Faculty Opinions recommendation of Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes.

AbstractHeterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles.

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Using single-cell transcriptomics to understand functional states and interactions in microbial eukaryotes

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0098 ◽

2019 ◽

Vol 374 (1786) ◽

pp. 20190098 ◽

Cited By ~ 5

Author(s):

Chuan Ku ◽

Arnau Sebé-Pedrós

Keyword(s):

Gene Expression ◽

Single Cell ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Interspecific Interactions ◽

Single Cells ◽

Life Cycles ◽

Modern Biology ◽

Microbial Eukaryotes ◽

Eukaryotic Microorganisms

Understanding the diversity and evolution of eukaryotic microorganisms remains one of the major challenges of modern biology. In recent years, we have advanced in the discovery and phylogenetic placement of new eukaryotic species and lineages, which in turn completely transformed our view on the eukaryotic tree of life. But we remain ignorant of the life cycles, physiology and cellular states of most of these microbial eukaryotes, as well as of their interactions with other organisms. Here, we discuss how high-throughput genome-wide gene expression analysis of eukaryotic single cells can shed light on protist biology. First, we review different single-cell transcriptomics methodologies with particular focus on microbial eukaryote applications. Then, we discuss single-cell gene expression analysis of protists in culture and what can be learnt from these approaches. Finally, we envision the application of single-cell transcriptomics to protist communities to interrogate not only community components, but also the gene expression signatures of distinct cellular and physiological states, as well as the transcriptional dynamics of interspecific interactions. Overall, we argue that single-cell transcriptomics can significantly contribute to our understanding of the biology of microbial eukaryotes. This article is part of a discussion meeting issue ‘Single cell ecology’.

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Quantifying long‐term recurrence in planktonic microbial eukaryotes

Molecular Ecology ◽

10.1111/mec.14929 ◽

2019 ◽

Vol 28 (5) ◽

pp. 923-935 ◽

Cited By ~ 22

Author(s):

Caterina R. Giner ◽

Vanessa Balagué ◽

Anders K. Krabberød ◽

Isabel Ferrera ◽

Albert Reñé ◽

...

Keyword(s):

Microbial Eukaryotes

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A fundamental difference between macrobiota and microbial eukaryotes: Protistan plankton has a species maximum in the freshwater‐marine transition zone of the Baltic Sea

Environmental Microbiology ◽

10.1111/1462-2920.14502 ◽

2018 ◽

Cited By ~ 2

Author(s):

Sabine Filker ◽

Steffen Kühner ◽

Melanie Heckwolf ◽

Jan Dierking ◽

Thorsten Stoeck

Keyword(s):

Baltic Sea ◽

Transition Zone ◽

Fundamental Difference ◽

The Baltic Sea ◽

Microbial Eukaryotes ◽

The Baltic

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SIGAR: Inferring features of genome architecture and DNA rearrangements by split read mapping

10.1101/2020.05.05.079426 ◽

2020 ◽

Author(s):

Yi Feng ◽

Leslie Y. Beh ◽

Wei-Jen Chang ◽

Laura F. Landweber

Keyword(s):

Genome Assembly ◽

Repetitive Sequences ◽

Genome Architecture ◽

Dna Rearrangements ◽

High Quality ◽

Microbial Eukaryotes ◽

Ciliate Species ◽

Split Read ◽

High Level ◽

Genome Assemblies

AbstractCiliates are microbial eukaryotes with distinct somatic and germline genomes. Post-zygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programmed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. While many high-quality somatic genomes have been assembled, a high quality germline genome assembly is difficult to obtain due to its smaller DNA content and abundance of repetitive sequences. To overcome these hurdles, we propose a new pipeline SIGAR (Splitread Inference of Genome Architecture and Rearrangements) to infer germline genome architecture and rearrangement features without a germline genome assembly, requiring only short germline DNA sequencing reads. As a proof of principle, 93% of rearrangement junctions identified by SIGAR in the ciliate Oxytricha trifallax were validated by the existing germline assembly. We then applied SIGAR to six diverse ciliate species without germline genome assemblies, including Ichthyophthirius multifilii, a fish pathogen. Despite the high level of somatic DNA contamination in each sample, SIGAR successfully inferred rearrangement junctions, short eliminated sequences and potential scrambled genes in each species. This pipeline enables pilot surveys or exploration of DNA rearrangements in species with limited DNA material access, thereby providing new insights into the evolution of chromosome rearrangements.

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Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies

mSystems ◽

10.1128/msystems.00201-17 ◽

2018 ◽

Vol 3 (2) ◽

Cited By ~ 28

Author(s):

Isabelle Laforest-Lapointe ◽

Marie-Claire Arrieta

Keyword(s):

Microbial Communities ◽

Microbial Ecology ◽

High Throughput Sequencing ◽

Sequencing Technology ◽

Human Gut ◽

Microbial Eukaryotes ◽

Host Health ◽

High Level ◽

Eukaryotic Organisms ◽

New Evidence

ABSTRACTHuman-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health. In this perspective, we discuss new evidence on eukaryotes as fundamental species of the human gut and emphasize that future microbiome studies should characterize the multitrophic interactions between microeukaryotes, other microorganisms, and the host.

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