Monitoring of reproductive health in the striped catfish Pangasianodon hypophthalmus (Sauvage, 1878) from the Saen Saep Canal, Thailand

Khlong Saen Saep is one of the most important and large canal systems in Bangkok, Thailand. However, the emergence of heavily polluted water has occasionally been reported due to the domestic sewage and industrial effluents discharged into the system. This situation may affect the reproductive status of aquatic lives residing in this canal. To evaluate the reproductive status of the canal inhabitant, the striped catfish Pangasianodon hypophthalmus (Sauvage, 1878)—a common dweller of the Saen Saep Canal—was collected from two selected stations, the Bumpen Nua Temple and the Kamalun Islam Mosque. The fish gonads were then anatomically and histologically examined. The results indicated that neither parasites nor ovary with external abnormality were found. Nevertheless, several histological alterations were detected, including vacuolar degeneration of previtellogenic oocytes, accumulation of melanomacrophage centers (MMCs), and atretic oocytes. Moreover, severe histopathological changes, such as the eosinophilic cytoplasm of spermatogonia, MMCs, blood congestion, and syncytium of spermatozoa, were observed in the fish testis. Our study suggested that the environmental stress and pollutions previously reported from the Saen Saep Canal possibly underpin the gonadal impairments of P. hypophthalmus examined and may have adverse impact on the reproductive health of others living in this canal syste

Rhizarian ‘Novel Clade 10’ Revealed as Abundant and Diverse Planktonic and Terrestrial Flagellates, including Aquavolon n. gen.

0000-0002-6719-5565The file attached is the Published/publisher’s pdf version of the articleThis is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited

The mitochondrial genome sequence of the ciliate Paramecium caudatum reveals a shift in nucleotide composition and codon usage within the genus Paramecium

<p>Abstract</p> <p>Background</p> <p>Despite the fact that the organization of the ciliate mitochondrial genome is exceptional, only few ciliate mitochondrial genomes have been sequenced until today. All ciliate mitochondrial genomes are linear. They are 40 kb to 47 kb long and contain some 50 tightly packed genes without introns. Earlier studies documented that the mitochondrial guanine + cytosine contents are very different between <it>Paramecium tetraurelia </it>and all studied <it>Tetrahymena </it>species. This raises the question of whether the high mitochondrial G+C content observed in <it>P. tetraurelia </it>is a characteristic property of <it>Paramecium </it>mtDNA, or whether it is an exception of the ciliate mitochondrial genomes known so far. To test this question, we determined the mitochondrial genome sequence of <it>Paramecium caudatum </it>and compared the gene content and sequence properties to the closely related <it>P. tetraurelia</it>.</p> <p>Results</p> <p>The guanine + cytosine content of the <it>P. caudatum </it>mitochondrial genome was significantly lower than that of <it>P. tetraurelia </it>(22.4% vs. 41.2%). This difference in the mitochondrial nucleotide composition was accompanied by significantly different codon usage patterns in both species, i.e. within <it>P. caudatum </it>clearly A/T ending codons dominated, whereas for <it>P. tetraurelia </it>the synonymous codons were more balanced with a higher number of G/C ending codons. Further analyses indicated that the nucleotide composition of most members of the genus <it>Paramecium </it>resembles that of <it>P. caudatum </it>and that the shift observed in <it>P. tetraurelia </it>is restricted to the <it>P. aurelia </it>species complex.</p> <p>Conclusions</p> <p>Surprisingly, the codon usage bias in the <it>P. caudatum </it>mitochondrial genome, exemplified by the effective number of codons, is more similar to the distantly related <it>T. pyriformis </it>and other single-celled eukaryotes such as <it>Chlamydomonas</it>, than to the closely related <it>P. tetraurelia</it>. These differences in base composition and codon usage bias were, however, not reflected in the amino acid composition. Most probably, the observed picture is best explained by a hitherto unknown (neutral or adaptive) mechanism that increased the guanine + cytosine content in <it>P. tetraurelia </it>mtDNA on the one hand, and strong purifying selection on the ancestral amino acid composition on the other hand. These contradicting forces are counterbalanced by a considerably altered codon usage pattern.</p

Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora)

Recent advances in molecular technology have revolutionized research on allaspects of the biology of organisms, including ciliates, and created unprece-dented opportunities for pursuing a more integrative approach to investigationsof biodiversity. However, this goal is complicated by large gaps and inconsis-tencies that still exist in the foundation of basic information about biodiversityof ciliates. The present paper reviews issues relating to the taxonomy of cili-ates and presents specific recommendations for best practice in the observa-tion and documentation of their biodiversity. This effort stems from aworkshop that explored ways to implement six Grand Challenges proposed bythe International Research Coordination Network for Biodiversity of Ciliates(IRCN-BC). As part of its commitment to strengthening the knowledge basethat supports research on biodiversity of ciliates, the IRCN-BC proposes topopulate The Ciliate Guide, an online database, with biodiversity-related dataand metadata to create a resource that will facilitate accurate taxonomic identi-fications and promote sharing of data

Parasites, pathogens and commensals in the “low-impact” non-native amphipod host Gammarus roeselii

Background: Whilst vastly understudied, pathogens of non-native species (NNS) are increasingly recognised as important threats to native wildlife. This study builds upon recent recommendations for improved screening for pathogens in NNS by focusing on populations of Gammarus roeselii in Chojna, north-western Poland. At this location, and in other parts of continental Europe, G. roeselii is considered a well-established and relatively ‘low-impact’ invader, with little understanding about its underlying pathogen profile and even less on potential spill-over of these pathogens to native species. Results: Using a combination of histological, ultrastructural and phylogenetic approaches, we define a pathogen profile for non-native populations of G. roeselii in Poland. This profile comprised acanthocephalans (Polymorphus minutus Goese, 1782 and Pomphorhynchus sp.), digenean trematodes, commensal rotifers, commensal and parasitic ciliated protists, gregarines, microsporidia, a putative rickettsia-like organism, filamentous bacteria and two viral pathogens, the majority of which are previously unknown to science. To demonstrate potential for such pathogenic risks to be characterised from a taxonomic perspective, one of the pathogens, a novel microsporidian, is described based upon its pathology, developmental cycle and SSU rRNA gene phylogeny. The novel microsporidian Cucumispora roeselii n. sp. displayed closest morphological and phylogenetic similarity to two previously described taxa, Cucumispora dikerogammari Ovcharenko, 2010 and Cucumispora ornata Bojko, 2015. Conclusions: In addition to our discovery extending the host range for the genus Cucumispora Ovcharenko, 2010 outside of the amphipod host genus Dikerogammarus Stebbing, we reveal significant potential for the co-transfer of (previously unknown) pathogens alongside this host when invading novel locations. This study highlights the importance of pre-invasion screening of low-impact NNS and, provides a means to document and potentially mitigate the additional risks posed by previously unknown pathogens

Environmental Barcoding Reveals Massive Dinoflagellate Diversity in Marine Environments

Rowena F. Stern is with University of British Columbia, Ales Horak is with University of British Columbia, Rose L. Andrew is with University of British Columbia, Mary-Alice Coffroth is with State University of New York at Buffalo, Robert A. Andersen is with the Bigelow Laboratory for Ocean Sciences, Frithjof C. Küpper is with the Scottish Marine Institute, Ian Jameson is with CSIRO Marine and Atmospheric Research, Mona Hoppenrath is with the German Center for Marine Biodiversity Research, Benoît Véron is with University of Caen Lower Normandy and the National Institute for Environmental Studies, Fumai Kasai is with the National Institute for Environmental Studies, Jerry Brand is with UT Austin, Erick R. James is with University of British Columbia, Patrick J. Keeling is with University of British Columbia.Background -- Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known “species”, as a reference to measure the natural diversity in three marine environments. Methodology/Principal Findings -- In this study, we assembled a large cytochrome c oxidase 1 (COI) barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean), including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species. Conclusions/Significance -- COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a massive amount of natural diversity in dinoflagellates. This highlights the extent to which we underestimate microbial diversity in the environment.This project was funded by Genome Canada and the Canadian Barcode of Life Network. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Biological Sciences, School o

Tracing the origins of centrioles, cilia, and flagella

Centrioles/basal bodies (CBBs) are microtubule-based cylindrical organelles that nucleate the formation of centrosomes, cilia, and flagella. CBBs, cilia, and flagella are ancestral structures; they are present in all major eukaryotic groups. Despite the conservation of their core structure, there is variability in their architecture, function, and biogenesis. Recent genomic and functional studies have provided insight into the evolution of the structure and function of these organelles

Comparative morphology and molecular evolution of marine interstitial cercozoans

The Cercozoa is an extremely diverse and poorly understood group of amoeboflagellated microeukaryotes that are united mainly by molecular phylogenetic data; a concrete synapomorphy at the morphological level has yet to be identified for the group. In order to better understand the biodiversity and evolutionary history of this lineage, I explored several marine benthic habitats in British Columbia, Canada and characterized novel cercozoans with high-resolution light microscopy and electron microscopy. Comparative ultrastructural studies using scanning and transmission electron microscopy on some of the newly discovered taxa demonstrated several novel features, including putative primary endosymbionts in one lineage (i.e., Auranticordis) and homologous patterns of muciferous bodies beneath the cell surface in another lineage. I coupled these morphological data with molecular phylogenetic analyses of small subunit (SSU) and large subunit (LSU) rDNA sequences and comparative analyses of polyubiquitin genes. This approach provided evidence that a concatenation of SSU and LSU rDNA sequences improves the phylogenetic resolution within the Cercozoa and that an insertion of one or two amino acids at the junctions between monomers in the polyubiquitin gene is a universal molecular signature for cercozoans (and foraminiferans). This study also enabled me to discover and describe eleven new species and five new genera, which underscores how poorly we currently understand the diversity of these marine microeukaryotic predators. The acquired SSU rDNA sequences from these novel lineages enabled me to provide the cellular identities of several environmental DNA sequence clades previously containing only uncharacterized taxa; these data also demonstrated the effectiveness of using a 600-bp fragment of the SSU rRNA gene for delimiting cercozoan species with limited morphological variation.Science, Faculty ofZoology, Department ofGraduat