scholarly journals Soil and Rhizosphere Bacterial Diversity in Maize Agro- Ecosystem

2017 ◽  
Vol 6 (3) ◽  
pp. 35 ◽  
Author(s):  
Maria Teresa Federici Rodriguez ◽  
Natalia Bajsa Valverde ◽  
Paula Lagurara ◽  
Santiago Revale ◽  
Jackson Antonio Marcondes de Souza ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Management Practices ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Community Diversity ◽  
Rrna Gene ◽  
Phenological Stages ◽  
Maize Production ◽  
Maize Cultivars ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis

Management practices used in maize production have an impact on soil agro- ecosystems where different microbial communities coexist. Soil inhabiting bacteria are numerous and diverse, but we know very little about their ecological distribution. Here we analyzed the bacterial community diversity in the rhizosphere of two transgenic maize cultivars, in agricultural soil before sowing and in non-cultivated soil in an experimental site in the south region of Uruguay. We followed two culture-independent methods: DGGE (denaturing gradient gel electrophoresis) and 454-pyrosequencing of 16S rRNA gene amplicon. Through pyrosequencing, the three environments analyzed presented differences in terms of bacterial composition. However, no differences were found in the relative abundance of the ten most represented phyla in the rhizosphere of the two cultivars at different phenological stages. We found significant differences of Bacteroidetes, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia phyla when comparing agricultural and non-cultivated soils, as well as a significant enrichment of members of the phylum Gemmatimonadetes in all rhizosphere samples compared to soil. Through DGGE analysis we evidenced that maize rhizosphere bacterial communities changed at different phenological stages in both cultivars. We also provided baseline information about bacterial specific taxa within maize agro- ecosystem for further evaluation of possible rhizosphere bacterial community shifts of genetically modified maize cultivars under different management practices.

scholarly journals Bacterial Community Structure and Diversity in a Century-Old Manure-Treated Agroecosystem

2004 ◽  
Vol 70 (10) ◽  
pp. 5868-5874 ◽  
Author(s):  
H. Y. Sun ◽  
S. P. Deng ◽  
W. R. Raun
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Management Practices ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Lime Treatment ◽  
Soil Microbial Community Structure ◽  
Treated Soil

ABSTRACT Changes in soil microbial community structure and diversity may reflect environmental impact. We examined 16S rRNA gene fingerprints of bacterial communities in six agroecosystems by PCR amplification and denaturing gradient gel electrophoresis (PCR-DGGE) separation. These soils were treated with manure for over a century or different fertilizers for over 70 years. Bacterial community structure and diversity were affected by soil management practices, as evidenced by changes in the PCR-DGGE banding patterns. Bacterial community structure in the manure-treated soil was more closely related to the structure in the untreated soil than that in soils treated with inorganic fertilizers. Lime treatment had little effect on bacterial community structure. Soils treated with P and N-P had bacterial community structures more closely related to each other than to those of soils given other treatments. Among the soils tested, a significantly higher number of bacterial ribotypes and a more even distribution of the bacterial community existed in the manure-treated soil. Of the 99 clones obtained from the soil treated with manure for over a century, two (both Pseudomonas spp.) exhibited 100% similarity to sequences in the GenBank database. Two of the clones were possible chimeras. Based on similarity matching, the remaining 97 clones formed six major clusters. Fifty-six out of 97 were assigned taxonomic units which grouped into five major taxa: α-, β-, and γ-Proteobacteria (36 clones), Acidobacteria (16 clones), Bacteroidetes (2 clones), Nitrospirae (1 clone), and Firmicutes (1 clone). Forty-one clones remained unclassified. Results from this study suggested that bacterial community structure was closely related to agroecosystem management practices conducted for over 70 years.

scholarly journals Bacterial Communities from Shoreline Environments (Costa da Morte, Northwestern Spain) Affected by the Prestige Oil Spill

2009 ◽  
Vol 75 (11) ◽  
pp. 3407-3418 ◽  
Author(s):  
Jorge Alonso-Gutiérrez ◽  
Antonio Figueras ◽  
Joan Albaigés ◽  
Núria Jiménez ◽  
Marc Viñas ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Oil Spill ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Mycolic Acids ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis ◽  
Northwestern Spain

ABSTRACT The bacterial communities in two different shoreline matrices, rocks and sand, from the Costa da Morte, northwestern Spain, were investigated 12 months after being affected by the Prestige oil spill. Culture-based and culture-independent approaches were used to compare the bacterial diversity present in these environments with that at a nonoiled site. A long-term effect of fuel on the microbial communities in the oiled sand and rock was suggested by the higher proportion of alkane and polyaromatic hydrocarbon (PAH) degraders and the differences in denaturing gradient gel electrophoresis patterns compared with those of the reference site. Members of the classes Alphaproteobacteria and Actinobacteria were the prevailing groups of bacteria detected in both matrices, although the sand bacterial community exhibited higher species richness than the rock bacterial community did. Culture-dependent and -independent approaches suggested that the genus Rhodococcus could play a key role in the in situ degradation of the alkane fraction of the Prestige fuel together with other members of the suborder Corynebacterineae. Moreover, other members of this suborder, such as Mycobacterium spp., together with Sphingomonadaceae bacteria (mainly Lutibacterium anuloederans), were related as well to the degradation of the aromatic fraction of the Prestige fuel. The multiapproach methodology applied in the present study allowed us to assess the complexity of autochthonous microbial communities related to the degradation of heavy fuel from the Prestige and to isolate some of their components for a further physiological study. Since several Corynebacterineae members related to the degradation of alkanes and PAHs were frequently detected in this and other supralittoral environments affected by the Prestige oil spill along the northwestern Spanish coast, the addition of mycolic acids to bioremediation amendments is proposed to favor the presence of these degraders in long-term fuel pollution-affected areas with similar characteristics.

scholarly journals Combining Culture-Dependent and -Independent Methodologies for Estimation of Richness of Estuarine Bacterioplankton Consuming Riverine Dissolved Organic Matter

2003 ◽  
Vol 69 (6) ◽  
pp. 3607-3616 ◽  
Author(s):  
Veljo Kisand ◽  
Johan Wikner
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Experimental System ◽  
Community Diversity ◽  
Rrna Gene ◽  
Solid Media ◽  
Gradient Gel Electrophoresis ◽  
Culture Dependent

ABSTRACT Three different methods for analyzing natural microbial community diversity were combined to maximize an estimate of the richness of bacterioplankton catabolizing riverine dissolved organic matter (RDOM). We also evaluated the ability of culture-dependent quantitative DNA-DNA hybridization, a 16S rRNA gene clone library, and denaturing gradient gel electrophoresis (DGGE) to detect bacterial taxa in the same sample. Forty-two different cultivatable strains were isolated from rich and poor solid media. In addition, 50 unique clones were obtained by cloning of the bacterial 16S rDNA gene amplified by PCR from the community DNA into an Escherichia coli vector. Twenty-three unique bands were sequenced from 12 DGGE profiles, excluding a composite fuzzy band of the Cytophaga-Flavobacterium group. The different methods gave similar distributions of taxa at the genus level and higher. However, the match at the species level among the methods was poor, and only one species was identified by all three methods. Consequently, all three methods identified unique subsets of bacterial species, amounting to a total richness of 97 operational taxonomic units in the experimental system. The confidence in the results was, however, dependent on the current precision of the phylogenetic determination and definition of the species. Bacterial consumers of RDOM in the studied estuary were primarily both cultivatable and uncultivable taxa of the Cytophaga-Flavobacterium group, a concordant result among the methods applied. Culture-independent methods also suggested several not-yet-cultivated β-proteobacteria to be RDOM consumers.

Design of PCR Primers for the mcrA Genes Detection of Methanogen Communities

2011 ◽  
Vol 135-136 ◽  
pp. 408-413 ◽  
Author(s):  
Nguyen Ngoc Tuan ◽  
Shir Ly Huang
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Biogas Production ◽  
Pcr Primers ◽  
Molecular Techniques ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Mcra Gene ◽  
Catabolic Genes ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis

Methanogens play an important role to carbon cycling, catalyzing the production of methane and carbon dioxide, both potent green house gases, during organic matter degradation in anaerobic environments. Therefore, it is necessary to better understand microorganisms that produce natural gas. Indeed, methanogens are difficult to perform through culture based methods. In addition, the culture independent methods using the 16S rRNA gene also revealed some disadvantages. For these reasons, the culture independent molecular techniques using the specific catabolic genes such as methyl coenzyme M reductase (MCR) were studied. In this study, a primer set which can amplify specific fragments from a wide variety of mcrA gene was designed based on the homologous regions of 100 mcrA genes listed in the GenBank. PCR with the mcrA primers amplified DNA fragments of the expected size from all the six samples which obtained from biogas production reactors. In addition, denaturing gradient gel electrophoresis PCR analysis using our designed primers also revealed the diversity of mcrA gene in each sample. These results revealed that our primers were successfully to detect the mcrA genes and it is also helpful to know the diversity of mcrA genes in methanogen communities.

scholarly journals Elucidating the Key Member of a Linuron-Mineralizing Bacterial Community by PCR and Reverse Transcription-PCR Denaturing Gradient Gel Electrophoresis 16S rRNA Gene Fingerprinting and Cultivation

2005 ◽  
Vol 71 (7) ◽  
pp. 4144-4148 ◽  
Author(s):  
Sebastian R. Sørensen ◽  
Jim Rasmussen ◽  
Carsten S. Jacobsen ◽  
Ole S. Jacobsen ◽  
René K. Juhler ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gel Electrophoresis ◽  
Agricultural Soil ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Carbon And Nitrogen ◽  
Reverse Transcription Pcr ◽  
Gradient Gel Electrophoresis

ABSTRACT A bacterial community from Danish agricultural soil was enriched with linuron [N-(3,4-dichlorophenyl)-N′-methoxy-N′-methylurea] as the sole carbon and nitrogen source. The community mineralized [ring-U-14C]linuron completely to 14CO2 and 14C-biomass. Denaturing gradient gel electrophoresis analysis and cultivation revealed that a Variovorax sp. was responsible for the mineralization activity.

scholarly journals Biodiversity in Oscypek, a Traditional Polish Cheese, Determined by Culture-Dependent and -Independent Approaches

2012 ◽  
Vol 78 (6) ◽  
pp. 1890-1898 ◽  
Author(s):  
Ángel Alegría ◽  
Pawel Szczesny ◽  
Baltasar Mayo ◽  
Jacek Bardowski ◽  
Magdalena Kowalczyk
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Starter Cultures ◽  
Rrna Gene ◽  
Content Type ◽  
Protected Designation Of Origin ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis ◽  
Microbial Groups ◽  
The Tatra Mountains ◽  
Culture Dependent

ABSTRACTOscypek is a traditional Polish scalded-smoked cheese, with a protected-designation-of-origin (PDO) status, manufactured from raw sheep's milk without starter cultures in the Tatra Mountains region of Poland. This study was undertaken in order to gain insight into the microbiota that develops and evolves during the manufacture and ripening stages of Oscypek. To this end, we made use of both culturing and the culture-independent methods of PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing of 16S rRNA gene amplicons. The culture-dependent technique and PCR-DGGE fingerprinting detected the predominant microorganisms in traditional Oscypek, whereas the next-generation sequencing technique (454 pyrosequencing) revealed greater bacterial diversity. Besides members of the most abundant bacterial genera in dairy products, e.g.,Lactococcus,Lactobacillus,Leuconostoc,Streptococcus, andEnterococcus, identified by all three methods, other, subdominant bacteria belonging to the familiesBifidobacteriaceaeandMoraxellaceae(mostlyEnhydrobacter), as well as various minor bacteria, were identified by pyrosequencing. The presence of bifidobacterial sequences in a cheese system is reported for the first time. In addition to bacteria, a great diversity of yeast species was demonstrated in Oscypek by the PCR-DGGE method. Culturing methods enabled the determination of a number of viable microorganisms from different microbial groups and their isolation for potential future applications in specific cheese starter cultures.

Sign in / Sign up

Export Citation Format

Share Document