Metagenomic analysis of the microbiota of a laboratory mite population of Neoseiulus californicus (mesostigmata, phytoseiidae) and the optimisation of microbiota composition to improve mite breeding efficiency

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Abstract

Experimental modelling of the microbiota of a biocontrol population of the predatory mite, Neoseiulus californicus bred on the spider mite, Tetranychus urticae was carried out to both eliminate bacterial pathogens and increase the viability of the mite line. We produced an isofemale line of N. californicus BioDefence2 and a derived line with an optimised microbiota BioDefence3. The microbiota was optimised by a sequential treatment of the mite line with tetracycline to eliminate pathogenic bacteria, followed by a treatment with the probiotic bacterium, Bacillus subtilis to restore the viability of the mite line. The microbiotas of the BioDefence2 and BioDefence3 mite lines were compared using metagenomic 16S rRNA gene data. The metagenomic data were extracted from the hologenomes of the mite lines obtained through Oxford Nanopore long read sequencing. The bacterial species comprising the microbiotas of the original and optimised mite lines were identified. The saprophytic soil bacteria, Stenotrophomonas maltophilia, Acinetobacter johnsonii and Enterobacter hormaechei, also known as opportunistic human pathogens, form the basis of the N. californicus microbiota. The optimization of the microbiota eliminates the intracellular bacterium, Renibacterium salmoninarum, a well-known fish pathogen. The effect of mite microbiota optimisation on the viability of the biocontrol population of N. californicus is discussed. The results obtained may provide a basis for improving the technology of N. californicus rearing.

Full Text

Restricted Access

About the authors

B. V. Andrianov

Vavilov Institute of General Genetics, Russian Academy of Sciences

Author for correspondence.
Email: andrianovb@mail.ru
Russian Federation, Moscow, 119333

L. A. Uroshlev

Vavilov Institute of General Genetics, Russian Academy of Sciences

Email: leoniduroshlev@gmail.com
Russian Federation, Moscow, 119333

O. V. Vasilenko

All-Russia Collection of Microorganisms, G. K. Skryabin Institute of the Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences

Email: ovvasilenko@gmail.com
Russian Federation, Pushchino, 142290

Y. I. Meshkov

All-Russia Scientific Research Institute of Phytopathology

Email: yimeshkov@rambler.ru
Russian Federation, Moscow Oblast, Odintsovsky District, Bolshiye Vyazyomy, 143050

References

  1. Akyazi R., Liburd O.E., 2019. Biological Control of the Twospotted Spider Mite (Trombidiformes: Tetranychidae) with the Predatory Mite Neoseiulus californicus (Mesotigmata: Phytoseiidae) in Blackberries // Florida Entomologist. V. 102. P. 373– 381. https://doi.org/10.1653/024.102.0217
  2. Andrianov B.V., 2022. Bacterial Symbionts and Pathogens in Populations of Phytoseiidae Mites (Phytoseiidae, Mesostigmata) // Biology Bulletin Reviews. V. 12. P. S78–S84. https://doi.org/10.1134/S2079086422070027
  3. Becnel J.J., Jeyaprakash A., Hoy M.A., Shapiro A., 2002. Morphological and molecular characterization of a new microsporidian species from the predatory mite Metaseiulus occidentalis (Nesbitt) (Acari, Phytoseiidae) // Journal of Invertebrate Pathology. V. 79. № 3. P. 163–172. https://doi.org/10.1016/s0022-2011(02)00032-0
  4. Breeuwer J.A.J., Jacobs G., 1996. Wolbachia: intracellular manipulators of mite reproduction // Experimental and Applied Acarology. V. 20. P. 421–434.
  5. Emms D.M., Kelly S., 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics // Genome Biology. V. 20. P. 238. https://doi.org/10.1186/s13059-019-1832-y
  6. Enigl M., Schausberger P., 2007. Incidence of the endosymbionts Wolbachia, Cardinium and Spiroplasma in phytoseiid mites and associated prey // Experimental and Applied Acarology. V. 42. P. 75–85. https://doi.org/10.1007/s10493-007-9080-3
  7. Famah S.N., Hanna R., Breeuwer J.A., et al., 2014. The endosymbionts Wolbachia and Cardinium and their effects in three populations of the predatory mite Neoseiulus paspalivorus // Experimental and Applied Acarology. V. 64. P. 207–221. https://doi.org/10.1007/s10493-014-9820-0
  8. Glinushkin A.P., Yakovleva I.N., Meshkov Y.I., 2019. The impact of pesticides used in greenhouses, on the predatory mite Neoseiulus californicus (parasitiformes, phytoseiidae) // Rossiiskaia selskokhoziaistvennaia nauka. V. 3. P. 32–34. https://doi.org/10.31857/S2500-26272019332-34
  9. Gols R., Schutte C., Stouthamer R., et al., 2007. PCR-based identification of the pathogenic bacterium, Acaricomes phytoseiuli, in the biological control agent Phytoseiulus persimilis (Acari: Phytoseiidae) // Biological Control. V. 42. P. 316–325. https://doi.org/10.1016/j.biocontrol.2007.06.001
  10. Hejnar P., Bardon J., Sauer P, Kolár M., 2007. Stenotrophomonas maltophilia as a part of normal oral bacterial flora in captive snakes and its susceptibility to antibiotics // Veterinary Microbiology. V. 121. P. 357–362. https://doi.org/10.1016/j.vetmic.2006.12.026
  11. Hoy M., Jeyaprakash A., 2005. Microbial diversity in the predatory mite Metaseiulus occidentalis (Acari: Phytoseiidae) and its prey, Tetranychus urticae (Acari: Tetranychidae) // Biological Control. V. 32. P. 427– 441. https://doi.org/10.1016/j.biocontrol.2004.12.012
  12. Hoy M.A., Jeyaprakash A., 2008. Symbionts, including pathogens, of the predatory mite Metaseiulus occidentalis: current and future analysis methods // Experimental and Applied Acarology. V. 46. P. 329–347. https://doi.org/10.1007/s10493-008-9185-3
  13. Johanowicz D.L., Hoy M.A., 1996. Wolbachia in a Predator–Prey System: 16S Ribosomal DNA Analysis of Two Phytoseiids (Acari: Phytoseiidae) and Their Prey (Acari: Tetranychidae) // Annals of the Entomological Society of America. V. 89. P. 435–441. https://doi.org/10.1093/aesa/89.3.435
  14. Kim D., Song L., Breitwieser F.P., Salzberg S.L., 2016. Centrifuge: rapid and sensitive classification of metagenomic sequences // Genome Research. V. 12. P. 1721– 1729. https://doi.org/10.1101/gr.210641.116
  15. Koren S., Walenz B.P., Berlin K., Miller J.R., Bergman N.H., Phillippy A.M., 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation // Genome Research. V. 27. P. 722–736. https://doi.org/10.1101/gr.215087.116
  16. Manni M., Berkeley M.R., Seppey M., Simao F.A., Zdobnov E.M., 2021. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes // Molecular Biology and Evolution. V. 38. P. 4647–4654. https://doi.org/10.1093/molbev/msab199
  17. Merlin B.L., Moraes G.J., Cônsoli F.L., 2023. The Microbiota of a Mite Prey-Predator System on Different Host Plants Are Characterized by Dysbiosis and Potential Functional Redundancy // Microbial Ecology. V. 85. P. 1590–1607. https://doi.org/10.1007/s00248-022-02032-6
  18. Ondov B.D., Bergman N.H., Phillippy A.M., 2011. Interactive metagenomic visualization in a Web browser // BMC Bioinformatics. V. 12. P. 385. https://doi.org/10.1186/1471-2105-12-385
  19. Pekas A., Palevsky E., Sumner J.C. et al., 2017. Comparison of bacterial microbiota of the predatory mite Neoseiulus cucumeris (Acari: Phytoseiidae) and its factitious prey Tyrophagus putrescentiae (Acari: Acaridae) // Scientific Reports. V. 7. P. Article № 2. https://doi.org/10.1038/s41598-017-00046-6
  20. Rozas-Serri M., Lobos C., Correa R., et al., 2020. Atlantic Salmon Pre-smolt Survivors of Renibacterium salmoninarum Infection Show Inhibited Cell-Mediated Adaptive Immune Response and a Higher Risk of Death During the Late Stage of Infection at Lower Water Temperatures // Frontiers in Immunology. V. 11. Article № 13787. https://doi.org/10.3389/fimmu.2020.01378
  21. Sanchez N.E., Greco N.M., Cedola C.V., 2008. Biological Control by Neoseiulus californicus (McGregor) (Acari: Phytoseiidae). In: Capinera J.L. (eds) Encyclopedia of Entomology. Dordrecht: Springer. P. 493–495. https://doi.org/10.1007/978-1-4020-6359-6_319
  22. Schütte C., Gols R., Kleespies R.G., Poitevin O., Dicke M., 2008. Novel bacterial pathogen Acaricomes phytoseiuli causes severe disease symptoms and histopathological changes in the predatory mite Phytoseiulus persimilis (Acari, Phytoseiidae) // Journal of Invertebrate Pathology. V. 2. P. 127–135. https://doi.org/10.1016/j.jip.2008.03.006
  23. Sonoda S., Kohara Y., Siqingerile, Toyoshima S., Kishimoto H., Hinomoto N., 2012. Phytoseiid mite species composition in Japanese peach orchards estimated using quantitative sequencing // Experimental and Applied Acarology. V. 56. № 1. P. 9–22. https://doi.org/10.1007/s10493-011-9485-x
  24. Stanke M., Keller O., Gunduz I., Hayes A., Waack S., Morgenstern B., 2006. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Research. V. 34. № 2. P. 435–439. https://doi.org/10.1093/nar/gkl200
  25. Sumner-Kalkun J.C., Baxter I., Perotti M.A., 2023. Bacterial microbiota of three commercially mass-reared predatory mite species (Mesostigmata: Phytoseiidae): pathogenic and beneficial interactions // Frontiers in Arachnid Science. V. 2. Article № 1242716. https://doi.org/10.3389/frchs.2023.1242716
  26. Weeks A.R., Velten R., Stouthamer R., 2003. Incidence of a new sex-ratio-distorting endosymbiotic bacterium among arthropods // Proceedings of the Royal Society B.V. 270. P. 1857–1865. https://doi.org/10.1098/rspb.2003.2425
  27. Wu K., Hoy M.A., 2012. Cardinium is associated with reproductive incompatibility in the predatory mite Metaseiulus occidentalis (Acari: Phytoseiidae) // Journal of Invertebrate Pathology. V. 110. P. 359–365.
  28. Yang W., Yi Y., Xia Bo, 2023. Unveiling the duality of Pantoea dispersa: A mini review // Science of The Total Environment. V. 873. Article № 162320. https://doi.org/10.1016/j.scitotenv.2023.162320

Supplementary files

Supplementary Files
Action
1. JATS XML
Download
2. Fig. 1. Experimental setup for breeding laboratory lines of N. Californicus: a – rafts of bean leaves that are infected with spider mites and on which N. californicus mites feed under controlled conditions; b – a female of N. californicus, a maturing egg shines in the center of the body. Photo by Yu. I. Meshkov.

Download (181KB)
Indexing metadata
3. Fig. 2. Comparison of microbiota of BioDefence sublines. The color indicates the number of NumResds of each taxon, which is a rank estimate of the number of this species in the microbiota. The inset in the center shows the legend for the colors of the diagram with the matching color and number of NumResds. The numbers in the sectors of the diagram correspond to the number of bacterial species: a – microbiota of the BioDefence2 line, b – microbiota of the BioDefence3 line.

Download (819KB)
Indexing metadata
4. Fig. 3. Demographic structure of ticks in the BioDefence2 and BioDefence3 lines on the 7th day of the experiment. The blue color shows the BioDefence2 line, the red color shows the BioDefence3 line. The segments indicate 95% confidence intervals of the fraction error. On the vertical axis – the proportion of a group of ticks in the entire sample. On the horizontal axis there are groups of ticks. The data of 30 repetitions of the experiment on sheet clippings for each of the lines are summarized. A total of 1,576 ticks of all ages of the BioDefence2 line and 1,967 ticks of the BioDefence3 line were obtained.

Download (86KB)
Indexing metadata

Copyright (c) 2024 Russian Academy of Sciences