Department Aquatic Ecology

Examination of faecal material has demonstrated how a broad range of organisms are distributed by bird movements. Such research has largely focused on dispersal of plant seeds by frugivores and of freshwater organisms by waterbirds. However, with few exceptions (e.g. avian influenza, Ebola virus), there is a dearth of evidence for transport of parasites and pathogens. High-throughput sequencing methods now provide a powerful means of addressing this knowledge gap by elucidating faecal contents in unprecedented detail. We collected faeces excreted by a range of migratory waterbirds in south-west Spain and pooled faecal DNA to create libraries reflective of feeding behavior. We created sets of libraries using high-throughput metagenomic and amplicon sequencing. For the latter we employed two sets of primers to broadly target the V4 region of the 18S rRNA gene (one set amplifying the region across all eukaryotes, the other excluding amplification of metazoans). Libraries revealed a wide diversity of eukaryotes, including parasites of the faecal producers themselves, parasites of food items, or those incidentally ingested. We also detected novel microbial eukaryotic taxa and found that parasite assemblage profiles were relatively distinct. Comparing the performance of the methods used supports their joint use for future studies of diversity and abundance. Because viable stages of many parasites are likely to be present in faeces, our results suggest significant levels of bird-mediated dispersal of parasites (both from avian and other hosts). Our methods revealed much hidden biodiversity, and allowed identification of the individuals who produced the faecal samples to species level, facilitating the study of interaction networks.

Biological quality elements have been developed worldwide to assess whether a water body is in a good status or not. However, current studies mainly focus on a single taxonomic group or a small set of species, often limited by methods of morphological identification, and lack further aspects of biodiversity (e.g., across taxa and multiple attributes) and ecosystem functions. Here, we advance a framework for assessing the river's ecological status based on complete biodiversity data measured by environmental DNA (eDNA) metabarcoding and measurements of ecosystem functions in addition to physicochemical elements across a large riverine system in China. We identified 40 indicators of biodiversity and ecosystem functions, covering five taxonomic groups from bacteria to invertebrates, and associated with multiple attributes of biodiversity and ecosystem functions. Our data show that human impact on ecosystems could be accurately predicted by these eDNA-based indicators and ecosystem functions, using cross-validation with a known stressor gradient. Moreover, indices based on these indicators of biodiversity and ecosystem functions not only distinguish the physicochemical characteristics of the sites but also improve the assessment accuracy of 20–30% for the river’s ecological status. Overall, by incorporating eDNA-based biodiversity with physicochemical and ecosystem functional elements, the multidimensional perspectives of ecosystem states provide additional information to protect and maintain a good ecological status of rivers.

1. River regulation globally has reduced the riverine connectivity (longitudinal, lateral and vertically) with significant consequences for their abiotic and biotic components. To restore the ecological integrity of regulated rivers, artificial floods are increasingly being employed in large-scale flow restoration efforts. Despite considerable recognition regarding the ecological and geomorphological effects of artificial floods on benthic habitats, understanding the implications for the hyporheic zone is essentially absent. This void in our management knowledge base is considerable given that one of the most widely associated consequences of flow regulation is excessive deposition of fine sediment (sedimentation; particles <2 mm) that often disconnects the hyporheic zone from surface waters.
2. In this study, we examined the effects of an artificial flood on the hyporheic zone of the River Spöl in Switzerland. Fine sediment content of shallow benthic substrates (ca. 10 cm) was significantly reduced following the flood. The flushing of fine sediment was also apparent in hyporheic substrates (depths of 0.25 and 0.50 m), resulting in a reconnection of previously clogged interstitial pathways. The opening of interstitial pore space enhanced physicochemical conditions in the hyporheic zone, such as improved dissolved oxygen concentrations, and supported greater taxa richness.
3. Alterations in the composition of shallower hyporheic assemblages (0.25 m) were evident following the flood. These results indicated that benthic pore space became more connected to surface waters following the flood, thereby enhancing accessibility for interstitial organisms.
4. Our results suggest that artificial floods can be an effective management tool to restore spatial heterogeneity in sediment composition and pore space and improve vertical connectivity for macroinvertebrates. We anticipate that artificial floods would be required on a regular basis given the re-accumulation of fine sediment 10 months later in our study system. We encourage river managers and scientists to consider flow disturbance and restoration in a holistic manner that encompasses the multiple spatial dimensions of connectivity, including the hyporheic ecotone.