Phytoplankton and water quality of Lake Kuchane (Pskov region, Russia)

The phytoplankton communities of Lake Kuchane, located in the Mikhailovskoye Museum-Reserve, were studied during different 2016–2017 seasons for the first time. 213 specific and intraspecific taxa from 9 phylums were identified in the phytoplankton, namely: Bacillariophyta, Chlorophyta, Chrysophyta, Euglenophyta, Cyanobacteria, Dinophyta, Cryptophyta, Charophyta, and Xanthophyta. The ratio of the main phylums of microalgae during the studied seasons was similar. The floristic complex of the lake's algoflora consisted of diatoms (36.6%), green (27.2%) and golden (10.8%) algae. Most of the phytoplankton genera contained one species taxon only. The specific composition of the phytoplankton community in 2017 was similar from spring to autumn. The minimum specific similarity of the phytoplankton communities was noted in July, 2016, and August, 2017. According to the level of biomass of planktonic algae, the lake belongs to oligotrophic water bodies. The planktonic algoflora of Lake Kuchane is characterized by the predominance of cosmopolitan freshwater forms of microalgae. In relation to pH, the predominant representatives preferred slightly alkaline waters. The Milius trophic index varied in the range 18.0–39.6 with a maximum value in summer. The Pantle–Bukk saprobity index almost did not change during the entire study. The waters of Lake Kuchane corresponded to the betamesosaprobic self-purification zone, quality class III.

A synthesis tree of the Copepoda: integrating phylogenetic and taxonomic data reveals multiple origins of parasitism

The Copepoda is a clade of pancrustaceans containing 14,485 species that are extremely varied in their morphology and lifestyle. Not only do copepods dominate marine plankton and sediment communities and make up a sizeable component of the freshwater plankton, but over 6,000 species are symbiotically associated with every major phylum of marine metazoans, mostly as parasites. Unfortunately, our understanding of copepod evolutionary relationships is relatively limited in part because of their extremely divergent morphology, sparse taxon sampling in molecular phylogenetic analyses, a reliance on only a handful of molecular markers, and little taxonomic overlap between phylogenetic studies. Here, a synthesis tree method is used to integrate published phylogenies into a more comprehensive tree of copepods by leveraging phylogenetic and taxonomic data. A literature review in this study finds fewer than 500 species of copepods have been sampled in molecular phylogenetic studies. Using the Open Tree of Life platform, those taxa that have been sampled in previous phylogenetic studies are grafted together and combined with the underlying copepod taxonomic hierarchy from the Open Tree of Life Taxonomy to make a synthesis phylogeny of all copepod species. Taxon sampling with respect to molecular phylogenetic analyses is reviewed for all orders of copepods and shows only 3% of copepod species have been sampled in phylogenetic studies. The resulting synthesis phylogeny reveals copepods have transitioned to a parasitic lifestyle on at least 14 occasions. We examine the underlying phylogenetic, taxonomic, and natural history data supporting these transitions to parasitism; review the species diversity of each parasitic clade; and identify key areas for further phylogenetic investigation.

Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification

Columnea latent viroid (CLVd) is a member of the Pospiviroid family and its naked circular RNA genome typically forms native “rod-like” secondary structures. In this work, the CLVd taxonomy was reevaluated based on sequence similarity and phylogenetic analysis, as well as the evaluation of the symptom development and disease severity of four selected CLVd isolates in a range of host species. The phylogenetic analysis showed that all CLVd isolates were clustered into five distinct clades: (I) severe isolates originally found in tomato crops in Thailand, (II) ornamental isolates, (III) mild isolates originally found in tomato crops in Thailand, and two clades (IV and V) containing mild isolates originating mainly from tomato crops in European countries, with different virulence levels on several hosts. Our analysis demonstrated that some CLVd isolates have a sequence similarity of less than 90% within the species taxon, as well as distinct biological characteristics (symptom development and virulence), both of which are important ICTV criteria for viroid classification. For these reasons, we propose that CLVd should be re-classified into at least three main taxonomic lineages: a “CLVd-tomato Asian lineage” (I), a “CLVd-tomato European lineage” (IV) and a “CLVd-ornamental European lineage” (II), plus two minor lineages (III and V), fitting the ICTV criteria.

'Candidatus Phytoplasma dypsidis', a novel taxon associated with a lethal wilt disease of palms in Australia

A phytoplasma was initially detected in Dypsis poivriana by nested and real-time PCR from the botanical gardens in Cairns, Queensland, Australia in 2017. Further surveys in the Cairns region identified phytoplasma infections in eight additional dying ornamental palm species (Euterpe precatoria, Cocos nucifera, Verschaffeltia splendida, Brassiophoenix drymophloeodes, Burretiokentia hapala, Cyrtostachys renda, Reinhardtia gracilis, Carpoxylon macrospermum), a Phoenix species, a Euterpe species and two native palms (Archontophoenix alexandrae). Analysis of 16S rRNA gene sequences showed that this phytoplasma is distinct as it shared less than 97.5 % similarity with all other ‘Candidatus Phytoplasma’ species. At 96.3 % similarity, the most closely related formally described member of the provisional 'Ca. Phytoplasma' genus was 'Ca. Phytoplasma noviguineense', a novel taxon from the island of New Guinea found in monocotyledonous plants. It was slightly more closely related (96.6–96.8 %) to four palm-infecting strains from the Americas, which belong to strain group 16SrIV and which have not been assigned to a formal 'Candidatus Phytoplasma’ species taxon. Phylogenetic analysis of the 16S rRNA gene and ribosomal protein genes of the phytoplasma isolate from a dying coconut palm revealed that the phytoplasma represented a distinct lineage within the phytoplasma clade. As the nucleotide identity with other phytoplasmas is less than 97.5 % and the phylogenetic analyses show that it is distinct, a novel taxon 'Candidatus Phytoplasma dypsidis' is proposed for the phytoplasma found in Australia. Strain RID7692 (GenBank accession no. MT536195) is the reference strain. The impact and preliminary aspects of the epidemiology of the disease outbreak associated with this novel taxon are described.

Diversity and composition of algal epiphytes on the Mediterranean seagrass Cymodocea nodosa: a scale-based study

Cymodocea nodosa, a typical marine angiosperm species in the Mediterranean Sea, hosts a range of epiphytic algae. Epiphyte abundance varies at different spatial scales, yet epiphyte diversity and community composition are poorly understood. This study explores the epiphytes on C. nodosa from two reference meadows (Thasos, Vrasidas) and one anthropogenically stressed meadow (Nea Karvali) in the northern Aegean Sea (Kavala Gulf, Greece). A nested destructive sampling design at three spatial scales (metres, hundreds of metres, kilometres) and stereoscopic/microscopic observations were used. Light microscopy revealed a total of 19 taxa of macroalgae populating the leaves of C. nodosa. The most commonly encountered taxa with highest cover (%) were Hydrolithon cruciatum and Feldmannia mitchelliae. DNA sequencing (18S rDNA) confirms the presence of a number of dinoflagellate and red algal epiphytes, and this represents the first application of DNA metabarcoding to study the diversity of seagrass epiphytes. Epiphytic communities studied at species/taxon and functional (Ecological Status Groups) levels separated the reference low-stressed meadows from the degraded one, with the functional approach having higher success. The ecological evaluation index classified the studied meadows into different Ecological Status Classes according to anthropogenic stress.

Potential use of molecular and structural characterization of the gut bacterial community for postmortem interval estimation in Sprague Dawley rats

Once the body dies, the indigenous microbes of the host begin to break down the body from the inside and play a key role thereafter. This study aimed to investigate the probable shift in the composition of the rectal microbiota at different time intervals up to 15 days after death and to explore bacterial taxa important for estimating the time since death. At the phylum level, Proteobacteria and Firmicutes showed major shifts when checked at 11 different intervals and emerged at most of the postmortem intervals. At the species level, Enterococcus faecalis and Proteus mirabilis showed a downward and upward trend, respectively, after day 5 postmortem. The phylum-, family-, genus-, and species-taxon richness decreased initially and then increased considerably. The turning point occurred on day 9, when the genus, rather than the phylum, family, or species, provided the most information for estimating the time since death. We constructed a prediction model using genus-level data from high-throughput sequencing, and seven bacterial taxa, namely, Enterococcus, Proteus, Lactobacillus, unidentified Clostridiales, Vagococcus, unidentified Corynebacteriaceae, and unidentified Enterobacteriaceae, were included in this model. The abovementioned bacteria showed potential for estimating the shortest time since death.

Species

The diversity of life is not seamless but comes in relatively discrete packages, species. Is that packaging real, or an artefact of our limited temporal perspective on the history of life? If all living forms are descended from one or a few ancestors, there may be no real distinction between living and ancestral forms, or between closely related living animals. Received wisdom holds that species are the ’units of evolution’, for it is they that evolve. They are the upshot of evolutionary processes, but, if species and not just their component organisms compete with one another, they are also important agents in the evolutionary process. If so, species are real units in nature, not arbitrary segmentations of seamless variation. The ’species problem’ has been approached from two angles. One focus has been on specific taxa of the tree of life. What would settle whether some arbitrarily chosen organism is a member of homo sapiens or canis familiaris? This is sometimes known as the ’species taxon’ problem. An alternate way of approaching diversity has been to ask what all species have in common. What do all the populations we think of as species share? This is the ’species category’ problem. One idea is to group organisms into species by appealing to the overall similarity. This ’phenetic’ conception is in retreat. Most contemporary species definitions are relational, the animals that compose pan troglodytes are a species, not because they are all very similar (they are very like the pygmy chimps as well) but because of their relations amongst themselves and with their ancestors. The most famous relational definition is the ’biological species concept’, according to which conspecific organisms are organisms that can interbreed, however different they look. Relational species definitions aim to define a category of theoretical and explanatory interest to evolutionary and ecological theory. Given that there are many explanatory interests, one problem in evaluating these accounts is to determine whether they are genuinely rivals.

Properties of stumps that promote the growth and survival of Japanese cedar saplings in a natural old-growth forest

In a natural forest that has experienced logging and lacks large fallen logs, cut stumps are expected to become a suitable substrate for regeneration. We investigated the properties of stumps that promoted the natural regeneration of coniferous species in a natural old-growth forest dominated by Cryptomeria japonica (L.f.) D. Don. A comparison of C. japonica saplings growing in three microsites (ground, stumps, and fallen logs) revealed that sapling density was highest on the stumps; 75% of saplings were distributed on stumps, which occupied only 3% of the projected forest area. The mortality of saplings during the 3-year study period did not differ significantly among the three microsites. Six properties of stumps were quantified: height, diameter at ground level, decay class, species taxon, type (i.e., cause of occurrence: logging or natural disturbance), and light conditions. Of these properties, the type of stump was the most influential. The density of saplings was significantly greater on stumps produced by logging than on naturally broken stumps. Taller stumps exhibited a significantly higher density of saplings; indeed, there were no saplings on stumps less than 60 cm in height. Saplings on stumps were concentrated in higher positions on the stump, and survivorship tended to be greater when their root location was higher. We concluded that the height of the microsite was an important factor for regeneration of C. japonica at this research site, where saplings were under competition with dense undergrowth vegetation. Most of the fallen logs were less than 60 cm in height and it appeared unlikely that they would function as regeneration sites for C. japonica.

The Larval Salivary-Gland Polytene Chromosomes of Anopheles (Cellia) Annulipes Sl Walker (Diptera, Culicidae)

A photomap of the larval salivary gland chromosomes of An. annulipes from colony material arbitrarily chosen as standard for this taxon is presented. Also illustrated are seven types of X chromosomes which have been revealed in this multi-species taxon.

Porcine haemophili and actinobacilli: characterization by means of API test strips and possible taxonomic implications

Thirty Haemophilus strains and six Actinobacillus strains, all of porcine origin, were examined for their biochemical reactivity on API 20E and API ZYM test strips using dense cell suspensions (supplemented with NAD as appropriate) as strip inocula. When combined with a test for V-factor dependency, the use of both strips allowed adequate differentiation of closely related organisms. Numerical taxonomic analysis of the data demonstrated that the majority of the haemophili and actinobacilli studied could be placed in one of four major clusters; these clusters contained, respectively, the H. pleuropneumoniae – A. pleuropneumoniae strains, the H. parasuis strains, strains belonging to Haemophilus taxon "minor group," and strains belonging to an unusual group of mannitol-positive, urease-negative haemophili. A representative of Haemophilus species taxon C and an unusual Actinobacillus isolate appeared to be comparatively unrelated to organisms in the four major clusters. Although it may, on occasion, be difficult to place an unusual isolate in any one particular group, owing to the uncertain taxonomy of some of these organisms, it is concluded that API test strips can serve as useful tools for the characterization and differentiation of porcine haemophili and actinobacilli.