Next Article in Journal
A Discovery of Relevant Hepatoprotective Effects and Underlying Mechanisms of Dietary Clostridium butyricum Against Corticosterone-Induced Liver Injury in Pekin Ducks
Next Article in Special Issue
Effects of Vertical Water Mass Segregation on Bacterial Community Structure in the Beaufort Sea
Previous Article in Journal
Nanomaterials as Delivery Vehicles and Components of New Strategies to Combat Bacterial Infections: Advantages and Limitations
Previous Article in Special Issue
Unveiling of Concealed Processes for the Degradation of Pharmaceutical Compounds by Neopestalotiopsis sp.
Open AccessArticle

Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

1
Microorganism Resources Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Incheon 22689, Korea
2
Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Korea
*
Author to whom correspondence should be addressed.
Microorganisms 2019, 7(9), 357; https://doi.org/10.3390/microorganisms7090357
Received: 5 August 2019 / Revised: 10 September 2019 / Accepted: 13 September 2019 / Published: 16 September 2019
Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis. View Full-Text
Keywords: heavy metals; soil; PacBio; 16S rRNA gene; mines heavy metals; soil; PacBio; 16S rRNA gene; mines
Show Figures

Figure 1

MDPI and ACS Style

Hur, M.; Park, S.-J. Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System. Microorganisms 2019, 7, 357.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop