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

• Published in: The ISME Journal Vol. 5; no. 7; pp. 1201 - 1212
• Main Authors: A Turk, Kendra, Rees, Andrew P, Zehr, Jonathan P, Pereira, Nicole, Swift, Paul, Shelley, Rachel, Lohan, Maeve, Woodward, E Malcolm S, Gilbert, Jack
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.07.2011; Oxford University Press; Nature Publishing Group
• Subjects: 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; Cyanobacteria - enzymology; Cyanobacteria - genetics; Ecology; Evolutionary Biology; Gene Library; Iron - analysis; Islands; Life Sciences; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; NITROGEN FIXATION; NITROGENASE; Nitrogenase - genetics; Nutrient concentrations; NUTRIENTS; Original; original-article; Phylogeny; PRODUCTIVITY; Proteobacteria - enzymology; Proteobacteria - genetics; Reverse Transcriptase Polymerase Chain Reaction; Seawater - analysis; Seawater - microbiology; Surface water; SURFACE WATERS; TARGETS; Water analysis; Water Microbiology; Water sampling; Cape Verde; molecular; nitrogen fixation; Atlantic; nitrogenase
• ISSN: 1751-7362; 1751-7370; 1751-7370
• DOI: 10.1038/ismej.2010.205

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.