Endosymbiotic adaptations in three new bacterial species associated withDictyostelium discoideum:Paraburkholderia agricolarissp. nov.,Paraburkholderia hayleyellasp. nov., andParaburkholderia bonnieasp. nov

Abstract

Here we give names to three new species of Paraburkholderia that can remain in symbiosis indefinitely in the spores of a soil dwelling eukaryote, Dictyostelium discoideum. The new species P. agricolaris sp. nov., P. hayleyella sp. nov., and P. bonniea sp. nov. are widespread across the eastern USA and were isolated as internal symbionts of wild-collected D. discoideum. We describe these sp. nov. using several approaches. Evidence that they are each a distinct new species comes from their phylogenetic position, average nucleotide identity, genome-genome distance, carbon usage, reduced length, cooler optimal growth temperature, metabolic tests, and their previously described ability to invade D. discoideum amoebae and form a symbiotic relationship. All three of these new species facilitate the prolonged carriage of food bacteria by D. discoideum, though they themselves are not food. Further studies of the interactions of these three new species with D. discoideum should be fruitful for understanding the ecology and evolution of symbioses.

Paraburkholderia Symbionts Display Variable Infection Patterns That Are Not Predictive of Amoeba Host Outcomes

“…We hypothesized that if infection outcomes were variable across strains, we would be able to interrogate the relationship between infection patterns and host outcomes. These thirteen Paraburkholderia strains represent the three-known natural Paraburkholderia symbiont species of D. discoideum [29]. Phenotypic, metabolic, and phylogenetic comparisons have been done for representative strains of each of these species [29].…”

“…These thirteen Paraburkholderia strains represent the three-known natural Paraburkholderia symbiont species of D. discoideum [29]. Phenotypic, metabolic, and phylogenetic comparisons have been done for representative strains of each of these species [29]. For all thirteen strains used in this study 16S rRNA and phaC, atpD, gltB, lepA, and trpB house-keeping gene sequences have been previously analyzed for the construction of a phylogeny [25].…”

“…D. discoideum has effective innate immune mechanisms that function to resist or eliminate pathogens during vegetative and multicellular stages [ 4 , 17 , 18 , 19 , 20 , 21 , 22 ]. Despite the many challenges a bacterium faces to effectively colonize D. discoideum , bacteria belonging to the Paraburkholderia genus are prevalent and stable endosymbionts of D. discoideum [ 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. These bacteria comprise three novel species, P. bonniea, P. agricolaris, and P. hayleyella, which intracellularly infect D. discoideum amoeba and persist through the social stage to continue transmission in spore cells and sori contents [ 25 , 26 , 29 ].…”

“…Despite the many challenges a bacterium faces to effectively colonize D. discoideum , bacteria belonging to the Paraburkholderia genus are prevalent and stable endosymbionts of D. discoideum [ 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. These bacteria comprise three novel species, P. bonniea, P. agricolaris, and P. hayleyella, which intracellularly infect D. discoideum amoeba and persist through the social stage to continue transmission in spore cells and sori contents [ 25 , 26 , 29 ]. These species and related members have previously been described as belonging to the Burkholderia genus but have since been proposed as species of the recently nominated Paraburkholderia genera [ 30 ].…”

Novel Chlamydiae andAmoebophilusendosymbionts are prevalent in wild isolates of the model social amoebaDictyostelium discoideum

“…The D. discoideum microbiome is composed of both persistent and transient bacterial associates (Brock et al, 2018). Three different newly named Paraburkholderia species, P. agricolaris, P. hayleyella, and P. bonniea are persistent bacterial symbionts that intracellularly infect vegetative amoebae and spore cells (Brock et al, 2020(Brock et al, , 2011Haselkorn et al, 2018;Khojandi et al, 2019;Shu et al, 2018). While these Paraburkholderia themselves do not nourish D. discoideum, they confer farming to their hosts by allowing food bacteria to survive in the fruiting body.…”