A primary aim of microbial ecology is to determine patterns and drivers of community distribution, interaction, and assembly amidst complexity and uncertainty. Microbial community composition has been shown to change across gradients of environment, geographic distance, salinity, temperature, oxygen, nutrients, pH, day length, and biotic factors 1-6 . These patterns have been identified mostly by focusing on one sample type and region at a time, with insights extra polated across environments and geography to produce generalized principles. To assess how microbes are distributed across environments globally-or whether microbial community dynamics follow funda mental ecological 'laws' at a planetary scale-requires either a massive monolithic cross environment survey or a practical methodology for coordinating many independent surveys. New studies of microbial environments are rapidly accumulating; however, our ability to extract meaningful information from across datasets is outstripped by the rate of data generation. Previous meta analyses have suggested robust gen eral trends in community composition, including the importance of salinity 1 and animal association 2 . These findings, although derived from relatively small and uncontrolled sample sets, support the util ity of meta analysis to reveal basic patterns of microbial diversity and suggest that a scalable and accessible analytical framework is needed.The Earth Microbiome Project (EMP, http://www.earthmicrobiome. org) was founded in 2010 to sample the Earth's microbial communities at an unprecedented scale in order to advance our understanding of the organizing biogeographic principles that govern microbial commu nity structure 7,8 . We recognized that open and collaborative science, including scientific crowdsourcing and standardized methods 8 , would help to reduce technical variation among individual studies, which can overwhelm biological variation and make general trends difficult to detect 9 . Comprising around 100 studies, over half of which have yielded peer reviewed publications (Supplementary Table 1), the EMP has now dwarfed by 100 fold the sampling and sequencing depth of earlier meta analysis efforts 1,2 ; concurrently, powerful analysis tools have been developed, opening a new and larger window into the distri bution of microbial diversity on Earth. In establishing a scalable frame work to catalogue microbiota globally, we provide both a resource for the exploration of myriad questions and a starting point for the guided acquisition of new data to answer them. As an example of using this Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of r...

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The biogeochemical properties of an extensive bloom (∼250,000 km2) of the coccolithophore, Emiliania huxleyi, in the north east Atlantic Ocean were investigated in June 1991. Satellite (NOAA‐AVHRR) imagery showed that the bloom was centered initially at 60°–63°N by 13°–28°W and lasted approximately 3 weeks. Spatial variations in satellite‐measured reflectance were well correlated with surface measurements of the beam attenuation coefficient, levels of particulate inorganic carbon, and coccolith density. Rates of both photosynthesis and calcification were typically relatively low within the coccolithophore‐rich waters, suggesting the population was in a late stage of development at the time of the field observations. Levels of dimethyl sulphide (DMS) in surface waters were high compared to average ocean values, with the greatest concentrations in localized areas characterized by relatively high rates of photosynthesis, calcification, and grazing by microzooplankton. The estimated spatially averaged flux of DMS to the atmosphere was 1122 nmol m−2 h−1, somewhat greater than that determined for the same region in June‐July 1987. Coccolith production (1 × 106 tonnes calcite‐C) had a significant impact on the state of the CO2 system, causing relative increases of up to 50 μatm in surface pCO2 in association with alkalinity and water temperature changes. Gradients in pCO2 were as great as 100 μatm over horizontal distances of 20–40 km. The environmental implications of these findings are discussed in relation to the spatial and temporal distributions of E. huxleyi.

a b s t r a c tMetabolic activity in the water column below the euphotic zone is ultimately fuelled by the vertical flux of organic material from the surface. Over time, the deep ocean is presumably at steady state, with sources and sinks balanced. But recently compiled global budgets and intensive local field studies suggest that estimates of metabolic activity in the dark ocean exceed the influx of organic substrates. This imbalance indicates either the existence of unaccounted sources of organic carbon or that metabolic activity in the dark ocean is being over-estimated. Budgets of organic carbon flux and metabolic activity in the dark ocean have uncertainties associated with environmental variability, measurement capabilities, conversion parameters, and processes that are not well sampled. We present these issues and quantify associated uncertainties where possible, using a Monte Carlo analysis of a published data set to determine the probability that the imbalance can be explained purely by uncertainties in measurements and conversion factors. A sensitivity analysis demonstrates that the bacterial growth efficiencies and assumed cell carbon contents have the greatest effects on the magnitude of the carbon imbalance. Two poorly quantified sources, lateral advection of particles and a population of slowly settling particles, are discussed as providing a means of closing regional carbon budgets. Finally, we make recommendations concerning future research directions to reduce important uncertainties and allow a better determination of the magnitude and causes of the unbalanced carbon budgets.

OutlineThis chapter reviews the current state of knowledge of the process and measurement of microplankton respiration in marine surface waters. The principal approaches are outlined and their potentials and limitations discussed. A global database, containing 1662 observations has been compiled and analyzed for the spatial and temporal distribution of surface water respiration. The database is tiny compared to that of photosynthesis and biased with respect to season, latitude, community structure, and depth. Measurements and models show that the major portions of respiration lies in that attributable to bacteria (12-59%) and to algae A global estimate of 13.5 Pmol O 2 a −1 is derived from the mean depth-integrated rate, which significantly exceeds contemporary estimates of ocean plankton production (2.3-4.3 Pmol O 2 a −1 ). This difference is at variance with the results of mass-balance calculations, which suggest a small difference (ca. 0.18) between oceanic production and respiration. The reasons for this are discussed. IntroductionThis chapter reviews our present understanding of the process of marine planktonic respiration, and the methodologies used for its determination. We collate the global database of measured respiration and use it to assess how far we can determine seasonal, regional, and latitudinal patterns of distribution. Measurements of respiration are not yet routine within national and international marine biogeochemical programs. A significant relationship between respiration and more routinely measured parameters would substantially progress our ability to determine its spatial and temporal variability. We investigate whether such a relationship exists. Linked to this is the importance of an appreciation of the distribution of respiration within the microbial food web, and so improved food web model parameterization and verification. When considered on comparable time and space scales, the balance between plankton respiration and photosynthesis indicates the potential amount of photosynthetically fixed carbon available for export from the upper mixed layer. We assume that the epipelagic zone of the open oceans approaches this ideal, and analyze the distributions of respiration and photosynthesis in order to assess the global balance between photosynthesis and respiration. Available approaches and their constraintsRates of planktonic respiration can be derived in a number of ways: (i) from the measurement of the rate of production/consumption of a product 147