Phylogenetic evidence for a new genotype of Acanthamoeba (Amoebozoa, Acanthamoebida)

Acanthamoeba are widespread free-living amoebae, able to cause infection in animals, with keratitis and granulomatous encephalitis as major diseases in humans. Recent developments in the subgenus classification are based on the determination of the nucleotide sequence of the 18S rDNA. By this mean, Acanthamoeba have been clustered into 15 sequence types or genotypes, called T1 to T15. In this study, we analysed near full 18S rDNA of an Acanthamoeba recovered from an environmental sample and various unidentified Acanthamoeba sequences retrieved from GenBank. We provided phylogenetic evidence for a new genotype, which we proposed to name T1

More Acanthamoeba Genotypes: Limits to Use rDNA Fragments to Describe New Genotype

Strains of the genus Acanthamoeba are usually assigned to sequence types or genotypes according to pair-wise similarity values of the nuclear gene for the small subunit of ribosomal RNA. This classification system was established by comparing full or nearly full gene sequences, > 2000 bp. For practical reasons, diagnostic fragments of smaller lengths have been identified and used for rapid and economic identification of large number of strains. While the use of these small fragments in diagnostics applications remains valid when and only if the reference full sequence-type is available, we contest their use to identify and describe new genotypes. We report herein the case of a new genotype described on the basis of solely a small partial sequence and discuss the poor reliability of this fragment to correctly infer phylogenetic relationships, and its limits in the description of new genotypes of Acanthamoeba

" Candidatus Mesochlamydia elodeae” (Chlamydiae: Parachlamydiaceae ), a novel chlamydia parasite of free-living amoebae

Vannella sp. isolated from waterweed Elodea sp. was found infected by a chlamydia-like organism. This organism behaves like a parasite, causing the death through burst of its host. Once the vannellae degenerated, the parasite was successfully kept in laboratory within a Saccamoeba sp. isolated from the same waterweed sample, which revealed in fine through electron microscopy to harbor two bacterial endosymbionts: the chlamydial parasite we introduce and another endosymbiont initially and naturally present in the host. Herein, we provide molecular-based identification of both the amoeba host and its two endosymbionts, with special focus on the chlamydia parasite. High sequence similarity values of the 18S rDNA permitted to assign the amoeba to the species Saccamoeba lacustris (Amoebozoa, Tubulinea). The bacterial endosymbiont naturally harbored by the host belonged to Sphingomonas koreensis (Alpha-Proteobacteria). The chlamydial parasite showed a strict specificity for Saccamoeba spp., being unable to infect a variety of other amoebae, including Acanthamoeba, and it was itself infected by a bacteriophage. Sequence similarity values of the 16S rDNA and phylogenetic analysis indicated that this strain is a new member of the family Parachlamydiaceae, for which we propose the name "Candidatus Mesochlamydia elodeae.

Molecular Phylogenetics Evidence for a Novel Lineage of Amoebae Within Discosea (Amoebozoa: Lobosa)

Some amoebae were recovered from freshwater samples on agar plates. Due to a fungal contamination tightly associated with these amoebae, it was impossible to correctly characterize them on a morphological base, but sequences of the small subunit ribosomal RNA gene (SSU rDNA) were successfully obtained from three strains. Phylogenetic analysis performed on these SSU rDNA allowed to identify these amoebae as members of a new lineage, related to the Dermamoebida, which includes also several other environmental SSU sequences

Molecular Identification of a Phage-infected Protochlamydia Strain Naturally Harboured by Non-Encysting Naegleria

A thermophilic strain of Naegleria clarki, isolated from a pond, has previously been investigated for its peculiarity to host a cytoplasmic symbiont, which causes a loss of the ability to form cysts. This endosymbiont, called Pcb, was itself infected by a phage, and exhibited chlamydia-like features resembling to another symbiont of Naegleria previously described as Protochlamydia naegleriophila. We report in this study, the results of amoeba host range and 16S rDNA molecular phylogeny of this strain, showing that Pcb is a new strain of the Naegleria endosymbiont chlamydial species Protochlamydia naegleriophila (Chlamydiae: Parachlamydiaceae)

Microsporidia-like parasites of amoebae belong to the early fungal lineage Rozellomycota

Molecular phylogenies based on the small subunit ribosomal RNA gene (SSU or 18S ribosomal DNA (rDNA)) revealed recently the existence of a relatively large and widespread group of eukaryotes, branching at the base of the fungal tree. This group, comprising almost exclusively environmental clones, includes the endoparasitic chytrid Rozella as the unique known representative. Rozella emerged as the first fungal lineage in molecular phylogenies and as the sister group of the Microsporidia. Here we report rDNA molecular phylogenetic analyses of two endonuclear parasites of free-living naked amoebae having microsporidia-like ultrastructural features but belonging to the rozellids. Similar to microsporidia, these endoparasites form unflagellated walled spores and grow inside the host cells as unwalled nonphagotrophic meronts. Our endonuclear parasites are microsporidia-like rozellids, for which we propose the name Paramicrosporidium, appearing to be the until now lacking morphological missing link between Fungi and Microsporidia. These features contrast with the recent description of the rozellids as an intermediate wall-less lineage of organisms between protists and true Fungi. We thus reconsider the rozellid clade as the most basal fungal lineage, naming it Rozellomycota

Monitoring the December 2015 summit eruptions of Mt. Etna (Italy): Implications on eruptive dynamics

A lengthy period of eruptive activity fromthe summit craters ofMt. Etna started in January 2011. It culminated in early December 2015 with a spectacular sequence of intense eruptive events involving all four summit craters (Voragine, Bocca Nuova,NewSoutheast Crater, and Northeast Crater). The activity consisted of high eruption columns, Strombolian explosions, lava flows andwidespread ash falls that repeatedly interferedwith air traffic. The most powerful episode occurred on 3 December 2015 from the Voragine. After three further potent episodes fromthe Voragine, activity shifted to the NewSoutheast Crater on 6 December 2015, where Strombolian activity and lava flow emission lasted for two days and were fed by the most primitive magma of the study period. Activity once more shifted to the Northeast Crater, where ash emission and weak Strombolian activity took place for several days. Sporadic ash emissions from all craters continued until 18 December, when all activity ceased. Although resembling the summit eruptions of 1998–1999, which also involved all four summit craters, thismultifaceted eruptive sequence occurred in an exceptionally short time window of less than three days, unprecedented in the recent activity of Mt. Etna. It also produced important morphostructural changes of the summit area with the coalescence of Voragine and Bocca Nuova in a single large crater, the “Central Crater”, reproducing themorphological setting of the summit cone before the formation of Bocca Nuova in 1968. The December 2015 volcanic crisis was followed closely by the staff of the Etna Observatory to monitor the on-going activity and forecast its evolution, in accordance with protocols agreed with the Italian Civil Protection Department.Published53-695V. Dinamica dei processi eruttivi e post-eruttiviJCR Journa

Stress, strain and mass changes at Mt. Etna during the period between the 1991–93 and 2001 flank eruptions

During the ~8-year period between the 1991–93 and 2001 flank eruptions, the eruptive activity of Mt. Etna was confined to the summit craters. Deformation and tomography studies indicate that this activity was fed by a magma accumulation zone centered NE of the summit, at a depth of 5 to 9 km below sea level. The most significant gravity changes measured during the same period were induced by mass redistributions at shallower depth below the southeastern flank of the volcano, where minor ground deformation was observed (i.e., vertical displacements within 2 cm). The mismatch between the position of pressure and mass sources is difficult to explain under the assumption that both are directly related to magma dynamics. Past studies have suggested that the gravity changes observed during 1994–2001 may primarily reflect changes in the rate of microfracturing along the NNW–SSE fracture/weakness zone (FWZ) that crosses the SE slope of Etna. We use the finite element method to shed new light on the complex relations between stress, strain and mass changes that occurred at Etna during the studied period. In particular, following previous results on the degradation of the mechanical properties of rocks, we perform a set of simulations assuming that the part of the medium containing the FWZ is characterized by a lower Young's modulus than would be expected from interpolation of tomographic data. We find that the presence of the FWZ creates a distortion of the displacement field induced by the deeper pressure source, locally resulting in a weak extensional regime. This finding supports the hypothesis of a cause–effect relationship between pressurization beneath the NW flank and tensile extension beneath the SE slope of the volcano. We propose that this extensional regime enhanced the propagation of pressurized gas, that, in turn, amplified the tensile strain across the FWZ. We also find that decreasing the value of Young's modulus in the FWZ allows for a larger amount of extension at depth, with no change in the magnitude of surface displacements. This result provides an indication of how the changes in the rate of microfracturing at depth, which are needed to induce the observed gravity changes, might have occurred without large ground deformation