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Institution

Bedford Institute of Oceanography

FacilityDartmouth, Nova Scotia, Canada
About: Bedford Institute of Oceanography is a facility organization based out in Dartmouth, Nova Scotia, Canada. It is known for research contribution in the topics: Population & Arctic. The organization has 1782 authors who have published 3741 publications receiving 172740 citations. The organization is also known as: BIO.


Papers
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Journal ArticleDOI
TL;DR: 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, which yielded an extensive dataset consisting of 7.7 million sequencing reads.
Abstract: 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.

1,982 citations

Journal ArticleDOI
TL;DR: Eight different mathematical formulations of the photosynthesis—light curve for phytoplankton were recast in terms of the same two parameters: the initial slope α, and the assimilation number PmB.
Abstract: Eight different mathematical formulations of the photosynthesis—light curve for phytoplankton (up to and including light saturation) were recast in terms of the same two parameters: the initial slope α, and the assimilation number PmB. Each equation was tested for its ability to describe empirical data from natural populations of marine phytoplankton: the results of 188 light-saturation experiments at three coastal locations in Nova Scotia over a 2-year period. The most consistently useful mathematical representation of the data was found to be the hyperbolic tangent function.

1,952 citations

Journal ArticleDOI
TL;DR: This review highlights the best available methods for insuring ageing accuracy and quantifying ageing precision, whether in support of large-scale production ageing or a small-scale research project.
Abstract: Many calcified structures produce periodic growth increments useful for age determination at the annual or daily scale. However, age determination is invariably accompanied by various sources of error, some of which can have a serious effect on age-structured calculations. This review highlights the best available methods for insuring ageing accuracy and quantifying ageing precision, whether in support of large-scale production ageing or a small-scale research project. Included in this review is a critical overview of methods used to initiate and pursue an accurate and controlled ageing program, including (but not limited to) validation of an ageing method. The distinction between validation of absolute age and increment periodicity is emphasized, as is the importance of determining the age of first increment formation. Based on an analysis of 372 papers reporting age validation since 1983, considerable progress has been made in age validation efforts in recent years. Nevertheless, several of the age validation methods which have been used routinely are of dubious value, particularly marginal increment analysis. The two major measures of precision, average percent error and coefficient of variation, are shown to be functionally equivalent, and a conversion factor relating the two is presented. Through use of quality control monitoring, ageing errors are readily detected and quantified; reference collections are the key to both quality control and reduction of costs. Although some level of random ageing error is unavoidable, such error can often be corrected after the fact using statistical (‘digital sharpening)’ methods.

1,842 citations

Journal ArticleDOI
TL;DR: This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists, and proposes a scheme that is based on nameless ranked systematics.
Abstract: This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional ''kingdoms.'' The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.

1,620 citations

Journal ArticleDOI
TL;DR: A detailed description of the techniques and analytical procedures for sampling, grain size determinations, and for precise and accurate AAS determination of the major and trace metals in marine sediments and suspended particulate matter is given in this paper.

1,307 citations


Authors

Showing all 1790 results

NameH-indexPapersCitations
David M. Karl11246148702
Thomas F. Stocker9937558271
R. Lawrence Edwards8639050047
Robie W. Macdonald7929223460
Trevor Platt7728526220
Daniel Vaulot7619220464
Leonard A. Barrie7417717356
James P. M. Syvitski7430428538
Jeffrey A. Hutchings6823018211
John C. Beier6530914184
Steven E. Campana6518818404
Shubha Sathyendranath6424618141
Richard J. Geider6414818910
William C. Leggett6418613134
David J.W. Piper6036411711
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Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
20234
202214
2021129
2020136
2019139
201891