Article

Identifying the Dominant Soil Bacterial taxa in Libraries. of 16S rRNA and 16S rRNA Genes

Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia.
Applied and Environmental Microbiology (Impact Factor: 3.67). 04/2006; 72(3):1719-28. DOI: 10.1128/AEM.72.3.1719-1728.2006
Source: PubMed
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Available from: Peter H Janssen, Sep 15, 2014
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    • "Brevundimonas sp. belongs to the class Proteobacteria, which has been shown to contain Asresistant bacteria (Janssen, 2006). Among three PV tissues, Bacillus sp. was present only in the roots. "
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    ABSTRACT: The ability of As-resistant endophytic bacteria in As transformation and plant growth promotion was determined. The endophytes were isolated from As-hyperaccumulator Pteris vittata (PV) after growing for 60 d in a soil containing 200 mg kg(-1) arsenate (AsV). They were isolated in presence of 10 mM AsV from PV roots, stems, and leaflets, representing 4 phyla and 17 genera. All endophytes showed at least one plant growth promoting characteristics including IAA synthesis, siderophore production and P solubilization. The root endophytes had higher P solubilization ability than the leaflet (60.0 vs. 18.3 mg L(-1)). In presence of 10 mM AsV, 6 endophytes had greater growth than the control, suggesting As-stimulated growth. Furthermore, root endophytes were more resistant to AsV while the leaflet endophytes were more tolerant to arsenite (AsIII), which corresponded to the dominant As species in PV tissues. Bacterial As resistance was positively correlated to their ability in AsV reduction but not AsIII oxidation. The roles of those endophytes in promoting plant growth and As resistance in P. vittata warrant further investigation.
    Full-text · Article · Feb 2016 · Chemosphere
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    • "Acidobacteria play an important role in soil ecological processes, and this phylum is one of the most widely distributed and diverse bacterial phyla in various natural environments (Hugenholtz et al., 1998;Tringe et al., 2005;Janssen, 2006). Based on data analysis of the 16S rRNA gene, members of this phylum commonly represent 10e50% of total soil bacterial communities (Barns et al., 1999;Dunbar et al., 1999;Branco et al., 2005;Fracchia et al., 2006;Penn et al., 2006;Lee et al., 2008). "
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    ABSTRACT: Although Acidobacteria are ubiquitous and are commonly one of the most abundant bacterial phyla in soils, knowledge regarding their diversity and distribution is still limited. Our previous studies discovered the biogeographical distribution patterns of bacterial and fungal communities in the black soil zone of northeast China. In this study, we further investigated the diversity and composition of acidobacterial communities generated with the Acidobacteria-specific primers ACIDO/342r in the same soil samples using quantitative PCR and Illumina MiSeq sequencing methods. A total of 412,203 acidobacterial 16S rRNA gene sequences were obtained from 26 soil samples that were collected from arable lands across the black soil zone. These sequences belonged to 21 subgroups, and GP1, GP3, GP4 and GP6 were the most abundant subgroups, accounting for 22.63%, 17.17%, 23.82% and 27.47% of acidobacterial sequences across all soils, respectively. The abundance of Acidobacteria displayed a more significant positive correlation with soil carbon content than with soil pH, and the relative abundance of certain subgroups was significantly positive or negative related with soil pH. The OTU richness, phylogenetic diversity and community composition of Acidobacteria were significantly correlated with soil pH. A variance partitioning analysis showed that the soil pH contributed 25% of the community variation, while the geographic distance explained only approximately 5% of the variation. These results indicated that soil pH was a main factor structuring acidobacterial communities in the black soil zone of northeast China. Our results also suggested that the Acidobacteria-specific primers could be better used for studying the distribution of acidobacterial communities in soils.
    Full-text · Article · Jan 2016 · Soil Biology and Biochemistry
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    • "However, the correlation to OM and soil DOC further supports the importance of soil carbon input to bacterial community response, and suggests this family of bacteria might grow more readily on carbon derived from root exudates as opposed to litter inputs. Along the same lines, clades within Proteobacteria (Janssen, 2006;Nacke et al., 2011) and Actinobacteria are often correlated to changes in carbon availability (Fierer et al., 2007;Goldfarb et al., 2011;Pfeiffer et al., 2013). Proteobacteria are the dominant bacteria in the rhizosphere of lodgepole pine trees (Chow et al., 2002) and multiple studies have observed an increase in g-Proteobacteria (Fierer et al., 2007;Eilers et al., 2010) and b-Proteobacteria (Goldfarb et al., 2011) in response to the addition of more labile, low molecular weight organic carbon compounds (Padmanabhan et al., 2003;Cleveland et al., 2007), along with an increase in the abundance of the Mycobacteriaceae family of the Actinobacteria phylum. "
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    ABSTRACT: Unprecedented insect-induced tree mortality has been observed globally and while hydrologic and biogeochemical changes have been recorded, alterations to terrestrial microbial communities, which influence as well as respond to these shifts, are not well understood. The objective of this work was to better understand how bacterial communities are coupled to perturbations in biogeochemically-relevant soil physicochemical parameters resulting from beetle-induced tree death. To this end, soils beneath trees across a beetle-kill spectrum were contrasted in the central Rocky Mountains at both heavily impacted (Chimney, 85% mortality) and moderately impacted (Niwot, 18% mortality) field sites. Soil organic matter (OM), dissolved organic carbon (DOC) and dissolved organic nitrogen were all significantly altered when contrasting soils under healthy versus beetle-attacked trees at Chimney. Bacterial alpha diversity measurements were found to increase with tree death and beta diversity measures showed significant clustering with relation to tree phase. The site was characterized by a significantly higher relative abundance of bacterial clades under healthy trees that were correlated to OM and DOC concentrations. In contrast, compositional changes in soil bacterial communities and edaphic parameters associated with tree phase were not observed at the less impacted Niwot site. Our findings reveal a coupled response between shifts in organic carbon cycling and the bacterial assemblage as a result of large-scale, beetle-induced tree mortality with implications for heterotrophic respiration in near-surface soils and suggests a possible dependence on the level of forest mortality before manifestation.
    Full-text · Article · Dec 2015 · Soil Biology and Biochemistry
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