Illumina MiSeq sequencing investigation on the contrasting soil bacterial community structures in different iron mining areas

Abstract

Mine activities leaked heavy metals into surrounding soil and may affected indigenous microbial communities. In the present study, the diversity and composition of the bacterial community in soil collected from three regions which have different pollution degree, heavy pollution, moderate pollution, and non-pollution, within the catchment of Chao River in Beijing City, were compared using the Illumina MiSeq sequencing technique. Rarefaction results showed that the polluted area had significant higher bacterial alpha diversity than those from unpolluted area. Principal component analysis (PCA) showed that microbial communities in the polluted areas had significant differences compared with the unpolluted area. Moreover, PCA at phylum level and Matastats results demonstrated that communities in locations shared similar phyla diversity, indicating that the bacterial community changes under metal pollution were not reflected on phyla structure. At genus level, the relative abundance of dominant genera changed in sites with degrees of pollution. Genera Bradyrhizobium, Rhodanobacter, Reyranella, and Rhizomicrobium significantly decreased with increasing pollution degree, and their dominance decreased, whereas several genera (e.g., Steroidobacter, Massilia, Arthrobacter, Flavisolibacter, and Roseiflexus) increased and became new dominant genera in the heavily metal-polluted area. The potential resistant bacteria, found within the genera of Thiobacillus, Pseudomonas, Arthrobacter, Microcoleus, Leptolyngbya, and Rhodobacter, are less than 2.0 % in the indigenous bacterial communities, which play an important role in soil ecosystem. This effort to profile the background diversity may set the first stage for better understanding the mechanism underlying the community structure changes under in situ mild heavy metal pollution.

Characterization of a Microbial Consortium for the Bioremoval of Polycyclic Aromatic Hydrocarbons (PAHs) in Water

“…The next sample most related to the ore waste was the sample with phenanthrene, whereas naphthalene and pyrene have a distinct community structure and are not as related to each other. This confirms that each carbon source, with respect to the target PAHs, performs a selective pressure on the microbial community, as was pointed out by Hong et al [40], Sawulski et al [42], and Wei et al [43]. …”

“…Hong et al obtained lower diversity in a microbial consortium from mining soil samples, reporting a Chao index of 1091–1522 [40]. This index is lower to the reported in this study (32,348–39,895).…”

The bacterial community structure and functional profile in the heavy metal contaminated paddy soils, surrounding a nonferrous smelter in South Korea

“…Previously, other DNA‐based studies have shown the negative or very weak impact of the heavy metals on the microbial diversity in the soils (Bamborough & Cummings, ; Gans, Wolinsky, & Dunbar, ; Sheik et al., ). In some cases, an increase in the bacterial alpha diversity indices in the heavy metal polluted soils has also been observed (Hong et al., ). The diversity of bacterial community in the metal polluted soils estimated using DNA‐based methods may not change due to fact that some bacterial community members might display low activity profiles due to pollution while RNA‐based methods may reveal reduction in community diversity due heavy metals (Nunes et al., ).…”

“…The pollution of the soils by the heavy metals poses a serious threat to ecosystems and human health (Liu et al, 2016). Studies have shown that the pollution by heavy metals affects plant growth and genetic variation, changes the composition of the soil microbial community, and reduces microbial activity (Ellis, Morgan, Weightman, & Fry, 2003;Hong, Si, Xing, & Li, 2015;Li et al, 2006;Linton, Shotbolt, & Thomas, 2007;Moffett et al, 2003;Müller, Westergaard, Christensen, & Sørensen, 2001;Singh et al, 2014;Xie et al, 2016;Zhou et al, 2011). The resilience and metal tolerance mechanisms, allowing the microbial populations not only to survive but also maintain the main functions of their communities, have been observed in the soil that has a long-term history of heavy metal contamination (Azarbad et al, 2015(Azarbad et al, , 2016.…”

Oilseed rape cultivation increases the microbial richness and diversity in soils contaminated with cadmium

“…More and more evidences have suggested that metal contamination has been extensively shown to decrease species diversity and alter microbial community structure (Dahlin et al 1997;Abaye et al 2005). Hong et al (2015) found that the variable degree of heavy metals in the soil in iron mining areas increased bacterial alpha diversity and changed the dominant genera. Cadmium pollution of soil reportedly can change the taxonomic diversity and functionality of the microbial communities, and further affect soil quality and plant growth (de Campos et al 2013;Hill et al 2000;Li et al 2014;Tipayno et al 2011).…”