Life cycle of the Early Cambrian acritarchs

XV lnternational A.P.L.E. Symposium of Palynolog

A Single-Tube HNB-Based Loop-Mediated Isothermal Amplification for the Robust Detection of the Ostreid Herpesvirus 1

The Ostreid herpesvirus 1 species affects shellfish, contributing significantly to high economic losses during production. To counteract the threat related to mortality, there is a need for the development of novel point-of-care testing (POCT) that can be implemented in aquaculture production to prevent disease outbreaks. In this study, a simple, rapid and specific colorimetric loop-mediated isothermal amplification (LAMP) assay has been developed for the detection of Ostreid herpesvirus1 (OsHV-1) and its variants infecting Crassostrea gigas (C. gigas). The LAMP assay has been optimized to use hydroxynaphthol blue (HNB) for visual colorimetric distinction of positive and negative templates. The effect of an additional Tte UvrD helicase enzyme used in the reaction was also evaluated with an improved reaction time of 10 min. Additionally, this study provides a robust workflow for optimization of primers for uncultured viruses using designed target plasmid when DNA availability is limited.info:eu-repo/semantics/publishedVersio

Pectobacterium and Dickeya species detected in vegetables in Northern Ireland

Publication history: Accepted - 22 January 2019; Published online - 7 February 2019.Destructive soft rot Pectobacteriaceae affect a number of vegetable crops and cause high economic loses in the field and storage. The diversity of Pectobacterium and Dickeya causing soft rot of vegetables in Northern Ireland is unknown. This study provides details of Pectobacterium and Dickeya spp. detected in vegetables from several locations in Northern Ireland in the years 2015–2017. Soft rot Pectobacteriaceae were identified based on DNA sequences. Thirty one strains were selected for further phylogenetic analysis based on the recA gene region. Results from the testing of over 3456 potato samples for plant health statutory purposes in years 2005–2017 demonstrated that Dickeya spp. is not the major pathogen causing soft rot or blackleg in Northern Ireland. The most predominant species causing soft rot of vegetables in Northern Ireland were Pectobacterium atrosepticum and Pectobacterium carotovorum subsp. carotovorum. Pectobacterium atrosepticum was also detected on hosts other than potato. Testing of bacteria isolated from carrots led to the detection of P. carotovorum and Dickeya sp. This is the first study to provide knowledge about Pectobacterium and Dickeya spp. diversity causing soft rot of vegetables in Northern Ireland confirmed by real-time PCR and DNA sequences. This is also the first report of the detection of D. aquatica from a source other than water

Current Trends and Challenges for Rapid SMART Diagnostics at Point-of-Site Testing for Marine Toxins

Publication history: Accepted - 24 March 2021; Published - 3 April 2021.In the past twenty years marine biotoxin analysis in routine regulatory monitoring has advanced significantly in Europe (EU) and other regions from the use of the mouse bioassay (MBA) towards the high-end analytical techniques such as high-performance liquid chromatography (HPLC) with tandem mass spectrometry (MS). Previously, acceptance of these advanced methods, in progressing away from the MBA, was hindered by a lack of commercial certified analytical standards for method development and validation. This has now been addressed whereby the availability of a wide range of analytical standards from several companies in the EU, North America and Asia has enhanced the development and validation of methods to the required regulatory standards. However, the cost of the high-end analytical equipment, lengthy procedures and the need for qualified personnel to perform analysis can still be a challenge for routine monitoring laboratories. In developing regions, aquaculture production is increasing and alternative inexpensive Sensitive, Measurable, Accurate and Real-Time (SMART) rapid point-of-site testing (POST) methods suitable for novice end users that can be validated and internationally accepted remain an objective for both regulators and the industry. The range of commercial testing kits on the market for marine toxin analysis remains limited and even more so those meeting the requirements for use in regulatory control. Individual assays include enzyme-linked immunosorbent assays (ELISA) and lateral flow membrane-based immunoassays (LFIA) for EU-regulated toxins, such as okadaic acid (OA) and dinophysistoxins (DTXs), saxitoxin (STX) and its analogues and domoic acid (DA) in the form of three separate tests offering varying costs and benefits for the industry. It can be observed from the literature that not only are developments and improvements ongoing for these assays, but there are also novel assays being developed using upcoming state-of-the-art biosensor technology. This review focuses on both currently available methods and recent advances in innovative methods for marine biotoxin testing and the end-user practicalities that need to be observed. Furthermore, it highlights trends that are influencing assay developments such as multiplexing capabilities and rapid POST, indicating potential detection methods that will shape the future market.This research was funded by the UK BBSRC project “Safe and Sustainable Shellfish: Introducing local testing and management solutions” (reference BB/S004211/1)

Middle Ordovician acritarchs and problematic organic-walled microfossils from the Saq-Hanadir transitional beds in the QSIM-801 well, Saudi Arabia

Core samples from the QSIM-801 water well, drilled in central Saudi Arabia, cover a 93-foot interval spanning the transition between the Sajir Member of the Saq Formation, that consists mainly of sandstones of tidal sand flat environments, and the Hanadir Member of the Qasim Formation, characterized by argillaceous graptolitic mudstones, corresponding to a tidal delta front. The samples contain abundant, exceptionally well-preserved and diverse palynomorphs, which include cryptospores, acritarchs and chitinozoans, other problematic organic-walled microfossils as well as other organic particles such as cuticle-like fragments. The studied interval is biostratigraphically well constrained by the presence of chitinozoans of the formosa and pissotensis Zones of late-early to late Darriwilian age (Middle Ordovician) in the uppermost Saq Formation and Hanadir Member. The biostratigraphic age of the Sajir Member considered to span the Dapingian–Darriwilian boundary, is re-discussed based on the results herein. The uppermost part of the Sajir Member yielded the ichnofossil, Phycodes fusiforme. Acritarch assemblages from the Sajir Member of the Saq Formation are poorly diversified and dominated by sphaeromorphs. More diverse assemblages of acritarchs, associated with enigmatic forms, occur in the Hanadir Member of the Qasim Formation. The contact between the two formations and the transition between the palynomorph assemblages are sharp, suggesting a stratigraphic hiatus. A quantitative analysis allows us to discuss the paleoenvironmental changes and possibly climatic changes associated with an hypothesis of ice house conditions during this period. Among the diagnostic acritarch taxa observed are Frankea breviuscula, F. longiuscula, Baltisphaeridium ternatum, Dasydorus cirritus, Dicrodiacrodium ancoriforme, Poikilofusa ciliaris, Pterospermopsis colbathii and Uncinisphaera fusticula. These are associated with other typical forms known to range across the Lower–Middle Ordovician boundary, such as Aremoricanium rigaudae, Aureotesta clathrata, Barakella fortunata, B. rara, Baltisphaeridium klabavense, Glaucotesta latiramosa and Striatotheca spp. Galeate and peteinoid acritarchs are also well represented, as well as tiny forms of ultraplanctonic size. Three new species of acritarchs are proposed: Frankea longiuscula var. darriwilense var. nov, Micrhystridium regulum sp. nov, and Tyrannus proteus sp. nov. Repeated occurrences throughout the section of cryptospores, problematic microfossils such as organic filaments, cuticle-like tissues, striated and pigmented leiospheres frequently in clusters, are interpreted to reflect recurrent terrestrial and freshwater inputs in the depositional environment. Single-specimen, high-resolution analyses using Confocal Laser Scanning Microscopy on the enigmatic form Tyrannus proteus sp. nov. show fluorescence emission spectra and microstructural properties significantly different from those of typical marine acritarchs from the same levels

The Ediacaran microbiota and the survival of Snowball Earth conditions

Recently recovered assemblage of late Ediacaran cyanobacteria, phytoplankton and some microfossils of uncertain origin from the subsurface Włodawa Formation on the Lublin Slope in Poland, allowed to extend their stratigraphic ranges and provided a new evidence that more species survived the Cryogenian Period. Numerous other species of unicellular eukaryotes (informally called acritarchs) and prokaryotes (also coenobial and colonial) have been documented in recent years to lived-over to the Ediacaran, enlarging the global list of biota surviving the Neoproterozoic icehouse intervals. This compelling record revives the issue how marine biota could coup with the catastrophic consequences imposed by the global glaciations and/or to what extent the environmental and climatic change reduced the life habitats. For this purpose, the metabolic processes, modes of life and ecologic habitats of the biota are inferred and analyzed. The reviewed biota are autotrophic and aerobic: benthic cyanobacteria, which were solitary and largely colonial, living in functionally complex communities of mat-builders, and planktic and/or facultative benthic eukaryotes, which reproduced also sexually and some had advanced life cycle with alternating vegetative and reproductive generations. The environmental requirements of these microorganisms are well-oxygenated open marine waters in the photic zone, and permanent seafloor substrate for benthic and periodic access to bottom sediment for some planktic species with sexual reproduction to rest the cyst. Such natural habitats must have been preserved throughout the Cryogenian Period, and in a substantial extent (environmental “critical mass”) to sustain viable populations in the lineages that are represented by surviving species. Modern analogues of extraordinary adaptations of diverse biota to extreme conditions have their limitations when applied to the Cryogenian Period. Modern extreme environments (like those in Antarctica) with highly specialized organisms are maintained over relatively short time intervals (thousands of years) and may occasionally/periodically be in contact with the outside world to replenish their genetic stock. This is in a sharp contrast to the millions of years of environmental and genetic isolation invoked for the Cryogenian. The global fossil record, enlarged by recent new findings, is briefly reviewed to understand the impact of the Cryogenian glaciations on biodiversity and the rate of survival of microbiota. The Snowball Earth Hypothesis and its modified versions are discussed in pursuit of an environmentally plausible Earth System model consistent with the survival of biota. The radical version of the Snowball Earth Hypothesis is ruled out. An Earth System model with open marine water, ice-free shelf (at least seasonally) and access to the sea floor is obligatory for the Cryogenian in order to satisfy the living requirements of the biota that survived the period. The palaeobiological findings are entirely consistent with sedimentaological findings that require open marine water and well-functioning hydrologic cycle. The Slushball Earth model accommodates more adequately these requirements.Neoproterozoic microbial diversification, Neoproterozic Ice Age

New records of late Ediacaran microbiota from Poland

New records of organic-walled microfossils, including cyanobacteria, phytoplankton (certain acritarchs) and some microbiota of unknown biological affinities, are reported from the late Ediacaran Włodawa Formation in the Łopiennik IG-1 borehole, Poland. The microfossil association consists mostly of known species, which originated prior to the Cryogenian Period, evidence that these microorganisms survived the Neoproterozoic glacial epochs. The longevity of most of the species is extended herein to ca. 545 Ma. One species is new but described as gen. et sp. indet., because only a single specimen is available. Although the microfossils represent both prokaryotic and eukaryotic groups of organisms, and benthic and planktic modes of life, all, with the exception of Valkyria, are photoautotrophic aerobes. Metabolic processes of nutrition, respiration and reproductive cycles, and ecologic habitats of these biota and the evolutionary lineages to which they belong are analyzed with respect to the basic requirements needed to survive prolonged periods of environmental perturbation.All recorded here cyanobacteria are benthic microbial mat-dwellers, requiring ample water and regular oxygen supply and sun light for their metabolism. Planktic species of Leiosphaeridia studied here are considered to be green algae (chlorophyceans), forming resting cysts and alternating sexual/vegetative generations in their life cycle. They also required habitats of well-oxygenated open water in the photic zone and periodic access to bottom sediment (to rest the cyst) in order to survive the glacial epochs, as they evidently did. It is argued that the natural habitats of all these biota must have been preserved and ecologically functional throughout the Cryogenian Period, and have been robust enough to sustain viable populations and genetic stocks of at least some evolutionary lineages known at the time. This is a primary constraint imposed by contemporaneous marine biosphere on the Earth System model, which can be accepted among hypothetical versions of the Snowball Earth hypotheses based on sedimentological, geochemical, physical and other geological records. The Slushball Earth model, or comparable, is thus favoured over strict Snowball Earth model because it reconciles the habitable conditions with other envisaged geo- and physical conditions during the period.Neoproterozoic microbial diversification, Neoproterozoic Ice Age