Dataset Information

Aphotic N2 fixation in the Eastern Tropical South Pacific Ocean.

ABSTRACT: We examined rates of N2 fixation from the surface to 2000 m depth in the Eastern Tropical South Pacific (ETSP) during El Niño (2010) and La Niña (2011). Replicated vertical profiles performed under oxygen-free conditions show that N2 fixation takes place both in euphotic and aphotic waters, with rates reaching 155 to 509 µmol N m(-2) d(-1) in 2010 and 24±14 to 118±87 µmol N m(-2) d(-1) in 2011. In the aphotic layers, volumetric N2 fixation rates were relatively low (<1.00 nmol N L(-1) d(-1)), but when integrated over the whole aphotic layer, they accounted for 87-90% of total rates (euphotic+aphotic) for the two cruises. Phylogenetic studies performed in microcosms experiments confirm the presence of diazotrophs in the deep waters of the Oxygen Minimum Zone (OMZ), which were comprised of non-cyanobacterial diazotrophs affiliated with nifH clusters 1K (predominantly comprised of ?-proteobacteria), 1G (predominantly comprised of ?-proteobacteria), and 3 (sulfate reducing genera of the ?-proteobacteria and Clostridium spp., Vibrio spp.). Organic and inorganic nutrient addition bioassays revealed that amino acids significantly stimulated N2 fixation in the core of the OMZ at all stations tested and as did simple carbohydrates at stations located nearest the coast of Peru/Chile. The episodic supply of these substrates from upper layers are hypothesized to explain the observed variability of N2 fixation in the ETSP.

SUBMITTER: Bonnet S

PROVIDER: S-EPMC3861260 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Aphotic N2 fixation in the Eastern Tropical South Pacific Ocean.

Bonnet Sophie S Dekaezemacker Julien J Turk-Kubo Kendra A KA Moutin Thierry T Hamersley Robert M RM Grosso Olivier O Zehr Jonathan P JP Capone Douglas G DG

PloS one 20131212 12

We examined rates of N2 fixation from the surface to 2000 m depth in the Eastern Tropical South Pacific (ETSP) during El Niño (2010) and La Niña (2011). Replicated vertical profiles performed under oxygen-free conditions show that N2 fixation takes place both in euphotic and aphotic waters, with rates reaching 155 to 509 µmol N m(-2) d(-1) in 2010 and 24±14 to 118±87 µmol N m(-2) d(-1) in 2011. In the aphotic layers, volumetric N2 fixation rates were relatively low (<1.00 nmol N L(-1) d(-1)), bu ...[more]

PMID: 24349048

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Project description:The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed "fragment recruitment," addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed "extreme assembly," made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.

Dataset Information

Aphotic N2 fixation in the Eastern Tropical South Pacific Ocean.

Publications

Aphotic N2 fixation in the Eastern Tropical South Pacific Ocean.

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