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Comparative metagenomics of anode-associated microbiomes developed in rice paddy-field microbial fuel cells.

Kouzuma A, Kasai T, Nakagawa G, Yamamuro A, Abe T, Watanabe K - PLoS ONE (2013)

Bottom Line: In sediment-type microbial fuel cells (sMFCs) operating in rice paddy fields, rice-root exudates are converted to electricity by anode-associated rhizosphere microbes.Pyrotag sequencing showed that Geobacteraceae bacteria were associated with the anodes of all three systems, but the dominant Geobacter species in each MFC were different.Our findings suggest that G. psychrophilus and its related species preferentially grow on the anodes of rhizosphere sMFCs and generate electricity through syntrophic interactions with organisms that excrete electron donors.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan.

ABSTRACT
In sediment-type microbial fuel cells (sMFCs) operating in rice paddy fields, rice-root exudates are converted to electricity by anode-associated rhizosphere microbes. Previous studies have shown that members of the family Geobacteraceae are enriched on the anodes of rhizosphere sMFCs. To deepen our understanding of rhizosphere microbes involved in electricity generation in sMFCs, here, we conducted comparative analyses of anode-associated microbiomes in three MFC systems: a rice paddy-field sMFC, and acetate- and glucose-fed MFCs in which pieces of graphite felt that had functioned as anodes in rice paddy-field sMFC were used as rhizosphere microbe-bearing anodes. After electric outputs became stable, microbiomes associated with the anodes of these MFC systems were analyzed by pyrotag sequencing of 16S rRNA gene amplicons and Illumina shotgun metagenomics. Pyrotag sequencing showed that Geobacteraceae bacteria were associated with the anodes of all three systems, but the dominant Geobacter species in each MFC were different. Specifically, species closely related to G. metallireducens comprised 90% of the anode Geobacteraceae in the acetate-fed MFC, but were only relatively minor components of the rhizosphere sMFC and glucose-fed MFC, whereas species closely related to G. psychrophilus were abundantly detected. This trend was confirmed by the phylogenetic assignments of predicted genes in shotgun metagenome sequences of the anode microbiomes. Our findings suggest that G. psychrophilus and its related species preferentially grow on the anodes of rhizosphere sMFCs and generate electricity through syntrophic interactions with organisms that excrete electron donors.

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Metagenomic insights into the genus Geobacter obtained by MEGAN analyses.(A) Sub-genus level distribution of genes affiliated with the genus Geobacter based on BLAST homology. ‘Geobacter’ in the figures represents genes that were assigned to Geobacter at the genus level, but not to any genome-sequenced strain. (B) A partial MEGAN tree showing taxonomic distribution of genes encoding the acetate-catabolizing enzymes acetyl-CoA synthetase (EC 6.2.1.1), phosphate acetyltransferase (2.3.1.8), and acetate kinase (2.7.2.1), assigned to the class Deltaproteobacteria. LCA parameters: Min score, 50; top percent, 1.0; Min support, 2.
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pone-0077443-g006: Metagenomic insights into the genus Geobacter obtained by MEGAN analyses.(A) Sub-genus level distribution of genes affiliated with the genus Geobacter based on BLAST homology. ‘Geobacter’ in the figures represents genes that were assigned to Geobacter at the genus level, but not to any genome-sequenced strain. (B) A partial MEGAN tree showing taxonomic distribution of genes encoding the acetate-catabolizing enzymes acetyl-CoA synthetase (EC 6.2.1.1), phosphate acetyltransferase (2.3.1.8), and acetate kinase (2.7.2.1), assigned to the class Deltaproteobacteria. LCA parameters: Min score, 50; top percent, 1.0; Min support, 2.

Mentions: Genes assigned to the genus Geobacter based on BLAST homology were extracted, and we attempted to assign them to the eight genome-sequenced Geobacter strains (Figure 6A). The analysis showed that the Geobacter genes in the bulk soil could not be assigned to any strain, suggesting that the Geobacter strains in the bulk soil were not closely related to the eight fully sequenced stains. For the other samples, approximately half of the genes were not assigned to any isolated strain, while the remaining genes displayed characteristic distributions. Specifically, a high proportion (approximately 70%) of genes assigned to G. sulfurreducens was identified in the AM-anode biofilm, whereas the gene distribution pattern of the anode-associated soil was similar to that of the GM-anode biofilm. These results suggest that Geobacter EAB present in the anode-associated soil were similar to those in the GM-anode biofilm.


Comparative metagenomics of anode-associated microbiomes developed in rice paddy-field microbial fuel cells.

Kouzuma A, Kasai T, Nakagawa G, Yamamuro A, Abe T, Watanabe K - PLoS ONE (2013)

Metagenomic insights into the genus Geobacter obtained by MEGAN analyses.(A) Sub-genus level distribution of genes affiliated with the genus Geobacter based on BLAST homology. ‘Geobacter’ in the figures represents genes that were assigned to Geobacter at the genus level, but not to any genome-sequenced strain. (B) A partial MEGAN tree showing taxonomic distribution of genes encoding the acetate-catabolizing enzymes acetyl-CoA synthetase (EC 6.2.1.1), phosphate acetyltransferase (2.3.1.8), and acetate kinase (2.7.2.1), assigned to the class Deltaproteobacteria. LCA parameters: Min score, 50; top percent, 1.0; Min support, 2.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815305&req=5

pone-0077443-g006: Metagenomic insights into the genus Geobacter obtained by MEGAN analyses.(A) Sub-genus level distribution of genes affiliated with the genus Geobacter based on BLAST homology. ‘Geobacter’ in the figures represents genes that were assigned to Geobacter at the genus level, but not to any genome-sequenced strain. (B) A partial MEGAN tree showing taxonomic distribution of genes encoding the acetate-catabolizing enzymes acetyl-CoA synthetase (EC 6.2.1.1), phosphate acetyltransferase (2.3.1.8), and acetate kinase (2.7.2.1), assigned to the class Deltaproteobacteria. LCA parameters: Min score, 50; top percent, 1.0; Min support, 2.
Mentions: Genes assigned to the genus Geobacter based on BLAST homology were extracted, and we attempted to assign them to the eight genome-sequenced Geobacter strains (Figure 6A). The analysis showed that the Geobacter genes in the bulk soil could not be assigned to any strain, suggesting that the Geobacter strains in the bulk soil were not closely related to the eight fully sequenced stains. For the other samples, approximately half of the genes were not assigned to any isolated strain, while the remaining genes displayed characteristic distributions. Specifically, a high proportion (approximately 70%) of genes assigned to G. sulfurreducens was identified in the AM-anode biofilm, whereas the gene distribution pattern of the anode-associated soil was similar to that of the GM-anode biofilm. These results suggest that Geobacter EAB present in the anode-associated soil were similar to those in the GM-anode biofilm.

Bottom Line: In sediment-type microbial fuel cells (sMFCs) operating in rice paddy fields, rice-root exudates are converted to electricity by anode-associated rhizosphere microbes.Pyrotag sequencing showed that Geobacteraceae bacteria were associated with the anodes of all three systems, but the dominant Geobacter species in each MFC were different.Our findings suggest that G. psychrophilus and its related species preferentially grow on the anodes of rhizosphere sMFCs and generate electricity through syntrophic interactions with organisms that excrete electron donors.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan.

ABSTRACT
In sediment-type microbial fuel cells (sMFCs) operating in rice paddy fields, rice-root exudates are converted to electricity by anode-associated rhizosphere microbes. Previous studies have shown that members of the family Geobacteraceae are enriched on the anodes of rhizosphere sMFCs. To deepen our understanding of rhizosphere microbes involved in electricity generation in sMFCs, here, we conducted comparative analyses of anode-associated microbiomes in three MFC systems: a rice paddy-field sMFC, and acetate- and glucose-fed MFCs in which pieces of graphite felt that had functioned as anodes in rice paddy-field sMFC were used as rhizosphere microbe-bearing anodes. After electric outputs became stable, microbiomes associated with the anodes of these MFC systems were analyzed by pyrotag sequencing of 16S rRNA gene amplicons and Illumina shotgun metagenomics. Pyrotag sequencing showed that Geobacteraceae bacteria were associated with the anodes of all three systems, but the dominant Geobacter species in each MFC were different. Specifically, species closely related to G. metallireducens comprised 90% of the anode Geobacteraceae in the acetate-fed MFC, but were only relatively minor components of the rhizosphere sMFC and glucose-fed MFC, whereas species closely related to G. psychrophilus were abundantly detected. This trend was confirmed by the phylogenetic assignments of predicted genes in shotgun metagenome sequences of the anode microbiomes. Our findings suggest that G. psychrophilus and its related species preferentially grow on the anodes of rhizosphere sMFCs and generate electricity through syntrophic interactions with organisms that excrete electron donors.

Show MeSH
Related in: MedlinePlus