scholarly journals Changes in rhizosphere bacterial communities associated with tree decline: grapevine esca syndrome case study

2019 ◽  
Vol 65 (12) ◽  
pp. 930-943 ◽  
Author(s):  
Maria Ludovica Saccà ◽  
Luisa Maria Manici ◽  
Francesco Caputo ◽  
Salvatore Frisullo
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Amplicon Sequencing ◽  
Dna Fingerprint ◽  
Esca Disease ◽  
Gradient Gel Electrophoresis ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs ◽  
Total Bacteria

An investigation was carried out on rhizosphere bacteria to determine if they may be associated with perennial crops affected by nonspecific decline, a phenomenon that is difficult to diagnose and prevent. Esca disease of grapevine was chosen for this case study because of its easy foliar symptom identification. Ribosomal DNA fingerprint analysis by polymerase chain reaction – denaturing gradient gel electrophoresis (PCR–DGGE), quantitative PCR (qPCR), and rDNA amplicon sequencing by next-generation sequencing (NGS) were adopted to investigate the bacterial communities associated with grapevines, which were selected for the presence and absence of external foliar symptoms in 11 vineyards. According to PCR–DGGE and qPCR, bacterial communities differed in site of origin (vineyards), but not between symptomatic and asymptomatic plants, whereas qPCR gave a significantly higher presence of total bacteria and Pseudomonas spp. in asymptomatic plants. NGS confirmed no difference between symptomatic and asymptomatic plants, apart from a few minor genera (<0.5%) such as Salinibacterium, Flavobacterium, Nocardia, and Janthinobacterium, which were, in all cases, higher in asymptomatic plants and whose functional role should be the object of further investigation. The fact that total bacteria and Pseudomonas were more abundant in the rhizosphere of asymptomatic grapevines and that some bacterial genera were associated with the latter, represents a new element when investigating the multiple-origin phenomenon such as esca disease of grapevine.

Model plants for studying the interaction between Methylobacterium mesophilicum and Xylella fastidiosa

2006 ◽  
Vol 52 (5) ◽  
pp. 419-426 ◽  
Author(s):  
Fernando D Andreote ◽  
Paulo T Lacava ◽  
Cláudia S Gai ◽  
Welington L Araújo ◽  
Walter Maccheroni, Jr. ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Xylella Fastidiosa ◽  
Specific Primers ◽  
Gradient Gel Electrophoresis ◽  
Polymerase Chain ◽  
Methylobacterium Mesophilicum ◽  
Biofilm Structure ◽  
Nicotiana Clevelandii

Over the last few years, endophytic bacterial communities associated with citrus have been studied as key components interacting with Xylella fastidiosa. In this study, we investigated the possible interaction between the citrus endophyte Methylobacterium mesophilicum SR1.6/6 and X. fastidiosa in model plants such as Catharanthus roseus (Madagaskar periwinkle) and Nicotiana clevelandii (Clevelands tobacco). The aim of this study was to establish the fate of M. mesophilicum SR1.6/6 after inoculation of C. roseus and N. clevelandii plants, using PCR–DGGE (polymerase chain reaction – denaturing gradient gel electrophoresis) and plating techniques. Shifts in the indigenous endophytic bacterial communities were observed in plants inoculated with strain SR1.6/6, using specific primers targeting α- and β-Proteobacteria. Cells of strain SR1.6/6 were observed in a biofilm structure on the root and hypocotyl surfaces of in vitro seedlings inoculated with M. mesophilicum SR1.6/6. This emphasizes the importance of these tissues as main points of entrance for this organism. The results showed that C. roseus and N. clevelandii could be used as model plants to study the interaction between M. mesophilicum and X. fastidiosa.Key words: endophytic, Methylobacterium, model plants, DGGE.

Effects of Long-Term Elevated CO2 on Rhizosphere and Bulk Soil Bacterial Community Structure in Pinus sylvestriformis Seedlings Fields

2011 ◽  
Vol 343-344 ◽  
pp. 351-356
Author(s):  
Xia Jia ◽  
Chun Juan Zhou
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pinus Sylvestriformis ◽  
Soil Bacterial Community Structure ◽  
Gradient Gel Electrophoresis ◽  
Polymerase Chain

The effect of long-term elevated CO2(as open top chambers) on rhizosphere and bulk bacterial community structure in Pinus sylvestriformis seedlings field was investigated in July, August, and September. The bacterial communities were processed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis of bacterial 16S rDNA fragments amplified by PCR (Polymerase Chain Reaction) from DNA extracted directly from soil. DGGE profiles from rhizosphere samples showed large changes in rhizosphere bacterial community under elevated CO2compared to ambient except for that in September. For bulk samples, bacterial community structure changed when exposed to elevated CO2in three months. With the exception of bulk samples in August, a similitude of bacterial communities structures existed between different elevated CO2concentrations by analyzing UPGMA dendrogram based on Jaccard’s coefficient.

scholarly journals The Effects of Different Oxytetracycline and Copper Treatments on the Performance of Anaerobic Digesters and the Dynamics of Bacterial Communities

2018 ◽  
Vol 2018 ◽  
pp. 1-6
Author(s):  
Yun Zhang ◽  
Xin Ke ◽  
Wei Sun ◽  
Guangcai Zhang ◽  
Xiaodan Gao ◽  
...  
Keyword(s):  
Methane Production ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Anaerobic Digesters ◽  
Animal Manures ◽  
Ph Values ◽  
Gradient Gel Electrophoresis ◽  
The Common ◽  
Polymerase Chain ◽  
Chelation Reaction

Oxytetracycline and copper are the common residues in animal manures. Meanwhile, anaerobic digestion is considered as a clean biotechnology for the disposal of animal manures. In this paper, the performance of anaerobic digesters and the dynamics of bacterial communities under the different treatments of oxytetracycline and copper were discussed. The parameters of methane production and pH values were studied to reflect the performance of anaerobic digester. Results showed that the changes of methane production and pH values were not obvious compared with the control. This means that the treatments of oxytetracycline and copper almost have no effects on the performance of anaerobic digesters. This phenomenon might be due to the chelation reaction between oxytetracycline and copper. This chelation reaction might reduce the toxicity of oxytetracycline. The study on the dynamics of bacterial communities was based on the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) method. Results indicated that the bacterial communities had significant differences under the different treatments of oxytetracycline and copper. UnculturedBacteroidetesbacterium (CU922272.1) and unculturedBacteroidetesbacterium (AB780945.1) showed adaptability to the different treatments of oxytetracycline and copper and were the dominant bacterial communities.

Bacterial communities associated with lesions of two forms of shell disease in the American lobster (Homarus americanus, Milne Edwards) from Atlantic Canada

2013 ◽  
Vol 59 (6) ◽  
pp. 380-390 ◽  
Author(s):  
Robert A. Quinn ◽  
Richard J. Cawthorn ◽  
Rachael L. Summerfield ◽  
Roxanna Smolowitz ◽  
Andrei Y. Chistoserdov
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Homarus Americanus ◽  
American Lobster ◽  
Atlantic Canada ◽  
Yellow Color ◽  
Gradient Gel Electrophoresis ◽  
Shell Disease ◽  
Polymerase Chain ◽  
Vibrio Spp

Shell disease is a major threat to the American lobster (Homarus americanus, Milne Edwards) fishery. Here we describe the composition of microbial communities associated with lesions of 2 forms of shell disease in Atlantic Canada, (i) a trauma shell disease (TSD) characterized by massive lesions and (ii) an enzootic shell disease (EnSD) characterized by irregularly shaped lesions with a distinct orange to yellow color. The microbiology of the lesions was described by polymerase chain reaction and denaturing gradient gel electrophoresis of 16S rDNA amplified from scrapings of the shell lesions and was compared with communities of unaffected carapaces and previously described forms of shell diseases. Both TSD and EnSD lesions were dominated by members of Alphaproteobacteria, Gammaproteobacteria, and Flavobacteria, all commonly detected in other forms of shell disease; however, unique members of Epsilonproteobacteria were also present. Two Vibrio spp. and 2 Pseudoalteromonas spp. were dominant in lesions of TSD and a Tenacibaculum sp. and Tenacibaculum ovolyticum were dominant in lesions of EnSD. The TSD and EnSD in this study contained similar taxa as other shell disease forms; however, their microbiology is mostly different and neither resembles that of epizootic shell disease.

scholarly journals Impact of Intensive Land-Based Fish Culture in Qingdao, China, on the Bacterial Communities in Surrounding Marine Waters and Sediments

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Qiufen Li ◽  
Yan Zhang ◽  
David Juck ◽  
Nathalie Fortin ◽  
Charles W. Greer
Keyword(s):  
Bacterial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Fish Culture ◽  
Fish Ponds ◽  
Marine Area ◽  
Gradient Gel Electrophoresis ◽  
Reducing Bacteria ◽  
The Impact ◽  
Nitrate Reducing Bacteria

The impact of intensive land-based fish culture in Qingdao, China, on the bacterial communities in surrounding marine environment was analyzed. Culture-based studies showed that the highest counts of heterotrophic, ammonium-oxidizing, nitrifying, and nitrate-reducing bacteria were found in fish ponds and the effluent channel, with lower counts in the adjacent marine area and the lowest counts in the samples taken from 500 m off the effluent channel. Denaturing gradient gel electrophoresis (DGGE) analysis was used to assess total bacterial diversity. Fewer bands were observed from the samples taken from near the effluent channel compared with more distant sediment samples, suggesting that excess nutrients from the aquaculture facility may be reducing the diversity of bacterial communities in nearby sediments. Phylogenetic analysis of the sequenced DGGE bands indicated that the bacteria community of fish-culture-associated environments was mainly composed of Flavobacteriaceae, gamma- and deltaproteobacteria, including generaGelidibacter, Psychroserpen, Lacinutrix,andCroceimarina.

scholarly journals Investigations on the Effects of Dietary Essential Oils and Different Husbandry Conditions on the Gut Ecology in Piglets after Weaning

2009 ◽  
Vol 2009 ◽  
pp. 1-9 ◽  
Author(s):  
P. Janczyk ◽  
R. Pieper ◽  
V. Urubschurov ◽  
K. R. Wendler ◽  
W. B. Souffrant
Keyword(s):  
Essential Oils ◽  
Dry Matter ◽  
Distal Part ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Control Diet ◽  
Short Chain Fatty Acids ◽  
Growth Promoters ◽  
Gradient Gel Electrophoresis ◽  
Antibiotic Growth Promoters ◽  
Polymerase Chain

Essential oils (EO) are being considered as possible alternatives to in-feed antibiotic growth promoters in pig nutrition. The effects of an EO mixture consisting of limonene, eugenol and pinene (10.0, 2.0, and 4.8 mg/kg diet, resp.) on gut physiology and ecology were studied in piglets. The experiment was conducted at low (commercial farm) and high hygienic conditions (experimental farm), to elucidate interactions between EO supplementation and husbandry methods. Piglets were weaned at 28 days of age, when they were offered either a control diet (C) or C with EO. Four piglets were sacrificed in each group on day 29, 30, 33 and 39. Digesta from the third distal part of the small intestine and from the colon were sampled and analysed for pH, dry matter, lactic acid, short chain fatty acids and ammonia concentrations. Enterobacteria, enterococci, lactobacilli and yeast counts were obtained by plating. Genomic DNA was extracted from digesta and polymerase chain reaction—denaturing gradient gel electrophoresis was performed. Individual microbial communities were identified at each farm. Age affected the intestinal parameters. No effects of the EO with exception for a significant reduction in colon bacterial diversity at 39 days of age could be recorded at experimental farm.

The assessment of the coke wastewater treatment efficacy in rotating biological contractor

2015 ◽  
Vol 73 (5) ◽  
pp. 1202-1210 ◽  
Author(s):  
G. Cema ◽  
S. Żabczyński ◽  
A. Ziembińska-Buczyńska
Keyword(s):  
Biological Treatment ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rotating Biological Contactor ◽  
Coke Wastewater ◽  
Promising Tool ◽  
Start Up ◽  
Gradient Gel Electrophoresis ◽  
Real Wastewater ◽  
Polymerase Chain ◽  
Anammox Process

Coke wastewater is known to be relatively difficult for biological treatment. Nonetheless, biofilm-based systems seem to be promising tool for such treatment. That is why a rotating biological contactor (RBC) system focused on the Anammox process was used in this study. The experiment was divided into two parts with synthetic and then real wastewater. It was proven that it is possible to treat coke wastewater with RBC but such a procedure requires a very long start-up period for the nitritation (190 days), as well as for the Anammox process, where stable nitrogen removal over 70% was achieved after 400 days of experiment. Interestingly, it was possible at a relatively low (20.2 ± 2.2 °C) temperature. The polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE) based monitoring of the bacterial community showed that its biodiversity decreased when the real wastewater was treated and it was composed mainly of GC-rich genotypes, probably because of the modeling influence of this wastewater and the genotypes specialization.

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