Abstract
Soil organic matter (SOM) has a key role in the carbon (C) cycle and consists of particulate organic matter (POM) and mineral-associated organic matter (MAOM), which differ in stability and turnover. This study investigates C dynamics and microbial abundance at two alpine sites (1526 and 2500 m a.s.l). Soil samples were fractionated, and the C:N ratio, pH, and microbial abundances were analysed. While the MAOM/POM ratio remained stable across sites, the higher-elevation soil, dominated by N-poor alpine graminoids, showed an increased C:N ratio, consistent with reduced decomposition and transfer of litter into mineral-associated pools under colder, more acidic conditions. Bacteria predominated in MAOM, supporting their role in SOM stabilisation, whereas fungal abundance was highest in MAOM only at 2500 m. Fungal abundance remained stable across sites, indicating greater tolerance to low temperatures and pH compared to bacteria, which declined at higher altitudes. This suggests fungi play a key role in decomposition in colder environments. Correlations between fungi and bacteria were context-dependent: negative in MAOM and positive in POM, but only at 2500 m. These findings highlight how the composition and stability of SOM and microbial abundance differ between fractions and at different elevations, underscoring the value of integrating microbial data with SOM fractionation to better understand alpine soil C dynamics.
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High stability and metabolic capacity of bacterial community promote the rapid reduction of easily decomposing carbon in soil
Microbial trait multifunctionality drives soil organic matter formation potential
Conceptualizing soil fauna effects on labile and stabilized soil organic matter
Data availability
The data used to support the findings of this study are available from the corresponding author upon request.
References
Bardgett, R. D., Freeman, C. & Ostle, N. J. Microbial contributions to climate change through carbon cycle feedbacks. ISME J. 2, 805–814 (2008).
Oldfield, E. E., Bradford, M. A. & Wood, S. A. Global meta-analysis of the relationship between soil organic matter and crop yields. Soil 5, 15–32 (2019).
Kirschbaum, M. U. F. Will changes in soil organic carbon act as a positive or negative feedback on global warming?. Biogeochemistry 48, 21–51 (2000).
Scharlemann, J. P. W., Tanner, E. V. J., Hiederer, R. & Kapos, V. Global soil carbon: Understanding and managing the largest terrestrial carbon pool. Carbon Manag. 5, 81–91 (2014).
Davidson, E. A. & Janssens, I. A. Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature 440, 165–173 (2006).
Dungait, J. A. J., Hopkins, D. W., Gregory, A. S. & Whitmore, A. P. Soil organic matter turnover is governed by accessibility not recalcitrance. Glob. Change Biol. 18, 1781–1796 (2012).
Lehmann, J. & Kleber, M. The contentious nature of soil organic matter. Nature 528, 60–68 (2015).
Nottingham, A. T. et al. Climate warming and soil carbon in tropical forests: insights from an elevation gradient in the Peruvian Andes. Bioscience 65, 906–921 (2015).
Cotrufo, M. F., Ranalli, M. G., Haddix, M. L., Six, J. & Lugato, E. Soil carbon storage informed by particulate and mineral-associated organic matter. Nat. Geosci. 12, 989–994 (2019).
Lavallee, J. M., Soong, J. L. & Cotrufo, M. F. Conceptualizing soil organic matter into particulate and mineral-associated forms to address global change in the 21st century. Glob. Change Biol. 26, 261–273 (2020).
Cotrufo, M. F. et al. Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nat. Geosci. 8, 776–779 (2015).
de Boer, W., Folman, L. B., Summerbell, R. C. & Boddy, L. Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol. Rev. 29, 795–811 (2005).
Xuan, M., Ai, L., Wu, F., Zhang, X. & Ni, X. Biomarkers evidence shows a preferential occlusion of microbial necromass in mineral-associated and not particle organic matter. Geoderma 450, 117030 (2024).
Kuzyakov, Y. & Blagodatskaya, E. Microbial hotspots and hot moments in soil: Concept and review. Soil Biol. Biochem. 83, 184–199 (2015).
Schimel, J. P. & Schaeffer, S. M. Microbial control over carbon cycling in soil. Front. Microbiol. 3, 1–11 (2012).
Fernandez, C. W. & Kennedy, P. G. Revisiting the ‘Gadgil effect’: do interguild fungal interactions control carbon cycling in forest soils?. New Phytol. 209, 1382–1394 (2016).
Rousk, J. & Bååth, E. Growth of saprotrophic fungi and bacteria in soil. FEMS Microbiol. Ecol. 78, 17–30 (2011).
Kallenbach, C. M., Grandy, A. S., Frey, S. D. & Diefendorf, A. F. Microbial physiology and necromass regulate agricultural soil carbon accumulation. Soil Biol. Biochem. 91, 279–290 (2015).
Liang, C., Schimel, J. P. & Jastrow, J. D. The importance of anabolism in microbial control over soil carbon storage. Nat. Microbiol. 2, 17105 (2017).
Margesin, R., Jud, M., Tscherko, D. & Schinner, F. Microbial communities and activities in alpine and subalpine soils. FEMS Microbiol. Ecol. 67, 208–218 (2009).
Körner, C., Paulsen, J. & Spehn, E. M. A definition of mountains and their bioclimatic belts for global comparisons of biodiversity data. Alp Botany 121, 73 (2011).
Sundqvist, M. K., Sanders, N. J. & Wardle, D. A. Community and ecosystem responses to elevational gradients: processes, mechanisms, and insights for global change. Annu. Rev. Ecol. Evol. Syst. 44, 261–280 (2013).
Tang, M. et al. Elevational is the main factor controlling the soil microbial community structure in alpine tundra of the Changbai Mountain. Sci. Rep. 10, 12442 (2020).
He, W. et al. Elevational control on microbial residues contributions to soil organic carbon: Dual regulation by soil moisture and total nitrogen dynamics in semi-arid mountain soils. Soil Ecol. Lett. 7, 250350 (2025).
Cotrufo, M. F., Wallenstein, M. D., Boot, C. M., Denef, K. & Paul, E. The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: do labile plant inputs form stable soil organic matter?. Glob. Change Biol. 19, 988–995 (2013).
Manzoni, S. & Cotrufo, M. F. Mechanisms of soil organic carbon and nitrogen stabilization in mineral-associated organic matter – insights from modeling in phase space. Biogeosciences 21, 4077–4098 (2024).
Zaccone, C., Beneduce, L., Lotti, C., Martino, G. & Plaza, C. DNA occurrence in organic matter fractions isolated from amended, agricultural soils. Appl. Soil. Ecol. 130, 134–142 (2018).
European Soil Data Centre. Soil Sampling Protocol. (2024).
Just, C., Poeplau, C., Don, A., van Wesemael, B., Kögel-Knabner, I. & Wiesmeier, M. A simple approach to isolate slow and fast cycling organic carbon fractions in central European soils—importance of dispersion method. Front. Soil Sci. 1, (2021).
Wasimuddin, et al. Evaluation of primer pairs for microbiome profiling from soils to humans within the One Health framework. Mol. Ecol. Resour. 20, 1558–1571 (2020).
Toju, H., Tanabe, A. S., Yamamoto, S. & Sato, H. High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples. PLoS ONE 7, e40863 (2012).
R Core Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2022).
Wang, Y., Sun, J. & Lee, T. M. Altitude dependence of alpine grassland ecosystem multifunctionality across the Tibetan Plateau. J. Environ. Manag. 332, 117358 (2023).
Růžek, M., Tahovská, K., Guggenberger, G. & Oulehle, F. Litter decomposition in European coniferous and broadleaf forests under experimentally elevated acidity and nitrogen addition. Plant Soil 463, 471–485 (2021).
Manzoni, S., Taylor, P., Richter, A., Porporato, A. & Ågren, G. I. Environmental and stoichiometric controls on microbial carbon-use efficiency in soils. New Phytol. 196, 79–91 (2012).
von Lützow, M. & Kögel-Knabner, I. Temperature sensitivity of soil organic matter decomposition—what do we know?. Biol. Fertil. Soils 46, 1–15 (2009).
Zhang, Y. et al. Drivers of mountain soil organic carbon stock dynamics: A review. J. Soils Sediments 23, 64–76 (2023).
Leuthold, S. J., Lavallee, J. M., Basso, B., Brinton, W. F. & Cotrufo, M. F. Shifts in controls and abundance of particulate and mineral-associated organic matter fractions among subfield yield stability zones. Soil 10, 307–319 (2024).
Kögel-Knabner, I. The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter. Soil Biol. Biochem. 34, 139–162 (2002).
Grandy, A. S., Strickland, M. S., Lauber, C. L., Bradford, M. A. & Fierer, N. The influence of microbial communities, management, and soil texture on soil organic matter chemistry. Geoderma 150, 278–286 (2009).
Miltner, A., Bombach, P., Schmidt-Brücken, B. & Kästner, M. SOM genesis: microbial biomass as a significant source. Biogeochemistry 111, 41–55 (2012).
Kaiser, C., Franklin, O., Dieckmann, U. & Richter, A. Microbial community dynamics alleviate stoichiometric constraints during litter decay. Ecol. Lett. 17, 680–690 (2014).
Lang, A. K., Pett-Ridge, J., McFarlane, K. J. & Phillips, R. P. Climate, soil mineralogy and mycorrhizal fungi influence soil organic matter fractions in eastern US temperate forests. J. Ecol. 111, 1254–1269 (2023).
Wang, J. et al. The fungal community structure regulates elevational variations in soil organic carbon fractions in a Wugong mountain meadow. J. Fungi 10, 772 (2024).
Clemmensen, K. E. et al. Roots and associated fungi drive long-term carbon sequestration in boreal forest. Science 339, 1615–1618 (2013).
Ryberg, M., Andreasen, M. & Björk, R. G. Weak habitat specificity in ectomycorrhizal communities associated with Salix herbacea and Salix polaris in alpine tundra. Mycorrhiza 21, 289–296 (2011).
Six, J., Frey, S. D., Thiet, R. K. & Batten, K. M. Bacterial and fungal contributions to carbon sequestration in agroecosystems. Soil Sci. Soc. Am. J. 70, 555–569 (2006).
Sinsabaugh, R. L. et al. Stoichiometry of microbial carbon use efficiency in soils. Ecol. Monogr. 86, 172–189 (2016).
Strickland, M. S. & Rousk, J. Considering fungal:bacterial dominance in soils – Methods, controls, and ecosystem implications. Soil Biol. Biochem. 42, 1385–1395 (2010).
Delgado-Baquerizo, M. et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat. Ecol. Evol. 4, 210–220 (2020).
Khan, M. T., Supronienė, S., Žvirdauskienė, R. & Aleinikovienė, J. Climate, soil, and microbes: interactions shaping organic matter decomposition in croplands. Agronomy 15, 1928 (2025).
Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. 103, 626–631 (2006).
Treseder, K. K. & Lennon, J. T. Fungal traits that drive ecosystem dynamics on land. Microbiol. Mol. Biol. Rev. 79, 243–262 (2015).
Waring, B. G., Averill, C. & Hawkes, C. V. Differences in fungal and bacterial physiology alter soil carbon and nitrogen cycling: insights from meta-analysis and theoretical models. Ecol. Lett. 16, 887–894 (2013).
Wang, C. & Kuzyakov, Y. Mechanisms and implications of bacterial–fungal competition for soil resources. ISME J. 18, 1–15 (2024).
Fierer, N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. 15, 579–590 (2017).
Philippot, L., Griffiths, B. S. & Langenheder, S. Microbial community resilience across ecosystems and multiple disturbances. Microbiol. Mol. Biol. Rev. 85, 1–31 (2021).
Acknowledgements
We want to offer special thanks to Dr. Angela Augusti, who, although no longer with us, continues to inspire us through her dedication and contributions to research. The authors are grateful to Fondazione Montagna Sicura (http://www.fondazionemontagnasicura.org/en/), which made the realization of this study possible.
Funding
This study was supported by the Italian Ministry of University and Research, PRIN 2020 (Projects of Relevant National Interest), Prot. 20204KF4RW, CUP: I53C21000140001 and by the Open Access Publishing Fund of the Free University of Bozen-Bolzano.
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I.F. and L.F. contributed equally to the present study (first authors) by conceptualizing the work, conducting the investigation, performing formal analysis, curating the data, preparing visualizations, and writing the original draft of the manuscript. R.T. and P.B. contributed to resource provision and participated in reviewing and editing the manuscript. A.A., O.G., L.Z., and L.M. contributed resources and assisted in reviewing and editing the manuscript. L.B. supervised the research, contributed to the methodology and resource acquisition, and participated in manuscript review and editing. T.M. conceptualized the work, supervised the project, contributed to the methodology and resource provision, and participated in reviewing and editing the manuscript. All authors discussed and commented on the methods and results and contributed to the final version of the paper.
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Fracasso, I., Foley, L., Tiziani, R. et al. Soil organic carbon fractions and their associated bacterial and fungal abundance in alpine ecosystems.
Sci Rep (2025). https://doi.org/10.1038/s41598-025-31187-8
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DOI: https://doi.org/10.1038/s41598-025-31187-8
Keywords
- Carbon fractions
- POM
- MAOM
- Soil ecology
- Fungal abundance
- Bacterial abundance
Source: Ecology - nature.com
