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

Abstract

To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community.

Fig 1. Principle coordinate analysis (PCoA) plot (environmental variables as vectors) showing differences in bacterial community structure (a) and As functional gene structure (b) of the five As contaminated soils from different geographical locations.

Soil codes: B1, Faridpur, Bangladesh; B2, Sonargaon, Bangladesh; C1, Chenzhou, China; C2, Qiyang, China; UK, Rothamsted, UK.

Fig 2. Composition of microbial communities in the five soils at the phylum level.

Circles from inside out correspond to the soils B1, B2, C1, C2 and UK, respectively. See Fig 1 caption for the soil codes.

Fig 3. Relative abundance of the Proteobacteria community composition in the five soils.

A, The relative abundance of the Proteobacteria; B, Relative abundance of the Alphaproteobacteria. See Fig 1 caption for the soil codes.

Fig 4. Heatmap of the 10 most abundant genera in each soil.

The 10 most abundant genera in each sample were selected (a total of 27 genera for all five soils), and their abundances were compared to those in other soils. The color intensity in each cell shows the percentage of a genus in a soil. See Fig 1 caption for the soil codes.

Fig 5. Variation partitioning analyses of As functional genes (A) and microbial community (B) explained by the soil selected properties and geographic locations.

The diagram represents the biological variation partitioned into the relative effects of each factor or a combination of factors, in which arrow thickness was proportional to the respective percentages of explained variation. Letter ′a′represents the combined effect of soil properties and geographic location. Letter ′b′represents the effect that could not be explained by any of the variables tested. And letters ′c′ and ′d′ represent the effect of soil properties and geographic location, respectively.