Skip to main content
Springer Nature - PMC COVID-19 Collection logoLink to Springer Nature - PMC COVID-19 Collection
. 2020 Nov 13;3(1):1–5. doi: 10.1007/s42832-020-0068-9

Lessons learned from COVID-19 on potentially pathogenic soil microorganisms

Haifeng Qian 1,, Qi Zhang 1, Tao Lu 1, W J G M Peijnenburg 2,3, Josep Penuelas 4,5, Yong-Guan Zhu 6,7,8
PMCID: PMC7661327  PMID: 40477108

The content is available as a PDF (749.4 KB).

Acknowledgments

This work was financially supported by the National Natural Science Foundation of China (41907210, 21777144, 21976161).

References

  1. Aundy, K., Munder, A., Aravind R., Eapen, S.J., Tümmler, B., Raaijmakers, J.M., 2012. Friend or foe: Genetic and functional characterization of plant endophytic Pseudomonas aeruginosa. Environmental Microbiology 15, 764–779. [DOI] [PubMed] [Google Scholar]
  2. Banerjee, S., Walder, F., Büchi, L., Meyer, M., Held, A., Gattinger, A., Keller, T., Charles, R., Van der Heijden, M., 2019. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME Journal 13, 1722–1736. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bassler, B., 1999. How bacteria talk to each other: regulation of gene expression by quorum sensing. Current Opinion in Microbiology 2, 582–587. [DOI] [PubMed] [Google Scholar]
  4. Bellas, C., Anesio, A., Barker, G., 2015. Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions. Frontiers in Microbiology 6, 656. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Berg, G., Eberl, L., Hartmann, A., 2005. The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environmental Microbiology 7, 1673–1685. [DOI] [PubMed] [Google Scholar]
  6. Boris, R., Nikolai, T., Alan, J.P., 2012. Climate change and zoonotic infections in the Russian Arctic. International Journal of Circumpolar Health 71, 18792. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Danovaro, R., Dell’Anno, A., Corinaldesi, C., Magagnini, M., Noble, R., Tamburini, C., Weinbauer, M., 2008. Major viral impact on the functioning of benthic deep-sea ecosystems. Nature 454, 1084–1087. [DOI] [PubMed] [Google Scholar]
  8. Foley, J., Defries, R., Asner, G., Barford, C., Bonan, G., Carpenter, S., Chapin III, F.S., Coe, M., Daily, G., Gibbs, H., Helkowski, J., Holloway, T., Howard, E., Kucharik, C., Monfreda, C., Patz, J., Prentice, I., Ramankutty, N., Snyder, P., 2005. Global consequences of land use. Science 309, 570–574. [DOI] [PubMed] [Google Scholar]
  9. Foley, J., Ramankutty, N., Brauman, K., Cassidy, E., Gerber, J., Johnston, M., Mueller, N., O’Connell, C., Ray, D., West, P., Balzer, C., Bennett, E., Carpenter, S., Hill, J., Monfreda, C., Polasky, S., Rockström, J., Sheehan, J., Siebert, S., Zaks, D., 2011. Solutions for a cultivated planet. Nature 478, 337–342. [DOI] [PubMed] [Google Scholar]
  10. Frenken, T., Brussaard, C., Velthuis, M., Aben, R., Kazanjian, G., Hilt, S., Kosten, S., Peeters, E., de Senerpont Domis, L., Stephan, S., Donk, E., Van de Waal, D., 2020. Warming advances virus population dynamics in a temperate freshwater plankton community. Limnology and Oceanography Letters 5, 295–304. [Google Scholar]
  11. Gans, J., Wolinsky, M., Dunbar, J., 2005. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309, 1387–1390. [DOI] [PubMed] [Google Scholar]
  12. Gattuso, J.-P., Magnan, A.; Billé, R., Cheung, W., Howes, E. L., Joos, F., Allemand, D., Bopp, L., Cooley, S., Eakin, C. M., Hoegh-Guldberg, O., Kelly, R., Pörtner, H.-O., Rogers, A., Baxter, J., Laffoley, D., Osborn, D., Rankovic, A., Rochette, J., Turley, C., 2015. Contrasting futures for ocean and society from different anthropogenic CO2 emissions scenarios. Science 349, 1–10. [DOI] [PubMed] [Google Scholar]
  13. Hofmann, A., Fischer, D., Hartmann, A., Schmid, M., 2014. Colonization of plants by human pathogenic bacteria in the course of organic vegetable production. Frontiers in Microbiology 5, 191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kwak, M.J., Kong, H.G., Choi, K., Kwon, S.K., Song, J.Y., Lee, J., Lee, P.A., Choi, S.Y., Seo, M., Lee, H.J., Jung, E.J., Park, H., Roy, N., Kim, H., Lee, M.M., Rubin, E.M., Lee, S.W., Kim, J.F., 2018. Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nature Biotechnology 36, 1100–1109. [DOI] [PubMed] [Google Scholar]
  15. Labbé, M., Girard, C., Vincent, W., Culley, A., 2020. Extreme viral partitioning in a marine-derived high arctic lake. MSphere 5, e00334–e20. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lawson, C., Harcombe, W., Hatzenpichler, R., Lindemann, S., Löffler, F., O’Malley, M., Martín, H., Pfleger, B., Raskin, L., Venturelli, O., Weissbrodt, D., Noguera, D., McMahon, K., 2019. Common principles and best practices for engineering microbiomes. Nature Reviews. Microbiology 17, 1–17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Leclerc, M., Doré, T., Gilligan, C., Lucas, P., Filipe, J., 2013. Host growth can cause invasive spread of crops by soilborne pathogens. PLoS One 8, e63003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Locatelli, A., Spor, A., Jolivet, C., Piveteau, P., Hartmann, A., 2013. Biotic and abiotic soil properties influence survival of listeria monocytogenes in soil. PLoS One 8, e75969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lynch, J., Hsiao, E., 2019. Microbiomes as sources of emergent host phenotypes. Science 365, 1405–1409. [DOI] [PubMed] [Google Scholar]
  20. Maurhofer, M., Keel, C., Schnider, U., Voisard, C., Haas, D., Défago, G., 1992. Influence of enhanced antibiotic production in pseudomonas fluorescens strain CHA0 on its disease suppressive capacity. Phytopathology 82, 190–195. [Google Scholar]
  21. Mendes, R., Garbeva, P., Raaijmakers, J., 2013. The rhizosphere microbiome: Significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiology Reviews 37, 34–63. [DOI] [PubMed] [Google Scholar]
  22. Mendes, R., Kruijt, M., Bruijn, I., Dekkers, E., Voort, M., Schneider, J., Piceno, Y., DeSantis, T., Andersen, G., Bakker, P., Raaijmakers, J., 2011. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332, 1097–1100. [DOI] [PubMed] [Google Scholar]
  23. Mueller, E., Wisnoski, N., Peralta, A., Lennon, J., 2019. Microbial rescue effects: How microbiomes can save hosts from extinction. Functional Ecology 00, 1–10. [Google Scholar]
  24. Mundt, C., 2002. Use of multiline cultivars and cultivar mixtures for disease management. Annual Review of Phytopathology 40, 381–410. [DOI] [PubMed] [Google Scholar]
  25. Raaijmakers, J., Mazzola, M., 2016. Soil immune responses. Science 352, 1392–1393. [DOI] [PubMed] [Google Scholar]
  26. Schierstaedt, J., Jechalke, S., Nesme, J., Neuhaus, K., Sørensen, S., Grosch, R., Smalla, K., Schikora, A., 2020. Salmonella persistence in soil depends on reciprocal interactions with indigenous microorganisms. Environmental Microbiology 22, 2639–2652. [DOI] [PubMed] [Google Scholar]
  27. Steffan, J.J., Derby, J.A., Brevik, E.C., 2020. Soil pathogens that may potentially cause pandemics, including SARS coronaviruses. Current Opinion in Environmental Science & Health. 10.1016/j.coesh.2020.08.005. [DOI] [PMC free article] [PubMed]
  28. Stocker, T., Qin, D., Plattner, G.K., Tignor, M., Allen, S.K., Boschung, J., Nauels, A., Xia, Y., Bex, V., Midgley, P.M., 2013. Climate Change 2013: The Physical Science Basis. Cambridge University Press, Cambridge 33–115. [Google Scholar]
  29. Teplitski, M., Barak, J., Schneider, K., 2009. Human enteric pathogens in produce: Un-answered ecological questions with direct implications for food safety. Current Opinion in Biotechnology 20, 166–171. [DOI] [PubMed] [Google Scholar]
  30. Tyler, H., Triplett, E., 2008. Plants as a habitat for beneficial and/or human pathogenic bacteria. Annual Review of Phytopathology 46, 53–73. [DOI] [PubMed] [Google Scholar]
  31. Vannier, N., Agler, M., Hacquard, S., 2019. Microbiota-mediated disease resistance in plants. PLoS Pathogens 15, e1007740. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Williamson, K., Fuhrmann, J., Wommack, K.E., Radosevich, M., 2017. Viruses in soil ecosystems: an unknown quantity within an unexplored territory. Annual Review of Virology 4, 201–219. [DOI] [PubMed] [Google Scholar]
  33. Wu, S.P., 2017. Prevention and control of emerging infectious diseases, an eternal topic of mankind. Electronic Journal of Emerging Infectious Diseases 2, 1–4. [Google Scholar]
  34. Zhang, G.L., Gao, Z.L., 2018. Emerging infectious diseases and the strategy of prevention and control. Chinese Journal of Viral Diseases 8, 252–256. [Google Scholar]
  35. Zhong, Z., Rapp, J., Wainaina, J., Solonenko, N., Maughan, H., Carpenter, S., Cooper, Z., Jang, H.B., Bolduc, B., Deming, J., Sullivan, M., 2020. Viral ecogenomics of arctic cryopeg brine and sea ice. mSystems 5, e00246–e20. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Zhu, Y.G., Gillings, M., Penuelas, J., 2020. Integrating biomedical, ecological, and sustainability sciences to manage emerging infectious diseases. One Earth 3, 23–26. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Zhu, Y.G., Gillings, M., Simonet, P., Stekel, D., Banwart, S., Penuelas, J., 2017. Microbial mass movements. Science 357, 1099–1100. [DOI] [PubMed] [Google Scholar]

Articles from Soil Ecology Letters are provided here courtesy of Nature Publishing Group

RESOURCES