Microbial Community Structure and Metabolic Potential of the Hyporheic Zone of a Large Mid-Stream Channel Bar

Abstract

To develop a greater understanding of hyporheic zone microbial biogeochemistry, we sampled pore fluids from a piezometer array associated with the McCarran Ranch channel bar (MRCB); a partially submerged cobble island in the Truckee River, NV, USA. Flowing surface water and pumped pore fluids were characterized by prokaryotic community structure, metabolic potential, and aqueous physicochemistry. Concentrations of potential respiratory electron acceptors were highest in surface water and riverbed porewater and sequentially depleted in porewaters along the inferred flowpath (O₂, then NO₃^?, then SO₄^2?). Correspondingly, cultivable nitrate reducers/denitrifiers were most abundant in surface water and riverbed porewater, despite oxic conditions. Cultivable sulfate reducers were overall most abundant in surface water. Prokaryotic community reconstruction from 16S rRNA gene sequences indicates that the surface water community was less diverse than that of porewater and supports a shift in metabolic strategy, from aerobic heterotrophy in surface water (e.g., Comamonadaceae and Sporichthyaceae) to chemolithotrophy and anaerobic metabolisms (e.g., Hydrogenophaga spp., Ferribacterium spp., Methanobacterium spp.) along the hyporheic flow path. These data indicate that prokaryotic communities within the MRCB are phylogenetically and metabolically diverse and contribute to biogeochemical cycling in this common yet relatively understudied habitat.     

Microbial Community Dynamics Associated with Rhizosphere Carbon Flow

Root-deposited photosynthate (rhizodeposition) is an important source of readily available carbon (C) for microbes in the vicinity of growing roots. Plant nutrient availability is controlled, to a large extent, by the cycling of this and other organic materials through the soil microbial community. Currently, our understanding of microbial community dynamics associated with rhizodeposition is limited. We used a ¹³C pulse-chase labeling procedure to examine the incorporation of rhizodeposition into individual phospholipid fatty acids (PLFAs) in the bulk and rhizosphere soils of greenhouse-grown annual ryegrass (Lolium multiflorum Lam. var. Gulf). Labeling took place during a growth stage in transition between active root growth and rapid shoot growth on one set of plants (labeling period 1) and 9 days later during the rapid shoot growth stage on another set of plants (labeling period 2). Temporal differences in microbial community composition were more apparent than spatial differences, with a greater relative abundance of PLFAs from gram-positive organisms (i15:0 and a15:0) in the second labeling period. Although more abundant, gram-positive organisms appeared to be less actively utilizing rhizodeposited C in labeling period 2 than in labeling period 1. Gram-negative bacteria associated with the 16:1ω5 PLFA were more active in utilizing ¹³C-labeled rhizodeposits in the second labeling period than in the first labeling period. In both labeling periods, however, the fungal PLFA 18:2ω6,9 was the most highly labeled. These results demonstrate the effectiveness of using ¹³C labeling and PLFA analysis to examine the microbial dynamics associated with rhizosphere C cycling by focusing on the members actively involved.     

Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity

The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum), another by a shrub (Rhamnus davurica), and the third by a tree (Ailanthus altissima). The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs) closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that nitrogen cycling bacteria and functions are important factors in plant invasions. Whether the changes in microbial communities are driven by direct plant microbial interactions or a result of plant-driven changes in soil properties remains to be determined.     

Microbial Community Structure and Denitrification in a Wetland Mitigation Bank

Wetland mitigation is implemented to replace ecosystem functions provided by wetlands; however, restoration efforts frequently fail to establish equivalent levels of ecosystem services. Delivery of microbially mediated ecosystem functions, such as denitrification, is influenced by both the structure and activity of the microbial community. The objective of this study was to compare the relationship between soil and vegetation factors and microbial community structure and function in restored and reference wetlands within a mitigation bank. Microbial community composition was assessed using terminal restriction fragment length polymorphism targeting the 16S rRNA gene (total bacteria) and the nosZ gene (denitrifiers). Comparisons of microbial function were based on potential denitrification rates. Bacterial community structures differed significantly between restored and reference wetlands; denitrifier community assemblages were similar among reference sites but highly variable among restored sites throughout the mitigation bank. Potential denitrification was highest in the reference wetland sites. These data demonstrate that wetland restoration efforts in this mitigation bank have not successfully restored denitrification and that differences in potential denitrification rates may be due to distinct microbial assemblages observed in restored and reference (natural) wetlands. Further, we have identified gradients in soil moisture and soil fertility that were associated with differences in microbial community structure. Microbial function was influenced by bacterial community composition and soil fertility. Identifying soil factors that are primary ecological drivers of soil bacterial communities, especially denitrifying populations, can potentially aid the development of predictive models for restoration of biogeochemical transformations and enhance the success of wetland restoration efforts.Wetlands provide more ecosystem services (e.g., flood control, water purification, nutrient cycling, and habitat for wildlife) per hectare than any other ecosystem (16). Riparian wetlands, in particular, are sites of intense biogeochemical activity and play an important role in improving water quality, recycling nutrients, and detoxifying chemicals (41). Changing patterns of land use over the last century have resulted in the loss of over half of the wetlands in the contiguous United States (17) and about 60% of wetlands in the Midwestern United States (82). The loss of ecosystem services through conversion of wetlands to alternative (primarily agricultural) land uses exacerbates nutrient pollution and eutrophication of downstream ecosystems (57). Declines in wetland acreage have continued despite a federal policy goal of no-net-loss of wetland acreage and function adopted in 1990 (7, 55). Wetland mitigation projects provide compensation for impacted wetlands and aim to replace the critical functions provided by wetlands. Despite decades of wetland mitigation, however, restoration efforts frequently fail to reestablish desired levels of ecosystem services. Restoration outcomes remain uncertain, and more information is necessary in order to improve monitoring and assessment of wetland development (13, 18, 50, 80).One approach to wetland compensation is through mitigation banks. These sites are areas that are restored, established, enhanced, or preserved for replacement of wetlands that will be affected by future land use change. Mitigation banks are considered “third-party” compensatory mitigation, where the permittee (e.g., developer planning to destroy a wetland) is responsible for purchasing wetland credits in acreage, but the wetland bank is established and managed by another party (24). Wetland mitigation banks have unique characteristics that distinguish them from smaller individual restoration projects (7, 69, 81). Due to their size, wetland mitigation banks are especially heterogeneous and may have a great deal of within-site variability in hydrology and nutrient status, making it challenging to implement a single restoration design. Thus, wetland mitigation banks require intense management and monitoring for improved success (7, 69, 81).Restoration efforts such as mitigation banks aim to replace chemical, physical, and biological ecosystem functions of wetlands that have been lost through anthropogenic disturbance (24). Monitoring of wetland mitigation sites has largely focused on measures of macro-scale community structure (e.g., vegetation surveys) (52) along with measures of hydrology and soil type (24). Measurement of vegetation is a common proxy for wetland performance but does not provide an accurate assessment of wetland function (6, 52). Quantitative assessment is achievable, however, for ecosystem services such as water quality improvement through nitrate removal, where well-characterized microbial mechanisms underlie denitrification processes.The link between microbial community structure and function in a restoration context is a topic of current interest (33). Relating microbial community composition and dynamics to chemical, physical, and biological variables can help to reveal important ecological drivers of microbial communities and their activities (26, 35, 42). Conserved bacterial functional genes related to specific biogeochemical transformations allow evaluation of the community structure of microbial populations directly involved in these processes (49, 60, 63, 77, 79). Assessing the diversity of microorganisms that are specifically involved in denitrification is possible through amplification of the nosZ gene, which encodes the catalytic subunit of nitrous oxide reductase, the enzyme responsible for the final step of denitrification (60, 63, 66). Phylogenetically diverse microorganisms can carry out denitrification though the majority of previously described denitrifiers belong to subphyla within the Proteobacteria (53, 56, 60, 61). Denitrification is a facultative process that occurs only under anaerobic conditions (53, 75). Complete denitrification to N₂ is more prevalent in anaerobic, saturated wetland ecosystems (14, 76), and incomplete denitrification to N₂O is the less desirable, more common endpoint of denitrification under more aerobic, drier conditions (14, 62). While the environmental factors (e.g., oxygen, carbon, nitrate, and pH) that influence bulk denitrification rates have been well characterized (31, 72), the influence of these factors on the composition of denitrifier communities, particularly in a restoration context, is unclear. Understanding the relationship between the microbial populations responsible for nitrogen transformations and easily measured environmental parameters (e.g., soil chemical and physical measures) could lead to assessment metrics that are linked directly to ecosystem functions such as denitrification and bridge the current gap in functional assessment methods (36, 60, 70).The objectives of this study were (i) to compare the microbial and plant community composition in restored wetlands to the composition in adjacent reference floodplain forest wetlands; (ii) to assess the relationship between microbial community composition (based on terminal restriction fragment length polymorphism [T-RFLP]) and potential denitrification activity throughout the mitigation bank; and (iii) to examine soil factors correlated with microbial community composition using both phylogenetic and functional gene markers. As soil environmental conditions affect microbial community structure and activity, we expected that sites where wetland hydrology and soil chemistry have been successfully restored would harbor microbial assemblages that are similar in composition and denitrification function to those observed in reference wetlands within this mitigation bank.     

Taxonomic Profiling and Metagenome Analysis of a Microbial Community from a Habitat Contaminated with Industrial Discharges

Industrial units, manufacturing dyes, chemicals, solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canal bank (N 22°57.878′; E 072°38.478′), Ahmedabad, Gujarat, India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be “Proteobacteria” and “Pseudomonas,” respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other “-omic” studies, will help in designing future bioremediation strategies in effluent treatment plants and environmental clean-up projects.     

高寒地区不同海拔梯度西北小檗生境土壤微生物群落结构及多样性分析

以青海高原2 300～4 000 m海拔范围的6处西北小檗(Berberis vernae)生境土壤为试材,采用高通量测序方法,分析不同海拔梯度西北小檗生境土壤微生物群落结构及多样性。研究结果表明:(1)在西北小檗生境土壤中,细菌群落组成主要包括10个细菌门21个细菌属,真菌群落由子囊菌门、担子菌门等8个真菌门59个真菌属组成。(2)低海拔位置的海东乐都1号样点(hdld1) 0～20 cm土层的细菌群落丰富性及多样性均最高,黄南泽库样点(hnzk) 0～20 cm土层的真菌群落丰富度最高,西宁大通样点(xndt) 0～20 cm土层的真菌群落多样性最高;随着海拔的升高,0～20 cm、40～60 cm土层的细菌群落丰富度及多样性呈现出先降低再升高再降低的趋势,20～40 cm土层的细菌群落丰富度及多样性则呈现出先升高后降低的趋势,0～20 cm、20～40 cm土层土壤微生物真菌群落丰富度呈现出先升高再降低再升高的趋势,0～20 cm、40～60 cm土层真菌群落多样性呈现先升高再降低的趋势,40～60 cm土层的真菌丰富度及20～40 cm土层的真菌多样性的变化趋势不明显。(3)硝态氮、速效磷和速效钾对土壤微生物群落的影响较明显。综上可知,高寒地区不同海拔梯度西北小檗生境土壤微生物群落结构多样性呈现出一定的海拔差异趋势,其海拔差异主要受到环境条件、土壤理化性质和植被分布的影响。     

Community Structure of Fishes and Habitat Complexity on a Tropical Rocky Shore

The relationship between the variables of reef fish community structure (fish richness, fish diversity and total number of fishes) and those of habitat complexity (total surface area, substratum diversity, topographic complexity, number of holes, percent cover of turf algae, zoanthids, millepores, massive corals, bare rock, encrusting calcareous algae, urchins, other sessile organisms and Sargassum) were examined on three different rocky shores (FA, FB and FT) at Arraial do Cabo, a tropical region located on Brazilian southeastern coast (23° S, 42° W). Fish abundance and vertical distribution were assessed by a visual census technique using strip transects. Percentage cover of benthic organisms and other substratum types were calculated by replicated transects using a chain laid down on the substratum. Topographic complexity was determined by the chain link method and number of holes were estimated by direct counts on replicated transects. More than 91 fishes belonging to 37 families were seen in all study sites during one year of visual census effort. FA and FB sites had similar fish community structure and habitat complexity characteristics, while FT showed different habitat characteristics and higher fish diversity and richness, plus total number of fishes. Vertical distribution of fishes along the rocky shores studied seemed to be predictable and was determined by factors such as feeding habits and behavior, availability of refuges and social interactions. The habitat variables that best explained the higher diversity and number of fishes observed in FT site were total surface area of rocky shores and the abundance of benthic sessile invertebrates; these conditions were typical of rocky shores more exposed to wave surge.     

Microbial Community Composition of Floodplains Shallow-Water Seeps in the Bolshaya Rechka Floodplain,Western Siberia

Microbiology - Recently discovered fields of seeps in western Siberia are an important, previously unknown source of methane. Seeps are located in the floodplains of small rivers and vary in shape,...     

Microbial Community Structure and Carbon-Utilization Diversity in a Mine Tailings Revegetation Study

Restoration of metals‐contaminated environments requires a functional microbial community for successful plant community establishment, soil development, and biogeochemical cycling. Our research measured microbial community structure and carbon‐utilization diversity in treatment plots from a mine waste revegetation project near Butte, Montana. Treatments included two controls (raw tailings) either (1) with or (2) without tilling, (3) shallow‐tilled lime addition, (4) deep‐tilled lime addition, (5) lime slurry injection, (6) topsoil addition, and (7) an undisturbed area near the tailings. Microbial community structural differences were assayed by plate counts of heterotrophic bacteria, actinomycetes, fungi, and bacterial endospores, and quantification of arbuscular mycorrhizae colonization. Metabolic diversity differences were assessed by carbon‐utilization profiles generated with Biolog microtiter plates. Heterotrophic bacteria counts were significantly higher in the limed and topsoil treatment plots than the control plots, and the actinomycete and fungal counts increased in the tilled control plot as well. Endospore counts were significantly higher in the topsoil addition and the undisturbed plots than the other treatment plots. Carbon‐utilization activity was very low in untreated plots, intermediate in lime‐treated plots, and very high in topsoil and undisturbed plots. Arbuscular mycorrhizae (AM) colonization levels of two grass species showed low levels of colonization on control, shallow‐limed, and lime slurry‐injected plots, and high levels on the deep‐limed and topsoil‐addition plots. Plant and soil system components increased across the treatment plots, but individual components responded differently to changing environmental conditions.     

Seasonal Variation in the Structure of a Marine Benthic Microbial Community

Abstract The patterns of seasonal variation in the structure of a marine benthic microbial community were examined using phospholipid fatty acid analysis (PLFA). Principal component analysis of PLFA profiles indicated a strong seasonal pattern dominated the variance within the data set. Three functional groups of microorganisms (phototrophic microeukaryotes, and two groups of anaerobic bacteria) were disproportionately abundant in the communities that mapped to either extreme of the first principle component. Phototrophic microeukaryotes were most abundant and exhibited the greatest relative abundance during periods of cold water. In contrast, the two functional groups of anaerobic bacteria showed the greatest relative abundance during times of warm water. Differential responses by these groups, and macrofaunal deposit feeders, to light intensity and water temperature were offered as the proximal causes of the observed patterns. Received: 28 April 1997; Accepted: 10 September 1997     

Differences in Hyporheic-Zone Microbial Community Structure along a Heavy-Metal Contamination Gradient

The hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. The microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. Using a suite of methods (denaturing gradient gel electrophoresis, 16S rRNA phylogeny, phospholipid fatty acid analysis, direct microscopic enumeration, and quantitative PCR), we compared the microbial communities inhabiting the hyporheic zone of six different river sites that encompass a wide range of sediment metal loads resulting from large base-metal mining activity in the region. There was no correlation between sediment metal content and the total hyporheic microbial biomass present within each site. However, microbial community structure showed a significant linear relationship with the sediment metal loads. The abundances of four phylogenetic groups (groups I, II, III, and IV) most closely related to α-, β-, and γ-proteobacteria and the cyanobacteria, respectively, were determined. The sediment metal content gradient was positively correlated with group III abundance and negatively correlated with group II abundance. No correlation was apparent with regard to group I or IV abundance. This is the first documentation of a relationship between fluvially deposited heavy-metal contamination and hyporheic microbial community structure. The information presented here may be useful in predicting long-term effects of heavy-metal contamination in streams and provides a basis for further studies of metal effects on hyporheic microbial communities.     

Microbial Community Structure in Three Deep-Sea Carbonate Crusts

Carbonate crusts in marine environments can act as sinks for carbon dioxide. Therefore, understanding carbonate crust formation could be important for understanding global warming. In the present study, the microbial communities of three carbonate crust samples from deep-sea mud volcanoes in the eastern Mediterranean were characterized by sequencing 16S ribosomal RNA (rRNA) genes amplified from DNA directly retrieved from the samples. In combination with the mineralogical composition of the crusts and lipid analyses, sequence data were used to assess the possible role of prokaryotes in crust formation. Collectively, the obtained data showed the presence of highly diverse communities, which were distinct in each of the carbonate crusts studied. Bacterial 16S rRNA gene sequences were found in all crusts and the majority was classified as α-, γ-, and δ- Proteobacteria. Interestingly, sequences of Proteobacteria related to Halomonas and Halovibrio sp., which can play an active role in carbonate mineral formation, were present in all crusts. Archaeal 16S rRNA gene sequences were retrieved from two of the crusts studied. Several of those were closely related to archaeal sequences of organisms that have previously been linked to the anaerobic oxidation of methane (AOM). However, the majority of archaeal sequences were not related to sequences of organisms known to be involved in AOM. In combination with the strongly negative δ ¹³C values of archaeal lipids, these results open the possibility that organisms with a role in AOM may be more diverse within the Archaea than previously suggested. Different communities found in the crusts could carry out similar processes that might play a role in carbonate crust formation.     

Silicon-Mediated Tomato Resistance Against Ralstonia solanacearum is Associated with Modification of Soil Microbial Community Structure and Activity

Bacterial wilt caused by Ralstonia solanacearum is a serious soil-borne disease of Solanaceae crops. In this study, the soil microbial effects of silicon-induced tomato resistance against R. solanacearum were investigated through pot experiment. The results showed that exogenous 2.0 mM Si treatment reduced the disease index of bacterial wilt by 19.18 % to 52.7 % compared with non-Si-treated plants. The uptake of Si was significantly increased in the Si-treated tomato plants, where the Si content was higher in the roots than that in the shoots. R. solanacearum inoculation resulted in a significant increase of soil urease activity and reduction of soil sucrase activity, but had no effects on soil acid phosphatase activity. Si supply significantly increased soil urease and soil acid phosphatase activity under pathogen-inoculated conditions. Compared with the non-inoculated treatment, R. solanacearum infection significantly reduced the amount of soil bacteria and actinomycetes by 52.5 % and 16.5 %, respectively, but increased the ratio of soil fungi/soil bacteria by 93.6 %. After R. solanacearum inoculation, Si amendments significantly increased the amount of soil bacteria and actinomycetes and reduced soil fungi/soil bacteria ratio by 53.6 %. The results suggested that Si amendment is an effective approach to control R. solanacearum. Moreover, Si-mediated resistance in tomato against R. solanacearum is associated with the changes of soil microorganism amount and soil enzyme activity.     

Microbial Diversity and Community Structure on Corroding Concretes

The objective of this study was to analyze bacterial diversity in two different concrete samples to understand the dominant types of bacteria that may contribute to concrete corrosion. Two concrete samples, HN-1 from the sunny side and HN-2 from dark and damp side, were collected from Zijin Mountain in Nanjing and genomic DNA was extracted. The partial bacterial 16S rRNA gene fragment was PCR amplified and two clone libraries were constructed. Amplified ribosomal DNA restriction analysis (ARDRA) was performed by digestion of the 16S rRNA gene and each unique restriction fragment polymorphism pattern was designated as an operational taxonomic unit (OTU). Phylogenetic trees of bacterial 16S rDNA nucleotide sequences were constructed. Sample HN-1 and HN-2 contained 21 OTUs and 26 OTUs, respectively. Proteobacteria and Planctomycetes were the predominant bacteria in both samples, and they are distributed among Herbaspirillum, Archangium, Phyllobacteriaceae and Planctomycetaceae. Cyanobacteria and Rubrobacter sp. are dominant in HN-1; while Acidobacteriaceae, Adhaeribacter sp. and Nitrospira sp. are predominant in HN-2. This distribution pattern was consistent with local environmental conditions of these two samples. The inferred physiological characteristics of these bacteria, based on relatedness of the DNA clone sequences to cultivated species, revealed different mechanisms of concrete corrosion depending on the local environmental conditions.     

Changes in Cystic Fibrosis Airway Microbial Community Associated with a Severe Decline in Lung Function

Cystic fibrosis (CF) is a genetic disease resulting in chronic polymicrobial infections of the airways and progressive decline in lung function. To gain insight into the underlying causes of severe lung diseases, we aimed at comparing the airway microbiota detected in sputum of CF patients with stable lung function (S) versus those with a substantial decline in lung function (SD). Microbiota composition was investigated by using culture-based and culture-independent methods, and by performing multivariate and statistical analyses. Culture-based methods identified some microbial species associated with a worse lung function, i.e. Pseudomonas aeruginosa, Rothia mucilaginosa, Streptococcus pneumoniae and Candida albicans, but only the presence of S. pneumoniae and R. mucilaginosa was found to be associated with increased severe decline in forced expiratory volume in 1 second (FEV₁). Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis revealed a higher bacterial diversity than that detected by culture-based methods. Molecular signatures with a statistically significant odds ratio for SD status were detected, and classified as Pseudomonas, Burkholderia and Shewanella, while for other Terminal Restriction Fragments (T-RFs) no species assignation was achieved. The analysis of T-RFLP data using ecological biodiversity indices showed reduced Evenness in SD patients compared to S ones, suggesting an impaired ecology of the bacterial community in SD patients. Statistically significant differences of the ecological biodiversity indices among the three sub-groups of FEV₁ (normal/mild vs moderate vs severe) were also found, suggesting that the patients with moderate lung disease experienced changes in the airway assembly of taxa. Overall, changes in CF airway microbial community associated with a severe lung function decline were detected, allowing us to define some discriminatory species as well as some discriminatory T-RFs that represent good candidates for the development of predictive biomarkers of substantial decline in lung function.     

Biophysical Heterogeneity,Hydrologic Connectivity,and Productivity of a Montane Floodplain Forest

Ecosystems - Floodplains display exceptional variation in habitat type, connectivity, and vegetation structure that make them ideal landscapes in which to address biophysical controls on primary...     

生物造粒流化床微生物落结构及其动态变化

为了研究生物造粒流化床污水处理反应器颗粒污泥中微生物群落结构及其动态变化,分别从生物造粒流化床10、60、110cm处取颗粒污泥,通过细胞裂解直接提取颗粒污泥细菌基因组DNA。以细菌和古细菌16S rRNA基因通用引物530F/1490R,对活性污泥中提取的细菌基因组DNA进行PCR扩增,长约1kb的PCR扩增产物纯化后经变性梯度凝胶电泳(DGGE)分离,获得微生物群落的DNA特征指纹图谱。结果显示,生物造粒流化床反应器颗粒污泥中的微生物群落非常丰富,在10cm处微生物的种属达到23种,60cm处为21种,110cm处为20种;生物造粒流化床不同高度都有一些各自的特有种属和共有种属,反应器不同高度的微生物群落演替不明显,微生物群落相似性为83.1%,群落结构较为稳定。     

生物造粒流化床微生物群落结构及其动态变化

为了研究生物适粒流化床污水处理反应器颗粒污泥中微生物群落结构及其动态变化,分别从生物造粒流化床10、60、110 cm处取颗粒污泥,通过细胞裂解直接提取颗粒污泥细菌基因组DNA.以细菌和古细菌16S rRNA基因通用引物530F/1490R,对活性污泥中提取的细菌基因组DNA进行PCR扩增,长约1 kb的PCR扩增产物纯化后经变性梯度凝胶电泳(DGGE)分离,获得微生物群落的DNA特征指纹图谱.结果显示,生物造粒流化床反应器颗粒污泥中的微生物群落非常丰富,在10 cm处微生物的种属达到23种,60 cm处为21种,110 cm处为20种;生物造粒流化床不同高度都有一些各自的特有种属和共有种属,反应器不同高度的微生物群落演替不明显,微生物群落相似性为83.1%,群落结构较为稳定.