Linking molecular size, composition and carbon turnover of extractable soil microbial compounds

Ashish A. Malik*, Vanessa Nina Roth, Mathieu Hébert, Luc Tremblay, Thorsten Dittmar, Gerd Gleixner

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

30 Citations (Scopus)


Microbial contribution to the maintenance and turnover of soil organic matter is significant. Yet, we do not have a thorough understanding of how biochemical composition of soil microbial biomass is related to carbon turnover and persistence of different microbial components. Using a suite of state-of-the-art analytical techniques, we investigated the molecular characteristics of extractable microbial biomass and linked it to its carbon turnover time. A 13CO2 plant pulse labelling experiment was used to trace plant carbon into rhizosphere soil microbial biomass, which was obtained by chloroform fumigation extraction (CFE). 13C content in molecular size classes of extracted microbial compounds was analysed using size exclusion chromatography (SEC) coupled online to high performance liquid chromatography-isotope ratio mass spectrometry (SEC-HPLC-IRMS). Molecular characterization of microbial compounds was performed using complementary approaches, namely SEC-HPLC coupled to Fourier transform infrared spectroscopy (SEC-HPLC-FTIR) and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS). SEC-HPLC-FTIR suggests that mid to high molecular weight (MW) microbial compounds were richer in aliphatic CH bonds, carbohydrate-like compounds and possibly PO derivatives from phospholipids. On the contrary, the lower size range was characterized by more oxidised compounds with hydroxyl, carbonyl, ether and/or carboxyl groups. ESI-FT-ICR-MS suggests that microbial compounds were largely aliphatic and richer in N than the background detrital material. Both molecular characterization tools suggest that CFE derived microbial biomass was largely lipid, carbohydrate and protein derived. SEC-HPLC-IRMS analysis revealed that 13C enrichment decreased with increasing MW of microbial compounds and the turnover time was deduced as 12.8 ± 0.6, 18.5 ± 0.6 and 22.9 ± 0.7 days for low, mid and high MW size classes, respectively. We conclude that low MW compounds represent the rapidly turned-over metabolite fraction of extractable soil microbial biomass consisting of organic acids, alcohols, amino acids and sugars; whereas, larger structural compounds are part of the cell envelope (likely membrane lipids, proteins or polysaccharides) with a much lower renewal rate. This relation of microbial carbon turnover to its molecular size, structure and composition thus highlights the significance of cellular biochemistry in determining the microbial contribution to soil carbon cycling and specifically soil organic matter formation.

Original languageEnglish
Pages (from-to)66-73
Number of pages8
JournalSoil Biology and Biochemistry
Early online date5 Jun 2016
Publication statusPublished - 1 Sept 2016

Bibliographical note

This truly collaborative project was funded by the Max-Planck-Gesellschaft (MPG)/Max Planck Society, the Natural Science and Engineering Research Council of Canada (NSERC), and the New Brunswick Innovation Foundation (NBIF). We acknowledge Deutsche Forschungsgemeinschaft (DFG)/German Research Foundation for the PhD fellowship to A.A.M. in the research training group 1257 ‘Alteration and element mobility at microbe-mineral interface’. V.-N. R. received financial support from the foundation “Zwillenberg-Tietz Stiftung” and Deutsche Forschungsgemeinschaft (DFG)/German Research Foundation as part of the collaborative research centre (CRC) 1076 “AquaDiva”. A.A.M. has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 655240. We thank Steffen Ruehlow for technical support with stable isotope analyses; Agnes Fastnacht, Karl Kuebler and Iris Kuhlmann for support in establishing the experimental setup and K. Klapproth for technical support with FT-ICR-MS measurements. We also thank the reviewers and the editor for constructive comments that helped improve the manuscript.


  • Chloroform fumigation extraction
  • Microbial biomass
  • Soil carbon


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