Microbial ecology of biotechnological processes

The investigation of phylogenetic diversity and functionality of complex microbial communities in relation to changes in the environmental conditions represents a major challenge of microbial ecology research. Nowadays, particular attention is paid to microbial communities occurring at environmental sites contaminated by recalcitrant and toxic organic compounds. Extended research has evidenced that such communities evolve some metabolic abilities leading to the partial degradation or complete mineralization of the contaminants. Determination of such biodegradation potential can be the starting point for the development of cost effective biotechnological processes for the bioremediation of contaminated matrices. This work showed how metagenomics-based microbial ecology investigations supported the choice or the development of three different bioremediation strategies. First, PCR-DGGE and PCR-cloning approaches served the molecular characterization of microbial communities enriched through sequential development stages of an aerobic cometabolic process for the treatment of groundwater contaminated by chlorinated aliphatic hydrocarbons inside an immobilized-biomass packed bed bioreactor (PBR). In this case the analyses revealed homogeneous growth and structure of immobilized communities throughout the PBR and the occurrence of dominant microbial phylotypes of the genera Rhodococcus, Comamonas and Acidovorax, which probably drive the biodegradation process. The same molecular approaches were employed to characterize sludge microbial communities selected and enriched during the treatment of municipal wastewater coupled with the production of polyhydroxyalkanoates (PHA). Known PHA-accumulating microorganisms identified were affiliated with the genera Zooglea, Acidovorax and Hydrogenophaga. Finally, the molecular investigation concerned communities of polycyclic aromatic hydrocarbon (PAH) contaminated soil subjected to rhizoremediation with willow roots or fertilization-based treatments. The metabolic ability to biodegrade naphthalene, as a representative model for PAH, was assessed by means of stable isotope probing in combination with high-throughput sequencing analysis. The phylogenetic diversity of microbial populations able to derive carbon from naphthalene was evaluated as a function of the type of treatment.

Targeting p-Conjugated Multiple Donor-Acceptor Motifs Exemplified by Tetrathiafulvalene-Linked Quinoxalines and Tetrabenz bc,ef,hi,uv ovalenes: Synthesis, Spectroscopic, Electrochemical, and Theoretical Characterization

An efficient synthetic approach to a symmetrically functionalized tetrathiafulvalene (TTF) derivative with two diamine moieties, 2-[5,6-diamino-4,7-bis(4-pentylphenoxy)-1,3-benzodithiol-2-ylidene]-4,7- bis(4-pentylphenoxy)-1,3-benzodithiole-5,6-diamine (2), is reported. The subsequent Schiff-base reactions of 2 afford large p-conjugated multiple donoracceptor (DA) arrays, for example, the triad 2-[4,9-bis(4-pentylphenoxy)-1,3-dithiolo[4,5-g]quinoxalin-2-ylidene]-4,9 -bis(4-pentylphenoxy)-1,3-dithiolo[4,5-g]quinoxaline (8) and the corresponding tetrabenz[bc,ef,hi,uv]ovalene-fused pentad 1, in good yields and high purity. The novel redox-active nanographene 1 is so far the largest known TTF-functionalized polycyclic aromatic hydrocarbon (PAH) with a well-resolved 1H NMR spectrum. The electrochemically highly amphoteric pentad 1 and triad 8 exhibit various electronically excited charge-transfer states in different oxidation states, thus leading to intense optical intramolecular charge-transfer (ICT) absorbances over a wide spectral range. The chemical and electrochemical oxidations of 1 result in an unprecedented TTF+ radical cation dimerization, thereby leading to the formation of [1+]2 at room temperature in solution due to the stabilizing effect, which arises from strong pp interactions. Moreover, ICT fluorescence is observed with large solvent-dependent Stokes shifts and quantum efficiencies of 0.05 for 1 and 0.035 for 8 in dichloromethane.

Bioremediation with White-Rot Fungi at Fisherville Mill: Analyses of Gene Expression and Number 6 Fuel Oil Degradation

Extracellular enzymes that white-rot fungi secrete during lignin decay have been proposed as promising agents for oxidizing pollutants. We investigated the abilities of the white-rot fungi Punctularia strigosozonata, Irpex lacteus, Trichaptum biforme, Phlebia radiata, Trametes versicolor, and Pleurotus ostreatus to degrade Number 6 fuel oil in wood sawdust cultures. Our goals are to advise bioremediation efforts at a brownfield redevelopment site on the Blackstone River in Grafton, Massachusetts and to contribute to the understanding of decay mechanisms in white-rot fungi. All species tested degraded a C10 alkane. When cultivated for 6 months, Irpex lacteus, T. biforme, P. radiata, T. versicolor and P. ostreatus also degraded a C14 alkane and the polycyclic aromatic hydrocarbon phenanthrene. Gene expression analyses of P. strigosozonata indicate differential gene expression in the presence of Number 6 oil and on pine and aspen sawdust.

Influence of perylenediimide–pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity

Aromatic pi–pi stacking interactions are ubiquitous in nature, medicinal chemistry and materials sciences. They play a crucial role in the stacking of nucleobases, thus stabilising the DNA double helix. The following paper describes a series of chimeric DNA–polycyclic aromatic hydrocarbon (PAH) hybrids. The PAH building blocks are electron-rich pyrene and electron-poor perylenediimide (PDI), and were incorporated into complementary DNA strands. The hybrids contain different numbers of pyrene–PDI interactions that were found to directly influence duplex stability. As the pyrene–PDI ratio approaches 1:1, the stability of the duplexes increases with an average value of 7.5 °C per pyrene–PDI supramolecular interaction indicating the importance of electrostatic complementarity for aromatic pi–pi stacking interactions.

Linking Ah receptor mediated effects of sediments and impacts on fish to key pollutants in the Yangtze Three Gorges Reservoir, China – A comprehensive perspective

The Three Gorges Reservoir (TGR), created in consequence of the Yangtze River's impoundment by the Three Gorges Dam, faces numerous anthropogenic impacts that challenge its unique ecosystem. Organic pollutants, particularly aryl hydrocarbon receptor (AhR) agonists, have been widely detected in the Yangtze River, but only little research was yet done on AhR-mediated activities. Hence, in order to assess effects of organic pollution, with particular focus on AhR-mediated activities, several sites in the TGR area were examined applying the "triad approach". It combines chemical analysis, in vitro, in vivo and in situ investigations to a holistic assessment. Sediments and the benthic fish species Pelteobagrus vachellii were sampled in 2011/2012, respectively, to identify relevant endpoints. Sediment was tested in vitro with the ethoxyresorufin-O-deethylase (EROD) induction assay, and in vivo with the Fish Embryo Toxicity Test and Sediment Contact Assay with Danio rerio. Activities of phase I (EROD) and phase II (glutathione-S-transferase) biotransformation enzymes, pollutant metabolites and histopathological alterations were studied in situ in P. vachellii. EROD induction was tested in vitro and in situ to evaluate possible relationships. Two sites, near Chongqing and Kaixian city, were identified as regional hot-spots and further investigated in 2013. The sediments induced in the in vitro/in vivo bioassays AhR-mediated activities and embryotoxic/teratogenic effects - particularly on the cardiovascular system. These endpoints could be significantly correlated to each other and respective chemical data. However, particle-bound pollutants showed only low bioavailability. The in situ investigations suggested a rather poor condition of P. vachellii, with histopathological alterations in liver and excretory kidney. Fish from Chongqing city exhibited significant hepatic EROD induction and obvious parasitic infestations. The polycyclic aromatic hydrocarbon (PAH) metabolite 1-hydroxypyrene was detected in bile of fish from all sites. All endpoints in combination with the chemical data suggest a pivotal role of PAHs in the observed ecotoxicological impacts.

Geochemistry and pyrolysis at DSDP Hole 77-535

There are substantial differences in the character of organic matter contained in the Pleistocene and Cretaceous sedimentary sequences of DSDP Site 535. The argillaceous Pleistocene section contains type III, gas-prone organic matter whereas the calcareous Cretaceous section is dominated by type II, oil-prone organic matter. A more detailed investigation of the Cretaceous section reveals that the finely laminated limestones of Valanginian to Barremian age are of good to excellent source quality. The indigenous organic matter contained within this organically rich section is thermally immature, not having undergone sufficient thermal diagenesis for the generation and expulsion of hydrocarbons. Within this stratigraphic section, however, staining by mature hydrocarbons was detected. These stains are associated with a fractured interval. These fractures may in turn represent potential migration pathways.

Organic geochemistry of ODP Leg 135 sediment samples

The average total organic carbon (TOC) content obtained after Rock-Eval/TOC analysis of 156 sediment samples from the eight sites cored during Leg 135 is 0.05%. Hence, the TOC content of Leg 135 sediments is extremely low. The organic matter that is present in these samples is probably mostly reworked and oxidized material. Ten sediment samples were selected for extraction and analysis by gas chromatography and gas chromatography-mass spectrometry. Very low amounts of extractable hydrocarbons were obtained and some aspects of the biomarker distributions suggest that these hydrocarbons are not representative of the organic matter indigenous to the samples. A sample of an oil seep from Pili, Tongatapu was also analyzed. The seep is a biodegraded, mature oil that shows many characteristics in common with previously published analyses of oil seeps from Tongatapu. Biomarker evidence indicates that its source is a mature, marine carbonate of probable Late Cretaceous-Early Tertiary age. The source rock responsible for the Tongatapu oil seeps remains unknown.

Composition of swamp waters from the lower Tom' River Basin

New data on chemical and trace component compositions of acidic and low acidic swamp waters and other types of low mineralized waters are reported in the paper. Special attention is paid to dissolved organic compounds: fulvic and humic acids, bitumen, and hydrocarbons. For the first time detailed data on organic trace components (alkanes, pentacyclic terpenoids, steranes, alkylbenzenes, naphthalenes, phenanthrenes, tetraarenes, etc.) in the swamp waters of the Western Siberia: are reported.

Hydrocarbons, sterols and alkenones at time series station KERFIX

Hydrocarbons, sterols and alkenones were analyzed in samples collected from a 10 month sediment trap time series deployed in the Indian Ocean sector of the Southern Ocean. Fluxes and within-class distributions varied seasonally. During higher mass and organic carbon (OC) flux periods, which occurred in austral summer and fall, fresh marine inputs were predominant. Vertical fluxes were most intense in January, but limited to one week in duration. They were, however, low compared with other oceanic regions. In contrast, low mass and OC flux periods were characterized by a strong unresolved complex mixture (UCM) in the hydrocarbon fraction and a high proportion of stanols as a result of zooplanktonic grazing. Terrigenous inputs were not detectable. The alkenone compositions were consistent with previous data on suspended particles from Antarctic waters. However, UK'37 values diverged from the linear and exponential fits established by Sikes et al. (1997, doi:10.1016/S0016-7037(97)00017-3) in the low temperature range. The seasonal pattern of alkenone production implied that IPT (integrated production temperature) is likely to be strongly imprinted by austral summer and fall SST (sea surface temperature).

Lithology, stage, organic carbon, d13C, hydrocarbons and fatty acids at DSDP Hole 93-603B

Organic-matter-rich Upper Cretaceous claystones from DSDP Hole 603B, lower continental rise, had organic carbon values ranging from 1.7 to 13.7%, C/N ratios from 32 to 72, and d13C values from -23.5 to -27.1 per mil. Lipid class maxima for the unbound alkanes (C29 and C31), unbound fatty acids (C28 and C30), and bound fatty acids (C24, C26 , and C28) and the strong odd-carbon and even-carbon preferences, respectively, suggested that the organic matter in these sediments was partially the result of input from continental plant waxes. Transport of the organic-matter-rich sediments to the deep sea from the near-shore environment probably resulted from turbiditic flow under oxygen-stressed conditions.

Organic geochemistry of sediments at DSDP Legs 56-57 Holes

The quantity, type, and maturity of the organic matter of Quaternary and Tertiary sediments from the Japan Trench (DSDP Leg 56, Sites 434 and 436; and Leg 57, Sites 438, 439 and 440) were determined. The hydrocarbons in lipid extracts were analyzed by capillary- column gas chromatography and combined gas chromatography/ mass spectrometry. Kerogen concentrates were investigated by microscopy, and vitrinite-reflectance values were determined. Measured organic-carbon values were in the range of 0.13 to 1.00 per cent. Extract yields, however, were extremely low. Normalized to organic carbon, total extracts ranged from 4.1 to 15.7 mg/g Corg. Gas chromatography of non-aromatic hydrocarbons showed that all sediments, except one Oligocene sample, contained very immature, mainly terrigenous organic material. This was indicated by n-alkane maxima at C29 and C31 and high odd-carbon-number predominances. Unsaturated steroid hydrocarbons were found to be major cyclic compounds in lower- and middle-Miocene samples from the upper inner trench slope (Sites 438 and 439). Perylene was the dominating aromatic hydrocarbon in all but the Oligocene sample. Microscopy showed kerogens rich in terrigenous organic particles, with a major portion of recycled vitrinite. Nevertheless, almost all the liptinite particles appeared to be primary. This is a paradox, as the bulk of the samples were composed of hemipelagic mineral matter with a major siliceous biogenic (planktonic) component. A trend of reduced size and increased roundness can be seen for the vitrinite/ inertinite particles from west to east (from upper inner trench slope to outer trench slope). All sediments but one are relatively immature, with mean huminite-reflectance values (Ro)in the range of 0.30 to 0.45 per cent. The oldest and deepest sediment investigated, an Oligocene sandstone from Site 439, yielded a mean vitrinitereflectance value of 0.74 per cent and a mature n-alkane distribution. This sample may indicate a geothermal event in late Oligocene time. It failed to affect the overlying lower Miocene and may have been caused by an intrusion. Boulders of acidic igneous rocks in the Oligocene can be interpreted as witnesses of nearby volcanic activity accompanied by intrusions.

Estudo da absorção das espécies pesadas do gás natural em octanol: efeitos da temperatura e vazão

In the oil industry, natural gas is a vital component of the world energy supply and an important source of hydrocarbons. It is one of the cleanest, safest and most relevant of all energy sources, and helps to meet the world's growing demand for clean energy in the future. With the growing share of natural gas in the Brazil energy matrix, the main purpose of its use has been the supply of electricity by thermal power generation. In the current production process, as in a Natural Gas Processing Unit (NGPU), natural gas undergoes various separation units aimed at producing liquefied natural gas and fuel gas. The latter should be specified to meet the thermal machines specifications. In the case of remote wells, the process of absorption of heavy components aims the match of fuel gas application and thereby is an alternative to increase the energy matrix. Currently, due to the high demand for this raw gas, research and development techniques aimed at adjusting natural gas are studied. Conventional methods employed today, such as physical absorption, show good results. The objective of this dissertation is to evaluate the removal of heavy components of natural gas by absorption. In this research it was used as the absorbent octyl alcohol (1-octanol). The influence of temperature (5 and 40 °C) and flowrate (25 and 50 ml/min) on the absorption process was studied. Absorption capacity expressed by the amount absorbed and kinetic parameters, expressed by the mass transfer coefficient, were evaluated. As expected from the literature, it was observed that the absorption of heavy hydrocarbon fraction is favored by lowering the temperature. Moreover, both temperature and flowrate favors mass transfer (kinetic effect). The absorption kinetics for removal of heavy components was monitored by chromatographic analysis and the experimental results demonstrated a high percentage of recovery of heavy components. Furthermore, it was observed that the use of octyl alcohol as absorbent was feasible for the requested separation process.

Estudo da absorção das espécies pesadas do gás natural em octanol: efeitos da temperatura e vazão

In the oil industry, natural gas is a vital component of the world energy supply and an important source of hydrocarbons. It is one of the cleanest, safest and most relevant of all energy sources, and helps to meet the world's growing demand for clean energy in the future. With the growing share of natural gas in the Brazil energy matrix, the main purpose of its use has been the supply of electricity by thermal power generation. In the current production process, as in a Natural Gas Processing Unit (NGPU), natural gas undergoes various separation units aimed at producing liquefied natural gas and fuel gas. The latter should be specified to meet the thermal machines specifications. In the case of remote wells, the process of absorption of heavy components aims the match of fuel gas application and thereby is an alternative to increase the energy matrix. Currently, due to the high demand for this raw gas, research and development techniques aimed at adjusting natural gas are studied. Conventional methods employed today, such as physical absorption, show good results. The objective of this dissertation is to evaluate the removal of heavy components of natural gas by absorption. In this research it was used as the absorbent octyl alcohol (1-octanol). The influence of temperature (5 and 40 °C) and flowrate (25 and 50 ml/min) on the absorption process was studied. Absorption capacity expressed by the amount absorbed and kinetic parameters, expressed by the mass transfer coefficient, were evaluated. As expected from the literature, it was observed that the absorption of heavy hydrocarbon fraction is favored by lowering the temperature. Moreover, both temperature and flowrate favors mass transfer (kinetic effect). The absorption kinetics for removal of heavy components was monitored by chromatographic analysis and the experimental results demonstrated a high percentage of recovery of heavy components. Furthermore, it was observed that the use of octyl alcohol as absorbent was feasible for the requested separation process.