Molecular evidence for zooplankton-associated nitrogen-fixing anaerobes based on amplification of the nifH gene

Braun, Sarah; Proctor, Lita M.; Zani, Sabino; Mellon, Mark T.; Zehr, Jonathan P.

doi:10.1111/j.1574-6941.1999.tb00582.x

Cited by 90 publications

(23 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The presence of nifH sequences related to anaerobic microorganisms suggests that anoxic microsites exist in the oxygenated water column. It has been suggested that these bacteria thrive on particles or in association with zooplankton [9], [41], [45], [58]. However, their presence in prefiltered surface samples (Sargasso DNA2; [24], [41]) as well indicates that they may be facultative anaerobes thriving even in the fully oxygenated free-living phase.…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2011

View full text Add to dashboard Cite

Cyanobacteria are thought to be the main N2-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 N2 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.

show abstract

Section: Resultsmentioning

confidence: 99%

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

et al. 2011

View full text Add to dashboard Cite

show abstract

“…Potential sources of hydrogen in the ocean photic zone include photochemical reactions [27], algal metabolism [28], and heterotroph activity in anoxic microenvironments [29]. Hydrogenase-like genes are also harbored by the marine plankton Roseobacter clade isolates Roseovarius sp.…”

Section: Resultsmentioning

confidence: 99%

Assembling the Marine Metagenome, One Cell at a Time

et al. 2009

View full text Add to dashboard Cite

The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms. We employed fluorescence-activated cell sorting and multiple displacement amplification to obtain hundreds of micrograms of genomic DNA from individual, uncultured cells of two marine flavobacteria from the Gulf of Maine that were phylogenetically distant from existing cultured strains. Shotgun sequencing and genome finishing yielded 1.9 Mbp in 17 contigs and 1.5 Mbp in 21 contigs for the two flavobacteria, with estimated genome recoveries of about 91% and 78%, respectively. Only 0.24% of the assembling sequences were contaminants and were removed from further analysis using rigorous quality control. In contrast to all cultured strains of marine flavobacteria, the two single cell genomes were excellent Global Ocean Sampling (GOS) metagenome fragment recruiters, demonstrating their numerical significance in the ocean. The geographic distribution of GOS recruits along the Northwest Atlantic coast coincided with ocean surface currents. Metabolic reconstruction indicated diverse potential energy sources, including biopolymer degradation, proteorhodopsin photometabolism, and hydrogen oxidation. Compared to cultured relatives, the two uncultured flavobacteria have small genome sizes, few non-coding nucleotides, and few paralogous genes, suggesting adaptations to narrow ecological niches. These features may have contributed to the abundance of the two taxa in specific regions of the ocean, and may have hindered their cultivation. We demonstrate the power of single cell DNA sequencing to generate reference genomes of uncultured taxa from a complex microbial community of marine bacterioplankton. A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa.

show abstract

“…The relatively large energy demands associated with N 2 fixation appear to have largely relegated this process to phototrophic microorganisms found in the well-lit regions of the upper ocean. However, several Gammaproteobacteria and Alphaproteobacteria, as well as several presumed anaerobic bacteria, appear to have the capability of fixing N 2 in the open ocean (Zehr et al 1998;Braun et al 1999;Church et al 2005), although the potential importance of heterotrophic N 2 fixation remains unknown.…”

Section: Nitrogenmentioning

confidence: 99%