scholarly journals Phyllosphere and carposphere bacterial communities in olive plants subjected to different cultural practices

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Silvia Pascazio ◽  
Carmine Crecchio ◽  
Patrizia Ricciuti ◽  
Assunta Maria Palese ◽  
Cristos Xiloyannis ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Cultural Practices ◽  
Plant Protection ◽  
Bacterial Species ◽  
Agricultural Practices ◽  
Fruit Pulp ◽  
Gradient Gel Electrophoresis ◽  
Olive Trees

The aim of this study was to characterize phyllosphere and carposphere bacterial communities of olive trees subjected for 13 years to two different soil management systems (sustainable and conventional) in a mature olive grove located in Southern Italy. Amplified DNA fragments of the 16S ribosomal RNA eubacterial gene (16S <em>rRNA</em>) of bacteria living on leaf and fruit surface, and in fruit pulp were analyzed by denaturing gradient gel electrophoresis (DGGE). A clone library of 16S <em>rRNA</em> amplicons extracted from the bacteria living in pulp homogenates and a phylogenetic analysis were performed. Generally, the DGGE patterns of the bacteria from both the treatments clustered separately. The medium-term sustainable orchard management resulted in a higher number of bacterial species from olive fruit pulp. Phyllosphere and carposphere communities evaluated by DGGE were affected by the type of the agricultural practices adopted. A better understanding of phyllosphere and carposphere microbiota of cultivated olive plants could be useful for the promotion of plant growth, a better plant protection and a higher crop quality.

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 Assessing the Microbial Communities in Four Different Daqusby Using PCR-DGGE, PLFA, and Biolog Analyses

2020 ◽  
Vol 69 (1) ◽  
pp. 27-37
Author(s):  
YUXI LING ◽  
WENYING LI ◽  
TONG TONG ◽  
ZUMING LI ◽  
QIAN LI ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phospholipid Fatty Acid ◽  
Bacterial Species ◽  
Carbon Sources ◽  
Bacterial Biomass ◽  
Biolog Ecoplates ◽  
Different Types ◽  
Gradient Gel Electrophoresis ◽  
Plfa Analysis

Daqu made from raw wheat, barley or pea is used as an inoculum for the fermentation of Chinese Baijiu. In this study, the microbial communities of four different types of Daqus (sauce-flavor Wuling Daqu, sauce and strong-flavor Baisha Daqu, strong-flavor Deshan Daqu, and light-flavor Niulanshan Daqu) were analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), phospholipid fatty acid (PLFA) analysis, and Biolog EcoPlates analysis (Biolog). Clear differences were seen between the microbial communities of the four Daqus. PCR-DGGE showed differences in the number and brightness of bands between the Daqus, indicating the presence of unique bacterial species in Deshan Daqu, Wuling Daqu, and Niulanshan Daqu. Lactobacillus sanfranciscensis, Bacillus thermoamylovorans, and some unclassified bacteria were unique to Wuling Daqu, Deshan Daqu, and Niulanshan Daqu, respectively. Moreover, some bacterial species were observed in all four Daqus. A total of 26 PLFAs between C12 to C20 were detected from the four Daqus by PLFA analysis. Wuling Daqu had the highest total and fungal biomasses, Baisha Daqu had the highest bacterial biomass, and Niulanshan Daqu had the highest ratio of fungal biomass to bacterial biomass. The Biolog results indicated differences in the carbon source use and mode of the four Daqus, and also demonstrated that each Daqu had varying abilities to utilize different types of carbon sources. The cluster analysis of the three methods showed that the microbial communities of the four Daqus were different. This study also demonstrates the applicability of the three analytical methods in the evaluating of the microbial communities of Daqus.

scholarly journals Aquaponics using a fish farm effluent shifts bacterial communities profile in halophytes rhizosphere and endosphere

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Vanessa Oliveira ◽  
Patrícia Martins ◽  
Bruna Marques ◽  
Daniel F. R. Cleary ◽  
Ana I. Lillebø ◽  
...  
Keyword(s):  
Natural Environment ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Nutrient Loads ◽  
Marine Aquaculture ◽  
Aquaculture Effluents ◽  
Specific Effects ◽  
Salicornia Ramosissima ◽  
Gradient Gel Electrophoresis ◽  
Species Specific

AbstractThe intensification of marine aquaculture raises multiple sustainability issues, namely the handling of nutrient-rich effluents that can adversely impact ecosystems. As integrated multi-trophic aquaculture (IMTA) gains momentum, the use of halophyte plants to phytoremediate aquaculture effluents has received growing attention, particularly in aquaponics. It is, therefore, important to obtain a more in-depth knowledge of the microbial communities present in the root systems of these plants, both in their natural environment (sediment) and in aquaponics, in order to understand their nutrient removal potential. The present study used denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing to assess the bacterial community present in the endosphere and rhizosphere of three halophyte plants: Halimione portulacoides, Salicornia ramosissima and Sarcocornia perennis. Species-specific effects were recorded in the profile and diversity of the bacterial communities present in halophyte roots, with significant differences also recorded for the same halophyte species grown in contrasting environments (sediment vs. aquaponics). In aquaponics the most abundant groups belonged to the orders Rhodocyclales, Campylobacterales, Rhodobacterales and Desulfobacterales, while in the natural environment (sediment) the most abundant groups belonged to the orders Rhizobiales, Sphingomonadales and Alteromonadales. An overall enrichment in bacterial taxa involved in nutrient cycling was recorded in the roots of halophytes grown in aquaponics (such as Denitromonas, Mesorhizobium, Colwellia, Dokdonella and Arcobacter), thereby highlighting their potential to reduce the nutrient loads from aquaculture effluents.

scholarly journals Monitoring Biofilm Formation and Microbial Interactions that May Occur During a Salmonella Contamination Incident across the Network of a Water Bottling Plant

2019 ◽  
Vol 7 (8) ◽  
pp. 236
Author(s):  
Karampoula ◽  
Doulgeraki ◽  
Fotiadis ◽  
Tampakaki ◽  
Nychas
Keyword(s):  
Bacterial Communities ◽  
Biofilm Formation ◽  
Fluorescent Protein ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Yellow Fluorescent Protein ◽  
Foodborne Pathogen ◽  
Microbial Interactions ◽  
Enhanced Yellow Fluorescent Protein ◽  
Serovar Typhimurium ◽  
Gradient Gel Electrophoresis

The present study aims to monitor the ability of Salmonella to colonize and compete as a member of the mixed species biofilm within key points at a water bottling plant, in case of a contamination incident with this major foodborne pathogen. To achieve this goal, bacterial communities throughout the production line were collected and their identities were investigated by microbial counts and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). These bacterial communities alone or along with constructed Salmonella enterica serovar Typhimurium (ST) fluorescence-based bioreporters were left to form a biofilm on stainless steel for 6 days at 20 °C. ST bioreporters were constructed by introducing plasmids expressing EYFP (enhanced yellow fluorescent protein) fusions of the genes csgB, csrA, sspH2, and fliD into ST 14028S. The bead vortexing-plate counting method was applied for the enumeration of the biofilm population, while the behavior of the bioreporters was evaluated by fluorescence microscopy. From a set of 16 samples that were collected from the plant, species of Citrobacter, Staphylococcus, Pseudomonas, Bacillus, and Exiguobacterium were identified. The presence of these indigenous bacteria neither inhibited nor enhanced the biofilm formation of ST in mixed bacterial communities (p > 0.05). Furthermore, the csrA-based bioreporter was shown to be induced in multispecies biofilms with Citrobacter. In conclusion, this study enhanced our knowledge of bacterial interactions occurring within a biofilm in a water bottling plant.

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.

scholarly journals Bacterial Chitinolytic Communities Respond to Chitin and pH Alteration in Soil

2012 ◽  
Vol 79 (1) ◽  
pp. 263-272 ◽  
Author(s):  
Anna M. Kielak ◽  
Mariana Silvia Cretoiu ◽  
Alexander V. Semenov ◽  
Søren J. Sørensen ◽  
Jan Dirk van Elsas
Keyword(s):  
16S Rrna ◽  
Bacterial Communities ◽  
Plant Pathogens ◽  
Structural Changes ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Acid Soil ◽  
Rrna Gene ◽  
Content Type ◽  
Soil Suppressiveness ◽  
Gradient Gel Electrophoresis

ABSTRACTChitin amendment is a promising soil management strategy that may enhance the suppressiveness of soil toward plant pathogens. However, we understand very little of the effects of added chitin, including the putative successions that take place in the degradative process. We performed an experiment in moderately acid soil in which the level of chitin, next to the pH, was altered. Examination of chitinase activities revealed fast responses to the added crude chitin, with peaks of enzymatic activity occurring on day 7. PCR-denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA andchiAgenes showed structural changes of the phylogenetically and functionally based bacterial communities following chitin addition and pH alteration. Pyrosequencing analysis indicated (i) that the diversity ofchiAgene types in soil is enormous and (i) that differentchiAgene types are selected by the addition of chitin at different prevailing soil pH values. Interestingly, a major role of Gram-negative bacteria versus a minor one ofActinobacteriain the immediate response to the added chitin (based on 16S rRNA gene abundance andchiAgene types) was indicated. The results of this study enhance our understanding of the response of the soil bacterial communities to chitin and are of use for both the understanding of soil suppressiveness and the possible mining of soil for novel enzymes.

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.

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