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

<div><p>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.</p></div

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

<p>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.</p

Diversity indices based on the 16S rRNA gene sequences from the five geographically distributed soils contaminated with different levels of arsenic.

<p>See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0176696#pone.0176696.g001" target="_blank">Fig 1</a> caption for the soil codes.</p

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

<p>Circles from inside out correspond to the soils B1, B2, C1, C2 and UK, respectively. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0176696#pone.0176696.g001" target="_blank">Fig 1</a> caption for the soil codes.</p

Relative abundance of the <i>Proteobacteria</i> community composition in the five soils.

<p>A, The relative abundance of the <i>Proteobacteria</i>; B, Relative abundance of the <i>Alphaproteobacteria</i>. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0176696#pone.0176696.g001" target="_blank">Fig 1</a> caption for the soil codes.</p

Heatmap of the 10 most abundant genera in each soil.

<p>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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0176696#pone.0176696.g001" target="_blank">Fig 1</a> caption for the soil codes.</p

Numbers of genes predicted to be up-expressed or down-expressed (down) genes (log ratio ≥1 and p

05) of the mutant during the time course experiment. C1', C5', C10', C20', C40' and C60' are the time points of 1, 5, 10, 20, 40, and 60 minutes after adding iron chelator. F1', F5', F10', F20', F40' and F60' are the time points of 1, 5, 10, 20, 40, and 60 minutes after adding iron back to the iron-depleted culture. Total genes (A) and genes related to (B) anaerobic energy transport and (C) aerobic energy transport that are up-expressed or down-expressed are shown.<p><b>Copyright information:</b></p><p>Taken from "Characterization of the Fur gene: roles in iron and acid tolerance response"</p><p>http://www.biomedcentral.com/1471-2164/9/S1/S11</p><p>BMC Genomics 2008;9(Suppl 1):S11-S11.</p><p>Published online 20 Mar 2008</p><p>PMCID:PMC2386053.</p><p></p

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.

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

Soil respiratory carbon (C) release represented by O₂ depletion flux without additional substrate (a) and with the addition of glucose (b), C₃ (c), and C₄ (d) substrate under the four treatments: UC: unclipped control; UW: unclipped and warmed; CC: clipped control; CW: clipped and warmed.

<p>Soil respiratory carbon (C) release represented by O₂ depletion flux without additional substrate (a) and with the addition of glucose (b), C₃ (c), and C₄ (d) substrate under the four treatments: UC: unclipped control; UW: unclipped and warmed; CC: clipped control; CW: clipped and warmed.</p

Warming- and clipping-induced changes in soil respiratory C release (%) with the addition of C₃ plant material, C₄ plant material, or glucose or without substrate addition during the incubation period under four treatments: UC: unclipped control; UW: unclipped and warmed; CC: clipped and control; CW: clipped and warmed.

<p>The comparisons included the effects of warming on soil respiratory C release with (CW/CC) and without (UW/UC) clipping, and the effects of clipping under control (CC/UC) and warming (CW/UW) treatments. Vertical bars and their error bars represent means and standard errors (<i>n</i> = 4). The different letters indicate statistical significance.</p