Ecological influence of sediment bypass tunnels on macroinvertebrates in dam-fragmented rivers by DNA metabarcoding

Abstract

Sediment bypass tunnels (SBTs) are guiding structures used to reduce sediment accumulation in reservoirs during high flows by transporting sediments to downstream reaches during operation. Previous studies monitoring the ecological effects of SBT operations on downstream reaches suggest a positive influence of SBTs on riverbed sediment conditions and macroinvertebrate communities based on traditional morphology-based surveys. Morphology-based macroinvertebrate assessments are costly and time-consuming, and the large number of morphologically cryptic, small-sized and undescribed species usually results in coarse taxonomic identification. Here, we used DNA metabarcoding analysis to assess the influence of SBT operations on macroinvertebrates downstream of SBT outlets by estimating species diversity and pairwise community dissimilarity between upstream and downstream locations in dam-fragmented rivers with operational SBTs in comparison to dam-fragmented (i.e., no SBTs) and free-flowing rivers (i.e., no dam). We found that macroinvertebrate community dissimilarity decreases with increasing operation time and frequency of SBTs. These factors of SBT operation influence changes in riverbed features, e.g. sediment relations, that subsequently effect the recovery of downstream macroinvertebrate communities to their respective upstream communities. Macroinvertebrate abundance using morphologically-identified specimens was positively correlated to read abundance using metabarcoding. This supports and reinforces the use of quantitative estimates for diversity analysis with metabarcoding data.

Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring

“…However, recent metabarcoding studies have tested and found such positive correlation using relative abundances of morphologically identified taxa. Most of these studies were taxonomically limited to the family Nematoda (Porazinska et al, 2010), Chironomidae (Carew et al, 2013) or calanoid copepods (Clarke et al, 2017) that include similarly-sized species, while a handful tested environmental samples composed of macroinvertebrate taxa with varying size (e.g., Aylagas et al, 2016; Elbrecht et al, 2017; Krehenwinkel et al, 2017; Serrana et al, 2018). However, more tests with wider taxonomic and body size ranges such as macroinvertebrate communities are necessary to verify this relationship for taxonomically diverse communities for use in stream assessment.…”

Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16s rDNA amplicon sequencing

“…Also, method-specific or unique taxa could result from having abundant taxa with polymorphisms (Laroche et al, 2017). On the other hand, setting a more stringent parameter for quality filtering could reduce the rate of detecting false positives (Ficetola et al, 2015;Serrana et al, 2018). Given that we employed a relatively lax read quality filtering parameter in this study, the false positive detection could result from low-quality passing reads.…”

A practical guide to DNA metabarcoding for entomological ecologists

“…Water samples were usually vacuum‐pumped and filtered through a membrane to collect aquatic eDNA. Preserving the filter membrane in ethanol (Spens et al ., ; Macher et al ., ; Serrana et al ., ) or Longmire's buffer (Longmire et al ., ; Grey et al ., ; Lacoursiere‐Roussel et al ., ), is effective. Temperature is a key factor for DNA preservation.…”