Recovery of As-Yet-Uncultured Soil Acidobacteria on Dilute Solid Media

George, Isabelle; Hartmann, Manuela; Liles, Mark R.; Agathos, Spiros N.

doi:10.1128/aem.05956-11

Cited by 62 publications

(30 citation statements)

References 36 publications

(34 reference statements)

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“…The contrasting tendencies of pH preference displayed by different classes of Acidobacteria in this site were in agreement with some recent studies (Rousk et al, 2010;George et al, 2011;Foesel et al, 2014). Unlike most other phyla, Acidobacteria seemed to be unaffected by contamination levels that suggests a role as generalists in hydrocarboncontaminated soils (Mukherjee et al, 2013).…”

Section: Discussionsupporting

confidence: 79%

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

et al. 2014

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Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites.

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Section: Discussionsupporting

confidence: 79%

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

et al. 2014

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“…Furthermore, differential abundance analysis revealed that Acidobacteria groups 1, 2 and 3 favoured low moisture levels, whereas the other Acidobacteria classes present at Gi-FACE favoured either medium or high moisture levels. The data from Gi-FACE, therefore, provide evidence of ecological distinctness for individual acidobacterial classes, which contributes to our knowledge of these poorly known, albeit abundant soil bacteria (Quaiser et al, 2003;Janssen, 2006;Jones et al, 2009;Castro et al, 2010, George et al, 2011Griffiths et al, 2011).…”

Section: Class Order Familymentioning

confidence: 83%

The soil microbiome at the Gi-FACE experiment responds to a moisture gradient but not to CO2 enrichment

et al. 2016

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The soil bacterial community at the Giessen free-air CO 2 enrichment (Gi-FACE) experiment was analysed by tag sequencing of the 16S rRNA gene. No substantial effects of CO 2 levels on bacterial community composition were detected. However, the soil moisture gradient at Gi-FACE had a significant effect on bacterial community composition. Different groups within the Acidobacteria and Verrucomicrobia phyla were affected differently by soil moisture content. These results suggest that modest increases in atmospheric CO 2 may cause only minor changes in soil bacterial community composition and indicate that the functional responses of the soil community to CO 2 enrichment previously reported at Gi-FACE are due to factors other than changes in bacterial community composition. The effects of the moisture gradient revealed new information about the relationships between poorly known Acidobacteria and Verrucomicrobia and soil moisture content. This study contrasts with the relatively small number of other temperate grassland free-air CO 2 enrichment microbiome studies in the use of moderate CO 2 enrichment and the resulting minor changes in the soil microbiome. Thus, it will facilitate the development of further climate change mitigation studies. In addition, the moisture gradient found at Gi-FACE contributes new knowledge in soil microbial ecology, particularly regarding the abundance and moisture relationships of the soil Verrucomicrobia.

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“…The isolation of bacteria from forest topsoil was described by Lladó et al (28) Cultivation proceeded for up to 15 weeks, because long-term culturing was previously demonstrated to yield slow-growing bacteria from nutrient-limiting environments (34). The strains were stored in a sterile 20% glycerol solution at Ϫ80°C and subcultured on GY-VL55 agar plates at 24°C.…”

Section: Methodsmentioning

confidence: 99%

Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation

García‐Fraile

Benada

Cajthaml

et al. 2016

Appl Environ Microbiol

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dUnderstanding the activity of bacteria in coniferous forests is highly important, due to the role of these environments as a global carbon sink. In a study of the microbial biodiversity of montane coniferous forest soil in the Bohemian Forest National Park (Czech Republic), we succeeded in isolating bacterial strain S55 T , which belongs to one of the most abundant operational taxonomic units (OTUs) in active bacterial populations, according to the analysis of RNA-derived 16S rRNA amplicons. The 16S rRNA gene sequence analysis showed that the species most closely related to strain S55 T include Bryocella elongata SN10 T also reveals the presence of enzymatic machinery required for organic matter decomposition. Soil metatranscriptomic analyses found 132 genes from strain S55 T he decomposition of organic matter from plant residues in forest soils depends on microbial enzymes and environmental factors, such as temperature, moisture, pH, and soil texture. In fact, the carbon cycle in forest soils is completed principally through lignocellulose-degrading microorganisms present in the soil and guts of animals (1). The main plant cell wall polymers are polysaccharides (cellulose and hemicelluloses) and lignin. The degradation of these polymers requires the activity of extracellular enzymes (cellulases, xylanases, laccases, and peroxidases) produced from fungal and bacterial inhabitants of soil (2-6).Bacteria belonging to the phylum Acidobacteria are common in the environment. Acidobacteria are difficult to isolate and maintain in culture, but estimations based on culture-independent studies suggest that approximately 20% (7) of the bacteria in soils worldwide belong to this phylum. Particularly, in some acidic soils, members of Acidobacteria might constitute Ͼ50% of the total bacterial community (8, 9), although they can also be abundant in more-neutral soils (10-13). Thus, this phylum is as abundant in soils as is Proteobacteria. Subdivision 1 of Acidobacteria contains most of the officially described taxa within this phylum; currently, there are only 21 validated species classified in 7 genera, plus the not-yet-validated proposed new genus and species "Acidipila rosea" (14). Most of these bacteria have been isolated from acidic soils, wetlands, tundra, and peat (15)(16)(17)(18)(19)(20). The Acidobacteria phylum was originally described as including four or five subgroups or subdivisions (10, 21). As the number of available 16S rRNA gene sequences increased, the work of Barns et al. (11) expanded the known diversity encompassed within the phylum to the current 26 subdivisions. The abundance of these bacteria in soils suggests that acidobacteria play important roles in soil ecological processes. pH is the most important environmental variable affecting acidobacterial abundance (8). Besides pH, a negative correlation with organic carbon availability and total nitrogen concentration in soils was observed, suggesting an oligotrophic lifestyle of Acidobacteria (22,23). Oligotrophy and preferential colonization of bulk so...

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Recovery of As-Yet-Uncultured Soil Acidobacteria on Dilute Solid Media

Cited by 62 publications

References 36 publications

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

The soil microbiome at the Gi-FACE experiment responds to a moisture gradient but not to CO2 enrichment

Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation

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