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The diversity and abundance of As(III) oxidizers on root iron plaque is critical for arsenic bioavailability to rice.

Hu M, Li F, Liu C, Wu W - Sci Rep (2015)

Bottom Line: Iron plaque is a strong adsorbent on rice roots, acting as a barrier to prevent metal uptake by rice.The microbial composition and diversity of the root iron plaque were significantly different from those of the bulk and rhizosphere soils.Using the aoxB gene as an identifying marker, we determined that the arsenite-oxidizing microbiota on the iron plaque was dominated by Acidovorax and Hydrogenophaga-affiliated bacteria.

View Article: PubMed Central - PubMed

Affiliation: Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China.

ABSTRACT
Iron plaque is a strong adsorbent on rice roots, acting as a barrier to prevent metal uptake by rice. However, the role of root iron plaque microbes in governing metal redox cycling and metal bioavailability is unknown. In this study, the microbial community structure on the iron plaque of rice roots from an arsenic-contaminated paddy soil was explored using high-throughput next-generation sequencing. The microbial composition and diversity of the root iron plaque were significantly different from those of the bulk and rhizosphere soils. Using the aoxB gene as an identifying marker, we determined that the arsenite-oxidizing microbiota on the iron plaque was dominated by Acidovorax and Hydrogenophaga-affiliated bacteria. More importantly, the abundance of arsenite-oxidizing bacteria (AsOB) on the root iron plaque was significantly negatively correlated with the arsenic concentration in the rice root, straw and grain, indicating that the microbes on the iron plaque, particularly the AsOB, were actively catalyzing arsenic transformation and greatly influencing metal uptake by rice. This exploratory research represents a preliminary examination of the microbial community structure of the root iron plaque formed under arsenic pollution and emphasizes the importance of the root iron plaque environment in arsenic biogeochemical cycling compared with the soil-rhizosphere biotope.

No MeSH data available.


Related in: MedlinePlus

Taxonomic composition of arsenite-oxidizing bacteria of iron plaque at genus level.
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f4: Taxonomic composition of arsenite-oxidizing bacteria of iron plaque at genus level.

Mentions: Quantification of the number of aoxB gene copies using real-time qPCR revealed that the aoxB genes of the root iron plaque were present at 1.08 × 107 to 1.78 × 108 copies per g wet roots. The abundance of the aoxB gene was significantly negatively correlated with the total As content in the roots and straw (Pearson correlation coefficients of −0.853 and −0.663, respectively; all P < 0.001). However, there was no significant correlation between aoxB gene abundance and As concentration in the grain (Fig. 3). To obtain insights into the taxonomic composition of the AsOB on the root iron plaque, a clone library was constructed from the DNA extracted from the iron plaque using the aoxB gene as a functional marker. A total of 28 different aoxB OTUs (97% similarity level) were recovered from 96 sequenced clones. A blastx search of the NCBI-nr database and subsequent phylogenetic inferences from the deduced amino acid sequences revealed that the AsOB on the root iron plaque were dominated by Acidovorax (accounting for 28.4% of the total library), unclassified bacteria (22.4%), Hydrogenophaga (14.9%) and Sinorhizobium (10.4%) (Fig. 4). The most abundant OTU, OTU15, was nearly identical to the aoxB amino acid sequences found in two species, Acidovorax sp. NO1 (100% amino acid identity) and Acidovorax sp. 75 (97% amino acid identity) (Supplementary Fig. S4). The other 5 OTUs that clustered near the aoxB gene were from Albidiferax ferrireducens T118 (with 91% amino acid identity), which also belongs to the Comamonadaceae family. OTU19 was the second most abundant OTU affiliated with the uncultured bacteria. The other aoxB-like OTUs were categorized as rare (i.e., OTUs containing less than three representative sequences). Furthermore, many of these rare OTUs formed unique clades and were associated with Acinetobacter sp. 33, Burkholderia vietnamiensis AU4i, Ralstonia sp. 22, Agrobacterium tumefaciens and Aminobacter sp. 86 (Supplementary Fig. S4).


The diversity and abundance of As(III) oxidizers on root iron plaque is critical for arsenic bioavailability to rice.

Hu M, Li F, Liu C, Wu W - Sci Rep (2015)

Taxonomic composition of arsenite-oxidizing bacteria of iron plaque at genus level.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4555042&req=5

f4: Taxonomic composition of arsenite-oxidizing bacteria of iron plaque at genus level.
Mentions: Quantification of the number of aoxB gene copies using real-time qPCR revealed that the aoxB genes of the root iron plaque were present at 1.08 × 107 to 1.78 × 108 copies per g wet roots. The abundance of the aoxB gene was significantly negatively correlated with the total As content in the roots and straw (Pearson correlation coefficients of −0.853 and −0.663, respectively; all P < 0.001). However, there was no significant correlation between aoxB gene abundance and As concentration in the grain (Fig. 3). To obtain insights into the taxonomic composition of the AsOB on the root iron plaque, a clone library was constructed from the DNA extracted from the iron plaque using the aoxB gene as a functional marker. A total of 28 different aoxB OTUs (97% similarity level) were recovered from 96 sequenced clones. A blastx search of the NCBI-nr database and subsequent phylogenetic inferences from the deduced amino acid sequences revealed that the AsOB on the root iron plaque were dominated by Acidovorax (accounting for 28.4% of the total library), unclassified bacteria (22.4%), Hydrogenophaga (14.9%) and Sinorhizobium (10.4%) (Fig. 4). The most abundant OTU, OTU15, was nearly identical to the aoxB amino acid sequences found in two species, Acidovorax sp. NO1 (100% amino acid identity) and Acidovorax sp. 75 (97% amino acid identity) (Supplementary Fig. S4). The other 5 OTUs that clustered near the aoxB gene were from Albidiferax ferrireducens T118 (with 91% amino acid identity), which also belongs to the Comamonadaceae family. OTU19 was the second most abundant OTU affiliated with the uncultured bacteria. The other aoxB-like OTUs were categorized as rare (i.e., OTUs containing less than three representative sequences). Furthermore, many of these rare OTUs formed unique clades and were associated with Acinetobacter sp. 33, Burkholderia vietnamiensis AU4i, Ralstonia sp. 22, Agrobacterium tumefaciens and Aminobacter sp. 86 (Supplementary Fig. S4).

Bottom Line: Iron plaque is a strong adsorbent on rice roots, acting as a barrier to prevent metal uptake by rice.The microbial composition and diversity of the root iron plaque were significantly different from those of the bulk and rhizosphere soils.Using the aoxB gene as an identifying marker, we determined that the arsenite-oxidizing microbiota on the iron plaque was dominated by Acidovorax and Hydrogenophaga-affiliated bacteria.

View Article: PubMed Central - PubMed

Affiliation: Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China.

ABSTRACT
Iron plaque is a strong adsorbent on rice roots, acting as a barrier to prevent metal uptake by rice. However, the role of root iron plaque microbes in governing metal redox cycling and metal bioavailability is unknown. In this study, the microbial community structure on the iron plaque of rice roots from an arsenic-contaminated paddy soil was explored using high-throughput next-generation sequencing. The microbial composition and diversity of the root iron plaque were significantly different from those of the bulk and rhizosphere soils. Using the aoxB gene as an identifying marker, we determined that the arsenite-oxidizing microbiota on the iron plaque was dominated by Acidovorax and Hydrogenophaga-affiliated bacteria. More importantly, the abundance of arsenite-oxidizing bacteria (AsOB) on the root iron plaque was significantly negatively correlated with the arsenic concentration in the rice root, straw and grain, indicating that the microbes on the iron plaque, particularly the AsOB, were actively catalyzing arsenic transformation and greatly influencing metal uptake by rice. This exploratory research represents a preliminary examination of the microbial community structure of the root iron plaque formed under arsenic pollution and emphasizes the importance of the root iron plaque environment in arsenic biogeochemical cycling compared with the soil-rhizosphere biotope.

No MeSH data available.


Related in: MedlinePlus