Metagenomic analysis revealed highly diverse microbial arsenic metabolism genes in paddy soils with low-arsenic contents

Abstract

a b s t r a c tMicrobe-mediated arsenic (As) metabolism plays a critical role in global As cycle, and As metabolism involves different types of genes encoding proteins facilitating its biotransformation and transportation processes. Here, we used metagenomic analysis based on high-throughput sequencing and constructed As metabolism protein databases to analyze As metabolism genes in five paddy soils with low-As contents. The results showed that highly diverse As metabolism genes were present in these paddy soils, with varied abundances and distribution for different types and subtypes of these genes. Arsenate reduction genes (ars) dominated in all soil samples, and significant correlation existed between the abundance of arr (arsenate respiration), aio (arsenite oxidation), and arsM (arsenite methylation) genes, indicating the co-existence and close-relation of different As resistance systems of microbes in wetland environments similar to these paddy soils after long-term evolution. Among all soil parameters, pH was an important factor controlling the distribution of As metabolism gene in five paddy soils (p ¼ 0.018). To the best of our knowledge, this is the first study using high-throughput sequencing and metagenomics approach in characterizing As metabolism genes in the five paddy soil, showing their great potential in As biotransformation, and therefore in mitigating arsenic risk to humans.

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

“…Zhang et al [41] revealed a strong correlation between arsC and arsM gene copies based on quantitative PCR, and suggested that similar compositions of microbial communities were involved in As(V) reduction and As(III) methylation in paddy soils. Previous studies revealed that the As(V) reduction, As(III) oxidation, and As(III) methylation processes co-exist and are closely related in microbes in paddy soils [41–43]. Similarly, significant correlations between the structures of the ars , aioB , and arsM genes were also observed in this study, suggesting that these different As transformation systems co-exist and are closely related in microbes in both paddy and upland soil.…”

“…In addition, in the soils studied, other soil properties such as pH represent additional stressors for microbial communities that may impact their diversity. Metagenomics studies also showed that microbial-mediated As metabolic processes in paddy soils correlated significantly with pH [40]. Zhang et al [41] revealed a strong correlation between arsC and arsM gene copies based on quantitative PCR, and suggested that similar compositions of microbial communities were involved in As(V) reduction and As(III) methylation in paddy soils.…”

Understanding arsenic dynamics in agronomic systems to predict and prevent uptake by crop plants

“…This approach measures the presence and expression of specific genes, rather than attempting to isolate and study the microbes that carry them, 98% of which – it is estimated - do not grow in culture 134 . Microbially mediated arsenic metabolic processes that play a major role in arsenic cycling in agronomic systems include arsenite oxidation (via the aio genes), arsenate respiration (via the arr genes), arsenate reduction (via the ars genes) and arsenite methylation (via the arsM genes) 135 . Interested readers are referred to the recent excellent work of Andres and Bertin 132 for a comprehensive review of this subject.…”

Arsenic Methylation Dynamics in a Rice Paddy Soil Anaerobic Enrichment Culture

“…Assessments of As methylation in soils and other environments have been hindered partly by limited databases for taxonomic classification. 20,21,49 The more extensive 726 protein sequence database developed for this study, along with a primer pair having greater degeneracy to amplify a broad range of arsM sequences, has enabled a deeper examination of arsM phylogenetic diversity. This study demonstrates the utility of these new tools, in conjunction with analyses of physiological responses to As, in probing relationships between community structure and biomethylation function.…”