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Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach.

Ishii S, Suzuki S, Tenney A, Norden-Krichmar TM, Nealson KH, Bretschger O - Sci Rep (2015)

Bottom Line: Potential metabolic switches between eleven dominant members were mainly observed for acetate, hydrogen, and ethanol metabolisms.These results have enabled the estimation of a multi-species metabolic network and the associated short-term responses to EET stimuli that induce changes to metabolic flow and cooperative or competitive microbial interactions.This systematic meta-omics approach represents a next step towards understanding complex microbial roles within a community and how community members respond to specific environmental stimuli.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA.

ABSTRACT
Microorganisms almost always exist as mixed communities in nature. While the significance of microbial community activities is well appreciated, a thorough understanding about how microbial communities respond to environmental perturbations has not yet been achieved. Here we have used a combination of metagenomic, genome binning, and stimulus-induced metatranscriptomic approaches to estimate the metabolic network and stimuli-induced metabolic switches existing in a complex microbial biofilm that was producing electrical current via extracellular electron transfer (EET) to a solid electrode surface. Two stimuli were employed: to increase EET and to stop EET. An analysis of cell activity marker genes after stimuli exposure revealed that only two strains within eleven binned genomes had strong transcriptional responses to increased EET rates, with one responding positively and the other responding negatively. Potential metabolic switches between eleven dominant members were mainly observed for acetate, hydrogen, and ethanol metabolisms. These results have enabled the estimation of a multi-species metabolic network and the associated short-term responses to EET stimuli that induce changes to metabolic flow and cooperative or competitive microbial interactions. This systematic meta-omics approach represents a next step towards understanding complex microbial roles within a community and how community members respond to specific environmental stimuli.

No MeSH data available.


Related in: MedlinePlus

Overall gene expression levels and dynamics related to microbial cell activities for each Bin-genome.Mean gene expression levels were calculated from all CDSs in each Bin-genome (A). Gene expression levels and changes for selected marker gene families related to transcription (B), translation (C), replication (D), and energy and stress (E) were calculated (see Supplementary Data 1). Normalized gene expression levels (mRNA-RPKM/DNA-RPKM) for each Bin-genome under the three operational conditions is described by the size of circle, while gene expression dynamics (mRNA-RPKM/mRNA-RPKM) is described by the circle color of SP (expression fold-change from MFC to SP) and the circle color of OC (expression fold-change from SP to OC).
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f3: Overall gene expression levels and dynamics related to microbial cell activities for each Bin-genome.Mean gene expression levels were calculated from all CDSs in each Bin-genome (A). Gene expression levels and changes for selected marker gene families related to transcription (B), translation (C), replication (D), and energy and stress (E) were calculated (see Supplementary Data 1). Normalized gene expression levels (mRNA-RPKM/DNA-RPKM) for each Bin-genome under the three operational conditions is described by the size of circle, while gene expression dynamics (mRNA-RPKM/mRNA-RPKM) is described by the circle color of SP (expression fold-change from MFC to SP) and the circle color of OC (expression fold-change from SP to OC).

Mentions: To compare the gene expression trends of cell activity-associated marker genes between the dominant strains, gene expression levels (mRNA-RPKM) were normalized by the DNA frequencies (DNA-RPKM), and both gene expression levels and dynamic changes were co-visualized in Fig. 3. The selected marker genes encode proteins that are ubiquitously essential for all life, including transcription, translation, and replication (Fig. 3B–D). In addition, genes encoding ATP synthase, superoxide reductase, and catalase were also employed as indicators for energy synthesis or stress responses, respectively (Fig. 3E). By combining them, we will enable to discuss about microbial cell activity dynamics for each strain within the given community.


Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach.

Ishii S, Suzuki S, Tenney A, Norden-Krichmar TM, Nealson KH, Bretschger O - Sci Rep (2015)

Overall gene expression levels and dynamics related to microbial cell activities for each Bin-genome.Mean gene expression levels were calculated from all CDSs in each Bin-genome (A). Gene expression levels and changes for selected marker gene families related to transcription (B), translation (C), replication (D), and energy and stress (E) were calculated (see Supplementary Data 1). Normalized gene expression levels (mRNA-RPKM/DNA-RPKM) for each Bin-genome under the three operational conditions is described by the size of circle, while gene expression dynamics (mRNA-RPKM/mRNA-RPKM) is described by the circle color of SP (expression fold-change from MFC to SP) and the circle color of OC (expression fold-change from SP to OC).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595844&req=5

f3: Overall gene expression levels and dynamics related to microbial cell activities for each Bin-genome.Mean gene expression levels were calculated from all CDSs in each Bin-genome (A). Gene expression levels and changes for selected marker gene families related to transcription (B), translation (C), replication (D), and energy and stress (E) were calculated (see Supplementary Data 1). Normalized gene expression levels (mRNA-RPKM/DNA-RPKM) for each Bin-genome under the three operational conditions is described by the size of circle, while gene expression dynamics (mRNA-RPKM/mRNA-RPKM) is described by the circle color of SP (expression fold-change from MFC to SP) and the circle color of OC (expression fold-change from SP to OC).
Mentions: To compare the gene expression trends of cell activity-associated marker genes between the dominant strains, gene expression levels (mRNA-RPKM) were normalized by the DNA frequencies (DNA-RPKM), and both gene expression levels and dynamic changes were co-visualized in Fig. 3. The selected marker genes encode proteins that are ubiquitously essential for all life, including transcription, translation, and replication (Fig. 3B–D). In addition, genes encoding ATP synthase, superoxide reductase, and catalase were also employed as indicators for energy synthesis or stress responses, respectively (Fig. 3E). By combining them, we will enable to discuss about microbial cell activity dynamics for each strain within the given community.

Bottom Line: Potential metabolic switches between eleven dominant members were mainly observed for acetate, hydrogen, and ethanol metabolisms.These results have enabled the estimation of a multi-species metabolic network and the associated short-term responses to EET stimuli that induce changes to metabolic flow and cooperative or competitive microbial interactions.This systematic meta-omics approach represents a next step towards understanding complex microbial roles within a community and how community members respond to specific environmental stimuli.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA.

ABSTRACT
Microorganisms almost always exist as mixed communities in nature. While the significance of microbial community activities is well appreciated, a thorough understanding about how microbial communities respond to environmental perturbations has not yet been achieved. Here we have used a combination of metagenomic, genome binning, and stimulus-induced metatranscriptomic approaches to estimate the metabolic network and stimuli-induced metabolic switches existing in a complex microbial biofilm that was producing electrical current via extracellular electron transfer (EET) to a solid electrode surface. Two stimuli were employed: to increase EET and to stop EET. An analysis of cell activity marker genes after stimuli exposure revealed that only two strains within eleven binned genomes had strong transcriptional responses to increased EET rates, with one responding positively and the other responding negatively. Potential metabolic switches between eleven dominant members were mainly observed for acetate, hydrogen, and ethanol metabolisms. These results have enabled the estimation of a multi-species metabolic network and the associated short-term responses to EET stimuli that induce changes to metabolic flow and cooperative or competitive microbial interactions. This systematic meta-omics approach represents a next step towards understanding complex microbial roles within a community and how community members respond to specific environmental stimuli.

No MeSH data available.


Related in: MedlinePlus