New and poorly known "araphid" diatom species (Bacillariophyta) from regions near Lake Titicaca, South America and a discussion on the continued use of morphological characters in "araphid" diatom taxonomy.
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ABSTRACT:
SUBMITTER: Morales EA
PROVIDER: S-EPMC8688410 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Latin America, like other areas in the world, is faced with the problem of high arsenic (As) background in surface and groundwater, with impacts on human health. We studied As biogeochemical cycling by periphyton in Lake Titicaca and the mine-impacted Lake Uru Uru. As concentration was measured in water, sediment, totora plants (Schoenoplectus californicus) and periphyton growing on stems, and As speciation was determined by X-ray absorption spectroscopy in bulk and EDTA-extracted periphyton. Dissolved arsenic was between 5.0 and 15 ?g L-1 in Lake Titicaca and reached 78.5 ?g L-1 in Lake Uru Uru. As accumulation in periphyton was highly variable. We report the highest As bioaccumulation factors ever measured (BAFsperiphyton up to 245,000) in one zone of Lake Titicaca, with As present as As(V) and monomethyl-As (MMA(V)). Non-accumulating periphyton found in the other sites presented BAFsperiphyton between 1281 and 11,962, with As present as As(III), As(V) and arsenosugars. DNA analysis evidenced several taxa possibly related to this phenomenon. Further screening of bacterial and algal isolates would be necessary to identify the organism(s) responsible for As hyperaccumulation. Impacts on the ecosystem and human health appear limited, but such organisms or consortia would be of great interest for the treatment of As contaminated water.
| S-EPMC6650431 | biostudies-literature
Project description:This study deals with Ulnaria species found and described from two regions of China with large climate differences during the period of 2014-2022. The first region, located in the Wuling Mountains and Hunan province, has a subtropical climate and the second in Qinghai, a northwest province of China, has a highland continental climate which is characterized by a cold and long winter and warm, short summer. Previously there were nine new Ulnaria species published from the first region. This study describes 14 additional new Ulnaria taxa, nine of which were found in the first region and five of which were found in the second region. A key to the Ulnaria species that have been described from China is provided. The main morphological characteristics for 63 Ulnaria taxa are summarized in Appendices which allow the division of these Ulnaria taxa into three groups: the seven members of group one all possess both uniseriate striae and valve marginal spines, the 42 members of group two all possess uniseriate or mostly uniseriate striae but without the valve marginal spines, and the 14 members of group three all possess mostly biseriate striae and without valve marginal spines. To summarize the morphological characters of the published Ulnaria taxa and 14 taxa described in this study several conclusions for the characterization of Ulnaria are drawn: 1) each cell has two valve-appressed, long plate-like plastids; 2) living cells of many Ulnaria species often lie in girdle view on a slide because they have deep mantles and some copulae associated with either the epivalve or the hypovalve so that the cell depth is often larger than the valve width; 3) the basic structures forming a valve include sternum, virgae, and vimines/viminules; 4) the valvocopula is a closed hoop which has a similar ultrastructure in all Ulnaria taxa but differs from the other copulae in structure; 5) the configuration of girdle bands is a common condition; 6) the life history of Ulnaria can be divided into the four series of successive stages: auxospore, initial cell, pre-normal vegetative cell, and normal vegetative cell, which is very similar to the life history of Hannaeainaequidentata (Lagerstedt) Genkal and Kharitonov; 7) the closed valvocopula is proposed as a definition character for the genus Ulnaria because demonstrating all girdle bands closed is impracticable.
| S-EPMC10314368 | biostudies-literature
Project description:Microplastic pollution is a widespread environmental concern. Like other anthropogenic pollutants, microplastics can reach aquatic ecosystems through rivers and interact with the aquatic biota. For instance, Lake Titicaca (between Bolivia and Peru), one of the great ancient lakes in South America (3,809 m a.s.l.), shows a pollution problem, particularly in the southern shallow basin (Lago Menor) in Bolivia. Nevertheless, our knowledge of the presence of microplastics and their interaction with the biota of Lake Titicaca is limited. Therefore, this study evaluated the presence of microplastics in the stomach content of the four fish species targeted by local fisheries in Lago Menor of Lake Titicaca (Orestias luteus, Orestias agassizii, Trichomycterus dispar, and Odonthestes bonariensis; N = 1,283), and looked for relationships with trophic guilds or fishing areas. Additionally, surface water was analyzed to evaluate the presence of microplastics in the water. The evaluation of microplastics was carried out by visual observations. We observed that the frequency of microplastic ingestion was low in all species (<5%). Conversely, microplastic was present in the water, with the highest quantity at the southern part of Lago Menor (103 ± 20 particles per L), without differences in the microplastic number between sites. Most microplastics counted in stomach contents were fibers, whereas water samples mainly contained fragments. Our results point to microplastic pollution in Lago Menor of Lake Titicaca. However, we could not determine the pollution rate due to considerable methodological limitations. Further research will be needed to robustly detect microplastics in Lake Titicaca and their impact on the fish species in the lake.
| S-EPMC9653051 | biostudies-literature
Project description:Since the 1980s, many have suggested we are in the midst of a massive extinction crisis, yet only 799 (0.04%) of the 1.9 million known recent species are recorded as extinct, questioning the reality of the crisis. This low figure is due to the fact that the status of very few invertebrates, which represent the bulk of biodiversity, have been evaluated. Here we show, based on extrapolation from a random sample of land snail species via two independent approaches, that we may already have lost 7% (130,000 extinctions) of the species on Earth. However, this loss is masked by the emphasis on terrestrial vertebrates, the target of most conservation actions. Projections of species extinction rates are controversial because invertebrates are essentially excluded from these scenarios. Invertebrates can and must be assessed if we are to obtain a more realistic picture of the sixth extinction crisis.
| S-EPMC4485135 | biostudies-literature
Project description:BackgroundDiatoms are one of the most species-rich groups of eukaryotic microbes known. Diatoms are also the only group of eukaryotic micro-algae with a diplontic life history, suggesting that the ancestral diatom switched to a life history dominated by a duplicated genome. A key mechanism of speciation among diatoms could be a propensity for additional stable genome duplications. Across eukaryotic taxa, genome size is directly correlated to cell size and inversely correlated to physiological rates. Differences in relative genome size, cell size, and acclimated growth rates were analyzed in isolates of the diatom Ditylum brightwellii. Ditylum brightwellii consists of two main populations with identical 18s rDNA sequences; one population is distributed globally at temperate latitudes and the second appears to be localized to the Pacific Northwest coast of the USA. These two populations co-occur within the Puget Sound estuary of WA, USA, although their peak abundances differ depending on local conditions.ResultsAll isolates from the more regionally-localized population (population 2) possessed 1.94 +/- 0.74 times the amount of DNA, grew more slowly, and were generally larger than isolates from the more globally distributed population (population 1). The ITS1 sequences, cell sizes, and genome sizes of isolates from New Zealand were the same as population 1 isolates from Puget Sound, but their growth rates were within the range of the slower-growing population 2 isolates. Importantly, the observed genome size difference between isolates from the two populations was stable regardless of time in culture or the changes in cell size that accompany the diatom life history.ConclusionsThe observed two-fold difference in genome size between the D. brightwellii populations suggests that whole genome duplication occurred within cells of population 1 ultimately giving rise to population 2 cells. The apparent regional localization of population 2 is consistent with a recent divergence between the populations, which are likely cryptic species. Genome size variation is known to occur in other diatom genera; we hypothesize that genome duplication may be an active and important mechanism of genetic and physiological diversification and speciation in diatoms.
| S-EPMC2821323 | biostudies-literature
Project description:BackgroundThe taxonomic classification of the suborder Tintinnina Kofoid & Campbell, 1929, a species-rich group of planktonic ciliated protistans with a characteristic lorica, has long been ambiguous largely due to the lack of cytological and molecular data for most species. Tintinnopsis is the largest, most widespread, and most taxonomically complex genus within this group with about 170 species occurring in nearshore waters. Previous molecular phylogenetic studies have revealed that Tintinnopsis is polyphyletic.ResultsHere we document the live morphology, infraciliature, gene sequences, and habitat characteristics of three poorly known tintinnine species, viz. Tintinnopsis karajacensis Brandt, 1896, Tintinnopsis gracilis Kofoid & Campbell, 1929, and Tintinnopsis tocantinensis Kofoid & Campbell, 1929, isolated from the coastal waters of China. Based on a unique cytological feature (i.e., an elongated ciliary tuft with densely arranged kinetids) in the former two species, Antetintinnopsis gen. nov. is erected with Antetintinnopsis hemispiralis (Yin, 1956) comb. nov. (original combination: Tintinnopsis hemispiralis Yin, 1956) designated as the type species. Moreover, A. karajacensis (Brandt, 1896) comb. nov. (original combination: Tintinnopsis karajacensis Brandt, 1896) and A. gracilis (Kofoid & Campbell, 1929) comb. nov. (original combination: Tintinnopsis gracilis Kofoid & Campbell, 1929) are placed in a highly supported clade that branches separately from Tintinnopsis clades in phylogenetic trees based on SSU rDNA and LSU rDNA sequence data, thus supporting the establishment of the new genus. One other species is assigned to Antetintinnopsis gen. nov., namely A. subacuta (Jörgensen, 1899) comb. nov. (original combination Tintinnopsis subacuta Jörgensen, 1899).ConclusionsThe findings of the phylogenetic analyses support the assertion that cytological characters are taxonomically informative for tintinnines. This study also contributes to the broadening of our understanding of the tintinnine biodiversity and evolution.
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Project description:Lake Titicaca, situated in the Altiplano high plateau, is the only ancient lake in South America. This 2- to 3-My-old (where My is million years) water body has had a complex history that included at least five major hydrological phases during the Pleistocene. It is generally assumed that these physical events helped shape the evolutionary history of the lake's biota. Herein, we study an endemic species assemblage in Lake Titicaca, composed of members of the microgastropod genus Heleobia, to determine whether the lake has functioned as a reservoir of relic species or the site of local diversification, to evaluate congruence of the regional paleohydrology and the evolutionary history of this assemblage, and to assess whether the geographic distributions of endemic lineages are hierarchical. Our phylogenetic analyses indicate that the Titicaca/Altiplano Heleobia fauna (together with few extralimital taxa) forms a species flock. A molecular clock analysis suggests that the most recent common ancestor (MRCAs) of the Altiplano taxa evolved 0.53 (0.28-0.80) My ago and the MRCAs of the Altiplano taxa and their extralimital sister group 0.92 (0.46-1.52) My ago. The endemic species of Lake Titicaca are younger than the lake itself, implying primarily intralacustrine speciation. Moreover, the timing of evolutionary branching events and the ages of two precursors of Lake Titicaca, lakes Cabana and Ballivián, is congruent. Although Lake Titicaca appears to have been the principal site of speciation for the regional Heleobia fauna, the contemporary spatial patterns of endemism have been masked by immigration and/or emigration events of local riverine taxa, which we attribute to the unstable hydrographic history of the Altiplano. Thus, a hierarchical distribution of endemism is not evident, but instead there is a single genetic break between two regional clades. We also discuss our findings in relation to studies of other regional biota and suggest that salinity tolerance was the most likely limiting factor in the evolution of Altiplano species flocks.
| S-EPMC3434920 | biostudies-literature
Project description:This study seeks to determine the phylogenetic position of the diatom genus Rhoicosphenia. Currently, four hypotheses based on the morphology of the siliceous valve and its various ultrastructural components, sexual reproduction, and chloroplasts have been proposed. Two previous morphological studies have tentatively placed Rhoicosphenia near members of the Achnanthidiaceae and Gomphonemataceae, and no molecular studies have been completed. The position of Rhoicosphenia as sister to 'monoraphid' diatoms is problematic due to the apparent non-monophyly of that group, so hypotheses of 'monoraphid' monophyly are also tested. Using an analysis of morphological and cytological features, as well as sequences from three genes, SSU, LSU, and rbcL, recovered from several freshwater Rhoicosphenia populations that have similar morphology to Rhoicosphenia abbreviata (Agardh) Lange-Bertalot, we have analyzed the phylogenetic position of Rhoicosphenia in the context of raphid diatoms. Further, we have used topology testing to determine the statistical likelihoods of these relationships. The hypothesis that Rhoicosphenia is a member of the Achnanthidiaceae cannot be rejected, while the hypothesis that it is a member of the Gomphonemataceae can be rejected. In our analyses, members of the Achnanthidiaceae are basal to Rhoicosphenia, and Rhoicosphenia is basal to the Cymbellales, or a basal member of the Cymbellales, which includes the Gomphonemataceae. Hypothesis testing rejects the monophyly of 'monoraphid' diatoms.
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Project description:Deep convolutional neural networks are emerging as the state of the art method for supervised classification of images also in the context of taxonomic identification. Different morphologies and imaging technologies applied across organismal groups lead to highly specific image domains, which need customization of deep learning solutions. Here we provide an example using deep convolutional neural networks (CNNs) for taxonomic identification of the morphologically diverse microalgal group of diatoms. Using a combination of high-resolution slide scanning microscopy, web-based collaborative image annotation and diatom-tailored image analysis, we assembled a diatom image database from two Southern Ocean expeditions. We use these data to investigate the effect of CNN architecture, background masking, data set size and possible concept drift upon image classification performance. Surprisingly, VGG16, a relatively old network architecture, showed the best performance and generalizing ability on our images. Different from a previous study, we found that background masking slightly improved performance. In general, training only a classifier on top of convolutional layers pre-trained on extensive, but not domain-specific image data showed surprisingly high performance (F1 scores around 97%) with already relatively few (100-300) examples per class, indicating that domain adaptation to a novel taxonomic group can be feasible with a limited investment of effort.
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Project description:Acrophialophora fusispora is an emerging opportunistic fungus capable of causing human infections. The taxonomy of the genus is not yet resolved and, in order to facilitate identification of clinical specimens, we have studied a set of clinical and environmental Acrophialophora isolates by morphological and molecular analyses. This set included the available type strains of Acrophialophora species and similar fungi, some of which were considered by various authors to be synonyms of A. fusispora. Sequence analysis of the large subunit (LSU) and internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA and a fragment of the β-tubulin (Tub) gene revealed that Acrophialophora belongs in the family Chaetomiaceae and comprises three different species, i.e., A. fusispora, Acrophialophora levis, and Acrophialophora seudatica; the latter was previously included in the genus Ampullifera. The most prevalent species among clinical isolates was A. levis (72.7%), followed by A. fusispora (27.3%), both of which were isolated mostly from respiratory specimens (72.7%), as well as subcutaneous and corneal tissue samples. In general, of the eight antifungal drugs tested, voriconazole had the greatest in vitro activity, while all other agents showed poor in vitro activity against these fungi.
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