Towards DNA metabarcoding-based haplotype for monitoring terrestrial arthropod communities

Whole-organism community DNA (wocDNA) metabarcoding has become a necessary
and powerful tool to study mixed communities from bulk samples by
detecting short DNA sequences. This review integrates the use of
arthropods as ecological indicators through wocDNA metabarcoding, covering
key methodological aspects from sampling design to bioinformatics, and
highlighting ASV-based (Amplicon Sequence Variants) pipelines for
incorporating haplotype-level variation. The success of wocDNA
metabarcoding relies on proper sampling methods, good laboratory
practices, cleaning of bulk samples, selecting suitable arthropod sizes,
efficient DNA extractions, accurate library quantification, appropriate
genetic markers for accurate taxonomic identification, and effective
sequence filtering. Incorporating haplotype data into monitoring unveils
intraspecific variation that could complement species-level diversity,
thus enhancing conventional analyses. Choosing abundance- or
incidence-based approaches is key for selecting appropriate statistical
methods. WocDNA metabarcoding provides biodiversity estimates for
entire communities and allows researchers to derive insights that can
inform the formulation or refinement of hypotheses. These refined
hypotheses, based on the obtained biodiversity estimates, can then guide
ecosystem conservation.