Marine N₂ fixing microorganisms, termed diazotrophs, are a key functional group in marine pelagic ecosystems. The biological fixation of dinitrogen (N₂) to bioavailable nitrogen provides an important new source of nitrogen for pelagic marine ecosystems and influences primary productivity and organic matter export to the deep ocean. As one of a series of efforts to collect biomass and rates specific to different phytoplankton functional groups, we have constructed a database on diazotrophic organisms in the global pelagic upper ocean by compiling about 12 000 direct field measurements of cyanobacterial diazotroph abundances (based on microscopic cell counts or qPCR assays targeting the nifH genes) and N₂ fixation rates. Biomass conversion factors are estimated based on cell sizes to convert abundance data to diazotrophic biomass. The database is limited spatially, lacking large regions of the ocean especially in the Indian Ocean. The data are approximately log-normal distributed, and large variances exist in most sub-databases with non-zero values differing 5 to 8 orders of magnitude. Reporting the geometric mean and the range of one geometric standard error below and above the geometric mean, the pelagic N₂ fixation rate in the global ocean is estimated to be 62 (52–73) Tg N yr⁻¹ and the pelagic diazotrophic biomass in the global ocean is estimated to be 2.1 (1.4–3.1) Tg C from cell counts and to 89 (43–150) Tg C from nifH-based abundances. Reporting the arithmetic mean and one standard error instead, these three global estimates are 140 ± 9.2 Tg N yr⁻¹, 18 ± 1.8 Tg C and 590 ± 70 Tg C, respectively. Uncertainties related to biomass conversion factors can change the estimate of geometric mean pelagic diazotrophic biomass in the global ocean by about ±70%. It was recently established that the most commonly applied method used to measure N₂ fixation has underestimated the true rates. As a result, one can expect that future rate measurements will shift the mean N₂ fixation rate upward and may result in significantly higher estimates for the global N₂ fixation. The evolving database can nevertheless be used to study spatial and temporal distributions and variations of marine N₂ fixation, to validate geochemical estimates and to parameterize and validate biogeochemical models, keeping in mind that future rate measurements may rise in the future. The database is stored in PANGAEA (doi:10.1594/PANGAEA.774851).

This paper reviews progress on understanding biological carbon sequestration in the ocean with special reference to the microbial formation and transformation of recalcitrant dissolved organic carbon (RDOC), the microbial carbon pump (MCP). We propose that RDOC is a concept with a wide continuum of recalcitrance. Most RDOC compounds maintain their levels of recalcitrance only in a specific environmental context (RDOC_t). The ocean RDOC pool also contains compounds that may be inaccessible to microbes due to their extremely low concentration (RDOC_c). This differentiation allows us to appreciate the linkage between microbial source and RDOC composition on a range of temporal and spatial scales. Analyses of biomarkers and isotopic records show intensive MCP processes in the Proterozoic oceans when the MCP could have played a significant role in regulating climate. Understanding the dynamics of the MCP in conjunction with the better constrained biological pump (BP) over geological timescales could help to predict future climate trends. Integration of the MCP and the BP will require new research approaches and opportunities. Major goals include understanding the interactions between particulate organic carbon (POC) and RDOC that contribute to sequestration efficiency, and the concurrent determination of the chemical composition of organic carbon, microbial community composition and enzymatic activity. Molecular biomarkers and isotopic tracers should be employed to link water column processes to sediment records, as well as to link present-day observations to paleo-evolution. Ecosystem models need to be developed based on empirical relationships derived from bioassay experiments and field investigations in order to predict the dynamics of carbon cycling along the stability continuum of POC and RDOC under potential global change scenarios. We propose that inorganic nutrient input to coastal waters may reduce the capacity for carbon sequestration as RDOC. The nutrient regime enabling maximum carbon storage from combined POC flux and RDOC formation should therefore be sought.

We present a summary of biomass data for 11 plankton functional types (PFTs) plus phytoplankton pigment data, compiled as part of the MARine Ecosystem biomass DATa (MAREDAT) initiative. The goal of the MAREDAT initiative is to provide, in due course, global gridded data products with coverage of all planktic components of the global ocean ecosystem. This special issue is the first step towards achieving this. The PFTs presented here include picophytoplankton, diazotrophs, coccolithophores, Phaeocystis, diatoms, picoheterotrophs, microzooplankton, foraminifers, mesozooplankton, pteropods and macrozooplankton. All variables have been gridded onto a World Ocean Atlas (WOA) grid (1° × 1° × 33 vertical levels × monthly climatologies). The results show that abundance is much better constrained than their carbon content/elemental composition, and coastal seas and other high productivity regions have much better coverage than the much larger volumes where biomass is relatively low. The data show that (1) the global total heterotrophic biomass (2.0–4.6 Pg C) is at least as high as the total autotrophic biomass (0.5–2.4 Pg C excluding nanophytoplankton and autotrophic dinoflagellates); (2) the biomass of zooplankton calcifiers (0.03–0.67 Pg C) is substantially higher than that of coccolithophores (0.001–0.03 Pg C); (3) patchiness of biomass distribution increases with organism size; and (4) although zooplankton biomass measurements below 200 m are rare, the limited measurements available suggest that Bacteria and Archaea are not the only important heterotrophs in the deep sea. More data will be needed to characterise ocean ecosystem functioning and associated biogeochemistry in the Southern Hemisphere and below 200 m. Future efforts to understand marine ecosystem composition and functioning will be helped both by further archiving of historical data and future sampling at new locations. Microzooplankton database: doi:10.1594/PANGAEA.779970 All MAREDAT databases: http://www.pangaea.de/search?&q=maredat

We characterize the realized ecological niches of 133 phytoplankton taxa in the open ocean based on observations from the MAREDAT initiative and a statistical species distribution model (MaxEnt). The models find that the physical conditions (mixed layer depth, temperature, light) govern large‐scale patterns in phytoplankton biogeography over nutrient availability. Strongest differences in the realized niche centers were found between diatoms and coccolithophores. Diatoms (87 species) occur in habitats with significantly lower temperatures, light intensity and salinity, with deeper mixed layers, and with higher nitrate and silicate concentrations than coccolithophores (40 species). However, we could not statistically separate the realized niches of coccolithophores from those of diazotrophs (two genera) and picophytoplankton (two genera). Phaeocystis (two species) niches only clearly differed from diatom niches for temperature. While the realized niches of diatoms cover the majority of niche space, the niches of picophytoplankton and coccolithophores spread across an intermediate fraction and diazotroph and colonial Phaeocystis niches only occur within a relatively confined range of environmental conditions in the open ocean. Our estimates of the realized niches roughly match the predictions of Reynolds' C‐S‐R model for the global ocean, namely that taxa classified as nutrient stress tolerant have niches at lower nutrient and higher irradiance conditions than light stress tolerant taxa. Yet, there is considerable within‐class variability in niche centers, and many taxa occupy broad niches, suggesting that more complex approaches may be necessary to capture all aspects of phytoplankton ecology.

A future, more acidic ocean could be less productive, despite the fertilizing effects of elevated CO₂.