New insight into the bark beetle ips typographus bacteriome reveals unexplored diversity potentially beneficial to the host

. 2023 Jun 09 ; 18 (1) : 53. [epub] 20230609

Status PubMed-not-MEDLINE Jazyk angličtina Země Velká Británie, Anglie Médium electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid37296446

Grantová podpora
19-09072S Grantová Agentura České Republiky

Odkazy

PubMed 37296446
PubMed Central PMC10257263
DOI 10.1186/s40793-023-00510-z
PII: 10.1186/s40793-023-00510-z
Knihovny.cz E-zdroje

BACKGROUND: Ips typographus (European spruce bark beetle) is the most destructive pest of spruce forests in Europe. As for other animals, it has been proposed that the microbiome plays important roles in the biology of bark beetles. About the bacteriome, there still are many uncertainties regarding the taxonomical composition, insect-bacteriome interactions, and their potential roles in the beetle ecology. Here, we aim to deep into the ecological functions and taxonomical composition of I. typographus associated bacteria. RESULTS: We assessed the metabolic potential of a collection of isolates obtained from different life stages of I. typographus beetles. All strains showed the capacity to hydrolyse one or more complex polysaccharides into simpler molecules, which may provide an additional carbon source to its host. Also, 83.9% of the strains isolated showed antagonistic effect against one or more entomopathogenic fungi, which could assist the beetle in its fight against this pathogenic threat. Using culture-dependent and -independent techniques, we present a taxonomical analysis of the bacteriome associated with the I. typographus beetle during its different life stages. We have observed an evolution of its bacteriome, which is diverse at the larval phase, substantially diminished in pupae, greater in the teneral adult phase, and similar to that of the larval stage in mature adults. Our results suggest that taxa belonging to the Erwiniaceae family, and the Pseudoxanthomonas and Pseudomonas genera, as well as an undescribed genus within the Enterobactereaceae family, are part of the core microbiome and may perform vital roles in maintaining beetle fitness. CONCLUSION: Our results indicate that isolates within the bacteriome of I. typographus beetle have the metabolic potential to increase beetle fitness by proving additional and assimilable carbon sources for the beetle, and by antagonizing fungi entomopathogens. Furthermore, we observed that isolates from adult beetles are more likely to have these capacities but those obtained from larvae showed strongest antifungal activity. Our taxonomical analysis showed that Erwinia typographi, Pseudomonas bohemica, and Pseudomonas typographi species along with Pseudoxanthomonas genus, and putative new taxa belonging to the Erwiniaceae and Enterobacterales group are repeatedly present within the bacteriome of I. typographus beetles, indicating that these species might be part of the core microbiome. In addition to Pseudomonas and Erwinia group, Staphylococcus, Acinetobacter, Curtobacterium, Streptomyces, and Bacillus genera seem to also have interesting metabolic capacities but are present in a lower frequency. Future studies involving bacterial-insect interactions or analysing other potential roles would provide more insights into the bacteriome capacity to be beneficial to the beetle.

Zobrazit více v PubMed

García-Fraile P. Roles of bacteria in the bark beetle holobiont – how do they shape this forest pest? Ann Appl Biol. 2018;172:111–25. doi: 10.1111/aab.12406. DOI

Vitali V, Büntgen U, Bauhus J. Seasonality matters—the effects of past and projected seasonal climate change on the growth of native and exotic conifer species in Central Europe. Dendrochronologia. 2018;48:1–9. doi: 10.1016/j.dendro.2018.01.001. DOI

Schebeck M, Hansen EM, Schopf A, Ragland GJ, Stauffer C, Bentz BJ. Diapause and overwintering of two spruce bark beetle species. Physiol Entomol. 2017;42:200–10. doi: 10.1111/phen.12200. PubMed DOI PMC

Biedermann PHW, Müller J, Grégoire JC, Gruppe A, Hagge J, Hammerbacher A, et al. Bark Beetle Population Dynamics in the Anthropocene: Challenges and Solutions. Trends Ecol Evol. 2019;34:914–24. doi: 10.1016/j.tree.2019.06.002. PubMed DOI

Wood TG, Thomas RJ. The mutualistic association between Macrotermitinae and Termitomyces. Insect-fungus interactions. 1989;14:69–92. 10.1016/C2009-0-02797-4.

Mattanovich J, Ehrenhöfer M, Schafellner C, Tausz M, Führer E. The role of sulphur compounds for breeding success of Ips typographus L. (Col., Scolytidae) on Norway Spruce (Picea abies [L.] Karst) J Appl Entomol. 2001;125:425–31. doi: 10.1046/j.1439-0418.2001.00572.x. DOI

Morales-Jiménez J, Vera-Ponce de León A, García-Domínguez A, Martínez-Romero E, Zúñiga G, Hernández-Rodríguez C. Nitrogen-Fixing and uricolytic Bacteria Associated with the gut of Dendroctonus rhizophagus and Dendroctonus valens (Curculionidae: Scolytinae) Microb Ecol. 2013;66:200–10. doi: 10.1007/s00248-013-0206-3. PubMed DOI

Wegensteiner R, Weiser J. Annual variation of pathogen occurrence and pathogen prevalence in Ips typographus (Coleoptera, Scolytidae) from the BOKU University Forest Demonstration Centre. J Pest Sci. 2004;77:221–8. doi: 10.1007/s10340-004-0056-3. DOI

Wegensteiner R, Wermelinger B, Herrmann M. Natural enemies of Bark Beetles: Predators, Parasitoids, Pathogens, and nematodes. In Bark Beetles: Biology and Ecology of native and invasive species. Elsevier sci. 2015;7:247–304. doi: 10.1016/B978-0-12-417156-5.00007-1. DOI

Wermelinger B. Ecology and management of the spruce bark beetle Ips typographus—a review of recent research. For Ecol Manag. 2004;202:67–82. doi: 10.1016/j.foreco.2004.07.018. DOI

Morales-Jiménez J, Zúñiga G, Ramírez-Saad HC, Hernández-Rodríguez C. Gut-Associated Bacteria throughout the life cycle of the Bark Beetle Dendroctonus rhizophagus Thomas and Bright (Curculionidae: Scolytinae) and their cellulolytic activities. Microb Ecol. 2012;64:268–78. doi: 10.1007/s00248-011-9999-0. PubMed DOI

Boone CK, Keefover-Ring K, Mapes AC, Adams AS, Bohlmann J, Raffa KF. Bacteria Associated with a tree-killing insect reduce concentrations of Plant Defense Compounds. J Chem Ecol. 2013;39:1003–6. doi: 10.1007/s10886-013-0313-0. PubMed DOI

Six DL. The bark beetle holobiont: why microbes matter. J Chem Ecol. 2013;39:989–1002. doi: 10.1007/s10886-013-0318-8. PubMed DOI

Cheng C, Wickham JD, Chen L, Xu D, Lu M, Sun J. Bacterial microbiota protect an invasive bark beetle from a pine defensive compound. Microbiome. 2018;6:1–16. doi: 10.1186/s40168-018-0518-0. PubMed DOI PMC

Six DL. Bark beetle-fungus symbioses. Insect symbiosis. 2003;1:97–114. doi: 10.1201/9780203009918. PubMed DOI PMC

Chakraborty A, Modlinger R, Ashraf MZ, Synek J, Schlyter F, Roy A. Core Mycobiome and their ecological relevance in the gut of five Ips bark beetles (Coleoptera: Curculionidae: Scolytinae) Front Microbiol. 2020;11:2134. doi: 10.3389/fmicb.2020.568853. PubMed DOI PMC

Chakraborty A, Ashraf MZ, Modlinger R, Synek J, Schlyter F, Roy A. Unravelling the gut bacteriome of Ips (Coleoptera: Curculionidae: Scolytinae): identifying core bacterial assemblage and their ecological relevance. Sci Rep. 2020;10:1–17. doi: 10.1038/s41598-020-75203-5. PubMed DOI PMC

Fang JX, Zhang SF, Liu F, Zhang X, Zhang FB, Guo XB, et al. Differences in gut bacterial Communities of Ips typographus (Coleoptera: Curculionidae) Induced by Enantiomer-Specific α-Pinene. Environ Entomol. 2020;49(5):1198–205. doi: 10.1093/ee/nvaa098. PubMed DOI

Veselská T, Švec K, Kostovčík M, Peral-Aranega E, Garcia-Fraile P, Křížková B et al. Proportions of taxa belonging to the gut core microbiome change throughout the life cycle and season of the bark beetle Ips typographus. FEMS Microbiol Ecol. Under review. PubMed

Fabryová A, Kostovčík M, Díez-Méndez A, Jiménez-Gómez A, Celador-Lera L, Saati-Santamaría Z, et al. On the bright side of a forest pest-the metabolic potential of bark beetles’ bacterial associates. Sci Total Environ. 2018;619–620:9–17. doi: 10.1016/j.scitotenv.2017.11.074. PubMed DOI

Peral-Aranega E, Saati-Santamaría Z, Kolařik M, Rivas R, García-Fraile P. Bacteria belonging to pseudomonas typographi sp. Nov. from the bark beetle ips typographus have genomic potential to aid in the host ecology. Insects. 2020;11:1–22. doi: 10.3390/insects11090593. PubMed DOI PMC

Skrodenytee-Arbaciauskiene V, Radziute S, Stunzenas V, Buda V. Erwinia typographi sp. nov., isolated from bark beetle (Ips typographus) gut. IJSEM. 2012;62:942–8. doi: 10.1099/ijs.0.030304-0. PubMed DOI

Cain CC, Henry AT, Waldo RH, Casida J, Falkinham JO. Identification and characteristics of a novel Burkholderia strain with broad-spectrum antimicrobial activity. Appl Environ Microbiol. 2000;66:4139–41. doi: 10.1128/AEM.66.9.4139-4141.2000. PubMed DOI PMC

Raaijmakers JM, de Bruijn I, Nybroe O, Ongena M. Natural functions of lipopeptides from Bacillus and Pseudomonas: more than surfactants and antibiotics. FEMS Microbiol Rev. 2010;34:1037–62. doi: 10.1111/j.1574-6976.2010.00221.x. PubMed DOI

Winding A, Binnerup SJ, Pritchard H. Non-target effects of bacterial biological control agents suppressing root pathogenic fungi. FEMS Microbiol Ecol. 2004;47:129–41. doi: 10.1016/S0168-6496(03)00261-7. PubMed DOI

González-Dominici LI, Saati-Santamaría Z, García-Fraile P. Genome analysis and genomic comparison of the Novel Species Arthrobacter ipsi Reveal its potential protective role in its Bark Beetle host. Microb Ecol. 2021;81:471–82. doi: 10.1007/s00248-020-01593-8. PubMed DOI

Saati-Santamaría Z, López-Mondéjar R, Jiménez-Gómez A, Díez-Méndez A, Vetrovský T, Igual JM, et al. Discovery of phloeophagus beetles as a source of pseudomonas strains that produce potentially new bioactive substances and description of pseudomonas bohemica sp. nov. Front Microbiol. 2018;9:913. doi: 10.3389/fmicb.2018.00913. PubMed DOI PMC

Rivas R, García-Fraile P, Mateos PF, Martínez-Molina E, Velázquez E. Characterization of xylanolytic bacteria present in the bract phyllosphere of the date palm Phoenix dactylifera. Lett Appl Microbiol. 2007;44:181–7. doi: 10.1111/j.1472-765X.2006.02050.x. PubMed DOI

Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95–8.

Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, et al. Introducing EzTaxon-e: a prokaryotic 16s rRNA gene sequence database with phylotypes that represent uncultured species. IJSEM. 2012;62:716–21. doi: 10.1099/ijs.0.038075-0. PubMed DOI

Sagova-Mareckova M, Cermak L, Novotna J, Plhackova K, Forstova J, Kopecky J. Innovative methods for soil DNA purification tested in soils with widely differing characteristics. Appl Environ Microbiol. 2008;74(9):2902–7. doi: 10.1128/AEM.02161-07. PubMed DOI PMC

Chelius MK, Triplett EW. The diversity of Archaea and Bacteria in Association with the roots of Zea mays L. Microb Ecol. 2001;252–63. 10.1007/s002480000087. PubMed

Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N. The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol. 2010;12(11):2885–93. doi: 10.1111/j.1462-2920.2010.02258.x. PubMed DOI PMC

Minard G, Tran F-H, Dubost A, Tran-Van V, Mavingui P, et al. Pyrosequencing 16S rRNA genes of bacteria associated with wild tiger mosquito Aedes albopictus: a pilot study. Front Cell Infect Microbiol. 2014;4:59. doi: 10.3389/fcimb.2014.00059. PubMed DOI PMC

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 2019;37(8):852–7. doi: 10.7287/peerj.preprints.27295v1. PubMed DOI PMC

Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP. Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000research. 2016;5. https://doi.org/10.12688%2Ff1000research.8986.2. PubMed PMC

Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome. 2018;6(1):1–17. doi: 10.1186/s40168-018-0470-z. PubMed DOI PMC

Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018;35:1547–9. doi: 10.1093/molbev/msy096. PubMed DOI PMC

Thompson JD, Higgins DG, Gibson TJ, CLUSTAL W. Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673–80. doi: 10.1093/nar/22.22.4673. PubMed DOI PMC

Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947–8. doi: 10.1093/bioinformatics/btm404. PubMed DOI

Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993;10(3):512–26. doi: 10.1093/oxfordjournals.molbev.a040023. PubMed DOI

Mateos PF, Jimenez-Zurdo JI, Chen J, Squartini AS, Haack SK, Martinez-Molina E, et al. Cell-associated pectinolytic and cellulolytic enzymes in Rhizobium leguminosarum biovar trifolii. App Environ Microbiol. 1992;58:1816–22. doi: 10.1128/aem.58.6.1816-1822.1992. PubMed DOI PMC

García-Fraile P, Rivas R, Willems A, Peix A, Martens M, Martínez-Molina E, et al. Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba. IJSEM. 2007;57:844–8. doi: 10.1099/ijs.0.64680-0. PubMed DOI

Jiménez-Gómez A, Saati-Santamaría Z, Igual JM, Rivas R, Mateos PF, García-Fraile P. Genome insights into the Novel Species Microvirga brassicacearum, a rapeseed endophyte with biotechnological potential. Microorganisms. 2019;7:354. doi: 10.3390/microorganisms7090354. PubMed DOI PMC

Kubátová A, Dvořák L. Entomopathogenic fungi associated with insect hibernating in underground shelters. Czech Mycol. 2005;57:221–37. doi: 10.33585/cmy.57303. DOI

Pažoutová S, Šrůtka P, Holuša J, Chudíčková M, Kolařík M. Diversity of xylariaceous symbionts in Xiphydria woodwasps: role of vector and a host tree. Fungal Ecol. 2010;3:392–401. doi: 10.1016/j.funeco.2010.07.002. DOI

Sulochana MB, Jayachandra SY, Kumar SKA, Dayanand A. Antifungal attributes of siderophore produced by the Pseudomonas aeruginosa JAS-25. J Basic Microbiol. 2014;54:418–24. doi: 10.1002/jobm.201200770. PubMed DOI

Biedermann PHW, Müller J, Grégoire JC, Gruppe A, Hagge J, Hammerbacher A, et al. Bark Beetle Population Dynamics in the Anthropocene: Challenges and Solutions. Trends Ecol Evol. 2019;34:914–24. doi: 10.1016/j.tree.2019.06.002. PubMed DOI

Claesson MJ, Wang Q, O’Sullivan O, Greene-Diniz R, Cole JR, Ross RP, O’Toole PW. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res. 2010;38(22):e200–0. doi: 10.1093/nar/gkq873. PubMed DOI PMC

De Vries EJ, Jacobs G, Sabelis MW, Menken SB, Breeuwer JA. Diet–dependent effects of gut bacteria on their insect host: the symbiosis of Erwinia sp. and western flower thrips. Proc. Royal Soc. B, 2004;271(1553):2171–2178. 10.1098/rspb.2004.2817. PubMed PMC

Saati-Santamaría Z, Rivas R, Kolařik M, García-Fraile P. A new perspective of Pseudomonas—host interactions: distribution and potential ecological functions of the genus Pseudomonas within the Bark Beetle Holobiont. Biology. 2021;10(2):16. doi: 10.3390/biology10020164. PubMed DOI PMC

Yilmax H, Sezen K, Kati H, Demirbaǧ Z. The first study on the bacterial flora of the European spruce bark beetle, Dendroctonus micans (Coleoptera: Scolytidae) Biología. 2006;61:679–86. doi: 10.2478/s11756-006-0140-7. DOI

Hu X, Yu J, Wang C, Chen H. Cellulolytic Bacteria Associated with the gut of Dendroctonus armandi Larvae (Coleoptera: Curculionidae: Scolytinae) Forests. 2014;5:455–65. doi: 10.3390/f5030455. DOI

Bright M, Bulgheresi S. A complex journey: transmission of microbial symbionts. Nat Rev Microbiol. 2010;8:218–30. doi: 10.1038/nrmicro2262. PubMed DOI PMC

Carter DO, Metcalf JL, Bibat A, Knight R. Seasonal variation of postmortem microbial communities. Forensic Sci Med Pathol. 2015;11(2):202–7. doi: 10.1007/s12024-015-9667-7. PubMed DOI PMC

Muthukrishnan S, Mun S, Noh MY, Geisbrecht ER, Arakane Y. Insect cuticular chitin contributes to form and function. Curr Pharm Des. 2020;26(29):3530–45. doi: 10.2174/1381612826666200523175409. PubMed DOI PMC

Banskar S, Mourya DT, Shouche YS. Bacterial diversity indicates dietary overlap among bats of different feeding habits. Microbiol Res. 2016;182:99–108. doi: 10.1016/j.micres.2015.10.006. PubMed DOI

Six DL. Ecological and evolutionary determinants of bark beetle—fungus symbioses. Insects. 2012;3(1):339–66. doi: 10.3390/insects3010339. PubMed DOI PMC

Wilson MK, Abergel RJ, Raymond KN, Arceneaux JEL, Byers BR. Siderophores of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis. Biochem Biophys Res Commun. 2006;348:320–5. doi: 10.1016/j.bbrc.2006.07.055. PubMed DOI

Yu X, Ai C, Xin L, Zhou G. The siderophore-producing bacterium, Bacillus subtilis CAS15, has a biocontrol effect on Fusarium wilt and promotes the growth of pepper. Eur J Soil Biol. 2011;47:138–45. doi: 10.1016/j.ejsobi.2010.11.001. DOI

Raaska L, Mattila-Sandholm T. Effects of iron level on the anatagonistic action of siderophores from non-pathogenic Staphylococcus spp. J Ind Microbiol Biotechnol. 1995;15(6):480–5. doi: 10.1007/BF01570018. DOI

Nagpure A, Choudhary B, Kumar S, Gupta RK. Isolation and characterization of chitinolytic Streptomyces sp. MT7 and its antagonism towards wood-rotting fungi. Ann Microbiol. 2014;64:531–41. doi: 10.1007/s13213-013-0686-x. DOI

El-Goorani MA, Hassanein F, Shoeib A. Antibacterial and antifungal spectra of antibiotics produced by different strains of Erwinia herbicola (Pantoea agglomerans) J phytopathol. 1992;136:335–9. doi: 10.1111/j.1439-0434.1992.tb01316.x. DOI

Tenning P, van Rijsbergen R, Zhao Y, Joos H. Cloning and transfer of genes for antifungal compounds from Erwinia herbicola to Escherichia coli. Mol. Plant Microbe Interact. 1993;6:474–80. doi: 10.1094/mpmi-6-474. PubMed DOI

Liu CH, Chen X, Liu TT, Lian B, Gu Y, Caer V, Xue YR, Wang BT. Study of the antifungal activity of Acinetobacter baumannii LCH001 in vitro and identification of its antifungal components. Appl Microbiol Biotech. 2007;76(2):459–66. doi: 10.1007/s00253-007-1010-0. PubMed DOI

Prapagdee B, Kuekulvong C, Mongkolsuk S. Antifungal potential of extracellular metabolites produced by Streptomyces hygroscopicus against phytopathogenic fungi. Int J Biol Sci. 2008;4(5):330. doi: 10.7150/ijbs.4.330. PubMed DOI PMC

León M, Yaryura PM, Montecchia MS, Hernández AI, Correa OS, Pucheu NL et al. Antifungal Activity of Selected Indigenous Pseudomonas and Bacillus from the Soybean Rhizosphere. Int J Microbiol. 2009;2009. 10.1155/2009/572049. PubMed PMC

Kupferschmied P, Maurhofer M, Keel C. Promise for plant pest control: root-associated pseudomonads with insecticidal activities. Front Plant Sci. 2013;4:287. doi: 10.3389/fpls.2013.00287. PubMed DOI PMC

Bhattacharjee R. An overview of fungal and bacterial biopesticides to control plant pathogens/diseases. Afr J Microbiol Res. 2014;8:1749–62. doi: 10.5897/AJMR2013.6356. DOI

Alijani Z, Amini J, Ashengroph M, Bahramnejad B. Antifungal activity of volatile compounds produced by Staphylococcus sciuri strain MarR44 and its potential for the biocontrol of Colletotrichum nymphaeae, causal agent strawberry anthracnose. Int J Food Microbiol. 2019;307:108276. doi: 10.1016/j.ijfoodmicro.2019.108276. PubMed DOI

Augustine SK, Bhavsar SP, Kapadnis BP. A non-polyene antifungal antibiotic from Streptomyces albidoflavus PU 23. J Biosci. 2005;30:201–11. doi: 10.1007/BF02703700. PubMed DOI

Erler F, Ates AO. Potential of two entomopathogenic fungi, Beauveria bassiana and metarhizium anisopliae (Coleoptera: Scarabaeidae), as biological control agents against the June beetle. J Insect Sci. 2015;15(1):44. doi: 10.1093/jisesa/iev029. PubMed DOI PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...