Reliability for detecting composition and changes of microbial communities by T-RFLP genetic profiling

Terminal restriction fragment length polymorphism (T-RFLP) analysis is commonly used for profiling microbial communities in various environments. However, it may suffer from biases during the analytic process. This study addressed the potential of T-RFLP profiles (1) to reflect real community structures and diversities, as well as (2) to reliably detect changing components of microbial community structures. For this purpose, defined artificial communities of 30 SSU rRNA gene clones, derived from nine bacterial phyla, were used. PCR amplification efficiency was one primary bias with a maximum variability factor of 3.5 among clones. PCR downstream analyses such as enzymatic restriction and capillary electrophoresis introduced a maximum bias factor of 4 to terminal restriction fragment (T-RF) signal intensities, resulting in a total maximum bias factor of 14 in the final T-RFLP profiles. In addition, the quotient between amplification efficiency and T-RF size allowed predicting T-RF abundances in the profiles with high accuracy. Although these biases impaired detection of real community structures, the relative changes in structures and diversities were reliably reflected in the T-RFLP profiles. These data support the suitability of T-RFLP profiling for monitoring effects on microbial communities.     

Spatiotemporal heterogeneity of plankton communities in Lake Donghu, China, as revealed by PCR–denaturing gradient gel electrophoresis and its relation to biotic and abiotic factors

The 16S and 18S rRNA genes of planktonic organisms derived from five stations with nutrient gradients in Lake Donghu, China, were studied by PCR–denaturing gradient gel electrophoresis (DGGE) fingerprinting, and the relationships between the genetic diversity of the plankton community and biotic/abiotic factors are discussed. The concentrations of total nitrogen (TN), total phosphorus (TP), NH₄-N and As were found to be significantly related ( P <0.05) to morphological composition of the plankton community. Both chemical and morphological analyses suggested that temporal heterogeneity was comparatively higher than spatial heterogeneity in Lake Donghu. Although the morphological composition was not identical to the DGGE fingerprints in characterizing habitat similarity, the two strongest eutrophic stations (I and II) were always initially grouped into one cluster. Canonical correspondence analysis suggested that the factors strongly correlated with the first two ordination axes were seasonally different. The concentrations of TN and TP and the densities of rotifers and crustaceans were generally the main factors related to the DGGE patterns of the plankton communities. The study suggested that genetic diversity as depicted by metagenomic techniques (such as PCR-DGGE fingerprinting) is a promising tool for ecological study of plankton communities and that such techniques are likely to play an increasingly important role in assessing the environmental conditions of aquatic habitats.     

Symptoms, Wood Lesions and Fungi Associated with Esca in Organic Vineyards in Languedoc-Roussillon (France)

We analysed symptoms, wood lesions and fungi associated with esca in mature organic vineyards in the Languedoc‐Roussillon region. Most previous surveys concerning esca syndrome were conducted in conventionally managed vineyards in other regions. We first found that esca may be present at a very low level in vineyards that were not treated with sodium arsenite. Affected vines displayed three types of symptoms: leaves with interveinal necrosis, wilt of entire branches and these two symptoms in combination. During the 3‐year survey, not all affected vines displayed symptoms every year and the same vine rarely displayed the same symptom or combination of symptoms in successive years. The incidence of esca appeared to be correlated with the percentage of vines that died during the survey but no correlation was found with either mortality before the survey or with the age of the vineyard. Observation of cross‐sections of a total of 210 vines with esca symptoms and isolation of fungi from the wood lesions led to similar results to those obtained in conventionally managed vineyards. Four different lesions were identified: a white rot lesion, a brown lesion in a central position, a brown lesion in a sectorial position and a scattered black spotting in healthy wood. The most frequently observed fungal species were Fomitiporia mediterranea (Fom), Phaeomoniella chlamydospora, Phaeoacremonium aleophilum and Eutypa lata. The white rot lesion caused by Fom was generally accompanied by one or more other lesions in the same vine. Similarly, Fom was generally isolated with one or several other fungi. No relationship was detected between the expression of external symptoms and any specific lesion or fungus. Our study also showed that esca and Eutypa dieback are often superimposed in our region of sampling.     

Phylogenetic characterization of bacterial consortia obtained of corroding gas pipelines in Mexico

Characterization of the microbial populations formed in gas pipelines is essential to understand the metallic surface-microbe interaction, their role in metal corrosion, and to implement efficient monitoring and control strategies. Microbial community analysis in a corroded gas pipeline in a petroleum-producing facility in the Southeast region in Mexico was performed by traditional cultivation techniques and identification based on 16S rRNA gene sequence. In all samples, thin bacterial biofilms were observed and pitting corrosion was reveled after removing the biofilms. Six pure or mixed cultures of anaerobic bacteria were obtained and their 16S rRNA libraries were constructed, respectively. At least two members of each RFLP profile were sequenced and the phylogenetic affiliations of cloned bacterial 16S rRNA genes indicated that native biofilms were mainly colonized by Desulfovibrio vulgaris and Desulfovibrio desulfuricans, sulfate-reducing bacteria members; Citrobacter freundii, an Enterobacteriaceae member; Clostridium celerecrescens and Clostridium sporogenes, spore-forming anaerobic species and Cetobacterium somerae, a microaerotolerant, non-spore-forming fusobacteria. Some of these species have been observed consistently in other steel pipelines previously, but Cetobacterium members and C. celerecrescens are described for the fist time in this corroded gas pipeline. The potential role of each species in biofilm formation and steel corrosion is discussed.     

Bacterial community diversity assessment in municipal solid waste compost amended soil using DGGE and ARISA fingerprinting methods

Bacterial community structure and diversity of Tunisian agricultural soil treated with different amounts of municipal solid waste compost (MSWC) and other fertilizers were studied using DGGE and ARISA fingerprinting methods. Sequence analysis of dominant DGGE bands revealed the presence of three major clusters, Cytophaga/Flexibacter/Bacteroides (CFB) group, Proteobacteria and Acidobacteria group. Using ARISA profiles, dominant populations were assigned to low and high GC Gram positive bacteria, Cyanobacteria, Spirochetes and Cytophagales. The two methods revealed the absence of significant bacterial community shifts related to the different MSWC applications. Moreover, indigenous bacterial population of the used loam-clayey soil was observed to limit proliferation and survival of Proteobacteria, initially dominant in MSWC and farmyard manure. Effectiveness of the two methods for soil bacterial community studying was shown. While DGGE was more accurate for bacterial identification, ARISA was more practical for handling and rapid estimation of dominant bacteria.     

Arthropod community diversity and trophic structure: a comparison between extremes of plant stress

Abstract.  1. Previous studies have shown that plant stress and plant vigour impact the preference and performance of many insect species. Global climate-change scenarios suggest that some regions such as continental interiors may become increasingly subject to severe drought. In combination, these two issues suggest that drought-driven plant stress may impact insect communities on a landscape scale. While there have been many population studies relating plant stress to the life history of individual herbivore species, far less is known about how plant stress affects entire communities.
2. To study the effect of plant stress on arthropod communities, arthropods were sampled from the canopies of pinyon pines ( Pinus edulis ) growing at sites with a history of chronically high environmental stress (e.g. lower water potentials, soil moisture, and reduced growth rates), and those growing under more favourable conditions. Sampling in these environments yielded >59 000 arthropods, representing 287 species from 14 orders and 80 families, and revealed three major community patterns.
3. First, chronic stress significantly altered community composition. Second, trees growing under high stress supported about 1/10th the number of arthropods, and roughly half the species as trees growing under more favourable conditions. Third, of the 33 abundant herbivore species that exhibited a significantly skewed distribution towards either high- or low-stress trees, 73% were skewed with higher numbers on low-stress trees.
4. The pattern of potentially reduced arthropod diversity and abundance on stressed pines observed in this study may further compound the loss of species resulting from the recent, landscape-scale drought-induced mortality of pines in the southwestern USA.     

高寒草甸植物群落中物种多样性与群落变异性的关系及其机制初探

通过对高寒草甸植物群落中采集的群落数据进行分析,探讨了物种构成的相似性、统计平均、种群变异性和净协方差等机制对形成高寒草甸植物群落中多样性与群落地上生物量变异性之间关系的影响。结果表明,地上生物量的年际变异性随着多样性的增加而减小。物种构成相似性是多样性一变异性负关系产生的原因之一,而相似性与多样性之间并无显著相关关系;统计平均效应是另一个多样性一变异性负关系的主要决定者;净协方差效应、种群变异性对多样性一变异性关系产生的影响不显著或非常有限。     

我国土壤动物群落生态学研究综述

总结了我国土壤动物群落生态学研究的特点,即区域分布集中于中国东部、研究的生态系统类型广泛、研究角度多种多样与应用研究发展迅速。并从土壤动物群落与环境关系、土壤动物群落的组成和多样性、土壤动物群落结构、土壤动物群落功能、土壤动物群落演替与受干扰生态系统的土壤动物群落6个方面综述其最新研究成果。在此基础上指出我国土壤动物群落生态学中有待开拓的研究领域是基础研究、特色区域和生态系统的研究、土地覆盖/土地利用对土壤动物的影响研究、土壤动物多样性及其保护研究、土壤动物在土壤生态系统和陆地生态系统物质循环和能量流动中的作用研究、全球变化响应研究与土壤动物应用研究。     

鼎湖山森林群落多样性垂直分布格局的研究

根据鼎湖山10 m×1 200 m的植物固定样带调查,沿海拔梯度对植物群落分布格局及生物多样性特性进行了分析。结果表明,本固定样带有3个森林类型,5个群落类型,构成一演替序列,但在垂直梯度上有交错现象。生物多样性指数为:乔木层,中生性阔叶林>针阔混交林>阳生性阔叶林;草本层,针阔混交林>阔叶林。阳性草本植物为主的草本群大部分生长在阳性树种为主的阔叶林和针阔混交林下,但是林下微环境变化对草本层植物优势度的影响也较大,以耐荫植物为主的草本群在阳性树种为主的阔叶林和针阔混交林也有分布,表明相同群落类型林下小环境的变化。     

淮南地区屋宇生态系粉螨群落组成和多样性研究

为了调查屋宇生态系中粉螨群落的物种组成和多样性,选取屋宇生态系中4种不同环境的灰尘进行粉螨采集、分类鉴定及数据分析。结果表明,44.9%标本发现粉螨,其中床面灰尘样本粉螨的阳性率为69%,地面灰尘粉螨的阳性率为52%,衣物灰尘粉螨的阳性率为32.5%和家具灰尘粉螨的阳性率为26%,检获粉螨14种,隶属于5科11属。多样性分析结果表明,4种环境的物种丰富度指数Rmargalef为0.400~1.170,Shannon-Wiener指数(H′)为1.574~2.480,Pielou指数(J)为0.967~0.978,说明温湿度及粉螨孳生食性对不同环境中粉螨群落的组成和多样性起直接限制作用,而人类干扰也是较为重要的影响因素。