Denaturing Gradient Gel Electrophoresis Profiles Research Articles

Impact of whole grain highland hull-less barley on the denaturing gradient gel electrophoresis profiles of gut microbial communities in rats fed high-fat diets.

While next-generation sequencing has overshadowed polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), the latter still holds promise for advancing gut microbiota analysis due to its unique advantages. In this study, we used optimized nested PCR-DGGE to investigate the gut microbiota profile of high-fat diet rats after administering whole grain highland hull-less barley. High-throughput sequencing was employed to validate the DGGE results. Our results proved the reliability of PCR-DGGE for analyzing the dominant taxonomic composition while also providing visual evidence of a notable relationship between the composition of cecal and fecal microbial communities, highlighting substantial differences in both richness and abundance.

Cyanobacterial Root Associations of Leafless Epiphytic Orchids.

The leafless orchids are rare epiphytic plants with extremely reduced leaves, and their aerial roots adopted for photosynthesis. The beneficial plant–microbial interactions contribute significantly to host nutrition, fitness, and growth. However, there are no data available on the bacterial associations, inhabiting leafless orchids. Here, we describe the diversity of cyanobacteria, which colonize the roots of greenhouse Microcoelia moreauae and Chiloschista parishii. The biodiversity and structure of the cyanobacterial community were analyzed using a complex approach, comprising traditional cultivable techniques, denaturing gradient gel electrophoresis (DGGE), and phylogenetic analysis, as well as the light and scanning electron microscopy (SEM). A wide diversity of associated bacteria colonize the root surface, forming massive biofilms on the aerial roots. The dominant populations of filamentous nitrogen-fixing cyanobacteria belonged to the orders Oscillatoriales, Synechococcales, and Nostocales. The composition of the cyanobacterial community varied, depending on the nitrogen supply. Two major groups prevailed under nitrogen-limiting conditions, belonging to Leptolyngbya sp. and Komarekiella sp. The latter was characterized by DGGE profiling and sequencing, as well as by its distinctive features of morphological plasticity. The leading role of these phototrophophic and diazotrophic cyanobacteria is discussed in terms of the epiphytic lifestyle of the leafless orchids.

Multidrug-resistant epi-endophytic bacterial community in Posidonia oceanica of Mahdia coast as biomonitoring factor for antibiotic contamination.

Faced with the significant disturbances, mainly of anthropogenic origin, which affect the Mediterranean coastal ecosystem, Posidonia oceanica (L.) Delile has often been used to assess the state of health of this environment. The present study aims to determine the multidrug resistance patterns among isolated and identified epi-endophytic bacterial strains in P. oceanica seagrass collected from Mahdia coastal seawater (Tunisia). To investigate the bacterial community structure and diversity from coastal seawater samples from Mahdia, total DNA extraction and 16S rRNA gene amplification were performed and analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE profiles showed that some bands were specific to a given site, while other bands were found to be common to more than one sample. In the other hand, bacterial strains were isolated from 1mL of leaves and epiphytes suspension of P. oceanica seagrass in marine agar. Forty-three isolates were obtained, seven of them were selected and identified on the basis of 16S rRNA gene sequence analysis. These isolates belonged to the genus Bacillus, exhibiting 98-100% of identity with known sequences. Susceptibility patterns of these strains were studied toward commonly used antibiotics in Tunisia. All identified isolates were resistant to Aztreonam (72.1%), Ceftazidime (60.5%), Amoxicillin (56%) and Rifampicin (51.2%). S5-L13 strain had presented the highest multidrug resistance with a MAR index of 0.67.

Community-Based 16S rDNA Fingerprinting Analysis of Geographically Distinct Marine Sediments of Unexplored Coastal Regions of Palk Bay and Gulf of Mannar.

The present study aims to carefully delineate the bacterial community composition in marine sediments from different geographical coastal regions of Palk Bay and Gulf of Mannar that are known for human recreational activities. Bacterial richness in different marine sediments was assessed using 16S rRNA gene-based Denaturing Gradient Gel Electrophoresis (DGGE) which is a widely deployed fingerprinting technique. The DGGE profiles revealed that the bacterial community profiles of sediment from different coastal regions were complex and dynamic. The most dominant phylum present in the marine sediment samples were Proteobacteria followed by Cyanobacteria, Bacteriodetes, Firmicutes, Acidobacteria, and Actinobacteria. Cosmopolitan presence of Thioalkalivibrio sp. was observed in all the marine sediments. Sequencing of the abundant band reveals the presence of Vibrio spp. in all the marine sediments. Comparative illumina data analysis revealed the presence of 51 different Vibrio species in which Vibrio alginolyticus holds the highest abundance (67.2%) followed by V. harveyi (13.5%). This is the one of the very few reports that compared the complex microbial community composition of the marine sediments of different geographical regions of unexplored coastal region. Further in-depth analysis needs to be taken to understand the presence of complex microbial compositions and their functions through high-throughput whole metagenome sequencing and metaproteomic approaches.

Simultaneous nitrification and phosphate removal by bioaugmented aerobic granules treating a fluoroorganic compound.

The presence of toxic compounds in wastewater can cause problems for organic matter and nutrient removal. In this study, the long-term effect of a model xenobiotic, 2-fluorophenol (2-FP), on ammonia-oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and phosphate accumulating organisms (PAO) in aerobic granular sludge was investigated. Phosphate (P) and ammonium (N) removal efficiencies were high (>93%) and, after bioaugmentation with 2-FP degrading strain FP1, 2-FP was completely degraded. Neither N nor P removal were affected by 50 mg L-1 of 2-FP in the feed stream. Changes in the aerobic granule bacterial communities were followed. Numerical analysis of the denaturing gradient gel electrophoresis (DGGE) profiles showed low diversity for the ammonia monooxygenase (amoA) gene with an even distribution of species. PAOs, including denitrifying PAO (dPAO), and AOB were present in the 2-FP degrading granules, although dPAO population decreased throughout the 444 days reactor operation. The results demonstrated that the aerobic granules bioaugmented with FP1 strain successfully removed N, P and 2-FP simultaneously.

Denaturing gradient gel electrophoresis and multi-SIR profiles of soil microbial communities from a karst doline at Aggtelek National Park, Hungary

Soils play an important role in the ecosystem of karstic landscapes both as a buffer zone and as a source of acidity to belowground water. Although the microbiota of karstic soils is known to have a great effect on karstification processes, the activity and composition of these communities are largely unknown. This study gives a comparative analysis of soil microbial profiles from different parts of a doline located at Aggtelek, Hungary. The aim was to reveal the relationships between the vegetation type and genetic fingerprints and substrate utilisation (multi-SIR) profiles of the soil microbiota. Soil samples were collected in early and late springs along a transect in a doline covered with different types of vegetation. Genetic fingerprints of bacterial communities were examined by denaturing gradient gel electrophoresis (DGGE) based on the 16S rRNA gene, along with multi-SIR profiles of the microbial communities measured by the MicroResp method using 15 different carbon sources. Genetic fingerprinting indicated that vegetation cover had a strong effect on the composition of soil bacterial communities. Procrustean analysis showed only a weak connection between DGGE and multi-SIR profiles, probably due to the high functional redundancy of the communities. Seasonality had a significant effect on substrate usage, which can be an important factor to consider in future studies.

BACTERIAL PROFILES OF KARVACHAR HOT SPRING IDENTIFIED BY COMBINATION OF DIFFERENT MOLECULAR APPROACHES

Molecular techniques, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA genes clone library construction and metagenomic analysis, were used to describe the bacterial composition of the Karvachar geothermal spring. It was shown the predominance of bacteria belonging to the phyla Proteobacteria, Bacteroidetes, Firmicutes and Cyanobacteria in the studied spring. Representatives of phylum Firmicutes were not detected in the clone library, while DGGE profiling and metagenome analysis confirmed the presence of Firmicutes as one of the major components in the bacterial community.

Emulsion PCR (ePCR) as a Tool to Improve the Power of DGGE Analysis for Microbial Population Studies.

To the authors’ knowledge, this is the first report of the use of emulsion-Polymerase chain reaction (e-PCR) coupled with denaturing gradient gel electrophoresis (DGGE) analysis. In the present work the effectiveness of ePCR in improving the power of the DGGE technique for microbial population studies was tested. Our results indicated that ePCR results in uniform amplification of several DNA molecules, overcoming the major limitations of conventional PCR, such as preferential amplification and DNA concentration dependence. Moreover, ePCR-DGGE resulted in higher sensitivity when compared to conventional PCR-DGGE methods used for studying microbial populations in a complex matrix. In fact, compared to conventional PCR, the DGGE profiles of ePCR products permitted the detection of a higher number of the species that were present in the tested sample.

Diverse Arbuscular Mycorrhizal Fungi (AMF) Communities Colonize Plants Inhabiting a Constructed Wetland for Wastewater Treatment

Constructed wetlands (CWs) are biological wastewater treatment systems that comprise several components where plants and associated organisms play an important role in water depuration. Microbial studies emphasize bacterial dynamics, whereas studies of arbuscular mycorrhizal fungi (AMF) are scarce and the functional role of AMF in aquatic and wetland plants is poorly understood. The aim of this study was to analyze the AMF communities colonizing the roots of Canna indica, Canna flaccida, and Watsonia borbonica inhabiting a CW treating wastewater of a tourism unit. The dynamics of the AMF communities were evaluated by Denaturing Gradient Gel Electrophoresis (DGGE) of 18S rRNA gene amplification products along cold (C) and hot (H) seasons for three consecutive years. DGGE profiles allowed the estimation of AMF species richness (S), and Shannon-Wienner (H) and Pielou (J) indexes, for the different plant species, showing differences between species and along the years. Excised bands from DGGE were analyzed and identified through sequencing for arbuscular mycorrhiza, revealing the presence of AMF strains closely related to Glomus sp., Rhizophagus sp. and Acaulospora sp. genera. Concomitant water quality analyses showed that the system was effective in organic and nutrient removal during the sampling period. Findings from this study suggest that AMF diversity found in the CW is influenced by the water constituents, season, and plant species.

Bifidobacterias como indicadoras de contaminación fecal en aguas tropicales

Human fecal pollution in water constitute a serious risk to the public health, nevertheless the indicator microorganisms commonly used to detect the levels of fecal pollution does not identify the specific source. The detection of certain Bifidobacterium species as B. adolescentis and B. dentium have been proposed as an effective marker of human fecal contamination, but this has not yet been demonstrated in tropical environmental conditions. The aim of the present work was to determine the Bifidobacteria profile in one sample of water from the Mesolandia Swamp in the Colombian Caribbean and feces samples of 260 human and 94 domestic animals from a human settlement around the swamp. DNA from all the samples was amplified by PCR using specific specie primers based on the 16S rRNA gene sequence and separated by DGGE (Denaturing Gradient Gel Electrophoresis). DGGE bands were excised, reamplified, sequenced, and compared to GenBank database. Bifidobacterial DGGE profiles showed that eight species of Bifidobacterium that were found in the water sample, were also present in the human and animal feces. Bifidobacterium adolescentis and B. dentium described as potential human fecal pollution indicators were found in domestic animals. In this study under the environmental and experimental conditions evaluated was not possible to find a Bifidobacterium species as specific marker of human fecal contamination in tropical areas. However, the applied method in this study could be useful to detect fecal pollution in tropical waters allowing a nearest approximation to the origin of the fecal pollution compared with cultural traditional methods, since it was possible to find identical DNA sequences in the water and in the fecal samples.

Structural shifts in the intestinal microbiota of rats treated with cyclosporine A after orthotropic liver transplantation.

Understanding the effect of immunosuppressive agents on intestinal microbiota is important to reduce the mortality and morbidity from orthotopic liver transplantation (OLT). We investigated the relationship between the commonly used immunosuppressive agent cyclosporine A (CSA) and the intestinal microbial variation in an OLT model. The rat samples were divided as follows: (1) N group (normal control); (2) I group (isograft LT, Brown Norway [BN] rat to BN); (3) R group (allograft LT, Lewis to BN rat); and (4) CSA group (R group treated with CSA). The intestinal microbiota was assayed by denaturing gradient gel electrophoresis profiles and by using real-time polymerase chain reaction. The liver histopathology and the alanine/aspartate aminotransferase ratio after LT were both ameliorated by CSA. In the CSA group, the numbers of rDNA gene copies of Clostridium cluster I, Clostridium cluster XIV, and Enterobacteriaceae decreased, whereas those of Faecalibacterium prausnitzii increased compared with the R group. Cluster analysis indicated that the samples from the N, I, and CSA groups were clustered, whereas the other clusters contained the samples from the R group. Hence, CSA ameliorates hepatic graft injury and partially restores gut microbiota following LT, and these may benefit hepatic graft rejection.

Trace and major element contents, microbial communities, and enzymatic activities of urban soils of Marrakech city along an anthropization gradient

Due to their close proximity with the population, urban soils are extensively affected by human activities that release considerable technogenic inputs resulting in an overall soil degradation and leading to an increase of water-extractable fraction of trace elements. This work aimed to determine the influence of anthropization on trace and major element concentrations and to assess how it might also affect soil biochemical and microbiological parameters in an urban area of Marrakech city, Morocco. The work was carried out on nine topsoils located along an anthropogenic gradient from a suburban area to the city center. The percentage of technogenic fraction (TGF) (e.g., building material, plastic, wood, metallic material, bones, glass, paper, fabric) was used to quantify the degree of human interference in the different soils. Physicochemical parameters were measured: pH (in water solution), TOC (Anne method), TKN, and Olsen phosphorus. The total fraction of trace and major elements (ISO NF 11446) and their water-soluble fraction were analyzed with an ICP-OES. Enumeration of cultivable microorganisms (bacteria, fungi, actinomycetes) was conducted on culture media. Dehydrogenase, alkaline phosphatase, and urease activities were colorimetrically measured, and the structure and diversity of soil bacterial communities were determined by denaturing gradient gel electrophoresis (DGGE) technique. In general, trace and major element concentrations showed increasing levels along the anthropogenic gradient, except for Ca, Mg, B, and Cd. However, trace element concentrations remained below the standard international limits for soils. Total numbers of microorganisms (bacteria, fungi, and actinomycetes) varied significantly among sites, with bacterial counts directly related to the anthropogenic gradient, significantly increasing from suburban area to the city center. Dehydrogenase activity decreased throughout the anthropogenic gradient, while phosphatase and urease activities varied between sites independently of the gradient. DGGE profiles showed that bacterial diversity was higher in the most anthropized soils, where their community structure seemed to be influenced by the total concentrations of Zn, As, Cr, Cu, Ni, Pb, and the technogenic fraction. Overall, trace and major element concentrations and the technogenic fraction were higher with increasing levels of urbanization. Microbiological and biochemical parameters appeared significantly influenced by the anthropogenic inputs without being systematically inhibited along the anthropogenic gradient. Dehydrogenase activity decreased along the anthropization gradient, and thus may be used as a proxy to assess the effect of anthropization on soil biological functions.

MOLECULAR ANALYSIS OF GUT BACTERIAL ENDOSYMBIONTS DIVERSITY IN RED PALM WEEVIL LARVAE, Rhynchophorus ferrugineus (COLEOPTERA; CURCULIONIDAE)

Red palm weevil, Rhynchophorus ferrugineus (Oliver, 1790), Order; Coleoptera, Family; Curculionidae, is considered as the biggest threat facing date palm cultivators. The larva feed on trunk tender tissue and can cause palm death within 6-8 months after infection. Insect gut harbors a community of bacteria that lives in an endosymbiotic relationship with the insect and it is strongly evident that it plays a key role in insect life. Deciphering and identification of insect microbiota could lead to the development of new symbiotiont-based control approaches. In this work we studied the diversity of the endosymbiont bacterial community of red palm weevil larval midgut in Egypt, by using Denaturing Gradient Gel Electrophoresis (DGGE), based on 16S rRNA genes PCR amplification. We used three groups of field caught larva sampled from two different places; El-Badrashin and Agricultural Research Center (ARC) in Giza governorate, Egypt. DGGE profiling patterns has shown the relative prevalence of bacterial phylotypes affiliated to family Firmicute; Leuconostoc lactis, Lactococcus lactis, Lactobacillus nagelli and bacterial phylotypes affiliated to family Actinobaceria; Cellulomonas cellasea, Bifidobacterium minimum, which suggest that they have a potential role in nutrition, physiology and immunomodulation of the insect.

Selection of metabolic pathways for continuous hydrogen production under thermophilic and mesophilic temperature conditions in anaerobic fluidized bed reactors

This study evaluated the influence of hydraulic retention time (HRT) on hydrogen (H2) production in anaerobic fluidized bed reactors at mesophilic (30 °C, AFBR-M) and thermophilic (55 °C, AFBR-T) temperatures. Reactors were fed sucrose-based synthetic wastewater (5000 mg chemical oxygen demand·L−1) in the HRT of 8, 6, 4, 2, or 1 h. H2 production rate increased from 67.8 ± 14.8 to 194.9 ± 57.0 ml H2·h−1 L−1 (AFBR-T) and from 72.0 ± 10.0 to 344.4 ± 74.0 mL H2·h−1·l−1 (AFBR-M) when HRT decreased from 8 to 1 h. Maximum H2 yields for AFBR-T and AFBR-M were 1.93 ± 0.21 and 2.68 ± 0.48 mol H2·mol−1 sucrose, respectively. The main metabolites were acetic acid (31.3%–41.5%) and butyric acid (10.2%–20.7%) (AFBR-M) and acetate (20.1%–39.3%) and ethanol (14.3%–29.9%) (AFBR-T). Denaturing gradient gel electrophoresis profiles revealed selective enrichment of microbial populations responsible for H2 production by the aceto-butyric route (AFBR-M) and ethanol-type fermentation (AFBR-T).

Use of the PCR-DGGE Method for the Analysis of the Bacterial Community Structure in Soil Treated With the Cephalosporin Antibiotic Cefuroxime and/or Inoculated With a Multidrug-Resistant Pseudomonas putida Strain MC1.

The widespread use of cefuroxime (XM) has resulted in the increase in its concentration in hospital and domestic wastewaters. Due to the limited removal of antibiotics and antibiotic-resistant genes in conventional systems, the drugs enter the surface water and soils. Moreover, the introduction of XM and/or XM-resistant bacteria into soil may cause a significant modification of the biodiversity of soil bacterial communities. Therefore, the goal of this research was to assess the genetic diversity of a bacterial community in the cefuroxime (XM1 – 1 mg/kg and XM10 – 10 mg/kg) and/or antibiotic-resistant Pseudomonas putida strain MC1 (Ps – 1.6 × 107 cells/g)-treated soils as determined by the DGGE (denaturing gradient gel electrophoresis) method. The obtained data were also evaluated using a multivariate analysis and the resistance (RS)/resilience (RL) concept. Strain MC1 was isolated from raw sewage in the presence of XM and was resistant not only to this antibiotic but also to vancomycin, clindamycin and erythromycin. The DGGE patterns revealed that the XM10 and XM10+Ps treatments modified the composition of the bacterial community by the alteration of the DGGE profiles as well as a decline in the DGGE indices, in particular on days 30, 60, and 90. In turn, the XM1 and XM1+Ps or Ps treatments did not affect the values of richness and diversity of the soil bacteria members. A principal component analysis (PCA) also indicated that XM markedly changed the diversity of bacterial assemblages in the second part of the experiment. Moreover, there were differences in the RS/RL of the DGGE indices to the disturbances caused by XM and/or Ps. Considering the mean values of the RS index, the resistance was categorized in the following order: diversity (0.997) > evenness (0.993) > richness (0.970). The soil RL index was found to be negative, thus reflecting the progressing detrimental impact of XM on the genetic biodiversity of bacteria within the experiment. These results indicate that the introduction of XM at higher dosages into the soil environment may exert a potential risk for functioning of microorganism.

Intestinal Microbiota Ecological Response to Oral Administrations of Hydrogen-Rich Water and Lactulose in Female Piglets Fed a Fusarium Toxin-Contaminated Diet.

The objective of the current experiment was to explore the intestinal microbiota ecological response to oral administrations of hydrogen-rich water (HRW) and lactulose (LAC) in female piglets fed a Fusarium mycotoxin-contaminated diet. A total of 24 individually-housed female piglets (Landrace × large × white; initial average body weight, 7.25 ± 1.02 kg) were randomly assigned to receive four treatments (six pigs/treatment): uncontaminated basal diet (negative control, NC), mycotoxin-contaminated diet (MC), MC diet + HRW (MC + HRW), and MC diet + LAC (MC + LAC) for 25 days. Hydrogen levels in the mucosa of different intestine segments were measured at the end of the experiment. Fecal scoring and diarrhea rate were recorded every day during the whole period of the experiment. Short-chain fatty acids (SCFAs) profiles in the digesta of the foregut and hindgut samples were assayed. The populations of selected bacteria and denaturing gradient gel electrophoresis (DGGE) profiles of total bacteria and methanogenic Archaea were also evaluated. Results showed that Fusarium mycotoxins not only reduced the hydrogen levels in the caecum but also shifted the SCFAs production, and populations and communities of microbiota. HRW treatment increased the hydrogen levels of the stomach and duodenum. HRW and LAC groups also had higher colon and caecum hydrogen levels than the MC group. Both HRW and LAC protected against the mycotoxin-contaminated diet-induced higher diarrhea rate and lower SCFA production in the digesta of the colon and caecum. In addition, the DGGE profile results indicated that HRW and LAC might shift the pathways of hydrogen-utilization bacteria, and change the diversity of intestine microbiota. Moreover, HRW and LAC administrations reversed the mycotoxin-contaminated diet-induced changing of the populations of Escherichia coli (E. coli) and Bifidobacterium in ileum digesta and hydrogen-utilizing bacteria in colon digesta.

Use of PCR-denaturing gradient gel electrophoresis for the discrimination of Candida species isolated from natural habitats

Candida species are opportunistic microbes that cause chronic infections for a human being. Therefore, the exact identification of Candida species is extremely important for improved therapeutic strategy against these species. Identification based on conventional methods cannot differentiate between some of yeasts species, hence PCR based molecular techniques and sequencing could be an alternative tool for the yeasts identification. A quick molecular method based on the polymerase chain reaction (PCR) and Denaturing Gradient Gel Electrophoresis (DGGE) was applied for distinguishing strains belonging to the Candida species. Six different species designated as AH-20, AH-21, AH-22, AH-23, AH-24 and AH-25 were isolated from soil samples, and their exact identification was detected based on the D1/D2 domain of the 26S rRNA gene amplification and sequence determination. Alignment results and the comparison of 26S rRNA gene sequences of the isolates to 26S rRNA gene sequences available in the GenBank database, as well as the phylogenetic analysis, confirmed the accurate position of the isolates as Candida intermedia strain AH-20, Candida boidinii strain AH-21, Candida tropicalis strain AH-22, Candida mengyuniae strain AH-23, Candida maltosa strain AH-24 and Candida maltosa strain AH-25. Fragments of the D1/D2 domain of 26S rRNA gene were amplified using NL1-GC/LS2 primers and separated by the DGGE. Results showed that all Candida species reported in this study were well discriminated by a distinct band in the DGGE profile. Our results demonstrated that DGGE technique using NL1-GC/LS2 primers could use for the rapid discrimination of yeast strains belonging to the same genera.

Biofertigation of Forage With Effluents of Green Line of a Cattle Slaughterhouse: Microbial Diversity and Leaf Dry Mass Productivity

The wastewater has been an environmental problem, but your used as fertilizers could reduce or eliminate the application of commercial fertilizers in soil. Arbuscular mycorrhizal fungi (AMF) and nitrogen fixing bacteria (NFB) are a good parameter to analyze the impacts of this fertigationon soil. We aimed to evaluate the distribution and diversity of AMF and NFB before and after applications of wastewater or manure from green line of a cattle slaughterhouse in the irrigation of B. brizantha cv Marandu in Cerrado soil and leaf biomass productivity. The experimental design was performed in completely randomized blocks with ten biofertigation managements. The seeds of the forage were distributed in grooves with spacing of 5 cm. This seeds were covered with a soil layer. NFB and AMF diversity was performed by denaturing gradient gel electrophoresis (DGGE). The leaf biomass productivity in the biofertigation managements was higher than in the managements without the use wastewater/manure. After biofertigation managements, changes in the DGGE profile of the NFB and AMF communities were observed. These changes may be due to the difference in the sample collection period and in the soil humidification. Thus, these DGGE profiles was a good parameter to diagnose the efficacy of wastewater/manure as an alternative biotechnological irrigation.

Root growth improvement of mesquite seedlings and bacterial rhizosphere and soil community changes are induced by inoculation with plant growth‐promoting bacteria and promote restoration of eroded desert soil

AbstractSoil degradation is an ecological disturbance, usually human‐caused, that negatively affects the vegetation and climate of an ecosystem, particularly arid and semiarid environments. These degraded soils can be restored by using native perennial plants inoculated with specific microorganisms. We studied the changes in root growth and the rhizosphere bacterial community of mesquite seedlings (Prosopis articulata) after inoculation with the endophytic bacteria Bacillus pumilus ES4, over 3 cycles of growth in the same soil under desert climatic conditions, and found that inoculation significantly enhanced root biomass during the growth cycles but not shoot biomass or root and shoot lengths. Fluorescent in situ hybridization analysis demonstrated that B. pumilus colonized the root cap, apical meristem, and elongation zone, forming small colonies, on roots from soil‐grown mesquite. Inoculation also significantly changed the bacterial community structure of rhizophere and nonrhizosphere (without plants) soils based on denaturing gradient gel electrophoresis profiles. The changes were highly stable, and the bacterial community structure was maintained throughout the experimental period and not affected by plant replacement. The 16S rRNA pyrosequencing confirmed the changes on structure of bacterial community and revealed an impact on the top taxonomic levels analyzed. The rhizospheres of inoculated plants showed a significant increase in the abundance of Proteobacteria and Acidobacteria coupled with a concomitant decrease in Actinobacteria, whereas an opposite response was observed in nonrhizospheric degraded soils. Overall, inoculation with B. pumilus reduced bacterial diversity but increased the Rhizobium population in the soil. The class Bacilli, despite B. pumilus inoculum, showed minimal variation.

Analysis of the Intestinal Microbiota in Autistic Patients by Denaturing Gradient Gel Electrophoresis

To analyze the differences in the composition of the intestinal microbiota between the autistic and healthy children, we selected 45 autistic and 20 control children aged 2 to 9 years to collect their fecal samples. The total microbial genome DNA of each fecal sample was extracted, and the V3 regions of microbial 16S rRNA genes were amplified. The intestinal microbial composition of both study groups was detected by PCR-based denaturing gradient gel electrophoresis. Quantity One and Biodap software were used to analyze the diversity and similarity of bacterial populations, and SPSS software was used for statistical analysis. The denaturant gradient gel electrophoresis profiles documented significant differences in the composition of intestinal microflora between the autism and control groups. Analysis of the excised bands demonstrated the abundance of bacteria species assigned to the genus Escherichia/Shigella in the gastrointestinal tract of the autism group but a low content in the control group. An opposite result was obtained for the Bacteroides genus. These data indicate that intestinal microbial composition may is correlated with the occurrence of the autism.