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SCIENCE CHINA Life Sciences, Volume 61 , Issue 7 : 787-798(2018) https://doi.org/10.1007/s11427-017-9177-1

Comparative transcriptomic insights into the mechanisms of electron transfer in Geobacter co-cultures with activated carbon and magnetite

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  • ReceivedAug 25, 2017
  • AcceptedSep 15, 2017
  • PublishedOct 31, 2017

Abstract

Both activated carbon and magnetite have been reported to promote the syntrophic growth of Geobacter metallireducens and Geobacter sulfurreducens co-cultures, the first model to show direct interspecies electron transfer (DIET); however, differential transcriptomics of the promotion on co-cultures with these two conductive materials are unknown. Here, the comparative transcriptomic analysis of G. metallireducens and G. sulfurreducens co-cultures with granular activated carbon (GAC) and magnetite was reported. More than 2.6-fold reduced transcript abundances were determined for the uptake hydrogenase genes of G. sulfurreducens as well as other hydrogenases in those co-cultures to which conductive materials had been added. This is consistent with electron transfer in G. metallireducens-G. sulfurreducens co-cultures as evinced by direct interspecies electron transfer (DIET). Transcript abundance for the structural component of electrically conductive pili (e-pili), PilA, was 2.2-fold higher in G. metallireducens, and, in contrast, was 14.9-fold lower in G. sulfurreducens in co-cultures with GAC than in Geobacters co-cultures without GAC. However, it was 9.3-fold higher in G. sulfurreducens in co-cultures with magnetite than in Geobacters co-cultures. Mutation results showed that GAC can be substituted for the e-pili of both strains but magnetite can only compensate for that of G. sulfurreducens, indicating that the e-pili is a more important electron acceptor for the electron donor strain of G. metallireducens than for G. sulfurreducens. Transcript abundance for G. metallireducens c-type cytochrome gene GMET_RS14535, a homologue to c-type cytochrome gene omcE of G. sulfurreducens was 9.8-fold lower in co-cultures with GAC addition, while that for OmcS of G. sulfurreducens was 25.1-fold higher in co-cultures with magnetite, than in that without magnetite. Gene deletion studies showed that neither GAC nor magnetite can completely substitute the cytochrome (OmcE homologous) of G. metallireducens but compensate for the cytochrome (OmcS) of G. sulfurreducens. Moreover, some genes associated with central metabolism were up-regulated in the presence of both GAC and magnetite; however, tricarboxylic acid cycle gene transcripts in G. sulfurreducens were not highly-expressed in each of these amended co-cultures, suggesting that there was considerable redundancy in the pathways utilised by G. sulfurreducens for electron transfer to reduce fumarate with the amendment of GAC or magnetite. These results support the DIET model of G. metallireducens and G. sulfurreducens and suggest that e-pili and cytochromes of the electron donor strain are more important than that of the electron acceptor strain, indicating that comparative transcriptomics may be a promising route by which to reveal different responses of electron donor and acceptor during DIET in co-cultures.


Funded by

General Programme of the National Natural Science Foundation of China(41371257,41573071)

Shandong Natural Science Fund for Distinguished Young Scholars(JQ201608)

Young Taishan Scholars Programme of Shandong Province(tsqn20161054)

Key Research Project for Frontier Science of the Chinese Academy of Sciences(QYZDJ-SSW-DQC015)


Acknowledgment

This work was supported by the Major Research plan (91751112) and the General Programme (41371257, 41573071) of the National Natural Science Foundation of China, Shandong Natural Science Fund for Distinguished Young Scholars (JQ201608), the Young Taishan Scholars Programme of Shandong Province (tsqn20161054) and the Key Research Project for Frontier Science of the Chinese Academy of Sciences (QYZDJ-SSW-DQC015).


Interest statement

The author(s) declare that they have no conflict of interest.


Supplement

SUPPORTING INFORMATION

Figure S1 Heat map comparison of global gene expression of G. metallireducens and G. sulfurreducens in co-cultures of G.m_G.s, G.m_G.s_GAC, and G.m_G.s_magnetite.

Table S1 Statistical data of unique Illumina sequence reads of G. metallireducens and G. sulfurreducens transcripts from co-cultures of G.m_G.s, G.m_G.s_GAC, and G.m_G.s_magnetite

Table S2 Genes predicated to encode proteins that were differentially expressed in G. metallireducens cells grown in both co-cultures of G.m_G.s_GAC and G.m_G.s_magnetite compared with those grown in G.m_G.s. The values were normalised log base2 (ratio: G.m_G.s_GAC/G.m_G.s, G.m_G.s_magnetite/G.m_G.s)

Table S3 Genes predicated to encode proteins that were differentially expressed in G. sulfurreducens cells grown in both co-cultures of G.m_G.s_GAC and G.m_G.s_magnetite compared with those grown in G.m_G.s. The values were normalised log base2 (ratio: G.m_G.s_GAC/G.m_G.s, G.m_G.s_magnetite/G.m_G.s)

Table S4 Genes predicated to encode proteins that were differentially expressed in G. metallireducens cells grown in co-cultures of G.m_G.s_GAC but not G.m_G.s_magnetite compared with those grown in G.m_G.s. The values are normalised log base2 (ratio: G.m_G.s_GAC/G.m_G.s)

Table S5 Genes predicated to encode proteins that were differentially expressed in G. metallireducens cells grown in co-cultures G.m_G.s_magnetite but not G.m_G.s_GAC compared with those grown in G.m_G.s. The values are normalised log base2 (ratio: G.m_G.s_magnetite/G.m_G.s)

Table S6 Genes predicated to encode proteins that were differentially expressed in G. sulfurreducens cells grown in co-cultures of G.m_G.s_GAC but not G.m_G.s_magnetite compared with those grown in G.m_G.s. The values are normalised log base2 (ratio: G.m_G.s_GAC/G.m_G.s)

Table S7 Genes predicated to encode proteins that were differentially expressed in G. sulfurreducens cells grown in co-cultures of G.m_G.s_magnetite but not G.m_G.s_GAC compared with those grown in G.m_G.s. The values are normalised log base2 (ratio: G.m_G.s_magnetite/G.m_G.s)

Table S8 Genes predicated to encode electron transport proteins that were differentially expressed in G. metallireducens cells grown in both co-cultures of G.m_G.s_GAC and G.m_G.s_magnetite compared with those grown in G.m_G.s. The values were normalised log base2 (ratio: G.m_G.s_GAC/G.m_G.s, G.m_G.s_magnetite/G.m_G.s)

Table S9 Genes predicated to encode electron transport proteins that were differentially expressed in G. sulfurreducens cells grown in both co-cultures of G.m_G.s_GAC and G.m_G.s_magnetite compared with those grown in G.m_G.s. The values were normalised log base2 (ratio: G.m_G.s_GAC/G.m_G.s, G.m_G.s_magnetite/G.m_G.s)

Table S10 Genes predicated to encode electron transport proteins that were differentially expressed in G. metallireducens cells grown in co-cultures of G.m_G.s_GAC but not G.m_G.s_magnetite compared with those grown in G.m_G.s. The values are normalised log base2 (ratio: G.m_G.s_GAC/G.m_G.s)

Table S11 Genes predicated to encode electron transport proteins that were differentially expressed in G. sulfurreducens cells grown in co-cultures of G.m_G.s_GAC but not G.m_G.s_magnetite compared with those grown in G.m_G.s. The values are normalised log base2 (ratio: G.m_G.s_GAC/G.m_G.s)

Table S12 Genes predicated to encode electron transport proteins that were differentially expressed in G. metallireducens cells grown in co-cultures of G.m_G.s_magnetite but not GAC G.m_G.s_GAC compared with those grown in G.m_G.s. The values are normalised log base2 (ratio: G.m_G.s_magnetite/G.m_G.s)

Table S13 Genes predicated to encode electron transport proteins that were differentially expressed in G. sulfurreducens cells grown in co-cultures of G.m_G.s_magnetite but not G.m_G.s_GAC compared with those grown in G.m_G.s. The values are normalised log base2 (ratio: G.m_G.s_magnetite/G.m_G.s)

Table S14 Comparison of differentially expressed genes involved in DIET (cytochromes, pili and flagella) in G. metallireducens upon amendment by GAC and magnetite

Table S15 Comparison of differentially expressed genes involved in interspecies electron transfer (hydrogen/formate transfer, cytochromes, and pili) in G. sulfurreducens upon amendment by GAC and magnetite

Table S16 Comparison of differentially expressed genes involved in central metabolism in G. metallireducens-G. sulfurreducens co-cultures upon amendment by GAC and magnetite

The supporting information is available online at http://life.scichina.com and https://link.springer.com. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.


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  • Figure 1

    Ethanol consumption (A) and succinate production from fumarate reduction (B) by syntrophic co-cultures of G. metallireducens and G. sulfurreducens with amendments of granular activated carbon (GAC) and magnetite. The error bars represent standard deviations of the mean for triplicate cultures.

  • Figure 2

    Numbers of differentially expressed genes of G. metallireducens and G. sulfurreducens in co-cultures with GAC and magnetite. Column chart (A) and Venn diagram (B) show numbers of up-regulated, or down-regulated, and shared, or unique, differentially expressed genes of the two strains, respectively.

  • Figure 3

    Schematic models of differentially expressed genes (FDR≤0.001,︱log base 2 Ratio︱≥1) encoded proteins involved in DIET (cytochromes, pili and flagella) and central metabolic pathways in G. metallireducens-G. sulfurreducens co-cultures with the amendment of GAC (A), and magnetite (B). Red rectangles indicated that genes encoding for pili and cytochromes were analysed by deletion mutant studies.

  • Figure 4

    Succinate production from fumarate reduction by syntrophic co-cultures of G. metallireducens/G. sulfurreducens with the amendment of GAC (25 g L−1) initiated with wild-type strains and deletion mutants of the two Geobacacter species. Co-cultures initiated with either the PilA (A)- or cytochrome (GMET_RS14535) (B)-deficient strains of G. metallireducens and G. sulfurreducens wild type, and co-cultures initiated with either the PilA (C)- or cytochrome OmcS (D)-deficient strains of G. sulfurreducens and G. metallireducens wild type. The error bars represent standard deviations of the mean for triplicate cultures.

  • Figure 5

    Succinate production from fumarate reduction by syntrophic co-cultures of G. metallireducens /G. sulfurreducens with addition of magnetite (5 mmol L−1) initiated with wild-type strains and deletion mutants of two Geobacacter species. Co-cultures initiated with either the PilA (A)- or cytochrome (GMET_RS14535) (B)-deficient strains of G. metallireducens and G. sulfurreducens wild-type, and co-cultures initiated with either the PilA (C)- or cytochrome OmcS (D)-deficient strains of G. sulfurreducens and G. metallireducens wild-type. The error bars represent standard deviations of the mean for triplicate cultures.

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