Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data

  title={Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data},
  author={Jean-David Grattepanche and Laura M Walker and Brittany M Ott and Daniela Lopes Paim Pinto and Charles F. Delwiche and Christopher E. Lane and Laura A. Katz},
Despite their diversity and ecological importance, many areas of the SAR—Stramenopila, Alveolata, and Rhizaria—clade are poorly understood as the majority (90%) of SAR species lack molecular data and only 5% of species are from well‐sampled families. Here, we review and summarize the state of knowledge about the three major clades of SAR, describing the diversity within each clade and identifying synapomorphies when possible. We also assess the “dark area” of SAR: the morphologically described… 
Seed bank and seasonal patterns of the eukaryotic SAR (Stramenopila, Alveolata and Rhizaria) clade in a New England vernal pool
The protist community over a portion of the hydroperiod as the vernal pool transitions from its winter stage through its drying out in late summer is characterized, suggesting seasonality within microbial communities, suggesting a larger community of autotrophs in the winter followed by an increase in heterotrophic communities in the summer.
On the origin of TSAR: morphology, diversity and phylogeny of Telonemia
Six new telonemid strains are established, including the description of five new species and a new genus, and the origin of TSAR from flagellates with complex morphology and reconstruction of the ancestral structure of stramenopiles, alveolates and rhizarians, and their main synapomorphic characters are elucidated.
New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life
All phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup, and propose the moniker ‘TSAR’ to accommodate this new mega-assemblage in the phylogeny of eukaryotes.
New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life
All phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup, and propose the moniker “TSAR” to accommodate this new mega-assemblage in the phylogeny of eukaryotes.
Consistent patterns of high alpha and low beta diversity in tropical parasitic and free‐living protists
The results suggest that the biogeographies of macro‐ and micro‐organismal eukaryotes in lowland Neotropical rainforests are partially structured by the same general processes.
EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution
The EukRef pipeline and tools allow users interested in a particular group of microbial eukaryotes to retrieve all sequences belonging to that group from International Nucleotide Sequence Database Collaboration, to place those sequences in a phylogenetic tree, and to curate taxonomic and environmental information for the group.
A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis
The variety of Earth’s organisms is manifold. However, it is the small-scale marine community that makes the world goes round. Microbial organisms of pro- and eukaryotic origin drive the carbon
Phaeoviral Infections Are Present in Macrocystis, Ecklonia and Undaria (Laminariales) and Are Influenced by Wave Exposure in Ectocarpales
Phaeoviral infection is a widely occurring phenomenon in both lineages, and that phaeoviruses have diversified with their hosts at least since the divergence of the Laminariales and Ectocarpales.
Environmental DNA from a small sample of reservoir water can tell volumes about its biodiversity
Clustering into Amplicon Sequence Variants showed that 12S and 16S are able to detect predominant haplotypes of fishes, suggesting they are suitable to study population genetics of this group.
Diversity of Microbial Eukaryotes Along the West Antarctic Peninsula in Austral Spring
During a cruise from October to November 2019, along the West Antarctic Peninsula, between 64.32 and 68.37°S, we assessed the diversity and composition of the active microbial eukaryotic community


Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data.
Publicly available 18S barcoding data was used to define biases that may limit analyses and to gain an overview of the planktonic microbial eukaryotic diversity in freshwater ecosystems, and it was showed that Fungi, Stramenopiles and Viridiplantae play central role in lake ecosystems.
The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages.
Many freshwater phylogenetic groups identified in this study appeared unrelated to picoeukaryotic sequences identified in marine ecosystems, suggesting that aspects of eukaryote microbial diversity are specific to certain aquatic environments.
Taxon-rich phylogenomic analyses resolve the eukaryotic tree of life and reveal the power of subsampling by sites.
A taxon-rich phylogenomic analysis including 232 eukaryotes selected to maximize taxonomic diversity and up to 1554 genes chosen as vertically inherited based on their broad distribution among eukarian lineages finds strong support for five major clades, including Amoebozoa, Excavata, Opisthokonta, Archaeplastida, and SAR.
Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans
This study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.
A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts).
The first extensive phylogenomic analysis of stramenopiles, including representatives of most major lineages, provides a robust phylogenetic framework to investigate the evolution and diversification of this group of ecologically relevant protists.
A Molecular Genetic Timescale for the Diversification of Autotrophic Stramenopiles (Ochrophyta): Substantive Underestimation of Putative Fossil Ages
The evolutionary timescale of the autotrophic stramenopiles reconstructed here is generally older than previously inferred from molecular clocks, which casts serious doubt on the taxonomic validity of putative xanthophyte/phaeophyte fossils from the Proterozoic, which predate by as much as a half billion years or more the age suggested by the molecular genetic data.
A molecular view of microbial diversity and the biosphere.
Over three decades of molecular-phylogenetic studies, researchers have compiled an increasingly robust map of evolutionary diversification showing that the main diversity of life is microbial,
How discordant morphological and molecular evolution among microorganisms can revise our notions of biodiversity on Earth
It is argued that hypotheses about discordance can be tested using the concept of neutral morphologies, or more broadly neutral phenotypes, as a null hypothesis, and examples of such discordance are highlighted, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria.
Biology and systematics of heterokont and haptophyte algae.
  • R. Andersen
  • Environmental Science
    American journal of botany
  • 2004
This paper reviews what is currently known of phylogenetic relationships of heterokont and haptophyte algae and suggests they may be part of a large assemblage (chromalveolates) that includes heterokent algae and other stramenopiles, alveolate, and cryptophytes.
Phylogenetic and Ecological Analysis of Novel Marine Stramenopiles
A comparative analysis of novel stramenopiles is carried out, including new sequences from coastal genetic libraries presented here and sequences from recent reports from the open ocean and marine anoxic sites, confirming that they are fundamental members of the marine eukaryotic picoplankton.