Nitrification and denitrification: Probing the nitrogen cycle in aquatic environments

@article{Ward2004NitrificationAD,
  title={Nitrification and denitrification: Probing the nitrogen cycle in aquatic environments},
  author={Bess B. Ward},
  journal={Microbial Ecology},
  year={2004},
  volume={32},
  pages={247-261}
}
  • B. Ward
  • Published 1 November 1996
  • Biology
  • Microbial Ecology
Methods designed to detect microorganisms involved in the biogeochemistry of nitrogen in the marine environment are rapidly being developed and deployed in ecological investigations. Probes based on phylogenetic sequences (usually rRNA) and those based on the sequences of functional genes or proteins have both been demonstrated in the nitrogen cycle. The most progress has been made for ammonia oxidizers; several sets of PCR primers have been described and their specificity may be optimized to… 
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References

SHOWING 1-10 OF 73 REFERENCES
Functional and Taxonomic Probes for Bacteria in the Nitrogen Cycle
TLDR
Although quantification is still rudimentary, comparison among immunofluorescence enumeration, PCR amplification and quantitative hybridization allow an assessment of genotype vs phenotype abundances.
Numbers, activities, and diversity of autotrophic ammonia-oxidizing bacteria in a freshwater, eutrophic lake sediment
TLDR
Pure-culture isolations from a positive MPN tube inoculated with oxygenated sediment and representing a single point in a seasonal cycle produced ammonia-oxidizing strains belonging to the genus Nitrosospira, which extend the serological diversity of this group of bacteria.
Molecular analysis of enrichment cultures of marine ammonia oxidisers.
TLDR
The approach enabled analysis of ammonia oxidiser enrichments at an early stage and without the requirement for isolation of pure cultures, significantly reducing the time required and facilitating quantitative assessment of relatedness of strains.
Aerobic denitrification: a controversy revived
During studies on the denitrifying mixotroph, Thiosphaera pantotropha, it has been found that this organism is capable of simultaneously utilizing nitrate and oxygen as terminal electron acceptors in
Distribution and Diversity of Dissimilatory NO2− Reductases in Denitrifying Bacteria
Denitrification is the biological reduction of nitrogenous oxides to gaseous products during anaerobic bacterial growth. Some organisms, Thiosphaera pantotropha in particular, appear to denitrify in
Detection of ammonium-oxidizing bacteria of the beta-subclass of the class Proteobacteria in aquatic samples with the PCR
TLDR
This is the first report describing PCR primers specific for ammonium-oxidizing bacteria and the successful amplification of nitrifier genes coding for rRNA from DNA extracts from natural samples.
Production of NO and N2O by soil nitrifying bacteria
The composition of the atmosphere is influenced both directly and indirectly by biological activity. Evidence is presented here to suggest that nitrification in soil is a potentially significant
Marine ammonia- and nitrite-oxidizing bacteria: serological diversity determined by immunofluorescence in culture and in the environment.
TLDR
Ammonium- and nitrite-oxidizing bacteria were enumerated in samples taken in a depth profile in the Southern California Bight by immunofluorescence assays for two ammonium oxidizers and two nitrite oxidizers.
Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria
TLDR
The nitrifiers, as a group, apparently are not derived from an ancestral nitrifying phenotype, and consideration of physiology and phylogenetic distribution suggested that nitrite-oxidizing bacteria of the alpha and gamma subdivisions are derived from immediate photosynthetic ancestry.
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