title: Community structure and in situ activity of nitrifying bacteria in Phragmites root-associated biofilms.
abstract: The amount of oxygen released by Phragmites roots and the community structure and in situ activity of nitrifying bacteria in the root biofilms were analyzed by the combined use of 16S rRNA gene-cloning analysis, quantitative PCR (qPCR) assay and microelectrodes. Axial and radial O₂ microprofiles were obtained for individual roots of Phragmites in a horizontal flow reactor fed with artificial medium continuously. Axial O₂ profiles revealed that O₂ was released at a rate of 0.21 μmol O₂ cm⁻² (root surface area) h⁻¹ only in the apical region (up to ca. 40 mm from the root apex), where there was a high abundance (10⁷ to 10⁸ copies g⁻¹ biomass) of Nitrosomonas-like AOB and Nitrospira-like NOB. This abundance, however, sharply declined to the detection limit at positions more basal than 80 mm. Phylogenetic analysis based on 16S rRNA gene identified strains related to Nitrosomonas oligotropha and Nitrosomonas cryotolerans as the predominant AOB and strains related to Nitrospira marina and Nitrospira moscoviensis as the predominant NOB in the root biofilms. Based on radial O₂ microprofiles, the oxic region only extended about 0.5 mm into the surrounding sediment due to a high rate of O₂ consumption in the rhizosphere. The net NH₄⁺ and O₂ consumption rates in the apical region were higher than those determined at the oxic sediment surface in which the abundance of AOB and NOB was one order of magnitude lower than in the rhizosphere. These results clearly indicated that Phragmites root biofilms played an important role in nitrification in the waterlogged anoxic sediment.
authors.affiliation: Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo Hokkaido 060-8628, Japan. sokabe@eng.hokudai.ac.jp
authors.forename: Satoshi
authors.initials: S
authors.lastname: Okabe
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Hisashi
authors.initials: H
authors.lastname: Satoh
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D018407:Bacterial Physiological Phenomena; D018441:Biofilms; D058448:Biota; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D010100:Oxygen / Q000378:metabolism; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology*; D006109:Poaceae / Q000382:microbiology*; D000644:Quaternary Ammonium Compounds / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D000644:Quaternary Ammonium Compounds; D012336:RNA, Ribosomal, 16S; D010100:Oxygen