scholarly journals Epiphyton as a Niche for Ammonia-Oxidizing Bacteria: Detailed Comparison with Benthic and Pelagic Compartments in Shallow Freshwater Lakes

2008 ◽  
Vol 74 (7) ◽  
pp. 1963-1971 ◽  
Author(s):  
M. Coci ◽  
P. L. E. Bodelier ◽  
H. J. Laanbroek
Keyword(s):  
Bacterial Community ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Submerged Macrophytes ◽  
Bacterial Community Composition ◽  
Detailed Comparison ◽  
Ammonia Oxidizing Bacteria ◽  
Freshwater Lakes ◽  
Gradient Gel Electrophoresis ◽  
Potential Activity ◽  
Nitrosomonas Oligotropha

ABSTRACT Next to the benthic and pelagic compartments, the epiphyton of submerged macrophytes may offer an additional niche for ammonia-oxidizing bacteria in shallow freshwater lakes. In this study, we explored the potential activities and community compositions of ammonia-oxidizing bacteria of the epiphytic, benthic, and pelagic compartments of seven shallow freshwater lakes which differed in their trophic status, distribution of submerged macrophytes, and restoration history. PCR-denaturing gradient gel electrophoresis analyses demonstrated that the epiphytic compartment was inhabited by species belonging to cluster 3 of the Nitrosospira lineage and to the Nitrosomonas oligotropha lineage. Both the ammonia-oxidizing bacterial community compositions and the potential activities differed significantly between compartments. Interestingly, both the ammonia-oxidizing bacterial community composition and potential activity were influenced by the restoration status of the different lakes investigated.

scholarly journals Succession of Bacterial Communities during Early Plant Development: Transition from Seed to Root and Effect of Compost Amendment

2006 ◽  
Vol 72 (6) ◽  
pp. 3975-3983 ◽  
Author(s):  
Stefan J. Green ◽  
Ehud Inbar ◽  
Frederick C. Michel ◽  
Yitzhak Hadar ◽  
Dror Minz
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Bacterial Populations ◽  
Specific Pcr ◽  
Compost Amendment ◽  
The Family ◽  
Gradient Gel Electrophoresis ◽  
Root Surfaces

ABSTRACT Compost amendments to soils and potting mixes are routinely applied to improve soil fertility and plant growth and health. These amendments, which contain high levels of organic matter and microbial cells, can influence microbial communities associated with plants grown in such soils. The purpose of this study was to follow the bacterial community compositions of seed and subsequent root surfaces in the presence and absence of compost in the potting mix. The bacterial community compositions of potting mixes, seed, and root surfaces sampled at three stages of plant growth were analyzed via general and newly developed Bacteroidetes-specific, PCR-denaturing gradient gel electrophoresis methodologies. These analyses revealed that seed surfaces were colonized primarily by populations detected in the initial potting mixes, many of which were not detected in subsequent root analyses. The most persistent bacterial populations detected in this study belonged to the genus Chryseobacterium (Bacteroidetes) and the family Oxalobacteraceae (Betaproteobacteria). The patterns of colonization by populations within these taxa differed significantly and may reflect differences in the physiology of these organisms. Overall, analyses of bacterial community composition revealed a surprising prevalence and diversity of Bacteroidetes in all treatments.

scholarly journals Bacterial Community Composition in Lake Tanganyika: Vertical and Horizontal Heterogeneity

2005 ◽  
Vol 71 (9) ◽  
pp. 5029-5037 ◽  
Author(s):  
Aaike De Wever ◽  
Koenraad Muylaert ◽  
Katleen Van der Gucht ◽  
Samuel Pirlot ◽  
Christine Cocquyt ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Lake Tanganyika ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Latitudinal Variation ◽  
Nutrient Concentrations ◽  
Water Column Stratification ◽  
16S Rna ◽  
Gradient Gel Electrophoresis

ABSTRACT Vertical and latitudinal differences in bacterial community composition (BCC) in Lake Tanganyika were studied during the dry season of 2002 by means of denaturing gradient gel electrophoresis analysis of PCR-amplified 16S RNA fragments. Dominant bands were sequenced and identified as members of the Cyanobacteria, Actinobacteria, Nitrospirae, green nonsulfur bacteria, and Firmicutes divisions and the Gamma- and Deltaproteobacteria subdivisions. The BCC in the lake displayed both vertical and latitudinal variation. Vertical changes in BCC were related to the thermal water column stratification, which influences oxygen and nutrient concentrations. Latitudinal variation was related to upwelling of deep water and increased primary production in the south of the lake. The number of bands per sample increased with bacterial production in the epilimnion of the lake, suggesting a positive diversity-productivity relationship.

Spatial distribution of bacterial communities in sediment of a eutrophic lake revealed by denaturing gradient gel electrophoresis and multivariate analysis

2008 ◽  
Vol 54 (12) ◽  
pp. 1053-1063 ◽  
Author(s):  
Jin Zeng ◽  
Liu-Yan Yang ◽  
Yi Liang ◽  
Jia-Yun Li ◽  
Lin Xiao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Eutrophic Lake ◽  
Freshwater Ecosystems ◽  
Scaling Analysis ◽  
Gradient Gel Electrophoresis ◽  
Lake Xuanwu

Bacterial community structure and the effects of several environmental factors on the microbial community distribution were investigated in the sediment of the eutrophic Lake Xuanwu. Profiles of bacterial communities were generated using denaturing gradient gel electrophoresis (DGGE), and the results were interpreted with multivariate statistical analysis. Five major variables in sediment were examined in a principal component analysis, which indicates notable differences of physicochemical parameters among different sites of the lake. To assess changes in the genetic diversity of bacterial communities of different sampling sites, DGGE band patterns were analyzed by multidimensional scaling analysis, which indicated that sampling sites having similar environmental characteristics also have the similar microbial communities. Canonical correspondence analysis demonstrated that pH and redox potential had significant effects on the bacterial community composition in the sediments. Analysis of DNA sequences revealed that the dominant bacterial groups in Lake Xuanwu belonged to Proteobacteria , Actinobacteria , Verrucomicrobia , and Nitrospirae , which are commonly isolated from freshwater ecosystems.

scholarly journals Bacterial Community Composition in Produced Water of Diyarbakır Oil Fields in Turkey : Bacterial communities in produced waters of south-eastern Turkey reported in detail for the first time

2020 ◽  
Vol 64 (4) ◽  
pp. 452-466
Author(s):  
Tuğçe Tüccar ◽  
Esra Ilhan-Sungur ◽  
Gerard Muyzer
Keyword(s):  
Bacterial Community ◽  
Water Samples ◽  
Bacterial Communities ◽  
Produced Water ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Oil Fields ◽  
Rrna Gene ◽  
Gradient Gel Electrophoresis ◽  
First Time

Oil fields harbour a wide variety of microorganisms with different metabolic capabilities. To examine the microbial ecology of petroleum reservoirs, a molecular-based approach was used to assess the composition of bacterial communities in produced water of Diyarbakır oil fields in Turkey. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments was performed to characterise the bacterial community structure of produced water samples and to identify predominant community members after sequencing of separated DGGE bands. The majority of bacterial sequences retrieved from DGGE analysis of produced water samples belonged to unclassified bacteria (50%). Among the classified bacteria, Proteobacteria (29.2%), Firmicutes (8.3%), Bacteroidetes (8.3%) and Actinobacteria (4.2%) groups were identified. Pseudomonas was the dominant genus detected in the produced water samples. The results of this research provide, for the first time, insight into the complexity of microbial communities in the Diyarbakır oil reservoirs and their dominant constituents.

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