Articles | Volume 11, issue 1
https://doi.org/10.5194/soil-11-247-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/soil-11-247-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Review article
| 
12 Mar 2025
Review article |
| 12 Mar 2025
| 12 Mar 2025
Impacts of soil storage on microbial parameters
Nathalie Fromin
CORRESPONDING AUTHOR
CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
Related subject area
Soil biodiversity and soil health
Moderate N fertilizer reduction with straw return modulates cropland functions and microbial traits in a meadow soil
Ectomycorrhizal fungal network complexity determines soil multi-enzymatic activity
Unraveling biogeographical patterns and environmental drivers of soil fungal diversity at the French national scale
Biochar promotes soil aggregate stability and associated organic carbon sequestration and regulates microbial community structures in Mollisols from northeast China
Only a minority of bacteria grow after wetting in both natural and post-mining biocrusts in a hyperarid phosphate mine
Lower functional redundancy in “narrow” than “broad” functions in global soil metagenomics
Pairing litter decomposition with microbial community structures using the Tea Bag Index (TBI)
Network complexity of rubber plantations is lower than tropical forests for soil bacteria but not for fungi
Changes in soil physicochemical properties and bacterial communities at different soil depths after long-term straw mulching under a no-till system
Microbial communities and their predictive functional profiles in the arid soil of Saudi Arabia
Development of a soil biological quality index for soils of semi-arid tropics
What do we know about how the terrestrial multicellular soil fauna reacts to microplastic?
Soil microbial biomass and function are altered by 12 years of crop rotation
Soil denitrifier community size changes with land use change to perennial bioenergy cropping systems
Knowledge needs, available practices, and future challenges in agricultural soils
Technological advancements and their importance for nematode identification
Fire affects root decomposition, soil food web structure, and carbon flow in tallgrass prairie
Case study of microarthropod communities to assess soil quality in different managed vineyards
A meta-analysis of soil biodiversity impacts on the carbon cycle
Yan Duan, Minghui Cao, Wenling Zhong, Yuming Wang, Zheng Ni, Mengxia Zhang, Jiangye Li, Yumei Li, Xianghai Meng, and Lifang Wu
SOIL, 10, 779–794, https://doi.org/10.5194/soil-10-779-2024, https://doi.org/10.5194/soil-10-779-2024, 2024
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Nitrogen (N) fertilization has received worldwide attention due to its effects on soil functions. However, soil multifunctionality and the underlying microbial mechanisms remain unclear. Therefore, we carried out in situ field and incubation experiments. We propose that straw return with 25 % N fertilizer reduction may achieve high soil multifunctionality by regulating the soil C:N ratio and N input level and specific keystone taxa-driven community contributions to soil functions.
Jorge Prieto-Rubio, José L. Garrido, Julio M. Alcántara, Concepción Azcón-Aguilar, Ana Rincón, and Álvaro López-García
SOIL, 10, 425–439, https://doi.org/10.5194/soil-10-425-2024, https://doi.org/10.5194/soil-10-425-2024, 2024
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Changes in soil biological activity when microbial taxa interact remain little understood. To address this, we approach network analyses of ectomycorrhizal fungal communities. The study highlights how distinct fungi contribute to explaining community structure, whilst others mainly do for soil enzymatic activity. This differentiation between structural and functional roles of ectomycorrhizal fungi adds new insights to understand soil fungal community complexity and its functionality in soils.
Christophe Djemiel, Samuel Dequiedt, Walid Horrigue, Arthur Bailly, Mélanie Lelièvre, Julie Tripied, Charles Guilland, Solène Perrin, Gwendoline Comment, Nicolas P. A. Saby, Claudy Jolivet, Antonio Bispo, Line Boulonne, Antoine Pierart, Patrick Wincker, Corinne Cruaud, Pierre-Alain Maron, Sébastien Terrat, and Lionel Ranjard
SOIL, 10, 251–273, https://doi.org/10.5194/soil-10-251-2024, https://doi.org/10.5194/soil-10-251-2024, 2024
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The fungal kingdom has been diversifying for more than 800 million years by colonizing a large number of habitats on Earth. Based on a unique dataset (18S rDNA meta-barcoding), we described the spatial distribution of fungal diversity at the scale of France and the environmental drivers by tackling biogeographical patterns. We also explored the fungal network interactions across land uses and climate types.
Jing Sun, Xinrui Lu, Guoshuang Chen, Nana Luo, Qilin Zhang, and Xiujun Li
SOIL, 9, 261–275, https://doi.org/10.5194/soil-9-261-2023, https://doi.org/10.5194/soil-9-261-2023, 2023
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A field experiment was conducted to compare and analyze the effects of combined application of biochar and nitrogen fertilizer on soil aggregate stability mechanism, the dynamic characteristics of aggregate organic carbon, and the microbial community structure in northeast black soil. We provide a scientific basis for formulating effective strategies to slow down soil quality degradation and ensure the sustainable development of the agroecosystem.
Talia Gabay, Eva Petrova, Osnat Gillor, Yaron Ziv, and Roey Angel
SOIL, 9, 231–242, https://doi.org/10.5194/soil-9-231-2023, https://doi.org/10.5194/soil-9-231-2023, 2023
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This paper evaluates bacterial growth in biocrusts after a large-scale mining disturbance in a hyperarid desert, using a stable isotope probing assay.
We discovered that biocrust bacteria from both natural and post-mining plots resumed photosynthetic activity but did not grow following hydration. Our paper provides insights into the effects of a large-scale disturbance (mining) on biocrusts and their response to hydration, with implications for biocrust restoration practices in Zin mines.
Huaihai Chen, Kayan Ma, Yu Huang, Qi Fu, Yingbo Qiu, Jiajiang Lin, Christopher W. Schadt, and Hao Chen
SOIL, 8, 297–308, https://doi.org/10.5194/soil-8-297-2022, https://doi.org/10.5194/soil-8-297-2022, 2022
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By analyzing and generalizing microbial taxonomic and functional profiles, we provide strong evidence that the degree of soil microbial functional redundancy differs significantly between “broad” and “narrow” functions across the globe. Future sequencing efforts will likely increase our confidence in comparative metagenomes and provide time-series information to further identify to what extent microbial functional redundancy regulates dynamic ecological fluxes across space and time.
Anne Daebeler, Eva Petrová, Elena Kinz, Susanne Grausenburger, Helene Berthold, Taru Sandén, Roey Angel, and the high-school students of biology project groups I, II, and
III from 2018–2019
SOIL, 8, 163–176, https://doi.org/10.5194/soil-8-163-2022, https://doi.org/10.5194/soil-8-163-2022, 2022
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In this citizen science project, we combined a standardised litter bag method (Tea Bag Index) with microbiome analysis of bacteria and fungi colonising the teabags to gain a holistic understanding of the carbon degradation dynamics in temperate European soils. Our method focuses only on the active part of the soil microbiome. The results show that about one-third of the prokaryotes and one-fifth of the fungal species (ASVs) in the soil were enriched in response to the presence of fresh OM.
Guoyu Lan, Chuan Yang, Zhixiang Wu, Rui Sun, Bangqian Chen, and Xicai Zhang
SOIL, 8, 149–161, https://doi.org/10.5194/soil-8-149-2022, https://doi.org/10.5194/soil-8-149-2022, 2022
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Forest conversion alters both bacterial and fungal soil networks: it reduces bacterial network complexity and enhances fungal network complexity. This is because forest conversion changes the soil pH and other soil properties, which alters the bacterial composition and subsequent network structure. Our study demonstrates the impact of forest conversion on soil network structure, which has important implications for ecosystem functions and the health of soil ecosystems in tropical regions.
Zijun Zhou, Zengqiang Li, Kun Chen, Zhaoming Chen, Xiangzhong Zeng, Hua Yu, Song Guo, Yuxian Shangguan, Qingrui Chen, Hongzhu Fan, Shihua Tu, Mingjiang He, and Yusheng Qin
SOIL, 7, 595–609, https://doi.org/10.5194/soil-7-595-2021, https://doi.org/10.5194/soil-7-595-2021, 2021
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Straw mulching is not always combined with no-till systems during conservation tillage. We explored the effects of long-term straw mulching on soil attributes with soil depths under a no-till system. Compared to straw removal, straw mulching had various effects on soil properties at different depths, the biggest difference occurring at the topsoil depth. Overall, straw mulch is highly recommended for use under the no-till system because of its benefits to soil fertility and bacterial abundance.
Munawwar A. Khan and Shams T. Khan
SOIL, 6, 513–521, https://doi.org/10.5194/soil-6-513-2020, https://doi.org/10.5194/soil-6-513-2020, 2020
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Soil is a renewable resource for purposes ranging from agriculture to mineralization. Soil microbiome plays vital roles in facilitating process like providing nutrients to plants, or their mobilization for plant uptake, consequently improving plant growth and productivity. Therefore, understanding of these microbial communities and their role in soil is crucial for exploring the possibility of using microbial community inoculants for improving desert soil fertility and agricultural potential.
Selvaraj Aravindh, Chinnappan Chinnadurai, and Dananjeyan Balachandar
SOIL, 6, 483–497, https://doi.org/10.5194/soil-6-483-2020, https://doi.org/10.5194/soil-6-483-2020, 2020
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Soil quality is important for functioning of the agricultural ecosystem to sustain productivity. It is combination of several physical, chemical, and biological attributes. In the present work, we developed a soil biological quality index, a sub-set of the soil quality index (SBQI) using six important biological variables. These variables were computed from long-term manurial experimental soils and transformed into a unitless 10-scaled SBQI. This will provide constraints of soil processes.
Frederick Büks, Nicolette Loes van Schaik, and Martin Kaupenjohann
SOIL, 6, 245–267, https://doi.org/10.5194/soil-6-245-2020, https://doi.org/10.5194/soil-6-245-2020, 2020
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Via anthropogenic input, microplastics (MPs) today represent a part of the soil organic matter. We analyzed studies on passive translocation, active ingestion, bioaccumulation and adverse effects of MPs on multicellular soil faunal life. These studies on a wide range of soil organisms found a recurring pattern of adverse effects on motility, growth, metabolism, reproduction, mortality and gut microbiome. However, the shape and type of the experimental MP often did not match natural conditions.
Marshall D. McDaniel and A. Stuart Grandy
SOIL, 2, 583–599, https://doi.org/10.5194/soil-2-583-2016, https://doi.org/10.5194/soil-2-583-2016, 2016
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Modern agriculture is dominated by monoculture crop production, having negative effects on soil biology. We used a 12-year crop rotation experiment to examine the effects of increasing crop diversity on soil microorganisms and their activity. Crop rotations increased microbial biomass by up to 112 %, and increased potential ability to supply nitrogen as much as 58 %, compared to monoculture corn. Collectively, our findings show that soil health is increased when crop diversity is increased.
Karen A. Thompson, Bill Deen, and Kari E. Dunfield
SOIL, 2, 523–535, https://doi.org/10.5194/soil-2-523-2016, https://doi.org/10.5194/soil-2-523-2016, 2016
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Dedicated bioenergy crops are required for future energy production; however the effects of land use change from traditional crops to biofuel crops on soil microbial communities, which drive greenhouse gas production, are largely unknown. We used quantitative PCR to enumerate these microbial communities to assess the sustainability of different bioenergy crops, including miscanthus and corn. We found that miscanthus may be a suitable crop for bioenergy production in variable Ontario conditions.
Georgina Key, Mike G. Whitfield, Julia Cooper, Franciska T. De Vries, Martin Collison, Thanasis Dedousis, Richard Heathcote, Brendan Roth, Shamal Mohammed, Andrew Molyneux, Wim H. Van der Putten, Lynn V. Dicks, William J. Sutherland, and Richard D. Bardgett
SOIL, 2, 511–521, https://doi.org/10.5194/soil-2-511-2016, https://doi.org/10.5194/soil-2-511-2016, 2016
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Enhancing soil health is key to providing ecosystem services and food security. There are often trade-offs to using a particular practice, or it is not fully understood. This work aimed to identify practices beneficial to soil health and gaps in our knowledge. We reviewed existing research on agricultural practices and an expert panel assessed their effectiveness. The three most beneficial practices used a mix of organic or inorganic material, cover crops, or crop rotations.
Mohammed Ahmed, Melanie Sapp, Thomas Prior, Gerrit Karssen, and Matthew Alan Back
SOIL, 2, 257–270, https://doi.org/10.5194/soil-2-257-2016, https://doi.org/10.5194/soil-2-257-2016, 2016
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This review covers the history and advances made in the area of nematode taxonomy. It highlights the success and limitations of the classical approach to nematode taxonomy and provides reader with a bit of background to the applications of protein and DNA-based methods for identification nematodes. The review also outlines the pros and cons of the use of DNA barcoding in nematology and explains how DNA metabarcoding has been applied in nematology through next-generation sequencing.
E. Ashley Shaw, Karolien Denef, Cecilia Milano de Tomasel, M. Francesca Cotrufo, and Diana H. Wall
SOIL, 2, 199–210, https://doi.org/10.5194/soil-2-199-2016, https://doi.org/10.5194/soil-2-199-2016, 2016
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We investigated fire's effects on root decomposition and carbon (C) flow to the soil food web. We used 13C-labeled dead roots buried in microcosms constructed from two burn treatment soils (annual and infrequent burn). Our results showed greater root decomposition and C flow to the soil food web for the annual burn compared to infrequent burn treatment. Thus, roots are a more important C source for decomposers in annually burned areas where surface plant litter is frequently removed by fire.
E. Gagnarli, D. Goggioli, F. Tarchi, S. Guidi, R. Nannelli, N. Vignozzi, G. Valboa, M. R. Lottero, L. Corino, and S. Simoni
SOIL, 1, 527–536, https://doi.org/10.5194/soil-1-527-2015, https://doi.org/10.5194/soil-1-527-2015, 2015
M.-A. de Graaff, J. Adkins, P. Kardol, and H. L. Throop
SOIL, 1, 257–271, https://doi.org/10.5194/soil-1-257-2015, https://doi.org/10.5194/soil-1-257-2015, 2015
Cited articles
Abellan, A. M., Wic Baena, C., García Morote, F. A., Picazo Cordoba, M. I., Candel Pérez, D., and Lucas-Borja, M. E.: Influence of the soil storage method on soil enzymatic activities, For. Syst., 20, 379, https://doi.org/10.5424/fs/20112003-11081, 2011.
Achat, D. L., L. Augusto, A. Gallet-Budynek, and Bakker, M. R.: Drying-induced changes in phosphorus status of soils with contrasting soil organic matter contents – Implications for laboratory approaches, Geoderma, 187-188, 41–48, https://doi.org/10.1016/j.geoderma.2012.04.014, 2012.
Barnard, R. L., Osborne C. A., and Firestone M. K.: Responses of soil bacterial and fungal communities to extreme desiccation and rewetting, ISME J., 7, 2229–2241, https://doi.org/10.1038/ismej.2013.104, 2013.
Barria, C., Malecki M., and Arraiano C. M.: Bacterial adaptation to cold, Microbiology, 159, 2437–2443, https://doi.org/10.1099/mic.0.052209-0, 2013.
Bartlett, R. J. and James, B.: Studying dried, stored soil samples-some pitfalls, Soil Sci. Soc. Am. J., 44, 721–724, https://doi.org/10.2136/sssaj1980.03615995004400040011x, 1980.
Benucci, G. M. N., Rennick, B., and Bonito, G.: Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities?, PLoS ONE, 15, e0237368, https://doi.org/10.1371/journal.pone.0237368, 2020.
Birch, H. F.: The effect of soil drying on humus decomposition and nitrogen availability, Plant Soil, 10, 9–31, https://doi.org/10.1007/BF01343734, 1958.
Blake, L., Goulding, K. W. T., Mott, C. J. B., and Poulton, P. R.: Temporal changes in chemical properties of air-dried stored soils and their interpretation for long-term experiments, Eur. J. Soil Sci., 51, 345–353, https://https://doi.org/10.1046/j.1365-2389.2000.00307.x, 2000.
Brandt, F. B., Breidenbach, B., Brenzinger, K., and Conrad, R.: Impact of short-term storage temperature on determination of microbial community composition and abundance in aerated forest soil and anoxic pond sediment samples, Syst. Appl. Microbiol., 37, 570–577, https://doi.org/10.1016/j.syapm.2014.10.007, 2014.
Breitenbeck, G. A. and Bremmer, J. M.: Effects of storing soils at various temperatures on their capacity for denitrification, Soil Biol. Biochem., 19, 377-380, https://doi.org/10.1016/0038-0717(87)90026-5, 1987.
Brock, M. T., Morrisson, H. G., Maignien, L., and Weinig, C.: Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities, FEMS Microbiol. Lett., 371, fnae044, https://doi.org/10.1093/femsle/fnae044, 2024.
Brohon, B., Delolme, C., and Gourdon, R.: Qualification of soils through microbial activities measurements influence of the storage period on int-reductase, phosphatase and respiration, Chemosphere, 38, 1973–1984, https://doi.org/10.1016/S0045-6535(98)00410-X, 1999.
Černohlávková, J., Jarkovský, J., Nešporová, M., and Hofman, J.: Variability of soil microbial properties: Effects of sampling, handling and storage, Ecotox. Environ. Safe., 72, 2102–2108, https://doi.org/10.1016/j.ecoenv.2009.04.023, 2009.
Chattopadhyay, M.: Mechanism of bacterial adaptation to low temperature, J. Biosciences, 31, 157–165, https://doi.org/10.1007/BF02705244, 2006.
Chirinda, N., Olesen, J. E., and Porter, J. R.: Post-cold-storage conditioning time affects soil denitrifying enzyme activity, Commun. Soil Sci. Plan., 42, 2160-2167, https://doi.org.inee.bib.cnrs.fr/10.1080/00103624.2011.596244, 2011.
Clark, I. M. and Hirsch, P. R.: Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted Broadbalk experiment, Soil Biol. Biochem., 40, 1090–1102, https://https://doi.org/10.1016/j.soilbio.2007.11.021, 2008.
Creamer, R. E., Stone, D., Berry, P., and Kuiper, I.: Measuring respiration profiles of soil microbial communities across Europe using MicroResp™ method, Appl. Soil Ecol., 97, 36–43, https://doi.org/10.1016/j.apsoil.2015.08.004, 2016.
Cui, H., Wang, C., Gu, Z., Zhu, H., Fu, S., and Yao, Q.: Evaluation of soil storage methods for soil microbial community using genetic and metabolic fingerprintings, Eur. J. Soil Biol., 63, 55–63, https://doi.org/10.1016/j.ejsobi.2014.05.006, 2014.
D'Amico, S., Collins, T., Marx, J.-C., Feller, G., and Gerday, C.: Psychrophilic microorganisms: challenges for life, EMBO Rep., 7, 385–389, https://doi.org/10.1038/sj.embor.7400662, 2006.
Dadenko, E. V., Kazeev, K. S., Kolesnikov, S. I., and Val'kov, V. F.: Changes in the enzymatic activity of soil samples upon their storage, Eurasian Soil Sci., 42, 1380–1385, https://doi.org/10.1134/S1064229309120084, 2009.
De Castro Lopes, A. A., Gomes de Sousa, D. M., Bueno, dos Reis Junior, F. B., and Mendes, I. C.: Air-drying and long-term storage effects on β-glucosidase, acid phosphatase and arylsulfatase activities in a tropical Savannah Oxisol, Appl. Soil Ecol., 93, 68–77, https://doi.org/10.1016/j.apsoil.2015.04.001, 2015.
De Nobili, M., Contin, M., and Brookes, P. C.: Microbial biomass dynamics in recently air-dried and rewetted soils compared to others stored air-dry for up to 103 years, Soil Biol. Biochem., 38, 2871–2881, https://doi.org/10.1016/j.soilbio.2006.04.044, 2006.
de Vries, F. T., Griffiths, R. I., Bailey, M., Carig, H., Girlanda, M., Gweon, H. S., Hallin, S., Kaisermann, A., Keith, A. M., Kretzschmar, M., Lemanceau, P., Lumini, E., Mason, K. E., Oliver, A., Ostle, N., Prosser, J. I., Thion, C., Thomson, B., and Bardgett, R. D.: Soil bacterial networks are less stable under drought than fungal networks, Nat. Commun., 9, 3033, https://doi.org/10.1038/s41467-018-05516-7, 2018.
DeForest, J. L.: The influence of time, storage temperature, and substrate age on potential soil enzyme activity in acidic forest soils using MUB-linked substrates and l-DOPA, Soil Biol. Biochem., 41, 1180–1186, https://doi.org/10.1016/j.soilbio.2009.02.029, 2009.
Delavaux, C. S., Bever, J. D., Karpinnen, E. M., and Bainard, L. D.: Keeping it cool: Soil sample cold pack storage and DNA, Ecol. Evol., 10, 4652–4664, https://doi.org/10.1002/ece3.6219, 2020.
Delgado-Baquerizo, M. Reich, P. B, Trivedi, C., Eldridge, D. J., Abades, S., Alfaro, F. D., Bastida, F., Berhe, A. A., Cutler, N. A., Gallardo, A., García-Velázquez, L., Hart, S. C., Hayes, P. E., He, J. Z., Hseu, Z. Y., Hu, H. W., Kirchmair, M., Neuhauser, S., Pérez, C. A., Reed, S. C., Santos, F., Sullivan, B. W., Trivedi, P., Wang, J. T., Weber-Grullon, L., Williams, M. A., and Singh, B. K.: Multiple elements of soil biodiversity drive ecosystem functions across biomes, Nat. Ecol. Evol., 4, 210–220, https://doi.org/10.1038/s41559-019-1084-y, 2020.
Evans, S. E. and Wallenstein, M. D.: Soil microbial community response to drying and rewetting stress: does historical precipitation regime matter?, Biogeochemistry, 109, 101–116, https://doi.org/10.1007/s10533-011-9638-3, 2012.
Evans, S. E. and Wallenstein, M. D.: Climate change alters ecological strategies of soil bacteria, Ecol. Lett., 17, 155–164, https://doi.org/10.1111/ele.12206, 2014.
Fardoux, J., P. Fernandes, A. Niane-Badiane, and Chotte, J.-L.: Effet du séchage d'échantillons d'un sol ferrugineux tropical sur la détermination de la biomasse microbienne, Etudes et Gestion des Sols, 7, 385–394, 2000.
Fierer, N. and Schimel, J. P.: A proposed mechanism for the pulse in carbon dioxide production commonly observed following rapid rewetting of a dry soil, Soil Sci. Soc. Am. J., 67, 798–805, https://doi.org/10.2136/sssaj2003.0798, 2002.
Finn, D. R., Schroeder, J., Samad, M. S., Poeplau, C., and Tebbe, C.: Importance of sample pre-treatments for the DNA-based characterization of microbiomes in cropland and forest soils, Soil Biol. Biochem., 184, 109077, https://doi.org/10.1016/j.soilbio.2023.109077, 2023.
Gillespie, L., Hättenschwiler, S., Milcu, A., Wambsganss, J., Shihan, A., and Fromin, N.: Tree species mixing affects soil microbial functioning indirectly via root and litter traits and soil parameters in European forests, Funct. Ecol., 35, 2190–2204, https://doi.org/10.1111/1365-2435.13877, 2021.
Ginn, B. R., Habteselassie, M. Y., Meile, C., and Thompson, A.: Effects of sample storage on microbial Fe-reduction in tropical rainforest soils, Soil Biol. Biochem., 68, 44–51, https://doi.org/10.1016/j.soilbio.2013.09.012, 2014.
Goberna, M., Insam, H., Pascual, J. A., and Sánchez, J.: Storage effects on the community level physiological profiles of Mediterranean forest soils, Soil Biol. Biochem., 37, 173–178, https://doi.org/10.1016/j.soilbio.2004.06.014, 2005.
Gonzalez-Quiñones, V., Banning, N. C., Ballesta, R. J., and Murphy, D. V.: Influence of cold storage on soil microbial community level physiological profiles and implications for soil quality monitoring, Soil Biol. Biochem., 41, 1574–1576, https://doi.org/10.1016/j.soilbio.2009.04.004, 2009.
Graham, E. B., Knelman, J. E. Schindlbacher, A., Siciliano, S., Breulmann, M., Yannarell, A., Beman, J. M., Abell, G., Philippot, L., Prosser, J., Foulquier, A., Yuste, J. C., Glanville, H. C., Jones, D. L., Angel, R., Salminen, J., Newton, R. J., Bürgmann, H., Ingram, L. J., Hamer, U., Siljanen, H. M. P, Peltoniemi, K., Potthast, K., Bañeras, L., Hartmann, M., Banerjee, S., Yu, R. Q., Nogaro, G., Richter, A., Koranda, M., Castle, S. C., Goberna, M., Song, B., Chatterjee, A., Nunes, O. C., Lopes, A. R., Cao, Y., Kaisermann, A., Hallin, S., Strickland, M. S., Garcia-Pausas, J., Barba, J., Kang, H., Isobe, K., Papaspyrou, S., Pastorelli, R., Lagomarsino, A., Lindström, E. S., Basiliko, N., and Nemergut, D. R.: Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?, Front. Microbiol., 7, 214, https://doi.org/10.3389/fmicb.2016.00214, 2016.
Guerrieri, A, Bonin, A., Münkemüller, T., Gielly, L., Thuiller, W., and Ficetola, G. F.: Effects of soil preservation for biodiversity monitoring using environmental DNA, Mol. Ecol., 30, 3313–3325, https://doi.org/10.1111/mec.15674, 2020.
Hamer, U., Unger, M., and Makeschin, F.: Impact of air-drying and rewetting on PLFA profiles of soil microbial communities, J. Plant Nutr. Soil Sc., 170, 259–264, https://doi.org/10.1002/jpln.200625001, 2007.
Harry, M., Gambier, B., and Garnier-Sillam, E.: Soil conservation for DNA preservation for bacterial molecular studies, Eur. J Soil Biol., 36, 51–55, https://doi.org/10.1016/S1164-5563(00)00044-3, 2000.
Hill, G. T., Mitkowski, N. A., Aldrich-Wolfe, L., Emele, L. R., Jurkonie, D. D., Ficke, A., Maldonado-Ramirez, S., Lynch, S. T., and Nelson, E. B.: Methods for assessing the composition and diversity of soil microbial communities, Appl. Soil Ecol., 15, 25–36, https://doi.org/10.1016/S0929-1393(00)00069-X, 2000.
Hu, X., Jia, Z., Liu, J. Gu, H., Zhou, B., Wei, D., Jin, J., Liu, X., and Wang, G.: The preservation of bacterial community legacies in archived agricultural soils, Soil Till. Res., 231, 105739, https://doi.org/10.1016/j.still.2023.105739, 2023.
Ivarson, K. C. and Sowden, F. J.: Effect of frost action and storage of soil at freezing temperatures on the free amino acids, free sugars and respiratory activity, Can. J. Soil Sci., 50, 191–198, https://doi.org/10.4141/cjss70-027, 1970.
Jansson, J. K. and Tas, N.: The microbial ecology of permafrost, Nat. Rev. Microbiol., 12, 414–425, https://doi-org.inee.bib.cnrs.fr/10.1038/nrmicro3262, 2014.
Jones, A. R., Gupta, V. V. S. R., Buckley, S., Brackin, R., Schmidt, S., and Dalal, R. C.: Drying and rewetting effects on organic matter mineralisation of contrasting soils after 36 years of storage, Geoderma, 342, 12–19, https://doi.org/10.1016/j.geoderma.2019.01.053, 2019.
Kaiser, M., Kleber, M., and Berhe, A. A.: How air-drying and rewetting modify soil organic matter characteristics: An assessment to improve data interpretation and inference, Soil Biol. Biochem., 80, 324–340, https://doi.org/10.1016/j.soilbio.2014.10.018, 2015.
Kaneda, T.: Iso and antesio-fatty acids in bacteria: biosynthesis, function, and taxonomic significance, Microbiol Rev., 55, 288–302, https://doi.org/10.1128/mr.55.2.288-302.1991, 1991.
Karimi, B., Terrat, S., Dequiedt, S., Saby, N. P. A., Horrigue, W., Lelièvre, M., Nowak, V., Jolivet, C., Arrouays, D., Wincker, P., Cruaud, C., Bispo, A., Maron, P., Prévost-Bouré, N. C., and Ranjard, L.: Biogeography of soil bacteria and archaea across France, Sci. Adv., 4, 1–14, https://doi.org/10.1126/sciadv.aat1808, 2018.
Kühnel, A., Wiesmeier, M., Spörlein, P., Schilling, B., and Kögel-Knabner, I.: Influence of drying vs. freezing of archived soil samples on soil organic matter fractions, J. Plant Nutr. Soil Sc., 182, 772–781, https://doi.org/10.1002/jpln.201800529, 2019.
Kushwaha, P., Soto Velazquez, A. L., McMahan, C., and Neilson, J.: Field to greenhouse: How stable is the soil microbiome after removal from the field?, Microorganisms, 12, 110, https://doi.org/10.3390/microorganisms12010110, 2024.
Lane, J. M., Delavaux, C. S., Van Koppen, L., Lu, P., Cade-Menum, B. J., Tremblay, J., and Bainard, L. D.: Soil sample storage conditions impact extracellular enzyme activity and bacterial amplicon diversity metrics in a semi-arid ecosystem, Soil Biol. Biochem., 175, 108858, https://doi.org/10.1016/j.soilbio.2022.108858, 2022.
Lauber, C. L., Zhou, N., Gordon, J. I., Knight, R., and Fierer, N.: Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples: Influence of short-term storage conditions on microbiota, FEMS Microbiol. Lett., 307, 80–86, https://doi.org/10.1111/j.1574-6968.2010.01965.x, 2010.
Lee, J. S., Daniels, B. L., Eberiel, D. T., and Farrell, R. E.: Polymer mineralization in soils: Effects of cold storage on microbial populations and biodegradation potential, J. Polym. Environ., 8, 81–89, https://doi.org/10.1023/A:1011522004419, 2000.
Lee, Y. B., Lorenz, N., Dick, L. K., and Dick, R. P.: Cold storage and pretreatment incubation effects on soil microbial properties, Soil Sci. Soc. Am. J., 71, 1299–1305, https://doi.org/10.2136/sssaj2006.0245, 2007.
Liu, Y., Yao, H., and Huang, C.: Assessing the effect of air-drying and storage on microbial biomass and community structure in paddy soils, Plant Soil, 317, 213–221, https://doi.org/10.1007/s11104-008-9803-1, 2009.
Luo, J., White, R. E., Ball, P. R., and Tillman, R. W.: Measuring denitrification activity in soils under pasture: Optimizing conditions for the short-term denitrification enzyme assay and effects of soil storage on denitrification activity, Soil Biol. Biochem., 28, 409–417, https://doi.org/10.1016/0038-0717(95)00151-4, 1996.
Makarov, M. I., Mulyukova, O. S., Malysheva, T. I., and Menyailo, O. V.: Influence of drying of the samples on the transformation of nitrogen and carbon compounds in mountain-meadow alpine soils, Eurasian Soil Sci., 46, 778–787, https://doi.org/10.1134/S1064229313070053, 2013.
Manter, D. K., Delgado, J. A., Blackburn, H. D., Harmel, D., Perez de Leon, A. A., and Honeycutt, C. W.: Why we need a national living soil repository, P. Natl. Acad. Sci. USA, 114, 13587–13590, https://doi.org/10.1073/pnas.1720262115, 2017.
Martí, E., Càliz, J., Montserrat, G., Garau, M. A., Cruañas, R., Vila, X., and Sierra, J.: Air-drying, cooling and freezing for soil sample storage affects the activity and the microbial communities from two mediterranean soils, Geomicrobiol. J., 29, 151–160, https://doi.org/10.1080/01490451.2010.530341, 2012.
Maslov, M. N., Maslova, O. A., and Tokareva, O. A.: Changes in labile and microbial pools of carbon and nitrogen in forest litter samples under different methods of storage, Eurasian Soil Sci., 52, 747–755, https://doi.org/10.1134/S106422931907010X, 2019.
Mazur, P.: Freezing of living cells: mechanisms and implications, Am. J. Physiol., 247, C125–C142, https://doi.org/10.1152/ajpcell.1984.247.3.C125, 1984.
Meisner, A., Baath, E., and Rousk, J.: Microbial growth response upon rewetting soil dried for four days or one year, Soil Biol. Biochem., 66, 188–192, https://doi.org/10.1016/j.soilbio.2013.07.014, 2013.
Meisner, A., Snoek, B. L., Nesme, J., Dent, E., Jacquiod, S., Classen, A. T., and Priemé, A.: Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles, ISME J., 15, 1207–1221, https://doi.org/10.1038/s41396-020-00844-3, 2021.
Meyer, N., Welp, G., and Amelung, W.: Effects of sieving and sample storage on soil respiration and its temperatire sensitivity (Q10) in mineral soils from Germany, Biol. Fert. Soils, 55, 825–832, https://doi.org/10.1007/s00374-019-01374-7, 2019.
Moreira, R. S., Chiba, M. K., Nunes, S. B., and de Maria, I. C.: Air-drying pretreatment effect on soil enzymatic activity, Plant Soil Environ., 63, 29–33, https://doi.org/10.17221/656/2016-PSE, 2017.
Moy, A. and Nkongolo, K.: Variation in microbial biomass and enzymatic activities in metal contaminated soils during storage at low temperature (4 °C), Chem. Ecol., 39, 688–709, https://doi.org/10.1080/02757540.2023.2253222, 2023.
Nannipieri, P., Ascher, J., Ceccherini, M. T., Landi, L., Pietramellara, G., and Renella, G.: Microbial diversity and soil functions, Eur. J. Soil Sci., 54, 655–670, https://doi.org/10.1111/ejss.4_12398, 2003.
Nicholson, P. B.: Storage of soils for direct microbial counts, Plant Soil, 36, 235–237, https://doi.org/10.1007/BF01373477, 1972.
Patten, D. K., Bremner, J. M., and Blackmer, A. M.: Effects of drying and air-dry storage of soils on their capacity for denitrification of nitrate, Soil Sci. Soc. Am. J., 44, 67–70, https://doi.org/10.2136/sssaj1980.03615995004400010015x, 1980.
Peoples, M. S. and Koide, R. T.: Considerations in the storage of soil samples for enzyme activity analysis, Appl. Soil Ecol., 62, 98–102, https://doi.org/10.1016/j.apsoil.2012.08.002, 2012.
Pesaro, M., Widmer, F., Nicollier, G., and Zeyer, J.: Effects of freeze-thaw stress during soil storage on microbial communities and methidathion degradation, Soil Biol. Biochem., 35, 1049–1061, https://doi.org/10.1016/S0038-0717(03)00147-0, 2003.
Petersen, S. O. and Klug, M. J.: Effects of sieving, storage, and incubation temperature on the phospholipid fatty acid profiles of a soil microbial community, Appl. Environ. Microb., 60, 2421–2430, https://doi.org/10.1128/AEM.60.7.2421-2430.1994, 1994.
Ramirez, M., Munoz, A., Lopez-Piniero, A., Albarran, A., Pena, D., Nunes, J. M. R., Gama, J., and Loures, L.: Evaluation of the microbial viability of soil samples from maize crops in freeze-storage under different management conditions in semi-arid climate, Sustainability, 9, 690, https://doi.org/10.3390/su9050690, 2017.
Rhymes, J. M., Cordero, I., Chomel, M., Lavallee, J. M., Straathof, A. L., Ashworth, D., Langridge, H., Semchenko, M., de Vries, F. T., Johnson, D., and Bardgett, R. D.: Are researchers following best storage practices for measuring soil biochemical properties?, SOIL, 7, 95–106, https://doi.org/10.5194/soil-7-95-2021, 2021.
Riepert, F. and Felgentreu, D.: Relevance of soil storage to biomass development, N-mineralisation and microbial activity using the higher plant growth test, ISO 11269-2, for testing of contaminated soils, Appl. Soil Ecol., 20, 57–68, https://doi.org/10.1016/S0929-1393(02)00006-9, 2002.
Ross, D. J.: Microbial biomass in a stored soil: A comparison of different estimation procedure, Soil Biol. Biochem., 23, 1005–1007, https://doi.org/10.1016/0038-0717(91)90183-K, 1991.
Ross, D. J., Tate, K. R., Cairns, A., and Meyrick, K. F.: Influence of storage on soil microbial biomass estimated by three biochemical procedures, Soil Biol. Biochem., 12, 369–374, https://doi.org/10.1016/0038-0717(80)90012-7, 1980.
Rubin, B. E. R., Gibbons, S. M., Kennedy, S., Hampton-Marcell, J., Owens, S., and Gilbert, J. A.: Investigating the impact of storage conditions on microbial community composition in soil samples, PLoS ONE, 8, e70460, https://doi.org/10.1371/journal.pone.0070460, 2013.
Schimel, J. P.: Life in dry soils: Effects of drought on soil microbial communities and processes, Annu. Rev. Ecol. Evol. S., 49, 409–432, https://doi.org/10.1146/annurev-ecolsys-110617-062614, 2018.
Schnecker, J., Wild, B., Fuchslueger, L., and Richter, A.: A field method to store samples from temperate mountain grassland soils for analysis of phospholipid fatty acids, Soil Biol. Biochem., 51, 81–83, https://doi.org/10.1016/j.soilbio.2012.03.029, 2012.
Schroeder, J., Kammann, L., Helfrich, M., Tebbe, C. C., and Poeplau, C.: Impact of common sample pre-treatments on key soil microbial properties, Soil Biol. Biochem, 160, 108321, https://doi.org/10.1016/j.soilbio.2021.108321, 2021.
Schutter, M. E. and Dick, R. P.: Comparison of fatty acid methyl ester (FAME) methods for characterizing microbial communities, Soil Sci. Soc. Am. J., 64, 1659–1668, https://doi.org/10.2136/sssaj2000.6451659x, 2000.
Sheppard, S. C. and Addison, J. A.: Soil sample handling and storage, in: Soil Sampling Methods of Analysis – Second Edition, edited by: Carter, M. R. and Gregorich, E. G., Canadian Society of Soil Science, CRC Press, ISBN 9780849335860, 2007.
Shishido, M. and Chanway, C. P.: Storage effects on indigenous soil microbial communities and PGPR efficacy, Soil Biol. Biochem., 30, 939–947, https://doi.org/10.1016/S0038-0717(97)00184-3, 1998.
Simek, M.: Changes in potential denitrification and respiration during the cold storage of soils, Folia Microbiol., 45, 187–190, https://doi.org/10.1007/BF02817422, 2000.
Simek, M. and Santruckova, H.: Influence of storage of soil samples on microbial biomass and its activity, Rost. Vyroba, 45, 415–419, 1999.
Sirois, S. H. and Buckley, D. H.: Factors governing extracellular DNA degradation dynamics in soil, Env. Microbiol. Rep., 11, 173–184, https://doi.org/10.1111/1758-2229.12725, 2019.
Smenderovac, E., Emilson, C., Rheault, K., Brazeau, E., Morency, M.-J., Gagné, P., Venier, L., and Martineau, C.: Drying as an effective method to store soil samples for DNA-based microbial community analyses: a comparative study, Sci. Rep., 14, 1725, https://doi.org/10.1038/s41598-023-50541-2, 2024.
Sparling, G. P. and Cheshire, M. V.: Effects of soil drying and storage on subsequent microbial-growth, Soil Biol. Biochem., 11, 317–319, https://doi.org/10.1016/0038-0717(79)90079-8, 1979.
Speir, T. W. and Ross, D., J.: A comparison of the effects of air-drying and acetone dehydration on soil enzyme activities, Soil Biol. Biochem., 13, 225–229, https://doi.org/10.1016/0038-0717(81)90025-0, 1981.
Stenberg, B., Johansson, M., Pell, M. Sjödahl-Svensson, K., Stenström, J., and Torstensson, L.: Microbial biomass and activities in soil as affected by frozen and cold storage, Soil Biol. Biochem., 30, 393–402, https://doi.org/10.1016/S0038-0717(97)00125-9, 1998.
Stotzky, G., Goos, R. D., and Timonin, M. I.: Microbial changes occurring in soil as a result of storage, Plant Soil, 16, 1–18, https://doi.org/10.1007/BF01378154, 1962.
Sun, S.-Q., Cai, H.-Y., Chang, S. X., and Bhatti, J. S.: Sample storage-induced changes in the quantity and quality of soil labile organic carbon, Sci. Rep., 5, 174976, https://doi.org/10.1038/srep17496, 2015.
Tabatabai, M. A. and Bremner, J. M.: Factors affecting soil arylsulfatase activity, Soil Sci. Soc. Am. J., 34, 427, https://doi.org/10.2136/sssaj1970.03615995003400030023x, 1970.
Tatangelo, V., Franzetti, A., Gandolfi, I., Bestetti, G., and Ambrosini, R.: Effect of preservation method on the assessment of bacterial community structure in soil and water samples, FEMS Microbiol. Lett., 356, 32–38, https://doi.org/10.1111/1574-6968.12475, 2014.
Tate, K. T. and Jenkinson, D. S.: Adenosine triphosphate (ATP) and microbial biomass in soil: Effects of storage at different temperatures and at different moisture levels, Commun. Soil Sci. Plan., 13, 899–908, https://doi.org/10.1080/00103628209367319, 2008.
Trabue, S. L., Palmquist, D. E., Lydick, T. M., and Singles, S. K.: Effects of soil storage on the microbial community and degradation of metsulfuron-methyl, J. Agr. Food Chem., 54, 142–151, https://doi.org/10.1021/jf0512048, 2006.
Turner, B. L. and Romero, T. E.: Stability of hydrolytic enzyme activity and microbial phosphorus during storage of tropical rain forest soils, Soil Biol. Biochem., 42, 459–465, https://doi.org/10.1016/j.soilbio.2009.11.029, 2010.
Tzeneva, V. A., Salles, J. F., Naumova, N., de Vos, W. M., Kuikman, P. J., Dolfing, J., and Smidt, H.: Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity, Res. Microbiol., 160, 89–98, https://doi.org/10.1016/j.resmic.2008.12.001, 2009.
Verchot, L. V.: Cold storage of a tropical soil decreases nitrification potential, Soil Sci. Soc. Am. J., 63, 1942–1944, https://doi.org/10.2136/sssaj1999.6361942x, 1999.
Veum, K. S., Lorenz, T., and Kremer, R. J.: Phospholipid fatty acid profiles of soils under variable handling and storage conditions, Agron. J., 111, 1090–1096, https://doi.org/10.2134/agronj2018.09.0628, 2019.
Villada, A., Vanguelova, E. I., Verhoef, A., and Shaw L. J.: Effect of air-drying pre-treatment on the characterization of forest carbon pools, Geoderma, 265, 53–61, https://doi.org/10.1016/j.geoderma.2015.11.003, 2016.
Wagg, C., Schlaeppi, K., Banerjee, S., Kuramae, E. E., and van der Heijden, M. G. A.: Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning, Nat. Commun., 10, 4841, https://doi.org/10.1038/s41467-019-12798-y, 2019.
Wakelin, S., Lombi, E., Donner, E., MacDonald, L., Black, A., and O'Callaghan, M.: Application of MicroResp™ for soil ecotoxicology, Environ. Pollut., 179, 177–184, https://doi.org/10.1016/j.envpol.2013.04.010, 2013.
Wallenius, K., Rita, H., Simpanen, S., Mikkonen, A., and Niemi, R. M.: Sample storage for soil enzyme activity and bacterial community profiles, J. Microbiol. Meth., 8, 48–55, https://doi.org/10.1016/j.mimet.2010.01.021, 2010.
Wang, J., Chapman, S. J., and Yao, H.: The effect of storage on microbial activity and bacterial community structure of drained and flooded paddy soil, J. Soil. Sediment., 15, 880–889, https://doi.org/10.1007/s11368-014-1053-7, 2015.
Wang, F., Che, R., Deng, Y., Wu, Y., Tang, L., Xu, Z., Wang, W., Liu, H., and Cui, X.: Air-drying and long time preservation of soil do not significantly impact microbial community composition and structure, Soil Biol. Biochem., 157, 108238, https://doi.org/10.1016/j.soilbio.2021.108238, 2021.
Wang, Y., Hayatsu, M., and Fujii, T.: Extraction of bacterial RNA from soil: Challenges and solutions, Microbes Environ., 27, 111–121, https://doi.org/10.1264/jsme2.ME11304, 2012.
Weißbecker, C., Buscot, F., and Wubet, T.: Preservation of nucleic acids by freeze-drying for next generation sequencing analyses of soil microbial communities, J. Plant Ecol., 10, 81–90, https://doi.org/10.1093/jpe/rtw042, 2017.
West, A. W., Ross, D. J., and Cowling, J. C.: Changes in microbial C, N, P and ATP contents, numbers and respiration on storage of soil, Soil Biol. Biochem., 18, 141–148, https://doi.org/10.1016/0038-0717(86)90018-0, 1986.
West, A. W., Sparling, G. P., Feltham, C. W., and Reynolds, J.: Microbial activity and survival in soils dried at different rates, Austr. J. Soil Res., 30, 209–222, https://doi.org/10.1071/SR9920209, 1992.
Wingfield, G. I.: Effects of time of soil collection and storage on microbial decomposition of cellulose in soil, B. Environ. Contam. Tox., 24, 671–675, https://doi.org/10.1007/BF01608172, 1980.
Włodarczyk, T., Szarlip, P., Kozieł, W., Nosalewicz, M., Brzezińska, M., Pazur, M., and Urbanek, E.: Effect of long storage and soil type on the actual denitrification and denitrification capacity to N2O formation, Int. Agrophys., 28, 371–381, https://doi.org/10.2478/intag-2014-0027, 2014.
Wu, Y., Ding, N., Wang, G., Xu, J., Wu, J., and Brookes, P. C.: Effects of different soil weights, storage times and extraction methods on soil phospholipid fatty acid analyses, Geoderma, 150, 171–178, https://doi.org/10.1016/j.geoderma.2009.02.003, 2009.
Yoshikura, J., Hayano, K., and Tsuru, S.: Effects of drying and preservation on β-glucosidases in soil, Soil Sci. Plant Nutr., 26, 37–42, https://doi.org/10.1080/00380768.1980.10433210, 1980.
Zantua, M. I. and Bremner, J. M.: Stability of urease in soils, Soil Biol. Biochem., 9, 135–140, https://doi.org/10.1016/0038-0717(77)90050-5, 1977.
Zorzona, R., Guerrero, C., Mataix-Solera, J., Arcenegui, V., Garcia-Orenes, F., Mataix-Beneyto, J.: Assessing air-drying and rewetting pre-treatment effect on some soil enzyme activities under Mediterranean conditions, Soil Biol. Biochem., 38, 2125–2134, https://doi.org/10.1016/j.soilbio.2006.01.010, 2006.
Zorzona, R., Guerrero, C., Mataix-Solera, J., Arcenegui, V., Garcia-Orenes, F., and Mataix-Beneyto, J.: Assessing the effects of air-drying and rewetting pre-treatment on soil microbial biomass, basal respiration, metabolic quotient and soluble carbon under Mediterranean conditions, Eur. J. Soil Biol., 43, 120–129, https://doi.org/10.1016/j.ejsobi.2006.11.004, 2007.
Zorzona, R., Mataix-Solera, Guerrero, C., J., Arcenegui, V., and Mataix-Beneyto, J.: Storage effects on biochemical properties of air-dried soil samples from Southeastern Spain, Arid Land Res. Manag., 23, 213–222, https://doi.org/10.1080/15324980903038727, 2009.
Short summary
Despite the massive use of soil storage, its impact on soil microbial parameters (SMPs) has been assessed in a very scattered way. I analysed 73 research articles dealing with the impact of storage practices on various SMPs. The results show significant effects of all storage practices on SMPs in a vast majority of cases. Storage practices should be carefully selected according to the conditions that prevail in the native soil environment and to the SMPs of interest.
Despite the massive use of soil storage, its impact on soil microbial parameters (SMPs) has been...
