A higher level classification of all living organisms

Applied and Environmental Microbiology

Soybean root rot caused by the oomycete Phytophthora sojae is a serious soil-borne disease threatening soybean production in China. Bacillus velezensis FZB42 is a model strain for Gram-positive plant growth-promoting rhizobacteria and is able to produce multiple antibiotics. In this study, we demonstrated that B. velezensis FZB42 can efficiently antagonize P. sojae. The underlying mechanism for the inhibition was then investigated. The FZB42 mutants deficient in the synthesis of lipopeptides (bacillomycin D and fengycin), known for antifungal activities, and polyketides (bacillaene, difficidin, and macrolactin), known for antibacterial activities, were not impaired in their antagonism toward P. sojae ; in contrast, mutants deficient in bacilysin biosynthesis completely lost their antagonistic activities toward P. sojae , indicating that bacilysin was responsible for the activity. Isolated pure bacilysin confirmed this inference. Bacilysin was previously shown to be antagonistic main...

Biodiversity Data Journal, 2016

The Greek Taxon Information System is an initiative of the LifeWatchGreece Research Infrastructure (ESFRI) that is resuming efforts to compile a complete checklist of all species reported from the Greek territory. Such an effort is necessary as a requirement for all signatories of the Convention on Biological Diversity (Greece is a signatory since 1994). Over an estimation published in 2004 according to which 50,000 species are present in Greece, belonging to most kingdoms except bacteria and viruses, a list of 35,000 valid species (and subspecies) has been assembled from previous national and European initiatives and specialized databases on various groups. A new database will be progressively set up in the LifeWatchGreece Infrastructure within the near future. Before the dissemination of this dataset, it is important that the checklists will be validated by specialists for each taxonomic group. The first step already accomplished was to build and publish Preliminary Checklists for some taxonomic groups of marine fauna, which have been validated by specialists on the basis of their expertise and secondary literature. The publication of these Preliminary Checklists is expected to increase the visibility and ‡ ‡ ‡ § © Bailly N et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. usability of the database in the future not only to the scientific community but also to the broader domain of biodiversity management, especially in cases where no such checklists have been published yet. The guidelines used to test the first taxonomic groups are presented in this paper.

Biota Neotropica

Inventory of cyanobacteria and microalgae cited for the National Park of the Chapada dos Guimarães (MT) and 80 new records from the region. Biota Neotropica.

Journal of Micropalaeontology

Integrated Ocean Drilling Program (IODP) Expedition 318 recovered a ∼ 170 m long Holocene organic-rich sedimentary sequence at Site U1357. Located within the narrow but deep Adélie Basin close to the Antarctic margin, the site accumulated sediments at exceptionally high sedimentation rates, which resulted in extraordinary preservation of the organic sedimentary component. Here, we present an overview of 74 different mainly marine microfossil taxa and/or types found within the organic component of the sediment, which include the remains of unicellular and higher organisms from three eukaryotic kingdoms (Chromista, Plantae, and Animalia). These remains include phytoplanktonic (phototrophic dinoflagellates and prasinophytes) and very diverse zooplanktonic (heterotrophic dinoflagellates, tintinnids, copepods) organisms. We illustrate each marine microfossil taxon or type identified by providing morphological details and photographic images, which will help with their identification in future studies. We also review their ecological preferences to aid future (palaeo)ecological and (palaeo)environmental studies. The planktonic assemblage shows a high degree of endemism related to the strong influence of the sea-ice system over Site U1357. In addition, we found the remains of various species of detritus feeders and bottom-dwelling scavengers (benthic foraminifers and annelid worms) indicative of high export productivity at Site U1357. This study shows the potential of organic microfossil remains for reconstructing past environmental conditions, such as sea-ice cover and (export) productivity.

Nature Communications

Understanding how species’ thermal limits have evolved across the tree of life is central to predicting species’ responses to climate change. Here, using experimentally-derived estimates of thermal tolerance limits for over 2000 terrestrial and aquatic species, we show that most of the variation in thermal tolerance can be attributed to a combination of adaptation to current climatic extremes, and the existence of evolutionary ‘attractors’ that reflect either boundaries or optima in thermal tolerance limits. Our results also reveal deep-time climate legacies in ectotherms, whereby orders that originated in cold paleoclimates have presently lower cold tolerance limits than those with warm thermal ancestry. Conversely, heat tolerance appears unrelated to climate ancestry. Cold tolerance has evolved more quickly than heat tolerance in endotherms and ectotherms. If the past tempo of evolution for upper thermal limits continues, adaptive responses in thermal limits will have limited pote...

Scientific Reports

Myxomycetes constitute a group within the Amoebozoa well known for their motile plasmodia and morphologically complex fruiting bodies. One obstacle hindering studies of myxomycete evolution is that their fossils are exceedingly rare, so evolutionary analyses of this supposedly ancient lineage of amoebozoans are restricted to extant taxa. Molecular data have significantly advanced myxomycete systematics, but the evolutionary history of individual lineages and their ecological adaptations remain unknown. Here, we report exquisitely preserved myxomycete sporocarps in amber from Myanmar, ca. 100 million years old, one of the few fossil myxomycetes, and the only definitive Mesozoic one. Six densely-arranged stalked sporocarps were engulfed in tree resin while young, with almost the entire spore mass still inside the sporotheca. All morphological features are indistinguishable from those of the modern, cosmopolitan genus Stemonitis, demonstrating that sporocarp morphology has been static ...

New Phytologist

At the colonization site of a foreign entity, plant cells alter their trajectory of growth and development. The resulting structurea plant gallaccommodates various needs of the foreigner, which are phylogenetically diverse: viruses, bacteria, protozoa, oomycetes, true fungi, parasitic plants, and many types of animals, including rotifers, nematodes, insects, and mites. The plant species that make galls also are diverse. We assume gall production costs the plant. All is well if the foreigner provides a gift that makes up for the cost. Nitrogen-fixing nodule-inducing bacteria provide nutritional services. Gall wasps pollinate fig trees. Unfortunately for plants, most galls are made for foes, some of which are deeply studied pathogens and pests: Agrobacterium tumefaciens, Rhodococcus fascians, Xanthomonas citri, Pseudomonas savastanoi, Pantoea agglomerans, 'Candidatus' phytoplasma, rust fungi, Ustilago smuts, root knot and cyst nematodes, and gall midges. Galls are an understudied phenomenon in plant developmental biology. We propose gall inception for discovering unifying features of the galls that plants make for friends and foes, talk about molecules that plants and gall-inducers use to get what they want from each other, raise the question of whether plants colonized by arbuscular mycorrhizal fungi respond in a gall-like manner, and present a research agenda.

Journal of Anatomy

Convergence is the tendency of independent species to evolve similarly when subjected to the same environmental conditions. The primitive blueprint for the circulatory system emerged around 700-600 Mya and exhibits diverse physiological adaptations across the radiations of vertebrates (Subphylum Vertebrata, Phylum Chordata). It has evolved from the early chordate circulatory system with a single layered tube in the tunicate (Subphylum Urchordata) or an amphioxus (Subphylum Cephalochordata), to a vertebrate circulatory system with a two-chambered heart made up of one atrium and one ventricle in gnathostome fish (Infraphylum Gnathostomata), to a system with a three-chambered heart made up of two atria which maybe partially divided or completely separated in amphibian tetrapods (Class Amphibia). Subsequent tetrapods, including crocodiles and alligators (Order Crocodylia, Subclass Crocodylomorpha, Class Reptilia), birds (Subclass Aves, Class Reptilia) and mammals (Class Mammalia) evolved a four-chambered heart. The structure and function of the circulatory system of each individual holds a vital role which benefits each species specifically. The special characteristics of the four-chamber mammalian heart are highlighted by the peculiar structure of the myocardial muscle.

Metabarcoding and Metagenomics

DNA metabarcoding has the capacity to bolster current biodiversity assessment techniques, including the early detection and monitoring of non-indigenous species (NIS). However, the success of this approach is greatly dependent on the availability, taxonomic coverage and reliability of reference sequences in genetic databases, whose deficiencies can potentially compromise species identifications at the taxonomic assignment step. In this study we assessed lacunae in availability of DNA sequence data from four barcodes (COI, 18S, rbcL and matK) for NIS occurring in European marine and coastal environments. NIS checklists were based on EASIN and AquaNIS databases. The highest coverage was found for COI for Animalia and rbcL for Plantae (up to 63%, for both) and 18S for Chromista (up to 51%), that greatly increased when only high impact species were taken into account (up to 82 to 89%). Results show that different markers have unbalanced representations in genetic databases, implying tha...

2019

The eukaryote pangenome has a chimeric structure encompassing genes unique to eukaryotes (~41%), and genes of bacterial (~50% of total) and archaeal ancestry (~9%). Crucially, bacterial sequences far exceed the set acquired from the proteobacterial ancestor of mitochondria. Extant eukaryotic lineages share a common ancestor (LECA) that had all the fundamental traits of eukaryotes including the mitochondrion. The current debate about eukaryote origins revolves around two competing scenarios. The fusion model posits that the eukaryotes derive from the "fusion" of an archaeon and a bacterium, and that the acquisition of the mitochondrion was pivotal to the evolution of other eukaryotic traits. The neomuran model maintains that the archaea and eukaryotes are sister groups devived from a bacterial ancestor, and that fundamental eukaryotic traits including phagocytosis were already in place before the evolution of the mitochondrion by endosymbiosis. Eukaryote placement within the archaea in phylogenomic analysis supports the fusion scenario. The predominance of bacterial sequences in the eukaryote pangenome, the bacterial stereochemistry of eukaryote membrane lipids, and similar trajectories in mitochondrial and chloroplast evolution favour the neomuran scenario. Phylogenomic analysis resolves two major eukaryotic domains, the Amorphea and Diaphoretika, with traditional Excavata being probably paraphyletic. The root of the eukaryote tree remains elusive. Paleontological evidence and molecular clock analysis date the eukaryote lineage to at least 1.5 GYA, the concestor of extant eukaryotes to about 1.2 GYA, and major extant lineages to 900 MYA or less. The chapter includes a review of mitochondrial properties and of locomotor organelles in bacteria, archaea and eukaryotes.

Scientific reports, 2018

Ubiquitin ligases (E3s) are basic components of the eukaryotic ubiquitination system. In this work, the emergence and diversification of fungal HECT ubiquitin ligases is described. Phylogenetic and structural data indicate that six HECT subfamilies (RSP5, TOM1, UFD4, HUL4, HUL4A and HUL5) existed in the common ancestor of all fungi. These six subfamilies have evolved very conservatively, with only occasional losses and duplications in particular fungal lineages. However, an early, drastic reduction in the number of HECT genes occurred in microsporidians, in parallel to the reduction of their genomes. A significant correlation between the total number of genes and the number of HECT-encoding genes present in fungi has been observed. However, transitions from unicellularity to multicellularity or vice versa apparently had no effect on the evolution of this family. Likely orthologs or co-orthologs of all fungal HECT genes have been detected in animals. Four genes are deduced to be pres...

Revista Caatinga

Forest management can lead to numerous changes of different magnitudes in the composition and diversity of soil organisms, according to the level of interference with the habitat. Within this context, this study aimed to test the influence of different types of forest management on the edaphic macrofauna community in a region of arboreal Caatinga. The study was carried out in Contendas do Sincorá National Forest, Contendas do Sincorá - Bahia. The experimental area consisted of three types of management (clear cutting, selective cutting by diameter at breast height and selective cutting by species), and a condition of unmanaged Caatinga, which was used as control. The macrofauna was sampled twice a year (March and November) using the soil monolith method. Densities, total number of individuals, total richness, average richness, and Shannon and Pielou rates were estimated. The soil macrofauna was shown to be sensitive to different forest management practices, which indicates that sele...

PloS one, 2016

Plant diversity affects species richness and abundance of taxa at higher trophic levels. However, plant diversity effects on omnivores (feeding on multiple trophic levels) and their trophic and non-trophic interactions are not yet studied because appropriate methods were lacking. A promising approach is the DNA-based analysis of gut contents using next generation sequencing (NGS) technologies. Here, we integrate NGS-based analysis into the framework of a biodiversity experiment where plant taxonomic and functional diversity were manipulated to directly assess environmental interactions involving the omnivorous ground beetle Pterostichus melanarius. Beetle regurgitates were used for NGS-based analysis with universal 18S rDNA primers for eukaryotes. We detected a wide range of taxa with the NGS approach in regurgitates, including organisms representing trophic, phoretic, parasitic, and neutral interactions with P. melanarius. Our findings suggest that the frequency of (i) trophic inte...

BMC evolutionary biology, 2017

Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive mo...

Journal of Systematics and Evolution, 2016

Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community-based approach. We use monophyly as the primary criterion for the recognition of taxa, but also aim to preserve existing taxa and circumscriptions that are both widely accepted and consistent with our understanding of pteridophyte phylogeny. In total, this classification treats an estimated 11 916 species in 337 genera, 51 families, 14 orders, and two classes. This classification is not intended as the final word on lycophyte and fern taxonomy, but rather a summary statement of current hypotheses, derived from the best available data and shaped by those most familiar with the plants in question. We hope that it will serve as a resource for those wanting references to the recent literature on pteridophyte phylogeny and classification, a framework for guiding future investigations, and a stimulus to further discourse.

Applied Sciences

Nowadays, microalgae and cyanobacteria have become a promising and sustainable source of useful products, thanks to their richness in bioactive metabolites of high value (antibiotics, toxins, pharmaceutically active compounds, plant growth regulators, and others). These photoautotroph microorganisms generate biomass using photosynthesis. This review, which distinguishes microalgae and Cyanobacteria, often called blue-green microalgae, aims to present their classification and taxonomic diversity as the ecological niches occupied by them. In addition, the usages of open ponds and photobioreactors to produce various microalgae and Cyanobacteria strains and the high-value bioactive compounds from these microorganisms are summarized. Finally, the numerous commercial applications of these phytoplanktons in different fields, such as food, dietary supplements, feed, cosmetic, and biofuel applications, are reviewed.

Viruses, 2018

Oxidative Medicine and Cellular Longevity, 2020

Bioactive constituents of numerous marine organisms have been investigated recently for their preclinical and clinical anticancer activity. Three marine organisms: black-spotted sea cucumber: Pearsonothuria graeffei (Pg), lollyfish: Holothuria atra (Ha), and sea hare: Aplysia dactylomela (Ad), were collected during winter 2019 from Gulf of Aqaba, Red Sea, Egypt, and macerated with ethanol into three different extracts: PgE, HaE, and AdE, where each was in vitro assessed for its antiproliferative and proapoptotic properties on HepG2, HCT-116, and MCF-7 cancer cells. PgE dose-dependently inhibited the growth of HepG2, HCT-116, and MCF-7 cells within IC50 values 16.22, 13.34, and 18.09 μg/mL, respectively, while the IC50 values for the antiproliferative activity of HaE were 12.48, 10.45, and 10.36 μg/mL, respectively, and the IC50 values of AdE were 6.51, 5.33, and 6.87 μg/mL, respectively. All extracts were found to induce G0/G1 cell cycle arrest for HepG2 cells side by side with thei...

BMC evolutionary biology, 2018

The class Diphyllatea belongs to a group of enigmatic unicellular eukaryotes that play a key role in reconstructing the morphological innovation and diversification of early eukaryotic evolution. Despite its evolutionary significance, very little is known about the phylogeny and species diversity of Diphyllatea. Only three species have described morphology, being taxonomically divided by flagella number, two or four, and cell size. Currently, one 18S rRNA Diphyllatea sequence is available, with environmental sequencing surveys reporting only a single partial sequence from a Diphyllatea-like organism. Accordingly, geographical distribution of Diphyllatea based on molecular data is limited, despite morphological data suggesting the class has a global distribution. We here present a first attempt to understand species distribution, diversity and higher order structure of Diphyllatea. We cultured 11 new strains, characterised these morphologically and amplified their rRNA for a combined...

Fungal Diversity, 2019

Inaccurate taxonomic placement of fossils can lead to the accumulation of errors in molecular clock studies and their generated evolutionary lineages. There are limited fossil data that can be used in divergence time estimations. Therefore, reliable morphological characterization and taxonomical identification of fossil fungi are extremely important. Most fossils of Dothideomycetes and Sordariomycetes are from the early Cenozoic (66-23 Mya), with fewer from the late Mesozoic (174-145 Mya). However, it is hard to distinguish some fossil descriptions as photographs and illustrations are unclear; thus, the validity of using these fossils in calibrations of molecular clocks is problematic. This study brings scattered paleobiological data on selected fossil Ascomycota, using descriptions, fossil images and illustrations, coupled with recent age estimations, and taxonomic and phylogenetic affinity of extant species. As an integrated approach, this study summarizes a historical fossil outline with a reliable minimum age for 16 calibrating points viz. crown of Aigialus, Anzia, Aspergillus, Asterina, Calicium chlorosporum-C. nobile, Capnodiales, Chaenotheca, Colletotrichum, Diaporthales, Meliola, Ophiocordyceps, Microthyriales, Microthyrium, Muyocopron, Pezizomycotina and Stigmatomyces. A scheme of Ascomycota ancient lineages is also provided in order to improve divergence time estimations.

Journal of Ichthyology, 2019

This article describes early development of the climbing perch Anabas testudineus in relation to its buoyancy dynamics. Main patterns of the ontogeny during the first 140 h of development are described. The climbing perch is characterized by positive buoyancy of eggs and early larvae not usually found in other freshwater fish. This allows the fish development close to the surface of the water and is enabled by a large oil globule in the yolk. The data on the spatial orientation of the larva body, their vertical distribution in the water column, the beginning of exogenous feeding and locomotion, and the fright reaction of the larvae at different ages are presented. The most significant changes in the behavior of the climbing perch larvae are associated with changing the shape of the yolk sac, beginning to function as a provisional hydrostatic organ from about the 80s hour of development.

The Linguistic Review, 2022

Contrary to the conventional three-way distinction of questions: polar questions, disjunctive questions, and wh-questions, we argue for a more revealing two-way distinction of polar versus constituent questions, the latter with two subtypes: disjunctive and wh-questions. Following Bhatt, Rajesh & Veneeta Dayal. 2020. Polar question particles: Hindi-Urdu kya. Natural Language & Linguistic Theory 38. 1115–1144 proposal that polar questions denote singleton sets of propositions and the standard view that disjunctive and wh-questions denote sets with multiple propositions, we further characterize this dichotomy pragmatically as confirmation-seeking (CS) and information-seeking (IS), i.e., polar questions seek confirmation of the proposition put forth, while constituent questions seek information specifically targeted by the interrogative constituent. This dichotomy is formally detected in Mandarin Chinese via the question particle ma versus ne, dichotomy of fragment questions, adverb na...

Revista Chilena de Historia Natural, 2021

Background In this article we would like to touch on the key role played by the microbiota in the maintenance of a sustainable environment in the entire planet. For obvious reasons, this article does not intend to review thoroughly this extremely complex topic, but rather to focus on the main threats that this natural scenario is presently facing. Methods Recent literature survey. Results Despite the relevance of microorganisms have in our planet, the effects of climate change on microbial communities have been scarcely and not systematically addressed in literature. Although the role of microorganisms in emissions of greenhouse gases has received some attention, there are several microbial processes that are affected by climate change with consequences that are presently under assessment. Among them, host-pathogen interactions, the microbiome of built environment, or relations among plants and beneficial microbes. Conclusions Further research is required to advance in knowledge of ...

Frontiers in immunology, 2017

Many essential functions of the human body are dependent on the symbiotic microbiota, which is present at especially high numbers and diversity in the gut. This intricate host-microbe relationship is a result of the long-term coevolution between the two. While the inheritance of mutational changes in the host evolution is almost exclusively vertical, the main mechanism of bacterial evolution is horizontal gene exchange. The gut conditions, with stable temperature, continuous food supply, constant physicochemical conditions, extremely high concentration of microbial cells and phages, and plenty of opportunities for conjugation on the surfaces of food particles and host tissues, represent one of the most favorable ecological niches for horizontal gene exchange. Thus, the gut microbial system genetically is very dynamic and capable of rapid response, at the genetic level, to selection, for example, by antibiotics. There are many other factors to which the microbiota may dynamically res...

TAXON

The widespread aquatic plant genus Callitriche is taxonomically very challenging, but noteworthy in many evolutionary aspects including a high overall diversity, extensive phenotypic plasticity, remarkable reproductive systems and a large variation in ploidy levels and chromosome numbers. We conducted a multi-level systematic study on 346 individuals of 25 taxa from 21 mostly European countries. Flow cytometric estimation of genome size, chromosome counting and direct sequencing of ITS and trnT-trnL DNA markers combined with RFLPs of the ITS region were applied in order to unravel the phylogenetic relationships among Callitriche taxa and to clarify the origin of polyploid species and hybrids. Additionally, ITS sequences from a recent worldwide phylogenetic study of the genus were included for comparison. We demonstrate that most of the traditionally recognized European Callitriche taxa are well defined by a combination of genome size and molecular markers. Several species showed remarkable intraspecific genetic variation; previously unknown cryptic taxa were revealed within C. stagnalis, C. truncata and North American C. heterophylla. The origin of selected polyploid taxa was investigated in detail. Diploid C. cophocarpa was confirmed to be the parental species of tetraploid C. platycarpa, but we did not find direct evidence for the putative allopolyploid origin of this species. The complex of C. brutia included three taxa; of these, C. hamulata is probably an allooctoploid derivative of C. brutia var. brutia and C. cophocarpa/C. platycarpa. The third member, C. brutia var. naftolskyi, was newly reclassified at the subspecies level; for the first time, chromosome numbers are provided for this poorly known taxon. For a single triploid sample, our results suggested an autopolyploid origin from C. stagnalis. Four Callitriche hybrids were revealed, two of which are newly described and validated here as C. ×nyrensis and C. brutia nothosubsp. neglecta. A tentative intrageneric concept of two sections (Callitriche, Pseudocallitriche) is adopted, with the need for a more detailed evaluation in the future.

iScience, 2021

Highlights We optimized single-cell methodology using a broad sample range, for EME We combined bioinformatic and bench protocols into a concise workflow We benchmarked the pipeline and used it on environmental samples We selected a set of QC criteria for best genome quality prediction

Mycological Progress, 2019

The diversity of yeasts has grown rapidly as the discovery of new species has benefited from intensified sampling and largely improved identification techniques. An environmental study typically reports the isolation of yeast species, some of which are new to science. Rare species represented by a few isolates often do not result in a taxonomic description. Nucleic acid sequences from these undescribed yeasts remain in public sequence databases, often without a proper taxonomic placement. This study presents a constrained phylogenetic analysis for many rare yeasts from unpublished but publicly available DNA sequences and from studies previously conducted by the authors of this work. We demonstrate that single isolates are an important source of taxonomic findings such as including new genera and species. Independent surveys performed during the last 20 years on a large geographic scale yielded a number of single strains, which were proved to be conspecific in the phylogenetic analyses presented here. The following new species were resolved and described: Vustinia terrea

Brazilian Journal of Pharmaceutical Sciences

Phellinus mushrooms have been traditionally used for various medicinal purposes. Protocatechuic acid, which was previously reported to be a component in some Phellinus mushrooms, has some pharmacological effects. This study aimed to validate a HPLC method for the quantitative analysis of the protocatechuic acid contents in the extracts from different Phellinus mushroom species collected in Thailand. HPLC was carried out using a C18 column and the gradient mobile phases of 0.1% formic acid in water and 0.1% formic acid in acetonitrile. Method validation was performed to assure the linearity, accuracy, precision, limit of detection and limit of quantitation of the analytical method. The linearity range of protocatechuic acid was 1-10 µg/ml. The average recovery was 104.16%. The method was shown to be precise with the RSD of repeatability and intermediate precision at less than 3%. The protocatechuic contents in 11 Phellinus mushrooms were in the range of less than 0.0099-0.4121 %w/w of the extract. The developed HPLC method was reliable and suitable for the quantitative analysis of protocatechuic acid content in Phellinus mushrooms.

Encyclopedia

Toxoplasma gondii is a ubiquitous zoonotic parasite with an obligatory intracellular lifestyle. It relies on a specialized set of cytoskeletal and secretory organelles for host cell invasion. When infecting its felid definitive host, T. gondii undergoes sexual reproduction in the intestinal epithelium, producing oocysts that are excreted with the feces and sporulate in the environment. In other hosts and/or tissues, T. gondii multiplies by asexual reproduction. Rapidly dividing tachyzoites expand through multiple tissues, particularly nervous and muscular tissues, and eventually convert to slowly dividing bradyzoites which produce tissue cysts, structures that evade the immune system and remain infective within the host. Infection normally occurs through ingestion of sporulated oocysts or tissue cysts. While T. gondii is able to infect virtually all warm-blooded animals, most infections in humans are asymptomatic, with clinical disease occurring most often in immunocompromised hosts...

Journal of Applied Phycology

Microalgae are emerging as an important renewable and sustainable source of high-value biomolecules having applications in food, cosmetics, pharmaceutical, agrochemicals and fuel industries. Deriving high-value biomolecules from micro-algae however faces numerous process and technological challenges. It is essential to develop innovative ways of intensifying processes used for valorising microalgae. Hydrodynamic cavitation (HC) offers an attractive platform for process intensification relevant to microalgae because of its scalability, ability to handle dense slurries, intense physicochemical effects, and low cost. Here we briefly review the overall processes involved in deriving high-value biomolecules from micro-algae. Opportunities for intensifying these processes and enhancing productivity of processing microalgae via HC are then identified and critically reviewed. The current state of the art and yet unresolved challenges are highlighted. An attempt is made to identify specific ...

Biogeosciences, 2020

Recent advances in fluorescence imaging facilitate actualistic studies of organisms used for palaeoceanographic reconstructions. Observations of cytoskeleton organisation and dynamics in living foraminifera foster understanding of morphogenetic and biomineralisation principles. This paper describes the organisation of a foraminiferal actin cytoskeleton using in vivo staining based on fluorescent SiR-actin. Surprisingly, the most distinctive pattern of SiR-actin staining in foraminifera is the prevalence of SiR-actin-labelled granules (ALGs) within pseudopodial structures. Fluorescent signals obtained from granules dominate over dispersed signals from the actin meshwork. SiR-actin-labelled granules are small (around 1 µm in diameter) actin-rich structures, demonstrating a wide range of motility behaviours, from almost stationarily oscillating around certain points to exhibiting rapid motion. These labelled microstructures are present both in Globothalamea (Amphistegina, Ammonia) and Tubothalamea (Quinqueloculina). They are found to be active in all kinds of pseudopodial ectoplasmic structures, including granuloreticulopodia, globopodia, and lamellipodia, as well as within the endoplasm. Several hypotheses are set up to explain either specific or non-specific actin staining. Two hypotheses regarding their function are proposed if specific actin labelling is taken into account: (1) granules are involved in endocytosis and intracellular transport of different kinds of cargo, or (2) they transport prefabricated and/or recycled actin fibres to the sites where they are needed. These hypotheses are not mutually exclusive. The first hypothesis is based on the presence of similar actin structures in fungi, fungi-like protists, and some plant cells. The later hypothesis is based on the assumption that actin granules are analogous to tubulin paracrystals responsible for efficient transport of tubulin. Actin patches transported in that manner are most likely involved in maintaining shape, rapid reorganisation, and elasticity of pseudopodial structures, as well as in adhesion to the substrate. Finally, our comparative studies suggest that a large proportion of SiR-actin-labelled granules probably represent fibrillar vesicles and elliptical fuzzy-coated vesicles often identified in transmission electron microscope images.

Fisheries Management and Ecology, 2020

Biological invasions are a major driver of global environmental change as invasive non‐native species can exert severe environmental impacts on invaded ecosystems. Estuaries are especially vulnerable to biological invasions, which in highly urbanised areas are further facilitated by introduction pathways linked to commercial activities. This study provides a risk screening of non‐native invasive species for the highly urbanised River Neretva Estuary (Eastern Adriatic Sea: Croatia and Bosnia–Herzegovina). In total, 12 species of non‐native aquatic organisms were identified and screened for their invasiveness with the Aquatic Species Invasiveness Screening Kit. Of these species, eight were classified as carrying a high risk of invasiveness under current climate conditions and nine under future climate conditions. Amongst the high‐risk species, blue crab Callinectes sapidus has already caused impacts in the risk assessment area, where it also represents an important economic resource. ...

Geological Society, London, Special Publications, 2020

Testate amoebae are a frequently used palaeoecological proxy for reconstructing changes in palaeohydrological conditions, particularly in studies of Sphagnum-dominated peatlands. Their use in palaeoecological studies has increased following the development of transfer functions, allowing for the quantitative reconstruction of water-table depth changes through time. Increasingly, they are included in non-pollen palynomorph (NPP) studies alongside a wide range of other proxies, representing a valuable tool, particularly in multi-proxy studies.Testate amoebae have been used for qualitative assessment of palaeohydrology in NPP studies and may aid the verification of environmental interpretations of conditions inferred from curves of NPP with unknown ecology and taxonomy. Their usefulness in such studies is limited by the destruction of tests owing to harsh chemical treatments used in pollen preparation methods. This makes community distribution data of testate amoebae derived by these m...

Fungal Diversity, 2018

High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum-and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.

Journal of Zoological Systematics and Evolutionary Research

Acari harbor numerous minute species of agricultural economic importance, mainly Tetranychidae and Phytoseiidae. Great efforts have been established by means of recovering morphological, molecular, and phylogenetic traits for species identification. Traditional identification still relies on external diagnostic characters, which are limited and usually exhibit large phenotypic plasticity within the species, rendering them useless for species delimitation and identification. We decided to increase the number of sequences of the Acari mitochondrial COI (Cytochrome C oxidase I) marker and ITS nuclear ribosomal DNA region for species identification in Tetranychidae and Phytoseiidae. The molecular data allow us to establish species boundaries and phylogenetic relationships among several clades of Acari, mainly Tetranychidae and Phytoseiidae. Sequence comparisons between complete COI and the Acari mitochondrial COI, ITS1-5,8S-ITS2, and ITS2 among all Acari sequences have demonstrated that...