汾河入黄口夏季微生物群落结构分析

【背景】河流交汇区日益成为流域生态治理的焦点和热点之一。【目的】探明汾河入黄口微生物群落结构及其主要环境影响因子。【方法】应用16S rRNA基因Illumina MiSeq高通量测序技术,分析了汾河入黄口夏季微生物群落结构,并利用典范对应分析(Canonical correspondence analysis,CCA)了解影响微生物群落的主要环境因子。【结果】多样性指数分析表明该区域微生物群落多样性较高。微生物多样性分析发现优势菌门为变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)、拟杆菌门(Bacteroidetes)和放线菌门(Actinobacteria);在属分类水平上,相对丰度最高的菌属为芽孢杆菌属(Bacillus),其次为乳球菌属(Lactococcus)和hgcI_clade。Spearman相关性分析及典范对应分析表明环境因子对水体微生物群落结构具有显著影响。【结论】汾河与黄河微生物群落组成具有一定的差异,不同环境因子对不同微生物的影响程度不同,p H和溶解氧(Dissolved oxygen,DO)是汾河入黄口微生物群落结构的主要影响因子。     

Broad-scale approaches to the determination of soil microbial community structure: Application of the community DNA hybridization technique

Broad-scale approaches seek to integrate information on whole microbial communities. It is widely recognized that culture techniques are too selective and unrepresentative to allow a realistic assessment of the overall structure of microbial communities. Techniques based on fatty acid or metabolic profiles determine the phenotypic composition of the community. Complementary information about the genotypic structure of soil microbial communities necessitates analysis of community DNA. To determine broad-scale differences in soil microbial community structure (i.e., differences at the whole community level, rather than specific differences in species composition), we have applied a community hybridization technique to determine the similarity and relative diversity of two samples by cross hybridization. In previous studies this assay failed with whole-soil community DNA. Usable hybridization signals were obtained using whole-soil DNA, in this study, by digesting the DNA with restriction enzymes before the labeling with a random-primer reaction. The community hybridization technique was tested using a graded series of microbial fractions, increasing in complexity, all isolated from the same soil sample. This demonstrated that single bacterial species and a mixture of cultivable bacteria were less complex and only 5% similar to whole-community DNA or bacteria directly extracted from the soil. Extracted bacterial and whole-community DNA were 75% similar to each other and equally complex. When DNA was extracted from four different agricultural soils, their similarities ranged from 35 to 75%. The potential usefulness of community hybridization applied to soil microbial communities is discussed.     

黄土丘陵沟壑区地形变化对土壤微生物群落功能多样性的影响

研究黄土高原丘陵沟壑区破碎地形对土壤微生物功能多样性的影响,对于理解复杂地形区生态过程与系统功能的空间变化具有重要意义。选择陕西省安塞县陈家洼为研究区,依据坡面地形变化选择不同坡位土壤,采用Biolog微平板培养法探究地形变化对土壤微生物群落功能多样性的影响。实验发现,土壤微生物群落培养的平均颜色变化率(AWCD)增长曲线总的呈现出坡下部坡中部坡上部的规律,且坡下部AWCD值与坡中部、坡上部间差异显著(P0.05);坡下部土壤微生物群落功能多样性显著高于坡中部和坡上部,但不同土层深度(0—10 cm、10—20 cm)间无显著性差异(P0.05);对土壤微生物群落功能多样性差异贡献较大的碳源是糖类、羧酸类和多酚化合物类碳源;土壤含水率高低是不同坡位土壤微生物群落功能多样性差异显著的主要原因;微生物群落丰富度(H)和均一度(D)与土壤全氮含量正相关,优势度(U)反之,土壤全碳、全磷和p H对土壤微生物群落结构和功能多样性差异作用不显著。     

Impact of chromium-contaminated wastewaters on the microbial community of a river

The influence of chromium on the microbial community structure was analyzed in a river system subjected to long-term chromium contamination, by plating and by sequencing 16S rRNA genes cloned from DNA extracted from the river sediments. We also analyzed the influence of chromium on the ability of the microbial community to resist and reduce Cr(VI) and on its resistance to antibiotics. Shifts in the microbial community structure were analyzed by amplified ribosomal DNA restriction analysis fingerprinting. The isolates obtained were phylogenetically related to Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria, whereas Acidobacteria and Deltaproteobacteria were only revealed by clone analyses. Cr(VI)-resistant and Cr(VI)-reducing strains were isolated in all sites examined. However, each sample site had a microbial community with a different antibiotic resistance pattern. Our study seems to indicate that in this river ecosystem chromium influenced the microbial communities, altering some of their functional characteristics, such as the percentage of the microbial community able to resist or to reduce Cr(VI) and the phylogenetic groups isolated, but it did not affect the structural diversity. Furthermore, the concentration of Cr(VI) in the sediments could not be correlated with a lower number of bacteria or lower index of generic diversity, neither with the ability of the microbial community to resist or to reduce higher Cr(VI) concentrations.     

植被对土壤微生物群落结构的影响

研究了不同土壤及覆盖其上的植被与土壤微生物群落结构和多样性的关系．植被使土壤中的微生物种类更丰富,群落多样性更高．表层土壤微生物群落中没有明显的优势种群,种间竞争作用较弱．并介绍了研究土壤微生物群落的分子生物学方法．     

Microbial community changes during the bioremediation of creosote-contaminated soil

AIMS: To investigate the effects of aeration on the ex situ biodegradation of polycyclic aromatic hydrocarbons (PAHs) in creosote-contaminated soil and its effect on the microbial community present. METHODS AND RESULTS: Aerated and nonaerated microcosms of soil excavated from a former timber treatment yard were maintained and sampled for PAH concentration and microbial community changes by terminal restriction fragment length polymorphism (TRFLP) analysis. After an experimental period of just 13 days, degradation was observed with all the PAHs monitored. Abiotic controls showed no loss of PAH. Results unexpectedly showed greater loss of the higher molecular weight PAHs in the nonaerated control. This may have been due to the soil excavation causing initial decompaction and aeration and the resulting changes caused in the microbial community composition, indicated by TRFLP analysis showing several ribotypes greatly increasing in relative abundance. Similar changes in both microcosms were observed but with several possible key differences. The species of micro-organisms putatively identified included Bacilli, pseudomonad, aeromonad, Vibrio and Clostridia species. CONCLUSIONS: Excavation of the contaminated soil leads to decompaction, aeration and increased nutrient availability, which in turn allow microbial biodegradation of the PAHs and a change in the microbial community structure. SIGNIFICANCE AND IMPACT OF THE STUDY: Understanding the changes occurring in the microbial community during biodegradation of all PAHs is essential for the development of improved site remediation protocols. TRFLP allows useful monitoring of the total microbial community.     

岷江干旱河谷造林对土壤微生物群落结构的影响

为了探讨不同造林时间和立地条件对土壤微生物群落结构的影响,采用磷脂脂肪酸(PLFAs)法测定了岷江干旱河谷地区不同造林时间(2002、2006和2011年)及不同立地条件(退耕地和宜林荒山地)营建的岷江柏人工林土壤微生物生物量及群落结构的变化情况。结果表明:由于造林时间较短,不同造林时间的人工林间土壤化学性质没有差异,但土壤微生物生物量和各菌群生物量差异显著,且随着造林时间的增加而增加。不同立地条件下则表现为退耕还林地土壤微生物生物量和各菌群生物量较高。说明土壤微生物对外界因素变化的反映更灵敏。相关性分析结果显示土壤全氮含量与土壤微生物生物量及各菌群生物量显著相关,是影响土壤微生物群落结构的关键因素。     

Changes in functional diversity of soil microbial community with addition of antibiotics sulfamethoxazole and chlortetracycline

Potential effects of antibiotics on agricultural soil microflora have recently become increasing concerns with antibiotic-contaminated biosolid now being used in agricultural land. However, changes of soil microbial community function caused by the antibiotic-associated disturbance are less addressed. This paper investigated the changes in microbial functional diversity by spiking sulfamethoxazole (SMX) and chlortetracycline (CTC) in a loam paddy soil and then incubating for 21 days. The dose-effect and time-dependent changes of antibiotic-associated disturbance on soil microbial community were analyzed with the soils sampled at 7 and 21 days using Biolog EcoPlate. At day 7 following treatment, SMX decreased functional diversity of soil microbial community, and the treatment of 100 mg SMX kg?1 dry soil had a significant inhibition of average well color development (AWCD) and Shannon index as compared to the control (p?相似文献   

The effect of earthworms on the physiological state of the microbial community at vermicomposting

The effect of earthworms on the microbial community of composts and vermicomposts was assayed by the following parameters: mineralization activity, the levels of physiologically active and growing microbial biomass, the requirement for growth factors, and the spectrum of assimilation of organic substrates by the microbial community. The substrate affinities of microbial enzyme systems in vermicompost were found to be lower than in compost without earthworms, which is evidence of a higher amount of r-strategists in the microbial community of vermicomposts. Physiologically active biomass of microorganisms is higher in peat-based vermicompost than in compost. The microorganisms of vermicomposts and composts experience deficiency in growth factors to a lesser extent than the microorganisms in soil. The presence of earthworms influences the physiological diversity: the Shannon index increases or decreases depending on the type of composted substrate and incubation time. The growth rate of microorganisms increases on various test substrates in the presence of worms.     

土壤样品长期保存对微生物群落代谢活性和功能类群的影响

【目的】评估土壤长期保存(4个月)对土壤微生物群落代谢活性的影响。【方法】采用Biolog? EcoPlateTM生态板研究4 °C风干保存和?20 °C低温冻存的农田土壤和森林土壤中微生物群落的碳源利用模式。【结果】与新鲜土壤样品相比,长期保存的土壤样品的微生物群落对碳源的利用能力大大降低,其多样性、均匀度和Simpson指数均降低;风干保存和低温冻存两者对土壤微生物的碳源利用的影响没有显著差异;除风干保存的土壤样品中利用多聚物类的微生物类群的代谢活性外,两种保存方法显著降低微生物群落的代谢活性,降低幅度为54.5%–99.8%。【结论】长期保存土壤可能会导致对微生物群落信息的低估,土壤微生物代谢活性研究的最佳样品为新鲜 土壤。     

人体鼻咽部微生物群落多样性研究进展

定殖于鼻咽部的微生物与人体始终处于动态生态平衡,对于维持人体健康发挥着重要作用,也与多种上呼吸道疾病的发生发展有密切关系。鼻咽部微生物之间及其与宿主之间的相互作用是引发人体上呼吸道疾病的重要因素。微生物的培养方法与分子生物学技术的结合使人们越来越深入地了解人体鼻咽部微生物群落的组成和结构。定殖于人体鼻咽部的微生物以肺炎链球菌(Streptococcus pneumoniae)和流感嗜血杆菌(Haemophilus influenzae)等潜在致病菌为主。本文将分别从鼻咽部微生物与机体的平衡关系、鼻咽部微生物群落的研究方法以及鼻咽部微生物群落的组成及其相互关系三个方面,综述近年来鼻咽部微生物群落结构的相关研究进展,从而为指导实践提供可靠的理论依据。     

Application of the microbial community coalescence concept to riverine networks

Flows of water, soil, litter, and anthropogenic materials in and around rivers lead to the mixing of their resident microbial communities and subsequently to a resultant community distinct from its precursors. Consideration of these events through a new conceptual lens, namely, community coalescence, could provide a means of integrating physical, environmental, and ecological mechanisms to predict microbial community assembly patterns better in these habitats. Here, we review field studies of microbial communities in riverine habitats where environmental mixing regularly occurs, interpret some of these studies within the community coalescence framework and posit novel hypotheses and insights that may be gained in riverine microbial ecology through the application of this concept. Particularly in the face of a changing climate and rivers under increasing anthropogenic pressures, knowledge about the factors governing microbial community assembly is essential to forecast and/or respond to changes in ecosystem function. Additionally, there is the potential for microbial ecology studies in rivers to become a driver of theory development: riverine systems are ideal for coalescence studies because regular and predictable environmental mixing occurs. Data appropriate for testing community coalescence theory could be collected with minimal alteration to existing study designs.     

Plant Species Composition Effects on Belowground Properties and the Resistance and Resilience of the Soil Microflora to a Drying Disturbance

We hypothesised that plant species composition and richness would affect soil chemical and microbial community properties, and that these in turn would affect soil microbial resistance and resilience to an experimentally imposed drying disturbance. We performed a container experiment that manipulated the composition and species richness of common pasture plant species (Trifolium repens, Lolium perenne, and Plantago lanceolata) by growing them in monoculture, and in all the possible two and three-way combinations, along with an unplanted control soil. Experimental units were harvested at four different times over a 16-month period to determine the effect of plant community development and seasonal changes in temperature and moisture on belowground properties. Results showed that plant species composition influenced soil chemistry, soil microbial community properties and soil microbial resistance and resilience. Soil from planted treatments generally showed reduced soil microbial resistance to drying compared to unplanted control soils. Soils from under T. repens showed a higher resistance and resilience than the soils from under P. lanceolata, and a higher resistance than soils from under L. perenne. We suggest that differences across soils in either resource limitation or soil microbial community structure may be responsible for these results. Plant species richness rarely affected soil microbial community properties or soil microbial resistance and resilience, despite having some significant effects on plant community biomass and soil nitrogen contents in some harvests. The effect that treatments had for most variables differed between harvests, suggesting that results can be altered by the stage of plant community development or by extrinsic environmental factors that varied with harvest timing. These results in combination show that soil microbial resistance and resilience was affected by plant community composition, and the time of measurement, but was largely unrelated to plant species richness.     

Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns

Winogradsky columns are model microbial ecosystems prepared by adding pond sediment to a clear cylinder with additional supplements and incubated with light. Environmental gradients develop within the column creating diverse niches that allow enrichment of specific bacteria. The enrichment culture can be used to study soil and sediment microbial community structure and function. In this study we used a 16S rRNA gene survey to characterize the microbial community dynamics during Winogradsky column development to determine the rate and extent of change from the source sediment community. Over a period of 60 days, the microbial community changed from the founding pond sediment population: Cyanobacteria, Chloroflexi, Nitrospirae, and Planctomycetes increased in relative abundance over time, while most Proteobacteria decreased in relative abundance. A unique, light-dependent surface biofilm community formed by 60 days that was less diverse and dominated by a few highly abundant bacteria. 67–72% of the surface community was comprised of highly enriched taxa that were rare in the source pond sediment, including the Cyanobacteria Anabaena, a member of the Gemmatimonadetes phylum, and a member of the Chloroflexi class Anaerolinea. This indicates that rare taxa can become abundant under appropriate environmental conditions and supports the hypothesis that rare taxa serve as a microbial seed bank. We also present preliminary findings that suggest that bacteriophages may be active in the Winogradsky community. The dynamics of certain taxa, most notably the Cyanobacteria, showed a bloom-and-decline pattern, consistent with bacteriophage predation as predicted in the kill-the-winner hypothesis. Time-lapse photography also supported the possibility of bacteriophage activity, revealing a pattern of colony clearance similar to formation of viral plaques. The Winogradsky column, a technique developed early in the history of microbial ecology to enrich soil microbes, may therefore be a useful model system to investigate both microbial and viral ecology.     

Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH

Although soil pH has been shown to be an important factor driving microbial communities, relatively little is known about the other potentially important factors that shape soil-borne microbial community structure. This study examined plant and microbial communities across a series of neutral pH fields (pH=7.0-7.5) representing a chronosequence of secondary succession after former arable fields were taken out of production. These fields ranged from 17 to >66 years since the time of abandonment, and an adjacent arable field was included as a reference. Hierarchical clustering analysis, nonmetric multidimensional scaling and analysis of similarity of 52 different plant species showed that the plant community composition was significantly different in the different chronosequences, and that plant species richness and diversity increased with time since abandonment. The microbial community structure, as analyzed by phylogenetic microarrays (PhyloChips), was significantly different in arable field and the early succession stage, but no distinct microbial communities were observed for the intermediate and the late succession stages. The most determinant factors in shaping the soil-borne microbial communities were phosphorous and NH(4)(+). Plant community composition and diversity did not have a significant effect on the belowground microbial community structure or diversity.     

Microbial community shift with decabromodiphenyl ether (BDE 209) in sediments of the Pearl River estuary, China

To compare the effect of decabromodiphenyl ether (BDE 209) on microbial community from the Pearl River estuary, the microbial community at three in situ sites and the responses of microbial community to BDE-209 stressor were investigated. Denaturing gradient gel electrophoresis analysis of 16S rRNA gene showed that microbial community at site A2 has less diversity than sites A1 and A3. Physicochemical parameters (NH₄-N, salinity and SiO₃-Si) could significantly impact the microbial community composition in this estuary. In laboratory-incubated experiments, results indicated high concentration of BDE 209 (100 mg/kg) could increase the microbial diversity at sites A1 and A2, whereas reduced the microbial diversity at site A3. The unweighted pair group method with arithmetic means cluster analysis and principal component analysis demonstrated that the community structure changes at sites A1 and A2 were driven by the BDE 209 concentration, whereas at site A3 they depended on the incubation time. Thirty-five days after the addition of 100 mg/kg BDE 209, Firmicutes were found to be the dominant bacteria at sites A1 and A2. These data suggest the BDE 209 may have different effects on the microbial community in the Pearl River estuary.     

短程硝化活性污泥微生物群落结构及羟胺代谢对短程硝化的影响

活性污泥法随着技术的成熟,已应用在高氨氮污水/废水处理中,通过不断发展衍生出的很多新型工艺也成为研究热点,短程硝化反应作为代表已逐渐体现出优越性。短程硝化能达到高效净化污水的目的,其反应中的代谢产物羟胺也和微生物类群及反应产物之间有着至关重要的影响。反应器中活性污泥的微生物群落结构和动态密切相关,探究微生物群落结构能帮助生物强化、优化参数,提高脱氮效率。本文主要总结了近年来有关短程硝化/半短程硝化活性污泥微生物群落组成与结构及其与反应器处理效率之间的关系,以及羟胺代谢对短程硝化的影响等方面的研究进展,这些研究加深了对微生物群落结构和污水处理工艺之间的认识,但充分发掘生物信息、提高工艺效能之路仍然充满挑战,还需利用氮平衡方法、Real-time PCR法等多种生物技术手段对短程硝化进行全方位研究,为实践提供坚实的理论基础。     

Seasonal Dynamics of Microbial Community Composition and Function in Oak Canopy and Open Grassland Soils

Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (¹³C-PLFA). Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and ¹³C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling microbial community composition and function.     

rRNA-targeted寡核苷酸探针识别活性污泥微生物群落结构与功能研究进展

活性污泥中微生物群落内部关系非常复杂 ,及时对活性污泥中优势菌群和群落内部关系进行监测是污水处理中采取正确措施的关键。历史研究表明传统培养方法经常导致活性污泥优势菌群检测的失败 ,而r RNA- targeted寡核苷酸探针作为一种快速原位监测活性污泥微生物群落结构和功能的新工具被引入 ,使我们对参与污水净化的微生物群落结构和优势菌群能有较全面的了解。就该方法在识别除磷污泥、脱氮污泥、污泥泡沫和膨胀污泥中微生物群落结构和功能的典型应用进行综述 ,分析了该方法存在的优点和缺点 ,并对目前已建立且应用于活性污泥微生物检测的 r RNA- targeted寡核苷酸探针进行了详细总结