Assessment of Soil Microbial Community Structure by Use of Taxon-Specific Quantitative PCR Assays

Fierer, Noah; Jackson, Jason A.; Vilgalys, Rytas; Jackson, Robert B.

doi:10.1128/aem.71.7.4117-4120.2005

Cited by 1,313 publications

(860 citation statements)

References 29 publications

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“…Interestingly, when applying the same approach in temperate grasslands, significant correlations were often found (r between 0.324 and 0.867, EE Kuramae et al, unpublished results). Incomplete primer specificity could also play a role, as this has been shown for some primers used in this study (Fierer et al, 2005).…”

Section: Phylochip Analysis Of Antarctic Soil Microbes E Yergeau Et Almentioning

confidence: 99%

“…Real-time PCR and PCR for microarray analyses Real-time PCR quantifications for Acidobacteria, Actinobacteria, Firmicutes, Alphaproteobacteria, Betaproteobacteria and bacteria were performed using primers and cycling conditions described in Fierer et al (2005). Real-time PCR quantifications were carried out on soil DNA using Absolute QPCR SYBR green mixes (AbGene, Epsom, UK) on a RotorGene 3000 (Corbett Research, Sydney, Australia) as described earlier (Yergeau et al, 2007a).…”

Section: Soil Samplesmentioning

confidence: 99%

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Environmental microarray analyses of Antarctic soil microbial communities

et al. 2008

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Antarctic ecosystems are fascinating in their limited trophic complexity, with decomposition and nutrient cycling functions being dominated by microbial activities. Not only are Antarctic habitats exposed to extreme environmental conditions, the Antarctic Peninsula is also experiencing unequalled effects of global warming. Owing to their uniqueness and the potential impact of global warming on these pristine systems, there is considerable interest in determining the structure and function of microbial communities in the Antarctic. We therefore utilized a recently designed 16S rRNA gene microarray, the PhyloChip, which targets 8741 bacterial and archaeal taxa, to interrogate microbial communities inhabiting densely vegetated and bare fell-field soils along a latitudinal gradient ranging from 51 °S (Falkland Islands) to 72 °S (Coal Nunatak). Results indicated a clear decrease in diversity with increasing latitude, with the two southernmost sites harboring the most distinct Bacterial and Archaeal communities. The microarray approach proved more sensitive in detecting the breadth of microbial diversity than polymerase chain reaction-based bacterial 16S rRNA gene libraries of modest size (∼190 clones per library). Furthermore, the relative signal intensities summed for phyla and families on the PhyloChip were significantly correlated with the relative occurrence of these taxa in clone libraries. PhyloChip data were also compared with functional gene microarray data obtained earlier, highlighting numerous significant relationships and providing evidence for a strong link between community composition and functional gene distribution in Antarctic soils. Integration of these PhyloChip data with other complementary methods provides an unprecedented understanding of the microbial diversity and community structure of terrestrial Antarctic habitats.

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Section: Phylochip Analysis Of Antarctic Soil Microbes E Yergeau Et Almentioning

confidence: 99%

Section: Soil Samplesmentioning

confidence: 99%

Environmental microarray analyses of Antarctic soil microbial communities

et al. 2008

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“…The optimal annealing temperature for msrA was 54°C. The 16S-rRNA gene in Bacteria was also enumerated with Eub338/Eub518 primers and protocols adapted from Fierer et al (2005). Additionally, the molarities of each primer used in reactions were optimized by combining forward and reverse primers at various concentrations.…”

Section: Quantitative Pcr Analysesmentioning

confidence: 99%

Fate and transport of tylosin-resistant bacteria and macrolide resistance genes in artificially drained agricultural fields receiving swine manure

Luby

Moorman

Soupir

2016

Science of The Total Environment

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Application of manure from swine treated with antibiotics introduces antibiotics and antibiotic resistance genes to soil with the potential for further movement in drainage water, which may contribute to the increase in antibiotic resistance in non-agricultural settings. We compared losses of antibiotic-resistant Enterococcus and macrolide-resistance (erm and msrA) genes in water draining from plots with or without swine manure application under chisel plow and no till conditions. Concentrations of ermB,ermC and ermF were all > 10 9 copies g − 1 in manure from tylosin-treated swine, and application of this manure resulted in short-term increases in the abundance of these genes in soil. Abundances of ermB, ermC and ermF in manured soil returned to levels identified in non-manured control plots by the spring following manure application. Tillage practices yielded no significant differences (p > 0.10) in enterococci or erm gene concentrations in drainage water and were therefore combined for further analysis. While enterococci and tylosin-resistant enterococci concentrations in drainage water showed no effects of manure application, ermB and ermF concentrations in drainage water from manured plots were significantly higher (p < 0.01) than concentrations coming from non-manured plots. ErmB and ermF were detected in 78% and 44%, respectively, of water samples draining from plots receiving manure. Although ermC had the highest concentrations of the three genes in drainage water, there was no effect of manure application on ermC abundance. MsrA was not detected in manure, soil or water. This study is the first to report significant increases in abundance of resistance genes in waters draining from agricultural land due to manure application. H I G H L I G H T S• Higher levels of ermB and ermF in drainage are attributable to manure.• Fall manure application resulted in transient increases in soil enterococci.• Manure application did not affect enterococci levels in drainage water. Application of manure from swine treated with antibiotics introduces antibiotics and antibiotic resistance genes to soil with the potential for further movement in drainage water, which may contribute to the increase in antibiotic resistance in non-agricultural settings. We compared losses of antibiotic-resistant Enterococcus and macrolide-resistance (erm and msrA) genes in water draining from plots with or without swine manure application under chisel plow and no till conditions. Concentrations of ermB, ermC and ermF were all N10 9 copies g −1 in manure from tylosin-treated swine, and application of this manure resulted in short-term increases in the abundance of these genes in soil. Abundances of ermB, ermC and ermF in manured soil returned to levels identified in non-manured control plots by the spring following manure application. Tillage practices yielded no significant differences (p N 0.10) in enterococci or erm gene concentrations in drainage water and were therefore combined for further analysis. While enterococci and tylosin...

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“…The bacterial rpoB gene was also selected, as this single-copy gene encodes a sub-unit of the bacterial RNA polymerase and thus provides an estimation of transcriptional activity. The primers used were: EUB338 and EUB518 for bacterial 16S (Fierer et al, 2005); NL1f and LS2r for fungal 28S (Bates and Garcia-Pichel, 2009); A364aF and A934b for archaeal 16S (Kemnitz et al, 2005); and rpoB-f-4 and rpoB-r-2 for bacterial rpoB gene (Silkie and Nelson, 2009).…”

Section: Abundance Of Genes and Transcriptsmentioning

confidence: 99%

Responses of soil bacterial and fungal communities to extreme desiccation and rewetting

2013

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The microbial response to summer desiccation reflects adaptation strategies, setting the stage for a large rainfall-induced soil CO 2 pulse upon rewetting, an important component of the ecosystem carbon budget. In three California annual grasslands, the present (DNA-based) and potentially active (RNA-based) soil bacterial and fungal communities were tracked over a summer season and in response to controlled rewetting of intact soil cores. Phylogenetic marker genes for bacterial (16S) and fungal (28S) RNA and DNA were sequenced, and the abundances of these genes and transcripts were measured. Although bacterial community composition differed among sites, all sites shared a similar response pattern of the present and potentially active bacterial community to dry-down and wet-up. In contrast, the fungal community was not detectably different among sites, and was largely unaffected by dry-down, showing marked resistance to dessication. The potentially active bacterial community changed significantly as summer dry-down progressed, then returned to pre-dry-down composition within several hours of rewetting, displaying spectacular resilience. Upon rewetting, transcript copies of bacterial rpoB genes increased consistently, reflecting rapid activity resumption. Acidobacteria and Actinobacteria were the most abundant phyla present and potentially active, and showed the largest changes in relative abundance. The relative increase (Actinobacteria) and decrease (Acidobacteria) with dry-down, and the reverse responses to rewetting reflected a differential response, which was conserved at the phylum level and consistent across sites. These contrasting desiccation-related bacterial life-strategies suggest that predicted changes in precipitation patterns may affect soil nutrient and carbon cycling by differentially impacting activity patterns of microbial communities.

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Assessment of Soil Microbial Community Structure by Use of Taxon-Specific Quantitative PCR Assays

Cited by 1,313 publications

References 29 publications

Environmental microarray analyses of Antarctic soil microbial communities

Environmental microarray analyses of Antarctic soil microbial communities

Fate and transport of tylosin-resistant bacteria and macrolide resistance genes in artificially drained agricultural fields receiving swine manure

Responses of soil bacterial and fungal communities to extreme desiccation and rewetting

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