Response of Soil Microbial Communities to Elevated Antimony and Arsenic Contamination Indicates the Relationship between the Innate Microbiota and Contaminant Fractions

Abstract

Mining of sulfide ore deposits containing metalloids, such as antimony and arsenic, has introduced serious soil contamination around the world, posing severe threats to food safety and human health. Hence, it is important to understand the behavior and composition of the microbial communities that control the mobilization or sequestration of these metal(loid)s. Here, we selected two sites in Southwest China with different levels of Sb and As contamination to study interactions among various Sb and As fractions and the soil microbiota, with a focus on the microbial response to metalloid contamination. Comprehensive geochemical analyses and 16S rRNA gene amplicon sequencing demonstrated distinct soil taxonomic inventories depending on Sb and As contamination levels. Stochastic gradient boosting indicated that citric acid extractable Sb(V) and As(V) contributed 5% and 15%, respectively, to influencing the community diversity. Random forest predicted that low concentrations of Sb(V) and As(V) could enhance the community diversity but generally, the Sb and As contamination impairs microbial diversity. Co-occurrence network analysis indicated a strong correlation between the indigenous microbial communities and various Sb and As fractions. A number of taxa were identified as core genera due to their elevated abundances and positive correlation with contaminant fractions (total Sb and As concentrations, bioavailable Sb and As extractable fractions, and Sb and As redox species). Shotgun metagenomics indicated that Sb and As biogeochemical redox reactions may exist in contaminated soils. All these observations suggest the potential for bioremediation of Sb- and As-contaminated soils.

Black soldier fly larvae (Hermetia illucens) strengthen the metabolic function of food waste biodegradation by gut microbiome

“…The size of each node is proportional to the number of connections (degree). Bigger nodes indicate stronger and more significant correlations with other nodes and, therefore, may be important members in the community (Sun et al ., ). The most densely connected node in each module is defined as a ‘hub’.…”

Microbial diversity in soils from antimony mining sites: geochemical control promotes species enrichment

“…Arthrobacter was positively correlated with Sb tot (p < 0.05), Sb avail (p < 0.05) and Pb avail (p < 0.05), while it was negatively correlated with As pbioavail as well as Hg pavail , which identified Arthrobacter as a core microorganism in the soils contaminated by Sb and As (Sun et al 2017). It was previously isolated from Pb-contaminated and Cd-contaminated soil and was not dependent on the concentration of metals in soils (Kozdrój and van Elsas 2001).…”

“…Recently, using Illumina sequencing of 16S rRNA, studies reported the investigation of the correlation between microbial community profiles and concentrations of Sb and As in soils and water (Sun et al 2016a, b;Xiao et al 2016Xiao et al , 2017. Recent work also includes the use of metagenomics and metagenomic binning to investigate the soil microflora response to As and Sb contamination, providing progresses using state-ofthe-art molecular tools to unravel the interactions between microbiota and Sb and As (Sun et al 2018;Sun et al 2017). Significant positive correlation was demonstrated between groups and the extractable fractions of Sb and As in soils (Sun et al 2016a, b;Xiao et al 2016Xiao et al , 2017.…”

Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir

“…Water bacterial and fungal community sequence reads were first filtered by the QIIME pipeline [ 22 ]. The quality-trimmer removed reads are shorter than 50 bp [ 23 ]. After quality filtering and chimera removal, the abundance-based coverage estimator (ACE) index, Chao richness estimator ( Chao 1), Shannon diversity ( H ') and Simpson diversity (1/ D ) indices were calculated by the MOTHUR package (version 1.22.2 ) using Operational Taxonomic Units (OTUs) grouped at 0.97 level [ 24 ].…”