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 Direct Molecular Approach to Monitoring Bacterial Colonization on Vacuum-Packaged Beef

2006 ◽  
Vol 72 (8) ◽  
pp. 5618-5622 ◽  
Author(s):  
Cecilia Fontana ◽  
Pier Sandro Cocconcelli ◽  
Graciela Vignolo
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Colonization ◽  
Lactobacillus Sakei ◽  
Lactobacillus Curvatus ◽  
Specific Primers ◽  
Specific Pcr ◽  
Gradient Gel Electrophoresis ◽  
Packaged Beef ◽  
Species Specific

ABSTRACT Denaturing gradient gel electrophoresis allowed us to monitor total bacterial communities and to establish a pattern of succession between species in vacuum-packaged beef stored at 2 and 8°C for 9 weeks and 14 days. Species-specific PCR was used to confirm the presence of Lactobacillus sakei and Lactobacillus curvatus. Multiplex PCRs using 16S rRNA-specific primers allowed differentiation between Leuconostoc species. These methods provided the desired information about microbial diversity by detecting the main microorganisms capable of colonizing this ecological niche.

scholarly journals Inter- and Intraspecific Variations of Bacterial Communities Associated with Marine Sponges from San Juan Island, Washington

2009 ◽  
Vol 75 (11) ◽  
pp. 3513-3521 ◽  
Author(s):  
On On Lee ◽  
Yue Him Wong ◽  
Pei-Yuan Qian
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Marine Sponges ◽  
San Juan ◽  
Specific Sequence ◽  
Intraspecific Variations ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis ◽  
Bacterial Associations ◽  
Species Specific

ABSTRACT This study attempted to assess whether conspecific or congeneric sponges around San Juan Island, Washington, harbor specific bacterial communities. We used a combination of culture-independent DNA fingerprinting techniques (terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis [DGGE]) and culture-dependent approaches. The results indicated that the bacterial communities in the water column consisted of more diverse bacterial ribotypes than and were drastically different from those associated with the sponges. High levels of similarity in sponge-associated bacterial communities were found only in Myxilla incrustans and Haliclona rufescens, while the bacterial communities in Halichondria panicea varied substantially among sites. Certain terminal restriction fragments or DGGE bands were consistently obtained for different individuals of M. incrustans and H. rufescens collected from different sites, suggesting that there are stable or even specific associations of certain bacteria in these two sponges. However, no specific bacterial associations were found for H. panicea or for any one sponge genus. Sequencing of nine DGGE bands resulted in recovery of seven sequences that best matched the sequences of uncultured Proteobacteria. Three of these sequences fell into the sponge-specific sequence clusters previously suggested. An uncultured alphaproteobacterium and a culturable Bacillus sp. were found exclusively in all M. incrustans sponges, while an uncultured gammaproteobacterium was unique to H. rufescens. In contrast, the cultivation approach indicated that sponges contained a large proportion of Firmicutes, especially Bacillus, and revealed large variations in the culturable bacterial communities associated with congeneric and conspecific sponges. This study revealed sponge species-specific but not genus- or site-specific associations between sponges and bacterial communities and emphasized the importance of using a combination of techniques for studying microbial communities.

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 Development and Validation of a Nested-PCR-Denaturing Gradient Gel Electrophoresis Method for Taxonomic Characterization of Bifidobacterial Communities

2003 ◽  
Vol 69 (11) ◽  
pp. 6380-6385 ◽  
Author(s):  
R. Temmerman ◽  
L. Masco ◽  
T. Vanhoutte ◽  
G. Huys ◽  
J. Swings
Keyword(s):  
Nested Pcr ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Temporal Changes ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Gradient Gel Electrophoresis ◽  
Species Specific ◽  
Taxonomic Characterization

ABSTRACT The taxonomic characterization of a bacterial community is difficult to combine with the monitoring of its temporal changes. None of the currently available identification techniques are able to visualize a “complete” community, whereas techniques designed for analyzing bacterial ecosystems generally display limited or labor-intensive identification potential. This paper describes the optimization and validation of a nested-PCR-denaturing gradient gel electrophoresis (DGGE) approach for the species-specific analysis of bifidobacterial communities from any ecosystem. The method comprises a Bifidobacterium-specific PCR step, followed by purification of the amplicons that serve as template DNA in a second PCR step that amplifies the V3 and V6-V8 regions of the 16S rRNA gene. A mix of both amplicons is analyzed on a DGGE gel, after which the band positions are compared with a previously constructed database of reference strains. The method was validated through the analysis of four artificial mixtures, mimicking the possible bifidobacterial microbiota of the human and chicken intestine, a rumen, and the environment, and of two fecal samples. Except for the species Bifidobacterium coryneforme and B. indicum, all currently known bifidobacteria originating from various ecosystems can be identified in a highly reproducible manner. Because no further cloning and sequencing of the DGGE bands is necessary, this nested-PCR-DGGE technique can be completed within a 24-h span, allowing the species-specific monitoring of temporal changes in the bifidobacterial community.

Molecular Analysis of Spoilage-Related Bacteria in Pasteurized Milk during Refrigeration by PCR and Denaturing Gradient Gel Electrophoresis

2009 ◽  
Vol 72 (3) ◽  
pp. 572-577 ◽  
Author(s):  
HONGFEI HE ◽  
JIN DONG ◽  
CHIN NYEAN LEE ◽  
YONG LI
Keyword(s):  
Shelf Life ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Plate Count ◽  
Pasteurized Milk ◽  
Milk Samples ◽  
Gradient Gel Electrophoresis ◽  
Aerobic Plate Count ◽  
Species Specific

Bacterial diversity in fluid milk products has been extensively studied in order to improve milk quality. Here, we illustrate the utility of viable counts and PCR–denaturing gradient gel electrophoresis (DGGE) for monitoring the microbial spoilage of pasteurized milk during shelf life. Five pasteurized milk samples stored at 4°C were examined at 10 and 5 days before expiration and on the expiration day. With bacterial DNA extracted directly from the samples, PCR-DGGE analysis indicated that Pseudomonas became dominant in four samples. Meanwhile, the aerobic plate count of these four samples exceeded the regulatory limit of 20,000 CFU/ml at 5 days before expiration, and the rapid psychrotrophic count markedly surpassed the aerobic plate count on the expiration day. Streptococcus and Buttiauxella spp. were detected in several samples. Sequence analysis of DGGE fragments revealed high diversity among Pseudomonas spp. in the milk samples. P. putida and P. migulae grew to high numbers during refrigerated storage. Further identification of Pseudomonas at the species level was facilitated by PCR and multiplex PCR using species-specific primers; consequently, P. fluorescens and P. fragi were observed. These results highlight an important role of Pseudomonas in the shelf life of pasteurized milk.

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.

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