Storage of soil samples leads to over-representation of the contribution of nitrate to plant-available nitrogen
Taleta Bailey
A B * , Nicole Robinson A , Mark Farrell B , Ben Macdonald C , Tim Weaver D , Diogenes L. Antille C , Aidan Chin A and Richard Brackin A
+ Author Affiliations
- Author Affiliations
A School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Qld, Australia.
B CSIRO Agriculture and Food, Waite Campus, Adelaide, SA, Australia.
C CSIRO Agriculture and Food, Black Mountain, Canberra, ACT, Australia.
D CSIRO Agriculture and Food, Myall Vale, Narrabri, NSW, Australia.
Soil Research 60(1) 22-32 https://doi.org/10.1071/SR21013
Submitted: 14 January 2021 Accepted: 15 June 2021 Published: 4 November 2021
© 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)
Abstract
Delays between soil sampling and processing for analysis are common in both research and agronomy, but the effects of storage conditions on measurements of plant-available nitrogen (N) are rarely considered. With increasing recognition of organic N pools in soils, such as amino acids and peptides, it is necessary to determine how sample handling impacts the outcomes of soil N quantification. In this study, we used in situ microdialysis to approximate plant availability of amino acids, ammonium and nitrate, then compared to both potassium chloride (KCl) extract and microdialysis samples taken from excavated soil samples when in the field, after 24 h refrigerated storage, and after storage for 1 month, either refrigerated or air-dried. Nitrate levels measured with microdialysis and KCl extracts increased immediately after soil sampling and continued to accumulate in the next day and 1 month stored samples. Amino acid and ammonium measurements remained more constant; however, microdialysis showed a decline in amino acid-N between in situ and next day samples. The proportional representation of N pools in the in-field extracts was most similar to in situ microdialysis. Soil samples should be processed for N analysis as close to sampling as possible, and the storage duration and conditions reported. The influence of storage must be considered in interpreting soil test results.
Keywords: air-dry, amino acids, ammonium, in situ soil sampling, microdialysis, nitrogen flux, organic nitrogen, refrigerated storage, soil testing.
References
Allen DE, Bloesch PM, Orton TG, Schroeder BL, Skocaj DM, Wang W, Masters B, Moody PM (2019) Nitrogen mineralisation in sugarcane soils in Queensland, Australia: I. Evaluation of soil tests for predicting nitrogen mineralisation. Soil Research 57, 738–754.| Nitrogen mineralisation in sugarcane soils in Queensland, Australia: I. Evaluation of soil tests for predicting nitrogen mineralisation.Crossref | GoogleScholarGoogle Scholar |
Andersson P, Berggren D (2005) Amino acids, total organic and inorganic nitrogen in forest floor soil solution at low and high nitrogen input. Water, Air, and Soil Pollution 162, 369–384.
| Amino acids, total organic and inorganic nitrogen in forest floor soil solution at low and high nitrogen input.Crossref | GoogleScholarGoogle Scholar |
Arnold J, Corre MD, Veldkamp E (2008) Cold storage and laboratory incubation of intact soil cores do not reflect in-situ nitrogen cycling rates of tropical forest soils. Soil Biology and Biochemistry 40, 2480–2483.
| Cold storage and laboratory incubation of intact soil cores do not reflect in-situ nitrogen cycling rates of tropical forest soils.Crossref | GoogleScholarGoogle Scholar |
Barraclough D, Puri G (1995) The use of 15N pool dilution and enrichment to separate the heterotrophic and autotrophic pathways of nitrification. Soil Biology and Biochemistry 27, 17–22.
| The use of 15N pool dilution and enrichment to separate the heterotrophic and autotrophic pathways of nitrification.Crossref | GoogleScholarGoogle Scholar |
Brackin R, Näsholm T, Robinson N, Guillou S, Vinall K, Lakshmanan P, Schmidt S, Inselsbacher E (2015) Nitrogen fluxes at the root-soil interface show a mismatch of nitrogen fertilizer supply and sugarcane root uptake capacity. Scientific Reports 5, 15727
| Nitrogen fluxes at the root-soil interface show a mismatch of nitrogen fertilizer supply and sugarcane root uptake capacity.Crossref | GoogleScholarGoogle Scholar | 26496834PubMed |
Brackin R, Atkinson BS, Sturrock CJ, Rasmussen A (2017) Roots-eye view: using microdialysis and microCT to non-destructively map root nutrient depletion and accumulation zones. Plant Cell and Environment 40, 3135–3142.
| Roots-eye view: using microdialysis and microCT to non-destructively map root nutrient depletion and accumulation zones.Crossref | GoogleScholarGoogle Scholar |
Brackin R, Buckley S, Pirie R, Visser F (2019) Predicting nitrogen mineralisation in Australian irrigated cotton cropping systems. Soil Research 57, 247–256.
| Predicting nitrogen mineralisation in Australian irrigated cotton cropping systems.Crossref | GoogleScholarGoogle Scholar |
Buckley S, Brackin R, Näsholm T, Schmidt S, Jämtgård S (2017) Improving in situ recovery of soil nitrogen using the microdialysis technique. Soil Biology and Biochemistry 114, 93–103.
| Improving in situ recovery of soil nitrogen using the microdialysis technique.Crossref | GoogleScholarGoogle Scholar |
Buckley S, Brackin R, Jämtgård S, Näsholm T, Schmidt S (2020) Microdialysis in soil environments: current practice and future perspectives. Soil Biology and Biochemistry 143, 107743
| Microdialysis in soil environments: current practice and future perspectives.Crossref | GoogleScholarGoogle Scholar |
Černohlávková J, Jarkovský J, Nešporová M, Hofman J (2009) Variability of soil microbial properties: effects of sampling, handling and storage. Ecotoxicology and Environmental Safety 72, 2102–2108.
| Variability of soil microbial properties: effects of sampling, handling and storage.Crossref | GoogleScholarGoogle Scholar | 19477519PubMed |
Crouse KK, Varco JJ, Jones WF (1994) Evaluation of methods for soil inorganic nitrogen analysis. Communications in Soil Science and Plant Analysis 25, 419–433.
| Evaluation of methods for soil inorganic nitrogen analysis.Crossref | GoogleScholarGoogle Scholar |
Dalgliesh N, Hochman Z, Huth N, Holzworth D (2016) ‘Field protocol to APSoil characterisations’. (CSIRO Agriculture and Food: Canberra, ACT, Australia) https://publications.csiro.au/rpr/download?pid=csiro:EP166550&dsid=DS4
Gütlein A, Dannenmann M, Kiese R (2016) Gross nitrogen turnover rates of a tropical lower montane forest soil: impacts of sample preparation and storage. Soil Biology and Biochemistry 95, 8–10.
| Gross nitrogen turnover rates of a tropical lower montane forest soil: impacts of sample preparation and storage.Crossref | GoogleScholarGoogle Scholar |
Hill EJ, Jones DL, Paterson E, Hill PW (2019) Hotspots and hot moments of amino acid N in soil: real-time insights using continuous microdialysis sampling. Soil Biology and Biochemistry 131, 40–43.
| Hotspots and hot moments of amino acid N in soil: real-time insights using continuous microdialysis sampling.Crossref | GoogleScholarGoogle Scholar |
Hobbie JE, Hobbie EA (2012) Amino acid cycling in plankton and soil microbes studied with radioisotopes: measured amino acids in soil do not reflect bioavailability. Biogeochemistry 107, 339–360.
| Amino acid cycling in plankton and soil microbes studied with radioisotopes: measured amino acids in soil do not reflect bioavailability.Crossref | GoogleScholarGoogle Scholar |
Holst J, Brackin R, Robinson N, Lakshmanan P, Schmidt S (2012) Soluble inorganic and organic nitrogen in two Australian soils under sugarcane cultivation. Agriculture, Ecosystems and Environment 155, 16–26.
| Soluble inorganic and organic nitrogen in two Australian soils under sugarcane cultivation.Crossref | GoogleScholarGoogle Scholar |
Inselsbacher E (2014) Recovery of individual soil nitrogen forms after sieving and extraction. Soil Biology and Biochemistry 71, 76–86.
| Recovery of individual soil nitrogen forms after sieving and extraction.Crossref | GoogleScholarGoogle Scholar |
Inselsbacher E, Näsholm T (2012a) The below-ground perspective of forest plants: soil provides mainly organic nitrogen for plants and mycorrhizal fungi. New Phytologist 195, 329–334.
| The below-ground perspective of forest plants: soil provides mainly organic nitrogen for plants and mycorrhizal fungi.Crossref | GoogleScholarGoogle Scholar |
Inselsbacher E, Näsholm T (2012b) A novel method to measure the effect of temperature on diffusion of plant-available nitrogen in soil. Plant and Soil 354, 251–257.
| A novel method to measure the effect of temperature on diffusion of plant-available nitrogen in soil.Crossref | GoogleScholarGoogle Scholar |
Inselsbacher E, Ripka K, Klaubauf S, Fedosoyenko D, Hackl E, Gorfer M, Hood-Novotny R, Von Wirén N, Sessitsch A, Zechmeister-Boltenstern S, Wanek W, Strauss J (2009) A cost-effective high-throughput microcosm system for studying nitrogen dynamics at the plant-microbe-soil interface. Plant and Soil 317, 293–307.
| A cost-effective high-throughput microcosm system for studying nitrogen dynamics at the plant-microbe-soil interface.Crossref | GoogleScholarGoogle Scholar |
Inselsbacher E, Öhlund J, Jämtgård S, Huss-Danell K, Näsholm T (2011) The potential of microdialysis to monitor organic and inorganic nitrogen compounds in soil. Soil Biology and Biochemistry 43, 1321–1332.
| The potential of microdialysis to monitor organic and inorganic nitrogen compounds in soil.Crossref | GoogleScholarGoogle Scholar |
Isbell RF (2016) ‘The Australian soil classification’. (CSIRO Publishing: Clayton, Vic., Australia)
Jämtgård S, Näsholm T, Huss-Danell K (2010) Nitrogen compounds in soil solutions of agricultural land. Soil Biology and Biochemistry 42, 2325–2330.
| Nitrogen compounds in soil solutions of agricultural land.Crossref | GoogleScholarGoogle Scholar |
Jones DL, Willett VB (2006) Experimental evaluation of methods to quantify dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soil. Soil Biology and Biochemistry 38, 991–999.
| Experimental evaluation of methods to quantify dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soil.Crossref | GoogleScholarGoogle Scholar |
Kuypers MMM, Marchant HK, Kartal B (2018) The microbial nitrogen-cycling network. Nature Reviews Microbiology 16, 263–276.
| The microbial nitrogen-cycling network.Crossref | GoogleScholarGoogle Scholar | 29398704PubMed |
Lee YB, Lorenz N, Dick LK, Dick RP (2007) Cold storage and pretreatment incubation effects on soil microbial properties. Soil Science Society of America Journal 71, 1299–1305.
| Cold storage and pretreatment incubation effects on soil microbial properties.Crossref | GoogleScholarGoogle Scholar |
Leinweber P, Kruse J, Baum C, Arcand M, Knight JD, Farrell R, Eckhardt K-U, Kiersch K, Jandl G (2013) Chapter two – Advances in understanding organic nitrogen chemistry in soils using state-of-the-art analytical techniques. In ‘Advances in agronomy’. (Ed. DL Sparks) pp. 83–151. (Academic Press: San Diego, CA, USA)
| Crossref |
Leitner S, Homyak PM, Blankinship JC, Eberwein J, Jenerette GD, Zechmeister-Boltenstern S, Schimel JP (2017) Linking NO and N2O emission pulses with the mobilization of mineral and organic N upon rewetting dry soils. Soil Biology and Biochemistry 115, 461–466.
| Linking NO and N2O emission pulses with the mobilization of mineral and organic N upon rewetting dry soils.Crossref | GoogleScholarGoogle Scholar |
Lenth R, Singmann H, Love J, Buerkner P, Herve M (2020) emmeans: estimated marginal means, aka least-squares means. R package version 1.7.0. https://CRAN.R-project.org/package=emmeans
Li KY, Zhao YY, Yuan XL, Zhao HB, Wang ZH, Li SX, Malhi SS (2012) Comparison of factors affecting soil nitrate nitrogen and ammonium nitrogen extraction. Communications in Soil Science and Plant Analysis 43, 571–588.
| Comparison of factors affecting soil nitrate nitrogen and ammonium nitrogen extraction.Crossref | GoogleScholarGoogle Scholar |
Ma BL, Ying J, Balchin D (2005) Impact of sample preservation methods on the extraction of inorganic nitrogen by potassium chloride. Journal of Plant Nutrition 28, 785–796.
| Impact of sample preservation methods on the extraction of inorganic nitrogen by potassium chloride.Crossref | GoogleScholarGoogle Scholar |
Macdonald BCT, Chang YF, Nadelko A, Tuomi S, Glover M (2017a) Tracking fertiliser and soil nitrogen in irrigated cotton: uptake, losses and the soil N stock. Soil Research 55, 264–272.
| Tracking fertiliser and soil nitrogen in irrigated cotton: uptake, losses and the soil N stock.Crossref | GoogleScholarGoogle Scholar |
Macdonald BCT, Ringrose-Voase AJ, Nadelko AJ, Farrell M, Tuomi S, Nachimuthu G (2017b) Dissolved organic nitrogen contributes significantly to leaching from furrow-irrigated cotton–wheat–maize rotations. Soil Research 55, 70–77.
| Dissolved organic nitrogen contributes significantly to leaching from furrow-irrigated cotton–wheat–maize rotations.Crossref | GoogleScholarGoogle Scholar |
Marshall TJ (1959) ‘Relations between water and soil’. (Commonwealth Agricultural Bureaux: Harpenden, UK)
Miranda KM, Espey MG, Wink DA (2001) A rapid, simple spectrophotometric method for simultaneous detection of nitrate and nitrite. Nitric Oxide 5, 62–71.
| A rapid, simple spectrophotometric method for simultaneous detection of nitrate and nitrite.Crossref | GoogleScholarGoogle Scholar | 11178938PubMed |
Miró M, Fitz WJ, Swoboda S, Wenzel WW (2010) In-situ sampling of soil pore water: evaluation of linear-type microdialysis probes and suction cups at varied moisture contents. Environmental Chemistry 7, 123–131.
| In-situ sampling of soil pore water: evaluation of linear-type microdialysis probes and suction cups at varied moisture contents.Crossref | GoogleScholarGoogle Scholar |
Mulvaney RL (1996) Nitrogen – inorganic forms. In ‘Methods of soil analysis: Part 3. Chemical methods, 5.3’. SSSA book series. (Eds DL Sparks, AL Page, PA Helmke, RH Loeppert, PN Soltanpour, MA Tabatabai, CT Johnston, ME Sumner) pp. 1123–1184. (John Wiley & Sons, Ltd: Madison, WI, USA)
| Crossref |
Nelson DW, Bremner JM (1972) Preservation of soil samples for inorganic nitrogen analyses1. Agronomy Journal 64, 196–199.
| Preservation of soil samples for inorganic nitrogen analyses1.Crossref | GoogleScholarGoogle Scholar |
Pinheiro J, Bates D, DebRoy S, Sarkar D, R Core Team (2020) nlme: linear and nonlinear mixed effects models. R package version 3. 1–152. https://CRAN.R-project.org/package=nlme
R Core Team (2020) R: A language and environment for statistical computing. R Foundation for Statistical Computing: Vienna, Austria. Available at https://www.R-project.org/
Randewig D, Marshall JD, Näsholm T, Jämtgård S (2019) Combining microdialysis with metabolomics to characterize the in situ composition of dissolved organic compounds in boreal forest soil. Soil Biology and Biochemistry 136, 107530
| Combining microdialysis with metabolomics to characterize the in situ composition of dissolved organic compounds in boreal forest soil.Crossref | GoogleScholarGoogle Scholar |
Ratliff LF, Ritchie JT, Cassel DK (1983) Field-measured limits of soil water availability as related to laboratory-measured properties. Soil Science Society of America Journal 47, 770–775.
| Field-measured limits of soil water availability as related to laboratory-measured properties.Crossref | GoogleScholarGoogle Scholar |
Rayment GE, Lyons DJ (2011) ‘Soil chemical methods – Australasia’. (CSIRO Publishing: Collingwood, Vic., Australia)
Robinson N, Brackin R, Vinall K, Soper F, Holst J, Gamage H, Paungfoo-Lonhienne C, Rennenberg H, Lakshmanan P, Schmidt S (2011) Nitrate paradigm does not hold up for sugarcane. PLoS One e19045
| Nitrate paradigm does not hold up for sugarcane.Crossref | GoogleScholarGoogle Scholar |
Rochester IJ, Bange M (2016) Nitrogen fertiliser requirements of high-yielding irrigated transgenic cotton. Crop and Pasture Science 67, 641–648.
| Nitrogen fertiliser requirements of high-yielding irrigated transgenic cotton.Crossref | GoogleScholarGoogle Scholar |
Ros GH, Temminghoff EJM, Hoffland E (2011) Nitrogen mineralization: a review and meta-analysis of the predictive value of soil tests. European Journal of Soil Science 62, 162–173.
| Nitrogen mineralization: a review and meta-analysis of the predictive value of soil tests.Crossref | GoogleScholarGoogle Scholar |
Rousk J, Jones DL (2010) Loss of low molecular weight dissolved organic carbon (DOC) and nitrogen (DON) in H2O and 0.5 M K2SO4 soil extracts. Soil Biology and Biochemistry 42, 2331–2335.
| Loss of low molecular weight dissolved organic carbon (DOC) and nitrogen (DON) in H2O and 0.5 M K2SO4 soil extracts.Crossref | GoogleScholarGoogle Scholar |
Schwenke G, Beange L, Cameron J, Bell M, Harden S (2019) What soil information do crop advisors use to develop nitrogen fertilizer recommendations for grain growers in New South Wales, Australia? Soil Use and Management 35, 85–93.
| What soil information do crop advisors use to develop nitrogen fertilizer recommendations for grain growers in New South Wales, Australia?Crossref | GoogleScholarGoogle Scholar |
Shaw R, Williams AP, Jones DL (2014) Assessing soil nitrogen availability using microdialysis-derived diffusive flux measurements. Soil Science Society of America Journal 78, 1797–1803.
| Assessing soil nitrogen availability using microdialysis-derived diffusive flux measurements.Crossref | GoogleScholarGoogle Scholar |
Soil Survey Staff (1999) ‘Soil taxonomy: a basic system of soil classification for making and interpreting soil surveys’. (United States Department of Agriculture, Natural Resources Conservation Service: Washington, DC, USA) https://www.nrcs.usda.gov/Internet/FSE_DOCUMENTS/nrcs142p2_051232.pdf
Stenberg B, Johansson M, Pell M, Sjödahl-Svensson K, Stenström J, Torstensson L (1998) Microbial biomass and activities in soil as affected by frozen and cold storage. Soil Biology and Biochemistry 30, 393–402.
| Microbial biomass and activities in soil as affected by frozen and cold storage.Crossref | GoogleScholarGoogle Scholar |
Verchot LV (1999) Cold storage of a tropical soil decreases nitrification potential. Soil Science Society of America Journal 63, 1942–1944.
| Cold storage of a tropical soil decreases nitrification potential.Crossref | GoogleScholarGoogle Scholar |
Warren CR (2014) Organic N molecules in the soil solution: what is known, what is unknown and the path forwards. Plant and Soil 375, 1–19.
| Organic N molecules in the soil solution: what is known, what is unknown and the path forwards.Crossref | GoogleScholarGoogle Scholar |
Warren CR (2018) Development of online microdialysis-mass spectrometry for continuous minimally invasive measurement of soil solution dynamics. Soil Biology and Biochemistry 123, 266–275.
| Development of online microdialysis-mass spectrometry for continuous minimally invasive measurement of soil solution dynamics.Crossref | GoogleScholarGoogle Scholar |
Wooliver R, Pellegrini AFA, Waring B, Houlton BZ, Averill C, Schimel J, Hedin LO, Bailey JK, Schweitzer JA (2019) Changing perspectives on terrestrial nitrogen cycling: the importance of weathering and evolved resource-use traits for understanding ecosystem responses to global change. Functional Ecology 33, 1818–1829.
| Changing perspectives on terrestrial nitrogen cycling: the importance of weathering and evolved resource-use traits for understanding ecosystem responses to global change.Crossref | GoogleScholarGoogle Scholar |
Zhang T, Chen HYH, Ruan H (2018) Global negative effects of nitrogen deposition on soil microbes. The ISME Journal 12, 1817–1825.
| Global negative effects of nitrogen deposition on soil microbes.Crossref | GoogleScholarGoogle Scholar | 29588494PubMed |
