scholarly journals The effect of combined application of Streptomyces rubrogriseus HDZ-9-47 with soil biofumigation on soil microbial and nematode communities

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Na Jin ◽  
Xiuliang Lu ◽  
Xueyan Wang ◽  
Qian Liu ◽  
Deliang Peng ◽  
...  
Keyword(s):  
Combination Treatment ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Soil Microbial Communities ◽  
Diversity Indices ◽  
Nematode Communities ◽  
Soil Microbial ◽  
Combined Application ◽  
Nematode Diversity ◽  
Gradient Gel Electrophoresis ◽  
Fungal Phytopathogens

AbstractMeloidogyne incognita causes significant damage to many different crops. Previous studies showed that Streptomyces rubrogriseus HDZ-9-47 is a promising biocontrol agent. Combining it with biofumigation improved its efficacy against M. incognita. In the present study, the reason for the improved efficacy of the combination was investigated by analyzing its impact on both the soil microbial and the nematode communities in the field. The results showed that the combined application reduced root galls by 41% and its control efficacy was greater than each treatment alone. Cultivation-based analyses showed that the combination treatment affected the soil microbial community. Actinomycetes and bacterial densities were negatively correlated with the root knot score. In contrast, the fungal densities were positively correlated with the root knot score. Denaturing gradient gel electrophoresis (DGGE) results showed that the combination of S. rubrogriseus HDZ-9-47 and biofumigation enriched beneficial microbes and reduced certain soil-borne fungal phytopathogens, thereby enhancing the efficacies of both S. rubrogriseus HDZ-9-47 and biofumigation against M. incognita. And HDZ-9-47 could colonize in soil. The total abundance of nematode and plant parasites, the ratio of soil fungivore nematode to fungivore plus bacterivore nematode, and the nematode diversity indices all decreased with the combination treatment. Overall, the results of this study demonstrate that combined application of HDZ-9-47 with biofumigation was a useful and effective approach to suppress M. incognita by manipulating soil microbial communities in field.

scholarly journals Denaturing gradient gel electrophoresis as a fingerprinting method for the analysis of soil microbial communities

2009 ◽  
Vol 55 (No. 10) ◽  
pp. 413-423 ◽  
Author(s):  
V. Valášková ◽  
P. Baldrian
Keyword(s):  
Microbial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Genes Encoding ◽  
Gradient Gel Electrophoresis ◽  
Temperature Gradient Gel Electrophoresis ◽  
Experimental Treatments ◽  
Multiple Samples

In soil microbial ecology, the effects of environmental factors and their gradients, temporal changes or the response to specific experimental treatments of microbial communities can only be effectively analyzed using methods that address the structural differences among whole communities. Fingerprinting methods are the most appropriate technique for this task when multiple samples must be analyzed. Among the methods currently used to compare microbial communities based on nucleic acid sequences, the techniques based on differences in the melting properties of double-stranded molecules, denaturing gradient gel electrophoresis (DGGE) or temperature gradient gel electrophoresis (TGGE), are the most widely used. Their main advantage is that they provide the possibility to further analyze whole sequences contained in fingerprints using molecular methods. In addition to the analysis of microbial communities based on DNA extracted from soils, DGGE/TGGE can also be used for the assessment of the active part of the community based on the analysis of RNA-derived sequences or for the analysis of sequences of functional genes encoding for proteins involved in important soil processes.

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

2020 ◽  
Author(s):  
Márton Mucsi ◽  
Gergely Krett ◽  
Tibor Szili-Kovács ◽  
János Móga ◽  
Andrea K. Borsodi
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Vegetation Type ◽  
Carbon Sources ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Soil Microbial ◽  
Gradient Gel Electrophoresis

Abstract 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.

scholarly journals PCR-Denaturing Gradient Gel Electrophoresis Analysis To Assess the Effects of a Genetically Modified Cucumber Mosaic Virus-Resistant Tomato Plant on Soil Microbial Communities

2010 ◽  
Vol 76 (10) ◽  
pp. 3370-3373 ◽  
Author(s):  
Chih-Hui Lin ◽  
Tzu-Ming Pan
Keyword(s):  
Microbial Communities ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Genetically Modified ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Gradient Gel Electrophoresis ◽  
Tomato Genotype

ABSTRACT The effects of a genetically modified cucumber mosaic virus (CMV)-resistant tomato on soil microbial communities were evaluated in this study. Soil position and environmental factors played more dominant roles than the tomato genotype in the variation of soil microbial communities.

scholarly journals Microbial Ecology Dynamics during Rye and Wheat Sourdough Preparation

2013 ◽  
Vol 79 (24) ◽  
pp. 7827-7836 ◽  
Author(s):  
Danilo Ercolini ◽  
Erica Pontonio ◽  
Francesca De Filippis ◽  
Fabio Minervini ◽  
Antonietta La Storia ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Microbial Ecology ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Content Type ◽  
Gradient Gel Electrophoresis ◽  
Plate Counts ◽  
Relative Abundances

ABSTRACTThe bacterial ecology during rye and wheat sourdough preparation was described by 16S rRNA gene pyrosequencing. Viable plate counts of presumptive lactic acid bacteria, the ratio between lactic acid bacteria and yeasts, the rate of acidification, a permutation analysis based on biochemical and microbial features, the number of operational taxonomic units (OTUs), and diversity indices all together demonstrated the maturity of the sourdoughs during 5 to 7 days of propagation. Flours were mainly contaminated by metabolically active genera (Acinetobacter,Pantoea,Pseudomonas,Comamonas,Enterobacter,Erwinia, andSphingomonas) belonging to the phylumProteobacteriaorBacteroidetes(genusChryseobacterium). Their relative abundances varied with the flour. Soon after 1 day of propagation, this population was almost completely inhibited except for theEnterobacteriaceae. Although members of the phylumFirmicuteswere present at very low or intermediate relative abundances in the flours, they became dominant soon after 1 day of propagation. Lactic acid bacteria were almost exclusively representative of theFirmicutesby this time.Weissellaspp. were already dominant in rye flour and stably persisted, though they were later flanked by theLactobacillus sakeigroup. There was a succession of species during 10 days of propagation of wheat sourdoughs. The fluctuation between dominating and subdominating populations ofL. sakeigroup,Leuconostocspp.,Weissellaspp., andLactococcus lactiswas demonstrated. Other subdominant species such asLactobacillus plantarumwere detectable throughout propagation. As shown by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis,Saccharomyces cerevisiaedominated throughout the sourdough propagation. Notwithstanding variations due to environmental and technology determinants, the results of this study represent a clear example of how the microbial ecology evolves during sourdough preparation.

Changes in the structure and diversity of bacterial communities during the process of adaptation to organic wastewater

2010 ◽  
Vol 56 (4) ◽  
pp. 352-355 ◽  
Author(s):  
Junmin Li ◽  
Zexin Jin ◽  
Binbin Yu
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Similarity Index ◽  
Pcr Amplification ◽  
Genotypic Diversity ◽  
Diversity Indices ◽  
Inhibitory Effect ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gradient Gel Electrophoresis

To explore changes in the structure and diversity of activated sludge-derived microbial communities during adaptation to gradual increases in the concentration of wastewater, RAPD–PCR and the combination of PCR amplification of 16S rRNA genes with denaturing gradient gel electrophoresis (DGGE) analysis were used. In bacterial communities exposed to 0%, 5%, 10%, 20%, or 40% wastewater, there were 27, 25, 18, 17 and 16 bands, respectively, based on DGGE data, while there were 69, 83, 97, 86, and 88 bands, respectively, based on RAPD data. The community similarity index among bacterial communities during the process of adaptation to different concentrations of wastewater was different based on DGGE and RAPD data. Based on DGGE and RAPD profiles, the Shannon–Weiner and Simpson’s diversity indices decreased sharply upon exposure to 10% wastewater, indicating that 10% wastewater might be a critical point at which the growth of bacteria could be significantly inhibited and the genotypic diversity could change. This indicated that changes in structure and diversity might have an inhibitory effect on the toxicity of organic matter and that selection and adaptation could play important roles in the changes.

scholarly journals Effects of Wildfire and Harvest Disturbances on Forest Soil Bacterial Communities

2007 ◽  
Vol 74 (1) ◽  
pp. 216-224 ◽  
Author(s):  
Nancy R. Smith ◽  
Barbara E. Kishchuk ◽  
William W. Mohn
Keyword(s):  
Microbial Biomass ◽  
Microbial Communities ◽  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Biomass Carbon ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Microbial Biomass Nitrogen ◽  
Soil Microbial

ABSTRACT Wildfires and harvesting are important disturbances to forest ecosystems, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. This study was conducted at sites with similar soil, climatic, and other properties in a spruce-dominated boreal forest near Chisholm, Alberta, Canada. Soil microbial communities were assessed following four treatments: control, harvest, burn, and burn plus timber salvage (burn-salvage). Burn treatments were at sites affected by a large wildfire in May 2001, and the communities were sampled 1 year after the fire. Microbial biomass carbon decreased 18%, 74%, and 53% in the harvest, burn, and burn-salvage treatments, respectively. Microbial biomass nitrogen decreased 25% in the harvest treatment, but increased in the burn treatments, probably because of microbial assimilation of the increased amounts of available NH4 + and NO3 − due to burning. Bacterial community composition was analyzed by nonparametric ordination of molecular fingerprint data of 119 samples from both ribosomal intergenic spacer analysis (RISA) and rRNA gene denaturing gradient gel electrophoresis. On the basis of multiresponse permutation procedures, community composition was significantly different among all treatments, with the greatest differences between the two burned treatments versus the two unburned treatments. The sequencing of DNA bands from RISA fingerprints revealed distinct distributions of bacterial divisions among the treatments. Gamma- and Alphaproteobacteria were highly characteristic of the unburned treatments, while Betaproteobacteria and members of Bacillus were highly characteristic of the burned treatments. Wildfire had distinct and more pronounced effects on the soil microbial community than did harvesting.

scholarly journals A Combined Application of Molecular Microbial Ecology and Elemental Analyses Can Advance the Understanding of Decomposition Dynamics

2021 ◽  
Vol 9 ◽  
Author(s):  
Chawki Bisker ◽  
Gillian Taylor ◽  
Helen Carney ◽  
Theresia Komang Ralebitso-Senior
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Soil Microbial Community ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Analytical Techniques ◽  
Calcium Content ◽  
Diversity Indices ◽  
Abiotic Factor ◽  
Soil Microbial ◽  
Hill Numbers

Introducing animal carbon-source to soil initiates biochemical and microbial processes that lead to its decomposition and recycling, which subsequently cause successional shifts in soil microbial community. To investigate the use of soil microbial community to inform criminal investigation, this study was designed to mimic clandestine graves. It compared the decomposition of stillborn piglets (Sus scrofa domesticus), as human analogues, to oak (Quercus robur) leaf litter and soil-only controls outdoors for 720 days. Environmental and edaphic parameters were monitored and showed soil microbial community alignment with temperature seasonality, which highlighted the importance of this abiotic factor. Denaturing gradient gel electrophoresis (DGGE) data were used to calculate Hill numbers and diversity indices of the bacterial 16S rRNA community did not distinguish mammalian- from plant-based decomposition consistently during the first or second year of the study. In contrast, the fungal 18S rRNA community allowed clear differentiation between different treatments (beta diversity) throughout the 720-day experiment and suggested the moment of the decomposing mammalian skin rupture. 16S rRNA-based NGS facilitated the identification of e.g., Pirellulaceae, Acidobacteria ii1-15_order and Candidatus xiphinematobacter as Year 2 bacterial markers of gravesoil at family, order and species taxonomic levels, respectively, and confirmed the similarity of the calculated Hill diversity metrics with those derived from DGGE profiling. Parallel soil elemental composition was measured by portable X-ray Fluorescence where calcium profiles for the piglet-associated soils were distinct from those without carrion. Also, soil calcium content and PMI correlated positively during the first year then negatively during the second. This study is one of the first to apply a multidisciplinary approach based on molecular and physicochemical analytical techniques to assess decomposition. It highlights the recognised potential of using soil microbial community in forensic investigations and provides a proof-of-concept for the application of a combined molecular and elemental approach to further understand the dynamics of decomposition. In addition, it sets the scene for further research in different conditions based on Hill numbers metrics instead of the classic ecological indices for soil necrobiome richness, diversity and evenness.

Changes in Fecal and Colonic Mucosal Microbiota of Patients with Refractory Constipation after a Subtotal Colectomy

2015 ◽  
Vol 81 (2) ◽  
pp. 198-206 ◽  
Author(s):  
Xiaobo Feng ◽  
Yong Su ◽  
Jun Jiang ◽  
Ning Li ◽  
Weiwei Ding ◽  
...  
Keyword(s):  
Subtotal Colectomy ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Intestinal Flora ◽  
Diversity Indices ◽  
Control Subjects ◽  
Before And After ◽  
Gradient Gel Electrophoresis ◽  
Healthy Control ◽  
Polymerase Chain ◽  
Bacterial Groups

The purpose of this study was to investigate the changes in gut microbiota of patients with refractory constipation 6 months after a subtotal colectomy. Feces and mucosal samples of five healthy volunteers and 17 patients with refractory constipation before and six months after subtotal colectomy were collected. Denaturing gradient gel electrophoresis (DGGE) and polymerase chain reaction techniques were used for quantitative analysis of main bacterial groups and archeal methanogens. No significant differences were found in the DGGE profiles among the three groups. After subtotal colectomy, a significantly decreased similarity coefficient was observed in the fecal. The Shannon diversity indices had no significant differences among the three groups. The numbers of predominant bacteria (Bacteriodetes, Clostridium coccoides group, and Clostridium leptum group) did not significantly change in patients before and after surgery compared with healthy control subjects, and the number of total bacteria, Firmicutes, Bacteriodetes, and Clostridium leptum group bacteria in the feces decreased after surgery. However, the numbers of these bacteria remained the same in mucosa from postoperative patients. The numbers of Bifidobacteria and Lactobacilli in feces and the number of Bifidobacteria in mucosa were significantly lower in preoperative compared with healthy control subjects and increased after the surgery. The number of methanogens in the mucosa was decreased in preoperative patients but returned to normal levels postoperatively. In conclusion, although there was no difference in the structure of the predominant bacteria between refractory constipated patients and healthy control subjects, the number of probiotics ( Bifidobacteria and Lactobacilli) was significantly lower in refractory constipated patients. However, subtotal colectomy can significantly normalize the number of intestinal flora.

scholarly journals Impacts of Inter- and Intralaboratory Variations on the Reproducibility of Microbial Community Analyses

2010 ◽  
Vol 76 (22) ◽  
pp. 7451-7458 ◽  
Author(s):  
Yao Pan ◽  
Levente Bodrossy ◽  
Peter Frenzel ◽  
Anne-Grethe Hestnes ◽  
Sascha Krause ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Sample ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Community Composition ◽  
Diversity Indices ◽  
Internal Standards ◽  
Microbial Biogeography ◽  
Yield And Quality ◽  
Gradient Gel Electrophoresis

ABSTRACT With the advent of molecular biological techniques, especially next-generation sequencing and metagenomics, the number of microbial biogeography studies is rapidly increasing. However, these studies involve the synthesis of data generated by different laboratories using different protocols, chemicals, etc., all with inherent biases. The aim of this study was to assess inter- as well as intralaboratory variations in microbial community composition when standardized protocols are applied to a single soil sample. Aliquots from a homogenized soil sample from a rice field in Italy were sent to five participating laboratories. DNA was extracted by two investigators per laboratory using an identical protocol. All DNA samples were sent to one laboratory to perform DNA quantification, quantitative PCR (QPCR), and microarray and denaturing gradient gel electrophoresis (DGGE) analyses of methanotrophic communities. Yields, as well as purity of DNA, were significantly different between laboratories but in some cases also between investigators within the same laboratory. The differences in yield and quality of the extracted DNA were reflected in QPCR, microarray, and DGGE analysis results. Diversity indices (Shannon-Wiener, evenness, and richness) differed significantly between laboratories. The observed differences have implications for every project in which microbial communities are compared in different habitats, even if assessed within the same laboratory. To be able to make sensible comparisons leading to valid conclusions, intralaboratory variation should be assessed. Standardization of DNA extraction protocols and possible use of internal standards in interlaboratory comparisons may help in rendering a “quantifiable” bias.

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