Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Cellular and extracellular C contributions to respiration after wetting dry soil


Wetting of dry soil triggers a pulse of microbial respiration that has been attributed to two broad mechanisms: (1) recycling of microbial cellular carbon (C), and (2) consumption of extracellular organic C made available to microbes by wetting. We evaluated these two mechanisms by measuring cumulative CO2 release, changes in the size and chemical composition of microbial biomass, and water-extractable organic carbon (WEOC) concentrations following artificial wetting of soil sampled from two depths at each of seven sites across California spanning a range of geologic parent materials. In samples collected from surface soil (0–10 cm depth), we found that cumulative CO2 release after wetting in the laboratory was most strongly correlated with microbial biomass. In these samples, the relative abundance of trehalose—a putative microbial osmolyte—decreased from 25% (SD = 12) to 16% (SD = 7) of the chloroform-labile fraction of the microbial biomass after wetting. This suggested a role for osmolyte consumption in generating the respiration pulse. In subsoil (40–50 cm depth, or sampled at contact with rock), however, the cumulative CO2 release after wetting was unrelated to microbial biomass and more strongly related to WEOC. The concentrations of selected microbial biomass constituents (e.g. trehalose and amino acids) in WEOC were negligible (< 1%), suggesting that cell lysis was not important in generating WEOC in this study. The amount of WEOC relative to total organic C was greatest in subsoil, and negatively related to ammonium oxalate-extractable Fe (Pearson’s R = 0.42, p < 0.01), suggesting a role for soil mineralogical properties in controlling WEOC release. Together, these findings suggest that microbial cellular C and extracellular C jointly contribute to the respiration pulse, and that their relative contribution depends on depth.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5


  1. Adu JK, Oades JM (1978) Physical factors influencing decomposition of organic materials in soil aggregates. Soil Biol Biochem 10(2):109–115

  2. Bailey VL, Smith AP, Tfaily M, Fansler SJ, Bond-Lamberty B (2017) Differences in soluble organic carbon chemistry in pore waters sampled from different pore size domains. Soil Biol Biochem 107:133–143

  3. Bates D, Maechler M, Bolker B, Walker S (2015) lme4: linear mixed-effects models using Eigen and S4. R package version 1(1–7):2014

  4. Birch HF (1958) The effect of soil drying on humus decomposition and nitrogen availability. Plant Soil 10(1):9–31

  5. Blazewicz SJ, Schwartz E, Firestone MK (2014) Growth and death of bacteria and fungi underlie rainfall-induced carbon dioxide pulses from seasonally dried soil. Ecology 95(5):1162–1172

  6. Boot CM, Schaeffer SM, Schimel JP (2013) Static osmolyte concentrations in microbial biomass during seasonal drought in a California grassland. Soil Biol Biochem 57:356–361

  7. Borken W, Matzner E (2009) Reappraisal of drying and wetting effects on C and N mineralization and fluxes in soils. Glob Change Biol 15(4):808–824

  8. Bottner P (1985) Response of microbial biomass to alternate moist and dry conditions in a soil incubated with 14C-and 15N-labelled plant material. Soil Biol Biochem 17(3):329–337

  9. Bratbak G, Dundas I (1984) Bacterial dry matter content and biomass estimations. Appl Environ Microbiol 48(4):755–757

  10. Cerli C, Celi L, Kalbitz K, Guggenberger G, Kaiser K (2012) Separation of light and heavy organic matter fractions in soil—testing for proper density cut-off and dispersion level. Geoderma 170:403–416

  11. Chadwick OA, Gavenda RT, Kelly EF, Ziegler K, Olson CG, Elliott WC, Hendricks DM (2003) The impact of climate on the biogeochemical functioning of volcanic soils. Chem Geol 202(3–4):195–223

  12. Chowdhury TR et al (2019) Metaphenomic responses of a native prairie soil microbiome to moisture perturbations. mSystems 4(4):e00061-19

  13. Clarke CE, Aguilar-Carrillo J, Roychoudhury AN (2011) Quantification of drying induced acidity at the mineral–water interface using ATR-FTIR spectroscopy. Geochim Cosmochim Acta 75(17):4846–4856

  14. Coward EK, Ohno T, Plante AF (2018) Adsorption and molecular fractionation of dissolved organic matter on iron-bearing mineral matrices of varying crystallinity. Environ Sci Technol 52(3):1036–1044

  15. Denef K, Six J, Bossuyt H, Frey SD, Elliott ET, Merckx R, Paustian K (2001) Influence of dry–wet cycles on the interrelationship between aggregate, particulate organic matter, and microbial community dynamics. Soil Biol Biochem 33(12–13):1599–1611

  16. Fierer N, Schimel JP (2002) Effects of drying–rewetting frequency on soil carbon and nitrogen transformations. Soil Biol Biochem 34(6):777–787

  17. Fierer N, Schimel JP (2003) A proposed mechanism for the pulse in carbon dioxide production commonly observed following the rapid rewetting of a dry soil. Soil Sci Soc Am J 67(3):798–805

  18. Fierer N, Schimel JP, Holden PA (2003) Variations in microbial community composition through two soil depth profiles. Soil Biol Biochem 35(1):167–176

  19. Fierer N, Chadwick OA, Trumbore SE (2005) Production of CO2 in soil profiles of a California annual grassland. Ecosystems 8(4):412–429

  20. Fursova O, Pogorelko G, Zabotina OA (2012) An efficient method for transient gene expression in monocots applied to modify the Brachypodium distachyon cell wall. Ann Bot 110(1):47–56

  21. Göransson H, Godbold DL, Jones DL, Rousk J (2013) Bacterial growth and respiration responses upon rewetting dry forest soils: impact of drought-legacy. Soil Biol Biochem 57:477–486

  22. Graham RC, O'Geen AT (2010) Soil mineralogy trends in California landscapes. Geoderma 154(3–4):418–437

  23. Guo X, Drury CF, Yang X, Reynolds WD, Zhang R (2012) Impacts of wet–dry cycles and a range of constant water contents on carbon mineralization in soils under three cropping treatments. Soil Sci Soc Am J 76(2):485–493

  24. Homyak PM, Blankinship JC, Slessarev EW, Shaeffer SM, Manzoni S, Schimel JP, (2018) Effects of altered dry-season length and plant inputs on soluble carbon. Ecology.

  25. Imhoff JF (1986) Osmoregulation and compatible solutes in eubacteria. FEMS Microbiol Rev 2(1–2):57–66

  26. Joergensen RG (1996) The fumigation-extraction method to estimate soil microbial biomass: calibration of the kEC value. Soil Biol Biochem 28(1):25–31

  27. Kaiser M, Kleber M, Berhe AA (2015) How air-drying and rewetting modify soil organic matter characteristics: an assessment to improve data interpretation and inference. Soil Biol Biochem 80:324–340

  28. Kakumanu ML, Cantrell CL, Williams MA (2013) Microbial community response to varying magnitudes of desiccation in soil: a test of the osmolyte accumulation hypothesis. Soil Biol Biochem 57:644–653

  29. Kakumanu ML, Ma L, Williams MA (2019) Drought-induced soil microbial amino acid and polysaccharide change and their implications for CN cycles in a climate change world. Sci Rep 9(1):10968

  30. Kaushik JK, Bhat R (2003) Why is trehalose an exceptional protein stabilizer? An analysis of the thermal stability of proteins in the presence of compatible osmolyte trehalose. J Biol Chem 278(29):26458–26465

  31. Kempf B, Bremer E (1998) Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments. Arch Microbiol 170(5):319–330

  32. Kieft TL (1987) Microbial biomass response to a rapid increase in water potential when dry soil is wetted. Soil Biol Biochem 19(2):119–126

  33. Killham K, Firestone MK (1984) Salt stress control of intracellular solutes in streptomycetes indigenous to saline soils. Appl Environ Microbiol 47(2):301–306

  34. Kim DG, Mu S, Kang S, Lee D (2010) Factors controlling soil CO2 effluxes and the effects of rewetting on effluxes in adjacent deciduous, coniferous, and mixed forests in Korea. Soil Biol Biochem 42(4):576–585

  35. Kramer MG, Sanderman J, Chadwick OA, Chorover J, Vitousek PM (2012) Long-term carbon storage through retention of dissolved aromatic acids by reactive particles in soil. Glob Change Biol 18(8):2594–2605

  36. Kuznetsova A, Brockhoff PB, Christensen RHB (2017) lmerTest package: tests in linear mixed effects models. J Stat Softw.

  37. Lawrence CR, Neff JC, Schimel JP (2009) Does adding microbial mechanisms of decomposition improve soil organic matter models? A comparison of four models using data from a pulsed rewetting experiment. Soil Biol Biochem 41(9):1923–1934

  38. Lee MS, Nakane K, Nakatsubo T, Mo WH, Koizumi H (2002) Effects of rainfall events on soil CO2 flux in a cool temperate deciduous broad-leaved forest. Ecol Res 17(3):401–409

  39. Leinemann T, Preusser S, Mikutta R, Kalbitz K, Cerli C, Höschen C, Mueller CW, Kandeler E, Guggenberger G (2018) Multiple exchange processes on mineral surfaces control the transport of dissolved organic matter through soil profiles. Soil Biol Biochem 118:79–90

  40. 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 Biol Biochem 115:461–466

  41. Lin Y, Prentice SE III, Tran T, Bingham NL, King JY, Chadwick OA (2016) Modeling deep soil properties on California grassland hillslopes using LiDAR digital elevation models. Geoderma Reg 7(1):67–75

  42. Lin Y, Slessarev EW, Yehl ST, D’Antonio CM, King JY (2018) Long-term nutrient fertilization increased soil carbon stocks in California grasslands. Ecosystems 22(4):754–766

  43. Loeppert RH, Inskeep WP (1996) Iron. In: Sparks DL (ed.) Methods of soil analysis part 3: SSSA Book Ser. 5. SSSA, Madison pp 639–664.

  44. Luke SG (2017) Evaluating significance in linear mixed-effects models in R. Behav Res Methods 49(4):1494–1502

  45. Lund V, Goksøyr J (1980) Effects of water fluctuations on microbial mass and activity in soil. Microb Ecol 6(2):115–123

  46. Lundquist EJ, Jackson LE, Scow KM (1999) Wet–dry cycles affect dissolved organic carbon in two California agricultural soils. Soil Biol Biochem 31(7):1031–1038

  47. Manzoni S, Schaeffer SM, Katul G, Porporato A, Schimel JP (2014) A theoretical analysis of microbial eco-physiological and diffusion limitations to carbon cycling in drying soils. Soil Biol Biochem 73:69–83

  48. Meisner A, Rousk J, Bååth E (2015) Prolonged drought changes the bacterial growth response to rewetting. Soil Biol Biochem 88:314–322

  49. Miller AE, Schimel JP, Meixner T, Sickman JO, Melack JM (2005) Episodic rewetting enhances carbon and nitrogen release from chaparral soils. Soil Biol Biochem 37(12):2195–2204

  50. Navarro-García F, Casermeiro MÁ, Schimel JP (2012) When structure means conservation: Effect of aggregate structure in controlling microbial responses to rewetting events. Soil Biol Biochem 44(1):1–8

  51. Newcomb CJ, Qafoku NP, Grate JW, Bailey VL, De Yoreo JJ (2017) Developing a molecular picture of soil organic matter–mineral interactions by quantifying organo–mineral binding. Nature communications 8(1):396

  52. Olshansky Y, Root RA, Chorover J (2018) Wet–dry cycles impact DOM retention in subsurface soils. Biogeosciences 15:821–832

  53. PRISM (2018) PRISM Climate Group. Oregon State University, Corvallis, OR

  54. Rasmussen C, Heckman K, Wieder WR, Keiluweit M, Lawrence CR, Berhe AA, Blankinship JC, Crow SE, Druhan JL, Hicks Pries CE, Marin-Spiotta E, Plante AF, Schädel C, Schimel JP, Sierra CA, Thompson A, Wagai R (2018) Beyond clay: towards an improved set of variables for predicting soil organic matter content. Biogeochemistry 137(3):297–306

  55. Reardon PN, Walter ED, Marean-Reardon CL, Lawrence CW, Kleber M, Washton NM (2018) Carbohydrates protect protein against abiotic fragmentation by soil minerals. Scientific reports 8(1):813

  56. Sampedro JG, Guerra G, Pardo JP, Uribe S (1998) Trehalose-mediated protection of the plasma membrane H+-ATPase from Kluyveromyces lactis during freeze-drying and rehydration. Cryobiology 37(2):131–138

  57. Sanderman J, Amundson R (2008) A comparative study of dissolved organic carbon transport and stabilization in California forest and grassland soils. Biogeochemistry 89(3):309–327

  58. Sanderman J, Baldock JA, Amundson R (2008) Dissolved organic carbon chemistry and dynamics in contrasting forest and grassland soils. Biogeochemistry 89(2):181–198

  59. Scheu S, Parkinson D (1994) Changes in bacterial and fungal biomass C, bacterial and fungal biovolume and ergosterol content after drying, remoistening and incubation of different layers of cool temperate forest soils. Soil Biol Biochem 26(11):1515–1525

  60. Schimel JP (2018) Life in dry soils: effects of drought on soil microbial communities and processes. Annu Rev Ecol Evol Syst 49:409–432

  61. Schimel J, Balser TC, Wallenstein M (2007) Microbial stress-response physiology and its implications for ecosystem function. Ecology 88(6):1386–1394

  62. Schimel JP, Wetterstedt JM, Holden PA, Trumbore SE (2011) Drying/rewetting-Cycles mobilize old C from deep soils from a California annual grassland. Soil Biol Biochem 43(5):1101–1103

  63. Setia R, Verma SL, Marschner P (2012) Measuring microbial biomass carbon by direct extraction–comparison with chloroform fumigation-extraction. Eur J Soil Biol 53:103–106

  64. Smith AP, Bond-Lamberty B, Benscoter BW, Tfaily MM, Hinkle CR, Liu C, Bailey VL (2017) Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought. Nat Commun 8(1):1335

  65. Soil Survey Staff, Natural Resources Conservation Service, United States Department of Agriculture. (2017) Web soil survey.

  66. Sørensen LH (1974) Rate of decomposition of organic matter in soil as influenced by repeated air drying-rewetting and repeated additions of organic material. Soil Biol Biochem 6(5):287–292

  67. Sun WQ, Davidson P (1998) Protein inactivation in amorphous sucrose and trehalose matrices: effects of phase separation and crystallization. Biochim Biophys Acta (BBA) 1425(1):235–244

  68. Todoruk TR, Langford CH, Kantzas A (2003) Pore-scale redistribution of water during wetting of air-dried soils as studied by low-field NMR relaxometry. Environ Sci Technol 37(12):2707–2713

  69. Torn MS, Trumbore SE, Chadwick OA, Vitousek PM, Hendricks DM (1997) Mineral control of soil organic carbon storage and turnover. Nature 389(6647):170

  70. Warren CR (2016) Do microbial osmolytes or extracellular depolymerisation products accumulate as soil dries? Soil Biol Biochem 98:54–63

  71. Welsh DT (2000) Ecological significance of compatible solute accumulation by micro-organisms: from single cells to global climate. FEMS Microbiol Rev 24(3):263–290

  72. West AW, Sparling GP (1986) Modifications to the substrate-induced respiration method to permit measurement of microbial biomass in soils of differing water contents. J Microbiol Methods 5(3–4):177–189

  73. Wiemken A (1990) Trehalose in yeast, stress protectant rather than reserve carbohydrate. Antonie Van Leeuwenhoek 58(3):209–217

  74. Williams MA, Xia K (2009) Characterization of the water soluble soil organic pool following the rewetting of dry soil in a drought-prone tallgrass prairie. Soil Biol Biochem 41(1):21–28

  75. Xiang SR, Doyle A, Holden PA, Schimel JP (2008) Drying and rewetting effects on C and N mineralization and microbial activity in surface and subsurface California grassland soils. Soil Biol Biochem 40(9):2281–2289

  76. Xu L, Baldocchi DD, Tang J (2004) How soil moisture, rain pulses, and growth alter the response of ecosystem respiration to temperature. Glob Biogeochem Cycles.

Download references


Field sampling was supported by a grant from the Oren Pollak Memorial Research Fund, administered by The Nature Conservancy. Site selection and sampling was made possible by managers and support staff at four sites administered by the University of California Natural Reserve System: the McLaughlin Reserve, Sedgwick Reserve, Blue Oak Ranch Reserve, and Hastings Natural History Reservation; and two sites managed by the University of California Division of Agriculture and Natural Resources: Hopland and Sierra Foothill Research and Extension Centers. Jennifer King, Keri Opalk, and Andrew Saunders assisted with TOC analysis, Aral Greene assisted with soil texture analysis, and David Lyons assisted with ICP analysis of soil extracts. EWS received support from the National Science Foundation Graduate Research Fellowship Program. We thank two anonymous reviewers for helpful comments on this manuscript.

Author information

EWS was responsible for study design, field sampling, sample analysis, and writing. YL and BYJ contributed to field sampling, laboratory incubations, and manuscript revision. PMH contributed to chemical analyses and manuscript revision. OAC, CMD, and JPS contributed to study design, data interpretation, and manuscript revision.

Correspondence to Eric W. Slessarev.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Responsible Editor: Melany Fisk.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Slessarev, E.W., Lin, Y., Jiménez, B.Y. et al. Cellular and extracellular C contributions to respiration after wetting dry soil. Biogeochemistry 147, 307–324 (2020).

Download citation


  • Soil carbon
  • Birch effect
  • Drought
  • Osmoregulation