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.

Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physicochemical observations. Samples and observations were collected monthly over 3 years at a welldescribed ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. Negative correlations, perhaps suggesting competition or predation, were also common. The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism. Possible 'keystone' species were evident. The network has statistical features similar to previously described ecological networks, and in network parlance has non-random, small world properties (that is, highly interconnected nodes). This approach provides new insights into the natural history of microbes.

Natural assemblages of marine bacteria were cultured on combinations of C and N sources (amino acids, glucose, and NH,') to span a range of substrate C: N ratios from 1.5 : 1 to 10 : 1.

Mixotrophs are important components of the bacterioplankton, phytoplankton, microzooplankton, and (sometimes) zooplankton in coastal and oceanic waters. Bacterivory among the phytoplankton may be important for alleviating inorganic nutrient stress and may increase primary production in oligotrophic waters. Mixotrophic phytoflagellates and dinoflagellates are often dominant components of the plankton during seasonal stratification. Many of the microzooplankton grazers, including ciliates and Rhizaria, are mixotrophic owing to their retention of functional algal organelles or maintenance of algal endosymbionts. Phototrophy among the microzooplankton may increase gross growth efficiency and carbon transfer through the microzooplankton to higher trophic levels. Characteristic assemblages of mixotrophs are associated with warm, temperate, and cold seas and with stratification, fronts, and upwelling zones. Modeling has indicated that mixotrophy has a profound impact on marine planktonic ecosystems and may enhance primary production, biomass transfer to higher trophic levels, and the functioning of the biological carbon pump.

Literature review and synthesis of growth rates of aquatic protists focused on the role of temperature in the formation of massive annual algal blooms in high-latitude ecosystems. Maximal growth rates of herbivorous protists equaled or exceeded maximal growth rates of phototrophic protists at temperatures above 15uC. Maximal growth rates of herbivorous protists declined more rapidly with decreasing temperature than did those of phototrophic protists, and at the very low temperatures common to high-latitude ecosystems, the maximal growth rates of herbivorous protists were less than half the maximal growth rates of phototrophic protists. Growth rates of herbivorous protists were consistently lower than those of bacterivorous protists and were unrelated to differences in cell volume between the two groups. Linear equations describing the relationship of the natural log of maximal growth rates of bacterivorous and herbivorous protists to temperature were generated and compared to published information for maximal growth rates of phototrophic protists and copepods. The three heterotrophic groups had similar slopes (0.12 for bacterivorous protists, 0.10 for herbivorous protists, and 0.13 for copepods) that were approximately double that of phototrophic protists (0.06). The massive annual algal blooms observed in high latitudes are due in part to a fundamental difference in the relationship between growth and temperature for phototrophic protists and their grazers.