Biology subjects

Shokralla, S.

Publications and source records attributed to Shokralla, S..

2 recordsLinked to original sources

bioRxiv2017

DNA Metabarcoding For High-Throughput Monitoring Of Estuarine Macrobenthic Communities

Benthic communities are key components of aquatic ecosystems biomonitoring. However, morphology-based species identifications remain a low-throughput, and sometimes ambiguous, approach. Despite metabarcoding methodologies have been applied for above-species taxa inventories in marine meiofaunal communities, a comprehensive approach providing species-level identifications for estuarine macrobenthic communities is still lacking. Here we report a combination of experimental and field studies demonstrating the aptitude of COI metabarcoding to provide robust species-level identifications within a framework of high-throughput monitoring of estuarine macrobenthic communities. To investigate the ability to recover DNA barcodes from all species present in a bulk DNA extract, we assembled 3 phylogenetically diverse communities, using 4 different primer pairs to generate PCR products of the COI barcode region. Between 78 and 83% of the species in the tested communities were recovered through HTS. Subsequently, we compared morphology and metabarcoding-based approaches to determine the species composition from four distinct sites of an estuary. Our results indicate that the species richness would be considerably underestimated if only morphological methods were used. Although further refinement is required for improving the efficiency and output of this approach, here we show the great aptitude of COI metabarcoding to provide high quality and auditable species identifications in macrobenthos monitoring.

genetics↗

bioRxiv2016

Environmental DNA Barcode Sequence Capture: Targeted, PCR-free Sequence Capture for Biodiversity Analysis from Bulk Environmental Samples

Environmental DNA analysis using PCR amplified marker genes has been a key application of high-throughput sequencing (HTS). However, PCR bias is a major drawback to gain accurate qualitative and quantitative biodiversity data. We developed a PCR-free approach using enrichment baits for species-specific mitochondrial cytochrome c oxidase 1(COI) DNA barcodes. The sequence capture was tested on species-rich bulk terrestrial and aquatic benthic samples. Hybridization capture recovered an average of 6 and 4.7 more arthropod orders than amplicon sequencing for terrestrial and benthic samples, respectively. For the terrestrial sample, the four most abundant arthropod orders comprised 94.0% of the sample biomass. These same four orders comprised 95.5% and 97.5% of the COI sequences recovered by amplification and capture, respectively. Hybridization capture recovered three arthropod orders that were detected by biomass analysis, but not by amplicon sequencing and two other insect orders that were not detected by either biomass or amplicon methods. These results indicate the advantage of using sequence capture for a more accurate analysis of biodiversity in bulk environmental samples. The protocol can be easily customized to other DNA barcode markers or gene regions of interest for a wide range of taxa or for a specific target group.

genomics↗