Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth.

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PubMed ID: 30658982

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Jiao S, Chen W, Wei G

Appl Environ Microbiol. Jan 2019

COMMENT: This work investigates the soil microbial communities response to chemical contamination studying the long-term changes in soil ecosystems. 16S analysis for taxonomic profiling and shotgun metagenomics approaches for functional profiling are used to study the temporal dynamic of soil microbiomes in response to different contaminats using soils planted with different common legumes.


We selected phenanthrene, n-octadecane, and cadmium as the pollutants, since they are prevalent in contaminated agro-soils. Three common legumes, Robinia pseudoacacia (woody), Medicago sativa (herbaceous), and Vicia villosa (herbaceous), were used in this study because of their wide distribution and suitability for a wide range of environments. We applied 16S ribosomal RNA gene amplicon sequencing to analyze the community structure,and used the total DNA shotgun sequencing approach to assess their functional profiles

In total, we obtained 21 soil samples 127 contaminated with phenanthrene + n-octadecane + CdCl2, including four time points (0, 10, 128 30, and 90 days), in three legume plant treatments with 90 days of growth.

The authors detect the changes in the microbiome only after 90 days

In the present study, we observed no significant difference in microbial community composition between the planted and unplanted samples after 10 or 30 days of incubation, while significant differences in the microbial taxonomic and functional profiling were detected after 90 days of incubation

Each type of legume select a different taxonomic profile in the soil microbiome

Different legume plants imposed stronger selection on taxonomic profiles compared with functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals strong resilience of soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants long-term changes in soil ecosystems.


Herein, our results revealed distinct patterns of resilience in microbial diversity and specific traits at both the taxonomic and functional levels, in response to inorganic and organic soil pollutants.

This realm of investigation could provide valuable insight into the restoration of polluted ecosystems and environmental management, and yet it remains understudied


Raquel Tobes