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

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

Variation partitioning analysis of microbial diversity variance among important geochemical variables, P, NO₃⁻<b>, and C/N, and their interactions.</b>

<p>Variation partitioning analysis of microbial diversity variance among important geochemical variables, P, NO₃⁻<b>, and C/N, and their interactions.</b></p

Selected physical and chemical properties of the soils<i>^a.</i>

a<p>average values of 6 subsamples at each depth.</p><p>pH, 1∶2.5 soil-H₂O suspension; As, 0.05 M (NH₄)₂SO₄ soluble concentration.</p><p>A depth of 0 m represents soil of 0.00–0.10 m underground; 1, 2, 3 and 4 m represent ±0.05 m at each depth underground. TC, total carbon; TN, total nitrogen.</p

Maximum-likelihood phylogenetic tree of the 236 different <i>nifH</i> gene sequences obtained from GeoChip 3.0 analysis.

<p>The width of each wedge is the number of <i>nifH</i> sequences within each cluster. The percentages and numbers in each bracket are the signal proportions and detected gene numbers of each cluster within each depth, respectively. The significant differences of gene abundance were analyzed by one-way ANOVA.</p

Average metabolic response (AMR) of the soil samples measured by the BioLog system, error bar indicates ± 1 SE (standard error, <i>N = </i>6) of the six biological replicates within each depth.

<p>Average metabolic response (AMR) of the soil samples measured by the BioLog system, error bar indicates ± 1 SE (standard error, <i>N = </i>6) of the six biological replicates within each depth.</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

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

Production of Nitrous Oxide from Nitrite in Stable Type II Methanotrophic Enrichments

The coupled aerobic–anoxic nitrous decomposition operation is a new process for wastewater treatment that removes nitrogen from wastewater and recovers energy from the nitrogen in three steps: (1) NH₄⁺ oxidation to NO₂^–, (2) NO₂^– reduction to N₂O, and (3) N₂O conversion to N₂ with energy production. Here, we demonstrate that type II methanotrophic enrichments can mediate step two by coupling oxidation of poly­(3-hydroxybutyrate) (P3HB) to NO₂^– reduction. Enrichments grown with NH₄⁺ and NO₂^– were subject to alternating 48-h aerobic and anoxic periods, in which CH₄ and NO₂^– were added together in a “coupled” mode of operation or separately in a “decoupled mode”. Community structure was stable in both modes and dominated by Methylocystis. In the coupled mode, production of P3HB and N₂O was low. In the decoupled mode, significant P3HB was produced, and oxidation of P3HB drove reduction of NO₂^– to N₂O with ∼70% conversion for >30 cycles (120 d). In batch tests of wasted cells from the decoupled mode, N₂O production rates increased at low O₂ or high NO₂^– levels. The results are significant for the development of engineered processes that remove nitrogen from wastewater and for understanding of conditions that favor environmental production of N₂O