1
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Hoang KL, Salguero-Gómez R, Pike VL, King KC. The impacts of host association and perturbation on symbiont fitness. Symbiosis 2024; 92:439-451. [PMID: 38666134 PMCID: PMC11039428 DOI: 10.1007/s13199-024-00984-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 03/04/2024] [Indexed: 04/28/2024]
Abstract
Symbiosis can benefit hosts in numerous ways, but less is known about whether interactions with hosts benefit symbionts-the smaller species in the relationship. To determine the fitness impact of host association on symbionts in likely mutualisms, we conducted a meta-analysis across 91 unique host-symbiont pairings under a range of spatial and temporal contexts. Specifically, we assess the consequences to symbiont fitness when in and out of symbiosis, as well as when the symbiosis is under suboptimal or varying environments and biological conditions (e.g., host age). We find that some intracellular symbionts associated with protists tend to have greater fitness when the symbiosis is under stressful conditions. Symbionts of plants and animals did not exhibit this trend, suggesting that symbionts of multicellular hosts are more robust to perturbations. Symbiont fitness also generally increased with host age. Lastly, we show that symbionts able to proliferate in- and outside host cells exhibit greater fitness than those found exclusively inside or outside cells. The ability to grow in multiple locations may thus help symbionts thrive. We discuss these fitness patterns in light of host-driven factors, whereby hosts exert influence over symbionts to suit their own needs. Supplementary Information The online version contains supplementary material available at 10.1007/s13199-024-00984-6.
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Affiliation(s)
- Kim L. Hoang
- Department of Biology, University of Oxford, Oxford, UK
- Emory University School of Medicine, Atlanta, GA USA
| | | | | | - Kayla C. King
- Department of Biology, University of Oxford, Oxford, UK
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, Canada
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2
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Horas EL, Metzger SM, Platzer B, Kelly JB, Becks L. Context-dependent costs and benefits of endosymbiotic interactions in a ciliate-algae system. Environ Microbiol 2022; 24:5924-5935. [PMID: 35799468 DOI: 10.1111/1462-2920.16112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/20/2022] [Indexed: 01/12/2023]
Abstract
Endosymbiosis, an interaction between two species where one lives within the other, has evolved multiple times independently, but the underlying mechanisms remain unclear. Evolutionary theory suggests that for an endosymbiotic interaction to remain stable over time, births of both partners should be higher than their deaths in symbiosis and deaths of both partners should be higher than their births when living independently. However, experimentally measuring this can be difficult and conclusions tend to focus on the host. Using a ciliate-algal system (Paramecium bursaria host and Chlorella endosymbionts), we estimated the benefits and costs of endosymbiosis for both organisms using fitness measurements in different biotic environments to test under which environmental conditions the net effects of the interaction were positive for both partners. We found that the net effects of harbouring endosymbionts were positive for the ciliate hosts as it allowed them to survive in conditions of low-quality bacteria food. The algae benefitted by being endosymbiotic when predators such as the hosts were present, but the net effects were dependent on the total density of hosts, decreasing as hosts densities increased. Overall, we show that including context-dependency of endosymbiosis is essential in understanding how these interactions have evolved.
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Affiliation(s)
- Elena L Horas
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Sarah M Metzger
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Konstanz, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Barbara Platzer
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Joseph B Kelly
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Lutz Becks
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Konstanz, Germany
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3
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Zachar I, Boza G. The Evolution of Microbial Facilitation: Sociogenesis, Symbiogenesis, and Transition in Individuality. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.798045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Metabolic cooperation is widespread, and it seems to be a ubiquitous and easily evolvable interaction in the microbial domain. Mutual metabolic cooperation, like syntrophy, is thought to have a crucial role in stabilizing interactions and communities, for example biofilms. Furthermore, cooperation is expected to feed back positively to the community under higher-level selection. In certain cases, cooperation can lead to a transition in individuality, when freely reproducing, unrelated entities (genes, microbes, etc.) irreversibly integrate to form a new evolutionary unit. The textbook example is endosymbiosis, prevalent among eukaryotes but virtually lacking among prokaryotes. Concerning the ubiquity of syntrophic microbial communities, it is intriguing why evolution has not lead to more transitions in individuality in the microbial domain. We set out to distinguish syntrophy-specific aspects of major transitions, to investigate why a transition in individuality within a syntrophic pair or community is so rare. We review the field of metabolic communities to identify potential evolutionary trajectories that may lead to a transition. Community properties, like joint metabolic capacity, functional profile, guild composition, assembly and interaction patterns are important concepts that may not only persist stably but according to thought-provoking theories, may provide the heritable information at a higher level of selection. We explore these ideas, relating to concepts of multilevel selection and of informational replication, to assess their relevance in the debate whether microbial communities may inherit community-level information or not.
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4
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Flemming FE, Grosser K, Schrallhammer M. Natural Shifts in Endosymbionts' Occurrence and Relative Frequency in Their Ciliate Host Population. Front Microbiol 2022; 12:791615. [PMID: 35087493 PMCID: PMC8787144 DOI: 10.3389/fmicb.2021.791615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/14/2021] [Indexed: 11/13/2022] Open
Abstract
The role of bacterial endosymbionts harbored by heterotrophic Paramecium species is complex. Obligate intracellular bacteria supposedly always inflict costs as the host is the only possible provider of resources. However, several experimental studies have shown that paramecia carrying bacterial endosymbionts can benefit from their infection. Here, we address the question which endosymbionts occur in natural paramecia populations isolated from a small lake over a period of 5 years and which factors might explain observed shifts and persistence in the symbionts occurrence. One hundred and nineteen monoclonal strains were investigated and approximately two-third harbored intracellular bacteria. The majority of infected paramecia carried the obligate endosymbiotic "Candidatus Megaira polyxenophila", followed by Caedimonas varicaedens, and Holospora undulata. The latter was only detected in a single strain. While "Ca. M. polyxenophila" was observed in seven out of 13 samplings, C. varicaedens presence was limited to a single sampling occasion. After the appearance of C. varicaedens, "Ca. M. polyxenophila" prevalence dramatically dropped with some delay but recovered to original levels at the end of our study. Potential mechanisms explaining these observations include differences in infectivity, host range, and impact on host fitness as well as host competitive capacities. Growth experiments revealed fitness advantages for infected paramecia harboring "Ca. M. polyxenophila" as well as C. varicaedens. Furthermore, we showed that cells carrying C. varicaedens gain a competitive advantage from the symbiosis-derived killer trait. Other characteristics like infectivity and overlapping host range were taken into consideration, but the observed temporal persistence of "Ca. M. polyxenophila" is most likely explained by the positive effect this symbiont provides to its host.
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Affiliation(s)
- Felicitas E. Flemming
- Microbiology, Institute of Biology II, Albert Ludwig University of Freiburg, Freiburg, Germany
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5
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Drew GC, Stevens EJ, King KC. Microbial evolution and transitions along the parasite-mutualist continuum. Nat Rev Microbiol 2021; 19:623-638. [PMID: 33875863 PMCID: PMC8054256 DOI: 10.1038/s41579-021-00550-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Virtually all plants and animals, including humans, are home to symbiotic microorganisms. Symbiotic interactions can be neutral, harmful or have beneficial effects on the host organism. However, growing evidence suggests that microbial symbionts can evolve rapidly, resulting in drastic transitions along the parasite-mutualist continuum. In this Review, we integrate theoretical and empirical findings to discuss the mechanisms underpinning these evolutionary shifts, as well as the ecological drivers and why some host-microorganism interactions may be stuck at the end of the continuum. In addition to having biomedical consequences, understanding the dynamic life of microorganisms reveals how symbioses can shape an organism's biology and the entire community, particularly in a changing world.
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Affiliation(s)
| | | | - Kayla C King
- Department of Zoology, University of Oxford, Oxford, UK.
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6
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Emergent RNA-RNA interactions can promote stability in a facultative phototrophic endosymbiosis. Proc Natl Acad Sci U S A 2021; 118:2108874118. [PMID: 34521754 PMCID: PMC8463893 DOI: 10.1073/pnas.2108874118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2021] [Indexed: 12/11/2022] Open
Abstract
Stable endosymbiosis between eukaryotic microbes has driven the evolution of further cellular complexity. Yet the mechanisms that can act to stabilize an emergent eukaryote–eukaryote endosymbiosis are unclear. Using the model facultative endosymbiotic system, Paramecium bursaria, we demonstrate that endosymbiont–host RNA–RNA interactions can drive a cost to host growth upon endosymbiont digestion. These RNA–RNA interactions are facilitated by the host RNA-interference system. For endosymbiont messenger RNA sharing a high level of sequence identity with host transcripts, this process can result in host gene knockdown. We propose that these endosymbiont–host RNA–RNA interactions—“RNA-interference collisions”—represent an emergent mechanism to sanction the host for breakdown of the endosymbiosis, promoting the stability of the facultative endosymbiotic interaction. Eukaryote–eukaryote endosymbiosis was responsible for the spread of chloroplast (plastid) organelles. Stability is required for the metabolic and genetic integration that drives the establishment of new organelles, yet the mechanisms that act to stabilize emergent endosymbioses—between two fundamentally selfish biological organisms—are unclear. Theory suggests that enforcement mechanisms, which punish misbehavior, may act to stabilize such interactions by resolving conflict. However, how such mechanisms can emerge in a facultative endosymbiosis has yet to be explored. Here, we propose that endosymbiont–host RNA–RNA interactions, arising from digestion of the endosymbiont population, can result in a cost to host growth for breakdown of the endosymbiosis. Using the model facultative endosymbiosis between Paramecium bursaria and Chlorella spp., we demonstrate that this mechanism is dependent on the host RNA-interference (RNAi) system. We reveal through small RNA (sRNA) sequencing that endosymbiont-derived messenger RNA (mRNA) released upon endosymbiont digestion can be processed by the host RNAi system into 23-nt sRNA. We predict multiple regions of shared sequence identity between endosymbiont and host mRNA, and demonstrate through delivery of synthetic endosymbiont sRNA that exposure to these regions can knock down expression of complementary host genes, resulting in a cost to host growth. This process of host gene knockdown in response to endosymbiont-derived RNA processing by host RNAi factors, which we term “RNAi collisions,” represents a mechanism that can promote stability in a facultative eukaryote–eukaryote endosymbiosis. Specifically, by imposing a cost for breakdown of the endosymbiosis, endosymbiont–host RNA–RNA interactions may drive maintenance of the symbiosis across fluctuating ecological conditions.
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7
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Abstract
Can hosts swap ancient symbionts for new ones? A new study shows that a novel partnership between a protist and an algal symbiont can rapidly evolve to both overcome initial incompatibility and adapt to environmental challenges.
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Affiliation(s)
- Stephanie Porter
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA.
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8
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Zeng Y, Wiens JJ. Do mutualistic interactions last longer than antagonistic interactions? Proc Biol Sci 2021; 288:20211457. [PMID: 34493078 PMCID: PMC8424312 DOI: 10.1098/rspb.2021.1457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/13/2021] [Indexed: 11/12/2022] Open
Abstract
Species interactions are crucial and ubiquitous across organisms. However, it remains unclear how long these interactions last over macroevolutionary timescales, and whether the nature of these interactions (mutualistic versus antagonistic) helps predict how long they persist. Here, we estimated the ages of diverse species interactions, based on phylogenies from 60 studies spanning the Tree of Life. We then tested if mutualistic interactions persist longer than antagonistic interactions. We found that the oldest mutualisms were significantly older than the oldest antagonisms across all organisms, and within plants, fungi, bacteria and protists. Surprisingly, this pattern was reversed in animals, with the oldest mutualisms significantly younger than the oldest antagonisms. We also found that many mutualisms were maintained for hundreds of millions of years (some greater than 1 billion years), providing strong evidence for the long-term stability of mutualisms and for niche conservatism in species interactions.
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Affiliation(s)
- Yichao Zeng
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - John J. Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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9
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Hoang KL, Gerardo NM, Morran LT. Association with a novel protective microbe facilitates host adaptation to a stressful environment. Evol Lett 2021; 5:118-129. [PMID: 33868708 PMCID: PMC8045907 DOI: 10.1002/evl3.223] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 02/02/2021] [Accepted: 02/18/2021] [Indexed: 01/19/2023] Open
Abstract
Protective symbionts can allow hosts to occupy otherwise uninhabitable niches. Despite the importance of symbionts in host evolution, we know little about how these associations arise. Encountering a microbe that can improve host fitness in a stressful environment may favor persistent interactions with that microbe, potentially facilitating a long-term association. The bacterium Bacillus subtilis protects Caenorhabditis elegans nematodes from heat shock by increasing host fecundity compared to the nonprotective Escherichia coli. In this study, we ask how the protection provided by the bacterium affects the host's evolutionary trajectory. Because of the stark fitness contrast between hosts heat shocked on B. subtilis versus E. coli, we tested whether the protection conferred by the bacteria could increase the rate of host adaptation to a stressful environment. We passaged nematodes on B. subtilis or E. coli, under heat stress or standard conditions for 20 host generations of selection. When assayed under heat stress, we found that hosts exhibited the greatest fitness increase when evolved with B. subtilis under stress compared to when evolved with E. coli or under standard (nonstressful) conditions. Furthermore, despite not directly selecting for increased B. subtilis fitness, we found that hosts evolved to harbor more B. subtilis as they adapted to heat stress. Our findings demonstrate that the context under which hosts evolve is important for the evolution of beneficial associations and that protective microbes can facilitate host adaptation to stress. In turn, such host adaptation can benefit the microbe.
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Affiliation(s)
- Kim L. Hoang
- Department of BiologyEmory UniversityAtlantaGeorgia30322USA
- Department of ZoologyUniversity of OxfordOxfordOX1 3SZUnited Kingdom
| | | | - Levi T. Morran
- Department of BiologyEmory UniversityAtlantaGeorgia30322USA
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10
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Cha S, Lim HG, Kwon S, Kim DH, Kang CW, Jung GY. Design of mutualistic microbial consortia for stable conversion of carbon monoxide to value-added chemicals. Metab Eng 2021; 64:146-153. [PMID: 33571657 DOI: 10.1016/j.ymben.2021.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/22/2020] [Accepted: 02/02/2021] [Indexed: 12/31/2022]
Abstract
Carbon monoxide (CO) is a promising carbon source for producing value-added biochemicals via microbial fermentation. However, its microbial conversion has been challenging because of difficulties in genetic engineering of CO-utilizing microorganisms and, more importantly, maintaining CO consumption which is negatively affected by the toxicity of CO and accumulated byproducts. To overcome these issues, we devised mutualistic microbial consortia, co-culturing Eubacterium limosum and genetically engineered Escherichia coli for the production of 3-hydroxypropionic acid (3-HP) and itaconic acid (ITA). During the co-culture, E. limosum assimilated CO and produced acetate, a toxic by-product, while E. coli utilized acetate as a sole carbon source. We found that this mutualistic interaction dramatically stabilized and improved CO consumption of E. limosum compared to monoculture. Consequently, the improved CO consumption allowed successful production of 3-HP and ITA from CO. This study is the first demonstration of value-added biochemical production from CO using a microbial consortium. Moreover, it suggests that synthetic mutualistic microbial consortium can serve as a powerful platform for the valorization of CO.
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Affiliation(s)
- Sanghak Cha
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Seokmu Kwon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Dong-Hwan Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Chae Won Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
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11
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Chomicki G, Kiers ET, Renner SS. The Evolution of Mutualistic Dependence. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-110218-024629] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
While the importance of mutualisms across the tree of life is recognized, it is not understood why some organisms evolve high levels of dependence on mutualistic partnerships, while other species remain autonomous or retain or regain minimal dependence on partners. We identify four main pathways leading to the evolution of mutualistic dependence. Then, we evaluate current evidence for three predictions: ( a) Mutualisms with different levels of dependence have distinct stabilizing mechanisms against exploitation and cheating, ( b) less dependent mutualists will return to autonomy more often than those that are highly dependent, and ( c) obligate mutualisms should be less context dependent than facultative ones. Although we find evidence supporting all three predictions, we stress that mutualistic partners follow diverse paths toward—and away from—dependence. We also highlight the need to better examine asymmetry in partner dependence. Recognizing how variation in dependence influences the stability, breakdown, and context dependence of mutualisms generates new hypotheses regarding how and why the benefits of mutualistic partnerships differ over time and space.
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Affiliation(s)
- Guillaume Chomicki
- Department of Bioscience, Durham University, Durham DH1 3LE, United Kingdom
| | - E. Toby Kiers
- Department of Ecological Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Susanne S. Renner
- Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), 80638 Munich, Germany
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12
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Stoy KS, Gibson AK, Gerardo NM, Morran LT. A need to consider the evolutionary genetics of host-symbiont mutualisms. J Evol Biol 2020; 33:1656-1668. [PMID: 33047414 DOI: 10.1111/jeb.13715] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/20/2020] [Accepted: 09/27/2020] [Indexed: 12/28/2022]
Abstract
Despite the ubiquity and importance of mutualistic interactions, we know little about the evolutionary genetics underlying their long-term persistence. As in antagonistic interactions, mutualistic symbioses are characterized by substantial levels of phenotypic and genetic diversity. In contrast to antagonistic interactions, however, we, by and large, do not understand how this variation arises, how it is maintained, nor its implications for future evolutionary change. Currently, we rely on phenotypic models to address the persistence of mutualistic symbioses, but the success of an interaction almost certainly depends heavily on genetic interactions. In this review, we argue that evolutionary genetic models could provide a framework for understanding the causes and consequences of diversity and why selection may favour processes that maintain variation in mutualistic interactions.
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Affiliation(s)
- Kayla S Stoy
- Department of Biology, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Program, Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, USA
| | - Amanda K Gibson
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Levi T Morran
- Department of Biology, Emory University, Atlanta, GA, USA
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13
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Fagorzi C, Ilie A, Decorosi F, Cangioli L, Viti C, Mengoni A, diCenzo GC. Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping. Genome Biol Evol 2020; 12:2521-2534. [PMID: 33283865 PMCID: PMC7719227 DOI: 10.1093/gbe/evaa221] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 01/03/2023] Open
Abstract
Rhizobium–legume symbioses serve as paradigmatic examples for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and interkingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF likely emerged several times within the genus Ensifer through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the “symbiotic” and “nonsymbiotic” clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the nonsymbiotic clade. Initial characterization of a subset of ten Ensifer strains identified several putative phenotypic differences between the clades. Tested strains of the nonsymbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, the tested strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.
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Affiliation(s)
- Camilla Fagorzi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Alexandru Ilie
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Francesca Decorosi
- Genexpress Laboratory, Department of Agriculture, Food, Environment and Forestry, University of Florence, Sesto Fiorentino, Italy
| | - Lisa Cangioli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Carlo Viti
- Genexpress Laboratory, Department of Agriculture, Food, Environment and Forestry, University of Florence, Sesto Fiorentino, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - George C diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.,Department of Biology, Queen's University, Kingston, Ontario, Canada
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14
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Zachar I, Boza G. Endosymbiosis before eukaryotes: mitochondrial establishment in protoeukaryotes. Cell Mol Life Sci 2020; 77:3503-3523. [PMID: 32008087 PMCID: PMC7452879 DOI: 10.1007/s00018-020-03462-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 12/25/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023]
Abstract
Endosymbiosis and organellogenesis are virtually unknown among prokaryotes. The single presumed example is the endosymbiogenetic origin of mitochondria, which is hidden behind the event horizon of the last eukaryotic common ancestor. While eukaryotes are monophyletic, it is unlikely that during billions of years, there were no other prokaryote-prokaryote endosymbioses as symbiosis is extremely common among prokaryotes, e.g., in biofilms. Therefore, it is even more precarious to draw conclusions about potentially existing (or once existing) prokaryotic endosymbioses based on a single example. It is yet unknown if the bacterial endosymbiont was captured by a prokaryote or by a (proto-)eukaryote, and if the process of internalization was parasitic infection, slow engulfment, or phagocytosis. In this review, we accordingly explore multiple mechanisms and processes that could drive the evolution of unicellular microbial symbioses with a special attention to prokaryote-prokaryote interactions and to the mitochondrion, possibly the single prokaryotic endosymbiosis that turned out to be a major evolutionary transition. We investigate the ecology and evolutionary stability of inter-species microbial interactions based on dependence, physical proximity, cost-benefit budget, and the types of benefits, investments, and controls. We identify challenges that had to be conquered for the mitochondrial host to establish a stable eukaryotic lineage. Any assumption about the initial interaction of the mitochondrial ancestor and its contemporary host based solely on their modern relationship is rather perilous. As a result, we warn against assuming an initial mutually beneficial interaction based on modern mitochondria-host cooperation. This assumption is twice fallacious: (i) endosymbioses are known to evolve from exploitative interactions and (ii) cooperativity does not necessarily lead to stable mutualism. We point out that the lack of evidence so far on the evolution of endosymbiosis from mutual syntrophy supports the idea that mitochondria emerged from an exploitative (parasitic or phagotrophic) interaction rather than from syntrophy.
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Affiliation(s)
- István Zachar
- Evolutionary Systems Research Group, Institute of Evolution, Centre for Ecological Research, Klebelsberg Kunó str. 3., Tihany, 8237, Hungary.
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Department of Plant Taxonomy and Ecology, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, 1117, Hungary.
- Center for the Conceptual Foundations of Science, Parmenides Foundation, Kirchplatz 1, 82049, Munich, Germany.
| | - Gergely Boza
- Evolutionary Systems Research Group, Institute of Evolution, Centre for Ecological Research, Klebelsberg Kunó str. 3., Tihany, 8237, Hungary
- Evolution and Ecology Program, International Institute for Applied Systems Analysis (IIASA), Schlossplatz 1, 2361, Laxenburg, Austria
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15
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Chomicki G, Werner GDA, West SA, Kiers ET. Compartmentalization drives the evolution of symbiotic cooperation. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190602. [PMID: 32772665 DOI: 10.1098/rstb.2019.0602] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Across the tree of life, hosts have evolved mechanisms to control and mediate interactions with symbiotic partners. We suggest that the evolution of physical structures that allow hosts to spatially separate symbionts, termed compartmentalization, is a common mechanism used by hosts. Such compartmentalization allows hosts to: (i) isolate symbionts and control their reproduction; (ii) reward cooperative symbionts and punish or stop interactions with non-cooperative symbionts; and (iii) reduce direct conflict among different symbionts strains in a single host. Compartmentalization has allowed hosts to increase the benefits that they obtain from symbiotic partners across a diversity of interactions, including legumes and rhizobia, plants and fungi, squid and Vibrio, insects and nutrient provisioning bacteria, plants and insects, and the human microbiome. In cases where compartmentalization has not evolved, we ask why not. We argue that when partners interact in a competitive hierarchy, or when hosts engage in partnerships which are less costly, compartmentalization is less likely to evolve. We conclude that compartmentalization is key to understanding the evolution of symbiotic cooperation. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Guillaume Chomicki
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Gijsbert D A Werner
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford OX1 3SZ, UK.,Netherlands Scientific Council for Government Policy, Buitenhof 34, 2513 AH Den Haag, The Netherlands
| | - Stuart A West
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - E Toby Kiers
- Department of Ecological Science, VU University, Amsterdam, The Netherlands
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16
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Medina Munoz M, Spencer N, Enomoto S, Dale C, Rio RVM. Quorum sensing sets the stage for the establishment and vertical transmission of Sodalis praecaptivus in tsetse flies. PLoS Genet 2020; 16:e1008992. [PMID: 32797092 PMCID: PMC7449468 DOI: 10.1371/journal.pgen.1008992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/26/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Bacterial virulence factors facilitate host colonization and set the stage for the evolution of parasitic and mutualistic interactions. The Sodalis-allied clade of bacteria exhibit striking diversity in the range of both plant and animal feeding insects they inhabit, suggesting the appropriation of universal molecular mechanisms that facilitate establishment. Here, we report on the infection of the tsetse fly by free-living Sodalis praecaptivus, a close relative of many Sodalis-allied symbionts. Key genes involved in quorum sensing, including the homoserine lactone synthase (ypeI) and response regulators (yenR and ypeR) are integral for the benign colonization of S. praecaptivus. Mutants lacking ypeI, yenR and ypeR compromised tsetse survival as a consequence of their inability to repress virulence. Genes under quorum sensing, including homologs of the binary insecticidal toxin PirAB and a putative symbiosis-promoting factor CpmAJ, demonstrated negative and positive impacts, respectively, on tsetse survival. Taken together with results obtained from experiments involving weevils, this work shows that quorum sensing virulence suppression plays an integral role in facilitating the establishment of Sodalis-allied symbionts in diverse insect hosts. This knowledge contributes to the understanding of the early evolutionary steps involved in the formation of insect-bacterial symbiosis. Further, despite having no established history of interaction with tsetse, S. praecaptivus can infect reproductive tissues, enabling vertical transmission through adenotrophic viviparity within a single host generation. This creates an option for the use of S. praecaptivus in the biocontrol of insect disease vectors via paratransgenesis.
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Affiliation(s)
- Miguel Medina Munoz
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States of America
| | - Noah Spencer
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States of America
| | - Shinichiro Enomoto
- Department of Biology, University of Utah, Salt Lake City, UT, United States of America
| | - Colin Dale
- Department of Biology, University of Utah, Salt Lake City, UT, United States of America
| | - Rita V. M. Rio
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States of America
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17
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Doulcier G, Lambert A, De Monte S, Rainey PB. Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity. eLife 2020; 9:e53433. [PMID: 32633717 PMCID: PMC7440921 DOI: 10.7554/elife.53433] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/12/2020] [Indexed: 01/23/2023] Open
Abstract
Interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on communities. Such scaffolding causes communities to participate directly in the process of evolution by natural selection and drives the evolution of cell-level interactions to the point where, despite underlying stochasticity, derived communities give rise to offspring communities that faithfully re-establish parental phenotype. The mechanism is akin to a developmental process (developmental correction) that arises from density-dependent interactions among cells. Knowledge of ecological factors affecting evolution of developmental correction has implications for understanding the evolutionary origin of major egalitarian transitions, symbioses, and for top-down engineering of microbial communities.
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Affiliation(s)
- Guilhem Doulcier
- Laboratoire de Génétique de l'Evolution, Chimie Biologie et Innovation, Université PSLParisFrance
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, Université PSLParisFrance
| | - Amaury Lambert
- Laboratoire de Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRSParisFrance
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, Université PSL, CNRS, INSERMParisFrance
| | - Silvia De Monte
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, Université PSLParisFrance
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Paul B Rainey
- Laboratoire de Génétique de l'Evolution, Chimie Biologie et Innovation, Université PSLParisFrance
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary BiologyPlönGermany
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18
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Better off alone? New insights in the symbiotic relationship between the flatworm Symsagittifera roscoffensis and the microalgae Tetraselmis convolutae. Symbiosis 2020. [DOI: 10.1007/s13199-020-00691-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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19
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Paraburkholderia Symbionts Display Variable Infection Patterns That Are Not Predictive of Amoeba Host Outcomes. Genes (Basel) 2020; 11:genes11060674. [PMID: 32575747 PMCID: PMC7349545 DOI: 10.3390/genes11060674] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/07/2020] [Accepted: 06/18/2020] [Indexed: 12/17/2022] Open
Abstract
Symbiotic interactions exist within a parasitism to mutualism continuum that is influenced, among others, by genes and context. Dynamics of intracellular invasion, replication, and prevalence may underscore both host survivability and symbiont stability. More infectious symbionts might exert higher corresponding costs to hosts, which could ultimately disadvantage both partners. Here, we quantify infection patterns of diverse Paraburkholderia symbiont genotypes in their amoeba host Dictyostelium discoideum and probe the relationship between these patterns and host outcomes. We exposed D. discoideum to thirteen strains of Paraburkholderia each belonging to one of the three symbiont species found to naturally infect D. discoideum: Paraburkholderia agricolaris, Paraburkholderia hayleyella, and Paraburkholderia bonniea. We quantified the infection prevalence and intracellular density of fluorescently labeled symbionts along with the final host population size using flow cytometry and confocal microscopy. We find that infection phenotypes vary across symbiont strains. Symbionts belonging to the same species generally display similar infection patterns but are interestingly distinct when it comes to host outcomes. This results in final infection loads that do not strongly correlate to final host outcomes, suggesting other genetic factors that are not a direct cause or consequence of symbiont abundance impact host fitness.
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20
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Tamarit D, Andersson SGE. Rethinking microbial symbioses. FEMS Microbiol Lett 2020; 367:5810346. [PMID: 32193538 PMCID: PMC7082701 DOI: 10.1093/femsle/fnz255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 12/23/2019] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniel Tamarit
- Molecular Evolution, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Siv G E Andersson
- Molecular Evolution, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
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