Long-term phosphorus fertilisation increased the diversity of the total bacterial community and the phoD phosphorus mineraliser group in pasture soils

Tan, Hao; Barret, Matthieu; Mooij, Marlies J.; Rice, Olivia; Morrissey, John P.; Dobson, Alan D. W.; Griffiths, Bryan S.; O’Gara, Fergal

doi:10.1007/s00374-012-0755-5

Cited by 286 publications

(210 citation statements)

References 71 publications

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“…The pairwise distance matrix was calculated from the alignment, and sequences were clustered using the k-furthest method as implemented in mothur, with a similarity cutoff at 75% to define the operational taxonomic units (OTUs), as calculated by Tan et al (10). OTU matrices were normalized to the smallest library size using the normalized.shared command in mothur to allow comparison between samples.…”

Section: Methodsmentioning

confidence: 99%

“…There is high sequence variability in the PhoA, PhoD, and PhoX proteins, not only between the families but also within each family (5,9). PhoD is widespread in both terrestrial and aquatic ecosystems (8,10).…”

mentioning

confidence: 99%

“…Subsequently, the ALPS primers were demonstrated to be specific to the phoD alkaline phosphatase gene (10). 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).…”

mentioning

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.…”

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phoD Alkaline Phosphatase Gene Diversity in Soil

Ragot

Kertesz

Bünemann

2015

Appl Environ Microbiol

236

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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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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phoD Alkaline Phosphatase Gene Diversity in Soil

Ragot

Kertesz

Bünemann

2015

Appl Environ Microbiol

236

151

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“…When only organic fertilizers are applied in organic agrosystems, phosphorus becomes a yield-limiting factor in the soils of different richness (Fageria et al, 2011;Tan et al, 2013). Therefore, the majority of authors suggest using the biomass of perennial grasses aftermath or annual plants cultivated as catch crops for green manure in organic agrosystems.…”

Section: Introductionmentioning

confidence: 99%

Pagrindinių mitybos elementų pokyčiai dirvožemyje taikant alternatyvias žemdirbystės sistemas

Masilionytė

Maikštėnienė

2016

Zemdirbyste-Agriculture

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Experiments were conducted at Joniškėlis Experimental Station of the Lithuanian Research Centre for Agriculture and Forestry in 2006-2013, on an Endocalcari-Endohypogleyic Cambisol (CMg-n-w-can), which is characterised by low phosphorus and high potassium contents with low (<2.0) and moderate (>2.1) humus content. The research was carried out in the crop rotation's grass-cereal sequence: perennial grasses (grown as green manure) → winter wheat. The aim of experiments is to determine the changes of biogenic soil elements in the organic cropping systems by using farmyard manure and aftermath of red clover for green manure or their combinations for winter wheat fertilization, and in sustainable cropping systems -by replenishing the amount of nutritional elements with mineral fertilizers. The NPK balance was negative in the organic cropping system in the soil with both low and moderate levels of soil humus when only green manure had been used as fertilizer for winter wheat. The NP balance was strongly positive and K was significantly in excess in the organic cropping system when the green manure had been used in combination with 40 Mg ha -1 of farmyard manure. A marked reduction in the available phosphorus content in the soil with different humus levels was established when green manure or 40 Mg ha -1 of farmyard manure or their combinations had been applied. Also, potassium levels increased in the organic cropping system where green or farmyard manure had been applied. When 40 Mg ha -1 of farmyard manure and N 30 mineral fertilizer had been used in the sustainable cropping system to promote straw mineralization, the nitrogen balance in the soil with the low humus content was slightly positive, but in the soil with moderate humus content it was strongly negative; in the soil of both humus levels phosphorus balance was slightly positive and potassium balance was significantly excessive. In the both soils with low and moderate humus content, in the sustainable cropping systems that had used the perennial grass aftermath as green manure with minimum rates of mineral fertilizer N 30 P 60 K 60 , N balance was negative, P -marginally positive. In the soil with low humus content K value was positive, in the soil with moderate humus content -marginally negative. In the sustainable cropping system, where perennial grass aftermath for green manure and N 30 P 60 K 60 had been used for winter wheat during two 4-field crop rotations the available phosphorus and potassium quantity in the soil low and moderate in humus status showed a trend towards decreasing.

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Impact of roots, microorganisms and microfauna on the fate of soil phosphorus in the rhizosphere

Hinsinger

Herrmann

Lesueur³

et al. 2015

Annual Plant Reviews Volume 48

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Phosphorus (P) occurs at low concentrations in soils because of the numerous processes responsible for P sorption or immobilisation. Soil P is also characterised by its restricted mobility, and thus the most limiting step of P acquisition is not its absorption by plant roots, but rather the many processes that determine the fate of soil P in the rhizosphere. This chapter describes these various processes, including those directly mediated by plants (which vary considerably with plant species), and those related to soil microbial and microfaunal activities. In order to overcome the restricted mobility of soil P, plants have evolved several features aimed at increasing the rhizosphere volume by increasing the absorptive surfaces, notably root elongation and branching. The formation of root hairs and mycorrhizas is also triggered by interactions with plant growth promoting microorganisms. Plants have also evolved strategies aimed at increasing soil P concentrations via the mobilisation of inorganic and organic pools of soil P. These imply changes in pH, and the release of P-mobilising compounds such as carboxylates and phosphatases, that are exuded by the roots themselves or by rhizosphere microorganisms. Finally, the soil microfauna (especially the predators of bacteria and fungi) play an important role in the cycling of soil P in the rhizosphere that deserves further consideration. (Résumé d'auteur

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Long-term phosphorus fertilisation increased the diversity of the total bacterial community and the phoD phosphorus mineraliser group in pasture soils

Cited by 286 publications

References 71 publications

phoD Alkaline Phosphatase Gene Diversity in Soil

phoD Alkaline Phosphatase Gene Diversity in Soil

Pagrindinių mitybos elementų pokyčiai dirvožemyje taikant alternatyvias žemdirbystės sistemas

Impact of roots, microorganisms and microfauna on the fate of soil phosphorus in the rhizosphere

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