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163 results for “Protist”
Soil protist functional composition shifts with atmospheric nitrogen deposition in subtropical forests
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Data from: Temperature and carbon dioxide interactively drive shifts in the compositional and functional structure of peatland protist communities
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Protists regulate microbially-mediated organic carbon turnover in soil aggregates
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Data from: Gene swamping alters evolution during range expansions in the protist Tetrahymena thermophila
<p>At species' range edges, individuals often face novel environmental conditions that may limit range expansion until populations adapt. The potential to adapt depends on genetic variation upon which selection can act. However, populations at species' range edges are often genetically depauperated. One mechanism to increase genetic variation is to reshuffle existing variation through sex. During range expansions, sex can, however, act as a double-edged sword. The gene swamping hypothesis predicts that for populations expanding along an abiotic gradient, sex can hinder adaptation if asymmetric dispersal leads to numerous maladapted dispersers from the range core swamping the range edge. In this study, we experimentally tested the gene swamping hypothesis by performing replicated range expansions in landscapes with or without an abiotic pH-gradient, using the ciliate <i>Tetrahymena thermophila</i>, while simultaneously manipulating the occurrence of gene flow and sex. We show that sex accelerated evolution of local adaptation in the absence of gene flow, but hindered it in the presence of gene flow. The effect of sex, however, was independent of the pH-gradient, indicating that not only abiotic gradients but also the biotic gradient in population density leads to gene swamping. Overall, our results show that gene swamping can affect adaptation in life-history strategies.</p>
Data from: Division of functional roles for termite gut protists revealed by single-cell transcriptomes
<p>The microbiome in the hindgut of wood-feeding termites comprises various species of bacteria, archaea, and protists. This gut community is indispensable for the termite, which thrives solely on recalcitrant and nitrogen-poor wood. However, the difficulty in culturing these microorganisms has hindered our understanding of the function of each species in the gut. Although protists predominate in the termite gut microbiome and play a major role in wood digestion, very few culture-independent studies have explored the contribution of each species to digestion. Here, we report single-cell transcriptomes of four protists species comprising the protist population in worldwide pest <em>Coptotermes formosanus</em>. Comparative transcriptomic analysis revealed that the expression patterns of the genes involved in wood digestion were different among species, reinforcing their division of roles in wood degradation. Transcriptomes, together with enzyme assays, also suggested that one of the protists, <em>Cononympha leidyi</em>, actively degrades chitin and assimilates it into amino acids. We propose that C. leidyi contributes to nitrogen recycling and inhibiting infection from entomopathogenic fungi through chitin degradation. Two of the genes for chitin degradation were further revealed to be acquired via lateral gene transfer (LGT) implying the importance of LGT in the evolution of symbiosis. Our single-cell-based approach successfully characterized the function of each protist in termite hindgut and explained why the gut community includes multiple species.</p>
Data from: Negative frequency-dependent selection is intensified at higher population densities in protist populations
Natural populations of free-living protists often exhibit high-levels of intraspecific diversity, yet this is puzzling as classic evolutionary theory predicts dominance by genotypes with high fitness, particularly in large populations where selection is efficient. Here, we test whether negative frequency-dependent selection (NFDS) plays a role in the maintenance of diversity in the marine flagellate Oxyrrhis marina using competition experiments between multiple pairs of strains. We observed strain-specific responses to frequency and density, but an overall signature of NFDS that was intensified at higher population densities. Because our strains were not selected a priori on the basis of particular traits expected to exhibit NFDS, these data represent a relatively unbiased estimate of the role for NFDS in maintaining diversity in protist populations. These findings could help to explain how bloom-forming plankton, which periodically achieve exceptionally high population densities, maintain substantial intraspecific diversity.
Data from: Environmental monitoring through protist NGS metabarcoding: assessing the impact of fish farming on benthic foraminifera communities
The measurement of species diversity represents a powerful tool for assessing the impacts of human activities on marine ecosystems. Traditionally, the impact of fish farming on the coastal environment is evaluated by monitoring the dynamics of macrobenthic infaunal populations. However, taxonomic sorting and morphology-based identification of the macrobenthos demands highly trained specialists and is extremely time-consuming and costly, what makes it unsuitable for large-scale biomonitoring efforts involving numerous samples. Here, we propose to alleviate this laborious task by developing protist metabarcoding tools based on next-generation sequencing (NGS) of environmental DNA and RNA extracted from sediment samples. In this study, we analysed the response of benthic foraminiferal communities to the variation of environmental gradients associated with salmon farms in Scotland. We investigated the foraminiferal diversity based on ribosomal minibarcode sequences generated by the Illumina NGS technology. We compared the molecular data with morphospecies counts and with environmental gradients, including distance to cages and Redox used as a proxy for sediment oxygenation. Our study revealed high variations between foraminiferal communities collected in the vicinity of fish farms and at distant locations. We found evidence for alpha diversity loss in strongly impacted sites, especially visible in the RNA data. We also detected some candidate bioindicator foraminiferal species. Based on this proof-of-concept study, we conclude that NGS metabarcoding using foraminifera and other protists has considerable potential to become a new tool for surveying the impact of aquaculture and other industrial activities in the marine environment.
Data from: Polar lakes may act as ecological islands to aquatic protists
A fundamental question in ecology is whether microorganisms follow the same patterns as multicellular organisms when it comes to population structure and levels of genetic diversity. Enormous population sizes, predominately asexual reproduction, and presumably high dispersal due to small body size could have profound implications on their genetic diversity and population structure. Here, we have analyzed the population genetic structure in a lake-dwelling microbial eukaryote (dinoflagellate) and tested the hypothesis that there is population genetic differentiation among nearby lake subpopulations. This dinoflagellate occurs in the marine-derived saline lakes of the Vestfold Hills, Antarctica, which are ice-covered most of the year. Clonal strains were isolated from four different lakes, and were genotyped using AFLP (Amplified Fragment Length Polymorphism). Our results show high genetic differentiation among lake populations despite their close geographical proximity (< 9 km). Moreover, genotype diversity was high within populations. Gene flow in this system is clearly limited, either due to physical or biological barriers. Our results discard the null hypothesis that there is free gene flow among protist lake populations. Instead, limnetic protist populations may differentiate genetically, and lakes act as ecological islands even on the microbial scale.
Data from: Constraints on the adult-offspring size relationship in protists
The relationship between adult and offspring size is an important aspect of reproductive strategy. Although this filial relationship has been extensively examined in plants and animals, we currently lack comparable data for protists, whose strategies may differ due to the distinct ecological and physiological constraints on single-celled organisms. Here, we report measurements of adult and offspring sizes in 3,888 species and subspecies of foraminifera, a class of large marine protists. Foraminifera exhibit a wide range of reproductive strategies; species of similar adult size may have offspring whose sizes vary 100-fold. Yet, a robust pattern emerges. The minimum (5th percentile), median, and maximum (95th percentile) offspring sizes exhibit a consistent pattern of increase with adult size independent of environmental change and taxonomic variation over the past 400 million years. The consistency of this pattern may arise from evolutionary optimization of the offspring size-fecundity trade-off and/or from cell-biological constraints that limit the range of reproductive strategies available to single-celled organisms. When compared with plants and animals, foraminifera extend the evidence that offspring size covaries with adult size across an additional five orders of magnitude in organism size.
Representative giant virus genomes for "Resolving environmental drivers and ecological patterns of active viruses infecting protists in the Southern Ocean"
<p>Nucleotide FASTA files of each representative giant virus genomes used in "Resolving environmental drivers and ecological patterns of active viruses infecting protists in the Southern Ocean". </p>
Figure 1. Enteromyces callianassae Lichtwardt, 1961 in First reports of protists in land crabs of the family Gecarcinidae (Crustacea: Decapoda: Brachyura) suggest a relatively widespread phenomenon
Figure 1. Enteromyces callianassae Lichtwardt, 1961: (a) distribution along the (cleared) stomach wall of a female Gecarcinus lateralis (Guérin, 1832) (carapace width 39 mm); (b) thalli attached to multiple holdfast systems; (c) holdfast on stomach wall; (d) multinucleate thalli.
Figure 2 in First reports of protists in land crabs of the family Gecarcinidae (Crustacea: Decapoda: Brachyura) suggest a relatively widespread phenomenon
Figure 2. Relative frequency of stomachs of Gecarcinus lateralis (Guérin, 1832) according to their fullness, with and without eccrinids (0 = empty stomach; 1 = 1–50%; 2 = 51–100%).
Supplementary material 4 from: Boenigk J, Wodniok S, Bock C, Beisser D, Hempel C, Grossmann L, Lange A, Jensen M (2018) Geographic distance and mountain ranges structure freshwater protist communities on a European scalе. Metabarcoding and Metagenomics 2: e21519. https://doi.org/10.3897/mbmg.2.21519
Richness is shown for different elevations. The number of lakes within this elevation range is indicated. While mean richness ranges around 750 OTUs it drops to around 400 OTUs at high elevations. The transition seems to be around or slightly below 1400m.
18S/16S raw amplicon data for Martínez Martínez et al. : "Coastal bacteria and protists assimilate viral carbon and nitrogen"
<p>Raw amplicon (18S and 16S rRNA) sequencing data (.fastq.gz) for Martínez Martínez <em>et al.</em> : "Coastal bacteria and protists assimilate viral carbon and nitrogen". Each sample has forward (*_1.fastq.gz) and reverse (*_2.fastq.gz) reads as separate files. </p>
Supplementary material 2 from: Cahoon AB, Huffman AG, Krager MM, Crowell RM (2018) A meta-barcoding census of freshwater planktonic protists in Appalachia – Natural Tunnel State Park, Virginia, USA. Metabarcoding and Metagenomics 2: e26939. https://doi.org/10.3897/mbmg.2.26939
Figure 2. Rarefaction analysis estimates demonstrate that family and genus collections were approaching saturation :
mTagBFP2-expressing vectors for electroporation of marine protists
<p>Plasmid maps and genbank sequence files for the plasmids used for electroporation of model organism <em>Nannochloropsis oceanica</em> and environmental samples following the protocol <a href="https://www.protocols.io/view/fabrication-of-dna-constructs-by-gibson-assembly-a-7r8hm9w">Matute et al.</a></p> <p>EMS initiative from Gordon and Betty Moore foundation.</p>
Arctic Biodiversity: Arctic Protists
Biogeography and other attributes for Arctic organisms, various sources.<p></p>
Data from: Direct effects of microalgae and protists on herring (Clupea harengus) yolk sac larvae
This study investigated effects of microalgae (Rhodomonas baltica) and heterotrophic protists (Oxyrrhis marina) on the daily growth, activity, condition and feeding success of Atlantic herring (Clupea harengus) larvae from hatch, through the end of the endogenous (yolk sac) period. Yolk sac larvae were reared in the presence and absence of microplankton and, each day, groups of larvae were provided access to copepods. Larvae reared with microalgae and protists exhibited precocious (2 days earlier) and ≥ 60% increased feeding incidence on copepods compared to larvae reared in only seawater (SW). In the absence and presence of microalgae and protists, survival and growth trajectories of yolk sac larvae were similar and digestive enzyme activity (trypsin) and nutritional condition (RNA-DNA ratio) markedly declined in all larvae directly after yolk sac depletion. Thus, microplankton promoted early feeding but was not sufficient to alter survival and growth during the yolk sac phase. Given the importance of early feeding, field programs should place greater emphasis on the protozooplankton-ichthyoplankton link to better understand match-mismatch dynamics and bottom-up drivers of year class success in marine fish.
FIGURES 1–3. 1 in Description of Parentocirrus brasiliensis sp. n. (Ciliophora: Spirotrichea), a new ciliate protist present in activated sludge
FIGURES 1–3. 1. Drawing of living specimen, showing ventral side. CV = contractile vacuole. 2. Drawing of silver impregnated specimen, showing ventral side. Macronuclear row dettached and displayed in the left. Ma = macronuclear nodules; Mi = micronuclei. 3. Drawing of silver impregnated specimen, showing dorsal side. Kineties are indicated by arabic algarisms. Arrows point to scattered kinetids. CC = caudal cirri.
FIGURES 8–10. Silver impregnated specimens. 8 in Description of Parentocirrus brasiliensis sp. n. (Ciliophora: Spirotrichea), a new ciliate protist present in activated sludge
FIGURES 8–10. Silver impregnated specimens. 8 – specimen with anomalous macronuclear apparatus. Arrowheads pointing to anteriormost and posteriormost macronuclear nodules, which are constricted in the equatorial region; 9 – specimen showing ventral ciliature variation. Arrowhead pointing to cirrus located between right ventral row and right marginal row; 10 – Dorsal side showing dorsal ciliature variation. Arrowhead pointing to posterior scattered kinetids. Legend: Ma = Macronuclear module; Mi = micronucleus. Scale bars: 10µm.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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