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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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Related in: MedlinePlus

MEGAN trees constructed for genes with high BLAST scores assigned to the KEGG maps.(A) citrate cycle and (B) glycolysis/gluconeogenesis. Normalized numbers of genes assigned to each taxonomic group are presented in the comparative tree views of MEGAN. The size of each node is scaled logarithmically to indicate numbers of assigned genes in the four samples.
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pone-0077443-g005: MEGAN trees constructed for genes with high BLAST scores assigned to the KEGG maps.(A) citrate cycle and (B) glycolysis/gluconeogenesis. Normalized numbers of genes assigned to each taxonomic group are presented in the comparative tree views of MEGAN. The size of each node is scaled logarithmically to indicate numbers of assigned genes in the four samples.

Mentions: In the MFC systems analyzed in the present study, the glycolytic pathway and citrate cycle should be important for electricity generation. We therefore investigated the taxonomic distributions of genes that were assigned by MEGAN to the KEGG maps of the “citrate cycle” and “glycolysis/gluconeogenesis” (Figure 5). The constructed MEGAN trees show that abundantly represented taxa involved in these catabolic pathways, such as Geobacter in the anode-biofilm samples, Comamonas in the AM-abode biofilm, and Clostridium in the GM-anode biofilm, were also detected in the 16S rRNA gene-sequence analyses (Figure 3B). We also found that genes in the bulk and anode-associated soils were similarly distributed to the MEGAN trees, and many of the detected genes were assigned only to higher ranks, except for Nitrospira and Rhizobiales. This trend may be attributed to the short gene lengths for the soil samples (Table 1). In the GM-anode biofilm, fermentative bacteria, including Anaerolinea [46], Clostridium [33], and Syntrophobacter [47] were overrepresented, suggesting the importance of fermentative bacteria and their syntrophic associations with EABs in the conversion of glucose into electricity.


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)

MEGAN trees constructed for genes with high BLAST scores assigned to the KEGG maps.(A) citrate cycle and (B) glycolysis/gluconeogenesis. Normalized numbers of genes assigned to each taxonomic group are presented in the comparative tree views of MEGAN. The size of each node is scaled logarithmically to indicate numbers of assigned genes in the four samples.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0077443-g005: MEGAN trees constructed for genes with high BLAST scores assigned to the KEGG maps.(A) citrate cycle and (B) glycolysis/gluconeogenesis. Normalized numbers of genes assigned to each taxonomic group are presented in the comparative tree views of MEGAN. The size of each node is scaled logarithmically to indicate numbers of assigned genes in the four samples.
Mentions: In the MFC systems analyzed in the present study, the glycolytic pathway and citrate cycle should be important for electricity generation. We therefore investigated the taxonomic distributions of genes that were assigned by MEGAN to the KEGG maps of the “citrate cycle” and “glycolysis/gluconeogenesis” (Figure 5). The constructed MEGAN trees show that abundantly represented taxa involved in these catabolic pathways, such as Geobacter in the anode-biofilm samples, Comamonas in the AM-abode biofilm, and Clostridium in the GM-anode biofilm, were also detected in the 16S rRNA gene-sequence analyses (Figure 3B). We also found that genes in the bulk and anode-associated soils were similarly distributed to the MEGAN trees, and many of the detected genes were assigned only to higher ranks, except for Nitrospira and Rhizobiales. This trend may be attributed to the short gene lengths for the soil samples (Table 1). In the GM-anode biofilm, fermentative bacteria, including Anaerolinea [46], Clostridium [33], and Syntrophobacter [47] were overrepresented, suggesting the importance of fermentative bacteria and their syntrophic associations with EABs in the conversion of glucose into electricity.

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