Diatom metabarcoding reveals differences in ecological preferences among genetic variants within some key species for biomonitoring

We applied DNA metabarcoding to evaluate the ecology of genetic variants within several diatom species that are important for biomonitoring. Benthic diatoms widely used as bioindicators biomonitoring programmes, including those European rivers demanded by Water Framework Directive (WFD). Morphological identification at level is required assessing ecological status in programmes. However, this a time-consuming task and requires expert knowledge. In addition, closely related species, which sometimes scarcely distinguishable on basis their morphology, can show different preferences; these may even vary single species. Not being able identify preferences shown or might have consequences especially if such differences occur common The key we studied were: Fistulifera saprophila (FSAP), regarded marker elevated nutrient levels, organic pollution hence poor status; Achnanthidium minutissimum (ADMI), usually indicates good Nitzschia inconspicua (NINC) N. soratensis (NSTS), two separated phylogenetically but almost impossible distinguish light microscope. Our dataset was based high-throughput sequencing using 312-bp rbc L marker. denoising pipeline DADA2 infer amplicon sequence (ASVs) from 554 environmental samples river campaigns Catalonia (NE Spain) France. Ecological groupings ASVs were distinguished according responses given Threshold Indicator Taxa ANalysis (TITAN); parameters most influenced occurrence tested boosted regression trees. could three ADMI FSAP. each clearly opposite calcium conductivity trees showed out four groupings, variables among explaining ASV distributions. third grouping FSAP had negative response total carbon positive altitude better represented less organically polluted waters higher than generally assumed analyses did not NINC NSTS confirmed earlier studies, more limited sampling, indicated Conductivity NSTS, distributed with levels NSTS. findings indicate potential use distinguishing This information, coupled broad knowledge generated over many years traditional microscope-based identifications, will facilitate development accurate biological indexes programmes future.