Monitoring of microbial hydrocarbon remediation in the soil

Bioremediation of hydrocarbon pollutants is advantageous owing to the cost-effectiveness of the technology and the ubiquity of hydrocarbon-degrading microorganisms in the soil. Soil microbial diversity is affected by hydrocarbon perturbation, thus selective enrichment of hydrocarbon utilizers occurs. Hydrocarbons interact with the soil matrix and soil microorganisms determining the fate of the contaminants relative to their chemical nature and microbial degradative capabilities, respectively. Provided the polluted soil has requisite values for environmental factors that influence microbial activities and there are no inhibitors of microbial metabolism, there is a good chance that there will be a viable and active population of hydrocarbon-utilizing microorganisms in the soil. Microbial methods for monitoring bioremediation of hydrocarbons include chemical, biochemical and microbiological molecular indices that measure rates of microbial activities to show that in the end the target goal of pollutant reduction to a safe and permissible level has been achieved. Enumeration and characterization of hydrocarbon degraders, use of micro titer plate-based most probable number technique, community level physiological profiling, phospholipid fatty acid analysis, 16S rRNA- and other nucleic acid-based molecular fingerprinting techniques, metagenomics, microarray analysis, respirometry and gas chromatography are some of the methods employed in bio-monitoring of hydrocarbon remediation as presented in this review

The Effects of Mary Rose Conservation Treatment on Iron Oxidation Processes and Microbial Communities Contributing to Acid Production in Marine Archaeological Timbers

The Tudor warship the Mary Rose has reached an important transition point in her conservation. The 19 year long process of spraying with polyethylene glycol (PEG) has been completed (April 29th 2013) and the hull is air drying under tightly controlled conditions. Acidophilic bacteria capable of oxidising iron and sulfur have been previously identified and enriched from unpreserved timbers of the Mary Rose, demonstrating that biological pathways of iron and sulfur oxidization existed potentially in this wood, before preservation with PEG. This study was designed to establish if the recycled PEG spray system was a reservoir of microorganisms capable of iron and sulfur oxidization during preservation of the Mary Rose. Microbial enrichments derived from PEG impregnated biofilm collected from underneath the Mary Rose hull, were examined to better understand the processes of cycling of iron. X-ray absorption spectroscopy was utilised to demonstrate the biological contribution to production of sulfuric acid in the wood. Using molecular microbiological techniques to examine these enrichment cultures, PEG was found to mediate a shift in the microbial community from a co-culture of Stenotrophomonas and Brevunidimonas sp, to a co-culture of Stenotrophomonas and the iron oxidising Alicyclobacillus sp. Evidence is presented that PEG is not an inert substance in relation to the redox cycling of iron. This is the first demonstration that solutions of PEG used in the conservation of the Mary Rose are promoting the oxidation of ferrous iron in acidic solutions, in which spontaneous abiotic oxidation does not occur in water. Critically, these results suggest PEG mediated redox cycling of iron between valence states in solutions of 75% PEG 200 and 50% PEG 2000 (v/v) at pH 3.0, with serious implications for the future use of PEG as a conservation material of iron rich wooden archaeological artefacts

Halomonas olivaria sp. nov., a moderately halophilic bacterium isolated from olive-processing effluents

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Halomonas olivaria sp nov., a moderately halophilic bacterium isolated from olive-processing effluents

A moderately halophilic, Gram-stain-negative, non-sporulating bacterium designed as strain TYRC17(T) was isolated from olive-processing effluents. The organism was a straight rod, motile by means of peritrichous flagella and able to respire both oxygen and nitrate. Growth occurred with 0-25 % (w/v) NaCl (optimum, 7%), at pH 5-11 (optimum, pH 7.0) and at 4-50 degrees C (optimally at 35 degrees C). It accumulated poly-beta-hydroxyalkanoate granules and produced exopolysaccharides. The predominant fatty acids were C-18:1 omega 7c, C-16:1 omega 7c and C-16:0. Ubiquinone 9 (Q-9) was the only respiratory quinone. The DNA G-FC content of TYRC17(T) was 53.9 mol%. Phylogenetic analyses of 16S rRNA gene sequences revealed that the strain represents a member of the genus Halomonas and more precisely of the subgroup containing Halomonas sulfidaeris, H. titanicae, H. variabilis, H. zhanjiangensis, H.alkaliantarctica, H. boliviensis and H. neptunia. TYRC17(T) showed high 16S-rRNA sequence identities in particular with the three last species listed (99.4-99.5 %). A multilocus sequence analysis (MLSA) using the 23S rRNA, gyrB, rpoD and secA genes allowed clarifying the phylogenetic position of TYRC17(T). This, combined with the level of DNA DNA hybridization between TYRC17(T) and its closest relatives ranging from 21.6 % to 48.4 %, indicated that TYRC17(T) did not represent any of these species. On the basis of phenotypic and genotypic characteristics, and also genomic and phylogenetic evidence, it was concluded that strain TYRC17(T) represented a novel species of the genus Halomonas. The name Halomonas olivaria sp. nov. is proposed with TYRC17(T) (=DSM 19074(T)=CCUG 53850B(T)) as the type strain

Pertinence des résidus de lysine de surface pour la fonctionnalisation de Laccase

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