Single-species (qPCR)
Pros - Single-species assays provide quantitative information about your organism of interest. While they do not yield actual counts of the organism (number of individuals) as you might get from a visual survey, they do give an idea of the amount of DNA of that target species present in the environment which should be more in locations where more of that species is present and less in locations where the species is rare or absent.
Cons - Since one must make a choice about species to focus on for single-species assays, you do lose the ability to understand the total community composition and the relative abundance of your focal organism in the whole community. While the cost for this assay may be cheaper than for metabarcoding (see Stage 3b), you only gain information about one organism so the cost per organism is ultimately more expensive in single-species assays compared to community-based assays. But, community-based assays have their own limitations too (see Stage 3b).
Community (Metabarcoding)
Pros - The main advantage of this approach is that it can generate community-level data for all species present in a sample. This is ideal for generating baseline biodiversity data or comparing biodiversity across different locations or through time.
Many studies have compared the results of DNA metabarcoding to conventional visual biodiversity surveys. Generally the eDNA metabarcoding approach identifies more species than a conventional visual survey, can be more rapid and cost effective, and removes the need for expertise in visually identifying the species present.
Cons - Metabarcoding data does have some limitations: