-
MBio Aug 2019Crude oil and gases in the seabed provide an important energy source for subsurface microorganisms. We investigated the role of archaea in the anaerobic degradation of...
Crude oil and gases in the seabed provide an important energy source for subsurface microorganisms. We investigated the role of archaea in the anaerobic degradation of non-methane alkanes in deep-sea oil seeps from the Gulf of Mexico. We identified microscopically the ethane and short-chain alkane oxidizers " Argoarchaeum" and " Syntrophoarchaeum" forming consortia with bacteria. Moreover, we found that the sediments contain large numbers of cells from the archaeal clade " Methanoliparia," which was previously proposed to perform methanogenic alkane degradation. " Methanoliparia" occurred abundantly as single cells attached to oil droplets in sediments without apparent bacterial or archaeal partners. Metagenome-assembled genomes of " Methanoliparia" encode a complete methanogenesis pathway including a canonical methyl-coenzyme M reductase (MCR) but also a highly divergent MCR related to those of alkane-degrading archaea and pathways for the oxidation of long-chain alkyl units. Its metabolic genomic potential and its global detection in hydrocarbon reservoirs suggest that " Methanoliparia" is an important methanogenic alkane degrader in subsurface environments, producing methane by alkane disproportionation as a single organism. Oil-rich sediments from the Gulf of Mexico were found to contain diverse alkane-degrading groups of archaea. The symbiotic, consortium-forming " Argoarchaeum" and " Syntrophoarchaeum" are likely responsible for the degradation of ethane and short-chain alkanes, with the help of sulfate-reducing bacteria. " Methanoliparia" occurs as single cells associated with oil droplets. These archaea encode two phylogenetically different methyl-coenzyme M reductases that may allow this organism to thrive as a methanogen on a substrate of long-chain alkanes. Based on a library survey, we show that "" is frequently detected in oil reservoirs and may be a key agent in the transformation of long-chain alkanes to methane. Our findings provide evidence for the important and diverse roles of archaea in alkane-rich marine habitats and support the notion of a significant functional versatility of the methyl coenzyme M reductase.
Topics: Alkanes; Anaerobiosis; Bacteria; Biodegradation, Environmental; Euryarchaeota; Fatty Acids; Geologic Sediments; Gulf of Mexico; Hydrocarbons; Metagenomics; Methane; Oil and Gas Fields; Oxidation-Reduction; Oxidoreductases; Phylogeny; RNA, Ribosomal, 16S
PubMed: 31431553
DOI: 10.1128/mBio.01814-19 -
Journal of Animal Science Oct 2020Precise techniques to estimate feed intake by ruminants are critical to enhance feed efficiency and to reduce greenhouse gas emissions and nutrient losses to the... (Meta-Analysis)
Meta-Analysis
Precise techniques to estimate feed intake by ruminants are critical to enhance feed efficiency and to reduce greenhouse gas emissions and nutrient losses to the environment. Using a meta-analysis, we evaluated the accuracy of the n-alkane technique to predict feed intake in cattle and sheep and assessed the relationships between feed intake and fecal recovery (FR) of n-alkanes. The database was composed of 28 studies, including 129 treatments (87 and 42 for cattle and sheep, respectively) and 402 animals (232 cattle and 170 sheep) fed at troughs, from published studies. Relationships between observed (in vivo measurement) and predicted feed intake by C31:C32 and C32:C33 n-alkane pairs were evaluated by regression. Meta-regression addressed the relationships between the difference in FR of n-alkane pairs and the error in intake estimation, as well as the amount and duration of C32 n-alkane dosing. Regression of observed intake on n-alkane-based estimates revealed good relationships in cattle (adjusted R2 = 0.99 for C31:C32, and adjusted R2 = 0.98 for C32:C33; P < 0.0001) and in sheep (adjusted R2 = 0.94 for C31:C32, and adjusted R2 = 0.96 for C32:C33; P < 0.0001). FR of natural n-alkanes showed a coefficient of variation of about 15% and 16% for C31 and C33, respectively, in cattle. In sheep, the coefficient of variation was 8% and 14% for C31 and C33, respectively. The relationships between the difference of FR of n-alkane pairs and the error in feed intake estimation in cattle were characterized by an adjusted R2 = 0.83 for C31:C32 (P < 0.0001) and adjusted R2 = 0.93 for C32:C33 (P < 0.0001). In sheep, they were characterized by an adjusted R2 = 0.69 for C31:C32 (P < 0.001) and adjusted R2 = 0.76 for C32:C33 (P < 0.001). The n-alkane technique provided the reliability for estimating feed intake in cattle and sheep in barn experiments. The present meta-analysis demonstrated that without correction for differences in FR of n-alkane pairs, deviation in feed intake prediction would occur. However, further research is necessary to determine the relationship between the n-alkane dosing procedure (daily amount and duration of dosing) and FR of n-alkane.
Topics: Alkanes; Animal Feed; Animals; Cattle; Eating; Feces; Reproducibility of Results; Ruminants; Sheep
PubMed: 32910189
DOI: 10.1093/jas/skaa304 -
Nature Communications Jun 2022Chiral organoborons are of great value in asymmetric synthesis, functional materials, and medicinal chemistry. The development of chiral bis(boryl) alkanes, especially...
Chiral organoborons are of great value in asymmetric synthesis, functional materials, and medicinal chemistry. The development of chiral bis(boryl) alkanes, especially optically enriched 1,1-diboron compounds, has been greatly inhibited by the lack of direct synthetic protocols. Therefore, it is very challenging to develop a simple and effective strategy to obtain chiral 1,1-diborylalkanes. Herein, we develop an enantioselective copper-catalyzed cascade double hydroboration of terminal alkynes and highly enantioenriched gem-diborylalkanes were readily obtained. Our strategy uses simple terminal alkynes and two different boranes to construct valuable chiral gem-bis(boryl) alkanes with one catalytic and one ligand pattern, which represents the simplest and most straightforward strategy for constructing such chiral gem-diborons.
Topics: Alkanes; Alkynes; Catalysis; Copper; Stereoisomerism
PubMed: 35725731
DOI: 10.1038/s41467-022-31234-2 -
Environment International Jun 2024Marine microorganisms are primary drivers of the elemental cycling. The interaction between heterotrophic prokaryotes and biomarker (n-alkane) in Kuroshio Extension (KE)...
Marine microorganisms are primary drivers of the elemental cycling. The interaction between heterotrophic prokaryotes and biomarker (n-alkane) in Kuroshio Extension (KE) remains unclear. Here, we categorize KE into three characteristic areas based on ocean temperatures and nutrient conditions: Cold Water Area (CWA), Mixed Area (MA), and Warm Water Area (WWA). A total of 49 samples were collected during two-year voyage to identify the source of n-alkane and associated degrading microorganisms. Total n-alkane concentrations (Σn-Alk) in surface water (SW) spanned from 1,308 ng L to 1,890 ng L, it was significantly higher (Tukey-Kramer test, p < 0.05) in MA than CWA and WWA. The Σn-Alk in surface sediments (SS) gradually increased from north to south, ranging from 5,982 ng g to 37,857 ng g. Bacteria and algae were the primary sources of n-alkane in both SW and SS. Proteobacteria was the most widely distributed among three areas. The presence of Rhodobacteraceae with alkB was the primary reason affecting n-alkane concentrations in SW. The Gammaproteobacteria with alkB and alkR chiefly affected n-alkane concentrations in SS. In summary, n-alkane s serve as an energy source for particular microorganisms, shaping the unique oceanographic patterns.
Topics: Alkanes; Seawater; Bacteria; Geologic Sediments; Japan; Environmental Monitoring
PubMed: 38795659
DOI: 10.1016/j.envint.2024.108757 -
Proceedings of the National Academy of... Nov 2016How hydrophobicity (HY) drives protein folding is studied. The 1971 Nozaki-Tanford method of measuring HY is modified to use gases as solutes, not crystals, and this...
How hydrophobicity (HY) drives protein folding is studied. The 1971 Nozaki-Tanford method of measuring HY is modified to use gases as solutes, not crystals, and this makes the method easy to use. Alkanes are found to be much more hydrophobic than rare gases, and the two different kinds of HY are termed intrinsic (rare gases) and extrinsic (alkanes). The HY values of rare gases are proportional to solvent-accessible surface area (ASA), whereas the HY values of alkanes depend on special hydration shells. Earlier work showed that hydration shells produce the hydration energetics of alkanes. Evidence is given here that the transfer energetics of alkanes to cyclohexane [Wolfenden R, Lewis CA, Jr, Yuan Y, Carter CW, Jr (2015) Proc Natl Acad Sci USA 112(24):7484-7488] measure the release of these shells. Alkane shells are stabilized importantly by van der Waals interactions between alkane carbon and water oxygen atoms. Thus, rare gases cannot form this type of shell. The very short (approximately picoseconds) lifetime of the van der Waals interaction probably explains why NMR efforts to detect alkane hydration shells have failed. The close similarity between the sizes of the opposing energetics for forming or releasing alkane shells confirms the presence of these shells on alkanes and supports Kauzmann's 1959 mechanism of protein folding. A space-filling model is given for the hydration shells on linear alkanes. The model reproduces the n values of Jorgensen et al. [Jorgensen WL, Gao J, Ravimohan C (1985) J Phys Chem 89:3470-3473] for the number of waters in alkane hydration shells.
Topics: Algorithms; Alkanes; Gases; Hydrophobic and Hydrophilic Interactions; Models, Chemical; Protein Folding; Solvents; Thermodynamics
PubMed: 27791131
DOI: 10.1073/pnas.1610541113 -
Applied and Environmental Microbiology Oct 2022Due to the barrier effect of lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria, transporters are required for hydrophobic alkane uptake. However,...
Due to the barrier effect of lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria, transporters are required for hydrophobic alkane uptake. However, there are few reports on long-chain alkane transporters. In this study, a potential ong-chain kane ransporter (AltL) was screened in Acinetobacter venetianus RAG-1 by comparative transcriptome analysis. Growth and degradation experiments showed that deletion led to the loss of -octacosane utilization capacity of RAG-1. To identify the function of AltL, we measured the existence and accumulation of alkanes in cells through the constructed alkane detection system and isotope transport experiment, which proved its long-chain alkane transport function. Growth experiments using different chain-length -alkanes and fatty acids as substrates showed that AltL was responsible for the transport of (very) long-chain -alkanes (C to C) and fatty acids (C to C) and was also involved in the uptake of medium-chain -alkanes (C to C). Subsequently, we analyzed the distribution of AltL in bacteria, and found that AltL homologs are widespread in -, -, and Deltaproteobacteria. An AltL homolog in Pseudomonas aeruginosa was also identified to participate in long-chain alkane transport by a gene deletion and growth assay. We also found that overexpression of in Pseudomonas aeruginosa enhanced the degradation of C to C -alkanes. In addition, structure analysis showed that AltL has longer extracellular loops than other FadL family members, which may be involved in the binding of alkanes. These results showed that AltL is a novel transporter and that it is mainly responsible for the transport of long-chain -alkanes and (very) long-chain fatty acids and has broad application potential. Petroleum pollution has caused great harm to the natural environment, and alkanes are the main components of petroleum. Many Gram-negative bacteria can use alkanes as carbon and energy sources, which is an important strategy for oil pollution remediation. Alkane uptake is the first step for its utilization. Hence, the characterization of transport proteins is of great significance for the recovery of oil pollution and other potential applications in industrial engineering bacteria. At present, some short- and medium-chain alkane transporters have been identified, but stronger hydrophobic long-chain alkane transporters have received little attention. In this study, the broad-spectrum transporter AltL, identified in RAG-1, makes up for the lack of research on the transport of long-chain alkanes and (very) long-chain fatty acids. Meanwhile, the structural features of longer extracellular loops might be related to its unique transport function on more hydrophobic and larger substrates, indicating it is a novel type alkane transporter.
Topics: Lipopolysaccharides; Fatty Acids; Biodegradation, Environmental; Alkanes; Petroleum; Membrane Transport Proteins; Pseudomonas aeruginosa; Bacteria; Carbon
PubMed: 36169310
DOI: 10.1128/aem.01294-22 -
Applied and Environmental Microbiology Nov 2017-Alkanes are ubiquitous in nature and are widely used by microorganisms as carbon sources. Alkane hydroxylation by alkane monooxygenases is a critical step in the...
-Alkanes are ubiquitous in nature and are widely used by microorganisms as carbon sources. Alkane hydroxylation by alkane monooxygenases is a critical step in the aerobic biodegradation of -alkanes, which plays important roles in natural alkane attenuation and is used in industrial and environmental applications. The alkane oxidation operon, , in the alkane-degrading strain sp. strain DQ12-45-1b is negatively autoregulated by the TetR family repressor AlkX via a product positive feedback mechanism. To predict the gene regulation mechanism, we determined the 3.1-Å crystal structure of an AlkX homodimer in a non-DNA-bound state. The structure showed traceable long electron density deep inside a hydrophobic cavity of each monomer along the long axis of the helix bundle, and further gas chromatography-mass spectrometry analysis of AlkX revealed that it contained the -derived long-chain fatty acid molecules as a ligand. Moreover, an unusual structural feature of AlkX is an extra helix, α6', forming a lid-like structure with α6 covering the inducer-binding pocket and occupying the space between the two symmetrical DNA-binding motifs in one dimer, indicating a distinct conformational transition mode in modulating DNA binding. Sequence alignment of AlkX homologs from strains showed that the residues involved in DNA and inducer binding are highly conserved, suggesting that the regulation mechanisms of -alkane hydroxylation are possibly a common characteristic of strains. With -alkanes being ubiquitous in nature, many bacteria from terrestrial and aquatic environments have evolved -alkane oxidation functions. Alkane hydroxylation by alkane monooxygenases is a critical step in the aerobic biodegradation of -alkanes, which plays important roles in natural alkane attenuation and petroleum-contaminating environment bioremediation. The gene regulation of the most common alkane hydroxylase, AlkB, has been studied widely in Gram-negative bacteria but has been less explored in Gram-positive bacteria. Our previous study showed that the TetR family regulator (TFR) AlkX negatively autoregulated the alkane oxidation operon, , in the Gram-positive strain sp. strain DQ12-45-1b. Although TFRs are one of the most common transcriptional regulator families in bacteria, the TFR involved in -alkane metabolism has been reported only recently. In this study, we determined the crystal structure of AlkX, which implies a distinct DNA/ligand binding mode. Our results shed light upon the regulation mechanism of the common alkane degradation process in nature.
Topics: Actinomycetales; Alkanes; Amino Acid Motifs; Bacterial Proteins; Biodegradation, Environmental; Gene Expression Regulation, Bacterial; Repressor Proteins
PubMed: 28821550
DOI: 10.1128/AEM.01447-17 -
Ecotoxicology and Environmental Safety Aug 2022In the process of marine oil spill remediation, adding highly efficient oil degrading microorganisms can effectively promote oil degradation. However, in practice, the...
In the process of marine oil spill remediation, adding highly efficient oil degrading microorganisms can effectively promote oil degradation. However, in practice, the effect is far less than expected due to the inadaptability of microorganisms to the environment and their disadvantage in the competition with indigenous bacteria for nutrients. In this article, four strains of oil degrading bacteria were isolated from seawater in Jiaozhou Bay, China, where a crude oil pipeline explosion occurred seven years ago. Results of high-throughput sequencing, diesel degradation tests and surface activity tests indicated that Peseudomonas aeruginosa ZS1 was a highly efficient petroleum degrading bacterium with the ability to produce surface active substances. A diesel oil-degrading bacterial consortium (named SA) was constructed by ZS1 and another oil degrading bacteria by diesel degradation test. Degradation products analysis indicated that SA has a good ability to degrade short chain alkanes, especially n-alkanes (C-C). Community structure analysis showed that OTUs of Alcanivorax, Peseudomona, Ruegeria, Pseudophaeobacter, Hyphomonas and Thalassospira on genus level increased after the oil spill and remained stable throughout the recovery period. Most of these enriched microorganisms were related to known alkane and hydrocarbon degraders by the previous study. However, it is the first time to report that Pseudophaeobacter was enriched by using diesel as the sole carbon source. The results also indicated that ZS1 may have a dominant position in competition with indigenous bacteria. Oil pollution has an obvious selective effect on marine microorganisms. Although the oil degradation was promoted after SA injection, the recovery of microbial community structure took a longer time.
Topics: Alkanes; Bacteria; Biodegradation, Environmental; Hydrocarbons; Petroleum; Petroleum Pollution; Seawater
PubMed: 35738097
DOI: 10.1016/j.ecoenv.2022.113769 -
Applied and Environmental Microbiology Aug 2019Methanogenic degradation of -alkanes is prevalent in -alkane-impacted anoxic oil reservoirs and oil-polluted sites. However, little is known about the initial activation...
Methanogenic degradation of -alkanes is prevalent in -alkane-impacted anoxic oil reservoirs and oil-polluted sites. However, little is known about the initial activation mechanism of the substrate, especially -alkanes with a chain length above C Here, a methanogenic C to C-alkane-degrading enrichment culture was established from production water of a low-temperature oil reservoir. At the end of the incubation (364 days), C to C (1-methylalkyl)succinates were detected in the -alkane-amended enrichment culture, suggesting that fumarate addition had occurred in the degradation process. This evidence is supported further by the positive amplification of the gene encoding the alpha subunit of alkylsuccinate synthase. A phylogenetic analysis shows these amplicons to be affiliated with and clades. Together with the high abundance of these clades in the bacterial community, these two species are postulated to be the key players in the degradation of C to C-alkanes in the present study. Our results provide evidence that long -alkanes are activated via a fumarate addition mechanism under methanogenic conditions. Methanogenic hydrocarbon degradation is the major process for oil degradation in subsurface oil reservoirs and is blamed for the formation of heavy oil and oil sands. Addition of -alkanes to fumarate yielding alkyl-substituted succinates is a well-characterized anaerobic activation mechanism for hydrocarbons and is the most common activation mechanism in the anaerobic biodegradation of -alkanes with chain lengths less than C However, the activation mechanism involved in the methanogenic biodegradation of -alkanes longer than C is still uncertain. In this study, we analyzed a methanogenic enrichment culture amended with a mixture of C to C-alkanes. These -alkanes can be activated via fumarate addition by mixed cultures containing and species under methanogenic conditions. These observations provide a fundamental understanding of long--alkane metabolism under methanogenic conditions and have important applications for the remediation of oil-contaminated sites and for energy recovery from oil reservoirs.
Topics: Alkanes; Archaea; Bacterial Proteins; Biodegradation, Environmental; Chemoautotrophic Growth; Deltaproteobacteria; Fumarates; Methane; Phylogeny
PubMed: 31175186
DOI: 10.1128/AEM.00985-19 -
Nature Structural & Molecular Biology Apr 2023Alkane monooxygenase (AlkB) is a widely occurring integral membrane metalloenzyme that catalyzes the initial step in the functionalization of recalcitrant alkanes with...
Alkane monooxygenase (AlkB) is a widely occurring integral membrane metalloenzyme that catalyzes the initial step in the functionalization of recalcitrant alkanes with high terminal selectivity. AlkB enables diverse microorganisms to use alkanes as their sole carbon and energy source. Here we present the 48.6-kDa cryo-electron microscopy structure of a natural fusion from Fontimonas thermophila between AlkB and its electron donor AlkG at 2.76 Å resolution. The AlkB portion contains six transmembrane helices with an alkane entry tunnel within its transmembrane domain. A dodecane substrate is oriented by hydrophobic tunnel-lining residues to present a terminal C-H bond toward a diiron active site. AlkG, an [Fe-4S] rubredoxin, docks via electrostatic interactions and sequentially transfers electrons to the diiron center. The archetypal structural complex presented reveals the basis for terminal C-H selectivity and functionalization within this broadly distributed evolutionary class of enzymes.
Topics: Cryoelectron Microscopy; Cytochrome P-450 CYP4A; Alkanes
PubMed: 36997762
DOI: 10.1038/s41594-023-00958-0