Laura J Raiger Iustman, Paula M Tribelli, José G Ibarra, Mariela V Catone, Esmeralda C Solar Venero, Nancy I López
{"title":"Genome sequence analysis of Pseudomonas extremaustralis provides new insights into environmental adaptability and extreme conditions resistance.","authors":"Laura J Raiger Iustman, Paula M Tribelli, José G Ibarra, Mariela V Catone, Esmeralda C Solar Venero, Nancy I López","doi":"10.1007/s00792-014-0700-7","DOIUrl":"https://doi.org/10.1007/s00792-014-0700-7","url":null,"abstract":"<p><p>The genome of the Antarctic bacterium Pseudomonas extremaustralis was analyzed searching for genes involved in environmental adaptability focusing on anaerobic metabolism, osmoregulation, cold adaptation, exopolysaccharide production and degradation of complex compounds. Experimental evidences demonstrated the functionality of several of these pathways, including arginine and pyruvate fermentation, alginate production and growth under cold conditions. Phylogenetic analysis along with genomic island prediction allowed the detection of genes with probable foreign origin such as those coding for acetate kinase, osmotic resistance and colanic acid biosynthesis. These findings suggest that in P. extremaustralis the horizontal transfer events and/or gene redundancy could play a key role in the survival under unfavorable conditions. Comparative genome analysis of these traits in other representative Pseudomonas species highlighted several similarities and differences with this extremophile bacterium. </p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"207-20"},"PeriodicalIF":2.9,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-014-0700-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32747567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mitsuhiro Yoshida, Yukari Yoshida-Takashima, Takuro Nunoura, Ken Takai
{"title":"Genomic characterization of a temperate phage of the psychrotolerant deep-sea bacterium Aurantimonas sp.","authors":"Mitsuhiro Yoshida, Yukari Yoshida-Takashima, Takuro Nunoura, Ken Takai","doi":"10.1007/s00792-014-0702-5","DOIUrl":"https://doi.org/10.1007/s00792-014-0702-5","url":null,"abstract":"<p><p>A temperate phage (termed AmM-1) was identified from the psychrotolerant Rhizobiales bacterium Aurantimonas sp. C5-1, which was isolated from bathypelagic water (water depth = 1,500 m) in the northwest Pacific. The AmM-1 genome is 47,800 bp in length and contains 67 coding sequences. Although phage AmM-1 morphologically belongs to the family Myoviridae, its genomic structure, particularly modular genome organization, is similar to that of lambda-type phages of Siphoviridae. Genetic and phylogenetic analyses of the structural core genes also revealed that AmM-1 has a mosaic genomic structure that includes a lambda-like head (Siphoviridae) and P2-like tail (Myoviridae). The sequences of the structural core genes of AmM-1 are distinct from those of previously characterized phage groups but similar to those of recently identified one prophage element and one phage of marine Rhizobiales bacteria: a potential prophage element in the marine psychrotolerant Aureimonas ureilytica DSM 18598 genome and the temperate phage RR-1A infecting Rhizobium radiobacter P007 isolated from deep subseafloor sediment. The mosaic genome structure of AmM-1 suggests the occurrence of genetic exchange between distinct temperate phages in marine Rhizobiales populations. </p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"49-58"},"PeriodicalIF":2.9,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-014-0702-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32780111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tássio Brito de Oliveira, Eleni Gomes, Andre Rodrigues
{"title":"Thermophilic fungi in the new age of fungal taxonomy.","authors":"Tássio Brito de Oliveira, Eleni Gomes, Andre Rodrigues","doi":"10.1007/s00792-014-0707-0","DOIUrl":"https://doi.org/10.1007/s00792-014-0707-0","url":null,"abstract":"<p><p>Thermophilic fungi are of wide interest due to their potential to produce heat-tolerant enzymes for biotechnological processes. However, the taxonomy of such organisms remains obscure, especially given new developments in the nomenclature of fungi. Here, we examine the taxonomy of the thermophilic fungi most commonly used in industry in light of the recent taxonomic changes following the adoption of the International Code of Nomenclature for Algae, Fungi and Plants and also based on the movement One Fungus = One Name. Despite the widespread use of these fungi in applied research, several thermotolerant fungi still remain classified as thermophiles. Furthermore, we found that while some thermophilic fungi have had their genomes sequenced, many taxa still do not have barcode sequences of reference strains available in public databases. This lack of basic information is a limiting factor for the species identification of thermophilic fungi and for metagenomic studies in this field. Based on next-generation sequencing, such studies generate large amounts of data, which may reveal new species of thermophilic fungi in different substrates (composting systems, geothermal areas, piles of plant material). As discussed in this study, there are intrinsic problems associated with this method, considering the actual state of the taxonomy of thermophilic fungi. To overcome such difficulties, the taxonomic classification of this group should move towards standardizing the commonly used species names in industry and to assess the possibility of including new systems for describing species based on environmental sequences. </p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"31-7"},"PeriodicalIF":2.9,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-014-0707-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32815933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The saci_2123 gene of the hyperthermoacidophile Sulfolobus acidocaldarius encodes an ATP-binding cassette multidrug transporter.","authors":"Nuan Yang, Arnold J M Driessen","doi":"10.1007/s00792-014-0688-z","DOIUrl":"https://doi.org/10.1007/s00792-014-0688-z","url":null,"abstract":"<p><p>Multidrug resistance (MDR) transporters are capable of secreting structurally and functionally unrelated toxic compounds from the cell. Among this group are ATP-binding cassette (ABC) transporters. These membrane proteins are typically arranged as either hetero- or homo-dimers of ABC half-transporters with each subunit consisting of a membrane domain fused at the C-terminus to an ATP-binding domain, or as full transporters in which the two subunits are fused into a single polypeptide. The saci_2123 gene of the thermoacidophilic archaeon Sulfolobus acidocaldarius is the only gene in the genome that encodes an ATP-binding cassette half-transporter, while a homologous gene is present in the genomes of S. solfataricus, S. tokodaii and S islandicus. Saci_2123 shares homology with well-characterized bacterial and mammalian MDR transporters. The saci_2132 gene is up-regulated when cells are exposed to drugs. A deletion mutant of saci_2132 was found to be more vulnerable to a set of toxic compounds, including detergents, antibiotics and uncouplers as compared to the wild-type strain, while the drug resistance could be restored through the plasmid-based expression of saci_2132. These data demonstrate that Saci_2132 is an archaeal ABC-MDR transporter and therefore it was termed Smr1 (Sulfolobus multidrug resistance transporter 1). </p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"101-8"},"PeriodicalIF":2.9,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-014-0688-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32598360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Biofilms constructed for the removal of hydrocarbon pollutants from hypersaline liquids.","authors":"D M Al-Mailem, M Eliyas, M Khanafer, S S Radwan","doi":"10.1007/s00792-014-0698-x","DOIUrl":"https://doi.org/10.1007/s00792-014-0698-x","url":null,"abstract":"<p><p>Hydrocarbonoclastic biofilms were established on sterile glass plates vertically submerged for 1 month in a hypersaline soil/water suspension containing 0.3% crude oil. The culture-dependent analysis of the microbial community in those biofilms revealed hydrocarbonoclastic species in the magnitude of 10(3) cells cm(-2). Those species belonged to the halophilic bacterial genera Marinobacter, Halomonas, Dietzia, Bacillus, Arhodomonas, Aeromonas and Kocuria as well as to the haloarchaeal genera Haloferax and Halobacterium. Those organisms were not evenly distributed over the biofilm surface area. The culture-independent analysis revealed a different community composition, which was based on four uncultured and four cultured taxa. Depending on the culture conditions and the sort of chemical amendments, the biofilms succeeded in removing in 2 weeks up to about 60-70% of crude oil, pure n-hexadecane and pure phenanthrene in hypersaline pond water samples. The amendment with KCl, MgSO4 and a vitamin mixture composed of thiamin, pyridoxine, vitamin B12, biotin, riboflavin and folic acid was most effective.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"189-96"},"PeriodicalIF":2.9,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-014-0698-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32729437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mauricio Quiroz, Xavier Triadó-Margarit, Emilio O Casamayor, Gonzalo Gajardo
{"title":"Comparison of Artemia-bacteria associations in brines, laboratory cultures and the gut environment: a study based on Chilean hypersaline environments.","authors":"Mauricio Quiroz, Xavier Triadó-Margarit, Emilio O Casamayor, Gonzalo Gajardo","doi":"10.1007/s00792-014-0694-1","DOIUrl":"https://doi.org/10.1007/s00792-014-0694-1","url":null,"abstract":"<p><p>The brine shrimp Artemia (Crustacea) and a diversity of halophilic microorganisms coexist in natural brines, salterns and laboratory cultures; part of such environmental microbial diversity is represented in the gut of Artemia individuals. Bacterial diversity in these environments was assessed by 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) fingerprinting. Eight natural locations in Chile, where A. franciscana or A. persimilis occur, were sampled for analysis of free-living and gut-associated bacteria in water from nature and laboratory cultures. The highest ecological diversity (Shannon's index, H') was found in brines, it decreased in the gut of wild and laboratory animals, and in laboratory water. Significant differences in H' existed between brines and laboratory water, and between brines and gut of wild animals. The greatest similarity of bacterial community composition was between brines and the gut of field animals, suggesting a transient state of the gut microbiota. Sequences retrieved from DGGE patterns (n = 83) exhibited an average of 97.8% identity with 41 bacterial genera from the phyla Proteobacteria (55.4% of sequences match), Bacteroidetes (22.9%), Actinobacteria (16.9%) and Firmicutes (4.8%). Environment-exclusive genera distribution was seen in Sphingomonas and Paenibacillus (gut of field animals), Amaricoccus and Ornithinimicrobium (gut of laboratory animals), and Hydrogenophaga (water of laboratory cultures). The reported ecological and physiological capabilities of such bacteria can help to understand Artemia adaptation to natural and laboratory conditions.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"135-47"},"PeriodicalIF":2.9,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-014-0694-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32682949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fatma Ben Aissa, Anne Postec, Gaël Erauso, Claude Payri, Bernard Pelletier, Moktar Hamdi, Marie-Laure Fardeau, Bernard Ollivier
{"title":"Characterization of Alkaliphilus hydrothermalis sp. nov., a novel alkaliphilic anaerobic bacterium, isolated from a carbonaceous chimney of the Prony hydrothermal field, New Caledonia.","authors":"Fatma Ben Aissa, Anne Postec, Gaël Erauso, Claude Payri, Bernard Pelletier, Moktar Hamdi, Marie-Laure Fardeau, Bernard Ollivier","doi":"10.1007/s00792-014-0697-y","DOIUrl":"https://doi.org/10.1007/s00792-014-0697-y","url":null,"abstract":"<p><p>A novel anaerobic, alkaliphilic, Gram-positive staining bacterium was isolated from a hydrothermal chimney in the Prony Bay, New Caledonia. This strain designated FatMR1(T) grew at temperatures from 20 to 55 °C (optimum 37 °C) and at pH between 7.5 and 10.5 (optimum 8.8-9). NaCl is not required for growth (optimum 0.2-0.5%), but is tolerated up to 3%. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite are not used as terminal electron acceptors. Strain FatMR1(T) fermented pyruvate, yeast extract, peptone and biotrypcase and used fructose as the only sugar. The main fermentation products from fructose and proteinaceous compounds (e.g. peptone and biotrypcase) were acetate, H2 and CO2. Crotonate was disproportionated to acetate and butyrate. The predominant cellular fatty acids were C14:0 and C16:0. The G + C content of the genomic DNA was 37.1 mol%. On the basis of phylogenetic, genetic, and physiological properties, strain FatMR1(T) (=DSM 25890(T), =JCM 18390(T)) belonging to the phylum Firmicutes, class Clostridia, order Clostridiales, is proposed as a novel species of the genus Alkaliphilus, A. hydrothermalis sp. nov.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"183-8"},"PeriodicalIF":2.9,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-014-0697-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32749519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jan Kjølhede Vester, Mikkel Andreas Glaring, Peter Stougaard
{"title":"Improved cultivation and metagenomics as new tools for bioprospecting in cold environments.","authors":"Jan Kjølhede Vester, Mikkel Andreas Glaring, Peter Stougaard","doi":"10.1007/s00792-014-0704-3","DOIUrl":"https://doi.org/10.1007/s00792-014-0704-3","url":null,"abstract":"<p><p>Only a small minority of microorganisms from an environmental sample can be cultured in the laboratory leaving the enormous bioprospecting potential of the uncultured diversity unexplored. This resource can be accessed by improved cultivation methods in which the natural environment is brought into the laboratory or through metagenomic approaches where culture-independent DNA sequence information can be combined with functional screening. The coupling of these two approaches circumvents the need for pure, cultured isolates and can be used to generate targeted information on communities enriched for specific activities or properties. Bioprospecting in extreme environments is often associated with additional challenges such as low biomass, slow cell growth, complex sample matrices, restricted access, and problematic in situ analyses. In addition, the choice of vector system and expression host may be limited as few hosts are available for expression of genes with extremophilic properties. This review summarizes the methods developed for improved cultivation as well as the metagenomic approaches for bioprospecting with focus on the challenges faced by bioprospecting in cold environments. </p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"17-29"},"PeriodicalIF":2.9,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-014-0704-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32815934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J T Csotonyi, C Maltman, J Swiderski, E Stackebrandt, V Yurkov
{"title":"Extremely 'vanadiphilic' multiply metal-resistant and halophilic aerobic anoxygenic phototrophs, strains EG13 and EG8, from hypersaline springs in Canada.","authors":"J T Csotonyi, C Maltman, J Swiderski, E Stackebrandt, V Yurkov","doi":"10.1007/s00792-014-0693-2","DOIUrl":"https://doi.org/10.1007/s00792-014-0693-2","url":null,"abstract":"<p><p>Two pinkish peach-colored strains of obligately aerobic phototrophic bacteria, EG13 and EG8, were isolated from a saline spring effluent stream in west central Manitoba, Canada. The strains possessed bacteriochlorophyll a incorporated into a typical purple bacterial light-harvesting complex 1 (870 nm) and reaction center (801 nm). Analysis of 16S rRNA gene sequences indicated 100% identity among the isolates and 99% similarity to Roseovarius tolerans EL-172(T). The strains were physiologically well adapted to high salinity (0-22%), fluctuating pH (7-12) and temperature (7-40 °C) of the exposed hypersaline stream of East German Creek. EG8 and EG13 were also highly resistant to the toxic metal(loid) oxyanions tellurite, selenite and metavanadate (≥1000 μg/ml each). Most intriguingly, growth and pigment production of EG13 on glutamate minimal medium was stimulated by 1000-10000 μg/ml of sodium metavanadate compared to metal-free conditions. Phylogenetic analysis and phenotypic properties such as pigment composition and morphology indicate close relatedness to Roseovarius genus.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"127-34"},"PeriodicalIF":2.9,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-014-0693-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32658791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Benedetta Turchetti, Laura Selbmann, Robert A Blanchette, Simone Di Mauro, Elisabetta Marchegiani, Laura Zucconi, Brett E Arenz, Pietro Buzzini
{"title":"Cryptococcus vaughanmartiniae sp. nov. and Cryptococcus onofrii sp. nov.: two new species isolated from worldwide cold environments.","authors":"Benedetta Turchetti, Laura Selbmann, Robert A Blanchette, Simone Di Mauro, Elisabetta Marchegiani, Laura Zucconi, Brett E Arenz, Pietro Buzzini","doi":"10.1007/s00792-014-0692-3","DOIUrl":"https://doi.org/10.1007/s00792-014-0692-3","url":null,"abstract":"<p><p>Twenty yeast strains, representing a selection from a wider group of more than 60 isolates were isolated from cold environments worldwide (Antarctica, Iceland, Russia, USA, Italian and French Alps, Apennines). The strains were grouped based on their common morphological and physiological characteristics. A phylogeny based on D1/D2 ribosomal DNA sequences placed them in an intermediate position between Cryptococcus saitoi and Cryptococcus friedmannii; the ITS1 and ITS2 rDNA phylogeny demonstrated that these strains belong to two related but hitherto unknown species within the order Filobasidiales, albidus clade. These two novel species are described with the names Cryptococcus vaughanmartiniae (type strain DBVPG 4736(T)) and Cryptococcus onofrii (type strain DBVPG 5303(T)). </p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"149-59"},"PeriodicalIF":2.9,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-014-0692-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32682948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}