Stability in Natural Bacterial Communities: I. Nutrient Addition Effects on Rhizosphere Diazotroph Assemblage Composition

Abstract The ability of rhizosphere diazotrophs to remain competitive during increased nitrogen availability in situ was tested in a salt marsh grass stand. Nitrogen (16.3 g m^-2) or nitrogen (16.3 g m^-2) and phosphorus (18.0 g m^-2) were added to plots of short form Spartina alterniflora for either 2 weeks or 8 weeks. The diazotroph assemblage composition was monitored via the polymerase chain reaction using nifH specific primers followed by denaturing gradient gel electrophoresis (DGGE) analysis. DGGE profiles from the short-term experiments (2 and 8 weeks) were compared to profiles from control (no additions) and from long-term (>10 y) nutrient addition plots. Nitrogen fixation activity was assayed in each short-term treatment and control plot using an acetylene reduction technique. The control and nutrient addition DGGE profiles were very similar throughout the short-term experiments. One DGGE band that was prominent in the control plots was not found in the long-term nutrient addition plots. Diazotrophy may provide a competitive advantage for some species in this system, as indicated by results from the long-term nutrient amended plots. However, the rhizosphere environment in situ appears to limit the immediate impacts of increased nutrient availability on the diazotroph assemblage composition. Results from the short-term nutrient amended plots showed no measurable effect on the diazotroph assemblage. These results indicate substantial short-term stability of the diazotroph assemblage composition, but the potential for change in the face of long-term changes in nutrient availability.     

Stability in Natural Bacterial Communities: II. Plant Resource Allocation Effects on Rhizosphere Diazotroph Assemblage Composition

Abstract Plant rhizospheres are dynamic environments in which microbes compete for resources, particularly plant-derived organic carbon/energy sources. Altering plant productivity changes the availability of carbon/energy resources to rhizosphere microbiota. This limitation is expected to intensify competition for the remaining carbon supply and could cause the loss of poor competitors from the assemblage. We clipped or shaded plots of the salt marsh cord grass, Spartina alterniflora, to shift plant carbon resource allocation from the rhizosphere to the aboveground shoots. We then examined key porewater parameters (pH, salinity, H2S, NH⁺4), diazotrophic activity (by acetylene reduction assay), and diazotroph assemblage composition after 2 weeks or 8 weeks of treatment. The diazotroph assemblage composition was monitored via the polymerase chain reaction using nifH specific primers followed by denaturing gradient gel electrophoresis (DGGE) analysis. Porewater parameters and acetylene reduction rates did not differ significantly among treatments. The DGGE profiles also were very similar across the control and experimental treatments, indicating that no detectable diazotroph species were displaced from the assemblage. This implies that rhizosphere diazotrophs are able to compete successfully against nondiazotrophs, in spite of the high energy requirements of nitrogen fixation. These results show that the species composition of the diazotroph assemblage in the S. alterniflora rhizosphere is stable in the face of short-duration but potentially high-impact variations in carbon resource availability.     

转基因生防菌308R(pCPP430)对番茄根围菌群的影响

研究目的在于了解转基因生防菌308R(pCPP430)对番茄根围菌群代谢能力和群落结构的影响。实验中使用了两种互为补充的方法,即单一碳源利用测试(SCSU)和ERIC-PCR,对分别以308R(pCPP430)悬液、308R悬液和无菌水蘸根处理的番茄植株根围菌群进行比较。SCSU菌落计数的聚类分析表明,308R(pCPP430)和308R处理的根围菌重复之间相似性好,水处理的相似性差。主成分分析也得到了相同的结果。ERIC-PCR聚类结果表明,10种碳源,其中8种水处理和308R处理聚为一类。实验为生防菌与植物的互作提供一些依据,为根围菌群结构研究提供一些新的思路。     

Increased Killing of Bacillus subtilis on the Hair Roots of Transgenic T4 Lysozyme-Producing Potatoes

Transgenic potato plants expressing the phage T4 lysozyme gene which are resistant to the plant-pathogenic enterobacterium Erwinia carotovora subsp. carotovora have been constructed. The agricultural growth of these potatoes might have harmful effects on soil microbiota as a result of T4 lysozyme release into the rhizosphere. To assess the bactericidal effect of roots, we have developed a novel method to associate the cells of Bacillus subtilis with hair roots of plants and to quantify the survival of cells directly on the root surface by appropriate staining and fluorescence microscopy. With this technique, we found that the roots of potato plants (Désirée and transgenic control lines) without T4 lysozyme gene display measurable killing activity on root-adsorbed B. subtilis cells. Killing was largely independent of the plant age and growth of plants in greenhouse or field plots. Roots from potato lines expressing the T4 lysozyme gene always showed significantly (1.5- to 3.5-fold) higher killing. It is concluded that T4 lysozyme is released from the root epidermis cells and is active in the fluid film on the root surface. We discuss why strong negative effects of T4 lysozyme-producing potatoes on soil bacteria in field trials may not be observed. We propose that the novel method presented here to study interactions of bacteria with roots can be applied not only to bacterial killing but also to interactions leading to growth-sustaining effects of plants on bacteria.     

Effects of Abiotic Factors on the Phylogenetic Diversity of Bacterial Communities in Acidic Thermal Springs

Acidic thermal springs offer ideal environments for studying processes underlying extremophile microbial diversity. We used a carefully designed comparative analysis of acidic thermal springs in Yellowstone National Park to determine how abiotic factors (chemistry and temperature) shape acidophile microbial communities. Small-subunit rRNA gene sequences were PCR amplified, cloned, and sequenced, by using evolutionarily conserved bacterium-specific primers, directly from environmental DNA extracted from Amphitheater Springs and Roaring Mountain sediment samples. Energy-dispersive X-ray spectroscopy, X-ray diffraction, and colorimetric assays were used to analyze sediment chemistry, while an optical emission spectrometer was used to evaluate water chemistry and electronic probes were used to measure the pH, temperature, and E_h of the spring waters. Phylogenetic-statistical analyses found exceptionally strong correlations between bacterial community composition and sediment mineral chemistry, followed by weaker but significant correlations with temperature gradients. For example, sulfur-rich sediment samples contained a high diversity of uncultured organisms related to Hydrogenobaculum spp., while iron-rich sediments were dominated by uncultured organisms related to a diverse array of gram-positive iron oxidizers. A detailed analysis of redox chemistry indicated that the available energy sources and electron acceptors were sufficient to support the metabolic potential of Hydrogenobaculum spp. and iron oxidizers, respectively. Principal-component analysis found that two factors explained 95% of the genetic diversity, with most of the variance attributable to mineral chemistry and a smaller fraction attributable to temperature.     

Effects of Host Plant Factors on the Bacterial Communities Associated with Two Whitefly Sibling Species

Background

Although discrepancy in the specific traits and ecological characteristics of Bemisia tabaci between species are partially attributed to the B. tabaci-associated bacteria, the factors that affect the diversity of B. tabaci-associated bacteria are not well-understood. We used the metagenomic approach to characterize the B. tabaci-associated bacterial community because the approach is an effective tool to identify the bacteria.

Methodology and Results

To investigate the effects of the host plant and a virus, tomato yellow leaf curl virus (TYLCV), on the bacterial communities of B. tabaci sibling species B and Q, we analyzed the bacterial communities associated with whitefly B and Q collected from healthy cotton, healthy tomato, and TYLCV-infected tomato. The analysis used miseq-based sequencing of a variable region of the bacterial 16S rDNA gene. For the bacteria associated with B. tabaci, we found that the influence of the host plant species was greater than that of the whitefly cryptic species. With further analysis of host plants infected with the TYLCV, the virus had no significant effects on the B. tabaci-associated bacterial community.

Conclusions

The effects of different plant hosts and TYLCV-infection on the diversity of B. tabaci-associated bacterial communities were successfully analyzed in this study. To explain why B. tabaci sibling species with different host ranges differ in performance, the analysis of the bacterial community may be essential to the explanation.     

Effect of Elevated Tropospheric Ozone on the Structure of Bacterial Communities Inhabiting the Rhizosphere of Herbaceous Plants Native to Germany

Current elevated concentrations of ozone in the atmosphere, as they are observed during summer seasons, can cause severe effects on plant vegetation. This study was initiated to analyze whether ozone-stressed plants also transfer signals below ground and thereby alter the bacterial community composition in their rhizospheres. Herbaceous plants, native to Germany, with tolerance (Anthoxanthum odoratum, Achillea millefolium, Poa pratensis, Rumex acetosa, and Veronica chamaedrys) and sensitivity (Matricaria chamomilla, Sonchus asper, and Tanacetum vulgare) to ozone, raised in the greenhouse, were exposed in open-top chambers to two different ozone regimes, i.e., “summer stress” and a normal ozone background. DNA of bacterial cells from the rhizospheres was directly extracted, and partial sequences of the 16S rRNA genes were PCR amplified with primers targeting the following phylogenetic groups: Bacteria, α-Proteobacteria, Actinobacteria, and Pseudomonas, respectively. The diversity of the amplified products was analyzed by genetic profiling based on single-strand conformation polymorphism (SSCP). Neither the tolerant nor the sensitive plants, the latter with visible above-ground damage, showed ozone-induced differences in any of the SSCP profiles, with the single exception of Actinobacteria-targeted profiles from S. asper. To increase the stress, S. asper was germinated and raised in the continuous presence of an elevated level of ozone. SSCP profiles with Bacteria-specific primers combined with gene probe hybridizations indicated an ozone-related increase in a Xanthomonas-related 16S rRNA gene and a decrease in the respective gene from the plant plastids. The fact that only this latter unrealistic scenario caused a detectable effect demonstrated that ozone stress has a surprisingly small effect on the structural diversity of the bacterial community in rhizospheres.     

Potential of a 16S rRNA-Based Taxonomic Microarray for Analyzing the Rhizosphere Effects of Maize on Agrobacterium spp. and Bacterial Communities

Bacterial diversity is central to ecosystem sustainability and soil biological function, for which the role of roots is important. The high-throughput analysis potential of taxonomic microarray should match the breadth of bacterial diversity. Here, the power of this technology was evidenced through methodological verifications and analysis of maize rhizosphere effect based on a 16S rRNA-based microarray developed from the prototype of H. Sanguin et al. (Environ. Microbiol. 8:289-307, 2006). The current probe set was composed of 170 probes (41 new probes in this work) that targeted essentially the Proteobacteria. Cloning and sequencing of 16S rRNA amplicons were carried out on maize rhizosphere and bulk soil DNA. All tested clones that had a perfect match with corresponding probes were positive in the hybridization experiment. The hierarchically nested probes were reliable, but the level of taxonomic identification was variable, depending on the probe set specificity. The comparison of experimental and theoretical hybridizations revealed 0.91% false positives and 0.81% false negatives. The microarray detection threshold was estimated at 0.03% of a given DNA type based on DNA spiking experiments. A comparison of the maize rhizosphere and bulk soil hybridization results showed a significant rhizosphere effect, with a higher predominance of Agrobacterium spp. in the rhizosphere, as well as a lower prevalence of Acidobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes, a new taxon of interest in soil. In addition, well-known taxonomic groups such as Sphingomonas spp., Rhizobiaceae, and Actinobacteria were identified in both microbial habitats with strong hybridization signals. The taxonomic microarray developed in the present study was able to discriminate and characterize bacterial community composition in related biological samples, offering extensive possibilities for systematic exploration of bacterial diversity in ecosystems.     

Variable Effects of Dispersal on Productivity of Bacterial Communities Due to Changes in Functional Trait Composition

Previous studies have shown variable relationships between dispersal rate and ecosystem functioning, but the reasons for and mechanisms behind variable dispersal rate – functioning patterns are currently unknown. In this study we used six bacterial lake water communities in a laboratory experiment in order to investigate how dispersal among communities influences community productivity by evaluating three different mechanisms: 1) changes in taxonomic diversity, 2) changes in phylogenetic diversity or 3) changes in the composition of functional traits. The experiment was conducted in two phases; (A) a dialysis bag experiment where the dispersal rate among six communities was manipulated and the subsequent change in bacterial diversity and growth rate was recorded, and (B) a regrowth experiment where we manipulated available resources to study how well a taxon grows on certain organic carbon resources, i.e. their functional traits. From experiment (B) we could thus estimate changes in functional traits in communities in experiment (A). Bacterial production was affected by dispersal, but not consistently among lakes. Neither change in taxonomic or phylogenetic diversity with dispersal could explain the observed dispersal – productivity relationships. Instead, changes in trait composition with dispersal, especially the communities’ ability to use p-coumaric acid, an aromatic compound, could explain the observed dispersal – productivity relationships. Changes in this trait caused by dispersal seemed especially important for bacterial productivity in waters with a high aromaticity of the organic matter pool. We conclude that the effect of dispersal on bacterial communities can affect ecosystem functioning in different ways, through changes in functional key-traits which are important for the local environment.     

Inhibitory Effects of Trypanosoma cruzi Sialoglycoproteins on CD4+ T Cells Are Associated with Increased Susceptibility to Infection

Background

The Trypanosoma cruzi infection is associated with severe T cell unresponsiveness to antigens and mitogens characterized by decreased IL-2 synthesis. Trypanosoma cruzi mucin (Tc Muc) has been implicated in this phenomenom. These molecules contain a unique type of glycosylation consisting of several sialylated O-glycans linked to the protein backbone via N-acetylglucosamine residues.

Methodology/Principal Findings

In this study, we evaluated the ability of Tc Muc to modulate the activation of CD4⁺ T cells. Our data show that cross-linking of CD3 on naïve CD4⁺ T cells in the presence of Tc Muc resulted in the inhibition of both cytokine secretion and proliferation. We further show that the sialylated O-Linked Glycan residues from tc mucin potentiate the suppression of T cell response by inducing G1-phase cell cycle arrest associated with upregulation of mitogen inhibitor p27^kip1. These inhibitory effects cannot be reversed by the addition of exogenous IL-2, rendering CD4⁺ T cells anergic when activated by TCR triggering. Additionally, in vivo administration of Tc Muc during T. cruzi infection enhanced parasitemia and aggravated heart damage. Analysis of recall responses during infection showed lower frequencies of IFN-γ producing CD4⁺ T cells in the spleen of Tc Muc treated mice, compared to untreated controls.

Conclusions/Significance

Our results indicate that Tc Muc mediates inhibitory efects on CD4⁺ T expansion and cytokine production, by blocking cell cycle progression in the G1 phase. We propose that the sialyl motif of Tc Muc is able to interact with sialic acid-binding Ig-like lectins (Siglecs) on CD4⁺ T cells, which may allow the parasite to modulate the immune system.     

Effects of Spilled Oil on Bacterial Communities of Mediterranean Coastal Anoxic Sediments Chronically Subjected to Oil Hydrocarbon Contamination

The effects of spilled oil on sedimentary bacterial communities were examined in situ at 20 m water depth in a Mediterranean coastal area. Sediment collected at an experimental site chronically subjected to hydrocarbon inputs was reworked into PVC cores with or without a massive addition of crude Arabian light oil (∼20 g kg⁻¹ dry weight). Cores were reinserted into the sediment and incubated in situ at the sampling site (20 m water depth) for 135 and 503 days. The massive oil contamination induced significant shifts in the structure of the indigenous bacterial communities as shown by ribosomal intergenic spacer analysis (RISA). The vertical heterogeneity of the bacterial communities within the sediment was more pronounced in the oiled sediments particularly after 503 days of incubation. Response to oil of the deeper depth communities (8–10 cm) was slower than that of superficial depth communities (0–1 and 2–4 cm). Analysis of the oil composition by gas chromatography revealed a typical microbial alteration of n-alkanes during the experiment. Predominant RISA bands in oiled sediments were affiliated to hydrocarbonoclastic bacteria sequences. In particular, a 395-bp RISA band, which was the dominant band in all the oiled sediments for both incubation times, was closely related to hydrocarbonoclastic sulfate-reducing bacteria (SRB). These bacteria may have contributed to the main fingerprint changes and to the observed biodegradation of n-alkanes. This study provides useful information on bacterial dynamics in anoxic contaminated infralittoral sediments and highlights the need to assess more precisely the contribution of SRB to bioremediation in oil anoxic contaminated areas.     

Role of the Host Cell in Bacteriophage Morphogenesis: Effects of a Bacterial Mutation on T4 Head Assembly

In certain bacterial mutants, called groE, T4 phage head assembly is blocked specifically, implying that the host plays a direct role in head assembly. The block occurs early in the assembly process at the level of action of T4 gene 31.     

Functional Diversity of Culturable Bacterial Communities in the Rhizosphere in Relation to Fine-root and Soil Parameters in Alder Stands on Forest, Abandoned Agricultural, and Oil-shale Mining Areas

Grey alder (Alnus incana) and black alder (Alnus glutinosa) stands on forest land, abandoned agricultural, and reclaimed oil-shale mining areas were investigated with the aim of analysing the functional diversity and activity of microbial communities in the soil–root interface and in the bulk soil in relation to fine-root parameters, alder species, and soil type. Biolog Ecoplates were used to determine community-level physiological profiles (CLPP) of culturable bacteria in soil–root interface and bulk soil samples. CLPP were summarized as AWCD (average well color development, OD 48 h⁻¹) and by Shannon diversity index, which varied between 4.3 and 4.6 for soil–root interface. The soil–root interface/bulk soil ratio of AWCD was estimated. Substrate-induced respiration (SIR) and basal respiration (BAS) of bulk soil samples were measured and metabolic quotient (Q = BAS/SIR) was calculated. SIR and Q varied from 0.24 to 2.89 mg C g⁻¹ and from 0.12 to 0.51, respectively. Short-root morphological studies were carried out by WinRHIZO^TM Pro 2003b; mean specific root area (SRA) varied for grey alder and black alder from 69 to 103 and from 54 to 155 m² kg⁻¹, respectively. The greatest differences between AWCD values of culturable bacterial communities in soil–root interface and bulk soil were found for the young alder stands on oil-shale mining spoil and on abandoned agricultural land. Soil–root interface/bulk soil AWCD ratio, ratio for Shannon diversity indices, and SRA were positively correlated. Foliar assimilation efficiency (FOE) was negatively correlated with soil–root interface/bulk soil AWCD ratio. The impact of soil and alder species on short-root morphology was significant; short-root tip volume and mass were greater for black alder than grey alder. For the investigated microbiological characteristics, no alder-species-related differences were revealed.     

Upscaling from Rhizosphere to Whole Root System: Modelling the Effects of Phospholipid Surfactants on Water and Nutrient Uptake

While the rhizosphere presents a different chemical, physical and biological environment to bulk soil, most experimental and modelling investigations of plant growth and productivity are based on bulk soil parameters. In this study, water and nutrient acquisition by wheat (Triticum aestivum L.) roots was investigated using rhizosphere- and root-system-scale modelling. The physical and chemical properties of rhizosphere soil could be influenced by phospholipid surfactants in the root mucilage. Two models were compared: a 2-dimensional (2D) Finite Element Method rhizosphere model, and a 3-dimensional (3D) root architecture model, ROOTMAP. ROOTMAP was parameterised to reproduce the results of the detailed 2D model, and was modified to include a rhizosphere soil volume. Lecithin (a phospholipid surfactant) could be exuded into the rhizosphere soil volume, decreasing soil water content and hydraulic conductivity at any given soil water potential, and decreasing phosphate adsorption to soil particles. The rhizosphere-scale modelling (5 × 5 mm² soil area, 10 mm root length, uptake over 12 h) predicted a reduction in water uptake (up to 16% at 30 kPa) and an increase in phosphate uptake (up to 4%) with lecithin exudation into the rhizosphere, but little effect on nitrate uptake, with only a small reduction in dry soil (1.6% at 200 kPa). The 3D root model reproduced the water (y = 1.013x, R² = 0.996), nitrate (y = 1x, R² = 1) and phosphate (y = 0.978x, R² = 0.998) uptake predictions of the rhizosphere model, providing confidence that a whole root system model could reproduce the dynamics simulated by a Finite Element Method rhizosphere model. The 3D root architecture model was then used to scale-up the rhizosphere dynamics, simulating the effect of lecithin exudation on water, nitrate and phosphate acquisition by a wheat root system, growing over 41 d. When applied to growing and responsive roots, lecithin exudation increased P acquisition by up to 13% in nutrient-rich, and 49% in relatively nutrient-poor soil. A comparison of wheat (Triticum aestivum L.) and lupin (Lupinus angustifolius L.) root architectures, suggested an interaction between the P acquisition benefit of rhizosphere lecithin and root architecture, with the more highly-branched wheat root structure acquiring relatively more P in the presence of lecithin than the sparsely-branched lupin root system.     

Effects of T4 lysozyme release from transgenic potato roots on bacterial rhizosphere communities are negligible relative to natural factors

Rhizosphere bacterial communities of two transgenic potato lines which produce T4 lysozyme for protection against bacterial infections were analyzed in comparison to communities of wild-type plants and transgenic controls not harboring the lysozyme gene. Rhizosphere samples were taken from young, flowering, and senescent plants at two field sites in three consecutive years. The communities were characterized in a polyphasic approach. Cultivation-dependent methods included heterotrophic plate counts, determination of species composition and diversity based on fatty acid analysis of isolates, and community level catabolic profiling. Cultivation-independent analyses were based on denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments amplified from rhizosphere DNA using primers specific for Bacteria, Actinomycetales, or alpha- or beta-Proteobacteria. Several bands of the DGGE patterns were further characterized by sequence analysis. All methods revealed that environmental factors related to season, field site, or year but not to the T4 lysozyme expression of the transgenic plants influenced the rhizosphere communities. For one of the T4 lysozyme-producing cultivars, no deviation in the rhizosphere communities compared to the control lines was observed. For the other, differences were detected at some of the samplings between the rhizosphere community structure and those of one or all other cultivars which were not attributable to T4 lysozyme production but most likely to differences observed in the growth characteristics of this cultivar.     

Impact of Ectomycorrhizosphere on the Functional Diversity of Soil Bacterial and Fungal Communities from a Forest Stand in Relation to Nutrient Mobilization Processes

The ectomycorrhizal symbiosis alters the physicochemical and biological conditions in the surrounding soil, thus creating a particular environment called ectomycorrhizosphere, which selects microbial communities suspected to play a role in gross production and nutrient cycling. To assess the ectomycorrhizosphere effect on the structure of microbial communities potentially involved in the mobilization of nutrients from the soil minerals in a poor-nutrient environment, we compared the functional diversity of soil and ectomycorrhizosphere bacterial communities in a forest stand. Two hundred and sixty-four bacterial strains and 107 fungal strains were isolated from the bulk soil of an oak (Quercus petraea) stand and from oak–Scleroderma citrinum ectomycorrhizosphere and ectomycorrhizae, in two soil organo-mineral horizons (0 to 3 cm and 5 to 10 cm). They were characterized using two in vitro tests related to their capacities to mobilize iron and phosphorus. We demonstrated that the oak–S. citrinum ectomycorrhizosphere significantly structures the culturable bacterial communities in the two soil horizons by selecting very efficient strains for phosphorus and iron mobilization. This effect was also observed on the diversity of the phosphate-solubilizing fungal communities in the lower soil horizon. A previous study already demonstrated that Laccaria bicolor–Douglas fir ectomycorrhizosphere structures the functional diversity of Pseudomonas fluorescens population in a forest nursery soil. Comparing to it, our work highlights the consistency of the mycorrhizosphere effect on the functional diversity of bacterial and fungal communities in relation to the mineral weathering process, no matter the fungal symbiont, the age and species of the host tree, or the environment (nursery vs forest). We also demonstrated that the intensity of phosphorus and iron mobilization by the ectomycorrhizosphere bacteria isolated from the lower soil horizon was significantly higher compared to that which was isolated from the upper horizon. This reveals for the first time a stratification of the functional diversity of the culturable soil bacterial communities as related to phosphorus and iron mobilization.     

The Effect of Dissolved Organic Carbon on Bacterial Adhesion to Conditioning Films Adsorbed on Glass from Natural Seawater Collected during Different Seasons

Adhesion of three marine bacterial strains, i.e. Marinobacter hydrocarbonoclasticus, Psychrobacter sp. and Halomonas pacifica with different cell surface hydrophobicities was measured on glass in a stagnation point flow chamber. Prior to bacterial adhesion, the glass surface was conditioned for 1?h with natural seawater collected at different seasons in order to determine the effect of seawater composition on the conditioning film and bacterial adhesion to it. The presence of a conditioning film was demonstrated by an increase in water contact angle from 15° on bare glass to 50° on the conditioned glass, concurrent with an increase in the amount of adsorbed organic carbon and nitrogen, as measured by X-ray photoelectron spectroscopy. Multiple linear regression analysis on initial deposition rates, with as explanatory variables the temperature, salinity, pH and concentration of dissolved organic carbon (DOC) of the seawater at the time of collection, showed that the concentration of DOC was most strongly associated with the initial deposition rates of the three strains. Initial deposition rates of the two most hydrophilic strains to a conditioning film, increased with the concentration of DOC in the seawater, whereas the initial deposition rate of the most hydrophobic strain decreased with an increasing concentration of DOC.     

Characterization of Bacterial Communities in Feces from Healthy Elderly Volunteers and Hospitalized Elderly Patients by Using Real-Time PCR and Effects of Antibiotic Treatment on the Fecal Microbiota

Fecal bacteria were studied in healthy elderly volunteers (age, 63 to 90 years; n = 35) living in the local community, elderly hospitalized patients (age, 66 to 103; n = 38), and elderly hospitalized patients receiving antibiotic treatment (age, 65 to 100; n = 21). Group- and species-specific primer sets targeting 16S rRNA genes were used to quantitate intestinal bacteria by using DNA extracted from feces and real-time PCR. The principal difference between healthy elderly volunteers and both patient cohorts was a marked reduction in the Bacteroides-Prevotella group following hospitalization. Reductions in bifidobacteria, Desulfovibrio spp., Clostridium clostridiiforme, and Faecalibacterium prausnitzii were also found in the hospitalized patients. However, total 16S rRNA gene copy numbers (per gram of wet weight of feces) were generally lower in the stool samples of the two groups of hospitalized patients compared to the number in the stool samples of elderly volunteers living in the community, so the relative abundance (percentage of the group- and species-specific rRNA gene copies in relation to total bacterial rRNA gene copies) of bifidobacteria, Desulfovibrio spp., C. clostridiiforme, and F. prausnitzii did not change. Antibiotic treatment resulted in further reductions in the numbers of bacteria and their prevalence and, in some patients, complete elimination of certain bacterial communities. Conversely, the numbers of enterobacteria increased in the hospitalized patients who did not receive antibiotics, and due to profound changes in fecal microbiotas during antibiotic treatment, the opportunistic species Enterococcus faecalis proliferated.