Division of labor within psyllids: metagenomics reveals an ancient dual endosymbiosis with metabolic complementarity in the genus Cacopsylla
Language English Country United States Media print-electronic
Document type Journal Article
Grant support
I 4639-B
Province Bolzano, Austrian Science Fund FWF
2017/26/D/NZ8/00799
Polish National Science Center
PubMed
37768069
PubMed Central
PMC10654072
DOI
10.1128/msystems.00578-23
Knihovny.cz E-resources
- Keywords
- comparative genomics, endosymbionts, psyllids, symbiosis,
- MeSH
- Bacteria MeSH
- Enterobacteriaceae genetics MeSH
- Phylogeny MeSH
- Hemiptera * genetics MeSH
- Symbiosis genetics MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
Heritable beneficial bacterial endosymbionts have been crucial for the evolutionary success of numerous insects by enabling the exploitation of nutritionally limited food sources. Herein, we describe a previously unknown dual endosymbiosis in the psyllid genus Cacopsylla, consisting of the primary endosymbiont "Candidatus Carsonella ruddii" and a co-occurring Enterobacteriaceae bacterium for which we propose the name "Candidatus Psyllophila symbiotica." Its localization within the bacteriome and its small genome size confirm that Psyllophila is a co-primary endosymbiont widespread within the genus Cacopsylla. Despite its highly eroded genome, Psyllophila perfectly complements the tryptophan biosynthesis pathway that is incomplete in the co-occurring Carsonella. Moreover, the genome of Psyllophila is almost as small as Carsonella's, suggesting an ancient dual endosymbiosis that has now reached a precarious stage where any additional gene loss would make the system collapse. Hence, our results shed light on the dynamic interactions of psyllids and their endosymbionts over evolutionary time.
Competence Centre for Plant Health Free University of Bozen Bolzano Bolzano Italy
Faculty of Science University of South Bohemia České Budějovice Czech Republic
UMR 1345 Université d'Angers Institut Agro INRAE IRHS SFR Quasav Beaucouzé France
See more in PubMed
Moran NA, McCutcheon JP, Nakabachi A. 2008. Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet 42:165–190. doi:10.1146/annurev.genet.41.110306.130119 PubMed DOI
Buchner P. 1965. Endosymbiosis of animals with plant microorganisms. Interscience Publishers, New York.
Baumann P. 2005. Biology bacteriocyte-associated endosymbionts of plant sap-sucking insects. Annu Rev Microbiol 59:155–189. doi:10.1146/annurev.micro.59.030804.121041 PubMed DOI
Hansen AK, Moran NA. 2011. Aphid genome expression reveals host-symbiont cooperation in the production of amino acids. Proc Natl Acad Sci U S A 108:2849–2854. doi:10.1073/pnas.1013465108 PubMed DOI PMC
McCutcheon JP, von Dohlen CD. 2011. An interdependent metabolic patchwork in the nested symbiosis of mealybugs. Curr Biol 21:1366–1372. doi:10.1016/j.cub.2011.06.051 PubMed DOI PMC
Bennett GM, Moran NA. 2013. Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a phloem-feeding insect. Genome Biol Evol 5:1675–1688. doi:10.1093/gbe/evt118 PubMed DOI PMC
Akman L, Yamashita A, Watanabe H, Oshima K, Shiba T, Hattori M, Aksoy S. 2002. Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat Genet 32:402–407. doi:10.1038/ng986 PubMed DOI
Nováková E, Husník F, Šochová E, Hypša V. 2015. Arsenophonus and Sodalis symbionts in louse flies: an analogy to the Wigglesworthia and Sodalis system in tsetse flies. Appl Environ Microbiol 81:6189–6199. doi:10.1128/AEM.01487-15 PubMed DOI PMC
Reis F, Kirsch R, Pauchet Y, Bauer E, Bilz LC, Fukumori K, Fukatsu T, Kölsch G, Kaltenpoth M. 2020. Bacterial symbionts support larval sap feeding and adult folivory in (semi-)aquatic reed beetles. Nat Commun 11:2964. doi:10.1038/s41467-020-16687-7 PubMed DOI PMC
McCutcheon JP, Moran NA. 2012. Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol 10:13–26. doi:10.1038/nrmicro2670 PubMed DOI
Toft C, Andersson SGE. 2010. Evolutionary microbial genomics: insights into bacterial host adaptation. Nat Rev Genet 11:465–475. doi:10.1038/nrg2798 PubMed DOI
Manzano-Marín A, Latorre A. 2016. Snapshots of a shrinking partner: genome reduction in Serratia symbiotica. Sci Rep 6:32590. doi:10.1038/srep32590 PubMed DOI PMC
Pérez-Brocal V, Gil R, Ramos S, Lamelas A, Postigo M, Michelena JM, Silva FJ, Moya A, Latorre A. 2006. A small microbial genome: the end of a long symbiotic relationship?. Science 314:312–313. doi:10.1126/science.1130441 PubMed DOI
Monnin D, Jackson R, Kiers ET, Bunker M, Ellers J, Henry LM. 2020. Parallel evolution in the integration of a co-obligate aphid symbiosis. Curr Biol 30:1949–1957. doi:10.1016/j.cub.2020.03.011 PubMed DOI
Koga R, Bennett GM, Cryan JR, Moran NA. 2013. Evolutionary replacement of obligate symbionts in an ancient and diverse insect lineage. Environ Microbiol 15:2073–2081. doi:10.1111/1462-2920.12121 PubMed DOI
Koga R, Moran NA. 2014. Swapping symbionts in spittlebugs: evolutionary replacement of a reduced genome symbiont. ISME J 8:1237–1246. doi:10.1038/ismej.2013.235 PubMed DOI PMC
McCutcheon JP, Boyd BM, Dale C. 2019. The life of an insect endosymbiont from the cradle to the grave. Curr Biol 29:R485–R495. doi:10.1016/j.cub.2019.03.032 PubMed DOI
Manzano-Marín A, Szabó G, Simon J-C, Horn M, Latorre A. 2017. Happens in the best of subfamilies: establishment and repeated replacements of co-obligate secondary endosymbionts within lachninae aphids. Environ Microbiol 19:393–408. doi:10.1111/1462-2920.13633 PubMed DOI
Matsuura Y, Moriyama M, Łukasik P, Vanderpool D, Tanahashi M, Meng X-Y, McCutcheon JP, Fukatsu T. 2018. Recurrent symbiont recruitment from fungal parasites in cicadas. Proc Natl Acad Sci U S A 115:E5970–E5979. doi:10.1073/pnas.1803245115 PubMed DOI PMC
Ankrah NYD, Chouaia B, Douglas AE. 2018. The cost of metabolic interactions in symbioses between insects and bacteria with reduced genomes. mBio 9:mBio doi:10.1128/mBio.01433-18 PubMed DOI PMC
McCutcheon JP, Moran NA. 2007. Parallel Genomic evolution and metabolic interdependence in an ancient symbiosis. Proc Natl Acad Sci U S A 104:19392–19397. doi:10.1073/pnas.0708855104 PubMed DOI PMC
McCutcheon JP, McDonald BR, Moran NA. 2009. Convergent evolution of metabolic roles in bacterial co-symbionts of insects. Proc Natl Acad Sci U S A 106:15394–15399. doi:10.1073/pnas.0906424106 PubMed DOI PMC
McCutcheon JP, Moran NA. 2010. Functional convergence in reduced genomes of bacterial symbionts spanning 200 my of evolution. Genome Biol Evol 2:708–718. doi:10.1093/gbe/evq055 PubMed DOI PMC
Mao M, Yang X, Poff K, Bennett G. 2017. 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 9:1803–1815. doi:10.1093/gbe/evx134 PubMed DOI PMC
Bennett GM, Mao M. 2018. Comparative genomics of a quadripartite symbiosis in a planthopper host reveals the origins and rearranged nutritional responsibilities of anciently diverged bacterial lineages. Environ Microbiol 20:4461–4472. doi:10.1111/1462-2920.14367 PubMed DOI
Michalik A, Castillo Franco D, Kobiałka M, Szklarzewicz T, Stroiński A, Łukasik P. 2021. Alternative transmission patterns in independently acquired nutritional cosymbionts of Dictyopharidae planthoppers. mBio 12:e0122821. doi:10.1128/mBio.01228-21 PubMed DOI PMC
Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H. 2000. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407:81–86. doi:10.1038/35024074 PubMed DOI
Lamelas A, Gosalbes MJ, Manzano-Marín A, Peretó J, Moya A, Latorre A. 2011. Serratia symbiotica from the aphid Cinara cedri: a missing link from facultative to obligate insect endosymbiont. PLoS Genet 7:e1002357. doi:10.1371/journal.pgen.1002357 PubMed DOI PMC
Manzano-Marín A, Simon J-C, Latorre A. 2016. Reinventing the wheel and making it round again: evolutionary convergence in Buchnera-Serratia Symbiotic consortia between the distantly related Lachninae aphids Tuberolachnus salignus and Cinara cedri. Genome Biol Evol 8:1440–1458. doi:10.1093/gbe/evw085 PubMed DOI PMC
Yorimoto S, Hattori M, Kondo M, Shigenobu S. 2022. Complex host/symbiont integration of a multi-partner symbiotic system in the Eusocial aphid Ceratovacuna japonica. iScience 25:105478. doi:10.1016/j.isci.2022.105478 PubMed DOI PMC
Thao ML, Moran NA, Abbot P, Brennan EB, Burckhardt DH, Baumann P. 2000. Cospeciation of psyllids and their primary prokaryotic endosymbionts. Appl Environ Microbiol 66:2898–2905. doi:10.1128/AEM.66.7.2898-2905.2000 PubMed DOI PMC
Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA, Hattori M. 2006. The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314:267. doi:10.1126/science.1134196 PubMed DOI
Tamames J, Gil R, Latorre A, Peretó J, Silva FJ, Moya A. 2007. The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii. BMC Evol Biol 7:181. doi:10.1186/1471-2148-7-181 PubMed DOI PMC
Sloan DB, Moran NA. 2012. Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids. Mol Biol Evol 29:3781–3792. doi:10.1093/molbev/mss180 PubMed DOI PMC
Hall AAG, Morrow JL, Fromont C, Steinbauer MJ, Taylor GS, Johnson SN, Cook JM, Riegler M. 2016. Codivergence of the primary bacterial endosymbiont of psyllids versus host switches and replacement of their secondary bacterial endosymbionts. Environ Microbiol 18:2591–2603. doi:10.1111/1462-2920.13351 PubMed DOI
Fromont C, Riegler M, Cook JM. 2016. Phylogeographic analyses of bacterial endosymbionts in fig homotomids (Hemiptera: Psylloidea) reveal codiversification of both primary and secondary endosymbionts. FEMS Microbiol Ecol 92:fiw205. doi:10.1093/femsec/fiw205 PubMed DOI
Sloan DB, Nakabachi A, Richards S, Qu J, Murali SC, Gibbs RA, Moran NA. 2014. Parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects. Mol Biol Evol 31:857–871. doi:10.1093/molbev/msu004 PubMed DOI PMC
Fukatsu T, Nikoh N. 1998. Two intracellular symbiotic bacteria from the mulberry psyllid Anomoneura mori (Insecta, Homoptera). Appl Environ Microbiol 64:3599–3606. doi:10.1128/AEM.64.10.3599-3606.1998 PubMed DOI PMC
Subandiyah S, Nikoh N, Tsuyumu S, Somowiyarjo S, Fukatsu T. 2000. Complex endosymbiotic microbiota of the citrus psyllid Diaphorina citri (Homoptera: Psylloidea). Zoolog Sci 17:983–989. doi:10.2108/zsj.17.983 DOI
Nakabachi A, Ueoka R, Oshima K, Teta R, Mangoni A, Gurgui M, Oldham NJ, van Echten-Deckert G, Okamura K, Yamamoto K, Inoue H, Ohkuma M, Hongoh Y, Miyagishima S, Hattori M, Piel J, Fukatsu T. 2013. Defensive bacteriome symbiont with a drastically reduced genome. Curr Biol 23:1478–1484. doi:10.1016/j.cub.2013.06.027 PubMed DOI
Nakabachi A, Piel J, Malenovský I, Hirose Y. 2020. Comparative genomics underlines multiple roles of Profftella, an obligate symbiont of psyllids: providing toxins, vitamins, and carotenoids. Genome Biol Evol 12:1975–1987. doi:10.1093/gbe/evaa175 PubMed DOI PMC
Morrow JL, Hall AAG, Riegler M. 2017. Symbionts in waiting: the dynamics of incipient endosymbiont complementation and replacement in minimal bacterial communities of psyllids. Microbiome 5:58. doi:10.1186/s40168-017-0276-4 PubMed DOI PMC
Morrow JL, Om N, Beattie GAC, Chambers GA, Donovan NJ, Liefting LW, Riegler M, Holford P. 2020. Characterization of the bacterial communities of psyllids associated with Rutaceae in Bhutan by high throughput sequencing. BMC Microbiol 20:215. doi:10.1186/s12866-020-01895-4 PubMed DOI PMC
Kwak Y, Sun P, Meduri VR, Percy DM, Mauck KE, Hansen AK. 2021. Uncovering symbionts across the psyllid tree of life and the discovery of a new Liberibacter species, "Candidatus Liberibacter capsica". Front Microbiol 12:739763. doi:10.3389/fmicb.2021.739763 PubMed DOI PMC
Nakabachi A, Inoue H, Hirose Y. 2022. Microbiome analyses of 12 psyllid species of the family Psyllidae identified various bacteria including Fukatsuia and Serratia symbiotica, known as secondary symbionts of aphids. BMC Microbiol 22:15. doi:10.1186/s12866-021-02429-2 PubMed DOI PMC
Štarhová Serbina L, Gajski D, Pafčo B, Zurek L, Malenovský I, Nováková E, Schuler H, Dittmer J. 2022. Microbiome of pear psyllids: a tale about closely related species sharing their endosymbionts. Environ Microbiol 24:5788–5808. doi:10.1111/1462-2920.16180 PubMed DOI PMC
Schuler H, Dittmer J, Borruso L, Galli J, Fischnaller S, Anfora G, Rota-Stabelli O, Weil T, Janik K. 2022. Investigating the microbial community of Cacopsylla spp. as potential factor in vector competence of phytoplasma. Environ Microbiol 24:4771–4786. doi:10.1111/1462-2920.16138 PubMed DOI PMC
Dial DT, Weglarz KM, Aremu AO, Havill NP, Pearson TA, Burke GR, von Dohlen CD. 2022. Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae). ISME J 16:642–654. doi:10.1038/s41396-021-01102-w PubMed DOI PMC
Anbutsu H, Moriyama M, Nikoh N, Hosokawa T, Futahashi R, Tanahashi M, Meng XY, Kuriwada T, Mori N, Oshima K, Hattori M, Fujie M, Satoh N, Maeda T, Shigenobu S, Koga R, Fukatsu T. 2017. Small genome symbiont underlies cuticle hardness in beetles. Proc Natl Acad Sci U S A 114:E8382–E8391. doi:10.1073/pnas.1712857114 PubMed DOI PMC
Sloan DB, Moran NA. 2012. Endosymbiotic bacteria as a source of carotenoids in whiteflies. Biol Lett 8:986–989. doi:10.1098/rsbl.2012.0664 PubMed DOI PMC
Drohojowska J, Szwedo J, Müller P, Burckhardt D. 2020. New fossil from mid-cretaceous burmese amber confirms monophyly of Liadopsyllidae (Hemiptera: Psylloidea). Sci Rep 10:17607. doi:10.1038/s41598-020-74551-6 PubMed DOI PMC
Percy DM, Crampton‐Platt A, Sveinsson S, Lemmon AR, Lemmon EM, Ouvrard D, Burckhardt D. 2018. Resolving the psyllid tree of life: phylogenomic analyses of the superfamily Psylloidea (Hemiptera). Syst Entomol 43:762–776. doi:10.1111/syen.12302 DOI
Nakabachi A, Inoue H, Hirose Y. 2022. High-resolution microbiome analyses of nine psyllid species of the family Triozidae identified previously unrecognized but major bacterial populations, including Liberibacter and Wolbachia of supergroup O. Microbes Environ 37:ME22078. doi:10.1264/jsme2.ME22078 PubMed DOI PMC
Thao ML, Clark MA, Baumann L, Brennan EB, Moran NA, Baumann P. 2000. Secondary endosymbionts of psyllids have been acquired multiple times. Curr Microbiol 41:300–304. doi:10.1007/s002840010138 PubMed DOI
Morris JJ, Lenski RE, Zinser ER. 2012. The black queen hypothesis: evolution of dependencies through adaptive gene loss. mBio 3:e00036-12. doi:10.1128/mBio.00036-12 PubMed DOI PMC
Corretto E, Trenti M, Štarhová Serbina L, Howie JM, Dittmer J, Kerschbamer C, Candian V, Tedeschi R, Janik K, Schuler H. 2023. Multiple factors driving the acquisition efficiency of apple proliferation phytoplasma in Cacopsylla melanoneura. Journal of Pest Science, in press. doi:10.21203/rs.3.rs-2646791/v1 PubMed DOI PMC
Jarausch B, Tedeschi R, Sauvion N, Gross J, Jarausch W. 2019. Psyllid vectors, p 53–78. In Bertaccini A, Weintraub PG, Rao GP, Mori N (ed), Phytoplasmas: plant pathogenic bacteria II. Springer, Singapore. doi:10.1007/978-981-13-2832-9 DOI
Oettl S, Schlink K. 2015. Molecular identification of two vector species, Cacopsylla melanoneura and Cacopsylla picta (Hemiptera: Psyllidae), of apple proliferation disease and further common psyllids of northern Italy. J Econ Entomol 108:2174–2183. doi:10.1093/jee/tov204 PubMed DOI
Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094–3100. doi:10.1093/bioinformatics/bty191 PubMed DOI PMC
Kolmogorov M, Bickhart DM, Behsaz B, Gurevich A, Rayko M, Shin SB, Kuhn K, Yuan J, Polevikov E, Smith TPL, Pevzner PA. 2020. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat Methods 17:1103–1110. doi:10.1038/s41592-020-00971-x PubMed DOI PMC
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410. doi:10.1016/S0022-2836(05)80360-2 PubMed DOI
Zimin AV, Salzberg SL. 2020. The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies. PLoS Comput Biol 16:e1007981. doi:10.1371/journal.pcbi.1007981 PubMed DOI PMC
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736. doi:10.1101/gr.215087.116 PubMed DOI PMC
Pryszcz LP, Gabaldón T. 2016. Redundans: an assembly pipeline for highly heterozygous genomes. Nucleic Acids Res 44:e113. doi:10.1093/nar/gkw294 PubMed DOI PMC
Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. 2020. Using SPAdes de novo assembler. Curr Protoc Bioinformatics 70:e102. doi:10.1002/cpbi.102 PubMed DOI
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212. doi:10.1093/bioinformatics/btv351 PubMed DOI
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. doi:10.1093/nar/gkw569 PubMed DOI PMC
Emms DM, Kelly S. 2019. Orthofinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20:238. doi:10.1186/s13059-019-1832-y PubMed DOI PMC
R Core Team . 2021. R: A language and environment for statistical computing, R foundation for statistical computing, Vienna, Austria. Available from: https://www.R-project.org
Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. 2021. EggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 38:5825–5829. doi:10.1093/molbev/msab293 PubMed DOI PMC
Kanehisa M, Sato Y, Morishima K. 2016. BlastKOALA and Ghostkoala: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428:726–731. doi:10.1016/j.jmb.2015.11.006 PubMed DOI
Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. doi:10.1093/nar/gkh340 PubMed DOI PMC
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37:1530–1534. doi:10.1093/molbev/msaa131 PubMed DOI PMC
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. 2017. Modelfinder: fast model selection for accurate phylogenetic estimates. Nat Methods 14:587–589. doi:10.1038/nmeth.4285 PubMed DOI PMC
Chernomor O, von Haeseler A, Minh BQ. 2016. Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol 65:997–1008. doi:10.1093/sysbio/syw037 PubMed DOI PMC