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

Applied Soil Ecology - Tập 111 - Trang 48-56 - 2017
Tandra D. Fraser1, Derek H. Lynch2, Jonathan Gaiero3, Kamini Khosla3, Kari E. Dunfield3
1Centre for Agri-Environmental Research, School of Agriculture, Policy and Development, University of Reading, UK
2Department of Plant and Animal Science, Dalhousie University, Canada
3School of Environmental Science, University of Guelph, Canada

Tài liệu tham khảo

Alegria Terrazas, 2016, Chapter one – plant–microbiota interactions as a driver of the mineral turnover in the rhizosphere, 1, 10.1016/bs.aambs.2016.03.001 Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 1990, 403, 10.1016/S0022-2836(05)80360-2 Apel, 2007, Phosphate control of phoA, phoC and phoD gene expression in Streptomyces coelicolor reveals significant differences in binding of PhoP to their promoter regions, Microbiology, 153, 3527, 10.1099/mic.0.2007/007070-0 Araujo, 2008, Phosphatase and phytase activities in nodules of common bean genotypes at different levels of phosphorus supply, Plant Soil, 312, 129, 10.1007/s11104-008-9595-3 Araujo, 2008, Phosphatase and phytase activities in nodules of common bean genotypes at different levels of phosphorus supply, Plant Soil, 312, 129, 10.1007/s11104-008-9595-3 Brookes, 1984, Phosphorus in the soil microbial biomass, Soil Biol. Biochem., 16, 169, 10.1016/0038-0717(84)90108-1 Castorena, 2016, Micromapping of microbial hotspots and biofilms from different crops using digital image mosaics of soil thin sections, Geoderma, 279, 11, 10.1016/j.geoderma.2016.05.017 Eivazi, 1977, Phosphatases in soils, Soil Biol. Biochem., 9, 167, 10.1016/0038-0717(77)90070-0 Entz, 2001, Crop yield and soil nutrient status on 14 organic farms in the eastern portion of the northern Great Plains, Can. J. Plant Sci., 81, 351, 10.4141/P00-089 Ezawa, 2005, A new hypothesis on the strategy for acquisition of phosphorus in arbuscular mycorrhiza: up-regulation of secreted acid phosphatase gene in the host plant, Mol. Plant-Microbe Interact., 18, 1046, 10.1094/MPMI-18-1046 Fraser, 2015, Linking alkaline phosphatase activity with bacterial phoD gene abundance in soil from a long-term management trial, Geoderma, 257, 115, 10.1016/j.geoderma.2014.10.016 Fraser, 2015, Soil bacterial phoD gene abundance and expression in response to applied phosphorus and long-term management, Soil Biol. Biochem., 88, 137, 10.1016/j.soilbio.2015.04.014 Gandhi, 2012, A comparative analysis of three classes of bacterial non-specific acid phosphatases and archaeal phosphoesterases: evolutionary perspective, Acta Inf. Med., 20, 167, 10.5455/aim.2012.20.167-173 George, 2006, Depletion of organic phosphorus from Oxisols in relation to phosphatase activities in the rhizosphere, Eur. J. Soil Sci., 57, 47, 10.1111/j.1365-2389.2006.00767.x Giovanetti, 1980, An evaluation of techniques for measuring vesicular-arbuscular mycorrhizal infection in roots, New Phytol., 84, 489, 10.1111/j.1469-8137.1980.tb04556.x Gomez, 1995, Cloning, sequencing and characterization of the alkaline phosphatase gene (phoD) from Zymomonas mobilis, Fems Microbiol. Lett., 125, 237, 10.1111/j.1574-6968.1995.tb07364.x Hinsinger, 2001, Bioavailability of soil inorganic P in the rhizosphere as affected by root-induced chemical changes: a review, Plant Soil, 237, 173, 10.1023/A:1013351617532 Huang, 2014, Rhizosphere interactions: root exudates, microbes, and microbial communities, Bot.-Botanique, 92 Kier, 1979, Regulation of nonspecific acid phosphatase in Salmonella: phoN and phoP genes, J. Bacteriol., 138, 155, 10.1128/JB.138.1.155-161.1979 Knight, 2010, Classification and fertility status of organically managed fields across Saskatchewan, Canada, Can. J. Soil Sci., 90, 667, 10.4141/cjss09082 Koressaar, 2007, Enhancements and modifications of primer design program Primer3, Bioinformatics, 23, 1289, 10.1093/bioinformatics/btm091 Kouas, 2009, Effect of phosphorus deficiency on acid phosphatase and phytase activities in common bean (Phaseolus vulgaris L.) under symbiotic nitrogen fixation, Symbiosis, 73, 141, 10.1007/BF03179974 Krol, 2004, Global transcriptional analysis of the phosphate starvation response in Sinorhizobium meliloti strains 1021 and 2011, Mol. Genet. Genomics, 272, 1, 10.1007/s00438-004-1030-8 Lane, 2015, CEMAsuite: open source degenerate PCR primer design, Bioinformatics, 31, 3688, 10.1093/bioinformatics/btv420 Li, 2002, Purple acid phosphatases of Arabidopsis thaliana: comparative analysis and differential regulation by phosphate deprivation, J. Biol. Chem., 2002, 27772, 10.1074/jbc.M204183200 Li, 2012, Identification of soybean purple acid phosphatase genes and their expression responses to phosphorus availability and symbiosis, Ann. Bot., 109, 275, 10.1093/aob/mcr246 Lidbury, 2016, Comparative genomic, proteomic and exoproteomic analyses of three Pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria, Appl. Environ. Microbiol., 18, 3535 Main, 2013, Soil phosphorus effects on forage harvested and nitrogen fixation on Canadian organic dairy farms, Agron. J., 105, 1, 10.2134/agronj2012.0500 Marschner, 1986, Root-induced changes in the rhizosphere: importance for the mineral nutrition of plants, Z. Pflanzenernaehr. Bodenk., 149, 441, 10.1002/jpln.19861490408 Marschner, 2004, Development of specific rhizosphere bacterial communities in relation to plant species, nutrition and soil type, Plant Soil, 261, 199, 10.1023/B:PLSO.0000035569.80747.c5 Martin, 2007, Phosphorus status on Canadian organic farms, J. Sci. Food Agric., 87, 2737, 10.1002/jsfa.3077 Martinez, 2007, Aerobic uranium (VI) bioprecipitation by metal-resistant bacteria isolated from radionuclide- and metal-contaminated subsurface soils, Environ. Microbiol., 9, 3122, 10.1111/j.1462-2920.2007.01422.x Mehlich, 1984, Mehlich-3 soil test extractant – a modification of Mehlich-2 extractant, Commun. Soil Sci. Plant Anal., 15, 1409, 10.1080/00103628409367568 Murphy, 1962, A modified single solution method for the determination of phosphate in natural waters, Anal. Chim. Acta, 27, 31, 10.1016/S0003-2670(00)88444-5 Nannipieri, 2011, Role of phosphatase enzymes in soil, 215 Penheiter, 1997, Soybean root nodule acid phosphatase, Plant Physiol., 114, 597, 10.1104/pp.114.2.597 Penheiter, 1997, Soybean root nodule acid phosphatase, Plant Physiol., 114, 597, 10.1104/pp.114.2.597 Philippot, 2013, Going back to the roots: the microbial ecology of the rhizosphere, Nat. Rev. Microbiol., 11, 789, 10.1038/nrmicro3109 Ragot, 2015, phoD alkaline phosphatase gene diversity in soil, Appl. Environ. Microbiol., 18, 7281, 10.1128/AEM.01823-15 Raposo, 2004, Acid phosphatase activity and leaf phosphorus content in soybean cultivars, Scientia Agricola, 61, 439, 10.1590/S0103-90162004000400014 Rengel, 2005, Nutrient availability and management in the rhizosphere: exploiting genotypic differences, New Phytol., 168, 305, 10.1111/j.1469-8137.2005.01558.x Roberts, 2008, Nutrient budgets of Ontario organic dairy farms, Can. J. Soil Sci., 88, 107, 10.4141/S06-056 Rodrıguez, 2006, Genetics of phosphate solubilization and its potential applications for improving plant growth-promoting bacteria, Plant Soil, 287, 15, 10.1007/s11104-006-9056-9 Rossolini, 1998, Bacterial nonspecific acid phosphohydrolases: physiology, evolution and use as tools in microbial biotechnology, Cell. Mol. Life Sci., 54, 10.1007/s000180050212 Sakurai, 2008, Analysis of bacterial communities on alkaline phosphatase genes in soil supplied with organic matter, Soil Sci. Plant Nutr., 54, 62, 10.1111/j.1747-0765.2007.00210.x Shujie, 2011, Effects of phosphorus concentration on adaptive mechanisms of high- and low-P efficiency soybean genotypes when grown in solution, Plant Soil Environ., 57, 61, 10.17221/143/2010-PSE Sievers, 2011, Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Mol. Syst. Biol., 7, 10.1038/msb.2011.75 Spohn, 2013, Distribution of microbial- and root-derived phosphatase activities in the rhizosphere depending on P availability and C allocation – Coupling soil zymography with C-14 imaging, Soil Biol. Biochem., 67, 106, 10.1016/j.soilbio.2013.08.015 Spohn, 2015, Distribution of phosphatase activity and various bacterial phyla in the rhizosphere of Hordeum vulgare L. depending on P availability, Soil Biol. Biochem., 89, 44, 10.1016/j.soilbio.2015.06.018 Tabatabai, 1994, Soil enzymes, 775 Tarafdar, 1998, Organic phosphorus compounds as a phosphorus source for higher plants through the activity of phosphatases produced by plant roots and microorganisms, Biol. Fertil. Soils, 5, 308 Untergasser, 2012, Primer3-new capabilities and interfaces, Nucl. Acids Res., 40, 10.1093/nar/gks596 Vershinina, 2002, The Pho regulons of bacteria, Microbiology, 71, 497, 10.1023/A:1020547616096 Vierheilig, 1998, Ink and vinegar: a simple staining technique for arbuscular-mycorrhizal fungi, Appl. Environ. Microbiol., 64, 5004, 10.1128/AEM.64.12.5004-5007.1998 Voroney, 2008, Soil microbial biomass C, N, P, and S, 637 Wang, 2010, Genetic improvement for phosphorus efficiency in soybean: a radical approach, Ann. Bot., 106, 215, 10.1093/aob/mcq029 Wang, 2012, Phosphorus pools and other soil properties in the rhizosphere of wheat and legumes growing in three soils in monoculture or as a mixture of wheat and legume, Plant Soil, 354, 283, 10.1007/s11104-011-1065-7 Wang, 2015, Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling, Sci. Rep., 5, 14345, 10.1038/srep14345 Zhang, 2012, Soil phosphorus composition determined by P-31 NMR spectroscopy and relative phosphatase activities influenced by land use, Eur. J. Soil Biol., 52, 73, 10.1016/j.ejsobi.2012.07.001