Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum: Paraburkholderia agricolaris sp. nov., Paraburkholderia hayleyella sp. nov., and Paraburkholderia bonniea sp. nov.

Debra A Brock,Alexander S Bradley,Tamara S Haselkorn,Melanie K Suess,Suegene Noh,Mahboubeh Tavakoli-Nezhad,Joan E Strassmann,Alicia N.M Hubert,David C Queller,Susanne Disalvo,Katherine S Geist

doi:10.7717/peerj.9151

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.

Highlights

Eukaryote soil-dwelling amoebae are exposed to bacteria in their environments
Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum: Paraburkholderia agricolaris sp. nov., Paraburkholderia hayleyella sp. nov., and Paraburkholderia bonniea sp. nov
P. agricolaris BaQS159 is estimated to have a genome of approximately 8.7 megabase pairs (Mbp), which is similar size to other closely related Paraburkholderia (e.g., P. fungorum ATCC BAA-463 has a genome size of 9 Mbp) while P. hayleyella BhQS11 and P. bonniea BbQS859 are estimated to have a genome of less than half this size at approximately 4.1 Mbp each (Table S9)

Summary

Introduction

Eukaryote soil-dwelling amoebae are exposed to bacteria in their environments. Amoebae ingest bacteria, but some bacteria may foil their digestive systems and take up residenceHow to cite this article Brock DA, Noh S, Hubert ANM, Haselkorn TS, DiSalvo S, Suess MK, Bradley AS, Tavakoli-Nezhad M, Geist KS, Queller DC, Strassmann JE. 2020. Amoebae may be penetrated by bacteria using secretion systems (Tosetti, Croxatto & Greub, 2014). Some of these bacteria become permanent or semi-permanent residents (Oliver et al, 2010). Based on data presented here and data previously published (Brock et al, 2011; DiSalvo et al, 2015; Brock et al, 2016; Shu et al, 2018a; Shu et al, 2018b; Haselkorn et al, 2019), we name three new species in the plant beneficial and environmental Paraburkholderia clade of Burkholderia sensu lato

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