265
Views
4
CrossRef citations to date
0
Altmetric
Original Articles

Agriculturally relevant microbial community structure in long-term fertilized paddy soils as revealed by phospholipid fatty acid (PLFA) and pyrosequencing analyses

, , , , , & show all
Pages 1379-1393 | Received 04 Jul 2017, Accepted 29 Jan 2018, Published online: 08 Feb 2018

References

  • Ahn JH, Song J, Kim BY, Kim MS, Joa JH, Weon HY. 2012. Characterization of the bacterial and archaeal communities in rice field soils subjected to long-term fertilization practices. J Microbiol. 50:754–765.
  • Bardgett RD, Lovell RD, Hobbs PJ, Jarvis SC. 1999. Seasonal changes in soil microbial communities along a fertility gradient of temperate grasslands. Soil Biol Biochem. 31:1021–1030.
  • 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. Biol Fertil Soils. 34:311–318.
  • Da Costa PB, Beneduzi A, de Souza R, Schoenfeld R, Vargas LK, Passaglia LM. 2013. The effects of different fertilization conditions on bacterial plant growth promoting traits: guidelines for directed bacterial prospection and testing. Plant Soil. 368:267–280.
  • Daquiado AR, Kuppusamy S, Kim SY, Kim JH, Yoon YE, Kim PJ, Oh SH, Kwak YS, Lee YB. 2016. Pyrosequencing analysis of bacterial community diversity in long-term fertilized paddy field soil. Appl Soil Ecol. 108:84–91.
  • Datta M, Banik S, Gupta RK. 1982. Studies on the efficacy of a phytohormone producing phosphate solubilizing Bacillus firmus in augmenting paddy yield in acid soils of Nagaland. Plant Soil. 69:365–373.
  • Dedysh SN, Smirnova KV, Khmelenina VN, Suzina NE, Liesack W, Trotsenko YA. 2005. Methylotrophic autotrophy in Beijerinckia mobilis. J Bacteriol. 187:3884–3888.
  • Elfstrand S, Båth B, Mårtensson A. 2007. Influence of various forms of green manure amendment on soil microbial community composition, enzyme activity and nutrient levels in leek. Appl Soil Ecol. 36:70–82.
  • Eo J, Park KC. 2016. Long-term effects of imbalanced fertilization on the composition and diversity of soil bacterial community. Agric Ecosyst Environ. 231:176–182.
  • Francioli D, Schulz E, Lentendu G, Wubet T, Buscot F, Reitz T. 2016. Mineral vs. organic amendments: microbial community structure, activity and abundance of agriculturally relevant microbes are driven by long-term fertilization strategies. Front Microbiol. 7.
  • Frostegård Å, Bååth E, Tunlio A. 1993. Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty acid analysis. Soil Biol Biochem. 25:723–730.
  • Frostegård Å, Tunlid A, Bååth E. 1991. Microbial biomass measured as total lipid phosphate in soils of different organic content. J Microbiol Methods. 14:151–163.
  • Gordon JC, Wheeler CT. 2012. Biological nitrogen fixation in forest ecosystems: foundations and applications. The Hague (Netherland): Martinus Nijhoff/Dr W. Junk Publishers.
  • Gupta RS. 2000. The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev. 24:367–402.
  • Hartmann M, Frey B, Mayer J, Mäder P, Widmer F. 2015. Distinct soil microbial diversity under long-term organic and conventional farming. ISME J. 9:1177–1194.
  • Hirano K, Sugiyama T, Kosugi A, Nioh I, Asai T, Nakai H. 2001. Relationship between number of nitrogen-fixing rihzobacteria and growth pattern of rice varieties in the nature farming. Breeding Res. 3:3–12.
  • Hou H, Liu X, Liu G, Li Z, Liu Y, Huang Y, Ji J, Shao C, Wang F. 2011. Effect of long-term located organic-inorganic fertilizer application on rice yield and soil fertility in red soil area of China. Sci Agric Sinica. 44:516–523.
  • Irisarri P, Gonnet S, Monza J. 2001. Cyanobacteria in Uruguayan rice fields: diversity, nitrogen fixing ability and tolerance to herbicides and combined nitrogen. J Biotechnol. 91:95–103.
  • Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 3:442–453.
  • Kondo M. 1993. Acetylene reduction activity of paddy field soils. Tohoku Agric Res. 46:97–98.
  • Kuppusamy S, Thavamani P, Megharaj M, Venkateswarlu K, Lee YB, Naidu R. 2016. Pyrosequencing analysis of bacterial diversity in soils contaminated long-term with PAHs and heavy metals: implications to bioremediation. J Hazard Mater. 317:169–179.
  • Kuppusamy S, Yoon YE, Kim SY, Kim JH, Kim HT, Lee YB. 2017. Does long-term application of fertilizers enhance the micronutrient density in soil and crop? - Evidence from a field trial conducted on a 47-year-old rice paddy. J Soil Sediments. 18:49-62.
  • Lauber CL, Hamady M, Knight R, Fierer N. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol. 75:5111–5120.
  • Lee CH, Kang UG, Park KD, Lee DK, Kim PJ. 2008. Long-term fertilization effects on rice productivity and nutrient efficiency in Korean paddy. J Plant Nutri. 31:1496–1506.
  • Lentendu G, Wubet T, Chatzinotas A, Wilhelm C, Buscot F, Schlegel M. 2014. Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach. Mol Ecol. 23:3341–3355.
  • Lesaulnier C, Papamichail D, McCorkle S, Ollivier B, Skiena S, Taghavi S, Zak D, Van Der Lelie D. 2008. Elevated atmospheric CO2 affects soil microbial diversity associated with trembling aspen. Environ Microbiol. 10:926–941.
  • Marschner P, Kandeler E, Marschner B. 2003. Structure and function of the soil microbial community in a long-term fertilizer experiment. Soil Biol Biochem. 35:453–461.
  • Murase J, Hida A, Ogawa K, Nonoyama T, Yoshikawa N, Imai K. 2015. Impact of long-term fertilizer treatment on the microeukaryotic community structure of a rice field soil. Soil Biol Biochem. 80:237–243.
  • Navarrete AA, Kuramae EE, de Hollander M, Pijl AS, van Veen JA, Tsai SM. 2013. Acidobacterial community responses to agricultural management of soybean in Amazon forest soils. FEMS Microbiol Ecol. 83:607–621.
  • Nelson DW, Sommers L. 1982. Methods of soil analysis. Madison (US): American Society of Agronomy (ASA) and Soil Science Society of America (SSSA). Chapter 29, Total carbon, organic carbon, and organic matter; p. 239–579.
  • Peacock AG, Mullen MD, Ringelberg DB, Tyler DD, Hedrick DB, Gale PM, White DC. 2001. Soil microbial community responses to dairy manure or ammonium nitrate applications. Soil Biol Biochem. 33:1011–1019.
  • Podosokorskaya OA, Bonch-Osmolovskaya EA, Novikov AA, Kolganova TV, Kublanov IV. 2013. Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae. Int J Syst Evol Microbiol. 63:86–92.
  • Poulsen PH, Al-Soud WA, Bergmark L, Magid J, Hansen LH, Sørensen SJ. 2013. Effects of fertilization with urban and agricultural organic wastes in a field trial–prokaryotic diversity investigated by pyrosequencing. Soil Biol Biochem. 57:784–793.
  • Prasanna R, Nayak S. 2007. Influence of diverse rice soil ecologies on cyanobacterial diversity and abundance. Wetl Ecol Manag. 15:127–134.
  • Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig WG, Peplies J, Glockner FO. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35:7188–7196.
  • RDA. 1995. Standard investigation methods for agriculture experiment. Jeonju (South Korea): Rural Development Administration.
  • Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N. 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4:1340–1351.
  • Saison C, Degrange V, Oliver R, Millard P, Commeaux C, Montange D, Le Roux X. 2006. Alteration and resilience of the soil microbial community following compost amendment: effects of compost level and compost‐borne microbial community. Environ Microbiol. 8:247–257.
  • Sellstedt A, Richau KH. 2013. Aspects of nitrogen-fixing Actinobacteria, in particular free-living and symbiotic Frankia. FEMS Microbiol Lett. 342:179–186.
  • Shen C, Xiong J, Zhang H, Feng Y, Lin X, Li X, Liang W, Chu H. 2013. Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain. Soil Biol Biochem. 57:204–211.
  • Sun J, Zhang Q, Zhou J, Wei Q. 2014. Pyrosequencing technology reveals the impact of different manure doses on the bacterial community in apple rhizosphere soil. Appl Soil Ecol. 78:28–36.
  • Toribio J, Escalante AE, Caballero-Mellado J, González-González A, Zavala S, Souza V, Soberón-Chávez G. 2011. Characterization of a novel biosurfactant producing Pseudomonas koreensis lineage that is endemic to Cuatro Cienegas Basin. Syst Appl Microbiol. 34:531–535.
  • Trouve C, Chazal PM, Gueroux B, Sauvaitre N. 1998. Denitrification by new strains of Thiobacillus denitrificans under non-standard physicochemical conditions. Effect of temperature, pH, and sulphur source. Environ Technol. 19:601–610.
  • USEPA. 1998. Microwave assisted acid digestion of sediments, sludges, soils and oils. Washington (DC): United States Environmental Protection Agency (USEPA); p. 1–30.
  • Vanparys B, Heylen K, Lebbe L, De Vos P. 2006. Pseudomonas peli sp. nov. and Pseudomonas borbori sp. nov., isolated from a nitrifying inoculum. Int J Syst Evol Microbiol. 56:1875–1881.
  • Wu M, Qin H, Chen Z, Wu J, Wei W. 2011. Effect of long-term fertilization on bacterial composition in rice paddy soil. Biol Fert Soils. 47:397–405.
  • Yuan Y, Dai X, Xu M, Wang H, Fu X, Yang F. 2015. Responses of microbial community structure to land-use conversion and fertilization in southern. China Eur J Soil Biol. 70:1–6.
  • Zhao J, Ni T, Li Y, Xiong W, Ran W, Shen B, Shen Q, Zhang R, Smidt H. 2014. Responses of bacterial communities in arable soils in a rice-wheat cropping system to different fertilizer regimes and sampling times. PLoS One. 9:e85301.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.