TY - JOUR A1 - Alawi, Mashal A1 - Schneider, Beate A1 - Kallmeyer, Jens T1 - A procedure for separate recovery of extra- and intracellular DNA from a single marine sediment sample JF - Journal of microbiological methods N2 - Extracellular DNA (eDNA) is a ubiquitous biological compound in aquatic sediment and soil. Previous studies suggested that eDNA plays an important role in biogeochemical element cycling, horizontal gene transfer and stabilization of biofilm structures. Previous methods for eDNA extraction were either not suitable for oligotrophic sediments or only allowed quantification but no genetic analyses. Our procedure is based on cell detachment and eDNA liberation from sediment particles by sequential washing with an alkaline sodium phosphate buffer followed by a separation of cells and eDNA. The separated eDNA is then bound onto silica particles and purified, whereas the intracellular DNA from the separated cells is extracted using a commercial kit. The method provides extra- and intracellular DNA of high purity that is suitable for downstream applications like PCR. Extracellular DNA was extracted from organic-rich shallow sediment of the Baltic Sea, glacially influenced sediment of the Barents Sea and from the oligotrophic South Pacific Gyre. The eDNA concentration in these samples varied from 23 to 626 ng g(-1) wet weight sediment. A number of experiments were performed to verify each processing step. Although extraction efficiency is higher than other published methods, it is not fully quantitative. (C) 2014 Elsevier B.V. All rights reserved. KW - Extracellular DNA KW - eDNA KW - Intracellular DNA KW - South Pacific Gyre KW - Ancient DNA KW - Fossil DNA Y1 - 2014 U6 - https://doi.org/10.1016/j.mimet.2014.06.009 SN - 0167-7012 SN - 1872-8359 VL - 104 SP - 36 EP - 42 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Noah, Mareike A1 - Lappe, Michael A1 - Schneider, Beate A1 - Vieth-Hillebrand, Andrea A1 - Wilkes, Heinz A1 - Kallmeyer, Jens T1 - Tracing biogeochemical and microbial variability over a complete oil sand mining and recultivation process JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man N2 - Recultivation of disturbed oil sand mining areas is an issue of increasing importance. Nevertheless only little is known about the fate of organic matter, cell abundances and microbial community structures during oil sand processing, tailings management and initial soil development on reclamation sites. Thus the focus of this work is on biogeochemical changes of mined oil sands through the entire process chain until its use as substratum for newly developing soils on reclamation sites. Therefore, oil sand, mature fine tailings (MFTs) from tailings ponds and drying cells and tailings sand covered with peat-mineral mix (PMM) as part of land reclamation were analyzed. The sample set was selected to address the question whether changes in the above-mentioned biogeochemical parameters can be related to oil sand processing or biological processes and how these changes influence microbial activities and soil development. GC-MS analyses of oil-derived biomarkers reveal that these compounds remain unaffected by oil sand processing and biological activity. In contrast, changes in polycyclic aromatic hydrocarbon (PAH) abundance and pattern can be observed along the process chain. Especially naphthalenes, phenanthrenes and chrysenes are altered or absent on reclamation sites, Furthermore, root-bearing horizons on reclamation sites exhibit cell abundances at least ten times higher (10(8) to 10(9) cells g(-1)) than in oil sand and MFF samples (10(7) cells g(-1)) and show a higher diversity in their microbial community structure. Nitrate in the pore water and roots derived from the PMM seem to be the most important stimulants for microbial growth. The combined data show that the observed compositional changes are mostly related to biological activity and the addition of exogenous organic components (PMM), whereas oil extraction, tailings dewatering and compaction do not have significant influences on the evaluated compounds. Microbial community composition remains relatively stable through the entire process chain. (C) 2014 Elsevier B.V. All rights reserved. KW - Oil sands KW - Tailings ponds KW - Reclamation KW - PAN KW - Biomarker KW - Microbial community analysis Y1 - 2014 U6 - https://doi.org/10.1016/j.scitotenv.2014.08.020 SN - 0048-9697 SN - 1879-1026 VL - 499 SP - 297 EP - 310 PB - Elsevier CY - Amsterdam ER -