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Open AccessJournal ArticleDOI

Plankton networks driving carbon export in the oligotrophic ocean.

TLDR
It is shown that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.
Abstract
The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

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mixOmics: An R package for 'omics feature selection and multiple data integration

TL;DR: MixOmics is introduced, an R package dedicated to the multivariate analysis of biological data sets with a specific focus on data exploration, dimension reduction and visualisation and extends Projection to Latent Structure models for discriminant analysis.
Journal ArticleDOI

Scientists' Warning to Humanity: Microorganisms and Climate Change

Ricardo Cavicchioli, +34 more
TL;DR: This Consensus Statement documents the central role and global importance of microorganisms in climate change biology and puts humanity on notice that the impact of climate change will depend heavily on responses of micro organisms, which are essential for achieving an environmentally sustainable future.
Journal ArticleDOI

Marine DNA Viral Macro- and Microdiversity from Pole to Pole.

TL;DR: An ∼12-fold expanded global ocean DNA virome dataset is established of 195,728 viral populations, now including the Arctic Ocean, and it is validated that these populations form discrete genotypic clusters.
Journal ArticleDOI

Phage Puppet Masters of the Marine Microbial Realm

TL;DR: The ‘royal family model’ is proposed as a hypothesis to describe successional patterns of bacteria and phages over time in marine systems, where despite high richness and significant seasonal differences, only a small number of phages appear to continually dominate a given marine ecosystem.
References
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Journal ArticleDOI

Fast gapped-read alignment with Bowtie 2

TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar
- 01 Oct 2010 - 
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Journal ArticleDOI

WGCNA: an R package for weighted correlation network analysis.

TL;DR: The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis that includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software.
Journal ArticleDOI

Primary Production of the Biosphere: Integrating Terrestrial and Oceanic Components

TL;DR: Integrating conceptually similar models of the growth of marine and terrestrial primary producers yielded an estimated global net primary production of 104.9 petagrams of carbon per year, with roughly equal contributions from land and oceans.
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