Structure, Variation, and Co-occurrence of Soil Microbial Communities in Abandoned Sites of a Rare Earth Elements Mine

Abstract

Mining activity for rare earth elements (REEs) has caused serious environmental pollution, particularly for soil ecosystems. However, the effects of REEs on soil microbiota are still poorly understood. In this study, soils were collected from abandoned sites of a REEs mine, and the structure, diversity, and co-occurrence patterns of soil microbiota were evaluated by Illumina high-throughput sequencing targeting 16S rRNA genes. Although microbiota developed significantly along with the natural restoration, the microbial structure on the site abandoned for 10 years still significantly differed from that on the unmined site. Potential plant growth promoting bacteria (PGPB) were identified by comparing 16S sequences against a self-constructed PGPB database via BLAST, and it was found that siderophore-producing and phosphorus-solubilizing bacteria were more abundant in the studied soils than in reference soils. Canonical correspondence analysis indicated that species richness of plant community was the prime factor affecting microbial structure, followed by limiting nutrients (total carbon and total nitrogen) and REEs content. Further co-occurring network analysis revealed nonrandom assembly patterns of microbiota in the studied soils. These results increase our understanding of microbial variation and assembly pattern during natural restoration in REE contaminated soils.

Sludge Biochar Amendment and Alfalfa Revegetation Improve Soil Physicochemical Properties and Increase Diversity of Soil Microbes in Soils from a Rare Earth Element Mining Wasteland

“…The sensitivity of the response of a microbial community, specifically bacterial and fungal communities, reflects a change in soil quality [ 32 , 33 ]. For instance, a significant alteration of microbial community in IAC mining wasteland was demonstrated in our previous study [ 34 ] and some other reports [ 35 , 36 , 37 ]. In this study, we used sludge biochar as a soil ameliorant and alfalfa as the revegetation plant and conducted pot trials in a climate-controlled chamber, and we test the hypothesis that sludge biochar amendment and alfalfa plantation can ameliorate physicochemical properties and increase the microbial diversity of soil from IAC mining wastelands.…”

China’s most typical nonferrous organic-metal facilities own specific microbial communities

“…( d ) Abundance (%) of bacterial communities in different type of sites at the phylum level. Active: active sites in present study; Aband: abandoned sites in present study; SA, slightly acidic sites22; Pb-Zn, an abandoned Pb-Zn mine 23 , REE: a rare Earth element mine 24 ; CA, Chlor-alkali sites 25 . The inset Table in Fig.…”

“…3d ). Results of ANOVA using the data from these sites (active, abandoned, and literature 21 , 24 also indicated that TP and Fe had significant differences ( p < 0.05, Fig. 3 ).…”

Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region

“…On the contrary, a better efficiency of the biological control agents is obtained when microbial consortia and not single strains are used to control pathogenic fungi in soils and substrates (Danon et al, 2010 ; Jain et al, 2012 ; Pertot et al, 2017 ). Thus, it is becoming clearer and clearer that soil functionality depends on the community pattern and that the activity of the microorganisms directly involved in the targeted function is only possible in the presence of the different components of this community, without these components being directly involved in the function of interest (Tyc et al, 2014 ; Williams et al, 2014 ; Chao et al, 2016 ). Therefore, an alternative strategy to identify the members of the microbial consortium responsible for soil suppressiveness would be to erode diversity by performing serial dilutions of the suppressive soil until it loses its suppressiveness.…”