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DNA recovery from soils of diverse composition
Four methods for purifying crude DNA were evaluated for percent recovery, fragment size, speed, enzyme restriction, PCR amplification, and DNA-DNA hybridization and in general, all methods produced DNA pure enough for PCR amplification. Expand
DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.
It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available and reveal extensive gene diversity within the current concept of "species". Expand
Towards environmental systems biology of Shewanella
Systems-level analysis of the model species Shewanella oneidensis MR-1 and other members of this genus has provided new insights into the signal-transduction proteins, regulators, and metabolic and respiratory subsystems that govern the remarkable versatility of the shewanellae. Expand
Molecular Evidence for the Broad Distribution of Anaerobic Ammonium-Oxidizing Bacteria in Freshwater and Marine Sediments
This study provides evidence for the widespread distribution of anammox bacteria in that it detected closely related anamm ox 16S rRNA gene sequences in 11 geographically and biogeochemically diverse freshwater and marine sediments. Expand
The bacterial species definition in the genomic era
The analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available and the idea of biologically meaningful clusters of diversity may not be universally applicable in the microbial world. Expand
Simultaneous Recovery of RNA and DNA from Soils and Sediments
  • R. Hurt, Xiaoyun Qiu, +4 authors Jizhong Zhou
  • Biology, Medicine
  • Applied and Environmental Microbiology
  • 1 October 2001
A robust, simple, rapid, and effective method was developed for simultaneous recovery of both RNA and DNA from soils of diverse composition by adapting the previous grinding-based cell lysis method for DNA extraction. Expand
Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs.
The three strains share identical 16S rRNA gene sequences and represent a novel lineage of methane-oxidizing bacteria within the alpha-subclass of the class Proteobacteria and are only moderately related to type II methanotrophs of the Methylocystis-Methylosinus group. Expand
Cryptic Lineages of the Genus Escherichia
Evidence that Escherichia fergusonii has evolved at an accelerated rate compared to E. coli is found, suggesting that this species is younger than estimated by the molecular clock method. Expand
Phases of denitrification following oxygen depletion in soil
The short-term response of soil denitrification to reduced aeration was studied using the acetylene inhibition method for the assay of denitrification. Two distinct phases of denitrification rateExpand
Denitrification: ecological niches, competition and survival
It is suggested that organic carbon is more important than oxygen status in determining denitrifying enzyme content of habitats, and Michaelis-Menten theoretical models suggest the conditions required to achieve changes in partitioning between the two fates of nitrate. Expand