1
|
Younker IT, Molnar N, Scorza K, Weed R, Light SH, Pfister CA. Bacteria on the foundational kelp in kelp forest ecosystems: Insights from culturing, whole genome sequencing and metabolic assays. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13270. [PMID: 38778582 PMCID: PMC11112141 DOI: 10.1111/1758-2229.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/06/2024] [Indexed: 05/25/2024]
Abstract
In coastal marine ecosystems, kelp forests serve as a vital habitat for numerous species and significantly influence local nutrient cycles. Bull kelp, or Nereocystis luetkeana, is a foundational species in the iconic kelp forests of the northeast Pacific Ocean and harbours a complex microbial community with potential implications for kelp health. Here, we report the isolation and functional characterisation of 16 Nereocystis-associated bacterial species, comprising 13 Gammaproteobacteria, 2 Flavobacteriia and 1 Actinomycetia. Genome analyses of these isolates highlight metabolisms potentially beneficial to the host, such as B vitamin synthesis and nitrogen retention. Assays revealed that kelp-associated bacteria thrive on amino acids found in high concentrations in the ocean and in the kelp (glutamine and asparagine), generating ammonium that may facilitate host nitrogen acquisition. Multiple isolates have genes indicative of interactions with key elemental cycles in the ocean, including carbon, nitrogen and sulphur. We thus report a collection of kelp-associated microbial isolates that provide functional insight for the future study of kelp-microbe interactions.
Collapse
Affiliation(s)
- Isaac T. Younker
- Committee on MicrobiologyThe University of ChicagoChicagoIllinoisUSA
| | - Nichos Molnar
- The CollegeThe University of ChicagoChicagoIllinoisUSA
| | - Kaylie Scorza
- The CollegeThe University of ChicagoChicagoIllinoisUSA
| | - Roo Weed
- The Graduate Program in Biophysical SciencesThe University of ChicagoChicagoIllinoisUSA
| | - Samuel H. Light
- Department of MicrobiologyThe University of ChicagoChicagoIllinoisUSA
| | | |
Collapse
|
2
|
Maritan E, Quagliariello A, Frago E, Patarnello T, Martino ME. The role of animal hosts in shaping gut microbiome variation. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230071. [PMID: 38497257 PMCID: PMC10945410 DOI: 10.1098/rstb.2023.0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 03/19/2024] Open
Abstract
Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
Collapse
Affiliation(s)
- Elisa Maritan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Enric Frago
- CIRAD, UMR CBGP, INRAE, Institut Agro, IRD, Université Montpellier, 34398 Montpellier, France
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Maria Elena Martino
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| |
Collapse
|
3
|
Massey C, Nosker ME, Gale J, Scott S, Walker CJ, Cluff A, Wilcox S, Morrison A, Gottfredson Morgan SJ, Beltz J, Schmidt P, Chaston JM. Humidity determines penetrance of a latitudinal gradient in genetic selection on the microbiota by Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.591907. [PMID: 38746372 PMCID: PMC11092659 DOI: 10.1101/2024.05.02.591907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The fruit fly Drosophila melanogaster is a model for understanding how hosts and their microbial partners interact as the host adapts to wild environments. These interactions are readily interrogated because of the low taxonomic and numeric complexity of the flies' bacterial communities. Previous work has established that host genotype, the environment, diet, and interspecies microbial interactions can all influence host fitness and microbiota composition, but the specific processes and characters mediating these processes are incompletely understood. Here, we compared the variation in microbiota composition between wild-derived fly populations when flies could choose between the microorganisms in their diets and when flies were reared under environmental perturbation (different humidities). We also compared the colonization of the resident and transient microorganisms. We show that the ability to choose between microorganisms in the diet and the environmental condition of the flies can influence the relative abundance of the microbiota. There were also key differences in the abundances of the resident and transient microbiota. However, the microbiota only differed between populations when the flies were reared at humidities at or above 50% relative humidity. We also show that elevated humidity determined the penetrance of a gradient in host genetic selection on the microbiota that is associated with the latitude the flies were collected from. Finally, we show that the treatment-dependent variation in microbiota composition is associated with variation in host stress survival. Together, these findings emphasize that host genetic selection on the microbiota composition of a model animal host can be patterned with the source geography, and that such variation has the potential to influence their survival in the wild. Importance The fruit fly Drosophila melanogaster is a model for understanding how hosts and their microbial partners interact as hosts adapt in wild environments. Our understanding of what causes geographic variation in the fruit fly microbiota remains incomplete. Previous work has shown that the D. melanogaster microbiota has relatively low numerical and taxonomic complexity. Variation in the fly microbiota composition can be attributed to environmental characters and host genetic variation, and variation in microbiota composition can be patterned with the source location of the flies. In this work we explored three possible causes of patterned variation in microbiota composition. We show that host feeding choices, the host niche colonized by the bacteria, and a single environmental character can all contribute to variation in microbiota composition. We also show that penetrance of latitudinally-patterned host genetic selection is only observed at elevated humidities. Together, these results identify several factors that influence microbiota composition in wild fly genotypes and emphasize the interplay between environmental and host genetic factors in determining the microbiota composition of these model hosts.
Collapse
|
4
|
Glaser-Schmitt A, Ramnarine TJS, Parsch J. Rapid evolutionary change, constraints and the maintenance of polymorphism in natural populations of Drosophila melanogaster. Mol Ecol 2024; 33:e17024. [PMID: 37222070 DOI: 10.1111/mec.17024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/25/2023]
Abstract
Allele frequencies can shift rapidly within natural populations. Under certain conditions, repeated rapid allele frequency shifts can lead to the long-term maintenance of polymorphism. In recent years, studies of the model insect Drosophila melanogaster have suggested that this phenomenon is more common than previously believed and is often driven by some form of balancing selection, such as temporally fluctuating or sexually antagonistic selection. Here we discuss some of the general insights into rapid evolutionary change revealed by large-scale population genomic studies, as well as the functional and mechanistic causes of rapid adaptation uncovered by single-gene studies. As an example of the latter, we consider a regulatory polymorphism of the D. melanogaster fezzik gene. Polymorphism at this site has been maintained at intermediate frequency over an extended period of time. Regular observations from a single population over a period of 7 years revealed significant differences in the frequency of the derived allele and its variance across collections between the sexes. These patterns are highly unlikely to arise from genetic drift alone or from the action of sexually antagonistic or temporally fluctuating selection individually. Instead, the joint action of sexually antagonistic and temporally fluctuating selection can best explain the observed rapid and repeated allele frequency shifts. Temporal studies such as those reviewed here further our understanding of how rapid changes in selection can lead to the long-term maintenance of polymorphism as well as improve our knowledge of the forces driving and limiting adaptation in nature.
Collapse
Affiliation(s)
- Amanda Glaser-Schmitt
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Timothy J S Ramnarine
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| |
Collapse
|
5
|
Yim C, Bellis ES, DeLeo VL, Gamba D, Muscarella R, Lasky JR. Climate biogeography of Arabidopsis thaliana: linking distribution models and individual variation. JOURNAL OF BIOGEOGRAPHY 2024; 51:560-574. [PMID: 38596256 PMCID: PMC11000247 DOI: 10.1111/jbi.14737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/19/2023] [Indexed: 04/11/2024]
Abstract
AIM Patterns of individual variation are key to testing hypotheses about the mechanisms underlying biogeographic patterns. If species distributions are determined by environmental constraints, then populations near range margins may have reduced performance and be adapted to harsher environments. Model organisms are potentially important systems for biogeographical studies, given the available range-wide natural history collections, and the importance of providing biogeographical context to their genetic and phenotypic diversity. LOCATION Global. TAXON Arabidopsis thaliana ("Arabidopsis"). METHODS We fit occurrence records to climate data, and then projected the distribution of Arabidopsis under last glacial maximum, current, and future climates. We confronted model predictions with individual performance measured on 2,194 herbarium specimens, and we asked whether predicted suitability was associated with life-history and genomic variation measured on ~900 natural accessions. RESULTS The most important climate variables constraining the Arabidopsis distribution were winter cold in northern and high elevation regions and summer heat in southern regions. Herbarium specimens from regions with lower habitat suitability in both northern and southern regions were smaller, supporting the hypothesis that the distribution of Arabidopsis is constrained by climate-associated factors. Climate anomalies partly explained interannual variation in herbarium specimen size, but these did not closely correspond to local limiting factors identified in the distribution model. Late-flowering genotypes were absent from the lowest suitability regions, suggesting slower life histories are only viable closer to the center of the realized niche. We identified glacial refugia farther north than previously recognized, as well as refugia concordant with previous population genetic findings. Lower latitude populations, known to be genetically distinct, are most threatened by future climate change. The recently colonized range of Arabidopsis was well-predicted by our native-range model applied to certain regions but not others, suggesting it has colonized novel climates. MAIN CONCLUSIONS Integration of distribution models with performance data from vast natural history collections is a route forward for testing biogeographical hypotheses about species distributions and their relationship with evolutionary fitness across large scales.
Collapse
Affiliation(s)
- Christina Yim
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Emily S. Bellis
- Department of Biology, Pennsylvania State University, University Park, USA
- Department of Computer Science, Arkansas State University, Jonesboro, USA
| | - Victoria L. DeLeo
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Diana Gamba
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Robert Muscarella
- Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jesse R. Lasky
- Department of Biology, Pennsylvania State University, University Park, USA
| |
Collapse
|
6
|
Bitter MC, Berardi S, Oken H, Huynh A, Schmidt P, Petrov DA. Continuously fluctuating selection reveals extreme granularity and parallelism of adaptive tracking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.562586. [PMID: 37904939 PMCID: PMC10614893 DOI: 10.1101/2023.10.16.562586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Temporally fluctuating environmental conditions are a ubiquitous feature of natural habitats. Yet, how finely natural populations adaptively track fluctuating selection pressures via shifts in standing genetic variation is unknown. We generated high-frequency, genome-wide allele frequency data from a genetically diverse population of Drosophila melanogaster in extensively replicated field mesocosms from late June to mid-December, a period of ∼12 generations. Adaptation throughout the fundamental ecological phases of population expansion, peak density, and collapse was underpinned by extremely rapid, parallel changes in genomic variation across replicates. Yet, the dominant direction of selection fluctuated repeatedly, even within each of these ecological phases. Comparing patterns of allele frequency change to an independent dataset procured from the same experimental system demonstrated that the targets of selection are predictable across years. In concert, our results reveal fitness-relevance of standing variation that is likely to be masked by inference approaches based on static population sampling, or insufficiently resolved time-series data. We propose such fine-scaled temporally fluctuating selection may be an important force maintaining functional genetic variation in natural populations and an important stochastic force affecting levels of standing genetic variation genome-wide.
Collapse
|
7
|
O'Brien AM, Laurich JR, Frederickson ME. Evolutionary consequences of microbiomes for hosts: impacts on host fitness, traits, and heritability. Evolution 2024; 78:237-252. [PMID: 37828761 DOI: 10.1093/evolut/qpad183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/30/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023]
Abstract
An organism's phenotypes and fitness often depend on the interactive effects of its genome (Ghost), microbiome (Gmicrobe), and environment (E). These G × G, G × E, and G × G × E effects fundamentally shape host-microbiome (co)evolution and may be widespread, but are rarely compared within a single experiment. We collected and cultured Lemnaminor (duckweed) and its associated microbiome from 10 sites across an urban-to-rural ecotone. We factorially manipulated host genotype and microbiome in two environments (low and high zinc, an urban aquatic stressor) in an experiment with 200 treatments: 10 host genotypes × 10 microbiomes × 2 environments. Host genotype explained the most variation in L.minor fitness and traits, while microbiome effects often depended on host genotype (G × G). Microbiome composition predicted G × G effects: when compared in more similar microbiomes, duckweed genotypes had more similar effects on traits. Further, host fitness increased and microbes grew faster when applied microbiomes more closely matched the host's field microbiome, suggesting some local adaptation between hosts and microbiota. Finally, selection on and heritability of host traits shifted across microbiomes and zinc exposure. Thus, we found that microbiomes impact host fitness, trait expression, and heritability, with implications for host-microbiome evolution and microbiome breeding.
Collapse
Affiliation(s)
- Anna M O'Brien
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Jason R Laurich
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Megan E Frederickson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
8
|
Yan K, Lu DS, Ding CJ, Wang Y, Tian YR, Su XH, Dong YF, Wang YP. Rare and abundant bacterial communities in poplar rhizosphere soils respond differently to genetic effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168216. [PMID: 37923276 DOI: 10.1016/j.scitotenv.2023.168216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Interactions between plants and soil microbes are important to plant hybrid breeding under global change. However, the relationship between host plants and rhizosphere soil microorganisms has not been fully elucidated. Understanding the rhizosphere microbial structure of parents and progenies would provide a deeper insight into how genetic effects modulate the relationship between plants and soil. In this study, two family groups of poplar trees (A: parents and their two progenies; B: parents and their one progeny) with different genetic backgrounds (including seven genotypes) were selected from a common garden, and their rhizobacterial communities were analyzed to explore parent-progeny relationships. Our results showed significant differences in phylogenetic diversity, the number of 16S genes and the structure of rhizosphere bacterial communities (Adonis: R2 = 0.166, P < 0.01) between different family groups. Rhizosphere bacterial community structure was significantly dominated by genetic effects. Compared with abundant taxa, genetic effects were more powerful drivers of rare taxa. In addition, bacterial communities of hybrid progenies were all significantly more similar to their parents compared to the other group of parents, especially among rare taxa. The two poplar family groups exhibited differences between their rhizosphere bacterial co-occurrence networks. Group B had a relatively complex network with 2380 edges and 468 nodes, while group A had 1829 edges and 304 nodes. Soil organic carbon and carbon to nitrogen ratio (C/N) also influenced the rhizosphere bacterial community assembly. This was especially true for soil C/N, which explained 23 % of the β-nearest taxon index (βNTI) variation in rare taxa. Our results reveal the relationship of rhizosphere microorganisms between parents and progenies. This can help facilitate an understanding of the combination of plant breeding with microbes resource utilization and provide a theoretical basis for scientific advancement to support the development of forestry industry.
Collapse
Affiliation(s)
- Kun Yan
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - De Shan Lu
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Chang Jun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yan Wang
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Yong Ren Tian
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Xiao Hua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | | | - Yan Ping Wang
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China.
| |
Collapse
|
9
|
Härer A, Rennison DJ. The effects of host ecology and phylogeny on gut microbiota (non)parallelism across birds and mammals. mSphere 2023; 8:e0044223. [PMID: 38038446 PMCID: PMC10732045 DOI: 10.1128/msphere.00442-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE What are the roles of determinism and contingency in evolution? The paleontologist and evolutionary biologist Stephen J. Gould raised this question in his famous thought experiment of "replaying life's tape." Settings where independent lineages have repeatedly adapted to similar ecological niches (i.e., parallel evolution) are well suited to address this question. Here, we quantified whether repeated ecological shifts across 53 mammalian and 50 avian host species are associated with parallel gut microbiota changes. Our results indicate that parallel shifts in host diet are associated with greater gut microbiota parallelism (i.e., more deterministic). While further research will be necessary to obtain a comprehensive picture of the circumstances under which deterministic gut microbiota changes might be expected, our study can be instrumental in motivating the use of more quantitative methods in microbiota research. This, in turn, can help us better understand microbiota dynamics during adaptive evolution of their hosts.
Collapse
Affiliation(s)
- Andreas Härer
- Department of Ecology, Behavior & Evolution, School of Biological Sciences , University of California San Diego, La Jolla, California, USA
| | - Diana J. Rennison
- Department of Ecology, Behavior & Evolution, School of Biological Sciences , University of California San Diego, La Jolla, California, USA
| |
Collapse
|
10
|
Michel A, Minocher R, Niehoff PP, Li Y, Nota K, Gadhvi MA, Su J, Iyer N, Porter A, Ngobobo-As-Ibungu U, Binyinyi E, Nishuli Pekeyake R, Parducci L, Caillaud D, Guschanski K. Isolated Grauer's gorilla populations differ in diet and gut microbiome. Mol Ecol 2023; 32:6523-6542. [PMID: 35976262 DOI: 10.1111/mec.16663] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/30/2022]
Abstract
The animal gut microbiome has been implicated in a number of key biological processes, ranging from digestion to behaviour, and has also been suggested to facilitate local adaptation. Yet studies in wild animals rarely compare multiple populations that differ ecologically, which is the level at which local adaptation may occur. Further, few studies simultaneously characterize diet and gut microbiome from the same sample, despite their probable interdependence. Here, we investigate the interplay between diet and gut microbiome in three geographically isolated populations of the critically endangered Grauer's gorilla (Gorilla beringei graueri), which we show to be genetically differentiated. We find population- and social group-specific dietary and gut microbial profiles and covariation between diet and gut microbiome, despite the presence of core microbial taxa. There was no detectable effect of age, and only marginal effects of sex and genetic relatedness on the microbiome. Diet differed considerably across populations, with the high-altitude population consuming a lower diversity of plants compared to low-altitude populations, consistent with plant availability constraining dietary choices. The observed pattern of covariation between diet and gut microbiome is probably a result of long-term social and environmental factors. Our study suggests that the gut microbiome is sufficiently plastic to support flexible food selection and hence contribute to local adaptation.
Collapse
Affiliation(s)
- Alice Michel
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Department of Anthropology, University of California, Davis, California, USA
| | - Riana Minocher
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Department of Human Behavior, Ecology and Culture, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Peter-Philip Niehoff
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Yuhong Li
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Kevin Nota
- Plant Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Maya A Gadhvi
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jiancheng Su
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Neetha Iyer
- Department of Anthropology, University of California, Davis, California, USA
| | - Amy Porter
- Department of Anthropology, University of California, Davis, California, USA
| | | | - Escobar Binyinyi
- The Dian Fossey Gorilla Fund International, Kinshasa, Democratic Republic of the Congo
| | - Radar Nishuli Pekeyake
- Institut Congolais pour la Conservation de la Nature, Kinshasa, Democratic Republic of the Congo
| | - Laura Parducci
- Department of Human Behavior, Ecology and Culture, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Damien Caillaud
- Department of Anthropology, University of California, Davis, California, USA
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
11
|
Brinker P, Chen F, Chehida YB, Beukeboom LW, Fontaine MC, Salles JF. Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica, but not in the presence of the endosymbiont Wolbachia. Mol Ecol 2023; 32:6644-6658. [PMID: 36125236 DOI: 10.1111/mec.16699] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 09/11/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022]
Abstract
The microbial community composition is crucial for diverse life-history traits in many organisms. However, we still lack a sufficient understanding of how the host microbiome is acquired and maintained, a pressing issue in times of global environmental change. Here we investigated to what extent host genotype, environmental conditions, and the endosymbiont Wolbachia influence the bacterial communities in the parasitic wasp Asobara japonica. We sampled multiple wasp populations across 10 locations in their natural distribution range in Japan and sequenced the host genome (whole genome sequencing) and microbiome (16S rRNA gene). We compared the host population structure and bacterial community composition of wasps that reproduce sexually and are uninfected with Wolbachia with wasps that reproduce asexually and carry Wolbachia. The bacterial communities in asexual wasps were highly similar due to a strong effect of Wolbachia rather than host genomic structure. In contrast, in sexual wasps, bacterial communities appear primarily shaped by a combination of population structure and environmental conditions. Our research highlights that multiple factors shape the bacterial communities of an organism and that the presence of a single endosymbiont can strongly alter their compositions. This information is crucial to understanding how organisms and their associated microbiome will react in the face of environmental change.
Collapse
Affiliation(s)
- Pina Brinker
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Fangying Chen
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, UK
- Department of Biology, University of York, York, UK
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
- Centre de Recherche en Écologie et Évolution de la Santé (CREES), Montpellier, France
| | - Joana Falcao Salles
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| |
Collapse
|
12
|
McPherson AE, Abram PK, Curtis CI, Wannop ER, Dudzic JP, Perlman SJ. Dynamic changes in Wolbachia infection over a single generation of Drosophila suzukii, across a wide range of resource availability. Ecol Evol 2023; 13:e10722. [PMID: 38020682 PMCID: PMC10651314 DOI: 10.1002/ece3.10722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/19/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Wolbachia bacteria are maternally inherited symbionts that commonly infect terrestrial arthropods. Many Wolbachia reach high frequencies in their hosts by manipulating their reproduction, for example by causing reproductive incompatibilities between infected male and uninfected female hosts. However, not all strains manipulate reproduction, and a key unresolved question is how these non-manipulative Wolbachia persist in their hosts, often at intermediate to high frequencies. One such strain, wSuz, infects the invasive fruit pest Drosophila suzukii, spotted-wing drosophila. Here, we tested the hypothesis that wSuz infection provides a competitive benefit when resources are limited. Over the course of one season, we established population cages with varying amounts of food in a semi-field setting and seeded them with a 50:50 mixture of flies with and without Wolbachia. We predicted that Wolbachia-infected individuals should have higher survival and faster development than their uninfected counterparts when there was little available food. We found that while food availability strongly impacted fly fitness, there was no difference in development times or survival between Wolbachia-infected and uninfected flies. Interestingly, however, Wolbachia infection frequencies changed dramatically, with infections either increasing or decreasing by as much as 30% in a single generation, suggesting the possibility of unidentified factors shaping Wolbachia infection over the course of the season.
Collapse
Affiliation(s)
- Audrey E. McPherson
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
- Agriculture and Agri‐Food Canada, Agassiz Research and Development CentreAgassizBritish ColumbiaCanada
| | - Paul K. Abram
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
- Agriculture and Agri‐Food Canada, Agassiz Research and Development CentreAgassizBritish ColumbiaCanada
| | - Caitlin I. Curtis
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Erik R. Wannop
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Jan P. Dudzic
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Steve J. Perlman
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| |
Collapse
|
13
|
Xiao C, Duarri‐Redondo S, Thorhölludottir DAV, Chen Y, Schlötterer C. Non-additive effects between genotypes: Implications for competitive fitness assays. Ecol Evol 2023; 13:e10713. [PMID: 37941737 PMCID: PMC10630047 DOI: 10.1002/ece3.10713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/27/2023] [Accepted: 10/22/2023] [Indexed: 11/10/2023] Open
Abstract
Competitive fitness assays are widely used in evolutionary biology and typically rely on a reference strain to compare different focal genotypes. This approach implicitly relies on the absence of interaction between the competing genotypes. In other words, the performance of the reference strain must not depend on the competitor. This report scrutinized this assumption by competing diverged Drosophila simulans populations against a common reference strain. We detected strong evidence for interaction between the competing genotypes: (1) Frequency-dependent selection was common with opposite effects in genetically diverged populations. (2) Temporal heterogeneity of fitness estimates, which can be partially attributed to a competitor-specific delay in the eclosion of the reference strain. We propose that this inconsistent behavior of the reference strain can be considered a specific case of a genotype × environment interaction. Focal populations could modify the environment of the reference strain, either indirectly by altering the microbiome composition and food availability or directly by genotype-specific cannibalism. Our results provide new insights into the interaction of diverged genotypes and have important implications for the interpretation of competitive fitness assays.
Collapse
Affiliation(s)
- Changyi Xiao
- Institut für PopulationsgenetikVetmeduni ViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Sara Duarri‐Redondo
- Institut für PopulationsgenetikVetmeduni ViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Dagny A. V. Thorhölludottir
- Institut für PopulationsgenetikVetmeduni ViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Yiwen Chen
- Institut für PopulationsgenetikVetmeduni ViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | | |
Collapse
|
14
|
Santos J, Matos M, Flatt T, Chelo IM. Microbes are potential key players in the evolution of life histories and aging in Caenorhabditis elegans. Ecol Evol 2023; 13:e10537. [PMID: 37753311 PMCID: PMC10518755 DOI: 10.1002/ece3.10537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/07/2023] [Accepted: 09/01/2023] [Indexed: 09/28/2023] Open
Abstract
Microbes can have profound effects on host fitness and health and the appearance of late-onset diseases. Host-microbe interactions thus represent a major environmental context for healthy aging of the host and might also mediate trade-offs between life-history traits in the evolution of host senescence. Here, we have used the nematode Caenorhabditis elegans to study how host-microbe interactions may modulate the evolution of life histories and aging. We first characterized the effects of two non-pathogenic and one pathogenic Escherichia coli strains, together with the pathogenic Serratia marcescens DB11 strain, on population growth rates and survival of C. elegans from five different genetic backgrounds. We then focused on an outbred C. elegans population, to understand if microbe-specific effects on the reproductive schedule and in traits such as developmental rate and survival were also expressed in the presence of males and standing genetic variation, which could be relevant for the evolution of C. elegans and other nematode species in nature. Our results show that host-microbe interactions have a substantial host-genotype-dependent impact on the reproductive aging and survival of the nematode host. Although both pathogenic bacteria reduced host survival in comparison with benign strains, they differed in how they affected other host traits. Host fertility and population growth rate were affected by S. marcescens DB11 only during early adulthood, whereas this occurred at later ages with the pathogenic E. coli IAI1. In both cases, these effects were largely dependent on the host genotypes. Given such microbe-specific genotypic differences in host life history, we predict that the evolution of reproductive schedules and senescence might be critically contingent on host-microbe interactions in nature.
Collapse
Affiliation(s)
- Josiane Santos
- cE3c – Centre for Ecology, Evolution and Environmental Changes & CHANGE – Global Change and Sustainability InstituteLisboaPortugal
- Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Margarida Matos
- cE3c – Centre for Ecology, Evolution and Environmental Changes & CHANGE – Global Change and Sustainability InstituteLisboaPortugal
- Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Thomas Flatt
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Ivo M. Chelo
- cE3c – Centre for Ecology, Evolution and Environmental Changes & CHANGE – Global Change and Sustainability InstituteLisboaPortugal
- Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| |
Collapse
|
15
|
Téfit MA, Budiman T, Dupriest A, Yew JY. Environmental microbes promote phenotypic plasticity in reproduction and sleep behaviour. Mol Ecol 2023; 32:5186-5200. [PMID: 37577956 PMCID: PMC10544802 DOI: 10.1111/mec.17095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 06/13/2023] [Accepted: 07/25/2023] [Indexed: 08/15/2023]
Abstract
The microbiome has been hypothesized as a driving force of phenotypic variation in host organisms that is capable of extending metabolic processes, altering development and in some cases, conferring novel functions that are critical for survival. Only a few studies have directly shown a causal role for the environmental microbiome in altering host phenotypic features. To assess the extent to which environmental microbes induce variation in host life-history traits and behaviour, we inoculated axenic Drosophila melanogaster with microbes isolated from drosophilid populations collected from two different field sites and generated two populations with distinct bacterial and fungal profiles. We show that microbes isolated from environmental sites with modest abiotic differences induce large variation in host reproduction, fatty acid levels, stress tolerance and sleep behaviour. Importantly, clearing microbes from each experimental population removed the phenotypic differences. The results support the causal role of environmental microbes as drivers of host phenotypic plasticity and potentially, rapid adaptation and evolution.
Collapse
Affiliation(s)
- Mélisandre A Téfit
- School of Ocean and Earth Science and Technology, Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Tifanny Budiman
- School of Ocean and Earth Science and Technology, Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Adrianna Dupriest
- School of Ocean and Earth Science and Technology, Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Joanne Y Yew
- School of Ocean and Earth Science and Technology, Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| |
Collapse
|
16
|
Fernández-Ruiz N, Pinecki-Socias S, Estrada-Peña A, Wu-Chuang A, Maitre A, Obregón D, Cabezas-Cruz A, de Blas I, Nijhof AM. Decontamination protocols affect the internal microbiota of ticks. Parasit Vectors 2023; 16:189. [PMID: 37286996 DOI: 10.1186/s13071-023-05812-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/14/2023] [Indexed: 06/09/2023] Open
Abstract
Studies on the microbiota of ticks have promoted hypotheses about the combined effects of the bacterial community, its functional contributions to the tick's physiology or probable competition effects with some tick-borne pathogens. However, knowledge on the origin of the microbiota of newly hatched larvae is missing. This study aimed to elucidate the source(s) of the microbiota in unfed tick larvae, addressing the composition of the "core microbiota" and the best ways to decontaminate eggs for microbiota studies. We applied laboratory degree bleach washes and/or ultraviolet light treatments on engorged Rhipicephalus australis females and/or their eggs. No significant effects of these treatments on the reproductive parameters of females and the hatching rates of eggs were observed. However, the different treatments did show striking effects on the composition of the microbiota. The results indicated that bleach washes disrupted the internal tick microbiota in females, implying that bleach may have entered the tick and subsequently affected the microbiota. Furthermore, the analyses of results demonstrated that the ovary is a main source of tick microbiota, while the contribution of Gené's organ (a part of the female reproductive system that secretes a protective wax coat onto tick eggs) or the male's spermatophore requires further investigation. Further studies are needed to identify best practice protocols for the decontamination of ticks for microbiota studies.
Collapse
Affiliation(s)
- Natalia Fernández-Ruiz
- Faculty of Veterinary Medicine, University of Zaragoza, 50013, Zaragoza, Spain.
- Group of Research on Emerging Zoonoses, Instituto Agroalimentario de Aragón (IA2), 50013, Zaragoza, Spain.
| | - Sophia Pinecki-Socias
- Institute of Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Agustín Estrada-Peña
- Faculty of Veterinary Medicine, University of Zaragoza, 50013, Zaragoza, Spain
- Group of Research on Emerging Zoonoses, Instituto Agroalimentario de Aragón (IA2), 50013, Zaragoza, Spain
| | - Alejandra Wu-Chuang
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Apolline Maitre
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Dasiel Obregón
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Alejandro Cabezas-Cruz
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Ignacio de Blas
- Faculty of Veterinary Medicine, University of Zaragoza, 50013, Zaragoza, Spain
| | - Ard M Nijhof
- Institute of Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
- Veterinary Centre for Resistance Research, Freie Universität Berlin, 14163, Berlin, Germany
| |
Collapse
|
17
|
Kwoji ID, Aiyegoro OA, Okpeku M, Adeleke MA. 'Multi-omics' data integration: applications in probiotics studies. NPJ Sci Food 2023; 7:25. [PMID: 37277356 DOI: 10.1038/s41538-023-00199-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
The concept of probiotics is witnessing increasing attention due to its benefits in influencing the host microbiome and the modulation of host immunity through the strengthening of the gut barrier and stimulation of antibodies. These benefits, combined with the need for improved nutraceuticals, have resulted in the extensive characterization of probiotics leading to an outburst of data generated using several 'omics' technologies. The recent development in system biology approaches to microbial science is paving the way for integrating data generated from different omics techniques for understanding the flow of molecular information from one 'omics' level to the other with clear information on regulatory features and phenotypes. The limitations and tendencies of a 'single omics' application to ignore the influence of other molecular processes justify the need for 'multi-omics' application in probiotics selections and understanding its action on the host. Different omics techniques, including genomics, transcriptomics, proteomics, metabolomics and lipidomics, used for studying probiotics and their influence on the host and the microbiome are discussed in this review. Furthermore, the rationale for 'multi-omics' and multi-omics data integration platforms supporting probiotics and microbiome analyses was also elucidated. This review showed that multi-omics application is useful in selecting probiotics and understanding their functions on the host microbiome. Hence, recommend a multi-omics approach for holistically understanding probiotics and the microbiome.
Collapse
Affiliation(s)
- Iliya Dauda Kwoji
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa
| | - Olayinka Ayobami Aiyegoro
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, Northwest, South Africa
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa
| | - Matthew Adekunle Adeleke
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa.
| |
Collapse
|
18
|
Wan X, Takala TM, Huynh VA, Ahonen SL, Paulin L, Björkroth J, Sironen T, Kant R, Saris P. Comparative genomics of 40 Weissella paramesenteroides strains. Front Microbiol 2023; 14:1128028. [PMID: 37065164 PMCID: PMC10102382 DOI: 10.3389/fmicb.2023.1128028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Abstract
Weissella strains are often detected in spontaneously fermented foods. Because of their abilities to produce lactic acid and functional exopolysaccharides as well as their probiotic traits, Weissella spp. improve not only the sensorial properties but also nutritional values of the fermented food products. However, some Weissella species have been associated with human and animal diseases. In the era of vast genomic sequencing, new genomic/genome data are becoming available to the public on daily pace. Detailed genomic analyses are due to provide a full understanding of individual Weissella species. In this study, the genomes of six Weissella paramesenteroides strains were de novo sequenced. The genomes of 42 W. paramesenteroides strains were compared to discover their metabolic and functional potentials in food fermentation. Comparative genomics and metabolic pathway reconstructions revealed that W. paramesenteroides is a compact group of heterofermentative bacteria with good capacity of producing secondary metabolites and vitamin Bs. Since the strains rarely harbored plasmid DNA, they did not commonly possess the genes associated with bacteriocin production. All 42 strains were shown to bear vanT gene from the glycopeptide resistance gene cluster vanG. Yet none of the strains carried virulence genes.
Collapse
Affiliation(s)
- Xing Wan
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- *Correspondence: Xing Wan,
| | - Timo M. Takala
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Vy A. Huynh
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | | | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Johanna Björkroth
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdańsk, Gdynia, Poland
| | - Per Saris
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
- Per Saris,
| |
Collapse
|
19
|
Holmes IA, Grundler MC. Phylogenetically under-dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community. Mol Ecol 2023; 32:258-274. [PMID: 36221927 PMCID: PMC9797449 DOI: 10.1111/mec.16733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 12/31/2022]
Abstract
While key elements of fitness in vertebrate animals are impacted by their microbiomes, the host genetic characteristics that factor into microbiome composition are not fully understood. Here, we correlate host genomic heterozygosity and gut microbiome phylogenetic diversity across a community of reptiles in southwestern New Mexico to test hypotheses about the behaviour of host genes that drive microbiome assembly. We find that microbiome communities are phylogenetically under-dispersed relative to random expectations, and that host heterozygosity is not correlated with microbiome diversity. Our analyses reinforce results from functional genomic work that identify conserved host immune and nonimmune genes as key players in microbiome assembly, rather than gene families that rely on heterozygosity for their function.
Collapse
Affiliation(s)
- Iris A. Holmes
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Cornell Institute of Host Microbe Interactions and Disease and Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
| | - Michael C. Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA
| |
Collapse
|
20
|
Grieneisen L, Blekhman R, Archie E. How longitudinal data can contribute to our understanding of host genetic effects on the gut microbiome. Gut Microbes 2023; 15:2178797. [PMID: 36794811 PMCID: PMC9980606 DOI: 10.1080/19490976.2023.2178797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
A key component of microbiome research is understanding the role of host genetic influence on gut microbial composition. However, it can be difficult to link host genetics with gut microbial composition because host genetic similarity and environmental similarity are often correlated. Longitudinal microbiome data can supplement our understanding of the relative role of genetic processes in the microbiome. These data can reveal environmentally contingent host genetic effects, both in terms of controlling for environmental differences and in comparing how genetic effects differ by environment. Here, we explore four research areas where longitudinal data could lend new insights into host genetic effects on the microbiome: microbial heritability, microbial plasticity, microbial stability, and host and microbiome population genetics. We conclude with a discussion of methodological considerations for future studies.
Collapse
Affiliation(s)
- Laura Grieneisen
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, Canada
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Elizabeth Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| |
Collapse
|
21
|
Härer A, Rennison DJ. Quantifying (non)parallelism of gut microbial community change using multivariate vector analysis. Ecol Evol 2022; 12:e9674. [PMID: 36590339 PMCID: PMC9797641 DOI: 10.1002/ece3.9674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/26/2022] [Accepted: 12/09/2022] [Indexed: 12/30/2022] Open
Abstract
Parallel evolution of phenotypic traits is regarded as strong evidence for natural selection and has been studied extensively in a variety of taxa. However, we have limited knowledge of whether parallel evolution of host organisms is accompanied by parallel changes of their associated microbial communities (i.e., microbiotas), which are crucial for their hosts' ecology and evolution. Determining the extent of microbiota parallelism in nature can improve our ability to identify the factors that are associated with (putatively adaptive) shifts in microbial communities. While it has been emphasized that (non)parallel evolution is better considered as a quantitative continuum rather than a binary phenomenon, quantitative approaches have rarely been used to study microbiota parallelism. We advocate using multivariate vector analysis (i.e., phenotypic change vector analysis) to quantify direction and magnitude of microbiota changes and discuss the applicability of this approach for studying parallelism, and we compiled an R package for multivariate vector analysis of microbial communities ('multivarvector'). We exemplify its use by reanalyzing gut microbiota data from multiple fish species that exhibit parallel shifts in trophic ecology. We found that multivariate vector analysis results were largely consistent with other statistical methods, parallelism estimates were not affected by the taxonomic level at which the microbiota is studied, and parallelism might be stronger for gut microbiota function compared to taxonomic composition. This approach provides an analytical framework for quantitative comparisons across host lineages, thereby providing the potential to advance our capacity to predict microbiota changes. Hence, we emphasize that the development and application of quantitative measures, such as multivariate vector analysis, should be further explored in microbiota research in order to better understand the role of microbiota dynamics during their hosts' adaptive evolution, particularly in settings of parallel evolution.
Collapse
Affiliation(s)
- Andreas Härer
- School of Biological Sciences, Department of Ecology, Behavior, & EvolutionUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Diana J. Rennison
- School of Biological Sciences, Department of Ecology, Behavior, & EvolutionUniversity of California San DiegoLa JollaCaliforniaUSA
| |
Collapse
|
22
|
Juottonen H, Moghadam NN, Murphy L, Mappes J, Galarza JA. Host's genetic background determines the outcome of reciprocal faecal transplantation on life-history traits and microbiome composition. Anim Microbiome 2022; 4:67. [PMID: 36564793 PMCID: PMC9789590 DOI: 10.1186/s42523-022-00210-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Microbes play a role in their host's fundamental ecological, chemical, and physiological processes. Host life-history traits from defence to growth are therefore determined not only by the abiotic environment and genotype but also by microbiota composition. However, the relative importance and interactive effects of these factors may vary between organisms. Such connections remain particularly elusive in Lepidoptera, which have been argued to lack a permanent microbiome and have microbiota primarily determined by their diet and environment. We tested the microbiome specificity and its influence on life-history traits of two colour genotypes of the wood tiger moth (Arctia plantaginis) that differ in several traits, including growth. All individuals were grown in the laboratory for several generations with standardized conditions. We analyzed the bacterial community of the genotypes before and after a reciprocal frass (i.e., larval faeces) transplantation and followed growth rate, pupal mass, and the production of defensive secretion. RESULTS After transplantation, the fast-growing genotype grew significantly slower compared to the controls, but the slow-growing genotype did not change its growth rate. The frass transplant also increased the volume of defensive secretions in the fast-growing genotype but did not affect pupal mass. Overall, the fast-growing genotype appeared more susceptible to the transplantation than the slow-growing genotype. Microbiome differences between the genotypes strongly suggest genotype-based selective filtering of bacteria from the diet and environment. A novel cluster of insect-associated Erysipelotrichaceae was exclusive to the fast-growing genotype, and specific Enterococcaceae were characteristic to the slow-growing genotype. These Enterococcaceae became more prevalent in the fast-growing genotype after the transplant, which suggests that a slower growth rate is potentially related to their presence. CONCLUSIONS We show that reciprocal frass transplantation can reverse some genotype-specific life-history traits in a lepidopteran host. The results indicate that genotype-specific selective filtering can fine-tune the bacterial community at specific life stages and tissues like the larval frass, even against a background of a highly variable community with stochastic assembly. Altogether, our findings suggest that the host's genotype can influence its susceptibility to being colonized by microbiota, impacting key life-history traits.
Collapse
Affiliation(s)
- Heli Juottonen
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Neda N. Moghadam
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Liam Murphy
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Johanna Mappes
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland ,grid.7737.40000 0004 0410 2071Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikki Biocenter 3, 00014 Helsinki, Finland
| | - Juan A. Galarza
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland ,grid.7737.40000 0004 0410 2071Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikki Biocenter 3, 00014 Helsinki, Finland
| |
Collapse
|
23
|
Henry LP, Ayroles JF. Drosophila melanogaster microbiome is shaped by strict filtering and neutrality along a latitudinal cline. Mol Ecol 2022; 31:5861-5871. [PMID: 36094780 PMCID: PMC9643648 DOI: 10.1111/mec.16692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 01/13/2023]
Abstract
Microbiomes affect many aspects of host biology, but the eco-evolutionary forces that shape their diversity in natural populations remain poorly understood. Geographical gradients, such as latitudinal clines, generate predictable patterns in biodiversity at macroecological scales, but whether these macroscale processes apply to host-microbiome interactions is an open question. To address this question, we sampled the microbiomes of 13 natural populations of Drosophila melanogaster along a latitudinal cline in the eastern United States. The microbiomes were surprisingly consistent across the cline, as latitude did not predict either alpha or beta diversity. Only a narrow taxonomic range of bacteria were present in all microbiomes, indicating that strict taxonomic filtering by the host and neutral ecological dynamics are the primary factors shaping the fly microbiome. Our findings reveal the complexity of eco-evolutionary interactions shaping microbial variation in D. melanogaster and highlight the need for additional sampling of the microbiomes in natural populations along environmental gradients.
Collapse
Affiliation(s)
- Lucas P Henry
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Julien F Ayroles
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| |
Collapse
|
24
|
Aagaard A, Liu S, Tregenza T, Braad Lund M, Schramm A, Verhoeven KJF, Bechsgaard J, Bilde T. Adapting to climate with limited genetic diversity: Nucleotide, DNA methylation and microbiome variation among populations of the social spider Stegodyphus dumicola. Mol Ecol 2022; 31:5765-5783. [PMID: 36112081 PMCID: PMC9827990 DOI: 10.1111/mec.16696] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 02/06/2023]
Abstract
Understanding the role of genetic and nongenetic variants in modulating phenotypes is central to our knowledge of adaptive responses to local conditions and environmental change, particularly in species with such low population genetic diversity that it is likely to limit their evolutionary potential. A first step towards uncovering the molecular mechanisms underlying population-specific responses to the environment is to carry out environmental association studies. We associated climatic variation with genetic, epigenetic and microbiome variation in populations of a social spider with extremely low standing genetic diversity. We identified genetic variants that are associated strongly with environmental variation, particularly with average temperature, a pattern consistent with local adaptation. Variation in DNA methylation in many genes was strongly correlated with a wide set of climate parameters, thereby revealing a different pattern of associations than that of genetic variants, which show strong correlations to a more restricted range of climate parameters. DNA methylation levels were largely independent of cis-genetic variation and of overall genetic population structure, suggesting that DNA methylation can work as an independent mechanism. Microbiome composition also correlated with environmental variation, but most strong associations were with precipitation-related climatic factors. Our results suggest a role for both genetic and nongenetic mechanisms in shaping phenotypic responses to local environments.
Collapse
Affiliation(s)
- Anne Aagaard
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Shenglin Liu
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Tom Tregenza
- Centre for Ecology & Conservation, School of BiosciencesUniversity of ExeterPenryn CampusUK
| | - Marie Braad Lund
- Section for Microbiology, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Andreas Schramm
- Section for Microbiology, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Koen J. F. Verhoeven
- Terrestrial Ecology DepartmentNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Jesper Bechsgaard
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Trine Bilde
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
| |
Collapse
|
25
|
Önder BŞ, Aksoy CF. Seasonal variation in wing size and shape of Drosophila melanogaster reveals rapid adaptation to environmental changes. Sci Rep 2022; 12:14622. [PMID: 36028640 PMCID: PMC9418266 DOI: 10.1038/s41598-022-18891-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
Populations in seasonal fluctuating environments receive multiple environmental cues and must deal with this heterogenic environment to survive and reproduce. An enlarged literature shows that this situation can be resolved through rapid adaptation in Drosophila melanogaster populations. Long-term monitoring of a population in its natural habitat and quantitative measurement of its responses to seasonal environmental changes are important for understanding the adaptive response of D. melanogaster to temporal variable selection. Here, we use inbred lines of a D. melanogaster population collected at monthly intervals between May to October over a temporal scale spanning three consecutive years to understand the variation in wing size and wing shape over these timepoints. The wing size and shape of this population changed significantly between months and a seasonal cycle of this traits is repeated for three years. Our results suggest that the effects of environmental variables that generated variation in body size between populations such as latitudinal clines, are a selective pressure in a different manner in terms of seasonal variation. Temperature related variable have a significant nonlinear relation to this fluctuating pattern in size and shape, whereas precipitation and humidity have a sex-specific effect which is more significant in males.
Collapse
Affiliation(s)
- Banu Şebnem Önder
- Genetic Variation and Adaptation Laboratory, Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey.
| | - Cansu Fidan Aksoy
- Genetic Variation and Adaptation Laboratory, Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
| |
Collapse
|
26
|
Arellano AA, Sommer AJ, Coon KL. Beyond canonical models: why a broader understanding of Diptera-microbiota interactions is essential for vector-borne disease control. Evol Ecol 2022; 37:165-188. [PMID: 37153630 PMCID: PMC10162596 DOI: 10.1007/s10682-022-10197-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vector-borne diseases constitute a major global public health threat. The most significant arthropod disease vectors are predominantly comprised of members of the insect order Diptera (true flies), which have long been the focus of research into host-pathogen dynamics. Recent studies have revealed the underappreciated diversity and function of dipteran-associated gut microbial communities, with important implications for dipteran physiology, ecology, and pathogen transmission. However, the effective parameterization of these aspects into epidemiological models will require a comprehensive study of microbe-dipteran interactions across vectors and related species. Here, we synthesize recent research into microbial communities associated with major families of dipteran vectors and highlight the importance of development and expansion of experimentally tractable models across Diptera towards understanding the functional roles of the gut microbiota in modulating disease transmission. We then posit why further study of these and other dipteran insects is not only essential to a comprehensive understanding of how to integrate vector-microbiota interactions into existing epidemiological frameworks, but our understanding of the ecology and evolution of animal-microbe symbiosis more broadly.
Collapse
Affiliation(s)
- Aldo A. Arellano
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew J. Sommer
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kerri L. Coon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
27
|
Arias MB, Hartle-Mougiou K, Taboada S, Vogler AP, Riesgo A, Elfekih S. Unveiling biogeographic patterns in the worldwide distributed Ceratitis capitata (medfly) using populations genomics and microbiome composition. Mol Ecol 2022; 31:4866-4883. [PMID: 35838255 DOI: 10.1111/mec.16616] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022]
Abstract
Invasive species are among the most important, growing threats to food security and agricultural systems. The Mediterranean medfly, Ceratitis capitata, is one of the most damaging representatives of a group of rapidly expanding species in the Tephritidae family, due to their wide host range and high invasiveness potential. Here, we used restriction site-associated DNA sequencing (RADseq) to investigate the population genomic structure and phylogeographic history of medflies collected from six sampling sites, including Africa (South Africa), the Mediterranean (Spain, Greece), Latin America (Guatemala, Brazil) and Australia. A total of 1,907 single nucleotide polymorphisms (SNPs) were used to identify two genetic clusters separating native and introduced ranges, consistent with previous findings. In the introduced range, all individuals were assigned to one genetic cluster except for those in Brazil, which showed introgression of an additional genetic cluster that also appeared in South Africa, and which could not be previously identified using microsatellite markers. Moreover, we assessed the microbial composition variations in medfly populations from selected sampling sites using amplicon sequencing of the 16S ribosomal RNA (V4 region). Microbiome composition and structure were highly similar across geographic regions and host plants, and only the Brazilian specimens showed increased diversity levels and a unique composition of its microbiome compared to other sampling sites. The unique SNP patterns and microbiome features in the Brazilian specimens could point to a direct migration route from Africa with subsequent adaptation of the microbiota to the specific conditions present in Brazil. These findings significantly improve our understanding of the evolutionary history of the global medfly invasions and their adaptation to newly colonised environments.
Collapse
Affiliation(s)
- María Belén Arias
- Department of Life Sciences, Natural History Museum, London, UK.,School of Life Sciences, University of Essex, Colchester, UK
| | - Katherine Hartle-Mougiou
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
| | - Sergi Taboada
- Department of Life Sciences, Natural History Museum, London, UK.,Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain.,Departamento de Ciencias de la Vida, Universidad de Alcalá de Henares, Madrid, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
| | - Ana Riesgo
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Biodiversity and Evolutionary Biology, Museum Nacional de Ciencias Naturales, Madrid, Spain
| | - Samia Elfekih
- CSIRO Health & Biosecurity, Black Mountain, Canberra, Australia.,PEARG, School of BioSciences, Bio21 Institute, The University of Melbourne VIC, Australia
| |
Collapse
|
28
|
Paddock KJ, Finke DL, Kim KS, Sappington TW, Hibbard BE. Patterns of Microbiome Composition Vary Across Spatial Scales in a Specialist Insect. Front Microbiol 2022; 13:898744. [PMID: 35722352 PMCID: PMC9201478 DOI: 10.3389/fmicb.2022.898744] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/12/2022] [Indexed: 11/20/2022] Open
Abstract
Microbial communities associated with animals vary based on both intrinsic and extrinsic factors. Of many possible determinants affecting microbiome composition, host phylogeny, host diet, and local environment are the most important. How these factors interact across spatial scales is not well understood. Here, we seek to identify the main influences on microbiome composition in a specialist insect, the western corn rootworm (WCR; Diabrotica virgifera virgifera), by analyzing the bacterial communities of adults collected from their obligate host plant, corn (Zea mays), across several geographic locations and comparing the patterns in communities to its congeneric species, the northern corn rootworm (NCR; Diabrotica barberi). We found that bacterial communities of WCR and NCR shared a portion of their bacterial communities even when collected from disparate locations. However, within each species, the location of collection significantly influenced the composition of their microbiome. Correlations of geographic distance between sites with WCR bacterial community composition revealed different patterns at different spatial scales. Community similarity decreased with increased geographic distance at smaller spatial scales (~25 km between the nearest sites). At broad spatial scales (>200 km), community composition was not correlated with distances between sites, but instead reflected the historical invasion path of WCR across the United States. These results suggest bacterial communities are structured directly by dispersal dynamics at small, regional spatial scales, while landscape-level genetic or environmental differences may drive community composition across broad spatial scales in this specialist insect.
Collapse
Affiliation(s)
- Kyle J Paddock
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Deborah L Finke
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Kyung Seok Kim
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, United States
| | - Thomas W Sappington
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, United States
| | - Bruce E Hibbard
- USDA-ARS, Plant Genetics Research Unit, University of Missouri, Columbia, MO, United States
| |
Collapse
|
29
|
Ørsted M, Yashiro E, Hoffmann AA, Kristensen TN. Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness. PLoS Genet 2022; 18:e1010206. [PMID: 35604942 PMCID: PMC9166449 DOI: 10.1371/journal.pgen.1010206] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 06/03/2022] [Accepted: 04/18/2022] [Indexed: 11/23/2022] Open
Abstract
It is becoming increasingly clear that microbial symbionts influence key aspects of their host’s fitness, and vice versa. This may fundamentally change our thinking about how microbes and hosts interact in influencing fitness and adaptation to changing environments. Here we explore how reductions in population size commonly experienced by threatened species influence microbiome diversity. Consequences of such reductions are normally interpreted in terms of a loss of genetic variation, increased inbreeding and associated inbreeding depression. However, fitness effects of population bottlenecks might also be mediated through microbiome diversity, such as through loss of functionally important microbes. Here we utilise 50 Drosophila melanogaster lines with different histories of population bottlenecks to explore these questions. The lines were phenotyped for egg-to-adult viability and their genomes sequenced to estimate genetic variation. The bacterial 16S rRNA gene was amplified in these lines to investigate microbial diversity. We found that 1) host population bottlenecks constrained microbiome richness and diversity, 2) core microbiomes of hosts with low genetic variation were constituted from subsets of microbiomes found in flies with higher genetic variation, 3) both microbiome diversity and host genetic variation contributed to host population fitness, 4) connectivity and robustness of bacterial networks was low in the inbred lines regardless of host genetic variation, 5) reduced microbial diversity was associated with weaker evolutionary responses of hosts in stressful environments, and 6) these effects were unrelated to Wolbachia density. These findings suggest that population bottlenecks reduce hologenomic variation (combined host and microbial genetic variation). Thus, while the current biodiversity crisis focuses on population sizes and genetic variation of eukaryotes, an additional focal point should be the microbial diversity carried by the eukaryotes, which in turn may influence host fitness and adaptability with consequences for the persistence of populations. It is becoming increasingly clear that organisms and the microbes that live on or in them–their microbiome–affect each other in profound ways that we are just beginning to understand. For instance, a diverse microbiome can help maintain metabolic functions or fight pathogens causing diseases. A disrupted microbiome may be especially critical for animals and plants that occur in low numbers because of threats from e.g. human exploitation or climate change, as they may already suffer from genetic challenges such as inbreeding and reduced evolutionary potential. The importance of such a reduction in population size, called a bottleneck, on the microbial diversity and the potential interactive effects on host health remains unexplored. Here we experimentally test these associations by investigating the microbiomes of 50 inbred or non-inbred populations of vinegar flies. We found that restricting the population size constrain the host’s genetic variation and simultaneously decreases the diversity of the microbiome that they harbor, and that both effects were detrimental to host fitness. The microbial communities in inbred host populations were less robust than in their non-inbred counterparts, suggesting that we should increasingly consider the microbiome diversity, which may ultimately influence the health and persistence of threatened species.
Collapse
Affiliation(s)
- Michael Ørsted
- Section for Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
- Section for Bioscience and Engineering, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- * E-mail:
| | - Erika Yashiro
- Section for Bioscience and Engineering, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Institute for Plant Sciences, Department of Biology, University of Cologne, Cologne, Germany
| | - Ary A. Hoffmann
- Section for Bioscience and Engineering, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- School of Biosciences, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Torsten Nygaard Kristensen
- Section for Bioscience and Engineering, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| |
Collapse
|
30
|
Development of Resistance to Clarithromycin and Amoxicillin-Clavulanic Acid in Lactiplantibacillus plantarum In Vitro Is Followed by Genomic Rearrangements and Evolution of Virulence. Microbiol Spectr 2022; 10:e0236021. [PMID: 35579444 PMCID: PMC9241834 DOI: 10.1128/spectrum.02360-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ensuring the safety of the use of probiotics is a top priority. Obviously, in addition to studying the beneficial properties of lactic acid bacteria, considerable attention should be directed to assessing the virulence of microorganisms as well as investigating the possibility of its evolution under conditions of selective pressure. To assess the virulence of probiotics, it is now recommended to analyze the genomes of bacteria in relation to the profiles of the virulome, resistome, and mobilome as well as the analysis of phenotypic resistance and virulence in vitro. However, the corresponding procedure has not yet been standardized, and virulence analysis of strains in vivo using model organisms has not been performed. Our study is devoted to testing the assumption that the development of antibiotic resistance in probiotic bacteria under conditions of selective pressure of antimicrobial drugs may be accompanied by the evolution of virulence. In this regard, special attention is required for the widespread in nature commensals and probiotic bacteria actively used in pharmacology and the food industry. As a result of step-by-step selection from the Lactiplantibacillus plantarum 8p-a3 strain isolated from the “Lactobacterin” probiotic (Biomed, Russia), the L. plantarum 8p-a3-Clr-Amx strain was obtained, showing increased resistance simultaneously to amoxicillin-clavulanic acid and clarithromycin (antibiotics, the combined use of which is widely used for Helicobacter pylori eradication) compared to the parent strain (MIC8p-a3-Clr-Amx of 20 μg/mL and 10 μg/mL, and MIC8p-a3 of 0.5 μg/mL and 0.05 μg/mL, respectively). The results of a comparative analysis of antibiotic-resistant and parental strains indicate that the development of resistance to the corresponding antimicrobial drugs in L. plantarum in vitro is accompanied by the following: (i) significant changes in the genomic profile (point mutations as well as deletions, insertions, duplications, and displacement of DNA sequences) associated in part with the resistome and mobilome; (ii) changes in phenotypic sensitivity to a number of antimicrobial drugs; and (iii) an increase in the level of virulence against Drosophila melanogaster, a model organism for which L. plantarum is considered to be a symbiont. The data obtained by us indicate that the mechanisms of adaptation to antimicrobial drugs in L. plantarum are not limited to those described earlier and determine the need for comprehensive studies of antibiotic resistance scenarios as well as the trajectories of virulence evolution in probiotic bacteria in vivo and in vitro to develop a standardized system for detecting virulent strains of the corresponding microorganisms. IMPORTANCE Ensuring the safety of the use of probiotics is a top priority. We found that increased resistance to popular antimicrobial drugs in Lactiplantibacillus plantarum is accompanied by significant changes in the genomic profile and phenotypic sensitivity to a number of antimicrobial drugs as well as in the level of virulence of this bacterium against Drosophila. The data obtained in our work indicate that the mechanisms of antibiotic resistance in this bacterium are not limited to those described earlier and determine the need for comprehensive studies of the potential for the evolution of virulence in lactic acid bacteria in vivo and in vitro and to develop a reliable control system to detect virulent strains among probiotics.
Collapse
|
31
|
Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host. mBio 2022; 13:e0067922. [PMID: 35502903 PMCID: PMC9239044 DOI: 10.1128/mbio.00679-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections.
Collapse
|
32
|
McHugh KM, Burke MK. From microbes to mammals: The experimental evolution of aging and longevity across species. Evolution 2022; 76:692-707. [PMID: 35112358 DOI: 10.1111/evo.14442] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/09/2021] [Accepted: 12/01/2021] [Indexed: 01/21/2023]
Abstract
Senescence, the functional deterioration of cells or organisms associated with increased age, is pervasive across the tree of life. Yet our understanding of the genetic and physiological basis underlying age-related declines in health and reproduction remains limited. Experimental evolution allows empirical examination of the question of why aging occurs; imposing selection for age-specific fitness traits shifts patterns of aging in experimental populations, enabling investigations of the variation underlying senescence and the mechanisms governing it. Whole-genome sequencing of experimentally evolved populations may reveal candidate genomic variants underlying particular aging patterns; unfortunately, most study systems suffer from limitations that weaken associations between genotypes and phenotypes. In this review, we provide a survey of experimental evolution studies that have altered population-level patterns of reproductive timing and senescence in a variety of species. We discuss the specific selection conditions that have increased longevity, the phenotypic responses and trade-offs that accompany these increases, and examine genomic data collected from these experiments. Additionally, we consider how selected field studies complement laboratory experiments on life-history evolution. Finally, we address the strengths and weaknesses of existing study systems, and evaluate which model organisms appear most promising for future genomic investigations of the evolutionary biology of aging.
Collapse
Affiliation(s)
- Kaitlin M McHugh
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, 97331
| | - Molly K Burke
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, 97331
| |
Collapse
|
33
|
Ashra H, Nair S. Review: Trait plasticity during plant-insect interactions: From molecular mechanisms to impact on community dynamics. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 317:111188. [PMID: 35193737 DOI: 10.1016/j.plantsci.2022.111188] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Phenotypic plasticity, prevalent in all domains of life, enables organisms to cope with unpredictable or novel changes in their growing environment. Plants represent an interesting example of phenotypic plasticity which also directly represents and affects the dynamics of biological interactions occurring in a community. Insects, which interact with plants, manifest phenotypic plasticity in their developmental, physiological, morphological or behavioral traits in response to the various host plant defenses induced upon herbivory. However, plant-insect interactions are generally more complex and multidimensional because of their dynamic association with their respective microbiomes and macrobiomes. Moreover, these associations can alter plant and insect responses towards each other by modulating the degree of phenotypic plasticity in their various traits and studying them will provide insights into how plants and insects reciprocally affect each other's evolutionary trajectory. Further, we explore the consequences of phenotypic plasticity on relationships and interactions between plants and insects and its impact on their development, evolution, speciation and ecological organization. This overview, obtained after exploring and comparing data obtained from several inter-disciplinary studies, reveals how genetic and molecular mechanisms, underlying plasticity in traits, impact species interactions at the community level and also identifies mechanisms that could be exploited in breeding programs.
Collapse
Affiliation(s)
- Himani Ashra
- Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Suresh Nair
- Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110 067, India.
| |
Collapse
|
34
|
Rudman SM, Greenblum SI, Rajpurohit S, Betancourt NJ, Hanna J, Tilk S, Yokoyama T, Petrov DA, Schmidt P. Direct observation of adaptive tracking on ecological time scales in Drosophila. Science 2022; 375:eabj7484. [PMID: 35298245 PMCID: PMC10684103 DOI: 10.1126/science.abj7484] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Direct observation of evolution in response to natural environmental change can resolve fundamental questions about adaptation, including its pace, temporal dynamics, and underlying phenotypic and genomic architecture. We tracked the evolution of fitness-associated phenotypes and allele frequencies genome-wide in 10 replicate field populations of Drosophila melanogaster over 10 generations from summer to late fall. Adaptation was evident over each sampling interval (one to four generations), with exceptionally rapid phenotypic adaptation and large allele frequency shifts at many independent loci. The direction and basis of the adaptive response shifted repeatedly over time, consistent with the action of strong and rapidly fluctuating selection. Overall, we found clear phenotypic and genomic evidence of adaptive tracking occurring contemporaneously with environmental change, thus demonstrating the temporally dynamic nature of adaptation.
Collapse
Affiliation(s)
- Seth M. Rudman
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA
| | - Sharon I. Greenblum
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Subhash Rajpurohit
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biological and Life Sciences, Ahmedabad University, Ahmedabad 380009, GJ, India
| | | | - Jinjoo Hanna
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susanne Tilk
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Tuya Yokoyama
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
35
|
Pfister CA, Light SH, Bohannan B, Schmidt T, Martiny A, Hynson NA, Devkota S, David L, Whiteson K. Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes. mSystems 2022; 7:e0137421. [PMID: 35014872 PMCID: PMC8751383 DOI: 10.1128/msystems.01374-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 12/26/2022] Open
Abstract
Whether a microbe is free-living or associated with a host from across the tree of life, its existence depends on a limited number of elements and electron donors and acceptors. Yet divergent approaches have been used by investigators from different fields. The "environment first" research tradition emphasizes thermodynamics and biogeochemical principles, including the quantification of redox environments and elemental stoichiometry to identify transformations and thus an underlying microbe. The increasingly common "microbe first" research approach benefits from culturing and/or DNA sequencing methods to first identify a microbe and encoded metabolic functions. Here, the microbe itself serves as an indicator for environmental conditions and transformations. We illustrate the application of both approaches to the study of microbiomes and emphasize how both can reveal the selection of microbial metabolisms across diverse environments, anticipate alterations to microbiomes in host health, and understand the implications of a changing climate for microbial function.
Collapse
Affiliation(s)
- Catherine A. Pfister
- Department of Ecology & Evolution and The Microbiome Center, University of Chicago, Chicago, Illinois, USA
| | - Samuel H. Light
- Department of Microbiology & Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Brendan Bohannan
- Environmental Studies and Biology, University of Oregon, Eugene, Oregon, USA
| | - Thomas Schmidt
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam Martiny
- Earth System Science & Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - Nicole A. Hynson
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Suzanne Devkota
- Microbiome Research, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lawrence David
- Molecular Genetics & Microbiology, Duke University, Durham, North Carolina, USA
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
| |
Collapse
|
36
|
Couch CE, Epps CW. Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations. J Hered 2022; 113:221-234. [PMID: 34983061 DOI: 10.1093/jhered/esab078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/03/2022] [Indexed: 11/14/2022] Open
Abstract
In recent years, emerging sequencing technologies and computational tools have driven a tidal wave of research on host-associated microbiomes, particularly the gut microbiome. These studies demonstrate numerous connections between the gut microbiome and vital host functions, primarily in humans, model organisms, and domestic animals. As the adaptive importance of the gut microbiome becomes clearer, interest in studying the gut microbiomes of wild populations has increased, in part due to the potential for discovering conservation applications. The study of wildlife gut microbiomes holds many new challenges and opportunities due to the complex genetic, spatial, and environmental structure of wild host populations, and the potential for these factors to interact with the microbiome. The emerging picture of adaptive coevolution in host-microbiome relationships highlights the importance of understanding microbiome variation in the context of host population genetics and landscape heterogeneity across a wide range of host populations. We propose a conceptual framework for understanding wildlife gut microbiomes in relation to landscape variables and host population genetics, including the potential of approaches derived from landscape genetics. We use this framework to review current research, synthesize important trends, highlight implications for conservation, and recommend future directions for research. Specifically, we focus on how spatial structure and environmental variation interact with host population genetics and microbiome variation in natural populations, and what we can learn from how these patterns of covariation differ depending on host ecological and evolutionary traits.
Collapse
Affiliation(s)
- Claire E Couch
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Clinton W Epps
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| |
Collapse
|
37
|
Mostoufi SL, Singh ND. Diet-induced changes in titer support a discrete response of Wolbachia-associated plastic recombination in Drosophila melanogaster. G3 GENES|GENOMES|GENETICS 2022; 12:6428536. [PMID: 34791181 PMCID: PMC8728003 DOI: 10.1093/g3journal/jkab375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022]
Abstract
Plastic recombination in Drosophila melanogaster has been associated with a variety of extrinsic and intrinsic factors such as temperature, starvation, and parasite infection. The bacterial endosymbiont Wolbachia pipientis has also been associated with plastic recombination in D. melanogaster. Wolbachia infection is pervasive in arthropods and this infection induces a variety of phenotypes in its hosts, the strength of which can depend on bacterial titer. Here, we test the hypothesis that the magnitude of Wolbachia-associated plastic recombination in D. melanogaster depends on titer. To manipulate titer, we raised Wolbachia-infected and uninfected flies on diets that have previously been shown to increase or decrease Wolbachia titer relative to controls. We measured recombination in treated and control individuals using a standard backcrossing scheme with two X-linked visible markers. Our results recapitulate previous findings that Wolbachia infection is associated with increased recombination rate across the yellow-vermillion interval of the X chromosome. Our data show no significant effect of diet or diet by Wolbachia interactions on recombination, suggesting that diet-induced changes in Wolbachia titer have no effect on the magnitude of plastic recombination. These findings represent one of the first steps toward investigating Wolbachia-associated plastic recombination and demonstrate that the phenotype is a discrete response rather than a continuous one.
Collapse
Affiliation(s)
- Sabrina L Mostoufi
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Nadia D Singh
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| |
Collapse
|
38
|
Medvedeva ES, Mouzykantov AA, Kostenko VV, Baranova NB, Markelova MI, Sabouni RG, Khusnutdinova DR, Chernova OA, Chernov VM. Adaptation to Antimicrobials and Pathogenicity in Mycoplasmas: Development of Ciprofloxacin-Resistance and Evolution of Virulence in Acholeplasma laidlawii. DOKL BIOCHEM BIOPHYS 2021; 501:444-448. [PMID: 34966969 DOI: 10.1134/s1607672921060028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/22/2022]
Abstract
For the first time it was shown that the development of resistance to ciprofloxacin in vitro in Acholeplasma laidlawii, a mycoplasma which is widely spread in nature and which is the main contaminant of cell cultures and vaccines, is associated with diverse pathways of virulence evolution: virulome and virulence differ significantly between ciprofloxacin-resistant strains, including those with the same level of antimicrobial resistance.
Collapse
Affiliation(s)
- E S Medvedeva
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
| | - A A Mouzykantov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia.
| | - V V Kostenko
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia.,Kazan (Volga Region) Federal University, Kazan, Russia
| | - N B Baranova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
| | - M I Markelova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia.,Kazan (Volga Region) Federal University, Kazan, Russia
| | - R G Sabouni
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia.,Kazan (Volga Region) Federal University, Kazan, Russia
| | - D R Khusnutdinova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia.,Kazan (Volga Region) Federal University, Kazan, Russia
| | - O A Chernova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
| | - V M Chernov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
| |
Collapse
|
39
|
Mazzucco R, Schlötterer C. Long-term gut microbiome dynamics in Drosophila melanogaster reveal environment-specific associations between bacterial taxa at the family level. Proc Biol Sci 2021; 288:20212193. [PMID: 34905708 PMCID: PMC8670958 DOI: 10.1098/rspb.2021.2193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The influence of the microbiome on its host is well-documented, but the interplay of its members is not yet well-understood. Even for simple microbiomes, the interaction among members of the microbiome is difficult to study. Longitudinal studies provide a promising approach to studying such interactions through the temporal covariation of different taxonomic units. By contrast to most longitudinal studies, which span only a single host generation, we here present a post hoc analysis of a whole-genome dataset of 81 samples that follows microbiome composition for up to 180 host generations, which cover nearly 10 years. The microbiome diversity remained rather stable in replicated Drosophila melanogaster populations exposed to two different temperature regimes. The composition changed, however, systematically across replicates of the two temperature regimes. Significant associations between families, mostly specific to one temperature regime, indicate functional interdependence of different microbiome components. These associations also involve moderately abundant families, which emphasizes their functional importance, and highlights the importance of looking beyond the common constituents of the Drosophila microbiome.
Collapse
Affiliation(s)
- Rupert Mazzucco
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 1, Wien 1210, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 1, Wien 1210, Austria
| |
Collapse
|
40
|
Kapun M, Nunez JCB, Bogaerts-Márquez M, Murga-Moreno J, Paris M, Outten J, Coronado-Zamora M, Tern C, Rota-Stabelli O, Guerreiro MPG, Casillas S, Orengo DJ, Puerma E, Kankare M, Ometto L, Loeschcke V, Onder BS, Abbott JK, Schaeffer SW, Rajpurohit S, Behrman EL, Schou MF, Merritt TJS, Lazzaro BP, Glaser-Schmitt A, Argyridou E, Staubach F, Wang Y, Tauber E, Serga SV, Fabian DK, Dyer KA, Wheat CW, Parsch J, Grath S, Veselinovic MS, Stamenkovic-Radak M, Jelic M, Buendía-Ruíz AJ, Gómez-Julián MJ, Espinosa-Jimenez ML, Gallardo-Jiménez FD, Patenkovic A, Eric K, Tanaskovic M, Ullastres A, Guio L, Merenciano M, Guirao-Rico S, Horváth V, Obbard DJ, Pasyukova E, Alatortsev VE, Vieira CP, Vieira J, Torres JR, Kozeretska I, Maistrenko OM, Montchamp-Moreau C, Mukha DV, Machado HE, Lamb K, Paulo T, Yusuf L, Barbadilla A, Petrov D, Schmidt P, Gonzalez J, Flatt T, Bergland AO. Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource. Mol Biol Evol 2021; 38:5782-5805. [PMID: 34469576 PMCID: PMC8662648 DOI: 10.1093/molbev/msab259] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.
Collapse
Affiliation(s)
- Martin Kapun
- Department of Evolutionary Biology and Environmental Studies, University of
Zürich, Switzerland
- Department of Cell & Developmental Biology, Center of Anatomy and Cell
Biology, Medical University of Vienna, Vienna, Austria
| | - Joaquin C B Nunez
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | | | - Jesús Murga-Moreno
- Department of Genetics and Microbiology, Universitat Autònoma de
Barcelona, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Margot Paris
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Joseph Outten
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | | | - Courtney Tern
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment, University of Trento, San Michele all'
Adige, Italy
| | | | - Sònia Casillas
- Department of Genetics and Microbiology, Universitat Autònoma de
Barcelona, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia,
Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de
Barcelona, Barcelona, Spain
| | - Eva Puerma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia,
Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de
Barcelona, Barcelona, Spain
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of
Jyväskylä, Jyväskylä, Finland
| | - Lino Ometto
- Department of Biology and Biotechnology, University of Pavia,
Pavia, Italy
| | | | - Banu S Onder
- Department of Biology, Hacettepe University, Ankara, Turkey
| | | | - Stephen W Schaeffer
- Department of Biology, The Pennsylvania State University,
University Park, PA, USA
| | - Subhash Rajpurohit
- Department of Biology, University of Pennsylvania, Philadelphia,
PA, USA
- Division of Biological and Life Sciences, School of Arts and Sciences,
Ahmedabad University, Ahmedabad, India
| | - Emily L Behrman
- Department of Biology, University of Pennsylvania, Philadelphia,
PA, USA
- Janelia Research Campus, Ashburn, VA, USA
| | - Mads F Schou
- Department of Biology, Aarhus University, Aarhus, Denmark
- Department of Biology, Lund University, Lund, Sweden
| | - Thomas J S Merritt
- Department of Chemistry & Biochemistry, Laurentian
University, Sudbury, ON, Canada
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca, NY,
USA
| | - Amanda Glaser-Schmitt
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Eliza Argyridou
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Fabian Staubach
- Department of Evolution and Ecology, University of Freiburg,
Freiburg, Germany
| | - Yun Wang
- Department of Evolution and Ecology, University of Freiburg,
Freiburg, Germany
| | - Eran Tauber
- Department of Evolutionary and Environmental Biology, Institute of Evolution,
University of Haifa, Haifa, Israel
| | - Svitlana V Serga
- Department of General and Medical Genetics, Taras Shevchenko National
University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center, Ministry of Education
and Science of Ukraine, Kyiv, Ukraine
| | - Daniel K Fabian
- Department of Genetics, University of Cambridge, Cambridge,
United Kingdom
| | - Kelly A Dyer
- Department of Genetics, University of Georgia, Athens, GA,
USA
| | | | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Sonja Grath
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | | | | | - Mihailo Jelic
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | | | | | | | - Aleksandra Patenkovic
- Institute for Biological Research “Siniša Stanković”, National Institute of
Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Katarina Eric
- Institute for Biological Research “Siniša Stanković”, National Institute of
Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marija Tanaskovic
- Institute for Biological Research “Siniša Stanković”, National Institute of
Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Anna Ullastres
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Lain Guio
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Miriam Merenciano
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Sara Guirao-Rico
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Vivien Horváth
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh,
Edinburgh, United Kingdom
| | - Elena Pasyukova
- Institute of Molecular Genetics of the National Research Centre “Kurchatov
Institute”, Moscow, Russia
| | - Vladimir E Alatortsev
- Institute of Molecular Genetics of the National Research Centre “Kurchatov
Institute”, Moscow, Russia
| | - Cristina P Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do
Porto, Porto, Portugal
| | - Jorge Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do
Porto, Porto, Portugal
| | | | - Iryna Kozeretska
- Department of General and Medical Genetics, Taras Shevchenko National
University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center, Ministry of Education
and Science of Ukraine, Kyiv, Ukraine
| | - Oleksandr M Maistrenko
- Department of General and Medical Genetics, Taras Shevchenko National
University of Kyiv, Kyiv, Ukraine
- Structural and Computational Biology Unit, European Molecular Biology
Laboratory, Heidelberg, Germany
| | | | - Dmitry V Mukha
- Vavilov Institute of General Genetics, Russian Academy of
Sciences, Moscow, Russia
| | - Heather E Machado
- Department of Biology, Stanford University, Stanford, CA,
USA
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Keric Lamb
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | - Tânia Paulo
- Departamento de Biologia Animal, Instituto Gulbenkian de Ciência,
Oeiras, Portugal
| | - Leeban Yusuf
- Center for Biological Diversity, University of St. Andrews, St
Andrews, United Kingdom
| | - Antonio Barbadilla
- Department of Genetics and Microbiology, Universitat Autònoma de
Barcelona, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA,
USA
| | - Paul Schmidt
- Department of Biology, The Pennsylvania State University,
University Park, PA, USA
| | - Josefa Gonzalez
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Alan O Bergland
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| |
Collapse
|
41
|
An altered microbiome in a Parkinson's disease model Drosophila melanogaster has a negative effect on development. Sci Rep 2021; 11:23635. [PMID: 34880269 PMCID: PMC8654912 DOI: 10.1038/s41598-021-02624-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/08/2021] [Indexed: 11/30/2022] Open
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disease, besides Alzheimer’s Disease, characterized by multiple symptoms, including the well-known motor dysfunctions. It is well-established that there are differences in the fecal microbiota composition between Parkinson’s disease (PD) patients and control populations, but the mechanisms underlying these differences are not yet fully understood. To begin to close the gap between description and mechanism we studied the relationship between the microbiota and PD in a model organism, Drosophila melanogaster. First, fecal transfers were performed with a D. melanogaster model of PD that had a mutation in the parkin (park25) gene. Results indicate that the PD model feces had a negative effect on both pupation and eclosion in both control and park25 flies, with a greater effect in PD model flies. Analysis of the microbiota composition revealed differences between the control and park25 flies, consistent with many human studies. Conversely, gnotobiotic treatment of axenic embryos with feces-derived bacterial cultures did not affect eclosure. We speculate this result might be due to similarities in bacterial prevalence between mutant and control feces. Further, we confirmed a bacteria-potentiated impact on mutant and control fly phenotypes by measuring eclosure rate in park25 flies that were mono-associated with members of the fly microbiota. Both the fecal transfer and the mono-association results indicate a host genotype-microbiota interaction. Overall, this study concludes functional effects of the fly microbiota on PD model flies, providing support to the developing body of knowledge regarding the influence of the microbiota on PD.
Collapse
|
42
|
Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila. BMC Biol 2021; 19:187. [PMID: 34565363 PMCID: PMC8474910 DOI: 10.1186/s12915-021-01124-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
Background How microbes affect host fitness and environmental adaptation has become a fundamental research question in evolutionary biology. To better understand the role of microbial genomic variation for host fitness, we tested for associations of bacterial genomic variation and Drosophila melanogaster offspring number in a microbial Genome Wide Association Study (GWAS). Results We performed a microbial GWAS, leveraging strain variation in the genus Gluconobacter, a genus of bacteria that are commonly associated with Drosophila under natural conditions. We pinpoint the thiamine biosynthesis pathway (TBP) as contributing to differences in fitness conferred to the fly host. While an effect of thiamine on fly development has been described, we show that strain variation in TBP between bacterial isolates from wild-caught D. melanogaster contributes to variation in offspring production by the host. By tracing the evolutionary history of TBP genes in Gluconobacter, we find that TBP genes were most likely lost and reacquired by horizontal gene transfer (HGT). Conclusion Our study emphasizes the importance of strain variation and highlights that HGT can add to microbiome flexibility and potentially to host adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01124-y.
Collapse
|
43
|
Abstract
Can hosts swap ancient symbionts for new ones? A new study shows that a novel partnership between a protist and an algal symbiont can rapidly evolve to both overcome initial incompatibility and adapt to environmental challenges.
Collapse
Affiliation(s)
- Stephanie Porter
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA.
| |
Collapse
|
44
|
Affiliation(s)
- A M O'Brien
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
| | - T L Harrison
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
45
|
Rodrigues MF, Cogni R. Genomic Responses to Climate Change: Making the Most of the Drosophila Model. Front Genet 2021; 12:676218. [PMID: 34326859 PMCID: PMC8314211 DOI: 10.3389/fgene.2021.676218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/15/2021] [Indexed: 11/18/2022] Open
Abstract
It is pressing to understand how animal populations evolve in response to climate change. We argue that new sequencing technologies and the use of historical samples are opening unprecedented opportunities to investigate genome-wide responses to changing environments. However, there are important challenges in interpreting the emerging findings. First, it is essential to differentiate genetic adaptation from phenotypic plasticity. Second, it is extremely difficult to map genotype, phenotype, and fitness. Third, neutral demographic processes and natural selection affect genetic variation in similar ways. We argue that Drosophila melanogaster, a classical model organism with decades of climate adaptation research, is uniquely suited to overcome most of these challenges. In the near future, long-term time series genome-wide datasets of D. melanogaster natural populations will provide exciting opportunities to study adaptation to recent climate change and will lay the groundwork for related research in non-model systems.
Collapse
Affiliation(s)
- Murillo F. Rodrigues
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Rodrigo Cogni
- Department of Ecology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
46
|
Rodrigues MF, Vibranovski MD, Cogni R. Clinal and seasonal changes are correlated in Drosophila melanogaster natural populations. Evolution 2021; 75:2042-2054. [PMID: 34184262 DOI: 10.1111/evo.14300] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022]
Abstract
Spatial and seasonal variations in the environment are ubiquitous. Environmental heterogeneity can affect natural populations and lead to covariation between environment and allele frequencies. Drosophila melanogaster is known to harbor polymorphisms that change both with latitude and seasons. Identifying the role of selection in driving these changes is not trivial, because nonadaptive processes can cause similar patterns. Given the environment changes in similar ways across seasons and along the latitudinal gradient, one promising approach may be to look for parallelism between clinal and seasonal changes. Here, we test whether there is a genome-wide correlation between clinal and seasonal changes, and whether the pattern is consistent with selection. Allele frequency estimates were obtained from pooled samples from seven different locations along the east coast of the United States, and across seasons within Pennsylvania. We show that there is a genome-wide correlation between clinal and seasonal variations, which cannot be explained by linked selection alone. This pattern is stronger in genomic regions with higher functional content, consistent with natural selection. We derive a way to biologically interpret these correlations and show that around 3.7% of the common, autosomal variants could be under parallel seasonal and spatial selection. Our results highlight the contribution of natural selection in driving fluctuations in allele frequencies in natural fly populations and point to a shared genomic basis to climate adaptation that happens over space and time in D. melanogaster.
Collapse
Affiliation(s)
- Murillo F Rodrigues
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil.,Current Address: Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, 97403
| | - Maria D Vibranovski
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
| | - Rodrigo Cogni
- Department of Ecology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
| |
Collapse
|
47
|
Machado HE, Bergland AO, Taylor R, Tilk S, Behrman E, Dyer K, Fabian DK, Flatt T, González J, Karasov TL, Kim B, Kozeretska I, Lazzaro BP, Merritt TJS, Pool JE, O'Brien K, Rajpurohit S, Roy PR, Schaeffer SW, Serga S, Schmidt P, Petrov DA. Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila. eLife 2021; 10:e67577. [PMID: 34155971 PMCID: PMC8248982 DOI: 10.7554/elife.67577] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched in large chromosomal inversions, and we find a broad concordance between seasonal and spatial allele frequency change. The direction of allele frequency change at seasonally variable polymorphisms can be predicted by weather conditions in the weeks prior to sampling, linking the environment and the genomic response to selection. Our results suggest that fluctuating selection is an important evolutionary force affecting patterns of genetic variation in Drosophila.
Collapse
Affiliation(s)
- Heather E Machado
- Department of Biology, Stanford UniversityStanfordUnited States
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Alan O Bergland
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Biology, University of VirginiaCharlottesvilleUnited States
| | - Ryan Taylor
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Susanne Tilk
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Emily Behrman
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Kelly Dyer
- Department of Genetics, University of GeorgiaAthensUnited States
| | - Daniel K Fabian
- Institute of Population Genetics, Vetmeduni ViennaViennaAustria
- Centre for Pathogen Evolution, Department of Zoology, University of CambridgeCambridgeUnited Kingdom
| | - Thomas Flatt
- Institute of Population Genetics, Vetmeduni ViennaViennaAustria
- Department of Biology, University of FribourgFribourgSwitzerland
| | - Josefa González
- Institute of Evolutionary Biology, CSIC- Universitat Pompeu FabraBarcelonaSpain
| | - Talia L Karasov
- Department of Biology, University of UtahSalt Lake CityUnited States
| | - Bernard Kim
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Iryna Kozeretska
- Taras Shevchenko National University of KyivKyivUkraine
- National Antarctic Scientific Centre of Ukraine, Taras Shevchenko Blvd.KyivUkraine
| | - Brian P Lazzaro
- Department of Entomology, Cornell UniversityIthacaUnited States
| | - Thomas JS Merritt
- Department of Chemistry & Biochemistry, Laurentian UniversitySudburyCanada
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-MadisonMadisonUnited States
| | - Katherine O'Brien
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Subhash Rajpurohit
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Paula R Roy
- Department of Ecology and Evolutionary Biology, University of KansasLawrenceUnited States
| | - Stephen W Schaeffer
- Department of Biology, The Pennsylvania State UniversityUniversity ParkUnited States
| | - Svitlana Serga
- Taras Shevchenko National University of KyivKyivUkraine
- National Antarctic Scientific Centre of Ukraine, Taras Shevchenko Blvd.KyivUkraine
| | - Paul Schmidt
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
| |
Collapse
|
48
|
Mallott EK, Amato KR. Host specificity of the gut microbiome. Nat Rev Microbiol 2021; 19:639-653. [PMID: 34045709 DOI: 10.1038/s41579-021-00562-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 02/07/2023]
Abstract
Developing general principles of host-microorganism interactions necessitates a robust understanding of the eco-evolutionary processes that structure microbiota. Phylosymbiosis, or patterns of microbiome composition that can be predicted by host phylogeny, is a unique framework for interrogating these processes. Identifying the contexts in which phylosymbiosis does and does not occur facilitates an evaluation of the relative importance of different ecological processes in shaping the microbial community. In this Review, we summarize the prevalence of phylosymbiosis across the animal kingdom on the basis of the current literature and explore the microbial community assembly processes and related host traits that contribute to phylosymbiosis. We find that phylosymbiosis is less prevalent in taxonomically richer microbiomes and hypothesize that this pattern is a result of increased stochasticity in the assembly of complex microbial communities. We also note that despite hosting rich microbiomes, mammals commonly exhibit phylosymbiosis. We hypothesize that this pattern is a result of a unique combination of mammalian traits, including viviparous birth, lactation and the co-evolution of haemochorial placentas and the eutherian immune system, which compound to ensure deterministic microbial community assembly. Examining both the individual and the combined importance of these traits in driving phylosymbiosis provides a new framework for research in this area moving forward.
Collapse
Affiliation(s)
- Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, IL, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA.
| |
Collapse
|
49
|
Doña J, Virrueta Herrera S, Nyman T, Kunnasranta M, Johnson KP. Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites. Front Microbiol 2021; 12:642543. [PMID: 33935998 PMCID: PMC8085356 DOI: 10.3389/fmicb.2021.642543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
While interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louse Echinophthirius horridus sampled from individual Saimaa ringed seals Pusa hispida saimensis. Both genome-resolved and read-based metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how well-known processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems.
Collapse
Affiliation(s)
- Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Departamento de Biología Animal, Universidad de Granada, Granada, Spain
| | - Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Natural Resources Institute Finland, Joensuu, Finland
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| |
Collapse
|
50
|
Henry LP, Ayroles JF. Meta-analysis suggests the microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster. BMC Microbiol 2021; 21:108. [PMID: 33836662 PMCID: PMC8034159 DOI: 10.1186/s12866-021-02168-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 03/31/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Experimental evolution has a long history of uncovering fundamental insights into evolutionary processes, but has largely neglected one underappreciated component--the microbiome. As eukaryotic hosts evolve, the microbiome may also respond to selection. However, the microbial contribution to host evolution remains poorly understood. Here, we re-analyzed genomic data to characterize the metagenomes from ten Evolve and Resequence (E&R) experiments in Drosophila melanogaster to determine how the microbiome changed in response to host selection. RESULTS Bacterial diversity was significantly different in 5/10 studies, primarily in traits associated with metabolism or immunity. Duration of selection did not significantly influence bacterial diversity, highlighting the importance of associations with specific host traits. CONCLUSIONS Our genomic re-analysis suggests the microbiome often responds to host selection; thus, the microbiome may contribute to the response of Drosophila in E&R experiments. We outline important considerations for incorporating the microbiome into E&R experiments. The E&R approach may provide critical insights into host-microbiome interactions and fundamental insight into the genomic basis of adaptation.
Collapse
Affiliation(s)
- Lucas P Henry
- Department of Ecology & Evolutionary Biology, 150 Carl Icahn Laboratory, Princeton University, Princeton, NJ, 08544, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
| | - Julien F Ayroles
- Department of Ecology & Evolutionary Biology, 150 Carl Icahn Laboratory, Princeton University, Princeton, NJ, 08544, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
| |
Collapse
|