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Description of Naviculavanseea sp. nov. (Naviculales, Naviculaceae), a new species of diatom from the highly alkaline Lake Van (Republic of Türkiye) with complete characterisation of its organellar genomes and multigene phylogeny. PHYTOKEYS 2024; 241:27-48. [PMID: 38628637 PMCID: PMC11019260 DOI: 10.3897/phytokeys.241.118903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/19/2024] [Indexed: 04/19/2024]
Abstract
The current article describes Naviculavanseeasp. nov., a new species of diatom from Lake Van, a highly alkaline lake in Eastern Anatolia (Türkiye). The description is based on light and scanning electron microscopy performed on two monoclonal cultures. The complete nuclear rRNA clusters and plastid genomes have been sequenced for these two strains and the complete mitogenome for one of them. The plastome of both strains shows the probable loss of a functional ycf35 gene. They also exhibit two IB4 group I introns in their rrl, each encoding for a putative LAGLIDADG homing endonuclease, with the first L1917 IB4 intron reported amongst diatoms. The Maximum Likelihood phylogeny inferred from a concatenated alignment of 18S, rbcL and psbC distinguishes N.vanseea sp. nov. from the morphologically similar species Naviculacincta and Naviculamicrodigitoradiata.
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Maximising environmental pressure-response relationship signals from diatom-based metabarcoding in rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169445. [PMID: 38159778 DOI: 10.1016/j.scitotenv.2023.169445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
DNA metabarcoding has been performed on a large number of river phytobenthos samples collected from the UK, using rbcL primers optimised for diatoms. Within this dataset the composition of non-diatom sequence reads was studied and the effect of including these in models for evaluating the nutrient gradient was assessed. Whilst many non-diatom taxonomic groups were detected, few contained the full diversity expected in riverine environments. This may be due to the performance of the current primers in characterising the wider phytobenthic community and influenced by the sampling method employed, as both were developed specifically for diatoms. Nevertheless, the study identified considerable diversity in some groups, e.g. Eustigmatophyceae and a wider distribution than previously thought for freshwater Phaeophyceae. These results offer a strong case for the benefits of metabarcoding for expanding knowledge of aquatic biodiversity in the UK and elsewhere. Many of the ASVs associated with non-diatoms showed significant pressure responses; however, models that included non-diatoms had similar predictive strength to those based on diatoms alone. Whilst limitations of the primers for assessing non-diatoms may play a role in explaining these results, the diatoms provide a strong signal along the nutrient gradient and other algae, therefore, add little unique information. We recommend that future developments should use ASVs to calculate metrics, with links to reference databases made as a final step to generate lists of taxa to support interpretation. Any further exploration of the potential of non-diatoms would benefit from access to a well-curated reference database, similar to diat.barcode. Such a database does not yet exist, and we caution against the indiscriminate use of NCBI GenBank as a taxonomic resource as many rbcL sequences deposited have not been curated.
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Prey preference in a kleptoplastic dinoflagellate is linked to photosynthetic performance. THE ISME JOURNAL 2023; 17:1578-1588. [PMID: 37391621 PMCID: PMC10504301 DOI: 10.1038/s41396-023-01464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 07/02/2023]
Abstract
Dinoflagellates of the family Kryptoperidiniaceae, known as "dinotoms", possess diatom-derived endosymbionts and contain individuals at three successive evolutionary stages: a transiently maintained kleptoplastic stage; a stage containing multiple permanently maintained diatom endosymbionts; and a further permanent stage containing a single diatom endosymbiont. Kleptoplastic dinotoms were discovered only recently, in Durinskia capensis; until now it has not been investigated kleptoplastic behavior and the metabolic and genetic integration of host and prey. Here, we show D. capensis is able to use various diatom species as kleptoplastids and exhibits different photosynthetic capacities depending on the diatom species. This is in contrast with the prey diatoms in their free-living stage, as there are no differences in their photosynthetic capacities. Complete photosynthesis including both the light reactions and the Calvin cycle remain active only when D. capensis feeds on its habitual associate, the "essential" diatom Nitzschia captiva. The organelles of another edible diatom, N. inconspicua, are preserved intact after ingestion by D. capensis and expresses the psbC gene of the photosynthetic light reaction, while RuBisCO gene expression is lost. Our results indicate that edible but non-essential, "supplemental" diatoms are used by D. capensis for producing ATP and NADPH, but not for carbon fixation. D. capensis has established a species-specifically designed metabolic system allowing carbon fixation to be performed only by its essential diatoms. The ability of D. capensis to ingest supplemental diatoms as kleptoplastids may be a flexible ecological strategy, to use these diatoms as "emergency supplies" while no essential diatoms are available.
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Ethical Implications of Cleft Lip and Palate Repair in Patients with Trisomy 13 and Trisomy 18. Cleft Palate Craniofac J 2023:10556656231163722. [PMID: 36945782 DOI: 10.1177/10556656231163722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Children born with Trisomy 13 or 18 (T13/18) often have multiple congenital anomalies, many of which drastically shorten their lifespan. Among these defects are cleft lip and palate, the repair of which presents an ethical dilemma to the surgeon given the underlying comorbidities associated with T13/18. The authors present an ethical discussion and institutional experience in navigating this dilemma. METHODS The authors analyzed existing literature on T13 and T18 surgery and mortality. A retrospective study over ten years was also conducted to identify pediatric patients who underwent surgical correction of cleft lip and/or palate secondary to a confirmed diagnosis of T13/18. The authors identified two patients and examined their treatment course. RESULTS The authors' review of literature coupled with their institution's experience builds on the published successes of correcting cleft lip and palate in the setting of T13/18. It was found that both patients identified in the case series underwent successful correction with no surgical complications. CONCLUSION A careful balance must be struck between improved quality of life, benefits of treatment, and risks of surgery in children with T13/T18. Careful consideration should be given to the medical status of these complex patients. If the remaining medical comorbidities are well managed and under control, there is an ethical precedent for performing cleft lip and palate surgeries on these children. A diagnosis of T13/T18 alone is not enough to disqualify patients from cleft lip/palate surgery.
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Evaluation of two short overlapping rbcL markers for diatom metabarcoding of environmental samples: Effects on biomonitoring assessment and species resolution. CHEMOSPHERE 2022; 307:135933. [PMID: 35952789 DOI: 10.1016/j.chemosphere.2022.135933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/02/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Two short diatom rbcL barcodes, 331 bp and 263 bp in length, have frequently been used in diatom metabarcoding studies. They overlap in a common 263-bp region but differ in the presence or absence of a 68-bp tail at the 5' end. Though the effectiveness of both has been demonstrated in separate biomonitoring and diversity studies, the impact of the 68-bp non-shared region has not been evaluated. Here we compare the two barcodes in terms of the values of a biotic index (IPS) and the ecological status classes derived from their application to an extensive metabarcoding dataset from United Kingdom rivers; this comprised 1703 samples and was produced using the 331-bp primers. In addition, we assess the effectiveness of each barcode for discrimination of genetic variants around and below the species level. The strong correlation found in IPS values between barcodes (Pearson's R = 0.98) indicates that the choice of the barcode does not have major implications for current WFD ecological assessments, although a very few sites (55: 3.23% of those analysed) were downgraded from an acceptable WFD class ("Good") to an unacceptable one ("Moderate"). Analyses of the taxonomic resolution of the two barcodes indicate that for many ASVs, the use of either marker - 263-bp and 331-bp - gives unambiguous assignations at species level though with differences in bootstrap confidence values. Such differences are caused by the stochasticity involved in the naïve Bayesian classifier used and by the fact that genetic distance, regarding closely related species, is increased when using the 331-bp barcode. However, in three cases, species differentiation fails with the shorter marker, leading to underestimates of species diversity. Finally, two ASVs from Nitzschia species evidenced that the use of the shorter marker can sometimes lead to false positives when the extent and nature of infraspecific variation are poorly known.
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Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex. JOURNAL OF PHYCOLOGY 2022; 58:643-656. [PMID: 35861132 PMCID: PMC9804273 DOI: 10.1111/jpy.13281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
In contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes provide a wealth of genomic loci that can resolve relationships among taxonomically challenging lineages. Diatoms are a diverse group of aquatic microalgae that includes important bioindicator species and many such lineages. One example is Nitzschia palea, a widespread species complex with several morphologically defined taxonomic varieties, some of which are critical pollution indicators. Morphological differences among the varieties are subtle and phylogenetic studies based on a few genes fail to resolve their evolutionary relationships. We conducted morphometric and transcriptome analyses of 10 Nitzschia palea strains to resolve the relationships among strains and taxonomic varieties. Nitzschia palea was resolved into three clades, one of which corresponds to a group of strains with narrow linear-lanceolate valves. The other morphological group recovered in the shape outline analysis was not monophyletic and consisted of two clades. Gene-tree concordance analyses and phylogenetic network estimations revealed patterns of incomplete lineage sorting and gene flow between intraspecific lineages. We detected reticulated evolutionary patterns among lineages with different morphologies, resulting in a putative recent hybrid. Our study shows that phylogenomic analyses of unlinked nuclear loci, complemented with morphometrics, can resolve complex evolutionary histories of recently diverged species complexes.
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Assessment of a novel microalgae-cork based technology for removing antibiotics, pesticides and nitrates from groundwater. CHEMOSPHERE 2022; 301:134777. [PMID: 35500629 DOI: 10.1016/j.chemosphere.2022.134777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/01/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Groundwater pollution has increased in recent years due to the intensification of agricultural and livestock activities. This results in a significant reduction in available freshwater resources. Here, we have studied the long term assessment of a green technology (1-4 L/day) based on a photobioreactor (PBR) containing immobilised microalgae-bacteria in polyurethane foam (PF) followed by a cork filter (CF) for removing nitrates, pesticides (atrazine and bromacil), and antibiotics (sulfamethoxazole and sulfacetamide) from groundwater. The prototype was moderately effective for removing nitrates (58%) at an HRT of 8 days, while its efficiency decreased at a HRT of 4 and 2 days (<20% removal). The combined use of PBR-CF enabled antibiotics and pesticides to be attenuated by up to 95% at an HRT of 8 days, but their attenuation decreased with shorter HRT, with pesticides being the compounds most affected (reducing from 97 to 98% at an HRT of 8 days to 23-45% at an HRT of 2 days). Pesticide transformation products were identified after the CF, supporting biodegradation as the main attenuation process. A gene-based metataxonomic assessment linked the attenuation of micropollutants to the presence of specific pesticide biodegradation species (e.g. genus Phenylobacterium, Sphingomonadaceae, and Caulobacteraceae). Therefore, the results highlighted the potential use of microalgae and cork to treat polluted groundwater.
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Assessment of marine benthic diatom communities: insights from a combined morphological-metabarcoding approach in Mediterranean shallow coastal waters. MARINE POLLUTION BULLETIN 2022; 174:113183. [PMID: 35090287 DOI: 10.1016/j.marpolbul.2021.113183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 06/14/2023]
Abstract
We investigated the advantages and disadvantages of light microscope (LM)-based identifications and DNA metabarcoding, based on a 312-bp rbcL marker, for examining benthic diatom communities from Mediterranean shallow coastal environments. For this, we used biofilm samples collected from different substrata in the Ebro delta bays. We show that 1) Ebro delta bays harbour high-diversity diatom communities [LM identified 249 taxa] and 2) DNA metabarcoding effectively reflects this diversity at genus- but not species level, because of the incompleteness of the DNA reference library. Nevertheless, DNA metabarcoding offers new opportunities for detecting small, delicate and rare diatom species missed by LM and diatoms that lack silica frustules. The primers used, though designed for diatoms, successfully amplified rarely reported members of other stramenopile groups. Combining LM and DNA approaches offers stronger support for ecological studies of benthic microalgal communities in shallow coastal environments than using either approach on its own.
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DNA metabarcoding reveals differences in distribution patterns and ecological preferences among genetic variants within some key freshwater diatom species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149029. [PMID: 34375267 DOI: 10.1016/j.scitotenv.2021.149029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/16/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Our study evaluates differences in the distribution and ecology of genetic variants within several ecologically important diatom species that are also key for Water Framework Directive monitoring of European rivers: Fistulifera saprophila (FSAP), Achnanthidium minutissimum (ADMI), Nitzschia inconspicua (NINC) and Nitzschia soratensis (NSTS). We used DADA2 to infer amplicon sequence variants (ASVs) of a short rbcL barcode in 531 environmental samples from biomonitoring campaigns in Catalonia and France. ASVs within each species showed different distribution patterns. Threshold Indicator Taxa ANalysis revealed three ecological groupings of ASVs in both ADMI and FSAP. Two of these in each species were separated by opposite responses to calcium and conductivity. Boosted regression trees additionally showed that both variables greatly influenced the occurrence of these groupings. A third grouping in FSAP was characterized by a negative response to total organic carbon and hence was better represented in waters with higher ecological status than the other FSAP ASVs, contrasting with what is generally assumed for the species. In the two Nitzschia species, our analyses confirmed earlier studies: NINC preferred higher levels of calcium and conductivity. Our findings suggest that the broad ecological tolerance of some diatom species results from overlapping preferences among genetic variants, which individually show much more restricted preferences and distributions. This work shows the importance of studying the ecological preferences of genetic variants within species complexes, now possible with DNA metabarcoding. The results will help reveal and understand biogeographical distributions and facilitate the development of more accurate biological indexes for biomonitoring programmes.
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Ethics in the Labor and Delivery Unit. Anesthesiol Clin 2021; 39:839-849. [PMID: 34776112 DOI: 10.1016/j.anclin.2021.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Obstetric anesthesiologists can use the tenets of principlism to identify ethically supportable decisions. This approach begins with recognizing and upholding the fiduciary obligations that every physician has to their patient. For the pregnant patient, these obligations are both autonomy- and beneficence-based. Additional beneficence-based obligations arise in cases where the fetus is also considered a patient. Ethical dilemmas result from conflict between any of these obligations. A shared decision-making model that incorporates the foundational principles of ethics can be used to resolve these conflicts, leaving clinicians and patients confident that a sound decision-making process has taken place and an ethically supportable decision has been reached.
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Fetal heart rate mirrors maternal temperature during posterior fossa craniotomy: a case report. Int J Obstet Anesth 2021; 47:103193. [PMID: 34144352 DOI: 10.1016/j.ijoa.2021.103193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/27/2021] [Accepted: 05/19/2021] [Indexed: 11/15/2022]
Abstract
While it is well known that maternal temperature affects fetal heart rate, the exact relationship is not well described. The circumstances accompanying most cases of maternal hypothermia and rewarming (e.g. a drowning event) have precluded a precise quantitative description of this relationship. We describe hypothermia and controlled rewarming during resection of a maternal brain stem tumor in the early third trimester. Continuous electronic fetal heart rate and core temperature monitoring demonstrated a near linear relationship during the development of hypothermia and rewarming. Recognition of the close relationship between maternal temperature and fetal heart rate can help safeguard maternal and fetal health, and prevent unnecessary delivery during non-obstetric surgery in pregnancy.
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"You can't make me!" Managing adolescent dissent to anesthesia. Paediatr Anaesth 2021; 31:397-403. [PMID: 33386692 DOI: 10.1111/pan.14119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 11/28/2022]
Abstract
When adolescents require health care, the need to obtain consent from the parent/legal guardian and assent from the patient can create the potential for an ethical dilemma when these two parties are not in agreement. Here, we describe a representative and common case scenario in which both parent and adolescent patient gave consent and assent, respectively, with a full understanding of the risks and benefits of the procedure and anesthetic. At the time of anesthetic induction, however, the patient expresses that she no longer wishes to have the procedure. We identify a number of considerations that inform the ethical analysis of such cases and offer recommendations about the most appropriate path forward for a practitioner faced with a difficult decision about how to respond.
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Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.58056] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.
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A polyphasic approach to the study of the genus Nitzschia (Bacillariophyta): three new planktonic species from the Adriatic Sea. JOURNAL OF PHYCOLOGY 2021; 57:143-159. [PMID: 33089508 DOI: 10.1111/jpy.13085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/08/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
The paraphyletic diatom genus Nitzschia comprises over 1000 morphologically distinct pennate taxa, known from the benthos and plankton of freshwater, brackish, and marine environments. The principal diagnostic characters for delimitation of Nitzschia species include valve shape, the position and structure of the raphe, presence/absence and shape of the proximal raphe endings and terminal raphe fissures, areola structure, and specific morphometric features such as cell size, and stria and fibula density. In this study, we isolated 12 diatom strains into culture from samples collected at the surface or greater depths of the southeastern Adriatic Sea. Morphological analyses included LM, SEM, and TEM observations, which, along with specific morphometric features, allowed us to distinguish three new Nitzschia species. These findings were congruent with the results of phylogenetic analyses performed on nuclear-encoded SSU (18S) rDNA and chloroplast-encoded rbcL and psbC genes. One of the new species (Nitzschia dalmatica sp. nov.) formed a lineage within a clade of Bacillariaceae containing members of the Nitzschia sect. Dubiae, which was sister to Psammodictyon. A second lineage was part of a novel clade that is significantly distinct from other Nitzschia species sequenced so far and includes Nitzschia adhaerens sp. nov. and N. cf. adhaerens. A further new species was found, Nitzschia inordinata sp. nov., which appeared as the sister group to the N. adhaerens clade and the conopeoid Nitzschia species in our phylogenetic trees. Our findings contribute to the overall diversity of genus Nitzschia, especially in identifying some deep branches within the Bacillariaceae, and highlight under-scoring of this genus in marine plankton.
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Ripe for reassessment: A synthesis of available molecular data for the speciose diatom family Bacillariaceae. Mol Phylogenet Evol 2020; 158:106985. [PMID: 33059066 DOI: 10.1016/j.ympev.2020.106985] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/21/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023]
Abstract
The Bacillariaceae is a very species-rich family of raphid diatoms and includes the large and taxonomically difficult genus Nitzschia, whose species are often small-celled and finely structured and have few discrete morphological characters visible in the light microscope. The classification of Nitzschia is still mostly based on one developed in the second half of the 19th century by Grunow, who separated the genus into a series of sections largely on cell shape and symmetry, the position of the raphe, transverse extension of the fibulae, and folding of the valve. We assembled and analysed single-gene and concatenated alignments of nSSU, nLSU, rbcL, psbC and cox1 to test Grunow's and subsequent classifications and to examine selected morphological characters for their potential to help define monophyletic groups. The maximum likelihood trees were equivocal as to monophyly of the family itself but showed good support for each of eight main clades of Bacillariaceae, three of which corresponded more or less to existing genera (Hantzschia, Cylindrotheca and Bacillaria). The other five main clades and some subclades comprised groups of Nitzschia species or assemblies of Nitzschia species with other genera (Pseudo-nitzschia, Fragilariopsis, Neodenticula, Tryblionella, Psammodictyon). Relationships between most of the eight main clades were not resolved robustly but all analyses recovered Nitzschia as non-monophyletic. The Grunowian classification of Nitzschia into sections was not supported, though in some respects (e.g. treatment of sigmoid species) it is better than subsequent reclassifications. Several of the main clades and subclades are cryptic (lacking morphological synapomorphies) and homoplasy is common in both light microscopical and ultrastructural characters (to the extent that organisms initially assigned to the same species sometimes prove to belong to a different main clade). Nevertheless, some characters, including the structure of the raphe canal and girdle, seem to be sufficiently conservative evolutionarily to give a provisional estimate of relationships if molecular data are unavailable. No new formal classifications are proposed but various options are explored and research needs identified.
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The Taxonomy and Diversity of Proschkinia (Bacillariophyta), A Common But Enigmatic Genus from Marine Coasts. JOURNAL OF PHYCOLOGY 2020; 56:953-978. [PMID: 32259285 DOI: 10.1111/jpy.12998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/03/2020] [Indexed: 06/11/2023]
Abstract
Detailed morphological documentation is provided for established Proschkinia taxa, including the generitype, P. bulnheimii, and P. complanata, P. complanatula, P. complanatoides and P. hyalosirella, and six new species. All established taxa are characterized from original material from historical collections. The new species described in this paper (P. luticola, P. staurospeciosa, P. impar, P. modesta, P. fistulispectabilis, and P. rosowskii) were isolated from the Western Pacific (Yellow Sea coast of Korea) and the Atlantic (Scottish and Texas coasts). Thorough documentation of the frustule, valve and protoplast architecture revealed the combination of characters diagnostic of the genus Proschkinia: a single-lobed chloroplast; a broad girdle composed of U-shaped, perforated bands; the position of the conopeate raphe-sternum relative to the external and internal valve surface; and the presence of an occluded process through the valve, termed the "fistula". Seven strains of Proschkinia were grown in culture and five of these were sequenced for nuclear ribosomal SSU and plastid-encoded rbcL. Phylogenetic analysis recovered a clade of Proschkinia with Fistulifera, another fistula-bearing diatom genus, and together these were sister to a clade formed of the Stauroneidaceae; in turn, all of these were sister to a clade composed of Parlibellus and two monoraphid genera Astartiella and Schizostauron. Despite morphological similarities between Proschkinia and the Naviculaceae, these two taxa are distant in our analysis. We document the variation in the morphology of Proschkinia, including significant variability in the fistula, suggesting that fistula ultrastructure might be one of the key features for species identification within the genus.
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Evaluation and sensitivity analysis of diatom DNA metabarcoding for WFD bioassessment of Mediterranean rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138445. [PMID: 32334210 DOI: 10.1016/j.scitotenv.2020.138445] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
Our study of 164 diatom samples from Catalonia (NE Spain) is the first to evaluate the applicability of DNA metabarcoding, based on high throughput sequencing (HTS) using a 312-bp rbcL marker, for biomonitoring Mediterranean rivers. For this, we compared the values of a biotic index (IPS) and the ecological status classes derived from them, between light microscope-based (LM) and HTS methods. Very good correspondence between methods gives encouraging results concerning the applicability of DNA metabarcoding for Catalan rivers for the EU Water Framework Directive (WFD). However, in 10 sites, the ecological status class was downgraded from "Good"/"High" obtained by LM to "Moderate"/"Poor"/"Bad" by HTS; these "critical" sites are especially important, because the WFD requires remedial action by water managers for any river with Moderate or lower status. We investigated the contribution of each species to the IPS using a "leave-one-out" sensitivity analysis, paying special attention to critical sites. Discrepancies in IPS between LM and HTS were mainly due to the misidentification and overlooking in LM of a few species, which were better recovered by HTS. This bias was particularly important in the case of Fistulifera saprophila, whose clear underrepresentation in LM was important for explaining 8 out of the 10 critical sites and probably reflected destruction of weakly-silicified frustules during sample preparation. Differences between species in the rbcL copy number per cell affected the relative abundance obtained by HTS for Achnanthidium minutissimum, Nitzschia inconspicua and Ulnaria ulna, which were also identified by the sensitivity analysis as important for the WFD. Only minor IPS discrepancies were attributed to the incompleteness of the reference library, as most of the abundant and influential species (to the IPS) were well represented there. Finally, we propose that leave-one-out analysis is a good method for identifying priority species for isolation and barcoding.
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Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta). JOURNAL OF PHYCOLOGY 2019; 55:948-970. [PMID: 31106407 DOI: 10.1111/jpy.12886] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 04/24/2019] [Indexed: 06/09/2023]
Abstract
This paper explores the diversity and taxonomy of species within Fragilaria sensu stricto, an abundant and ecologically important diatom genus, taking advantage of cultured and DNA-barcoded material. The goal is to facilitate the identification of European taxa within this complex, providing a unified view on morphological and molecular diversity. There is a general agreement that the separation of species within the group of Fragilaria is difficult because morphological descriptions of species are not consistent between authorities, ongoing taxonomic revisions have resulted in species described with standards of the late 20th and 21st centuries alongside descriptions based on 19th century (light microscopical) criteria, and because not all diagnostic characters can be seen in all specimens encountered in routine analyses. Consequent confusion could blur potentially important ecological distinctions between species. Our study demonstrated that some species defined on morphological criteria could be confirmed using the rbcL chloroplast gene as a genetic marker, for example, Fragilaria gracilis, Fragilaria tenera, Fragilaria perminuta, and Fragilaria subconstricta. However, even for those species, preliminary identifications based on morphology often differed from identifications based on phylogenetic clustering combined with detailed morphological study. Clades were well-defined by rbcL, but based on morphology, the terminal taxa of these clades did not match the currently described Fragilaria species. To clarify recognition of these taxa, we describe three new species: Fragilaria agnesiae, Fragilaria heatherae, and Fragilaria joachimii.
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Discovery of a kleptoplastic 'dinotom' dinoflagellate and the unique nuclear dynamics of converting kleptoplastids to permanent plastids. Sci Rep 2019; 9:10474. [PMID: 31324824 PMCID: PMC6642167 DOI: 10.1038/s41598-019-46852-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 07/05/2019] [Indexed: 12/25/2022] Open
Abstract
A monophyletic group of dinoflagellates, called ‘dinotoms’, are known to possess evolutionarily intermediate plastids derived from diatoms. The diatoms maintain their nuclei, mitochondria, and the endoplasmic reticulum in addition with their plastids, while it has been observed that the host dinoflagellates retain the diatoms permanently by controlling diatom karyokinesis. Previously, we showed that dinotoms have repeatedly replaced their diatoms. Here, we show the process of replacements is at two different evolutionary stages in two closely related dinotoms, Durinskia capensis and D. kwazulunatalensis. We clarify that D. capensis is a kleptoplastic protist keeping its diatoms temporarily, only for two months. On the other hand, D. kwazulunatalensis is able to keep several diatoms permanently and exhibits unique dynamics to maintain the diatom nuclei: the nuclei change their morphologies into a complex string-shape alongside the plastids during interphase and these string-shaped nuclei then condense into multiple round nuclei when the host divides. These dynamics have been observed in other dinotoms that possess permanent diatoms, while they have never been observed in any other eukaryotes. We suggest that the establishment of this unique mechanism might be a critical step for dinotoms to be able to convert kleptoplastids into permanent plastids.
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Surgical interventions and anesthesia in the 1st year of life for lower urinary tract obstruction. J Pediatr Surg 2019; 54:820-824. [PMID: 30049573 DOI: 10.1016/j.jpedsurg.2018.06.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/14/2018] [Accepted: 06/26/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Patients with a prenatal diagnosis of lower urinary tract obstruction (LUTO) may undergo prenatal interventions, such as vesicoamniotic shunt (VAS) placement, as a temporary solution for relieving urinary tract obstruction. A recent FDA communication has raised awareness of the potential neurocognitive adverse effects of anesthesia in children. We hypothesized as to whether a prenatal LUTO staging system was predictive of the number of anesthesia events for prenatally diagnosed LUTO patients. METHODS We retrospectively reviewed the prenatal and postnatal clinical records for patients with prenatally diagnosed LUTO from 2012 to 2015. Patients were stratified by prenatal VAS status and by LUTO disease severity according to Ruano et al. (Ultrasound Obstet Gynecol. 2016). RESULTS 31 patients were identified with a prenatal LUTO diagnosis, and postnatal records were available for 21 patients (seven patients in each stage). When combining prenatal and postnatal anesthesia, there was a significant difference in the number of anesthesia encounters by stage (1.6, 3.7, and 6.7 for Stage I, II, and III respectively, p = .034). Upon univariate analysis, higher gestational age (GA) at birth was associated with a decreased number of anesthesia events in the first year (p = .031). CONCLUSIONS The majority of infants with prenatally diagnosed LUTO will undergo postnatal procedures with general anesthesia exposure in the first year of life. Patients with higher prenatal LUTO severity experienced a higher number of both prenatal and postnatal anesthesia encounters. In addition, higher GA at birth was associated with fewer anesthesia encounters in the first year. LEVEL OF EVIDENCE This is a prognostic study with Level IV evidence.
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Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. J Eukaryot Microbiol 2019; 66:4-119. [PMID: 30257078 PMCID: PMC6492006 DOI: 10.1111/jeu.12691] [Citation(s) in RCA: 566] [Impact Index Per Article: 113.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 09/04/2018] [Indexed: 12/22/2022]
Abstract
This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.
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Annotated 18S and 28S rDNA reference sequences of taxa in the planktonic diatom family Chaetocerotaceae. PLoS One 2018; 13:e0208929. [PMID: 30586452 PMCID: PMC6306197 DOI: 10.1371/journal.pone.0208929] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/26/2018] [Indexed: 02/07/2023] Open
Abstract
The species-rich diatom family Chaetocerotaceae is common in the coastal marine phytoplankton worldwide where it is responsible for a substantial part of the primary production. Despite its relevance for the global cycling of carbon and silica, many species are still described only morphologically, and numerous specimens do not fit any described taxa. Nowadays, studies to assess plankton biodiversity deploy high throughput sequencing metabarcoding of the 18S rDNA V4 region, but to translate the gathered metabarcodes into biologically meaningful taxa, there is a need for reference barcodes. However, 18S reference barcodes for this important family are still relatively scarce. We provide 18S rDNA and partial 28S rDNA reference sequences of 443 morphologically characterized chaetocerotacean strains. We gathered 164 of the 216 18S sequences and 244 of the 413 28S sequences of strains from the Gulf of Naples, Atlantic France, and Chile. Inferred phylogenies showed 84 terminal taxa in seven principal clades. Two of these clades included terminal taxa whose rDNA sequences contained spliceosomal and Group IC1 introns. Regarding the commonly used metabarcode markers in planktonic diversity studies, all terminal taxa can be discriminated with the 18S V4 hypervariable region; its primers fit their targets in all but two species, and the V4-tree topology is similar to that of the 18S. Hence V4-metabarcodes of unknown Chaetocerotaceae are assignable to the family. Regarding the V9 hypervariable region, most terminal taxa can be discriminated, but several contain introns in their primer targets. Moreover, poor phylogenetic resolution of the V9 region affects placement of metabarcodes of putative but unknown chaetocerotacean taxa, and hence, uncertainty in taxonomic assignment, even of higher taxa.
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Complete mitochondrial genome of a rare diatom (Bacillariophyta) Proschkinia and its phylogenetic and taxonomic implications. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 4:25-26. [PMID: 33365405 PMCID: PMC7510632 DOI: 10.1080/23802359.2018.1535852] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/19/2018] [Indexed: 11/02/2022]
Abstract
We obtained the complete mitogenome of Proschkinia sp. strain SZCZR1824, a strain belonging to a poorly known diatom genus with no previous molecular data. This genome is 48,863 bp long, with two group I introns in rnl and three group II introns in cox1. Using mitogenomic data, Proschkinia sp. was recovered with Fistulifera solaris, far distant from Navicula and Nitzschia, two genera with which Proschkinia has sometimes been associated based on morphology.
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Valve morphogenesis in Diploneis smithii (Bacillariophyta). JOURNAL OF PHYCOLOGY 2018; 54:171-186. [PMID: 29282746 DOI: 10.1111/jpy.12616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 12/01/2017] [Indexed: 06/07/2023]
Abstract
Diploneis species have perhaps the most complex valve structure among pennate diatoms. The development of this structure was studied in Diploneis smithii and begins with the formation of a primary band, which then develops secondary arms at both poles and the center, as in the classic Chiappino-Volcani model of raphid diatom ontogeny. Spine-like projections grow out from the primary band and secondary arms to establish the transapical ribs (virgae) of the mature valve and themselves develop spines, which are spaced first oppositely and then alternately and fuse with each other to delimit the stria pores. Subsequently, new pattern and structures develop both externally (formation of bifurcating projections that fuse to delimit the outer, sieve-like layer of the valve) and internally (growth and fusion of flanges from the first-formed ribs to create the longitudinal canals and deposition of a hymenate strip over the internal face of each stria). Comparisons are made with morphogenesis in other diatoms. Diploneis smithii ontogeny suggests how very slight developmental changes might have created the very variable external morphology of Diploneis species. It also indicates that the longitudinal canals of Diploneis and Fallacia have different origins, since the porous external wall is not formed as a unilaterally attached flap in Diploneis and the canal is internal to the first-formed rib-stria system in Diploneis, but external to it in Fallacia.
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Fetal bradycardia associated with maternal hypothermia after fetoscopic repair of neural tube defect. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2018; 51:411-412. [PMID: 28436065 DOI: 10.1002/uog.17501] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 03/31/2017] [Accepted: 04/14/2017] [Indexed: 06/07/2023]
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Perioperative Anesthetic Management for Cesarean Delivery in a Parturient With Type IV Loeys-Dietz Syndrome. ACTA ACUST UNITED AC 2017; 9:182-185. [DOI: 10.1213/xaa.0000000000000561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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A comparison of the Truview PCD and the GlideScope Cobalt AVL video-laryngoscopes to the Miller blade for successfully intubating manikins simulating normal and difficult pediatric airways. Paediatr Anaesth 2016; 26:613-20. [PMID: 27083381 DOI: 10.1111/pan.12906] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/15/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Video-laryngoscopes provide better glottic visualization, but tracheal intubation times are longer, compared to conventional direct laryngoscopy in adult patients with normal airways. The objective of this randomized crossover study was to compare times to successful tracheal intubation with video-laryngoscope and direct laryngoscopy in manikins simulating infants with normal and abnormal airways. METHODS Thirty experienced pediatric anesthesia practitioners performed tracheal intubation in three distinct manikins simulating infants with (i) a normal airway (ii), an anterior larynx, and (iii) the Pierre Robin sequence anatomy. These were performed using a standard Miller #1 blade, the GlideScope Cobalt AVL, and the Truview PCD video-laryngoscope, first in a normal neck and then an unstable cervical spine scenario (18 intubations/subject). The specific assigned order of devices and manikins for each participant was based on a three by three Latin square design to minimize carryover effects between the model and the device. Predefined times to intubation were analyzed by Cox regression model and Kaplan-Meier survival curves. RESULTS Intubation times were shorter and success rates were higher with the Miller blade compared to either the GlideScope or the Truview videoscope in all three manikins in both scenarios, but did not differ between the GlideScope and the Truview devices. Improved intubation times and success rates in the unstable cervical spine scenario compared to the normal neck were attributed to learning effects with sequential intubation. CONCLUSION Higher success rates and shorter intubation times with the Miller blade compared to either video-laryngoscope may reflect greater experience with direct laryngoscopy, need for more video-laryngoscopy training, or result from the manikin design. Individual practitioners may differ in their preference of device for intubating a child with anticipated difficult airway based on their previous experiences, self-assessment of their skills, and evaluation of the child's airway anatomy.
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Unusual pleuroamniotic shunt complication managed using a two-port in-CO2 fetoscopic technique: technical and ethical considerations. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2016; 47:123-124. [PMID: 26183219 DOI: 10.1002/uog.14947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/02/2015] [Accepted: 06/09/2015] [Indexed: 06/04/2023]
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59: Fetal endoscopic tracheal occlusion for severe isolated left-sided congenital diaphragmatic hernia: a USA tertiary care center experience. Am J Obstet Gynecol 2016. [DOI: 10.1016/j.ajog.2015.10.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Genotypic diversity and differentiation among populations of two benthic freshwater diatoms as revealed by microsatellites. Mol Ecol 2015; 24:4433-48. [DOI: 10.1111/mec.13336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 12/30/2022]
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Genetic and Physiological Diversity in the Diatom Nitzschia inconspicua. J Eukaryot Microbiol 2015; 62:815-32. [DOI: 10.1111/jeu.12240] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 05/22/2015] [Accepted: 05/22/2015] [Indexed: 11/30/2022]
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Spermatogenesis and auxospore structure in the multipolar centric diatom Hydrosera. JOURNAL OF PHYCOLOGY 2015; 51:144-158. [PMID: 26986265 DOI: 10.1111/jpy.12261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 11/18/2014] [Indexed: 06/05/2023]
Abstract
Spermatogenesis and auxospore development were studied in the freshwater centric diatom Hydrosera triquetra. Spermatogenesis was unusual, lacking depauperating cell divisions within the spermatogonangium. Instead, a series of mitoses occurred within an undivided cell to produce a multinucleate plasmodium with peripheral nuclei, which then underwent meiosis. 32 or 64 sperm budded off from the plasmodium leaving a large residual cell containing all the chloroplasts. Similar development apparently occurs in Pleurosira, Aulacodiscus, and Guinardia, these being so distantly related that independent evolution of plasmodial spermatogenesis seems likely. After presumed fertilization, the Hydrosera egg cell expanded distally to form a triangular end part. However, unlike in other triangular diatoms (Lithodesmium, Triceratium), the development of triradiate symmetry was not controlled by the "canonical" method of a perizonium that constrains expansion to small terminal areas of the auxospore wall. Instead, the auxospore wall lacked a perizonium and possessed only scales and a dense mat of thin, apparently entangled strips of imperforate silica. No such structures have been reported from any other centric diatoms, the closest analogs being instead the incunabular strips of some raphid diatoms (Nitzschia and Pinnularia). Whether these silica structures are formed by the normal method (intracellular deposition within a silica deposition vesicle) is unknown. As well as being more rounded than vegetative cells, the initial cell is aberrant in its structure, since it has a less polarized distribution of the "triptych" pores characteristic of the species.
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A Description of Biremis panamae sp. nov., a New Diatom Species from the Marine Littoral, with an Account of the Phylogenetic Position of Biremis D.G. Mann et E.J. Cox (Bacillariophyceae). PLoS One 2014; 9:e114508. [PMID: 25494095 PMCID: PMC4262420 DOI: 10.1371/journal.pone.0114508] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/05/2014] [Indexed: 11/18/2022] Open
Abstract
Here we present a formal description of Biremis panamae Barka, Witkowski et Weisenborn sp. nov., which was isolated from the marine littoral environment of the Pacific Ocean coast of Panama. The description is based on morphology (light and electron microscopy) and the rbcL, psbC and SSU sequences of one clone of this species. The new species is included in Biremis due to its morphological features; i.e. two marginal rows of foramina, chambered striae, and girdle composed of numerous punctate copulae. The new species also possesses a striated valve face which is not seen in most known representatives of marine littoral Biremis species. In this study we also present the relationship of Biremis to other taxa using morphology, DNA sequence data and observations of auxosporulation. Our results based on these three sources point to an evolutionary relationship between Biremis, Neidium and Scoliopleura. The unusual silicified incunabular caps present in them are known otherwise only in Muelleria, which is probably related to the Neidiaceae and Scoliotropidaceae. We also discuss the relationship between Biremis and the recently described Labellicula and Olifantiella.
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When is sampling complete? The effects of geographical range and marker choice on perceived diversity in Nitzschia palea (Bacillariophyta). Protist 2014; 165:245-59. [PMID: 24739436 DOI: 10.1016/j.protis.2014.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 10/25/2022]
Abstract
DNA barcoding, being developed for biomonitoring, requires a database of reference sequences and knowledge of how much sequences can deviate before they are assigned to separate species. The molecular hunt for hidden species also raises the question of species definitions. We examined whether there are objective criteria for sequence-based species delimitation in diatoms, using Nitzschia palea, an important monophyletic indicator species already known to contain cryptic diversity. Strains from a wide geographical range were sequenced for 28S rRNA, COI and rbcL. Homogeneity indices and the Chao index failed to objectively select a precise number of species existing in N. palea as well as an evolutionary method based on coalescence theory. COI always gave higher diversity estimations than 28S rRNA or rbcL. Mating data did not provide a precise calibration of molecular species thresholds. Rarefaction curves indicated that further MOTUs would be detected with more isolates than we sampled (81 clones, 42 localities). Although some genotypes had intercontinental distributions, there was a positive relationship between genetic and geographical distance, suggesting even higher richness than we assessed, given that many regions were not sampled. Overall, no objective criteria were found for species separation; instead barcoding will need a consensual approach to molecular species limits.
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Sperm ultrastructure in the diatoms Melosira and Thalassiosira and the significance of the 9 + 0 configuration. PROTOPLASMA 2013; 250:833-50. [PMID: 23149627 DOI: 10.1007/s00709-012-0465-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 10/15/2012] [Indexed: 05/16/2023]
Abstract
The most complete account to date of the ultrastructure of flagellate cells in diatoms is given for the sperm of Thalassiosira lacustris and Melosira moniliformis var. octogona, based on serial sections. The sperm are uniflagellate, with no trace of a second basal body, and possess a 9 + 0 axoneme. The significance of the 9 + 0 configuration is discussed: lack of the central pair microtubules and radial spokes does not compromise the mastigoneme-bearing flagellum's capacity to perform planar beats and thrust reversal and may perhaps be related to sensory/secretory function of the sperm flagellum during plasmogamy. The basal bodies of diatoms are confirmed to contain doublets rather than triplets, which may correlate with the absence of some centriolar proteins found in most cells producing active flagella. Whereas Melosira possesses a normal cartwheel structure in the long basal body, no such structure is present in Thalassiosira, which instead possesses 'intercalary fibres' linking the basal body doublets. No transitional helices or transitional plates are present in either species studied. Cones of microtubules are associated with the basal body and partially enclose the nucleus in M. moniliformis and T. lacustris. They do not appear to be true microtubular roots and may arise through transformation of the meiosis II spindle. A close association between cone microtubules and tubules containing mastigonemes may indicate a function in intracellular mastigoneme transport. No correlation can yet be detected between methods of spermatogenesis and phylogeny in diatoms, contrary to previous suggestions.
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An inordinate fondness? The number, distributions, and origins of diatom species. J Eukaryot Microbiol 2013. [PMID: 23710621 DOI: 10.1111/jeu-.12047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The number of extant species of diatoms is estimated here to be at least 30,000 and probably ca. 100,000, by extrapolation from an eclectic sample of genera and species complexes. Available data, although few, indicate that the pseudocryptic species being discovered in many genera are not functionally equivalent. Molecular sequence data show that some diatom species are ubiquitously dispersed. A good case can be made that at least some diatom species and even a few genera are endemics, but many such claims are still weak. The combination of very large species numbers and relatively rapid dispersal in diatoms is inconsistent with some versions of the "ubiquity hypothesis" of protist biogeography, and appears paradoxical. However, population genetic data indicate geographical structure in all the (few) marine and freshwater species that have been examined in detail, sometimes over distances of a few tens of kilometres. The mode of speciation may often be parapatric, in the context of a constantly shifting mosaic of temporarily isolated (meta) populations, but if our "intermediate dispersal hypothesis" is true (that long-distance dispersal is rare, but not extremely rare), allopatric speciation could also be maximized.
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An Inordinate Fondness? The Number, Distributions, and Origins of Diatom Species. J Eukaryot Microbiol 2013; 60:414-20. [DOI: 10.1111/jeu.12047] [Citation(s) in RCA: 226] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 03/05/2013] [Indexed: 11/28/2022]
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Abstract
A group of protist experts proposes a two-step DNA barcoding approach, comprising a universal eukaryotic pre-barcode followed by group-specific barcodes, to unveil the hidden biodiversity of microbial eukaryotes.
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Gametogenesis and auxospore development in Actinocyclus (Bacillariophyta). PLoS One 2012; 7:e41890. [PMID: 22870259 PMCID: PMC3411613 DOI: 10.1371/journal.pone.0041890] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 06/29/2012] [Indexed: 11/18/2022] Open
Abstract
cGametogenesis and auxospore development have been studied in detail in surprisingly few centric diatoms. We studied the development of sperm, eggs and auxospores in Actinocyclus sp., a radially symmetrical freshwater diatom collected from Japan, using LM and electron microscopy of living cultures and thin sections. Actinocyclus represents a deep branch of the 'radial centric' diatoms and should therefore contribute useful insights into the evolution of sexual reproduction in diatoms. Spermatogenesis was examined by LM and SEM and involved the formation of two spermatogonia (sperm mother-cells) in each spermatogonangium through an equal mitotic division. The spermatogonia produced a reduced 'lid' valve, resembling a large flat scale with irregular radial thickenings. Sperm formation was merogenous, producing four sperm per spermatogonium, which were released by dehiscence of the 'lid' valve. The sperm were spindle-shaped with numerous surface globules and, as usual for diatoms, the single anterior flagellum bore mastigonemes. One egg cell was produced per oogonium. Immature eggs produced a thin layer of circular silica scales before fertilization, while the eggs were still contained within the oogonium. Sperm were attracted in large numbers to each egg and were apparently able to contact the egg surface via a gap formed between the long hypotheca and shorter epitheca of the oogonium and a small underlying hole in the scale-case. Auxospores expanded isodiametrically and many new scales were added to its envelope during expansion. Finally, new slightly-domed initial valves were produced at right angles to the oogonium axis, after a strong contraction of the cell away from the auxospore wall. At different stages, Golgi bodies were associated with chloroplasts or mitochondria, contrasting with the constancy of Golgi-ER-mitochondrion (G-ER-M) units in some other centric diatoms, which has been suggested to have phylogenetic significance. Electron-dense bodies in the vacuole of Actinocyclus are probably acidocalcisomes containing polyphosphate.
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SCALY INCUNABULA, AUXOSPORE DEVELOPMENT, AND GIRDLE POLYMORPHISM IN SELLAPHORA MARVANII SP. NOV. (BACILLARIOPHYCEAE)(1). JOURNAL OF PHYCOLOGY 2011; 47:1368-1378. [PMID: 27020361 DOI: 10.1111/j.1529-8817.2011.01058.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Uniparental auxosporulation was observed in a monoclonal culture of a Sellaphora clone isolated from the epipelon of a fishpond in the Czech Republic. The cox1 sequence for the clone confirmed that it belonged to the Sellaphora pupula-bacillum species complex but showed significant differences from all previously characterized Sellaphora species, and it is therefore described as S. marvanii sp. nov. Protoplast, valve, and girdle structure resembled those of other Sellaphora species, but a novel finding for all diatoms was a change in girdle structure during the life cycle: the most advalvar girdle band (valvocopula) bore a single line of pores in enlarged postauxospore cells but was entirely plain in small cells and gametangia. The young auxospores were covered by incunabula containing large, delicate, ± circular scales, resembling those of centric diatom auxospores; similar scales have been reported in a few other raphid diatoms (Pseudo-nitzschia multiseries, Diploneis sp.) but contrast with the strip incunabula of some Nitzschia and Pinnularia and the helmet-like caps of Neidium. The scales persisted during auxospore expansion, mostly as two caps over the auxospore poles. The transverse perizonium comprised a very wide, closed primary band, flanked by numerous secondary bands whose open ends were strongly incurved toward the center. Initial valves were differentiated from their immediate descendants by the very strong external demarcation of the raphe sternum, irregular shape, and curved transapical profile.
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A time-calibrated multi-gene phylogeny of the diatom genus Pinnularia. Mol Phylogenet Evol 2011; 61:866-79. [PMID: 21930222 DOI: 10.1016/j.ympev.2011.08.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 08/17/2011] [Accepted: 08/31/2011] [Indexed: 10/17/2022]
Abstract
Pinnularia is an ecologically important and species-rich genus of freshwater diatoms (Bacillariophyceae) showing considerable variation in frustule morphology. Interspecific evolutionary relationships were inferred for 36 Pinnularia taxa using a five-locus dataset. A range of fossil taxa, including newly discovered Middle Eocene forms of Pinnularia, was used to calibrate a relaxed molecular clock analysis and investigate temporal aspects of the genus' diversification. The multi-gene approach resulted in a well-resolved phylogeny of three major clades and several subclades that were frequently, but not universally, delimited by valve morphology. The genus Caloneis was not recovered as monophyletic, confirming that, as currently delimited, this genus is not evolutionarily meaningful and should be merged with Pinnularia. The Pinnularia-Caloneis complex is estimated to have diverged between the Upper Cretaceous and the early Eocene, implying a ghost range of at least 10 million year (Ma) in the fossil record.
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Barcoding diatoms: exploring alternatives to COI-5P. Protist 2011; 162:405-22. [PMID: 21239228 DOI: 10.1016/j.protis.2010.09.005] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 09/12/2010] [Indexed: 11/15/2022]
Abstract
Diatoms are a diverse lineage with species that can be difficult to identify or cryptic, but DNA barcoding, a molecular technique, can assist identification and facilitate studies of speciation and biogeography. The most common region used for DNA barcoding, COI-5P, can distinguish diatom species, but has not displayed universality (i.e., successful PCR amplification from diverse taxa). Therefore, we have assessed the following alternative markers: ∼1400bp of rbcL; 748bp at the 3' end of rbcL (rbcL-3P); LSU D2/D3 and UPA. Sellaphora isolates were used to determine each marker's ability to discriminate among closely related species and culture collection material was utilized to explore further marker universality. All of the alternative markers investigated have greater universality than COI-5P. Both full and partial (3P) rbcL regions had the power to discriminate between all species, but rbcL-3P can be sequenced more easily. LSU D2/D3 could distinguish between all but the most closely related species (96%), whereas UPA only distinguished 20% of species. Our observations suggest that rbcL-3P should be used as the primary marker for diatom barcoding, while LSU D2/D3 should be sequenced as a secondary marker to facilitate environmental surveys.
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A Practice of Anesthesia for Infants and Children, 4th ed. Anesth Analg 2009. [DOI: 10.1213/ane.0b013e3181b576d7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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MOLECULAR EVIDENCE CONFIRMS SISTER RELATIONSHIP OF ARDISSONEA, CLIMACOSPHENIA, AND TOXARIUM WITHIN THE BIPOLAR CENTRIC DIATOMS (BACILLARIOPHYTA, MEDIOPHYCEAE), AND CLADISTIC ANALYSES CONFIRM THAT EXTREMELY ELONGATED SHAPE HAS ARISEN TWICE IN THE DIATOMS(1). JOURNAL OF PHYCOLOGY 2008; 44:1340-1348. [PMID: 27041731 DOI: 10.1111/j.1529-8817.2008.00560.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
With the use of a new kit from Qiagen to amplify total genome quantity, DNA was bulked up from two diatoms that are difficult to grow (Ardissonea and Climacosphenia), and the nuclear SSU rRNA gene was successfully amplified. Results of Bayesian analyses showed that these diatoms are sister to Toxarium and belong to the bi- and multipolar centric diatoms. The results indicate that extremely elongate shape has arisen at least twice in diatoms, in the true pennates, and in the bipolar centrics. The two lateral pattern centers of Ardissonea and Climacosphenia likely represent a modified annulus that subtends ribs internally as well as externally. Studies of sexual reproduction are needed to determine whether Ardissonea, Climacosphenia, and Toxarium achieve their elongate shape by similar means to each other and to true pennates, that is, by controlling the expansion of the auxospores by sequential addition of silicified bands (to form a properizonium or perizonium).
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Abstract
Diatoms are a species-rich group of photosynthetic eukaryotes, with enormous ecological significance and great potential for biotechnology. During the last decade, diatoms have begun to be studied intensively using modern molecular techniques and the genomes of four diatoms have been wholly or partially sequenced. Although new insights into the biology and evolution of diatoms are accumulating rapidly due to the availability of reverse genetic tools, the full potential of these molecular biological approaches can only be fully realized if experimental control of sexual crosses becomes firmly established and widely accessible to experimental biologists. Here we discuss the issue of choosing new models for diatom research, by taking into account the broader context of diatom mating systems and the place of sex in relation to the intricate cycle of cell size reduction and restitution that is characteristic of most diatoms. We illustrate the results of our efforts to select and develop experimental systems in diatoms, using species with typical life cycle attributes, which could be used as future model organisms to complement existing ones.
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Abstract
Auxosporulation of the freshwater epipelic diatom Pinnularia nodosa (Ehrenb.) W. Sm. was studied in a clonal culture. Interphase cells possessed two chloroplasts with invaginated pyrenoids. The nucleus contained a single small body of heterochromatin at one end, also visible during most of meiotic prophase. During auxosporulation, induced by transfer of stationary-phase cells to fresh medium and suppressed by high nitrogen (N), an unpaired mother cell produced a single auxospore. Although meiosis II and nuclear fusion were not observed, indirect evidence indicated that auxosporulation was autogamous (rarely reported in pennate diatoms), rather than apomictic; paedogamy was excluded. The protoplast produced after meiosis either (1) matured into a "pseudozygote," via an asymmetrical contraction after meiosis I to form a single spherical cell at one end of the mother cell (pathway 1); or (2) constricted into two spherical cells (pathway 2). In pathway 2, the "pseudogametes" never fused and only one or none developed into a pseudozygote and then into an auxospore. Pathway 2 could be suppressed by continuous light. During metamorphosis of the spherical pseudozygote into an elongate young auxospore, a complete covering of thin siliceous incunabular strips was formed, separate from the organic wall formed around the pseudozygote when first formed and from the perizonium. Mature auxospores produced via pathway 2 had 60% of the volume as those produced via pathway 1 and had smaller chloroplasts (through loss of fragments during protoplast cleavage), but they achieved exactly the same lengths, suggesting that absolute length is monitored during expansion.
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A MOLECULAR SYSTEMATIC APPROACH TO EXPLORE DIVERSITY WITHIN THE SELLAPHORA PUPULA SPECIES COMPLEX (BACILLARIOPHYTA)(1). JOURNAL OF PHYCOLOGY 2008; 44:215-231. [PMID: 27041057 DOI: 10.1111/j.1529-8817.2007.00454.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The common and cosmopolitan freshwater benthic diatom Sellaphora pupula (Kütz.) Mereschk. is a model system for studying the nature of species in microalgae; the biological significance of morphological variation in this species complex has been widely demonstrated. The aim of this study was to establish a two-gene phylogeny (18S rDNA and rbcL) for 23 Sellaphora taxa, including 19 S. pupula aggregate (agg.) demes or species, S. bacillum (Ehrenb.) D. G. Mann, and S. laevissima (Kütz.) D. G. Mann. A range of analyses on separate and combined data sets indicated that Sellaphora is a monophyletic group containing four major clades. Of the traditionally recognized species, S. bacillum and S. laevissima are natural groups, but S. pupula is paraphyletic or polyphyletic because S. bacillum groups with S. pupula"small lanceolate" and S. lanceolata. Thickened bars at the poles of valves within the core "pupula-bacillum" group may be a morphological synapomorphy; the fossil record suggests that this group is at least 12 million years old. Otherwise, there was no clear pattern in the distribution of different morphologies among the major clades; each clade was also heterogeneous with respect to mating system. More intensive and extensive sampling will doubtless uncover even greater diversity; the challenge lies in its interpretation. Our results demonstrate the limitations of paleoecological, ecological, and biogeographical research based on morphospecies.
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Genetic divergence and reproductive barriers among morphologically heterogeneous sympatric clones of Eunotia bilunaris sensu lato (Bacillariophyta). Protist 2007; 159:73-90. [PMID: 17964215 DOI: 10.1016/j.protis.2007.08.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Accepted: 08/03/2007] [Indexed: 11/26/2022]
Abstract
The study of reproductive isolation between populations, combined with estimates of genetic divergence, provides important insights into mechanisms of speciation. In this study, sixteen morphologically heterogeneous sympatric clones of Eunotia bilunaris sensu lato (Bacillariophyta) were brought into culture to study their phylogenetic relationships and pre- and postzygotic reproductive barriers. An ITS rDNA phylogeny was congruent with morphology and divided the clones into three groups ('slender', 'robust' and 'labile'), pointing to the presence of several species in E. bilunaris. Whereas most strains had a heterothallic mating system, four 'labile' clones displayed apomictic behaviour. A further 'labile' clone had a heterothallic mating behaviour, however, suggesting a very recent origin for apomixis. Despite high sequence divergence, hybridization occurred between clones belonging to different groups, but was 20-400 times less frequent than in intra-group matings. F1 hybrids had an intermediate morphology and were almost completely sterile; gamete formation was generally arrested in the early stages of meiosis I. The ITS divergence of 11.5-12.3% between the 'robust' and 'slender' clones seems to represent an upper limit of divergence in which cell pairing, gamete formation and auxosporulation are still possible but heavily reduced, and where hybrid sterility has already evolved.
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