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Bronstein JL, Sridhar H. Connecting and integrating cooperation within and between species. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230203. [PMID: 39034697 PMCID: PMC11293865 DOI: 10.1098/rstb.2023.0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 07/23/2024] Open
Abstract
There has long been a fundamental divide in the study of cooperation: researchers focus either on cooperation within species, including but not limited to sociality, or else on cooperation between species, commonly termed mutualism. Here, we explore the ecologically and evolutionarily significant ways in which within- and between-species cooperation interact. We highlight two primary cross-linkages. First, cooperation of one type can change the context in which cooperation of the other type functions, and thus potentially its outcome. We delineate three possibilities: (i) within-species cooperation modulates benefits for a heterospecific partner; (ii) between-species cooperation affects the dynamics of within-species cooperation; and (iii) both processes take place interactively. The second type of cross-linkage emerges when resources or services that cooperation makes available are obtainable either from members of the same species or from different species. This brings cooperation at the two levels into direct interaction, to some extent obscuring the distinction between them. We expand on these intersections between within- and between-species cooperation in a diversity of taxa and interaction types. These interactions have the potential to weave together social networks and trophic dynamics, contributing to the structure and functioning of ecological communities in ways that are just beginning to be explored. This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.
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Affiliation(s)
- Judith L. Bronstein
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ85721, USA
| | - Hari Sridhar
- Konrad Lorenz Institute for Evolution and Cognition Research, KlosterneuburgA-3400, Austria
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2
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Duron O. Nutritional symbiosis in ticks: singularities of the genus Ixodes. Trends Parasitol 2024; 40:696-706. [PMID: 38942646 DOI: 10.1016/j.pt.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 06/30/2024]
Abstract
Symbiosis with intracellular bacteria is essential for the nutrition of ticks, particularly through the biosynthesis of B vitamins. Yet, ticks of the genus Ixodes, which include major vectors of human pathogens, lack the nutritional symbionts usually found in other tick genera. This paradox raises questions about the mechanisms that Ixodes ticks use to prevent nutritional deficiencies. Nonetheless, Ixodes ticks commonly harbor other symbionts belonging to the order Rickettsiales. Although these obligate intracellular bacteria are primarily known as human pathogens, Rickettsiales symbionts often dominate the Ixodes microbial community without causing diseases. They also significantly influence Ixodes physiology, synthesize key B vitamins, and are crucial for immatures. These findings underscore unique associations between Rickettsiales and Ixodes ticks distinct from other tick genera.
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Affiliation(s)
- Olivier Duron
- MIVEGEC, University of Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Montpellier, France.
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3
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Michalik A, C. Franco D, Szklarzewicz T, Stroiński A, Łukasik P. Facultatively intrabacterial localization of a planthopper endosymbiont as an adaptation to its vertical transmission. mSystems 2024; 9:e0063424. [PMID: 38934538 PMCID: PMC11264691 DOI: 10.1128/msystems.00634-24] [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: 05/03/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Transovarial transmission is the most reliable way of passing on essential nutrient-providing endosymbionts from mothers to offspring. However, not all endosymbiotic microbes follow the complex path through the female host tissues to oocytes on their own. Here, we demonstrate an unusual transmission strategy adopted by one of the endosymbionts of the planthopper Trypetimorpha occidentalis (Hemiptera: Tropiduchidae) from Bulgaria. In this species, an Acetobacteraceae endosymbiont is transmitted transovarially within deep invaginations of cellular membranes of an ancient endosymbiont Sulcia-strikingly resembling recently described plant virus transmission. However, in males, Acetobacteraceae colonizes the same bacteriocytes as Sulcia but remains unenveloped. Then, the unusual endobacterial localization of Acetobacteraceae observed in females appears to be a unique adaptation to maternal transmission. Further, the symbiont's genomic features, including encoding essential amino acid biosynthetic pathways and its similarity to a recently described psyllid symbiont, suggest a unique combination of the ability to horizontally transmit among species and confer nutritional benefits. The close association with Acetobacteraceae symbiont correlates with the so-far-unreported level of genomic erosion of ancient nutritional symbionts of this planthopper. In Sulcia, this is reflected in substantial changes in genomic organization, reported for the first time in the symbiont renowned for its genomic stability. In Vidania, substantial gene loss resulted in one of the smallest genomes known, at 108.6 kb. Thus, the symbionts of T. occidentalis display a combination of unusual adaptations and genomic features that expand our understanding of how insect-microbe symbioses may transmit and evolve.IMPORTANCEReliable transmission across host generations is a major challenge for bacteria that associate with insects, and independently established symbionts have addressed this challenge in different ways. The facultatively endobacterial localization of Acetobacteraceae symbiont, enveloped by cells of ancient nutritional endosymbiont Sulcia in females but not males of the planthopper Trypetimorpha occidentalis, appears to be a unique adaptation to maternal transmission. Acetobacteraceae's genomic features indicate its unusual evolutionary history, and the genomic erosion experienced by ancient nutritional symbionts demonstrates the apparent consequences of such close association. Combined, this multi-partite symbiosis expands our understanding of the diversity of strategies that insect symbioses form and some of their evolutionary consequences.
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Affiliation(s)
- Anna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Diego C. Franco
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Teresa Szklarzewicz
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Adam Stroiński
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
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4
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Thia JA, Zhan D, Robinson K, Umina PA, Hoffmann AA, Yang Q. 'Drifting' Buchnera genomes track the microevolutionary trajectories of their aphid hosts. INSECT MOLECULAR BIOLOGY 2024. [PMID: 39031957 DOI: 10.1111/imb.12946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/08/2024] [Indexed: 07/22/2024]
Abstract
Evolution of Buchnera-aphid host symbioses is often studied among species at macroevolutionary scales. Investigations within species offer a different perspective about how eco-evolutionary processes shape patterns of genetic variation at microevolutionary scales. Our study leverages new and publicly available whole-genome sequencing data to study Buchnera-aphid host evolution in Myzus persicae, the peach potato aphid, a globally invasive and polyphagous pest. Across 43 different asexual, clonally reproducing isofemale strains, we examined patterns of genomic covariation between Buchnera and their aphid host and considered the distribution of mutations in protein-coding regions of the Buchnera genome. We found Buchnera polymorphisms within aphid strains, suggesting the presence of genetically different Buchnera strains within the same clonal lineage. Genetic distance between pairs of Buchnera samples was positively correlated to genetic distance between their aphid hosts, indicating shared evolutionary histories. However, there was no segregation of genetic variation for both M. persicae and Buchnera with plant host (Brassicaceae and non-tobacco Solanaceae) and no associations between genetic and geographic distance at global or regional spatial scales. Abundance patterns of non-synonymous mutations were similar to synonymous mutations in the Buchnera genome, and both mutation classes had similar site frequency spectra. We hypothesize that a predominance of neutral processes results in the Buchnera of M. persicae to simply 'drift' with the evolutionary trajectory of their aphid hosts. Our study presents a unique microevolutionary characterization of Buchnera-aphid host genomic covariation across multiple aphid clones. This provides a new perspective on the eco-evolutionary processes generating and maintaining polymorphisms in a major pest aphid species and its obligate primary endosymbiont.
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Affiliation(s)
- Joshua A Thia
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dongwu Zhan
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Katie Robinson
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
| | - Paul A Umina
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
- Cesar Australia Pty Ltd, Melbourne, Victoria, Australia
| | - Ary A Hoffmann
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Qiong Yang
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
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5
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Chen Q, Tian Y, Zhang J, Li J, Ren H, Chen G, Zhang X. Resilience mechanisms of Trichopria drosophilae (Hymenoptera: Diapriinae) under global extreme cooling: insights into parasitic response and physiological adaptation. JOURNAL OF ECONOMIC ENTOMOLOGY 2024:toae134. [PMID: 39018046 DOI: 10.1093/jee/toae134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 07/18/2024]
Abstract
Global climate warming and frequent extreme low-temperature events have made it essential to investigate the impact of low temperatures on parasitic wasps to protect and strengthen farmland biodiversity, which in turn enhances the biological control potential of natural enemies such as parasitic wasps. We systematically examined how low-temperature stress affects the parasitic functional response of Trichopria drosophilae to Drosophila suzukii (Diptera: Drosophilidae) pupae. Our findings indicate that the parasitic behavior of T. drosophilae towards D. suzukii pupae aligns with the Holling II functional response model following exposure to different temperatures. Within the temperature range of 8 °C to -8 °C, lower temperatures correlated decreased instantaneous attack rate of T. drosophilae and an increase in processing time. The search constant Q initially increased and then decreased with declining temperatures. Short-term low-temperature stress negatively impacted the parasitic and searching abilities of T. drosophilae but did not alter its parasitic functional response model. Notably, short-term low-temperature stress had minimal effects on the water content, protein content, and total sugar content of male and female T. drosophilae adults. However, as temperatures decreased, the activities of key enzymes, including GAPDH, SOD, T-AOC, and malondialdehyde (MDA), exhibited an initial increase followed by a decrease. Conversely, the activities of LDH and HOAD decreased, while the activities of CAT and POD increased. Further study on the effect of short-term low temperature on T. drosophilae can provide a research basis for the large-scale production and low-temperature refrigeration technology of T. drosophilae, and provide a scientific basis for its efficient use in the field.
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Affiliation(s)
- Qiang Chen
- College of Plant Protection, Yunnan Agricultural University, State Key Laboratory of Yunnan Biological Resources Protection and Utilization, Kunming 650201, China
| | - Ye Tian
- College of Plant Protection, Yunnan Agricultural University, State Key Laboratory of Yunnan Biological Resources Protection and Utilization, Kunming 650201, China
| | - Jinlong Zhang
- College of Plant Protection, Yunnan Agricultural University, State Key Laboratory of Yunnan Biological Resources Protection and Utilization, Kunming 650201, China
| | - Juan Li
- College of Plant Protection, Yunnan Agricultural University, State Key Laboratory of Yunnan Biological Resources Protection and Utilization, Kunming 650201, China
| | - Hui Ren
- College of Plant Protection, Yunnan Agricultural University, State Key Laboratory of Yunnan Biological Resources Protection and Utilization, Kunming 650201, China
| | - Guohua Chen
- College of Plant Protection, Yunnan Agricultural University, State Key Laboratory of Yunnan Biological Resources Protection and Utilization, Kunming 650201, China
| | - Xiaoming Zhang
- College of Plant Protection, Yunnan Agricultural University, State Key Laboratory of Yunnan Biological Resources Protection and Utilization, Kunming 650201, China
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6
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Gilbert SF. Inter-kingdom communication and the sympoietic way of life. Front Cell Dev Biol 2024; 12:1427798. [PMID: 39071805 PMCID: PMC11275584 DOI: 10.3389/fcell.2024.1427798] [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: 05/04/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024] Open
Abstract
Organisms are now seen as holobionts, consortia of several species that interact metabolically such that they sustain and scaffold each other's existence and propagation. Sympoiesis, the development of the symbiotic relationships that form holobionts, is critical for our understanding the origins and maintenance of biodiversity. Rather than being the read-out of a single genome, development has been found to be sympoietic, based on multigenomic interactions between zygote-derived cells and symbiotic microbes. These symbiotic and sympoietic interactions are predicated on the ability of cells from different kingdoms of life (e.g., bacteria and animals) to communicate with one another and to have their chemical signals interpreted in a manner that facilitates development. Sympoiesis, the creation of an entity by the interactions of other entities, is commonly seen in embryogenesis (e.g., the creation of lenses and retinas through the interaction of brain and epidermal compartments). In holobiont sympoiesis, interactions between partners of different domains of life interact to form organs and biofilms, wherein each of these domains acts as the environment for the other. If evolution is forged by changes in development, and if symbionts are routinely involved in our development, then changes in sympoiesis can constitute an important factor in evolution.
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Affiliation(s)
- Scott F. Gilbert
- Department of Biology, Swarthmore College, Swarthmore, PA, United States
- Evolutionary Phenomics Group, Biotechnology Institute, University of Helsinki, Helsinki, Finland
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7
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Uppal S, Waterworth SC, Nick A, Vogel H, Flórez LV, Kaltenpoth M, Kwan JC. Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576914. [PMID: 39026795 PMCID: PMC11257431 DOI: 10.1101/2024.01.23.576914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In some of the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work in Lagria villosa revealed the dominant genome-eroded symbiont of the genus Burkholderia produces the antifungal compound lagriamide and protects the beetle's eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from seven different host species within Lagriinae from five countries, to unravel the evolutionary history of this symbiotic relationship. In each host species, we detected one dominant genome-eroded Burkholderia symbiont encoding the lagriamide biosynthetic gene cluster (BGC). Surprisingly, however, we did not find evidence for host-symbiont co-diversification, or for a monophyly of the lagriamide-producing symbionts. Instead, our analyses support at least four independent acquisition events of lagriamide-encoding symbionts and subsequent genome erosion in each of these lineages. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide BGC. In conclusion, our results reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by high degree of specificity. They highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.
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Affiliation(s)
- Siddharth Uppal
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, USA
| | - Samantha C. Waterworth
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, USA
- Current address: National Cancer Institute, Frederick, Maryland, USA
| | - Alina Nick
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Heiko Vogel
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Laura V. Flórez
- Department of Plant and Environmental Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Jason C. Kwan
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, USA
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8
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Hanke DM, Wang Y, Dagan T. Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility. Nucleic Acids Res 2024; 52:7049-7062. [PMID: 38808675 PMCID: PMC11229322 DOI: 10.1093/nar/gkae430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/23/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024] Open
Abstract
Evidence for gene non-functionalization due to mutational processes is found in genomes in the form of pseudogenes. Pseudogenes are known to be rare in prokaryote chromosomes, with the exception of lineages that underwent an extreme genome reduction (e.g. obligatory symbionts). Much less is known about the frequency of pseudogenes in prokaryotic plasmids; those are genetic elements that can transfer between cells and may encode beneficial traits for their host. Non-functionalization of plasmid-encoded genes may alter the plasmid characteristics, e.g. mobility, or their effect on the host. Analyzing 10 832 prokaryotic genomes, we find that plasmid genomes are characterized by threefold-higher pseudogene density compared to chromosomes. The majority of plasmid pseudogenes correspond to deteriorated transposable elements. A detailed analysis of enterobacterial plasmids furthermore reveals frequent gene non-functionalization events associated with the loss of plasmid self-transmissibility. Reconstructing the evolution of closely related plasmids reveals that non-functionalization of the conjugation machinery led to the emergence of non-mobilizable plasmid types. Examples are virulence plasmids in Escherichia and Salmonella. Our study highlights non-functionalization of core plasmid mobility functions as one route for the evolution of domesticated plasmids. Pseudogenes in plasmids supply insights into past transitions in plasmid mobility that are akin to transitions in bacterial lifestyle.
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Affiliation(s)
- Dustin M Hanke
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Yiqing Wang
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
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9
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Sosa-Jiménez VM, Kvist S, Manzano-Marín A, Oceguera-Figueroa A. Discovery of a novel symbiotic lineage associated with a hematophagous leech from the genus Haementeria. Microbiol Spectr 2024; 12:e0428623. [PMID: 38842327 PMCID: PMC11218487 DOI: 10.1128/spectrum.04286-23] [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: 12/26/2023] [Accepted: 04/29/2024] [Indexed: 06/07/2024] Open
Abstract
Similarly to other strict blood feeders, leeches from the Haementeria genus (Hirudinida: Glossiphoniidae) have established a symbiotic association with bacteria harbored intracellularly in esophageal bacteriomes. Previous genome sequence analyses of these endosymbionts revealed co-divergence with their hosts, a strong genome reduction, and a simplified metabolism largely dedicated to the production of B vitamins, which are nutrients lacking from a blood diet. 'Candidatus Providencia siddallii' has been identified as the obligate nutritional endosymbiont of a monophyletic clade of Mexican and South American Haementeria spp. However, the Haementeria genus includes a sister clade of congeners from Central and South America, where the presence or absence of the aforementioned symbiont taxon remains unknown. In this work, we report on a novel bacterial endosymbiont found in a representative from this Haementeria clade. We found that this symbiont lineage has evolved from within the Pluralibacter genus, known mainly from clinical but also environmental strains. Similarly to Ca. Providencia siddallii, the Haementeria-associated Pluralibacter symbiont displays clear signs of genome reduction, accompanied by an A+T-biased sequence composition. Genomic analysis of its metabolic potential revealed a retention of pathways related to B vitamin biosynthesis, supporting its role as a nutritional endosymbiont. Finally, comparative genomics of both Haementeria symbiont lineages suggests that an ancient Providencia symbiont was likely replaced by the novel Pluralibacter one, thus constituting the first reported case of nutritional symbiont replacement in a leech without morphological changes in the bacteriome. IMPORTANCE Obligate symbiotic associations with a nutritional base have likely evolved more than once in strict blood-feeding leeches. Unlike those symbioses found in hematophagous arthropods, the nature, identity, and evolutionary history of these remains poorly studied. In this work, we further explored obligate nutritional associations between Haementeria leeches and their microbial symbionts, which led to the unexpected discovery of a novel symbiosis with a member of the Pluralibacter genus. When compared to Providencia siddallii, an obligate nutritional symbiont of other Haementeria leeches, this novel bacterial symbiont shows convergent retention of the metabolic pathways involved in B vitamin biosynthesis. Moreover, the genomic characteristics of this Pluralibacter symbiont suggest a more recent association than that of Pr. siddallii and Haementeria. We conclude that the once-thought stable associations between blood-feeding Glossiphoniidae and their symbionts (i.e., one bacteriome structure, one symbiont lineage) can break down, mirroring symbiont turnover observed in various arthropod lineages.
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Affiliation(s)
- Víctor Manuel Sosa-Jiménez
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autonoma de México, Ciudad de México, Mexico
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Alejandro Manzano-Marín
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alejandro Oceguera-Figueroa
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autonoma de México, Ciudad de México, Mexico
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10
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Henry LP, Fernandez M, Wolf S, Abhyankar V, Ayroles JF. Wolbachia impacts microbiome diversity and fitness-associated traits for Drosophila melanogaster in a seasonally fluctuating environment. Ecol Evol 2024; 14:e70004. [PMID: 39041013 PMCID: PMC11262851 DOI: 10.1002/ece3.70004] [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: 01/15/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 07/24/2024] Open
Abstract
The microbiome contributes to many different host traits, but its role in host adaptation remains enigmatic. The fitness benefits of the microbiome often depend on ecological conditions, but theory suggests that fluctuations in both the microbiome and environment modulate these fitness benefits. Moreover, vertically transmitted bacteria might constrain the ability of both the microbiome and host to respond to changing environments. Drosophila melanogaster provides an excellent system to investigate the impacts of interactions between the microbiome and the environment. To address this question, we created field mesocosms of D. melanogaster undergoing seasonal environmental change with and without the vertically transmitted bacteria, Wolbachia pipientis. Sampling temporal patterns in the microbiome revealed that Wolbachia constrained microbial diversity. Furthermore, Wolbachia and a dominant member of the microbiome, Commensalibacter, were associated with differences in two higher-order fitness traits, starvation resistance and lifespan. Our work here suggests that the interplay between the abiotic context and microbe-microbe interactions may shape key host phenotypes that underlie adaptation to changing environments. We conclude by exploring the consequences of complex interactions between Wolbachia and the microbiome for our understanding of eco-evolutionary processes that shape host-microbiome interactions.
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Affiliation(s)
- Lucas P. Henry
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
- Department of Biology, Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Michael Fernandez
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Scott Wolf
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Varada Abhyankar
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Julien F. Ayroles
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
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11
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Łukasik P, Kolasa MR. With a little help from my friends: the roles of microbial symbionts in insect populations and communities. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230122. [PMID: 38705185 PMCID: PMC11070262 DOI: 10.1098/rstb.2023.0122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/14/2023] [Indexed: 05/07/2024] Open
Abstract
To understand insect abundance, distribution and dynamics, we need to understand the relevant drivers of their populations and communities. While microbial symbionts are known to strongly affect many aspects of insect biology, we lack data on their effects on populations or community processes, or on insects' evolutionary responses at different timescales. How these effects change as the anthropogenic effects on ecosystems intensify is an area of intense research. Recent developments in sequencing and bioinformatics permit cost-effective microbial diversity surveys, tracking symbiont transmission, and identification of functions across insect populations and multi-species communities. In this review, we explore how different functional categories of symbionts can influence insect life-history traits, how these effects could affect insect populations and their interactions with other species, and how they may affect processes and patterns at the level of entire communities. We argue that insect-associated microbes should be considered important drivers of insect response and adaptation to environmental challenges and opportunities. We also outline the emerging approaches for surveying and characterizing insect-associated microbiota at population and community scales. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Michał R. Kolasa
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
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12
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Liang Y, Dikow RB, Su X, Wen J, Ren Z. Comparative genomics of the primary endosymbiont Buchnera aphidicola in aphid hosts and their coevolutionary relationships. BMC Biol 2024; 22:137. [PMID: 38902723 PMCID: PMC11188193 DOI: 10.1186/s12915-024-01934-w] [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: 05/04/2023] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Coevolution between modern aphids and their primary obligate, bacterial endosymbiont, Buchnera aphidicola, has been previously reported at different classification levels based on molecular phylogenetic analyses. However, the Buchnera genome remains poorly understood within the Rhus gall aphids. RESULTS We assembled the complete genome of the endosymbiont Buchnera in 16 aphid samples, representing 13 species in all six genera of Rhus gall aphids by shotgun genome skimming method. We compared the newly assembled genomes with those from GenBank to comprehensively investigate patterns of coevolution between the bacteria Buchnera and their aphid hosts. Buchnera genomes were mostly collinear, and the pan-genome contained 684 genes, in which the core genome contained 256 genes with some lineages having large numbers of tandem gene duplications. There has been substantial gene-loss in each Buchnera lineage. We also reconstructed the phylogeny for Buchnera and their host aphids, respectively, using 72 complete genomes of Buchnera, along with the complete mitochondrial genomes and three nuclear genes of 31 corresponding host aphid accessions. The cophylogenetic test demonstrated significant coevolution between these two partner groups at individual, species, generic, and tribal levels. CONCLUSIONS Buchnera exhibits very high levels of genomic sequence divergence but relative stability in gene order. The relationship between the symbionts Buchnera and its aphid hosts shows a significant coevolutionary pattern and supports complexity of the obligate symbiotic relationship.
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Affiliation(s)
- Yukang Liang
- School of Life Science and Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, 92 Wucheng Rd, Taiyuan Shanxi, 030006, China
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 600 Maryland Avenue SW, Washington, DC, 20024, USA
| | - Xu Su
- School of Geography and Life Science, Qinghai Normal University, 38 Wusixi Road, Xining, 810008, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, MRC-166, Washington, DC, 20013-7012, USA.
| | - Zhumei Ren
- School of Life Science and Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, 92 Wucheng Rd, Taiyuan Shanxi, 030006, China.
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13
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Huang Z, Wang D, Zhou J, He H, Wei C. Segregation of endosymbionts in complex symbiotic system of cicadas providing novel insights into microbial symbioses and evolutionary dynamics of symbiotic organs in sap-feeding insects. Front Zool 2024; 21:15. [PMID: 38863001 PMCID: PMC11165832 DOI: 10.1186/s12983-024-00536-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 06/03/2024] [Indexed: 06/13/2024] Open
Abstract
The most extraordinary systems of symbiosis in insects are found in the suborder Auchenorrhyncha of Hemiptera, which provide unique perspectives for uncovering complicated insect-microbe symbiosis. We investigated symbionts associated with bacteriomes and fat bodies in six cicada species, and compared transmitted cell number ratio of related symbionts in ovaries among species. We reveal that Sulcia and Hodgkinia or a yeast-like fungal symbiont (YLS) are segregated from other host tissues by the bacteriomes in the nymphal stage, then some of them may migrate to other organs (i.e., fat bodies and ovaries) during host development. Particularly, YLS resides together with Sulcia in the "symbiont ball" of each egg and the bacteriomes of young-instar nymphs, but finally migrates to the fat bodies of adults in the majority of Hodgkinia-free cicadas, whereas it resides in both bacteriome sheath and fat bodies of adults in a few other species. The transmitted Sulcia/YLS or Sulcia/Hodgkinia cell number ratio in ovaries varies significantly among species, which could be related to the distribution and/or lineage splitting of symbiont(s). Rickettsia localizes to the nuclei of bacteriomes and fat bodies in some species, but it was not observed to be transmitted to the ovaries, indicating that this symbiont may be acquired from environments or from father to offspring. The considerable difference in the transovarial transmission process of symbionts suggests that cellular mechanisms underlying the symbiont transmission are complex. Our results may provide novel insights into insect-microbe symbiosis.
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Affiliation(s)
- Zhi Huang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Key Laboratory of Integrated Pest Management On Crops in Northwest Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of National Forestry and Grassland Administration for Control of Forest Biological Disasters in Western China, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dandan Wang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Key Laboratory of Integrated Pest Management On Crops in Northwest Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jinrui Zhou
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Key Laboratory of Integrated Pest Management On Crops in Northwest Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hong He
- Key Laboratory of National Forestry and Grassland Administration for Control of Forest Biological Disasters in Western China, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Cong Wei
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Key Laboratory of Integrated Pest Management On Crops in Northwest Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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14
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Bennett GM, Kwak Y, Maynard R. Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again. Genome Biol Evol 2024; 16:evae112. [PMID: 38813885 PMCID: PMC11154151 DOI: 10.1093/gbe/evae112] [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: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution and Genome Biology and Evolution have provided an essential window into how these endosymbiotic interactions have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in Molecular Biology and Evolution and Genome Biology and Evolution, and insights from the field at large. The accumulated work illustrates how endosymbioses provide hosts with novel phenotypes that allow them to transition between adaptive landscapes to access environmental resources. Such endosymbiotic relationships have shaped and reshaped life on Earth. The early serial establishment of mitochondria and chloroplasts through endosymbioses permitted massive upscaling of cellular energetics, multicellularity, and terrestrial planetary greening. These endosymbioses are also the foundation upon which all later ones are built, including everything from land-plant endosymbioses with fungi and bacteria to nutritional endosymbioses found in invertebrate animals. Common evolutionary mechanisms have shaped this broad range of interactions. Endosymbionts generally experience adaptive and stochastic genome streamlining, the extent of which depends on several key factors (e.g. mode of transmission). Hosts, in contrast, adapt complex mechanisms of resource exchange, cellular integration and regulation, and genetic support mechanisms to prop up degraded symbionts. However, there are significant differences between endosymbiotic interactions not only in how partners have evolved with each other but also in the scope of their influence on biological diversity. These differences are important considerations for predicting how endosymbioses will persist and adapt to a changing planet.
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Affiliation(s)
- Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Younghwan Kwak
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Reo Maynard
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
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15
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Mulio SÅ, Zwolińska A, Klejdysz T, Prus‐Frankowska M, Michalik A, Kolasa M, Łukasik P. Limited variation in microbial communities across populations of Macrosteles leafhoppers (Hemiptera: Cicadellidae). ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13279. [PMID: 38855918 PMCID: PMC11163331 DOI: 10.1111/1758-2229.13279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/26/2024] [Indexed: 06/11/2024]
Abstract
Microbial symbionts play crucial roles in insect biology, yet their diversity, distribution, and temporal dynamics across host populations remain poorly understood. In this study, we investigated the spatio-temporal distribution of bacterial symbionts within the widely distributed and economically significant leafhopper genus Macrosteles, with a focus on Macrosteles laevis. Using host and symbiont marker gene amplicon sequencing, we explored the intricate relationships between these insects and their microbial partners. Our analysis of the cytochrome oxidase subunit I (COI) gene data revealed several intriguing findings. First, there was no strong genetic differentiation across M. laevis populations, suggesting gene flow among them. Second, we observed significant levels of heteroplasmy, indicating the presence of multiple mitochondrial haplotypes within individuals. Third, parasitoid infections were prevalent, highlighting the complex ecological interactions involving leafhoppers. The 16S rRNA data confirmed the universal presence of ancient nutritional endosymbionts-Sulcia and Nasuia-in M. laevis. Additionally, we found a high prevalence of Arsenophonus, another common symbiont. Interestingly, unlike most previously studied species, M. laevis exhibited only occasional cases of infection with known facultative endosymbionts and other bacteria. Notably, there was no significant variation in symbiont prevalence across different populations or among sampling years within the same population. Comparatively, facultative endosymbionts such as Rickettsia, Wolbachia, Cardinium and Lariskella were more common in other Macrosteles species. These findings underscore the importance of considering both host and symbiont dynamics when studying microbial associations. By simultaneously characterizing host and symbiont marker gene amplicons in large insect collections, we gain valuable insights into the intricate interplay between insects and their microbial partners. Understanding these dynamics contributes to our broader comprehension of host-microbe interactions in natural ecosystems.
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Affiliation(s)
- Sandra Åhlén Mulio
- Institute of Environmental Sciences, Faculty of BiologyJagiellonian UniversityKrakówPoland
| | - Agnieszka Zwolińska
- Department of Plant Physiology, Faculty of BiologyAdam Mickiewicz UniversityPoznanPoland
| | - Tomasz Klejdysz
- Institute of Plant Protection – National Research InstituteResearch Centre for Registration of AgrochemicalsPoznańPoland
| | - Monika Prus‐Frankowska
- Institute of Environmental Sciences, Faculty of BiologyJagiellonian UniversityKrakówPoland
| | - Anna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of BiologyJagiellonian UniversityKrakówPoland
| | - Michał Kolasa
- Institute of Environmental Sciences, Faculty of BiologyJagiellonian UniversityKrakówPoland
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of BiologyJagiellonian UniversityKrakówPoland
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16
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Zhang B, Xiao L, Lyu L, Zhao F, Miao M. Exploring the landscape of symbiotic diversity and distribution in unicellular ciliated protists. MICROBIOME 2024; 12:96. [PMID: 38790063 PMCID: PMC11127453 DOI: 10.1186/s40168-024-01809-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND The eukaryotic-bacterial symbiotic system plays an important role in various physiological, developmental, and evolutionary processes. However, our current understanding is largely limited to multicellular eukaryotes without adequate consideration of diverse unicellular protists, including ciliates. RESULTS To investigate the bacterial profiles associated with unicellular organisms, we collected 246 ciliate samples spanning the entire Ciliophora phylum and conducted single-cell based metagenome sequencing. This effort has yielded the most extensive collection of bacteria linked to unicellular protists to date. From this dataset, we identified 883 bacterial species capable of cohabiting with ciliates, unveiling the genomes of 116 novel bacterial cohabitants along with 7 novel archaeal cohabitants. Highlighting the intimate relationship between ciliates and their cohabitants, our study unveiled that over 90% of ciliates coexist with bacteria, with individual hosts fostering symbiotic relationships with multiple bacteria concurrently, resulting in the observation of seven distinct symbiotic patterns among bacteria. Our exploration of symbiotic mechanisms revealed the impact of host digestion on the intracellular diversity of cohabitants. Additionally, we identified the presence of eukaryotic-like proteins in bacteria as a potential contributing factor to their resistance against host digestion, thereby expanding their potential host range. CONCLUSIONS As the first large-scale analysis of prokaryotic associations with ciliate protists, this study provides a valuable resource for future research on eukaryotic-bacterial symbioses. Video Abstract.
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Affiliation(s)
- Bing Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Liwen Xiao
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liping Lyu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Fangqing Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
| | - Miao Miao
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
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17
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Renoz F, Parisot N, Baa-Puyoulet P, Gerlin L, Fakhour S, Charles H, Hance T, Calevro F. PacBio Hi-Fi genome assembly of Sipha maydis, a model for the study of multipartite mutualism in insects. Sci Data 2024; 11:450. [PMID: 38704391 PMCID: PMC11069519 DOI: 10.1038/s41597-024-03297-x] [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: 12/17/2023] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
Dependence on multiple nutritional endosymbionts has evolved repeatedly in insects feeding on unbalanced diets. However, reference genomes for species hosting multi-symbiotic nutritional systems are lacking, even though they are essential for deciphering the processes governing cooperative life between insects and anatomically integrated symbionts. The cereal aphid Sipha maydis is a promising model for addressing these issues, as it has evolved a nutritional dependence on two bacterial endosymbionts that complement each other. In this study, we used PacBio High fidelity (HiFi) long-read sequencing to generate a highly contiguous genome assembly of S. maydis with a length of 410 Mb, 3,570 contigs with a contig N50 length of 187 kb, and BUSCO completeness of 95.5%. We identified 117 Mb of repetitive sequences, accounting for 29% of the genome assembly, and predicted 24,453 protein-coding genes, of which 2,541 were predicted enzymes included in an integrated metabolic network with the two aphid-associated endosymbionts. These resources provide valuable genetic and metabolic information for understanding the evolution and functioning of multi-symbiotic systems in insects.
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Affiliation(s)
- François Renoz
- Biodiversity Research Centre, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, 1348, Belgium.
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR203, Villeurbanne, F-69621, France.
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8634, Japan.
| | - Nicolas Parisot
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR203, Villeurbanne, F-69621, France.
| | | | - Léo Gerlin
- Univ Lyon, INRAE, INSA Lyon, BF2I, UMR203, Villeurbanne, F-69621, France
| | - Samir Fakhour
- Biodiversity Research Centre, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, 1348, Belgium
- Department of Plant Protection, National Institute for Agricultural Research (INRA), Béni-Mellal, 23000, Morocco
| | - Hubert Charles
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR203, Villeurbanne, F-69621, France
| | - Thierry Hance
- Biodiversity Research Centre, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, 1348, Belgium
| | - Federica Calevro
- Univ Lyon, INRAE, INSA Lyon, BF2I, UMR203, Villeurbanne, F-69621, France.
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18
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García-Lozano M, Henzler C, Porras MÁG, Pons I, Berasategui A, Lanz C, Budde H, Oguchi K, Matsuura Y, Pauchet Y, Goffredi S, Fukatsu T, Windsor D, Salem H. Paleocene origin of a streamlined digestive symbiosis in leaf beetles. Curr Biol 2024; 34:1621-1634.e9. [PMID: 38377997 DOI: 10.1016/j.cub.2024.01.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024]
Abstract
Timing the acquisition of a beneficial microbe relative to the evolutionary history of its host can shed light on the adaptive impact of a partnership. Here, we investigated the onset and molecular evolution of an obligate symbiosis between Cassidinae leaf beetles and Candidatus Stammera capleta, a γ-proteobacterium. Residing extracellularly within foregut symbiotic organs, Stammera upgrades the digestive physiology of its host by supplementing plant cell wall-degrading enzymes. We observe that Stammera is a shared symbiont across tortoise and hispine beetles that collectively comprise the Cassidinae subfamily, despite differences in their folivorous habits. In contrast to its transcriptional profile during vertical transmission, Stammera elevates the expression of genes encoding digestive enzymes while in the foregut symbiotic organs, matching the nutritional requirements of its host. Despite the widespread distribution of Stammera across Cassidinae beetles, symbiont acquisition during the Paleocene (∼62 mya) did not coincide with the origin of the subfamily. Early diverging lineages lack the symbiont and the specialized organs that house it. Reconstructing the ancestral state of host-beneficial factors revealed that Stammera encoded three digestive enzymes at the onset of symbiosis, including polygalacturonase-a pectinase that is universally shared. Although non-symbiotic cassidines encode polygalacturonase endogenously, their repertoire of plant cell wall-degrading enzymes is more limited compared with symbiotic beetles supplemented with digestive enzymes from Stammera. Highlighting the potential impact of a symbiotic condition and an upgraded metabolic potential, Stammera-harboring beetles exploit a greater variety of plants and are more speciose compared with non-symbiotic members of the Cassidinae.
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Affiliation(s)
- Marleny García-Lozano
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Christine Henzler
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | | | - Inès Pons
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Aileen Berasategui
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany; Amsterdam Institute for Life and Environment, Vrije Universiteit, Amsterdam 1081 HV, the Netherlands
| | - Christa Lanz
- Genome Center, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Heike Budde
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Kohei Oguchi
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan; Misaki Marine Biological Station, The University of Tokyo, Miura 238-0225, Japan
| | - Yu Matsuura
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Yannick Pauchet
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Shana Goffredi
- Department of Biology, Occidental College, Los Angeles, CA 90041, USA
| | - Takema Fukatsu
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Donald Windsor
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
| | - Hassan Salem
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany; Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama.
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19
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Acar T, Moreau S, Jardinaud MF, Houdinet G, Maviane-Macia F, De Meyer F, Hoste B, Leroux O, Coen O, Le Ru A, Peeters N, Carlier A. The association between Dioscorea sansibarensis and Orrella dioscoreae as a model for hereditary leaf symbiosis. PLoS One 2024; 19:e0302377. [PMID: 38648204 PMCID: PMC11034651 DOI: 10.1371/journal.pone.0302377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Hereditary, or vertically-transmitted, symbioses affect a large number of animal species and some plants. The precise mechanisms underlying transmission of functions of these associations are often difficult to describe, due to the difficulty in separating the symbiotic partners. This is especially the case for plant-bacteria hereditary symbioses, which lack experimentally tractable model systems. Here, we demonstrate the potential of the leaf symbiosis between the wild yam Dioscorea sansibarensis and the bacterium Orrella dioscoreae (O. dioscoreae) as a model system for hereditary symbiosis. O. dioscoreae is easy to grow and genetically manipulate, which is unusual for hereditary symbionts. These properties allowed us to design an effective antimicrobial treatment to rid plants of bacteria and generate whole aposymbiotic plants, which can later be re-inoculated with bacterial cultures. Aposymbiotic plants did not differ morphologically from symbiotic plants and the leaf forerunner tip containing the symbiotic glands formed normally even in the absence of bacteria, but microscopic differences between symbiotic and aposymbiotic glands highlight the influence of bacteria on the development of trichomes and secretion of mucilage. This is to our knowledge the first leaf symbiosis where both host and symbiont can be grown separately and where the symbiont can be genetically altered and reintroduced to the host.
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Affiliation(s)
- Tessa Acar
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
- Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - Sandra Moreau
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | | | | | | | | | - Bart Hoste
- Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | | | - Olivier Coen
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Aurélie Le Ru
- Plateforme Imagerie TRI-FRAIB, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Nemo Peeters
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Aurelien Carlier
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
- Laboratory of Microbiology, Ghent University, Ghent, Belgium
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20
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Vasquez YM, Li Z, Xue AZ, Bennett GM. Chromosome-level genome assembly of the aster leafhopper (Macrosteles quadrilineatus) reveals the role of environment and microbial symbiosis in shaping pest insect genome evolution. Mol Ecol Resour 2024; 24:e13919. [PMID: 38146900 DOI: 10.1111/1755-0998.13919] [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: 08/22/2023] [Revised: 11/12/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
Leafhoppers comprise over 20,000 plant-sap feeding species, many of which are important agricultural pests. Most species rely on two ancestral bacterial symbionts, Sulcia and Nasuia, for essential nutrition lacking in their phloem and xylem plant sap diets. To understand how pest leafhopper genomes evolve and are shaped by microbial symbioses, we completed a chromosomal-level assembly of the aster leafhopper's genome (ALF; Macrosteles quadrilineatus). We compared ALF's genome to three other pest leafhoppers, Nephotettix cincticeps, Homalodisca vitripennis, and Empoasca onukii, which have distinct ecologies and symbiotic relationships. Despite diverging ~155 million years ago, leafhoppers have high levels of chromosomal synteny and gene family conservation. Conserved genes include those involved in plant chemical detoxification, resistance to various insecticides, and defence against environmental stress. Positive selection acting upon these genes further points to ongoing adaptive evolution in response to agricultural environments. In relation to leafhoppers' general dependence on symbionts, species that retain the ancestral symbiont, Sulcia, displayed gene enrichment of metabolic processes in their genomes. Leafhoppers with both Sulcia and its ancient partner, Nasuia, showed genomic enrichment in genes related to microbial population regulation and immune responses. Finally, horizontally transferred genes (HTGs) associated with symbiont support of Sulcia and Nasuia are only observed in leafhoppers that maintain symbionts. In contrast, HTGs involved in non-symbiotic functions are conserved across all species. The high-quality ALF genome provides deep insights into how host ecology and symbioses shape genome evolution and a wealth of genetic resources for pest control targets.
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Affiliation(s)
- Yumary M Vasquez
- Department of Life and Environmental Sciences, University of California, Merced, Merced, California, USA
| | - Zheng Li
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Allen Z Xue
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, Merced, California, USA
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21
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Brockhurst MA, Cameron DD, Beckerman AP. Fitness trade-offs and the origins of endosymbiosis. PLoS Biol 2024; 22:e3002580. [PMID: 38607979 PMCID: PMC11014431 DOI: 10.1371/journal.pbio.3002580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024] Open
Abstract
Endosymbiosis drives evolutionary innovation and underpins the function of diverse ecosystems. The mechanistic origins of symbioses, however, remain unclear, in part because early evolutionary events are obscured by subsequent evolution and genetic drift. This Essay highlights how experimental studies of facultative, host-switched, and synthetic symbioses are revealing the important role of fitness trade-offs between within-host and free-living niches during the early-stage evolution of new symbiotic associations. The mutational targets underpinning such trade-offs are commonly regulatory genes, such that single mutations have major phenotypic effects on multiple traits, thus enabling and reinforcing the transition to a symbiotic lifestyle.
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Affiliation(s)
- Michael A. Brockhurst
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Duncan D. Cameron
- Department of Environmental and Earth Sciences, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
| | - Andrew P. Beckerman
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, United Kingdom
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22
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Kempraj V, Auth J, Cha DH, Mason CJ. Impact of Larval Food Source on the Stability of the Bactrocera dorsalis Microbiome. MICROBIAL ECOLOGY 2024; 87:46. [PMID: 38407587 PMCID: PMC10896919 DOI: 10.1007/s00248-024-02352-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/27/2024]
Abstract
Bacterial symbionts are crucial to the biology of Bactrocera dorsalis. With larval diet (fruit host) being a key factor that determines microbiome composition and with B. dorsalis using more than 400 fruits as hosts, it is unclear if certain bacterial symbionts are preserved and are passed on to B. dorsalis progenies despite changes in larval diet. Here, we conducted a fly rearing experiment to characterize diet-induced changes in the microbiome of female B. dorsalis. In order to explicitly investigate the impacts of larval diet on the microbiome, including potential stable bacterial constituents of B. dorsalis, we performed 16S rRNA sequencing on the gut tissues of teneral female flies reared from four different host fruits (guava, mango, papaya, and rose apple) infested using a single cohort of wild B. dorsalis that emerged from tropical almond (mother flies). Although B. dorsalis-associated microbiota were predominantly shaped by the larval diet, some major bacterial species from the mother flies were retained in progenies raised on different larval diets. With some variation, Klebsiella (ASV 1 and 2), Morganella (ASV 3), and Providencia (ASV 6) were the major bacterial symbionts that were stable and made up 0.1-80% of the gut and ovipositor microbiome of female teneral flies reared on different host fruits. Our results suggest that certain groups of bacteria are stably associated with female B. dorsalis across larval diets. These findings provide a basis for unexplored research on symbiotic bacterial function in B. dorsalis and may aid in the development of novel management techniques against this devastating pest of horticultural importance.
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Affiliation(s)
- Vivek Kempraj
- USDA-ARS, Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye US Pacific Basin Agriculture Research Center, Hilo, HI, 96720, USA
- College of Tropical Agriculture and Human Resources, Komohana Research and Extension Center, University of Hawai'i, Hilo, HI, 96720, USA
| | - Jean Auth
- USDA-ARS, Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K Inouye US Pacific Basin Agriculture Research Center, Hilo, HI, 96720, USA
| | - Dong H Cha
- USDA-ARS, Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye US Pacific Basin Agriculture Research Center, Hilo, HI, 96720, USA.
| | - Charles J Mason
- USDA-ARS, Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K Inouye US Pacific Basin Agriculture Research Center, Hilo, HI, 96720, USA.
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23
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Hammer TJ. Why do hosts malfunction without microbes? Missing benefits versus evolutionary addiction. Trends Microbiol 2024; 32:132-141. [PMID: 37652785 DOI: 10.1016/j.tim.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 09/02/2023]
Abstract
Microbes are widely recognized to be vital to host health. This new consensus rests, in part, on experiments showing how hosts malfunction when microbes are removed. More and more microbial dependencies are being discovered, even in fundamental processes such as development, immunity, physiology, and behavior. But why do they exist? The default explanation is that microbes are beneficial; when hosts lose microbes, they also lose benefits. Here I call attention to evolutionary addiction, whereby a host trait evolves a need for microbes without having been improved by them. Evolutionary addiction should be considered when interpreting microbe-removal experiments, as it is a distinct and potentially common process. Further, it may have unique implications for the evolution and stability of host-microbe interactions.
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Affiliation(s)
- Tobin J Hammer
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA.
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24
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Feitosa-Junior OR, Lubbe A, Kosina SM, Martins-Junior J, Barbosa D, Baccari C, Zaini PA, Bowen BP, Northen TR, Lindow SE, da Silva AM. The Exometabolome of Xylella fastidiosa in Contact with Paraburkholderia phytofirmans Supernatant Reveals Changes in Nicotinamide, Amino Acids, Biotin, and Plant Hormones. Metabolites 2024; 14:82. [PMID: 38392974 PMCID: PMC10890622 DOI: 10.3390/metabo14020082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/25/2024] Open
Abstract
Microbial competition within plant tissues affects invading pathogens' fitness. Metabolomics is a great tool for studying their biochemical interactions by identifying accumulated metabolites. Xylella fastidiosa, a Gram-negative bacterium causing Pierce's disease (PD) in grapevines, secretes various virulence factors including cell wall-degrading enzymes, adhesion proteins, and quorum-sensing molecules. These factors, along with outer membrane vesicles, contribute to its pathogenicity. Previous studies demonstrated that co-inoculating X. fastidiosa with the Paraburkholderia phytofirmans strain PsJN suppressed PD symptoms. Here, we further investigated the interaction between the phytopathogen and the endophyte by analyzing the exometabolome of wild-type X. fastidiosa and a diffusible signaling factor (DSF) mutant lacking quorum sensing, cultivated with 20% P. phytofirmans spent media. Liquid chromatography-mass spectrometry (LC-MS) and the Method for Metabolite Annotation and Gene Integration (MAGI) were used to detect and map metabolites to genomes, revealing a total of 121 metabolites, of which 25 were further investigated. These metabolites potentially relate to host adaptation, virulence, and pathogenicity. Notably, this study presents the first comprehensive profile of X. fastidiosa in the presence of a P. phytofirmans spent media. The results highlight that P. phytofirmans and the absence of functional quorum sensing affect the ratios of glutamine to glutamate (Gln:Glu) in X. fastidiosa. Additionally, two compounds with plant metabolism and growth properties, 2-aminoisobutyric acid and gibberellic acid, were downregulated when X. fastidiosa interacted with P. phytofirmans. These findings suggest that P. phytofirmans-mediated disease suppression involves modulation of the exometabolome of X. fastidiosa, impacting plant immunity.
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Affiliation(s)
- Oseias R Feitosa-Junior
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, SP, Brazil
- The DOE Joint Genome Institute, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Andrea Lubbe
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joaquim Martins-Junior
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, SP, Brazil
| | - Deibs Barbosa
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, SP, Brazil
| | - Clelia Baccari
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Paulo A Zaini
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Benjamin P Bowen
- The DOE Joint Genome Institute, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Trent R Northen
- The DOE Joint Genome Institute, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Steven E Lindow
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Aline M da Silva
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, SP, Brazil
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25
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Song Q, Zhao F, Hou L, Miao M. Cellular interactions and evolutionary origins of endosymbiotic relationships with ciliates. THE ISME JOURNAL 2024; 18:wrae117. [PMID: 38916437 PMCID: PMC11253213 DOI: 10.1093/ismejo/wrae117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/26/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
As unicellular predators, ciliates engage in close associations with diverse microbes, laying the foundation for the establishment of endosymbiosis. Originally heterotrophic, ciliates demonstrate the ability to acquire phototrophy by phagocytizing unicellular algae or by sequestering algal plastids. This adaptation enables them to gain photosynthate and develop resistance to unfavorable environmental conditions. The integration of acquired phototrophy with intrinsic phagotrophy results in a trophic mode known as mixotrophy. Additionally, ciliates can harbor thousands of bacteria in various intracellular regions, including the cytoplasm and nucleus, exhibiting species specificity. Under prolonged and specific selective pressure within hosts, bacterial endosymbionts evolve unique lifestyles and undergo particular reductions in metabolic activities. Investigating the research advancements in various endosymbiotic cases within ciliates will contribute to elucidate patterns in cellular interaction and unravel the evolutionary origins of complex traits.
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Affiliation(s)
- Qi Song
- Medical School, University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Huairou District, Beijing 100049, China
| | - Fangqing Zhao
- Medical School, University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Huairou District, Beijing 100049, China
- Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, No. 1 Xiangshan Road, Hangzhou 310024, China
| | - Lina Hou
- Medical School, University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Huairou District, Beijing 100049, China
| | - Miao Miao
- Medical School, University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Huairou District, Beijing 100049, China
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26
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Bing XL, Liang ZJ, Tian J, Gong X, Huang SQ, Chen J, Hong XY. The influence of Acetobacter pomorum bacteria on the developmental progression of Drosophila suzukii via gluconic acid secretion. Mol Ecol 2024; 33:e17202. [PMID: 37947376 DOI: 10.1111/mec.17202] [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: 10/19/2022] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Insects are rich in various microorganisms, which play diverse roles in affecting host biology. Although most Drosophila species prefer rotten fruits, the agricultural pest Drosophila suzukii attacks ripening fruits before they are harvested. We have reported that the microbiota has positive and negative impacts on the agricultural pest D. suzukii on nutrient-poor and -rich diets, respectively. On nutrient-poor diets, microbes provide protein to facilitate larval development. But how they impede D. suzukii development on nutrient-rich diets is unknown. Here we report that Acetobacter pomorum (Apo), a commensal bacterium in many Drosophila species and rotting fruit, has several detrimental effects in D. suzukii. Feeding D. suzukii larvae nutrient-rich diets containing live Apo significantly delayed larval development and reduced the body weight of emerged adults. Apo induced larval immune responses and downregulated genes of digestion and juvenile hormone metabolism. Knockdown of these genes in germ-free larvae reproduced Apo-like weakened phenotypes. Apo was confirmed to secrete substantial amounts of gluconic acid. Adding gluconic acid to the D. suzukii larval diet hindered larval growth and decreased adult body weight. Moreover, the dose of gluconic acid that adversely affected D. suzukii did not negatively affect Drosophila melanogaster, suggesting that D. suzukii is less tolerant to acid than D. melanogaster. Taken together, these findings indicate that D. suzukii is negatively affected by gluconic acid, which may explain why it prefers ripening fruit over Apo-rich rotting fruit. These results show an insect's tolerance to microbes can influence its ecological niche.
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Affiliation(s)
- Xiao-Li Bing
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zi-Jian Liang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jia Tian
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xue Gong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Shao-Qiu Huang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jie Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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27
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Giovannini M, Petroni G, Castelli M. Novel evolutionary insights on the interactions of the Holosporales (Alphaproteobacteria) with eukaryotic hosts from comparative genomics. Environ Microbiol 2024; 26:e16562. [PMID: 38173299 DOI: 10.1111/1462-2920.16562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024]
Abstract
Holosporales are an alphaproteobacterial order engaging in obligate and complex associations with eukaryotes, in particular protists. The functional and evolutionary features of those interactions are still largely undisclosed. Here, we sequenced the genomes of two members of the species Bealeia paramacronuclearis (Holosporales, Holosporaceae) intracellularly associated with the ciliate protist Paramecium, which resulted in high correspondence. Consistent with the short-branched early-divergent phylogenetic position, Bealeia presents a larger functional repertoire than other Holosporaceae, comparable to those of other Holosporales families, particularly for energy metabolism and motility. Our analyses indicate that different Holosporales likely experienced at least partly autonomous genome reduction and adaptation to host interactions, for example regarding dependence on host biotin driven by multiple independent horizontal acquisitions of transporters. Among Alphaproteobacteria, this is reminiscent of the convergently evolved Rickettsiales, which however appear more diverse, possibly due to a probably more ancient origin. We identified in Bealeia and other Holosporales the plasmid-encoded putative genetic determinants of R-bodies, which may be involved in a killer trait towards symbiont-free hosts. While it is not clear whether these genes are ancestral or recently horizontally acquired, an intriguing and peculiar role of R-bodies is suggested in the evolution of the interactions of multiple Holosporales with their hosts.
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Affiliation(s)
| | | | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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28
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Michalik A, Bauer E, Szklarzewicz T, Kaltenpoth M. Nutrient supplementation by genome-eroded Burkholderia symbionts of scale insects. THE ISME JOURNAL 2023; 17:2221-2231. [PMID: 37833524 PMCID: PMC10689751 DOI: 10.1038/s41396-023-01528-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
Hemipterans are known as hosts to bacterial or fungal symbionts that supplement their unbalanced diet with essential nutrients. Among them, scale insects (Coccomorpha) are characterized by a particularly large diversity of symbiotic systems. Here, using microscopic and genomic approaches, we functionally characterized the symbionts of two scale insects belonging to the Eriococcidae family, Acanthococcus aceris and Gossyparia spuria. These species host Burkholderia bacteria that are localized in the cytoplasm of the fat body cells. Metagenome sequencing revealed very similar and highly reduced genomes (<900KBp) with a low GC content (~38%), making them the smallest and most AT-biased Burkholderia genomes yet sequenced. In their eroded genomes, both symbionts retain biosynthetic pathways for the essential amino acids leucine, isoleucine, valine, threonine, lysine, arginine, histidine, phenylalanine, and precursors for the semi-essential amino acid tyrosine, as well as the cobalamin-dependent methionine synthase MetH. A tryptophan biosynthesis pathway is conserved in the symbiont of G. spuria, but appeared pseudogenized in A. aceris, suggesting differential availability of tryptophan in the two host species' diets. In addition to the pathways for essential amino acid biosynthesis, both symbionts maintain biosynthetic pathways for multiple cofactors, including riboflavin, cobalamin, thiamine, and folate. The localization of Burkholderia symbionts and their genome traits indicate that the symbiosis between Burkholderia and eriococcids is younger than other hemipteran symbioses, but is functionally convergent. Our results add to the emerging picture of dynamic symbiont replacements in sap-sucking Hemiptera and highlight Burkholderia as widespread and versatile intra- and extracellular symbionts of animals, plants, and fungi.
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Affiliation(s)
- Anna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland.
| | - Eugen Bauer
- Department for Evolutionary Ecology, Institute for Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Teresa Szklarzewicz
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology, Institute for Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany.
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany.
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29
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Whittle M, Bonsall MB, Barreaux AMG, Ponton F, English S. A theoretical model for host-controlled regulation of symbiont density. J Evol Biol 2023; 36:1731-1744. [PMID: 37955420 DOI: 10.1111/jeb.14246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
There is growing empirical evidence that animal hosts actively control the density of their mutualistic symbionts according to their requirements. Such active regulation can be facilitated by compartmentalization of symbionts within host tissues, which confers a high degree of control of the symbiosis to the host. Here, we build a general theoretical framework to predict the underlying ecological drivers and evolutionary consequences of host-controlled endosymbiont density regulation for a mutually obligate association between a host and a compartmentalized, vertically transmitted symbiont. Building on the assumption that the costs and benefits of hosting a symbiont population increase with symbiont density, we use state-dependent dynamic programming to determine an optimal strategy for the host, i.e., that which maximizes host fitness, when regulating the density of symbionts. Simulations of active host-controlled regulation governed by the optimal strategy predict that the density of the symbiont should converge to a constant level during host development, and following perturbation. However, a similar trend also emerges from alternative strategies of symbiont regulation. The strategy which maximizes host fitness also promotes symbiont fitness compared to alternative strategies, suggesting that active host-controlled regulation of symbiont density could be adaptive for the symbiont as well as the host. Adaptation of the framework allowed the dynamics of symbiont density to be predicted for other host-symbiont ecologies, such as for non-essential symbionts, demonstrating the versatility of this modelling approach.
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Affiliation(s)
- Mathilda Whittle
- School of Biological Sciences, University of Bristol, Bristol, UK
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Michael B Bonsall
- Department of Biology, University of Oxford, Oxford, UK
- St Peter's College, Oxford, UK
| | - Antoine M G Barreaux
- UMR INTERTRYP, CIRAD, Montpellier, France
- Animal Health Theme, ICIPE, Nairobi, Kenya
| | - Fleur Ponton
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Sinead English
- School of Biological Sciences, University of Bristol, Bristol, UK
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30
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Gao X, Hu F, Cui H, Zhu X, Wang L, Zhang K, Li D, Ji J, Luo J, Cui J. Glyphosate decreases survival, increases fecundity, and alters the microbiome of the natural predator Harmonia axyridis (ladybird beetle). ENVIRONMENTAL RESEARCH 2023; 238:117174. [PMID: 37739152 DOI: 10.1016/j.envres.2023.117174] [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: 07/06/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023]
Abstract
Glyphosate is a widely-used herbicide that shows toxicity to non-target organisms. The predatory natural enemy Harmonia axyridis may ingest glyphosate present in pollen and aphid prey. The present study characterized the responses of adult H. axyridis to environmentally relevant concentrations of glyphosate (5, 10, and 20 mg/L) for one or five days. There were no obvious effects on adult H. axyridis survival rates or fecundity in response to 5 or 10 mg/L glyphosate. However, exposure to 20 mg/L glyphosate significantly reduced the survival rate and increased fecundity. Analysis of the adult H. axyridis microbiota with 16S rRNA sequencing demonstrated changes in the relative and/or total abundance of specific taxa, including Serratia, Enterobacter, Staphylococcus, and Hafnia-Obesumbacterium. These changes in symbiotic bacterial abundance may have led to changes in survival rates or fecundity of this beetle. This is the first report of herbicide-induced stimulation of fecundity in a non-target predatory natural enemy, reflecting potentially unexpected risks of glyphosate exposure in adult H. axyridis. Although glyphosate resistant crops have been widely planted, the results of this study indicate a need to strengthen glyphosate management to prevent over-use, which could cause glyphosate toxicity and threaten environmental and human health.
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Affiliation(s)
- Xueke Gao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Fangmei Hu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China; Zhongjian township People's Government of Qianxi county, Bijie, 551500, Guizhou, China
| | - Huanfei Cui
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiangzhen Zhu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Li Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Kaixin Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Dongyang Li
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Jichao Ji
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Junyu Luo
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Jinjie Cui
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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31
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Valdivia C, Newton JA, von Beeren C, O'Donnell S, Kronauer DJC, Russell JA, Łukasik P. Microbial symbionts are shared between ants and their associated beetles. Environ Microbiol 2023; 25:3466-3483. [PMID: 37968789 DOI: 10.1111/1462-2920.16544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023]
Abstract
The transmission of microbial symbionts across animal species could strongly affect their biology and evolution, but our understanding of transmission patterns and dynamics is limited. Army ants (Formicidae: Dorylinae) and their hundreds of closely associated insect guest species (myrmecophiles) can provide unique insights into interspecific microbial symbiont sharing. Here, we compared the microbiota of workers and larvae of the army ant Eciton burchellii with those of 13 myrmecophile beetle species using 16S rRNA amplicon sequencing. We found that the previously characterized specialized bacterial symbionts of army ant workers were largely absent from ant larvae and myrmecophiles, whose microbial communities were usually dominated by Rickettsia, Wolbachia, Rickettsiella and/or Weissella. Strikingly, different species of myrmecophiles and ant larvae often shared identical 16S rRNA genotypes of these common bacteria. Protein-coding gene sequences confirmed the close relationship of Weissella strains colonizing army ant larvae, some workers and several myrmecophile species. Unexpectedly, these strains were also similar to strains infecting dissimilar animals inhabiting very different habitats: trout and whales. Together, our data show that closely interacting species can share much of their microbiota, and some versatile microbial species can inhabit and possibly transmit across a diverse range of hosts and environments.
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Affiliation(s)
- Catalina Valdivia
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Justin A Newton
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Christoph von Beeren
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York, USA
| | - Sean O'Donnell
- Department of Biodiversity, Earth & Environmental Science, Drexel University, Philadelphia, Pennsylvania, USA
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, New York, New York, USA
| | - Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
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Kolasa M, Kajtoch Ł, Michalik A, Maryańska-Nadachowska A, Łukasik P. Till evolution do us part: The diversity of symbiotic associations across populations of Philaenus spittlebugs. Environ Microbiol 2023; 25:2431-2446. [PMID: 37525959 DOI: 10.1111/1462-2920.16473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 07/15/2023] [Indexed: 08/02/2023]
Abstract
Symbiotic bacteria have played crucial roles in the evolution of sap-feeding insects and can strongly affect host function. However, their diversity and distribution within species are not well understood; we do not know to what extent environmental factors or associations with other species may affect microbial community profiles. We addressed this question in Philaenus spittlebugs by surveying both insect and bacterial marker gene amplicons across multiple host populations. Host mitochondrial sequence data confirmed morphology-based identification of six species and revealed two divergent clades of Philaenus spumarius. All of them hosted the primary symbiont Sulcia that was almost always accompanied by Sodalis. Interestingly, populations and individuals often differed in the presence of Sodalis sequence variants, suggestive of intra-genome 16S rRNA variant polymorphism combined with rapid genome evolution and/or recent additional infections or replacements of the co-primary symbiont. The prevalence of facultative endosymbionts, including Wolbachia, Rickettsia, and Spiroplasma, varied among populations. Notably, cytochrome I oxidase (COI) amplicon data also showed that nearly a quarter of P. spumarius were infected by parasitoid flies (Verralia aucta). One of the Wolbachia operational taxonomic units (OTUs) was exclusively present in Verralia-parasitized specimens, suggestive of parasitoids as their source and highlighting the utility of host gene amplicon sequencing in microbiome studies.
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Affiliation(s)
- Michał Kolasa
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Krakow, Poland
| | - Łukasz Kajtoch
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Krakow, Poland
| | - Anna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | | | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
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Martin Říhová J, Gupta S, Darby AC, Nováková E, Hypša V. Arsenophonus symbiosis with louse flies: multiple origins, coevolutionary dynamics, and metabolic significance. mSystems 2023; 8:e0070623. [PMID: 37750682 PMCID: PMC10654098 DOI: 10.1128/msystems.00706-23] [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: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Insects that live exclusively on vertebrate blood utilize symbiotic bacteria as a source of essential compounds, e.g., B vitamins. In louse flies, the most frequent symbiont originated in genus Arsenophonus, known from a wide range of insects. Here, we analyze genomic traits, phylogenetic origins, and metabolic capacities of 11 Arsenophonus strains associated with louse flies. We show that in louse flies, Arsenophonus established symbiosis in at least four independent events, reaching different stages of symbiogenesis. This allowed for comparative genomic analysis, including convergence of metabolic capacities. The significance of the results is twofold. First, based on a comparison of independently originated Arsenophonus symbioses, it determines the importance of individual B vitamins for the insect host. This expands our theoretical insight into insect-bacteria symbiosis. The second outcome is of methodological significance. We show that the comparative approach reveals artifacts that would be difficult to identify based on a single-genome analysis.
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Affiliation(s)
- Jana Martin Říhová
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Shruti Gupta
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Alistair C. Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Eva Nováková
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
- Institute of Parasitology, Biology Centre, ASCR, v.v.i., České Budějovice, Czechia
| | - Václav Hypša
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
- Institute of Parasitology, Biology Centre, ASCR, v.v.i., České Budějovice, Czechia
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Sullivan TJ, Roberts H, Bultman TL. Genetic Covariation Between the Vertically Transmitted Endophyte Epichloë canadensis and Its Host Canada Wildrye. MICROBIAL ECOLOGY 2023; 86:1686-1695. [PMID: 36725749 DOI: 10.1007/s00248-022-02166-7] [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: 11/11/2022] [Accepted: 12/26/2022] [Indexed: 06/18/2023]
Abstract
Symbiotic mutualisms are thought to be stabilized by correlations between the interacting genotypes which may be strengthened via vertical transmission and/or reduced genetic variability within each species. Vertical transmission, however, may weaken interactions over time as the endosymbionts would acquire mutations that could not be purged. Additionally, temporal variation in a conditional mutualism could create genetic variation and increased variation in the interaction outcome. In this study, we assessed genetic variation in both members of a symbiosis, the endosymbiotic fungal endophyte Epichloë canadensis and its grass host Canada wildrye (Elymus canadensis). Both species exhibited comparable levels of diversity, mostly within populations rather than between. There were significant differences between populations, although not in the same pattern for the two species, and the differences were not correlated with geographic distance for either species. Interindividual genetic distance matrices for the two species were significantly correlated, although all combinations of discriminant analysis of principle components (DAPC) defined multilocus genotype groups were found suggesting that strict genotype matching is not necessary. Variation in interaction outcome is common in grass/endophyte interactions, and our results suggest that the accumulation of mutations overtime combined with temporal variation in selection pressures increasing genetic variation in the symbiosis may be the cause.
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Affiliation(s)
- T J Sullivan
- School of Sciences, Indiana University Kokomo, 2300 S. Washington St, Kokomo, IN, 46902, USA.
| | - Holly Roberts
- School of Sciences, Indiana University Kokomo, 2300 S. Washington St, Kokomo, IN, 46902, USA
| | - Thomas L Bultman
- Department of Biology, Hope College, 35 E. 12th St., Holland, MI, 49423, USA
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Moriyama M, Nishide Y, Toyoda A, Itoh T, Fukatsu T. Complete genomes of mutualistic bacterial co-symbionts " Candidatus Sulcia muelleri" and " Candidatus Nasuia deltocephalinicola" of the rice green leafhopper Nephotettix cincticeps. Microbiol Resour Announc 2023; 12:e0035323. [PMID: 37623315 PMCID: PMC10508130 DOI: 10.1128/mra.00353-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/22/2023] [Indexed: 08/26/2023] Open
Abstract
The genomes of obligate bacterial co-symbionts of the green rice leafhopper Nephotettix cincticeps, which is notorious as an agricultural pest, were determined. The streamlined genomes of "Candidatus Sulcia muelleri" and "Candidatus Nasuia deltocephalinicola" exhibited complementary metabolic pathways for synthesizing essential nutrients that contribute to host adaptation.
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Affiliation(s)
- Minoru Moriyama
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yudai Nishide
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics (NIG), Mishima, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Japan
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Manzano-Marín A, Kvist S, Oceguera-Figueroa A. Evolution of an Alternative Genetic Code in the Providencia Symbiont of the Hematophagous Leech Haementeria acuecueyetzin. Genome Biol Evol 2023; 15:evad164. [PMID: 37690114 PMCID: PMC10540940 DOI: 10.1093/gbe/evad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023] Open
Abstract
Strict blood-feeding animals are confronted with a strong B-vitamin deficiency. Blood-feeding leeches from the Glossiphoniidae family, similarly to hematophagous insects, have evolved specialized organs called bacteriomes to harbor symbiotic bacteria. Leeches of the Haementeria genus have two pairs of globular bacteriomes attached to the esophagus which house intracellular "Candidatus Providencia siddallii" bacteria. Previous work analyzing a draft genome of the Providencia symbiont of the Mexican leech Haementeria officinalis showed that, in this species, the bacteria hold a reduced genome capable of synthesizing B vitamins. In this work, we aimed to expand our knowledge on the diversity and evolution of Providencia symbionts of Haementeria. For this purpose, we sequenced the symbiont genomes of three selected leech species. We found that all genomes are highly syntenic and have kept a stable genetic repertoire, mirroring ancient insect endosymbionts. Additionally, we found B-vitamin pathways to be conserved among these symbionts, pointing to a conserved symbiotic role. Lastly and most notably, we found that the symbiont of H. acuecueyetzin has evolved an alternative genetic code, affecting a portion of its proteome and showing evidence of a lineage-specific and likely intermediate stage of genetic code reassignment.
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Affiliation(s)
- Alejandro Manzano-Marín
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, Toronto, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
- Present address: Swedish Museum of Natural History, Stockholm, Sweden
| | - Alejandro Oceguera-Figueroa
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autonoma de México, Ciudad de México, México
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Kolo AO, Raghavan R. Impact of endosymbionts on tick physiology and fitness. Parasitology 2023; 150:859-865. [PMID: 37722758 PMCID: PMC10577665 DOI: 10.1017/s0031182023000793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 09/20/2023]
Abstract
Ticks transmit pathogens and harbour non-pathogenic, vertically transmitted intracellular bacteria termed endosymbionts. Almost all ticks studied to date contain 1 or more of Coxiella, Francisella, Rickettsia or Candidatus Midichloria mitochondrii endosymbionts, indicative of their importance to tick physiology. Genomic and experimental data suggest that endosymbionts promote tick development and reproductive success. Here, we review the limited information currently available on the potential roles endosymbionts play in enhancing tick metabolism and fitness. Future studies that expand on these findings are needed to better understand endosymbionts’ contributions to tick biology. This knowledge could potentially be applied to design novel strategies that target endosymbiont function to control the spread of ticks and pathogens they vector.
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Affiliation(s)
- Agatha O. Kolo
- Department of Molecular Microbiology and Immunology, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Rahul Raghavan
- Department of Molecular Microbiology and Immunology, The University of Texas at San Antonio, San Antonio, TX, USA
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38
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Wolfgang A, Tack AJM, Berg G, Abdelfattah A. Reciprocal influence of soil, phyllosphere, and aphid microbiomes. ENVIRONMENTAL MICROBIOME 2023; 18:63. [PMID: 37480131 PMCID: PMC10362670 DOI: 10.1186/s40793-023-00515-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND The effect of soil on the plant microbiome is well-studied. However, less is known about the impact of the soil microbiome in multitrophic systems. Here we examined the effect of soil on plant and aphid microbiomes, and the reciprocal effect of aphid herbivory on the plant and soil microbiomes. We designed microcosms, which separate below and aboveground compartments, to grow oak seedlings with and without aphid herbivory in soils with three different microbiomes. We used amplicon sequencing and qPCR to characterize the bacterial and fungal communities in soils, phyllospheres, and aphids. RESULTS Soil microbiomes significantly affected the microbial communities of phyllospheres and, to a lesser extent, aphid microbiomes, indicating plant-mediated assembly processes from soil to aphids. While aphid herbivory significantly decreased microbial diversity in phyllospheres independent of soil microbiomes, the effect of aphid herbivory on the community composition in soil varied among the three soils. CONCLUSIONS This study provides experimental evidence for the reciprocal influence of soil, plant, and aphid microbiomes, with the potential for the development of new microbiome-based pest management strategies.
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Affiliation(s)
- Adrian Wolfgang
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria.
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany.
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39
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Cornwallis CK, van 't Padje A, Ellers J, Klein M, Jackson R, Kiers ET, West SA, Henry LM. Symbioses shape feeding niches and diversification across insects. Nat Ecol Evol 2023; 7:1022-1044. [PMID: 37202501 PMCID: PMC10333129 DOI: 10.1038/s41559-023-02058-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/15/2023] [Indexed: 05/20/2023]
Abstract
For over 300 million years, insects have relied on symbiotic microbes for nutrition and defence. However, it is unclear whether specific ecological conditions have repeatedly favoured the evolution of symbioses, and how this has influenced insect diversification. Here, using data on 1,850 microbe-insect symbioses across 402 insect families, we found that symbionts have allowed insects to specialize on a range of nutrient-imbalanced diets, including phloem, blood and wood. Across diets, the only limiting nutrient consistently associated with the evolution of obligate symbiosis was B vitamins. The shift to new diets, facilitated by symbionts, had mixed consequences for insect diversification. In some cases, such as herbivory, it resulted in spectacular species proliferation. In other niches, such as strict blood feeding, diversification has been severely constrained. Symbioses therefore appear to solve widespread nutrient deficiencies for insects, but the consequences for insect diversification depend on the feeding niche that is invaded.
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Affiliation(s)
| | - Anouk van 't Padje
- Amsterdam Institute for Life and Environment, section Ecology and Evolution, Vrije Universiteit, Amsterdam, the Netherlands
- Laboratory of Genetics, Wageningen University and Research, Wageningen, the Netherlands
| | - Jacintha Ellers
- Amsterdam Institute for Life and Environment, section Ecology and Evolution, Vrije Universiteit, Amsterdam, the Netherlands
| | - Malin Klein
- Amsterdam Institute for Life and Environment, section Ecology and Evolution, Vrije Universiteit, Amsterdam, the Netherlands
| | - Raphaella Jackson
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - E Toby Kiers
- Amsterdam Institute for Life and Environment, section Ecology and Evolution, Vrije Universiteit, Amsterdam, the Netherlands
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, UK
| | - Lee M Henry
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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40
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Zhao Y, Song Q, Song Y. The role of insect intestinal microbes in controlling of Empoasca onukii Matsuda (Hemiptera: Cicadellidae) pest infestations in the production of tea garden: a review. Arch Microbiol 2023; 205:267. [PMID: 37351731 DOI: 10.1007/s00203-023-03609-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/27/2023] [Accepted: 06/10/2023] [Indexed: 06/24/2023]
Abstract
Pests like the phytophagous bug Empoasca onukii Matsuda frequently harm tea plants. The harm this insect does to agricultural and environmentally sensitive places is extremely harmful since physical and chemical prevention and control are still the primary methods of handling it. Therefore, it is important to develop pest management strategies. Recent research has demonstrated that pathogenic fungus and the gut microbiota interact to induce host and death, and that the gut microbiota, which has a dramatic effect on the host, can engage in pest control. The advancement of genome editing technologies is also new to the field of pest management. The diversity, function, and research methodologies of insect gut microbiota are summarized in this work, and discusses E. onukii Matsuda control options as well as the importance of insect gut microbiome in pest management. In comparison to traditional pesticides and physical prevention and control, the interaction between pathogenic fungi represented by Beauveria bassiana and intestinal microorganisms, as well as their participation in pest management, causes physiological stress on the host, which meets the new requirements of modern agricultural green development and has a protective effect on habitat fragmentation areas (Karst region). Exploring additional harmful fungus for pest management and fully using the specific traits of insect gut microbiota to achieve "killing insects with bacteria" would be a promising technique from this standpoint.
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Affiliation(s)
- Yuanqi Zhao
- School of Karst Science, Guizhou Normal University, Guiyang, 550001, China
- State Engineering Technology Institute for Karst Desertification Control, Guiyang, 550001, China
| | - Qingfa Song
- School of Karst Science, Guizhou Normal University, Guiyang, 550001, China
- State Engineering Technology Institute for Karst Desertification Control, Guiyang, 550001, China
| | - Yuehua Song
- School of Karst Science, Guizhou Normal University, Guiyang, 550001, China.
- State Engineering Technology Institute for Karst Desertification Control, Guiyang, 550001, China.
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41
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Rose C, Lund MB, Søgård AM, Busck MM, Bechsgaard JS, Schramm A, Bilde T. Social transmission of bacterial symbionts homogenizes the microbiome within and across generations of group-living spiders. ISME COMMUNICATIONS 2023; 3:60. [PMID: 37330540 PMCID: PMC10276852 DOI: 10.1038/s43705-023-00256-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/12/2023] [Accepted: 05/12/2023] [Indexed: 06/19/2023]
Abstract
Disentangling modes and fidelity of symbiont transmission are key for understanding host-symbiont associations in wild populations. In group-living animals, social transmission may evolve to ensure high-fidelity transmission of symbionts, since non-reproducing helpers constitute a dead-end for vertical transmission. We investigated symbiont transmission in the social spider Stegodyphus dumicola, which lives in family groups where the majority of females are non-reproducing helpers, females feed offspring by regurgitation, and individuals feed communally on insect prey. Group members share temporally stable microbiomes across generations, while distinct variation in microbiome composition exists between groups. We hypothesized that horizontal transmission of symbionts is enhanced by social interactions, and investigated transmission routes within (horizontal) and across (vertical) generations using bacterial 16S rRNA gene amplicon sequencing in three experiments: (i) individuals were sampled at all life stages to assess at which life stage the microbiome is acquired. (ii) a cross-fostering design was employed to test whether offspring carry the microbiome from their natal nest, or acquire the microbiome of the foster nest via social transmission. (iii) adult spiders with different microbiome compositions were mixed to assess whether social transmission homogenizes microbiome composition among group members. We demonstrate that offspring hatch symbiont-free, and bacterial symbionts are transmitted vertically across generations by social interactions with the onset of regurgitation feeding by (foster)mothers in an early life stage. Social transmission governs horizontal inter-individual mixing and homogenization of microbiome composition among nest mates. We conclude that temporally stable host-symbiont associations in social species can be facilitated and maintained by high-fidelity social transmission.
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Affiliation(s)
- Clémence Rose
- Section for Genetics, Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark.
| | - Marie B Lund
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andrea M Søgård
- Section for Genetics, Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Mette M Busck
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Jesper S Bechsgaard
- Section for Genetics, Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Trine Bilde
- Section for Genetics, Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
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42
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Spencer N, Łukasik P, Meyer M, Veloso C, McCutcheon JP. No Transcriptional Compensation for Extreme Gene Dosage Imbalance in Fragmented Bacterial Endosymbionts of Cicadas. Genome Biol Evol 2023; 15:evad100. [PMID: 37267326 PMCID: PMC10287537 DOI: 10.1093/gbe/evad100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/04/2023] Open
Abstract
Bacteria that form long-term intracellular associations with host cells lose many genes, a process that often results in tiny, gene-dense, and stable genomes. Paradoxically, the some of the same evolutionary processes that drive genome reduction and simplification may also cause genome expansion and complexification. A bacterial endosymbiont of cicadas, Hodgkinia cicadicola, exemplifies this paradox. In many cicada species, a single Hodgkinia lineage with a tiny, gene-dense genome has split into several interdependent cell and genome lineages. Each new Hodgkinia lineage encodes a unique subset of the ancestral unsplit genome in a complementary way, such that the collective gene contents of all lineages match the total found in the ancestral single genome. This splitting creates genetically distinct Hodgkinia cells that must function together to carry out basic cellular processes. It also creates a gene dosage problem where some genes are encoded by only a small fraction of cells while others are much more abundant. Here, by sequencing DNA and RNA of Hodgkinia from different cicada species with different amounts of splitting-along with its structurally stable, unsplit partner endosymbiont Sulcia muelleri-we show that Hodgkinia does not transcriptionally compensate to rescue the wildly unbalanced gene and genome ratios that result from lineage splitting. We also find that Hodgkinia has a reduced capacity for basic transcriptional control independent of the splitting process. Our findings reveal another layer of degeneration further pushing the limits of canonical molecular and cell biology in Hodgkinia and may partially explain its propensity to go extinct through symbiont replacement.
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Affiliation(s)
- Noah Spencer
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Piotr Łukasik
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Mariah Meyer
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Claudio Veloso
- Department of Ecological Sciences, Science Faculty, University of Chile, Santiago, Chile
| | - John P McCutcheon
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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43
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Li MJ, Zhang B, Chen GH, Zhou SW, Liu JH, Lu M, Zhang JL, Yang SW, Zhang XM. Effects of short-term extreme temperature treatment on the development and reproductive capacity of Encarsia formosa. Front Physiol 2023; 14:1187743. [PMID: 37389122 PMCID: PMC10304823 DOI: 10.3389/fphys.2023.1187743] [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: 03/21/2023] [Accepted: 05/18/2023] [Indexed: 07/01/2023] Open
Abstract
Encarsia formosa is a natural enemy of the invasive pest Bemisia tabaci and is known to be a dominant parasitic. The frequency and magnitude of climate extremes, particularly temperature extremes, have increased, which has put insect populations at risk. However, the effects of temperature extremes on E. formosa are not well understood. To examine the impact of short-term extreme temperature exposure on the development and reproduction of E. formosa, eggs, larvae, pupae, and adults were exposed to high/low temperature treatments (HLT25, HLT50, LLT25, and LLT50). Our findings indicate that the pupal stage of E. formosa exhibited the strongest tolerance to both heat and cold, while adults exhibited a weaker tolerance. The shortest egg-to-adult development period of 12.65 days was observed in E. formosa exposed to HLT50 treatment during the egg-larval stage. The parasitism peak of the adult stage was delayed by 1-6 days after exposure to extreme temperatures during the egg-larval stage. Conversely, the parasitism peak was advanced by 1-3 days after exposure to extreme temperatures during the pupal and adult stages. The eclosion rate, total parasitism, eclosion rate of the F1 generation, and adult longevity of the F1 generation were lower in the treatment groups than in the control groups. The F1 generation's development period was prolonged to 15.49 and 15.19 days after exposure to HLT25 and HLT50 treatments, respectively, during the egg-larval stage. The F1 generation's development period was shortened to 13.33 days after exposure to LLT50 treatment during the pupal stage. Male individuals appeared in the F1 generation after exposure to HLT50 treatment during the pupal stage, with females accounting for only 56.38%. Our results demonstrate that short-term exposure to extreme temperatures has detrimental effects on the growth and reproduction of E. formosa. In field biocontrol against E. formosa, the release of E. formosa should be avoided as much as possible when the ambient temperature is higher than 35°C or lower than 0°C. During extreme temperature conditions, timely supplementation and release of E. formosa population, along with ventilation and cooling in greenhouse facilities during summer, are necessary for better pest control efficacy.
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Affiliation(s)
- Ming-Jiang Li
- National Key Laboratory for Conservation and Utilization of Biological Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, China
- Yunnan Yuntianhua Co., Ltd., Kunming, Yunnan, China
| | - Bo Zhang
- National Key Laboratory for Conservation and Utilization of Biological Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Guo-Hua Chen
- National Key Laboratory for Conservation and Utilization of Biological Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Shun-Wen Zhou
- National Key Laboratory for Conservation and Utilization of Biological Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Ji-Huan Liu
- National Key Laboratory for Conservation and Utilization of Biological Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Mei Lu
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Jin-Long Zhang
- National Key Laboratory for Conservation and Utilization of Biological Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Shao-Wu Yang
- National Key Laboratory for Conservation and Utilization of Biological Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, China
- Yunnan Urban Agricultural Engineering and Technological Research Center, College of Agronomy and Life Sciences, Kunming University, Kunming, China
| | - Xiao-Ming Zhang
- National Key Laboratory for Conservation and Utilization of Biological Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, China
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Boutry J, Buysse M, Tissot S, Cazevielle C, Hamede R, Dujon AM, Ujvari B, Giraudeau M, Klimovich A, Thomas F, Tökölyi J. Spontaneously occurring tumors in different wild-derived strains of hydra. Sci Rep 2023; 13:7449. [PMID: 37156860 PMCID: PMC10167321 DOI: 10.1038/s41598-023-34656-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 05/04/2023] [Indexed: 05/10/2023] Open
Abstract
Hydras are freshwater cnidarians widely used as a biological model to study different questions such as senescence or phenotypic plasticity but also tumoral development. The spontaneous tumors found in these organisms have been so far described in two female lab strains domesticated years ago (Hydra oligactis and Pelmatohydra robusta) and the extent to which these tumors can be representative of tumors within the diversity of wild hydras is completely unknown. In this study, we examined individuals isolated from recently sampled wild strains of different sex and geographical origin, which have developed outgrowths looking like tumors. These tumefactions have common features with the tumors previously described in lab strains: are composed of an accumulation of abnormal cells, resulting in a similar enlargement of the tissue layers. However, we also found diversity within these new types of tumors. Indeed, not only females, but also males seem prone to form these tumors. Finally, the microbiota associated to these tumors is different from the one involved in the previous lineages exhibiting tumors. We found that tumorous individuals hosted yet undescribed Chlamydiales vacuoles. This study brings new insights into the understanding of tumor susceptibility and diversity in brown hydras from different origins.
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Affiliation(s)
- Justine Boutry
- CREEC/CANECEV (CREES), MIVEGEC, Unité Mixte de Recherches, IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France.
| | - Marie Buysse
- MIVEGEC, Unité Mixte de Recherches, IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France
| | - Sophie Tissot
- CREEC/CANECEV (CREES), MIVEGEC, Unité Mixte de Recherches, IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France
| | - Chantal Cazevielle
- Institut des Neurosciences de Montpellier: Electronic Microscopy Facilities, INSERM U 1298, Université Montpellier, Montpellier, France
| | - Rodrigo Hamede
- CREEC/CANECEV (CREES), MIVEGEC, Unité Mixte de Recherches, IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Antoine M Dujon
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Beata Ujvari
- CREEC/CANECEV (CREES), MIVEGEC, Unité Mixte de Recherches, IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Mathieu Giraudeau
- Littoral Environnement et Sociétés (LIENSs), UMR 7266 CNRS-La Rochelle Université, 223 Rue Olympe de Gouges, 17000, La Rochelle, France
| | | | - Frédéric Thomas
- CREEC/CANECEV (CREES), MIVEGEC, Unité Mixte de Recherches, IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France
| | - Jácint Tökölyi
- MTA-DE "Momentum" Ecology, Evolution and Developmental Biology Research Group, Department of Evolutionary Zoology, University of Debrecen, Debrecen, 4032, Hungary.
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45
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Kiefer JST, Bauer E, Okude G, Fukatsu T, Kaltenpoth M, Engl T. Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles. THE ISME JOURNAL 2023:10.1038/s41396-023-01415-y. [PMID: 37085551 DOI: 10.1038/s41396-023-01415-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/23/2023]
Abstract
Many insects engage in stable nutritional symbioses with bacteria that supplement limiting essential nutrients to their host. While several plant sap-feeding Hemipteran lineages are known to be simultaneously associated with two or more endosymbionts with complementary biosynthetic pathways to synthesize amino acids or vitamins, such co-obligate symbioses have not been functionally characterized in other insect orders. Here, we report on the characterization of a dual co-obligate, bacteriome-localized symbiosis in a family of xylophagous beetles using comparative genomics, fluorescence microscopy, and phylogenetic analyses. Across the beetle family Bostrichidae, most investigated species harbored the Bacteroidota symbiont Shikimatogenerans bostrichidophilus that encodes the shikimate pathway to produce tyrosine precursors in its severely reduced genome, likely supplementing the beetles' cuticle biosynthesis, sclerotisation, and melanisation. One clade of Bostrichid beetles additionally housed the co-obligate symbiont Bostrichicola ureolyticus that is inferred to complement the function of Shikimatogenerans by recycling urea and provisioning the essential amino acid lysine, thereby providing additional benefits on nitrogen-poor diets. Both symbionts represent ancient associations within the Bostrichidae that have subsequently experienced genome erosion and co-speciation with their hosts. While Bostrichicola was repeatedly lost, Shikimatogenerans has been retained throughout the family and exhibits a perfect pattern of co-speciation. Our results reveal that co-obligate symbioses with complementary metabolic capabilities occur beyond the well-known sap-feeding Hemiptera and highlight the importance of symbiont-mediated cuticle supplementation and nitrogen recycling for herbivorous beetles.
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Affiliation(s)
- Julian Simon Thilo Kiefer
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Mainz, Germany
| | - Eugen Bauer
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Mainz, Germany
| | - Genta Okude
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8566, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, 113-0033, Japan
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8566, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, 113-0033, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8571, Japan
| | - Martin Kaltenpoth
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Mainz, Germany
- Department of Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Tobias Engl
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Mainz, Germany.
- Department of Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Jena, Germany.
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46
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Danneels B, Blignaut M, Marti G, Sieber S, Vandamme P, Meyer M, Carlier A. Cyclitol metabolism is a central feature of Burkholderia leaf symbionts. Environ Microbiol 2023; 25:454-472. [PMID: 36451580 DOI: 10.1111/1462-2920.16292] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled 17 new endophyte genomes representing endophytes from 13 plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.
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Affiliation(s)
- Bram Danneels
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | - Monique Blignaut
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Guillaume Marti
- Metatoul-AgromiX Platform, LRSV, Université de Toulouse, CNRS, UT3, INP, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Simon Sieber
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Marion Meyer
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Aurélien Carlier
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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Segredo-Otero E, Sanjuán R. Genetic complementation fosters evolvability in complex fitness landscapes. Sci Rep 2023; 13:662. [PMID: 36635310 PMCID: PMC9837146 DOI: 10.1038/s41598-022-26588-y] [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: 09/28/2022] [Accepted: 12/16/2022] [Indexed: 01/14/2023] Open
Abstract
The ability of natural selection to optimize traits depends on the topology of the genotype-fitness map (fitness landscape). Epistatic interactions produce rugged fitness landscapes, where adaptation is constrained by the presence of low-fitness intermediates. Here, we used simulations to explore how evolvability in rugged fitness landscapes is influenced by genetic complementation, a process whereby different sequence variants mutually compensate for their deleterious mutations. We designed our model inspired by viral populations, in which genetic variants are known to interact frequently through coinfection. Our simulations indicate that genetic complementation enables a more efficient exploration of rugged fitness landscapes. Although this benefit may be undermined by genetic parasites, its overall effect on evolvability remains positive in populations that exhibit strong relatedness between interacting sequences. Similar processes could operate in contexts other than viral coinfection, such as in the evolution of ploidy.
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Affiliation(s)
- Ernesto Segredo-Otero
- grid.4711.30000 0001 2183 4846Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/ Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/ Catedrático Agustín Escardino 9, 46980, Paterna, València, Spain.
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Hoffman T, Olsen B, Lundkvist Å. The Biological and Ecological Features of Northbound Migratory Birds, Ticks, and Tick-Borne Microorganisms in the African-Western Palearctic. Microorganisms 2023; 11:microorganisms11010158. [PMID: 36677450 PMCID: PMC9866947 DOI: 10.3390/microorganisms11010158] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Identifying the species that act as hosts, vectors, and vehicles of vector-borne pathogens is vital for revealing the transmission cycles, dispersal mechanisms, and establishment of vector-borne pathogens in nature. Ticks are common vectors for pathogens causing human and animal diseases, and they transmit a greater variety of pathogenic agents than any other arthropod vector group. Ticks depend on the movements by their vertebrate hosts for their dispersal, and tick species with long feeding periods are more likely to be transported over long distances. Wild birds are commonly parasitized by ticks, and their migration patterns enable the long-distance range expansion of ticks. The African-Palearctic migration system is one of the world's largest migrations systems. African-Western Palearctic birds create natural links between the African, European, and Asian continents when they migrate biannually between breeding grounds in the Palearctic and wintering grounds in Africa and thereby connect different biomes. Climate is an important geographical determinant of ticks, and with global warming, the distribution range and abundance of ticks in the Western Palearctic may increase. The introduction of exotic ticks and their microorganisms into the Western Palearctic via avian vehicles might therefore pose a greater risk for the public and animal health in the future.
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Affiliation(s)
- Tove Hoffman
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Björn Olsen
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, 751 85 Uppsala, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
- Correspondence:
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49
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Sloan DB, Warren JM, Williams AM, Kuster SA, Forsythe ES. Incompatibility and Interchangeability in Molecular Evolution. Genome Biol Evol 2023; 15:evac184. [PMID: 36583227 PMCID: PMC9839398 DOI: 10.1093/gbe/evac184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
There is remarkable variation in the rate at which genetic incompatibilities in molecular interactions accumulate. In some cases, minor changes-even single-nucleotide substitutions-create major incompatibilities when hybridization forces new variants to function in a novel genetic background from an isolated population. In other cases, genes or even entire functional pathways can be horizontally transferred between anciently divergent evolutionary lineages that span the tree of life with little evidence of incompatibilities. In this review, we explore whether there are general principles that can explain why certain genes are prone to incompatibilities while others maintain interchangeability. We summarize evidence pointing to four genetic features that may contribute to greater resistance to functional replacement: (1) function in multisubunit enzyme complexes and protein-protein interactions, (2) sensitivity to changes in gene dosage, (3) rapid rate of sequence evolution, and (4) overall importance to cell viability, which creates sensitivity to small perturbations in molecular function. We discuss the relative levels of support for these different hypotheses and lay out future directions that may help explain the striking contrasts in patterns of incompatibility and interchangeability throughout the history of molecular evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, Colorado
| | - Jessica M Warren
- Center for Mechanisms of Evolution, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Alissa M Williams
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Shady A Kuster
- Department of Biology, Colorado State University, Fort Collins, Colorado
| | - Evan S Forsythe
- Department of Biology, Colorado State University, Fort Collins, Colorado
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50
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Jackson R, Patapiou PA, Golding G, Helanterä H, Economou CK, Chapuisat M, Henry LM. Evidence of phylosymbiosis in Formica ants. Front Microbiol 2023; 14:1044286. [PMID: 37213490 PMCID: PMC10196114 DOI: 10.3389/fmicb.2023.1044286] [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: 09/14/2022] [Accepted: 03/31/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction Insects share intimate relationships with microbes that play important roles in their biology. Yet our understanding of how host-bound microbial communities assemble and perpetuate over evolutionary time is limited. Ants host a wide range of microbes with diverse functions and are an emerging model for studying the evolution of insect microbiomes. Here, we ask whether phylogenetically related ant species have formed distinct and stable microbiomes. Methods To answer this question, we investigated the microbial communities associated with queens of 14 Formica species from five clades, using deep coverage 16S rRNA amplicon sequencing. Results We reveal that Formica species and clades harbor highly defined microbial communities that are dominated by four bacteria genera: Wolbachia, Lactobacillus, Liliensternia, and Spiroplasma. Our analysis reveals that the composition of Formica microbiomes mirrors the phylogeny of the host, i.e., phylosymbiosis, in that related hosts harbor more similar microbial communities. In addition, we find there are significant correlations between microbe co-occurrences. Discussion Our results demonstrate Formica ants carry microbial communities that recapitulate the phylogeny of their hosts. Our data suggests that the co-occurrence of different bacteria genera may at least in part be due to synergistic and antagonistic interactions between microbes. Additional factors potentially contributing to the phylosymbiotic signal are discussed, including host phylogenetic relatedness, host-microbe genetic compatibility, modes of transmission, and similarities in host ecologies (e.g., diets). Overall, our results support the growing body of evidence that microbial community composition closely depends on the phylogeny of their hosts, despite bacteria having diverse modes of transmission and localization within the host.
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Affiliation(s)
- Raphaella Jackson
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Patapios A. Patapiou
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Gemma Golding
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Heikki Helanterä
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Chloe K. Economou
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Lee M. Henry
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
- *Correspondence: Lee M. Henry,
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