Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and "deep peat" lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.
Oxidation of ammonia, the first step in nitrification, is carried out in soil by bacterial and archaeal ammonia oxidizers and recent studies suggest possible selection for the latter in low-ammonium environments. In this study, we investigated the selection of ammonia-oxidizing archaea and bacteria in wetland soil vertical profiles at two sites differing in terms of the ammonium supply rate, but not significantly in terms of the groundwater level. One site received ammonium through decomposition of organic matter, while the second, polluted site received a greater supply, through constant leakage of an underground septic tank. Soil nitrification potential was significantly greater at the polluted site. Quantification of amoA genes demonstrated greater abundance of bacterial than archaeal amoA genes throughout the soil profile at the polluted site, whereas bacterial amoA genes at the unpolluted site were below the detection limit. At both sites, archaeal, but not the bacterial community structure was clearly stratified with depth, with regard to the soil redox potential imposed by groundwater level. However, depth-related changes in the archaeal community structure may also be associated with physiological functions other than ammonia oxidation.
The most important prerequisite for the application of PCR-based methods, among them the detection and quantifi cation of genetically modifi ed organisms (GMOs) is the ability to extract significant amounts of DNA of adequate quality from the sample under investigation. The sample of interest in our work was soybean lecithin with expected low DNA content. The aim of this study was to set up a fast and effective HPLC (High Performance Liquid Chromatography) method using CIM® (Convective Interaction Media, BIA Separations d.o.o., Ljubljana, Slovenia) DEAE (DiEthylAminoEthyl) anion-exchange disk monolithic columns (disks) for the isolation of DNA from soybean lecithin samples. As the reference isolation procedure we used CTAB (CethylTrimethylAmmonium Bromide) method, which is widely used in GMO detection. It was demonstrated, that CIM® DEAE disks allow effi cient isolation of DNA from soybean lecithin. Furthermore, in comparison with the CTAB method, the method was less time-consuming and reduced the use of some aggressive chemicals. The quality of isolated DNA was tested with spectrophotometric analysis, agarose gel electrophoresis and by amplification of soybean specifi c lectin gene with qualitative and real-time PCR. The isolated soybean DNA was of adequate quantity and quality for PCR analysis, even though mostly degraded, present in small amounts and contaminated with some impurities, among them potential PCR inhibitors. The study expanded the applicability of monolithic columns in the isolation of biomolecules from highly processed food materials and their potential use for nucleic acids detection.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.