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Chromium contamination accentuates changes in the microbiome and heavy metal resistome of a tropical agricultural soil

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Abstract

The impacts of hexavalent chromium (Cr) contamination on the microbiome, soil physicochemistry, and heavy metal resistome of a tropical agricultural soil were evaluated for 6 weeks in field-moist microcosms consisting of a Cr-inundated agricultural soil (SL9) and an untreated control (SL7). The physicochemistry of the two microcosms revealed a diminution in the total organic matter content and a significant dip in macronutrients phosphorus, potassium, and nitrogen concentration in the SL9 microcosm. Heavy metals analysis revealed the detection of seven heavy metals (Zn, Cu, Fe, Cd, Se, Pb, Cr) in the agricultural soil (SL7), whose concentrations drastically reduced in the SL9 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the preponderance of the phyla, classes, genera, and species of Actinobacteria (33.11%), Actinobacteria_class (38.20%), Candidatus Saccharimonas (11.67%), and Candidatus Saccharimonas aalborgensis (19.70%) in SL7, and Proteobacteria (47.52%), Betaproteobacteria (22.88%), Staphylococcus (16.18%), Staphylococcus aureus (9.76%) in SL9, respectively. Functional annotation of the two metagenomes for heavy metal resistance genes revealed diverse heavy metal resistomes involved in the uptake, transport, efflux, and detoxification of various heavy metals. It also revealed the exclusive detection in SL9 metagenome of resistance genes for chromium (chrB, chrF, chrR, nfsA, yieF), cadmium (czcB/czrB, czcD), and iron (fbpB, yqjH, rcnA, fetB, bfrA, fecE) not annotated in SL7 metagenome. The findings from this study revealed that Cr contamination induces significant shifts in the soil microbiome and heavy metal resistome, alters the soil physicochemistry, and facilitates the loss of prominent members of the microbiome not adapted to Cr stress.

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All data generated or analyzed during this study are included in this published article.

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Authors and Affiliations

  1. Department of Biological Sciences, Microbiology unit, Elizade University, Ilara-Mokin, Ondo State, Nigeria

    Lateef Babatunde Salam

  2. Department of Microbiology, Lagos State University, Ojo, Lagos, Nigeria

    Oluwafemi S. Obayori

  3. Department of Microbiology, University of Lagos, Akoka, Lagos, Nigeria

    Matthew O. Ilori & Olukayode O. Amund

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  1. Lateef Babatunde Salam
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  2. Oluwafemi S. Obayori
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  3. Matthew O. Ilori
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  4. Olukayode O. Amund
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Contributions

L.B.S. conceived the study, performed the experiments, and wrote the Methods and Results. O.S.O. coordinated the study and wrote the Introduction and Discussion. M.O.I. and O.O.A. contributed to the Discussion and overall scientific quality of the manuscript. All the authors reviewed and approved the final version of the manuscript.

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Correspondence to Lateef Babatunde Salam.

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Salam, L.B., Obayori, O.S., Ilori, M.O. et al. Chromium contamination accentuates changes in the microbiome and heavy metal resistome of a tropical agricultural soil. World J Microbiol Biotechnol 39, 228 (2023). https://doi.org/10.1007/s11274-023-03681-6

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