Abstract
Auchenorrhynchan insects (Hemiptera) generally depend on two bacterial symbionts for nutrition. These bacteria experience extreme genome reduction and loss of essential cell functions that require direct host support, or the replacement of failing symbionts with more capable ones. However, it remains unclear how hosts adapt to integrate symbionts into their systems, particularly when they are replaced. Here, we comparatively investigated the evolution of host-support mechanisms in the glassy-winged sharpshooter, Homalodisca vitripennis (GWSS), and the aster leafhopper, Macrosteles quadrilineatus (ALF). ALF harbors the ancestral co-symbionts of the Auchenorrhyncha that have tiny genomes, Sulcia (190 kb) and Nasuia (112 kb). In GWSS, Sulcia retains an expanded genome (245 kb), but Nasuia was replaced by the more capable Baumannia (686 kb). To support their symbionts, GWSS and ALF have evolved novel mechanisms via horizontal gene transfer, gene duplication, and co-option of mitochondrial support genes. However, GWSS has fewer support systems targeting essential bacterial processes. In particular, although both hosts use ancestral mechanisms to support Sulcia, GWSS does not encode all of the same support genes required to sustain Sulcia-ALF or Nasuia. Moreover, GWSS support of Baumannia is far more limited and tailored to its expanded capabilities. Our results demonstrate how symbiont replacements shape host genomes and the co-evolutionary process.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
Data availability
Raw Illumina reads from GWSS were submitted to the Sequence Read Archive (SRA) database under the accession number PRJNA342859, and the assembled transcriptome was submitted to the Transcriptome Shotgun Assembly (TSA) database under the accession number GICT00000000.
References
Baumann P. Biology of bacteriocyte-associated endosymbionts of plant sap-sucking insects. Annu Rev Microbiol. 2005;59:155–89.
Douglas AE. The microbial dimension in insect nutritional ecology. Funct Ecol. 2009;23:38–47.
Buchner P. Endosymbiosis of animals with plant microorganims. New York, NY: Interscience; 1965.
Moran NA, McCutcheon JP, Nakabachi A. Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet. 2008;42:165–90.
Koga R, Meng X-Y, Tsuchida T, Fukatsu T. Cellular mechanism for selective vertical transmission of an obligate insect symbiont at the bacteriocyte–embryo interface. Proc Natl Acad Sci USA. 2012;109:E1230–7.
Luan J, Sun X, Fei Z, Douglas AE. Maternal inheritance of a single somatic animal cell displayed by the bacteriocyte in the whitefly Bemisia tabaci. Curr Biol. 2018;28:459–65.
McCutcheon JP, Moran NA. Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol. 2012;10:13–26.
Moran NA, Bennett GM. The tiniest tiny genomes. Annu Rev Microbiol. 2014;68:195–215.
Hansen AK, Moran NA. Aphid genome expression reveals host–symbiont cooperation in the production of amino acids. Proc Natl Acad Sci USA. 2011;108:2849–54.
Sloan DB, Nakabachi A, Richards S, Qu J, Murali SC, Gibbs RA, et al. Parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects. Mol Biol Evol. 2014;31:857–71.
Husnik F, Nikoh N, Koga R, Ross L, Duncan RP, Fujie M, et al. Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis. Cell. 2013;153:1567–78.
Luan J-B, Chen W, Hasegawa DK, Simmons AM, Wintermantel WM, Ling K-S, et al. Metabolic coevolution in the bacterial symbiosis of whiteflies and related plant sap-feeding insects. Genome Biol Evol. 2015;7:2635–47.
Mao M, Yang X, Bennett GM. Evolution of host support for two ancient bacterial symbionts with differentially degraded genomes in a leafhopper host. Proc Natl Acad Sci USA. 2018;115:E11691–700.
Duncan RP, Husnik F, Van Leuven JT, Gilbert DG, Dávalos LM, McCutcheon JP, et al. Dynamic recruitment of amino acid transporters to the insect/symbiont interface. Mol Ecol. 2014;23:1608–23.
Husnik F, McCutcheon JP. Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis. Proc Natl Acad Sci USA. 2016;113:5416–24.
Chong RA, Park H, Moran NA. Genome evolution of the obligate endosymbiont Buchnera aphidicola. Mol Biol Evol. 2019;36:1481–9.
Łukasik P, Nazario K, Van Leuven JT, Campbell MA, Meyer M, Michalik A, et al. Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas. Proc Natl Acad Sci USA. 2018;115:E226–35.
Bennett GM, McCutcheon JP, McDonald BR, Moran NA. Lineage-specific patterns of genome deterioration in obligate symbionts of sharpshooter leafhoppers. Genome Biol Evol. 2015;8:296–301.
Koga R, Bennett GM, Cryan JR, Moran NA. Evolutionary replacement of obligate symbionts in an ancient and diverse insect lineage. Environ Microbiol. 2013;15:2073–81.
McCutcheon JP, Moran NA. Functional convergence in reduced genomes of bacterial symbionts spanning 200 My of evolution. Genome Biol Evol. 2010;2:708–18.
Manzano‐Marín A, Szabó G, Simon JC, Horn M, Latorre A. Happens in the best of subfamilies: establishment and repeated replacements of co‐obligate secondary endosymbionts within Lachninae aphids. Environ Microbiol. 2017;19:393–408.
Kaiser B. Licht-und elektronenmikroskopische untersuchung der symbionten von Graphocephala coccinea forstier (Homoptera: Jassidae). Int J Insect Morphol Embryol. 1980;9:79–88.
Nakabachi A, Shigenobu S, Sakazume N, Shiraki T, Hayashizaki Y, Carninci P, et al. Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera. Proc Natl Acad Sci USA. 2005;102:5477–82.
Braendle C, Miura T, Bickel R, Shingleton AW, Kambhampati S, Stern DL. Developmental origin and evolution of bacteriocytes in the aphid—Buchnera symbiosis. PLoS Biol. 2003;1:e21.
Moran NA, Tran P, Gerardo NM. Symbiosis and insect diversification: an ancient symbiont of sap-feeding insects from the bacterial phylum Bacteroidetes. Appl Environ Microbiol. 2005;71:8802–10.
Bennett GM, Mao M. Comparative genomics of a quadripartite symbiosis in a planthopper host reveals the origins and rearranged nutritional responsibilities of anciently diverged bacterial lineages. Environ Microbiol. 2018;20:4461–72.
Bell-Roberts L, Douglas AE, Werner GD. Match and mismatch between dietary switches and microbial partners in plant sap-feeding insects. Proc R Soc B. 2019;286:20190065.
Mao M, Yang X, Poff K, Bennett G. Comparative genomics of the dual-obligate symbionts from the treehopper, Entylia carinata (Hemiptera: Membracidae), provide insight into the origins and evolution of an ancient symbiosis. Genome Biol Evol. 2017;9:1803–15.
Bennett GM, Abbà S, Kube M, Marzachì C. Complete genome sequences of the obligate symbionts “Candidatus Sulcia muelleri” and “Ca. Nasuia deltocephalinicola” from the pestiferous Leafhopper Macrosteles quadripunctulatus (Hemiptera: Cicadellidae). Genome Announc. 2016;4:e01604–15.
Van Leuven JT, Mao M, Xing DD, Bennett GM, McCutcheon JP. Cicada endosymbionts have tRNAs that are correctly processed despite having genomes that do not encode all of the tRNA processing machinery. mBio. 2019;10:e01950–01918.
Moran NA, Dale C, Dunbar H, Smith WA, Ochman H. Intracellular symbionts of sharpshooters (Insecta: Hemiptera: Cicadellinae) form a distinct clade with a small genome. Environ Microbiol. 2003;5:116–26.
Takiya DM, Tran PL, Dietrich CH, Moran NA. Co‐cladogenesis spanning three phyla: leafhoppers (Insecta: Hemiptera: Cicadellidae) and their dual bacterial symbionts. Mol Ecol. 2006;15:4175–91.
Bennett GM, McCutcheon JP, MacDonald BR, Romanovicz D, Moran NA. Differential genome evolution between companion symbionts in an insect-bacterial symbiosis. mBio. 2014;5:e01697–14.
Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, Khouri H, et al. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol. 2006;4:e188.
Bennett GM, McCutcheon JP, McDonald BR, Moran NA. Lineage-specific patterns of genome deterioration in obligate symbionts of sharpshooter leafhoppers. Genome Biol Evol. 2016;8:296–301.
Kobiałka M, Michalik A, Szwedo J, Szklarzewicz T. Diversity of symbiotic microbiota in Deltocephalinae leafhoppers (Insecta, Hemiptera, Cicadellidae). Arthropod Struct Dev. 2018;467:268–78.
Bennett GM, Chong RA. Genome-wide transcriptional d in the companion bacterial symbionts of the glassy-winged sharpshooter (Cicadellidae: Homalodisca vitripennis) reveal differential gene expression in bacteria occupying multiple host organs. G3 Genes, Genomes, Genet. 2017;7:3073–82.
McCutcheon JP, Moran NA. Parallel genomic evolution and metabolic interdependence in an ancient symbiosis. Proc Natl Acad Sci USA. 2007;104:19392–7.
Bennett GM, Moran NA. Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a phloem-feeding insect. Genome Biol Evol. 2013;5:1675–88.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52.
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658–9.
Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet. 2000;16:276–7.
Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muñiz-Rascado L, et al. EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011;39:D583–90.
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 2011;12:323.
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.
Katoh K, Misawa K. Kuma K-i, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–66.
Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics. 2011;27:1164–5.
Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE). 2010; New Orleans, LA. p. 1–8.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Lartillot N, Rodrigue N, Stubbs D, Richer J. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst Biol. 2013;62:611–5.
Wilson AC, Duncan RP. Signatures of host/symbiont genome coevolution in insect nutritional endosymbioses. Proc Natl Acad Sci USA. 2015;112:10255–61.
Thomas GW, Dohmen E, Hughes DS, Murali SC, Poelchau M, Glastad K, et al. The genomic basis of arthropod diversity. BioRxiv. 2018. https://doi.org/10.1101/382945.
Janosi L, Shimizu I, Kaji A. Ribosome recycling factor (ribosome releasing factor) is essential for bacterial growth. Proc Natl Acad Sci USA. 1994;91:4249–53.
Hehenberger E, Gast RJ, Keeling PJ. A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis. Proc Natl Acad Sci USA. 2019;116:17934–42.
Carrie C, Small I. A reevaluation of dual-targeting of proteins to mitochondria and chloroplasts. Biochim Biophys Acta. 2013;1833:253–9.
Peeters N, Small I. Dual targeting to mitochondria and chloroplasts. Biochimica et Biochim Biophys Acta. 2001;1541:54–63.
Singer A, Poschmann G, Mühlich C, Valadez-Cano C, Hänsch S, Hüren V, et al. Massive protein import into the early-evolutionary-stage photosynthetic organelle of the amoeba Paulinella chromatophora. Curr Biol. 2017;27:2763–73.
Bayeva M, Khechaduri A, Wu R, Burke MA, Wasserstrom JA, Singh N, et al. ATP-binding cassette B10 regulates early steps of heme synthesis. Circ Res. 2013;113:279–87.
Bauerschmitt H, Funes S, Herrmann JM. The membrane-bound GTPase Guf1 promotes mitochondrial protein synthesis under suboptimal conditions. J Biol Chem. 2008;283:17139–46.
Price DR, Duncan RP, Shigenobu S, Wilson AC. Genome expansion and differential expression of amino acid transporters at the aphid/Buchnera symbiotic interface. Mol Biol Evol. 2011;28:3113–26.
Price DR, Tibbles K, Shigenobu S, Smertenko A, Russell CW, Douglas AE, et al. Sugar transporters of the major facilitator superfamily in aphids; from gene prediction to functional characterization. Insect Mol Biol. 2010;19:97–112.
Duncan RP, Nathanson L, Wilson AC. Novel male-biased expression in paralogs of the aphid slimfast nutrient amino acid transporter expansion. BMC Evol Biol. 2011;11:253.
Dahan RA, Duncan RP, Wilson AC, Dávalos LM. Amino acid transporter expansions associated with the evolution of obligate endosymbiosis in sap-feeding insects (Hemiptera: sternorrhyncha). BMC Evol Biol. 2015;15:52.
McCutcheon JP, McDonald BR, Moran NA. Convergent evolution of metabolic roles in bacterial co-symbionts of insects. Proc Natl Acad Sci USA. 2009;106:15394–9.
Wyatt G, Kalf G. The chemistry of insect hemolymph: II. trehalose and other carbohydrates. J gen physiol. 1957;40:833–47.
Mori H, Lee J-H, Okuyama M, Nishimoto M, Ohguchi M, Kim D, et al. Catalytic reaction mechanism based on α-secondary deuterium isotope effects in hydrolysis of trehalose by European honeybee trehalase. Biosci Biotechnol Biochem. 2009;73:2466–73.
Poliakov A, Russell C, Ponnala L, Hoops H, Sun Q, Douglas A, et al. Large-scale label-free quantitative proteomics of the pea aphid-Buchnera symbiosis. Mol cell Proteom. 2011;10:M110.007039.
Ankrah NY, Chouaia B, Douglas AE. The cost of metabolic interactions in symbioses between insects and bacteria with reduced genomes. mBio. 2018;9:e01433–18.
Douglas AE. How multi-partner endosymbioses function. Nat Rev Microbiol. 2016;14:731–43.
Balibar CJ, Hollis-Symynkywicz MF, Tao J. Pantethine rescues phosphopantothenoylcysteine synthetase and phosphopantothenoylcysteine decarboxylase deficiency in Escherichia coli but not in Pseudomonas aeruginosa. J Bacteriol. 2011;193:3304–12.
Rana A, Seinen E, Siudeja K, Muntendam R, Srinivasan B, Van Der Want JJ, et al. Pantethine rescues a Drosophila model for pantothenate kinase–associated neurodegeneration. Proc Natl Acad Sci USA. 2010;107:6988–93.
Andersen PC, Brodbeck BV, Mizell RF III. Feeding by the leafhopper, Homalodisca coagulata, in relation to xylem fluid chemistry and tension. J Insect Physiol. 1992;38:611–22.
Leigh JA, Dodsworth JA. Nitrogen regulation in bacteria and archaea. Annu Rev Microbiol. 2007;61:349–77.
Douglas AE. The B vitamin nutrition of insects: the contributions of diet, microbiome and horizontally-acquired genes. Curr Opin Insect Sci. 2017;23:65–69.
Klasson L, Andersson SG. Evolution of minimal-gene-sets in host-dependent bacteria. Trends Microbiol. 2004;12:37–43.
Mazel D, Pochet S, Marliere P. Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation. EMBO J. 1994;13:914–23.
Matsuura Y, Moriyama M, Łukasik P, Vanderpool D, Tanahashi M, Meng X-Y, et al. Recurrent symbiont recruitment from fungal parasites in cicadas. Proc Natl Acad Sci USA. 2018;115:E5970–9.
Sudakaran S, Kost C, Kaltenpoth M. Symbiont acquisition and replacement as a source of ecological innovation. Trends Microbiol. 2017;27:375–90.
Bennett GM, Moran NA. Heritable symbiosis: the advantages and perils of an evolutionary rabbit hole. Proc Natl Acad Sci USA. 2015;112:10169–76.
McCutcheon JP, Boyd BM, Dale C. The life of an insect endosymbiont from the cradle to the grave. Curr Biol. 2019;29:R485–95.
Wernegreen JJ. Endosymbiont evolution: predictions from theory and surprises from genomes. Ann N Y Acad Sci. 2015;1360:16–35.
Gil R, Latorre A. Unity makes strength: a review on mutualistic symbiosis in representative insect clades. Life. 2019;9:21.
Sabater-Muñoz B, Toft C, Alvarez-Ponce D, Fares MA. Chance and necessity in the genome evolution of endosymbiotic bacteria of insects. ISME J. 2017;11:1291–304.
Acknowledgements
We thank three anonymous reviewers for the helpful suggestions. We thank Dr Stephen Richards (University of California Davis), Adelaida Rhodes (Broad Institute), and the i5K team for help with accessing the GWSS genome. We thank Dr Nancy Moran (University of Texas Austin) and Dr Susan Ge (University of California Merced) for the use of laboratory resources. We also thank the UT Austin GSAF for sequencing. Dr Allen Yang and Dr Xiaoliang Liu provided valuable support with data analysis and immunoblot experiment. The data in this work were collected, in part, with a confocal microscope acquired through the National Science Foundation (NSF) MRI Award (DMR-1625733). This work was supported by a NSF Award (IOS1347116).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Mao, M., Bennett, G.M. Symbiont replacements reset the co-evolutionary relationship between insects and their heritable bacteria. ISME J 14, 1384–1395 (2020). https://doi.org/10.1038/s41396-020-0616-4
Received:
Revised:
Accepted:
Published:
Version of record:
Issue date:
DOI: https://doi.org/10.1038/s41396-020-0616-4
This article is cited by
-
Evolutionary dynamics of obligate endosymbiosis in the psyllid genus Cacopsylla
Communications Biology (2025)
-
Genome degradation results in nested symbiosis and endosymbiont replacement in cicadas
Nature Communications (2025)
-
Microbiota dynamics across different developmental stages of the pepper weevil (Anthonomus eugenii Cano)
Biologia (2025)
-
Symbiont Diversity of Rice-Associated Leafhoppers (Cicadellidae) in the Tropical Floodplains of the Tonle Sap Lake, Cambodia
Microbial Ecology (2025)
-
Transcriptome Analysis of the Fat Body of the Maize Pest Delphacodes kuscheli (Hemiptera: Delphacidae) Reveals Essential Roles of Fungal Endosymbionts
Microbial Ecology (2025)
