Contemporary issues, current best practice and ways forward in soil protist ecology

Abstract

Soil protists are increasingly studied due to a release from previous methodological constraints and the acknowledgement of their immense diversity and functional importance in ecosystems. However, these studies often lack sufficient depth in knowledge, which is visible in the form of falsely used terms and false‐ or over‐interpreted data with conclusions that cannot be drawn from the data obtained. As we welcome that also non‐experts include protists in their still mostly bacterial and/or fungal‐focused studies, our aim here is to help avoid some common errors. We provide suggestions for current terms to use when working on soil protists, like protist instead of protozoa, predator instead of grazer, microorganisms rather than microflora and other terms to be used to describe the prey spectrum of protists. We then highlight some dos and don'ts in soil protist ecology including challenges related to interpreting 18S rRNA gene amplicon sequencing data. We caution against the use of standard bioinformatic settings optimized for bacteria and the uncritical reliance on incomplete and partly erroneous reference databases. We also show why causal inferences cannot be drawn from sequence‐based correlation analyses or any sampling/monitoring, study in the field without thorough experimental confirmation and sound understanding of the biology of taxa. Together, we envision this work to help non‐experts to more easily include protists in their soil ecology analyses and obtain more reliable interpretations from their protist data and other biodiversity data that, in the end, will contribute to a better understanding of soil ecology.

In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities

“…This can be particularly problematic when analyses target complex mixtures of DNA(e.g. eDNA extracted from soil) that comprise the DNA of both nematodes and other organisms [58,59]. For instance, in vitro assessments of the EcoF-EcoR primers detected a very large number of non-nematode taxa, suggesting that this marker can be not appropriate for analyses only focusing on nematodes [48].…”

Toward a Common Set of Functional Traits for Soil Protists

“…Despite these challenges, the framework allowed us to develop a functional dataset on proglacial soils, representing a starting point toward the creation of a common trait repository. However, the use of a single generic eukaryotic marker limited the ability to target specific taxonomic groups (e.g., Amoebozoa or Heterolobosea; Geisen et al, 2023) and, therefore, the dataset presented is not complete, as widespread soil protist taxa are missing.…”

“…The traits of organisms are known to be closely linked to ecosystem functioning (Loreau et al, 2001;Cardinale et al, 2012;Naeem et al, 2012). Thus, refined information on their functional diversity is required to deepen our understanding of the relationships between soil protists and ecosystem functions, but also their role in biogeochemical cycles, and how abiotic and biotic drivers shape communities in space and time (Cardinale et al, 2012;Naeem et al, 2012;Briones, 2014;Geisen et al, 2023). Functional diversity represents the variety of morphological, ecological, behavioral, and physiological traits exhibited by different species (Hooper et al, 2005;Cadotte et al, 2011).…”

“…1). This can be related to the complexity of the study of protists ecology (Geisen et al, 2023), but also to the lack of a conceptual framework and comprehensive databases covering key functional traits (Dumack et al, 2020). So far, publicly available datasets are mostly restricted to a few major taxa such as Cercozoa and Endomyxa (Fiore-Donno et al, 2019;Dumack et al, 2020), phytoplankton (Laplace-Treyture et al, 2021, or a subset of Ciliophora and amoeboid protists (Gulin et al, 2022).…”