Protist feeding patterns and growth rate are related to their predatory impacts on soil bacterial communities

Abstract

Predatory protists are major consumers of soil micro-organisms. By selectively feeding on their prey, they can shape soil microbiome composition and functions. While different protists are known to show diverging impacts, it remains impossible to predict a priori the effect of a given species. Various protist traits including phylogenetic distance, growth rate and volume have been previously linked to the predatory impact of protists. Closely-related protists,however, also showed distinct prey choices which could mirror specificity in their dietary niche. We, therefore, aimed to estimate the dietary niche breadth and overlap of eight protist isolates on 20 bacterial species in plate assays. To assess the informative value of previously suggested and newly proposed (feeding-related) protist traits, we related them to the impacts of predation of each protist on a protist-free soil bacterial community in a soil microcosm via 16S rRNA gene amplicon sequencing. We could demonstrate that each protist showed a distinct feeding pattern in vitro. Further, the assayed protist feeding patterns and growth rates correlated well with the observed predatory impacts on the structure of soil bacterial communities. We thus conclude that in vitro screening has the potential to inform on the specific predatory impact of selected protists.

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

“…The first is that predatory protists are never fully specialized in a single prey species. While it has been widely acknowledged that food regimes of protists vary between species, all predatory protists known so far eat diverse bacterial and fungal species (Amacker et al, 2022; Geisen et al, 2016). The genus/family‐level resolution obtained by OTUs/ASVs adds another level of uncertainty in high‐detail assignment of functional groups as distinct protist species can differ in their feeding patterns (Amacker et al, 2022; Glucksman et al, 2010).…”

“…While it has been widely acknowledged that food regimes of protists vary between species, all predatory protists known so far eat diverse bacterial and fungal species (Amacker et al, 2022; Geisen et al, 2016). The genus/family‐level resolution obtained by OTUs/ASVs adds another level of uncertainty in high‐detail assignment of functional groups as distinct protist species can differ in their feeding patterns (Amacker et al, 2022; Glucksman et al, 2010). Species within the same genus can even differ in their coarse functional positions like Pythium species that can range from plant parasitic to animal parasitic (Rai et al, 2020).…”

Extensive Cryptic Diversity and Ecological Associations Uncovered among Mexican and Global Collections of Naegleria and Vermamoeba Species by 18S Ribosomal DNA, Internal Transcribed Spacer, and Cytochrome Oxidase Subunit I Sequence Analysis

“…Free-living amoebae (FLA) comprise a diverse and ancient assemblage of testate and naked predatory protists that feed on other microorganisms by phagocytosis, playing an essential role in shaping microbial communities ( 1 , 2 ). However, some microbes, including diverse opportunistic pathogens, have developed various molecular strategies to evade amoebal digestion, eventually using them as replication or survival niches ( 3 – 5 ) Over evolutionary time, these interactions developed into a notorious diversity of symbioses between protists, bacteria, and archaea ( 6 ).…”

Microbiome predators in changing soils

“…These approaches conflict with the fact that potentially millions of functionally diverse microbiome predator species exist (Geisen, Wall, & van der Putten, 2019). We now know that microbiome predators have species‐specific feeding differences that can change microbiome composition and functioning (Amacker et al, 2022; Glucksman et al, 2010), which can explain the major impact of microbiome predators on the microbiome (Geisen et al, 2016; Saleem et al, 2012). Yet, we are missing an understanding of the functional importance of microbiome predator communities for key ecosystem functions that soils provide, such as elemental cycling and plant performance (including growth, health, and yield).…”