Abstract:[Objective] Fungal diversity and community structures were revealed in Rehai hot springs in Tengchong, Yunnan, and effects of sediment geochemical properties on fungal distribution were analyzed.[Methods] Fungal ITS genes were detected in the sediment metagenomes by high-throughput pyrosequencing and bioinformatic analysis.[Results] Total 343484 valid reads from 5 hot springs were obtained, and these reads included 5 phyla, 20 classes, and 66 orders. The hot springs Jiemeiquan right (JMQR), Jiemeiquan left (JMQL), Hamazui (M), Qiaoquan (QQ) and Gumingquan (GMQP) were dominated by communities such as Agaricales, Eurotiales, Capnodiales, and Hypocreales. A total of 365 genera were discovered in the hot springs studied. There were total 212 genera detected in JMQR, 197 in JMQL, 222 in M, 270 in QQ, and 179 in GMQP. Schizophyllum was a dominant genus of fungal community in JMQR, and Penicillium was highly frequent in JMQL. Cladosporium dominanted fungal community in M and QQ, and Engyodontium was highly rich in GMQP. The geochemical variables such as NH₄⁺, temperature, and pH, exerted effects on distribution of different dominant fungi in the hot springs. The pH in the hot springs had significant effect on fungal community composition.[Conclusion] Rehai hot springs in Tengchong, Yunnan, harbor surprisingly fungal diversity. Fungi in different samples had distinct community structures. The pH in the hot springs could be one of the factors determining the fungal community.

Abstract:[Objective] The aim of this study was to understand the relationship between the diversity of culturable bacteria in the surface seawater and the hydrological environment.[Methods] We used MA, R2A and seawater medium to isolate bacteria from four different hydrological environments:the warm area, the cold area, the basin area and the intersection area. 16S rRNA was sequenced for classification and identification of the isolates, and phylogenetic tree was built for phylogenetic analysis.[Results] In total 407 bacteria were isolated from the samples and 154 strains were selected and sequenced by the Restriction Fragment Length Polymorphism analysis. These 154 strains were divided into 3 phyla, 18 genera and 27 species. The 3 phyla were Proteobacteria, Firmicutes and Actinobacteria. The dominant genera were Pseudoalteromonas,Psychrobacter, ect. The dominant species were Pseudoalteromonas agarivorans,Psychrobacter nivimaris, ect. And several psychropliles bacteria were separated such as Alteromonas fuliginea. Compared the bacterial diversity among different regions, γ-proteobacteria was dominant in all the four areas, and the bacterial diversity of intersection area was the highest, where 10 different genera were isolated. Bacterial diversity of basic area was the lowest, only had 4. In addition to the basin area, special species were isolated from the samples in other 3 areas.[Conclusion] Nordic Sea is rich in microbial resources, and the microbial diversity in the intersection area is higher than that in other regions.

Abstract:[Objective] To reveal the diversity and antimicrobial activity of culturable fungi from the deep-sea sediments in 4 different sites in South China Sea.[Methods] We used 4 different methods and 8 different media to study the culturable fungal diversity in 12 deep-sea sediments samples. We identified fungal isolates by colonial morphology observation and ITS-based phylogenetic analysis. We used disc diffusion and growth rate methods to test antibacterial and antifungal activities.[Results] A total of 125 fungi were isolated from the sediments. Based on the ITS sequence analysis and morphological characteristics, the isolates were grouped to 18 fungal species and 12 genera within 2 phyla. Most fungi belong to Ascomycota and only 2 isolates belong to Basidiomycota. The culturable fungal diversity was different among the 4 locations. Most of the fungal isolates exhibited antimicrobial activity. The genera Alternaria, Penicillium and Stemphylium displayed antibacterial activity against more than one indicator. Particularly, Alternaria tenuissima DN09, Alternaria alternata DN14 and Penicillium chrysogenum DN16 displayed activity against both Gram-positive and Gram-negative bacteria.[Conclusion] Higher diversity and antimicrobial activity of the culturable fungi isolated from deep-sea sediments in South China Sea provide the potential application of these fungi.

Abstract:[Objective] This study is aimed at studying the diversity of culturable actinobacteria in soils of the north Qinghai-Tibet Plateau and comparing the effect of different selective isolation media on the isolation of actinobacteria.[Methods] We used 9 isolation media to isolate actinobacteria from 14 soil samples collected from Ali, Naqu and Haixi districts on the Qinghai-Tibet Plateau. We added the fermentation broth of Micrococcus luteus to the medium to help the isolation. The isolates were identified based on the 16S rRNA gene sequences, and diversity of actinobacterial isolates were analyzed at different taxonomic levels.[Results] We isolated a total of 255 dereplicated strains, belonging to 8 orders, 14 families and 23 genera of the phylum Actinobacteria. The isolates were delineated into 94 OTUs, which corresponded to 94 putative species. Among them, at least 25 putative species were new, spanning 13 genera; and 108 strains, which contained 28 putative species, belonged to the genus Streptomyces, the most dominant genus of culturable actinobacteria from the soils. Addition of the Micrococcus luteus fermentation broth obviously increased the number and diversity of actinobacterial isolates. Diluted glucose-yeast extract-malt extract medium was suitable for the isolation of Streptomyces, and starch-glycerol-proline medium, sodium propionate-casein medium, etc. were suitable for the isolation of rare actinobacteria.[Conclusion] Soils of the north Qinghai-Tibet Plateau contain a high diversity of culturable actinobacteria and a number of novel actinobacterial species. Addition of the Micrococcus lutea fermentation broth into the isolation medium can effectively improve the isolation efficiency for actinobacteria.

Abstract:[Objective] To clone, express, purify and characterize flap endonuclease 1 from thermophilic archaea Pyrococcus furious.[Methods] We cloned fen1 gene from Pyrococcus furious (pFEN1), expressed it in Escherichia coli and purified the protein by affinity chromatography. We applied denaturing polyacrylamide gel electrophoresis to detect the enzymatic activities and studied its interaction with other proteins by using fluorescence labeled oligonucleotides as substrates.[Results] pFEN1 was overexpressed in E. coli. The presence of salts diminished the endonuclease activity of pFEN1, with cleavage greatly reduced at 100 mmol/L of NaCl. The activity of pFEN1 was detected only in the presence of magnesium (Mg²⁺) or manganese (Mn²⁺), and pFEN1 showed a higher endonucease activity under the catalysis of Mn²⁺. pFEN1 was thermally stable and had highest activity at temperature range of 60-65℃. Proliferating cell nuclear antigen (PCNA) can significantly promote the activity of pFEN1.[Conclusion] This study confirmed that pFEN1 is a Mg²⁺ or Mn²⁺ dependent endonuclease and PCNA can stimulate its activity.

Abstract:[Objective] To explore an efficiently expressed fluorescence protein, enhanced consensus green protein variant 123 (eCGP123), and its application on sub-cellular localization of proteins in the thermophilic acidophile Sulfolobus islandicus.[Methods] eCGP123 exhibits extreme thermostability, acid stability and reversible photo-switching. We optimized the sequence of eCGP123 gene according to S. islandicus codon usage. The protein purified from E. coli was characterized. We fused various proteins with different cellular localizations at C-terminal of eCGP123, including FtsZ from E. coli, and UpsE, PCNA1 and SiRe_1200 from S. islandicus. We constructed eCGP123 and its fusion proteins expression strains and analyzed their sub-cellular localizations in the host cells by laser confocal microscopy.[Results] Consistent with previous results, the optimized eCGP123 expressed from E. coli had the same absorption spectrum as the wild type green fluorescence protein and was thermostable in vitro. We found that the cell division proteins FtsZ and SiRe_1200 mainly localized at the mid-cell of E. coli and S. islandicus, respectively. The pili component protein UpsE evenly distributes in the cells as dots, while DNA replication clamp subunit PCNA1 formed several foci in certain area of a cell indicating the locations of DNA replication.[Conclusion] The optimized eCGP123 can utilized as a protein reporter for analysis of protein sub-cellular localizations in S. islandicus. This will be an important tool for functional studies of genes in the model species. However, more improvements are still needed for the application.

Abstract:Proteases and peptidases play important roles in nutrient metabolism, protein turnover and processing, and protein quality control in hyperthermophilic archaea. Due to their high stability and activity at high temperatures, proteases and peptidases from hyperthermophilic archaea are especially valuable to study mechanisms that stabilize protein structure and function at the maximum temperature capable of supporting life, and have great potential in industrial application. This review summarizes types, functions, catalytic properties, thermostabilizing mechanisms, and application potential of ATP-independent proteases and peptidases from hyperthermophilic archaea.

Abstract:Phosphorylation is one of the main types of protein post-translational modifications, which can be catalyzed by protein kinase, phosphotransferase, and phosphorylase. Among them, reversible protein phosphorylation mediated by protein kinases/phosphatases is an important mechanism of signal transduction in cells and plays regulatory roles in the processes of DNA replication, transcription, protein translation, and DNA repair. The study of protein kinases in archaea is still at the initial stage. Although phosphoproteomics studies showed that there are a large number of phosphorylated proteins in archaea, their specific enzymes and regulation mechanisms involved are still unclear. In this review, we summarized the putative functions of the protein kinases involved in the cellular processes including DNA metabolism, cell metabolism, cell cycle and cell mobility mechanism. Finally, we also proposed the perspectives of studies on archaeal protein kinases.

Abstract:Recent metagenomic surveys suggested that Epsilon-proteobacteria is abundant in deep-sea extreme environment such as hydrothermal vent and they play important role in carbon, nitrogen, hydrogen, and sulfur recycle in the ocean. A few studies have been carried out on this class of bacteria, mainly including 16S rRNA taxonomic identification and genomic sequence analysis from deep sequencing. This review summarized current understanding of ecological distribution and diversity of Epsilon-proteobacteria. Meanwhile, we elaborated diverse energy metabolism, powerful chemotaxis and motility, and relationships with benthic animals of Epsilon-proteobacteria. Meanwhile, we also discuss the adaptation mechanism of Epsilon-proteobacteria to deep-sea extreme environment to expedite our understanding and bioprospecting of the unique biological features of Epsilon-proteobacteria.

Abstract:The integrative genetic elements involved in the spreading of virulence factors, defense and DNA modification, and secondary metabolism have been characterized in bacteria, but similar investigations on the function of the hyperthermophilic archaeal counterparts are still very rare. This review summarizes the reported groups of integrative genetic elements, the mechanism of integration and maintenance of such genetic elements in hyperthermophilic archaea. The horizontal gene transfer processes mediated by integrative genetic elements play important roles in the genome evolution of hyperthermophilic archaea. Functional genomic studies of integrative genetic elements provide a new perspective for understanding the diversity and environmental adaptability of hyperthermophilic archaea.

Abstract:Microorganisms growing at high salinity and elevated alkaline environments have gained wide attention in term of their unique properties. According to the soluble composition, saline-alkaline environment can be two groups, i.e. "NaCl type" and "soda type (Na₂CO₃/NaHCO₃)". The alkaline pH of the former is relatively low, and that of the latter is higher. This review summarizes validated haloalkaliphilic type strains for optimal growth requiring Na⁺ concentrations above 0.5 mol/L and an alkaline pH of 9, and their biodiversity and physiological characteristics. The biodiversity of the halophilic bacteria is far greater than that of halophilic archaea. Halophilic bacteria are mainly composed of Bacilli (40% of the total), gamma-Proteobacteria (30%), Clostridia (11%), delta-Proteobacteria (6%) and Actinobacteria (6%); Halophilic archaea are Halobacteria (92%) and Methanomicrobia (8%). These extremophiles under double stress play essential roles and functions in biogeochemical processes and the ecological function.