Extremophiles最新文献

{"title":"Halorientalis salina sp. nov., Halorientalis marina sp. nov., Halorientalis litorea sp. nov.: three extremely halophilic archaea isolated from a salt lake and coarse sea salt.","authors":"Bei-Bei Wang,&nbsp;Ya-Ping Sun,&nbsp;Zhang-Ping Wu,&nbsp;Xi-Wen Zheng,&nbsp;Jing Hou,&nbsp;Heng-Lin Cui","doi":"10.1007/s00792-022-01275-y","DOIUrl":"https://doi.org/10.1007/s00792-022-01275-y","url":null,"abstract":"<p><p>Three halophilic archaeal strains, NEN8^T, GDY88^T and ZY14^T, were isolated from a salt lake in Tibet and coarse sea salt samples from Guangdong and Hebei, China, respectively. These strains formed three separate clades (showing 94.4-95.8% and 87.1-89.4% similarities, respectively) and then clustered with the current Halorientalis members (showing 90.7-97.6% and 87.0-91.2% similarities, respectively), as revealed by phylogenetic analyses based on 16S rRNA and rpoB' genes. The overall genome-related index, average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), average amino acid identity (AAI) and the percentage of conserved proteins (POCP) values, among the three strains and members of the genus Halorientalis were 76.0-88.0%, 21.3-37.2%, 69.0-88.3% and 57.7-78.1%, clearly below the threshold values for species demarcation. Strains NEN8^T, GDY88^T and ZY14^T could be distinguished from current Halorientalis species according to differential phenotypic characteristics. The major polar lipids of the three strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1) and disulfated mannosyl glucosyl diether (S₂-DGD). In addition, mannosyl glucosyl diether (DGD-1) was detected in strain NEN8^T and phosphatidic acid (PA), posssulfated galactosyl mannosyl glucosyl diether (S-TGD-1) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA) were observed in strain ZY14^T. These results revealed that strains NEN8^T (= CGMCC 1.17213^T = JCM 34155^T), GDY88^T (= CGMCC 1.18548^T = JCM 34481^T) and ZY14^T (= CGMCC 1.17178^T = JCM 34154^T) represent three novel species of the genus Halorientalis, for which the names Halorientalis salina sp. nov., Halorientalis marina sp. nov. and Halorientalis litorea sp. nov. are proposed.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40598033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic analysis of heavy metal-resistant Halobacterium salinarum isolated from Sfax solar saltern sediments.","authors":"Houda Baati,&nbsp;Mariem Siala,&nbsp;Chafai Azri,&nbsp;Emna Ammar,&nbsp;Christopher Dunlap,&nbsp;Mohamed Trigui","doi":"10.1007/s00792-022-01273-0","DOIUrl":"https://doi.org/10.1007/s00792-022-01273-0","url":null,"abstract":"<p><p>The draft genome sequences of five archaeal strains, isolated from Sfax solar saltern sediments and affiliated with Halobacterium salinarum, were analyzed in order to reveal their adaptive strategies to live in hypersaline environments polluted with heavy metals. The genomes of the strains (named AS1, AS2, AS8, AS11, and AS19) are found to contain 2,060,688; 2,467,461; 2,236,624; 2,432,692; and 2,428,727 bp respectively, with a G + C content of 65.5, 66.0, 67.0, and 66.2%. The majority of these genes (43.69-55.65%) are annotated as hypothetical proteins. Growth under osmotic stress is possible by genes coding for potassium uptake, sodium efflux, and kinases, as well as stress proteins, DNA repair systems, and proteasomal components. These strains harbor many genes responsible for metal transport/resistance, such as: copper-translocating P-type ATPases, ABC transporter, and cobalt-zinc-cadmium resistance protein. In addition, detoxification enzymes and secondary metabolites are also identified. The results show strain AS1, as compared to the other strains, is more adapted to heavy metals and may be used in the bioremediation of multi-metal contaminated environments. This study highlights the presence of several commercially valuable bioproducts (carotenoids, retinal proteins, exopolysaccharide, stress proteins, squalene, and siderophores) and enzymes (protease, sulfatase, phosphatase, phosphoesterase, and chitinase) that can be used in many industrial applications.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9288257/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40528280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Soil substrate culturing approaches recover diverse members of Actinomycetota from desert soils of Herring Island, East Antarctica.","authors":"Nicole Benaud,&nbsp;Devan S Chelliah,&nbsp;Sin Yin Wong,&nbsp;Belinda C Ferrari","doi":"10.1007/s00792-022-01271-2","DOIUrl":"https://doi.org/10.1007/s00792-022-01271-2","url":null,"abstract":"<p><p>Antimicrobial resistance is an escalating health crisis requiring urgent action. Most antimicrobials are natural products (NPs) sourced from Actinomycetota, particularly the Streptomyces. Underexplored and extreme environments are predicted to harbour novel microorganisms with the capacity to synthesise unique metabolites. Herring Island is a barren and rocky cold desert in East Antarctica, remote from anthropogenic impact. We aimed to recover rare and cold-adapted NP-producing bacteria, by employing two culturing methods which mimic the natural environment: direct soil culturing and the soil substrate membrane system. First, we analysed 16S rRNA gene amplicon sequencing data from 18 Herring Island soils and selected the soil sample with the highest Actinomycetota relative abundance (78%) for culturing experiments. We isolated 166 strains across three phyla, including novel and rare strains, with 94% of strains belonging to the Actinomycetota. These strains encompassed thirty-five 'species' groups, 18 of which were composed of Streptomyces strains. We screened representative strains for genes which encode polyketide synthases and non-ribosomal peptide synthetases, indicating that 69% have the capacity to synthesise polyketide and non-ribosomal peptide NPs. Fourteen Streptomyces strains displayed antimicrobial activity against selected bacterial and yeast pathogens using an in situ assay. Our results confirm that the cold-adapted bacteria of the harsh East Antarctic deserts are worthy targets in the search for bioactive compounds.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9279279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40590174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Incomplete denitrification phenotypes in diverse Thermus species from diverse geothermal spring sediments and adjacent soils in southwest China.","authors":"Chrisabelle C Mefferd, Enmin Zhou, Cale O Seymour, Noel A Bernardo, Shreya Srivastava, Amanda J Bengtson, Jian-Yu Jiao, Hailiang Dong, Wen-Jun Li, Brian P Hedlund","doi":"10.1007/s00792-022-01272-1","DOIUrl":"10.1007/s00792-022-01272-1","url":null,"abstract":"<p><p>A few members of the bacterial genus Thermus have been shown to be incomplete denitrifiers, terminating with nitrite (NO₂^-) or nitrous oxide (N₂O). However, the denitrification abilities of the genus as a whole remain poorly characterized. Here, we describe diverse denitrification phenotypes and genotypes of a collection of 24 strains representing ten species, all isolated from a variety of geothermal systems in China. Confirmed terminal products of nitrate reduction were nitrite or N₂O, while nitric oxide (NO) was inferred as the terminal product in some strains. Most strains produced N₂O; complete denitrification was not observed. Denitrification phenotypes were largely consistent with the presence of denitrification genes, and strains of the same species often had the same denitrification phenotypes and largely syntenous denitrification gene clusters. Genes for nirS and nirK coexisted in three Thermus brockianus and three Thermus oshimai genomes, which is a unique hallmark of some denitrifying Thermus strains and may be ecologically important. These results show that incomplete denitrification phenotypes are prominent, but variable, within and between Thermus species. The incomplete denitrification phenotypes described here suggest Thermus species may play important roles in consortial denitrification in high-temperature terrestrial biotopes where sufficient supply of oxidized inorganic nitrogen exists.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9270275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40481194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Strategies for anti-oxidative stress and anti-acid stress in bioleaching of LiCoO₂ using an acidophilic microbial consortium.","authors":"Dehong Liu,&nbsp;Hongjie Shi,&nbsp;Guanglin Chen,&nbsp;Xu Zhang,&nbsp;Tingyue Gu,&nbsp;Minglong Zhu,&nbsp;Wensong Tan","doi":"10.1007/s00792-022-01270-3","DOIUrl":"https://doi.org/10.1007/s00792-022-01270-3","url":null,"abstract":"<p><p>High metal ion concentrations and low pH cause severely inhibit the activity of an acidophilic microbial consortium (AMC) in bioleaching. This work investigated the effects of exogenous spermine on biofilm formation and the bioleaching efficiency of LiCoO₂ by AMC in 9K medium. After the addition of 1 mM spermine, the activities of glutathione peroxidase and catalase increased, while the amount of H₂O₂, intracellular reactive oxygen species (ROS) and malondialdehyde in AMC decreased. These results indicated that the ability of AMC biofilm to resist oxidative stress introduced by 3.5 g/L Li⁺ and 30.1 g/L Co²⁺ was improved by spermine. The activity of glutamate decarboxylase was promoted to restore the intracellular pH buffering ability of AMC. Electrochemical measurements showed that the oxidation rate of pyrite was increased by exogenous spermine. As a result, high bioleaching efficiencies of 97.1% for Li⁺ and 96.1% for Co²⁺ from a 5.0% (w v^-1) lithium cobalt oxide powder slurry were achieved. This work demonstrated that Tafel polarization can be used to monitor the AMC biofilm's ability of uptaking electrons from pyrite during bioleaching. The corrosion current density increased with 1 mM spermine, indicating enhanced electron uptake by the biofilm from pyrite.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40408442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Asgard archaea in saline environments.","authors":"Horia L Banciu,&nbsp;Ionuț M Gridan,&nbsp;Adrian V Zety,&nbsp;Andreea Baricz","doi":"10.1007/s00792-022-01266-z","DOIUrl":"https://doi.org/10.1007/s00792-022-01266-z","url":null,"abstract":"<p><p>Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40400878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Halomonas faecis sp. nov., a halophilic bacterium isolated from human faeces.","authors":"Zhu-Xiang Liu,&nbsp;Jin-Hua Chen,&nbsp;Ling-Ling Yang,&nbsp;Yu-Zhou Feng,&nbsp;Li-Ying Deng,&nbsp;Jian-Wu He,&nbsp;Shu-Kun Tang,&nbsp;Yi-Guang Chen","doi":"10.1007/s00792-022-01269-w","DOIUrl":"https://doi.org/10.1007/s00792-022-01269-w","url":null,"abstract":"<p><p>A novel moderately halophilic, Gram-stain-negative, catalase- and oxidase-positive, strictly aerobic, non-sporulating, non-motile rod, designated strain JSM 104105^T, was isolated from human faeces. Strain JSM 104105^T was able to grow with 0.5-18% (w/v) NaCl (optimum 4-9%), at pH 6-10.5 (optimum pH 7-8) and at 10-40 °C (optimum 30 °C) in complex media. The major cellular fatty acids were C_18:1ω7c, C_16:0, C_16:1ω7c and/or C_16:1ω6c, C_19:0 cyclo ω8c and C_12:0 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid and three unidentified phospholipids. The predominant respiratory quinone was Q-9 and the genomic DNA G + C content was 64.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 104105^T should be assigned to the genus Halomonas, and was most closely related to Halomonas gudaonensis SL014B-69^T (99.0% sequence similarity), followed by Halomonas azerbaijanica TBZ202^T (98.6%) and Halomonas lysinitropha 3(2)^T (97.3%). The whole genomic analysis showed that strain JSM 104105^T constituted a different taxon separated from the recognized Halomonas species. Combined data from phenotypic and genotypic studies demonstrated that strain JSM 104105^T represents a new species of the genus Halomonas, for which the name Halomonas faecis sp. nov. is proposed. The type strain is JSM 104105^T (= CCTCC AB 2014160^T = CGMCC 1.12945^T = KCTC 42146^T).</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39986819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evansella halocellulosilytica sp. nov., an alkali-halotolerant and cellulose-dissolving bacterium isolated from bauxite residue","authors":"Guo-Hong Liu, Manik Prabhu Narsing Rao, Qianqian Chen, Jian-mei Che, Huai Shi, Bo Liu, Wenjun Li","doi":"10.1007/s00792-022-01267-y","DOIUrl":"https://doi.org/10.1007/s00792-022-01267-y","url":null,"abstract":"","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49141223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial diversity and community structure in the rhizosphere of the halophyte Halocnemum strobilaceum in an Algerian arid saline soil","authors":"Sabrina Behairi, N. Baha, M. Barakat, Philippe Ortet, W. Achouak, T. Heulin, Y. Kaci","doi":"10.1007/s00792-022-01268-x","DOIUrl":"https://doi.org/10.1007/s00792-022-01268-x","url":null,"abstract":"","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44779785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simple sequence repeat insertion induced stability and potential ‘gain of function’ in the proteins of extremophilic bacteria","authors":"S. Mahfooz, G. Shankar, Jitendra Narayan, Pallavi Singh, Y. Akhter","doi":"10.1007/s00792-022-01265-0","DOIUrl":"https://doi.org/10.1007/s00792-022-01265-0","url":null,"abstract":"","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42405978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}