from eggs symptomatic and asymptomatic of fusariosis ( n = 680 eggs), tested for Fusarium infection by PCR amplifying the TEF-1α gene (n= 68 turtle internal egg swab samples) and sequenced eight amplicons for screening of FSSC membership on an Illumina Miseq. Hatchability was 72% for asymptomatic eggs, whilst only 8% of symptomatic eggs hatched. Eight percent of asymptomatic and 58% of symptomatic eggs tested positive for Fusarium spp. and sequencing revealed that nine sequence variants from three asymptomatic and four symptomatic eggs corresponded to F. keratoplasticum, F. solani and F. falciforme, the three major FSSC pathogens already reported in sea turtle egg fusariosis. Our study therefore suggests that observed hatching failure of eggs showing symptoms of fusariosis is at least partially caused by Fusarium pathogens within FSSC in a freshwater turtle. This report highlights that fusariosis is more widespread among the Testudines order than previously reported and is not limited to sea environments, which is of particular conservation concern.

As microbiome research moves away from model organisms to wildlife, new challenges for microbiome high throughput sequencing arise caused by the variety of wildlife diets. High levels of contamination are commonly observed emanating from the host (mitochondria) or diet (chloroplast). Such high contamination levels affect the overall sequencing depth of wildlife samples thus decreasing statistical power and leading to poor performance in downstream analysis. We developed an amplification protocol utilizing PNA-DNA clamps to maximize the use of resources and to increase the sampling depth of true microbiome sequences in samples with high levels of plastid contamination. We chose two study organisms, a bat (Leptonyteris yerbabuenae) and a bird (Mimus parvulus), both relying on heavy plant-based diets that sometimes lead to traces of plant-based faecal material producing high contamination signals from chloroplasts and mitochondria. On average, our protocol yielded a 13-fold increase in bacterial sequence amplification compared with the standard protocol (Earth Microbiome Protocol) used in wildlife research. For both focal species, we were able significantly to increase the percentage of sequences available for downstream analyses after the filtering of plastids and mitochondria. Our study presents the first results obtained by using PNA-DNA clamps to block the PCR amplification of chloroplast and mitochondrial DNA from the diet in the gut microbiome of wildlife. The method involves a cost-effective molecular technique instead of the filtering out of unwanted sequencing reads. As 33% and 26% of birds and bats, respectively, have a plant-based diet, the tool that we present here will optimize the sequencing and analysis of wild microbiomes.