Effects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil

• Published in: Bioresources and bioprocessing Vol. 7; no. 1; pp. 1 - 19
• Main Authors: Salam, Lateef B., Obayori, Oluwafemi S., Ilori, Mathew O., Amund, Olukayode O.
• Format: Journal Article
• Language: English
• Published: Singapore Springer Singapore 11-05-2020; Springer Nature B.V; SpringerOpen
• Subjects: Agricultural soil; Annotations; Biochemical Engineering; Cadmium; Chemistry; Chemistry and Materials Science; Chromium; Community structure; Copper; Deoxyribonucleic acid; Detoxification; DNA; DNA sequencing; Efflux; Environmental Engineering/Biotechnology; Heavy metals; Industrial and Production Engineering; Iron; Lead; Metals; Methylobacterium; Microbial community structure and function; Microbial contamination; Microbiomes; Microcosms; Microorganisms; Nodulation; Perturbation; Physicochemical properties; Proteobacteria; Selenium; Shotgun metagenomics; Soil contamination; Soil microcosm; Soil microorganisms; Soil moisture; Soil pollution; Soil structure; Soils; Statistical analysis; Statistical significance; Structure-function relationships; Zinc; Soil microcosm; Microbial community structure and function; Heavy metal resistome; Cadmium; Agricultural soil; Heavy metals; Shotgun metagenomics
• ISSN: 2197-4365; 2197-4365
• DOI: 10.1186/s40643-020-00314-w

The effects of cadmium (Cd) contamination on the microbial community structure, soil physicochemistry and heavy metal resistome of a tropical agricultural soil were evaluated in field-moist soil microcosms. A Cd-contaminated agricultural soil (SL5) and an untreated control (SL4) were compared over a period of 5 weeks. Analysis of the physicochemical properties and heavy metals content of the two microcosms revealed a statistically significant decrease in value of the soil physicochemical parameters (
P 
< 
0.05
) and concentration of heavy metals (Cd, Pb, Cr, Zn, Fe, Cu, Se) content of the agricultural soil in SL5 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the predominance of the phyla, classes, genera and species of
Proteobacteria
(37.38%),
Actinobacteria
(35.02%),
Prevotella
(6.93%), and
Conexibacter woesei
(8.93%) in SL4, and
Proteobacteria
(50.50%),
Alphaproteobacteria
(22.28%),
Methylobacterium
(9.14%), and
Methylobacterium radiotolerans
(12,80%) in SL5, respectively. Statistically significant (
P 
< 0.05) difference between the metagenomes was observed at genus and species delineations. Functional annotation of the two metagenomes revealed diverse heavy metal resistome for the uptake, transport, efflux and detoxification of various heavy metals. It also revealed the exclusive detection in SL5 metagenome of members of RND (resistance nodulation division) protein czcCBA efflux system (
czcA, czrA, czrB
), CDF (cation diffusion facilitator) transporters (
czcD
), and genes for enzymes that protect the microbial cells against cadmium stress (
sodA, sodB, ahpC
). The results obtained in this study showed that Cd contamination significantly affects the soil microbial community structure and function, modifies the heavy metal resistome, alters the soil physicochemistry and results in massive loss of some autochthonous members of the community not adapted to the Cd stress.