Limits...
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.

Show MeSH

Related in: MedlinePlus

Analyses of pyrotag-sequencing data for bacterial communities.(A) Rarefaction curves showing the diversity of OTUs (similarity cut off of 95%). (B) Relative abundances of major genus-level bacterial groups estimated using the RDP classifier. Detailed data are shown in Table S2.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3815305&req=5

pone-0077443-g003: Analyses of pyrotag-sequencing data for bacterial communities.(A) Rarefaction curves showing the diversity of OTUs (similarity cut off of 95%). (B) Relative abundances of major genus-level bacterial groups estimated using the RDP classifier. Detailed data are shown in Table S2.

Mentions: To compare the phylogenetic compositions of bacteria associated with anodes of the sMFC and acetate- and glucose-fed MFCs, pyrotag sequencing of 16S rRNA-gene amplicons [14] was conducted using DNA samples obtained from anode-associated soil of rhizosphere sMFCs (anode-associated soil), and the anode biofilms of acetate-fed MFCs (AM-anode biofilm) and glucose-fed MFC (GM-anode biofilm). Bulk soil of the rice paddy field (bulk soil) was also analyzed as a control. Comparisons of the overall OTUs detected in the samples indicated that the enrichment of anode-associated bacteria in these different MFC reactors resulted in a marked decrease (less than 25%) of phylogenetic diversity, as shown in the plotted rarefaction curves (Figure 3A). Concerning the total community structure at the genus level (Figure 3B), the bulk soil and anode-associated soil displayed similar profiles, in which Acidobacteria subgroup Gp6 was the most abundant, representing 6% of the total bacteria in these samples (see Table S1 for details). Consistent with a previous report for soil samples [32], a large number of uncultured Acidobacteria subgroups were also detected. Geobacter was also detected abundantly in these soil samples, representing approximately 2% and 3% of the total bacteria in the bulk and anode-associated soil, respectively. The ratios of Geobacteraceae sequences were previously reported to have increased from 0.13% to 0.74% in response to an increase in current density in a rhizosphere sMFC [7]. Here, Geobacter sequences were also more abundant in anode-associated soil than in bulk soil, suggesting Geobacter species were involved in electricity generation in the rhizosphere sMFCs.


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)

Analyses of pyrotag-sequencing data for bacterial communities.(A) Rarefaction curves showing the diversity of OTUs (similarity cut off of 95%). (B) Relative abundances of major genus-level bacterial groups estimated using the RDP classifier. Detailed data are shown in Table S2.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0077443-g003: Analyses of pyrotag-sequencing data for bacterial communities.(A) Rarefaction curves showing the diversity of OTUs (similarity cut off of 95%). (B) Relative abundances of major genus-level bacterial groups estimated using the RDP classifier. Detailed data are shown in Table S2.
Mentions: To compare the phylogenetic compositions of bacteria associated with anodes of the sMFC and acetate- and glucose-fed MFCs, pyrotag sequencing of 16S rRNA-gene amplicons [14] was conducted using DNA samples obtained from anode-associated soil of rhizosphere sMFCs (anode-associated soil), and the anode biofilms of acetate-fed MFCs (AM-anode biofilm) and glucose-fed MFC (GM-anode biofilm). Bulk soil of the rice paddy field (bulk soil) was also analyzed as a control. Comparisons of the overall OTUs detected in the samples indicated that the enrichment of anode-associated bacteria in these different MFC reactors resulted in a marked decrease (less than 25%) of phylogenetic diversity, as shown in the plotted rarefaction curves (Figure 3A). Concerning the total community structure at the genus level (Figure 3B), the bulk soil and anode-associated soil displayed similar profiles, in which Acidobacteria subgroup Gp6 was the most abundant, representing 6% of the total bacteria in these samples (see Table S1 for details). Consistent with a previous report for soil samples [32], a large number of uncultured Acidobacteria subgroups were also detected. Geobacter was also detected abundantly in these soil samples, representing approximately 2% and 3% of the total bacteria in the bulk and anode-associated soil, respectively. The ratios of Geobacteraceae sequences were previously reported to have increased from 0.13% to 0.74% in response to an increase in current density in a rhizosphere sMFC [7]. Here, Geobacter sequences were also more abundant in anode-associated soil than in bulk soil, suggesting Geobacter species were involved in electricity generation in the rhizosphere sMFCs.

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