Effects of glyphosate on soil fungal communities: A field study / Efecto del glifosato en las comunidades fúngicas del suelo: estudio a campo

ABSTRACT The driving forces behind many soil processes are microorganisms and they are able to respond immediately to environmental changes. The soil microbial community impacts on many soil properties. More than one-third of the terrestrial ecosystems are semiarid. However, a limited number of studies have been conducted to characterize soil fungal communities in semiarid grasslands, in particular those of agricultural fields. The aim of this study was to explore changes in the diversity and structure of soil fungal communities in semiarid grasslands, after different doses of glyphosate were applied under field conditions. Changes in soil fungal communities were examined using different approaches including culturing, calcofluor white stain and denaturing gradient gel electrophoresis (DGGE). The different approaches complement each other, revealing different aspects of the effect of glyphosate on soil fungal communities. We demonstrated a negative effect of glyphosate on soil fungal biomass at high doses and an early and transitory stimulatory effect on soil fungal biomass. We also found a negative effect of glyphosate on the species richness of cultivable fungi and changes in the molecular structure of soil fungal communities after double doses or long-term glyphosate application. In summary, our findings demonstrate an overall negative effect of glyphosate on soil fungal communities.

RESUMEN Los microorganismos del suelo son los responsables de llevar a cabo la mayoría de los procesos biológicos que ocurren en el suelo, y son capaces de reaccionar ante el estrés ambiental. Más de un tercio de los ecosistemas terrestres son semiáridos. Sin embargo, son escasos los estudios realizados para caracterizar las comunidades fúngicas en suelos agrícolas en ecosistemas semiáridos. El objetivo del presente trabajo fue estudiar los cambios que se producen en la biomasa, la diversidad y la estructura de las comunidades fúngicas del suelo, luego de la aplicación de distintas dosis de glifosato en condiciones de campo. Se emplearon diferentes técnicas incluidas el cultivo, la tinción directa con blanco de calcoflúor y PCR acoplada a electroforesis en geles de gradiente desnaturalizante (DGGE). Las distintas metodologías empleadas se complementan entre sí al detectar cada una distintos aspectos del efecto del glifosato en las comunidades fúngicas del suelo. Se encontró que el glifosato produce un efecto negativo sobre la biomasa fúngica, también se encontró un efecto transitorio estimulante inmediatamente posterior a la aplicación del herbicida. Además, se vio un efecto negativo sobre la riqueza de hongos cultivables, así como también cambios en la estructura molecular de las comunidades luego de aplicaciones repetidas. En conclusión, se demostró un efecto negativo generalizado sobre las comunidades fúngicas del suelo.

Arbuscular mycorrhizal fungal communities in the rhizosphere of a continuous cropping soybean system at the seedling stage

Abstract Arbuscular mycorrhizae (AM) fungi play a crucial role in the growth of soybean; however, the planting system employed is thought to have an effect on AM fungal communities in the rhizosphere. This study was performed to explore the influence of continuous soybean cropping on the diversity of Arbuscular mycorrhizal (AM) fungi, and to identify the dominant AM fungus during the seedling stage. Three soybean cultivars were planted under two and three years continuous cropping, respectively. The diversity of AM fungi in the rhizosphere soil at the seedling stage was subsequently analyzed using polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE). The results showed that an increase in cropping years improved the colonization rate of AM in all three soybean cultivars. Moreover, the dominant species were found to be Funneliformis mosseae and Glomus species. The results of cluster analysis further confirmed that the number of years of continuous cropping significantly affected the composition of rhizospheric AM fungal communities in different soybean cultivars.

Development and diversity of lactic acid producing bacteria and bifidobacteria in healthy full term Indian infants from Himachal Pradesh

BACKGROUND/AIMS: The initial microbial colonization is a crucial step for the healthy development of an infant. Previous studies from India reported the dominance of target microbial species among Indian infants without any analysis on the diversity of target groups. This is the first study from India with an objective to investigate the establishment and diversity of lactic acid producing bacteria (LAB) and bifidobacteria in vaginally delivered, full term, breastfed infants for the first 4 months after birth. METHODS: Present study used polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) based sequence analysis of LAB and bifidobacteria in healthy infants. The results were used to compare the development and early colonization by LAB and bifidobacteria using diversity indices during the initial months of development of gut microbiota in infants. RESULTS: During the first 4 months, the Shannon diversity index (H) of LAB increased from 1.16 to 1.318 and for bifidobacteria the H increased from 0.975 to 1.293 (P < 0.05). Higher Sorenson’s pair wise similarity coefficient was observed for LAB and bifidobacteria during 2nd and the 3rd month. The species of the genera Enterococcus, Streptococcus, and Lactobacillus were dominant among the LAB group whereas Bifidobacterium breve was dominant species among Bifidobacterium group. CONCLUSIONS: Our results indicate that in breast fed infants, the microbial diversity of LAB and bifidobacteria increased during the period of study.

Ecology and biotechnological potential of bacterial community from three marine sponges of the coast of Rio de Janeiro, Brazil

ABSTRACT Marine sponges has been a large reservoir of microbial diversity, with the presence of many species specific populations as well as producing biologically active compounds, which has attracted great biotechnological interest. In order to verify the influence of the environment in the composition of the bacterial community present in marine sponges and biotechnological potential of bacteria isolated from these organisms, three species of sponges and the waters surrounding them were collected in different beaches of Rio de Janeiro, Brazil. The profile of the bacterial community present in sponges and water was obtained by PCR-DGGE technique and the biotechnological potential of the strains isolated by producing amylase, cellulase, protease and biosurfactants. The results showed that despite the influence of the environment in the composition of the microbial community, studied marine sponges shown to have specific bacterial populations, with some, showing potential in the production of substances of biotechnological applications.

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

Abstract 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.

Establecimiento y evaluación de dos métodos de pre tratamiento de muestras de suelo para la extracción de ADN para el estudio de la diversidad bacteriana / Establishment and evaluation of two methods of pre-treatment of soil samples for the extraction of DNA for the study of bacterial diversity

La necesidad de ampliar los conocimientos respecto a los mecanismos bioquímicos y fisiológicos desarrollados por los microorganismos presentes en suelos requiere de una descripción completa de la diversidad microbiana, para lo cual en las últimas décadas se han desarrollado diferentes técnicas moleculares (qPCR, DGGE, T-RFLP, RAPD.) las mismas que requieren una adecuada técnica de extracción de ADN que aseguren el éxito de la descripción de la diversidad microbiana, considerando las características de las muestras de suelos a ser estudiadas. Los protocolos de extracción de ADN generalmente utilizados están basados en la separación de los microorganismos de la matriz antes de la extracción de ADN mediante lisis física o química y por otro lado, la extracción directa del ADN microbiano a partir de muestras de suelo, sin embargo la presencia de sustancias húmicas y fenólicas afectan la calidad del ADN extraído, lo que repercuten en el desarrollo de posteriores estudios moleculares. La finalidad de este estudio fue la de establecer procedimientos de pre tratamientos de 3 tipos de nuestras de suelo (arenoso, arcilloso y francos) para posteriormente describir la riqueza y diversidad bacteriana de las muestras en estudio mediante PCR DGGE. De esta manera se determinó que la adición de CaCO3 en muestras de suelos francos permite la identificación de una mayor diversidad y riqueza bacteriana (10 bandas). Asimismo, la adición de PVPP a suelos arenosos (8 bandas) y arcillosos (3 bandas) también permite obtener las características descritas anteriormente utilizando el método PCR-DGGE. Lo cual indica que los procedimientos de pre tratamiento con CaCO3 y PVPP son específicos para la extracción de ciertas comunidades microbianas.

The knowledge about biochemical and physiological mechanisms by microorganisms in soils are required for a complete description of microbial diversity, lately different molecular techniques have been developed to study this feature (qPCR, DGGE, T- RFLP, RAPD). DNA extraction techniques ensure the description of the microbial diversity success, according the soil samples characteristics. Generally, DNA extraction protocols used for separation of microorganism of matrix soil before DNA extraction by physical and chemical lysis. Other protocol is direct extraction of microbial DNA from soil samples, humic acids and phenolic substances affect the quality of DNA, which affect the development of subsequent molecular studies. The purpose of this study was to establish pretreatment procedures for different kind of soil samples (frank, sandy and clayey) in order to describe richness and bacterial diversity by PCR DGGE. In this sense, we determined the addition of CaCO3 in frank soils samples allows the identification of greater diversity and bacterial richness (10 bands) than the other method. Besides, PVPP pretreatment is no only useful to obtain bacterial diversity in sandy soil (8 bands), but also in clayey soils (3 bands) soils by PCR-DGGE method. This indicates that the pretreatment procedures with CaCO3 and PVPP are specific for soil microbial community's isolation.

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

Abstract 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.

Comparative analysis of the intestinal microbial flora diversity of adult and young African lions / 中国兽医学报

In this study,the intestinal microbial flora diversity of adult and young African lions in the same breeding environment was detected by PCR-DGGE technique.Total bacterial DNA was extracted and 16S rDNA V3 region was amplified,then conducting PCR-DGGE.Subsequently,the specific bands of DGGE were cloned and sequenced.The bacterial species were identified by comparing the sequence through BLAST.The results indicated that the intestinal microbial flora of adult African lions includes Clostridium,Lachnospiraceae bacterium,Anaerovorax,Lactococcus,Peptostreptococcus and Blautia.While the intestinal microbial flora of young African lions is lesser,most bacteria are common to adult and young lions,such as Bacteroidetes bacterium and rumen bacterium.The UPGMA clustering analysis of the DGGE fingerprint showed the similarities of the bacteria structures between adult and young African lions were only 34％.These results revealed that the intestinal microbial flora has significant difference in different stages of African lions.This study lays a foundation for the development of microecological agents in different growth stages of wild animals.

Study on dynamic changing regularity of microflora in fermentation process of Sojae Semen Praeparatum by PCR-DGGE / 中草药

Objective: To reveal the dynamic changing regularity of microflora in the fermentation process of Sojae Semen Praeparatum (SSP) and lay the foundation for revealing the mechanism of SSP processing by denaturing gradient gel electrophoresis (DGGE). Methods: The dynamic changes of microflora, both bacteria and fungi in fermentation process were monitored by PCR-denaturing gradient gel electrophoresis. According to the unweighted pair group method using arithmetic average clustering, the samples of SSP in various stages were analyzed. Results: Bacterial flora had diversity, and Aspergillus was the major fungus in the first stage called "yellow cladding". The major bacteria was Lactobacillus, while the major fungus was Cryptococcus at the "secondary fermentation" stage. The major microorganism was Bacillus subtillis and Pseudomonas putida on day 1, and Stenotrophomonas maltophilia, Sphingobacterium sp, and A. oryzae on day 3. Then on day 6, B. amyloliquefaciens, Aspergillus, and Trichosporon ovoides became the primary microorganisms. B. subtillis, T. ovoides, and A. niger were the major microorganism on day 3 of "secondary fermentation". On day 9 of this stage, the major strains were B. subtilis, L. concavus, L. nasuensis, and Cryptococcus randhawi. On day 15 of "secondary fermentation", they were B. subtilis, L. concavus, C. randhawi, Trichosporon, and two fungi cannot be cultured. Klebsiella oxytoca, B. subtilis, and L. concavus were dominant strains in the whole fermentation process. The composition of microflora in "yellow cladding" stage was different to that of the "secondary fermentation". The microbial community on day 3 and 6 was similar to 76.4%. While the lowest similarity between the samples on day 3 and 9, it was similar to 24.5% during samples on day 6 and 9 in "secondary fermentation" stage. The highest similarity of fungal composition was between day 3 and 6 samples, and the lowest one was between day 3 and 15 of "secondary fermentation", which was similar to 11.2% only. Conclusion: The results show that the unique flavor and function of SSP may be determined by the dynamic microbial communities and microbial flora in the fermentation process, and the secondary fermentation is proved to be irreplaceable from the microbiological point of view.

Effects of different forms of nitrogen on rhizosphere microbial community structure of Eichhornia crassipes (Pontederiaceae)

AbstractRhizosphere microbial communities are important for phytoremediation, plant nutrition, health and metabolism. Many factors, including plant species, pH and nutritional factors influence rhizosphere microbiology. In this study, we analysed the effects of different forms of nitrogen on the structures of rhizosphere microbial communities of E. crassipes. Using a conventional culture method with special media, bacteria, actinobacteria and molds were cultured. We found that the numbers of bacteria were largely similar across the three culture conditions, while the numbers of actinobacteria and molds from the rhizosphere of E. crassipes cultured in NH4Cl solution were two orders of magnitude higher than those from the rhizospheres of plants cultured in distilled water and KNO3 solution. Using a culture-independent method of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rDNA, we found that the form of nitrogen could influence the components of the rhizosphere microbial community. Pseudoxanthomonas, Enterobacter and Citrobacter were present in all of the samples cultured under the three different experimental conditions. The genus Reyranella was found only in samples cultured in KNO3 solution; Acinetobacter and Streptomyces were unique to samples cultured in NH4Cl solution, and Pseudomonas, Pseudacidovorax and Methylosinus were found only in samples cultured in distilled water. Pseudoxanthomonas and Acidovorax were the dominant genera in the rhizosphere microbial community of E. crassipes cultured in KNO3 solution, while Novosphingobium was the dominant genus in the sample cultured in a nitrogen-deficient medium. Our results provide a theoretical foundation for using E. crassipes as a phytoremediation plant and controlling the widespread distribution of E. crassipes around the world using principles of nutrient metabolism.

ResumenComunidades microbianas de la rizósfera son importantes para la fitorremediación, nutrición vegetal, salud y metabolismo. Muchos factores, incluyendo la especie de planta, el pH y los factores nutricionales influyen en la microbiología de la rizósfera. En este estudio, se analizaron los efectos de las diferentes formas del nitrógeno en la estructura de las comunidades microbianas de la rizósfera de E. crassipes. Mediante métodos de cultivo convencional con medios especiales se cultivaron: bacterias, actinobacterias y mohos. Se encontró que el número de bacterias era en gran parte similar a través de las tres condiciones de cultivo, mientras que el número de actinobacterias y mohos de la rizósfera de E. crassipes cultivadas en solución de NH4Cl era dos órdenes de magnitud superior a los de las rizósferas de plantas cultivadas en agua destilada y solución de KNO3. Utilizando un método de cultivo independiente de electroforesis en gel con gradiente de desnaturalización (PCR-DGGE) del ADNr 16S, se encontró que la forma de nitrógeno podría influir en los componentes de la comunidad microbiana de la rizósfera. Pseudoxanthomonas, Enterobacter y Citrobacter estaban presentes en todas las muestras cultivadas en las tres condiciones experimentales. El género Reyranella se encontró sólo en muestras cultivadas en solución de KNO3; Acinetobacter y Streptomyces eran las únicas muestras cultivadas en solución de NH4Cl, y Pseudomonas, Pseudacidovorax y Methylosinus se encontraron sólo en muestras cultivadas en agua destilada. Pseudoxanthomonas y Acidovorax eran los géneros dominantes en la comunidad microbiana de la rizósfera de E. crassipes cultivadas en solución de KNO3, mientras que Novos phingobium fue el género dominante en la muestra cultivada en un medio deficiente de nitrógeno. Nuestros resultados proporcionan una base teórica para el uso de E. crassipes como planta fitorremediadora y para controlar la distribución generalizada de E. crassipes en todo el mundo a través de los principios del metabolismo de nutrientes.

Evaluation of the microbial diversity in sequencing batch reactor treating linear alkylbenzene sulfonate under denitrifying and mesophilic conditions using swine sludge as inoculum

The objective of this study was to evaluate the degradation of Linear Alkylbenzene Sulfonate (LAS) in anaerobic sequencing batch reactor (ASBR) under denitrifying conditions using swine sludge as inoculum. The reactor was operated for 104 days with synthetic substrate containing nitrate, and LAS was added later (22 mg/L). Considering the added mass of the LAS, the adsorbed mass in the sludge and discarded along with the effluent, degradation of the surfactant at the end of operation was 87%, removal of chemical oxygen demand was 86% and nitrate was 98%. The bacterial community was evaluated by cutting the bands and sequencing of polymerase chain reaction (PCR) fragments and denaturing gradient gel electrophoresis (DGGE). The sequences obtained were related to the phylum Proteobacteria and the alpha-and beta-proteobacteria classes, these bacteria were probably involved in the degradation of LAS. The efficiently degraded LAS in the reactor was operated in batch sequences in denitrifying conditions.

Effects of dried whey on the intestinal bacterial community and probiotics in weaned laboratory rabbits / 中国比较医学杂志

Objective To investigate the effects of dried whey on the intestinal bacterial community and probiotics in weaned laboratory rabbits .Methods A single factor design was employed to investigate the effects of dried whey supplemented at levels of 0%, 2%, 5%and 10%, respectively, on 48 weaned (40-day-old) laboratory rabbits.At the day 30, eight rabbits in each group were taken and sacrificed after anesthesia .The total bacterial DNA from the ceacal content of each selected rabbit was drew to analyze the bacterial community and intestinal probiotics ( Bifidobacterium and Lactobacillius) population by PCR-DGGE and real-time fluorescence quantitative PCR, respectively.Results 1) The DGGE parameters of ceacal bacterial community were increased with the increasing dried whey supplemental levels .The number of DGGE band in 2%, 5%and 10%dried whey supplement groups (P0.05).Supplying dried whey has no significant effects on the homogeneity index (P>0.05).2) The population of Bifidobacterium and Lactobacillius in ceacal content had a trend of increase with the rising dried whey supplement levels .Compared with the 0% supplement group , the Lactobacillius population in the 2%, 5% and 10%supplement groups ( P <0.05 ) , the Bifidobacterium population in the 10% supplement group ( P <0.05 ) were significantly increased .Conclusions The results of our study indicate that: 1 ) Supplying dried whey in the feed of laboratory rabbit can effectively increase the diversity of ceacal bacterial community .2) Dried whey may effectively improve the intestinal probiotics population .

Microbial dynamics during azo dye degradation in a UASB reactor supplied with yeast extract

The present work aimed to investigate the microbial dynamics during the anaerobic treatment of the azo dye blue HRFL in bench scale upflow anaerobic sludge bed (UASB) reactor operated at ambient temperature. Sludge samples were collected under distinct operational phases, when the reactor were stable (low variation of color removal), to assess the effect of glucose and yeast extract as source of carbon and redox mediators, respectively. Reactors performance was evaluated based on COD (chemical oxygen demand) and color removal. The microbial dynamics were investigated by PCR-DGGE (Polimerase Chain Reaction - Denaturing Gradient of Gel Electrophoresis) technique by comparing the 16S rDNA profiles among samples. The results suggest that the composition of microorganisms changed from the beginning to the end of the reactor operation, probably in response to the presence of azo dye and/or its degradation byproducts. Despite the highest efficiency of color removal was observed in the presence of 500 mg/L of yeast extract (up to 93%), there were no differences regarding the microbial profiles that could indicate a microbial selection by the yeast extract addition. On the other hand Methosarcina barkeri was detected only in the end of operation when the best efficiencies on color removal occurred. Nevertheless the biomass selection observed in the last stages of UASB operation is probably a result of the washout of the sludge in response of accumulation of aromatic amines which led to tolerant and very active biomass that contributed to high efficiencies on color removal.

PCR Based Identification of Microbial Community in Usage Water of Slum Areas in Hyderabad.

Due to rapid urbanization in a context of economic constraints, the majority of urban residents in Hyderabad live in slums often characterized by a lack of basic services such as water and sewerage. Consequently, the urban poor often use inexpensive pit latrines and at the same time may draw domestic water from nearby local taps. Overcrowding in slums limits the adequate distance between taps and pit latrines so that micro-organisms migrate from latrines to water sources. Sanitary practices in these overcrowded slums are also poor, leading to contamination of this tap water. The DNA sequencing results indicated the microbial diversity, revealing that the dominant bacteria present in Khairathabad slum area of Hyderabad is Acinetobacter sp. whereas the dominant bacteria in Varasiguda slum area of Hyderabad is Alpha-proteobacteria. Futhermore, cluster analysis of the DGGE profiles indicated significant diversity in the bacterial community by depicting two distinct clusters for each waste water treatment plant. These data endorse the ability of PCR-DGGE method to identify and characterize bacterial community from Usage water.

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit MiniprepTM (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.

Analysis of alteration of gut microbial population under the exposure of graded hyperbaric pressures: Application of metagenomic approach.

Gastroenterological disorders are very common at hyperbaric conditions. The present study was conducted to find out the impact of gut flora on the gastrointestinal disorders created at such environmental circumstances. For this, male albino rat were exposed to graded hyperbaric pressures (915 and 1277 mmHg) and large intestinal content was examined for microbial composition using culture based and PCR-DGGE tools. After 30 day exposure, total aerobes (38.54 and 375.57 folds, 1.35 and 1.58 gdi) and E. coli (126.05 and 873.23 folds, 1.31 and 1.44 gdi) were increased whereas total anaerobes (7.01 × 104 and 8.84 × 103 folds, -1.56 and -1.39 gdi), Enterobacter spp. (-2.45 and -1.00 gdi) and Clostridium perfringens (12.88 and 54.16 folds, -1.38 and -1.75 gdi) were decreased significantly in respect to control after exposure of simulated hyperbaric pressures like at 915 and 1277 mmHg, respectively. Metagenomics study revealed an overall reduction in total microbial profile was noted than control at higher level hyperbaric pressure, i.e., 1277 mmHg air pressure for highest duration of exposure. Though, some new bands also appeared which indicated the expansion of dormant or new microbiota, Variation in the numbers of these newly dominated bacteria was correlated to dose and duration of hyperbaric treatment. The histological results clearly indicated that hyperbaric environment induced severe inflammation in the mucosal and submucosal layer of large intestine. Thus, the result suggest that hyperbaric pressure is an important exogenous factor that strongly modulated the intestinal morphology and microbial ecology, and induced several gastrointestinal ailments during hyperbarism.

Identification and assessment of kefir yeast potential for sugar/ethanol-resistance

Biochemical and molecular analysis was used for identification of different kefir yeasts species from Brazil, Canada and the United States of America. The sugar/ethanol-resistant activity of the yeasts was evaluated. Saccharomyces cerevisiae and Kluyveromyces marxianus had the highest growth rates, suggesting biotechnological applications possible for these strains.

Application of molecular fingerprinting for analysis of a PAH-contaminated soil microbiota growing in the presence of complex PAHs / Aplicação de técnica molecular para análise da microbiota de solo contaminado em misturas complexas de HPAs

Polycyclic aromatic hydrocarbons (PAHs) constitute a group of priority pollutants which are present at high concentrations in the soils of many industrial contaminated sites. Pollution by these compounds may stimulate growth of organisms able to live in these environments causing changes in the structure of the microbial community due to some cooperative process of metabolization of toxic compounds. A long-term PAH-contaminated soil was stored for several years and used to analyze the native microbiota regarding their ability to grow on pyrene, benzo[a]pyrene, as well as in mixtures of LMW- and HMW-PAHs. Molecular profiles of the microbial community was assessed by PCR-DGGE of 16S rRNA gene, and the number of bands observed in DGGE analyses was interpreted as dominant microbial members into the bacterial community. Results of PAH-contaminated soil microorganisms showed different profiles in the degradative dynamics when some nutrients were added. Predominant species may play a significative role while growing and surviving on PAHs, and some other metabolically active species have emerged to interact themselves in a cooperative catabolism of PAHs.

Os hidrocarbonetos poliaromáticos (HPAs) são considerados poluentes prioritários presentes em expressiva concentração no solo contaminado com derivados de petróleo. A poluição por esses compostos estimula o crescimento de microrganismos capazes de sobreviverem nestes ambientes contaminados, causando alterações na estrutura da comunidade microbiana do solo pelo processo de cooperação metabólica entre as populações. Um solo contaminado por um longo período de tempo foi coletado de uma área industrial (Port Melbourne, Austrália) e utilizado para análise da capacidade da comunidade microbiana em crescer em HPAs isolados e/ou em misturas como únicas fontes de carbono e energia. Os perfis moleculares foram obtidos por PCR-DGGE do fragmento da subunidade 16S do DNA ribossomal, sendo o número de bandas presentes nos géis de eletroforese interpretado como populações dominantes dentro da comunidade do solo. Resultados demonstraram diferentes perfis quando vitaminas e micronutrientes fizeram parte do meio líquido de crescimento da microbiota, além da presença dos HPAs. As espécies predominantes podem ter papel significativo na degradação desses compostos no solo a ser remediado, enquanto sobrevivem e interagem com outras populações por meio de mecanismos de catabolismo cooperativo.

Extraction of bulk DNA from Thar Desert soils for optimization of PCR-DGGE based microbial community analysis

A reliable method for characterizing microbial communities on the basis of their differences in the 16S ribosomal RNA (rRNA) gene sequences in the hot arid zone sandy soils has been optimized. A desert plant (Calligonum polygonoides) was chosen to provide the rhizospheric soil samples, collected from three different agro-ecological locations. Total community DNA was efficiently extracted at small-scale level using direct lysis with hot sodium dodecyl sulphate (SDS), glass bead beating and finally subjecting the sandy soil to liquid nitrogen freeze-thaw cycles. To amplify V3 region of bacterial 16S rRNA gene, universal conserved primers were used. Second round polymerase chain reaction (PCR) was attempted to increase product concentration and to minimize the effect of inhibitory substances. To enhance the detection sensitivity of the denaturing gradient gel electrophoresis (DGGE), the effect of change in template DNA concentration was studied. The separation of bands were greatly enhanced in the fingerprints obtained after the second round of PCR representing low abundant species which were not differentiated at single optimized concentration of DNA.

Remoção de etanol e benzeno em reator anaeróbio horizontal de leito fixo na presença de sulfato / Ethanol and benzene removal in a horizontal-flow anaerobic immobilized biomass reactor in the presence of sulfate

Reator anaeróbio horizontal de leito fixo (RAHLF), preenchido com espumas de poliuretano, foi usado para tratar benzeno em solução etanólica, sob condições sulfetogênicas. Benzeno foi adicionado em concentração inicial de 2,0 mg.l-1, seguido de aumentos que variaram até 10 mg.l-1. O etanol foi adicionado em concentrações de 170 mg.l-1 a 980 mg.l-1. Soluções de sulfato ferroso e sulfato de sódio foram usadas, nas concentrações de 91 e 550 mg.l-1, respectivamente. O reator foi operado a 30 (± 2) ºC com tempo de detenção hidráulica de 12 h. A remoção da matéria orgânica foi próxima a 90 por cento com taxa máxima de degradação de benzeno de 0,07 mg benzeno.mg-1SSV.d-1. O presente trabalho corrobora os dados obtidos por Cattony et al (2005), na medida em que torna mais consistente a proposta do uso de unidades compactas de RAHLF, para a biorremediação in situ de compostos aromáticos.

In this study it is reported the operation of a horizontal-flow anaerobic immobilized biomass (HAIB) reactor under sulfate-reducing condition which was also exposed to different amounts of ethanol and benzene. The HAIB reactor comprised of an immobilized biomass on polyurethane foam and ferrous and sodium sulfate solutions were used (91 and 550 mg.l-1, respectively), to promote a sulfate-reducing environment. Benzene was added at an initial concentration of 2.0 mg.l-1 followed by an increased to 9 e 10 mg.l-1, respectively. Ethanol was added at an initial concentration of 170 mg.l-1 followed by an increased range of 960 mg.l-1. The reactor was operated at 30 (± 2) ºC with hydraulic detention time of 12 h. Organic matter removal efficiency of 90 percent with a maximum benzene degradation rate of 0.07 mg benzene.mg-1VSS.d-1. Thus, this work corroborate the data obtained for Cattony et al (2005) and also demonstrate that compact units of HAIB reactors, under sulfate reducing conditions, are a potential alternative for in situ aromatic compounds bioremediation.