Investigating soil mesofauna cryptic diversity: Current challenges and perspectives

Abstract

Cryptic species lacking distinct morphological features are widespread among soil fauna, including such functionally significant groups as springtails, mites and enchytraeids. Their presence, diversity and biomass may impact ecosystem services provided by belowground ecosystems. However, traditionally, the potential effects of cryptic diversity in explaining the functional significance of different mesofauna species have been overlooked due to the widespread practice of morphology-based species identification. This review synthesizes the current state of knowledge on soil fauna cryptic species identification, emphasizing specific molecular techniques as the most reliable and precise method currently available for detecting and unravelling cryptic diversity. We analysed 326 scientific contributions available via Scopus or Web of Science, compiling information on genetic markers used to study cryptic diversity, including targeted gene regions, PCR primers and methods for estimating genetic distances. For comprehensive genetic analysis, combinations of mitochondrial Cytochrome c Oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) genes, together with nuclear markers such as 28S ribosomal RNA (28S rRNA) or Histone H3 (H3), are most commonly used. Our analysis revealed taxon-specific thresholds: while COI divergences greater than 3% typically indicate cryptic species in collembolans, higher thresholds appear justified for mites (up to 17%) and enchytraeids (up to 5%) when supported by conserved nuclear markers (28S/H3), ecological or geographic coherence and the absence of intermediate forms. Advances in molecular research have also facilitated the analysis of cryptic diversity within morphospecies an—approach widely applied in soil ecology, especially when species-level identification is hindered by limited taxonomic literature or expertise. However, our findings also demonstrated that it is a long way before methodological development in molecular approaches would ensure reliable cryptic species identifications in soil mesofauna. Even more should be done in linking the revealed cryptic diversity with its functional implications and possible differences in responding to environmental change. Besides these current limitations, we are positive that deeper integration of cryptic diversity knowledge into soil ecological research will significantly increase the reliability and precision of soil functions and services assessment.