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34 results for “microbial eukaryotes”
Trait Spreadsheet to DwCA: Trophic guild data for microbial eukaryotes
<p></p>https://eol-jira.bibalex.org/browse/DATA-1882<p></p>Updated: 2022-05-31 02:59
Trait Spreadsheet to DwCA: Habitat data for microbial eukaryotes
<p></p>https://eol-jira.bibalex.org/browse/DATA-1882<p></p>Updated: 2022-09-28 15:15
Data from: DNA metabarcoding reveals that 200-μm-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes
Microeukaryotic plankton (0.2–200 μm) are critical components of aquatic ecosystems and key players in global ecological processes. High-throughput sequencing is currently revolutionizing their study on an unprecedented scale. However, it is currently unclear whether we can accurately, effectively and quantitatively depict the microeukaryotic plankton communities using traditional size-fractionated filtering combined with molecular methods. To address this, we analysed the eukaryotic plankton communities both with, and without, prefiltering with a 200 μm pore-size sieve –by using SSU rDNA-based high-throughput sequencing on 16 samples with three replicates in each sample from two subtropical reservoirs sampled from January to October in 2013. We found that ~25% reads were classified as metazoan in both size groups. The species richness, alpha and beta diversity of plankton community and relative abundance of reads in 99.2% eukaryotic OTUs showed no significant changes after prefiltering with a 200 μm pore-size sieve. We further found that both >0.2 μm and 0.2–200 μm eukaryotic plankton communities, especially the abundant plankton subcommunities, exhibited very similar, and synchronous, spatiotemporal patterns and processes associated with almost identical environmental drivers. The lack of an effect on community structure from prefiltering suggests that environmental DNA from larger metazoa is introduced into the smaller size class. Therefore, size-fractionated filtering with 200 μm is insufficient to discriminate between the eukaryotic plankton size groups in metabarcoding approaches. Our results also highlight the importance of sequencing depth, and strict quality filtering of reads, when designing studies to characterize microeukaryotic plankton communities.
Data from: DNA metabarcoding reveals that 200-μm-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes
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Data from: Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill
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Data from: Effects of long term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach
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Data from: Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments
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Sequences of microbial eukaryotic genes obtained from the metagenome of the Mariana Trench
<p>nonredundant_eukaryotic_genes.faa contains the non-redundant amino acid sequences of predicted eukaryotic genes in all samples by MetaEuk.</p> <p>nonredundant_eukaryotic_genes.fna contains the non-redundant nucleotide sequences of predicted eukaryotic genes in all samples by MetaEuk.</p> <p>tax_for_per_gene.txt contains the taxonomic information of per non-redundant gene.</p>
Data from: Complex phylogeographic patterns in the freshwater alga Synura provide new insights on ubiquity versus endemism in microbial eukaryotes
The global distribution, abundance, and diversity of microscopic freshwater algae demonstrate an ability to overcome significant barriers such as dry land and oceans by exploiting a range of biotic and abiotic colonization vectors. If these vectors are considered unlimited and colonization occurs in proportion to population size, then globally ubiquitous distributions are predicted to arise. This model contrasts with observations that many freshwater microalgal taxa possess true biogeographies. Here, using a concatenated multi-gene dataset, we study the phylogeography of the freshwater heterokont alga Synura petersenii sensu lato. Our results suggest that this Synura morphotaxon contains both cosmopolitan and regionally endemic cryptic species, co-occurring in some cases, and masked by a common ultrastructural morphology. Phylogenies based on both proteins (seven protein-coding plastid and mitochondrial genes) and DNA (nine genes including ITS and 18S rDNA) reveal pronounced biogeographic delineations within phylotypes of this cryptic species complex, while retaining one clade that is globally distributed. Relaxed molecular clock calculations, constrained by fossil records, suggest that the genus Synura is considerably older than currently proposed. The availability of tectonically-relevant geological time (10^7-10^8 years) has enabled the development of the observed, complex biogeographic patterns. Our comprehensive analysis of freshwater algal biogeography suggests that neither ubiquity nor endemism wholly explain global patterns of microbial eukaryote distribution, and that processes of dispersal remain poorly understood.
Data from: Complex phylogeographic patterns in the freshwater alga Synura provide new insights on ubiquity versus endemism in microbial eukaryotes
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Data from: Long-term dynamics in microbial eukaryotes communities: a paleolimnological view based on sedimentary DNA
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Data from: Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes
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Data from: Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis
Under hypoxic conditions, some organisms use an electron transport chain consisting of only complex I and II (CII) to generate the proton gradient essential for ATP production. In these cases, CII functions as a fumarate reductase that accepts electrons from a low electron potential quinol, rhodoquinol (RQ). To clarify the origins of RQ-mediated fumarate reduction in eukaryotes, we investigated the origin and function of rqua, a gene encoding an RQ biosynthetic enzyme. Rqua is very patchily distributed across eukaryotes and bacteria adapted to hypoxia. Phylogenetic analyses suggest lateral gene transfer (LGT) of rqua from bacteria to eukaryotes occurred at least twice and the gene was transferred multiple times amongst protists. We demonstrate that RQUA functions in the mitochondrion-related organelles of the anaerobic protist Pygsuia and is correlated with the presence of RQ. These analyses reveal the role of gene transfer in the evolutionary remodeling of mitochondria in adaptation to hypoxia.
Data from: Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis
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