Characterization of depth-related microbial communities in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rRNA fragments

The characterization of microbial communities of different depth sediment samples was examined by a culture-independent method and compared with physicochemical parameters, those are organic matter （OM）, total nitrogen （TN）, total phosphorus （TP）, pH and redox potential （Eh）. Total genomic DNA was extracted from samples derived from different depths. After they were amplified with the GC-341 f/907r primer sets of partial bacterial 16S rRNA genes, the products were separated by denaturing gradient gel electrophoresis （DGGE）. The profile of DGGE fingerprints of different depth sediment samples revealed that the community structure remained relatively stable along the entire 45 cm sediment core, however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. The principle coordinates analysis suggested that the bacterial communities along the sediment core could be separated into two groups, which were located 0-20 cm and 21-45 cm, respectively. The sequencing dominant bands demonstrated that the major phylogenetic groups identified by DGGE belonged to Bacillus, Bacterium, Brevibacillus, Exiguobacterium, γ-Proteobacterium, Acinetobacter sp. and some uncultured or unidentified bacteria. The results indicated the existence of highly diverse bacterial community in the lake sediment core.

STUDY ON THE RELATIONSHIP BETWEEN MELTING POINT AND ACID DENATURING ACIDITY OF DNA BY ULTRAVIOLET SPECTROMETER

The relationship between meltillg point and acid denaturing acidity of DNA was studied by ultraviolet spectrometer. According to our investigation there exists a good linear relationship between melting point and acid denaturing acidity of DNA. The acid denaturing acidity. which could be obtained easily. may be used in the field of biochemistry as an alternative to melting point.

Signal Peptide and Denaturing Temperature are Critical Factors for Efficient Mammalian Expression and Immunoblotting of Cannabinoid Receptors

Many researchers employed mammalian expression system to artificially express cannabinoid receptors, but immunoblot data that directly prove efficient protein expression can hardly be seen in related research reports. In present study, we demonstrated cannabinoid receptor protein was not able to be properly expressed with routine mammalian expression system. This inefficient expression was rescued by endowing an exogenous signal peptide ahead of cannabinoid receptor peptide. In addition, the artificially synthesized cannabinoid receptor was found to aggregate under routine sample denaturing temperatures (i.e.,≥95°C), forming a large molecular weight band when analyzed by immuno-blotting. Only denaturing temperatures ≤75°C yielded a clear band at the predicted molecular weight. Collectively, we showed that efficient mammalian expression of cannabinoid receptors need a signal peptide sequence, and described the requirement for a low sample denaturing temperature in immuno-blot analysis. These findings provide very useful information for efficient mammalian expression and immuno-blotting of membrane receptors.

Denatured proteins show new vitality:Green synthesis of germanium oxide hollow microspheres with versatile functions by denaturing proteins around bubbles

The hollow structure has long attracted great attention because of its excellent properties.However,this special structure is usually synthesized through some complex approaches.Herein,we discovered that denatured bovine serum albumin(BSA)can trigger unusual biomineralization for the simple,green and shape-controllable synthesis of germanium oxide(GeOx)hollow microsphere(HMS).At high temperature(60℃),BSA was denatured,and a compact BSA layer was formed around the H2 bubbles.The denatured BSA layer was stable and suitable for anchoring and growing GeOx.By simply changing the BSA concentration and temperature,various morphologies of GeOx could be obtained.Due to the denatured protein skeletons and microenvironment-regulated collapse,GeOx HMS showed great potential for intelligently responsive pesticide delivery in the insect gut,showing superiority over traditional delivery systems,which early release pesticides in the mouth and stomach.Inspired by its large specific surface area,excellent biocompatibility,modifiable functional groups,and high electrocatalytic activity,GeOx HMS was also applied to versatile sensors for H_(2)O_(2) assays at physiological pH and rapid coronavirus COVID-19 detection.This work not only provides some evidence for understanding proteins in depth but also paves a new avenue for the biomineralization-inspired synthesis of hollow structures with versatile functions.

Monitoring of microbial community structure and succession in the biohydrogen production reactor by denaturing gradient gel electrophoresis(DGGE)

To study the structure of microbial communities in the biological hydrogen produc- tion reactor and determine the ecological function of hydrogen producing bacteria, anaerobic sludge was obtained from the continuous stirred tank reactor (CSTR) in different periods of time, and the diversity and dynamics of microbial communities were investigated by denaturing gra- dient gel electrophoresis (DGGE). The results of DGGE demonstrated that an obvious shift of microbial population happened from the beginning of star-up to the 28th day, and the ethanol type fermentation was established. After 28 days the structure of microbial community became stable, and the climax community was formed. Comparative analysis of 16S rDNA sequences from reamplifying and sequencing the prominent bands indicated that the dominant population belonged to low G+C Gram-positive bacteria (Clostridium sp. and Ethanologenbacterium sp.), β- proteobacteria (Acidovorax sp.), γ-proteobacteria (Kluyvera sp.), Bacteroides (uncultured bacte- rium SJA-168), and Spirochaetes (uncultured eubacterium E1-K13), respectively. The hydrogen production rate increased obviously with the increase of Ethanologenbacterium sp., Clostridium sp. and uncultured Spirochaetes after 21 days, meanwhile the succession of ethanol type fer- mentation was formed. Throughout the succession the microbial diversity increased however it decreased after 21 days. Some types of Clostridium sp. Acidovorax sp., Kluyvera sp., and Bac- teroides were dominant populations during all periods of time. These special populations were essential for the construction of climax community. Hydrogen production efficiency was de- pendent on both hydrogen producing bacteria and other populations. It implied that the co- metabolism of microbial community played a great role of biohydrogen production in the reactors.

Denaturing gradient gel electrophoresis fingerprinting of soil bacteria in the vicinity of the Chinese Great Wall Station, King George Island, Antarctica

Bacterial diversity was investigated in soil samples collected from 13 sites around the Great Wall Station, Fildes Peninsula, King George Island, Antarctica, using denaturing gradient gel electrophoresis （DGGE） of 16S rRNA genes. The classes α-, β-, and γ-Proteobacteria, as well as the phylum Actinobacteria, were found to be the dominant bacteria in the soils around the Great Wall Station. Although the selected samples were not contaminated by oil, a relationship between soil parameters, microbial biodiversity, and human impact was still seen. Sample sites in human impacted areas showed lower bacterial biodiversity （average H′= 2.65） when compared to nonimpacted sites （average H′= 3.05）. There was no statistically significant correlation between soil bacterial diversity and total organic carbon （TOC）, total nitrogen, or total phosphorus contents of the soil. Canonical correlation analysis showed that TOC content was the most important factor determining bacterial community profiles among the measured soil parameters. In conclusion, microbial biodiversity and community characteristics within relatively small scales （1.5 km） were determined as a function of local environment parameters and anthropogenic impact.

Concentration-Dependent Effect of Nickel Ions on Amyloid Fibril Formation Kinetics of Hen Egg White Lysozyme:a Raman Spectroscopy Study

Nickel,an important transi-tion metal element,is one of the trace elements for hu-man body and has a crucial impact on life and health.Some evidences show the excess exposure to metal ions might be associated with neurological diseases.Herein,we applied Raman spectroscopy to study the Ni(II)ion effect on kinetics of amyloid fibrillation of hen egg white lysozyme(HEWL)in thermal and acidic conditions.Using the well-known Raman indicators for protein tertiary and secondary structures,we monitored and analyzed the concentration effect of Ni(II)ions on the unfolding of tertiary structures and the transformation of sec-ondary structures.The experimental evidence validates the accelerator role of the metal ion in the kinetics.Notably,the additional analysis of the amide I band profile,combined with thioflavin-T fluorescence assays,clearly indicates the inhibitory effect of Ni(II)ions on the formation of amyloid fibrils with organizedβ-sheets structures.Instead,a more significant promotion influence is affirmed on the assembly into other aggregates with disordered struc-tures.The present results provide rich information about the specific metal-mediated protein fibrillation.

不同性状窖泥的细菌群落结构与酸酯含量分析

为了解不同性状窖泥细菌群落结构及酸酯代谢的差异,分别选取新窖泥、趋老熟窖泥和老熟窖泥,对其细菌16S r DNA的V3区进行变性梯度凝胶电泳分析和同源性比较,并结合窖泥主要有机酸及有机酸酯含量进行了典型相关分析。结果表明,老熟窖泥的细菌多样性指数及均匀度指数高于新窖泥和趋老熟窖泥,得到的39个优势条带,进行细菌DNA测序可分为14类;Clostridium XIVa、Aminobacterium均只在老熟窖泥中检测到;新窖泥和趋老熟窖泥与Lactococcus、Lactobacillus、乳酸、乳酸乙酯含量正相关,老熟窖泥与Clostridiales、己酸、己酸乙酯和丁酸含量正相关。

多功能农药降解基因工程菌株m-CDS-1环境释放安全评价

【目的】为了评价多功能农药降解基因工程菌株m-CDS-1的环境释放中间试验水平的安全性。【方法】通过农药检测、平板计数、Most probable number-PCR(MPN-PCR)和Denaturing Gradient Gel Electrophoresis(DGGE)等方法在江苏大丰进行了工程菌株m-CDS-1田间降解农药效果、定殖动态和对土壤微生物群落结构影响的研究。【结果】投加1.01×107CFU/g干土的工程菌株m-CDS-1在30d时均能完全降解10.71mg/kg的甲基对硫磷和1.29mg/kg的呋喃丹。平板计数表明工程菌株m-CDS-1在土壤中快速下降;MPN-PCR检测结果显示,在4d,15d和30d时,0～10cm混合土壤中该工程菌株的数目分别为2.15±0.98×106CFU/g干土,3.70±4.66×104CFU/g干土和检测不出。工程菌株m-CDS-1的投加不会对土壤可培养三大微生物菌群数量产生显著影响;基于细菌16S rDNA V3区的DGGE分析结果表明,施加农药对细菌菌落结构有显著影响,4d,11d,30d时农药施用区与空白对照区的图谱相似性分别为17.16%,49.81%和75.01%,但到60d时的相似性为98.62%。工程菌株m-CDS-1释放在前期对细菌群落结构有一定影响,4d,11d和30d工程菌株释放区相对于空白的相似性分别为49.57%,38.30%和83.30%。在60d时,空白、施药和施菌小区的图谱相似性都在90%以上。【结论】工程菌株m-CDS-1不仅可同时高效降解甲基对硫磷和呋喃丹,仍保持了实验室内的原有特性,而且不会成为优势菌群长期在土壤环境中存在,也不会对土壤微生物群落结构造成长期影响。

PCR指纹图谱技术在酸奶质量监测中的应用

用PCR指纹图谱技术对市售某品牌酸奶进行了短期动态监测,对于收集的3个生产批次的9个酸奶样品,用ERIC(EnterobacterialRepetitiveIntergenicConsensus,肠杆菌基因间保守重复序列)-PCR和PCR-DGGE(DenaturingGradientGelElectrophoresis,变性梯度凝胶电泳)指纹图谱技术对其菌种组成及其稳定性进行评价。ER-IC-PCR指纹图谱聚类分析结果显示,同一生产批次内3个不同包装的样品ERIC-PCR指纹图谱相似性为90%左右,而不同生产批次样品之间ERIC-PCR指纹图谱相似性有所下降,为82%。该结果进一步用DGGE指纹图谱进行证实。DGGE分析结果表明,G2样品明显缺少一条主带,经割胶回收测序发现,这条主带代表的微生物是Lacto-bacillusdelbrueckiisubsp.Bulgaricus,说明该产品不同生产批次间的稳定性不是很好。DGGE图谱和测序结果还显示,除G2样品外,该酸奶样品的菌种组成与产品标签说明是一致的。

一种快速的酸奶质量跟踪监测检验新方法

分析酸奶中的菌种组成是酸奶质量控制的重要指标。本文用PCR-DGGE(denaturinggra-dientgelelectrophoresis,变性梯度凝胶电泳)指纹图谱技术对市售某品牌酸奶在1个月内进行了动态监测,共收集了6个生产批次的18个酸奶样品,通过建立16SrDNAV3区PCR-DGGE分析、DGGE图谱条带割胶回收测序等一套完整的检测评价方法,结合常规分离培养方法,对样品微生物组成及其稳定性进行跟踪监测。结果显示,所有供试样品在整个动态监测期内DGGE指纹图谱都出现2条带,显示其微生物组成比较稳定,割胶回收测序结果表明其微生物组成与厂家标注完全一致,分别为Lacto-bacillusdelbrueckiisubsp.bulgaricus(保加利亚乳杆菌)和Streptococcusthermophilus(嗜热链球菌)。分离计数结果表明前者比后者低3个数量级,二者的DGGE条带亮度也有显著差别。本研究用菌种组成及其稳定性两个指标对酸奶样品质量进行评价,建立了DGGE评价方法,结果表明,该技术可以作为酸奶质量控制和动态监测的快速简便的新方法。

变性梯度凝胶电泳技术在微生物多样性研究中的应用

变性梯度凝胶电泳是不依赖于培养的、依据DNA分子的大小和所带电荷分析微生物多样性和动态变化的分子生物学技术,具有检测极限低、分析速度快及重复性好等优点。主要对变性梯度凝胶电泳原理、特点及其在微生物多样性应用方面进行综述。

Plankton community composition in the Three Gorges Reservoir Region revealed by PCR-DGGE and its relationships with environmental factors

To explore the relationships between community composition and the environment in a reservoir ecosystem, plankton communities from the Three Gorges Reservoir Region were studied by PCR-denaturing gradient gel electrophoresis fingerprinting. Bacterial and eukaryotic operational taxonomic units （OTUs）, generated by DGGE analysis of the PCR-amplified 16S and 18S rRNA genes, were used as surrogates for the dominant ＂biodiversity units＂. OTU composition among the sites was heterogeneous; 46.7% of the total bacterial OTUs （45） and 64.1% of the eukaryotic OTUs （39） were identified in less than half of the sampling sites. Unweighted pair group method with arithmetic averages （UPGMA） clustering of the OTUs suggested that the plankton communities in the Xiangxi Rive sites were not always significantly different from those from the Yangtze River sites, despite clear differences in their environmental characterizations. Canonical correspondence analysis （CCA） was applied to further investigate the relationships between OTU composition and the environmental factors. The first two CCA ordination axes suggested that the bacterial community composition was primarily correlated with the variables of NO3^--N, dissolved oxygen （DO）, and SiO3^2--Si, whereas, the eukaryotic community was mainly correlated with the concentrations of DO, PO4^3--P, and SiO3^2--Si.

Community analysis of ammonia and nitrite oxidizers in start-up of aerobic granular sludge reactor

A lab-scale sequencing batch reactor （SBR） was set-up and the aerobic granular sludge was successfully incubated using anaerobic granular sludge as seed sludge. Nitrogen was partially removed by simultaneous nitrification and denitrification （SND） via nitrite with free ammonia （FA） of about 10 mg/L. The denaturing gradient gel electrophoresis （DGGE） method was used to investigate community structure of α-Proteobacteria, β-Proteobacteria, ammonia oxidizing bacteria （AOB）, and Nitrospira populations during start-up. The population sizes of bacteria, AOB and Nitrospira were examined using real-time PCR method. The analysis of community structure and Shannon index showed that stable structure of AOB population was obtained at day 35, while the communities of α- Proteobacteria, β-Proteobacteria, and Nitrospira became stable after day 45. At stable stage, the average cell densities were 1.1× 10^12, 2.2×10^10 and 1.0×10^10 cells/L for bacteria, AOB and Nitrospira, respectively. The relationship between characteristics of nitrifying bacteria community and nitrogenous substrate utilization constant was discussed by calculating Pearson correlation. Certain correlation seemed to exist between population size, biodiversity, and degradation constant. And the influence of population size might be greater than that of biodiversity.

Microbial community structure in an integrated A/O reactor treating diluted livestock wastewater during start-up period

In order to investigate the correlation between reactor performance and the microorganisms,an integrated A/O reactor was operated for 72 days to treat diluted livestock wastewater.Chemical oxygen demand （COD） removal efficiency increased from 79% to 94%,with total nitrogen （TN） removal efficiency from 37% to 50% （HRT 7.4 hr） when the influent COD and TN were ca.1500 mg/L and 95 mg/L,respectively,and the outlet COD concentration was less than 100 mg/L at the end.Microbial community was monitored during start-up period by denaturing gradient gel electrophoresis （DGGE） based on 16S rRNA gene.DGGE profiles showed that microbial community had changed significantly during the start-up and these shifts were in accordance with the reactor performance.UPGMA clustering analysis showed that 14 anaerobic samples fell into five main groups and so did the aerobic ones,but the grouping patterns were different.Phylogenetic analysis indicated that microbial populations in the anaerobic compartment belonged to Firmicutes,Proteobacteria,Chloroflexi and Bacteroidetes,while Proteobacteria,Bacteroidetes,Firmicutes,Verrucomicrobiae and Nitrospira were present in the aerobic compartment.In the anaerobic compartment,more fermentative and acetogenic bacteria were detected during the start-up while denitrifying bacteria faded away.Two functional populations such as Nitrospira defluvii and Dechloromonas denitrificans were observed when nitrogen removal was high,indicating that simultaneous nitrification and denitrification occurred in the aerobic compartment.

Phylogenetic diversity and specificity of bacteria associated with Microcystis aeruginosa and other cyanobacteria

Interactions between bacteria and cyanobacteria have been suggested to have a potential to influence harmful algal bloom dynamics; however, little information on these interactions has been reported. In this study, the bacterial communities associated with five strains of Microcystis aeruginosa, three species of other Microcystis spp., and four representative species of non-Microcystis cyanobacteria were compared. Bacterial 16S rDNA fragments were amplified and separated by denaturing gradient gel electrophoresis （DGGE） followed by DNA sequence analysis. The similarities among bacterial communities associated with these cyanobacteria were compared to the digitized DGGE profiles using the cluster analyses. The bacterial community structure of all cyanobacterial cultures differed. Cluster analysis showed that the similarity values among M. aeruginosa cultures were higher than those of other cyanobacterial cultures. Sequence analysis of DGGE fragments indicated the presence of bacteria including, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria in the cyanobacterial cultures. Members of the Sphingomonadales were the prevalent group among the Microcystis-associated bacteria. The results provided further evidence for species-specific associations between cyanoabcteria and heterotrophic bacteria, which are useful for understanding interactions between Microcystis and their associated bacteria.

Effect of methamidophos on soil fungi community in microcosms by plate count,DGGE and clone library analysis

Methamidophos was widely used a pesticide in northern China. The potential influences of methamidophos on soil fungal community in black soil were assessed by plate count, 28S rDNA-PCR-DGGE, and clone library analysis. Three methamidophos levels （50, 150, and 250 mg/kg） were tested in soil microcosms. Results from plate count during a 60-d microcosm experiment showed that high concentrations of methamidophos （250 mg/kg） could significantly stimulate fungal populations. DGGE （denaturing gradient gel electrophoresis） fingerprinting patterns showed a significant difference between the responses of culturable and total fungi communities under the stress of methamidophos. Shannon diversity indices calculated from DGGE profiles indicated that culturable fungi in all microcosms with methamidophos treatment increased after 1 week of incubation. However, the diversity indices of total fungi decreased in the first week, as compared to the stimulation of culturable fungi. At the 8th week, however, all the microcosms treated by methamidophos were similar to the control microcosms in community structure as suggested by the Shannon diversity indices for both culturable and total fungi. In contrast, after 1 week the fungal structure of culturable and unculturable both were disturbed to different extent under the stresses of methamidophos by clustering analysis. Clone sequencing analysis indicated the stimulation of pathogenic and unculturable fungal populations by methamidophos treatment, suggetsing potential risks of plant disease outbreak.

Characterisation of the bacterial community in expressed prostatic secretions from patients with chronic prostatitis/chronic pelvic pain syndrome and infertile men： a preliminary investigation

The expressed prostatic secretions （EPSs） of men with chronic prostatitis/chronic pelvic pain syndrome （CP/CPPS）, infertile men and normal men were subjected to microbiological study. EPSs were collected from the subjects, which included 26 normal men, 11 infertile patients and 51 CP/CPPS patients. DNA was extracted from each specimen, and the V3 regions of the 16S rRNA genes were amplified using universal bacterial primers. The results showed that the EPS 16S rRNA gene-positive rate in the CP/CPPS and infertile patients was much higher than in the normal men, but without any difference among the three patient groups. The denaturing gradient gel electrophoresis （DGGE） method was used to characterize the EPS bacterial community structure of the prostate fluid from patients with CP/CPPS or infertility issues. Principal component analysis （PCA） and partial least squares （PLS） analyses of PCR-DGGE profiles revealed that the EPS bacterial community structure differed among the three groups. Three bands were identified as the key factors responsible for the discrepancy between CP/CPPS patients and infertile patients （P〈O.05）. Two bands were identified as priority factors in the discrepancy of category IliA and category IIIB prostatitis patients （P〈O.05）. According to this research, the ecological balance of the prostate and low urethra tract, when considered as a microenvironment, might play an important role in the maintenance of a healthy male reproductive tract.

Microbial Community Dynamics During Biogas Slurry and Cow Manure Compost

This study evaluated the microbial community dynamics and maturation time of two compost systems： biogas slurry compost and cow manure compost, with the aim of evaluating the potential utility of a biogas slurry compost system. Denaturing gradient gel electrophoresis （DGGE）, gene clone library, temperature, C/N ratio, and the germination index were employed for the investigation, cow manure compost was used as the control. Results showed that the basic strip and dominant strips of the DGGE bands for biogas slurry compost were similar to those of cow manure compost, but the brightness of the respective strips for each system were different. Shannon-Weaver indices of the two compost systems differed, possessing only 22% similarity in the primary and maturity stages of the compost process. Using bacterial 16S rRNA gene clone library analysis, 88 bacterial clones were detected. Further, 18 and 13 operational taxonomic units （OTUs） were present in biogas slurry and cow manure compost, respectively. The 18 OTUs of the biogas slurry compost belonged to nine bacterial genera, of which the dominant strains were Bacillus sp. and Carnobacterium sp.; the 13 OTUs of the cow manure compost belonged to eight bacterial genera, of which the dominant strains were Psychrobacter sp., Pseudomonas sp., and Clostridium sp. Results demonstrated that the duration of the thermophilic phase （more than 50°C） for biogas slurry compost was 8 d less than the according duration for cow manure compost, and the maturation times for biogas slurry and cow manure compost were 45 and 60 d, respectively. It is an effective biogas slurry assimilate technology by application of biogas slurry as nitrogen additives in the manufacture of organic fertilizer.

Effects on soil quality of biochar and straw amendment in conjunction with chemical fertilizers

The objective of this study was to evaluate the effects on chemical and microbiological properties of paddy soil of short-term biochar,straw,and chemical fertilizers compared with chemical fertilization alone.Five soil fertilization treatments were evaluated：regular chemical fertilizers（RF）,straw＋regular chemical fertilizers（SRF）,straw biochar＋regular chemical fertilizers（SCRF）,bamboo biochar（BC）＋regular chemical fertilizers（BCRF）,and straw biochar＋70%regular chemical fertilizers（SC＋70%RF）.Their effects were investigated after approximately 1.5 years.The soil p H and cation exchange capacity（CEC）were significantly higher in biochar-treated soils.The soil phosphorous（P）and potassium（K）contents increased with biochar application.The soil Colwell P content was significantly increased with the addition of straw biochar in the treatments of SCRF and SC＋70%RF.The oxygen（O）：carbon（C）ratio doubled in BC picked from the soil.This indicated that BC underwent a significant oxidation process in the soil.The denaturing gradient gel electrophoresis（DGGE）fingerprints of microbial communities differed among the treatments.Soils with added biochar had higher Shannon diversity and species richness indices than soils without biochars.The results suggest that biochar can improve soil fertility.