Linking alkaline phosphatase activity with bacterial phoD gene abundance in soil from a long-term management trial

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

doi:10.1016/j.geoderma.2014.10.016

Cited by 196 publications

(124 citation statements)

References 69 publications

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“…We predict that in these systems, the turnover of organic P by microorganisms is essential for maintaining long-term productivity. In a previous study, we demonstrated a general correlation between the abundance of an ALK gene (phoD) and ALK (pH 11.0) activity in a heavy clay soil (pH 7.4 H20 ) from the Northern Great Plains near Winnipeg, Canada (Fraser et al, 2015a) and a negative correlation with labile P (Fraser et al, 2015a). However, we predict that in soils with a neutral or lower pH that the bacterial phoC genes will be more predominant than the phoD genes.…”

Section: Introductionmentioning

confidence: 61%

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

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156

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Section: Introductionmentioning

confidence: 61%

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

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156

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“…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%

phoD Alkaline Phosphatase Gene Diversity in Soil

Ragot

Kertesz

Bünemann

2015

Appl Environ Microbiol

249

151

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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 ...

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“…The abundance and the compositions of APase-harboring bacteria have been related to P availability in soils fertilized with manure and P inorganic fertilizers (Chhabra et al 2013;Fraser et al 2015a;Sakurai et al 2008;Tan et al 2013). However, little is known of APase-harboring bacterial assemblages in pristine soils.…”

Section: Discussionmentioning

confidence: 99%

“…The phoD gene has been used as a molecular marker to provide information regarding the distribution and diversity of APase bacterial assemblages in soils (Tan et al 2013). The abundance of phoD has been shown to be an effective indicator of enzyme function due to its high inverse correlation with P availability and positive correlation with APase activities (Fraser et al 2015a). The presence and abundance of both phoA and phoX has been studied in aquatic ecosystems, including seawater and freshwater (Dai et al 2014(Dai et al , 2015; the phoX is more widely distributed among marine bacteria than the phoA (Sebastian and Ammerman 2009).…”

Section: Introductionmentioning

confidence: 99%

Bacterial alkaline phosphomonoesterase in the rhizospheres of plants grown in Chilean extreme environments

et al. 2016

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Bacterial alkaline phosphomonoesterases (APases) are relevant for organic phosphorus (Po) recycling in many soils. However, the abundance and diversity of bacterial APase in the rhizospheres of native plants are poorly known, particularly in extreme environments. In this research work, we studied the composition of total and APase-harboring bacterial communities, abundances of selected APase genes (phoD and phoX), and APase activities in rhizosphere soils from native plants grown in extreme environments of northern (Atacama Desert), central (Andes volcano; Quetrupillan and Mamuil Malal) and hot spring (Liquiñe), and southern polar (Patagonia and Antarctic) regions of Chile. Differences in the composition of bacterial communities in the rhizosphere soils were revealed by denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) of 16S ribosomal RNA (rRNA), phoD, and phoX genes. In general, the significant lowest bacterial diversities, APase gene abundances, and APase activities were observed in rhizosphere soils from Atacama Desert, whereas the highest values were observed in rhizosphere soils of Patagonia. In addition, APase gene abundances were positively correlated among them and with APase activity of rhizosphere soils, but negatively correlated with phosphorus (P) availability in rhizosphere soils. Although bacterial APases were observed in all studied rhizosphere soils, their relevance to soil Po recycling in soils of extreme environments remains unclear and further studies are needed.

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Linking alkaline phosphatase activity with bacterial phoD gene abundance in soil from a long-term management trial

Cited by 196 publications

References 69 publications

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

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

phoD Alkaline Phosphatase Gene Diversity in Soil

Bacterial alkaline phosphomonoesterase in the rhizospheres of plants grown in Chilean extreme environments

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