The biological pump is a process whereby CO(2) in the upper ocean is fixed by primary producers and transported to the deep ocean as sinking biogenic particles or as dissolved organic matter. The fate of most of this exported material is remineralization to CO(2), which accumulates in deep waters until it is eventually ventilated again at the sea surface. However, a proportion of the fixed carbon is not mineralized but is instead stored for millennia as recalcitrant dissolved organic matter. The processes and mechanisms involved in the generation of this large carbon reservoir are poorly understood. Here, we propose the microbial carbon pump as a conceptual framework to address this important, multifaceted biogeochemical problem.

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This paper presents standards and best practices for reporting genome sequences of uncultivated viruses.Supplementary informationThe online version of this article (doi:10.1038/nbt.4306) contains supplementary material, which is available to authorized users.

This review summarizes the present state of knowledge regarding the toxic, bloom-forming cyanobacterium, Microcystis, with a specific focus on its geographic distribution, toxins, genomics, phylogeny, and ecology. A global analysis found documentation suggesting geographic expansion of Microcystis, with recorded blooms in at least 108 countries, 79 of which have also reported the hepatatoxin microcystin. The production of microcystins (originally "Fast-Death Factor") by Microcystis and factors that control synthesis of this toxin are reviewed, as well as the putative ecophysiological roles of this metabolite. Molecular biological analyses have provided significant insight into the ecology and physiology of Microcystis, as well as revealed the highly dynamic, and potentially unstable, nature of its genome. A genetic sequence analysis of 27 Microcystis species, including 15 complete/draft genomes are presented. Using the strictest biological definition of what constitutes a bacterial species, these analyses indicate that all Microcystis species warrant placement into the same species complex since the average nucleotide identity values were above 95%, 16S rRNA nucleotide identity scores exceeded 99%, and DNA-DNA hybridization was consistently greater than 70%. The review further provides evidence from around the globe for the key role that both nitrogen and phosphorus play in controlling Microcystis bloom dynamics, and the effect of elevated temperature on bloom intensification. Finally, highlighted is the ability of Microcystis assemblages to minimize their mortality losses by resisting grazing by zooplankton and bivalves, as well as viral lysis, and discuss factors facilitating assemblage resilience.

Preventing harmful algal blooms (HABs) is needed to protect lakes and downstream ecosystems. Traditionally, reducing phosphorus (P) inputs was the prescribed solution for lakes, based on the assumption that P universally limits HAB formation. Reduction of P inputs has decreased HABs in many lakes, but was not successful in others. Thus, the "P-only" paradigm is overgeneralized. Whole-lake experiments indicate that HABs are often stimulated more by combined P and nitrogen (N) enrichment rather than N or P alone, indicating that the dynamics of both nutrients are important for HAB control. The changing paradigm from P-only to consideration of dual nutrient control is supported by studies indicating that (1) biological N fixation cannot always meet lake ecosystem N needs, and (2) that anthropogenic N and P loading has increased dramatically in recent decades. Sediment P accumulation supports long-term internal loading, while N may escape via denitrification, leading to perpetual N deficits. Hence, controlling both N and P inputs will help control HABs in some lakes and also reduce N export to downstream N-sensitive ecosystems. Managers should consider whether balanced control of N and P will most effectively reduce HABs along the freshwater-marine continuum.