Microscopic Eukaryotes Research Articles

Kotuikan Formation assemblage: A diverse organic-walled microbiota in the Mesoproterozoic Anabar succession, northern Siberia

Abundant and diverse microfossils from shales of the Lower Member of the ∼1500-Ma-old Kotuikan Formation in northern Siberia document early Mesoproterozoic life along the Siberian Platform. Similar to many Meso- and Neoproterozoic microbiota, the Kotuikan assemblage is dominated by prokaryotic cyanobacteria, both filamentous (oscillatorialeans and nostocaleans, which are represented primarily by cellular trichomes and by empty sheaths) and coccoidal (chroococcaleans, including solitary and colonial specimens). However, unlike Mesoproterozoic microbiota of shallow-water settings, the Kotuikan compressed organic-walled microfossil assemblage in the open shelf facies includes diverse microscopic eukaryotes: large (up to ∼1-mm diameter) megasphaeromorph acritarchs, branched filaments that are most likely of eukaryotic algae and coccoidal monostromatic colonies of chlorococcaleans, as well as other morphologically complex microorganisms.The Kotuikan assemblage contains numerous taxa previously recorded from Neoproterozoic successions (e.g., Elatera, Eosolena, Palaeastrum, Pterospermopsimorpha, Rugosoopsis and Navifusa), but these are long-ranging genera and no Neoproterozoic index fossils have been recorded. The microbiota is considered to be Mesoproterozoic in age because it contains a mixed assemblage of prokaryotic and eukaryotic microorganism remains including new taxa unknown in younger deposits. The Kotuikan assemblage documents the status of the marine biosphere at an early Mesoproterozoic time preceding the primary radiation of eukaryotes and representing an evolutionary stage transitional between the predominantly prokaryote-dominated Paleoproterozoic and the eukaryote-dominated Neoproterozoic microbiota.As reported in this study, 35 taxa were identified in the Kotuikan assemblage (of which five forms are described informally) that are assigned to 18 genera of microscopic prokaryotes and eukaryotes. Two new genera and five new species are proposed: Hirudiforma lancetica gen. and sp. nov., H. simmetrica gen. and sp. nov., Lineaforma elongata gen. and sp. nov., Elatera minor sp. nov., Eosolena minuta sp. nov.

Discrimination of plant-parasitic nematodes from complex soil communities using ecometagenetics.

Many plant pathogens are microscopic, cryptic, and difficult to diagnose. The new approach of ecometagenetics, involving ultrasequencing, bioinformatics, and biostatistics, has the potential to improve diagnoses of plant pathogens such as nematodes from the complex mixtures found in many agricultural and biosecurity situations. We tested this approach on a gradient of complexity ranging from a few individuals from a few species of known nematode pathogens in a relatively defined substrate to a complex and poorly known suite of nematode pathogens in a complex forest soil, including its associated biota of unknown protists, fungi, and other microscopic eukaryotes. We added three known but contrasting species (Pratylenchus neglectus, the closely related P. thornei, and Heterodera avenae) to half the set of substrates, leaving the other half without them. We then tested whether all nematode pathogens-known and unknown, indigenous, and experimentally added-were detected consistently present or absent. We always detected the Pratylenchus spp. correctly and with the number of sequence reads proportional to the numbers added. However, a single cyst of H. avenae was only identified approximately half the time it was present. Other plant-parasitic nematodes and nematodes from other trophic groups were detected well but other eukaryotes were detected less consistently. DNA sampling errors or informatic errors or both were involved in misidentification of H. avenae; however, the proportions of each varied in the different bioinformatic pipelines and with different parameters used. To a large extent, false-positive and false-negative errors were complementary: pipelines and parameters with the highest false-positive rates had the lowest false-negative rates and vice versa. Sources of error identified included assumptions in the bioinformatic pipelines, slight differences in primer regions, the number of sequence reads regarded as the minimum threshold for inclusion in analysis, and inaccessible DNA in resistant life stages. Identification of the sources of error allows us to suggest ways to improve identification using ecometagenetics.

Molecular examination of kalyptorhynch diversity (Platyhelminthes: Rhabdocoela), including descriptions of five meiofaunal species from the north-eastern Pacific Ocean

The spaces between sand grains are home to a myriad of microscopic marine eukaryotes, including kalyptorhynch rhabdocoels equipped with an eversible proboscis that enables them to capture microscopic prey living in these environments. The structure of the kalyptorhynch proboscis separates the two major subclades within the group: the Schizorhynchia (bifurcated proboscis) and the Eukalyptorhynchia (unbranched proboscis). A survey of meiofaunal metazoans in the Pacific north-west led to the discovery of three new schizorhynch species (Undicola tofinoensisgen. nov., sp. nov.,Schizorhinos vancouverensisgen. nov., sp. nov. andLinguabana tulaigen. nov., sp. nov.) and two new eukalyptorhynch species (Thinodactylaina tlaoquiahtensisgen. nov., sp. nov. andRostracilla nuuchahnulthensisgen. nov., sp. nov.). This survey also recovered the putative cosmopolitan eukalyptorhynch (Polycystididae)Gyratrix hermaphroditusEhrenberg, 1831. We performed molecular phylogenetic analyses on 18S rDNA sequences from all five novel isolates and from all available kalyptorhynch species in GenBank. The molecular data supported the monophyly of the Eukalyptorhynchia and Schizorhynchia and helped demonstrate the boundaries between different species within the Kalyptorhynchia.

Harmful and parasitic unicellular eukaryotes persist in a shallow lake under reconstruction (L. Karla, Greece)

The reconstructed Lake Karla, Greece, has been undergoing its water-filling period since November 2009. In this paper, we aimed at investigating whether the unicellular eukaryotes, including the toxic/parasitic ones, that have been found during mass fish kills in the lake (March–April 2010), persist during the first warm period of the lake (May, August, November 2010). Given that microscopic characterization of some of these eukaryotes is not adequate for their identification, we analysed the 18S rRNA gene diversity of plankton samples. All the found phylotypes belonged to the phyla of Mesomycetazoa, Chlorophyta, Fungi, Alveolata, Cercozoa, Cryptophyta and Stramenopiles. Some members of these groups seem to persist in Lake Karla as they have been found in early spring as well. These microscopic eukaryotes are either ichthyotoxic/parasitic (e.g. Pfiesteria sp./Pseudopfiesteria shumwayae, some Fungi, Mesomycetazoa, Lagenidium sp., Cercozoa) or indicative of hyper-eutrophic conditions (e.g. Oocystis sp., Scenedesmus spp.) and were rather abundant during the first spring–autumn period of the lake’s refilling process. These complex microscopic communities are expected to shape highly dynamic and variable food webs with the risk of repeated fish kills.

The Race to Name Earth's Species

[Extract] In their Review Can we name Earth's species before they go extinct? (25 January, p. 413), M. J. Costello et al. answer in the affirmative. I am not so sure. Costello et al. could be underestimating global biodiversity by concluding that Earth likely sustains only 2 to 8 million species of eukaryotes. Studies they review suggest that there might be 6.1 to 7.8 million species of terrestrial arthropods alone, as well as 0.3 to 1.0 million marine species and 0.3 to 0.4 million species of plants (1). Even if one ignores the relatively small number of vertebrate species, many other taxa—including nematodes and other worm phyla, fungi, and other terrestrial and freshwater invertebrates—could be impressively species-rich. Beyond this, there are myriad microscopic eukaryotes (2). I am also less sanguine than are Costello et al. about the world's undescribed biodiversity. Such species likely include many local endemics (3), small-sized or non-descript species, species that live in poorly explored places such as the rainforest canopy or deep oceans, morphologically cryptic species, and those that simply are very good at hiding (1). Even with improving genetic and other technologies, some of these taxa may be extremely difficult to find or catalog. Moreover, because the missing species are almost certainly a nonrandom component of all biodiversity, our incomplete view of life on Earth likely suffers from various selective biases. Finally, even with growing taxonomic expertise in developing nations, it is far from certain that sufficient effort will be focused on the world's imperiled biodiversity hotspots (4), which are likely to house the bulk of undescribed species (3, 5).

PRESERVATIONAL AND MORPHOLOGICAL VARIABILITY OF ASSEMBLAGES OF AGGLUTINATED EUKARYOTES IN CRYOGENIAN CAP CARBONATES OF NORTHERN NAMIBIA

Laminated carbonates of the Rasthof Formation, deposited in the aftermath of the early Cryogenian low-latitude glaciation (Sturtian, 717–662 Ma), preserve abundant round tests of agglutinated microscopic eukaryotes. Previously, fossil tests were reported in two localities (Ongongo and Okaaru) from microbially laminated carbonates in the Rasthof Formation, which revealed a previous unexplored Cryogenian taphonomic window. In order to better understand the lateral variability in these microfossil assemblages, this work systematically examines fossil tests from two additional localities, South Ombepera and Ombepera, and compares their preservation in thinly and thickly laminated microbial laminites. Cap carbonates in South Ombepera and Ombepera contain abundant, hollow, spheroidal agglutinated tests (50 to 225 µm in diameter). Some of these tests exhibit slitlike or triangular apertures. In contrast, much larger, oval tests with a tapering end dominate the assemblages at Okaaru, whereas oval, laterally compressed and round structures with slits, visors, or central apertures are found at Ongongo. The thinly laminated microbial laminites from Ombepera, South Ombepera, and Okaaru also preserve rare agglutinated tubes attributed to fossils of early Foraminifera. At all four localities, the thinly laminated microbial laminites preserve more microfossils than thickly laminated microbial laminites although these two facies commonly interfinger and are interbedded. This difference shows that conditions present during formation of the thinly laminated microbial laminites favored the preservation of round agglutinators, perhaps during early burial, lithification, and fossilization of the test walls.

TESTING THE LINK BETWEEN POPULATION GENETIC DIFFERENTIATION AND CLADE DIVERSIFICATION IN COSTA RICAN ORCHIDS

Species population genetics could be an important factor explaining variation in clade species richness. Here, we use newly generated amplified fragment length polymorphism (AFLP) data to test whether five pairs of sister clades of Costa Rican orchids that differ greatly in species richness also differ in average neutral genetic differentiation within species, expecting that if the strength of processes promoting differentiation within species is phylogenetically heritable, then clades with greater genetic differentiation should diversify more. Contrary to expectation, neutral genetic differentiation does not correlate directly with total diversification in the clades studied. Neutral genetic differentiation varies greatly among species and shows no heritability within clades. Half of the variation in neutral genetic differentiation among populations can be explained by ecological variables, and species-level traits explain the most variation. Unexpectedly, we find no isolation by distance in any species, but genetic differentiation is greater between populations occupying different niches. This pattern corresponds with those observed for microscopic eukaryotes and could reflect effective widespread dispersal of tiny and numerous orchid seeds. Although not providing a definitive answer to whether population genetics processes affect clade diversification, this work highlights the potential for addressing new macroevolutionary questions using a comparative population genetic approach.

Putative Cryogenian ciliates from Mongolia

Research Article| December 01, 2011 Putative Cryogenian ciliates from Mongolia T. Bosak; T. Bosak 1Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Search for other works by this author on: GSW Google Scholar F. Macdonald; F. Macdonald 2Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts 02138, USA Search for other works by this author on: GSW Google Scholar D. Lahr; D. Lahr 3Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA Search for other works by this author on: GSW Google Scholar E. Matys E. Matys 1Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Search for other works by this author on: GSW Google Scholar Geology (2011) 39 (12): 1123–1126. https://doi.org/10.1130/G32384.1 Article history received: 25 Apr 2011 rev-recd: 05 Jul 2011 accepted: 07 Jul 2011 first online: 09 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Search Site Citation T. Bosak, F. Macdonald, D. Lahr, E. Matys; Putative Cryogenian ciliates from Mongolia. Geology 2011;; 39 (12): 1123–1126. doi: https://doi.org/10.1130/G32384.1 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyGeology Search Advanced Search Abstract Major lineages of modern eukaryotes, represented primarily by microscopic taxa, are thought to have originated during the Neoproterozoic, but microfossils older than 635 Ma rarely have unambiguous relationships to modern microscopic eukaryotes. Here we report exceptionally preserved 715–635 m.y. old eukaryotic tests in limestone strata of Mongolia. The ∼100-μm-long organic-rich three-dimensional tests have flask-like shapes, constricted necks, distinct and often thickened collars, and flexible walls composed of densely packed alveolar structures. The combined morphological and ultrastructural characters of these Cryogenian tests are remarkably similar to the tests of tintinnids, modern planktonic ciliates. Eukaryotes forming recalcitrant organic or mineral-rich tests before 635 Ma may have increased export and burial fraction of organic carbon, driving an increase in atmospheric oxygen and the subsequent radiation of metazoans. You do not have access to this content, please speak to your institutional administrator if you feel you should have access.

Single-cell PCR on protargol-impregnated euplotid ciliates: a combined approach of morphological and molecular taxonomy

Ciliates are considered one of the most diverse protozoa and play significant roles in ecology. For successful taxonomic study of these microscopic eukaryotes, a staining procedure is necessary, due mainly to intrinsic difficulties in recognizing characteristics from living cells. Although molecular taxonomy has been used to resolve the ambiguities associated with traditional morphology-based taxonomy, extraction of genomic DNA from stained ciliate cells is not available yet. In the present study, we describe a method to extract genomic DNA from a single protargol-impregnated euplotid cell. By using HgCl2 as a fixative and modulating the exposure time of bleach solution in the protargol impregnation, high-quality genomic DNA can successfully be extracted from a stained single cell with minimal loss of morphological integrity. This technique will contribute to the effectiveness of combined approaches of molecular and morphological taxonomy from single ciliate cells.

Size is not everything: a meta-analysis of geographic variation in microscopic eukaryotes

Aim To analyse how important body size is for geographic variation in microscopic organisms in the marine environment and thereby determine the validity of the ‘everything is everywhere’ hypothesis. Location Marine environments, globally. Methods Studies on geographic variation in all marine eukaryotes smaller than 1 mm and all marine copepods were compiled from the literature and incorporated in multiple binomial regressions to analyse the effect of body size, lifestyle, environmental isolation and taxonomic affinity on the probability of different regions being reciprocally monophyletic. Sample size was also analysed, because a negative relationship between sample size and probability of being reciprocally monophyletic would indicate biases due to undersampling in the original studies. Separate analyses were performed for three potential types of barriers to gene flow for marine organisms (the water barrier of the middle of the oceans, the temperature barrier of the equator, and the land barrier of the continents). Results Environmental isolation was the only variable in the best-fitting model for the probability of populations from each side of an ocean being reciprocally monophyletic. The estimated importance of body size was quite large and the lack of this variable in the best-fitting model may be a power issue due to the small sample size (n= 40). Both environmental isolation and body size were important for the probability of monophyletic populations in different hemispheres. The analysis of isolation between different oceans did not produce clear results. The relationship between sample intensity and probability of being reciprocally monophyletic was positive for the isolation between different oceans and non-existent for the two other analyses. Main conclusions The results showed that body size was an important factor governing the potential for geographic variation but not the only important factor by far. These results clearly weaken the ‘everything is everywhere’ hypothesis as they showed that microscopic organisms may have geographic variation, albeit to a lesser degree than larger organisms.

Microscopic eukaryotes living in a dying lake (Lake Koronia, Greece)

The morphological and phylogenetic diversity of the microscopic eukaryotes of the Lake Koronia water column was investigated during a mass kill of birds and fish in August-September 2004. The dominant morphospecies corresponded to the known toxin-producing species Prymnesium parvum, followed by Amoebidium sp., a taxon belonging to the group of parasitic Mesomycetozoea, and the common chlorophyte Pediastrum boryanum. Prymnesium exhibited heteromorphic life-cycle stages (flagellate and nonmotile coccoid cells). Phylogenetic analysis with 18S rRNA gene suggested that these heteromorphic stages belonged to the Platychrysis-Prymnesium monophyletic group. The most abundant phylotype was almost identical to P. boryanum. The fungal phylotypes were related to the Chytridiomycota, and the ciliate-like ones were closely related to Enchelys polynucleata and Pattersoniella vitiphila. Two phylotypes representing novel members belonging to the Jakobida and the Apicomplexa were also found. The microscopic eukaryotes of Lake Koronia include several organisms that are related to parasitic life modes.

Insights into the diversity of eukaryotes in acid mine drainage biofilm communities.

Microscopic eukaryotes are known to have important ecosystem functions, but their diversity in most environments remains vastly unexplored. Here we analyzed an 18S rRNA gene library from a subsurface iron- and sulfur-oxidizing microbial community growing in highly acidic (pH < 0.9) runoff within the Richmond Mine at Iron Mountain (northern California). Phylogenetic analysis revealed that the majority (68%) of the sequences belonged to fungi. Protists falling into the deeply branching lineage named the acidophilic protist clade (APC) and the class Heterolobosea were also present. The APC group represents kingdom-level novelty, with <76% sequence similarity to 18S rRNA gene sequences of organisms from other environments. Fluorescently labeled oligonucleotide rRNA probes were designed to target each of these groups in biofilm samples, enabling abundance and morphological characterization. Results revealed that the populations vary significantly with the habitat and no group is ubiquitous. Surprisingly, many of the eukaryotic lineages (with the exception of the APC) are closely related to neutrophiles, suggesting that they recently adapted to this extreme environment. Molecular analyses presented here confirm that the number of eukaryotic species associated with the acid mine drainage (AMD) communities is low. This finding is consistent with previous results showing a limited diversity of archaea, bacteria, and viruses in AMD environments and suggests that the environmental pressures and interplay between the members of these communities limit species diversity at all trophic levels.

An interdisciplinary approach to assess the functional diversity of free-living microscopic eukaryotes

Free-living microbes are arguably ubiquitously dispersed. Molecular phylogeographies have been used to assess microbial distributions but can be difficult to interpret. Combinations of molecular and ecophysiological data have, however, proven useful in assessing the influence of dis- persal, local adaptation and historical contingency on distributions. A logical extension of this approach is to develop molecular markers for ecophysiological traits, which would allow the assess- ment of adaptations in large numbers of environmental isolates without requiring extensive cultur- ing. To assess this approach, we compared enzyme activity and gene expression of Na + /K + ATPase in response to salinity, and compared Na + /K + ATPase mRNA sequences, in 3 Brachionus plicatilis (Rotifera) sibling species. B. plicatilis siblings display different salinity tolerances, which in turn influence their distributions. Na + /K + ATPase is an important component of salinity tolerance and a potentially useful marker for ecophysiological variation. In all cases, Na + /K + ATPase enzyme activity and gene expression increased in response to salinity (5 to 50‰) and paralleled growth rate differ- ences: highest enzyme activity/gene expression occurred in the sibling species that displayed high- est growth. However, sequence variation in Na + /K + ATPase mRNAs was minor (~4%) and did not match gene expression patterns; thus, differences between siblings in Na + /K + ATPase occurred as a result of differential expression of highly similar gene transcripts. While we were not able to develop functional molecular markers for salinity tolerance in B. plicatilis, we highlight that the application of phylogenetic and functional markers will be a powerful tool for assessing the distributions of free- living microorganisms.