Dataset Information

Widespread Distribution and Expression of Gamma A (UMB), an Uncultured, Diazotrophic, ?-Proteobacterial nifH Phylotype.

ABSTRACT: Marine dinitrogen (N2) fixation studies have focused nearly exclusively on cyanobacterial diazotrophs; however ?-proteobacteria are an abundant component of the marine community and have been largely overlooked until recently. Here we present a phylogenetic analysis of all nifH ?-proteobacterial sequences available in public databases and qPCR data of a ?-proteobacterial phylotype, Gamma A (UMB), obtained during several research cruises. Our analysis revealed a complex diversity of diazotrophic ?-proteobacteria. One phylotype in particular, Gamma A, was described in several traditional and quantitative PCR studies. Though several ?-proteobacterial nifH sequences have been described as laboratory contaminants, Gamma A is part of a large cluster of sequences isolated from marine environments and distantly related to the clade of contaminants. Using a TaqMan probe and primer set, Gamma A nifH DNA abundance and expression were analyzed in nearly 1000 samples collected during 15 cruises to the Atlantic and Pacific Oceans. The data showed that Gamma A is an active, cosmopolitan diazotroph found throughout oxygenated, oligotrophic waters reaching maximum abundances of 8 x 104 nifH DNA copies l-1 and 5 x 105 nifH transcript copies l-1. Gamma A nifH transcript abundances were on average 3 fold higher than nifH DNA abundances. The widespread distribution and activity of Gamma A indicate that it has potential to be a globally important N2 fixing organism.

SUBMITTER: Langlois R

PROVIDER: S-EPMC4477881 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Widespread Distribution and Expression of Gamma A (UMB), an Uncultured, Diazotrophic, γ-Proteobacterial nifH Phylotype.

Langlois Rebecca R Großkopf Tobias T Mills Matthew M Takeda Shigenobu S LaRoche Julie J

PloS one 20150623 6

Marine dinitrogen (N2) fixation studies have focused nearly exclusively on cyanobacterial diazotrophs; however γ-proteobacteria are an abundant component of the marine community and have been largely overlooked until recently. Here we present a phylogenetic analysis of all nifH γ-proteobacterial sequences available in public databases and qPCR data of a γ-proteobacterial phylotype, Gamma A (UMB), obtained during several research cruises. Our analysis revealed a complex diversity of diazotrophic ...[more]

PMID: 26103055

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Project description:The Tropical North Atlantic (TNAtl) plays a critical role in the marine nitrogen cycle, as it supports high rates of biological nitrogen (N(2)) fixation, yet it is unclear whether this process is limited by the availability of iron (Fe), phosphate (P) or is co-limited by both. In order to investigate the impact of nutrient limitation on the N(2)-fixing microorganisms (diazotrophs) in the TNAtl, trace metal clean nutrient amendment experiments were conducted, and the expression of nitrogenase (nifH) in cyanobacterial diazotrophs in response to the addition of Fe, P, or Fe+P was measured using quantitative PCR. To provide context, N(2) fixation rates associated with the <10 ?m community and diel nifH expression in natural cyanobacterial populations were measured. In the western TNAtl, nifH expression in Crocosphaera, Trichodesmium, and Richelia was stimulated by Fe and Fe+P additions, but not by P, implying that diazotrophs may be Fe-limited in this region. In the eastern TNAtl, nifH expression in unicellular cyanobacteria UCYN-A and Crocosphaera was stimulated by P, implying P-limitation. In equatorial waters, nifH expression in Trichodesmium was highest in Fe+P treatments, implying co-limitation in this region. Nutrient additions did not measurably stimulate N(2) fixation rates in the <10 ?m fraction in most of the experiments, even when upregulation of nifH expression was evident. These results demonstrate the utility of using gene expression to investigate the physiological state of natural populations of microorganisms, while underscoring the complexity of nutrient limitation on diazotrophy, and providing evidence that diazotroph populations are slow to respond to the addition of limiting nutrients and may be limited by different nutrients on basin-wide spatial scales. This has important implications for our current understanding of controls on N(2) fixation in the TNAtl and may partially explain why it appears to be intermittently limited by Fe, P, or both.

Dataset Information

Widespread Distribution and Expression of Gamma A (UMB), an Uncultured, Diazotrophic, ?-Proteobacterial nifH Phylotype.

Publications

Widespread Distribution and Expression of Gamma A (UMB), an Uncultured, Diazotrophic, γ-Proteobacterial nifH Phylotype.

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