Groundwater
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PROVIDER: PRJNA817512 | ENA |
REPOSITORIES: ENA
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Project description:Community characteristics of autotrophic CO2-fixing bacteria in karst wetland groundwaters
| PRJNA821389 | ENA
Project description:Community characteristics of soil carbon-fixing microorganisms in Huixian karst wetlands
| PRJNA608833 | ENA
Project description:Gas fermentation has emerged as a sustainable route to produce fuels and chemicals by recycling inexpensive one-carbon (C1) feedstocks from gaseous and solid waste using gas-fermenting microbes. Currently, acetogens that utilise the Wood-Ljungdahl pathway to convert carbon oxides (CO and CO2) into valuable products are the most advanced biocatalysts for gas fermentation. However, our understanding of the functionalities of the genes involved in the C1-fixing gene cluster and its closely-linked genes is incomplete. Here, we investigate the role of two genes with unclear functions – hypothetical protein (hp; LABRINI_07945) and CooT nickel binding protein (nbp; LABRINI_07950) – directly adjacent and expressed at similar levels to the C1-fixing gene cluster in the gas-fermenting model-acetogen Clostridium autoethanogenum. Targeted deletion of either the hp or nbp gene using CRISPR/nCas9, and phenotypic characterisation in heterotrophic and autotrophic batch and autotrophic bioreactor continuous cultures revealed significant growth defects and altered by-product profiles for both ∆hp and ∆nbp strains. Variable effects of gene deletion on autotrophic batch growth on rich or minimal media suggest that both genes affect the utilisation of complex nutrients. Autotrophic chemostat cultures showed lower acetate and ethanol production rates and higher carbon flux to CO2 and biomass for both deletion strains. Additionally, proteome analysis revealed that disruption of either gene affects the expression of proteins of the C1-fixing gene cluster and ethanol synthesis pathways. Our work contributes to a better understanding of genotype-phenotype relationships in acetogens and offers engineering targets to improve carbon fixation efficiency in gas fermentation.
2023-05-10 | PXD040151 | Pride
Project description:Microbial community and its spatiotemporal characteristics in Huixian karst wetland soils.
| PRJNA805021 | ENA
Project description:Metagenome-assembled genomes (MAGs) have revealed the existence of novel bacterial and archaeal groups and provided insight into their genetic potential. However, metagenomics and even metatranscriptomics cannot resolve how the genetic potential translates into metabolic functions and physiological activity. Here, we present a novel approach for the quantitative and organism-specific assessment of the carbon flux through microbial communities with stable isotope probing-metaproteomics and integration of temporal dynamics in 13C incorporation by Stable Isotope Cluster Analysis (SIsCA). We used groundwater microcosms labeled with 13CO2 and D2O as model systems and stimulated them with reduced sulfur compounds to determine the ecosystem role of chemolithoautotrophic primary production. Raman microspectroscopy detected rapid deuterium incorporation in microbial cells from 12 days onwards, indicating activity of the groundwater organisms. SIsCA revealed that groundwater microorganisms fell into five distinct carbon assimilation strategies. Only one of these strategies, comprising less than 3.5% of the community, consisted of obligate autotrophs (Thiobacillus), with a 13C incorporation of approximately 95%. Instead, mixotrophic growth was the most successful strategy, and was represented by 12 of the 15 MAGs expressing pathways for autotrophic CO2 fixation, including Hydrogenophaga, Polaromonas and Dechloromonas, with varying 13C incorporation between 5% and 90%. Within 21 days, 43% of carbon in the community was replaced by 13C, increasing to 80% after 70 days. Of the 31 most abundant MAGs, 16 expressed pathways for sulfur oxidation, including strict heterotrophs. We concluded that chemolithoautotrophy drives the recycling of organic carbon and serves as a fill-up function in the groundwater. Mixotrophs preferred the uptake of organic carbon over the fixation of CO2, and heterotrophs oxidize inorganic compounds to preserve organic carbon. Our study showcases how next-generation physiology approach like SIsCA can move beyond metagenomics studies by providing information about expression of metabolic pathways and elucidating the role of MAGs in ecosystem functioning.
2022-05-20 | PXD024889 | Pride
Project description:The aim of this study was to understand how autotrophic (CO2-fixing) bacteria balance the different needs for substrate assimilation, growth functions, and resilience in order to thrive in their environment.To this end, the proteome of the model chemolithoautotroph Ralstonia eutropha a.k.a. Cupriavidus necator was studied in different environmental conditions (four limiting substrates, and five different growth rates). Cupriavidus was cultivated in substrate-limited chemostats with fructose, formate, succinate and ammonium limitation to obtain steady state cell samples. The dilution rate/growth rate was increased step-wise from 0.05 to 0.25 1/h in 0.05 steps. Protein quantity was determined by LC-MS, and enzyme utilization was investigated by resource balance analysis modeling.
2022-02-17 | PXD024819 | Pride
Project description:The melting of permafrost and its potential impact on greenhouse gas emissions is a major concern in the context of global warming. The fate of the carbon trapped in permafrost will largely depend on soil physico-chemical characteristics, among which are the quality and quantity of organic matter, pH and water content, and on microbial community composition. In this study, we used microarrays and real-time PCR (qPCR) targeting 16S rRNA genes to characterize the bacterial communities in three different soil types representative of various Arctic settings. The microbiological data were linked to soil physico-chemical characteristics and CO2 production rates. Microarray results indicated that soil characteristics, and especially the soil pH, were important parameters in structuring the bacterial communities at the genera/species levels. Shifts in community structure were also visible at the phyla/class levels, with the soil CO2 production rate being positively correlated to the relative abundance of the Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria. These results indicate that CO2 production in Arctic soils does not only depend on the environmental conditions, but also on the presence of specific groups of bacteria that have the capacity to actively degrade soil carbon.
2011-01-01 | GSE24800 | GEO
Project description:The synthetic microbial community used in this study was composed of the major functional guilds (cellulolytic fermenter, sulfate reducer, hydrogenotrophic methanogen and acetoclastic methanogen) that mediate the anaerobic conversion of cellulosic biomass to CH4 and CO2 in wetland soils. The choice of a facultative sulfate-reducing bacterium (Desulfovibrio vulgaris Hildenborough) introduced metabolic versatility and enabled investigations into the community response to sulfate intrusion. The growth status of these multi-species cultures was measured over a week by daily analysis of substrate consumption and product accumulation. The quad-cultures were analyzed with metaproteomics at the end of experiment to characterize the community structure and metabolic activities.
2023-02-17 | PXD035759 | Pride
Project description:Autotrophic conversion of CO2 to value-added biochemicals has received considerable attention for the sustainable route to replace the fossil fuels. Particularly, anaerobic acetogenic bacteria are naturally capable of reducing CO2 or CO to various metabolites. To fully utilize their biosynthetic potential, systemic understanding of the metabolic network with the transcriptional and translational regulation of the corresponding genes is highly demanded. Here, we complete a genome sequence of Eubacterium limosum ATCC8466 in a circular form of 4.4 Mb, followed by integrating genome-scale measurements of its transcriptome and translatome. Interestingly, the transcriptionally abundant genes encoding the Wood-Ljungdahl pathway were regulated at translational level with decreased translation efficiency (TE). To understand the regulation, the primary transcriptome was augmented, which determined 1,458 transcription start sites (TSS) and 1,253 5’-untranslated regions (5′UTR). The data supports that under the autotrophic condition the TE of genes for the Wood-Ljungdahl pathway and the energy conservation system were regulated by 5′UTR secondary structure. In addition, it was illustrated that the strain reallocates protein synthesis and energy economically, focusing more on translation of energy conservation system rather than on carbon metabolism under autotrophic growth. Thus, our results provide potential route for strain engineering to enhance syngas fermenting capacity.
2018-07-16 | GSE97613 | GEO