Bacterial communities in polluted seabed sediments: a molecular biology assay in Leghorn harbor

Seabed sediments of commercial ports are often characterized by high pollution levels. Differences in number and distribution of bacteria in such areas can be related to distribution of pollutants in the port and to sediment conditions. In this study, the bacterial communities of five sites from Leghorn Harbor seabed were characterized and the main bacterial groups identified. T-RFLP was used for all samples; two 16S rRNA libraries and in silico digestion of clones were used to identify fingerprint profiles. Library data, phylogenetic analysis, and T-RFLP coupled with in silico digestion of the obtained sequences evidenced the dominance of Proteobacteria and the high percentage of Bacteroidetes in all sites. The approach highlighted similar bacterial communities between samples coming from the five sites, suggesting a modest differentiation among bacterial communities of different harbor seabed sediments, and hence the capacity of bacterial communities to adapt to different levels and types of pollution

Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination

The prevailing view of the nuclear genetic code is that it is largely frozen and unambiguous. Flexibility in the nuclear genetic code has been demonstrated in ciliates that reassign standard stop codons to amino acids, resulting in seven variant genetic codes, including three previously undescribed ones reported here. Surprisingly, in two of these species, we find efficient translation of all 64 codons as standard amino acids and recognition of either one or all three stop codons. How, therefore, does the translation machinery interpret a “stop” codon? We provide evidence, based on ribosomal profiling and “stop” codon depletion shortly before coding sequence ends, that mRNA 3′ ends may contribute to distinguishing stop from sense in a context-dependent manner. We further propose that such context-dependent termination/readthrough suppression near transcript ends enables genetic code evolution

Free-living ciliates as potential reservoirs for eukaryotic parasites: Occurrence of a trypanosomatid in the macronucleus of Euplotes encysticus

Background: Flagellates of the family Trypanosomatidae are obligate endoparasites, which can be found in various hosts. Several genera infect insects and occur as monoxenous parasites especially in representatives of Diptera and Hemiptera. These trypanosomatid flagellates probably share the worldwide distribution of their hosts, which are often infested by large numbers of endoparasites. Traditionally, their taxonomy was based on morphology, host origin, and life cycle. Here we report the characterization of a trypanosomatid infection detected in a protozoan, a ciliate collected from a polluted freshwater pond in a suburb of New Delhi (India). Methods. Live observations and morphological studies applying light, fluorescence and transmission electron microscopy were conducted. Molecular analyses of host and parasite were performed and used for phylogenetic reconstructions and species (host) or genus level (parasite) identification. Results: Although the morphological characteristics were not revealing, a high similarity of the trypanosomatids 18S rRNA gene sequence to Herpetomonas ztiplika and Herpetomonas trimorpha (Kinetoplastida, Trypanosomatidae), both parasites of biting midges (Culicoides kibunensis and Culicoides truncorum, respectively) allowed the assignment to this genus. The majority of the host population displayed a heavy infection that significantly affected the shape of the host macronucleus, which was the main site of parasite localization. In addition, the growth rate of host cultures, identified as Euplotes encysticus according to cell morphology and 18S rRNA gene sequence, was severely impacted by the infection. Conclusions: The host-parasite system described here represents a recent example of free-living protists acting as environmental reservoirs for parasitic eukaryotic microorganisms

Preliminary data on the distribution, morphology and genetics of white-clawed crayfish and on their ectosymbionts in Lunigiana (Tuscany, Italy)

The white-clawed crayfish is a complex of species (Austropotamobius pallipes plus A. italicus, Crustacea) pivotal to riverine environments. Regrettably, it is endangered in many European countries due to a recent massive decline. We carried out a fine-scale survey on white-clawed crayfish distribution, morphology and genetics in an under-investigated region of central Italy (Lunigiana, Tuscany) to improve local knowledge and aid conservation management of the species. The torrential fauna of Lunigiana is scarcely known and habitat alterations due to the anthropic exploitation of the territory represent a potential threat to its persistence. We investigated crayfish occurrence in eight streams of the Magra River Basin. We performed nocturnal and diurnal transects, took morphometric measurements, collected samples for genetic analysis and checked for the occurrence of ectosymbionts. Crayfish were disclosed in two streams (Civasola, Verdesina). Morphometric and phylogenetic analysis (mtDNA COI gene Bayesian tree reconstruction) concurrently identified both populations as Austropotamobius italicus carinthiacus. In the Verdesina stream, crayfish were heavily infested by branchiobdellidans (Annelida). Verdesina crayfish were also significantly smaller than those found in the Civasola stream, where branchiobdellidans were absent. Hence, we hypothesized that such difference in size might be related to the high density of ectosymbionts. In the light of habitat features and of data herein provided, we propose that both Civasola and Verdesina streams should be considered as “natural ark sites” for A. italicus, with the Magra River Basin representing a regional stronghold for the conservation of the specie

Stress Hyperglycemia and Complications Following Traumatic Injuries in Individuals With/Without Diabetes: The Case of Orthopedic Surgery

Purpose: Hyperglycemia in trauma patients may stem from metabolic response to stress, both in the presence and the absence of underlying diabetes. We aimed to test the association of stress hyperglycemia with risks of adverse events subjects undergoing orthopedic surgery. Patients and Methods: In a prospective observational study, we enrolled 202 consecutive patients with hyperglycemia at hospital admission for trauma injuries requiring orthopedic surgery. Based on history, diabetes was present in 183, and 13 more were defined as unknown diabetes on the basis of HbA1c ≥48mmol/mol. Stress hyperglycemia was defined in subjects with/without diabetes by a stress hyperglycemia ratio (SHR) >1.14, calculated as admission glucose/average glucose, estimated from glycosylated hemoglobin. Logistic regression analysis was used to calculate the risk of post-surgery adverse events associated with different states of hyperglycemia, after correction for demographic and clinical confounders. Results: Stress hyperglycemia was diagnosed, either as superimposed to diabetes (54/196 cases, 27.6%) as well as in the 6 cases without diabetes. At least one complication was recorded in 68 cases (33.7%), the most common being systemic infection (22.8% of cases). In the total cohort, stress hyperglycemia, irrespective of the presence of diabetes, increased the risk of adverse events (any events, odds ratio [OR], 4.43; 95% confidence interval [CI], 2.11–9.30), cardiovascular events (OR, 7.09; 95% CI, 2.47–19.91), systemic infections (OR, 4.21; 95% CI, 1.97–9.03) and other adverse events (OR, 6.30; 95% CI, 1.41–28.03), after adjustment for confounders; hospital stay was much longer. The same was true when the analysis was limited to the diabetes cohort or by comparing pure stress hyperglycemia vs diabetes without stress hyperglycemia. Conclusion: The study highlights the importance of stress hyperglycemia for adverse events in the setting of orthopedic surgery following trauma injuries. This condition requires stricter management, considering the much longer length of hospital stay and higher costs

The neotypification of Frontonia vernalis (Ehrenberg, 1833) Ehrenberg, 1838 and the description of Frontonia paravernalis sp. nov. trigger a critical revision of frontoniid systematics

Background: Among Oligohymenophorea (Ciliophora, Alveolata) the subclass Peniculia stands as one of the most well-known groups. Frontonia is the largest genus of Peniculia, and its representatives are spread in any type of water bodies as well as in soil. At a first glance, Frontonia species exhibit an overall similar morphology, and form a well-recognizable taxon of ciliates. Despite the general morphological homogeneity, the phylogenetic analysis based on the 18S rDNA sequencing showed that Frontonia is a non-monophyletic group. The systematics of this genus should be deeply reviewed, although additional issues complicate the task solving. First, type species of the genus is not yet clearly established, and no type material is available. In this context, the situation of F. vernalis, one of the first Frontonia ever described, is somehow puzzled: the description of this ciliate made by Ehrenberg (in 1833 and 1838) contains several inaccuracies and subsequent misidentifications by other authors occurred. Moreover, the 18S rDNA sequence of a putative F. vernalis is available on GenBank, but no morphological description of the correspondent specimens is provided; thus, in our opinion, it should be only prudently associated with F. vernalis or at least indicated as “F. vernalis”. Results: In the present work, we provide the neotypification of F. vernalis newly found in Italy, presenting its multidisciplinary description and its neotype material. Similarly, we describe a novel species bearing Chlorella-like endosymbionts, Frontonia paravernalis sp. nov., retrieved in two far distant locations (Italy, Russia). A critical discussion on the status of Frontonia taxonomy and phylogeny is also presented, based on the 18S rDNA sequencing of both these two newly collected species and other 14 frontoniids isolated in different parts of the world. Finally, in the present study F. leucas was neotypified and proposed as the type species of the genus. Conclusions: Green frontoniids form a monophyletic clade of freshwater organisms characterized by having a single contractile vacuole and bearing intracytoplasmatic Chlorella-like symbionts. With the neotypification of F. vernalis and F. leucas a fundamental step in Frontonia systematics was taken, and the bases for further taxonomic studies were laid

Recalcitrant compounds removal in raw leachate and synthetic effluents using the white-rot fungus Bjerkandera adusta

Recalcitrant compounds limit the efficiency of conventional biological processes for wastewater treatment, representing one of the major issues in the field. This study focused on the treatment of three effluents with White-Rot-Fungus (WRF) Bjerkandera adusta MUT 2295 in batch tests, with biomass cultivated in attached form on polyurethane foam cubes (PUFs) to test its efficiency in the removal of the target effluents' recalcitrant fraction. Treatment efficiency of B. adusta was evaluated on landfill leachate (Canada) and two solutions containing synthetic recalcitrant compounds, which were prepared with tannic and humic acid. Chemical Oxygen Demand (COD) and color removal, the production of manganese peroxidases, and the consumption of a co-substrate (glucose) were monitored during the experiment. Biological Oxygen Demand (BOD5) and fungal dry weight were measured at the beginning and at the end of the experiment. After co-substrate addition, effluent COD was 2300 ± 85, 2545 ± 84, and 2580 ± 95 (mg/L) in raw leachate and tannic and humic acids, respectively. COD removal of 48%, 61%, and 48% was obtained in raw leachate and in the synthetic effluents containing tannic and humic acids, respectively. Color removal of 49%, 25%, and 42% was detected in raw leachate and in tannic and humic acid solutions, respectively. COD and color removals were associated with the increase of fungal dry weight, which was observed in all the trials. These results encourage the use of the selected fungal strain to remove tannic acid, while further investigations are required to optimize leachate and humic acid bioremediation

Rare Freshwater Ciliate Paramecium chlorelligerum Kahl, 1935 and Its Macronuclear Symbiotic Bacterium "Candidatus Holospora parva"

Ciliated protists often form symbioses with many diverse microorganisms. In particular, symbiotic associations between ciliates and green algae, as well as between ciliates and intracellular bacteria, are rather wide-spread in nature. In this study, we describe the com- plex symbiotic system between a very rare ciliate, Paramecium chlorelligerum, unicellular algae inhabiting its cytoplasm, and novel bacteria colonizing the host macronucleus. Para- mecium chlorelligerum, previously found only twice in Germany, was retrieved from a novel location in vicinity of St. Petersburg in Russia. Species identification was based on both clas- sical morphological methods and analysis of the small subunit rDNA. Numerous algae occu- pying the cytoplasm of this ciliate were identified with ultrastructural and molecular methods as representatives of the Meyerella genus, which before was not considered among symbi- otic algae. In the same locality at least fifteen other species of “green” ciliates were found, thus it is indeed a biodiversity hot-spot for such protists. A novel species of bacterial symbi- onts living in the macronucleus of Paramecium chlorelligerum cells was morphologically and ultrastructurally investigated in detail with the description of its life cycle and infection capabilities. The new endosymbiont was molecularly characterized following the full-cycle rRNA approach. Furthermore, phylogenetic analysis confirmed that the novel bacterium is a member of Holospora genus branching basally but sharing all characteristics of the genus except inducing connecting piece formation during the infected host nucleus division. We propose the name “Candidatus Holospora parva” for this newly described species. The described complex system raises new questions on how these microorganisms evolve and interact in symbiosis