Influence of heavy metals on rhizosphere microbial communities of Siam weed (Chromolaena odorata (L.)) using a 16S rRNA gene amplicon sequencing approach

Thanyaporn Ruangdech, Manoosak Wongphatcharachai, Christopher M Staley, Michael J Sadowsky, Kannika Sajjaphan

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


A 16S rRNA amplicon sequencing approach was used to assess the impacts of cadmium (Cd) and zinc (Zn) contamination on populations of rhizobacteria on Siam weed (Chromolaena odorata (L.)). Bacterial communities were characterized using the Illumina MiSeq platform and the V6 hypervariable region of the 16S rRNA gene. Among the 54,026 unique operational taxonomic units (OTUs) identified, 99.7% were classified as bacteria and the rest were classified as archaea. Several dominant bacterial phyla were observed in all samples—Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Bacteroidetes. These five phyla accounted for 89.2% of all OTUs identified among all sites, and only two OTUs could not be classified to a phylum. Comparison among samples containing low and high levels of Cd contamination using nonparametric Shannon and Shannon diversity indices showed that soils with low levels of diversity had a higher level of Cd (p < 0.05). These results indicated that levels of Cd may significantly alter bacterial species selection. The Cd- and Zn-resistant bacteria from each sample were subjected to heavy-metal minimum inhibitory concentration (MIC) analyses. The MIC values obtained from 1152 isolates were used to individually analyze the pattern of gene function using the BioNumerics software. The results of this analysis showed that 26.7% of the bacteria were resistant to Cd concentrations up to 320 mg/L and only 2.3% of bacteria were resistant to Zn at concentrations up to 3200 mg/L. The MIC analyses indicated that the number of resistant bacteria decreased with increasing metal concentrations and those bacteria resistant to Cd and Zn may contain more than one group of metal-resistance genes.

Original languageEnglish (US)
Pages (from-to)137-141
Number of pages5
JournalAgriculture and Natural Resources
Issue number3
StatePublished - Jun 2017

Bibliographical note

Funding Information:
This work was supported in part by a grant to the fifth author from the Kasetsart University Research and Development Institute (KURDI) , Bangkok, Thailand, by a grant to the fourth author from the University of Minnesota Agricultural Experiment Station , St. Paul, MN, USA and by a scholarship to the first author from The Capacity Building of Kasetsart University Students on Internationalization Program .

Publisher Copyright:
© 2017 Kasetsart University


  • 16S rRNA gene sequencing
  • Heavy metals
  • Microbial community
  • Rhizosphere
  • Siam weed


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