Experimental strategies to measure the microbial uptake and mineralization kinetics of dissolved organic carbon in soil

Abstract

Soil organic matter turnover rates are typically estimated from mass loss of the material over time or from on rates of carbon dioxide production. In the study, we investigated a new way to characterize the concentration-dependent kinetics of amino acids used by measuring microbial uptake and mineralization of ¹⁴C-alanine. We measured the depletion from soil solution after additions ¹⁴C-alanine. The microbial uptake of ¹⁴C-alanine from soil solution was concentration dependent and kinetic analysis indicated the operation of at least three distinct alanine transport systems of differing affinities. Most of the ¹⁴C-alanine depletion from the soil solution occurred rapidly within the first 10 – 30 min of the incubation after 10 μM to 1 mM substrate additions. At alanine concentrations less than 250 μM, the kinetic parameters for K_m and V_max of the higher-affinity transporter were 60.0 μM and 1.32 μmol g⁻¹ DW soil h⁻¹, respectively. The mineralization of alanine was determined and the half-time values for the rapid mineralization process were 45 min to 1.5 h after the addition at alanine concentrations below 1 mM. The time delay after its uptake into microbial biomass suggested that alanine uptake and subsequent respiration was uncoupled pattern. The microbial N uptake rate was calculated by microbial mineralization, and an estimated the K_m value of 1731.7±274.6 μM and V_max value of 486.0±38.5 μmol kg⁻¹ DW soil h⁻¹. This study provides an alternative approach for measuring the rate of turnover of compounds that turnover very rapidly in soil.

Keywords

¹⁴C tracer / Microbial uptake / Carbon mineralization / Turnover

References

[1] Balland-Bolou-Bi, C., Bolou-Bi, E.B., Alphonse, V., Giusti-Miller, S., Jusselme, M.D., Livet, A., Grimaldi, M., Bousserhine, N., 2019. Impact of microbial activity on the mobility of metallic elements (Fe, Al and Hg) in tropical soils. Geoderma 334, 146–154

[2] Boddy, E., Hill, P.W., Farrar, J., Jones, D.L., 2007. Fast turnover of low molecular weight components of the dissolved organic carbon pool of temperate grassland field soils. Soil Biology & Biochemistry 39, 827–835

[3] Boddy, E., Roberts, P., Hill, P.W., Farrar, J., Jones, D.L., 2008. Turnover of low molecular weight dissolved organic C (DOC) and microbial C exhibit different temperature sensitivities in Arctic tundra soils. Soil Biology & Biochemistry 40, 1557–1566

[4] Brailsford, F.L., Glanville, H.C., Golyshin, P.N., Yates, C.A., Jones, D.L., 2019. Microbial uptake kinetics of dissolved organic carbon (DOC) compound groups from river water and sediments. Scientific Reports 9, 11229

[5] Chavarría-Hernández, N., Torre, M.D.L., 2001. Population growth kinetics of the nematode, Steinernema feltiae, in submerged monoxenic culture. Biotechnology Letters 23, 311–315

[6] Declerck, S., D’Or, D., Cranenbrouck, S., Le, E.B., 2001. Modelling the sporulation dynamics of arbuscular mycorrhizal fungi in monoxenic culture. Mycorrhiza 11, 225–230

[7] Dippold, M., Biryukov, M., Kuzyakov, Y., 2014. Sorption affects amino acid pathways in soil: implications from position-specific labeling of alanine. Soil Biology & Biochemistry 72, 180–192

[8] Farrell, M., Hill, P.W., Farrar, J., DeLuca, T.H., Roberts, P., Kielland, K., Dahlgren, R., Murphy, D.V., Hobbs, P.J., Bardgett, R.D., Jones, D.L., 2013. Oligopeptides represent a preferred source of organic N uptake: a global phenomenon? Ecosystems (New York, N.Y.) 16, 133–145

[9] Farrell, M., Macdonald, L.M., Hill, P.W., Wanniarachchi, S.D., Farrar, J., Bardgett, R.D., Jones, D.L., 2014a. Amino acid dynamics across a grassland altitudinal gradient. Soil Biology & Biochemistry 76, 179–182

[10] Farrell, M., Prendergast-Miller, M., Jones, D.L., Hill, P.W., Condron, L.M., 2014b. Soil microbial organic nitrogen uptake is regulated by carbon availability. Soil Biology & Biochemistry 77, 261–267

[11] Fischer, H., Ingwersen, J., Kuzyakov, Y., 2010. Microbial uptake of low-molecular-weight organic substances out-competes sorption in soil. European Journal of Soil Science 4, 504–513

[12] Fisk, M.C., Schmidt, S.K., Seastedt, T., 1998. Topographic patterns of above- and below-ground production and nitrogen cycling in alpine tundra. Ecology 79, 2253–2266

[13] Ge, T., Roberts, P., Jones, D., Song, S., Huang, D., 2010. Dynamics of nitrogen speciation in horticultural soils in suburbs of Shanghai. Pedosphere 20, 261–272

[14] Ge, T., Roberts, P., Jones, D., Song, S., Iwasaki, K., Huang, D., 2009. Amino acids as a nitrogen source for tomato seedling: the use of dual labeled (¹³C, ¹⁵N) glycine to test for direct uptake by tomato seedling. Environmental and Experimental Botany 66, 357–361

[15] Ge, T., Wu, X., Liu, Q., Zhu, Z., Yuan, H., Wang, W., Whiteley, A.S., Wu, J.S., 2016. Effect of simulated tillage on microbial autotrophic CO₂ fixation in paddy and upland soils. Scientific Reports 6, 19784

[16] Ge, T., Yuan, H., Roberts, P., Jones, D., Qin, H., Tong, C., Huang, D., 2012. Amino acid and peptide dynamics in horticultural soils under conventional and organic management strategies. Journal of Soils and Sediments 12, 323–333

[17] Geisseler, D., Horwath, W.R., Joergensen, R.G., Ludwig, B., 2010. Pathways of nitrogen utilization by soil microorganisms – a review. Soil Biology & Biochemistry 42, 2058–2067

[18] Gunina, A., Smith, A.R., Kuzyakov, Y., Jones, D.L., 2017. Microbial uptake and utilization of low molecular weight organic substrates in soil depend on carbon oxidation state. Biogeochemistry 133, 1–12

[19] Hatté, C., Noury, C., Kheirbeik, L., Balesdent, J., 2017. Turnover of the soil organic matter amino acid fraction investigated by ¹³C and ¹⁴C signatures of carboxyl carbon. Radiocarbon 59, 1–9

[20] Hill, P.W., Farrar, J.F., Jones, D.L., 2008. Decoupling of microbial glucose uptake and mineralization in soil. Soil Biology & Biochemistry 40, 616–624

[21] Hill, P.W., Farrell, M., Roberts, P., Farrar, J., Grant, H., Newsham, K.K., Hopkins, D.W., Bardgett, R.D., Jones, D.L., 2011. Soil- and enantiomer-specific metabolism of amino acids and peptides by Antarctic soil microorganisms. Soil Biology & Biochemistry 43, 2410–2416

[22] Hill, P.W., Jones, D.L., 2019. Plant–microbe competition: does injection of isotopes of C and N into the rhizosphere effectively characterise plant use of soil N? New Phytologist 221, 796–806

[23] Hobbie, J.E., Hobbie, E.A., 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

[24] Hobbie, J.E., Hobbie, E.A., 2013. Microbes in nature are limited by carbon and energy: the starving-survival lifestyle in soil and consequences for estimating microbial rates. Frontiers in Microbiology 4, 1–11

[25] Jones, D.L., 1999. Amino acid biodegradation and its potential effects on organic nitrogen capture by plants. Soil Biology & Biochemistry 31, 613–622

[26] Jones, D.L., Hodge, A., 1999. Biodegradation kinetics and sorption reactions of three differently charged amino acids in soil and their effects on plant organic nitrogen availability. Soil Biology & Biochemistry 31, 1331–1342

[27] Jones, D.L., Kemmitt, S.J., Wright, D., Cuttle, S.P., Bol, R., Edwards, A.C., 2005. Rapid intrinsic rates of amino acid biodegradation in soils are unaffected by agricultural management strategy. Soil Biology & Biochemistry 37, 1267–1275

[28] Jones, D.L., Kielland, K., 2002. Soil amino acid turnover dominates the nitrogen flux in permafrost-dominated taiga forest soils. Soil Biology & Biochemistry 34, 209–219

[29] Jones, D.L., Murphy, D.V., 2007. Microbial response time to sugar and amino acid additions to soil. Soil Biology & Biochemistry 39, 2178–2182

[30] Knicker, H., 2011. Soil organic N- an under-rated player for C sequestration in soils? Soil Biology & Biochemistry 43, 1118–1129

[31] Kuzyakov, Y., Xu, X., 2013. Competition between roots and microorganisms for N: mechanisms and ecological relevance. New Phytologist 198, 656–669

[32] Lipson, D.A., Raab, T.K., Schmidt, S.K., Monson, R.K., 2001. An empirical model of amino acid transformations in alpine soil. Soil Biology & Biochemistry 33, 189–198

[33] Mcfarland, J.W., Ruess, R.W., Kielland, K., Hendrick, P.R., 2010. Glycine mineralization in situ closely correlates with soil carbon availability across six north american forest ecosystems. Biogeochemistry 99, 175–191

[34] Näsholm, T., Kielland, K., Ganeteg, U., 2009. Uptake of organic nitrogen by plants. New Phytologist 182, 31–48

[35] Nordin, A., Hogberg, P., Näsholm, T., 2001. Soil nitrogen form and plant nitrogen uptake along a boreal forest productivity gradient. Oecologia 129, 125–132

[36] Persson, J., Högberg, P., Ekblad, A., Högberg, M.N., Nordgren, A., Näsholm, T., 2003. Nitrogen acquisition from inorganic and organic sources by boreal forest plants in the field. Oecologia 137, 252–257

[37] Silvani, V.A., Bidondo, L.F., Bompadre, M.J., Colombo, R.P., Pérgola, M., Bompadre, A., Fracchia, S., Godess, A., 2014. Growth dynamics of geographically different arbuscular mycorrhizal fungal isolates belonging to the ‘rhizophagus clade’ under monoxenic conditions. Mycologia 106, 963–975

[38] Stöm, L., Ekberg, A., Mastepanov, M., Christensen, T., 2003. The effect of vascular plants on carbon turnover and methane emissions from a tundra wetland. Global Change Biology 9, 1185–1192

[39] Vinolas, L.C., Healey, J.R., Jones, D.L., 2001. Kinetics of soil microbial uptake of free amino acids. Biology and Fertility of Soils 33, 67–74

[40] Wilkinson, A., Hill, P.W., Farrar, J.F., Jones, D.L., Bardgett, R.D., 2014. Rapid microbial uptake and mineralization of amino acids and peptides along a grassland productivity gradient. Soil Biology & Biochemistry 72, 75–83

Acknowledgments

This study was financially supported by grants from the National Key Research and Development Program (2016YFE0101100), the Australia-China Joint Research Centre – Healthy Soils for Sustainable Food Production and Environmental Quality (ACSRF48165), the National Natural Science Foundation of China (41522107; 41430860), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB15020401), Royal Society Newton Advanced Fellowship (NA150182), Talented Young Scientist Program (TYSP) to Mostafa Zhran supported by China Science and Technology Exchange Center (Egypt-19-004) and the State Scholarship Fund of China Scholarship Council (CSC) to Baozhen Li.

RIGHTS & PERMISSIONS

2020 Higher Education Press