Further insights in the Tardigrada microbiome: phylogenetic position and prevalence of infection of four new Alphaproteobacteria putative endosymbionts

Abstract

Data from a previous study showed that microbiomes of six tardigrade species are species-specific and distinct from associated environmental microbes. We here performed a more in-depth analyses of those data, to identify and characterize new potential symbionts. The most abundant bacterial operational taxonomic units (OTUs) found in tardigrades are classified, and their prevalence in other environments is assessed using public databases. A subset of OTUs was selected for molecular phylogenetic analyses based on their affiliation with host-associated bacterial families in tardigrades. Almost 22.6% of the most abundant OTUs found do not match any sequence at 99% identity in the IMNGS database. These novel OTUs include four putative tardigrade endosymbionts from Alphaproteobacteria (Anaplasmataceae and Candidatus Tenuibacteraceae), which are characterized by 16S rRNA gene analysis and investigated for their infection rates in: Echiniscus trisetosus, Richtersisus coronifer and Macrobiotus macrocalix. These putative endosymbionts have an infection prevalence between 9.1% and 40.0%, and are, therefore, likely secondary symbionts, not essential for tardigrade survival and reproduction. Using fluorescence in situ hybridization (FISH), we detected bacteria on the cuticle and within the ovary of E. trisetosus, suggesting possible vertical transmission. This study highlights the great contribution in biodiversity discovery that neglected phyla can provide in microbiome and symbiosis studies.

Tardigrade community microbiomes in North American orchards include putative endosymbionts and plant pathogens

“…The life cycle of tardigrades poses a unique selective pressure on any permanent residents of the microbiota, as these organisms would also have to survive within the tardigrade during cryptobiosis. This would be especially true for the obligate endosymbiotic taxa Rickettsiales and Polynucleobacter previously observed in tardigrades (Vecchi et al 2018;Roberto Guidetti et al 2020;Kaczmarek et al 2020;Mioduchowska et al 2021), as well as for the Rickettsia identified in the current study (see below).…”

“…Our survey corroborates previous observations of putative endosymbionts of the obligate intracellular order Rickettsiales associated with tardigrades. Three of the four previous surveys of the tardigrade microbiome have detected OTUs of this order (Vecchi et al 2018;Roberto Guidetti et al 2020;Kaczmarek et al 2020;Mioduchowska et al 2021 and RDP analysis (Table S2, Table S3). The relative abundance of OTU 180 was significantly higher in tardigrades (0.88%) than in their lichen substrate (0.0012%) (Table S7) as well as significantly higher in 2020 (1.0%) than in 2019 (0.00026%) (Table S8, Table S9).…”

“…Tenuibacteraceae. These were differentially associated with different tardigrade species, and fluorescence in situ hybridization (FISH) detected bacteria within the ovaries of some tardigrades, suggesting that tardigrade endosymbionts are vertically transmitted (Roberto Guidetti et al 2020).…”

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

“…Tenuibacteraceae . These were differentially associated with different tardigrade species, and fluorescence in situ hybridization (FISH) detected bacteria within the ovaries of some tardigrades, suggesting that tardigrade endosymbionts are vertically transmitted ( Guidetti et al, 2020 ).…”

‘Candidatus Gromoviella agglomerans’, a novel intracellular Holosporaceae parasite of the ciliate Paramecium showing marked genome reduction

“…Tenuibacteraceae’ (Kroer et al ., 2016), have a distinctive host range, being found in association with metazoans, in particular arthropods and other ecdysozoans (e.g. Wang et al ., 2004; Koch et al ., 2013; Kroer et al ., 2016; Guidetti et al ., 2020), but to date never with protists. Interestingly, according to the data available (Wang et al ., 2004; Kroer et al ., 2016), these bacteria were found extracellularly, namely in the gut lumen.…”