title: Metal oxides, clay minerals and charcoal determine the composition of microbial communities in matured artificial soils and their response to phenanthrene.
abstract: Microbial communities in soil reside in a highly heterogeneous habitat where diverse mineral surfaces, complex organic matter and microorganisms interact with each other. This study aimed to elucidate the long-term effect of the soil mineral composition and charcoal on the microbial community composition established in matured artificial soils and their response to phenanthrene. One year after adding sterile manure to different artificial soils and inoculating microorganisms from a Cambisol, the matured soils were spiked with phenanthrene or not and incubated for another 70 days. 16S rRNA gene and internal transcribed spacer fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis. Metal oxides and clay minerals and to a lesser extent charcoal influenced the microbial community composition. Changes in the bacterial community composition in response to phenanthrene differed depending on the mineral composition and presence of charcoal, while no shifts in the fungal community composition were observed. The abundance of ring-hydroxylating dioxygenase genes was increased in phenanthrene-spiked soils except for charcoal-containing soils. Here we show that the formation of biogeochemical interfaces in soil is an ongoing process and that different properties present in artificial soils influenced the bacterial response to the phenanthrene spike.
authors: Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.
authors: Doreen
authors: D
authors: Babin
authors: Guo-Chun
authors: GC
authors: Ding
authors: Geertje Johanna
authors: GJ
authors: Pronk
authors: Katja
authors: K
authors: Heister
authors: Ingrid
authors: I
authors: Kögel-Knabner
authors: Kornelia
authors: K
authors: Smalla
mesh_terms: D000538:Aluminum Silicates; D001419:Bacteria / Q000145:classification / Q000187:drug effects / Q000235:genetics; D002606:Charcoal / Q000494:pharmacology; D000077215:Clay; D058645:Denaturing Gradient Gel Electrophoresis; D049308:Dioxygenases / Q000235:genetics; D017753:Ecosystem; D005658:Fungi / Q000145:classification / Q000187:drug effects / Q000235:genetics; D008372:Manure; D008670:Metals / Q000494:pharmacology; D008903:Minerals / Q000737:chemistry / Q000494:pharmacology; D010087:Oxides / Q000494:pharmacology; D010616:Phenanthrenes / Q000494:pharmacology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012987:Soil / Q000737:chemistry*; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000494:pharmacology*
chemical_list: D000538:Aluminum Silicates; D008372:Manure; D008670:Metals; D008903:Minerals; D010087:Oxides; D010616:Phenanthrenes; D012336:RNA, Ribosomal, 16S; D012987:Soil; D012989:Soil Pollutants; D002606:Charcoal; C031181:phenanthrene; D049308:Dioxygenases; D000077215:Clay
keywords: 16S rRNA genes; DGGE; ITS; RHDα genes; artificial soils