Environmental DNA and RNA Metabarcoding

Dear Colleagues,

The genetic, genomic, and bioinformatic assessment of environmental (e)DNA, and more recently, environmental (e)RNA, are leading to an information and application explosion towards new ecological understanding, through analyses of environmental samples from various sources, including water, plankton, soil, sediment, ice, air, digestive tract contents, etc. eDNA/eRNA sampling allows for the identification and screening monitoring of rare taxa, such as newly introduced ones, or endangered ones, as well as sampling from difficult-to-access areas, and has strong appeal for 'citizen science'. The use of short diagnostic DNA/RNA sequences to identify and distinguish among taxa, termed 'barcoding', has been extended to 'metabarcoding', which employs high-throughput sequencing and bioinformatics to analyze millions of sequence reads, and can be readily used on eDNA/eRNA samples. Notably, metabarcoding assays of eDNA can be used to determine the compositions and diversities of entire biological communities, ranging from microbes through plants and animals, with individual environmental samples (up to hundreds) distinguished by the addition of index tabs. Many metabarcoding assays and samples can be run together (i.e., hundreds), ranging from those employing standard barcode regions (e.g., mitochondrial DNA COI) to more targeted gene assays designed to exclusively amplify and distinguish among specific taxa, such as at the genus, species, and/or population level. Relative proportions of resultant sequence reads can be assessed in relationship to known biomass and/or numbers of individuals obtained from standard sampling, and taxon compositions can be compared to those from standard sampling and assessment techniques. A growing number of studies are showing strong relationships to ecological assessments of habitat types, conditions, connectivities, and anthropomorphic influences. A possible caveat is the lack of reference DNA sequences and museum-deposited voucher specimens, to match recovered DNA/RNA sequence reads.  Another need is standardized sampling methodology, the use of positive/negative controls, and appropriate bioinformatic pipelines to screen out errors. For this Special Issue, we will present state-of-the-art work on the use and application of metabarcoding to assess living communities from environmental DNA and/or RNA, assembling the most recent advances in our field in one place.

Dr. Carol Stepien
Dr. Mehrdad Hajibabaei
Guest Editors

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• barcoding
• environmental DNA
• environmental RNA
• Edna
• eRNA
• high-throughput sequencing
• metabarcoding
• metagenomics
• MiSeq
• next-generation sequencing