Aspergillus loretoensis , a single isolate from marine sediment of Loreto Bay, Baja California Sur, México resulting as a new obligate halophile species In the original publication the Figs. 3 and 4 are published inappropriately. The correct version of Figs. 3 and 4 is provided in this correction.

Production of highly catalytic, archaeal Pd(0) bionanoparticles using Sulfolobus tokodaii Abstract The thermo-acidophilic archaeon, Sulfolobus tokodaii, was utilized for the production of Pd(0) bionanoparticles from acidic Pd(II) solution. Use of active cells was essential to form well-dispersed Pd(0) nanoparticles located on the cell surface. The particle size could be manipulated by modifying the concentration of formate (as electron donor; e-donor) and by addition of enzymatic inhibitor (Cu2+) in the range of 14–63 nm mean size. Since robust Pd(II) reduction progressed in pre-grown S. tokodaii cells even in the presence of up to 500 mM Cl−, it was possible to conversely utilize the effect of Cl− to produce even finer and denser particles in the range of 8.7–15 nm mean size. This effect likely resulted from the increasing stability of anionic Pd(II)–chloride complex at elevated Cl− concentrations, eventually allowing involvement of greater number of initial Pd(0) crystal nucleation sites (enzymatic sites). The catalytic activity [evaluated based on Cr(VI) reduction reaction] of Pd(0) bionanoparticles of varying particle size formed under different conditions were compared. The finest Pd(0) bionanoparticles obtained at 50 mM Cl− (mean 8.7 nm; median 5.6 nm) exhibited the greatest specific Cr(VI) reduction rate, with four times higher catalytic activity compared to commercial Pd/C. The potential applicability of S. tokodaii cells in the recovery of highly catalytic Pd(0) nanoparticles from actual acidic chloride leachate was, thus, suggested.

Reference genes for real-time RT-PCR expression studies in an Antarctic Pseudomonas exposed to different temperature conditions Abstract Psychrophilic and psychrotolerant bacteria from permanently cold environments may be the most abundant extremophiles on Earth and yet little is known on how they cope with temperature stress. Real-time reverse transcription PCR (RT-qPCR) is a powerful technique that could shed light on this matter but it requires pre-validated reference genes for normalization of data to get accurate results. In this study, we assessed the expression stability of eight candidate genes for the psychrotolerant Antarctic isolate Pseudomonas sp. AU10 during exponential growth under 4 °C and 30 °C, and after a cold-shock. Using the software programs BestKeeper and geNorm we validated recA, ftsZ, 16S rRNA, and rpoD as reference genes and we suggested the combination of recA and ftsZ for qPCR data normalization. Our results provide a starting point for gene expression studies in Antarctic Pseudomonas concerning temperature-related physiology and also for the validation of reference genes in other cold-adapted bacterial species.

Endonucleases responsible for DNA repair of helix-distorting DNA lesions in the thermophilic crenarchaeon Sulfolobus acidocaldarius in vivo Abstract The DNA repair mechanisms of hyperthermophiles can provide important insights for understanding how genetic information is maintained under extreme environments. Recent biochemical studies have identified a novel endonuclease in hyperthermophilic archaea, NucS/EndoMS, that acts on branched DNA substrates and mismatched bases. NucS/EndoMS is thought to participate in the DNA repair of helix-distorting DNA lesions, including UV-induced DNA damage and DNA adducts, and mismatched bases; however, the specific in vivo role of NucS/EndoMS in hyperthermophilic archaeal DNA repair has not been reported. To explore the role of this protein, we knocked out the nucS/endoMS gene of the thermophilic crenarchaeon Sulfolobus acidocaldarius and characterized the mutant phenotypes. While the nucS/endoMS-deleted strain exhibited sensitivity to DNA adducts, it did not have high mutation rates or any sensitivity to UV irradiation. It has been proposed that the XPF endonuclease is involved in homologous recombination-mediated stalled-fork DNA repair. The xpf-deficient strain exhibited sensitivity to helix-distorting DNA lesions, but the sensitivity of the nucS/endoMS and xpf double knockout strain did not increase compared to that of the single knockout strains. We conclude that the endonuclease NucS/EndoMS works with XPF in homologous recombination-mediated stalled-fork DNA repair for the removal of helix-distorting DNA lesions in S. acidocaldarius.

Description of Halegenticoccus soli gen. nov., sp. nov., a halophilic archaeon isolated from a soil sample of Ebi lake Abstract Two extreme halophilic archaeal strains, SYSUA9-0T and SYSUA9-1, were isolated from Ebi lake of Xinjiang, China. The colonies were Gram-negative, coccoid, and non-motile. Strains were aerobic and grew at 25–50 °C (optimum at 37 °C), in the presence of 10–35% (w/v) NaCl (optimum at 20–22%), and pH 6.0–8.0 (optimum at 7.0). The 16S rRNA gene sequence result revealed that the two strains were closely related to Haloprofundus marisrubri SB9T (92.7% similarity). The DNA–DNA hybridization value (97% ± 1%) suggested that SYSUA9-0T and SYSUA9-1 were similar; however, their sequence similarities with other archaeal members suggested that they were novel candidates. The genomic G + C content of SYSUA9-0T was 66.9%. The average nucleotide identity value between SYSU A9-0T and Haloprofundus marisrubri SB9T was 69.1%, which was far below the cutoff value (95–96%) proposed to define the species boundary. The polar lipids were phosphatidylglycerol (PG), phosphatidylglycerolphosphate methylester (PGP-Me), sulfated mannosyl glucosyl diether, mannosyl glucosyldiether, and four unidentified glycolipids. Phenotypic, chemotaxonomic and comparative genome analysis suggested that SYSU A9-0T and SYSU A9-1 represent a novel species of a new genus within the family Haloferacaceae, for which the name Halegenticoccus soli gen. nov., sp. nov., is proposed. The type strain is SYAUA9-0T (= KCTC4241T = CGMCC 1.15765T).

A novel thermophilic Aeribacillus bacteriophage AP45 isolated from the Valley of Geysers, Kamchatka: genome analysis suggests the existence of a new genus within the Siphoviridae family Abstract A novel thermophilic bacteriophage AP45 and its host strain Aeribacillus sp. CEMTC656 were isolated from the Valley of Geysers, Kamchatka Peninsula, Russia. Bacteriophage AP45 was identified as a member of the Siphoviridae family by electron microscopy. It showed high thermostability and had a slow cycle of reproduction. The AP45 genome had 51,606 base pairs (bp) and contained 71 open reading frames (ORFs), 40 of them encoding proteins of predicted function. Genes encoding DNA and RNA polymerases were not identified, indicating that AP45 used host polymerases. Based on the ORF65 encoding putative endolysin, the recombinant protein rAP45Lys was developed and its peptidoglycan-hydrolyzing activity was demonstrated. The AP45 genome exhibited limited identity to other phage sequences; the highest identity, 36%, was with the genome of the thermophilic Geobacillus myovirus D6E. The majority of putative proteins encoded by the AP45 genome had higher similarity to proteins from bacteria belonging to the Bacillaceae family, than to bacteriophages. In addition, more than half of the putative ORFs in the AP45 genome were highly similar to prophage sequences of A. pallidus strain 8m3, which was isolated in north–east China. The AP45 phage and revealed prophages might be members of a new genus belonging to the Siphoviridae family.

Structural determinants increasing flexibility confer cold adaptation in psychrophilic phosphoglycerate kinase Abstract Crystal structures of phosphoglycerate kinase (PGK) from the psychrophile Pseudomonas sp. TACII 18 have been determined at high resolution by X-ray crystallography methods and compared with mesophilic, thermophilic and hyperthermophilic counterparts. PGK is a two-domain enzyme undergoing large domain movements to catalyze the production of ATP from 1,3-biphosphoglycerate and ADP. Whereas the conformational dynamics sustaining the catalytic mechanism of this hinge-bending enzyme now seems rather clear, the determinants which underlie high catalytic efficiency at low temperatures of this psychrophilic PGK were unknown. The comparison of the three-dimensional structures shows that multiple (global and local) specific adaptations have been brought about by this enzyme. Together, these reside in an overall increased flexibility of the cold-adapted PGK thereby allowing a better accessibility to the active site, but also a potentially more disordered transition state of the psychrophilic enzyme, due to the destabilization of some catalytic residues.

Aspergillus loretoensis , a single isolate from marine sediment of Loreto Bay, Baja California Sur, México resulting as a new obligate halophile species Abstract An obligate halophile fungal was isolated from 275 m deep marine sediments and is characterized here for the first time. Its optimal growth was at 15% NaCl even though it was able to grow at 25% and is incapable of growth with no NaCl. Based on its morphological characteristics as conidia chain production in a single phialide, the fungal is related to the genus Aspergillus, subgenus Polypaecilum. Phylogenetic molecular analysis using several markers (ITS1–2; RPB1; RPB2; Cct8; TSR1; CaM; BenA) places the fungal isolate closer to Aspergillus salinarus and A. baarnensis. However, its morphological and molecular differences establish it as a new species, Aspergillus loretoensis sp. nov.

Purification and biochemical characterization of a novel thermostable and halotolerant subtilisin SAPN, a serine protease from Melghiribacillus thermohalophilus Nari2A T for chitin extraction from crab and shrimp shell by-products Abstract The present study investigates the purification and biochemical characterization of a novel extracellular serine alkaline protease, subtilisin (called SAPN) from Melghiribacillus thermohalophilus Nari2AT. The highest yield of protease (395 IU/g) with white shrimp shell by-product (40 g/L) as a unique source of nutriments in the growth medium was achieved after 52 h at 55 °C. The monomeric enzyme of about 30 kDa was purified to homogeneity by ammonium sulfate fractionation, heat treatment, followed by sequential column chromatographies. The optimum pH and temperature values for subtilisin activity were pH 10 and 75 °C, respectively, and half lives of 9 and 5 h at 80 and 90 °C, respectively. The sequence of the 25 NH2-terminal residues pertaining of SAPN exhibited a high homology with those of Bacillus subtilisins. The inhibition by DFP and PMSF indicates that this enzyme belongs to the serine proteases family. SAPN was found to be effective in the deproteinization (DDP %) of blue swimming crab (Portunus segnis) and white shrimp (Metapenaeus monoceros) by-products, with a degree of 65 and 82%, respectively. The commercial and the two chitins obtained in this work showed a similar peak pattern in Fourier-Transform Infrared (FTIR) analysis, suggesting that SAPN is suitable for the bio-production of chitin from shell by-products.

Recombinant production and characterization of a novel esterase from a hypersaline lake, Acıgöl, by metagenomic approach Abstract The aim of this study was to isolate a novel esterase from a hypersaline lake by sequence-based metagenomics. The metagenomic DNA was isolated from the enriched hypersaline lake sediment. Degenerate primers targeting the conserved regions of lipolytic enzymes of halophilic microorganisms were used for polymerase chain reaction (PCR) and a whole gene was identified by genome walking. The gene was composed of 783 bp, which corresponds to 260 amino acids with a molecular weight of 28.2 kDa. The deduced amino acid sequence best matched with the esterase from Halomonas gudaonensis with an identity of 91%. Recombinantly expressed enzyme exhibited maximum activity towards pNP-hexanoate with a kcat value of 12.30 s−1. The optimum pH and temperature of the enzyme were found as 9 and 30 °C, respectively. The effects of NaCl, solvents, metal ions, detergents and enzyme inhibitors were also studied. In conclusion, a novel enzyme, named as hypersaline lake “Acıgöl” esterase (hAGEst), was identified by sequence-based metagenomics. The high expression level, the ability to maintain activity at cold temperatures and tolerance to DMSO and metal ions are the most outstanding properties of the hAGEst.