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Journal of Environmental Management Jan 2023Accurate reconstructions of past environments are critical and urgent because they can help understand how modern environments might respond to current climatic and...
Short-term microbial effects on n-alkane during the early phase degradation and consequential modification of biomarkers in a lowland subtropical rainforest in southern Taiwan: A litterbag experiment.
Accurate reconstructions of past environments are critical and urgent because they can help understand how modern environments might respond to current climatic and land-use changes. However, the effect of microbial degradation and consequential modification in plant-derived-biomarkers during the early degradation phase is not yet apparent, that might bias the paleoenvironmental investigation. In this regard, a litterbag experiment was conducted to reveal the microbial effects on n-alkane-associated biomarker changes associated with three habitats (ravine, windward, and leeward) in a lowland subtropical rainforest in southern Taiwan. Freshly collected leaves of plant species Iles rotunda, Ficus benjamina, and Castanopsis carlesii were distributed in the habitat leaf litterbag experiment for 15 and 75 days incubation, respectively. The results revealed that the average leaf decomposition rate was 19.4% ± 6.4% during the first 15 days and 39% ± 11% within 75 days incubation for all leaves. The overall leaf mass degradation of I. rotunda, F. benjamina and C. carlesii in the ravine after 75 days was 58%, 51% and 41%, respectively, which were higher than those in the windward (28%, 36% and 38%) and leeward habitats (35%, 26% and 42%, respectively) indicating higher decomposition rate in the ravine habitat than the others. The predominant n-alkanes in I. rotunda were C and C, whereas in F. benjamina these were C, C, and C, and in C. carlesii it was C. After 75 days, the ravine habitat showed a 60% decrease in the total n-alkane concentration compared to windward and leeward habitats, suggesting the microbial community associated with the ravine habitat has a higher efficiency of degrading n-alkanes. However, the biomarkers such as carbon preference index (CPI), average carbon length (ACL) and the C/C ratio did not show statistical difference in all habitats from 15 to 75 days incubation. The next-generation sequencing revealed that microbial communities changed significantly from 15 to 75 days in all habitats. The alkB gene-containing bacteria and their family lineages increased substantially during the first 15 days incubation in all habitats. Furthermore, several bacterial genera were exclusively present in the ravine habitat, whereas some were only in the leeward and windward habitats. Despite the heterogeneity of microbial proliferation, difference in biomass and n-alkane degradation among the three habitats, most of the n-alkane-associated biomarkers remained the same. Therefore, we concluded that the microbial effects on n-alkane degradation during the early phase in plant leaves had little influence on the results of most n-alkane biomarkers.
Topics: Alkanes; Rainforest; Taiwan; Carbon; Bacteria; Biomarkers
PubMed: 36402014
DOI: 10.1016/j.jenvman.2022.116780 -
Plant Physiology Feb 2024
Topics: Carbon Isotopes; Lipids; Alkanes
PubMed: 37988573
DOI: 10.1093/plphys/kiad619 -
Nature Microbiology Apr 2019Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth's climate. Recent results suggest that the diversity of...
Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth's climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea. Five of these MAGs represent under-sampled (Verstraetearchaeota, Methanonatronarchaeia, ANME-1 and GoM-Arc1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation substantially expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea ('Candidatus Methanoliparia'). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.
Topics: Alkanes; Archaea; Biodiversity; DNA, Archaeal; Metagenome; Methane; Oxidation-Reduction; Phylogeny
PubMed: 30833729
DOI: 10.1038/s41564-019-0363-3 -
FEMS Microbiology Letters Mar 2017Intracellular metabolic sensors can be used for efficient screening and optimization of microbial cell factories. In particular, the sensors are useful in acquiring...
Intracellular metabolic sensors can be used for efficient screening and optimization of microbial cell factories. In particular, the sensors are useful in acquiring information about pathway dynamics and bottlenecks in a straightforward manner. Here, we developed a twin-layer biosensor that functions simultaneously at two levels: through transcription factor mediated sensing and enzyme-metabolite interaction, providing insights into the dynamics of alkane metabolism. In addition, the sensor can be used for monitoring either alkane degradation or biosynthesis, depending on the used cellular context. Alkanes are monitored using a fluorescent reporter green fluorescent protein placed under a native alkane-inducible promoter, whereas a bacterial luciferase producing bioluminescence signal enzymatically detects a specific metabolic intermediate in the alkane production/degradation pathway. First, we employed the sensor to investigate the native alkane degradation route in Acinetobacter baylyi ADP1. The highest fluorescence and luminescence signals were obtained for dodecane. Second, we constructed a non-native alkane synthesis pathway in A. baylyi ADP1, of which the functionality was confirmed with the sensor. The twin-layer approach provides convenient means to study and optimize the kinetics and performance of the heterologous pathway and will facilitate the development of an efficient cell factory.
Topics: Acinetobacter; Alkanes; Biosensing Techniques; Carbohydrate Metabolism; Gene Expression; Genes, Reporter; Luminescent Measurements; Metabolic Networks and Pathways
PubMed: 28333269
DOI: 10.1093/femsle/fnx053 -
The Journal of Chemical Physics Mar 2010The structures of medium-length n-alkane species (C(8)-C(11)) adsorbed to a hydrophilic silica/vapor interface were examined using vibrational sum frequency...
The structures of medium-length n-alkane species (C(8)-C(11)) adsorbed to a hydrophilic silica/vapor interface were examined using vibrational sum frequency spectroscopy. Experiments sampling out-of-plane orientation show a clear pattern in vibrational band intensities that implies chains having primarily all-trans conformations lying flat along the interface. Further analysis shows that the methylene groups of the alkane chains have their local symmetry axes directed into and away from the surface. Spectra acquired under different polarization conditions interlock to reinforce this picture of interfacial structure and organization. Variation in signal intensities with chain length suggests that correlation between adsorbed monomers weakens with increasing chain length. This result stands in contrast with alkane behavior at neat liquid/vapor interfaces where longer length alkanes show considerably more surface induced ordering than short chain alkanes.
Topics: Adsorption; Alkanes; Molecular Conformation; Silicon Dioxide; Spectrum Analysis; Stereoisomerism; Surface Properties; Vibration
PubMed: 20331310
DOI: 10.1063/1.3336727 -
Nature Chemistry Jul 2022The σ-alkane complexes of transition metals, which contain an essentially intact alkane molecule weakly bound to the metal, have been well established as crucial...
The σ-alkane complexes of transition metals, which contain an essentially intact alkane molecule weakly bound to the metal, have been well established as crucial intermediates in the activation of the strong C-H σ-bonds found in alkanes. Methane, the simplest alkane, binds even more weakly than larger alkanes. Here we report an example of a long-lived methane complex formed by directly binding methane as an incoming ligand to a reactive organometallic complex. Photo-ejection of carbon monoxide from a cationic osmium-carbonyl complex dissolved in an inert hydrofluorocarbon solvent saturated with methane at -90 °C affords an osmium(II) complex, [η-CpOs(CO)(CH)], containing methane bound to the metal centre. Nuclear magnetic resonance (NMR) spectroscopy confirms the identity of the σ-methane complex and shows that the four protons of the metal-bound methane are in rapid exchange with each other. The methane ligand has a characteristically shielded H NMR resonance (δ -2.16), and the highly shielded carbon resonance (δ -56.3) shows coupling to the four attached protons (J = 127 Hz). The methane complex has an effective half-life of about 13 hours at -90 °C.
Topics: Alkanes; Ligands; Metals; Methane; Osmium; Protons
PubMed: 35469008
DOI: 10.1038/s41557-022-00929-w -
Journal of Computer-aided Molecular... May 2013Alkane/water partition coefficients (P(alk)) are less familiar to the molecular design community than their 1-octanol/water equivalents and access to both data and...
Alkane/water partition coefficients (P(alk)) are less familiar to the molecular design community than their 1-octanol/water equivalents and access to both data and prediction tools is much more limited. A method for predicting alkane/water partition coefficient from molecular structure is introduced. The basis for the ClogP(alk) model is the strong (R² = 0.987) relationship between alkane/water partition coefficient and molecular surface area (MSA) that was observed for saturated hydrocarbons. The model treats a molecule as a perturbation of a saturated hydrocarbon molecule with the same MSA and uses increments defined for functional groups to quantify the extent to which logP(alk) is perturbed by the introduction each functional group. Interactions between functional groups, such as intramolecular hydrogen bonds are also parameterized within a perturbation framework. The functional groups and interactions between them are specified substructurally in a transparent and reproducible manner using SMARTS notation. The ClogP(alk) model was parameterized using data measured for structurally prototypical compounds that dominate the literature on alkane/water partition coefficients and then validated using an external test set of 100 alkane/water logP measurements, the majority of which were for drugs.
Topics: 1-Octanol; Alkanes; Drug Discovery; Hydrogen Bonding; Models, Chemical; Molecular Structure; Quantitative Structure-Activity Relationship; Solubility; Water
PubMed: 23737238
DOI: 10.1007/s10822-013-9655-5 -
Applied and Environmental Microbiology Jan 2013Upon growth on n-hexadecane (C(16)), n-tetracosane (C(24)), and n-hexatriacontane (C(36)), Dietzia sp. strain DQ12-45-1b could produce different glycolipids,...
Upon growth on n-hexadecane (C(16)), n-tetracosane (C(24)), and n-hexatriacontane (C(36)), Dietzia sp. strain DQ12-45-1b could produce different glycolipids, phospholipids, and lipopeptides. Interestingly, cultivation with C(36) increased cell surface hydrophobic activity, which attenuated the negative effect of the decline of the emulsification activity. These results suggest that the mechanisms of biosurfactant production and cell surface hydrophobicity are dependent upon the chain lengths of the n-alkanes used as carbon sources.
Topics: Actinomycetales; Alkanes; DNA, Bacterial; Hydrophobic and Hydrophilic Interactions; Molecular Sequence Data; Sequence Analysis, DNA; Surface Properties; Surface-Active Agents
PubMed: 23104403
DOI: 10.1128/AEM.02497-12 -
Journal of Bacteriology Jul 2001In many microorganisms the first step for alkane degradation is the terminal oxidation of the molecule by an alkane hydroxylase. We report the characterization of a gene...
In many microorganisms the first step for alkane degradation is the terminal oxidation of the molecule by an alkane hydroxylase. We report the characterization of a gene coding for an alkane hydroxylase in a Burkholderia cepacia strain isolated from an oil-contaminated site. The protein encoded showed similarity to other known or predicted bacterial alkane hydroxylases, although it clustered on a separate branch together with the predicted alkane hydroxylase of a Mycobacterium tuberculosis strain. Introduction of the cloned B. cepacia gene into an alkane hydroxylase knockout mutant of Pseudomonas fluorescens CHAO restored its ability to grow on alkanes, which confirms that the gene analyzed encodes a functional alkane hydroxylase. The gene, which was named alkB, is not linked to other genes of the alkane oxidation pathway. Its promoter was identified, and its expression was analyzed under different growth conditions. Transcription was induced by alkanes of chain lengths containing 12 to at least 30 carbon atoms as well as by alkanols. Although the gene was efficiently expressed during exponential growth, transcription increased about fivefold when cells approached stationary phase, a characteristic not shared by the few alkane degraders whose regulation has been studied. Expression of the alkB gene was under carbon catabolite repression when cells were cultured in the presence of several organic acids and sugars or in a complex (rich) medium. The catabolic repression process showed several characteristics that are clearly different from what has been observed in other alkane degradation pathways.
Topics: Alkanes; Base Sequence; Burkholderia cepacia; Cytochrome P-450 CYP4A; Cytochrome P-450 Enzyme System; DNA, Bacterial; Gene Expression Regulation, Bacterial; Gene Expression Regulation, Enzymologic; Mixed Function Oxygenases; Molecular Sequence Data; Phylogeny; Promoter Regions, Genetic
PubMed: 11418560
DOI: 10.1128/JB.183.14.4202-4209.2001 -
International Journal of Cosmetic... Oct 2011Several studies have reported that 1,2-alkanediols show increasing anti-microbial activity as their alkane chain length increases. However, there are no reports on the...
Several studies have reported that 1,2-alkanediols show increasing anti-microbial activity as their alkane chain length increases. However, there are no reports on the influence of alkane chain length on the skin irritation potential of 1,2-alkanediols. To investigate the influence of alkane chain length on the skin irritation potential of 1,2-alkanediols. The objective and subjective (sensory) skin irritation potentials of five 1,2-alkanediols - 1,2-butanediol, 1,2-pentanediol, 1,2-hexanediol, 1,2-octanediol and 1,2-decanediol - were evaluated. We also estimated percutaneous absorption by measuring in vitro skin penetration using a Franz diffusion cell system. Like anti-microbial activity, sensory irritation potential increased as alkane chain length increased, most likely due to increasing membrane interference and/or intrinsic toxicity of 1,2-alkanediols. 1,2-Hexanediol showed the lowest objective skin irritation potential, which increased when the alkane chain length decreased or increased. Furthermore, percutaneous absorption negatively correlated with the alkane chain length of 1,2-alkanediols. These results show that a lower skin absorption potential is not indicative of a low skin irritation potential. Our results suggest that the factors and processes involved in skin irritation potential are complex and that skin irritation potential is influenced by intrinsic toxicity and the potential for penetration or integration in the lipid bilayer.
Topics: Adult; Alkanes; Anti-Infective Agents; Female; Humans; Irritants; Male; Microbial Sensitivity Tests; Skin
PubMed: 21585401
DOI: 10.1111/j.1468-2494.2011.00646.x