Farming practices and crop species influence the population of total and alkaline phosphatase gene harboring bacteria in tropical agro-ecosystem
The alkaline phosphatase (ALP) enzyme is encoded by the phoD gene reported majorly in bacteria. In the present study, we investigated variation in the phoD gene abundance, and the relationship between phoD gene abundance, ALP enzyme activity and available P under different farming practice (organic vs conventional), crop species (chickpea, mustard, soybean and maize) and their growth stages (pre-vegetation, vegetative, flowering, maturation and post-harvest). The qPCR analysis revealed variation in total bacterial and phoD gene copy number (copies g-1dws), ranging from 1.40X109 to 9.16X1010 and 1.72X105 to 1.43X107, respectively. The farming practices suggested significant effect with increased activity of ALP, and abundance of phoD and 16S rRNA genes in organic farming than the conventional one. The 16S rRNA and phoD gene abundance varied significantly along different growth stages of crops in the order: flowering > maturation > vegetative > post-harvest > pre-vegetation stages with maximum in maize and lowest in soybean in both the farming practice. In conclusion, farming practices, crop types and crop growth stages influenced soil available P and significantly affected ALP activity by regulating phoD bacterial population in agroecosystem.
<?xml version="1.0" encoding="UTF-8" standalone="yes"?> <!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.2d1 20170631//EN" "JATS-journalpublishing1.dtd"> <article xlink="http://www.w3.org/1999/xlink" dtd-version="1.0" article-type="agricultural-biotechnology" lang="en"> <front> <journal-meta> <journal-id journal-id-type="publisher">JIAR</journal-id> <journal-id journal-id-type="nlm-ta">Journ of innovation in applied research</journal-id> <journal-title-group> <journal-title>Journal of Innovation in Applied Research</journal-title> <abbrev-journal-title abbrev-type="pubmed">Journ of innovation in applied research</abbrev-journal-title> </journal-title-group> <issn pub-type="ppub">2231-2196</issn> <issn pub-type="opub">0975-5241</issn> <publisher> <publisher-name>Radiance Research Academy</publisher-name> </publisher> </journal-meta> <article-meta> <article-id pub-id-type="publisher-id">104</article-id> <article-id pub-id-type="doi">10.51323/JIAR.5.1.2022.52-68</article-id> <article-id pub-id-type="doi-url"/> <article-categories> <subj-group subj-group-type="heading"> <subject>Agricultural Biotechnology</subject> </subj-group> </article-categories> <title-group> <article-title>Farming practices and crop species influence the population of total and alkaline phosphatase gene harboring bacteria in tropical agro-ecosystem </article-title> </title-group> <contrib-group> <contrib contrib-type="author"> <name> <surname>eha</surname> <given-names>N</given-names> </name> </contrib> <contrib contrib-type="author"> <name> <surname>Bhardwaj</surname> <given-names>Yashpal</given-names> </name> </contrib> <contrib contrib-type="author"> <name> <surname>Dubey</surname> <given-names>Suresh Kumar</given-names> </name> </contrib> </contrib-group> <pub-date pub-type="ppub"> <day>30</day> <month>04</month> <year>2022</year> </pub-date> <volume>5</volume> <issue/> <fpage>52</fpage> <lpage>68</lpage> <permissions> <license license-type="open-access" href="http://creativecommons.org/licenses/by/4.0/"> <license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution (CC BY 4.0) Licence. You may share and adapt the material, but must give appropriate credit to the source, provide a link to the licence, and indicate if changes were made.</license-p> </license> </permissions> <abstract> <p>The alkaline phosphatase (ALP) enzyme is encoded by the phoD gene reported majorly in bacteria. In the present study, we investigated variation in the phoD gene abundance, and the relationship between phoD gene abundance, ALP enzyme activity and available P under different farming practice (organic vs conventional), crop species (chickpea, mustard, soybean and maize) and their growth stages (pre-vegetation, vegetative, flowering, maturation and post-harvest). The qPCR analysis revealed variation in total bacterial and phoD gene copy number (copies g-1dws), ranging from 1.40X109 to 9.16X1010 and 1.72X105 to 1.43X107, respectively. The farming practices suggested significant effect with increased activity of ALP, and abundance of phoD and 16S rRNA genes in organic farming than the conventional one. The 16S rRNA and phoD gene abundance varied significantly along different growth stages of crops in the order: flowering > maturation > vegetative > post-harvest > pre-vegetation stages with maximum in maize and lowest in soybean in both the farming practice. In conclusion, farming practices, crop types and crop growth stages influenced soil available P and significantly affected ALP activity by regulating phoD bacterial population in agroecosystem. </p> </abstract> <kwd-group> <kwd>phoD gene copy number</kwd> <kwd> alkaline phosphatase activity</kwd> <kwd> available P</kwd> <kwd> farming practices</kwd> <kwd> crops</kwd> </kwd-group> </article-meta> </front> </article>
Acuña J. J., Durán P., Lagos L. M., Ogram A., de la Luz Mora M., & Jorquera M. A., (2016). Bacterial alkaline phosphomonoesterase in the rhizospheres of plants grown in Chilean extreme environments. Biology and Fertility of Soils, 52, 763-773.
Allen S. E., Grimshaw H. M., & Rowland A. P., (1986). Chemical Analysis. In: Moore, P.D. and Chapman, S.B., Eds., Methods of Plant Ecology, Blackwell, Oxford, 285-344.
Apel A. K., Sola-Landa A., Rodríguez-García A., & Martín J. F., (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, 3527-3537.
Bardgett R., Mawdsley J., Edwards S., Hobbs P., Rodwell J., & Davies W. J., (1999). Plant species and nitrogen effects on soil biological properties of temperate upland grasslands. Functional Ecology, 13, 650-660.
Bhardwaj Y., Sharma M. P., Pandey J., & Dubey S. K., (2020). Variations in microbial community in a tropical dry deciduous forest across the season and topographical gradient assessed through signature fatty acid biomarkers. Ecological Research, 35, 139-153.
Bhat N. A., Riar A., Ramesh A., Iqbal S., Sharma M. P., Sharma S. K., & Bhullar G. S., (2017). Soil biological activity contributing to phosphorus availability in vertisols under long-term organic and conventional agricultural management. Frontiers in Plant Science, 8: 1523.
Brady N. C., & Weil R. R., (2007). The nature and properties of soils. Prentice Hall, New Jersey, USA.
Burns R., (1982). Enzyme activity in soil: location and a possible role in microbial ecology. Soil Biology and Biochemistry, 14, 423-427.
Chakraborty A., Chakrabarti K., Chakraborty A., & Ghosh S., (2011). Effect of long-term fertilizers and manure application on microbial biomass and microbial activity of a tropical agricultural soil. Biology and Fertility of Soils, 47, 227-233
Chandra R., Kumar N., & Tyagi A., (2007). Nutrient dynamics and decomposition rates during composting of sulphitation pressmud by different methods. Journal of Environmental Engineering and Science, 49, 183-188.
Chen X., Jiang N., Chen Z., Tian J., Sun N., Xu M., & Chen L., (2017). Response of soil phoD phosphatase gene to long-term combined applications of chemical fertilizers and organic materials. Applied Soil Ecology, 119, 197-204.
Chen X., Jiang N., Condron L. M., Dunfield K. E., Chen Z., Wang J., & Chen L., (2019a). Impact of long-term phosphorus fertilizer inputs on bacterial phoD gene community in a maize field, Northeast China. Science of Total Environment, 669, 1011-1018.
Chen X., Jiang N., Condron L. M., Dunfield K. E., Chen Z., Wang J., & Chen L., (2019b). Soil alkaline phosphatase activity and bacterial phoD gene abundance and diversity under long-term nitrogen and manure inputs. Geoderma, 349, 36–44.
Chhabra S., Brazil D., Morrissey J., Burke J., O’Gara F., Dowling D. N., (2013). Fertilization management affects the alkaline phosphatase bacterial community in barley rhizosphere soil. Biology and Fertility of Soils, 49, 31-39.
Crecchio C., Curci M., Mininni R., Ricciuti P., & Ruggiero P., (2001). Short-term effects of municipal solid waste compost amendments on soil carbon and nitrogen content, some enzyme activities and genetic diversity. Biology and Fertility of Soils, 34, 311-318.
Devare M., Jones C., & Thies J., (2004). Effect of Cry3Bb transgenic corn and tefluthrin on the soil microbial community: biomass, activity, and diversity. Journal of Environmental Quality, 33, 837-843.
Edmeades D. C., (2003). The long-term effects of manures and fertilisers on soil productivity and quality: a review. Nutrient Cycling in Agroecosystems, 66, 165-180.
Eisenhauer N., Lanoue A., Strecker T., Scheu S., Steinauer K., Thakur M. P., & Mommer L., (2017). Root biomass and exudates link plant diversity with soil bacterial and fungal biomass. Scientific Reports, 7, 1-8.
Fraser T., Lynch D. H., Entz M.H., & Dunfield K. E., (2015a). Linking alkaline phosphatase activity with bacterial phoD gene abundance in soil from a long-term management trial. Geoderma, 257, 115-122.
Fraser T. D., Lynch D. H., Bent E., Entz M. H., & Dunfield K. E., (2015b). Soil bacterial phoD gene abundance and expression in response to applied phosphorus and long-term management. Soil Biology and Biochemistry, 88, 137-147.
Fraser T. D,, Lynch D. H., Gaiero J., Khosla K., & Dunfield K. E. (2017). 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, 111, 48-56.
Garg S., & Bahl G., (2008). Phosphorus availability to maize as influenced by organic manures and fertilizer P associated phosphatase activity in soils. Bioresource Technology, 99, 5773-5777.
Grayston S.J., Wang S., Campbell C. D., & Edwards A. C., (1998). Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biology and Biochemistry, 30, 369-378.
Guo S., Wu J., Coleman K., Zhu H., Li Y., & Liu W., (2012). Soil organic carbon dynamics in a dryland cereal cropping system of the Loess Plateau under long-term nitrogen fertilizer applications. Plant and Soil, 353, 321-332.
Hallama M., Pekrun C., Mayer-Gruner P., Uksa M., Abdullaeva Y., Pilz S., Schloter, M., Lambers, H., & Kandeler, E., (2022). The role of microbes in the increase of organic phosphorus availability in the rhizosheath of cover crops. Plant and Soil, 1-21.
Hu Y., Xia Y., Sun Q., Liu K., Chen X., Ge T., Zhu B., Zhu Z., Zhang Z., & Su Y., (2018). Effects of long-term fertilization on phoD-harboring bacterial community in Karst soils. Science of Total Environment, 628, 53-63.
Jackson M., (1958). Soil chemical analysis. Prentice Hall. Inc., Englewood Cliffs, NJ 498, pp 183-204
Kaufman M. M., Steffen J. M., & Yates K. L., (2020). Sustainability of soil organic matter at organic mixed vegetable farms in Michigan, USA. Organic Agriculture, 10, 487-496.
Lagos L. M., Acuña J. J., Maruyama F., Ogram A., de la Luz Mora M., & Jorquera M. A., (2016). Effect of phosphorus addition on total and alkaline phosphomonoesterase-harboring bacterial populations in ryegrass rhizosphere microsites. Biology and Fertility of Soils, 52, 1007-1019.
Liu E., Yan C., Mei X., He W., Bing S. H., Ding L., Liu Q., Liu S., & Fan T., (2010). Long-term effect of chemical fertilizer, straw, and manure on soil chemical and biological properties in northwest China. Geoderma 158: 173-180.
Long X. E., Yao H., Huang Y., Wei W., & Zhu Y. G., (2018). Phosphate levels influence the utilisation of rice rhizodeposition carbon and the phosphate-solubilising microbial community in a paddy soil. Soil Biology and Biochemistry, 118, 103-114.
Luo G., Ling N., Nannipieri P., Chen H., Raza W., Wang M., Guo S., & Shen Q., (2017). Long-term fertilisation regimes affect the composition of the alkaline phosphomonoesterase encoding microbial community of a vertisol and its derivative soil fractions. Biology and Fertility of Soils, 53, 375-388.
Mandal A., Patra A. K., Singh D., Swarup A., & Masto R. E., (2007). Effect of long-term application of manure and fertilizer on biological and biochemical activities in soil during crop development stages. Bioresource technology, 98, 3585-3592.
McAndrew D. W., & Malhi S. S., (1992). Long-term N fertilization of a Solonetzic soil—effects on chemical and biological properties. Soil Biology and Biochemistry, 24, 619–623.
Muyzer G., De Waal E. C., & Uitterlinden A. G., (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology, 59, 695-700.
Nannipieri P., Giagnoni L., Landi L., & Renella G., (2011). Role of phosphatase enzymes in soil. Phosphorus in action, Springer. pp 215-243.
Neal A., McLaren T., Lourenço Campolino M., Hughes D., Marcos Coelho A., Gomes de Paula Lana U., Aparecida Gomes E., & Morais de Sousa S., (2021). Crop type exerts greater influence upon rhizosphere phosphohydrolase gene abundance and phylogenetic diversity than phosphorus fertilization. FEMS Microbiology Ecology, 97, fiab033.
Neal A. L., Rossmann M., Brearley C., Akkari E., Guyomar C., Clark I. M., Allen E., & Hirsch P. R., (2017). Land?use influences phosphatase gene microdiversity in soils. Environmental Microbiology, 19, 2740-2753.
Olsen S. R., (1954). Estimation of available phosphorus in soils by extraction with sodium bicarbonate, US Department of Agriculture.
Pershina E., Valkonen J., Kurki P., Ivanova E., Chirak E., Korvigo I., Provorov N., & Andronov E., (2015). Comparative analysis of prokaryotic communities associated with organic and conventional farming systems. PloS one 10:12, e0145072.
Ragot S. A., Huguenin-Elie O., Kertesz M. A., Frossard E., & Bünemann E. K., (2016). Total and active microbial communities and phoD as affected by phosphate depletion and pH in soil. Plant and soil, 408:, 15-30.
Ragot S. A., Kertesz M. A., & Bünemann E. K., (2015). phoD alkaline phosphatase gene diversity in soil. Applied and Environmental Microbiology, 81, 7281-7289.
Richardson A. E., (2001). Prospects for using soil microorganisms to improve the acquisition of phosphorus by plants. Functional Plant Biology, 28, 897-906.
Richardson A. E., Barea J. M., McNeill A. M., & Prigent-Combaret C., (2009). Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms. Plant and soil 321: 305-339.
Rochette P., Angers D. A., & Flanagan L. B., (1999). Maize residue decomposition measurement using soil surface carbon dioxide fluxes and natural abundance of carbon?13. Soil Science Society of America Journal, 63, 1385-1396.
Saha S., Prakash V., Kundu S., Kumar N., & Mina B. L., (2008). Soil enzymatic activity as affected by long term application of farm yard manure and mineral fertilizer under a rainfed soybean–wheat system in NW Himalaya. European Journal of Soil Biology, 44, 309-315.
Sakurai M., Wasaki J., Tomizawa Y., Shinano T., & Osaki M., (2008). Analysis of bacterial communities on alkaline phosphatase genes in soil supplied with organic matter. Soil Science and Plant Nutrition, 54, 62-71.
Singh A., & Dubey S. K., (2012). Temporal variation in methanogenic community structure and methane production potential of tropical rice ecosystem. Soil Biology and Biochemistry, 48, 162-166.
Singh A. K., Rai G. K., Singh M., & Dubey S. K., (2013). Bacterial community structure in the rhizosphere of a Cry1Ac Bt-Brinjal crop and comparison to its non-transgenic counterpart in the tropical soil. Microbial Ecology, 66, 927-939.
Smalla K., Wieland G., Buchner A., Zock A., Parzy J., Kaiser S., Roskot N., Heuer H., & Berg G., (2001). Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Applied and Environmental Microbiology, 67, 4742-4751.
Sun R., Zhang X. X., Guo X., Wang D., & Chu H., (2015). Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw. Soil Biology and Biochemistry, 88, 9-18.
Tabatabai M. A., & Bremner J. M., (1969). Use of p-nitrophenyl phosphate for assay of soil phosphatase activity. Soil Biology and Biochemistry, 1, 301-307.
Tamilselvi S., Chinnadurai C., Ilamurugu K., Arulmozhiselvan K., & Balachandar D., (2015). Effect of long-term nutrient managements on biological and biochemical properties of semi-arid tropical Alfisol during maize crop development stages. Ecological Indicators, 48, 76-87.
Tan H., Barret M., Mooij M. J., Rice O., Morrissey J. P., Dobson A., Griffiths B., & O’gara F., (2013). Long-term phosphorus fertilisation increased the diversity of the total bacterial community and the phoD phosphorus mineraliser group in pasture soils. Biology and Fertility of Soils, 49, 661-672.
Walkley A., (1947). A critical examination of a rapid method for determining organic carbon in soils-effect of variations in digestion conditions and of inorganic soil constituents. Soil science, 63, 251-264.
Wang X. Y., Ge Y., & Wang J., (2017). Positive effects of plant diversity on soil microbial biomass and activity are associated with more root biomass production. Journal of Plant Interactions, 12, 533-541.
Welsh C., Tenuta M., Flaten D., Thiessen?Martens J., & Entz M., (2009). High yielding organic crop management decreases plant?available but not recalcitrant soil phosphorus. Journal of Agronomy, 101, 1027-1035.
Wu J. R., Shien J.H., Shieh H. K., Hu C. C., Gong S. R., Chen L.Y., & Chang P. C., (2007). Cloning of the gene and characterization of the enzymatic properties of the monomeric alkaline phosphatase (PhoX) from Pasteurella multocida strain X-73. FEMS Microbiology Letters, 267, 113-120.
Yang C., Yang L., & Jianhua L., (2006). Organic phosphorus fractions in organically amended paddy soils in continuously and intermittently flooded conditions. Journal of Environmental Quality, 35, 1142-1150.
Zappa S., Rolland J. L., Flament D., Gueguen Y., Boudrant J., & Dietrich J., (2001). Characterization of a highly thermostable alkaline phosphatase from the euryarchaeon Pyrococcus abyssi. Applied and Environmental Microbiology, 67, 4504-4511.
Zhang G., Chen Z., Zhang A., Chen L., Wu Z., & Ma X., (2014). Phosphorus composition and phosphatase activities in soils affected by long-term application of pig manure and inorganic fertilizers. Communications in Soil Science and Plant Analysis, 45, 1866-1876.