Differential protein expression during growth on model and commercial mixtures of naphthenic acids in Pseudomonas fluorescens Pf‐5

Naphthenic acids (NAs) are carboxylic acids with the formula (CnH2n+ZO2) and are among the most toxic, persistent constituents of oil sands process-affected waters (OSPW), produced during oil sands extraction. Currently, the proteins and mechanisms involved in NA biodegradation are unknown. Using LC-MS/MS shotgun proteomics, we identified proteins overexpressed during the growth of Pseudomonas fluorescens Pf-5 on a model NA (4′-n-butylphenyl)-4-butanoic acid (n-BPBA) and commercial NA mixture (Acros). By day 11, >95% of n-BPBA was degraded. With Acros, a 17% reduction in intensity occurred with 10–18 carbon compounds of the Z family −2 to −14 (major NA species in this mixture). A total of 554 proteins (n-BPBA) and 631 proteins (Acros) were overexpressed during growth on NAs, including several transporters (e.g., ABC transporters), suggesting a cellular protective response from NA toxicity. Several proteins associated with fatty acid, lipid, and amino acid metabolism were also overexpressed, including acyl-CoA dehydrogenase and acyl-CoA thioesterase II, which catalyze part of the fatty acid beta-oxidation pathway. Indeed, multiple enzymes involved in the fatty acid oxidation pathway were upregulated. Given the presumed structural similarity between alkyl-carboxylic acid side chains and fatty acids, we postulate that P. fluorescens Pf-5 was using existing fatty acid catabolic pathways (among others) during NA degradation

Aerobic and Anaerobic Naphthenic Acid Biodegradation by Indigenous Tailings Pond Microorganisms

Surface mining of bitumen extraction from Alberta’s oil sands generates large volumes of oil sands process-affected water (OSPW) that is stored in tailings ponds. Naphthenic acids (NAs) are toxic, corrosive, and complex, cyclic carboxylic acids that accumulate in tailings ponds over time and must be removed for effective reclamation. This work has examined microbial NA biodegradation under aerobic and anaerobic conditions as a possible approach for reclamation. Phosphate stimulation of oxic OSPW resulted in growth of algae (Scenedesmus, Chlorella) and bacteria (Porphyrobacter, Planctomyces) capable of biodegrading low molecular weight NAs resulting in small decreases in acute toxicity. Several new NA-biodegrading bacteria were isolated from OSPW and identified. Additionally, this work has now shown that NA can be biodegraded under nitrate-, iron-, sulfate-reducing and methanogenic conditions and has identified microbial community members likely contributing to NA biodegradation. These findings show that the use of microorganisms for NA remediation may be possible.2 year

Natural and induced cadmium-accumulation in poplar and willow: implications for phytoremediation. Plant Soil 227

Abstract Potentially poplars and willows may be used for the in situ decontamination of soils polluted with Cd, such as pasturelands fertilised with Cd-rich superphosphate fertiliser. Poplar (Kawa and Argyle) and willow (Tangoio) clones were grown in soils containing a range (0.6-60.6 µg g −1 dry soil) of Cd concentrations. The willow clone accumulated significantly more Cd (9-167 µg g −1 dry matter) than the two poplar clones (6-75 µg g −1 ), which themselves were not significantly different. Poplar trees (Beaupré) sampled in situ from a contaminated site near the town of Auby, Northern France, were also found to accumulate significant quantities (up to 209 µg g −1 ) of Cd. The addition of chelating agents (0.5 and 2 g kg −1 EDTA, 0.5 g kg −1 DTPA and 0.5 g kg −1 NTA) to poplar (Kawa) clones caused a temporary increase in uptake of Cd. However, two of the chelating agents (2 g kg −1 EDTA and 0.5 g kg −1 NTA) also resulted in a significant reduction in growth, as well as abscission of leaves. If the results obtained in these pot experiments can be realised in the field, then a single crop of willows could remove over 100 years worth of fertiliser-induced Cd contamination from pasturelands

Evolutionary History of Copper Membrane Monooxygenases

Copper membrane monooxygenases (CuMMOs) oxidize ammonia, methane and some short-chain alkanes and alkenes. They are encoded by three genes, usually in an operon of xmoCAB . We aligned xmo operons from 66 microbial genomes, including members of the Alpha -, Beta -, and Gamma-proteobacteria, Verrucomicrobia, Actinobacteria, Thaumarchaeota and the candidate phylum NC10. Phylogenetic and compositional analyses were used to reconstruct the evolutionary history of the enzyme and detect potential lateral gene transfer (LGT) events. The phylogenetic analyses showed at least 10 clusters corresponding to a combination of substrate specificity and bacterial taxonomy, but with no overriding structure based on either function or taxonomy alone. Adaptation of the enzyme to preferentially oxidize either ammonia or methane has occurred more than once. Individual phylogenies of all three genes, xmoA, xmoB and xmoC , closely matched, indicating that this operon evolved or was consistently transferred as a unit, with the possible exception of the methane monooxygenase operons in Verrucomicrobia , where the pmoB gene has a distinct phylogeny from pmoA and pmoC . Compositional analyses indicated that some clusters of xmoCAB operons (for example, the pmoCAB in gammaproteobacterial methanotrophs and the amoCAB in betaproteobacterial nitrifiers) were compositionally very different from their genomes, possibly indicating recent lateral transfer of these operons. The combined phylogenetic and compositional analyses support the hypothesis that an ancestor of the nitrifying bacterium Nitrosococcus was the donor of methane monooxygenase (pMMO) to both the alphaproteobacterial and gammaproteobacterial methanotrophs, but that before this event the gammaproteobacterial methanotrophs originally possessed another CuMMO (Pxm), which has since been lost in many species

Nitrate leaching through oxisols of the Loyalty Islands (New Caledonia) under intensified agricultural practices. Geoderma

Scope of the journal The primary intention of the journal is to stimulate wide interdisciplinary cooperation and understanding among workers in the different fields of pedology. Therefore, the journal tries to bring together papers from the entire field of soil research, rather than to emphasize any one subdiscipline. Interdisciplinary work should preferably be focused on occurrence and dynamic characterization in space and time of soils in the field. . For 1998 volumes 81-86 are scheduled for publication. Subscription prices are available upon request from the publisher. Subscriptions are accepted on a prepaid basis only and are entered on a calendar year basis. Issues are sent by surface mail except to the following countries where air delivery via SAL is ensured: Argentina, Australia, Brazil, Canada, Hong Kong, India, Israel, Japan, Malaysia, Mexico, New Zealand, Pakistan, PR China, Singapore, South Africa, South Korea, Taiwan, Thailand, USA. For all other countries airmail rates are available upon request. Claims for missing issues must be made within six months of our publication (mailing) date. For orders, claims, product enquiries (no manuscript enquiries) please contact Customer Support Department at the Regional Sales Office nearest to you: Publication information G E O D E W ELSEVIER Abstract For the uplifted coral atolls of the Loyalty Islands (New Caledonia), the prime source of potable water is the freshwater lenses that underlie the islands. The recent adoption of more-intensive agricultural practices, particularly the use of nitrogeneous fertilizers, may, however, represent a threat for these fragile Pacific ecosystems. To assess the risk posed by nitrate leaching, experiments have been conducted on the permeable oxisols of the island of Maré, using both cropped and bare soil sites. Drainage below the root zone was found to be very important, about 50% of the rainfall, even on the cropped site. The soils are thin and permeable, and the frequent tropical storms have high rainfall intensities. Nitrate fertilizers thus have potential to be leached, in large amounts, even up to 100% of the nitrate supply, especially if fertilizers are not supplied according to weather conditions and in concert with the plant's ability to extract them. O 1998 Elsevier Science B.V. All rights reserved