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.

/pdf/the-sorcerer-ii-global-ocean-sampling-expedition-northwest-310cgsz0o9.pdf

The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific

http://people.rses.anu.edu.au/lambeck_k/pdf/230.pdf

Sea-level and deep water temperature changes derived from benthic foraminifera isotopic records

Global observations of nonlinear mesoscale eddies

/pdf/climate-models-and-their-evaluation-3l7t3uekup.pdf

Climate models and their evaluation

Salinity stratification is critical to the vertical circulation of the high-latitude ocean. We here examine the control of the vertical circulation in the northern seas, and the potential for altering it, by considering the budgets and storage of fresh water in the Arctic Ocean and in the convective regions to the south. We find that the present-day Greenland and Iceland seas, and probably also the Labrador Sea, are rather delicately poised with respect to their ability to sustain convection. Small variations in the fresh water supplied to the convective gyres from the Arctic Ocean via the East Greenland Current can alter or stop the convection in what may be a modern analog to the halocline catastrophes proposed for the distant past. The North Atlantic salinity anomaly of the 1960s and 1970s is a recent example; it must have had its origin in an increased fresh water discharge from the Arctic Ocean. Similarly, the freshening and cooling of the deep North Atlantic in recent years is a likely manifestation of the increased transfer of fresh water from the Arctic Ocean into the convective gyres. Finally, we note that because of the temperature dependence of compressibility, a slight salinity stratification in the convective gyres is required to efficiently ventilate the deep ocean.

Glavnoe upravlenie navigat︠s︡ii i okeanografii Ministerstva oborony Sssr

Papers

World ocean atlas

Атлас океанов = Atlas of the oceans