Molecular Retrieval of Large 16S rRNA Gene Fragments from an Italian Rice Paddy Soil Affiliated with the Class Actinobacteria

Lüdemann, Heiner; Conrad, Ralf

doi:10.1016/s0723-2020(00)80033-8

Cited by 19 publications

(14 citation statements)

References 9 publications

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“…Group‐specific primers used for Actinobacteria (27f/1165r: Lane, 1991; Lüdemann & Conrad, 2000) resulted in the successful amplification of the 16S rRNA gene of the target taxa and sequences exclusively belonging to the desired group were obtained. However, for the Betaproteobacteria 16S rRNA gene clones library, the primers used (680f/1492r: Lane, 1991; Overmann et al , 1999) revealed some nonspecific amplification, with 12.9% (27 OTUs) for Verrucomicrobia and 4.8% (10 OTUs) for Cyanobacteria .…”

Section: Discussionmentioning

confidence: 99%

Diversity and dynamics of free-living and particle-associatedBetaproteobacteriaandActinobacteriain relation to phytoplankton and zooplankton communities

Parveen

Reveilliez

Mary

et al. 2011

FEMS Microbiology Ecology

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The diversity of attached and free-living Actinobacteria and Betaproteobacteria, based on 16S rRNA gene sequences, was investigated in a mesotrophic lake during two periods of contrasting phytoplankton dominance. Comparison analyses showed a phylogenetic difference between attached and free-living communities for the two bacterial groups. For Betaproteobacteria, the betaI clade was detected at all sampling dates in free-living and attached bacterial communities and was the dominant clade contributing to 57.8% of the total retrieved operational taxonomic units (OTUs). For Actinobacteria, the acIV cluster was found to be dominant, followed by acI contributing to 45% and 25% of the total retrieved OTUs, respectively. This study allows the determination of eight new putative clades among the Betaproteobacteria termed lbI-lbVIII and a new putative clade named acLBI belonging to the Actinobacteria. The seasonal dynamics of phytoplankton and zooplankton communities have been reflected as changes in distinct bacterial phylotypes for both attached and free-living communities. For attached communities, relationships were observed between Actinobacteria and Chrysophyceae, and between Betaproteobacteria and Dinophyceae and Chlorophyceae biomass. On the other hand, within free-living communities, few actinobacterial clades were found to be dependent on either nutrients or phytoplankton communities, whereas Betaproteobacteria were mainly associated with biological parameters (i.e. phytoplankton and copepod communities).

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Section: Discussionmentioning

confidence: 99%

Diversity and dynamics of free-living and particle-associatedBetaproteobacteriaandActinobacteriain relation to phytoplankton and zooplankton communities

Parveen

Reveilliez

Mary

et al. 2011

FEMS Microbiology Ecology

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“…The few existing isolates of freshwater Actinobacteria belong to the acII cluster and to the newly proposed acSTL cluster. The isolates are derived from totally different habitats, such as lakes, the German Wadden Sea, paddy soil, or a phenol-degrading bioreactor (11,21,34,43). Recently, the isolation of a member of the acI cluster was reported (8).…”

Section: Discussionmentioning

confidence: 99%

“…At present only a few isolates of freshwater Actinobacteria exist. These isolates are derived from a variety of aquatic habitats and are representative of only a few phylogenetic lineages of freshwater Actinobacteria (11,21,34,43). Due to the rather small number of isolates and their affiliation with distinct phylogenetic lineages, almost nothing is known about their physiology and ecological role.…”

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confidence: 99%

Diversity and Seasonal Dynamics of Actinobacteria Populations in Four Lakes in Northeastern Germany

Allgaier

Grossart

2006

Appl Environ Microbiol

203

184

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The phylogenetic diversity and seasonal dynamics of freshwater Actinobacteria populations in four limnologically different lakes of the Mecklenburg-Brandenburg Lake District (northeastern Germany) were investigated. Fluorescence in situ hybridization was used to determine the seasonal abundances and dynamics of total Actinobacteria (probe HGC69a) and the three actinobacterial subclusters acI, acI-A, and acI-B (probes AcI-852, AcI-840-1, and AcI-840-2). Seasonal means of total Actinobacteria abundances in the epilimnia of the lakes varied from 13 to 36%, with maximum values of 30 to 58%, of all DAPI (4,6-diamidino-2-phenylindole)-stained cells. Around 80% of total Actinobacteria belonged to the acI cluster. The two subclusters acI-A and acI-B accounted for 60 to 91% of the acI cluster and showed seasonal means of 49% (acI-B) and 23% (acI-A) in relation to the acI cluster. Total Actinobacteria and members of the clusters acI and acI-B showed distinct seasonal changes in their absolute abundances, with maxima in late spring and fall/winter. In eight clone libraries constructed from the lakes, a total of 76 actinobacterial 16S rRNA gene sequences were identified from a total of 177 clones. The majority of the Actinobacteria sequences belonged to the acI and acIV cluster. Several new clusters and subclusters were found (acSTL, scB1-4, and acIVA-D). The majority of all obtained 16S rRNA gene sequences are distinct from those of already-cultured freshwater Actinobacteria.

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“… Set of PCR primers used for DGGE fingerprinting and clone library construction of different phylogenetic groups of bacteria [ 29] , [30], [31], [62], [63], [64], [65], [66], [67], [68], [69] . …”

Section: Supporting Informationmentioning

confidence: 99%

Do Patterns of Bacterial Diversity along Salinity Gradients Differ from Those Observed for Macroorganisms?

et al. 2011

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It is widely accepted that biodiversity is lower in more extreme environments. In this study, we sought to determine whether this trend, well documented for macroorganisms, also holds at the microbial level for bacteria. We used denaturing gradient gel electrophoresis (DGGE) with phylum-specific primers to quantify the taxon richness (i.e., the DGGE band numbers) of the bacterioplankton communities of 32 pristine Tibetan lakes that represent a broad salinity range (freshwater to hypersaline). For the lakes investigated, salinity was found to be the environmental variable with the strongest influence on the bacterial community composition. We found that the bacterial taxon richness in freshwater habitats increased with increasing salinity up to a value of 1‰. In saline systems (systems with >1‰ salinity), the expected decrease of taxon richness along a gradient of further increasing salinity was not observed. These patterns were consistently observed for two sets of samples taken in two different years. A comparison of 16S rRNA gene clone libraries revealed that the bacterial community of the lake with the highest salinity was characterized by a higher recent accelerated diversification than the community of a freshwater lake, whereas the phylogenetic diversity in the hypersaline lake was lower than that in the freshwater lake. These results suggest that different evolutionary forces may act on bacterial populations in freshwater and hypersaline lakes on the Tibetan Plateau, potentially resulting in different community structures and diversity patterns.

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Molecular Retrieval of Large 16S rRNA Gene Fragments from an Italian Rice Paddy Soil Affiliated with the Class Actinobacteria

Cited by 19 publications

References 9 publications

Diversity and dynamics of free-living and particle-associatedBetaproteobacteriaandActinobacteriain relation to phytoplankton and zooplankton communities

Diversity and dynamics of free-living and particle-associatedBetaproteobacteriaandActinobacteriain relation to phytoplankton and zooplankton communities

Diversity and Seasonal Dynamics of Actinobacteria Populations in Four Lakes in Northeastern Germany

Do Patterns of Bacterial Diversity along Salinity Gradients Differ from Those Observed for Macroorganisms?

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