A laboratory-based model ecosystem reveals genetic determinants of methanotroph phenotypic heterogeneity in a methane-oxygen counter gradient
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ABSTRACT:
PROVIDER: PRJNA1020120 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26147616_1.fastq.gz | Fastqsanger.gz | |||
| SRR26147616_2.fastq.gz | Fastqsanger.gz | |||
| SRR26147617_1.fastq.gz | Fastqsanger.gz | |||
| SRR26147617_2.fastq.gz | Fastqsanger.gz | |||
| SRR26147618_1.fastq.gz | Fastqsanger.gz |
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Project description:Connecting genes to phenotypic traits in bacteria is often challenging because of a lack of environmental cues in laboratory settings. However, laboratory-based model ecosystems offer a means to better account for natural conditions compared to standard planktonic cultures, aiding in the linking of genotypes and phenotypes. Here, we present a simple, cost-effective, laboratory-based model ecosystem to study aerobic methane-oxidizing bacteria (methanotrophs). This system, referred to as the gradient syringe, is made by inoculating bacteria into semi-solid agarose held within a disposable syringe. Empty space at one end of the syringe is flushed with methane gas, while the other end is open to the atmosphere through a sterile filter. We show this system replicates the methane-oxygen counter gradient typically found in the natural soil environment of methanotrophs. Culturing the methanotroph Methylomonas sp. strain LW13 in this system produced a distinct horizontal band at the intersection of the counter gradient, which we discovered was due not to increased cell growth at this location but instead to an increased amount of extracellular polymeric substances (EPS). We also discovered that different methanotrophic taxa formed EPS bands with distinct locations and morphologies when grown in the methane-oxygen counter gradient. By comparing transcriptomic data from LW13 growing within and surrounding this EPS band, we identified genes implicated in cell growth and EPS formation within the gradient syringe, and validated the involvement of these genes with knockout strains. This work highlights the use of a laboratory-based model ecosystem that more closely mimics the natural environment to uncover methanotroph phenotypes missing from standard planktonic cultures, and link these phenotypes their genetic determinants.
2023-10-05 | GSE243827 | GEO
Project description:Lakes are a significant source of atmospheric methane, although methane-oxidizing bacteria consume most methane diffusing upward from anoxic sediments. Diverse methane-oxidizing bacteria form an effective methane filter in the water column of stratified lakes, yet, niche partitioning of different methane-oxidizing bacteria along the oxygen-methane counter gradient remains poorly understood. In our study, we reveal vertical distribution patterns of active methane-oxidizing bacteria along the oxygen-methane counter gradient of four lakes, based on amplicon sequencing analysis of 16S rRNA and pmoA genes, and 16S rRNA and pmoA transcripts, and potential methane oxidation rates. Differential distribution patterns indicated that ecologically different methane-oxidizing bacteria occupied the methane-deficient and oxygen-deficient part above and below the oxygen-methane interface. The interface sometimes harbored additional taxa. Within the dominant Methylococcales, an uncultivated taxon (CABC2E06) occurred mainly under methane-deficient conditions, whereas Crenothrix-related taxa preferred oxygen-deficient conditions. Candidatus Methylomirabilis limnetica (NC10 phylum) abundantly populated the oxygen-deficient part in two of four lakes. We reason that the methane filter in lakes is structured and that methane-oxidizing bacteria may rely on niche-specific adaptations for methane oxidation along the oxygen-methane counter gradient. Niche partitioning of methane-oxidizing bacteria might support greater overall resource consumption, contributing to the high effectivity of the lacustrine methane filter.
| S-EPMC6908591 | biostudies-literature
Project description:The bacteria that grow on methane aerobically (methanotrophs) support populations of non-methanotrophs in the natural environment by excreting methane-derived carbon. One group of excreted compounds are short-chain organic acids, generated in highest abundance when cultures are grown under O2-starvation. We examined this O2-starvation condition in the methanotroph Methylomicrobium buryatense 5GB1C . Under prolonged O2-starvation in a closed vial, this methanotroph increases the amount of acetate excreted about 10-fold, but the formate, lactate, and succinate excreted do not respond to this culture condition. In bioreactor cultures, the amount of each excreted product is similar across a range of growth rates and limiting substrates, including O2-limitation. A set of mutants were generated in genes predicted to be involved in generating or regulating excretion of these compounds and tested for growth defects, and changes in excretion products. The phenotypes and associated metabolic flux modeling suggested that in M. buryatense 5GB1C, formate and acetate are excreted in response to redox imbalance, and the resulting metabolic state represents a combination of fermentation and respiration metabolism.
2017-08-24 | GSE101981 | GEO
Project description:Methanotrophs, which help regulate atmospheric levels of methane, are active in diverse natural and man-made environments. This range of habitats and the feast-famine cycles seen by many environmental methanotrophs suggest that methanotrophs dynamically mediate rates of methane oxidation. Global methane budgets require ways to account for this variability in time and space. Functional gene biomarker transcripts are increasingly being studied to inform the dynamics of diverse biogeochemical cycles. Previously, per-cell transcript levels of the methane oxidation biomarker, pmoA, were found to vary quantitatively with respect to methane oxidation rates in model aerobic methanotroph, Methylosinus trichosporium OB3b. In the present study, these trends were explored for two additional aerobic methanotroph pure cultures, Methylocystis parvus OBBP and Methylomicrobium album BG8. At steady-state conditions, per cell pmoA mRNA transcript levels strongly correlated with per cell methane oxidation across the three methanotrophs across many orders of magnitude of activity (R2 = 0.91). Additionally, genome-wide expression data (RNA-seq) were used to explore transcriptomic responses of steady state M. album BG8 cultures to short-term CH4 and O2 limitation. These limitations induced regulation of genes involved in central carbon metabolism (including carbon storage), cell motility, and stress response.
2021-11-17 | GSE188821 | GEO
Project description:Methylomicrobium buryatense 5GB1 is an obligate methylotroph, which grows on methane or methanol with similar growth rates. Core metabolic pathways are similar on both substrates, but recent studies of methane metabolism suggest that growth on methanol might have significant differences from growth on methane. In this study, both a targeted metabolomics approach as well as a 13C tracer approach have been taken to understand core carbon metabolism in M. buryatense 5GB1 during methanol growth, to determine whether such differences occur. Targeted metabolomics analyses were performed on both methane and methanol cultures to identify metabolic nodes with altered fluxes. Several key metabolites showed significant differences in pool size. Noticeably, 2-keto-3-deoxy-6-phosphogluconate (KDPG) showed much larger pools under methanol culture, suggesting the Entner-Doudoroff (ED) pathway was more active. Intermediates in other parts of metabolism also showed differences in pool sizes under methanol growth. A systematic shift of active core metabolism is proposed to explain the changes. In order to distinguish flux partition differences at the C3-C4 node, 13C tracer analysis was also applied to methanol-grown cultures. Using the experimental results as constraints, we applied flux balance analysis to determine the metabolic flux phenotype of M. buryatense 5GB1 growing on methanol. The resulting new insights into core metabolism of this methanotroph provide an improved basis for future strain design.
2019-04-17 | GSE110541 | GEO
Project description:uncultured putative methanotroph Metagenome
| PRJNA445632 | ENA
Project description:Here we present the assembled genome of the facultative methanotroph, Methylocystis strain SB2, along with assessment of its transcriptome when grown on methane vs. ethanol. As expected, transcriptomic analyses indicate methane is converted to carbon dioxide via the canonical methane oxidation pathway for energy generation, and that carbon is assimilated at the level of formaldehyde via the serine cycle. When grown on ethanol, it appears this strain converts ethanol to acetyl-CoA and then utilizes the TCA cycle for energy generation and the ethylmalonyl CoA pathway for the production of biomass. All cultures were grown in triplicates for subsequent DNA and RNA extraction as well as for subsequent sequencing using Illumina. Transcriptomic analysis results presented in this Series.
2014-03-20 | E-GEOD-51345 | biostudies-arrayexpress
Project description:We report here a methanotroph, Methylotuvimicrobium buryatense 5GB1C, that consumes methane at 500ppm at rates several times higher than any previously published. Analyses of bioreactor-based performance and RNAseq based transcriptomics suggest that this superior ability to utilize low methane is based at least in part on an extremely low non-growth associated maintenance energy and on a 5-fold higher methane specific affinity than previous reports.
2023-08-02 | GSE221011 | GEO
Project description:Non-targeted microbial metabolomics (DDA) of extracts from methanotroph cocultures
2024-07-25 | MSV000095439 | MassIVE
Project description:Although representatives with spiral-shaped cells are described for many functional groups of bacteria, this cell morphotype has never been observed among methanotrophs. Here, we show that spiral-shaped methanotrophic bacteria do exist in nature but elude isolation by conventional approaches due to the preference for growth under micro-oxic conditions. The helical cell shape may enable rapid motility of these bacteria in water-saturated, heterogeneous environments with high microbial biofilm content, therefore offering an advantage of fast cell positioning under desired high methane/low oxygen conditions. The pmoA genes encoding a subunit of particulate methane monooxygenase from these methanotrophs form a new genus-level lineage within the family Methylococcaceae, type Ib methanotrophs. Application of a pmoA-based microarray detected these bacteria in a variety of high-latitude freshwater environments including wetlands and lake sediments. As revealed by the environmental pmoA distribution analysis, type Ib methanotrophs tend to live very near the methane source, where oxygen is scarce. The former perception of type Ib methanotrophs as being typical for thermal habitats appears to be incorrect because only a minor proportion of pmoA sequences from these bacteria originated from environments with elevated temperatures.
| S-EPMC5113839 | biostudies-literature