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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Cell. Infect. Microbiol. | doi: 10.3389/fcimb.2018.00411

Diversity of free-living environmental bacteria and their interactions with a bactivorous amoeba

 Debra A. Brock1*,  Tamara S. Haselkorn2,  Justine R. Garcia1, Usman Bashir1, Tracy E. Douglas1, Jesse Galloway3, Fischer Brodie3,  David Queller1 and  Joan Strassmann1
  • 1Washington University in St. Louis, United States
  • 2University of Central Arkansas, United States
  • 3University of Virginia, Mountain Lake Biological Station, United States

A small subset of bacteria in soil interact directly with eukaryotes. Which ones do so can reveal what is important to a eukaryote and how eukaryote defenses might be breached. Soil amoebae are simple eukaryotic organisms and as such could be particularly good for understanding how eukaryote microbiomes originate and are maintained. One such amoeba, Dictyostelium discoideum, has both permanent and temporary associations with bacteria. Here we focus on culturable bacterial associates in order to interrogate their relationship with D. discoideum. To do this, we isolated over 250 D. discoideum fruiting body samples from soil and deer feces at Mountain Lake Biological Station. In one-third of the wild D. discoideum we tested, one to six bacterial species were found per fruiting body sorus (spore mass) for a total of 174 bacterial isolates. The remaining two-thirds of D. discoideum fruiting body samples did not contain culturable bacteria, as is thought to be the norm. A majority (71.4%) of the unique bacterial haplotypes are in Proteobacteria. The rest are in either Actinobacteria, Bacteriodetes, or Firmicutes. The highest bacterial diversity was found in D. discoideum fruiting bodies originating from deer feces (27 OTUs), greater than either of those originating in shallow (11 OTUs) or in deep soil (4 OTUs). Rarefaction curves and the Chao1 estimator for species richness indicated the diversity in any substrate was not fully sampled, but for soil it came close. A majority of the D. discoideum-associated bacteria were edible by D. discoideum and supported its growth (75.2% for feces and 81.8% for soil habitats). However, we found several bacteria genera were able to evade phagocytosis and persist in D. discoideum cells through one or more social cycles. This study focuses not on the entire D. discoideum microbiome, but on the culturable subset of bacteria that have important eukaryote interactions as prey, symbionts, or pathogens. These eukaryote and bacteria interactions may provide fertile ground for investigations of bacteria using amoebas to gain an initial foothold in eukaryotes and of the origins of symbiosis and simple microbiomes.

Keywords: Dictyostelium, Bacteria, microbiome, Symbiosis, Amoebae, Persistence, predation

Received: 01 Aug 2018; Accepted: 05 Nov 2018.

Edited by:

Sascha Thewes, Freie Universität Berlin, Germany

Reviewed by:

Eric D. Cambronne, University of Texas at Austin, United States
Frank C. Gibson, III, University of Florida, United States
Pauline Schaap, University of Dundee, United Kingdom  

Copyright: © 2018 Brock, Haselkorn, Garcia, Bashir, Douglas, Galloway, Brodie, Queller and Strassmann. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Debra A. Brock, Washington University in St. Louis, St. Louis, United States, dbrock@wustl.edu