Unraveling the interaction between soil microbiomes and their potential for restoring polluted soils

Abstract

Soils are not exempt from anthropogenic pollution, which can eventually cause disturbance of the microbial communities and areas without any kind of productivity. Among soil microbiota, bacteria play an important role in pollutant degradation, enabling them to thrive in contaminated sites. Given this, several techniques have been used to increase the number of pollutant-degrading bacteria in situ or for subsequent addition. Additionally, bacteriophages exhibit a high tolerance to pollutants and enhance bacterial metabolic activity through phage-encoded auxiliary metabolic genes (AMGs), thereby augmenting their skills for nutrient assimilation, resistance to phage infection, antibiotic resistance, heavy metal resistance, and degradation of pesticides and xenobiotics, among others. Several phage-encoded AMGs have been described during the last few years, but their diversity, distribution, and function have not been extensively explored, warranting further studies. Here, we highlight soil microbiome interactions, especially bacterium and phage interactions to understand this unexplored world with a high potential for restoring polluted soils.

Graphical abstract

Keywords

Auxiliary metabolic genes / Microbiome / Pollutants / Soils / Viruses

References

[1] Chao H, Balcazar J L, Wu Y, Cai A, Ye M, Sun M, Hu F. (2023). Phages in vermicomposts enrich functional gene content and facilitate pesticide degradation in soil. Environment International, 179: 108175

[2] Domínguez J, Aira M, Crandall K A, Pérez-Losada M. (2021). Earthworms drastically change fungal and bacterial communities during vermicomposting of sewage sludge. Scientific Reports, 11(1): 15556

[3] Huang D, Yu P, Ye M, Schwarz C, Jiang X, Alvarez P J. (2021). Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress. Microbiome, 9(1): 150

[4] Miner G L, Delgado J A, Ippolito J A, Stewart C E. (2020). Soil health management practices and crop productivity. Agricultural & Environmental Letters, 5(1): e20023

[5] Sun M, Yuan S, Xia R, Ye M, Balcázar J L. (2023). Underexplored viral auxiliary metabolic genes in soil: diversity and eco-evolutionary significance. Environmental Microbiology, 25(4): 800–810

[6] Tomei M C, Daugulis A J. (2013). Ex situ bioremediation of contaminated soils: an overview of conventional and innovative technologies. Critical Reviews in Environmental Science and Technology, 43(20): 2107–2139

[7] Trubl G, Jang H B, Roux S, Emerson J B, Solonenko N, Vik D R, Solden L, Ellenbogen J, Runyon A T, Bolduc B. . (2018). Soil viruses are underexplored players in ecosystem carbon processing. mSystems, 3(5): e00076–18

[8] WilliamsonK E (2010). Soil phage ecology: abundance, distribution, and interactions with bacterial hosts. In: Witzany G, editor. Biocommunication in Soil Microorganisms. Berlin: Springer Berlin Heidelberg, 113–136

[9] Zheng X, Jahn M T, Sun M, Friman V P, Balcazar J L, Wang J, Shi Y, Gong X, Hu F, Zhu Y G. (2022). Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes. ISME Journal, 16(5): 1397–1408

Author Contributions Carlos O. Lomeli-Ortega:

Conceptualization (equal); writing – original draft (lead); writing – review and editing (equal). Mingming Sun: writing – original draft (supporting); writing – review and edition (equal). José Luis Balcázar: Funding acquisition (lead); conceptualization (equal); writing – original draft (supporting); writing – review and editing (Supporting).

ORCID

Carlos O. Lomeli Ortega: https://orcid.org/0000-0003-4969-3699

Mingming Sun: https://orcid.org/0000-0002-5550-6813

José Luis Balcázar: https://orcid.org/0000-0002-6866-9347

Acknowledgements

This project has received funding from the European Union’s Horizon Europe 2020 Research and Innovation Program under the Marie Skłodowska-Curie (No. 101106707). The authors acknowledge funding from Generalitat de Catalunya through Consolidated Research Group 2021 SGR 01282 and from the CERCA program.

Conflict of Interests

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Data Availability Statement

The data that support the findings of this study are available from the corresponding author, C.O.L.O., upon reasonable request.

RIGHTS & PERMISSIONS

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