DOI: 10.5061/dryad.70rxwdc72
title: Impact of soil inoculation on crop residue breakdown and carbon and nitrogen cycling in organically and conventionally managed agricultural soils

description: Organic agriculture relies on organic fertilizers and amendments to
 provide nutrients to plants and will therefore depend on decomposer
 communities to release nutrients from these organic inputs. However, after
 conversion of conventional to organic agriculture it may take up to
 decades before decomposer communities become adapted to the new resource
 inputs. The aim of the present study is to investigate if the functional
 capacity of soil communities for decomposing recalcitrant crop residue
 types can be enhanced by inoculating soil communities from organically
 into conventionally managed soils. We used a microcosm incubation
 experiment to test how soil inoculation, agricultural management history,
 and crop residue type affect carbon and nitrogen cycling with crop residue
 addition. We collected soil samples from 5 pairs of conventional and
 nearby organic fields and set up a reciprocal inoculation experiment under
 controlled lab conditions. We inoculated soil from each conventional field
 with soil from the paired organic field and vice versa. To each soil mix,
 five types of crop residues were added: a cover crop mixture, carrot
 leaves (Daucus carota), alfalfa (Medicago sativa), hay (Lolium perenne),
 and straw (Triticum aestivum). There was one control treatment without any
 addition. Soils were incubated for 34 days and we measured mass loss of
 the crop residues from litter bags, cumulative soil respiration,
 cumulative potential plant available nutrients, permanganate oxidizable
 carbon (POXC), and substrate-induced respiration (SIR). Initial soil
 abiotic conditions (soil organic matter content, pH, C:N ratio, plant
 available nutrients), soil microbial biomass and soil bacterial and fungal
 community composition were also determined. We did not find clear effects
 of inoculation on mass loss and cumulative respiration. Instead, effects
 of crop residue type on all parameters were substantial. Crop residues
 with higher C:N ratios generally had lower mass loss and cumulative
 respiration, and resulted in lower nitrogen availability but higher POXC
 contents. Organic management enhanced cumulative respiration. There was
 little overlap in bacterial and fungal ASVs between the organic and
 conventional soils within each pair, resulting in a potential increase in
 diversity as a result of soil inoculation. We conclude that decomposition
 of crop residues declined with their recalcitrance, and that soils from
 organically managed fields did not increase the capacity of the soil
 community to decompose recalcitrant residues. Further studies are needed
 to determine whether compositional differences between soils from organic
 and conventional fields are a response to farming practices or whether
 management also has functional implications for soil fertility.
description: We sampled ten fields in the east of the Netherlands. Five
 organic and five conventionally managed arable fields that were a
 subselection from the Chronosequence 2017 (sampled 1.5 years
 earlier). These soil samples are
 characterized. Then; we used these soils for an
 mesocosm incubation experiment; see material and methods section
 below. We set up a 34-day incubation experiment of
 soils from fields with contrasting arable management (organic vs
 conventional) and inoculated each soil with a 10% inoculum from the
 contrasting management regime. We then added plant residues ranging in
 recalcitrance (based on lignin content and C:N ratio) and measured litter
 mass loss, C respiration at different time points, and potential
 cumulative plant available nitrogen using resin bags. Before and directly
 after the experiment we determined permanganate-oxidizable carbon (POXC)
 as an indicator for carbon stabilization and substrate induced respiration
 (SIR) as a proxy for microbial biomass (Hurisso et al., 2016; Neely et
 al., 1991). We also characterized initial soil microbial communities by
 phospholipid fatty acids analysis (PLFA) and 16S and ITS
 metabarcoding. <strong>SOIL
 SAMPLING</strong> Soils were taken from sandy
 fields in the east of the Netherlands near Oploo and Deventer. Soils were
 classified as Anthrosols with a very low elutriable fraction and an
 A-horizon of at least 30cm. Gross coordinates can be found in table S1. We
 sampled 10 fields; 5 organic and 5 conventional which were paired. Soil
 cores (0-30 cm) were taken at 3 locations in each field with a minimum
 distance of 25 m between the cores and 10 m between the cores and the
 field border. Per field, cores were combined to a composite sample per
 field. Sampling depth was 0-30 cm. Soil was transported in a cooler box,
 stored at 4 °C, and sieved the day after collection (4 mm).
 <strong>EXPERIMENTAL SET-UP</strong>
 We used 500 mL air-tight pots with gas-sampling septa which were
 filled with 230 gram dry-weight equivalent soil. We had five replicated
 pairs of field fresh soil from the conventional field and the organic
 field. For both we created inoculation treatments by mixing soils within a
 pair from the contrasting management in ratio 1:9. The inoculation of
 conventional (10%) into organic soil was actually a control for
 inoculation, because we expected only an inoculation effect in
 conventional soils that were inoculated with organic soils.
 We added five types of crop residues to the soils, with a single
 residue per pot. In addition, for each inoculation treatment per field we
 had control pots where no crop residues were added. 5 replicates x 2
 management types x with/without inoculation x 5 substrates plus 1 control
 resulted in total in 120 pots. Crop residues that we used were a cover
 crop mixture, carrot leaves (Daucus carota), alfalfa (Medicago sativa),
 hay (Lolium perenne), straw (Triticum aestivum). We collected them from
 the shop, but the cover crop mixture was self-grown at the field. This was
 the TERRALIFE® - SOLARIGOL-mixture from DSV Zaden (DSV Zaden,
 Venzelderheide). The amount of residues added to each pot was standardized
 based on C content, with an addition of 1.04 gram C / 230 gram soil. To
 determine the C content of the crop residues we collected xxx subsamples
 for each residue, which were ground and measured for total C and N content
 using a CN elemental analyser (Interscience flashEA© 1112 series), after
 grinding using TissueLyser II (Qiagen, Hilden Germany). In total we added
 2.78 g carrot leaves (Daucus carota), 2.73 g cover crop mixture, 2.58
 alfalfa (Medicago sativa), 2.67 g hay (Lolium perenne) and 2.47 g wheat
 straw (Triticum aestivum). As the amount of added residue was standardized
 by carbon, amounts of added nitrogen varied between the crop residues and
 ranged from 0.013 for wheat straw to 0.116 gram for the cover mixture per
 pot (Table S2). Before the addition of the crop
 residues to the pots, all residues were cut into small pieces (5-10 mm).
 For all residues, 25% was put into a litter bag and the rest was mixed
 though the soil with a sterilized spoon. Litter bags were buried in the
 soils. Pots were places in an incubator at 18 °C and 65% water content in
 the dark for 34 days. We left the lids of the pot slightly open to prevent
 moisture loss, but allow gas diffusion. Pots were randomized.
 On days 1, 3, 4, 7, 10, 14, 23 and 32 we collected head space gas
 samples, to measure soil respiration. Before collecting the samples, we
 closed the lids for four hours. Then we took a 12 mL headspace gas sample
 using a syringe and 0.6mm needle. Samples were kept in pre-evacuated 6 ml
 exetainers. In each sample, the CO2 concentration was measured using a
 Trace GC ultra (Thermo Scientific, Waltham US). Cumulative potential plant
 available nitrogen was measured using resin bags that were buried in the
 pots and incubated during the whole experiment. Resin bags were
 constructed of nylon stockings, and contained 10 g of a 1:1 mixture of
 cation and anion exchange resins, preloaded with H+ and Cl-,
 respectively.
description: # Impact of soil inoculation on crop residue breakdown and carbon and
 nitrogen cycling in organically and conventionally managed agricultural
 soils
 [https://doi.org/10.5061/dryad.70rxwdc72](https://doi.org/10.5061/dryad.70rxwdc72) ## Description of the data and file structure This README_VRijsselKoorneef_2024_VitalSoilsChronosequencedataNIOO2017.txt file was generated on 2024-03-07 by Sophie Quirina van Rijssel GENERAL INFORMATION 1\. Title of Dataset: Vital Soils Inoculation decomposition experiment Conventional and Organic Agriculture 2019 2\. Author Information ``` A. Principal Investigator Contact Information Name: Sophie Q. van Rijssel Institution: Netherlands Institute of Ecology Current adress: PO box PO Box 47, 6700 AA, Wageningen, The Netherlands. sophie.vanrijssel@wur.nl B. Associate or Co-investigator Contact Information Name: Eva Kuipers contact: eva.kuipers@gmail.com C. Alternate Contact Information Name: Ciska Veen Institution: Netherlands Institute of Ecology Adress: PO box 50, 6700 AB 12 Wageningen, The Netherlands. Email: c.veen@nioo.knaw.nl ``` 3\. Date of data collection (single date, range, approximate date) : field visit (= soil collection) = Oktober 2018. Experiment ran till januari 2019 4\. Geographic location of data collection : Netherlands, near Oploo and Deventer 5\. Information about funding sources that supported the collection of the data: This work was funded by the Dutch Research Council (NWO-Groen ALWGR.2015.5). The data is gathered by Netherland Institute of Ecology (NIOO-KNAW) and Wageningen University and Research. **DATA & FILE OVERVIEW** Explanations of headers and units in the data file:  general points: ".start" indicates the status before experiment set-up which is actually fresh field measurement. This number is put in all treatments as the same, measurement was being done in triplo but the average was put in hte dataframe. Number : a unique number temake analyses easier. this is randomly assigned. Code : a unique numeric code that identifies the sample Field : Field where the sample was taken; this is an agricultural arable field located in the Netherlands managed by a farmer that applied either conventional or organic management FieldCode2017 : how the field is named in the "Vital Soils Chronosequence 2017" to be able to trace back. Substrate : The type of crop residue that was mixed with the soil. All where dried and cut into 1 cm pieces. ``` Cover crop = Cover crop mixture (DSV Terralife Solarigol) Carrot leaves = Carrot leaves (Daucus carota), bought from the supermarket Alfalfa = Alfalfa (Medicago sativa) Hay = Hay (Lolium perenne) Straw = Wheat straw (Triticum aestivum). ``` Management : Indicates whether the arable field was managed conventional or organically (according to Dutch SKAL regulations ([www.skal.nl](http://www.skal.nl)) which are in line with european legislation). (“Stichting Keur Alternatief voortgebrachte Landbouwproducten” which is translated as “Control authority for organic production”). Inoculation : treatment indicated whether there was soil added from the contrasting management or not replicate : Indicates whether it is the first, second, third, fourth of fifth pair of two fields (one conventional and one organically managed) Pair : identifies which conventional and organically fields are paired (conventional as reference fields of the organic fields). Organic.Soil.percentage : a different expression of management and inoculation. it indicates the % of organically managed soil ``` 0% = conventional soil 10% = 90% conventional soil with 10% inoculum of organic managed soil 90% = 90% organic soil with 10% inoculum of conventional managed soil (this is actually a double blind control since the interest is on whether convetional soil functioning can be enhanced. 100% = organically managed soil ``` Year : nr of years the organic fields received organic management pH : pH-water, measured on fresh soil, without unit. decimal = , CN.ratio_soil.start : Carbon : nitrogen element ratio, analysed using element analyzer, measured in the field soil that was first dried and grinded. Since it is a ratio is it without unit. P.Olsen.start : Stock P as measured in NaHCO3 measured in the field soil (indicated by .start), commonly known as P-Olsen. unit= [mg/kg] Bacterial.richness : Observed Amplicon sequencing variant richness for bacteria based on rarefied data from 16S. measured in the field soil. Bacterial.Shannon : Shannon diversity index for bacteria based on rarefied data from 16S. measured in the field soil. Bacterial.PLFAs : Sum of phospholipid fatty acid (PLFA) markers for bacteria. Measured in the field soil. (check paper method for markers) Fungal.richness : Observed Amplicon sequencing variant richness for fungi based on rarefied data from ITS. measured in the field soil. Fungal.Shannon : Shannon diversity index for for fungi based on rarefied data from ITS. measured in the field soil. Fungal.PLFA : Sum of phospholipid fatty acid (PLFA) markers for fungi. Measured in the field soil (check paper method for markers) SOM.start : Soil organic matter content measured in the field soil ``` Soil Organic matter, measured by loss of ignition (LOI). unit = fraction. See methods of paper for measurement details. ``` SOM.start.perc : see above, multiplied to get it in % instead of fraction POXC.start : permangate oxidizable carbon measured in the field soil unit = [gC/kg soil] Average POXC of pseudoreplicates 1 and 2 calculated via y=ax expressed on a soil weight basis POXC.end : permangate oxidizable carbon measured after the experiment unit = [gC/kg soil] Average POXC of pseudoreplicates 1 and 2 calculated via y=ax expressed on a soil weight basis SIR.start : Substrate Induced Respiration based on yeast extract. unit = [ug/g/day]. percentC.substrate: % carbon in the crop residue (measured as triplo in element analyzer, but averaged) percentN.substrate: % nitrogen in the crop residue (measured as triplo in element analyzer, but averaged) C.N.substrate: carbon-to-nitrogen ratio of the crop residues litter.weight.litterbag : amount of litter that was put inside the litterbag. unit = [gram] litter.weight.mixed.g : amount of litter that was mixed through the soil. unit = [gram] litter.weight.total : sum of weigth of litter inside and outside of litter bag. So it is the total of litter inside the meocosm unit = [gram] Mass.loss.perc : percentage of litter weight loss inside litter bag. gram.soil.in.pot : the amount of soil added in the microcosm. unit = [gram] percentN_soil.start : N content of the soil, measured by the element analyzer. unit = % no3.start : concentration of no3 in the field soil. Measured in kcl extract (see NIOO protocol). unit = [mg/kg] nh4.start : concentration of nh4 in the field soil. Measured in kcl extract (see NIOO protocol). unit = [mg/kg] no3.resin : amount of no3 that was taken up in the ion-exchange resin bag. This is cumulative over hte experiment and could be compared with potential plant available mineral nitrogen. Measured in kcl extract (see NIOO protocol). unit = [mg/L] nh4.resin : amount of nh4 that was taken up in the ion-exchange resin bag. This is cumulative over hte experiment and could be compared with potential plant available mineral nitrogen. Measured in kcl extract (see NIOO protocol). unit = [mg/L] percentC_soil.start : C content of the soil, measured by the element analyzer. unit = % respiration.day1 : Respiration measurement on first the day of incubation, after pots were air-closed for 4 hours. unit = [µg CO2-C/pot/h] respiration.day3 : Respiration measurement on day three of incubation, after pots were air-closed for 4 hours. unit = [µg CO2-C/pot/h] respiration.day4 : Respiration measurement on day four of incubation, after pots were air-closed for 4 hours. unit = [µg CO2-C/pot/h] respiration.day7 : Respiration measurement on day seven of incubation, after pots were air-closed for 4 hours. unit = [µg CO2-C/pot/h] respiration.day10 : Respiration measurement on day ten of incubation, after pots were air-closed for 4 hours. unit = [µg CO2-C/pot/h] respiration.day23 : Respiration measurement on day 23 of incubation, after pots were air-closed for 4 hours. unit = [µg CO2-C/pot/h] respiration.day32 : Respiration measurement on last the day of incubation. . Based on all respiration measurements cumulative respiration was calculated by taking into account the number of measurements and the time by making a figure and calculating the area below the line. unit = [µg CO2-C/pot/h] ### Files and variables #### File: CSV\_Inoculation\_Incubation\_Decomposition\_experiment\_Vital\_Soils\_Sophie\_2018.xlsx **Description:**  ##### Variables * Number : a unique number temake analyses easier. this is randomly assigned. * Code : a unique numeric code that identifies the sample * Field : Field where the sample was taken; this is an agricultural arable field located in the Netherlands managed by a farmer that applied either conventional or organic management * FieldCode2017 : how the field is named in the "Vital Soils Chronosequence 2017" to be able to trace back. * Substrate : The type of crop residue that was mixed with the soil. All where dried and cut into 1 cm pieces. * Cover crop = Cover crop mixture (DSV Terralife Solarigol) * Carrot leaves = Carrot leaves (Daucus carota), bought from the supermarket * Alfalfa = Alfalfa (Medicago sativa) * Hay = Hay (Lolium perenne) * Straw = Wheat straw (Triticum aestivum). * Management : Indicates whether the arable field was managed conventional or organically (according to Dutch SKAL regulations ([www.skal.nl](http://www.skal.nl)) which are in line with european legislation). (“Stichting Keur Alternatief voortgebrachte Landbouwproducten” which is translated as “Control authority for organic production”). * Inoculation : treatment indicated whether there was soil added from the contrasting management or not * replicate : Indicates whether it is the first, second, third, fourth of fifth pair of two fields (one conventional and one organically managed) * Pair : identifies which conventional and organically fields are paired (conventional as reference fields of the organic fields). * Organic.Soil.percentage : a different expression of management and inoculation. it indicates the % of organically managed soil * 0% = conventional soil * 10% = 90% conventional soil with 10% inoculum of organic managed soil * 90% = 90% organic soil with 10% inoculum of conventional managed soil (this is actually a double blind control since the interest is on whether convetional soil functioning can be enhanced. * 100% = organically managed soil * Year : nr of years the organic fields received organic management * pH : pH-water, measured on fresh soil, without unit. decimal = , * CN.ratio_soil.start : Carbon : nitrogen element ratio, analysed using element analyzer, measured in the field soil that was first dried and grinded. Since it is a ratio is it without unit. * P.Olsen.start : Stock P as measured in NaHCO3 measured in the field soil (indicated by .start), commonly known as P-Olsen. unit= [mg/kg] * Bacterial.richness : Observed Amplicon sequencing variant richness for bacteria based on rarefied data from 16S. measured in the field soil. * Bacterial.Shannon : Shannon diversity index for bacteria based on rarefied data from 16S. measured in the field soil. * Bacterial.PLFAs : Sum of phospholipid fatty acid (PLFA) markers for bacteria. Measured in the field soil. (check paper method for markers) * Fungal.richness : Observed Amplicon sequencing variant richness for fungi based on rarefied data from ITS. measured in the field soil. * Fungal.Shannon : Shannon diversity index for for fungi based on rarefied data from ITS. measured in the field soil. * Fungal.PLFA : Sum of phospholipid fatty acid (PLFA) markers for fungi. Measured in the field soil (check paper method for markers) * SOM.start : Soil organic matter content measured in the field soil. Soil Organic matter was measured by loss of ignition (LOI). unit = fraction.See methods of paper for measurement details. * SOM.start.perc : see above, multiplied to get it in % instead of fraction * POXC.start : permangate oxidizable carbon measured in the field soil unit = [gC/kg soil] Average POXC of pseudoreplicates 1 and 2 calculated via y=ax expressed on a soil weight basis POXC.end : permangate oxidizable carbon measured after the experiment unit = [gC/kg soil] Average POXC of pseudoreplicates 1 and 2 calculated via y=ax expressed on a soil weight basis SIR.start : Substrate Induced Respiration based on yeast extract. unit = [ug/g/day]. * percentC.substrate: % carbon in the crop residue (measured as triplo in element analyzer, but averaged) * percentN.substrate: % nitrogen in the crop residue (measured as triplo in element analyzer, but averaged) * C.N.substrate: carbon-to-nitrogen ratio of the crop residues * litter.weight.litterbag : amount of litter that was put inside the litterbag. unit = [gram] * litter.weight.mixed.g : amount of litter that was mixed through the soil. unit = [gram] * litter.weight.total : sum of weigth of litter inside and outside of litter bag. So it is the total of litter inside the meocosm unit = [gram] * Mass.loss.perc : percentage of litter weight loss inside litter bag. * gram.soil.in.pot : the amount of soil added in the microcosm. unit = [gram] * percentN_soil.start : N content of the soil, measured by the element analyzer. unit = % * no3.start : concentration of no3 in the field soil. Measured in kcl extract (see NIOO protocol). unit = [mg/kg] * nh4.start : concentration of nh4 in the field soil. Measured in kcl extract (see NIOO protocol). unit = [mg/kg] * no3.resin : amount of no3 that was taken up in the ion-exchange resin bag. This is cumulative over hte experiment and could be compared with potential plant available mineral nitrogen. Measured in kcl extract (see NIOO protocol). unit = [mg/L] * nh4.resin : amount of nh4 that was taken up in the ion-exchange resin bag. This is cumulative over hte experiment and could be compared with potential plant available mineral nitrogen. Measured in kcl extract (see NIOO protocol). unit = [mg/L] * percentC_soil.start : C content of the soil, measured by the element analyzer. unit = % * respiration.day1 : Respiration measurement on first the day of incubation, after pots were air-closed for 4 hours. unit = [µg CO2-C/pot/h] * respiration.day3 : Respiration measurement on day three of incubation, after pots were air-closed for 4 hours. unit = [µg CO2-C/pot/h] * respiration.day4 : Respiration measurement on day four of incubation, after pots were air-closed for 4 hours. unit = [µg CO2-C/pot/h] * respiration.day7 : Respiration measurement on day seven of incubation, after pots were air-closed for 4 hours. unit = [µg CO2-C/pot/h] * respiration.day10 : Respiration measurement on day ten of incubation, after pots were air-closed for 4 hours. unit = [µg CO2-C/pot/h] * respiration.day23 : Respiration measurement on day 23 of incubation, after pots were air-closed for 4 hours. unit = [µg CO2-C/pot/h] * respiration.day32 : Respiration measurement on last the day of incubation. . Based on all respiration measurements cumulative respiration was calculated by taking into account the number of measurements and the time by making a figure and calculating the area below the line. unit = [µg CO2-C/pot/h] ## Code/software The data is a csv file. So you can open and read it via multiple options. For example with R. The R code can be found in GitHub, see publication.