Abstract:

Abstract:[Objective] Streptomyces sp. PRh5 is an endophytic actinomycete from Dongxiang wild rice, and shows strong antimicrobial activity in vitro. In order to further study Streptomyces sp. PRh5 antimicrobial mechanism and secondary metabolites biosynthetic gene clusters, it is necessary to decipher the strain genome. [Methods] The genome was sequenced using high-throughput sequencing, and then analyzed using relevant software for genome assembly, gene prediction and functional annotation, cluster of orthologous group (COG) cluster analysis, synteny analysis and total secondary metabolite biosynthesis gene clusters prediction. [Results] The whole genome was assembled into 290 contigs, and the genome size is about 11.1 Mb with GC content of 71.1%. This Whole Genome Shotgun project has been deposited at GenBank under the accession JABQ00000000. According to genome sequences analysis, 50 secondary metabolite biosynthetic gene clusters were predicted. [Conclusion] The results will provide genome sequences for future functional genomics, biosynthetic pathways and heterologous expression of secondary metabolites on Streptomyces sp. PRh5.

Abstract:

Abstract:[Objective] To identify a chitinase producing marine bacterium CAU904 isolated from China Nan Hai and optimize the fermentation conditions for chitinase production. [Methods] Strain CAU904 was identified based on its morphological characters and 16S rDNA sequence. The fermentation conditions for chitinase production by strain CAU94 were optimized using the one-factor-at-a-time method. [Results] The strain CAU904 was identified as Paenibacillus barengoltzii, and the optimal fermentation conditions were obtained as follows: 0.5% colloidal chitin, 0.2% yeast extract, 0.1% Tween 80 (medium pH 7.0) 45 °C for 72 h. Under the optimized fermentation conditions, the highest chitinase activity of 8.2 U/mL was achieved, which was 5.4 folds higher than that obtained before. The chitinase zymogram analysis showed that at least 11 chitinases were secreted into the fermentation broth, and three major bands had molecular masses of 54, 47 and 38 kD, respectively. [Conclusion] The results can be helpful for further study on the purification and application of the chitinases from Paenibacillus barengoltzii.

Abstract:[Objective] To interpret the effect of sodium lactate (a carbohydrate metabolite) on cell growth and astaxanthin accumlation during Phaffia rhodozyma fermentation, based on the metabolic regulation mechanism of astaxanthin synthesis. [Methods] The astaxanthin producing strain Phaffia rhodozyma JMU-VDL668 was cultured in shake flasks and 7 L bioreactor respectively. The effect of sodium lactate on the synthetic metabolic flow of astaxanthin was studied with the method of metabolic flux analysis. [Results] It was found that adding sodium lactate into 7 L bioreactor increased astaxanthin accumulation significantly, and the production of astaxanthin reached 17.70 mg/L, which was 26% higher than the production of the control group. The regulation mechanism of sodium lactate on astaxanthin synthesis was studied by means of metabolic flux analysis, and it was shown that sodium lactate could adjust metabolic flux distribution at the nodes of pyruvate and acetyl-CoA. Lactate was catalyzed by dehydrogenase and directly into later half of the metabolic network. Thus the flux of acetyl-CoA and the flux down to TCA cycle were significantly increased. [Conclusion] Adding sodium lactate during fermentation could provide more precursors (acetyl-CoA etc.) and energy, and so improved astaxanthin synthesis.

Abstract:[Objective] To obtain microorganism strains for comprehensive utilization of cellulose, an ambient temperature cellulase-producing strain was isolated and identified. The optimal culture conditions for enzyme production were determined. [Methods] Filter paper medium was used to enrich the microorganism cultures. CMC-Na medium was used to screen the cellulose-degrading strains initially under the condition of ambient temperature. A strain, KZ-2, was isolated and purified using LB medium, followed by identification utilizing morphological, physiological and biochemical properties, and 16S rRNA gene sequence profiles. Single factor test based on incubation time, culture temperate, initial pH and sodium chloride (NaCl) concentration was performed to optimize the conditions for cellulase production. [Results] Strain KZ-2, capable of producing extracellular cellulase under ambient temperature, was isolated from decomposing maize straw. It was identified as a strain of Enterobacter sp. and potentially to be a novel species. The optimized enzyme production could be obtained when the strain was cultivated for 120 hours at 25-35 °C with initial pH 4.5-5.5, NaCl concentration of 1.0%-2.0%. The maximum cellulase activity of 80.93 U/mL was achieved under the optimal conditions. Initial enzymatic property analyses of the cellulase produced demonstrated that the enzyme was most active at pH 7.0 with a temperature of 50 °C. [Conclusion] The cellulose-degrading strain KZ-2 is able to secrete cellulase under ambient temperature and is potentially a novel species. The strain is expected to be further studied and developed to explore its marketing values.

Abstract:[Objective] The purpose of this research was to analyze the changes of enzyme activities and relationships amony enzymes on decomposing needle litter of Pinus armandii by saprophytic fungi and explore fungal decomposition capacities of the litter. [Methods] Basing on morphological characteristics and sequence alignment analysis of rDNA-ITS region, five dominant strains isolated from Pinus armandii needle litter from Erlang Mount were identified. These five isolates were used as the fungal strains and the needle litter was used as the natural substrate. The fungi abilities to degrade the needle in terms of the loss in total organic matter (TOM) and the enzyme activities of endoglucanase (EG), xylanase (Xyl), lignin peroxidase (LiP), manganese peroxidase (MnP) and acid phosphatase (AP) by fermentation were tested. [Results] The five isolates were identified as Mucor sp., Pestalotiopsis sp., Allantophomopsis sp., Phoma sp. and Hypocrea sp., respectively. The loss in TOM caused by the five fungi was between 6.63%?15.77%. AP activity in the case of Pestalotiopsis sp. was the highest and the activities of EG, Xyl, LiP were relatively high. LiP activity was the highest in Allantophomopsis sp., which had high activity of MnP. Whereas EG and Xyl activities were low for Hypocrea sp. which can secrete LiP and higher AP. The results of correlation analysis showed that AP activity was negatively correlated with the loss in TOM. Moreover, there was a certain synergy between EG, Xyl and AP, especially between EG and AP. [Conclusion] In the present study, the five saprophytic fungi can degrade needle litter of Pinus armandii and the ability from highest to lowest was as followed: Pestalotiopsis sp., Allantophomopsis sp., Hypocrea sp., Phoma sp., Mucor sp.. Enzyme activities and enzymes synergy had an influence on decomposition of the needle litter. Pestalotiopsis sp., Hypocrea sp. and Allantophomopsis sp. were found to not only be capable of producing lignocelluloses-degrading enzymes but cause higher loss in TOM. These three strains were regarded as lignocelluloses-degrading fungi.

Abstract:[Objective] To isolate and obtain an electrochemically bacterium (exoelectrogen), strain WJ5-4, from anode leacheate of MFC using biowaste as substrate and to study its electrical characteristics. [Methods] The strain was identified by morphological observation, physiological and biochemical properties and 16S rDNA sequence analysis. MFC (microbial fuel cell) was constructed using strain WJ5-4 as exoelectrogen and using biowaste as substrate. The electrical properties of strain WJ5-4 was studied on different inoculation concentration and solid content. [Results] The strain WJ5-4 belonged to Nitratireductor, when inoculation concentration was 200 mL, the maximum power density was 135.16 mW/m2, stable working voltage was 370 mV and degradation of TOC (total organic carbon) was up to 41.46%. When solid content was 23%, power density was 163.69 mW/m2, the voltage was 434 mV, and degradation of TOC was up to 46.29%. [Conclusion] Strain WJ5-4 could produce electricity using higher solid content biowaste, and the electricity production cycle was longer. These results would provide reliable basis for further treatment of biowaste by the means of MFC.

Abstract:[Objective] Identification and reporting two Aspergillus isolates as a new Chinese record species, i.e, A. germanicus. [Methods] Polyphasic studies using morphological characters and clamodulin gene, β-tubulin gene and rDNA ITS1-5.8S-ITS2 sequences. [Results] Based on the comparisions of morphological and molecular characters of the two Aspergillus isolates (AS3.15303 and AS3.15304, isolated from soil in Shandong Province, China) with the ex-type of A. germanicus (CBS 123887), the two Chinese isolates were identified as A. germanicus. [Conclusion] We confirmed that A. germanicus was a new Chinese record of Aspergillus section Usti.

Abstract:[Objective] The aim of this study was to investigate the effects of antimicrobial compounds of Kluyveromyces marxianus (K2 and K8) on wild pathogenic Escherichia coli and its cell surface characteristics. [Methods] K2 and K8 were extracted by ethyl acetate, and the inhibition zones of K2 and K8 against E. coli O8 were determined by Oxford cup method. The organic acids were determined by HPLC, and the concentrations of killer toxin were determined by enhanced BCA Protein Assay Kit. The minimum inhibition concentration (MIC) and the minimum bactericidal concentration (MBC) were determined by broth dilution method, the effects of K2 and K8 on the growth curve of E. coli O8 were determined by turbidimetry. Moreover, the effects of K2 and K8 on the hydrophobicity of the E. coli O8 cell surface was determined using the microbial adhesion to solvents method, and the permeation of E. coli O8 cell membrane were determined by measuring the release of β-galactosidase activity into the culture medium using ONPG as a substrate. [Results] The aqueous phases of pH 2.0 and pH 8.0 had higher inhibition zones, they were dried for 48 h by freeze-drying, then, K2 and K8 were obtained, the main components were propanoic acid and some other organic acids, and killer toxins. The MICs of K2 and K8 were 0.025 g/mL and 0.100 g/mL, respectively. The MBCs of K2 and K8 were 0.100 g/mL and 0.200 g/mL, respectively. The growth curve of E. coli O8 was S-shape. It changed obviously after adding K2 and K8. E. coli O8 was basic character, and had a hydrophilic surface. The hydrophobicity increased after adding K2 and K8. In addition, the release of the β-galactosidase in permeation of E. coli O8 was promoted gradually by K2 and K8, and it also caused membrane lesions allowing ONPG uptake into cells. These two factors resulted in the increasing permeation. K2 was better than K8. [Conclusion] K2 and K8 could inhibit the growth of pathogenic E. coli O8 and influence its cell surface characteristics.

Abstract:[Objective] In order to find out the difference of conidia germination rate, germination speed of Nomuraea rileyi strain Nr0815 which was isolated from the infected larva of Argyrogramma agnata Staudinger (Lepidoptera: Noctuidae) in the eight botanical edible oils at different temperatures. [Methods] The absorbance of Nr0815 conidia in eight botanical edible oils was measured by ultraviolet spectrophotometer, the conidia germination rate in different oils and the germination speed at different observation period within 72 h at different temperatures were observed using slide germination method. [Results] The conidia of N. rileyi showed a good dispersion in the tested botanical edible oils. The conidia of N. rileyi in all botanical edible oils was normally germinated at the temperature ranged from 10 to 30 °C, among of them, the maximum accumulative germination rate of N. rileyi conidia was in the soybean oil, germination speed in other oils increased with the extend of time within 72 h except for that in the soybean oil and rape oil at 23 °C, and the maximum germination speed was at 48-72 h. The germination speed was slowest under 10 °C, and it began to germinate after 48 h. From the development of germ tube, the germ tube length of N. rileyi in soybean oil was the longest at 23 °C, the length was (24.89±1.04) μm, and the minimum germ tube length was from that in the sunflower seed oil, the length was (9.10±1.00) μm. [Conclusion] The temperature and botanical edible oil affected the conidia germination of N. rileyi, and the result provided theoretical basis for the development and utilization of conidia oil formulation of N. rileyi.

Abstract:[Objective] Generally, traditional λ-Red recombination system possessed low efficiency, complicated processes, inconsistent protocols, high false-positive rate and instability for multi-gene-knock-out/knock-in during manipulation on chromosome gene of Escherichia coli. In order to solve these problems, this study established a high efficiency and standard strategy of gene knock-out/in. [Methods] Based on λ-Red recombination system, new template plasmids were developed. A pSC101 derivative replication origin was used to diminish the false-positive problem. Convenient genetic manipulation was achieved by using high-copy-number plasmid and multiple cloning sites. New genetic marker was used to facilitate continuous multi-gene knock-out/in. A series of key targets within primary metabolite networks of E. coli were then knocked out/in using our methods. [Results] New λ-Red plasmids system, named SC101-Cre-LoxP-MCS system, was developed. The positive colonies were selected on two-resistance plate and 100% positive rate was achieved. [Conclusion] The efficiency of gene recombination was improved by the new method of gene knock-out/knock-in. This new system provides a rapid genetic manipulation. Our new strategy provides important insights into gene function research and genetic engineering bacteria with new genetic characteristics.

Abstract:Immobilized microorganism is newly applied in bioremediation, which is high efficient, stabile and safe. Recently, it has been widely used in the purification of various polluted water, including the increasingly serious pollution of the offshore aquaculture water. This paper we first introduce the method of immobilized microorganism technology and the selection of carrier. Then we summarize the research advance in application of immobilized microorganism technology in the seriously polluted offshore aquaculture water. Finally we analyze the current problems existing in the application of the technology and discuss the future research needs.

Abstract:Microalgae have been considered as promising candidates in integrating CO2 mitigation, nutrients degradation in water systems, and energy capture from sunlight. Therefore, it is important for sustainable development via acceleration of microalgae research to address the problems of environmental pollution and energy shortage. However, high cost in biomass recovery is the major bottleneck in microalgal-based industrial applications, and a cost-effective method in microalgal biomass recovery is the key to this issue. Here, we reviewed the methods for microalgae harvesting, including sedimentation, centrifugation, filtration and flocculation. Among these methods, the progress and prospect in flocculation are especially focused so that to propose options for the cost-effective biomass recovery and microalgal industrialization.

Abstract:The loop-mediated isothermal amplification (LAMP) technique has been widely applied in the detection of nucleic acid because of its high specificity and sensitivity, time efficiency, and independent of thermo cycling equipment. After the invention of LAMP many studies have been done to modify and improve this method. This article has summarized these studies and reviewed the recent developments of LAMP technology from the following four aspects: methodology improvements; Shortening of reaction time and simplification of templates preprocessing; multiple products analysis; inhibition of false positive pollution. The objective of this review is to provide the theoretical foundation for the development of future novel nucleic acid detection platforms which will based on the LAMP technique.

Abstract:Indole is widespread in the natural environment, as more than 145 Gram-positive and Gram-negative bacteria can produce indole, including many pathogenic bacteria. More and more mechanism studies have revealed that indole acts as an important intercellular signal molecule in some enteric pathogens such as Escherichia coli, Edwardsiella tarda and Vibrio cholera, and controls diverse aspects of bacterial physiology, such as virulence, drug resistance, biofilm formation, motility, plasmid stability, acid resistance and spore formation. More importantly, indole and its derivatives regulate competition of microbial consortia and benefit digestive and immune system in human. We discuss our current study on the role of indole signaling in Edwardsiella tarda and review the progress of study on indole signaling in diverse bacterial species. Thus, better understanding of the indole signaling mechanism will help to develop new anti-infection strategies and their biotechnology applications.

Abstract:Cooperation is ubiquitous in nature. Intuitively, the behavior is easy to be exploited by selfish cheaters unless a specific mechanism is at work. Cooperation has also been found in microbial world and intrigues many evolutionary biologists. Here, we provide a conceptual overview of several cooperation mechanisms based on microbial population models, including kin selection, Simpson’s paradox, repression of competition, evolutionary game theory and so on.

Abstract:The cyclic lipopeptides (CLPs) produced by Pseudomonas were made up of a cyclized oligopeptide lactone ring coupled to a fatty acid tail. CLPs were synthesized by nonribosomal peptide synthetases in Pseudomonas and the genetic regulation of CLPs syntheses was strict and comprehensive. GacA/GacS two-component signal transduction system and N-AHL-mediated quorum sensing system played an important role in global regulation of CLPs production in Pseudomonas. Here, we reviewed some research advances on the systems involved in CLPs syntheses. We discussed the method using PCR to obtain some cyclic lipopeptides and prospected the applications of bioengineering technology in enhancing the production of CLPs in Pseudomonas. It was also discussed the genome mining combining with genetic regulation research to obtain new cyclic lipopeptides.

Abstract:Gut microbes are associated with the human health directly. Up till now, scientists have conducted many researches on the impact factors of gut microbiota structure both in human and animal models (i.e. mice and pigs), and got many achievements. In this paper, we focused on the impact factors of human’s gut microbiota structure, including the age, the host genotype, the postnatal environment, diet, antibiotic and so on. By recognizing and controlling these factors can help human keeping a healthy life.

Abstract:Nitrification (oxidation of ammonia to nitrate via nitrite) plays a crucial role in the global nitrogen cycling. Along with the discovery of ammonia monooxygenase coding gene (amoA) sequences in archaea and the successful cultivation (isolation and enrichment) of ammonia-oxidizing archaea (AOA), it has been found that AOA was more abundant than AOB in most environments. And the contribution of AOA vs AOB to the nitrogen cycling is still under debate. In this mini-review, the ecological distribution, evolution, abundance and potential function involved the microbial nitrification were summarized based on the current knowledge. Furthermore, the perspective insights were discussed for the future research.

Abstract:[Objective] This study was to investigate the genetic nature of multiple amplicons from PCR experiments on ‘Candidatus Liberibacter asiaticus’ infected citrus samples and to provide reference for molecular biological studies of fastidious prokaryotes. [Methods] Two short tandem repeats (STR) loci in the ‘Ca. L. asiaticus’ genome were amplified by conventional PCR. PCR products were separated by PAGE. Polymorphic bands were collected, cloned, and sequenced. [Results] The primers from the two STR loci generated multiple amplicons from a single ‘Ca. L. asiaticus’ infected citrus sample. Sequence analyses showed that these amplicons could be from ‘Ca. L. asiaticus’, other bacteria and citrus host. [Conclusion] The main source of amplicon variations was due to changes of STR numbers in the targeted loci. However, amplification of host and endophytic bacterial DNA could also contribute to the multi-band phenomenon.

Abstract:[Objective] To establish a rapid detection technology LAMP for Eucalyptus dieback. [Methods] The pathogen against on Eucalyptus was studied. Based on the species-specific conserved region of beta-tubulin gene on Cylindrocladium scoparium, a set of primers (inner primer: FIP/BIP, outer primer: F3/B3, Loop primers: LooPF/LooPB) were designed, a LAMP assay for rapid detection of C. scoparium was developed, evaluated and optimized. [Results] The LAMP reaction system (50 μL) consisted of Bst DNA polymerase (8 U) 1 μL, Betaine solution (5 mol/L) 3.0 μL, dNTPs (2.5 mmol/L) 3.5 μL, 10×Thermopol Ⅱ 2.5 μL, MgCl2 (100 mmol/L) 2 μL, FIP/BIP (40 μmol/L) 1 μL, F3/B3 (10 μmol/L) 0.5 μL, LooPF/LooPB (10 μmol/L) 1 μL, DNA template 2 μL, with ddH2O up to the volume of 50 μL. Response procedures acted as the mixture was in 65 °C water bath pot for about 45 min first, and then inactivated 5 min under the 90 °C to end of reaction. Specificity assays showed that the amplification results of 12 test isolates can be distinguished though visual inspection, ultraviolet light, added fluorescent dye SYBR Green I, and electrophoresis test strip, and the 4 pathogens were positive, and that of the other 8 pathogens were negative. The detection limit of LAMP was 40 pg pure genomic DNA per 50 μL reaction, which fits entirely in the field test. The wild field effectiveness showed that the different physiological small kinds different regions of C. scoparium can be detected with the method of LAMP, meanwhile the ultraviolet light and electrophoresis test strip were significantly. [Conclusion] Summing up the above, the LAMP rapid detection can be applied in filed effectively.