Sheep-urine-induced changes in soil microbial community structure

Soil microbial communities play an important role in nutrient cycling and nutrient availability, especially in unimproved soils. In grazed pastures, sheep urine causes local changes in nutrient concentration which may be a source of heterogeneity in microbial community structure. In the present study, we investigated the effects of synthetic urine on soil microbial community structure, using physiological (community level physiological profiling, CLPP), biochemical (phospholipid fatty acid analysis, PLFA) and molecular (denaturing gradient gel electrophoresis, DGGE) fingerprinting methods. PLFA data suggested that synthetic urine treatment had no significant effect on total microbial (total PLFA), total bacterial or fungal biomass; however, significant changes in microbial community structure were observed with both PLFA and DGGE data. PLFA data suggested that synthetic urine induced a shift towards communities with higher concentrations of branched fatty acids. DGGE banding patterns derived from control and treated soils differed, due to a higher proportion of DNA sequences migrating only to the upper regions of the gel in synthetic urine-treated samples. The shifts in community structure measured by PLFA and DGGE were significantly correlated with one another, suggesting that both datasets reflected the same changes in microbial communities. Synthetic urine treatment preferentially stimulated the use of rhizosphere-C in sole-carbon-source utilisation profiles. The changes caused by synthetic urine addition accounted for only 10-15% of the total variability in community structure, suggesting that overall microbial community structure was reasonably stable and that changes were confined to a small proportion of the communities.     

微生物燃料电池利用乳酸产电性能与微生物群落分布特征

【目的】为探讨以乳酸为基质的微生物燃料电池(Microbial fuel cell,MFC)产电性能以及微生物群落在阳极膜、悬浮液、阳极沉淀污泥中的分布特征,【方法】试验建立了双室MFC,以乳酸为阳极主要碳源,研究了反应器的启动过程及产电效能,同时以电镜和PCR-变性梯度凝胶电泳(Denaturing gradient gelelectrophoresis,DGGE)技术解析了微生物群落的空间分布特征。【结果】结果表明,反应器启动第7天时外电压达到0.56 V,当外阻为80Ω时,电流密度为415 mA/m2,MFC的功率密度达到最大值82 mW/m2。电镜观察发现大量杆菌附着在阳极表面,结合较为紧密;DGGE图谱显示阳极膜表面微生物与种泥最为相似,与阳极悬浮液、底部沉淀污泥中的主要菌群一致,条带序列与睾丸酮丛毛单胞菌(Comamonas testosteroni)和布氏弓形菌(Arcobacter butzleri)等最为相似。【结论】本研究表明以乳酸为基质MFC可产生较高的功率密度,阳极附着的优势菌与接种污泥来源密切相关。     

基于PCR-DGGE技术的红树林区微生物群落结构

【目的】为了解红树林沉积物中细菌的群落结构特征。【方法】应用PCR-DGGE技术对福建浮宫红树林的16个采样站位样品细菌的群落结构进行了研究。根据DGGE指纹图谱,对它们的遗传多样性进行了分析。【结果】各站位样品细菌多样性指数(H)、丰度(S)和均匀度(EH)均有所不同,这些差异与它们所处站位的不同有关,红树林区细菌多样性高于非红树林区细菌多样性。对不同站位细菌群落相似性分析,它们的相似性系数也存在一定的规律,同一断面的细菌群落结构相近性较高。对DGGE的优势条带序列分析,同源性最高的微生物分别属于变形菌门(Proteobacteria)、酸菌门(Acidobacteria)和绿菌门(Chlorobi),它们均为未培养微生物,分别来自于河口海岸沉积物。【结论】应用PCR-DGGE技术更能客观地反映红树林沉积物中真实的细菌群落结构信息。另外,研究也表明红树林区微生物多样性丰富,在红树林区研究开发未知微生物资源具有巨大的潜力。     

The host species affects the microbial community in the goat rumen

AIMS: This study was carried out to determine whether bacterial and ciliate populations in goat rumen vary significantly between different goat species living in the same environment. METHODS AND RESULTS: Bacterial and ciliate communities in the rumen of three goat species were analysed at the molecular level using denaturing gradient gel electrophoresis. The microbial community varied considerably among goats living in the same environment. Interspecies variation in the bacterial population was noticeably greater than intraspecies variation. In contrast, there was considerable variation in the ciliate population among goats within the same species, and intraspecies similarities were no greater than those observed across species. CONCLUSIONS: Because environmental factors and diets were identical for all goats, differences in bacterial populations reflect species-specific differences in rumen microbes. SIGNIFICANCE AND IMPACT OF THE STUDY: Factors related to the host species have an important effect on determining the bacterial composition in the goat rumen.     

应用PCR与温度梯度凝胶电泳分析龈上菌斑微生物群落

目的应用PCR与温度梯度凝胶电泳(PCR—TGGE)分子技术对成年健康口腔的龈上菌斑中微生物群落组成进行分析。方法8例成年个体包括4男4女,年龄19～29岁,分别采取每例个体上下颌牙周龈上菌斑样品,共18份(个体Subl间隔10天采集2次样品)。提取菌斑DNA,PCR扩增16SrDNAV3可变区,产物经TGGE后进行相似系数分析。结果同一个体的上下颌微生物群落组成相似性系数为81％～95％,而不同个体的龈上菌斑微生物群落组成相似性系数,均在60％以下。结论不同个体具有其独特的牙周微生物群落,而且在一定时期内组成稳定。     

云冈石窟石质文物表面及周边岩石样品中微生物群落分析

【目的】通过对云冈石窟石质文物表面及云冈石窟周边岩石样品中微生物的研究,建立可用于快速检测石质文物中微生物的方法。【方法】选取云冈石窟石质样品和云冈石窟周边岩石样品作为研究对象,应用PCR-DGGE技术对样品中的微生物群落结构进行了分析研究。【结果】根据系统发育树聚类分析,可以得出云冈石窟中检测出的微生物主要分为四大类群:γ-变形菌纲、鞘脂杆菌门、α-变形菌纲和放线菌纲;根据GenBank数据库中的序列比对结果,可以知道云冈石窟周边类似岩石样品中的微生物主要属于γ-变形菌纲、厚壁菌门和α-变形菌纲等。【结论】本实验成功检测出云冈石窟石质样品表面及云冈石窟周边岩石样品中的微生物类群,为云冈石窟的保护工作提供了有力依据,同时也证明了DEEG和分子克隆技术相结合的方法是检测石质文物中微生物群落结构的一种可操作性强、快速、准确的检测手段。     

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 production 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 gradient 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. andEthanologenbacterium sp.), β-proteobacteria (Acidovorax sp.), γ-proteobacteria (Kluyvera sp.), Bacteroides (uncultured bacterium SJA-168), and Spirochaetes (uncultured eubacterium E1-K13), respectively. The hydrogen production rate increased obviously with the increase ofEthanologenbacterium sp.,Clostridium sp. and uncultured Spirochaetes after 21 days, meanwhile the succession of ethanol type fermentation was formed. Throughout the succession the microbial diversity increased however it decreased after 21 days. Some types ofClostridium sp.Acidovorax sp.,Kluyvera sp., and Bacteroides were dominant populations during all periods of time. These special populations were essential for the construction of climax community. Hydrogen production efficiency was dependent on both hydrogen producing bacteria and other populations. It implied that the cometabolism of microbial community played a great role of biohydrogen production in the reactors.     

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

Biohydrogen production has been concerned ex-tremely as a new technology of energy resource pro-duction by many scientists[1—4]. Enhancement of hy-drogen production efficiency and cutting down the operating cost are very important problems, which are the limiting factors for the industrialization of hydro-gen production process. The fermentation hydrogen production technology offers a new method to resolve these difficulties[5—8]. Compared with photosynthetic hydrogen production possesses, f…     

Impacts of 2,4-D application on soil microbial community structure and on populations associated with 2,4-D degradation

The effect of 2,4-dichlorophenoxyacetic acid (2,4-D) application rate on microbial community structure and on the diversity of dominant 2,4-D degrading bacteria in an agricultural soil was examined using cultivation-independent molecular techniques coupled with traditional isolation and enumeration methods. Fingerprints of microbial communities established under increasing concentrations of 2,4-D (0-500 mg kg-1) in batch soil microcosms were obtained using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene segments. While a 2,4-D concentration of at least 100 mg kg-1 was required to obtain an apparent change in the community structure as visualized by DGGE, the greatest impact of 2,4-D concentration occurred in the 500 mg kg-1 treatment, resulting in significantly reduced diversity of the dominant populations and enrichment by Burkholderia-like populations. The greatest diversity of 2,4-D degrading isolates was cultivated from the 10 mg kg-1 treatment, indicating that under these conditions, cultivation was more sensitive than DGGE for detecting changes in community structure. Most of these isolates harbored homologs of Ralstonia eutrophus JMP134 and Burkholderia cepacia tfdA catabolic genes. Results from this study revealed that agriculturally relevant application rates of 2,4-D may provide a temporary selective advantage for organisms capable of utilizing 2,4-D as a carbon and energy source.     

不同覆土基质微生物结构特征研究及其对双孢蘑菇产量的影响

覆土是影响双孢蘑菇产量、质量和出菇整齐度的重要因子,利用现代分子生态学的方法快速、准确地对不同覆土基质微生物结构特征进行检测,以进一步了解微生物群落与双孢蘑菇相互作用关系。测定了不同覆土的理化特性,应用PCR技术对不同覆土材料提取总DNA,扩增细菌16S rDNA和真菌28S rDNA,运用变性梯度凝胶电泳技术对PCR产物进行分析,研究双孢蘑菇不同覆土基质微生物结构特征。结果表明：不同处理的覆土材料微生物群落的基因具有多样性,其中细菌群落基因多样性存在差异,使用纯泥炭与粉碎稻草处理差异最大,相似性仅为62%;通过真菌28S rDNA变性梯度凝胶电泳结果显示,粉碎稻草处理多样性指数最高,达3.576,但随着泥炭比例的提高,覆土处理中真菌群落的多样性相对减少;栽培试验发现,双孢蘑菇子实体形成量、总产量可能与覆土中的真菌群落多样性呈负相关。     

Summer warming accelerates sub‐arctic peatland nitrogen cycling without changing enzyme pools or microbial community structure

The balance of primary production and decomposition in northern peatlands may shift due to climate change, with potential feedbacks to atmospheric CO₂ concentrations. Nitrogen availability will modulate this shift, but little is known about the drivers of soil nitrogen dynamics in these environments. We used a long‐term (9 years) open top chamber (OTC) experiment in an ombrotrophic Sphagnum peat bog in sub‐arctic Sweden, to test for the interactive effects of spring warming, summer warming and winter snow addition on soil nitrogen fluxes, potential activities of nitrogen cycle enzymes, and soil microbial community composition. These simultaneous measurements allowed us to identify the level of organization at which climate change impacts are apparent, an important requirement for developing truly mechanistic understanding. Organic‐N pools and fluxes were an order of magnitude higher than inorganic‐N pools and fluxes. Summer warming approximately doubled fluxes of soil organic nitrogen and ammonia over the growing season. Such a large increase under 1 °C warming is unlikely to be due to kinetic effects, and we propose that it is linked to an observed seasonal decrease in microbial biomass, suggesting that N flux is driven by a substantial late‐season dieback of microbes. This change in N cycle dynamics was not reflected in any of the measured potential peptidase activities. Moreover, the soil microbial community structure was apparently stable across treatments, suggesting a non‐specific microbial dieback. Our results show that in these widespread peat bogs, where many plant species are capable of organic‐N uptake, organic soil N dynamics are quantitatively far more important than the commonly studied inorganic‐N dynamics. Understanding of climate change effects on organic soil N cycling in this system will be advanced by closer investigation of the seasonal dynamics of the microbial biomass and the input of substrates that maintain it.     

Reactor performance and microbial community of an EGSB reactor operated at 20 and 15°C

Aims:  To investigate the effects of low temperatures on the performance and microbial community of anaerobic wastewater treatment.
Methods and Results:  An expanded granular sludge bed (EGSB) reactor was employed to treat synthetic brewery wastewater at 20 and 15°C. Reactor performance was represented by chemical oxygen demand (COD) removal efficiency, while the microbial community was analysed using denaturing gradient gel electrophoresis (DGGE) and clone technology. When the hydraulic retention time (HRT) was maintained at 18 h, COD removal efficiencies above 85% were obtained at both 20 and 15°C, with influent COD concentrations up to 7300 and 4100 mg l⁻¹, respectively. At 15°C, the COD removal efficiency was more easily manipulated by increasing the influent COD concentration. DGGE and clone results for both temperatures revealed that Methanosaeta and Methanobacterium were two dominant methanogens, and that the majority of the eubacterial clones were represented by Firmicutes . When the temperature decreased from 20 to 15°C, both archaeal and eubacterial communities had higher diversity, and the proportion of Methanosaeta (acetate-utilizing methanogens) decreased markedly from 60·0% to 49·3%, together with an increase in proportions of hydrogen-utilizing methanogens (especially Methanospirillum ).
Conclusions:  The feasibility of psychrophilic anaerobic treatment of low and medium strength organic wastewaters was demonstrated, although lower temperature could significantly affect both reactor performance and the anaerobic microbial community.
Significance and Impact of the Study:  The findings enrich the theory involving the microbial community and the application of anaerobic treatment in a psychrophilic environment.     

云南不同海拔花椒园昆虫群落结构及动态

调查了4种不同海拔花椒园昆虫群落组成及结构的周年变化,应用群落特征参数及主分量分析方法分析了昆虫群落特征及其在时间过程中的主导因素和时间格局.结果表明,随着海拔的逐渐上升,昆虫群落中种类数量逐渐减少,种群数量相对增加,群落多样性、丰富度及均匀度等指数逐渐下降,随时间的变化而波动的趋势逐渐明显,主导昆虫群落变化的最主要因子由天敌亚群落的物种数和个体数量综合因子逐渐转向害虫亚群落的物种数和个体数量综合因子.     

接种微生物菌剂对猪粪堆肥过程中细菌群落多样性的影响

利用PCR-DGGE方法研究了接种外源微生物菌剂对鲜猪粪高温好氧堆肥过程中细菌群落多样性的影响.结果表明：接种外源微生物菌剂可以促进堆肥的顺利进行,比不接种处理的高温期提前2 d.DGGE图谱分析表明,堆肥中优势细菌群落组成发生了明显的更迭现象,不同堆肥时期细菌群落的Shannon-Wiener指数呈显著差异.目的条带克隆测序结果表明,整个堆肥过程Clostridium stercorarium subsp. thermolacticum sp.一直是优势菌属,不经培养细菌、Bacillus coagulans sp.、Clostridium thermocellum sp.在接种外源微生物菌剂处理的第10、16天成为优势菌属,不经培养的Firmicutes sp.和不经培养的 delta proteobacterium分别在未接种外源微生物菌剂处理堆肥发酵的第5天和第16天成为优势菌属.非优势菌属Ureibacillus thermosphaericus、不经培养的Silvimonas sp.出现在堆肥腐熟后期,不经培养的土壤细菌主要出现在堆肥初期和高温初期.UPGMC聚类分析表明,接种外源微生物菌剂明显影响了堆肥不同时期的细菌群落结构组成.堆肥化过程中细菌DGGE图谱主成分分析表明,细菌群落变化主要受外源接种微生物菌剂的影响.     

Polyphasic microbial community analysis of petroleum hydrocarbon-contaminated soils from two northern Canadian communities

The cold-adapted bacterial communities in petroleum hydrocarbon-contaminated and non-impacted soils from two northern Canadian environments, Kuujjuaq, Que., and Alert, Nunavut, were analyzed using a polyphasic approach. Denaturing gradient gel electrophoresis (DGGE) separation of 16S rDNA PCR fragments from soil total community DNA revealed a high level of bacterial diversity, as estimated by the total number of bands visualized. Dendrogram analysis clustered the sample sites on the basis of geographical location. Comparison of the overall microbial molecular diversity suggested that in the Kuujjuaq sites, contamination negatively impacted diversity whereas in the Alert samples, diversity was maintained or increased as compared to uncontaminated controls. Extraction and sequencing analysis of selected 16S rDNA bands demonstrated a range of similarity of 86-100% to reference organisms, with 63.6% of the bands representing high G+C Gram-positive organisms in the order Actinomycetales and 36.4% in the class Proteobacteria. Community level physiological profiles generated using Biolog GN plates were analyzed by cluster analysis. Based on substrate oxidation rates, the samples clustered into groups similar to those of the DGGE dendrograms, i.e. separation based upon geographic origin. The coinciding results reached using culture-independent and -dependent analyses reinforces the conclusion that geographical origin of the samples, rather than petroleum contamination level, was more important in determining species diversity within these cold-adapted bacterial communities.     

Bacterial community structure, compartmentalization and activity in a microbial fuel cell

AIMS: To characterize bacterial populations and their activities within a microbial fuel cell (MFC), using cultivation-independent and cultivation approaches. METHODS AND RESULTS: Electron microscopic observations showed that the fuel cell electrode had a microbial biofilm attached to its surface with loosely associated microbial clumps. Bacterial 16S rRNA gene libraries were constructed and analysed from each of four compartments within the fuel cell: the planktonic community; the membrane biofilm; bacterial clumps (BC) and the anode biofilm. Results showed that the bacterial community structure varied significantly between these compartments. It was observed that Gammaproteobacteria phylotypes were present at higher numbers within libraries from the BC and electrode biofilm compared with other parts of the fuel cell. Community structure of the MFC determined by analyses of bacterial 16S rRNA gene libraries and anaerobic cultivation showed excellent agreement with community profiles from denaturing gradient gel electrophoresis (DGGE) analysis. CONCLUSIONS: Members of the family Enterobacteriaceae, such as Klebsiella sp. and Enterobacter sp. and other Gammaproteobacteria with Fe(III)-reducing and electrochemical activity had a significant potential for energy generation in this system. SIGNIFICANCE AND IMPACT OF THE STUDY: This study has shown that electrochemically active bacteria can be enriched using an electrochemical fuel cell.     

浓香型白酒大曲微生物群落结构研究进展

大曲通常作为发酵剂用于酿造传统中国白酒,其提供各类微生物菌系和酶系启动白酒发酵,影响白酒风味和独特风格。近年来,对大曲微生物群落结构的研究成为研究热点,研究人员对大曲微生物群落结构、基因功能和功能微生物等进行了广泛而深入的研究,对大曲微生物组成、变迁规律和功能的认识逐渐清晰。本文综述了浓香型大曲微生物群落结构分析方法、主要微生物组成、重要功能微生物和微生物溯源,为研究大曲微生物群落结构、优化大曲生产工艺和改善白酒品质提供一定的理论依据。     

Effects of different sources of physically effective fiber on rumen microbial populations

Physically effective fiber is needed by dairy cattle to prevent ruminal acidosis. This study aimed to examine the effects of different sources of physically effective fiber on the populations of fibrolytic bacteria and methanogens. Five ruminally cannulated Holstein cows were each fed five diets differing in physically effective fiber sources over 15 weeks (21 days/period) in a Latin Square design: (1) 44.1% corn silage, (2) 34.0% corn silage plus 11.5% alfalfa hay, (3) 34.0% corn silage plus 5.1% wheat straw, (4) 36.1% corn silage plus 10.1% wheat straw, and (5) 34.0% corn silage plus 5.5% corn stover. The impact of the physically effective fiber sources on total bacteria and archaea were examined using denaturing gradient gel electrophoresis. Specific real-time PCR assays were used to quantify total bacteria, total archaea, the genus Butyrivibrio, Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens and three uncultured rumen bacteria that were identified from adhering ruminal fractions in a previous study. No significant differences were observed among the different sources of physical effective fiber with respect to the microbial populations quantified. Any of the physically effective fiber sources may be fed to dairy cattle without negative impact on the ruminal microbial community.