PCR-DGGE Fingerprinting Research Articles

Diversity of Microflora Surviving Decontamination Treatments of Pasteurized Meat Carcasses Assessed Using Cultivation-Based and Nested Pcr-Dgge Fingerprinting Methods

Diversity of Microflora Surviving Decontamination Treatments of Pasteurized Meat Carcasses Assessed Using Cultivation-Based and Nested Pcr-Dgge Fingerprinting Methods

Diversity of Microflora Surviving Decontamination Treatments of Pasteurized Meat Carcasses Assessed Using Cultivation-Based and Nested PCR-DGGE Fingerprinting Methods

Diversity of Microflora Surviving Decontamination Treatments of Pasteurized Meat Carcasses Assessed Using Cultivation-Based and Nested PCR-DGGE Fingerprinting Methods

PHENOLIC CONTENT, ANTIOXIDANT ACTIVITY AND BIODIVERSITY CHANGES DURING SPONTANEOUS FERMENTATION OF CARICA PAPAYA LEAF

The spontaneous fermentation was carried out on Carica papaya leaf (CPL) in view of its potential improvement on antioxidant functionality and cultivation of lactic acid bacteria. The effect of the spontaneous fermentation on the total phenolic content and antioxidant activity of CPL, as well as biodiversity profiling were evaluated in this study. Total phenolic content and antioxidant capacity of the fermented CPL were 31.14 mg GAE g-1 and 405.8 mM TE g-1 respectively, higher than the unfermented CPL (5.71 mg GAE/g and 130.5 mM TE g-1) respectively. Microbial community was predominantly lactic acid bacteria (LAB) and yeasts, both populated at 104 to 108 CFU/mL during most part of the fermentation. Presumptive Enterobacteriaceae showed up briefly at the onset of the fermentation before disappearing. PCR-DGGE fingerprinting revealed Lactobacillus plantarum (Lb. plantarum) as the sole dominant bacterial species. More diverse yeasts community was detected by PCR-DGGE where succession of Zygosaccharomyces, Saccharomyces, Candida and Aspergillus genera were detected along fermentation time. Spontaneous fermentation successfully enhanced the total phenolic content and antioxidant capacity of the CPL. The cultivation of lactic acid bacteria was indicated by the presence of Lb. plantarum, whereas the disappearance of Enterobacteriaceae conferred a safe consumption of the fermented CPL.

Insights into the Bacterial Diversity of the Acidic Akhtala Mine Tailing in Armenia Using Molecular Approaches.

The impact of the heavy metal contamination and acidity on the bacterial community was studied in samples collected from the Akhtala copper mine tailing using molecular approaches. The bacterial community structure analysis by PCR-DGGE fingerprinting revealed an abundance of Firmicutes, Acidobacteria, and Proteobacteria in different layers of the Akhtala tailing. 454 pyrotag sequence analyses revealed that a significant part of the sequences originated from Proteobacteria (49%) and Bacteroidetes (43%). Bacterial taxa are distributed also in phyla Saccharibacteria (2%), Verrucomicrobia (1.5%), Gammatimonadetes (1%), and some minor additional bacterial groups. The main primary producers in the Akhtala tailing appear to be obligate autotrophic Thiobacillus and Sulfuritalea species. Representatives of Lutibacter and Lysobacter genera are the most abundant acid-tolerant heterotrophs in the studied tailing. The presence of a large number of yet-uncultivated species emphasizes the importance of the future exploration of the tailing as an important source of novel bacteria.

Biofouling in membrane bioreactors: nexus between polyacrylonitrile surface charge and community composition

The influence of membrane surface charge on biofouling community composition during activated sludge filtration in a membrane bioreactor was investigated in this study using polyacrylonitrile-based membranes. Membranes with different surface properties were synthesized by phase inversion followed by a layer-by-layer modification. Various characterization results showed that the membranes differed only in their surface chemical composition and charge, ie two of them were negative, one neutral and one positive. Membrane fouling experiments were performed for 40 days and the biofouling communities were analyzed. PCR-DGGE fingerprinting indicated selective enrichment of bacterial populations from the sludge suspension within the biofilms at any time point. The biofilm community composition seemed to change with time. However, no difference was observed between the biofilm community of differently charged membranes at specific time points. It could be concluded that membrane charges do not play a decisive role in the long-term selection of the key bacterial foulants.

Analysis of the bacterial community composition of the epiphytes on diseased Gracilaria lemaneiformis using PCR-DGGE fingerprinting technology

PDF HTML阅读 XML下载 导出引用 引用提醒 PCR-DGGE指纹图谱技术分析发病龙须菜附生菌菌群组成 DOI: 作者: 作者单位: 1. 汕头大学 理学院 生物系, 广东省海洋生物技术重点实验室, 广东 汕头 515063;2. 汕头大学 理学院, 汕头大学-马尔凯理工大学藻类联合研究中心, 广东 汕头 515063;3. 福建省水产研究所, 福建省海洋生物增养殖与高值化利用重点实验室, 福建 厦门 361013 作者简介: 裴鹏兵(1990-),男,硕士研究生,研究方向为水生环境保护与修复.E-mail:peipengbing1990@126.com 通讯作者: 中图分类号: S917;Q935 基金项目: 广东省海洋渔业科技与产业发展专项项目（A201405B06）；福建省海洋生物增养殖与高值化利用重点实验室开放课题基金项目（2016fjscq02）. Analysis of the bacterial community composition of the epiphytes on diseased Gracilaria lemaneiformis using PCR-DGGE fingerprinting technology Author: Affiliation: 1. Guangdong Provincial Key Laboratory of Marine Biotechnology, Department of Biology, College of Science, Shantou University, Shantou 515063, China;2. Inauguration of STU-UNIVPM Joint Algal Research Center, College of Science, Shantou University, Shantou 515063, China;3. Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen 361013, China Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:本研究以07-2品系龙须菜（）为实验材料，提取自然条件下代表不同病变程度的健康、病间、白化藻体的附生菌DNA，经PCR扩增16S rDNA基因的V3可变区并进行变性梯度凝胶电泳（DGGE），分离V3片段，再对目的条带进行克隆鉴定。实验结果经数据化后计算龙须菜附生菌数目并比较附生菌菌群多样性，通过非度量多维尺度分析（nMDS）及多元梯度分析（RDA）来比较附生菌菌群组成相似性及优势菌群。实验结果表明，随着龙须菜病变程度的加深，附生菌菌落数及菌群多样性逐渐增加（<0.05）。nMDS分析结果表明，健康藻体与白化藻体在附生菌菌群组成上存在差异，病间藻体在附生菌菌群组成上与健康藻体更为接近。RDA分析结果表明，龙须菜健康藻体附生菌可能的优势菌群是海洋单胞菌属（）、红杆菌科（Rhodobacteraceae）、假交替单胞菌属（、红杆菌科、玫瑰变色菌属（）。从上述结果可以看出，龙须菜健康藻体与发病藻体在附生菌菌群组成及优势菌上存在较大差异，而介于两者之间的藻体在菌群组成上更偏向于健康藻体。 Abstract:, one of the important sources of agar, is the third most widely cultivated seaweed in China, after . In recent years, there has been a large-scale decrease in the cultivation of , resulting in huge economic losses for the seaweed cultivation industry. Epiphytes grow as an integral part on the surfaces of large algae, and the variations in the seaweed-associated microbial community compositions are typically associated with disease occurrence. In this study, the 07-2 strain was used as experimental material. DNA of epiphytes from the healthy, adjacent, and bleached fronds was extracted, and the V3 variables amplified from 16S rDNA genes were carried out by denaturing gradient gel electrophoresis (DGGE). Finally, the 23 objective bands were cloned and identified. The number and diversity index of the bacterial community of the epiphytes from the three fronds were calculated after digitization of the experimental results. The similarity among the dominant species in the bacterial communities were compared by non-metric multidimensional scaling (nMDS) and redundancy analysis (RDA). The results show that the colony forming units and bacterial community diversity increased gradually with the aggravation in the degree of lesion in <0.05). The nMDS results indicate that the bacterial community composition of the epiphytes varies between the healthy and bleached fronds, while the composition of adjacent fronds is closer compared with that between healthy fronds. The RDA results reveal that the potential dominant bacteria of the epiphytes of the healthy and adjacent fronds are Pseudoalteromonas, respectively. However, the potential dominant bacteria of the epiphytes of the bleached fronds were not identified. The dominant bacteria of the epiphytes of the bleached attached fronds were . It can be seen from the above results that there is a significant difference between the healthy fronds and the diseased fronds of in terms of the bacterial community composition and dominant bacteria of the epiphytes, while the epiphytic bacterial community composition of the adjacent fronds was more similar than that of the healthy fronds. 参考文献 相似文献 引证文献

Effect of bacterial probiotics bio encapsulated into Artemia franciscana on weight and length of the shortfin silverside (Chirostoma humboldtianum), and PCR DGGE characterization of its intestinal bacterial community

The shortfin silverside ( Chirostoma humboldtianum ) is a native fish of central Mexico with high value for artisanal fisheries. So far, attempts aimed to establish intensive culturing have failed. In this study, we evaluated the effect of probiotic strains; Bifidobacterium animalis subsp. lactis BB-12, Lactobacillus johnsonii C4, and Bacillus sp. B2 bio-encapsulated into Artemia franciscana on Chirostoma humboldtianum weight and length. Their influence on the fish intestinal bacterial communities was also assessed. The final weight and final length of the fishes fed with bio-encapsulated Bifidobacterium animalis BB-12, and L. johnsonii C4 were statistically different and higher than the control group. According to PCR-DGGE fingerprints of 16S rRNA gene, the intestinal content bacterial community associated with the shortfin silverside seems to be molded in early larval stages and only slight changes could be induced by the use of bio-encapsulated bacterial. An increase in fish survival rate and an improvement in weight and length were detected using L. johnsonii C4 bioencapsulated into A. franciscana , in spite of its small impact on the structure of the bacterial community associated with the intestinal content of shortfin silverside. The use of L. johnsonii C4 bio-encapsulated into A. franciscana could be an excellent option to improve the yield during intensive culturing of the shortfin silverside.

Root colonization by host-specific rhizobacteria alters indigenous root endophyte and rhizosphere soil bacterial communities and promotes the growth of mandarin orange

We assessed whether colonization of mandarin orange roots by host-specific plant growth promoting rhizobacteria (PGPR) can influence the composition of root endophyte, rhizosphere and non-rhizosphere bacterial communities and plant growth. The ability to colonize root by four host-specific PGPR, namely Enterobacter hormaechei RCE1, Enterobacter asburiae RCE2, Enterobacter ludwigii RCE5 and Klebsiella pneumoniae RCE7, was tested in axenically grown mandarin orange seedlings. The combined results of scanning and transmission electron microscopic images showed that PGPR inoculants successfully colonised on surface and within root tissues of axenic mandarin orange seedlings. The effect of root inoculation of 90 days old mandarin orange seedlings grown in natural soil with RCE1, RCE2, RCE5 and RCE7 either individually or as a consortium was evaluated in terms of plant biomass yield at 90, 180 and 360 days of post inoculation (dpi). Inoculation thus enhanced plant biomass yield over the uninoculated control. NMDS and hierarchical clustering of PCR DGGE fingerprints indicated that both the PGPR inoculation and plant age affected bacterial communities in root tissues and rhizosphere soils. Based on sequencing, the majority of the root endophyte and rhizosphere PCR-DGGE bands were from gammaproteobacteria, and the other were from Firmicutes and Deinococcus-Thermus. In conclusion, host-specific PGPR successfully colonized mandarin orange root tissue and rhizosphere soil and enhanced plant growth.

The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China.

In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure.

Microbial communities after wood ash fertilization in a boreal drained peatland forest

Wood ash contains all the essential plant nutrients except nitrogen, and thus supports tree growth especially on peatlands where mineral nutrients often are in short supply. Here we report the effects of wood ash fertilization on the soil microbial community in a boreal drained peatland, characterized by phospholipid fatty acid (PLFA) composition, and more specifically the fungal community, characterized with PCR-DGGE fingerprinting and sequencing methods. We investigated the microbial communities in unfertilized and ash-fertilized sample plots (loose wood ash 5000 or 15 000 kg ha−1) 6 years after fertilization. Microbial function measured as heterotrophic basal respiration increased over 30% in the surface peat layer after wood ash fertilization, yet the result was statistically insignificant. The higher amount of wood ash induced a shift in the microbial community in the surface peat layer (0–10 cm) along with an increase in pH. A higher relative proportion of fungal-specific PLFA 18:2ω6 and an increased fungal:bacterial ratio indicated that fungi benefited from the higher amount of wood ash in the topmost layer. Also, the lower amount of wood ash seemed to have stimulated actinobacteria. Our results indicated that higher pH and extra nutrients due to wood ash fertilization promoted the appearance of mycorrhizal and wood-decomposing fungi directly or via increased tree growth. We suggest that wood ash as a fertilizer would be a natural and economical choice to improve the nutrient status of drained peatlands used for forestry since it maintains the positive feedback between fungi and trees.

Inter-Population Differences and Seasonal Dynamic of the Bacterial Gut Community in the Endangered Land SnailHelix pomatia(Gastropoda: Helicidae)

ABSTRACT Among the multifaceted environmental factors, the bacterial community ingested with soil and food might play an important role in physiological processes of terrestrial gastropods, with consequences on population dynamics and species distribution patterns. Therefore, we investigated the bacterial gut community structure and seasonal dynamic in three populations of the protected endangered land snail Helix pomatia. The PCR-DGGE fingerprinting analysis followed by Nonmetric Multidimensional Scaling (NMDS) showed that Gamma-and Alphaproteobacteria were common to all populations, while Mollicutes and Betaproteobacteria were population specific. Allochthonous strains might be transiently abundant in the gut of foraging snails with respect to habitat conditions. Autochthonous strains were permanently present in the gut, even after expulsion of the gut content at hibernation beginning. Some of these permanent strains are known to have ice-nucleating activity, which is consistent with the limited cold ha...

The impact of different DNA extraction methods on the analysis of microbial diversity of oral saliva from healthy youths by polymerase chain reaction-denaturing gradient gel electrophoresis

Background/purposePolymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), as a conventional molecular technique, was utilized to analyze the diversity of oral microbiota. However, studies found that the results of PCR-DGGE were affected by the DNA isolation method. This study compared QIAamp DNA Micro Kit extraction method with the phenol and chloroform extraction method for DNA isolation of saliva of healthy youths and analyzed PCR-DGGE fingerprints. Materials and methodsIn the first stage, samples were divided into two after collection from eight health youths. Two methods were used to isolate the DNA for PCR-DGGE analysis. In the second stage, another 16 samples were collected from 14 youths. The better method, QIAamp DNA Micro Kit, was used to isolate the DNA for PCR-DGGE analysis. The cluster analysis was performed with unweighted pair-group method with arithmetic means. ResultsThe results in the first stage showed that the QIAamp DNA Micro Kit extraction method was more suitable for DNA extraction of saliva than the phenol-chloroform extraction method. In the second stage, the bands were changed into numbers “0”, “1”, and “2” to analyze the similarity of samples according to the bands' lightness. The similarity indices of different periods from the same individual showed that the microbiological composition was very similar (>0.95), while those from different individuals varied greatly (<0.90). ConclusionPCR-DGGE was more accurate in assessing oral microbial diversity by QIAamp DNA Micro Kit. Different individuals had large differences in oral microbial diversity but also had some common microbial dominant communities.

Analysis of effect of nicotine on microbial community structure in sediment using PCR-DGGE fingerprinting

Solid or liquid waste containing a high concentration of nicotine can pollute sediment in rivers and lakes, and may destroy the ecological balance if it is directly discharged into the environment without any treatment. In this study, the polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) method was used to analyze the variation of the microbial community structure in the control and nicotine-contaminated sediment samples with nicotine concentration and time of exposure. The results demonstrated that the growth of some bacterial species in the nicotine-contaminated sediment samples was inhibited during the exposure. Some bacteria decreased in species diversity and in quantity with the increase of nicotine concentration or time of exposure, while other bacteria were enriched under the effect of nicotine, and their DGGE bands changed from undertones to deep colors. The microbial community structure, however, showed a wide variation in the nicotine-contaminated sediment samples, especially in the sediment samples treated with high-concentration nicotine. The Jaccard index was only 35.1% between the initial sediment sample and the sediment sample with a nicotine concentration of 0.030 μg/g after 28 d of exposure. Diversity indices showed that the contaminated groups had a similar trend over time. The diversity indices of contaminated groups all decreased in the first 7 d after exposure, then increased until day 42. It has been found that nicotine decreased the diversity of the microbial community in the sediment.

Raising nutrients removal efficiency by improving the internal recycling strategy in an anoxic/oxic-membrane bioreactor package plant

The effects of two internal mixed liquor recycling strategies on nutrients removal from municipal wastewater were investigated in an anoxic/oxic-membrane bioreactor package plant with a capacity of 100 m3/d. In the original strategy, in which the mixed liquor was directly pumped back to the anoxic tank from the membrane tank, the removal efficiencies of total nitrogen (TN) and total phosphorus (TP) decreased significantly due to the high dissolved oxygen concentration in the anoxic tank with an increase of the internal recycling rate from 50 to 100%. In contrast, in the improved internal strategy, i.e., the mixed liquor in the membrane tank was returned to the oxic tank with a recycling rate of 150%, and meantime, the mixed liquor in the oxic tank was refluxed to the anoxic tank at a recycling rate of 250%, the average effluent concentration of chemical oxygen demand, NH4+-N, TN, and TP were 25.3, 0.55, 28.89, and 1.71 mg/L, respectively. When external acetic acid (2.66 L/d) was added, the effluent concentration of TN decreased to 8.5 mg/L. In addition, a reduction of membrane fouling with the high nutrients removal efficiency was achieved by the improved strategy as compared with that of the original strategy. PCR–DGGE fingerprints showed that bacterial community in the activated sludge from the tanks had a high similarity under the conditions of the improved strategy. The bacteria belong mainly to phyla-proteobacteria, Firmicutes, and Bacteroidetes, which were important for nitrogen and phosphate removal.

열대 해양 해면 Cinachyrella sp.와 Plakortis sp.의 공생세균 군집의 계통학적 다양성

The bacterial community structures of two marine sponges, Cinachyrella sp. and Plakortis sp., collected from Chuuk in the South Pacific in February 2012 were analyzed by PCR-DGGE (Denaturing Gradient Gel Electrophoresis) fingerprinting. After isolation of the total genomic DNAs from the sponges, the V3 regions of the 16S rRNA genes were amplified and subjected to DGGE profiling. The two species of sponges displayed different DGGE band patterns. The sequences derived from the DGGE bands revealed 85-100% similarities to known bacterial species in the public database. The bacterial community of Cinachyrella sp. was composed of 6 classes: Actinobacteria, Bacteroidetes, Chloroflexi, and Proteobacteria (Alpha-, Gamma-, Delta-). The bacterial community of Plakortis sp. included 7 classes: Actinobacteria, Chloroflexi, Firmicutes, Spirochaetes, and Proteobacteria (Alpha-, Gamma-, Delta-). Though Actinobacteria, Chloroflexi and Proteobacteria were commonly found in both sponges, the predominant bacterial communities differed between the two. Namely, the predominant bacterial groups in Cinachyrella sp. and Plakortis sp. were Proteobacteria and Chloroflexi, respectively. The sponge-associated bacteria are sponge host-specific, as each of the tested sponges from the same geographical location had different predominant bacterial diversity.

Spatial heterogeneity in a deep artificial lake plankton community revealed by PCR-DGGE fingerprinting

To explore the spatial heterogeneity of plankton communities in a deep artificial lake (Songhua Lake, China), samples were collected at seven sites. Samples were investigated by denaturing gradient gel electrophoresis (DGGE) analysis of the PCR-amplified 16S and 18S rRNA genes and specific bands were sequenced. Cluster analysis of the DGGE profiles revealed that all of the samples grouped into two distinct clusters, in accordance with sampling site; while in each cluster, the divergence of sub-clusters correlated with sampling depth. Sequence analysis of selected dominant DGGE bands revealed that most sequenced phylotypes (84%) exhibited ≥97% similarity to the closest sequences in GenBank, and were affiliated with ten common freshwater plankton phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Bacillariophyta, Pyrrophyta, Cryptophyta, Ciliophora, Stramenopiles, and Rotifera). Several of these groups are also found worldwide, indicating the cosmopolitan distribution of the phylotypes. The relationships between DGGE patterns and environmental factors were analyzed by redundancy analysis (RDA). The results suggested that, total nitrogen, nitrate, nitrite, ammonia, and CODMn concentrations, and water temperature were strongly correlated with the variation in plankton composition.

Accumulation and Distribution of Cadmium in Flue-Cured Tobacco and Its Impact on Rhizosphere Microbial Community

To explore the accumulation and distribution of Cadmium (Cd) in flue-cured tobacco and the effect on soil microbial community structure in the rhizosphere, pot experiments were conducted with different treatment levels of Cd (0, 2, 4, 8, and 16 mg·kg -1 ). The Cd accumulation in different organs of flue-cured tobacco was analyzed, and the bacteria and fungi community structures in the rhizosphere were examined using PCR-DGGE fingerprinting with universal bacteria and fungi primers. Results showed that the order of Cd contents in different organs of flue-cured tobacco was: leaf > stem > root. Increasing Cd concentration in the pot soil elevated Cd contents in different organs of flue-cured tobacco. As to the soil microbial community, the bacterial fingerprinting bands in rhizosphere with 4 mg·kg -1 Cd level were significantly less than other treatments. Some bacteria disappeared with increasing soil Cd concentrations. Nevertheless, some special bacteria apparently had a strong restoration capability in the rhizosphere at a high Cd contamination level (16 mg·kg -1 ). Among the 8 clusters of bacterial communities identified by the sequencing, the Bacterium ellin, Acidobacteria bacterium ellin, and Mycobacterium had strong resistance and adaptability to Cd contamination of different concentrations, whereas the Leptolyngbya had strong adaptability to Cd contamination of moderate concentration, which could become the dominant population at this level. The fungi community diversity in the rhizosphere with different concentrations of Cd was significantly different from the pattern of bacteria. Some fungi appeared with the increase of Cd concentration, but some fungi disappeared at the moderate Cd concentration (4 mg·kg -1 ). Among the 4 clusters of fungal communities identified by the sequencing, the Fusarium and unknown species were the dominant species in the fungi community, which existed in all treatments and had strong adaptability to different Cd concentrations. The Acremonium sclerotigenum was sensitive to Cd contamination and disappeared at Cd concentrations greater than 2 mg·kg -1

The date palm tree rhizosphere is a niche for plant growth promoting bacteria in the oasis ecosystem.

In arid ecosystems environmental factors such as geoclimatic conditions and agricultural practices are of major importance in shaping the diversity and functionality of plant-associated bacterial communities. Assessing the influence of such factors is a key to understand (i) the driving forces determining the shape of root-associated bacterial communities and (ii) the plant growth promoting (PGP) services they provide. Desert oasis environment was chosen as model ecosystem where agriculture is possible by the microclimate determined by the date palm cultivation. The bacterial communities in the soil fractions associated with the root system of date palms cultivated in seven oases in Tunisia were assessed by culture-independent and dependent approaches. According to 16S rRNA gene PCR-DGGE fingerprinting, the shapes of the date palm rhizosphere bacterial communities correlate with geoclimatic features along a north-south aridity transect. Despite the fact that the date palm root bacterial community structure was strongly influenced by macroecological factors, the potential rhizosphere services reflected in the PGP traits of isolates screened in vitro were conserved among the different oases. Such services were exerted by the 83% of the screened isolates. The comparable numbers and types of PGP traits indicate their importance in maintaining the plant functional homeostasis despite the different environmental selection pressures.

Sponging up metals: Bacteria associated with the marine sponge Spongia officinalis

The present study explored the bacteria of the sponge Spongia officinalis in a metal-polluted environment, using PCR-DGGE fingerprinting, culture-dependent approaches and in situ hybridization. The sponge samples collected over three consecutive years in the Western Mediterranean Sea contained high concentrations of zinc, nickel, lead and copper determined by ICP-MS. DGGE signatures indicated a sponge specific bacterial association and suggested spatial and temporal variations. The bacterial culturable fraction associated with S. officinalis and tolerant to heavy metals was isolated using metal-enriched microbiological media. The obtained 63 aerobic strains were phylogenetically affiliated to the phyla Proteobacteria, Actinobacteria, and Firmicutes. All isolates showed high tolerances to the selected heavy metals. The predominant genus Pseudovibrio was localized via CARD-FISH in the sponge surface tissue and validated as a sponge-associated epibiont. This study is the first step in understanding the potential involvement of the associated bacteria in sponge's tolerance to heavy metals.

Long-term impact of farm management and crops on soil microorganisms assessed by combined DGGE and PLFA analyses.

In the present study, long-term organic and conventional managements were compared at the experimental field of Monsampolo del Tronto (Marche region, Italy) with the aim of investigating soil chemical fertility and microbial community structure. A polyphasic approach, combining soil fertility indicators with microbiological analyses (plate counts, PCR-denaturing gradient gel electrophoresis [DGGE] and phospholipid fatty acid analysis [PLFA]) was applied. Organic matter, N as well as some important macro and micronutrients (K, P, Mg, Mn, Cu, and Zn) for crop growth, were more available under organic management. Bacterial counts were higher in organic management. A significant influence of management system and management x crop interaction was observed for total mesophilic bacteria, nitrogen fixing bacteria and actinobacteria. Interestingly, cultivable fungi were not detected in all analyzed samples. PLFA biomass was higher in the organic and Gram positive bacteria dominated the microbial community in both systems. Even if fungal biomass was higher in organic management, fungal PCR-DGGE fingerprinting revealed that the two systems were very similar in terms of fungal species suggesting that 10 years were not enough to establish a new dynamic equilibrium among ecosystem components. A better knowledge of soil biota and in particular of fungal community structure will be useful for the development of sustainable management strategies.