Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT

Ferroplasmaceae represent ubiquitous iron-oxidising extreme acidophiles with a number of unique physiological traits. In a genome-based study of Ferroplasma acidiphilum YT, the only species of the genus Ferroplasma with a validly published name, we assessed its central metabolism and genome stability during a long-term cultivation experiment. Consistently with physiology, the genome analysis points to F. acidiphilum YT having an obligate peptidolytic oligotrophic lifestyle alongside with anaplerotic carbon assimilation. This narrow trophic specialisation abridges the sugar uptake, although all genes for glycolysis and gluconeogenesis, including bifunctional unidirectional fructose 1,6-bisphosphate aldolase/phosphatase, have been identified. Pyruvate and 2-oxoglutarate dehydrogenases are substituted by ‘ancient’ CoA-dependent pyruvate and alpha-ketoglutarate ferredoxin oxidoreductases. In the lab culture, after ~550 generations, the strain exhibited the mutation rate of ≥1.3 × 10−8 single nucleotide substitutions per site per generation, which is among the highest values recorded for unicellular organisms. All but one base substitutions were G:C to A:T, their distribution between coding and non-coding regions and synonymous-to-non-synonymous mutation ratios suggest the neutral drift being a prevalent mode in genome evolution in the lab culture. Mutations in nature seem to occur with lower frequencies, as suggested by a remarkable genomic conservation in F. acidiphilum YT variants from geographically distant populations

Arthroscopic second generation autologous chondrocyte implantation at 48 months follow-up

none7openE. Kon; G. Filardo; M. Delcogliano; S. Zaffagnini; C. Montaperto; F. Iacono; M. MarcacciE. Kon; G. Filardo; M. Delcogliano; S. Zaffagnini; C. Montaperto; F. Iacono; M. Marcacc

New geological, geophysical and biological insights on the hydrothermal system of the Panarea – Basiluzzo Volcanic complex (Aeolian Islands, Tyrrhenian Sea)

Since the exhalative crisis of 2002 cruises were carried out to investigate morphology, magnetic and gravity fields, fluid escape, plume anomalies, biological and microbiological activity, benthic fluxes, early diagenesis, mineralogy and geochemistry of water and sediments of the hydrothermal system of Panarea. The volcanic complex was mapped by multibeam, including backscatter analysis, and magnetometric surveys were done to detect low magnetization in areas with hydrothermal activity, i.e., vents, sulphide deposits, chimney fields. CTD by ship and on ROV detected acidic plumes at bottom (minimum pH value 6.5) and mid depths. An Automatic Benthic Chamber was deployed on a terrace (40m) and in depressions with gas-charged and hydrothermally altered sediments (80m). At the 40m site, strong releases of Dissolved Inorganic Carbon (DIC) and Fe, Mn, Zn (75.7, 2.0, 2.9, 3.4 µmol m -2 day -1 ) were found. Average decrease of pH in the chamber was ~4 units day -1 with a H + benthic flux of 0.32 µmol m -2 day -1 ). DIC values of seawater had average 2.3, increasing to 3.1 on degassing vents, while 7.5 µmol was measured on top of a bubbling core. ROV dives explored and sampled several sites; active chimneys (black, red crusts and yellowish-orange precipitates at top) were recovered on the SE flanks of Basiluzzo; pH value of 5 was measured aboard on sediments. XRD and XRF data on the external crust showed Fe-Mn oxyhydroxides, including goethite and opal, with Co, Ce, Sr, Zn and Cu enrichments, whereas the inner part are depleted of Fe, Mn and other metals, mostly under detection limits. SEM imagery shows porous filamentous minerals, that are probably bacterial in origin. Dives to SW discovered fields of partially or totally relict chimneys at the same depth (~200m). Chimneys are present on the edges of slope failures and settled on areas of relative lower positive magnetic anomaly, indicating possible shallow depth level of hydrothermal alteration. Reddish crusts and sediments, and acid, gas boiling water (pH 5.5) were cored at 90 m depth upslope of the \u27active\u27 chimneys; upslope from the \u27relict\u27 chimney\u27s fields, oxized-normal sediments were found. Biological investigations on the sediments revealed a community strongly dominated by the amphipod Ampelisca ledoyeri (43.8 % of the total abundance), probably dwelling in the tube-patches. Rare species were detected on the chimney\u27s samples. The phylogenetic diversity of microbial communities in the precipitates collected on chimneys and on Bottaro vent was analyzed by bacterial and archaeal 16S rDNA clone libraries, showing a dominance of sulfur-oxidazing epsilon and gamma proteobacteria. Very interesting groups of archaea were revealed including methanotrophic Thermoplasmatales and members of SM1 candidate division. Overall prokaryotic diversity was found similar to that of deep sea hydrothermal vents and other sulfidic habitats. White microbial mats were found in an area S of Panarea, on a N-S oriented fracture

Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y-T

Golyshina OV, Tran H, Reva ON, et al. Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y-T. SCIENTIFIC REPORTS. 2017;7(1): 3682.Ferroplasmaceae represent ubiquitous iron-oxidising extreme acidophiles with a number of unique physiological traits. In a genome-based study of Ferroplasma acidiphilum Y-T, the only species of the genus Ferroplasma with a validly published name, we assessed its central metabolism and genome stability during a long-term cultivation experiment. Consistently with physiology, the genome analysis points to F. acidiphilum Y-T having an obligate peptidolytic oligotrophic lifestyle alongside with anaplerotic carbon assimilation. This narrow trophic specialisation abridges the sugar uptake, although all genes for glycolysis and gluconeogenesis, including bifunctional unidirectional fructose 1,6-bisphosphate aldolase/phosphatase, have been identified. Pyruvate and 2-oxoglutarate dehydrogenases are substituted by 'ancient' CoA-dependent pyruvate and alpha-ketoglutarate ferredoxin oxidoreductases. In the lab culture, after -550 generations, the strain exhibited the mutation rate of >= 1.3 x 10(-8) single nucleotide substitutions per site per generation, which is among the highest values recorded for unicellular organisms. All but one base substitutions were G: C to A: T, their distribution between coding and non-coding regions and synonymous-to-non-synonymous mutation ratios suggest the neutral drift being a prevalent mode in genome evolution in the lab culture. Mutations in nature seem to occur with lower frequencies, as suggested by a remarkable genomic conservation in F. acidiphilum Y-T variants from geographically distant populations