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A global, empirical, harmonised dataset of soil organic carbon changes under perennial crops

Abstract

A global, unified dataset on Soil Organic Carbon (SOC) changes under perennial crops has not existed till now. We present a global, harmonised database on SOC change resulting from perennial crop cultivation. It contains information about 1605 paired-comparison empirical values (some of which are aggregated data) from 180 different peer-reviewed studies, 709 sites, on 58 different perennial crop types, from 32 countries in temperate, tropical and boreal areas; including species used for food, bioenergy and bio-products. The database also contains information on climate, soil characteristics, management and topography. This is the first such global compilation and will act as a baseline for SOC changes in perennial crops. It will be key to supporting global modelling of land use and carbon cycle feedbacks, and supporting agricultural policy development.

 Design Type(s) data integration objective • data collection and processing objective • factorial design Measurement Type(s) amount of carbon atom in soil Technology Type(s) digital curation Factor Type(s) climate • Species • experimental condition • age Sample Characteristic(s) Brazil • cultivated environment • Canada • United States of America • New Zealand • Italy • Germany • Cameroon • India • Sri Lanka • Venezuela • Kingdom of Denmark • Republic of Ireland • French Republic • United Kingdom • Kingdom of Spain • Costa Rica • Ethiopia • Ghana • Indonesia • Mexico • Nigeria • Republic of South Africa • Portuguese Republic • China • Malaysia • Turkey • Israel • Sweden • italy • Georgia • Puerto Rico • Tanzania • Australia

Machine-accessible metadata file describing the reported data (ISA-Tab format)

Background & Summary

Perennial crops are those crops that have a productive life cycle longer than a year, such as apple trees or sugarcane. Perennial crops comprise 30% of global croplands1. Despite their large spatial coverage, the effects of perennial crop plantations on soil properties are not fully understood and results from the literature to date are inconclusive. For example, studies have reported both soil organic carbon (SOC) higher2,3, lower4,5 or equal to6 after transition to perennial crops. This variation could be due to the diverse nature of published studies which have been carried out in different climates and soil types, with a wide range of crops and management practices. Furthermore, a variety of experimental designs, sampling strategies (frequency and soil depth) and analytical methods have also been used. As a result, studies are not directly comparable and conclusions on the effect of perennial crop cultivation on SOC stocks, and the underlying mechanisms, cannot be easily derived.

Accordingly, a major problem contributing to a lack of clear conclusions is that no harmonised data exist. The dataset we present fills that gap: we have compiled the largest dataset to date comprising studies which assess the effects on SOC and soil texture parameters of (a) temporal dynamics, e.g. presenting values across years (b) land use change to perennial crop, e.g. from annual crop or forest to perennial crop and (c) different management practices, e.g. soil amendments. We have included basic climate information: mean annual temperature and precipitation, and topography and bioclimatic region. We have also harmonised the data entry values. The process of harmonising data is to combine data from different and heterogeneous sources and formats into a single, consistent, integrated dataset. Information about SOC carbon stocks already exist and is available in repositories such as the harmonized world soil database7,8 from the Global Soil Information System (GLOSIS) or SoilGrids9. The dataset we present not only complements those SOC stock data but provides further information on SOC changes.

We have included different final end-use types of perennials: (i) food and beverage crops such as citrus or coffee, (ii) bioenergy crops such as Miscanthus or switchgrass, (iii) short rotation coppice trees such as poplar and willow, (iv) animal-feed such us Brachiaria or Atriplex, (v) agroforestry and (vi) other bio-products such as cotton or ramie.

The data are at figshare10. In total, the dataset contains information from 1605 ID entries in 180 studies, 709 field studies, 58 crops, from 32 countries in all continents except for Antarctica, covering all the bio-climatic areas suitable for agriculture (Fig. 1). The list of crops and countries included is in Online-only Table 1.Some areas are still under-represented but we hope that publication of this dataset will encourage those gaps to be filled. Every ID-entry is a paired-comparison point. The ID-entry contains either single SOC measurements, when possible, or aggregated data at plot level when it was not possible to obtain individual values. This has been clearly indicated in the dataset, as is the number of subsamples in the aggregated data specified, where these data were available. Data aggregated at larger scale, i.e. local or regional, was not considered. Each ID-entry contains information on SOC dynamics, which can be either temporal data or paired comparison data including the crop age and time since conversion to perennial, which can be used as a surrogate of temporal information (see methods for more details). For every ID-entry, the dataset contains: information from the original study on crop type, crop age, climate, basic physio-chemical soil characteristics and SOC, number of samples, the original study source, plus additional information about climate, soil properties and biogeographical regions from global databases (details in Online-only Table 2). We only included studies that have information about the perennial crop plantation establishment date and crop age. This was an essential condition since otherwise temporal carbon dynamics cannot be quantified. The aforementioned essential requirements required us to discard many papers reporting some SOC changes in perennial crops, most of which lacked information about crop age. A second common cause for discarding papers was the reporting of SOC change alone rather than as empirical pair-wise values. Aggregation at a larger scales was also frequent.

This harmonized dataset will be of value to support global modelling of land use change and carbon cycle feedbacks, to underpin development of climate-smart agricultural strategies, policy development for sustainable agriculture, to calculate potential carbon savings from global deployment of perennial bioenergy crops, and to support the 4 per mille initiative11,12, among others. Indeed, as the first of many potential analyses using these data, an empirical model of global patterns of SOC changes under perennial crops is being developed using these datasets.

Methods

Empirical data gathering

We compiled the dataset from a systematic search of the literature and by consulting researchers globally to identify and share available data. We furthermore searched in ISI Web of Knowledge, GoogleScholar and figshare using the keywords “perennial crop”, “soil organic carbon” and “soil organic carbon perennial”. We additionally followed references from papers identified in these searches and contacted some authors via email.

For every ID-entry, we added all the available data from the original study in the original units given in the study. This included information about location, climate, crop, soil characteristics, and number of soil samples, temporal/paired site data and original study source. Full details and a list of all entries are presented in Online-only Table 2. Besides, we classified the crops in three main groups: woody plants, palms and grasses (Online-only Table 1).

For ID-entry, two SOC and soil characteristics values are given. The first pair of the set is named “Current SOC and soil characteristic” and indicates the values of SOC at the most recent time point (for temporal data), the perennial land use (for paired site data including different land use) or new management versus traditional (for paired site data including different crop management). The paired SOC and soil characteristic values are under “Previous SOC and soil characteristic”.

Extra fields added to the dataset: climate, topography, soil characteristics

We added additional values of climate variables, topography, soil characteristics and FAO ecoregion classification values from different global free-source datasets. In every case, we used the geographical coordinates given in the original sources to extract additional information. We did not use this information to gap-filling but provide it alongside in a complementary dataset. The data points can be matched and merged using the ID-entry.

Climate information for the plot was extracted from the WorldClim v2 dataset13, which uses average monthly climate data for 1970–2000 (http://www.worldclim.org/). In addition, we added a climatic water deficit index14, and calculated an indicator of water or climate stress P/(T + 10), where P is the annual precipitation and T the annual mean temperature. Details and units are presented in Online-only Table 3.

Information about soil texture and chemical properties was obtained from the SoilGrid Database15, which provides information at 250 m resolution at seven soil depths (https://soilgrids.org/#!/?layer=TAXNWRB_250m&vector=1). Details and units are given in Online-only Table 3.

To characterise the ecoregions, we used the FAO map of Eco-floristic regions (cdiac.ess-dive.lbl.gov/ftp/global_carbon/ecofloristic_zones.zip). Details and regions are given in Online-only Table 3.

Elevation information was extracted from the SRTM version 4.1, resolution approx. 250 m16, from the server http://srtm.csi.cgiar.org/SELECTION/inputCoord.asp. Using that elevation information, we created a digital elevation model, DEM using QGIS17 and derived the values of elevation, slope, aspect, hillshade and roughness at the plot coordinates. Details and units are given in Online-only Table 3. We also added the slope class from the FAO Agro-Ecological Zones (GAEZ v3.0), server (http://www.fao.org/geonetwork/srv/). The classes are: class 1, slope 0–2%; class 2: 2–5%; class 3: 5–8%; class 4: 8–16%; class 5: 16–30%; class 6: 30–45% and class 7: >45%.

Unifying units

For soil properties, values of soil texture, clay, sand and silt were transformed to percentages if they were not in that unit in the original study. To do so, values of g/kg were divided by 10.

Values of soil bulk density (BD), texture and pH were not gap-filled but left as NA when not provided. This was to avoid masking which data were empirical and which data were not. Only 51% of the studies reported the values of BD, and 43% soil texture. But information on BD, texture and pH for each point can be found in the fields added to those obtained from the SoilGrids dataset, at the soil depth of the middle depth of the sample point. This information can be used to gap fill those fields if necessary.

Values of SOC in the original studies where either in concentration, g/kg, (SOCcon) or in carbon stocks, Mg/ha (SOCstock). We initially considered transforming the values using the equation18:

$$SO{C}_{stock}=SO{C}_{con}\,\ast \,Bulk\,Density\,\ast \,depth\,\ast \,(1\,-\,rock\,fragments\,fraction).$$

However, that transformation would have added extra uncertainty and thus was not consistent with our principle of providing the SOC values as raw and close to empirical values as possible. Furthermore, when comparing the SOC values from transformed against untransformed data, we found a biased mismatch between the range of data using original units and the transformed data. We hypothesise that this may be due to the use of aggregated data or single use of BD for multiple samples19,20, or the use of different methodology21, or different sampling depth or soil core ring sizes, or lack of information about rock fragments. Considering this, we concluded that such a transformation was not appropriate, in line with previous reports5. Therefore, in this dataset, we provide SOC values using the units of the original study, which means about 30% are in g/kg (SOCcon) and the other 70% in Mg/ha (SOCstock).

For climate variables, temperature and precipitation, the values reported in the original study were kept. Otherwise, we added the values obtained from the WorldClim dataset, which has a lag time of 30 years, averaging climate values from 1970 to 2000. The “temperature” and “precipitation” fields were the only ones that were gap-filled in the provided main database (in about 1% of the cases). Average values of temperature and precipitation were provided in most of the original studies, however, the period of time was specified hardly any case.

Data aggregation quantification

We added a new field to indicate whether the original dataset contains information about a single SOC empirical measurement or aggregated data (in the “Data” section, Online-only Table 2). In addition, the entries “N plots” and “N samples” specify the number of empirical measurements per entry, when provided in the original studies. We added a new field called “N measured” which is the number of plots multiplied by the number of samples. Therefore, this value also indicates the level of data aggregation. When only the number of plots or samples per plot were indicated in the original study, this was the value given in this field. When neither of these values were reported in the original study, the number of measurements was set to 1. In the dataset, 108 data-points contained a single measurement, 965 ID-entries were aggregated data, and for the remaining 532 samples no details of aggregation were provided. From the 965 entries with aggregated data, only 319 (33%) reported the standard deviation or variation in the original study.

Data Records

The dataset, in spreadsheet format, can be found in the figshare repository10 with the title “A global dataset of harmonised empirical values of soil organic carbon changes under perennial crops v1.0”

The creators are: Alicia Ledo, Jonathan Hillier, Pete Smith, Eduardo Aguilera, Sergey Blagodatskiy, Francis Q. Brearley, Ashim Datta, Eugenio Diaz-Pines, Axel Don, Marta Dondini, Jennifer Dunn, Diana Marisa Feliciano, Mark A. Liebig, Rong Lang, Mireia Llorente, Yuri Lopes Zinn, Niall McNamara, Stephen Ogle, Zhangcai Qin, Pere Robira, Rebecca Rowe, José Luis Vicente Vicente, Jeanette Whitaker, Qian Yue, Ayalsew Zerihun.

The list of crops and countries is presented in Online-only Table 1. A summary Table summarising the different types of data included is in Table 1, and the percentage of data points in each category can be seen in Fig. 2.

Metadata information in ISA format (www.isa-tools.org) is provided in the associated Scientific Data Descriptor. The dataset we present is compliant with the FAIR principles for scientific data22: findable, accessible, intraoperative and reusable.

Technical Validation

Variable distribution and unusual point values

We evaluated the distribution of all the quantitative variables. We examined the outliers and/or extreme points for potential errors. The distribution of all variables can be found in Supplementary Material 1 (Scatterplots, box-and-whiskers and histograms).

Quantifying errors and standard deviations in SOC

We analysed the effect of the number of samples per plot in terms of uncertainty. To this end, we calculated the relative standard deviation (sd) of the SOC mean values for ID-entries with more than one measurement and reporting the sd of SOC values. Overall, the value of relative standard deviation of SOC mean values, sd/SOC, which is indeed the coefficient of variation (cv), decreased as the number of samples increased (Fig. 3). In other words, a greater sampling effort seems to decrease the cv. According to these data, the relative standard deviation is generally under 10–15% after gathering 20 sample points. Nonetheless, this depends on the soil characteristics and the sampling spatial distribution. All in all, having 20–30 replicates per plot seems to be an adequate sample size in SOC studies to constrain the coefficient of variation below 15% (Fig. 3).

On the SOC errors

Assessing SOC stocks is a complex process which involves several steps and measurements. It should thus be borne in mind that many types of error may have crept in the original data acquisition. Besides, while some errors may be random, others may be systematic thus introducing bias, the latter is of a greater concern and efforts should be made to minimise it. Not to mention that assessing SOC stocks is a complex matter itself. The dataset may contain different types of errors from different sources. For example measurement errors in the field, lab analytical and measurement errors and post-process data errors and transformations are all possible. A further description and comments on SOC errors is beyond the scope of this data paper and can be found elsewhere, e.g.18,19,23,24,25,26 among others.

SOC measurement and stock estimation also usually involve measuring or estimating other soil parameters, namely BD, and SOC concentration and determination accuracy are often affected by other properties such as texture and iron oxide contents. Mathematical relationships to link those parameters may introduce further bias18. However, measurement and analytical errors can lead to both under- and over-estimation. If this is the case and the errors are randomly distributed, they somewhat compensate for each other in large datasets. Non-random, systematic errors, may also mask trends in the data. However, it is not possible to know to which extent these kind of errors are present in the SOC perennials dataset given the available source information. In any case, we recommend quantifying sources of uncertainty when possible, and at different temporal and spatial scales23 and due to data aggregation19.

Different sampling depth is another potential source of error and uncertainty when comparing data from different studies27. In this dataset we have brought together SOC at different depths (the sample depth is clearly indicated in the dataset), but we suggest that values of SOC measured at different depths should not be mixed without using a suitable pedo-transfer function (PTF). Presenting new PTF for perennials is beyond the scope of this data paper yet is currently being explored for future publication.

A call for unification in reporting soil properties data

An increasing number of studies18,19,21 are reporting problems in comparing SOC data, and some of the given reasons have been mentioned in the previous subsection. Values of bulk density and soil texture are measured in most studies but only at times reported in the resulting manuscript. This first source of uncertainty, and potential errors and bias, can be remedied by including this information in publications. Thus, we formally appeal to researchers to measure and report BD and soil texture in future SOC studies. BD is technically simpler to measure than texture, which is a time consuming analytics and could be constrained by budget and or time. However, easy methods to estimate soil texture directly in the field have been proposed and evaluated as accurate enough for most purposes28.

A second essential piece of information not always detailed in published papers is the number of samples and replicates. We encourage researchers to provide all of the relevant data and measurements done, and for reviewers to request that authors provide this information, for the sake of transparency, reproducibility and quantification of uncertainty.

A particular drawback in current SOC studies is the lack of standardised carbon values to be reported. Until now, some studies use SOC concentration values (g/kg), while others use carbon stocks (Mg/ha) or volumetric values (g/m3). This is not a matter of different units, since those carbon pools are different things. Nonetheless, they are interchangeable if and only if the required soil variables are accurately measured and provided (SOC content, BD, soil texture, rock fragment, maximum depth), as we suggested and discussed in the previous sections. This lack of consensus and unification is not only limiting values of some relevant studies5, but is hampering our understanding of soil carbon dynamics. It is timely that we gather and unify knowledge to better understand of the carbon cycle in general, and SOC dynamics in particular. This understanding is key to realistic estimation of the potential of SOC storage in perennial crops as a climate change mitigation option, and a potential tool to deliver the goals of the 4 per 1000 initiative. This knowledge is also important to predict potential changes on SOC dynamics under climate change conditions and to underpin development of climate-smart agricultural strategies.

The ISRIC WDC GlobalSoilMap from the World Soil Information Service (WoSIS) has recently provided some standards and procedures to acquire, harmonise and provide soil data7,29. In further SOC analysis and work, it may be adequate to align with those protocols.

The minimum information we recommend that should be provided in SOC studies is: (i) number of plots and number of replicates per plot (ii) depth of measurement and number of layers considered, (iii) BD and equivalent soil mass, (iv) soil texture, (v) rock fragment fractions (vi) SOC in concentration and stocks, (vii) method used to measure SOC and BD, (viii) climate, or at least mean annual temperature, precipitation and elevation, (ix) soil management (if any), and (x) land use (historic land use is also highly desirable). The WoSIS repository has a shorter list of requirements. Nevertheless, to align with its standards, cation exchange capacity, electrical conductivity and water holding capacity are also required29.

References

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Acknowledgements

We acknowledge Deborah McGrath, Richard Harper and Stanley Sochacki for providing the paper contributing data. This study was initially funded by the NERC project (NE/N017854/1). It was finished by the BBSRC project BB/P027784/1 (AFRICAP), which supported A. Ledo. Y.L. Zinn is supported by CNPq (grant #302038/2016-7). A. Datta is thankful to the Director, and HSCM, ICAR-CSSRI for providing necessary facilities during attachement training study. Data provided by N. McNamara and J. Whitaker are from the Energy Technologies Institute “Ecosystem Land Use Project” (www.elum.ac.uk). An anonymous reviewer provided useful comments to improve the first version of the manuscript.

Author information

Authors

Contributions

A.L., J.H., P.S., initiated and designed the study. A.L. gathered and analysed the data. J.H., E.A., S.B., F.Q.B., A.D., E.D.-P., A.D., M.D., J.D., D.M.F., M.L., M.L.l., Y.L.Z., N.M., S.O., Z.Q., P.R., R.R., J.L.V.V., J.W., Q.Y. and A.Z. contributed data. All authors contributed ideas and wrote the associated data descriptor.

Corresponding author

Correspondence to Alicia Ledo.

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Ledo, A., Hillier, J., Smith, P. et al. A global, empirical, harmonised dataset of soil organic carbon changes under perennial crops. Sci Data 6, 57 (2019). https://doi.org/10.1038/s41597-019-0062-1

• Accepted:

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• DOI: https://doi.org/10.1038/s41597-019-0062-1

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