Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles

Abstract

Molecular surveys in planktonic marine systems have unveiled a large novel diversity of small protists. A large part of this diversity belongs to basal heterotrophic stramenopiles and is distributed in a set of polyphyletic ribogroups (described from rDNA sequences) collectively named as MAST (MArine STramenopiles). In the few groups investigated, MAST cells are globally distributed and abundant bacterial grazers, therefore having a putatively large impact on marine ecosystem functioning. The main aim of this study is to reevaluate the MAST ribogroups described so far and to determine whether additional groups can be found. For this purpose, we used traditional and state-of-the-art molecular tools, combining 18S rDNA sequences from publicly available clone libraries, single amplified genomes (SAGs) of planktonic protists, and a pyrosequencing survey from coastal waters and sediments. Our analysis indicated a final set of 18 MAST groups plus 5 new ribogroups within Ochrophyta (named as MOCH). The MAST ribogroups were then analyzed in more detail. Seven were typical of anoxic systems and one of oxic sediments. The rest were clearly members of oxic marine picoplankton. We characterized the genetic diversity within each MAST group and defined subclades for the more diverse (46 subclades in 8 groups). The analyses of sequences within subclades revealed further ecological specializations. Our data provide a renovated framework for phylogenetic classification of the numerous MAST ribogroups and support the notion of a tight link between phylogeny and ecological distribution. These diverse and largely uncultured protists are widespread and ecologically relevant members of marine microbial assemblages.

Geographic distance and mountain ranges structure freshwater protist communities on a European scalе

“…Distribution patterns are further obscured by partly inappropriate species delimitation in protists (Mann andVanormelingen 2013, Scoble andCavalier-Smith 2014). Appropriate species delimitation (and thus species distributions) are even more nebulous for the vast number of (so far) uncultivatable protist lineages (Massana et al 2013). Assertions on the absolute species numbers and species inventory are therefore imprecise and subject to numerous assumptions.…”

Discordant Temporal Turnovers of Sediment Bacterial and Eukaryotic Communities in Response to Dredging: Nonresilience and Functional Changes

“…In the eukaryotic community, DO was positively correlated with Bicoecea (r ϭ 0.589, P Ͻ 0.001) but negatively correlated with Bacillariophyta (r ϭ Ϫ0.376, P ϭ 0.005). The results further proved that oxygen was a key driver of protist community structure (19), which creates an apparent phylogenetic dichotomy between oxic and anoxic assemblages (29)(30)(31). In addition, pH and seasonal temperature variation were important factors influencing sediment community structure (32).…”

“…The difference can be ascribed to the alterations in sediment geochemical attributes. Oxygen status is the most important factor that strongly regulates cell metabolism in sediments (19). Dredging disturbance causes a direct increase in sediment DO and E h (Table S1), resulting in the stimulation of aerobic populations and repression of anaerobic groups.…”

“…However, in these studies, the samples were collected discontinuously at two time points before and after dredging; therefore, it is difficult to analyze the succession and the stability of the bacterial community. Furthermore, little attention has been paid to uncultured microeukaryotes in sediments, despite their crucial roles in the ecosystem (19). It is still unknown whether bacterial, microeukaryotic, and macrobenthic communities exhibit similar responses to dredging, as well as whether they contribute to the resulting ecological functional changes.…”

Novel Diversity of Deeply Branching Holomycota and Unicellular Holozoans Revealed by Metabarcoding in Middle Paraná River, Argentina

“…Nevertheless, molecular surveys of biodiversity have redrawn a completely different paradigm, in which unicellular eukaryotes represent the majority of the total eukaryotic richness, while remaining mostly undescribed (Pawlowski et al, 2012;del Campo et al, 2014). Many studies have overcome this limitation using molecular data to define new clades (López-García et al, 2001;Massana et al, 2004Massana et al, , 2014Šlapeta et al, 2005;Guillou et al, 2008;Marande et al, 2009;Jones et al, 2011;del Campo and Ruiz-Trillo, 2013). However, the complete view of the molecular eukaryotic diversity remains unsolved.…”