Is it worth the extra mile? Comparing environmental DNA and RNA metabarcoding for vertebrate and invertebrate biodiversity surveys in a lowland stream
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PROVIDER: PRJEB64868 | ENA |
REPOSITORIES: ENA
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Project description:The aim of the present study was to assess the impact of surrounding land use on the structure and functioning of lowland stream ecosystems. To this end, five different land use types were selected (forest, extensive grassland, intensive grassland, cropland and wastewater treatment plant) each represented by four replicate streams, in which diel dissolved oxygen concentrations were recorded, sediment and water quality parameters were measured and macroinvertebrate community composition was determined. Chironomus sp., Oligochaeta and Gastropoda dominated the cropland and wastewater treatment plant (WWTP) streams, while Plecoptera and most Trichoptera only occurred in forest and extensive grassland streams. Forest streams communities were related to a high oxygen saturation, a high C/N ratio in the sediment and woody debris and coarse particulate organic matter (CPOM) substrate cover. Macroinvertebrate communities in cropland and WWTP streams were related to a low oxygen saturation in water and sediment and high concentrations of dissolved nitrogen, phosphorus and carbon. It is concluded that land use specific impacts on lowland streams are likely exerted via fine sediment accumulation in deposition zones, affecting oxygen regimes, sediment oxygen demand and stream metabolism, ultimately changing macroinvertebrate community composition. This study supports therefore the importance of including the catchment scale in ecological stream quality assessments, combining structural and functional endpoints.
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Project description:Land use is known to affect water quality yet the impact it has on aquatic microbial communities in tropical systems is poorly understood. We used 16S metabarcoding to assess the impact of land use on bacterial communities in the water column of four streams in central Panama. Each stream was influenced by a common Neotropical land use: mature forest, secondary forest, silvopasture and traditional cattle pasture. Bacterial community diversity and composition were significantly influenced by nearby land uses. Streams bordered by forests had higher phylogenetic diversity (Faith's PD) and similar community structure (based on weighted UniFrac distance), whereas the stream surrounded by traditional cattle pasture had lower diversity and unique bacterial communities. The silvopasture stream showed strong seasonal shifts, with communities similar to forested catchments during the wet seasons and cattle pasture during dry seasons. We demonstrate that natural forest regrowth and targeted management, such as maintaining and restoring riparian corridors, benefit stream-water microbiomes in tropical landscapes and can provide a rapid and efficient approach to balancing agricultural activities and water quality protection.
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Project description:Metabarcoding reveals strong spatial structure and temporal turnover of zooplankton communities among marine and freshwater ports
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Project description:An important question in biology is why some animals are able to regenerate, whereas others are not. The basal chordate amphioxus is uniquely positioned to address the evolution of regeneration. We report here the high regeneration potential of the European amphioxus Branchiostoma lanceolatum. Adults regenerate both anterior and posterior structures, including neural tube, notochord, fin, and muscle. Development of a classifier based on tail regeneration profiles predicts the assignment of young and old adults to their own class with >94% accuracy. The process involves loss of differentiated characteristics, formation of an msx-expressing blastema, and neurogenesis. Moreover, regeneration is linked to the activation of satellite-like Pax3/7 progenitor cells, the extent of which declines with size and age. Our results provide a framework for understanding the evolution and diversity of regeneration mechanisms in vertebrates.
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Project description:BackgroundFreshwater ecosystems, such as streams, are facing increasing pressures from agricultural land use and recent literature stresses the importance of robust biomonitoring to detect trends in insect decline globally. Aquatic insects and other macroinvertebrates are often used as indicators of ecological condition in freshwater biomonitoring programs; however, these diverse groups can present challenges to morphological identification and coarse-level taxonomic resolution can mask patterns in community composition. Here, we incorporate molecular identification (DNA metabarcoding) into a stream biomonitoring sampling design to explore the diversity and variability of aquatic macroinvertebrate communities at small spatial scales. While individual stream reaches can be very heterogenous, most community ecology studies focus on larger, landscape-level patterns of community composition. A high degree of community variability at the local scale has important implications for both biomonitoring and ecological research, and the incorporation of DNA metabarcoding into local biodiversity assessments will inform future sampling protocols.ResultsWe sampled twenty streams in southern Ontario, Canada, for aquatic macroinvertebrates across multiple time points and assessed local community variability by comparing field replicates taken ten meters apart within the same stream. Using bulk-tissue DNA metabarcoding, we revealed that aquatic macroinvertebrate communities are highly diverse at small spatial scales with unprecedented levels of local taxonomic turnover. We detected over 1600 Operational Taxonomic Units (OTUs) from 149 families, and a single insect family, the Chironomidae, contained over one third of the total number of OTUs detected in our study. Benthic communities were largely comprised of rare taxa detected only once per stream despite multiple biological replicates (24-94% rare taxa per site). In addition to numerous rare taxa, our species pool estimates indicated that there was a large proportion of taxa that remained undetected by our sampling regime (14-94% per site). Our sites were located across a gradient of agricultural activity, and while we predicted that increased land use would homogenize benthic communities, this was not supported as within-stream dissimilarity was unrelated to land use. Within-stream dissimilarity estimates were consistently high for all levels of taxonomic resolution (invertebrate families, invertebrate OTUs, chironomid OTUs), indicating stream communities are very dissimilar at small spatial scales.
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