Nitrogenase Gene Amplicons from Global Marine Surface Waters Are Dominated by Genes of Non-Cyanobacteria

• Published in: PloS one Vol. 6; no. 4; p. e19223
• Main Authors: Farnelid, Hanna, Andersson, Anders F., Bertilsson, Stefan, Al-Soud, Waleed Abu, Hansen, Lars H., Sørensen, Søren, Steward, Grieg F., Hagström, Åke, Riemann, Lasse
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 29.04.2011; Public Library of Science (PLoS)
• Subjects: Amino acids; AMPLIFICATION; Anaerobic bacteria; Analysis; ATLANTIC-OCEAN; Bacteria; BALTIC SEA PROPER; Biologi; Biology; Carbon; Cell and molecular biology; Cell- och molekylärbiologi; CHESAPEAKE BAY; Cloning, Molecular; Clusters; Conservation of Natural Resources; Coral reefs; Cyanobacteria; Cyanobacteria - enzymology; Cyanobacteria - genetics; Deoxyribonucleic acid; DISTRIBUTIONS; Divergence; DIVERSITY; DNA; DNA Primers - genetics; DNA, Bacterial - metabolism; DNA, Complementary - metabolism; Ecology; Enzymes; EXPRESSION; Gene pool; Genes; Genetic testing; Geographical distribution; Geography; Microbiology; Microorganisms; Mikrobiologi; Multigene Family; N-2-FIXING CYANOBACTERIA; NATURAL SCIENCES; NATURVETENSKAP; NIFH GENE; Nitrogen; Nitrogen Fixation; Nitrogenase; Nitrogenase - genetics; Nitrogenase - metabolism; NORTH PACIFIC-OCEAN; Oceans and Seas; Pelagic zone; Phylogeny; Plankton; Polar environments; Polymerase Chain Reaction - methods; Proteins; Proteobacteria; Proteobacteria - genetics; Quality Control; Reproducibility of Results; Ribonucleic acid; RNA; Sequence Analysis, DNA; Sociology; Surface water; Transcription; Type 2 diabetes; Water Microbiology
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0019223

Cyanobacteria are thought to be the main N(2)-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations world-wide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III) were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N(2) fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.