Ontology highlight
ABSTRACT:
PROVIDER: PRJNA967366 | ENA |
REPOSITORIES: ENA
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Project description:Abstract. Microbial gas fermentation remains a promising biotechnology for the production of a variety of industrially relevant chemicals under relatively benign conditions using ubiquitous feedstocks, such as carbon dioxide. Implementation of these gas fermentation processes requires an understanding of the microbial response to different ratios of the gaseous feedstocks (carbon dioxide, oxygen, and hydrogen) supplied to the reactor. Here, we used Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337) as a microbial biocatalyst due to its metabolic diversity, genetic tractability, and ability to grow to high cell densities during aerobic fermentation in bioreactors. Specifically, we investigate whether the supply of different proportions of hydrogen and carbon dioxide in the gas stream (1:1, 3:1, and 8:1 H2:CO2) affects the physiology of C. necator, with a focus on the accumulation of single cell protein (SCP) and poly-3-hydroxybutyrate (PHB) within the microbial biomass. We found that an 8:1 ratio of H2:CO2 led to both the highest overall biomass production and PHB content within the biomass after a seven-day incubation. Intracellular SCP content varied as a function of both length of incubation and gas ratio supplied. We conducted a proteomic analysis to determine whether differences in productivity could be correlated with changes in protein expression over time and across treatment groups. This study highlights the importance of considering gaseous substrate composition and its potential effects on microbial physiology and metabolism during fermentation.
2026-05-15 | PXD064900 | Pride
Project description:The response of soil microbial community to climate warming through both function shift and composition reorganization may profoundly influence global nutrient cycles, leading to potential significant carbon release from the terrain to the atmosphere. Despite the observed carbon flux change in northern permafrost, it remains unclear how soil microbial community contributes to this ecosystem alteration. Here, we applied microarray-based GeoChip 4.0 to investigate the functional and compositional response of subsurface (15~25cm) soil microbial community under about one year’s artificial heating (+2°C) in the Carbon in Permafrost Experimental Heating Research site on Alaska’s moist acidic tundra. Statistical analyses of GeoChip signal intensities showed significant microbial function shift in AK samples. Detrended correspondence analysis and dissimilarity tests (MRPP and ANOSIM) indicated significant functional structure difference between the warmed and the control communities. ANOVA revealed that 60% of the 70 detected individual genes in carbon, nitrogen, phosphorous and sulfur cyclings were substantially increased (p<0.05) by heating. 18 out of 33 detected carbon degradation genes were more abundant in warming samples in AK site, regardless of the discrepancy of labile or recalcitrant C, indicating a high temperature sensitivity of carbon degradation genes in rich carbon pool environment. These results demonstrated a rapid response of northern permafrost soil microbial community to warming. Considering the large carbon storage in northern permafrost region, microbial activity in this region may cause dramatic positive feedback to climate change, which is important and necessary to be integrated into climate change models.
2016-02-22 | GSE77866 | GEO
Project description:Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. Microbial functional diversity, measured by a metagenomic tool named GeoChip, and phylogenetic diversity are increased with temperature, while microbial biomass were similar or decreased. Nevertheless, the effects of climate change was overridden by maize cropping, underscoring the need to disentangle them in research. Mantel tests and canonical correspondence analysis (CCA) demonstrated that vegetation, climatic factors (e.g., temperature and precipitation), soil nitrogen components and CO2 efflux were significantly correlated to the microbial community composition. Further investigation unveiled strong correlations between carbon cycling genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycling genes and nitrification, which provides mechanistic understanding of these microbe-mediated processes and empowers an interesting possibility of incorporating bacterial gene abundance in greenhouse gas emission modeling.
2013-10-30 | GSE51592 | GEO
Project description:An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and its impact on host physiology. This research can be confounded by poorly-understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multi-way interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the Drosophila gut microbiome (from single taxa to the five-member community of Acetobacter and Lactobacillus species) under three nutrient regimes. We show that the metabolic function of Drosophila gut bacteria is dynamic, influenced by community composition and responsive to dietary modulation. Furthermore, we show that ecological interactions such as competition and mutualism identified from the growth patterns of gut bacteria are underlain by a diversity of metabolic interactions, and show that the bacteria tend to compete for amino acids and B vitamins more frequently than for carbon sources. Our results reveal that in addition to fermentation products such as acetate, intermediates of the tricarboxylic acid (TCA) cycle including 2-oxoglutarate and succinate are produced at high flux and cross-fed between bacterial taxa suggesting important roles for TCA cycle intermediates in modulating Drosophila gut microbe interactions and the potential to influence host traits. These metabolic models provide specific predictions of the patterns of ecological and metabolic interactions among gut bacteria under different nutrient regimes, with potentially important consequences for overall community metabolic function and nutritional interactions with the host.
2021-07-01 | MODEL2002040005 | BioModels
Project description:An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and its impact on host physiology. This research can be confounded by poorly-understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multi-way interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the Drosophila gut microbiome (from single taxa to the five-member community of Acetobacter and Lactobacillus species) under three nutrient regimes. We show that the metabolic function of Drosophila gut bacteria is dynamic, influenced by community composition and responsive to dietary modulation. Furthermore, we show that ecological interactions such as competition and mutualism identified from the growth patterns of gut bacteria are underlain by a diversity of metabolic interactions, and show that the bacteria tend to compete for amino acids and B vitamins more frequently than for carbon sources. Our results reveal that in addition to fermentation products such as acetate, intermediates of the tricarboxylic acid (TCA) cycle including 2-oxoglutarate and succinate are produced at high flux and cross-fed between bacterial taxa suggesting important roles for TCA cycle intermediates in modulating Drosophila gut microbe interactions and the potential to influence host traits. These metabolic models provide specific predictions of the patterns of ecological and metabolic interactions among gut bacteria under different nutrient regimes, with potentially important consequences for overall community metabolic function and nutritional interactions with the host.
2021-07-01 | MODEL2002040006 | BioModels
Project description:An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and its impact on host physiology. This research can be confounded by poorly-understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multi-way interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the Drosophila gut microbiome (from single taxa to the five-member community of Acetobacter and Lactobacillus species) under three nutrient regimes. We show that the metabolic function of Drosophila gut bacteria is dynamic, influenced by community composition and responsive to dietary modulation. Furthermore, we show that ecological interactions such as competition and mutualism identified from the growth patterns of gut bacteria are underlain by a diversity of metabolic interactions, and show that the bacteria tend to compete for amino acids and B vitamins more frequently than for carbon sources. Our results reveal that in addition to fermentation products such as acetate, intermediates of the tricarboxylic acid (TCA) cycle including 2-oxoglutarate and succinate are produced at high flux and cross-fed between bacterial taxa suggesting important roles for TCA cycle intermediates in modulating Drosophila gut microbe interactions and the potential to influence host traits. These metabolic models provide specific predictions of the patterns of ecological and metabolic interactions among gut bacteria under different nutrient regimes, with potentially important consequences for overall community metabolic function and nutritional interactions with the host.
2021-07-01 | MODEL2002040003 | BioModels
Project description:An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and its impact on host physiology. This research can be confounded by poorly-understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multi-way interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the Drosophila gut microbiome (from single taxa to the five-member community of Acetobacter and Lactobacillus species) under three nutrient regimes. We show that the metabolic function of Drosophila gut bacteria is dynamic, influenced by community composition and responsive to dietary modulation. Furthermore, we show that ecological interactions such as competition and mutualism identified from the growth patterns of gut bacteria are underlain by a diversity of metabolic interactions, and show that the bacteria tend to compete for amino acids and B vitamins more frequently than for carbon sources. Our results reveal that in addition to fermentation products such as acetate, intermediates of the tricarboxylic acid (TCA) cycle including 2-oxoglutarate and succinate are produced at high flux and cross-fed between bacterial taxa suggesting important roles for TCA cycle intermediates in modulating Drosophila gut microbe interactions and the potential to influence host traits. These metabolic models provide specific predictions of the patterns of ecological and metabolic interactions among gut bacteria under different nutrient regimes, with potentially important consequences for overall community metabolic function and nutritional interactions with the host.
2021-07-01 | MODEL2002040004 | BioModels