Exploring the oceanic microeukaryotic interactome with metaomics approaches

Abstract

THE MICROBIAL OCEANOur collective awareness of the significance of marine ecosystems has increased steadily during the last 40 yr, progressing in concert with the development of new technologies that have allowed us to dig deeper into the microbial world. A number of key events can be identified from this period, for example the formulation of the microbial-loop concept, the discovery of abundant photoautotrophic (Synechococcus and Prochlorococcus) and heterotrophic (SAR11) pico-sized prokaryotic plankton as well as novel lineages of heterotrophic picoeukaryotes (e.g. MALV and MAST), the recognition of the importance of Archaea in oceanic plankton, the realization that the majority of marine microbes cannot be cultured, the discovery of the rare biosphere and the key role of viruses in oceanic communities (Kirchman 2008 ABSTRACT: Biological communities are systems composed of many interacting parts (species, populations or single cells) that in combination constitute the functional basis of the biosphere. Animal and plant ecologists have advanced substantially our understanding of ecological interactions. In contrast, our knowledge of ecological interaction in microbes is still rudimentary. This represents a major knowledge gap, as microbes are key players in almost all ecosystems, particularly in the oceans. Several studies still pool together widely different marine microbes into broad functional categories (e.g. grazers) and therefore overlook fine-grained species/population-specific interactions. Increasing our understanding of ecological interactions is particularly needed for oceanic microeukaryotes, which include a large diversity of poorly understood symbiotic relationships that range from mutualistic to parasitic. The reason for the current state of affairs is that determining ecological interactions between microbes has proven to be highly challenging. However, recent technological developments in genomics and transcriptomics (metaomics for short), coupled with microfluidics and high-performance computing are making it increasingly feasible to determine ecological interactions at the microscale. Here, we present our views on how this field will advance thanks to the progress in metaomics approaches as well as potential avenues for future research.

A Hard Day's Night: Diel Shifts in Microbial Eukaryotic Activity in the North Pacific Subtropical Gyre

“…Network analyses from a recent global ocean survey (de Vargas et al, 2015;Lima-Mendez et al, 2015) detected a significant number of associations involving parasitic Syndiniales, but these interactions were derived from rDNA sequences. Due to the variable rDNA copy number among alveolates, the number of OTU correlations in those studies may be inflated (Krabberød et al, 2017). However, the use of rRNA sequences in the present study, which presumably provides a better characterization of active protists, supported putative host-parasite relationships between OTUs within the Syndiniales and numerous other alveolates (Tables 2, 3A, Table S4).…”

Disentangling environmental effects in microbial association networks

“…Microorganisms have crucial roles in the biosphere by contributing to global biogeochemical cycles Falkowski et al (2008) and underpinning diverse food webs. The importance of microbes for the functioning of ecosystems cannot be understood without considering their ecological interactions DeLong (2009); Krabberød et al (2017). These allow transferring carbon and energy to upper trophic levels, and the recycling of nutrients and energy Worden et al (2015).…”

“…Although microbial communities are highly interconnected Layeghifard et al (2017), our knowledge about ecological interactions in the microbial world is still limited Bjorbaekmo et al (2019); Krabberød et al (2017).…”

Assessing the viral content of uncultured picoeukaryotes in the global‐ocean by single cell genomics

“…From these, SCG emerged as a powerful complement to cultivation and metagenomics by providing genomic information from individual uncultured cells (Stepanauskas, 2012). Furthermore, it has an incredible potential for cell-specific analyses of organismal interactions, such as parasitism, symbiosis and predation (Krabberød, Bjorbaekmo, Shalchian-Tabrizi, & Logares, 2017;Stepanauskas, 2012), giving comprehensive insights of in situ virus-host associations. Indeed, this effective approach has revealed new associations between viruses and bacterial (Labonté et al, 2015;Roux et al, 2014) or archaeal cells (Chow, Winget, White, Hallam, & Suttle, 2015;Labonté et al, 2015;Munson-McGee et al, 2018).…”