51
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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: 2] [Impact Index Per Article: 0.7] [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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Abstract
Recent human activity has profoundly transformed Earth biomes on a scale and at rates that are unprecedented. Given the central role of symbioses in ecosystem processes, functions, and services throughout the Earth biosphere, the impacts of human-driven change on symbioses are critical to understand. Symbioses are not merely collections of organisms, but co-evolved partners that arise from the synergistic combination and action of different genetic programs. They function with varying degrees of permanence and selection as emergent units with substantial potential for combinatorial and evolutionary innovation in both structure and function. Following an articulation of operational definitions of symbiosis and related concepts and characteristics of the Anthropocene, we outline a basic typology of anthropogenic change (AC) and a conceptual framework for how AC might mechanistically impact symbioses with select case examples to highlight our perspective. We discuss surprising connections between symbiosis and the Anthropocene, suggesting ways in which new symbioses could arise due to AC, how symbioses could be agents of ecosystem change, and how symbioses, broadly defined, of humans and "farmed" organisms may have launched the Anthropocene. We conclude with reflections on the robustness of symbioses to AC and our perspective on the importance of symbioses as ecosystem keystones and the need to tackle anthropogenic challenges as wise and humble stewards embedded within the system.
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Affiliation(s)
- Erik F. Y. Hom
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS 38677 USA
| | - Alexandra S. Penn
- Department of Sociology and Centre for Evaluation of Complexity Across the Nexus, University of Surrey, Guildford, Surrey, GU2 7XH UK
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53
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Henry LP, Bruijning M, Forsberg SKG, Ayroles JF. The microbiome extends host evolutionary potential. Nat Commun 2021; 12:5141. [PMID: 34446709 PMCID: PMC8390463 DOI: 10.1038/s41467-021-25315-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 08/03/2021] [Indexed: 02/07/2023] Open
Abstract
The microbiome shapes many host traits, yet the biology of microbiomes challenges traditional evolutionary models. Here, we illustrate how integrating the microbiome into quantitative genetics can help untangle complexities of host-microbiome evolution. We describe two general ways in which the microbiome may affect host evolutionary potential: by shifting the mean host phenotype and by changing the variance in host phenotype in the population. We synthesize the literature across diverse taxa and discuss how these scenarios could shape the host response to selection. We conclude by outlining key avenues of research to improve our understanding of the complex interplay between hosts and microbiomes.
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Affiliation(s)
- Lucas P. Henry
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA ,grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
| | - Marjolein Bruijning
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA
| | - Simon K. G. Forsberg
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA ,grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA ,grid.8993.b0000 0004 1936 9457Dept. of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Julien F. Ayroles
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA ,grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
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54
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Abstract
Many microorganisms with high prevalence in host populations are beneficial to the host and maintained by specialized transmission mechanisms. Although microbial promotion of host fitness and specificity of the associations undoubtedly enhance microbial prevalence, it is an open question whether these symbiotic traits are also a prerequisite for the evolutionary origin of prevalent microbial taxa. To address this issue, we investigate how processes without positive microbial effects on host fitness or host choice can influence the prevalence of certain microbes in a host population. Specifically, we develop a theoretical model to assess the conditions under which particular microbes can become enriched in animal hosts even when they are not providing a specific benefit to a particular host. We find increased prevalence of specific microbes in a host when both show some overlap in their lifecycles, and especially when both share dispersal routes across a patchy habitat distribution. Our results emphasize that host enrichment per se is not a reliable indicator of beneficial host-microbe interactions. The resulting increase in time spent associated with a host may nevertheless give rise to new selection conditions, which can favor microbial adaptations toward a host-associated lifestyle, and, thus, it could be the foundation for subsequent evolution of mutually beneficial coevolved symbioses.
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55
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Cavalcanti GS, Alker AT, Delherbe N, Malter KE, Shikuma NJ. The Influence of Bacteria on Animal Metamorphosis. Annu Rev Microbiol 2021; 74:137-158. [PMID: 32905754 DOI: 10.1146/annurev-micro-011320-012753] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The swimming larvae of many marine animals identify a location on the seafloor to settle and undergo metamorphosis based on the presence of specific surface-bound bacteria. While bacteria-stimulated metamorphosis underpins processes such as the fouling of ship hulls, animal development in aquaculture, and the recruitment of new animals to coral reef ecosystems, little is known about the mechanisms governing this microbe-animal interaction. Here we review what is known and what we hope to learn about how bacteria and the factors they produce stimulate animal metamorphosis. With a few emerging model systems, including the tubeworm Hydroides elegans, corals, and the hydrozoan Hydractinia, we have begun to identify bacterial cues that stimulate animal metamorphosis and test hypotheses addressing their mechanisms of action. By understanding the mechanisms by which bacteria promote animal metamorphosis, we begin to illustrate how, and explore why, the developmental decision of metamorphosis relies on cues from environmental bacteria.
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Affiliation(s)
- Giselle S Cavalcanti
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, California 92182, USA; , , , ,
| | - Amanda T Alker
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, California 92182, USA; , , , ,
| | - Nathalie Delherbe
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, California 92182, USA; , , , ,
| | - Kyle E Malter
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, California 92182, USA; , , , ,
| | - Nicholas J Shikuma
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, California 92182, USA; , , , ,
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56
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Hayward A, Poulin R, Nakagawa S. A broadscale analysis of host-symbiont cophylogeny reveals the drivers of phylogenetic congruence. Ecol Lett 2021; 24:1681-1696. [PMID: 33987932 DOI: 10.1111/ele.13757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/21/2021] [Accepted: 03/24/2021] [Indexed: 02/06/2023]
Abstract
Symbioses exert substantial biological influence, with great evolutionary and ecological relevance for disease, major evolutionary transitions, and the structure and function of ecological communities. Yet, much remains unknown about the patterns and processes that characterise symbioses. A major unanswered question is the extent to which symbiont phylogenies mirror those of their hosts and if patterns differ for parasites and mutualists. Addressing this question offers fundamental insights into evolutionary processes, such as whether symbionts typically codiverge with their hosts or if diversity is generated via host switches. Here, we perform a meta-analysis of host-symbiont phylogenetic congruence, encompassing 212 host-symbiont cophylogenetic studies that include ~10,000 species. Our analysis supersedes previous qualitative assessments by utilising a quantitative framework. We show that symbiont phylogeny broadly reflects host phylogeny across biodiversity and life-history, demonstrating a general pattern of phylogenetic congruence in host-symbiont interactions. We reveal two key aspects of symbiont life-history that promote closer ties between hosts and symbionts: vertical transmission and mutualism. Mode of symbiosis and mode of transmission are intimately interlinked, but vertical transmission is the dominant factor. Given the pervasiveness of symbioses, these findings provide important insights into the processes responsible for generating and maintaining the Earth's rich biodiversity.
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Affiliation(s)
- Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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57
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Abstract
Host-adapted microorganisms are generally assumed to have evolved from free-living, environmental microorganisms, as examples of the reverse process are rare. In the phylum Gammaproteobacteria, family Moraxellaceae, the genus Psychrobacter includes strains from a broad ecological distribution including animal bodies as well as sea ice and other nonhost environments. To elucidate the relationship between these ecological niches and Psychrobacter's evolutionary history, we performed tandem genomic analyses with phenotyping of 85 Psychrobacter accessions. Phylogenomic analysis of the family Moraxellaceae reveals that basal members of the Psychrobacter clade are Moraxella spp., a group of often-pathogenic organisms. Psychrobacter exhibited two broad growth patterns in our phenotypic screen: one group that we called the "flexible ecotype" (FE) had the ability to grow between 4 and 37°C, and the other, which we called the "restricted ecotype" (RE), could grow between 4 and 25°C. The FE group includes phylogenetically basal strains, and FE strains exhibit increased transposon copy numbers, smaller genomes, and a higher likelihood to be bile salt resistant. The RE group contains only phylogenetically derived strains and has increased proportions of lipid metabolism and biofilm formation genes, functions that are adaptive to cold stress. In a 16S rRNA gene survey of polar bear fecal samples, we detect both FE and RE strains, but in in vivo colonizations of gnotobiotic mice, only FE strains persist. Our results indicate the ability to grow at 37°C, seemingly necessary for mammalian gut colonization, is an ancestral trait for Psychrobacter, which likely evolved from a pathobiont.IMPORTANCE Host-associated microbes are generally assumed to have evolved from free-living ones. The evolutionary transition of microbes in the opposite direction, from host associated toward free living, has been predicted based on phylogenetic data but not studied in depth. Here, we provide evidence that the genus Psychrobacter, particularly well known for inhabiting low-temperature, high-salt environments such as sea ice, permafrost soils, and frozen foodstuffs, has evolved from a mammalian-associated ancestor. We show that some Psychrobacter strains retain seemingly ancestral genomic and phenotypic traits that correspond with host association while others have diverged to psychrotrophic or psychrophilic lifestyles.
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58
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Nourabadi N, Nishiguchi MK. pH Adaptation Drives Diverse Phenotypes in a Beneficial Bacterium-Host Mutualism. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.611411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abiotic variation can influence the evolution of specific phenotypes that contribute to the diversity of bacterial strains observed in the natural environment. Environmentally transmitted symbiotic bacteria are particularly vulnerable to abiotic fluctuations, given that they must accommodate the transition between the free-living state and the host's internal environment. This type of life history strategy can strongly influence the success of a symbiont, and whether adapting to changes outside the host will allow a greater capacity to survive in symbiosis with the host partner. One example of how environmental breadth is advantageous to the symbiosis is the beneficial association between Vibrio fischeri and sepiolid squids (Cephalopoda: Sepiolidae). Since Vibrio bacteria are environmentally transmitted, they are subject to a wide variety of abiotic variables prior to infecting juvenile squids and must be poised to survive in the host light organ. In order to better understand how a changing abiotic factor (e.g., pH) influences the diversification of symbionts and their eventual symbiotic competence, we used an experimental evolution approach to ascertain how pH adaptation affects symbiont fitness. Results show that low pH adapted Vibrio strains have more efficient colonization rates compared to their ancestral strains. In addition, growth rates had significant differences compared to ancestral strains (pH 6.5–6.8, and 7.2). Bioluminescence production (a marker for symbiont competence) of pH evolved strains also improved at pH 6.5–7.2. Results imply that the evolution and diversification of Vibrio strains adapted to low pH outside the squid improves fitness inside the squid by allowing a higher success rate for host colonization and symbiotic competence.
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59
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Lebov JF, Bohannan BJM. Msh Pilus Mutations Increase the Ability of a Free-Living Bacterium to Colonize a Piscine Host. Genes (Basel) 2021; 12:genes12020127. [PMID: 33498301 PMCID: PMC7909257 DOI: 10.3390/genes12020127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
Symbioses between animals and bacteria are ubiquitous. To better understand these relationships, it is essential to unravel how bacteria evolve to colonize hosts. Previously, we serially passaged the free-living bacterium, Shewanella oneidensis, through the digestive tracts of germ-free larval zebrafish (Danio rerio) to uncover the evolutionary changes involved in the initiation of a novel symbiosis with a vertebrate host. After 20 passages, we discovered an adaptive missense mutation in the mshL gene of the msh pilus operon, which improved host colonization, increased swimming motility, and reduced surface adhesion. In the present study, we determined that this mutation was a loss-of-function mutation and found that it improved zebrafish colonization by augmenting S. oneidensis representation in the water column outside larvae through a reduced association with environmental surfaces. Additionally, we found that strains containing the mshL mutation were able to immigrate into host digestive tracts at higher rates per capita. However, mutant and evolved strains exhibited no evidence of a competitive advantage after colonizing hosts. Our results demonstrate that bacterial behaviors outside the host can play a dominant role in facilitating the onset of novel host associations.
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Affiliation(s)
- Jarrett F. Lebov
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA;
- Correspondence:
| | - Brendan J. M. Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA;
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60
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Badji CA, Sol-Mochkovitch Z, Fallais C, Sochard C, Simon JC, Outreman Y, Anton S. Alarm Pheromone Responses Depend on Genotype, but Not on the Presence of Facultative Endosymbionts in the Pea Aphid Acyrthosiphon pisum. INSECTS 2021; 12:43. [PMID: 33430009 PMCID: PMC7826508 DOI: 10.3390/insects12010043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 11/17/2022]
Abstract
Aphids use an alarm pheromone, E-β farnesene (EBF), to warn conspecifics of potential danger. The antennal sensitivity and behavioural escape responses to EBF can be influenced by different factors. In the pea aphid, Acyrthosiphon pisum, different biotypes are adapted to different legume species, and within each biotype, different genotypes exist, which can carry or not Hamiltonella defensa, a bacterial symbiont that can confer protection against natural enemies. We investigate here the influence of the aphid genotype and symbiotic status on the escape behaviour using a four-way olfactometer and antennal sensitivity for EBF using electroantennograms (EAGs). Whereas the investigated three genotypes from two biotypes showed significantly different escape and locomotor behaviours in the presence of certain EBF doses, the infection with H. defensa did not significantly modify the escape behaviour and only marginally influenced the locomotor behaviour at high doses of EBF. Dose-response curves of EAG amplitudes after stimulation with EBF differed significantly between aphid genotypes in correlation with behavioural differences, whereas antennal sensitivity to EBF did not change significantly as a function of the symbiotic status. The protective symbiont H. defensa does thus not modify the olfactory sensitivity to the alarm pheromone. How EBF sensitivity is modified between genotypes or biotypes remains to be investigated.
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Affiliation(s)
- Cesar Auguste Badji
- IGEPP, INRAE, Institut Agro, University Rennes, CEDEX, 49045 Angers, France; (C.A.B.); (Z.S.-M.); (C.F.)
| | - Zoé Sol-Mochkovitch
- IGEPP, INRAE, Institut Agro, University Rennes, CEDEX, 49045 Angers, France; (C.A.B.); (Z.S.-M.); (C.F.)
| | - Charlotte Fallais
- IGEPP, INRAE, Institut Agro, University Rennes, CEDEX, 49045 Angers, France; (C.A.B.); (Z.S.-M.); (C.F.)
| | - Corentin Sochard
- IGEPP, INRAE, Institut Agro, University Rennes, CEDEX, 35000 Rennes, France; (C.S.); (Y.O.)
| | | | - Yannick Outreman
- IGEPP, INRAE, Institut Agro, University Rennes, CEDEX, 35000 Rennes, France; (C.S.); (Y.O.)
| | - Sylvia Anton
- IGEPP, INRAE, Institut Agro, University Rennes, CEDEX, 49045 Angers, France; (C.A.B.); (Z.S.-M.); (C.F.)
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61
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Maher AMD, Asaiyah M, Quinn S, Burke R, Wolff H, Bode HB, Griffin CT. Competition and Co-existence of Two Photorhabdus Symbionts with a Nematode Host. MICROBIAL ECOLOGY 2021; 81:223-239. [PMID: 32827089 DOI: 10.1007/s00248-020-01573-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
Photorhabdus spp. (Enterobacteriales: Morganellaceae) occur exclusively as symbionts of Heterorhabditis nematodes for which they provide numerous services, including killing insects and providing nutrition and defence within the cadavers. Unusually, two species (Photorhabdus cinerea and Photorhabdus temperata) associate with a single population of Heterorhabditis downesi at a dune grassland site. Building on previous work, we investigated competition between these two Photorhabdus species both at the regional (between insects) and local (within insect) level by trait comparison and co-culture experiments. There was no difference between the species with respect to supporting nematode reproduction and protection of cadavers against invertebrate scavengers, but P. cinerea was superior to P. temperata in several traits: faster growth rate, greater antibacterial and antifungal activity and colonisation of a higher proportion of nematodes in co-culture. Moreover, where both bacterial symbionts colonised single nematode infective juveniles, P. cinerea tended to dominate in numbers. Differences between Photorhabdus species were detected in the suite of secondary metabolites produced: P. temperata produced several compounds not produced by P. cinerea including anthraquinone pigments. Bioluminescence emitted by P. temperata also tended to be brighter than that from P. cinerea. Bioluminescence and pigmentation may protect cadavers against scavengers that rely on sight. We conclude that while P. cinerea may show greater local level (within-cadaver) competitive success, co-existence of the two Photorhabdus species in the spatially heterogeneous environment of the dunes is favoured by differing specialisations in defence of the cadaver against differing locally important threats.
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Affiliation(s)
- Abigail M D Maher
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Mohamed Asaiyah
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Sarajane Quinn
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Riona Burke
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Hendrik Wolff
- Molecular Biotechnology, Department of Biosciences, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, and Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, and Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
| | - Christine T Griffin
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland.
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62
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Goldstein SL, Klassen JL. Pseudonocardia Symbionts of Fungus-Growing Ants and the Evolution of Defensive Secondary Metabolism. Front Microbiol 2020; 11:621041. [PMID: 33424822 PMCID: PMC7793712 DOI: 10.3389/fmicb.2020.621041] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 12/03/2020] [Indexed: 12/16/2022] Open
Abstract
Actinobacteria belonging to the genus Pseudonocardia have evolved a close relationship with multiple species of fungus-growing ants, where these bacteria produce diverse secondary metabolites that protect the ants and their fungal mutualists from disease. Recent research has charted the phylogenetic diversity of this symbiosis, revealing multiple instances where the ants and Pseudonocardia have formed stable relationships in which these bacteria are housed on specific regions of the ant's cuticle. Parallel chemical and genomic analyses have also revealed that symbiotic Pseudonocardia produce diverse secondary metabolites with antifungal and antibacterial bioactivities, and highlighted the importance of plasmid recombination and horizontal gene transfer for maintaining these symbiotic traits. Here, we propose a multi-level model for the evolution of Pseudonocardia and their secondary metabolites that includes symbiont transmission within and between ant colonies, and the potentially independent movement and diversification of their secondary metabolite biosynthetic genes. Because of their well-studied ecology and experimental tractability, Pseudonocardia symbionts of fungus-growing ants are an especially useful model system to understand the evolution of secondary metabolites, and also comprise a significant source of novel antibiotic and antifungal agents.
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Affiliation(s)
- Sarah L Goldstein
- Department of Molecular and Cell Biology, University of Connecticut, Mansfield, CT, United States
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Mansfield, CT, United States
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63
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Weiler J, Zilio G, Zeballos N, Nørgaard L, Conce Alberto WD, Krenek S, Kaltz O, Bright L. Among-Strain Variation in Resistance of Paramecium caudatum to the Endonuclear Parasite Holospora undulata: Geographic and Lineage-Specific Patterns. Front Microbiol 2020; 11:603046. [PMID: 33381098 PMCID: PMC7767928 DOI: 10.3389/fmicb.2020.603046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/24/2020] [Indexed: 01/04/2023] Open
Abstract
Resistance is a key determinant in interactions between hosts and their parasites. Understanding the amount and distribution of variation in this trait between strains can provide insights into (co)evolutionary processes and their potential to shape patterns of diversity in natural populations. Using controlled inoculation in experimental mass cultures, we investigated the quantitative variation in resistance to the bacterial parasite Holospora undulata across a worldwide collection of strains of its ciliate host Paramecium caudatum. We combined the observed variation with available information on the phylogeny and biogeography of the strains. We found substantial variation in resistance among strains, with upper-bound values of broad-sense heritability >0.5 (intraclass correlation coefficients). Strain estimates of resistance were repeatable between laboratories and ranged from total resistance to near-complete susceptibility. Early (1 week post inoculation) measurements provided higher estimates of resistance heritability than did later measurements (2-3 weeks), possibly due to diverging epidemiological dynamics in replicate cultures of the same strains. Genetic distance (based on a neutral marker) was positively correlated with the difference in resistance phenotype between strains (r = 0.45), essentially reflecting differences between highly divergent clades (haplogroups) within the host species. Haplogroup A strains, mostly European, were less resistant to the parasite (49% infection prevalence) than non-European haplogroup B strains (28%). At a smaller geographical scale (within Europe), strains that are geographically closer to the parasite origin (Southern Germany) were more susceptible to infection than those from further away. These patterns are consistent with a picture of local parasite adaptation. Our study demonstrates ample natural variation in resistance on which selection can act and hints at symbiont adaptation producing signatures in geographic and lineage-specific patterns of resistance in this model system.
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Affiliation(s)
- Jared Weiler
- Department of Biology, State University of New York, College at New Paltz, New Paltz, NY, United States
| | - Giacomo Zilio
- ISEM, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Nathalie Zeballos
- ISEM, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Louise Nørgaard
- ISEM, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
- School of Biological Sciences and Centre for Geometric Biology, Monash University, Melbourne, VIC, Australia
| | - Winiffer D. Conce Alberto
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Sascha Krenek
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Oliver Kaltz
- ISEM, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Lydia Bright
- Department of Biology, State University of New York, College at New Paltz, New Paltz, NY, United States
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64
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Oliveira BFR, Lopes IR, Canellas ALB, Muricy G, Dobson ADW, Laport MS. Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea. Microorganisms 2020; 8:E1978. [PMID: 33322780 PMCID: PMC7764410 DOI: 10.3390/microorganisms8121978] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/12/2020] [Accepted: 11/25/2020] [Indexed: 01/28/2023] Open
Abstract
Marine sponges are excellent examples of invertebrate-microbe symbioses. In this holobiont, the partnership has elegantly evolved by either transmitting key microbial associates through the host germline and/or capturing microorganisms from the surrounding seawater. We report here on the prokaryotic microbiota during different developmental stages of Plakina cyanorosea and their surrounding environmental samples by a 16S rRNA metabarcoding approach. In comparison with their source adults, larvae housed slightly richer and more diverse microbial communities, which are structurally more related to the environmental microbiota. In addition to the thaumarchaeal Nitrosopumilus, parental sponges were broadly dominated by Alpha- and Gamma-proteobacteria, while the offspring were particularly enriched in the Vibrionales, Alteromonodales, Enterobacterales orders and the Clostridia and Bacteroidia classes. An enterobacterial operational taxonomic unit (OTU) was the dominant member of the strict core microbiota. The most abundant and unique OTUs were not significantly enriched amongst the microbiomes from host specimens included in the sponge microbiome project. In a wider context, Oscarella and Plakina are the sponge genera with higher divergence in their associated microbiota compared to their Homoscleromorpha counterparts. Our results indicate that P. cyanorosea is a low microbial abundance sponge (LMA), which appears to heavily depend on the horizontal transmission of its microbial partners that likely help the sponge host in the adaptation to its habitat.
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Affiliation(s)
- Bruno F. R. Oliveira
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland;
| | - Isabelle R. Lopes
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
| | - Anna L. B. Canellas
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
| | - Guilherme Muricy
- Laboratório de Biologia de Porifera, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940040, Brazil;
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland;
- Environmental Research Institute, University College Cork, T23 XE10 Cork, Ireland
| | - Marinella S. Laport
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
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65
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Energetic requirements of the transition from solitary to group living. ECOLOGICAL COMPLEXITY 2020. [DOI: 10.1016/j.ecocom.2020.100874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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66
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Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity. mSystems 2020; 5:5/6/e01045-20. [PMID: 33144315 PMCID: PMC7646530 DOI: 10.1128/msystems.01045-20] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Large-scale metagenome assemblies of human microbiomes have produced a vast catalogue of previously unseen microbial genomes; however, comparatively few microbial genomes derive from other vertebrates. Here, we generated 5,596 metagenome-assembled genomes (MAGs) from the gut metagenomes of 180 predominantly wild animal species representing 5 classes, in addition to 14 existing animal gut metagenome data sets. The MAGs comprised 1,522 species-level genome bins (SGBs), most of which were novel at the species, genus, or family level, and the majority were enriched in host versus environment metagenomes. Many traits distinguished SGBs enriched in host or environmental biomes, including the number of antimicrobial resistance genes. We identified 1,986 diverse biosynthetic gene clusters; only 23 clustered with any MIBiG database references. Gene-based assembly revealed tremendous gene diversity, much of it host or environment specific. Our MAG and gene data sets greatly expand the microbial genome repertoire and provide a broad view of microbial adaptations to the vertebrate gut.IMPORTANCE Microbiome studies on a select few mammalian species (e.g., humans, mice, and cattle) have revealed a great deal of novel genomic diversity in the gut microbiome. However, little is known of the microbial diversity in the gut of other vertebrates. We studied the gut microbiomes of a large set of mostly wild animal species consisting of mammals, birds, reptiles, amphibians, and fish. Unfortunately, we found that existing reference databases commonly used for metagenomic analyses failed to capture the microbiome diversity among vertebrates. To increase database representation, we applied advanced metagenome assembly methods to our animal gut data and to many public gut metagenome data sets that had not been used to obtain microbial genomes. Our resulting genome and gene cluster collections comprised a great deal of novel taxonomic and genomic diversity, which we extensively characterized. Our findings substantially expand what is known of microbial genomic diversity in the vertebrate gut.
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67
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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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68
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Abstract
Host-associated microbial communities have an important role in shaping the health and fitness of plants and animals. Most studies have focused on the bacterial, fungal or viral communities, but often the archaeal component has been neglected. The archaeal community, the so-called archaeome, is now increasingly recognized as an important component of host-associated microbiomes. It is composed of various lineages, including mainly Methanobacteriales and Methanomassiliicoccales (Euryarchaeota), as well as representatives of the Thaumarchaeota. Host-archaeome interactions have mostly been delineated from methanogenic archaea in the gastrointestinal tract, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. In this Review, we discuss the diversity and potential roles of the archaea associated with protists, plants and animals. We also present the current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeome in both health and disease.
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69
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Bao Y, Qi B, Huang W, Liu B, Li Y. The fungal community in non-rhizosphere soil of Panax ginseng are driven by different cultivation modes and increased cultivation periods. PeerJ 2020; 8:e9930. [PMID: 33088612 PMCID: PMC7568858 DOI: 10.7717/peerj.9930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/21/2020] [Indexed: 11/25/2022] Open
Abstract
Continuous cropping obstacles severely hindered the sustained development of the ginseng industry. Among the obstacles, an imbalance of soil microbiome community was considered one of the major culprits. The fungal community is an essential part of the soil microbiome community. Extensive characterization of the fungal community composition and variation during ginseng cultivation will help us understand the mechanism underlying continuous cropping obstacles. By using a high-throughput amplicon sequencing method, the non-rhizospheric fungal community of farmland cultivated ginseng of 2 years old (C2) and 5 years old (C5), understory wild ginseng of 15 years old (W15) and 35 years old (W35), fallow fields which have been abandoned for 10 (F10) years were characterized. Farmland cultivated ginseng and understory wild ginseng harbored distinct non-rhizospheric fungal communities, and extension of cultivation periods enlarged the fungal community difference between two cultivation modes. Extended cultivation periods significantly decreased the OTU richness and PD whole tree indices, and OTU number and cultivation periods were negatively correlated. Extension of cultivation periods led to an increased abundance of pathotrophs. Still, the increased abundance of pathotrophs may not be the leading cause of severe continuous cropping obstacles in farmland cultivated ginseng. Compared with understory wild ginseng, farmland cultivated ginseng had a lower abundance of symbiotrophs and a higher abundance of saprotrophs. This changed symbiotrophs/saprotrophs ratio may have some correlation with the severe continuous cropping obstacles that occurred in farmland cultivated ginseng. Fallowing on the fungal community of the non-rhizosphere soil was generally opposite of that of extension of ginseng cultivation periods. The impacts of farmland cultivation on the fungal community of the non-rhizosphere soil can last for decades, even if the following is practiced.
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Affiliation(s)
- Yu Bao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, People's Republic of China
| | - Bao Qi
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, People's Republic of China
| | - Wei Huang
- Key Laboratory of Applied Statistics of Ministry of Education, Northeast Normal University, Changchun, People's Republic of China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, People's Republic of China
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, People's Republic of China
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70
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Rapid evolution destabilizes species interactions in a fluctuating environment. ISME JOURNAL 2020; 15:450-460. [PMID: 33024292 DOI: 10.1038/s41396-020-00787-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 12/16/2022]
Abstract
Positive species interactions underlie the functioning of ecosystems. Given their importance, it is crucial to understand the stability of positive interactions over evolutionary timescales, in both constant and fluctuating environments; e.g., environments interrupted with periods of competition. We addressed this question using a two-species microbial system in which we modulated interactions according to the nutrient provided. We evolved in parallel four experimental replicates of species growing in isolation or together in consortia for 200 generations in both a constant and fluctuating environment with daily changes between commensalism and competition. We sequenced full genomes of single clones isolated at different time points during the experiment. We found that the two species coexisted over 200 generations in the constant commensal environment. In contrast, in the fluctuating environment, coexistence broke down when one of the species went extinct in two out of four cases. We showed that extinction was highly deterministic: when we replayed the evolution experiment from an intermediate time point we repeatably reproduced species extinction. We further show that these dynamics were driven by adaptive mutations in a small set of genes. In conclusion, in a fluctuating environment, rapid evolution destabilizes the long-term stability of positive pairwise interactions.
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71
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Origin and elaboration of a major evolutionary transition in individuality. Nature 2020; 585:239-244. [DOI: 10.1038/s41586-020-2653-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 06/03/2020] [Indexed: 11/09/2022]
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72
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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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73
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Nelsen MP, Lücking R, Boyce CK, Lumbsch HT, Ree RH. The macroevolutionary dynamics of symbiotic and phenotypic diversification in lichens. Proc Natl Acad Sci U S A 2020; 117:21495-21503. [PMID: 32796103 PMCID: PMC7474681 DOI: 10.1073/pnas.2001913117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Symbioses are evolutionarily pervasive and play fundamental roles in structuring ecosystems, yet our understanding of their macroevolutionary origins, persistence, and consequences is incomplete. We traced the macroevolutionary history of symbiotic and phenotypic diversification in an iconic symbiosis, lichens. By inferring the most comprehensive time-scaled phylogeny of lichen-forming fungi (LFF) to date (over 3,300 species), we identified shifts among symbiont classes that broadly coincided with the convergent evolution of phylogenetically or functionally similar associations in diverse lineages (plants, fungi, bacteria). While a relatively recent loss of lichenization in Lecanoromycetes was previously identified, our work instead suggests lichenization was abandoned far earlier, interrupting what had previously been considered a direct switch between trebouxiophycean and trentepohlialean algal symbionts. Consequently, some of the most diverse clades of LFF are instead derived from nonlichenized ancestors and re-evolved lichenization with Trentepohliales algae, a clade that also facilitated lichenization in unrelated lineages of LFF. Furthermore, while symbiont identity and symbiotic phenotype influence the ecology and physiology of lichens, they are not correlated with rates of lineage birth and death, suggesting more complex dynamics underly lichen diversification. Finally, diversification patterns of LFF differed from those of wood-rotting and ectomycorrhizal taxa, likely reflecting contrasts in their fundamental biological properties. Together, our work provides a timeline for the ecological contributions of lichens, and reshapes our understanding of symbiotic persistence in a classic model of symbiosis.
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Affiliation(s)
- Matthew P Nelsen
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605;
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, 14195 Berlin, Germany
| | - C Kevin Boyce
- Department of Geological Sciences, Stanford University, Stanford, CA 94305
| | - H Thorsten Lumbsch
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605
| | - Richard H Ree
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605
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74
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Molecular causes of an evolutionary shift along the parasitism-mutualism continuum in a bacterial symbiont. Proc Natl Acad Sci U S A 2020; 117:21658-21666. [PMID: 32817434 PMCID: PMC7474615 DOI: 10.1073/pnas.2005536117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Symbiotic relationships with microbes are ubiquitous among living beings and can be parasitic, such as in bacterial pathogens, or mutualistic, as in beneficial microbiomes. Among other factors, the outcome of microbe–host relationships is determined by the mode of symbiont transmission from host to host. Here we describe how bacterial symbionts increased in infectivity and virulence toward their amoeba host when transmission to a new host was essential for survival. The enhanced parasitism is a result of genomic changes and a pronounced switch of gene expression altering the symbionts’ mechanisms for host interaction. Our study provides both a molecular explanation as well as a blueprint for how changes in gene expression are sufficient to confer enhanced parasitism in microbes. Symbiosis with microbes is a ubiquitous phenomenon with a massive impact on all living organisms, shaping the world around us today. Theoretical and experimental studies show that vertical transmission of symbionts leads to the evolution of mutualistic traits, whereas horizontal transmission facilitates the emergence of parasitic features. However, these studies focused on phenotypic data, and we know little about underlying molecular changes at the genomic level. Here, we combined an experimental evolution approach with infection assays, genome resequencing, and global gene expression analysis to study the effect of transmission mode on an obligate intracellular bacterial symbiont. We show that a dramatic shift in the frequency of genetic variants, coupled with major changes in gene expression, allow the symbiont to alter its position in the parasitism–mutualism continuum depending on the mode of between-host transmission. We found that increased parasitism in horizontally transmitted chlamydiae residing in amoebae was a result of processes occurring at the infectious stage of the symbiont’s developmental cycle. Specifically, genes involved in energy production required for extracellular survival and the type III secretion system—the symbiont’s primary virulence mechanism—were significantly up-regulated. Our results identify the genomic and transcriptional dynamics sufficient to favor parasitic or mutualistic strategies.
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75
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Phenotypic Parallelism during Experimental Adaptation of a Free-Living Bacterium to the Zebrafish Gut. mBio 2020; 11:mBio.01519-20. [PMID: 32817106 PMCID: PMC7439477 DOI: 10.1128/mbio.01519-20] [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] [Indexed: 12/20/2022] Open
Abstract
Although animals encounter many bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. We used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of Shewanella oneidensis through the intestines of larval zebrafish (Danio rerio). Our results demonstrate that adaptation to the zebrafish gut is complex, with multiple evolutionary pathways capable of improving colonization, but that motility plays an important role during the onset of host association. Although animals encounter a plethora of bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. However, our understanding of how bacteria initiate symbioses with animal hosts remains underexplored, and this process is central to the assembly and function of gut bacterial communities. Therefore, we used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of Shewanella oneidensis through the intestines of larval zebrafish (Danio rerio). After approximately 200 bacterial generations, isolates from evolved populations improved their ability to colonize larval zebrafish during competition against their unpassaged ancestor. Genome sequencing revealed unique sets of mutations in the two evolved isolates exhibiting the highest mean competitive fitness. One isolate exhibited increased swimming motility and decreased biofilm formation compared to the ancestor, and we identified a missense mutation in the mannose-sensitive hemagglutinin pilus operon that is sufficient to increase fitness and reproduce these phenotypes. The second isolate exhibited enhanced swimming motility but unchanged biofilm formation, and here the genetic basis for adaptation is less clear. These parallel enhancements in motility and fitness resemble the behavior of a closely related Shewanella strain previously isolated from larval zebrafish and suggest phenotypic convergence with this isolate. Our results demonstrate that adaptation to the zebrafish gut is complex, with multiple evolutionary pathways capable of improving colonization, but that motility plays an important role during the onset of host association.
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76
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Douglas AE. Housing microbial symbionts: evolutionary origins and diversification of symbiotic organs in animals. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190603. [PMID: 32772661 DOI: 10.1098/rstb.2019.0603] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In many animal hosts, microbial symbionts are housed within specialized structures known as symbiotic organs, but the evolutionary origins of these structures have rarely been investigated. Here, I adopt an evolutionary developmental (evo-devo) approach, specifically to apply knowledge of the development of symbiotic organs to gain insights into their evolutionary origins and diversification. In particular, host genetic changes associated with evolution of symbiotic organs can be inferred from studies to identify the host genes that orchestrate the development of symbiotic organs, recognizing that microbial products may also play a key role in triggering the developmental programme in some associations. These studies may also reveal whether higher animal taxonomic groups (order, class, phylum, etc.) possess a common genetic regulatory network for symbiosis that is latent in taxa lacking symbiotic organs, and activated at the origination of symbiosis in different host lineages. In this way, apparent instances of convergent evolution of symbiotic organs may be homologous in terms of a common genetic blueprint for symbiosis. Advances in genetic technologies, including reverse genetic tools and genome editing, will facilitate the application of evo-devo approaches to investigate the evolution of symbiotic organs in animals. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Angela E Douglas
- Department of Entomology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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77
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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: 47] [Impact Index Per Article: 11.8] [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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78
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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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79
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Nguyen PL, van Baalen M. On the difficult evolutionary transition from the free-living lifestyle to obligate symbiosis. PLoS One 2020; 15:e0235811. [PMID: 32730262 PMCID: PMC7392539 DOI: 10.1371/journal.pone.0235811] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
Obligate symbiosis evolved from free-living individuals most likely via the intermediate stage of facultative symbiosis. However, why should facultative symbionts, who can live independently but also benefit from their partners if these are available, give up this best of both worlds? Using the adaptive dynamics approach, we analyse a simple model, focusing on one partner of the symbiosis, to gain more insight into the selective forces that make individuals forgo the ability to reproduce in the free-living state. Our results suggest that, similar to the parasitism-mutualism continuum, the free-living way of life and obligate symbiosis are two extremes of a continuum of the ability to reproduce independently of a partner. More importantly, facultative symbiosis should be the rule as for many parameter combinations completely giving up independent reproduction or adopting a pure free-living strategy is not so easy. We also show that if host encounter comes at a cost, individuals that put more effort into increasing the chances to meet with their partners are more likely to give up the ability to reproduce independently. Finally, our model does not specify the ecological interactions between hosts and symbionts but we discuss briefly how the ecological nature of an interaction can influence the transition from facultative to obligate symbiosis.
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Affiliation(s)
| | - Minus van Baalen
- Institut de Biologie de l’École Normale Supérieur, Paris, France
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80
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Abstract
Bacteria form diverse interactions with eukaryotic hosts. This is well represented by the Rhizobiales, a clade of Alphaproteobacteria strategically important for their large diversity of lifestyles with implications for agricultural and medical research. To investigate their lifestyle evolution, we compiled a comprehensive data set of genomes and lifestyle information for over 1,000 Rhizobiales genomes. We show that the origins of major host-associated lineages in Rhizobiales broadly coincided with the emergences of their host plants/animals, suggesting bacterium-host interactions as a driving force in the evolution of Rhizobiales. We further found that, in addition to gene gains, preexisting traits and recurrent losses of specific genomic traits may have played underrecognized roles in the origin of host-associated lineages, providing clues to genetic engineering of microbial agricultural inoculants and prevention of the emergence of potential plant/animal pathogens. Members of the order Rhizobiales include those capable of nitrogen fixation in nodules as well as pathogens of animals and plants. This lifestyle diversity has important implications for agricultural and medical research. Leveraging large-scale genomic data, we infer that Rhizobiales originated as a free-living ancestor ∼1,500 million years ago (Mya) and that the later emergence of host-associated lifestyles broadly coincided with the rise of their eukaryotic hosts. In particular, the first nodulating lineage arose from either Azorhizobium or Bradyrhizobium 150 to 80 Mya, a time range in general concurrent with the emergence of legumes. The rates of lifestyle transitions are highly variable; nodule association is more likely to be lost than gained, whereas animal association likely represents an evolutionary dead end. We searched for statistical correlations between gene presence and lifestyle and identified genes likely contributing to the transition and adaptation to the same lifestyle in divergent lineages. Among the genes potentially promoting successful transitions to major nodulation lineages, the nod and nif clusters for nodulation and nitrogen fixation, respectively, were repeatedly acquired during each transition; the fix, dct, and phb clusters involved in energy conservation under micro-oxic conditions were present in the nonnodulating ancestors; and the secretion systems were acquired in lineage-specific patterns. Our study data suggest that increased eukaryote diversity drives lifestyle diversification of bacteria and highlight both acquired and preexisting traits facilitating the origin of host association. IMPORTANCE Bacteria form diverse interactions with eukaryotic hosts. This is well represented by the Rhizobiales, a clade of Alphaproteobacteria strategically important for their large diversity of lifestyles with implications for agricultural and medical research. To investigate their lifestyle evolution, we compiled a comprehensive data set of genomes and lifestyle information for over 1,000 Rhizobiales genomes. We show that the origins of major host-associated lineages in Rhizobiales broadly coincided with the emergences of their host plants/animals, suggesting bacterium-host interactions as a driving force in the evolution of Rhizobiales. We further found that, in addition to gene gains, preexisting traits and recurrent losses of specific genomic traits may have played underrecognized roles in the origin of host-associated lineages, providing clues to genetic engineering of microbial agricultural inoculants and prevention of the emergence of potential plant/animal pathogens.
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81
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Abstract
Host-beneficial endosymbioses, which are formed when a microorganism takes up residence inside another cell and provides a fitness advantage to the host, have had a dramatic influence on the evolution of life. These intimate relationships have yielded the mitochondrion and the plastid (chloroplast) - the ancient organelles that in part define eukaryotic life - along with many more recent associations involving a wide variety of hosts and microbial partners. These relationships are often envisioned as stable associations that appear cooperative and persist for extremely long periods of time. But recent evidence suggests that this stable state is often born from turbulent and conflicting origins, and that the apparent stability of many beneficial endosymbiotic relationships - although certainly real in many cases - is not an inevitable outcome of these associations. Here we review how stable endosymbioses form, how they are maintained, and how they sometimes break down and are reborn. We focus on relationships formed by insects and their resident microorganisms because these symbioses have been the focus of significant empirical work over the last two decades. We review these relationships over five life stages: origin, birth, middle age, old age, and death.
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82
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Sørensen MES, Lowe CD, Minter EJA, Wood AJ, Cameron DD, Brockhurst MA. The role of exploitation in the establishment of mutualistic microbial symbioses. FEMS Microbiol Lett 2020; 366:5528313. [PMID: 31271421 PMCID: PMC6638607 DOI: 10.1093/femsle/fnz148] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022] Open
Abstract
Evolutionary theory suggests that the conditions required for the establishment of mutualistic symbioses through mutualism alone are highly restrictive, often requiring the evolution of complex stabilising mechanisms. Exploitation, whereby initially the host benefits at the expense of its symbiotic partner and mutual benefits evolve subsequently through trade-offs, offers an arguably simpler route to the establishment of mutualistic symbiosis. In this review, we discuss the theoretical and experimental evidence supporting a role for host exploitation in the establishment and evolution of mutualistic microbial symbioses, including data from both extant and experimentally evolved symbioses. We conclude that exploitation rather than mutualism may often explain the origin of mutualistic microbial symbioses.
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Affiliation(s)
- Megan E S Sørensen
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Chris D Lowe
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Ewan J A Minter
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - A Jamie Wood
- Department of Biology, University of York, York YO10 5DD, UK.,Department of Mathematics, University of York, York YO10 5DD, UK
| | - Duncan D Cameron
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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83
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Dharampal PS, Diaz-Garcia L, Haase MAB, Zalapa J, Currie CR, Hittinger CT, Steffan SA. Microbial Diversity Associated with the Pollen Stores of Captive-Bred Bumble Bee Colonies. INSECTS 2020; 11:insects11040250. [PMID: 32316296 PMCID: PMC7240610 DOI: 10.3390/insects11040250] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/14/2022]
Abstract
The pollen stores of bumble bees host diverse microbiota that influence overall colony fitness. Yet, the taxonomic identity of these symbiotic microbes is relatively unknown. In this descriptive study, we characterized the microbial community of pollen provisions within captive-bred bumble bee hives obtained from two commercial suppliers located in North America. Findings from 16S rRNA and ITS gene-based analyses revealed that pollen provisions from the captive-bred hives shared several microbial taxa that have been previously detected among wild populations. While diverse microbes across phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Ascomycota were detected in all commercial hives, significant differences were detected at finer-scale taxonomic resolution based on the supplier source. The causative agent of chalkbrood disease in honey bees, Ascosphaera apis, was detected in all hives obtained from one supplier source, although none of the hives showed symptoms of infection. The shared core microbiota across both commercial supplier sources consisted of two ubiquitous bee-associated groups, Lactobacillus and Wickerhamiella/Starmerella clade yeasts that potentially contribute to the beneficial function of the microbiome of bumble bee pollen provisions.
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Affiliation(s)
- Prarthana S. Dharampal
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA;
- Correspondence:
| | - Luis Diaz-Garcia
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA; (L.D.-G.); (J.Z.)
- Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Aguascalientes 20676, Mexico
| | - Max A. B. Haase
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.A.B.H.); (C.T.H.)
| | - Juan Zalapa
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA; (L.D.-G.); (J.Z.)
- USDA-ARS, Vegetable Crop Research Unit, Madison, WI 53706, USA
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.A.B.H.); (C.T.H.)
| | - Shawn A. Steffan
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA;
- USDA-ARS, Vegetable Crop Research Unit, Madison, WI 53706, USA
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84
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Binetruy F, Buysse M, Lejarre Q, Barosi R, Villa M, Rahola N, Paupy C, Ayala D, Duron O. Microbial community structure reveals instability of nutritional symbiosis during the evolutionary radiation of Amblyomma ticks. Mol Ecol 2020; 29:1016-1029. [PMID: 32034827 DOI: 10.1111/mec.15373] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 12/14/2022]
Abstract
Mutualistic interactions with microbes have facilitated the adaptation of major eukaryotic lineages to restricted diet niches. Hence, ticks with their strictly blood-feeding lifestyle are associated with intracellular bacterial symbionts through an essential B vitamin supplementation. In this study, examination of bacterial diversity in 25 tick species of the genus Amblyomma showed that three intracellular bacteria, Coxiella-like endosymbionts (LE), Francisella-LE and Rickettsia, are remarkably common. No other bacterium is as uniformly present in Amblyomma ticks. Almost all Amblyomma species were found to harbour a nutritive obligate symbiont, Coxiella-LE or Francisella-LE, that is able to synthesize B vitamins. However, despite the co-evolved and obligate nature of these mutualistic interactions, the structure of microbiomes does not mirror the Amblyomma phylogeny, with a clear exclusion pattern between Coxiella-LE and Francisella-LE across tick species. Coxiella-LE, but not Francisella-LE, form evolutionarily stable associations with ticks, commonly leading to co-cladogenesis. We further found evidence for symbiont replacements during the radiation of Amblyomma, with recent, and probably ongoing, invasions by Francisella-LE and subsequent replacements of ancestral Coxiella-LE through transient co-infections. Nutritional symbiosis in Amblyomma ticks is thus not a stable evolutionary state, but instead arises from conflicting origins between unrelated but competing symbionts with similar metabolic capabilities.
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Affiliation(s)
- Florian Binetruy
- MIVEGEC (Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France
| | - Marie Buysse
- MIVEGEC (Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France
| | - Quentin Lejarre
- MIVEGEC (Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France.,CIRMF (Centre International de Recherches Médicales de Franceville), Franceville, Gabon
| | - Roxanne Barosi
- MIVEGEC (Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France
| | - Manon Villa
- MIVEGEC (Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France
| | - Nil Rahola
- MIVEGEC (Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France.,CIRMF (Centre International de Recherches Médicales de Franceville), Franceville, Gabon
| | - Christophe Paupy
- MIVEGEC (Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France
| | - Diego Ayala
- MIVEGEC (Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France.,CIRMF (Centre International de Recherches Médicales de Franceville), Franceville, Gabon
| | - Olivier Duron
- MIVEGEC (Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France
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85
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Gano-Cohen KA, Wendlandt CE, Al Moussawi K, Stokes PJ, Quides KW, Weisberg AJ, Chang JH, Sachs JL. Recurrent mutualism breakdown events in a legume rhizobia metapopulation. Proc Biol Sci 2020; 287:20192549. [PMID: 31992172 DOI: 10.1098/rspb.2019.2549] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Bacterial mutualists generate major fitness benefits for eukaryotes, reshaping the host phenotype and its interactions with the environment. Yet, microbial mutualist populations are predicted to generate mutants that defect from providing costly services to hosts while maintaining the capacity to exploit host resources. Here, we examined the mutualist service of symbiotic nitrogen fixation in a metapopulation of root-nodulating Bradyrhizobium spp. that associate with the native legume Acmispon strigosus. We quantified mutualism traits of 85 Bradyrhizobium isolates gathered from a 700 km transect in California spanning 10 sampled A. strigosus populations. We clonally inoculated each Bradyrhizobium isolate onto A. strigosus hosts and quantified nodulation capacity and net effects of infection, including host growth and isotopic nitrogen concentration. Six Bradyrhizobium isolates from five populations were categorized as ineffective because they formed nodules but did not enhance host growth via nitrogen fixation. Six additional isolates from three populations failed to form root nodules. Phylogenetic reconstruction inferred two types of mutualism breakdown, including three to four independent losses of effectiveness and five losses of nodulation capacity on A. strigosus. The evolutionary and genomic drivers of these mutualism breakdown events remain poorly understood.
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Affiliation(s)
- Kelsey A Gano-Cohen
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Camille E Wendlandt
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Khadija Al Moussawi
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA, USA
| | - Peter J Stokes
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Kenjiro W Quides
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA, USA
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Joel L Sachs
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.,Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.,Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA, USA.,Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
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86
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Abstract
Little is known about the establishment of symbioses. A new study finds that two independent protist-algae symbioses utilize convergent patterns of nutrient exchange, suggesting that certain complementary host and symbiont traits can increase the likelihood of establishing beneficial symbiotic interactions.
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Affiliation(s)
- Levi T Morran
- Department of Biology, Emory University, Atlanta, GA, USA.
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87
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Abstract
The evolution of a mutualism requires reciprocal interactions whereby one species provides a service that the other species cannot perform or performs less efficiently. Services exchanged in insect-fungus mutualisms include nutrition, protection, and dispersal. In ectosymbioses, which are the focus of this review, fungi can be consumed by insects or can degrade plant polymers or defensive compounds, thereby making a substrate available to insects. They can also protect against environmental factors and produce compounds antagonistic to microbial competitors. Insects disperse fungi and can also provide fungal growth substrates and protection. Insect-fungus mutualisms can transition from facultative to obligate, whereby each partner is no longer viable on its own. Obligate dependency has (a) resulted in the evolution of morphological adaptations in insects and fungi, (b) driven the evolution of social behaviors in some groups of insects, and (c) led to the loss of sexuality in some fungal mutualists.
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Affiliation(s)
- Peter H W Biedermann
- Research Group Insect-Fungus Symbiosis, Department of Animal Ecology and Tropical Biology, University of Würzburg, 97074 Würzburg, Germany;
| | - Fernando E Vega
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705, USA;
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88
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Sørensen MES, Wood AJ, Minter EJA, Lowe CD, Cameron DD, Brockhurst MA. Comparison of Independent Evolutionary Origins Reveals Both Convergence and Divergence in the Metabolic Mechanisms of Symbiosis. Curr Biol 2020; 30:328-334.e4. [PMID: 31902722 DOI: 10.1016/j.cub.2019.11.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/17/2019] [Accepted: 11/18/2019] [Indexed: 11/28/2022]
Abstract
Through the merger of previously independent lineages, symbiosis promotes the acquisition of new traits and exploitation of inaccessible ecological niches [1, 2], driving evolutionary innovation and important ecosystem functions [3-6]. The transient nature of establishment makes study of symbiotic origins difficult, but experimental comparison of independent origins could reveal the degree of convergence in the underpinning mechanisms [7, 8]. We compared the metabolic mechanisms of two independent origins of Paramecium bursaria-Chlorella photosymbiosis [9-11] using a reciprocal metabolomic pulse-chase method. This showed convergent patterns of nutrient exchange and utilization for host-derived nitrogen in the Chlorella genotypes [12, 13] and symbiont-derived carbon in the P. bursaria genotypes [14, 15]. Consistent with a convergent primary nutrient exchange, partner-switched host-symbiont pairings were functional. Direct competition of hosts containing native or recombined symbionts against isogenic symbiont-free hosts showed that the fitness benefits of symbiosis for hosts increased with irradiance but varied by genotype. Global metabolism varied more between the Chlorella than the P. bursaria genotypes and suggested divergent mechanisms of light management. Specifically, the algal symbiont genotypes either produced photo-protective carotenoid pigments at high irradiance or more chlorophyll, resulting in corresponding differences in photosynthetic efficiency and non-photochemical quenching among host-symbiont pairings. These data suggest that the multiple origins of P. bursaria-Chlorella symbiosis use a convergent nutrient exchange, whereas other photosynthetic traits linked to functioning of photosymbiosis have diverged. Although convergence enables partner switching among diverse strains, phenotypic mismatches resulting from divergence of secondary symbiotic traits could mediate host-symbiont specificity in nature.
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Affiliation(s)
- Megan E S Sørensen
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - A Jamie Wood
- Department of Biology, University of York, York YO10 5DD, UK
| | - Ewan J A Minter
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Chris D Lowe
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Duncan D Cameron
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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89
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Kamm K, Osigus HJ, Stadler PF, DeSalle R, Schierwater B. Genome analyses of a placozoan rickettsial endosymbiont show a combination of mutualistic and parasitic traits. Sci Rep 2019; 9:17561. [PMID: 31772223 PMCID: PMC6879607 DOI: 10.1038/s41598-019-54037-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 10/25/2019] [Indexed: 12/16/2022] Open
Abstract
Symbiotic relationships between eukaryotic hosts and bacteria range from parasitism to mutualism and may deeply influence both partners' fitness. The presence of intracellular bacteria in the metazoan phylum Placozoa has been reported several times, but without any knowledge about the nature of this relationship and possible implications for the placozoan holobiont. This information may be of crucial significance since little is known about placozoan ecology and how different species adapt to different environmental conditions, despite being almost invariable at the morphological level. We here report on the novel genome of the rickettsial endosymbiont of Trichoplax sp. H2 (strain "Panama"). The combination of eliminated and retained metabolic pathways of the bacterium indicates a potential for a mutualistic as well as for a parasitic relationship, whose outcome could depend on the environmental context. In particular we show that the endosymbiont is dependent on the host for growth and reproduction and that the latter could benefit from a supply with essential amino acids and important cofactors. These findings call for further studies to clarify the actual benefit for the placozoan host and to investigate a possible role of the endosymbiont for ecological separation between placozoan species.
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Affiliation(s)
- Kai Kamm
- University of Veterinary Medicine Hannover, Foundation, Institute of Animal Ecology, Bünteweg 17d, D-30559, Hannover, Germany.
| | - Hans-Jürgen Osigus
- University of Veterinary Medicine Hannover, Foundation, Institute of Animal Ecology, Bünteweg 17d, D-30559, Hannover, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Bernd Schierwater
- University of Veterinary Medicine Hannover, Foundation, Institute of Animal Ecology, Bünteweg 17d, D-30559, Hannover, Germany. .,Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA.
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90
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Haselkorn TS, DiSalvo S, Miller JW, Bashir U, Brock DA, Queller DC, Strassmann JE. The specificity of Burkholderia symbionts in the social amoeba farming symbiosis: Prevalence, species, genetic and phenotypic diversity. Mol Ecol 2019; 28:847-862. [PMID: 30575161 DOI: 10.1111/mec.14982] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/13/2018] [Accepted: 10/25/2018] [Indexed: 01/10/2023]
Abstract
The establishment of symbioses between eukaryotic hosts and bacterial symbionts in nature is a dynamic process. The formation of such relationships depends on the life history of both partners. Bacterial symbionts of amoebae may have unique evolutionary trajectories to the symbiont lifestyle, because bacteria are typically ingested as prey. To persist after ingestion, bacteria must first survive phagocytosis. In the social amoeba Dictyostelium discoideum, certain strains of Burkholderia bacteria are able to resist amoebal digestion and maintain a persistent relationship that includes carriage throughout the amoeba's social cycle that culminates in spore formation. Some Burkholderia strains allow their host to carry other bacteria, as food. This carried food is released in new environments in a trait called farming. To better understand the diversity and prevalence of Burkholderia symbionts and the traits they impart to their amoebae hosts, we first screened 700 natural isolates of D. discoideum and found 25% infected with Burkholderia. We next used a multilocus phylogenetic analysis and identified two independent transitions by Burkholderia to the symbiotic lifestyle. Finally, we tested the ability of 38 strains of Burkholderia from D. discoideum, as well as strains isolated from other sources, for traits relevant to symbiosis in D. discoideum. Only D. discoideum native isolates belonging to the Burkholderia agricolaris, B. hayleyella, and B. bonniea species were able to form persistent symbiotic associations with D. discoideum. The Burkholderia-Dictyostelium relationship provides a promising arena for further studies of the pathway to symbiosis in a unique system.
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Affiliation(s)
| | - Susanne DiSalvo
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, Illinois
| | - Jacob W Miller
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, Illinois
| | - Usman Bashir
- Department of Biology, Washington University in St. Louis, Missouri
| | - Debra A Brock
- Department of Biology, Washington University in St. Louis, Missouri
| | - David C Queller
- Department of Biology, Washington University in St. Louis, Missouri
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91
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Potential Interactions between Clade SUP05 Sulfur-Oxidizing Bacteria and Phages in Hydrothermal Vent Sponges. Appl Environ Microbiol 2019; 85:AEM.00992-19. [PMID: 31492669 DOI: 10.1128/aem.00992-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/03/2019] [Indexed: 01/27/2023] Open
Abstract
In deep-sea hydrothermal vent environments, sulfur-oxidizing bacteria belonging to the clade SUP05 are crucial symbionts of invertebrate animals. Marine viruses, as the most abundant biological entities in the ocean, play essential roles in regulating the sulfur metabolism of the SUP05 bacteria. To date, vent sponge-associated SUP05 and their phages have not been well documented. The current study analyzed microbiomes of Haplosclerida sponges from hydrothermal vents in the Okinawa Trough and recovered the dominant SUP05 genome, designated VS-SUP05. Phylogenetic analysis showed that VS-SUP05 was closely related to endosymbiotic SUP05 strains from mussels living in deep-sea hydrothermal vent fields. Homology and metabolic pathway comparisons against free-living and symbiotic SUP05 strains revealed that the VS-SUP05 genome shared many features with the deep-sea mussel symbionts. Supporting a potentially symbiotic lifestyle, the VS-SUP05 genome contained genes involved in the synthesis of essential amino acids and cofactors that are desired by the host. Analysis of sponge-associated viral sequences revealed putative VS-SUP05 phages, all of which were double-stranded viruses belonging to the families Myoviridae, Siphoviridae, Podoviridae, and Microviridae Among the phage sequences, one contig contained metabolic genes (iscR, iscS, and iscU) involved in iron-sulfur cluster formation. Interestingly, genome sequence comparison revealed horizontal transfer of the iscS gene among phages, VS-SUP05, and other symbiotic SUP05 strains, indicating an interaction between marine phages and SUP05 symbionts. Overall, our findings confirm the presence of SUP05 bacteria and their phages in sponges from deep-sea vents and imply a beneficial interaction that allows adaptation of the host sponge to the hydrothermal vent environment.IMPORTANCE Chemosynthetic SUP05 bacteria dominate the microbial communities of deep-sea hydrothermal vents around the world, SUP05 bacteria utilize reduced chemical compounds in vent fluids and commonly form symbioses with invertebrate organisms. This symbiotic relationship could be key to adapting to such unique and extreme environments. Viruses are the most abundant biological entities on the planet and have been identified in hydrothermal vent environments. However, their interactions with the symbiotic microbes of the SUP05 clade, along with their role in the symbiotic system, remain unclear. Here, using metagenomic sequence-based analyses, we determined that bacteriophages may support metabolism in SUP05 bacteria and play a role in the sponge-associated symbiosis system in hydrothermal vent environments.
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92
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Fitness costs of the cultivable symbiont Serratia symbiotica and its phenotypic consequences to aphids in presence of environmental stressors. Evol Ecol 2019. [DOI: 10.1007/s10682-019-10012-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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93
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Baker LJ, Freed LL, Easson CG, Lopez JV, Fenolio D, Sutton TT, Nyholm SV, Hendry TA. Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment. eLife 2019; 8:47606. [PMID: 31571583 PMCID: PMC6773444 DOI: 10.7554/elife.47606] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/21/2019] [Indexed: 11/13/2022] Open
Abstract
Deep-sea anglerfishes are relatively abundant and diverse, but their luminescent bacterial symbionts remain enigmatic. The genomes of two symbiont species have qualities common to vertically transmitted, host-dependent bacteria. However, a number of traits suggest that these symbionts may be environmentally acquired. To determine how anglerfish symbionts are transmitted, we analyzed bacteria-host codivergence across six diverse anglerfish genera. Most of the anglerfish species surveyed shared a common species of symbiont. Only one other symbiont species was found, which had a specific relationship with one anglerfish species, Cryptopsaras couesii. Host and symbiont phylogenies lacked congruence, and there was no statistical support for codivergence broadly. We also recovered symbiont-specific gene sequences from water collected near hosts, suggesting environmental persistence of symbionts. Based on these results we conclude that diverse anglerfishes share symbionts that are acquired from the environment, and that these bacteria have undergone extreme genome reduction although they are not vertically transmitted. The deep sea is home to many different species of anglerfish, a group of animals in which females often display a dangling lure on the top of their heads. This organ shelters bacteria that make light, a partnership (known as symbiosis) that benefits both parties. The bacteria get a safe environment in which to grow, while the animal may use the light to confuse predators as well as attract prey and mates. The genetic information of these bacteria has changed since they became associated with their host. Their genomes have become smaller and more specialized, limiting their ability to survive outside of the fish. This phenomenon is also observed in other symbiotic bacteria, but mostly in microorganisms that are directly transmitted from parent to offspring, never having to live on their own. Yet, some evidence suggests that the bacteria in the lure of anglerfish may be spending time in the water until they find a new host, crossing thousands of meters of ocean in the process. To explore this paradox, Baker et al. looked into the type of bacteria carried by different groups of anglerfish. If each type of fish has its own kind of bacteria, this would suggest that the microorganisms are passed from one generation to the next, and are evolving with their hosts. On the other hand, if the same sort of bacteria can be found in different anglerfish species, this would imply that the bacteria pass from host to host and evolve independently from the fish. Genetic data analysis showed that amongst six groups of anglerfishes, one species of bacteria is shared across five groups while another is specific to one type of fish. The analyses also revealed that anglerfish and their bacteria are most likely not evolving together. This means that the bacteria must make the difficult journey from host to host by persisting in the deep sea, which was confirmed by finding the genetic information of these bacteria in the water near the fish. Anglerfish and the bacteria that light up their lure are hard to study, as they live so deep in the ocean. In fact, many symbiotic relationships are equally difficult to investigate. Examining genetic information can help to give an insight into how hosts and bacteria interact across the tree of life.
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Affiliation(s)
- Lydia J Baker
- Department of Microbiology, Cornell University, New York, United States
| | - Lindsay L Freed
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States
| | - Cole G Easson
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States.,Department of Biology, Middle Tennessee State University, Murfreesboro, United States
| | - Jose V Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States
| | - Danté Fenolio
- Center for Conservation and Research, San Antonio Zoo, San Antonio, United States
| | - Tracey T Sutton
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States
| | - Spencer V Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States
| | - Tory A Hendry
- Department of Microbiology, Cornell University, New York, United States
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94
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Vertical transmission of sponge microbiota is inconsistent and unfaithful. Nat Ecol Evol 2019; 3:1172-1183. [PMID: 31285574 DOI: 10.1038/s41559-019-0935-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 05/29/2019] [Indexed: 01/18/2023]
Abstract
Co-evolutionary theory predicts that if beneficial microbial symbionts improve host fitness, they should be faithfully transmitted to offspring. More recently, the hologenome theory of evolution predicts resemblance between parent and offspring microbiomes and high partner fidelity between host species and their vertically transmitted microbes. Here, we test these ideas in multiple coexisting host species with highly diverse microbiota, leveraging known parent-offspring pairs sampled from eight species of wild marine sponges (Porifera). We found that the processes governing vertical transmission were both neutral and selective. A neutral model was a better fit to larval (R2 = 0.66) than to the adult microbiota (R2 = 0.27), suggesting that the importance of non-neutral processes increases as the sponge host matures. Microbes that are enriched above neutral expectations in adults were disproportionately transferred to offspring. Patterns of vertical transmission were, however, incomplete: larval sponges shared, on average, 44.8% of microbes with their parents, which was not higher than the fraction they shared with nearby non-parental adults. Vertical transmission was also inconsistent across siblings, as larval sponges from the same parent shared only 17% of microbes. Finally, we found no evidence that vertically transmitted microbes are faithful to a single sponge host species. Surprisingly, larvae were as likely to share vertically transmitted microbes with larvae from other sponge species as they were with their own species. Our study demonstrates that common predictions of vertical transmission that stem from species-poor systems are not necessarily true when scaling up to diverse and complex microbiomes.
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95
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Hammer TJ, Sanders JG, Fierer N. Not all animals need a microbiome. FEMS Microbiol Lett 2019; 366:5499024. [DOI: 10.1093/femsle/fnz117] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/25/2019] [Indexed: 02/07/2023] Open
Abstract
ABSTRACTIt is often taken for granted that all animals host and depend upon a microbiome, yet this has only been shown for a small proportion of species. We propose that animals span a continuum of reliance on microbial symbionts. At one end are the famously symbiont-dependent species such as aphids, humans, corals and cows, in which microbes are abundant and important to host fitness. In the middle are species that may tolerate some microbial colonization but are only minimally or facultatively dependent. At the other end are species that lack beneficial symbionts altogether. While their existence may seem improbable, animals are capable of limiting microbial growth in and on their bodies, and a microbially independent lifestyle may be favored by selection under some circumstances. There is already evidence for several ‘microbiome-free’ lineages that represent distantly related branches in the animal phylogeny. We discuss why these animals have received such little attention, highlighting the potential for contaminants, transients, and parasites to masquerade as beneficial symbionts. We also suggest ways to explore microbiomes that address the limitations of DNA sequencing. We call for further research on microbiome-free taxa to provide a more complete understanding of the ecology and evolution of macrobe-microbe interactions.
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Affiliation(s)
- Tobin J Hammer
- Department of Integrative Biology, University of Texas at Austin, 2506 Speedway, NMS 4.216, Austin, TX 78712, USA
| | - Jon G Sanders
- Cornell Institute of Host–Microbe Interactions and Disease, Cornell University, E145 Corson Hall, Ithaca, NY 14853, USA
| | - Noah Fierer
- Department of Ecology & Evolutionary Biology, University of Colorado at Boulder, 216 UCB, Boulder, CO 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, CIRES Bldg. Rm. 318, Boulder, CO 80309, USA
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96
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Abstract
Tripartite symbioses between bacteriophages, the epithelial cell layers of the human gut, and bacterial symbionts may play an important and unrecognized role in the function of the gut microbiome. Traditionally, phages residing within the gut were considered to interact only with their bacterial hosts and thereby to facilitate indirect interactions with the epithelial cell layers, and yet a growing body of literature is demonstrating the surprising and diverse ways in which phages directly interact with the eukaryotic cells, organs, and systems of the body. Tripartite symbioses between bacteriophages, the epithelial cell layers of the human gut, and bacterial symbionts may play an important and unrecognized role in the function of the gut microbiome. Traditionally, phages residing within the gut were considered to interact only with their bacterial hosts and thereby to facilitate indirect interactions with the epithelial cell layers, and yet a growing body of literature is demonstrating the surprising and diverse ways in which phages directly interact with the eukaryotic cells, organs, and systems of the body. Phages can adhere to mucosal surfaces, bind and transcytose epithelial cells, and deliver proteins and nucleic acids to eukaryotic cells directly. These interactions could establish positive-feedback loops leading to the selection of bacterial hosts and their phage symbionts in the gut. The members of my laboratory are working to expand our knowledge on the phage-eukaryote interactions and to redefine the concept of tripartite symbioses within the human body.
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97
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98
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Dixon GB, Kenkel CD. Molecular convergence and positive selection associated with the evolution of symbiont transmission mode in stony corals. Proc Biol Sci 2019; 286:20190111. [PMID: 30991927 PMCID: PMC6501935 DOI: 10.1098/rspb.2019.0111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/28/2019] [Indexed: 02/06/2023] Open
Abstract
Heritable symbioses have been critical for the evolution of life. The genetic consequences of evolving a heritable symbiosis from the perspective of the symbiont are well established, but concomitant changes in the host remain unresolved. In stony corals, heritable, vertical transmission has evolved repeatedly, providing a unique opportunity to investigate the genomic basis of this complex trait. We conducted a comparative analysis of 25 coral transcriptomes to identify orthologous genes exhibiting signatures of positive selection and convergent amino acid substitutions in vertically transmitting lineages. The frequency of convergence events tends to be higher among vertically transmitting lineages, consistent with the proposed role of selection in driving the evolution of convergent transmission mode phenotypes. Of 10 774 orthologous genes, 403 exhibited at least one molecular convergence event and evidence of positive selection in at least one vertically transmitting lineage. Functional enrichments among these top candidate genes include processes previously implicated in symbiosis including endocytosis, immune response, cytoskeletal protein binding and cytoplasmic membrane-bounded vesicles. Finally, several novel candidates were identified among 100 genes showing evidence of positive selection at the particular convergence event, highlighting the value of our approach for generating new insight into host mechanisms associated with the evolution of heritable symbioses.
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Affiliation(s)
- Groves B. Dixon
- Department of Integrative Biology, The University of Texas at Austin, 1 University Station C0990, Austin, TX 78712, USA
| | - Carly D. Kenkel
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
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99
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Gano‐Cohen KA, Wendlandt CE, Stokes PJ, Blanton MA, Quides KW, Zomorrodian A, Adinata ES, Sachs JL. Interspecific conflict and the evolution of ineffective rhizobia. Ecol Lett 2019; 22:914-924. [DOI: 10.1111/ele.13247] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/07/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Kelsey A. Gano‐Cohen
- Department of Microbiology and Plant Pathology University of California Riverside CA USA
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Camille E. Wendlandt
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
- Department of Botany and Plant Sciences University of California Riverside CA USA
| | - Peter J. Stokes
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Mia A. Blanton
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Kenjiro W. Quides
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Avissa Zomorrodian
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Eunice S. Adinata
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Joel L. Sachs
- Department of Microbiology and Plant Pathology University of California Riverside CA USA
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
- Department of Botany and Plant Sciences University of California Riverside CA USA
- Institute for Integrative Genome Biology University of California Riverside CA USA
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100
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Adaptations and evolution of a heritable leaf nodule symbiosis between Dioscorea sansibarensis and Orrella dioscoreae. ISME JOURNAL 2019; 13:1831-1844. [PMID: 30877285 DOI: 10.1038/s41396-019-0398-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022]
Abstract
Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis between a wild yam species from Madagascar, Dioscorea sansibarensis and bacteria of the species Orrella dioscoreae. Using whole-genome sequencing of plastids and bacteria from wild-collected samples, we show phylogenetic patterns consistent with a dominant vertical mode of transmission of the symbionts. Unique so far among leaf nodule symbioses, the bacteria can be cultured and are amenable to comparative transcriptomics, revealing a potential role in complementing the host's arsenal of secondary metabolites. We propose a recent establishment of a vertical mode of transmission in this symbiosis which, together with a large effective population size explains the cultivability and apparent lack of genome reductive evolution in O. dioscoreae. We leverage these unique features to reveal pathways and functions under positive selection in these specialized endophytes, highlighting the candidate mechanisms enabling a permanent association in the phyllosphere.
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