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Proceedings of the National Academy of... Jul 2021Reports of biogenic methane (CH) synthesis associated with a range of organisms have steadily accumulated in the literature. This has not happened without controversy...
Reports of biogenic methane (CH) synthesis associated with a range of organisms have steadily accumulated in the literature. This has not happened without controversy and in most cases the process is poorly understood at the gene and enzyme levels. In marine and freshwater environments, CH supersaturation of oxic surface waters has been termed the "methane paradox" because biological CH synthesis is viewed to be a strictly anaerobic process carried out by O-sensitive methanogens. Interest in this phenomenon has surged within the past decade because of the importance of understanding sources and sinks of this potent greenhouse gas. In our work on Yellowstone Lake in Yellowstone National Park, we demonstrate microbiological conversion of methylamine to CH and isolate and characterize an sp. capable of this activity. Furthermore, we identify and clone a gene critical to this process (encodes pyridoxylamine phosphate-dependent aspartate aminotransferase) and demonstrate that this property can be transferred to with this gene and will occur as a purified enzyme. This previously unrecognized process sheds light on environmental cycling of CH, suggesting that O-insensitive, ecologically relevant aerobic CH synthesis is likely of widespread distribution in the environment and should be considered in CH modeling efforts.
Topics: Aerobiosis; Bacteria; Betaine; DNA Mutational Analysis; Methane; Microbiota; Mutation; Water
PubMed: 34183407
DOI: 10.1073/pnas.2019229118 -
Biotechnology and Bioengineering Dec 2020Aerobic granular sludge (AGS) technology allows simultaneous nitrogen, phosphorus, and carbon removal in compact wastewater treatment processes. To operate, design, and...
Aerobic granular sludge (AGS) technology allows simultaneous nitrogen, phosphorus, and carbon removal in compact wastewater treatment processes. To operate, design, and model AGS reactors, it is essential to properly understand the diffusive transport within the granules. In this study, diffusive mass transfer within full-scale and lab-scale AGS was characterized with nuclear magnetic resonance (NMR) methods. Self-diffusion coefficients of water inside the granules were determined with pulsed-field gradient NMR, while the granule structure was visualized with NMR imaging. A reaction-diffusion granule-scale model was set up to evaluate the impact of heterogeneous diffusion on granule performance. The self-diffusion coefficient of water in AGS was ∼70% of the self-diffusion coefficient of free water. There was no significant difference between self-diffusion in AGS from full-scale treatment plants and from lab-scale reactors. The results of the model showed that diffusional heterogeneity did not lead to a major change of flux into the granule (<1%). This study shows that differences between granular sludges and heterogeneity within granules have little impact on the kinetic properties of AGS. Thus, a relatively simple approach is sufficient to describe mass transport by diffusion into the granules.
Topics: Aerobiosis; Sewage; Waste Disposal, Fluid; Water Purification
PubMed: 32725888
DOI: 10.1002/bit.27522 -
Microbiology (Reading, England) Jun 2015Carnitine is a quaternary amine compound found at high concentration in animal tissues, particularly muscle, and is most well studied for its contribution to fatty acid... (Review)
Review
Carnitine is a quaternary amine compound found at high concentration in animal tissues, particularly muscle, and is most well studied for its contribution to fatty acid transport into mitochondria. In bacteria, carnitine is an important osmoprotectant, and can also enhance thermotolerance, cryotolerance and barotolerance. Carnitine can be transported into the cell or acquired from metabolic precursors, where it can serve directly as a compatible solute for stress protection or be metabolized through one of a few distinct pathways as a nutrient source. In this review, we summarize what is known about carnitine physiology and metabolism in bacteria. In particular, recent advances in the aerobic and anaerobic metabolic pathways as well as the use of carnitine as an electron acceptor have addressed some long-standing questions in the field.
Topics: Aerobiosis; Anaerobiosis; Animals; Bacterial Physiological Phenomena; Carnitine; Cold Temperature; Electron Transport; Hot Temperature; Hydrostatic Pressure; Metabolic Networks and Pathways; Osmotic Pressure; Stress, Physiological
PubMed: 25787873
DOI: 10.1099/mic.0.000080 -
Applied Microbiology and Biotechnology Jun 2020Lignocellulose is a widely available renewable carbon source and a promising feedstock for the production of various chemicals in biorefineries. However, its... (Review)
Review
Lignocellulose is a widely available renewable carbon source and a promising feedstock for the production of various chemicals in biorefineries. However, its recalcitrant nature is a major hurdle that must be overcome to enable economic conversion processes. Deconstruction of lignocellulose is part of the global carbon cycle, and efficient microbial degradation systems have evolved that might serve as models to improve commercial conversion processes. Biofilms-matrix encased, spatially organized clusters of microbial cells and the predominating lifestyle in nature-have been recognized for their essential role in the degradation of cellulose in nature, e.g., in soils or in the digestive tracts of ruminant animals. Cellulolytic biofilms allow for a high concentration of enzymes at the boundary layer between the solid substrate and the liquid phase and the more complete capture of hydrolysis products directly at the hydrolysis site, which is energetically favorable. Furthermore, enhanced expression of genes for carbohydrate active enzymes as a response to the attachment on solid substrate has been demonstrated for cellulolytic aerobic fungi and anerobic bacteria. In natural multispecies biofilms, the vicinity of different microbial species allows the creation of efficient food webs and synergistic interactions thereby, e.g., avoiding the accumulation of inhibiting metabolites. In this review, these topics are discussed and attempts to realize the benefits of biofilms in targeted applications such as the consolidated bioprocessing of lignocellulose are highlighted. KEY POINTS: Multispecies biofilms enable efficient lignocellulose destruction in the biosphere. Cellulose degradation by anaerobic bacteria often occurs by monolayered biofilms. Fungal biofilms immobilize enzymes and substrates in an external digestion system. Surface attached cultures typically show higher expression of cellulolytic enzymes.
Topics: Aerobiosis; Anaerobiosis; Bacteria, Anaerobic; Biofilms; Cellulose; Fungi; Hydrolysis; Lignin
PubMed: 32337627
DOI: 10.1007/s00253-020-10595-y -
Philosophical Transactions of the Royal... Sep 2016Flapping flight is energetically more costly than running, although it is less costly to fly a given body mass a given distance per unit time than it is for a similar... (Review)
Review
Flapping flight is energetically more costly than running, although it is less costly to fly a given body mass a given distance per unit time than it is for a similar mass to run the same distance per unit time. This is mainly because birds can fly faster than they can run. Oxygen transfer and transport are enhanced in migrating birds compared with those in non-migrators: at the gas-exchange regions of the lungs the effective area is greater and the diffusion distance smaller. Also, migrating birds have larger hearts and haemoglobin concentrations in the blood, and capillary density in the flight muscles tends to be higher. Species like bar-headed geese migrate at high altitudes, where the availability of oxygen is reduced and the energy cost of flapping flight increased compared with those at sea level. Physiological adaptations to these conditions include haemoglobin with a higher affinity for oxygen than that in lowland birds, a greater effective ventilation of the gas-exchange surface of the lungs and a greater capillary-to-muscle fibre ratio. Migrating birds use fatty acids as their source of energy, so they have to be transported at a sufficient rate to meet the high demand. Since fatty acids are insoluble in water, birds maintain high concentrations of fatty acid-binding proteins to transport fatty acids across the cell membrane and within the cytoplasm. The concentrations of these proteins, together with that of a key enzyme in the β-oxidation of fatty acids, increase before migration.This article is part of the themed issue 'Moving in a moving medium: new perspectives on flight'.
Topics: Aerobiosis; Animal Migration; Animals; Birds; Energy Metabolism; Flight, Animal
PubMed: 27528774
DOI: 10.1098/rstb.2015.0384 -
Journal of the American Chemical Society Aug 2016Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea... (Review)
Review
Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (MMO) and methyl coenzyme M reductase (MCR) enzymes. Although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in traditional industrial hosts. With turnover numbers of 0.16-13 s(-1), these enzymes pose a considerable upstream problem in the biological production of fuels or chemicals from methane. Methane oxidation enzymes will need to be engineered to be faster to enable high volumetric productivities; however, efforts to do so and to engineer simpler enzymes have been minimally successful. Moreover, known methane-oxidizing enzymes have different expression levels, carbon and energy efficiencies, require auxiliary systems for biosynthesis and function, and vary considerably in terms of complexity and reductant requirements. The pros and cons of using each methane-oxidizing enzyme for Bio-GTL are considered in detail. The future for these enzymes is bright, but a renewed focus on studying them will be critical to the successful development of biological processes that utilize methane as a feedstock.
Topics: Aerobiosis; Archaea; Enzymes; Gases; Methane; Oxidation-Reduction
PubMed: 27366961
DOI: 10.1021/jacs.6b04568 -
Microbial Physiology 2024The denitrifying betaproteobacterium Aromatoleum aromaticum EbN1T is a facultative anaerobic degradation specialist and belongs to the environmental bacteria studied... (Review)
Review
The denitrifying betaproteobacterium Aromatoleum aromaticum EbN1T is a facultative anaerobic degradation specialist and belongs to the environmental bacteria studied best on the proteogenomic level. This review summarizes the current state of knowledge about the anaerobic and aerobic degradation (to CO2) of 47 organic growth substrates (23 aromatic, 21 aliphatic, and 3 amino acids) as well as the modes of respiratory energy conservation (denitrification vs. O2-respiration). The constructed catabolic network is comprised of 256 genes, which occupy ∼7.5% of the coding regions of the genome. In total, 219 encoded proteins have been identified by differential proteomics, yielding a proteome coverage of ∼74% of the network. Its degradation section is composed of 31 peripheral and 4 central pathways, with several peripheral modules (e.g., for 4-ethylphenol, 2-phenylethylamine, indoleacetate, and phenylpropanoids) discovered only after the complete genome [Arch Microbiol. 2005 Jan;183(1):27-36] and a first proteomic survey [Proteomics. 2007 Jun;7(13):2222-39] of A. aromaticum EbN1T were reported. The activation of recalcitrant aromatic compounds involves a suite of biochemically intriguing reactions ranging from C-H-bond activation (e.g., ethylbenzene dehydrogenase) via carboxylation (e.g., acetophenone carboxylase) to oxidative deamination (e.g., benzylamine), reductive dearomatization (benzoyl-CoA), and epoxide-forming oxygenases (e.g., phenylacetyl-CoA). The peripheral reaction sequences are substrate-specifically induced, mediated by specific transcriptional regulators with in vivo response thresholds in the nanomolar range. While lipophilic substrates (e.g., phenolics) enter the cells via passive diffusion, polar ones require active uptake that is driven by specific transporters. Next to the protein repertoire for canonical complexes I-III, denitrification, and O2-respiration (low- and high-affinity oxidases), the genome encodes an Ndh-II, a tetrathionate reductase, two ETF:quinone oxidoreductases, and two Rnf-type complexes, broadening the electron transfer flexibility of the strain. Taken together, the detailed catabolic network presented here forms a solid basis for future systems biology-level studies with A. aromaticum EbN1T.
Topics: Bacterial Proteins; Anaerobiosis; Metabolic Networks and Pathways; Aerobiosis; Proteome; Proteomics; Denitrification; Rhodocyclaceae
PubMed: 37816339
DOI: 10.1159/000534425 -
Biochimica Et Biophysica Acta.... Nov 2020Ubiquinone is an important component of the electron transfer chains in proteobacteria and eukaryotes. The biosynthesis of ubiquinone requires multiple steps, most of... (Review)
Review
Ubiquinone is an important component of the electron transfer chains in proteobacteria and eukaryotes. The biosynthesis of ubiquinone requires multiple steps, most of which are common to bacteria and eukaryotes. Whereas the enzymes of the mitochondrial pathway that produces ubiquinone are highly similar across eukaryotes, recent results point to a rather high diversity of pathways in bacteria. This review focuses on ubiquinone in bacteria, highlighting newly discovered functions and detailing the proteins that are known to participate to its biosynthetic pathways. Novel results showing that ubiquinone can be produced by a pathway independent of dioxygen suggest that ubiquinone may participate to anaerobiosis, in addition to its well-established role for aerobiosis. We also discuss the supramolecular organization of ubiquinone biosynthesis proteins and we summarize the current understanding of the evolution of the ubiquinone pathways relative to those of other isoprenoid quinones like menaquinone and plastoquinone.
Topics: Aerobiosis; Anaerobiosis; Bacteria; Biosynthetic Pathways; Electron Transport; Ubiquinone
PubMed: 32663475
DOI: 10.1016/j.bbabio.2020.148259 -
Current Hypertension Reports Mar 2015Previously considered a disease isolated to the pulmonary circulation, pulmonary arterial hypertension is now being recognized as a systemic disorder that is associated... (Review)
Review
Previously considered a disease isolated to the pulmonary circulation, pulmonary arterial hypertension is now being recognized as a systemic disorder that is associated with significant metabolic dysfunction. Numerous animal models have demonstrated the development of pulmonary arterial hypertension following the onset of insulin resistance, indicating that insulin resistance may be causal. Recent publications highlighting alterations in aerobic glycolysis, fatty acid oxidation, and the tricarboxylic acid cycle in the pulmonary circulation and right ventricle have expanded our understanding of the complex pathobiology of this disease. By targeting these derangements in metabolism, numerous researchers are investigating noninvasive techniques to monitor disease activity and therapeutics that address the underlying metabolic condition. In the following review, we will explore pre-clinical and clinical studies investigating the metabolic dysfunction seen in pulmonary arterial hypertension.
Topics: Aerobiosis; Animals; Glycolysis; Humans; Hypertension, Pulmonary; Insulin Resistance; Metabolic Syndrome; Oxidation-Reduction; Pulmonary Circulation
PubMed: 25754317
DOI: 10.1007/s11906-014-0524-y -
Journal of Hazardous Materials Jun 2020This review summarises the current state of knowledge on the biodegradation and fate of the gasoline ether oxygenate ethyl tert-butyl ether (ETBE) in soil and... (Review)
Review
This review summarises the current state of knowledge on the biodegradation and fate of the gasoline ether oxygenate ethyl tert-butyl ether (ETBE) in soil and groundwater. Microorganisms have been identified in soil and groundwater with the ability to degrade ETBE aerobically as a carbon and energy source, or via cometabolism using alkanes as growth substrates. Aerobic biodegradation of ETBE initially occurs via hydroxylation of the ethoxy carbon by a monooxygenase enzyme, with subsequent formation of intermediates which include acetaldehyde, tert-butyl acetate (TBAc), tert-butyl alcohol (TBA), 2-hydroxy-2-methyl-1-propanol (MHP) and 2-hydroxyisobutyric acid (2-HIBA). Slow cell growth and low biomass yields on ETBE are believed to result from the ether structure and slow degradation kinetics, with potential limitations on ETBE metabolism. Genes known to facilitate transformation of ETBE include ethB (within the ethRABCD cluster), encoding a cytochrome P450 monooxygenase, and alkB-encoding alkane hydroxylases. Other genes have been identified in microorganisms but their activity and specificity towards ETBE remains poorly characterised. Microorganisms and pathways supporting anaerobic biodegradation of ETBE have not been identified, although this potential has been demonstrated in limited field and laboratory studies. The presence of co-contaminants (other ether oxygenates, hydrocarbons and organic compounds) in soil and groundwater may limit aerobic biodegradation of ETBE by preferential metabolism and consumption of available dissolved oxygen or enhance ETBE biodegradation through cometabolism. Both ETBE-degrading microorganisms and alkane-oxidising bacteria have been characterised, with potential for use in bioaugmentation and biostimulation of ETBE degradation in groundwater.
Topics: Aerobiosis; Anaerobiosis; Bacteria; Ethyl Ethers; Soil Pollutants; Water Pollutants, Chemical
PubMed: 32145642
DOI: 10.1016/j.jhazmat.2020.122046