Articles | Volume 2, issue 4
https://doi.org/10.5194/soil-2-499-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/soil-2-499-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Original research article
| 
04 Oct 2016
Original research article |
| 04 Oct 2016
Enzymatic biofilm digestion in soil aggregates facilitates the release of particulate organic matter by sonication
Frederick Büks
CORRESPONDING AUTHOR
Chair of Soil Science, Department of Ecology, Technische
Universität Berlin, Berlin, Germany
Martin Kaupenjohann
Chair of Soil Science, Department of Ecology, Technische
Universität Berlin, Berlin, Germany
Related authors
Frederick Büks, Sabine Dumke, and Julia König
EGUsphere, https://doi.org/10.5194/egusphere-2025-771, https://doi.org/10.5194/egusphere-2025-771, 2025
This preprint is open for discussion and under review for Biogeosciences (BG).
Short summary
Short summary
Ultrasonication followed by density fractionation is a frequently used method to determine soil structural stability and the amount of occluded particulate organic matter. Our analyses of three sandy, silty and loamy soils showed that air-drying and gentle rewetting changes SOM fractions depending on the subsequent time of reincubation compared to field-fresh samples. This is important, since e.g. the measurement of archived soils require the handling of air-dried samples.
Frederick Büks
Biogeosciences, 20, 1529–1535, https://doi.org/10.5194/bg-20-1529-2023, https://doi.org/10.5194/bg-20-1529-2023, 2023
Short summary
Short summary
Ultrasonication with density fractionation of soils is a commonly used method to separate soil organic matter pools, which is, e.g., important to calculate carbon turnover in landscapes. It is shown that the approach that merges soil and dense solution without mixing has a low recovery rate and causes co-extraction of parts of the retained labile pool along with the intermediate pool. An alternative method with high recovery rates and no cross-contamination was recommended.
Frederick Büks and Martin Kaupenjohann
SOIL, 8, 373–380, https://doi.org/10.5194/soil-8-373-2022, https://doi.org/10.5194/soil-8-373-2022, 2022
Short summary
Short summary
The adverse effect of microplastic (MP) on soil biota and soil structure depends on MP particle size and surface characteristics. Since weathering plays a major role in the genesis of these, it must be considered in both the analysis of environmental MP and the production of artificial MP for laboratory experiments. This work integrates recent findings on adverse effects and the genesis of its surface characteristics and discusses how to reproduce them to obtain closer-to-nature designer MP.
Frederick Büks, Gilles Kayser, Antonia Zieger, Friederike Lang, and Martin Kaupenjohann
Biogeosciences, 18, 159–167, https://doi.org/10.5194/bg-18-159-2021, https://doi.org/10.5194/bg-18-159-2021, 2021
Short summary
Short summary
Ultrasonication/density fractionation is a common method used to extract particulate organic matter (POM) and, recently, microplastic (MP) from soil samples. In this study, ultrasonic treatment with mechanical stress increasing from 0 to 500 J mL−1 caused comminution and a reduced recovery rate of soil-derived POMs but no such effects with MP particles. In consequence, the extraction of MP from soils is not affected by particle size and recovery rate artifacts.
Frederick Büks and Martin Kaupenjohann
SOIL, 6, 649–662, https://doi.org/10.5194/soil-6-649-2020, https://doi.org/10.5194/soil-6-649-2020, 2020
Short summary
Short summary
Laboratory experiments that assess microplastic (MP) impact on the terrestrial environment require information on common soil MP concentrations. We reviewed item numbers and mass concentrations recorded in 23 studies, with 223 sampling sites in total with respect to the underlying entry pathways, land uses and vicinities. Common values included amounts of up to 13 000 items kg−1 and 4.5 mg kg−1 dry soil. Based on the collected data, we identified problems in past field studies.
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
Short summary
Short summary
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.
Frederick Büks, Philip Rebensburg, Peter Lentzsch, and Martin Kaupenjohann
SOIL Discuss., https://doi.org/10.5194/soil-2016-73, https://doi.org/10.5194/soil-2016-73, 2016
Revised manuscript has not been submitted
Short summary
Short summary
Microbial communities play a role in soil aggregate formation. However, the influence of the microbial community structure on POM occlusion within soil aggregates is still unproved. In this experiment, sterile sandy agricultural soil was incubated in two variants – inoculated with soil extract and infected with air-born microorganisms. After 76 days of incubation soils show a strongly differing microbial populations structure, but no significant difference in POM occlusion.
Frederick Büks, Philip Rebensburg, Peter Lentzsch, and Martin Kaupenjohann
SOIL Discuss., https://doi.org/10.5194/soil-2016-14, https://doi.org/10.5194/soil-2016-14, 2016
Revised manuscript not accepted
Short summary
Short summary
Soil microbial biofilms are supposed to increase agglomeration of soil particles and therefore reduce erodibility. After inoculation with two strongly differing microbial communities, a sandy agricultural soil did not develop significant differences in aggregate stability. This leads to the assumption that mechanical properties of biofilms do not vary considerably across different biological/chemical compositions, which implies that aggregate stability is a resilient factor of soil fertility.
Frederick Büks, Sabine Dumke, and Julia König
EGUsphere, https://doi.org/10.5194/egusphere-2025-771, https://doi.org/10.5194/egusphere-2025-771, 2025
This preprint is open for discussion and under review for Biogeosciences (BG).
Short summary
Short summary
Ultrasonication followed by density fractionation is a frequently used method to determine soil structural stability and the amount of occluded particulate organic matter. Our analyses of three sandy, silty and loamy soils showed that air-drying and gentle rewetting changes SOM fractions depending on the subsequent time of reincubation compared to field-fresh samples. This is important, since e.g. the measurement of archived soils require the handling of air-dried samples.
Frederick Büks
Biogeosciences, 20, 1529–1535, https://doi.org/10.5194/bg-20-1529-2023, https://doi.org/10.5194/bg-20-1529-2023, 2023
Short summary
Short summary
Ultrasonication with density fractionation of soils is a commonly used method to separate soil organic matter pools, which is, e.g., important to calculate carbon turnover in landscapes. It is shown that the approach that merges soil and dense solution without mixing has a low recovery rate and causes co-extraction of parts of the retained labile pool along with the intermediate pool. An alternative method with high recovery rates and no cross-contamination was recommended.
Frederick Büks and Martin Kaupenjohann
SOIL, 8, 373–380, https://doi.org/10.5194/soil-8-373-2022, https://doi.org/10.5194/soil-8-373-2022, 2022
Short summary
Short summary
The adverse effect of microplastic (MP) on soil biota and soil structure depends on MP particle size and surface characteristics. Since weathering plays a major role in the genesis of these, it must be considered in both the analysis of environmental MP and the production of artificial MP for laboratory experiments. This work integrates recent findings on adverse effects and the genesis of its surface characteristics and discusses how to reproduce them to obtain closer-to-nature designer MP.
Frederick Büks, Gilles Kayser, Antonia Zieger, Friederike Lang, and Martin Kaupenjohann
Biogeosciences, 18, 159–167, https://doi.org/10.5194/bg-18-159-2021, https://doi.org/10.5194/bg-18-159-2021, 2021
Short summary
Short summary
Ultrasonication/density fractionation is a common method used to extract particulate organic matter (POM) and, recently, microplastic (MP) from soil samples. In this study, ultrasonic treatment with mechanical stress increasing from 0 to 500 J mL−1 caused comminution and a reduced recovery rate of soil-derived POMs but no such effects with MP particles. In consequence, the extraction of MP from soils is not affected by particle size and recovery rate artifacts.
Frederick Büks and Martin Kaupenjohann
SOIL, 6, 649–662, https://doi.org/10.5194/soil-6-649-2020, https://doi.org/10.5194/soil-6-649-2020, 2020
Short summary
Short summary
Laboratory experiments that assess microplastic (MP) impact on the terrestrial environment require information on common soil MP concentrations. We reviewed item numbers and mass concentrations recorded in 23 studies, with 223 sampling sites in total with respect to the underlying entry pathways, land uses and vicinities. Common values included amounts of up to 13 000 items kg−1 and 4.5 mg kg−1 dry soil. Based on the collected data, we identified problems in past field studies.
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
Short summary
Short summary
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.
Lisa Thieme, Daniel Graeber, Diana Hofmann, Sebastian Bischoff, Martin T. Schwarz, Bernhard Steffen, Ulf-Niklas Meyer, Martin Kaupenjohann, Wolfgang Wilcke, Beate Michalzik, and Jan Siemens
Biogeosciences, 16, 1411–1432, https://doi.org/10.5194/bg-16-1411-2019, https://doi.org/10.5194/bg-16-1411-2019, 2019
Short summary
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To improve our understanding of the effects of tree species selection and management intensity on dissolved organic matter (DOM), we studied solution samples along the water flow path through forests with spectroscopic methods and biodegradation tests. There are distinct changes in DOM composition and biodegradability following the water path. Aboveground DOM was influenced by tree species selection but not by management intensity. Differences became aligned in mineral soil.
Antonia Zieger, Klaus Kaiser, Pedro Ríos Guayasamín, and Martin Kaupenjohann
Biogeosciences, 15, 2743–2760, https://doi.org/10.5194/bg-15-2743-2018, https://doi.org/10.5194/bg-15-2743-2018, 2018
Short summary
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We tested a current theory, which proposes an upper limit for organic carbon (OC) stocks independent of increasing carbon input for a soil with already large OC stocks. The soil received a large additional carbon input as sawdust. In response, only the OC stock in 25–50 cm depth increased significantly. We assume, that due to saturation in 0–25 cm, added OC migrates downwards and becomes retained in 25–50 cm. This indicates the possibility to sustainably increase already large OC stocks further.
Frederick Büks, Philip Rebensburg, Peter Lentzsch, and Martin Kaupenjohann
SOIL Discuss., https://doi.org/10.5194/soil-2016-73, https://doi.org/10.5194/soil-2016-73, 2016
Revised manuscript has not been submitted
Short summary
Short summary
Microbial communities play a role in soil aggregate formation. However, the influence of the microbial community structure on POM occlusion within soil aggregates is still unproved. In this experiment, sterile sandy agricultural soil was incubated in two variants – inoculated with soil extract and infected with air-born microorganisms. After 76 days of incubation soils show a strongly differing microbial populations structure, but no significant difference in POM occlusion.
Lisa Thieme, Daniel Graeber, Martin Kaupenjohann, and Jan Siemens
Biogeosciences, 13, 4697–4705, https://doi.org/10.5194/bg-13-4697-2016, https://doi.org/10.5194/bg-13-4697-2016, 2016
Short summary
Short summary
Freezing can affect dissolved organic matter properties and concentrations. Nevertheless, water samples are regularly frozen for sample preservation. To test, if fast-freezing with liquid nitrogen instead of normal freezing at −18 °C can prevent changes in DOM characteristics, we compared fresh and differently frozen terrestrial water samples. We found that fast-freezing with liquid nitrogen can prevent bulk organic matter concentrations but not its spectroscopic properties.
Ariane Krause, Thomas Nehls, Eckhard George, and Martin Kaupenjohann
SOIL, 2, 147–162, https://doi.org/10.5194/soil-2-147-2016, https://doi.org/10.5194/soil-2-147-2016, 2016
Short summary
Short summary
In a field experiment in Tanzania, we used substrates from local projects as soil amenders for intercropping relevant local crops, aiming to advance the practical application of known principles for smallholder agriculture in SSA, i.e. biochar and biogas application and EcoSan practices. We studied the short-term effects on crop productivity, plant nutrition and soil properties. By mitigating P scarcity and acidification, yields were increased by up to 400 % compared to the control.
Frederick Büks, Philip Rebensburg, Peter Lentzsch, and Martin Kaupenjohann
SOIL Discuss., https://doi.org/10.5194/soil-2016-14, https://doi.org/10.5194/soil-2016-14, 2016
Revised manuscript not accepted
Short summary
Short summary
Soil microbial biofilms are supposed to increase agglomeration of soil particles and therefore reduce erodibility. After inoculation with two strongly differing microbial communities, a sandy agricultural soil did not develop significant differences in aggregate stability. This leads to the assumption that mechanical properties of biofilms do not vary considerably across different biological/chemical compositions, which implies that aggregate stability is a resilient factor of soil fertility.
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We have started to address this issue because the application of wetting agents is very widespread within the European Union and is often considered desirable because it increases the effectiveness of pesticides. While pesticides are thoroughly tested for their impact on the environment as a whole, testing for the effects of wetting agents is minimal. Today, there is no research on their impact on the soil environment.
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Mario Kirchhoff, Tobias Romes, Irene Marzolff, Manuel Seeger, Ali Aït Hssaine, and Johannes B. Ries
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This study found that the influence of argan trees on soil properties in southern Morocco is mostly limited to the area covered by the tree crown. However, the tree influences the bare soil outside the crown positively in specific directions because wind and water can move litter and soil particles from under the tree to the areas between the trees. These findings, based on soil samples around argan trees, could help structure reforestation measures.
Florian Wilken, Peter Fiener, Michael Ketterer, Katrin Meusburger, Daniel Iragi Muhindo, Kristof van Oost, and Sebastian Doetterl
SOIL, 7, 399–414, https://doi.org/10.5194/soil-7-399-2021, https://doi.org/10.5194/soil-7-399-2021, 2021
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This study demonstrates the usability of fallout radionuclides 239Pu and 240Pu as a tool to assess soil degradation processes in tropical Africa, which is particularly valuable in regions with limited infrastructure and challenging monitoring conditions for landscape-scale soil degradation monitoring. The study shows no indication of soil redistribution in forest sites but substantial soil redistribution in cropland (sedimentation >40 cm in 55 years) with high variability.
Ming Lu, David S. Powlson, Yi Liang, Dave R. Chadwick, Shengbi Long, Dunyi Liu, and Xinping Chen
SOIL, 7, 333–346, https://doi.org/10.5194/soil-7-333-2021, https://doi.org/10.5194/soil-7-333-2021, 2021
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Land use changes are an important anthropogenic perturbation that can cause soil degradation, but the impacts of land conversion from growing cereals to vegetables have received little attention. Using a combination of soil analyses from paired sites and data from farmer surveys, we found significant soil degradation in intensive vegetable cropping under paddy rice–oilseed rape rotation in southwestern China. This study may alert others to the potential land degradation in the subtropics.
Claire Froger, Nicolas P. A. Saby, Claudy C. Jolivet, Line Boulonne, Giovanni Caria, Xavier Freulon, Chantal de Fouquet, Hélène Roussel, Franck Marot, and Antonio Bispo
SOIL, 7, 161–178, https://doi.org/10.5194/soil-7-161-2021, https://doi.org/10.5194/soil-7-161-2021, 2021
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Pollution of French soils by polycyclic aromatic hydrocarbons (PAHs), known as carcinogenic pollutants, was quantified in this work using an extended data set of 2154 soils sampled across France. The map of PAH concentrations in French soils revealed strong trends in regions with heavy industries and around cities. The PAH signatures indicated the influence of PAH emissions in Europe during the industrial revolution. Health risks posed by PAHs in soils were low but need to be considered.
Shixiu Zhang, Liang Chang, Neil B. McLaughlin, Shuyan Cui, Haitao Wu, Donghui Wu, Wenju Liang, and Aizhen Liang
SOIL, 7, 71–82, https://doi.org/10.5194/soil-7-71-2021, https://doi.org/10.5194/soil-7-71-2021, 2021
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Long-term conservation tillage results in more complex and heterogeneous activities of soil organisms relative to conventional tillage. This study used an energetic food web modelling approach to calculate the mineralized N delivered by the whole soil community assemblages and highlighted the essential role of soil food web complexity in coupling N mineralization and soybean yield after a 14-year application of conservation tillage in a black soil of Northeast China.
Florian Wilken, Michael Ketterer, Sylvia Koszinski, Michael Sommer, and Peter Fiener
SOIL, 6, 549–564, https://doi.org/10.5194/soil-6-549-2020, https://doi.org/10.5194/soil-6-549-2020, 2020
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Soil redistribution by water and tillage erosion processes on arable land is a major threat to sustainable use of soil resources. We unravel the role of tillage and water erosion from fallout radionuclide (239+240Pu) activities in a ground moraine landscape. Our results show that tillage erosion dominates soil redistribution processes and has a major impact on the hydrological and sedimentological connectivity, which started before the onset of highly mechanised farming since the 1960s.
José A. Gómez, Gema Guzmán, Arsenio Toloza, Christian Resch, Roberto García-Ruíz, and Lionel Mabit
SOIL, 6, 179–194, https://doi.org/10.5194/soil-6-179-2020, https://doi.org/10.5194/soil-6-179-2020, 2020
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The long-term evolution of soil organic carbon in an olive orchard (planted in 1856) was evaluated and compared to an adjacent undisturbed natural area. Total soil organic carbon in the top 40 cm of the soil in the orchard was reduced to 25 % of that in the undisturbed area. The deposition downslope in the orchard of sediment coming from the eroded upslope area did not increase the accumulation of organic carbon in soil, but it quadrupled available phosphorus and improved overall soil quality.
Donia Jendoubi, Hanspeter Liniger, and Chinwe Ifejika Speranza
SOIL, 5, 239–251, https://doi.org/10.5194/soil-5-239-2019, https://doi.org/10.5194/soil-5-239-2019, 2019
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This paper is original research done in north-western Tunisia; it presents the impacts of the topography (slope and aspect) and the land use systems in the SOC storage in a Mediterranean area. It provides a soil spectral library, describes the variation of SOC under different conditions, and highlights the positive impact of agroforestry as good management in improving the SOC. Therefore this finding is very important to support decision making and inform sustainable land management in Tunisia.
Tor-Gunnar Vågen, Leigh Ann Winowiecki, Constance Neely, Sabrina Chesterman, and Mieke Bourne
SOIL, 4, 259–266, https://doi.org/10.5194/soil-4-259-2018, https://doi.org/10.5194/soil-4-259-2018, 2018
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Land degradation impacts the health and livelihoods of about 1.5 billion people worldwide. The state of the environment and food security are strongly interlinked in tropical landscapes. This paper demonstrates the integration of soil organic carbon (SOC) and land health maps with socioeconomic datasets into an online, open-access platform called the Resilience Diagnostic and Decision Support Tool for Turkana County in Kenya.
Dick J. Brus and Jan J. H. van den Akker
SOIL, 4, 37–45, https://doi.org/10.5194/soil-4-37-2018, https://doi.org/10.5194/soil-4-37-2018, 2018
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Subsoil compaction is an important soil threat. It is caused by heavy machines used in agriculture. The aim of this study was to estimate how large the area with overcompacted subsoils is in the Netherlands. This was done by selecting locations randomly and determining the porosity and bulk density of the soil at these locations. It appeared that 43 % of the soils in the Netherlands is overcompacted, and so we conclude that subsoil compaction is indeed a serious problem in the Netherlands.
E. V. Taguas, C. Arroyo, A. Lora, G. Guzmán, K. Vanderlinden, and J. A. Gómez
SOIL, 1, 651–664, https://doi.org/10.5194/soil-1-651-2015, https://doi.org/10.5194/soil-1-651-2015, 2015
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Biodiversity indices for spontaneous grass cover were measured in two olive orchards in southern Spain with contrasting site conditions and management to evaluate their potential for biodiversity metrics of soil degradation. Biodiversity indices were relatively high for agricultural areas. No correlation between the biodiversity indicators and soil quality features were observed. The mere use of vegetation presence as a proxy might mask relative intense soil degradation processes.
A. Kaiser, F. Neugirg, F. Haas, J. Schmidt, M. Becht, and M. Schindewolf
SOIL, 1, 613–620, https://doi.org/10.5194/soil-1-613-2015, https://doi.org/10.5194/soil-1-613-2015, 2015
A. Ola, I. C. Dodd, and J. N. Quinton
SOIL, 1, 603–612, https://doi.org/10.5194/soil-1-603-2015, https://doi.org/10.5194/soil-1-603-2015, 2015
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Plant roots are crucial in soil erosion control. Moreover, some species respond to nutrient-rich patches by lateral root proliferation. At the soil surface dense mats of roots may block soil pores thereby limiting infiltration, enhancing runoff; whereas at depth local increases in shear strength may reinforce soils at the shear plane. This review considers the potential of manipulating plant roots to control erosion.
C. Castillo, M. R. James, M. D. Redel-Macías, R. Pérez, and J. A. Gómez
SOIL, 1, 583–594, https://doi.org/10.5194/soil-1-583-2015, https://doi.org/10.5194/soil-1-583-2015, 2015
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- We present SF3M, a new graphical user interface for implementing a complete 3-D photo-reconstruction workflow based on freely available software, in combination with a low-cost survey design for the reconstruction of a several-hundred-metres-long gully network.
- This methodology implied using inexpensive means, little manpower, in a short time span, being a promising tool for gully erosion evaluation in scenarios with demanding budget and time constraints and reduced operator expertise.
J. Casalí, R. Giménez, and M. A. Campo-Bescós
SOIL, 1, 509–513, https://doi.org/10.5194/soil-1-509-2015, https://doi.org/10.5194/soil-1-509-2015, 2015
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Despite gullies having been intensively studied in the past decades, there is no general consensus on such basic aspects as the correct determination of the geometry (width and depth) of these erosion features. Therefore, a measurement protocol is proposed to characterize the geometry of a gully by its effective width and effective depth, which, together with its length, would permit the definition of the equivalent prismatic gully (EPG); this would facilitate the comparison between gullies.
E. A. C. Costantini, A. E. Agnelli, A. Fabiani, E. Gagnarli, S. Mocali, S. Priori, S. Simoni, and G. Valboa
SOIL, 1, 443–457, https://doi.org/10.5194/soil-1-443-2015, https://doi.org/10.5194/soil-1-443-2015, 2015
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Earthworks carried out before planting a new vineyard caused, in the surface soil layer, an increase in lime and a decline in soil OC and N contents, along with a reduction in the abundance and diversity of microbial and mesofauna communities. Five years after the new vineyard establishment, soil was still far from its original quality and this limited vine development. The reduced OM input resulting from the management and the poor residue biomass was a major factor in delaying soil resilience.
J. P. van Leeuwen, D. Moraetis, G. J. Lair, J. Bloem, N. P. Nikolaidis, L. Hemerik, and P. C. de Ruiter
SOIL Discuss., https://doi.org/10.5194/soild-2-187-2015, https://doi.org/10.5194/soild-2-187-2015, 2015
Manuscript not accepted for further review
R. Zornoza, J. A. Acosta, F. Bastida, S. G. Domínguez, D. M. Toledo, and A. Faz
SOIL, 1, 173–185, https://doi.org/10.5194/soil-1-173-2015, https://doi.org/10.5194/soil-1-173-2015, 2015
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Short summary
Soil aggregate stability and POM occlusion are integral markers for soil quality. Besides physico-chemical interactions, biofilms are considered to aggregate primary particles, but experimental proof is still missing. In our experiment, soil aggregate samples were treated with biofilm degrading enzymes and showed a reduced POM occlusion and an increased bacteria DNA release compared with untreated samples. Thus, biofilms are assumed to be an important factor of POM occlusion in soil aggregates.
Soil aggregate stability and POM occlusion are integral markers for soil quality. Besides...
