scholarly journals Viral and Flagellate Control of Prokaryotic Production and Community Structure in Offshore Mediterranean Waters

2009 ◽  
Vol 75 (14) ◽  
pp. 4801-4812 ◽  
Author(s):  
Osana Bonilla-Findji ◽  
Gerhard J. Herndl ◽  
Jean-Pierre Gattuso ◽  
Markus G. Weinbauer
Keyword(s):  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Leucine Incorporation ◽  
Rrna Gene ◽  
Highly Active ◽  
Prokaryotic Abundance ◽  
Gradient Gel Electrophoresis ◽  
Upper Mixed Layer ◽  
Differential Filtration

ABSTRACT A dilution and size fractionation approach was used to study the separate and combined effects of viruses and flagellates on prokaryotic production ([3H]leucine incorporation) and community composition (16S rRNA gene PCR and denaturing gradient gel electrophoresis [DGGE]) in the upper mixed layer and the deep chlorophyll maximum in the offshore Mediterranean Sea. Four experiments were established using differential filtration: a resource control without predators (C treatment), treatment in the presence of viruses (V treatment), treatment in the presence of flagellates (F treatment), and treatment in the presence of both predators (VF treatment). The V and VF treatments increased prokaryotic abundance (1.4- to 2.3-fold) and the number of DGGE bands (by up to 43%) and decreased prokaryotic production compared to the level for the C treatment (by 22 to 99%). For the F treatment, significant differences compared to the level for the C treatment were found as well, but trends were not consistent across experiments. The relative abundances of the high-nucleic-acid subgroups of prokaryotes with high scatter (HNAhs) in flow cytometer settings were lower in the V and VF treatments than in the C and F treatments. These differences were probably due to lysis of very active HNA prokaryotes in the V and VF treatments. Our results indicate that the presence of viruses or viruses plus flagellates sustains prokaryotic diversity and controls prokaryotic production by regulating the proportion of the highly active members of the community. Our data also suggest that lysis and grazing control influences the relationship between bacterial community composition and prokaryotic production.

scholarly journals Geobacteraceae Community Composition Is Related to Hydrochemistry and Biodegradation in an Iron-Reducing Aquifer Polluted by a Neighboring Landfill

2005 ◽  
Vol 71 (10) ◽  
pp. 5983-5991 ◽  
Author(s):  
Bin Lin ◽  
Martin Braster ◽  
Boris M. van Breukelen ◽  
Henk W. van Verseveld ◽  
Hans V. Westerhoff ◽  
...  
Keyword(s):  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Organic Micropollutants ◽  
Pollution Levels ◽  
Large Pool ◽  
Groundwater Samples ◽  
Leachate Plume ◽  
Gradient Gel Electrophoresis ◽  
Specific Species

ABSTRACT Relationships between community composition of the iron-reducing Geobacteraceae, pollution levels, and the occurrence of biodegradation were established for an iron-reducing aquifer polluted with landfill leachate by using cultivation-independent Geobacteraceae 16S rRNA gene-targeting techniques. Numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles and sequencing revealed a high Geobacteraceae diversity and showed that community composition within the leachate plume differed considerably from that of the unpolluted aquifer. This suggests that pollution has selected for specific species out of a large pool of Geobacteraceae. DGGE profiles of polluted groundwater taken near the landfill (6- to 39-m distance) clustered together. DGGE profiles from less-polluted groundwater taken further downstream did not fall in the same cluster. Several individual DGGE bands were indicative of either the redox process or the level of pollution. This included a pollution-indicative band that dominated the DGGE profiles from groundwater samples taken close to the landfill (6 to 39 m distance). The clustering of these profiles and the dominance by a single DGGE band corresponded to the part of the aquifer where organic micropollutants and reactive dissolved organic matter were attenuated at relatively high rates.

scholarly journals Effects of Wildfire and Harvest Disturbances on Forest Soil Bacterial Communities

2007 ◽  
Vol 74 (1) ◽  
pp. 216-224 ◽  
Author(s):  
Nancy R. Smith ◽  
Barbara E. Kishchuk ◽  
William W. Mohn
Keyword(s):  
Microbial Biomass ◽  
Microbial Communities ◽  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Biomass Carbon ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Microbial Biomass Nitrogen ◽  
Soil Microbial

ABSTRACT Wildfires and harvesting are important disturbances to forest ecosystems, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. This study was conducted at sites with similar soil, climatic, and other properties in a spruce-dominated boreal forest near Chisholm, Alberta, Canada. Soil microbial communities were assessed following four treatments: control, harvest, burn, and burn plus timber salvage (burn-salvage). Burn treatments were at sites affected by a large wildfire in May 2001, and the communities were sampled 1 year after the fire. Microbial biomass carbon decreased 18%, 74%, and 53% in the harvest, burn, and burn-salvage treatments, respectively. Microbial biomass nitrogen decreased 25% in the harvest treatment, but increased in the burn treatments, probably because of microbial assimilation of the increased amounts of available NH4 + and NO3 − due to burning. Bacterial community composition was analyzed by nonparametric ordination of molecular fingerprint data of 119 samples from both ribosomal intergenic spacer analysis (RISA) and rRNA gene denaturing gradient gel electrophoresis. On the basis of multiresponse permutation procedures, community composition was significantly different among all treatments, with the greatest differences between the two burned treatments versus the two unburned treatments. The sequencing of DNA bands from RISA fingerprints revealed distinct distributions of bacterial divisions among the treatments. Gamma- and Alphaproteobacteria were highly characteristic of the unburned treatments, while Betaproteobacteria and members of Bacillus were highly characteristic of the burned treatments. Wildfire had distinct and more pronounced effects on the soil microbial community than did harvesting.

Bacterial abundance, growth and community composition in oligotrophic, metal-rich running waters of Southern New Caledonia

2021 ◽  
Author(s):  
Chiaki Motegi ◽  
Yvan Bettarel ◽  
Aurélie Dufour ◽  
Xavier Mari ◽  
Christophe Migon ◽  
...  
Keyword(s):  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
New Caledonia ◽  
Bacterial Community Composition ◽  
Growth Efficiency ◽  
Rrna Gene ◽  
Running Waters ◽  
High Coverage ◽  
Running Water ◽  
P Limitation

<p>The basic bacterial ecology and diversity was investigated in five running water systems of Southern New Caledonia. These running waters were characterized by potential P-limitation and high concentrations of Ni, Fe, Mn, Cr and Co. The low concentrations of dissolved organic carbon, bacterial and viral abundance, bacterial production and growth efficiency support the characterization of the running waters as oligotroph to ultraoligotroph. Despite these similarities, there were strong differences (<50% similarity) in bacterial community composition between some habitats based on 16S rRNA gene and denaturing gradient gel electrophoresis (DGGE) fingerprints. The high coverage of sequenced DGGE bands found for <em>Betaproteobacteria</em> is typical for freshwater systems, however, we found also a strong representation of <em>Gammaproteobacteria</em>. Indeed the three bands found at all stations were related to <em>Limnohabitans</em> (<em>Comamonadaceae</em>) and <em>Alteromonadaceae</em>. Strong differences were also found between the free-living and the attached bacterial fraction with <em>Gammaproteobacteria </em>dominating in two systems. A higher representation of <em>Gammaproteobacteria </em>seems typical for metal-rich freshwater habitats. Consistent with fresh water habitats, majority of phylotypes detected in the sediment was affiliated to proteobacteria. Also, none of the sequences showed a 100% identity with data bases, and 10 of the 22 and 2 of the 23 sequences had similarities higher than 97% in the freshwater and sediment. This could indicate specific adaptations of the community composition either due to the high metal concentrations or due to the geographical isolation of the New Caledonia. </p>

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.

scholarly journals Bacterial Origin and Community Composition in the Barley Phytosphere as a Function of Habitat and Presowing Conditions

2000 ◽  
Vol 66 (10) ◽  
pp. 4372-4377 ◽  
Author(s):  
Bo Normander ◽  
Jim I. Prosser
Keyword(s):  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Pcr Amplification ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Populations ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis

ABSTRACT An understanding of the factors influencing colonization of the rhizosphere is essential for improved establishment of biocontrol agents. The aim of this study was to determine the origin and composition of bacterial communities in the developing barley (Hordeum vulgare) phytosphere, using denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified from extracted DNA. Discrete community compositions were identified in the endorhizosphere, rhizoplane, and rhizosphere soil of plants grown in an agricultural soil for up to 36 days. Cluster analysis revealed that DGGE profiles of the rhizoplane more closely resembled those in the soil than the profiles found in the root tissue or on the seed, suggesting that rhizoplane bacteria primarily originated from the surrounding soil. No change in bacterial community composition was observed in relation to plant age. Pregermination of the seeds for up to 6 days improved the survival of seed-associated bacteria on roots grown in soil, but only in the upper, nongrowing part of the rhizoplane. The potential occurrence of skewed PCR amplification was examined, and only minor cases of PCR bias for mixtures of two different DNA samples were observed, even when one of the samples contained plant DNA. The results demonstrate the application of culture-independent, molecular techniques in assessment of rhizosphere bacterial populations and the importance of the indigenous soil population in colonization of the rhizosphere.

scholarly journals Microbial Biogeography along an Estuarine Salinity Gradient: Combined Influences of Bacterial Growth and Residence Time

2004 ◽  
Vol 70 (3) ◽  
pp. 1494-1505 ◽  
Author(s):  
Byron C. Crump ◽  
Charles S. Hopkinson ◽  
Mitchell L. Sogin ◽  
John E. Hobbie
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Residence Time ◽  
Doubling Time ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Salinity Gradient ◽  
Bacterial Community Composition ◽  
River Estuary ◽  
Leucine Incorporation ◽  
Bacterioplankton Community

ABSTRACT Shifts in bacterioplankton community composition along the salinity gradient of the Parker River estuary and Plum Island Sound, in northeastern Massachusetts, were related to residence time and bacterial community doubling time in spring, summer, and fall seasons. Bacterial community composition was characterized with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA. Average community doubling time was calculated from bacterial production ([14C]leucine incorporation) and bacterial abundance (direct counts). Freshwater and marine populations advected into the estuary represented a large fraction of the bacterioplankton community in all seasons. However, a unique estuarine community formed at intermediate salinities in summer and fall, when average doubling time was much shorter than water residence time, but not in spring, when doubling time was similar to residence time. Sequencing of DNA in DGGE bands demonstrated that most bands represented single phylotypes and that matching bands from different samples represented identical phylotypes. Most river and coastal ocean bacterioplankton were members of common freshwater and marine phylogenetic clusters within the phyla Proteobacteria, Bacteroidetes, and Actinobacteria. Estuarine bacterioplankton also belonged to these phyla but were related to clones and isolates from several different environments, including marine water columns, freshwater sediments, and soil.

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