Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.

Arranging organisms into functional groups aids ecological research by grouping organisms (irrespective of phylogenetic origin) that interact with environmental factors in similar ways. Planktonic protists traditionally have been split between photoautotrophic "phytoplankton" and phagotrophic "microzooplankton". However, there is a growing recognition of the importance of mixotrophy in euphotic aquatic systems, where many protists often combine photoautotrophic and phagotrophic modes of nutrition. Such organisms do not align with the traditional dichotomy of phytoplankton and microzooplankton. To reflect this understanding, we propose a new functional grouping of planktonic protists in an eco-physiological context: (i) phagoheterotrophs lacking phototrophic capacity, (ii) photoautotrophs lacking phagotrophic capacity, (iii) constitutive mixotrophs (CMs) as phagotrophs with an inherent capacity for phototrophy, and (iv) non-constitutive mixotrophs (NCMs) that acquire their phototrophic capacity by ingesting specific (SNCM) or general non-specific (GNCM) prey. For the first time, we incorporate these functional groups within a foodweb structure and show, using model outputs, that there is scope for significant changes in trophic dynamics depending on the protist functional type description. Accordingly, to better reflect the role of mixotrophy, we recommend that as important tools for explanatory and predictive research, aquatic food-web and biogeochemical models need to redefine the protist groups within their frameworks.

We examined the fate of planktonic bacterial production and the balance between bacterial growth and grazing mortality in the surface waters of Upton Lake, New York. Growth rates were measured by the incorporation of t3H]thymidine into DNA. Grazing rates on bacteria were determined with small cells produced by a mutant strain ofEscherichia coli and made either fluorescent or radioactive to monitor feeding. Bacterial community turnover times calculated from either growth or grazing rates ranged from 1.5 to 16 d. On the basis of these data and results from 29 other studies, most bacterial communities appear to have turnover times substantially > 1 d. Our measurements of feeding rates on bacteria frequently exceeded estimates of growth. Limitations of precision and doubts about the accuracy of methods make attempts to balance measurements of bacterial growth and grazing with current techniques unrealistic. The fate of bacterial production depends on planktonic community structure. Flagellates were the primary consumers of bacteria in winter and fall. At other times, Daphnia galeata consumed most of the bacterial production. Ciliates and rotifers were never important bacterial grazers. In Upton Lake large populations of Daphnia effectively "break" the microbial loop and funnel bacterial production to higher consumers.

The incorporation of lipids into the copepod Acartia tonsa and its eggs was measured when it was fed either a bacterivorous ciliate (Pleuronema sp.) or a diatom (Thalassiosira weissfogii). Egg production was lo-fold higher on the diatom diet, whereas hatch success of eggs was the same for algal and ciliate diets. Adult copepods fed diatoms contained more total fatty acid and sterols than copepods fed the ciliate diet, and individual lipids reflected the dietary source. Eggs from diatom-fed copepods had fewer fatty acids but more sterols than eggs from copepods on a ciliate diet. Ciliate-fed copepods and their eggs contained significant amounts of odd chain-length and branched fatty acids diagnostic of bacteria. These fatty acids, in particular the iso C,, and C17, were also elevated in ciliates feeding on bacteria in culture, suggesting the direct transfer of bacterial fatty acids from ciliates to copepods and their eggs. We also observed the assimilation of tetrahymanol, a triterpenoid alcohol specific to ciliates, into adults and eggs when copepods were fed a ciliate diet. Tetrahymanol accounted for 6.6 + 1.9% of total neutral lipids in adults and 35.4 + 6.5% in eggs. These results suggest that bacterivorous ciliates may not provide copepods with adequate nutritional requirements for long-term survival, but that lipids unique to bacteria and ciliates can be assimilated by and may provide useful tracers of consumption by copepods.

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A variety of methods have been used to estimate the degree of control exercised upon marine bacterioplankton by grazing organisms. These include filtration or dilution of samples to reduce grazers, the use of specific inhibitors to prevent growth or grazing, and the use of artificial particles or radio-labelled bacteria as tracers for the natural bacterioplankton. Each of these techniques has drawbacks which may lead to under-or overestimates of grazing. In addition, they tell us little about which organisms are doing the grazing or the degree to which viruses or lytic bacteria compete with grazers for bacterial production.Because measurements of grazing and bacterioplankton growth rates are uncertain, exact comparisons are not presently possible. Thus measurements of bacterial and bacterivore abundance, concentrated on comparisons between seasons, on diel cycles and on spatial variations, have been used to evaluate mechanisms controlling bacterial populations. These give an idea of the degree of coupling between bacterial growth and bacterivore activity and of the time scales over which growth and grazing balance. Combined with laboratory studies of grazing, they currently provide the best insight into what controls populations of bacteria in the sea.

Up to 60 percent of the total marine primary production (or about one-fourth of the total global carbon dioxide fixation) passes through the free-living bacterioplankton. Grazing by bacteriovores is probably the predominant fate of the bacteria, although data are scarce. Evidence is presented that previously uncharacterized, small eukaryotes that are able to pass even 0.6-micrometer filters may be responsible for a large fraction (more than 50 percent) of the total grazing in coastal waters. These organisms have not yet been observed microscopically.