Nitrogen-fixation activity and the abundance and taxonomy of nifH genes in agricultural, pristine, and urban prairie stream sediments chronically exposed to different levels of nitrogen loading

Arch Microbiol. 2018 May;200(4):623-633. doi: 10.1007/s00203-018-1475-5. Epub 2018 Jan 15.


Small streams exert great influences on the retention and attenuation of nitrogen (N) within stream networks. Human land use can lead to increased transport of dissolved inorganic N compounds and downstream eutrophication. Microbial activity in streams is important for maintaining an actively functioning N cycle. Chronically high N loading in streams affects the rates of the central processes of the N cycle by increasing rates of nitrification and denitrification, with biota exhibiting decreased efficiency of N use. The LINXII project measured N-cycle parameters in small streams using 15NO3- tracer release experiments. We concurrently measured N2 fixation rates in six streams of three types (agricultural, pristine, and urban prairie streams) as part of this broader study of major N-cycle processes. Nitrogen fixation in streams was significantly negatively correlated with nitrate levels, dissolved inorganic N levels, and denitrification rates. Algal mat and leaf litter samples generally exhibited the highest rates of N2 fixation. The abundance of nifH genes, as measured by real-time PCR, was marginally correlated with N2-fixation rates, but not to other N-cycle processes or stream characteristics. The nifH sequences observed were assigned to cyanobacteria, Deltaproteobacteria, Methylococcus, and Rhizobia. Seasonal changes, disturbances, and varying inputs may encourage a diverse, flexible, stable N2-fixing guild. Patchiness in the streams should be considered when assessing the overall impact of N2 fixation, since algal biomass exhibited high rates of N2 fixation.

Keywords: Multirate; Nitrogen fixation; Real-time PCR; Streams; nifH.

MeSH terms

  • Agriculture
  • Bacterial Proteins / genetics*
  • Cyanobacteria / enzymology
  • Cyanobacteria / genetics
  • Eutrophication
  • Geologic Sediments / microbiology
  • Grassland
  • Kinetics
  • Molecular Typing
  • Nitrates / metabolism*
  • Nitrification
  • Nitrogen Fixation
  • Oxidoreductases / genetics*
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Rivers / microbiology


  • Bacterial Proteins
  • Nitrates
  • RNA, Ribosomal, 16S
  • Oxidoreductases
  • nitrogenase reductase