Nazia Mojib, Amin Farhoomand, Dale T Andersen, Asim K Bej
{"title":"UV and cold tolerance of a pigment-producing Antarctic Janthinobacterium sp. Ant5-2.","authors":"Nazia Mojib, Amin Farhoomand, Dale T Andersen, Asim K Bej","doi":"10.1007/s00792-013-0525-9","DOIUrl":"10.1007/s00792-013-0525-9","url":null,"abstract":"<p><p>In this paper, we describe the UV and cold tolerance of a purple violet pigment (PVP)-producing Antarctic bacterium, Janthinobacterium sp. Ant5-2 (PVP(+)) and compared its physiological adaptations with a pigmentless mutant strain (PVP(-)). A spontaneous deletion of vioA that codes for tryptophan monooxygenase, the first gene involved in the biosynthesis of PVP was found in PVP(-) strain. The PVP(-) culture exhibited significantly reduced survival during exponential and stationary growth phase following exposure to UVB (320 nm) and UVC (254 nm) (dose range: 0-300 J/m²) when compared to wild-type (PVP(+)) cultures. In addition, upon biochemical inhibition of pigment synthesis by 2(5H)-furanone, wild-type PVP(+) cultures exhibited approximately 50-fold growth reduction at a higher dose (300 J/m²) of UV. Increased resistance to UV was observed upon inducing starvation state in both PVP(+) and PVP(-) cultures. There was 80% (SD = ±8) reduction in extrapolymeric substance (EPS) production in the PVP(-) cultures along with a compromised survival to freeze-thaw cycles when compared to the PVP(+) cultures. Perhaps synthesis of PVP and EPS are among the key adaptive features that define the survival of this bacterium in Antarctic extreme conditions, especially during austral summer months.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"367-78"},"PeriodicalIF":0.0,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31414070","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}
Yukari Yoshida-Takashima, Yoshihiro Takaki, Shigeru Shimamura, Takuro Nunoura, Ken Takai
{"title":"Genome sequence of a novel deep-sea vent epsilonproteobacterial phage provides new insight into the co-evolution of Epsilonproteobacteria and their phages.","authors":"Yukari Yoshida-Takashima, Yoshihiro Takaki, Shigeru Shimamura, Takuro Nunoura, Ken Takai","doi":"10.1007/s00792-013-0529-5","DOIUrl":"https://doi.org/10.1007/s00792-013-0529-5","url":null,"abstract":"<p><p>Epsilonproteobacteria are among the predominant primary producers in deep-sea hydrothermal vent ecosystems. However, phages infecting deep-sea vent Epsilonproteobacteria have never been isolated and characterized. Here, we successfully isolated a novel temperate phage, NrS-1, that infected a deep-sea vent chemolithoautotrophic isolate of Epsilonproteobacteria, Nitratiruptor sp. SB155-2, and its entire genome sequence was obtained and analyzed. The NrS-1 genome is linear, circularly permuted, and terminally redundant. The NrS-1 genome is 37,159 bp in length and contains 51 coding sequences. Five major structural proteins including major capsid protein and tape measure protein were identified by SDS-PAGE and mass spectrometry analysis. NrS-1 belongs to the family Siphoviridae, but its sequence and genomic organization are distinct from those of any other previously known Siphoviridae phages. Homologues of genes encoded in the NrS-1 genome were widely distributed among the genomes of diverse Epsilonproteobacteria. The distribution patterns had little relation to the evolutionary traits and ecological and physiological differentiation of the host epsilonproteobacterial species. The widespread occurrence of phage genes in diverse Epsilonproteobacteria supports early co-evolution between temperate phages and Epsilonproteobacteria prior to the divergence of their habitats and physiological adaptation.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"405-19"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0529-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31414071","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":"Glycine betaine is the main organic osmotic solute in a stratified microbial community in a hypersaline evaporitic gypsum crust.","authors":"Aharon Oren, Rahel Elevi Bardavid, Nesya Kandel, Zeev Aizenshtat, Jan Jehlička","doi":"10.1007/s00792-013-0522-z","DOIUrl":"https://doi.org/10.1007/s00792-013-0522-z","url":null,"abstract":"<p><p>We have examined the organic osmotic solutes content within the stratified microbial communities in an evaporitic gypsum crust found in an evaporation pond (~194 g/l total dissolved salts) of the salterns of the Israel Salt Company, Eilat. We extracted intracellular solutes from the upper three pigmented layers of the crust: a yellow-orange layer dominated by unicellular cyanobacteria, a green layer with filamentous cyanobacteria, and a layer colored red-purple by purple sulfur bacteria; dense communities of heterotrophic bacteria were present in all layers. The solutes were analyzed by Raman spectroscopy, (1)H and (13)C nuclear magnetic resonance, and HPLC. All layers contained glycine betaine as the only detectable osmotic solute; ectoine and other solutes known to be produced by many halophilic and halotolerant prokaryotes were not found. In this first attempt to assess the osmotic solute content within complex natural communities of halophilic microorganisms, the predominant role of glycine betaine as an osmolyte was established. Most heterotrophic bacteria cannot produce glycine betaine but preferentially use it when it is supplied. Presence of glycine betaine produced by the photoautotrophic members of the community, therefore, may relieve the heterotrophs from the need to synthesize other compounds at a high-energy cost.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"445-51"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0522-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31315611","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}
Kimberly M Webb, Jerry Yu, Courtney K Robinson, Tomiya Noboru, Yuan C Lee, Jocelyne DiRuggiero
{"title":"Effects of intracellular Mn on the radiation resistance of the halophilic archaeon Halobacterium salinarum.","authors":"Kimberly M Webb, Jerry Yu, Courtney K Robinson, Tomiya Noboru, Yuan C Lee, Jocelyne DiRuggiero","doi":"10.1007/s00792-013-0533-9","DOIUrl":"https://doi.org/10.1007/s00792-013-0533-9","url":null,"abstract":"<p><p>Ionizing radiation (IR) is of particular interest in biology because its exposure results in severe oxidative stress to the cell's macromolecules. Our recent work with extremophiles supports the idea that IR resistance is most likely achieved by a metabolic route, effected by manganese (Mn) antioxidants. Biochemical analysis of \"super-IR resistant\" mutants of H. salinarum, evolved over multiple cycles of exposure to high doses of IR, confirmed the key role for Mn antioxidants in the IR resistance of this organism. Analysis of the proteome of H. salinarum \"super-IR resistant\" mutants revealed increased expression for proteins involved in energy metabolism, replenishing the cell with reducing equivalents depleted by the oxidative stress inflicted by IR. Maintenance of redox homeostasis was also activated by the over-expression of coenzyme biosynthesis pathways involved in redox reactions. We propose that in H. salinarum, increased tolerance to IR is a combination of metabolic regulatory adjustments and the accumulation of Mn-antioxidant complexes.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"485-97"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0533-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40227882","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}
Shanli Mou, Xiaowen Zhang, Naihao Ye, Jinlai Miao, Shaona Cao, Dong Xu, Xiao Fan, Meiling An
{"title":"Analysis of ΔpH and the xanthophyll cycle in NPQ of the Antarctic sea ice alga Chlamydomonas sp. ICE-L.","authors":"Shanli Mou, Xiaowen Zhang, Naihao Ye, Jinlai Miao, Shaona Cao, Dong Xu, Xiao Fan, Meiling An","doi":"10.1007/s00792-013-0532-x","DOIUrl":"https://doi.org/10.1007/s00792-013-0532-x","url":null,"abstract":"<p><p>Non-photochemical fluorescence quenching (NPQ) is mainly associated with the transthylakoid proton gradient (ΔpH) and xanthophyll cycle. However, the exact mechanism of NPQ is different in different oxygenic photosynthetic organisms. In this study, several inhibitors were used to study NPQ kinetics in the sea ice alga Chlamydomonas sp. ICE-L and to determine the functions of ΔpH and the xanthophyll cycle in the NPQ process. NH4Cl and nigericin, uncouplers of ΔpH, inhibited NPQ completely and zeaxanthin (Z) was not detected in 1 mM NH4Cl-treated samples. Moreover, Z and NPQ were increased in the samples containing N,N'-dicyclohexyl-carbodiimide (DCCD) under low light conditions. We conclude that ΔpH plays a major role in NPQ, and activation of the xanthophyll cycle is related to ΔpH. In dithiothreitol (DTT)-treated samples, no Z was observed and NPQ decreased. NPQ was completely inhibited when NH4Cl was added suggesting that part of the NPQ process is related to the xanthophyll cycle and the remainder depends on ΔpH. Moreover, lutein and β-carotene were also essential for NPQ. These results indicate that NPQ in the sea ice alga Chlamydomonas sp. ICE-L is mainly dependent on ΔpH which affects the protonation of PSII proteins and de-epoxidation of the xanthophyll cycle, and the transthylakoid proton gradient alone can induce NPQ.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"477-84"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0532-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31308678","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}
Carolina Belfiore, Omar F Ordoñez, María Eugenia Farías
{"title":"Proteomic approach of adaptive response to arsenic stress in Exiguobacterium sp. S17, an extremophile strain isolated from a high-altitude Andean Lake stromatolite.","authors":"Carolina Belfiore, Omar F Ordoñez, María Eugenia Farías","doi":"10.1007/s00792-013-0523-y","DOIUrl":"https://doi.org/10.1007/s00792-013-0523-y","url":null,"abstract":"<p><p>The North-Western part of Argentina is particularly rich in wetlands located in the Puna in an altitude between 3,600 and 4,600 m above sea level. Most of these high-altitude Andean lakes are inhospitable areas due to extreme habitat conditions such as high contents of toxic elements, particularly arsenic. Exiguobacterium sp. S17, isolated from stromatolites in Laguna Socompa, exhibited remarkable tolerance to high arsenic concentration, i.e., it tolerated arsenic concentration such as 10 mM of As(III) and 150 mM of As(V). A proteomics approach was conducted to reveal the mechanisms that provide the observed outstanding resistance of Exiguobacterium sp. S17 against arsenic. A comparative analysis of S17, exposed and unexposed to arsenic revealed 25 differentially expressed proteins. Identification of these proteins was performed by MALDI-TOF/MS revealing upregulation of proteins involved in energy metabolism, stress, transport, and in protein synthesis being expressed under arsenic stress. To our knowledge, this work represents the first proteomic study of arsenic tolerance in an Exiguobacterium strain.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"421-31"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0523-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31425682","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":"Next-generation sequencing-based transcriptome profiling analysis of Pohlia nutans reveals insight into the stress-relevant genes in Antarctic moss.","authors":"Shenghao Liu, Nengfei Wang, Pengying Zhang, Bailin Cong, Xuezheng Lin, Shouqiang Wang, Guangmin Xia, Xiaohang Huang","doi":"10.1007/s00792-013-0528-6","DOIUrl":"https://doi.org/10.1007/s00792-013-0528-6","url":null,"abstract":"<p><p>Genome-wide characterization of the Pohlia nutans transcriptome is essential for clarifying the role of stress-relevant genes in Antarctic moss adapting to the extreme polar environment. High-throughput Illumina sequencing was used to analyze the gene expression profile of P. nutans after cold treatment. A total of 93,488 unigenes, with an average length of 405 bp, were obtained. Gene annotation showed that 16,781 unigenes had significant similarity to known functional protein-coding genes, most of which were annotated using the GO, KOG and KEGG pathway databases. Global profiling of the differentially expressed genes revealed that 3,796 unigenes were significantly upregulated after cold treatment, while 1,405 unigenes were significantly downregulated. In addition, 816 receptor-like kinases and 1,309 transcription factors were identified from P. nutans. This overall survey of transcripts and stress-relevant genes can contribute to understanding the stress-resistance mechanism of Antarctic moss and will accelerate the practical exploitation of the genetic resources for this organism.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"391-403"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0528-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40227881","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":"Isolation and characterization of two novel alkalitolerant sulfidogens from a Thiopaq bioreactor, Desulfonatronum alkalitolerans sp. nov., and Sulfurospirillum alkalitolerans sp. nov.","authors":"D Y Sorokin, T P Tourova, G Muyzer","doi":"10.1007/s00792-013-0538-4","DOIUrl":"https://doi.org/10.1007/s00792-013-0538-4","url":null,"abstract":"<p><p>Two obligately anaerobic sulfidogenic bacterial strains were isolated from the full-scale Thiopaq bioreactor in Lelystad (The Netherlands) removing H2S from biogas under oxygen-limiting and moderately haloalkaline conditions. Strain HSRB-L represents a dominant culturable sulfate-reducing bacterium in the reactor. It utilizes formate, H2 (with acetate as C-source) and lactate as e-donors, and sulfate, thiosulfate and sulfite as e-acceptors. It is haloalkalitolerant, with a pH range for lithotrophic growth from 7.5 to 9.7 (optimum at 8.5-9) and a salt range from 0.1 to 1.75 M total Na(+) (optimum at 0.6 M). The strain is a member of the genus Desulfonatronum and is proposed as a novel species D. alkalitolerans. The second strain, strain HTRB-L1, represents a dominant thiosulfate/sulfur reducer in the reactor. It is an obligate anaerobe utilizing formate and H2 (with acetate as C-source), lactate, pyruvate and fumarate as e-donors, and thiosulfate (incomplete reduction), sulfur, arsenate and fumarate as e-acceptors. With lactate as e-donor it also grows as an ammonifyer in the presence of nitrate and nitrite. HTRB-L1 is haloalkalitolerant, with a pH range for lithotrophic growth from 7.1 to 9.7 (optimum at 8.5) and a salt range from 0.6 to 1.5 M total Na(+) (optimum at 0.6 M). Phylogenetic analysis showed that strain HTRB-L1 is a novel species within the genus Sulfurospirillum (Epsilonproteobacteria) for which a name Sulfurospirillum alkalitolerans is proposed.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"535-43"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0538-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31338724","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}
Tong-Wei Guan, Yun Teng, Ling-Ling Yang, Xiao-Ping Zhang, Zhen-Ming Che
{"title":"Isoptericola salitolerans sp. nov., a halotolerant filamentous actinobacterium isolated from a salt lake, China.","authors":"Tong-Wei Guan, Yun Teng, Ling-Ling Yang, Xiao-Ping Zhang, Zhen-Ming Che","doi":"10.1007/s00792-013-0531-y","DOIUrl":"https://doi.org/10.1007/s00792-013-0531-y","url":null,"abstract":"<p><p>A novel bacterial strain, TRM F109(T), was isolated from hypersaline habitat in Sichuan Province, China. It was a Gram-positive, aerobic, non-motile, halotolerant, filamentous bacterium. Phylogenetic analysis based on 16S rRNA gene sequences revealed levels of similarity of 97.0-98.4% to the type strains of recognized species of the genus Isoptericola. Chemotaxonomic data also supported the placement of strain TRM F109(T) within the genus Isoptericola. The low levels of DNA-DNA relatedness between the novel strain and the type strains of recognized species of the genus Isoptericola, in combination with differential phenotypic data, demonstrate that strain TRM F109(T) represents a novel species of the genus Isoptericola, for which the name Isoptericola salitolerans sp. nov. is proposed. The type strain is TRM F109(T) (=JCM 15901(T)=KCTC 19617(T)).</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"471-6"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0531-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31414072","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":"Oil-bioremediation potential of two hydrocarbonoclastic, diazotrophic Marinobacter strains from hypersaline areas along the Arabian Gulf coasts.","authors":"D M Al-Mailem, M Eliyas, S S Radwan","doi":"10.1007/s00792-013-0530-z","DOIUrl":"https://doi.org/10.1007/s00792-013-0530-z","url":null,"abstract":"<p><p>Two halophilic, hydrocarbonoclastics bacteria, Marinobacter sedimentarum and M. flavimaris, with diazotrophic potential occured in hypersaline waters and soils in southern and northern coasts of Kuwait. Their numbers were in the magnitude of 10(3) colony forming units g(-1). The ambient salinity in the hypersaline environments was between 3.2 and 3.5 M NaCl. The partial 16S rRNA gene sequences of the two strains showed, respectively, 99 and 100% similarities to the sequences in the GenBank. The two strains failed to grow in the absence of NaCl, exhibited best growth and hydrocarbon biodegradation in the presence of 1 to 1.5 M NaCl, and still grew and maintained their hydrocarbonoclastic activity at salinities up to 5 M NaCl. Both species utilized Tween 80, a wide range of individual aliphatic hydrocarbons (C9-C40) and the aromatics benzene, biphenyl, phenanthrene, anthracene and naphthalene as sole sources of carbon and energy. Experimental evidence was provided for their nitrogen-fixation potential. The two halophilic Marinobacter strains successfully mineralized crude oil in nutrient media as well as in hypersaline soil and water microcosms without the use of any nitrogen fertilizers.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"463-70"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0530-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40238312","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}