Tardigrade Community Microbiomes in North American Orchards Include Putative Endosymbionts and Plant Pathogens

Abstract

The microbiome of tardigrades, a phylum of microscopic animals best known for their ability to survive extreme conditions, is poorly studied worldwide and completely unknown in North America. An improved understanding of tardigrade-associated bacteria is particularly important because tardigrades have been shown to act as vectors of the plant pathogen Xanthomonas campestris in the laboratory. However, the potential role of tardigrades as reservoirs and vectors of phytopathogens has not been investigated further. This study analyzed the microbiota of tardigrades from six apple orchards in central Iowa, United States, and is the first analysis of the microbiota of North American tardigrades. It is also the first ever study of the tardigrade microbiome in an agricultural setting. We utilized 16S rRNA gene amplicon sequencing to characterize the tardigrade community microbiome across four contrasts: location, substrate type (moss or lichen), collection year, and tardigrades vs. their substrate. Alpha diversity of the tardigrade community microbiome differed significantly by location and year of collection but not by substrate type. Our work also corroborated earlier findings, demonstrating that tardigrades harbor a distinct microbiota from their environment. We also identified tardigrade-associated taxa that belong to genera known to contain phytopathogens (Pseudomonas, Ralstonia, and the Pantoea/Erwinia complex). Finally, we observed members of the genera Rickettsia and Wolbachia in the tardigrade microbiome; because these are obligate intracellular genera, we consider these taxa to be putative endosymbionts of tardigrades. These results suggest the presence of putative endosymbionts and phytopathogens in the microbiota of wild tardigrades in North America.

Pinpointing the microbiota of tardigrades: what is really there?

“…The issue of potential contamination in tardigrade microbiota studies was first mentioned by Tibbs-Cortes et al (2022), who applied a decontamination strategy in the analysis of microbiota of tardigrade communities extracted from environmental samples. A novel component of our study is information regarding the diversity of contamination sources that may affect microbial community profiles.…”

“…The authors found that microorganisms present in the environment are also present in tardigrades, and spotted significant differences between the microbiota of fully-fed and starved tardigrades. A recent tardigrade microbiota study conducted by Tibbs-Cortes et al (2022), characterized microbiota of tardigrade communities (tardigrades extracted from samples, without species identification) in American orchards, with the application of decontamination strategy. Using the same samples, the authors observed signs of Rickettsia infection in two of 55 tardigrade individuals using FISH (Tibbs-Cortes et al 2023).…”

Playing Peekaboo with a Master Manipulator: Metagenetic Detection and Phylogenetic Analysis of Wolbachia Supergroups in Freshwater Invertebrates

“…In 2018-2021, our team discovered Wolbachia infections in Tardigrada [34], Bivalvia [35] and Crustacea [32]. Later, Tibbs-Cortes et al [36] also confirmed Wolbachia infection in the microbiome of Tardigrada. This allows us to suspect that more extensive sequencing would bring more new data of infections in new host taxa, potentially revising our understanding of Wolbachia evolution.…”

“…To check whether all Wolbachia infections found in Tardigrada represented the same supergroup, we carried out the phylogenetic reconstructions of tardigrade Wolbachia 16S rRNA sequences identified in our study and in previous surveys [34,36]. All of these sequences were also compared with other Rickettsiales sequences obtained by Mioduchowska et al [34] and Tibbs-Cortes et al [36].…”

“…To check whether all Wolbachia infections found in Tardigrada represented the same supergroup, we carried out the phylogenetic reconstructions of tardigrade Wolbachia 16S rRNA sequences identified in our study and in previous surveys [34,36]. All of these sequences were also compared with other Rickettsiales sequences obtained by Mioduchowska et al [34] and Tibbs-Cortes et al [36]. Reconstructed phylogenetic relationships positioned our new sequences together with Wolbachia sequences from previous studies in a clade consisting of strains belonging to the supergroup A (Figure 4).…”