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

Moonsuk Hur,Soo-Je Park

doi:10.3390/microorganisms7090357

Abstract

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.

Highlights

As of 2017, 4677 out of 5544 mines in Korea have been abandoned owing to environmental concerns and/or economic factors
In the case of metal mines, most mines in Korea are in disuse due to soil pollution caused by waste rock and mine tailings with acid mine drainage (AMD) [1]
The mine tailings dams and/or AMD contaminated by heavy metals, including iron and cadmium, have led to serious environmental problems related to crops and public health through the contamination of the water supply and food chain, respectively

Summary

Introduction

As of 2017, 4677 out of 5544 mines (for coal, metal, and nonmetals) in Korea have been abandoned owing to environmental concerns and/or economic factors. The mine tailings dams and/or AMD contaminated by heavy metals, including iron and cadmium, have led to serious environmental problems related to crops and public health through the contamination of the water supply and food chain, respectively. These contaminated areas have been reclaimed by a long-term plan under the Ministry of Environment in Korea, there are rising concerns regarding soil contamination by heavy metals [2,3]. Most previous studies have focused on identifying microbial community structures in polluted soils or isolating useful microorganisms for the removal of heavy metals see review in [7]. Numerous unrecognized bacteria and archaea have been identified by NGS technology, and the results can serve as fundamental taxonomic information in (meta)genome analysis with putatively deduced functional characterizations [18,19]

Objectives

Methods

Results