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Scott TJ, Stephenson CJ, Rao S, Queller DC, Strassmann JE. Unpredictable soil conditions can affect the prevalence of a microbial symbiosis. PeerJ 2024; 12:e17445. [PMID: 38784393 PMCID: PMC11114107 DOI: 10.7717/peerj.17445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
The evolution of symbiotic interactions may be affected by unpredictable conditions. However, a link between prevalence of these conditions and symbiosis has not been widely demonstrated. We test for these associations using Dictyostelium discoideum social amoebae and their bacterial endosymbionts. D. discoideum commonly hosts endosymbiotic bacteria from three taxa: Paraburkholderia, Amoebophilus and Chlamydiae. Three species of facultative Paraburkholderia endosymbionts are the best studied and give hosts the ability to carry prey bacteria through the dispersal stage to new environments. Amoebophilus and Chlamydiae are obligate endosymbiont lineages with no measurable impact on host fitness. We tested whether the frequency of both single infections and coinfections of these symbionts were associated with the unpredictability of their soil environments by using symbiont presence-absence data from D. discoideum isolates from 21 locations across the eastern United States. We found that symbiosis across all infection types, symbiosis with Amoebophilus and Chlamydiae obligate endosymbionts, and symbiosis involving coinfections were not associated with any of our measures. However, unpredictable precipitation was associated with symbiosis in two species of Paraburkholderia, suggesting a link between unpredictable conditions and symbiosis.
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Affiliation(s)
- Trey J. Scott
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Calum J. Stephenson
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Sandeep Rao
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - David C. Queller
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Joan E. Strassmann
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
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Souza LS, Solowiej-Wedderburn J, Bonforti A, Libby E. Modeling endosymbioses: Insights and hypotheses from theoretical approaches. PLoS Biol 2024; 22:e3002583. [PMID: 38598454 PMCID: PMC11006130 DOI: 10.1371/journal.pbio.3002583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024] Open
Abstract
Endosymbiotic relationships are pervasive across diverse taxa of life, offering key avenues for eco-evolutionary dynamics. Although a variety of experimental and empirical frameworks have shed light on critical aspects of endosymbiosis, theoretical frameworks (mathematical models) are especially well-suited for certain tasks. Mathematical models can integrate multiple factors to determine the net outcome of endosymbiotic relationships, identify broad patterns that connect endosymbioses with other systems, simplify biological complexity, generate hypotheses for underlying mechanisms, evaluate different hypotheses, identify constraints that limit certain biological interactions, and open new lines of inquiry. This Essay highlights the utility of mathematical models in endosymbiosis research, particularly in generating relevant hypotheses. Despite their limitations, mathematical models can be used to address known unknowns and discover unknown unknowns.
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Affiliation(s)
- Lucas Santana Souza
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
- Integrated Science Lab, Umeå University, Umeå, Sweden
| | - Josephine Solowiej-Wedderburn
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
- Integrated Science Lab, Umeå University, Umeå, Sweden
| | - Adriano Bonforti
- Integrated Science Lab, Umeå University, Umeå, Sweden
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, Norrbyn, Sweden
| | - Eric Libby
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
- Integrated Science Lab, Umeå University, Umeå, Sweden
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Steele MI, Peiser JM, Shreenidhi PM, Strassmann JE, Queller DC. Predation-resistant Pseudomonas bacteria engage in symbiont-like behavior with the social amoeba Dictyostelium discoideum. ISME J 2023; 17:2352-2361. [PMID: 37884792 PMCID: PMC10689837 DOI: 10.1038/s41396-023-01535-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023]
Abstract
The soil amoeba Dictyostelium discoideum acts as both a predator and potential host for diverse bacteria. We tested fifteen Pseudomonas strains that were isolated from transiently infected wild D. discoideum for ability to escape predation and infect D. discoideum fruiting bodies. Three predation-resistant strains frequently caused extracellular infections of fruiting bodies but were not found within spores. Furthermore, infection by one of these species induces secondary infections and suppresses predation of otherwise edible bacteria. Another strain can persist inside of amoebae after being phagocytosed but is rarely taken up. We sequenced isolate genomes and discovered that predation-resistant isolates are not monophyletic. Many Pseudomonas isolates encode secretion systems and toxins known to improve resistance to phagocytosis in other species, as well as diverse secondary metabolite biosynthetic gene clusters that may contribute to predation resistance. However, the distribution of these genes alone cannot explain why some strains are edible and others are not. Each lineage may employ a unique mechanism for resistance.
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Affiliation(s)
- Margaret I Steele
- Biology Department, Washington University in St. Louis, St. Louis, MO, USA.
| | - Jessica M Peiser
- Biology Department, Washington University in St. Louis, St. Louis, MO, USA
| | - P M Shreenidhi
- Biology Department, Washington University in St. Louis, St. Louis, MO, USA
| | - Joan E Strassmann
- Biology Department, Washington University in St. Louis, St. Louis, MO, USA
| | - David C Queller
- Biology Department, Washington University in St. Louis, St. Louis, MO, USA
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Scott TJ, Larsen TJ, Brock DA, Uhm SYS, Queller DC, Strassmann JE. Symbiotic bacteria, immune-like sentinel cells, and the response to pathogens in a social amoeba. R Soc Open Sci 2023; 10:230727. [PMID: 37593719 PMCID: PMC10427822 DOI: 10.1098/rsos.230727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/27/2023] [Indexed: 08/19/2023]
Abstract
Some endosymbionts living within a host must modulate their hosts' immune systems in order to infect and persist. We studied the effect of a bacterial endosymbiont on a facultatively multicellular social amoeba host. Aggregates of the amoeba Dictyostelium discoideum contain a subpopulation of sentinel cells that function akin to the immune systems of more conventional multicellular organisms. Sentinel cells sequester and discard toxins from D. discoideum aggregates and may play a central role in defence against pathogens. We measured the number and functionality of sentinel cells in aggregates of D. discoideum infected by bacterial endosymbionts in the genus Paraburkholderia. Infected D. discoideum produced fewer and less functional sentinel cells, suggesting that Paraburkholderia may interfere with its host's immune system. Despite impaired sentinel cells, however, infected D. discoideum were less sensitive to ethidium bromide toxicity, suggesting that Paraburkholderia may also have a protective effect on its host. By contrast, D. discoideum infected by Paraburkholderia did not show differences in their sensitivity to two non-symbiotic pathogens. Our results expand previous work on yet another aspect of the complicated relationship between D. discoideum and Paraburkholderia, which has considerable potential as a model for the study of symbiosis.
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Affiliation(s)
- Trey J. Scott
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tyler J. Larsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Debra A. Brock
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - So Yeon Stacey Uhm
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - David C. Queller
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Joan E. Strassmann
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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Mather RV, Larsen TJ, Brock DA, Queller DC, Strassmann JE. Paraburkholderia symbionts isolated from Dictyostelium discoideum induce bacterial carriage in other Dictyostelium species. Proc Biol Sci 2023; 290:20230977. [PMID: 37464760 PMCID: PMC10354463 DOI: 10.1098/rspb.2023.0977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
The social amoeba Dictyostelium discoideum engages in a complex relationship with bacterial endosymbionts in the genus Paraburkholderia, which can benefit their host by imbuing it with the ability to carry prey bacteria throughout its life cycle. The relationship between D. discoideum and Paraburkholderia has been shown to take place across many strains and a large geographical area, but little is known about Paraburkholderia's potential interaction with other dictyostelid species. We explore the ability of three Paraburkholderia species to stably infect and induce bacterial carriage in other dictyostelid hosts. We found that all three Paraburkholderia species successfully infected and induced carriage in seven species of Dictyostelium hosts. While the overall behaviour was qualitatively similar to that previously observed in infections of D. discoideum, differences in the outcomes of different host/symbiont combinations suggest a degree of specialization between partners. Paraburkholderia was unable to maintain a stable association with the more distantly related host Polysphondylium violaceum. Our results suggest that the mechanisms and evolutionary history of Paraburkholderia's symbiotic relationships may be general within Dictyostelium hosts, but not so general that it can associate with hosts of other genera. Our work further develops an emerging model system for the study of symbiosis in microbes.
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Affiliation(s)
- Rory Vu Mather
- Department of Biology, Washington University in St Louis, St Louis, MO 63130-4899, USA
- Harvard Medical School, Boston, MA 02115-6027, USA
| | - Tyler J. Larsen
- Department of Biology, Washington University in St Louis, St Louis, MO 63130-4899, USA
| | - Debra A. Brock
- Department of Biology, Washington University in St Louis, St Louis, MO 63130-4899, USA
| | - David C. Queller
- Department of Biology, Washington University in St Louis, St Louis, MO 63130-4899, USA
| | - Joan E. Strassmann
- Department of Biology, Washington University in St Louis, St Louis, MO 63130-4899, USA
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Medina JM, Queller DC, Strassmann JE, Garcia JR. The social amoeba Dictyostelium discoideum rescues Paraburkholderia hayleyella, but not P. agricolaris, from interspecific competition. FEMS Microbiol Ecol 2023; 99:fiad055. [PMID: 37226596 PMCID: PMC10243984 DOI: 10.1093/femsec/fiad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 05/26/2023] Open
Abstract
Bacterial endosymbionts can provide benefits for their eukaryotic hosts, but it is often unclear if endosymbionts benefit from these relationships. The social amoeba Dictyostelium discoideum associates with three species of Paraburkholderia endosymbionts, including P. agricolaris and P. hayleyella. These endosymbionts can be costly to the host but are beneficial in certain contexts because they allow D. discoideum to carry prey bacteria through the dispersal stage. In experiments where no other species are present, P. hayleyella benefits from D. discoideum while P. agricolaris does not. However, the presence of other species may influence this symbiosis. We tested if P. agricolaris and P. hayleyella benefit from D. discoideum in the context of resource competition with Klebsiella pneumoniae, the typical laboratory prey of D. discoideum. Without D. discoideum, K. pneumoniae depressed the growth of both Paraburkholderia symbionts, consistent with competition. P. hayleyella was more harmed by interspecific competition than P. agricolaris. We found that P. hayleyella was rescued from competition by D. discoideum, while P. agricolaris was not. This may be because P. hayleyella is more specialized as an endosymbiont; it has a highly reduced genome compared to P. agricolaris and may have lost genes relevant for resource competition outside of its host.
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Affiliation(s)
- James M Medina
- Department of Biology, One Brookings Drive, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - David C Queller
- Department of Biology, One Brookings Drive, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Joan E Strassmann
- Department of Biology, One Brookings Drive, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Justine R Garcia
- Department of Biology, New Mexico Highlands University, 1005 Diamond Ave, Las Vegas, NM 87701, USA
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Wang Z, Huang W, Mai Y, Tian Y, Wu B, Wang C, Yan Q, He Z, Shu L. Environmental stress promotes the persistence of facultative bacterial symbionts in amoebae. Ecol Evol 2023; 13:e9899. [PMID: 36937064 PMCID: PMC10019945 DOI: 10.1002/ece3.9899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
Amoebae are one major group of protists that are widely found in natural and engineered environments. They are a significant threat to human health not only because many of them are pathogenic but also due to their unique role as an environmental shelter for pathogens. However, one unsolved issue in the amoeba-bacteria relationship is why so many bacteria live within amoeba hosts while they can also live independently in the environments. By using a facultative amoeba- Paraburkholderia bacteria system, this study shows that facultative bacteria have higher survival rates within amoebae under various environmental stressors. In addition, bacteria survive longer within the amoeba spore than in free living. This study demonstrates that environmental stress can promote the persistence of facultative bacterial symbionts in amoebae. Furthermore, environmental stress may potentially select and produce more amoeba-resisting bacteria, which may increase the biosafety risk related to amoebae and their intracellular bacteria.
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Affiliation(s)
- Zihe Wang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for BiocontrolSun Yat‐sen UniversityGuangzhouChina
| | - Wei Huang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for BiocontrolSun Yat‐sen UniversityGuangzhouChina
| | - Yingwen Mai
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for BiocontrolSun Yat‐sen UniversityGuangzhouChina
| | - Yuehui Tian
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for BiocontrolSun Yat‐sen UniversityGuangzhouChina
| | - Bo Wu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for BiocontrolSun Yat‐sen UniversityGuangzhouChina
| | - Cheng Wang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for BiocontrolSun Yat‐sen UniversityGuangzhouChina
| | - Qingyun Yan
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for BiocontrolSun Yat‐sen UniversityGuangzhouChina
| | - Zhili He
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for BiocontrolSun Yat‐sen UniversityGuangzhouChina
| | - Longfei Shu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for BiocontrolSun Yat‐sen UniversityGuangzhouChina
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Hasik AZ, de Angeli Dutra D, Doherty JF, Duffy MA, Poulin R, Siepielski AM. Resetting our expectations for parasites and their effects on species interactions: a meta-analysis. Ecol Lett 2023; 26:184-199. [PMID: 36335559 PMCID: PMC10099232 DOI: 10.1111/ele.14139] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/08/2022]
Abstract
Despite the ubiquitous nature of parasitism, how parasitism alters the outcome of host-species interactions such as competition, mutualism and predation remains unknown. Using a phylogenetically informed meta-analysis of 154 studies, we examined how the mean and variance in the outcomes of species interactions differed between parasitized and non-parasitized hosts. Overall, parasitism did not significantly affect the mean or variance of host-species interaction outcomes, nor did the shared evolutionary histories of hosts and parasites have an effect. Instead, there was considerable variation in outcomes, ranging from strongly detrimental to strongly beneficial for infected hosts. Trophically-transmitted parasites increased the negative effects of predation, parasites increased and decreased the negative effects of interspecific competition for parasitized and non-parasitized heterospecifics, respectively, and parasites had particularly strong negative effects on host species interactions in freshwater and marine habitats, yet were beneficial in terrestrial environments. Our results illuminate the diverse ways in which parasites modify critical linkages in ecological networks, implying that whether the cumulative effects of parasitism are considered detrimental depends not only on the interactions between hosts and their parasites but also on the many other interactions that hosts experience.
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Affiliation(s)
- Adam Z Hasik
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA.,Jacob Blaustein Center for Scientific Cooperation, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | | | - Jean-François Doherty
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Meghan A Duffy
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Adam M Siepielski
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
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Noh S, Capodanno BJ, Xu S, Hamilton MC, Strassmann JE, Queller DC. Reduced and Nonreduced Genomes in Paraburkholderia Symbionts of Social Amoebas. mSystems 2022; 7:e0056222. [PMID: 36098425 DOI: 10.1128/msystems.00562-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The social amoeba Dictyostelium discoideum is a predatory soil protist frequently used for studying host-pathogen interactions. A subset of D. discoideum strains isolated from soil persistently carry symbiotic Paraburkholderia, recently formally described as P. agricolaris, P. bonniea, and P. hayleyella. The three facultative symbiont species of D. discoideum present a unique opportunity to study a naturally occurring symbiosis in a laboratory model protist. There is a large difference in genome size between P. agricolaris (8.7 million base pairs [Mbp]) versus P. hayleyella and P. bonniea (4.1 Mbp). We took a comparative genomics approach and compared the three genomes of D. discoideum symbionts to 12 additional Paraburkholderia genomes to test for genome evolution patterns that frequently accompany host adaptation. Overall, P. agricolaris is difficult to distinguish from other Paraburkholderia based on its genome size and content, but the reduced genomes of P. bonniea and P. hayleyella display characteristics indicative of genome streamlining rather than deterioration during adaptation to their protist hosts. In addition, D. discoideum-symbiont genomes have increased secretion system and motility genes that may mediate interactions with their host. Specifically, adjacent BurBor-like type 3 and T6SS-5-like type 6 secretion system operons shared among all three D. discoideum-symbiont genomes may be important for host interaction. Horizontal transfer of these secretion system operons within the amoeba host environment may have contributed to the unique ability of these symbionts to establish and maintain a symbiotic relationship with D. discoideum. IMPORTANCE Protists are a diverse group of typically single cell eukaryotes. Bacteria and archaea that form long-term symbiotic relationships with protists may evolve in additional ways than those in relationships with multicellular eukaryotes such as plants, animals, or fungi. Social amoebas are a predatory soil protist sometimes found with symbiotic bacteria living inside their cells. They present a unique opportunity to explore a naturally occurring symbiosis in a protist frequently used for studying host-pathogen interactions. We show that one amoeba-symbiont species is similar to other related bacteria in genome size and content, while the two reduced-genome-symbiont species show characteristics of genome streamlining rather than deterioration during adaptation to their host. We also identify sets of genes present in all three amoeba-symbiont genomes that are potentially used for host-symbiont interactions. Because the amoeba symbionts are distantly related, the amoeba host environment may be where these genes were shared among symbionts.
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