Species Diversity of Periphyton Communities in the Littoral of a Temperate Lake

Species diversity of littoral periphyton sampled from Elk Lake (B. C., Canada) was dependent on station location and period of substrate exposure. Site differences were not statistically related to physico-chemical variables. However, diversity was negatively correlated with age of the communities and standing crop, and appeared to be associated with biological interaction or competition for available substrate surface. Further investigation revealed that the Shannon-Weaver index, as commonly applied, was inappropriate for data summarization since it reflected only the changes in evenness of the most abundant species. Components of the diversity index, as illustrated by the periphyton, were discussed.     

Diversity of Bacterial Communities in Container Habitats of Mosquitoes

We investigated the bacterial diversity of microbial communities in water-filled, human-made and natural container habitats of the mosquitoes Aedes aegypti and Aedes albopictus in suburban landscapes of New Orleans, Louisiana in 2003. We collected water samples from three classes of containers, including tires (n = 12), cemetery urns (n = 23), and miscellaneous containers that included two tree holes (n = 19). Total genomic DNA was extracted from water samples, and 16S ribosomal DNA fragments (operational taxonomic units, OTUs) were amplified by PCR and separated by denaturing gradient gel electrophoresis (DGGE). The bacterial communities in containers represented diverse DGGE-DNA banding patterns that were not related to the class of container or to the local spatial distribution of containers. Mean richness and evenness of OTUs were highest in water samples from tires. Bacterial phylotypes were identified by comparative sequence analysis of 90 16S rDNA DGGE band amplicons. The majority of sequences were placed in five major taxa: Alpha-, Beta- and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and an unclassified group; Proteobacteria and Bacteroidetes were the predominant heterotrophic bacteria in containers. The bacterial communities in human-made containers consisted mainly of undescribed species, and a phylogenetic analysis based on 16S rRNA sequences suggested that species composition was independent of both container type and the spatial distribution of containers. Comparative PCR-based, cultivation-independent rRNA surveys of microbial communities associated with mosquito habitats can provide significant insight into community organization and dynamics of bacterial species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Diversity of Planktonic and Attached Bacterial Communities in a Phenol-Contaminated Sandstone Aquifer

Polluted aquifers contain indigenous microbial communities with the potential for in situ bioremediation. However, the effect of hydrogeochemical gradients on in situ microbial communities (especially at the plume fringe, where natural attenuation is higher) is still not clear. In this study, we used culture-independent techniques to investigate the diversity of in situ planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer. Within the upper and lower plume fringes, denaturing gradient gel electrophoresis profiles indicated that planktonic community structure was influenced by the steep hydrogeochemical gradient of the plume rather than the spatial location in the aquifer. Under the same hydrogeochemical conditions (in the lower plume fringe, 30 m below ground level), 16S rRNA gene cloning and sequencing showed that planktonic and attached bacterial communities differed markedly and that the attached community was more diverse. The 16S rRNA gene phylogeny also suggested that a phylogenetically diverse bacterial community operated at this depth (30 mbgl), with biodegradation of phenolic compounds by nitrate-reducing Azoarcus and Acidovorax strains potentially being an important process. The presence of acetogenic and sulphate-reducing bacteria only in the planktonic clone library indicates that some natural attenuation processes may occur preferentially in one of the two growth phases (attached or planktonic). Therefore, this study has provided a better understanding of the microbial ecology of this phenol-contaminated aquifer, and it highlights the need for investigating both planktonic and attached microbial communities when assessing the potential for natural attenuation in contaminated aquifers.     

Minerals Affect the Specific Diversity of Forest Soil Bacterial Communities

Minerals constitute an ecological niche poorly investigated in the soil, in spite of their important role in biogeochemical cycles and plant nutrition. To evaluate the impact of minerals on the structure of the soil bacterial communities, we compared the bacterial diversity on mineral surfaces and in the surrounding soil. Three pure and calibrated minerals (apatite, plagioclase and a mix of phlogopite-quartz) were buried into the organo-mineral layer of a forest soil. After a 4-year incubation in soil conditions, mineral weathering and microbial colonization were evaluated. Apatite and plagioclase were the only two significantly weathered minerals. The analysis of the 16S rRNA gene sequences generated by the cloning-sequencing procedure revealed that bacterial diversity was higher in the surrounding soil and on the unweathered phlogopite-quartz samples compared with the other minerals. Moreover, a multivariate analysis based on the relative abundance of the main taxonomic groups in each compartments of origin demonstrated that the bacterial communities from the bulk soil differed from that colonizing the minerals. A significant correlation was obtained between the dissolution rate of the minerals and the relative abundance of Beta-proteobacteria detected. Notably, many sequences coming from bacteria colonizing the mineral surfaces, whatever the mineral, harbored high similarity with efficient mineral weathering bacteria belonging to Burkholderia and Collimonas genera, previously isolated on the same experimental site. Taken together, the present results provide new highlights concerning the bacterial communities colonizing minerals surfaces in the soil and suggests that the minerals create true ecological niches: the mineralosphere.     

Distinctive Bacterial Communities in the Rhizoplane of Four Tropical Tree Species

It is known that the microbial community of the rhizosphere is not only influenced by factors such as root exudates, phenology, and nutrient uptake but also by the plant species. However, studies of bacterial communities associated with tropical rainforest tree root surfaces, or rhizoplane, are lacking. Here, we analyzed the bacterial community of root surfaces of four species of native trees, Agathis borneensis, Dipterocarpus kerrii, Dyera costulata, and Gnetum gnemon, and nearby bulk soils, in a rainforest arboretum in Malaysia, using 454 pyrosequencing of the 16S rRNA gene. The rhizoplane bacterial communities for each of the four tree species sampled clustered separately from one another on an ordination, suggesting that these assemblages are linked to chemical and biological characteristics of the host or possibly to the mycorrhizal fungi present. Bacterial communities of the rhizoplane had various similarities to surrounding bulk soils. Acidobacteria, Alphaproteobacteria, and Betaproteobacteria were dominant in rhizoplane communities and in bulk soils from the same depth (0–10?cm). In contrast, the relative abundance of certain bacterial lineages on the rhizoplane was different from that in bulk soils: Bacteroidetes and Betaproteobacteria, which are known as copiotrophs, were much more abundant in the rhizoplane in comparison to bulk soil. At the genus level, Burkholderia, Acidobacterium, Dyella, and Edaphobacter were more abundant in the rhizoplane. Burkholderia, which are known as both pathogens and mutualists of plants, were especially abundant on the rhizoplane of all tree species sampled. The Burkholderia species present included known mutualists of tropical crops and also known N fixers. The host-specific character of tropical tree rhizoplane bacterial communities may have implications for understanding nutrient cycling, recruitment, and structuring of tree species diversity in tropical forests. Such understanding may prove to be useful in both tropical forestry and conservation.     

Species Diversity and Substrate Utilization Patterns of Thermophilic Bacterial Communities in Hot Aerobic Poultry and Cattle Manure Composts

This study investigated the species diversity and substrate utilization patterns of culturable thermophilic bacterial communities in hot aerobic poultry and cattle manure composts by coupling 16S rDNA analysis with Biolog data. Based on the phylogenetic relationships of 16S rDNA sequences, 34 thermophilic (grown at 60 degrees C) bacteria isolated during aerobic composting of poultry manure and cattle manure were classified as Bacillus licheniformis, B. atrophaeus, Geobacillus stearothermophilus, G. thermodenitrificans, Brevibacillus thermoruber, Ureibacillus terrenus, U. thermosphaericus, and Paenibacillus cookii. In this study, B. atrophaeus, Br. thermoruber, and P. cookii were recorded for the first time in hot compost. Physiological profiles of these bacteria, obtained from the Biolog Gram-positive (GP) microplate system, were subjected to principal component analysis (PCA). All isolates were categorized into eight different PCA groups based on their substrate utilization patterns. The bacterial community from poultry manure compost comprised more divergent species (21 isolates, seven species) and utilized more diverse substrates (eight PCA groups) than that from cattle manure compost (13 isolates, five species, and four PCA groups). Many thermophilic bacteria isolated in this study could use a variety of carboxylic acids. Isolate B110 (from poultry manure compost), which is 97.6% similar to U. terrenus in its 16S rDNA sequence, possesses particularly high activity in utilizing a broad spectrum of substrates. This isolate may have potential applications in industry.     

Bacterial Communities in Central European Bumblebees: Low Diversity and High Specificity

Recent studies on the microbial flora of the honeybee gut have revealed an apparently highly specific community of resident bacteria that might play a role in immune defence and food preservation for their hosts. However, at present, very little is known about the diversity and ecology of bacteria occurring in non-domesticated bees like bumblebees, which are of similar importance as honeybees for the pollination of agricultural and wild flowers. To fill this gap in knowledge, we examined six of the most common bumblebee species in Central Europe from three locations in Germany and Switzerland for their bacterial communities. We used a culture-independent molecular approach based on sequencing the 16S rRNA gene from a selection of individuals and examining a larger number of samples by terminal restriction fragment length polymorphism profiles. The gut flora was dominated by very few and mostly undescribed groups of bacteria belonging to the Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria. This core set of bacteria was present in all of the examined bumblebee species. These bacteria are similar to, but distinct from, bacteria previously described from the honeybee gut. Significant differences were observed between the communities of bacteria in the different bumblebee species; the effect of sampling location was less strong. A novel group of Betaproteobacteria additionally shows evidence for host species-specific genotypes. The gut flora of bumblebees therefore is apparently composed of relatively few highly specialized bacteria, indicating a strong interaction and possibly important functions with their hosts.     

Diversity of Bacterial Communities in a Profile of a Winter Wheat Field: Known and Unknown Members

In soils, bacteria are very abundant and diverse. They are involved in various agro-ecosystem processes such as the nitrogen cycle, organic matter degradation, and soil formation. Yet, little is known about the distribution and composition of bacterial communities through the soil profile, particularly in agricultural soils, as most studies have focused only on topsoils or forest and grassland soils. In the present work, we have used bar-coded pyrosequencing analysis of the V3 region of the 16S rRNA gene to analyze bacterial diversity in a profile (depths 10, 25, and 45 cm) of a well-characterized field of winter wheat. Taxonomic assignment was carried out with the Ribosomal Database Project (RDP) Classifier program with three bootstrap scores: a main run at 0.80, a confirmation run at 0.99, and a run at 0 to gain information on the unknown bacteria. Our results show that biomass and bacterial quantity and diversity decreased greatly with depth. Depth also had an impact, in terms of relative sequence abundance, on 81 % of the most represented taxonomic ranks, notably the ranks Proteobacteria, Bacteroidetes, Actinobacteridae, and Acidobacteria. Bacterial community composition differed more strongly between the topsoil (10 and 25 cm) and subsoil (45 cm) than between levels in the topsoil, mainly because of shifts in the carbon, nitrogen, and potassium contents. The subsoil also contained more unknown bacteria, 53.96 % on the average, than did the topsoil, with 42.06 % at 10 cm and 45.59 % at 25 cm. Most of these unknown bacteria seem to belong to Deltaproteobacteria, Actinobacteria, Rhizobiales, and Acidobacteria.     

闽北地区森林群落物种多样性的测定

采用8个物种多样性指数对闽北地区的8个森林群落类型物种多样性进行测定,并选用4个种一多度关系模型(对数正态分布、Weibull分布、对数级数分布、生态位优先占领模型)分析其物种-多度关系,把多样性指数与对数正态分布、Weibull分布和生态位优先占领模型的有关参数进行线性回归,以分析多度模型参数描述物种多样性的可行性。结果表明：(1)多数物种多样性指数对群落的测度是一致的,(2)对数正态分布、Weibull分布和生态位优先占领模型对8个群落的物种多度拟合效果很好;(3)对数正态分布、Weibull分布和生态位优先占领模型有关模型参数与部分物种多样性指数的线性关系达显著或极显著水平。通过闽北地区8个类型森林群落物种多样性指数测定,使生物多样性较准确地数量化,同时还说明采用改进单纯形法进行非线性分布函数的拟合是简单有效的,可推广应用。     

浙江仙居俞坑森林群落物种多样性研究

分别采用物种丰富度、物种多样性指数和群落均匀度指标对浙江省仙居县俞坑森林群落的物种多样性进行测定和分析。结果表明：本木植物的物种多样性以生境优越的常绿阔叶林为高,木本植物的物种丰富度、物种多样性指数明显大于草本植物。在群落垂直结构中,木本植物等2层的物种丰富度、物种多样性指数均显著大于第1层。物种丰富度以木本第3层最大,草本层最小;而物种多样性指数、群落均匀度则以木本第2层最大、草本层最小。木本植物各层次、草本层的物种多样性各项指标在群落各样地间均有一定的差异。     

Bacterial Diversity in Attached Communities of a Cold High-Sulfide Water Body in European Russia

Microbiology - Bacterial diversity in attached communities of the anoxic part of the Solodovka wetland (Samara region, Russia), which feeds on cold karst springs with a high (>3 mM) sulfide...     

北京山区辽东栎（Quercus liaotungensis）群落物种多样性的研究

根据８３块样地资料,研究了北京山区辽东栎群落的数量分类与排序及其与群落的物种多样性关系,发现ＤＣＡ排序轴的第１轴与群落的物种多样性关系密切,并证明了群落的各类生长型多样性指数应是一个整体。群落的物种丰富度和多样性指数随海拔升高总的变化趋势是上升的,但有较大的波动,而均匀度指数则呈较稳定的上升趋势。研究结果还证明了北京山区辽东栎群落不同演替阶段的多样性动态符合群落演替过程中多样性动态的一般规律。     

Effects of Plant Biomass, Plant Diversity, and Water Content on Bacterial Communities in Soil Lysimeters: Implications for the Determinants of Bacterial Diversity

Soils may comprise tens of thousands to millions of bacterial species. It is still unclear whether this high level of diversity is governed by functional redundancy or by a multitude of ecological niches. In order to address this question, we analyzed the reproducibility of bacterial community composition after different experimental manipulations. Soil lysimeters were planted with four different types of plant communities, and the water content was adjusted. Group-specific phylogenetic fingerprinting by PCR-denaturing gradient gel electrophoresis revealed clear differences in the composition of Alphaproteobacteria, Betaproteobacteria, Bacteroidetes, Chloroflexi, Planctomycetes, and Verrucomicrobia populations in soils without plants compared to that of populations in planted soils, whereas no influence of plant species composition on bacterial diversity could be discerned. These results indicate that the presence of higher plant species affects the species composition of bacterial groups in a reproducible manner and even outside of the rhizosphere. In contrast, the environmental factors tested did not affect the composition of Acidobacteria, Actinobacteria, Archaea, and Firmicutes populations. One-third (52 out of 160) of the sequence types were found to be specifically and reproducibly associated with the absence or presence of plants. Unexpectedly, this was also true for numerous minor constituents of the soil bacterial assemblage. Subsequently, one of the low-abundance phylotypes (beta10) was selected for studying the interdependence under particular experimental conditions and the underlying causes in more detail. This so-far-uncultured phylotype of the Betaproteobacteria species represented up to 0.18% of all bacterial cells in planted lysimeters compared to 0.017% in unplanted systems. A cultured representative of this phylotype exhibited high physiological flexibility and was capable of utilizing major constituents of root exudates. Our results suggest that the bacterial species composition in soil is determined to a significant extent by abiotic and biotic factors, rather than by mere chance, thereby reflecting a multitude of distinct ecological niches.     

Disturbance Promotes Non-Indigenous Bacterial Invasion in Soil Microcosms: Analysis of the Roles of Resource Availability and Community Structure

Background

Invasion-biology is largely based on non-experimental observation of larger organisms. Here, we apply an experimental approach to the subject. By using microbial-based microcosm-experiments, invasion-biology can be placed on firmer experimental, and hence, less anecdotal ground. A better understanding of the mechanisms that govern invasion-success of bacteria in soil communities will provide knowledge on the factors that hinder successful establishment of bacteria artificially inoculated into soil, e.g. for remediation purposes. Further, it will yield valuable information on general principles of invasion biology in other domains of life.

Methodology/Principal Findings

Here, we studied invasion and establishment success of GFP-tagged Pseudomonas fluorescens DSM 50090 in laboratory microcosms during a 42-day period. We used soil heating to create a disturbance gradient, and hypothesized that increased disturbance would facilitate invasion; our experiments confirmed this hypothesis. We suggest that the key factors associated with the heating disturbance that explain the enhanced invasion success are increased carbon substrate availability and reduced diversity, and thus, competition- and predation-release. In a second experiment we therefore separated the effects of increased carbon availability and decreased diversity. Here, we demonstrated that the effect of the indigenous soil community on bacterial invasion was stronger than that of resource availability. In particular, introduced bacteria established better in a long term perspective at lower diversity and predation pressure.

Conclusion

We propose increased use of microbial systems, for experimental study of invasion scenarios. They offer a simple and cost-efficient way to study and understand biological invasion. Consequently such systems can help us to better predict the mechanisms controlling changes in stability of communities and ecosystems. This is becoming increasingly relevant since anthropogenic disturbance causes increasing global change, which promotes invasion. Moreover, a thorough understanding of factors controlling invasion and establishment of artificially amended micro-organisms will mean a major step forward for soil-remediation microbiology.     

拉鲁湿地主要植物群落结构及物种多样性

2002年6~9月对拉鲁湿地植物种类、群落结构、生物量以及物种多样性进行了调查研究.结果表明:(1)拉鲁湿地共有植物30科52属85种,主要有芦苇[Phragmites australis(Cav.)Trin.ex Steud.](A)、尼伯尔酸模(RumexnepalensisSpreng)(B)、水葱(Scirpus validusVahl)(C)、穗状狐尾藻(MyriophyllumspicatumL.)(D)、灯芯草(Juncus effususL.)(E)、针叶苔草(CarexonoeiFranch.et Sav.)和黑褐苔草(CarexatrofuscaSchkuhr)(F)、藏北嵩草(KobresialittledaleiC.B.Clarke)(G)、藏蓟[Cirsiumlanatum(Roxb.ex Willd.)Spreng.](H)等8个主要植物群落.(2)在8个主要植物群落中,嵩草群落所含物种数最多,为44种,穗状狐尾藻群落最少,仅8种;芦苇群落生物量最高,为124.5~1 027.0 g/m2,藏蓟群落生物量最低,为124.5~220.5 g/m2;优势种芦苇的生物量最高,为183.5~660.0 g/m2,藏蓟生物量最低,为43.1~76.3 g/m2.(3)各群落的垂直结构特点是:芦苇群落、水葱群落、穗状狐尾藻群落具有挺水层、浮叶层和沉水层,其他群落只具有可分为高、低两层的草本层.(4)在各群落的相似性方面,嵩草群落与藏蓟群落、水葱群落与芦苇群落和尼伯尔酸模群落的相似性要明显高于其他群落,其Jaccard系数分别为0.549 0、0.538 5、0.500 0;芦苇群落、尼伯尔酸模群落、水葱群落、穗状狐尾藻群落与藏蓟群落以及芦苇群落、穗状狐尾藻群落与嵩草群落在建群种上没有相似之处,Jaccard系数为0.     

太行山南段森林群落物种多样性研究

分别用多样性指数、丰富度指数、均匀度指数对山西太行山南段森林群落的物种多样性及其与环境的关系进行了分析.结果表明:(1)3个植被型的物种多样性指数的顺序为:落叶阔叶林>温性针阔叶混交林>温性针叶林.(2)落叶阔叶林中各群系的物种多样性指数的顺序为:漆树 青麸杨林>鹅耳枥 青榨槭林>青檀林>辽东栎林>栓皮栎林>白桦林>红桦林>山杨 白桦林.(3)温性针叶林中各群系的物种多样性指数的顺序为南方红豆杉林>油松林>白皮松林>侧柏林.(4)物种丰富度指数在群落梯度上的总体趋势表现为草本层>灌木层>乔木层;多样性指数的趋势则为灌木层>乔木层>草本层;各群落灌木层物种均匀度指数大于乔木层和草本层,乔木层均匀度与草本层相差不明显.(5)各群落多样性指数在海拔梯度上表现出明显的规律,呈单峰曲线变化,即中等海拔高度上的群落物种多样性较高,而高海拔和低海拔多样性较低,这主要是由于在中海拔(大约1 500 m)地段水热条件组合较好、人类活动干扰较少所致.     

Diversity and Structure of Bacterial Communities in Arctic versus Antarctic Pack Ice

A comprehensive assessment of bacterial diversity and community composition in arctic and antarctic pack ice was conducted through cultivation and cultivation-independent molecular techniques. We sequenced 16S rRNA genes from 115 and 87 pure cultures of bacteria isolated from arctic and antarctic pack ice, respectively. Most of the 33 arctic phylotypes were >97% identical to previously described antarctic species or to our own antarctic isolates. At both poles, the α- and γ-proteobacteria and the Cytophaga-Flavobacterium group were the dominant taxonomic bacterial groups identified by cultivation as well as by molecular methods. The analysis of 16S rRNA gene clone libraries from multiple arctic and antarctic pack ice samples revealed a high incidence of closely overlapping 16S rRNA gene clone and isolate sequences. Simultaneous analysis of environmental samples with fluorescence in situ hybridization (FISH) showed that ~95% of 4′,6′-diamidino-2-phenylindole (DAPI)-stained cells hybridized with the general bacterial probe EUB338. More than 90% of those were further assignable. Approximately 50 and 36% were identified as γ-proteobacteria in arctic and antarctic samples,respectively. Approximately 25% were identified as α-proteobacteria, and 25% were identified as belonging to the Cytophaga-Flavobacterium group. For the quantification of specific members of the sea ice community, new oligonucleotide probes were developed which target the genera Octadecabacter, Glaciecola, Psychrobacter, Marinobacter, Shewanella, and Polaribacter. High FISH detection rates of these groups as well as high viable counts corroborated the overlap of clone and isolate sequences. A terrestrial influence on the arctic pack ice community was suggested by the presence of limnic phylotypes.