A NOVEL DESIGN OF PERISTALTIC CARBON NANO PUMP AND AN ANALYSIS OF HELIUM FLOW

A novel nano-scale pump that can transport atoms or small molecules with a peristaltic motion is designed. It is proven by molecular-dynamics simulations that the introduced nano-pump design works properly. The designed nano-pump consists of one main carbon nanotube named the flow tube and two rotors where multi-walled carbon nanotubes are attached. The pumping of helium atoms by the designed peristaltic carbon nano-pump is investigated by molecular-dynamics simulations. For varying rotor speeds and blade counts, time-averaged velocity, temperature, and pressure results of pumped helium atoms are calculated, and relationships between them are modeled as polynomial surfaces. The results showed that rotor frequency increases the velocity of helium linearly and the temperature and pressure of helium non-linearly. Furthermore, the blade count of the proposed mechanism does not substantially affect the velocity as per the previous studies in the literature.

Selective Isolation of Bifidobacterium From Human Faeces Using Pangenomics, Metagenomics, and Enzymology

Bifidobacterium, an important genus for human health, is difficult to isolate. We applied metagenomics, pangenomics, and enzymology to determine the dominant glycoside hydrolase (GH) families of Bifidobacterium and designed selective medium for Bifidobacterium isolation. Pangenomics results showed that the GH13, GH3, GH42, and GH43 families were highly conserved in Bifidobacterium. Metagenomic analysis of GH families in human faecal samples was performed. The results indicated that Bifidobacterium contains core GHs for utilizing raffinose, D-trehalose anhydrous, D(+)-cellobiose, melibiose, lactulose, lactose, D(+)-sucrose, resistant starch, pullulan, xylan, and glucan. These carbohydrates as the main carbon sources were applied for selective media, which were more conducive to the growth of bifidobacteria. In the medium with lactose, raffinose and xylan as the main carbon sources, the ratio of cultivable bifidobacteria to cultivable microorganisms were 89.39% ± 2.50%, 71.45% ± 0.99%, and 53.95% ± 1.22%, respectively, whereas the ratio in the ordinary Gifu anaerobic medium was only 17.90% ± 0.58%. Furthermore, the species significantly (p < 0.05) varied among samples from different individuals. Results suggested that xylan might be a prebiotic that benefits host health, and it is feasible to screen and isolate bifidobacteria using the oligosaccharides corresponding to the specific GHs of bifidobacteria as the carbon sources of the selective media.

Structural Insights into the Methane-Generating Enzyme from a Methoxydotrophic Methanogen Reveal a Restrained Gallery of Post-Translational Modifications

Methanogenic archaea operate an ancient, if not primordial, metabolic pathway that releases methane as an end-product. This last step is orchestrated by the methyl-coenzyme M reductase (MCR), which uses a nickel-containing F430-cofactor as the catalyst. MCR astounds the scientific world by its unique reaction chemistry, its numerous post-translational modifications, and its importance in biotechnology not only for production but also for capturing the greenhouse gas methane. In this report, we investigated MCR natively isolated from Methermicoccus shengliensis. This methanogen was isolated from a high-temperature oil reservoir and has recently been shown to convert lignin and coal derivatives into methane through a process called methoxydotrophic methanogenesis. A methoxydotrophic culture was obtained by growing M. shengliensis with 3,4,5-trimethoxybenzoate as the main carbon and energy source. Under these conditions, MCR represents more than 12% of the total protein content. The native MCR structure refined at a resolution of 1.6-Å precisely depicts the organization of a dimer of heterotrimers. Despite subtle surface remodeling and complete conservation of its active site with other homologues, MCR from the thermophile M. shengliensis contains the most limited number of post-translational modifications reported so far, questioning their physiological relevance in other relatives.

Rhodotorula Strains Isolated from Seawater That Can Biotransform Raw Glycerol into Docosahexaenoic Acid (DHA) and Carotenoids for Animal Nutrition

Due to the overexploitation of industrial fisheries, as the principal source of fish oil, as well as the increasing replacement of synthetic pigments for animal nutrition, we need to find sustainable sources for these essential nutrient productions. Marine Rhodotorula strains NCYC4007 and NCYC1146 were used to determine the biosynthesis of docosahexaenoic acid (DHA) and carotenoids by biotransforming raw glycerol, a waste product of biodiesel. To evaluate the presence of inhibitory substances in raw glycerol, both strains were also grown in the presence of analytical grade glycerol and glucose as the main carbon source separately. With raw glycerol, NCYC4007 showed a significant correlation between DHA production and intracellular phosphorous concentrations. NCYC1146, a new Rhodotorula strain genetically described in this work, can produce canthaxanthin but only when glycerol is used as a main carbon source. Then, NCYC4007 could synthesize DHA as a phospholipid, and the production of canthaxanthin depends on the kind of carbon source used by NCYC1146. Finally, malate dehydrogenase activity and glucose production can be used as a proxy of the metabolisms in these marine Rhodotorula. This is the first evidence that marine Rhodotorula are capable of synthesizing DHA and canthaxanthin using an alternative and low-cost source of carbon to potentially scale their sustainable production for animal nutrition.

Fast Location and Isolation of Phenanthrene-degrading Halophilic Microbial Community and its Degradation Pathway

Microbial consortium WZ-4, which could degrade phenanthrene (PHE) as the main carbon and energy source, was isolated from the aerobic sludge of Weizhou wastewater treatment plant. Under the condition of high salinity (3%), the degradation of PHE (100 mg/L) was 87.76% in 7d. Its metabolites, genome sequence and biodegradation pathway were studied. The main metabolites include 1,2-dihydroxynaphthalene, 1-hydroxy-2-naphthalene, 5,6-benzocoumarin and phthalic acid. 12 PHE degrading enzyme genes appeared in the metagenome sequencing of WZ-4, and the genes involved in PHE degradation were included phdE, phdF, phdG, and pcaL. Based on the metabolites detected by GC-MS and the potential PHE-degrading genes identified by BLAST search, biodegradation pathway of PHE by WZ-4 was predicted.

FTIR Analysis of Biodegradation of Polystyrene by Intestinal Bacteria Isolated from Zophobas Morio and Tenebrio Molitor

Since the 1970s, polystyrene (PS) plastic marine pollution has become a global concern. Tenebrio molitor and Zophobas morio beetle larva actively respond to a diet of primarily polystyrene. The tantalizing evidence indicates that the gut bacteria of these beetle larva enables them not only to consume polystyrene, but to successfully biodegrade polystyrene. Heretofore, data collection to verify polystyrene degradation by the gut bacteria of these larva has taken up to six months per test. Our laboratory created a platform by dissolving PS into a liquid mineral culture medium to examine PS degradation by the gut bacteria. Under investigation, PS works as main carbon source supporting the growth of gut bacteria. Fourier-transform Infrared spectroscopy (FTIR) is an effective method which can provide relevant information on chemical changes. This study presents a methodology using FTIR and Visible Light Spectrometry as an efficient methodology to verify the physiological degradation of polystyrene.

Enhancing Phenol Conversion Rates in Saline Anaerobic Membrane Bioreactor Using Acetate and Butyrate as Additional Carbon and Energy Sources

Phenolic industrial wastewater, such as those from coal gasification, are considered a challenge for conventional anaerobic wastewater treatment systems because of its extreme characteristics such as presence of recalcitrant compounds, high toxicity, and salinity. However, anaerobic membrane bioreactors (AnMBRs) are considered of potential interest since they retain all micro-organism that are required for conversion of the complex organics. In this study, the degradation of phenol as main carbon and energy source (CES) in AnMBRs at high salinity (8.0 g Na+⋅L–1) was evaluated, as well as the effect of acetate and an acetate-butyrate mixture as additional CES on the specific phenol conversion rate and microbial community structure. Three different experiments in two lab-scale (6.5 L) AnMBRs (35°C) were conducted. The first reactor (R1) was fed with phenol as the main CES, the second reactor was fed with phenol and either acetate [2 g COD⋅L–1], or a 2:1 acetate-butyrate [2 g COD⋅L–1] mixture as additional CES. Results showed that phenol conversion could not be sustained when phenol was the sole CES. In contrast, when the reactor was fed with acetate or an acetate-butyrate mixture, specific phenol conversion rates of 115 and 210 mgPh⋅gVSS–1 d–1, were found, respectively. The syntrophic phenol degrader Syntrophorhabdus sp. and the acetoclastic methanogen Methanosaeta sp. were the dominant bacteria and archaea, respectively, with corresponding relative abundances of up to 63 and 26%. The findings showed that dosage of additional CES allowed the development of a highly active phenol-degrading biomass, potentially improving the treatment of industrial and chemical wastewaters.

The seawater carbon inventory at the Paleocene–Eocene Thermal Maximum

The Paleocene–Eocene Thermal Maximum (PETM) (55.6 Mya) was a geologically rapid carbon-release event that is considered the closest natural analog to anthropogenic CO2 emissions. Recent work has used boron-based proxies in planktic foraminifera to characterize the extent of surface-ocean acidification that occurred during the event. However, seawater acidity alone provides an incomplete constraint on the nature and source of carbon release. Here, we apply previously undescribed culture calibrations for the B/Ca proxy in planktic foraminifera and use them to calculate relative changes in seawater-dissolved inorganic carbon (DIC) concentration, surmising that Pacific surface-ocean DIC increased by +1,010−646+1,415 µmol/kg during the peak-PETM. Making reasonable assumptions for the pre-PETM oceanic DIC inventory, we provide a fully data-driven estimate of the PETM carbon source. Our reconstruction yields a mean source carbon δ13C of −10‰ and a mean increase in the oceanic C inventory of +14,900 petagrams of carbon (PgC), pointing to volcanic CO2 emissions as the main carbon source responsible for PETM warming.

Biodiversity and niche partitioning in an anaerobic benzene degrading culture

ABSTRACTA key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and free energy source and nitrate as the electron acceptor. We demonstrate that only a few community members are able to degrade benzene, and that most of the others feed on the metabolic left-overs or on the contents of dead cells making up a food web with different trophic levels. As a result of niche partitioning, a high species richness is maintained and the complexity of a natural community is stabilized in a relatively simple environment. This view highlights the importance of species interactions and interdependencies, which drive microbial community structure and function. These mechanisms may well be conserved across ecosystems.