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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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Neighbor-joining tree based on 16S rRNA gene sequences showing phylogenetic relationships in the genus Geobacter.Refer to Table 2 for the major OTUs. Desulfuromonas acetoxidans was used as an outgroup. Bootstrap values (100 trials, only > 50 are shown) are indicated at branching points. The bar indicates 2% sequence divergence. Accession numbers are shown in parentheses.
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pone-0077443-g004: Neighbor-joining tree based on 16S rRNA gene sequences showing phylogenetic relationships in the genus Geobacter.Refer to Table 2 for the major OTUs. Desulfuromonas acetoxidans was used as an outgroup. Bootstrap values (100 trials, only > 50 are shown) are indicated at branching points. The bar indicates 2% sequence divergence. Accession numbers are shown in parentheses.

Mentions: Analyses of sequences affiliated with the family Geobacteraceae identified several major OTUs (>5% of the total Geobacteraceae sequences) from the AM- and GM-anode biofilm samples (Table 2). Examination of the phylogenetic relationships among these Geobacteraceae OTUs and several reference strains revealed that the dominant Geobacter OTU in the AM-anode biofilm (OTU ACE575, 89%) was affiliated with a distinct cluster comprised of G. grbicium, G. metallireducens, and G. sulfurreducens (Figure 4 and Table 2). This phylogenetic group was previously referred to as the G. metallireducens clade [39]. Notably, however, this group of Geobacter OTUs was only present as minor components in the other MFC samples. Relatives of G. sulfurreducens, which is a well-characterized EAB that has high electricity-generating capacity in the presence of acetate [40], are frequently detected in acetate-fed bioelectrochemical systems [41-43]. Together, the present results suggest that these Geobacter strains are preferentially selected in anode biofilms when acetate is supplied as the sole substrate.


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)

Neighbor-joining tree based on 16S rRNA gene sequences showing phylogenetic relationships in the genus Geobacter.Refer to Table 2 for the major OTUs. Desulfuromonas acetoxidans was used as an outgroup. Bootstrap values (100 trials, only > 50 are shown) are indicated at branching points. The bar indicates 2% sequence divergence. Accession numbers are shown in parentheses.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0077443-g004: Neighbor-joining tree based on 16S rRNA gene sequences showing phylogenetic relationships in the genus Geobacter.Refer to Table 2 for the major OTUs. Desulfuromonas acetoxidans was used as an outgroup. Bootstrap values (100 trials, only > 50 are shown) are indicated at branching points. The bar indicates 2% sequence divergence. Accession numbers are shown in parentheses.
Mentions: Analyses of sequences affiliated with the family Geobacteraceae identified several major OTUs (>5% of the total Geobacteraceae sequences) from the AM- and GM-anode biofilm samples (Table 2). Examination of the phylogenetic relationships among these Geobacteraceae OTUs and several reference strains revealed that the dominant Geobacter OTU in the AM-anode biofilm (OTU ACE575, 89%) was affiliated with a distinct cluster comprised of G. grbicium, G. metallireducens, and G. sulfurreducens (Figure 4 and Table 2). This phylogenetic group was previously referred to as the G. metallireducens clade [39]. Notably, however, this group of Geobacter OTUs was only present as minor components in the other MFC samples. Relatives of G. sulfurreducens, which is a well-characterized EAB that has high electricity-generating capacity in the presence of acetate [40], are frequently detected in acetate-fed bioelectrochemical systems [41-43]. Together, the present results suggest that these Geobacter strains are preferentially selected in anode biofilms when acetate is supplied as the sole substrate.

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