Prominent Effect of Soil Network Heterogeneity on Microbial Invasion

Using a network representation for real soil samples and mathematical models for microbial spread, we show that the structural heterogeneity of the soil habitat may have a very significant influence on the size of microbial invasions of the soil pore space. In particular, neglecting the soil structural heterogeneity may lead to a substantial underestimation of microbial invasion. Such effects are explained in terms of a crucial interplay between heterogeneity in microbial spread and heterogeneity in the topology of soil networks. The main influence of network topology on invasion is linked to the existence of long channels in soil networks that may act as bridges for transmission of microorganisms between distant parts of soil.

Influence of milk type and addition of passion fruit peel powder on fermentation kinetics, texture profile and bacterial viability in probiotic yoghurts

The effect of the addition of passion fruit peel powder (PFPP) on the fermentation kinetics and texture parameters, post-acidification and bacteria counts of probiotic yoghurts made with two milk types were evaluated during 28 days of storage at 4 degrees C. Milks were fermented by Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus (CY340), and one strain of probiotic bacteria: Lactobacillus acidophilus (L10 and NCFM), Bifidobacterium animalis subsp. lactis (8104 and HN019). The addition of PFPP reduced significantly fermentation time of skim milk co-fermented by the strains L10, NCFM and HN019. At the end of 28-day shelf-life, counts of B. lactis Bl04 were about 1 Log CFU mL(-1) higher in whole yoghurt fermented with PFPP regarding its control but, in general, the addition of PFPP had less influence on counts than the milk type itself. The titratable acidity in yoghurts with PFPP was significantly higher than in their respective controls, and in skim yoghurts higher than in the whole ones. The PFPP increased firmness, consistency (except for the NCFM strain of L acidophilus) and cohesiveness of all skim yoghurts. The results point out the suitability of using passion fruit by-product in the formulation of both skim and whole probiotic yoghurts. (C) 2012 Elsevier Ltd. All rights reserved.

Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis

The endemic marine sponge Arenosclera brasiliensis (Porifera, Demospongiae, Haplosclerida) is a known source of secondary metabolites such as arenosclerins A-C. In the present study, we established the composition of the A. brasiliensis microbiome and the metabolic pathways associated with this community. We used 454 shotgun pyrosequencing to generate approximately 640,000 high-quality sponge-derived sequences (similar to 150 Mb). Clustering analysis including sponge, seawater and twenty-three other metagenomes derived from marine animal microbiomes shows that A. brasiliensis contains a specific microbiome. Fourteen bacterial phyla (including Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Cloroflexi) were consistently found in the A. brasiliensis metagenomes. The A. brasiliensis microbiome is enriched for Betaproteobacteria (e.g., Burkholderia) and Gammaproteobacteria (e.g., Pseudomonas and Alteromonas) compared with the surrounding planktonic microbial communities. Functional analysis based on Rapid Annotation using Subsystem Technology (RAST) indicated that the A. brasiliensis microbiome is enriched for sequences associated with membrane transport and one-carbon metabolism. In addition, there was an overrepresentation of sequences associated with aerobic and anaerobic metabolism as well as the synthesis and degradation of secondary metabolites. This study represents the first analysis of sponge-associated microbial communities via shotgun pyrosequencing, a strategy commonly applied in similar analyses in other marine invertebrate hosts, such as corals and algae. We demonstrate that A. brasiliensis has a unique microbiome that is distinct from that of the surrounding planktonic microbes and from other marine organisms, indicating a species-specific microbiome.

Microbial transformation of the sesquiterpene lactone tagitinin C by the fungus Aspergillus terreus

The biotransformation of the sesquiterpene lactone tagitinin C by the fungus Aspergillus terreus MT 5.3 yielded a rare derivative that was elucidated by spectrometric methods. The fungus led to the formation of a different product through an unusual epoxidation reaction between C4 and C5, formation of a C3,C10 ether bridge, and a methoxylation of the C1 of tagitinin C. The chemical structure of the product, namely 1 beta-methoxy-3 alpha-hydroxy-3,10 beta-4,5 alpha-diepoxy-8 beta-isobutyroyloxygermacr-11(13)-en-6 alpha,12-olide, is the same as that of a derivative that was recently isolated from the flowers of a Brazilian population of Mexican sunflower (Tithonia diversifolia), which is the source of the substrate tagitinin C. The in vitro cytotoxic activity of the substrate and the biotransformed product were evaluated in HL-60 cells using an MTT assay, and both compounds were found to be cytotoxic. We show that soil fungi may be useful in the biotransformation of sesquiterpene lactones, thereby leading to unusual changes in their chemical structures that may preserve or alter their biological activities, and may also mimic plant biosynthetic pathways for production of secondary metabolites.

Biotechnological Utilization of Biodiesel-Derived Glycerol for the Production of Ribonucleotides and Microbial Biomass

Ten yeast strains were evaluated concerning their capabilities to assimilate biodiesel-derived glycerol in batch cultivation. The influence of glycerol concentration, temperature, pH and yeast extract concentration on biomass production was studied for the yeast selected. Further, the effect of agitation on glycerol utilization by the yeast Hansenula anomala was also studied. The yeast H. anomala CCT 2648 showed the highest biomass yield (0.30 g g(-1)) and productivity (0.19 g L-1 h(-1)). Citric acid, succinic acid, acetic acid and ethanol were found as the main metabolites produced. The increase of yeast extract concentration from 1 to 3 g L-1 resulted in high biomass production. The highest biomass concentration (21 g L-1), yield (0.45 g g(-1)) and productivity (0.31 g L-1 h(-1)), as well as ribonucleotide production (13.13 mg g(-1)), were observed at 700 rpm and 0.5 vvm. These results demonstrated that glycerol from biodiesel production process showed to be a feasible substrate for producing biomass and ribonucleotides by yeast species.

Microbial characterization and removal of anionic surfactant in an expanded granular sludge bed reactor

This study evaluated linear alkylbenzene sulfonate removal in an expanded granular sludge bed reactor with hydraulic retention times of 26 h and 32 h. Sludge bed and separator phase biomass were phylogenetically characterized (sequencing 16S rRNA) and quantified (most probable number) to determine the total anaerobic bacteria and methanogenic Archaea. The reactor was fed with a mineral medium supplemented with 14 mg l(-1) LAS, ethanol and methanol. The stage I-32 h consisted of biomass adaptation (without LAS influent) until reactor stability was achieved (COD removal >97%). In stage II-32 h, LAS removal was 74% due to factors such as dilution, degradation and adsorption. Higher HRT values increased the LAS removal (stage III: 26 h - 48% and stage IV: 32 h - 64%), probably due to increased contact time between the biomass and LAS. The clone libraries were different between samples from the sludge bed (Synergitetes and Proteobacteria) and the separator phase (Firmicutes and Proteobacteria) biomass. (C) 2011 Elsevier Ltd. All rights reserved.

Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes

Abstract Background The metabolic capacity for nitrogen fixation is known to be present in several prokaryotic species scattered across taxonomic groups. Experimental detection of nitrogen fixation in microbes requires species-specific conditions, making it difficult to obtain a comprehensive census of this trait. The recent and rapid increase in the availability of microbial genome sequences affords novel opportunities to re-examine the occurrence and distribution of nitrogen fixation genes. The current practice for computational prediction of nitrogen fixation is to use the presence of the nifH and/or nifD genes. Results Based on a careful comparison of the repertoire of nitrogen fixation genes in known diazotroph species we propose a new criterion for computational prediction of nitrogen fixation: the presence of a minimum set of six genes coding for structural and biosynthetic components, namely NifHDK and NifENB. Using this criterion, we conducted a comprehensive search in fully sequenced genomes and identified 149 diazotrophic species, including 82 known diazotrophs and 67 species not known to fix nitrogen. The taxonomic distribution of nitrogen fixation in Archaea was limited to the Euryarchaeota phylum; within the Bacteria domain we predict that nitrogen fixation occurs in 13 different phyla. Of these, seven phyla had not hitherto been known to contain species capable of nitrogen fixation. Our analyses also identified protein sequences that are similar to nitrogenase in organisms that do not meet the minimum-gene-set criteria. The existence of nitrogenase-like proteins lacking conserved co-factor ligands in both diazotrophs and non-diazotrophs suggests their potential for performing other, as yet unidentified, metabolic functions. Conclusions Our predictions expand the known phylogenetic diversity of nitrogen fixation, and suggest that this trait may be much more common in nature than it is currently thought. The diverse phylogenetic distribution of nitrogenase-like proteins indicates potential new roles for anciently duplicated and divergent members of this group of enzymes.

Microbial load in instruments used in surgeries classified as clean

Introduction / objectives The number of orthopedic surgery, especially surgery of total hip and knee, have been more frequent due to technological advances. This study aims to determine the microbial load in the instruments used in clean surgeries, quantifying and identifying the genus and species of microbial growth.Methods Orthopedic surgical instruments were immersed, after use, in sterile water, sonicated in ultrasonic washer and consecutively shaken. Then, the lavage was filtered through a 0.45micron membrane, the result was incubated in aerobic medium, anaerobic medium and medium for fungi and yeasts. Results In clean surgeries, results showed that 47% of used instruments had microbiological growth in the range of 1 to 100 CFU/instrument. The most prevalent organism was Staphylococcus coagulase negative (28%), followed by Bacillus subtilis (11%).This study refuted the hypothesis that clean surgeries happen in micro-organismsfree surgery field. Conclusion The microbiological findings reinforce the importance of antibiotic prophylaxis, practice already well established for this category of surgical procedure.

Economic viability of retrofiting emitters in center pivot irrigation systems

Although several studies have been conducted to evaluate the uniformity of water application under center pivot irrigation systems, there are few studies concerning the economic perspective of such coefficient. The aim of this study is to present a methodology to accomplish an economic analysis as support for the decision-making to retrofit emitters in center pivot irrigation systems, and to attribute an economic meaning to the uniformity coefficient of water application taking into account the response function productivity to the amount of water applied and the sale price of the crops. In the hypothetic calculation example considering the variation of revenue of potato crop under center pivot irrigation system, it was verified that the area with uniformity coefficient of water application of 90% brought an income increase of BR$ 1,992.00, considering an area about 1,0 ha. Thus, it can be concluded that the methodology presented has met the objectives proposed in the study and made it possible to attribute an economical meaning to the coefficient of water uniformity application.

Viability of recently harvested and stored Xylopia aromatica (Lam.) Mart. (Annonaceae) seeds

Xylopia aromatica is a native species from Brazil's "Cerrado", recommended for restoration ecology and also as a medicine. Its seeds have embryos with morphophysiological dormancy, making nursery propagation difficult. The objective of this study was to verify the efficiency of X-ray and tetrazolium tests for evaluating the viability of three seed lots, stored for different periods. All seeds were X-rayed (13 kV, 350 seconds) and samples used for tetrazolium and germination tests. In the tetrazolium test, seeds were submitted to six treatments at two temperatures (25 and 30 °C) with imbibition in distilled water and immersion in three concentrations of tetrazolium solution (0.5, 0.75 and 1%) at the two imbibition temperatures. Seeds for the germination test were placed for imbibition in distilled water and a 500 ppm Promalin® (6-Benzyladenine + GA4 + GA7) solution and later sown in sterilized sand. The embryo could not be observed with the X-ray test. However, those seeds observed with an undamaged endosperm did not differ in the percentages of seeds with firm and stained endosperms observed in the tetrazolium test for all the lots. The tetrazolium test is efficient for evaluating seed viability, principally if imbibed at 30 °C and immersed in a 0.5% solution at 30 °C.

Fluoride modulates preosteoblasts viability and matrix metalloproteinases-2 and -9 activities

This study evaluated the influence of fluoride on cell viability and activity of matrix metalloproteinases (MMP) -2 and -9 secreted by preosteoblasts. Preosteoblasts (MC3T3-E1 murine cell line) were cultured in MEM medium supplement with 10% Fetal Bovine Serum (FBS) and nucleosides/ribonucleosides without ascorbic acid. Adherent cells were treated with different concentrations of F (as sodium fluoride-NaF) in medium (5 x 10-6 M, 10-5 M, 10-4 M and 10-3 M) for 24, 48, 72 and 96 h at 37ºC, 5% CO2. Control cells were cultivated in MEM only. After each period, preosteoblast viability was assessed by MTT assay. MMP-2 and -9 activities were performed by gel zymography. Also, alkaline phosphatase (ALP) activity was quantified by colorimetry in all experimental groups. It was shown that cultured cells with the highest dose of F (10-3 M) for 96 h decreased preosteoblast viability while lower doses of F did not alter it, when compared to untreated cells. No differences were observed in ALP activity among groups. Moreover, compared to control, the treatment of cells with F at low dose slightly increased MMP-2 and -9 activities after 24 h. It was concluded that F modulates preosteoblast viability in a dose-dependent manner and also may regulate extracellular matrix remodeling.

Effects of microbial inoculants and amino acid production by-product on fermentation and chemical composition of sugarcane silages

The objective of this study was to evaluate the chemical composition, fermentation patterns and aerobic stability of sugarcane silages with addition of amino acid production (monosodium glutamate) by-product (APB) and microbial inoculants. Mature sugarcane was chopped and ensiled in laboratory silos (n = 4/treatment) without additives (control) and with APB (10 g/kg), Pioneer 1174® (PIO, 1.0 mg/kg, Lactobacillus plantarum + Streptoccoccus faecium, Pioneer), Lalsil Cana (2.0 mg/kg, Lactobacillus buchineri, Lallemand) or Mercosil Maís 11C33® (1.0 mg/kg, Lactobacillus buchineri + Lactobacillus plantarum + Streptoccoccus faecium, Timac Agro). Fresh silage and silage liquor samples were obtained to assess pH, chemical composition and organic acid concentrations. Silage temperature was recorded throughout seven days to evaluate aerobic stability. The addition of APB decreased lactic acid levels, increased pH and N-NH3 and did not alter ethanol, acetic and butyric acids concentrations or dry matter (DM) losses. Microbial inoculants enhanced acetic acid levels, although only Pioneer 1174® and Mercosil Maís 11C33® lowered ethanol, butyric acid and DM losses. The addition of APB increased CP content and did not modify DM, soluble carbohydrates contents or in vitro dry matter digestibility. Additives did not alter silage maximum temperature or temperature increasing rate; however, Pioneer 1174® and Mercosil Maís 11C33® increased the time elapsed to reach maximum temperature. Monosodium glutamate production by-product does not alter fermentation patterns or aerobic stability of sugarcane silages, whereas homofermentative bacteria can provide silages of good quality.

Comparison of different protocols for the extraction of microbial DNA from reef corals

This study aimed to test different protocols for the extraction of microbial DNA from the coral Mussismilia harttii. Four different commercial kits were tested, three of them based on methods for DNA extraction from soil (FastDNA SPIN Kit for soil, MP Bio, PowerSoil DNA Isolation Kit, MoBio, and ZR Soil Microbe DNA Kit, Zymo Research) and one kit for DNA extraction from plants (UltraClean Plant DNA Isolation Kit, MoBio). Five polyps of the same colony of M. harttii were macerated and aliquots were submitted to DNA extraction by the different kits. After extraction, the DNA was quantified and PCR-DGGE was used to study the molecular fingerprint of Bacteria and Eukarya. Among the four kits tested, the ZR Soil Microbe DNA Kit was the most efficient with respect to the amount of DNA extracted, yielding about three times more DNA than the other kits. Also, we observed a higher number and intensities of DGGE bands for both Bacteria and Eukarya with the same kit. Considering these results, we suggested that the ZR Soil Microbe DNA Kit is the best adapted for the study of the microbial communities of corals.

Microbial Translocation Is Associated with Extensive Immune Activation in Dengue Virus Infected Patients with Severe Disease

Background: Severe dengue virus (DENV) disease is associated with extensive immune activation, characterized by a cytokine storm. Previously, elevated lipopolysaccharide (LPS) levels in dengue were found to correlate with clinical disease severity. In the present cross-sectional study we identified markers of microbial translocation and immune activation, which are associated with severe manifestations of DENV infection. Methods: Serum samples from DENV-infected patients were collected during the outbreak in 2010 in the State of Sa˜o Paulo, Brazil. Levels of LPS, lipopolysaccharide binding protein (LBP), soluble CD14 (sCD14) and IgM and IgG endotoxin core antibodies were determined by ELISA. Thirty cytokines were quantified using a multiplex luminex system. Patients were classified according to the 2009 WHO classification and the occurrence of plasma leakage/shock and hemorrhage. Moreover, a (non-supervised) cluster analysis based on the expression of the quantified cytokines was applied to identify groups of patients with similar cytokine profiles. Markers of microbial translocation were linked to groups with similar clinical disease severity and clusters with similar cytokine profiles. Results: Cluster analysis indicated that LPS levels were significantly increased in patients with a profound pro-inflammatory cytokine profile. LBP and sCD14 showed significantly increased levels in patients with severe disease in the clinical classification and in patients with severe inflammation in the cluster analysis. With both the clinical classification and the cluster analysis, levels of IL-6, IL-8, sIL-2R, MCP-1, RANTES, HGF, G-CSF and EGF were associated with severe disease. Conclusions: The present study provides evidence that both microbial translocation and extensive immune activation occur during severe DENV infection and may play an important role in the pathogenesis.