Soil bacterial phoD gene abundance and expression in response to applied phosphorus and long-term management

Fraser, Tandra D.; Lynch, D. R.; Bent, Elizabeth; Entz, Martin H.; Dunfield, Kari E.

doi:10.1016/j.soilbio.2015.04.014

Cited by 171 publications

(108 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In contrast, Fraser et al (16) reported lower numbers, which are in the same range as in the six soils analyzed in this study. They found between 137 and 163 OTUs in soils from organic and conventional cropping systems and prairie, with a sequencing depth of 11,537 to 54,468 reads.…”

Section: Resultscontrasting

confidence: 49%

“…Previous studies using the ALPS primers have reported an effect of the application of organic and conventional fertilizers, crop management, vegetation, and pH (10,(12)(13)(14)(15)(16)50). The plant community has been reported to have an impact on phoD diversity and community structure in monocultures (14,15).…”

Section: Resultsmentioning

confidence: 99%

“…They were used to assess alkaline phosphatase gene diversity and structure in several soils by PCR-denaturing gradient gel electrophoresis (DGGE) (12)(13)(14)(15) and by 454 sequencing (10,16). These studies showed that crop management, application of organic and conventional fertilizers, and vegetation all affect the phoD alkaline phosphatase gene diversity.…”

mentioning

confidence: 99%

See 2 more Smart Citations

phoD Alkaline Phosphatase Gene Diversity in Soil

Ragot

Kertesz

Bünemann

2015

Appl Environ Microbiol

249

151

View full text Add to dashboard Cite

bPhosphatase enzymes are responsible for much of the recycling of organic phosphorus in soils. The PhoD alkaline phosphatase takes part in this process by hydrolyzing a range of organic phosphoesters. We analyzed the taxonomic and environmental distribution of phoD genes using whole-genome and metagenome databases. phoD alkaline phosphatase was found to be spread across 20 bacterial phyla and was ubiquitous in the environment, with the greatest abundance in soil. To study the great diversity of phoD, we developed a new set of primers which targets phoD genes in soil. The primer set was validated by 454 sequencing of six soils collected from two continents with different climates and soil properties and was compared to previously published primers. Up to 685 different phoD operational taxonomic units were found in each soil, which was 7 times higher than with previously published primers. The new primers amplified sequences belonging to 13 phyla, including 71 families. The most prevalent phoD genes identified in these soils were affiliated with the orders Actinomycetales (13 to 35%), Bacillales (1 to 29%), Gloeobacterales (1 to 18%), Rhizobiales (18 to 27%), and Pseudomonadales (0 to 22%). The primers also amplified phoD genes from additional orders, including Burkholderiales, Caulobacterales, Deinococcales, Planctomycetales, and Xanthomonadales, which represented the major differences in phoD composition between samples, highlighting the singularity of each community. Additionally, the phoD bacterial community structure was strongly related to soil pH, which varied between 4.2 and 6.8. These primers reveal the diversity of phoD in soil and represent a valuable tool for the study of phoD alkaline phosphatase in environmental samples. P hosphorus (P) is an essential macronutrient for all living cells (1). Despite its relative abundance in soils, P is one of the main limiting nutrients for terrestrial organisms (2). P is present in organic and inorganic forms in soil, but only the inorganic orthophosphate ions in soil solutions are readily available for plants (3). To sustain crop productivity, large amounts of P fertilizers are therefore used in agriculture, both as inorganic fertilizers (e.g., triple super phosphate) and organic fertilizers (e.g., manure). After application, some of the inorganic P is rapidly taken up by plants and microorganisms, while the remaining P is immobilized as insoluble and bound P forms in the soil. Microorganisms can access and recycle P from these recalcitrant P forms by solubilization of inorganic P and by mineralization of organic P via enzymatic processes mediated primarily by phosphatases, which hydrolyze the orthophosphate group from organic compounds (3). When facing P scarcity, microorganisms upregulate expression of functional genes coding for phosphatases (phosphomonoesterases, phosphodiesterases, phytases), high-affinity phosphate transporters, and enzymes for phosphonate utilization, which together constitute the Pho regulon (4). The phosphomonoesters which are hydrolyzed ...

show abstract

Section: Resultscontrasting

confidence: 49%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

phoD Alkaline Phosphatase Gene Diversity in Soil

Ragot

Kertesz

Bünemann

2015

Appl Environ Microbiol

249

151

View full text Add to dashboard Cite

show abstract

“…Previous studies have confirmed the presence of a phosphate regulon (Pho) in some bacteria, consisting of a suite of genes responsible for phosphate acquisition induced under conditions of phosphate starvation, including phosphatase production (Apel et al, 2007;Krol and Becker, 2004;Lidbury et al, 2016;Vershinina and Znamenskaya, 2002). Some experiments have demonstrated increased phosphatase activity under phosphate-limited conditions (Fraser et al, 2015a,b;Kier et al, 1979;Zhang et al, 2012), although others have found no correlation (Fraser et al, 2015b).…”

Section: Introductionmentioning

confidence: 99%

Quantification of bacterial non-specific acid ( phoC) and alkaline ( phoD ) phosphatase genes in bulk and rhizosphere soil from organically managed soybean fields

Fraser

Lynch

Gaiero

et al. 2017

Applied Soil Ecology

Self Cite

156

View full text Add to dashboard Cite

“…Furthermore, we observed higher soil acid phosphomonoesterase activity at the northern slope over time probably because of the lower soil P availability at this slope than in the comparable south-facing one. Indeed, an increase in P-acquiring enzyme activities is expected under conditions of soil P deficiency (Fraser et al 2015).…”

Section: Discussionmentioning

confidence: 99%

Chemical and microbiological changes in Norway spruce deadwood during the early stage of decomposition as a function of exposure in an alpine setting

Bardelli

Gómez-Brandòn

Fornasier³

et al. 2018

Arctic, Antarctic, and Alpine Research

View full text Add to dashboard Cite

Alpine ecosystems are vulnerable to ever-changing environmental conditions, leading to shifts in vegetation distribution and composition with implications on soil functionality and carbon (C) turnover. Although deadwood represents an important global C stock, scarce information is available on how slope exposure influences the wood-inhabiting microbiota throughout the decomposition process in an Alpine setting. We therefore evaluated the impact of slope exposure (north-vs. south-facing sites) on physicochemical and microbiological properties (microbial abundance based on real-time PCR: fungal 18S rRNA, dinitrogen reductase [nifH]; microbial biomass: double strand DNA; and microbial activity: hydrolytic enzyme activities of the main nutrient cycles) of Picea abies wood blocks and the underlying soil in a field experiment in the Italian Alps during a three-year period. Overall, a higher abundance of fungi and nitrogen-fixing bacteria was recorded in the soil at the north-facing site where cooler and moister conditions were observed. In contrast, no exposure effects were found for these two microbial groups in the wood blocks, while their abundance increased over time, accompanied by more acidic conditions with progressing decay. The impact of exposure was also enzyme specific and time dependent for both the P. abies wood blocks and the underlying soil.ARTICLE HISTORY

show abstract

Soil bacterial phoD gene abundance and expression in response to applied phosphorus and long-term management

Cited by 171 publications

References 44 publications

phoD Alkaline Phosphatase Gene Diversity in Soil

phoD Alkaline Phosphatase Gene Diversity in Soil

Quantification of bacterial non-specific acid ( phoC) and alkaline ( phoD ) phosphatase genes in bulk and rhizosphere soil from organically managed soybean fields

Chemical and microbiological changes in Norway spruce deadwood during the early stage of decomposition as a function of exposure in an alpine setting

Contact Info

Product

Resources

About