Chain Reaction-denaturing Gradient Gel Electrophoresis Research Articles

Diversity of Soil Microbial Communities from an Iron Mining Area (Oued Zem, Morocco)

Abstract Microbial communities in the soil were collected from 20 samples of an iron mining area (Ait Ammar, Oued Zem, Morocco), and unaffected samples were analysed to identify the effects of metal concentrations on functional diversity (Biolog® EcoPlates), and structural diversity (polymerase chain reaction-denaturing gradient gel electrophoresis of 16S rDNA). Aliivibrio fischeri is mainly used for evaluating polluted soil. The functional diversity was assessed by using such indices as area under substrate utilisation curve, richness, Shannon- Weaver and evenness indices. The analysis of similarities and the non-metric multidimensional scaling analyses of DGGE profiles showed that metals in the soil do not have a significant influence on bacteria. Principal component analysis of Biolog data revealed the similarity in the metabolic profiles of mining samples. These results suggest that the direction and the distance from the iron mine tailings do not have significant effects on the metabolic and structural diversity of the soil bacterial population. The toxicity of metals in soils heavily contaminated with Fe and P did not affect the quantities of microbial populations and did not significantly change the microbial diversity of contaminated soils.

Impact of tree species on barley rhizosphere-associated fungi in an agroforestry ecosystem as revealed by 18S rDNA PCR-DGGE

Agroforestry systems have been considered a form of sustainable land use. Woody species in agroforestry systems can improve soil physicochemical properties by supplying leaf or stem litter. However, little is known about fungal community structure and diversity in agroforestry systems. In the present study, the culture-independent 18S rDNA-based polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) method was used to investigate fungal community structure in rhizosphere and bulk soil in Populus euramevicana-barley and Taxodium distichum-barley agroforestry systems. DGGE profiling and cluster analysis revealed that the fungal community structure in the rhizosphere was more complex than that of bulk soil. Our results also indicated that the rhizosphere fungal community in barley was less affected by T. distichum than by P. euramevicana. In addition, an increase in the relative abundance of certain rhizosphere fungal populations was detected in this agroforestry system. Sequencing of prominent DGGE bands revealed an increase in the rhizosphere of a fungal species belonging to the genera Chaetomium, which includes potential biocontrol agents. A rare cellulolytic fungus, Acremonium alcalophilum, was found in the bulk soil from P. euramevicana and barley grown under P. euramevicana. Taken together, our findings may provide new insights into agroforestry practices.

Influence of experimental extreme water pulses on greenhouse gas emissions from soils

Climate models predict increased frequency and intensity of storm events, but it is unclear how extreme precipitation events influence the dynamics of soil fluxes for multiple greenhouse gases (GHGs). Intact soil mesocosms (0–10 cm depth) from a temperate forested watershed in the piedmont region of Maryland [two upland forest soils, and two hydric soils (i.e., wetland, creek bank)] were exposed to experimental water pulses with periods of drying, forcing soils towards extreme wet conditions under controlled temperature. Automated measurements (hourly resolution) of soil CO2, CH4, and N2O fluxes were coupled with porewater chemistry analyses (i.e., pH, Eh, Fe, S, NO3 −), and polymerase chain reaction–denaturing gradient gel electrophoresis to characterize changes in microbial community structure. Automated measurements quantified unexpected increases in emissions up to 245% for CO2 (Wetland), >23,000% for CH4 (Creek), and >110,000% for N2O (Forest Soils) following pulse events. The Creek soil produced the highest soil CO2 emissions, the Wetland soil produced the highest CH4 emissions, and the Forest soils produced the highest N2O emissions during the experiment. Using carbon dioxide equivalencies of the three GHGs, we determined the Creek soil contributed the most to a 20-year global warming potential (GWP; 30.3%). Forest soils contributed the most to the 100-year GWP (up to 53.7%) as a result of large N2O emissions. These results provide insights on the influence of extreme wet conditions on porewater chemistry and factors controlling soil GHGs fluxes. Finally, this study addresses the need to test biogeochemical thresholds and responses of ecosystem functions to climate extremes.

Use of Psychrotolerant Lactic Acid Bacteria (Lactobacillus spp. and Leuconostoc spp.) Isolated from Chinese Traditional Paocai for the Quality Improvement of Paocai Products.

To improve the quality of Chinese traditional Paocai, two psychrotolerant lactic acid bacteria (LAB) strains were isolated from Paocai, and the quality of Chinese Paocai product using these two strains as starter cultures was compared to a control sample fermented with aged brine at 10 °C. The results suggested that the physicochemical and sensory features of Paocai fermented with psychrotolerant LAB were more suitable for industrial applications. The nitrite content of Paocai fermented with psychrotolerant LAB was 1 mg/kg, which was significantly lower than that of the control Paocai (P < 0.05). Low-temperature fermentation with the starter cultures of psychrotolerant LAB could effectively prevent overacidity and over-ripening of the Paocai products. Additionally, Paocai fermented with psychrotolerant LAB harbored relatively simple microbial flora as revealed by polymerase chain reaction-denaturing gradient gel electrophoresis. This study provides a basis for improving the quality of Chinese traditional Paocai and the large-scale production of low-temperature Chinese traditional Paocai products.

Study of the treatment of domestic sewage using PVA gel beads as a biomass carrier

Abstract Technologies for domestic sewage treatment with low excess sludge yield rate and highly efficient biological treatment methods are needed, and the moving-bed biofilm reactor has great promise for meeting this need. To provide technical support for the treatment of typical domestic sewage, this paper provides an estimate of the bacterial diversity in polyvinyl alcohol (PVA) gel beads determined by a 16S-rRNA gene-based polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach, proposes a method for reducing the excess sludge yield rate, and describes the startup and continuous operation of the PVA technology. Domestic sewage was treated by a moving-bed biofilm reactor system using PVA gel beads as a biomass carrier. A significant amount of sphalerite, filamentous bacteria and bacillus were observed on the surface and internal structure of the PVA-gel beads by scanning electron microscope. Clostridiaceae bacterium, Alpha proteobacterium, Phenylobacterium haematophilum and Rhodobacter were identified as dominant bacteria strains using 16S-rRNA PCR-DGGE. The active sludge tanks were found to play a significant role in the reduction of excess sludge.

Evaluating the Effects of Metals on Microorganisms in Flooded Paddy Soils Using the SEM/AVS-Based Approach and Measurements of Exchangeable Metal Concentrations.

We examined possible adverse effects of heavy metals on microbial activity, biomass, and community composition using the simultaneously extracted metals (SEM)/acid-volatile sulfide (AVS)-based approach and measurements of exchangeable metal concentrations in three paddy soils (wastewater-contaminated soil, mine-contaminated soil, and noncontaminated soil) incubated for 60days under flooded conditions. Incubation under flooding increased pH and decreased Eh in all samples. AVS increased when Eh decreased to approximately -200mV for the mine-contaminated and noncontaminated soils, while the wastewater-contaminated soil originally had a high concentration of AVS despite its air-dried condition. Addition of rice straw or alkaline material containing calcium carbonate and gypsum increased AVS levels under flooded conditions. We observed no apparent relationship between soil enzyme activity (β-D-glucosidase and acid phosphatase) and concentrations of SEM, [∑SEM-AVS], and exchangeable metals. Bacterial and fungal community composition, assessed using polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) analysis targeting rRNA genes, was largely influenced by site of collection and incubation time, but metal contamination did not influence community composition. We observed significant negative correlations between biomass C and [∑SEM-AVS] and between biomass C and ∑SEM, suggesting that [∑SEM-AVS] and ∑SEM might reflect the bioavailability of organic matter to microorganisms in these soils.

A preliminary analysis of changes in composition of intestinal microbiota during infancy using polymerase chain reaction-denaturing gradient gel electrophoresis

To investigate the composition of bacteria in the stools of infants and the colonization of intestinal microbiota during infancy. Fresh stools were collected from 15 healthy infants at 0, 2, 4, 7, 10, 14, and 28 days and 3, 6, and 12 months after birth. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze the composition of intestinal microbiota, perform sequencing of dominant bacteria, and to analyze the changes in the composition of intestinal microbiota during infancy. DGGE fingerprint showed that the composition of intestinal microbiota during infancy changed significantly over time after birth. The cloning and sequencing results indicated that Proteobacteria colonized the earliest, mainly the obligate aerobes Enterobacter and Pseudomonas, followed by the obligate anaerobes (Clostridium hathewayi and Veillonella parvula) and the facultative anaerobe Clostridium ramosum in Firmicutes, and Verrucomicrobia. Actinobacteria colonized the latest, mainly Bifidobacterium, and gradually became dominant bacteria. During infancy, obligate aerobes colonize the intestinal tract the earliest, followed by obligate anaerobes and facultative anaerobes. Proteobacteria colonizes the earliest, followed by Firmicutes and Verrucomicrobia, and Actinobacteria, mainly Bifidobacterium, colonizes the latest.

The Influence of Micro-Oxygen Addition on Desulfurization Performance and Microbial Communities during Waste-Activated Sludge Digestion in a Rusty Scrap Iron-Loaded Anaerobic Digester

In this study, micro-oxygen was integrated into a rusty scrap iron (RSI)-loaded anaerobic digester. Under an optimal RSI dosage of 20 g/L, increasing O2 levels were added stepwise in seven stages in a semi-continuous experiment. Results showed the average methane yield was 306 mL/g COD (chemical oxygen demand), and the hydrogen sulphide (H2S) concentration was 1933 ppmv with RSI addition. O2 addition induced the microbial oxidation of sulphide by stimulating sulfur-oxidizing bacteria and chemical corrosion of iron, which promoted the generation of FeS and Fe2S3. In the 6th phase of the semi-continuous test, deep desulfurization was achieved without negatively impacting system performance. Average methane yield was 301.1 mL/g COD, and H2S concentration was 75 ppmv. Sulfur mass balance was described, with 84.0%, 11.90% and 0.21% of sulfur present in solid, liquid and gaseous phases, respectively. The Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analysis revealed that RSI addition could enrich the diversity of hydrogenotrophic methanogens and iron-reducing bacteria to benefit methanogenesis and organic mineralization, and impoverish the methanotroph (Methylocella silvestris) to reduce the consumption of methane. Micro-oxygen supplementation could enhance the diversity of iron-oxidizing bacteria arising from the improvement of Fe(II) release rate and enrich the sulphur-oxidising bacteria to achieved desulfurization. These results demonstrated that RSI addition in combination with micro-oxygenation represents a promising method for simultaneously controlling biogas H2S concentration and improving digestion performance.

Effects of Different Vegetation Types and Reclamation Years on Soil Bacterial Community Structure in Reclaimed Mine Areas

Effects of different vegetation types (Ulmus pumila, Larix gmelinii, Armeniaca vulgaris, Picea asperata and Robinia pseudoacacia) and reclamation years (15 and 20 years) on soil bacterial community structure in reclaimed Antaibao opencast mine areas were investigated using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and clone sequencing. For 20-year reclaimed soils, the significantly highest and lowest bacterial diversity were found in U. pumila and A. vulgaris stand, respectively, whereas no significant differences were found between the other three vegetation types. Under 15-year plantations, soil bacterial diversity index of P. asperata was significantly higher than that of R. pseudoacacia. Soil bacterial diversity index significantly increased in R. pseudoacacia planted soils but decreased in P. asperata treatment with the increase of reclaimed years. No significant change of soil bacterial community structure was observed in the same reclamation years based on the similarity coefficient analysis, cluster analysis and principal component analysis (PCA). Pearson correlation analysis demonstrated that bacterial diversity index was significantly positively correlated with soil pH. Nitrospira, Sphingomonas, Arthrobacter, Brachybacterium, Rhizobium as well as Mesorhizobium, which play important roles in the nitrogen cycle, degradation of polycyclic aromatic hydrocarbons and other organic matter, were identified by clone sequencing of the DGGE bands. Our results indicated that U. pumila and P. asperata were conducive to the recovery of soil bacterial diversity. The most dominant bacterial community from reclaimed mine soil would be beneficial for restoring wasteland contaminated soil and improving soil fertility.

Dynamic changes of yak (Bos grunniens) gut microbiota during growth revealed by polymerase chain reaction-denaturing gradient gel electrophoresis and metagenomics.

ObjectiveTo understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages.MethodsThe denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon contents of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analyze the DGGE fingerprint. The Illumina sequences were assembled, predicted to genes and functionally annotated, and then classified by querying protein sequences of the genes against the Kyoto encyclopedia of genes and genomes (KEGG) database.ResultsMetagenomic sequencing showed that more than 85% of ribosomal RNA (rRNA) gene sequences belonged to the phylum Firmicutes and Bacteroidetes, indicating that the family Ruminococcaceae (46.5%), Rikenellaceae (11.3%), Lachnospiraceae (10.0%), and Bacteroidaceae (6.3%) were dominant gut microbes. Over 50% of non-rRNA gene sequences represented the metabolic pathways of amino acids (14.4%), proteins (12.3%), sugars (11.9%), nucleotides (6.8%), lipids (1.7%), xenobiotics (1.4%), coenzymes, and vitamins (3.6%). Gene functional classification showed that most of enzyme-coding genes were related to cellulose digestion and amino acids metabolic pathways.ConclusionYaks’ age had a substantial effect on gut microbial composition. Comparative metagenomics of gut microbiota in 0.5-, 1.5-, and 2.5-year-old yaks revealed that the abundance of the class Clostridia, Bacteroidia, and Lentisphaeria, as well as the phylum Firmicutes, Bacteroidetes, Lentisphaerae, Tenericutes, and Cyanobacteria, varied more greatly during yaks’ growth, especially in young animals (0.5 and 1.5 years old). Gut microbes, including Bacteroides, Clostridium, and Lentisphaeria, make a contribution to the energy metabolism and synthesis of amino acid, which are essential to the normal growth of yaks.

Analysis of microbial diversity in Shenqu with different fermentation times by PCR-DGGE.

Shenqu is a fermented product that is widely used in traditional Chinese medicine (TCM) to treat indigestion; however, the microbial strains in the fermentation process are still unknown. The aim of this study was to investigate microbial diversity in Shenqu using different fermentation time periods. DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) profiles indicated that a strain of Pediococcus acidilactici (band 9) is the predominant bacteria during fermentation and that the predominant fungi were uncultured Rhizopus, Aspergillus oryzae, and Rhizopus oryzae. In addition, pathogenic bacteria, such as Enterobacter cloacae, Klebsiella oxytoca, Erwinia billingiae, and Pantoea vagan were detected in Shenqu. DGGE analysis showed that bacterial and fungal diversity declined over the course of fermentation. This determination of the predominant bacterial and fungal strains responsible for fermentation may contribute to further Shenqu research, such as optimization of the fermentation process.

The Denitrification Characteristics and Microbial Community in the Cathode of an MFC with Aerobic Denitrification at High Temperatures.

Microbial fuel cells (MFCs) have attracted much attention due to their ability to generate electricity while treating wastewater. The performance of a double-chamber MFC with simultaneous nitrification and denitrification (SND) in the cathode for treating synthetic high concentration ammonia wastewater was investigated at different dissolved oxygen (DO) concentrations and high temperatures. The results showed that electrode denitrification and traditional heterotrophic denitrification co-existed in the cathode chamber. Electrode denitrification by aerobic denitrification bacterium (ADB) is beneficial for achieving a higher voltage of the MFC at high DO concentrations (3.0–4.2 mg/L), while traditional heterotrophic denitrification is conducive to higher total nitrogen (TN) removal at low DO (0.5–1.0 mg/L) concentrations. Under high DO conditions, the nitrous oxide production and TN removal efficiency were higher with a 50 Ω external resistance than with a 100 Ω resistance, which demonstrated that electrode denitrification by ADB occurred in the cathode of the MFC. Sufficient electrons were inferred to be provided by the electrode to allow ADB survival at low carbon:nitrogen ratios (≤0.3). Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) results showed that increasing the DO resulted in a change of the predominant species from thermophilic autotrophic nitrifiers and facultative heterotrophic denitrifiers at low DO concentrations to thermophilic ADB at high DO concentrations. The predominant phylum changed from Firmicutes to Proteobacteria, and the predominant class changed from Bacilli to Alpha, Beta, and Gamma Proteobacteria.

Different phenanthrene-degrading bacteria cultured by in situ soil substrate membrane system and traditional cultivation

Polycyclic aromatic hydrocarbons (PAHs) constitute a large, diverse group of organic compounds that commonly have detrimental biological effects that pose a great environmental threat. Hence, development of isolation and culture techniques for PAH-degrading bacteria is necessary. In this study, a variety of phenanthrene-degrading bacteria were enriched and isolated using an in situ soil substrate membrane system (SSMS) and a traditional cultivation method with phenanthrene as the sole carbon source. In the traditional method, the major species of phenanthrene-degrading bacteria found was Pseudomonas (Gammaproteobacteria). By contrast, the major phenanthrene-degrading bacteria observed using SSMS were Sphingomonas (Alphaproteobacteria). Phenanthrene utilization by bacteria with SSMS was higher than traditional cultivation method. High throughput functional microarray, Geochip, and polymerase chain reaction-denaturing gradient gel electrophoresis were used to characterize the response of soil bacterial communities upon addition of phenanthrene. Results indicated that members of the class Alphaproteobacteria were the dominant bacteria in phenanthrene-contaminated soils, and their characteristic phenanthrene-degrading genes have important role in degradation of contaminants. Sphingomonas was isolated using SSMS and found to be capable of adapting to nutrient-poor environments by utilizing a variety of substrates. The SSMS method is more suitable for the growth of Sphingomonas in simulated environmental conditions.

Effects of Cry1Ab Bt maize straw return on bacterial community of earthworm Eisenia fetida

The eco-toxicological effects of Bacillus thuringiensis (Bt) maize on earthworm life-history traits were widely studied and the results were controversial, while their effects on earthworm bacterial community have been rarely studied. Here, effects of two hybrids of Bt maize [5422Bt1 (event Bt11) and 5422CBCL (MON810)] straw return on Eisenia fetida bacterial community were investigated by the terminal restriction fragment length polymorphism (T-RFLP) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) combing with DNA sequencing, compared to near-isogenic non-Bt maize (5422). Bt maize straw return had significant effects on soil nutrients, especially for available nitrogen (N). The significant differences were shown in soil bacterial community between Bt and non-Bt maize treatments on the 75th and 90th d, which was closely correlated with soil available N, P and K rather than Cry1Ab protein. There was no statistically significant difference in the bacterial community of earthworm gut contents between Bt and non-Bt maize treatments. The significant differences in the bacterial community of earthworm casts were found among three maize varieties treatments, which were closely correlated with Cry1Ab protein and N levels. The differentiated bacterial species in earthworm casts mainly belonged to Proteobacteria, including Brevundimonas, Caulobacter, Pseudomonas, Stenotrophomonas, Methylobacterium, Asticcacaulis and Achromobacter etc., which were associated with the mineralization, metabolic process and degradation of plants residues. Therefore, Bt maize straw return caused changes in the bacterial community of E. fetida casts, which was possibly caused by the direct (Cry1Ab protein) and non-expected effects (N levels) of Bt maize straw.

Inhibitory effects of soybean oligosaccharides and water-soluble soybean fibre on formation of putrefactive compounds from soy protein by gut microbiota

Soybeans are part of the traditional food consumed in Asia countries. In this study, we investigated inhibitory effects of soybean oligosaccharides and water-soluble soybean fibre (Soyafibe) on putrefactive compounds from soy protein by gut microbiota in rats. Caecal microbial fermentation products and microbiota in rats fed 20% soy protein (SP-1) and whole soybean flour (SFL: protein content was 20%) diets were determined. The caecal environment in rats fed 20% soy protein without dietary fibre (SP-2) or with 2% Soyafibe (SFB) was also determined. Compared to SP-1 and SP-2 group, low indole content with high lactic acid was shown in SFL and SFB group, respectively. Using the 16S rRNA genes polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing. Prevotella, Gram-negative anaerobic rods, were detected as dominant in both SFL and SFB groups. Our findings indicated that fermentable polysaccharides in soybeans have inhibitory effects on the formation of putrefactive compounds generated from soy protein by the microbiota.

Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) Profile of Bacterial Community from Agricultural Soils in Bauchi, North-East Nigeria

The population dynamics of bacterial community was investigated in three Agricultural soils, designated as Loamy sand (A), Peaty coarse (B) and Loamy coarse sand (C) in North-East, Nigeria. The soil chemical properties were characterized to fully understand their nature. Metagenomic approach was used to extract soil DNA using the fast DNA Spin Kit extraction technique. The PCR-electrophoresed DNA bands were excised and subjected to a full scale Denaturing Gradient Gel Electrophoresis (DGGE) analysis. DGGE fingerprinting for the PCR-16S rDNA product revealed a diverse profile of complex population of bacterial community in the study area. The study shows that more bacterial community can be fully investigated using molecular techniques rather than traditional culture method. The implication of the results obtained is discussed.

Hydrocarbon Degradation and Bacterial Community Responses During Remediation of Sediment Artificially Contaminated with Heavy Oil.

Natural biodegradation of heavy oil in the marine environment can be accelerated by the addition of nutrients or seeding of pre-selected microorganisms. In this study, a microcosm experiment was conducted to investigate the effects of inorganic nutrient supplementation (biostimulation) and bacterial consortium amendment (bioaugmentation) on the natural degradative processes of artificially contaminated sediment. Our results revealed that the addition of nutrients had greater effect on remediation than the addition of bacterial cells. Supplementation of inorganic nutrients promoted and sustained the growth of oil-degrading and heterotrophic bacteria throughout the experimental period. Highest reduction in the total petroleum hydrocarbons, and of their components, n-alkanes, polycylic aromatic hydrocarbons (PAHs) and alkyl PAHs, were obtained in the biostimulated microcosms. Changes in the bacterial community were monitored by the PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) method targeting the 16S rDNA gene. Results revealed different responses of the bacterial community to the addition of heavy oil and remediation agents. Shifts in the bacterial communities in the seawater were more dynamic than in the sediment. Results of this study showed that addition of remediation agents significantly enhanced the natural biodegradation of heavy oil in a sediment-seawater microcosm trial.

Análisis molecular de las bacterias asociadas a los depósitos de desechos de Atta cephalotes (Hymenoptera: Formicidae)

La composición bacteriana asociada a depósitos de desechos de las hormigas Atta cephalotes en cautiverio, se analizó empleando métodos de microbiología molecular. Ocho cepas bacterianas se aislaron utilizando métodos dependientes de cultivo, pertenecientes a los fila Firmicutes, Proteobacterias y Actinobacterias. De acuerdo con el análisis molecular de los perfiles de electroforesis en gel de gradiente desnaturalizante (PCR-DGGE) de las tres áreas de desecho de A. cephalotes, se encontraron diferencias en las comunidades bacterianas presentes en la fracción total (FT, ADN extraído directamente del área de desecho) y en la fracción cultivable (FC, ADN obtenido después del cultivo). En la fracción total se encontró similitudes superiores al 60 % entre los perfiles de los tiempos (0 y 15 días) para dos de las áreas de desecho (1H y 3H). El análisis de las secuencias del ADN obtenido de las bandas del DGGE reveló el predominio de los fila Proteobacteria, Firmicutes y Bacteroidetes, incluyendo cinco géneros (Ralstonia, Burkholderia, Bacillus sp., Enterobacter sp. y Myroides sp.) y un grupo de bacterias no cultivadas hasta el momento, siendo Bacillus el grupo dominante en todas las muestras analizadas. Los géneros encontrados se destacan por su potencial en la degradación de materia orgánica, como promotores de crecimiento de plantas y por su actividad antimicrobiana. En este estudio mostramos el primer análisis molecular de la comunidad bacteriana asociada a las áreas de desecho de las hormigas A. cephalotes en nidos artificiales. Nuestro trabajo revela la presencia de microbios asociados consistentemente en los depósitos y sugiere que las comunidades residentes están determinadas por la degradación de residuos de la planta y de las hormigas. Se requiere mayor investigación para evidenciar su función y su posible aplicación.

Identification of yeasts by polymerase-chain-reaction-mediated denaturing gradient gel electrophoresis in marcha, an ethnic amylolytic starter of India

BackgroundMarcha is an ethnic amylolytic starter that is used to ferment boiled cereals to produce alcoholic drinks, commonly called jaanr, in the Himalayan Regions of Sikkim and Darjeeling of India. MethodsThe aim of this study was to investigate yeast flora of marcha collected from Sikkim in India by phenotypic characterization and polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE). ResultsThe average load of yeast in marcha was 6.0×108 colony-forming units/g. The phenotypic characterization of yeast isolates from marcha showed the presence of Candida, Pichia, Torulospora, Schizosaccharomyces, Kluveromyces, Issatchenki, and Saccharomycopsis. The PCR-DGGE bands showed the dominance of Wickerhamomyces anomalus (72%) and Pichia anomalus (28%) in marcha. W. anomalus was reported for the first time from marcha using PCR-mediated DGGE. ConclusionThis is the first report on the yeast community associated with marcha analyzed by PCR-mediated DGGE.

Soil contamination assessment for Pb, Zn and Cd in a slag disposal area using the integration of geochemical and microbiological data.

Improper disposal of mining waste is still considered a global problem, and further details on the contamination by potentially toxic metals are required for a proper assessment. In this context, it is important to have a combined view of the chemical and biological changes in the mining dump area. Thus, the objective of this study was to evaluate the Pb, Zn and Cd contamination in a slag disposal area using the integration of geochemical and microbiological data. Analyses of soil organic matter (SOM), pH, Eh, pseudo-total concentration of metals, sequential extraction and microbial community by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) were conducted. Metal availability was evaluated based on the geoaccumulation index (I geo), ecological risk ([Formula: see text]), Risk Assessment Code (RAC) and experimental data, and different reference values were tested to assist in the interpretation of the indices. The soil pH was slightly acidic to neutral, the Eh values indicated oxidized conditions and the average SOM content varied from 12.10 to 53.60gkg-1. The average pseudo-total concentrations of metals were in the order of Zn > Pb > Cd. Pb and Zn were mainly bound to the residual fraction and Fe-Mn oxides, and a significant proportion of Cd was bound to the exchangeable and carbonate fractions. The topsoil (0-20cm) is highly contaminated (I geo) with Cd and has a very high potential ecological risk ([Formula: see text]). Higher bacterial diversity was mainly associated with higher metal concentrations. It is concluded that the integration of geochemical and microbiological data can provide an appropriate evaluation of mining waste-contaminated areas.