Environmental Microbiology Reports (2017) 9(1), 41–43 doi:10.1111/1758-2229.12514 Acknowledging and incorporating mixed nutrition into aquatic protistan ecology, finally David A. Caron*, Department of Biological Sciences, organelles from their prey). These species (e.g. many University of Southern California, 3616 Trousdale dinoflagellates and ciliates) possess ‘acquired phototro- Parkway, Los Angeles, CA, 90089-0371, USA phy’ as a consequence of chloroplast retention. They can be generalists, consuming and acquiring chloro- We often instinctively think of life on our planet being plasts from a variety of algal prey, or highly specialized composed of species capable of obtaining the organic in their preferred prey. Finally, numerous physically- matter and energy they need for growth from inorganic intimate, often-mutualistic associations exist between compounds (autotrophy) or species that utilize pre- heterotrophic protistan species and intact photosynthetic formed organic matter produced by autotrophs to meet algae or cyanobacteria that are generally now included their energy and carbon needs (heterotrophy). This is under the broad definition of mixotrophy. These associa- particularly true for terrestrial, macroscopic life forms, tions constitute efficient and productive relationships in where there exists an obvious dichotomy between most which feeding and nutrient remineralization by the het- phototrophs (plants) and heterotrophs (animals, fungi). erotrophic host support photosynthesis and growth of That perspective was also extrapolated to single-celled the symbionts which in turn contribute to host nutrition. eukaryotic organisms (the protists) many years ago as These associations (holobionts) have been described for one way of organizing the enormous diversity that exists well over a century for the larger Rhizaria (e.g. foraminif- among those species (Whittaker, 1969). That description era and radiolaria) (Haeckel, 1887) but they also exist was somewhat justified at the time by the fact that many among other protistan phyla such as the ciliates, includ- protists exhibit either phototrophic nutrition (microalgae,) ing the ciliate-symbiont model system of Paramecium- or heterotrophic nutrition (protozoa), and as a practical Chlorella (Brown and Nielson, 1974). way to organize the enormous diversity of species within Given that mixotrophic nutrition and the organisms the kingdom Protista. However, recent phylogenies that that conduct it have been known for quite some time, have been proposed for the domain Eukarya (Burki, why is this subject only now receiving attention by a 2014) recognize that photosynthetic and heterotrophic broad audience of aquatic microbiologists? One reason ability are not always phylogenetically informative, and is that only recently have the three general categories of often not mutually exclusive behaviors. Many, perhaps mixotrophy noted above been formally defined (Mitra even a dominant proportion of protists, it turns out, et al., 2016). Additionally, new information now appear- exhibit some combination of these nutritional modes (an ing in the literature indicates that we may have grossly ability generally referred to as mixotrophy). underestimated the collective abundances of these spe- Mixotrophic protists occur throughout the eukaryotic cies in aquatic ecosystems, and therefore poorly charac- tree of life although, functionally, most of these species terized their impacts on food web structure and function can be grouped into one of three general behavioral cat- in the plankton. Evidence over the last few years has egories (Mitra et al., 2016; Stoecker et al., 2016). Firstly, indicated substantial abundances of phagotrophic phyto- phagotrophic phytoflagellates are species that possess flagellates in the ocean (Unrein et al., 2014). The inges- chloroplasts but also engulf and digest small prey such tion of prey by these algae may provide them with a as bacteria and cyanobacteria by phagocytosis. We mechanism for obtaining vital nutrients for photosynthe- have long been aware that species within several algal sis, relative to algae that do not possess phagotrophic classes exhibit this behavior (Porter, 1988). Secondly, ability. If so, mixotrophy bestows an ecological advan- kleptoplastidic protists are heterotrophic species that tage in low-nutrient environments, and implicates those feed on algae, partially digest them, but retain their algae as a significant source of bacterial mortality in the chloroplasts in a functional state (and occasionally other plankton (overlapping with the ecological role attributed to small heterotrophic protists). Mixotrophic algae are also widespread in many freshwater ecosystems, although a clear generality across all freshwater ecosys- *For correspondence. E-mail [email protected]. tems is not yet possible because of the vast number of VC 2016 Society for Applied Microbiology and John Wiley & Sons Ltd 42 Crystal ball those environments and the limited number of studies mixotrophic species. How are photosynthetic and hetero- that have been conducted to date. For their part, klepto- trophic processes regulated within single-celled phago- plastidic ciliates and dinoflagellates are typically a signifi- trophic phytoflagellates? How does prey availability cant, and sometimes dominant portion of the affect cellular metabolism in those species? How are microzooplankton in planktonic ecosystem (Stoecker prey chloroplasts stabilized and controlled in the host et al., 1987; Stoecker, 1999). Photosynthesis by the cytoplasm of kleptoplastidic heterotrophic protists? How acquired chloroplasts of these species increases the are endosymbionts captured, recognized and maintained efficiency of trophic transfer of carbon and nutrients in at the molecular level in symbiont-bearing protists? the plankton (Stoecker, 1998). Finally, recent publica- Genetic approaches to answer these questions are at tions from a global ocean survey indicate a much great- the forefront. Such studies are identifying changes in er contribution of large, symbiont-bearing Rhizaria to gene expression that accompany shifts in the nutritional plankton communities in oceanic ecosystems (Biard mode of mixotrophic algae (Liu et al., 2015), transcrip- et al., 2016). These beautiful and delicate associations tional activity of chloroplasts in kleptoplastidic ciliates constitute microhabitats of high rates of photosynthesis, (Johnson et al., 2007), and the molecular signaling that and the hosts are also important generalist consumers takes place between heterotrophic hosts and symbiotic in the oceanic plankton (Caron and Swanberg, 1990). algae in the establishment of mutualistic associations Another reason for the recent upsurgence in scientific (Balzano et al., 2015). At present, such applications interest in mixotrophic protists is that global biogeo- make use primarily of transcriptomics because of the chemical models of the ocean still do not have the pre- daunting size of eukaryotic genomes, but genome dictive accuracy that we desire and need for the sequencing of microbial eukaryotes (including mixotro- climatological challenges of the coming decades. The phic species) is rapidly becoming economically feasible. limitations of these models are certainly not solely a Functional genomics, enabled by sequenced genomes, consequence of the fact that they lack mixotrophic will greatly expand the investigative tools available for behavior. However, some prescient work on this topic understanding the physiology of mixotrophic protists. has shown that the incorporation of even a highly simpli- The ‘end game’ of understanding and incorporating fied form of mixotrophy into biogeochemical models mixotrophy into the paradigm of the microbial food web changes modeled outcomes. It increases the transfer of will not be realized in the near future, of course, but it is carbon to higher trophic levels, and the sinking of par- at least entrenched in the minds of more researchers ticles (Mitra et al., 2014; Ward and Follows, 2016). Such these days. Full acknowledgment of the importance of findings, if substantiated with further study and complex- this behavior, and incorporation into biogeochemical mod- ity, have important implications for a variety of ocean els will entail an accurate determination of the contribution processes ranging from fisheries biology to removing of mixotroph abundances and biomass, their impact on carbon from surface waters of the ocean (the so-called energy flow, organic carbon production and utilization, and ‘biological carbon pump’). nutrient cycling. Given its ubiquitous occurrence and I suggest that the time is overdue to address the glar- important ecological consequences, the continued ing omission of mixed nutrition among protists in our col- absence of mixed nutrition in our conceptualization of lective scientific psyche regarding plankton food web aquatic food webs seems unwarranted and unwise. Much structure and, moreover, that we are uniquely poised to work remains on properly defining and parameterizing do so at this time. Recent decades of field and culture these plankton categories, but I predict (and hope) that studies have opened our eyes to the tremendous diver- sity of these species, yielded some insights into their will change radically within the next decade. physiological abilities, and outlined the potential ecologi- Acknowledgements cal consequences of mixotrophic nutrition. Cutting-edge approaches and techniques are now enabling new ways This work was supported in part