Journal Article

Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic

Rees, Andrew P, Gilbert, Jack, A Turk, Kendra, Pereira, Nicole, Lohan, Maeve, Zehr, Jonathan P, Woodward, E Malcolm S, Swift, Paul, Shelley, Rachel

2011

Overview

Expression of nifH in 28 surface water samples collected during fall 2007 from six stations in the vicinity of the Cape Verde Islands (north-east Atlantic) was examined using reverse transcription-polymerase chain reaction (RT-PCR)-based clone libraries and quantitative RT-PCR (RT-qPCR) analysis of seven diazotrophic phylotypes. Biological nitrogen fixation (BNF) rates and nutrient concentrations were determined for these stations, which were selected based on a range in surface chlorophyll concentrations to target a gradient of primary productivity. BNF rates greater than 6 nmolN l −1  h −1 were measured at two of the near-shore stations where high concentrations of Fe and PO 4 3− were also measured. Six hundred and five nifH transcripts were amplified by RT-PCR, of which 76% are described by six operational taxonomic units, including Trichodesmium and the uncultivated UCYN-A, and four non-cyanobacterial diazotrophs that clustered with uncultivated Proteobacteria . Although all five cyanobacterial phylotypes quantified in RT-qPCR assays were detected at different stations in this study, UCYN-A contributed most significantly to the pool of nifH transcripts in both coastal and oligotrophic waters. A comparison of results from RT-PCR clone libraries and RT-qPCR indicated that a γ-proteobacterial phylotype was preferentially amplified in clone libraries, which underscores the need to use caution interpreting clone-library-based nifH studies, especially when considering the importance of uncultivated proteobacterial diazotrophs.

• Publisher: Nature Publishing Group UK,Oxford University Press,Nature Publishing Group
• Subject: 60 APPLIED LIFE SCIENCES / 631/158/2446/2447 / 631/208/199 / 631/326/2565/855 / 631/326/47 / Bacterial Proteins - genetics / BASIC BIOLOGICAL SCIENCES / Biomedical and Life Sciences / Cabo Verde / CAPE VERDE ISLANDS / CHAIN REACTIONS / CHLOROPHYLL / Chlorophyll - analysis / Coastal waters / Cyanobacteria - enzymology / Cyanobacteria - genetics / Ecology / Evolutionary Biology / Gene Library / Iron - analysis / Islands / Libraries / Life Sciences / Microbial Ecology / Microbial Genetics and Genomics / Microbiology / NITROGEN FIXATION / NITROGENASE / Nitrogenase - genetics / Nitrogenation / Nutrient concentrations / NUTRIENTS / Original / original-article / Phylogeny / Polymerase chain reaction / PRODUCTIVITY / Proteobacteria - enzymology / Proteobacteria - genetics / Reverse Transcriptase Polymerase Chain Reaction / Reverse transcription / Seawater - analysis / Seawater - microbiology / Surface water / SURFACE WATERS / TARGETS / Water analysis / Water Microbiology / Water sampling