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Evaluation and Optimization of DNA Extraction and Purification Procedures for Soil and Sediment Samples
- D. N. Miller, J. Bryant, E. Madsen, W. Ghiorse
- Medicine, ChemistryApplied and Environmental Microbiology
- 1 November 1999
It is indicated that for these types of samples, optimum DNA recovery requires brief, low-speed bead mill homogenization in the presence of a phosphate-buffered SDS-chloroform mixture, followed by Sephadex G-200 column purification.
Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil
Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB) and the yield of the greenhouse gas N2O in the strain My1 culture was lower but comparable to that of soil AOB.
Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment
- M. Moré, J. B. Herrick, M. C. Silva, W. Ghiorse, E. Madsen
- Medicine, BiologyApplied and Environmental Microbiology
- 1 May 1994
This study reports improvements in two of the key steps, lysis of indigenous cells and DNA purification, required for achieving a rapid nonselective protocol for extracting nucleic acids directly…
Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil.
Nitrification of excess ammonia in soil causes eutrophication of water resources and emission of atmospheric N(2) O gas. The first step of nitrification, ammonia oxidation, is mediated by Archaea as…
Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food
- J. Jung, S. H. Lee, C. Jeon
- Biology, EngineeringApplied and Environmental Microbiology
- 11 February 2011
In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process of Kimchi, and provide insights into the kimchi microbial community.
Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment
- C. Jeon, W. Park, P. Padmanabhan, C. DeRito, J. Snape, E. Madsen
- Biology, Environmental ScienceProceedings of the National Academy of Sciences…
- 3 November 2003
Microorganisms maintain the biosphere by catalyzing biogeochemical processes, including biodegradation of organic chemical pollutants. Yet seldom have the responsible agents and their respective…
Comparative Survey of Rumen Microbial Communities and Metabolites across One Caprine and Three Bovine Groups, Using Bar-Coded Pyrosequencing and 1H Nuclear Magnetic Resonance Spectroscopy
- H. Lee, J. Jung, Y. Oh, Sang-Suk Lee, E. Madsen, C. Jeon
- Biology, MedicineApplied and Environmental Microbiology
- 15 June 2012
The data indicate that bovine host breeds override diet as the key factor that determines bacterial community and metabolite profiles in the rumen.
In Situ, Real-Time Catabolic Gene Expression: Extraction and Characterization of Naphthalene Dioxygenase mRNA Transcripts from Groundwater
Results are the first to directly document in situ transcription of genes encoding naphthalene catabolism at a contaminated site by indigenous microorganisms, indicating that diverse dioxygenase transcripts had been retrieved from groundwater.
High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy
- H. Lee, Sang Eun Jeong, P. Kim, E. Madsen, C. Jeon
- Environmental ScienceFront. Microbiol.
- 25 June 2015
Based on contrasts between absolute abundances of methanogens and methanotrophs at depths sampled across rhizosphere and bulk soils (especially millimeter-scale slices at the surface), it is identified populations of meethanogens (Methanosaeta, Methanoregula, Methanocella, MethANobacterium, and Methanosphaerula), and meethanotrophic populations that are likely physiologically active in situ.
Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment.
Comparative 16S rDNA analysis indicated that strain CJ2T is related to the family Comamonadaceae and that the nearest phylogenetic relative was Polaromonas vacuolata 34-PT (97.1% similarity).