Impact of Continuous Cucumis sativus L. Cropping on the Incidence of Root Diseases and Bacterial Community Structure

2012 ◽  
Vol 518-523 ◽  
pp. 5472-5479
Author(s):  
Yuan Sen Hu ◽  
Cui Xiang Li ◽  
Li Kun Gu
Keyword(s):  
Bacterial Community ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Diversity Index ◽  
Disease Incidence ◽  
Bacterial Species ◽  
Root Disease ◽  
Continuous Cropping ◽  
Culturable Bacteria ◽  
Uncultured Bacterium ◽  
Physiological Diversity

To investigate the change of cucumber root disease incidence and bacterial community shift in monocultrue soil, we established 4 treatments of greenhouse-pot cucumber, each representing various monoculture times, and monitored the bacterial variation in rhizosphere/bulk soil and root disease index. Results showed that culturable bacteria numbers gradually decreased as monoculture continued, a significant (P<0.05) difference was observed in rhizosphere samples of the fourth cropping (FC) and the third cropping (TC) soil in contrast to that of non-continuous cropping (NC). The Eco-Physiological diversity index also declined with consecutive cucumber cropping. Analysis by denaturing gradient gel electrophoresis (DGGE) showed that a few dominant bacterial species, including Pseudomonas sp. (95% similarity), Bacteriovorax sp. (93% similarity) and 2 uncultured soil bacteria, declined in population, while Sphingomonas sp. (100% similarity) and one uncultured bacterium increased. For all samples analyzed using DGGE or culture dependent approach, the bacterial population shift was more sensitive in the rhizosphere than in bulk soils, less bacterial diversity and higher root disease incidences were both detected in continuous monocultured soils.

scholarly journals Variation of rhizosphere microbial community in continuous mono-maize seed production

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yunchen Zhao ◽  
Wenjiang Fu ◽  
Changwei Hu ◽  
Guangquan Chen ◽  
Zhanwen Xiao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Seed Production ◽  
Disease Incidence ◽  
Bacterial Species ◽  
Curvularia Lunata ◽  
Continuous Cropping ◽  
Maize Seed ◽  
Bacterial Phyla ◽  
Soil Microbial ◽  
Pathogen Invasion

AbstractSoil microbe is crucial to a healthy soil, therefore its diversities and abundances under different conditions are still need fully understand.The aims of the study were to characterize the community structure and diversity of microbe in the rhizosphere soil after continuous maize seed production, and the relationship between the disease incidence of four diseases and the variation of the rhizosphere microbe. The results showed that different fungal and bacterial species were predominant in different cropping year, and long-term maize seed production had a huge impact on structure and diversity of soil microbial. Ascomycota and Mortierellomycota were the dominant fungal phyla and Mortierella and Ascomycetes represented for a large proportion of genus. A relative increase of Fusarium and Gibberella and a relative decrease of Mortierella, Chrysosporium, Podospora, and Chaetomium were observed with the increase of cropping year. Pathogenic Fusarium, Curvularia, Curvularia-lunata, Cladosporium, Gibberella-baccata, and Plectosphaerellaceae were over-presented and varied at different continuous cropping year, led to different maize disease incidence. Proteobacteria and Actinobacteria ranked in the top two of all bacterial phyla, and genus Pseudarthrobacter, Roseiflexus and RB41 dominated top 3. Haliangium and Streptomyces decreased with the continuous cropping year and mono-cropping of maize seed production increased disease incidence with the increase of cropping year, while the major disease was different. Continuous cropping of maize seed production induced the decrease of protective microbe and biocontrol genera, while pathogenic pathogen increased, and maize are in danger of pathogen invasion. Field management show great effects on soil microbial community.

Effect of nanoparticles on the bacterial community of the cucumber phyllosphere

2009 ◽  
Vol 6 (2) ◽  
pp. 141-145
Author(s):  
Chang Li-Yan ◽  
Wang Qi ◽  
Mei Ru-Hong
Keyword(s):  
Bacterial Community ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Titanium Dioxide Nanoparticles ◽  
Rapid Development ◽  
Chain Reaction ◽  
Uncultured Bacterium ◽  
Gradient Gel Electrophoresis ◽  
Polymerase Chain ◽  
The Impact ◽  
Phyllosphere Bacteria

AbstractWith the rapid development of nanotechnology, the security of nanomaterials has been an increasing cause for concern. In this study, the impact of titanium dioxide nanoparticles (nano-TiO2) on the phyllosphere bacterial community were analysed by both a culturable-dependent method and a polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) method. The quantity of culturable phyllosphere bacteria was significantly reduced with an increased concentration of nano-TiO2. With increasing concentrations from 0.002 to 20 mg/ml of nano-TiO2, the quantity of culturable phyllosphere bacteria decreased from 1.8×106to 3.1×105cfu/g. The phyllosphere bacteria community was analysed by PCR-DGGE, and when the concentrations of nano-TiO2were higher than 0.02 mg/ml, the DGGE bands were significantly lower than in the control. Sequencing results of the bands from the DGGE gel showed that there were at least seven genera in the phyllosphere bacteria. Only one uncultured bacterium was unaffected by the concentration of nano-TiO2.

scholarly journals Metagenomic Analysis of Bacteria Phylum Firmicutes and Bacteroidetes in Women with Type 2 Diabetes

2019 ◽  
Vol 26 (3) ◽  
pp. 110
Author(s):  
Zulhaerati Zulhaerati ◽  
Sri Budiarti ◽  
Rika Indri Astuti
Keyword(s):  
Insulin Resistance ◽  
Type 2 Diabetes ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Metagenomic Analysis ◽  
Rrna Gene ◽  
Healthy Controls ◽  
Microbial Composition ◽  
Uncultured Bacterium

Diabetes mellitus (DM) is a serious health problem in Indonesia. Type 2 diabetes is a metabolic disease which primarily caused by obesity-linked insulin resistance. There is a link between insulin resistance and bacterial populations in the gut. Therefore, the aims of this study was to analyze composition of bacteria belong to the phylum Firmicutes and Bacteroidetes in women with type 2 diabetes and non-diabetic persons as control. The study included five female adults type 2 diabetes patients and five healthy controls. The bacteria composition was analyzed for abundance by denaturing gradient gel electrophoresis (DGGE). Metagenomic analysis based on 16S rRNA gene was represented by 12 DGGE bands. The twelve respective bands showed the similarity ranging from 77 up to 98%. Diversity of microbial composition in women type 2 diabetes was represented by five DGGE bands are Bacteroides fragilis, Bacteroides vulgatus, uncultured Bacteroides sp. clone Lb4eF4, uncultured bacterium clone 16sms90-5g05, and uncultured bacterium clone Malaga 1F14. Four DGGE bands in women healthy controls are closely related to uncultured bacterium isolate DGGE gel band Eub42, uncultured bacterium isolate DGGE gel band K115, uncultured bacterium clone HFV04255, and Enterococcus sp. the finding shows bacterial species belong to the phylum Bacteroidetes was mostly found in women diabetic group, while those belong to the phylum Firmicutes was mostly found in healthy controls.

scholarly journals Study of the Ecology of Fresh Sausages and Characterization of Populations of Lactic Acid Bacteria by Molecular Methods

2004 ◽  
Vol 70 (4) ◽  
pp. 1883-1894 ◽  
Author(s):  
Luca Cocolin ◽  
Kalliopi Rantsiou ◽  
Lucilla Iacumin ◽  
Rosalinda Urso ◽  
Carlo Cantoni ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Leuconostoc Mesenteroides ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Storage Temperature ◽  
Bacterial Species ◽  
Debaryomyces Hansenii ◽  
Molecular Methods ◽  
Uncultured Bacterium ◽  
Dna And Rna

ABSTRACT In this study, a polyphasic approach was used to study the ecology of fresh sausages and to characterize populations of lactic acid bacteria (LAB). The microbial profile of fresh sausages was monitored from the production day to the 10th day of storage at 4°C. Samples were collected on days 0, 3, 6, and 10, and culture-dependent and -independent methods of detection and identification were applied. Traditional plating and isolation of LAB strains, which were subsequently identified by molecular methods, and the application of PCR-denaturing gradient gel electrophoresis (DGGE) to DNA and RNA extracted directly from the fresh sausage samples allowed the study in detail of the changes in the bacterial and yeast populations during storage. Brochothrix thermosphacta and Lactobacillus sakei were the main populations present. In particular, B. thermosphacta was present throughout the process, as determined by both DNA and RNA analysis. Other bacterial species, mainly Staphylococcus xylosus, Leuconostoc mesenteroides, and L. curvatus, were detected by DGGE. Moreover, an uncultured bacterium and an uncultured Staphylococcus sp. were present, too. LAB strains isolated at day 0 were identified as Lactococcus lactis subsp. lactis, L. casei, and Enterococcus casseliflavus, and on day 3 a strain of Leuconostoc mesenteroides was identified. The remaining strains isolated belonged to L. sakei. Concerning the yeast ecology, only Debaryomyces hansenii was established in the fresh sausages. Capronia mansonii was initially present, but it was not detected after the first 3 days. At last, L. sakei isolates were characterized by randomly amplified polymorphic DNA PCR and repetitive DNA element PCR. The results obtained underlined how different populations took over at different steps of the process. This is believed to be the result of the selection of the particular population, possibly due to the low storage temperature employed.

scholarly journals Bdellovibrio and Like Organisms Enhanced Growth and Survival of Penaeus monodon and Altered Bacterial Community Structures in Its Rearing Water

2014 ◽  
Vol 80 (20) ◽  
pp. 6346-6354 ◽  
Author(s):  
Huanhuan Li ◽  
Cheng Chen ◽  
Qiuping Sun ◽  
Renliang Liu ◽  
Junpeng Cai
Keyword(s):  
Bacterial Community ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Penaeus Monodon ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Community Structures ◽  
Bacterial Strains ◽  
Content Type ◽  
Growth And Survival

ABSTRACTIn this study, a 96-h laboratory reduction test was conducted with strain BDHSH06 (GenBank accession no.EF011103) as the test strain forBdellovibrioand like organisms (BALOs) and 20 susceptible marine bacterial strains forming microcosms as the targets. The results showed that BDHSH06 reduced the levels of approximately 50% of prey bacterial strains within 96 h in the seawater microcosms. An 85-day black tiger shrimp (Penaeus monodon) rearing experiment was performed. The shrimp survival rate, body length, and weight in the test tanks were 48.1% ± 1.2%, 99.8 ± 10.0 mm, and 6.36 ± 1.50 g, respectively, which were values significantly (P< 0.05) higher than those for the control,viz., 31.0% ± 2.1%, 86.0 ± 11.1 mm, and 4.21 ± 1.56 g, respectively. With the addition of BDHSH06, total bacterial andVibrionumbers were significantly reduced (P< 0.05) by 1.3 to 4.5 log CFU · ml−1and CFU · g−1in both water and shrimp intestines, respectively, compared to those in the control. The effect of BDHSH06 on bacterial community structures in the rearing water was also examined using PCR amplification of the 16S rRNA gene and denaturing gradient gel electrophoresis (DGGE). The DGGE profiles of rearing water samples from the control and test tanks revealed that the amounts of 44% of the bacterial species were reduced when BDHSH06 was added to the rearing water over the 85-day rearing period, and among these, approximately 57.1% were nonculturable. The results of this study demonstrated that BDHSH06 can be used as a biocontrol/probiotic agent inP. monodonculture.

scholarly journals MICROBIAL COMMUNITY OF BLACK BAND DISEASE ON INFECTION, HEALTHY, AND DEAD PART OF SCLERACTINIAN Montipora sp. COLONY AT SERIBU ISLANDS, INDONESIA

2014 ◽  
Vol 9 (2) ◽  
pp. 165 ◽  
Author(s):  
Ofri Johan ◽  
Dietriech Geoffrey Bengen ◽  
Neviaty Putri Zamani ◽  
Suharsono Suharsono ◽  
David Smith ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Disease Outbreaks ◽  
Desulfovibrio Desulfuricans ◽  
Sample Type ◽  
Black Band Disease ◽  
Gradient Gel Electrophoresis ◽  
Black Band

It is crucial to understand the microbial community associated with the host when attempting to discern the pathogen responsible for disease outbreaks in scleractinian corals. This study determines changes in the bacterial community associated with Montipora sp. in response to black band disease in Indonesian waters. Healthy, diseased, and dead Montipora sp. (n = 3 for each sample type per location) were collected from three different locations (Pari Island, Pramuka Island, and Peteloran Island). DGGE (Denaturing Gradient Gel Electrophoresis) was carried out to identify the bacterial community associated with each sample type and histological analysis was conducted to identify pathogens associated with specific tissues. Various Desulfovibrio species were found as novelty to be associated with infection samples, including Desulfovibrio desulfuricans, Desulfovibrio magneticus, and Desulfovibrio gigas, Bacillus benzoevorans, Bacillus farraginis in genus which previously associated with pathogenicity in corals. Various bacterial species associated with uninfected corals were lost in diseased and dead samples. Unlike healthy samples, coral tissues such as the epidermis, endodermis, zooxanthellae were not present on dead samples under histological observation. Liberated zooxanthellae and cyanobacteria were found in black band diseased Montipora sp. samples.

scholarly journals Diazotrophic Bacterial Community of Degraded Pastures

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
João Tiago Correia Oliveira ◽  
Everthon Fernandes Figueredo ◽  
Williane Patrícia da Silva Diniz ◽  
Lucianne Ferreira Paes de Oliveira ◽  
Pedro Avelino Maia de Andrade ◽  
...  
Keyword(s):  
Population Density ◽  
Bacterial Community ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Diversity Index ◽  
Most Probable Number ◽  
Probable Number ◽  
Pasture Degradation ◽  
Gradient Gel Electrophoresis ◽  
Degree Of Severity ◽  
Degraded Pastures

Pasture degradation can cause changes in diazotrophic bacterial communities. Thus, this study aimed to evaluate the culturable and total diazotrophic bacterial community, associated with regions of the rhizosphere and roots ofBrachiaria decumbensStapf. pastures in different stages of degradation. Samples of roots and rhizospheric soil were collected from slightly, partially, and highly degraded pastures. McCrady’s table was used to obtain the Most Probable Number (MPN) of bacteria per gram of sample, in order to determine population density and calculate the Shannon-Weaver diversity index. The diversity of total diazotrophic bacterial community was determined by the technique of Denaturing Gradient Gel Electrophoresis (DGGE) of thenifH gene, while the diversity of the culturable diazotrophic bacteria was determined by the Polymerase Chain Reaction (BOX-PCR) technique. The increase in the degradation stage of theB. decumbensStapf. pasture did not reduce the population density of the cultivated diazotrophic bacterial community, suggesting that the degradation at any degree of severity was highly harmful to the bacteria. The structure of the total diazotrophic bacterial community associated withB. decumbensStapf. was altered by the pasture degradation stage, suggesting a high adaptive capacity of the bacteria to altered environments.

scholarly journals Bacterial Community Dynamics and Polycyclic Aromatic Hydrocarbon Degradation during Bioremediation of Heavily Creosote-Contaminated Soil

2005 ◽  
Vol 71 (11) ◽  
pp. 7008-7018 ◽  
Author(s):  
Marc Viñas ◽  
Jordi Sabaté ◽  
María José Espuny ◽  
Anna M. Solanas
Keyword(s):  
Bacterial Community ◽  
Polycyclic Aromatic Hydrocarbon ◽  
Aromatic Hydrocarbon ◽  
Contaminated Soil ◽  
Community Dynamics ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Nutrient Treatment ◽  
Bacterial Community Dynamics ◽  
Polycyclic Aromatic

ABSTRACT Bacterial community dynamics and biodegradation processes were examined in a highly creosote-contaminated soil undergoing a range of laboratory-based bioremediation treatments. The dynamics of the eubacterial community, the number of heterotrophs and polycyclic aromatic hydrocarbon (PAH) degraders, and the total petroleum hydrocarbon (TPH) and PAH concentrations were monitored during the bioremediation process. TPH and PAHs were significantly degraded in all treatments (72 to 79% and 83 to 87%, respectively), and the biodegradation values were higher when nutrients were not added, especially for benzo(a)anthracene and chrysene. The moisture content and aeration were determined to be the key factors associated with PAH bioremediation. Neither biosurfactant addition, bioaugmentation, nor ferric octate addition led to differences in PAH or TPH biodegradation compared to biodegradation with nutrient treatment. All treatments resulted in a high first-order degradation rate during the first 45 days, which was markedly reduced after 90 days. A sharp increase in the size of the heterotrophic and PAH-degrading microbial populations was observed, which coincided with the highest rates of TPH and PAH biodegradation. At the end of the incubation period, PAH degraders were more prevalent in samples to which nutrients had not been added. Denaturing gradient gel electrophoresis analysis and principal-component analysis confirmed that there was a remarkable shift in the composition of the bacterial community due to both the biodegradation process and the addition of nutrients. At early stages of biodegradation, the α-Proteobacteria group (genera Sphingomonas and Azospirillum) was the dominant group in all treatments. At later stages, the γ-Proteobacteria group (genus Xanthomonas), the α-Proteobacteria group (genus Sphingomonas), and the Cytophaga-Flexibacter-Bacteroides group (Bacteroidetes) were the dominant groups in the nonnutrient treatment, while the γ-Proteobacteria group (genus Xathomonas), the β-Proteobacteria group (genera Alcaligenes and Achromobacter), and the α-Proteobacteria group (genus Sphingomonas) were the dominant groups in the nutrient treatment. This study shows that specific bacterial phylotypes are associated both with different phases of PAH degradation and with nutrient addition in a preadapted PAH-contaminated soil. Our findings also suggest that there are complex interactions between bacterial species and medium conditions that influence the biodegradation capacity of the microbial communities involved in bioremediation processes.

scholarly journals PENDEKATAN CULTURE INDEPENDENT UNTUK ANALISIS KOMUNITAS BAKTERI

OSEANA ◽  
2019 ◽  
Vol 42 (1) ◽  
pp. 9-17
Author(s):  
Nur Fitriah Afianti ◽  
Yeti Darmayati
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Target Genes ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Single Strand Conformation Polymorphism ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Culturable Bacteria ◽  
Culture Independent ◽  
Culture Dependent

CULTURE INDEPENDENT APPROACH FOR BACTERIAL COMMUNITY ANALYSIS. Analysis of bacterial community can be through two approaches, through cultivation (culture dependent) and without cultivation (culture independent). Culture dependent approach is conventional method which only covered few bacteria because not all bacteria could be cultured. Culture independent approach with molecular techniques based on DNA communities can provide more information about the structure and diversity of bacteria in nature, both culturable bacteria and unculturable bacteria. 16S rRNA gene is commonly target gene used in bacterial communities analysis. Other specific target genes also being developed for specific groups of bacteria. Several methods are developed for the analysis of molecular markers 16S rRNA or other specific genes, including Denaturing Gradient Gel Electrophoresis (DGGE), Terminal Restriction Fragment Length Polymorphism (TRFLP), and Single Strand Conformation Polymorphism (SSCP).

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