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Classification of significant differential gene expression (DGE) in M. album BG8, based on COG classification from the eggNOG 5.0 database. Positive and negative values on the x axis indicate numbers of genes in that COG category that were upregulated and downregulated, respectively, compared to steady-state conditions. Unclassified, category S ("Function Unknown") and categories with fewer than two genes with DGE are not shown.
Source publication
Methanotrophs are naturally occurring microorganisms capable of oxidizing methane, having an impact on global net methane emissions. Additionally, they have also gained interest for their biotechnological applications in single-cell protein production, biofuels, and bioplastics.
Contexts in source publication
Context 1
... substrate limitation. Transcriptome sequencing (RNA-seq) samples from M. album BG8 under short-term substrate limitation yielded 170.4 million reads across the 8 multiplexed samples from the four conditions (Table S5). Gene counts showed agreement after normalization, with medians consistent across samples and between biological replicates (Fig. S4). Biological replicates were examined using principal-component analysis (PCA) of normalized logarithmic transformed read counts using DESeq2 (59). Similarity was observed between duplicate biological replicates for the substrate-limiting conditions. Steady-state samples showed less uniformity due to one replicate from the 4.2-day RT ...
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... samples had similar expression profiles regardless of 2.8-or 4.2-day RT, with only 4 genes showing significant DGE. EggNOG 5.0 was used to categorize genes showing DGE between substrate-limited and corresponding steady-state samples, categorizing 74% and 81% of differentially expressed genes of the methane-and oxygen-limited samples, respectively (Fig. ...
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... CH 4 -and O 2 -limited conditions triggered upregulation of several of genes related to cell motility, flagella, and chemotaxis (identifier in Clusters of Orthologous Groups [COG] database: N) (Fig. 4 and Data Set S2). Upregulation of motility genes has been linked to nutrient limitation, with motile cells seeking more favorable conditions (61). In methanotrophs, growth conditions influence expression of motility and adhesion genes. Similar expression patterns have been observed in M. album BG8 and Methylocystis sp. strain Rockwell ...
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... flagellum genes were upregulated. In this study, both limitation of CH 4 and limitation of O 2 resulted in a strong consistent downregulation of translation, ribosomal structure, and biogenesis (COG: J) genes, with effects on ribosomal protein genes more pronounced in methane limitation, while oxygen limitation mostly affected translational genes (Fig. 4 and Data Set ...
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... strong effect was observed in genes involved in energy production and conversion (COG: C) (Fig. 4). For methanotrophs, these changes in expression of genes for energy production and conversion are hypothesized to be in response to the available substrate, to compensate for differences in energy available and minimize effect on core metabolic pathways (66). A visual representation of the response of central metabolic pathway genes ...
Citations
... Cytochrome c L , in turn, is oxidized by a typical class I cytochrome c (cytochrome c H ), which is also specific for methanol oxidation (Kang-Yun et al. 2022). Importantly, all three components-MDH, cytochrome c L , and cytochrome c H -are soluble and reside within the periplasm of gramnegative methylotrophs (Tentori et al. 2022). In contrast, gram-positive methylotrophs employ an NAD-linked MDH for methanol oxidation, while methanol-oxidizing yeast species use a methanol oxidase system for the same purpose. ...
... The extensive dataset of pMMO gene sequences from various methanotrophs offers the opportunity to utilize pmo as a "functional gene probe" in molecular ecology studies, enabling investigations into the diversity of methanotrophs within natural environments. This utilization has been recently explored and reviewed in publications such as Tentori et al. (2022) and Tyne et al. (2023). ...
The potential consequences for mankind could be disastrous due to global warming, which arises from an increase in the average temperature on Earth. The elevation in temperature primarily stems from the escalation in the concentration of greenhouse gases (GHG) such as CO2, CH4, and N2O within the atmosphere. Among these gases, methane (CH4) is particularly significant in driving alterations to the worldwide climate. Methanotrophic bacteria possess the distinctive ability to employ methane as both as source of carbon and energy. These bacteria show great potential as exceptional biocatalysts in advancing C1 bioconversion technology. The present review describes recent findings in methanotrophs including aerobic and anaerobic methanotroph bacteria, phenotypic characteristics, biotechnological potential, their physiology, ecology, and native multi-carbon utilizing pathways, and their molecular biology. The existing understanding of methanogenesis and methanotrophy in soil, as well as anaerobic methane oxidation and methanotrophy in temperate and extreme environments, is also covered in this discussion. New types of methanogens and communities of methanotrophic bacteria have been identified from various ecosystems and thoroughly examined for a range of biotechnological uses. Grasping the processes of methanogenesis and methanotrophy holds significant importance in the development of innovative agricultural techniques and industrial procedures that contribute to a more favorable equilibrium of GHG. This current review centers on the diversity of emerging methanogen and methanotroph species and their effects on the environment. By amalgamating advanced genetic analysis with ecological insights, this study pioneers a holistic approach to unraveling the biopotential of methanotrophs, offering unprecedented avenues for biotechnological applications.
Key points
• The physiology of methanotrophic bacteria is fundamentally determined.
• Native multi-carbon utilizing pathways in methanotrophic bacteria are summarized.
• The genes responsible for encoding methane monooxygenase are discussed.
... Methane. In some bacteria, strong transcriptional responses accompany growth under nutrient limitation and at low growth rates: Bacteria often decrease expression of the translation and transcription apparatus, up-regulate functions involved in motility and chemotaxis, and up-regulate amino acid synthesis pathways (25,(29)(30)(31). To understand how M. buryatense 5GB1C responds to low methane at the transcriptional level, we quantified holistic gene expression of cultures grown at 500 ppm and 1,000 ppm at methane-limited steady-state in the bioreactor, with growth rates of 0.009 h −1 and 0.02 h −1 , respectively. ...
... These changes also reflect decreased need at the low growth rates. By contrast, many genes related to flagellar protein synthesis and chemotaxis are up-regulated (Fig. 3F), as bacteria tend to be more active in searching for nutrients and more favorable environments under stress (29). ...
The rapid increase of the potent greenhouse gas methane in the atmosphere creates great urgency to develop and deploy technologies for methane mitigation. One approach to removing methane is to use bacteria for which methane is their carbon and energy source (methanotrophs). Such bacteria naturally convert methane to CO2 and biomass, a value-added product and a cobenefit of methane removal. Typically, methanotrophs grow best at around 5,000 to 10,000 ppm methane, but methane in the atmosphere is 1.9 ppm. Air above emission sites such as landfills, anaerobic digestor effluents, rice paddy effluents, and oil and gas wells contains elevated methane in the 500 ppm range. If such sites are targeted for methane removal, technology harnessing aerobic methanotroph metabolism has the potential to become economically and environmentally viable. The first step in developing such methane removal technology is to identify methanotrophs with enhanced ability to grow and consume methane at 500 ppm and lower. We report here that some existing methanotrophic strains grow well at 500 ppm methane, and one of them, Methylotuvimicrobium buryatense 5GB1C, consumes such low methane at enhanced rates compared to previously published values. Analyses of bioreactor-based performance and RNAseq-based transcriptomics suggest that this ability to utilize low methane is based at least in part on extremely low non-growth-associated maintenance energy and on high methane specific affinity. This bacterium is a candidate to develop technology for methane removal at emission sites. If appropriately scaled, such technology has the potential to slow global warming by 2050.
From the view of a circular economy, the bioconversion of methane into cell protein and carbohydrates could provide alternative food resources while cutting greenhouse gases, considering renewable gases from anaerobic...
The remediation of volatile chlorinated hydrocarbons in the quasi-vadose zone has become a significant challenge. We applied an integrated approach to assess the biodegradability of trichloroethylene to identify the biotransformation mechanism. The formation of the functional zone biochemical layer was assessed by analyzing the distribution of landfill gas, physical and chemical properties of cover soil, spatial-temporal variations of micro-ecology, biodegradability of landfill cover soil and distributional difference metabolic pathway. Real-time online monitoring showed that trichloroethylene continuously undergoes anaerobic dichlorination and simultaneous aerobic/anaerobic conversion-aerobic co-metabolic degradation on the vertical gradient of the landfill cover system and reduction in trans-1,2-dichloroethylene in the anoxic zone but not 1,1-dichloroethylene. PCR and diversity sequencing revealed the abundance and spatial distribution of known dichlorination-related genes within the landfill cover, with 6.61 ± 0.25 × 104-6.78 ± 0.09 × 106 and 1.17 ± 0.78 × 103-7.82 ± 0.07 × 105 copies per g/soil of pmoA and tceA, respectively. In addition, dominant bacteria and diversity were significantly linked with physicochemical factors, and Mesorhizobium, Pseudoxanthomonas and Gemmatimonas were responsible for biodegradation in the aerobic, anoxic and anaerobic zones. Metagenome sequencing identified 6 degradation pathways of trichloroethylene that may occur in the landfill cover; the main pathway was incomplete dechlorination accompanied by cometabolic degradation. These results indicate that the anoxic zone is important for trichloroethylene degradation.
