Biogeochemistry
https://doi.org/10.1007/s10533-023-01029-8
Predicting high resolution total phosphorus concentrations
for soils of the Upper Mississippi River Basin using machine
learning
Christine L. Dolph · Se Jong Cho · Jacques C. Finlay · Amy T. Hansen ·
Brent Dalzell
Received: 17 November 2022 / Accepted: 8 February 2023
© The Author(s), under exclusive licence to Springer Nature Switzerland AG 2023
Abstract The spatial distribution of soil phospho-
rus (P) is important to both biogeochemical processes
and the management of agricultural landscapes,
where it is critical for both crop production and con-
servation planning. Recent advances in the avail-
ability of large environmental datasets together with
big data analytical tools like machine learning have
created opportunities for evaluating and predicting
spatial patterns in complex environmental variables
like soil P. Here, we apply a random forest machine
learning model to publicly available soil P datasets
together with nearly 300 geospatial attributes sum-
marizing aspects of soil type, land cover, land use,
topography, nutrient inputs, and climate to predict
Responsible Editor: Justin B Richardson.
Supplementary Information The online version
contains supplementary material available at https://​doi.​
org/​10.​1007/​s10533-​023-​01029-8.
C. L. Dolph (*) · J. C. Finlay
Department of Ecology, Evolution and Behavior,
University of Minnesota, 140 Gortner Laboratory, 1479
Gortner Ave, St. Paul, MN 55108, USA
e-mail: dolph008@umn.edu
S. J. Cho
The National Socio‑Environmental Synthesis Center,
University of Maryland, Annapolis, MD 21401, USA
S. J. Cho
US Geological Survey, Water Resources Mission Area,
Reston, VA 20192, USA
total soil P at a 100 m grid scale for the Upper Mis-
sissippi River Basin (UMRB), USA. The UMRB
is one of the most intensively farmed regions in the
world and is characterized by widespread water qual-
ity degradation arising from P-associated eutrophica-
tion. Although potentially complex interacting drivers
determine total soil P, the predictive accuracy of our
random forest model was relatively high (R2 = 0.58
and RMSE = 129.3 for an independent validation
dataset). At the regional scale represented by our
model, the variables with the greatest comparative
importance for predicting soil P included a combina-
tion of soil sample depth, land use/land cover, under-
lying soil physical and geochemical properties, land-
scape features (such as slope, elevation and proximity
to the stream network), nutrient inputs, and climate-
related factors. An important product of this research
is a fine-scale (100 m) raster data layer of predicted
total soil P values for the UMRB for public use. This
A. T. Hansen
Civil, Environmental, and Architectural Engineering
Department, University of Kansas, 1530 W. 15Th St,
Lawrence, KS 66045, USA
B. Dalzell
ARS Soil and Water Management Research Unit, U.S.
Department of Agriculture, 439 Borlaug Hall, 1991 Upper
Buford Circle, St. Paul, MN 55108, USA
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dataset can be used to improve conservation planning
and modeling efforts to improve water quality in the
region.
Keywords Soil phosphorus · Modeling · Random
forest · Conservation · Data mining · Water quality
Introduction
Phosphorus (P) is an essential nutrient in terrestrial
and aquatic systems, with strong influences on plant
productivity, element cycling and many other aspects
of ecosystems (Vitousek et al. 2010). In excess, P has
strong negative impacts on water quality and aquatic
ecosystems arising from diverse effects of eutrophi-
cation (Schindler 2006; Clark and Longo 2018).
Because soils are the main source of phosphorus for
terrestrial and freshwater ecosystems, understanding
of ecosystem dynamics and management of phos-
phorus enrichment due to human activities requires
knowledge of distributions of soil P. While a large
majority of total soil phosphorus exists in diverse
forms that are not immediately available to plants
(i.e., primary and secondary minerals, organic P),
these pools of soil P determine general P availability
and influence losses to aquatic ecosystems (Hou et al.
2016; Vitousek et al. 2010). Thus, knowledge of total
soil P distributions can provide fundamental informa-
tion for research and management in terrestrial and
aquatic ecosystems.
In the Cornbelt and Great Plains regions of the
United States and Canada, decades of agricultural
practices including the conversion of perennial veg-
etation into row crops, intensive inputs of synthetic
fertilizers, and the spreading of manure from concen-
trated animal feeding operations (CAFOs), have led
to an accumulation of legacy phosphorus in soils well
beyond their retention capacity (Goyette et al. 2018).
Wastewater sources also contribute to P export,
although their impact is comparatively small for most
industrially managed agricultural watersheds (Board-
man et al. 2019). In many areas across the region,
legacy P continues to be compounded by ongoing fer-
tilizer and manure inputs, exacerbating the challenges
of addressing nonpoint source pollution (Stackpoole
et al. 2019; Boardman et al. 2019; Van Meter et al.
2021). These anthropogenic P inputs are overlaid on
complex underlying controls on soil P content and
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Biogeochemistry
transport, including soil parent material, soil texture,
and landscape geomorphology (Records et al. 2016).
Field work efforts to measure soil P at high spa-
tial resolution can be time intensive and costly, if not
infeasible, across large spatial extents. Although soil
P is predicted quite well at small spatial scales by
coincident soil properties such as pH, texture, parti-
cle size and soil organic matter (e.g., Hosseini et al.
2017), such microscale soil attributes are generally
not available at regional scales. Moreover, P het-
erogeneity at regional scales may also be affected by
broader scale drivers such as climate, parent material,
and glacial history. Thus, efforts to predict soil P from
existing geospatial and climatic datasets have con-
siderable utility within larger biophysical modeling
efforts designed to support conservation planning.
Recent advances in the availability of large envi-
ronmental datasets together with analytical tools like
machine learning models have created new opportuni-
ties for predicting spatial patterning in complex envi-
ronmental outcomes (Zhong et al. 2021). Total P at the
soil surface represents a critical pool of P that is poten-
tially erodible, reactive, and eventually bioavailable and
thus highly relevant to both crop production and water
quality. Machine learning represents a potentially use-
ful tool to help predict spatial variability in total soil P,
which is driven by complex, interacting drivers. Previ-
ously, machine learning has been used together with
detailed geospatial data to predict soil P across smaller
geographic areas, ranging from a single field to small
catchments to subregions with areal extents of up to a
few hundred ­km2 (Matos-Moreira et al. 2017; Jeong
et al. 2017; Sahabiev et al. 2021; Kaya et al. 2022; Kaya
and Başayığıt 2022). Machine learning has also been
used to predict soil attributes such as % carbon and total
nitrogen content at continental scales (Ramcharan et al.
2018), as well as nutrient concentrations in river net-
works (e.g., Shen et al. 2020; Sadayappan et al. 2022).
In this study, we develop a random forest machine
learning model from large, publicly available datasets
of soil P and nearly 300 predictive variables includ-
ing soil type, land cover, topography, nutrient inputs,
hydrology and climate to predict total surface soil P at a
100 m grid scale for the entire Upper Mississippi River
Basin (UMRB), USA. The UMRB is one of the most
intensively farmed regions in the world and is charac-
terized by widespread water quality degradation aris-
ing from P-associated eutrophication (Jacobson et al.
2011). Predicting the spatial variability of total soil P
Biogeochemistry

Fig. 1  Map of the study

region showing a) locations
of soil P samples from the
USGS National Geochemi-
cal Survey database (purple
dots, n = 6,664) and from
the National Cooperative
Soil Survey (NCSS) Soil
Characterization Database
(in orange, n = 558) across
the Midwestern regional
extent used in this study,
with the Upper Mississippi
River Basin (UMRB) out-
lined in bold and. b) close
up of the UMRB showing
land cover classes from the
2019 National Land Cover
Dataset (Dewitz, 2021) and
locations of major rivers
and cities

for this landscape has direct implications for conserva- Methods

tion planning for water quality improvement and for
understanding the resilience of soils for crop production
(Qiao et al. 2022). Our objectives for this research were
to (1) highlight the potential of underutilized publicly-
funded and available datasets to support conservation
planning; (2) predict soil P at a fine (100 m) resolution
across the UMRB and provide results in an open access
data framework for use in future conservation planning
and analysis; (3) identify geospatial attributes important
in predicting soil P at regional scales.
Study area
The focus of this study is the Upper Mississippi River
Basin (UMRB), which comprises the uppermost trib-
utaries to the Mississippi River, from the headwaters
at Lake Itasca in Minnesota down to the confluence
of the Mississippi and Missouri Rivers at St. Louis,
Missouri (Fig. 1).
The UMRB covers nearly half a million square
kilometers (492,027 k­m2) of the upper Midwestern

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Fig. 2  Schematic showing the workflow for machine learning development. Input data and R scripts are available at https://​github.​
com/​cldol​ph/​SoilP
United States, including large parts of Minnesota,
Wisconsin, Iowa, Missouri, Illinois, and smaller areas
of Indiana, North Dakota, and South Dakota, and cor-
responds to the HUC2-scale watershed (HUC ID = 07)
in the USGS Watershed Boundary Dataset (2021).
The UMRB is intensively farmed for large scale mon-
ocultures of primarily corn and soybeans. CAFOs are
also prolific in the basin, particularly across Iowa and
southern Minnesota (Harun and Ogneva-Himmel-
berger 2013). Overall, cultivated crops comprise 49%
of total basin land area (Dewitz, 2019); nearly 90% of
those crops are corn and soybeans (USDA 2022). The
intensity of agricultural land use varies across a gradi-
ent from north to south, with the uppermost parts of
the basin (in Minnesota and Wisconsin) characterized
by relatively higher amounts of forest and wetland
cover compared to the southern regions of the basin,
where crop land use can exceed 85%. However, even
the northern areas of the basin are undergoing rapid
land use change from wetland and forest cover towards
more agriculture (Green et al. 2018). The precipitation
gradient varies from comparatively drier in the north
and west to wetter in the south and east. Soil textures
in the basin are largely silty loam and loam, but also
include areas of poorly drained clays as well as areas
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Biogeochemistry
of well drained sands. Topography in the UMRB
includes widespread flat and gently rolling areas,
as well as steeper terrain and large bluffs near many
rivers and streams. Elevation across the basin ranges
from 85 to 640 m above sea level.
Data processing and analysis overview
Data processing and analysis was done in R Studio v.
2022.07.1 (RStudio Team 2022). All of the input data
and methods used to generate the machine learning
model for predicting soil P—including data acquisi-
tion, data preprocessing, data splitting, model training,
evaluation and interpretation—are publicly available
at https://​github.​com/​cldol​ph/​SoilP. The workflow
used to develop the model is summarized in Fig. 2.
Soil phosphorus data
For model training and testing, we used nearly 7,000
soil P measurements from two spatially extensive
datasets: (1) the USGS National Geochemical Survey
(NGS) Database (USGS 2004), and (2) the National
Cooperative Soil Survey (NCSS) Characterization
Dataset (NCSS 2021). Both of these datasets are
Biogeochemistry
publicly available1 and contain information about soil
P, among other soil attributes. We focused on total
soil P rather than soil test P in our model develop-
ment for several reasons. First, the NGS does not
contain information about soil test P. Although the
NCSS does contain information about various soil
test P measures (e.g., Bray 1 P, Olsen P, etc.), soil test
P is not measured consistently across the geography
of the dataset. Because different soil test P measures
extract variable amounts of P, they may not be readily
comparable to one another (Wuenscher et al. 2015),
making it difficult to compile and interpret multiple
soil test P measures into one cohesive dataset. By
contrast, total soil P data across the NGS and NCSS
was considerably more extensive compared to any
one soil test P measure, creating the opportunity for
stronger machine learning models. Second, total soil
P is a fundamental ecosystem property with broad
applications in conservation, biogeochemistry, and
agronomy (Correll 1998; Sharpley et al. 2009; Shen
et al. 2011). While soil test P may more directly indi-
cate the crop availability and risk of loss of soluble P
to downstream water bodies (e.g., Vadas et al. 2005),
total P provides a more consistent and integrative
measurement of soil P status. Moreover, previous
work has shown total P to correlate with soil test P
measures (especially when other soil properties are
also accounted for; Allen and Mallarino 2006), and
thus total P can be related to the potential for both
erosive and soluble P losses. Finally, water quality
monitoring and management efforts are often pegged
to estimates of total P in aquatic systems, rather than
estimates of ‘bioavailable’ P (Correll 1998). The
complexity of P cycling and transformation in ter-
restrial and aquatic environments is a good reason to
track total P in our initial machine learning efforts.
Future applications of this approach may be applied
to soil test P, particularly as more data is available
from high frequency sampling to account for high
variability in these forms, as the bioavailability of dif-
ferent components of total P may change over time.
Soil P estimates from these two datasets provided
only partial spatial cover of the UMRB (Fig. 1). To
expand our potential to predict soil P for different
types of soils and landcover conditions present across
1
NGS: https://​mrdata.​usgs.​gov/​geoch​em/; NCSS: https://​ncssl​
abdat​amart.​sc.​egov.​usda.​gov/
the UMRB, we expanded the regional range of data
used to build our predictive model to include loca-
tions that were outside of the UMRB boundary but
that shared potentially similar soils, climate and/
or land management. This expanded study region
included the following 13 U.S. states: Arkansas, Illi-
nois, Indiana, Iowa, Kansas, Minnesota, Missouri,
Nebraska, North Dakota, Ohio, South Dakota, Wis-
consin (Fig. 1).
National geochemical survey dataset (NGS)
The NGS contains 284 geochemical attributes for soil
and stream sediment samples across the United States
(n = 77,212). While the primary focus of the dataset is
stream sediments, the dataset contains a considerable
number of soil samples (n = 19,992). Of these soil
samples, 19,574 samples contain information about
total soil P. Total soil P estimates (% dry weight) were
obtained using inductively coupled plasma spectrom-
etry after acid dissolution (USGS 2004). We con-
verted soil P estimates to mg/kg by multiplying %
weight estimates by 10,000.
Samples in the NGS dataset were collected
between 1900 and 2008. Since we were most inter-
ested in developing modeling approaches capable of
predicting relatively current soil P conditions from
concurrent spatial attribute data, we subsampled the
dataset to those collected between 2000 and 2008,
leaving 9,589 samples. We further restricted samples
to those found in our geographic study region, leaving
a total of 6,664 soil P samples (Fig. 1).
For most samples, the NGS contains information
about soil depth. However, depth was represented
inconsistently across the dataset, with some samples
associated with minimum and maximum numeric
depth estimates (in inches), some samples associated
with a soil horizon category (i.e., “A”, “B”, etc.), and
some samples lacking any kind of information about
depth or horizon.
For samples where numeric depth information was
available, we designated a predictor variable ‘depth’
as the maximum depth pertaining to that sample. For
soil samples without numeric depth measurements,
we assumed a maximum depth of 30 cm if samples
were listed as occurring in the soil A horizon (cor-
responding to the surface or plowable layer). We also
assumed a maximum depth of 30 cm for samples with
no depth or horizon information provided (that is, we
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assumed samples without depth information were
surface samples). If samples occurred in any other
soil horizon (and if no numeric depth information
was provided) we designated samples as ‘subsurface’,
and assigned them a maximum depth of 76 cm based
on information from samples where depth data were
present (and corresponding primarily to the soil B
horizon).
National cooperative soil survey
The NCSS contains data commonly requested for
agronomic and biogeochemical purposes for 404,080
soil samples across the United States analyzed by
the Kellogg Soil Survey Laboratory and cooperat-
ing universities. Of these, 10,678 samples contained
information about total P, with 961 samples occur-
ring in our study region. As for the NGS dataset, we
filtered samples to include only those collected since
2000, leaving 558 samples in the remaining NCSS
dataset. Total soil P estimates (mg/kg) were obtained
using inductively coupled plasma spectrometry after
acid dissolution (Soil Survey Staff 2014). All samples
included an estimate of the top and bottom depth of
the soil horizon sampled in centimeters. We used the
estimate of horizon bottom depth as the estimate of
depth associated with each sample.
After subsampling the data, the combined NGS
and NCSS datasets yielded a total of 7,222 soil P
samples for model development and testing across the
Midwestern United States (Fig. 1).
Predictive variables
To predict soil P across the UMRB, we sought attrib-
utes that had previously been identified as known
drivers of P abundance, including soil properties such
as parent material, mineral and organic content, grain
size and texture, as well as attributes describing land-
scape position, land use, climate and anthropogenic
inputs (Records et al. 2016; Deiss et al. 2018; He
et al. 2021). We used geospatial attributes from mul-
tiple publicly available datasets to summarize aspects
of these potential drivers of soil P. These datasets
included: (i) the National Hydrography Dataset Plus
v2 (NHDPlusv2)2; (ii) the National Land Cover
2
https://​nhdpl​us.​com/​NHDPl​us/​NHDPl​usV2_​data.​php
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Database (NLCD) for 20063; (iii) the National Wet-
lands Inventory4; (iv) the gridded Soil Survey Geo-
graphic (gSSURGO) Database (10 m resolution)5;
and v) the U.S. EPA StreamCat dataset6. Overall, we
included 268 attributes derived from these datasets at
multiple spatial scales as predictors in soil P models.
Each of these datasets are described in more detail
below and specific attributes used in soil P models are
listed in Supplementary Information (SI) Table S1.
Once soil samples were joined to all predictors, 6,683
soil samples had complete attribute information avail-
able for use in modeling.
National hydrograph dataset plus v2 (NHDPlusv2)
We sought to include information about near chan-
nel areas (i.e., the 100 m buffer surrounding the
stream network) in our predictor dataset, because of
the possibility for these environments to accumulate
P relative to upland areas. For example, in a review
of the effects of conservation practices on water qual-
ity, Dodd and Sharpley (2015) found that near chan-
nel areas such as riparian buffers, including grass
and vegetative filter strips and wetlands, accumu-
lated labile forms of soil P over time. We derived a
categorical attribute indicating whether soil samples
were collected in the 100 m riparian buffer of various
stream categories defined in the NHDPlusv2 layer,
including ditches, intermittent streams, and perennial
streams. The NHDPlusv2 includes a digital stream
network layer for the conterminous United States,
divided into reaches (i.e., unique links in the network)
as well as catchment boundaries associated with each
reach. Catchments (i.e., local drainage areas) include
the immediate land area draining into each individual
stream reach excluding areas draining to upstream
reaches. Buffering of the stream layer was con-
ducted in ArcMap version 10.8.1. We also used the
NHDPlusv2 layer to assign soil P samples to NHD
catchments, which were subsequently used to link
soil samples to predictive variables in the StreamCat
database (see below).
3
https://​www.​mrlc.​gov/​data/​nlcd-​2006-​land-​cover-​conus
4
https://​www.​fws.​gov/​wetla​nds/​data/​data-​downl​oad.​html
5
https://​nrcs.​app.​box.​com/v/​soils
6
https://​www.​epa.​gov/​natio​nal-​aquat​ic-​resou​rce-​surve​ys/​strea​
mcat-​datas​et
Biogeochemistry
National land cover database (NLCD)
Land use is a likely driver of soil P dynamics through
multiple potential pathways, including alteration of
P inputs and outputs associated with different land
cover regimes, and through management practices
that may alter biological, chemical and physical pro-
cesses that affect P composition (Liu et al. 2018). We
used the NLCD to summarize aspects of land cover
for the UMRB. NLCD layers contain information
about 16 land cover classes across the United States at
30 m resolution. We chose NLCD 2006 because most
soil P samples in our dataset (85%) were collected
between 2000 and 2006, and all were collected before
2011. We used the spatial join function in ArcMap to
link land cover classes to soil P sample locations.
National wetlands inventory
Similar to riparian buffers, wetlands can accumulate
P by intercepting P-rich runoff from surrounding
drainage areas (Dodds and Sharpley 2015); thus we
sought to include wetland presence and type as pre-
dictors in machine learning models for soil P. The
NWI is a publicly available dataset that captures dis-
tribution and attribute information for wetlands in
all 50 U.S. states. We derived a categorical attribute
indicating whether soil samples were collected from a
series of possible wetland types included in the NWI,
including freshwater emergent wetlands, freshwater
forested/shrub wetlands, freshwater ponds, lakes, or
riverine wetlands, or from non-wetland areas.
gSSURGO
A large body of previous work has identified the
importance of soil properties such as mineral and
organic content, parent material, and soil texture to
P abundance (e.g., Records et al. 2016). We used the
10 m resolution raster gSSURGO dataset (Soil Sur-
vey Staff 2021) to assign soil properties to P sample
locations. The gSSURGO database is organized by
map unit soil polygons where each map unit is linked
to hundreds of detailed soil attributes. We selected 81
attributes from the gSSURGO dataset with the poten-
tial to control soil P abundance –including aspects
of parent material, grain size, organic matter con-
tent, and mineral content (Records et al. 2016)—and
linked them by location to soil P sample locations.
For gSSURGO attributes that are mapped at scales
smaller than the map unit, we preprocessed numeric
SSURGO attributes by taking the weighted average
of values for all components in a map unit, where
weights were the proportional contribution by area
of each component to the map unit. For categorical
SSURGO attributes, we selected the attribute value
for the component comprising the highest percent
area of the map unit. If two attribute values com-
prised the same percent area of the map unit, we pref-
erentially selected the component attribute with the
higher slope value because surface P runoff is likely
to be higher for soils with greater slope.
StreamCat dataset
U.S. EPA’s StreamCat dataset contains information
for over 600 different environmental metrics linked to
individual stream reaches in the NHDv2Plus dataset
(Hill et al. 2015). These metrics summarize diverse
geospatial attributes including land use, impervious
surfaces and road density, soil type, point source and
nutrient inputs, and climatic factors (temperature and
precipitation) at the catchment and watershed scale
draining into each reach. In contrast to the 30 m pixel
gridded NLCD 2006 data, StreamCat attributes are
summarized at the catchment (local drainage area)
and watershed scales and thus offered the potential to
capture land use trends at a slightly broader, but still
local, geographic scale that might be relevant to soil P
concentrations. We included attributes from Stream-
Cat variables potentially relevant to soil P across our
study region (Table S1). These tables included 220
attributes summarized at the watershed and catch-
ment in our dataset.
Random forest modeling
Random forest regression is a nonparametric ensem-
ble learning method that utilizes predictions from
multiple decision trees to improve model accuracy.
Each tree is composed of branches (“nodes”) rep-
resenting yes–no questions where features (i.e.,
predictive variables) are used to split the depend-
ent variable into two groups that minimize in-group
variability and maximize between group variability.
We selected random forest as our modeling method
because these models can be highly accurate, are
relatively fast to develop, can handle categorical and
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numerical attributes, are robust to outliers, and can
handle both non-linear and unbalanced data, all of
which were pertinent criteria for our dataset. Ran-
dom forest models also require very few assumptions
of the input datasets. At the same time, some limita-
tions of random forest modeling methods should be
noted: mainly, the machine-learning techniques are
characterized by the data mechanisms as ‘black box’
or ‘gray box’ algorithmic approaches (Jeong et al.
2016). Particularly, random forest is built on non-
parametric advanced classification and regression
tree (CART) analysis methods and models may not
be fully described mechanistically (Breiman 2001).
Also, the random forest algorithm has the potential
to overfit data, and may become impractical for mak-
ing predictions beyond the training data range (Jeong
et al. 2016). Given the inherent random forest struc-
ture, permutation of many trees may make the algo-
rithm slow for real-time prediction (Breiman 2001).
Random forest model development followed
the general scheme for machine learning models
articulated by Zhong et al. 2021 (Fig. 2). We used a
tidymodels framework (Kuhn and Wickham 2020) in
R (R Core Team 2022) to develop random forest mod-
els for predicting soil P from the assembled predic-
tors. Models were evaluated based on ­R2 and RMSE
values (Chicco et al. 2021). Within this framework,
we used both the ranger package (Wright and Ziegler
2017) and the randomForest (Liaw and Wiener 2002)
packages at different points in the modeling process.
Both ranger and randomForest have been shown to
perform as well or better than other machine learning
approaches for predictive purposes (Hagenauer et al.
2019) and have been shown to produce very simi-
lar model results to one another (Wright and Ziegler
2017). We used the ranger package for initial model
tuning, due to its considerably faster implementation
relative to randomForest (Wright and Ziegler 2017).
Once optimal hyperparameter values had been iden-
tified using this approach, we applied these hyperpa-
rameter values to a randomForest implementation to
create our final model, because randomForest model
objects (but not ranger model objects) are compatible
with conditional permutation methods for estimating
the relative importance of predictors to model out-
comes (see rationale for the approach we took to eval-
uate predictor importance below). Prior to switching
from ranger to randomForest implementations, we
confirmed that the two approaches produced nearly
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the exact same results in terms of model performance
(as measured by R ­ 2 and RMSE for actual vs predicted
values on an independent test dataset), when the same
hyperparameter values were used. A complete R
script detailing our approach can be found at https://​
github.​com/​cldol​ph/​SoilP.
Additional data curation
After pre-processing soil predictors as described
above, we linked attributes to soil P samples and
removed variables that did not contain useful infor-
mation (e.g., all rows = 0). We also excluded attrib-
utes where information was missing (‘NA’) for > 20%
of soil P samples. Finally, we also excluded three
attributes from the gSSURGO dataset (pmkind, tax-
partsize, and texcl) with category levels that did not
encompass the entire set of the categories contained
within the UMRB grid dataset (see below). Many of
the remaining attributes still contained some missing
values. Because random forest models cannot handle
missing values in predictor variables, we used the
missRanger package in R (Mayer 2021) to impute the
remaining missing values for the training and testing
datasets. missRanger imputes missing values for each
variable by building a random forest model for each
variable that uses all other variables in the dataset as
covariables. Prior to random forest modeling, we nor-
malized (i.e., centered and scaled) numeric attributes
to have a mean of zero and a standard deviation of
one.
Model tuning
For the soil P random forest model, we used 90% of
the data for model training, and the remaining 10%
for model testing. Using the training dataset and the
ranger implementation for random forest modeling,
we applied tenfold cross validation to tune model
hyperparameters across a range of possible values.
The hyperparameters selected for tuning were: mtry
(i.e., number of variables randomly sampled as can-
didates at each split) and min_n (i.e., the minimum
number of data points in a node). The trees hyper-
parameter (i.e., number of trees) was set to 1000
across all models. K-fold cross validation can assist
in avoiding model over-fitting and works by partition-
ing training data into K equal sized “folds” (in our
case 10). The model is iteratively trained on various
Biogeochemistry
combinations of tuning hyperparameters across K-1
folds, leaving the remaining fold to evaluate model
performance for each combination. We defined a grid
of 20 potential combinations of hyper-parameters
using the tune_grid () function from the tidymodels
collection of packages in R. This approach draws
hyperparameter values semi-randomly from parame-
ter space such that the various combinations cover the
whole space of potential values. We selected hyper-
parameter values using out-of-bag (OOB) RMSE and
­R2 for the associated models.
Once hyperparameter values were tuned, we re-
ran the random forest model using the randomFor-
est package, to create a randomForest object that was
compatible with our selected measure of predictive
variable importance (see next section). We evaluated
overall model performance based on the independent
test dataset (comprising 10% of the original dataset).
Predictive variable importance
Many implementations of random forest models
come with default measures used to quantify the rela-
tive importance of individual predictive variables to
model performance. However, recent work has shown
that many of these default strategies, including those
based on measures of impurity or permutation-based
metrics, can produce biased results when model pre-
dictors (1) vary in their scale of measurement; (2)
vary in their number of categories; or (3) are highly
correlated to one another (Hooker et al. 2021). When
these conditions apply, as they do for predictors in
our soil P dataset, alternative measures of importance
such as conditional permutation importance (CPI)
may be more appropriate, and less biased towards col-
linear predictive variables (Debeer and Strobl 2020;
Hooker et al. 2021). CPI aims to capture the depend-
ence between a predictor and the response variable,
conditionally on the values of all other predictors.
That is, CPI is a measure that can be used to assess
how much each variable contributes to accurately pre-
dicting the response variable, given what we know
from all other predictive variables. The tradeoff is that
CPI methods can be computationally expensive. To
derive less biased estimates of variable importance
to the random forest model performance, we imple-
mented the CPI approach from the permimp package
in R (Debeer et al. 2021). This approach builds upon
the widely used party package for CPI, while offering
improved computational speed, accounting for non-
linear dependence between predictors, less sensitivity
to dataset sample size, and greater stability of results
(Debeer and Strobl 2020). To date, permimp can be
applied to randomForest or cforest model objects in
R (but not to ranger objects). In permimp, a thresh-
old value, equal to 1—the p-value for the associa-
tion between predictor variables, is used to determine
whether to include a predictor in the conditioning for
the predictor of interest. We used the default value for
the threshold parameter in permimp (0.95) because
Debeer and Strobl (2020) advised utilizing threshold
values close to 1 for larger datasets.
Predicting soil P across the Upper Mississippi River
Basin
One of our goals of this effort was to predict soil P
values for unsampled locations across the UMRB.
To do this, we created a grid of points spaced 100 m
apart across the entire UMRB (UMRB grid), using
the Create Fishnet tool in ArcMap version 10.8. We
linked these locations to the same set of attributes
used in our random forest model (i.e., attributes from
the NHDPlusv2, NLCD 2006, NWI, gSSURGO, and
StreamCat datasets). We excluded grid locations that
coincided with locations of open water. We used the
High-Performance Cluster at the University of Min-
nesota’s Supercomputing Institute (https://​www.​msi.​
umn.​edu/) to assign attributes to the UMRB grid
points, and to generate predictions for the grid loca-
tions using the random forest model we developed.
For this effort, we assigned all predictions to the soil
surface (max depth = 30 cm). Lastly, we used the
Inverse Distance Weighting (IDW) tool in ArcMap
version 10.8 to interpolate a raster surface of soil P
values at the 100 m grid scale for the UMRB.
Results
Soil phosphorus
Mean soil total P for the broader Midwestern
region included in the study was 580 mg/kg (range
17–4370 mg/kg). The distribution of soil P val-
ues showed a slight right skew (Fig. 3). The dataset
was comprised of 1,761 samples that could be con-
sidered to occur in the “plowable layer” at the soil
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Fig. 3  Distribution of P
concentrations for all soil
samples included in the
dataset (n = 6,683). Blue
dashed line indicates mean
value (580 mg/kg). Black
dot-dash line indicates
cut off (1000 mg/kg) for
samples used in the random
forest model
surface (i.e., <  = 30 cm deep), and 5,128 samples that
occurred at depths > 30 cm (i.e., ‘subsurface’ sam-
ples). Surface soil samples had a mean total P con-
centration of 585.6 mg/kg (range = 80—4370 mg/kg).
Subsurface soil samples had a mean total P concentra-
tion of 592.6 mg/kg (range = 17—4280 mg/kg). The
dataset contained 1,085 samples that were located in
“near channel” or riparian areas (i.e., within a 100 m
buffer of the NHDv2Plus stream network), and 5,798
samples that were non riparian or located outside of
the stream buffer zone (Fig. S5). The dataset also
contained 309 samples that were located within wet-
land soils, and 6,574 that were located in nonwetland
soils.
Across all samples, 352 samples (5%) had soil
P > 1000 mg/kg and were distributed throughout the
study region (Figure S1). A very small number of
samples (n = 5) had soil P > 3000 mg/kg. All of these
samples occurred in the National Geochemical Sur-
vey dataset. We examined the original field notes for
these samples to ascertain if these values could be
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Biogeochemistry
attributed to error or other specific site features, but
there was no obvious information pointing to sam-
pling or analytical error.
Relative to samples with soil P < 1000 mg/kg,
samples with very high soil P were located in areas
with higher median crop productivity index for corn,
lower available water storage in the root zone, rela-
tively higher contribution of groundwater to streams
in the local catchment and watershed, relatively
higher rates of N deposition (as ­NO3−, ­NH4+ and
inorganic N), higher pesticide and fertilizer use,
higher precipitation and runoff, and higher cropland
cover in the catchment, watershed and riparian zone
(See SI Table S2). Higher contributions of groundwa-
ter to stream and river flow could indicate high per-
meability (like karst), a large contribution of drain tile
(Schilling and Libra 2003), or a lower contribution of
surface water such as in the drier western part of the
basin. Overall, predictor values for samples with high
soil P suggest that very high soil P samples occur on
average in areas with greater precipitation and well
Biogeochemistry
Fig. 4  Actual vs predicted total soil P (mg/kg) for soil sam-
ples in the independent test dataset (i.e., not used to build the
model). R2 = 0.58, RMSE = 0.129.3, p < 0.0001. Note that the
random forest model was run using centered and scaled values
of P, but unscaled values are shown here for easier interpreta-
tion
drained soils, which are also associated with areas of
more intense agriculture in the UMRB. This rationale
makes sense for samples located in parts of the study
region (e.g., Iowa), where these conditions are likely
to occur. However, the spatial distribution of sam-
ples with high soil P (Figure S1) indicates that many
of them also occurred in northern areas of the basin
characterized by relatively little agriculture (e.g.,
northern Minnesota).
Model performance
The original model included all soil P samples in
model training and testing; however, this resulted in
a model that tended to underpredict soil P for sam-
ples > 1000 mg/kg (SI Figure S2). As a result, we
decided to increase model prediction accuracy for the
vast majority (95%) of soil samples in our dataset by
excluding the 5% of samples with soil P > 1000 mg/
kg from the training and testing datasets (see Dis-
cussion). The final selected hyperparameters for the
random forest model based on model tuning with ten-
fold cross validation for this dataset were mtry = 50,
trees = 1000, min_n = 3. Evaluation of predicted vs
actual soil P values for the independent test dataset
indicated a model RMSE of 0129.3, and an R ­ 2 of
0.58, for soil P samples < 1000 mg/kg (Fig. 4).
Predictive variable importance
Using the permimp function to estimate conditional
permutation importance (CPI) for predictors in our
model indicated that soil sample depth had by far
the strongest relative impact on model performance,
followed by land use in the immediate area (i.e., the
30 m grid cell) in which the soil sample was collected
(Fig. 5). The remaining top predictive variables are
shown ranked by importance in Fig. 5 and Table 1.
In addition to sample depth and local land use, the
top predictors ranked for importance included aspects
of catchment- and watershed-scale land use (includ-
ing aspects of urban land use, the extent of impervi-
ous surfaces, open water cover, barren land cover,
and urban and agricultural land use in riparian areas),
underlying soil properties (e.g., soil characteristics
such as organic matter and mineral content, water
storage and permeability), landscape properties (such
as slope, elevation, and whether sites were located
adjacent to the stream network), inputs (includ-
ing atmospheric deposition as well as fertilizer and
manure inputs), and climate factors (including tem-
perature and precipitation; Table 1). Additional pre-
dictors beyond this set did not appear to contribute
strongly to model accuracy once all other variables
had been accounted for.
Examining some of these attributes in relation
to soil P in more detail, we find that the highest
soil P concentrations (> 750 mg/kg) were found
almost exclusively in samples collected at a depth
of 100 cm or shallower, i.e., comparatively closer to
the surface. Nearly all samples deeper than 100 cm
had soil P < 750 mg/kg (SI Figure S3). Among
NLCD land use categories, samples collected in
areas designated as open water, shrub/scrub, culti-
vated crops, developed/open space and grassland/
herbaceous had higher mean soil P concentrations
than the total dataset average, whereas other cate-
gories had comparatively lower soil P (Figure S4).
Riparian soils (i.e., soils located within 100 m of
the NHDv2Plus stream network) had significantly
higher soil P (mean soil P = 646 mg/kg) compared
to non-riparian soils (mean soil P = 580 mg/kg;
unpaired t test t = − 7.04, df = 1456., p < 0.00001;
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Fig. 5  Conditional Permutation Importance (CPI) values
of covariates in the random forest model for soil P samples
with soil P < 1000 mg/kg. CPI is a measure that can be used
to assess how much each variable ‘adds’ to accurately predict-
ing the response variable, given what we know from all other
Figure S5). However, caution should be used when
applying univariate relationships to aid in the inter-
pretation of importance values for the random forest
model. Because the random forest model is based
a series of successive data splitting events (i.e.,
decision trees) where data is binned into branches
of groups based on predictive variable split points,
the predictor values useful in parsing these groups
may not be readily apparent from univariate
relationships.
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covariates. Additional covariates beyond those shown did not
show a strong impact on model performance, once all other
covariates were accounted for. Full covariate descriptions are
listed in Table 1
Predicting soil P for the Upper Mississippi River
Basin
Figure 6 shows predicted total soil P values for the
soil surface (max depth = 30 cm) of the UMRB at the
100 m grid scale, based on the random forest model.
The predictions indicate the highest concentrations of
total soil P in northern Iowa, southern Minnesota, and
north-central Illinois. The lowest predicted concen-
trations occurred in northern and north/north-central
Biogeochemistry

Table 1  Top covariates, as ranked by conditional permutation importance (CPI), to the performance of the random forest model
Abbreviation Category Short description Source layer

Depth_cm Underlying soil properties Soil depth (cm) NGS/NCSS

NLC06 Land use Land use category in the 30 m grid cell where soil sample NLCD 2006
was collected
PctImp2006CatRp100 Land use % Impervious in riparian zones within catchment StreamCat
PctImp2006Cat Land use % Impervious within catchment StreamCat
PctBl2006Ws Land use % Barren land within watershed StreamCat
P2O5Cat Underlying soil properties Mean % lithological phosphorous oxide content in surface StreamCat
geology within catchment
PctOw2006WsRp100 Land use % Open water in riparian zones within watershed StreamCat
slope_r Landscape properties Mean slope in gSSURGO map unit gSSURGO
RdDensCatRp100 Land use Road density in riparian zones within catchment StreamCat
nccpi3corn Underlying soil properties National commodity crop productivity index for corn in gSSURGO
gSSURGO map unit
PctGlacLakeCrsCat Underlying soil properties % of catchment area classified as coarse-textured glacial StreamCat
outwash & glacial lake sediment
NO3_2008Cat Inputs Mean NO3 wet deposition within catchment StreamCat
HydrlCondCat Underlying soil properties Mean lithological hydraulic conductivity in surface geol- StreamCat
ogy within catchment
sieveno200_r Underlying soil properties Mean soil fraction passing a #200 sieve (0.074 mm square gSSURGO
opening) for gSSURGO map unit
PctUrbOp2006CatRp100 Land use % Developed, open space in riparian zones within catch- StreamCat
ment
NO3_2008Ws Inputs Mean NO3 wet deposition within watershed StreamCat
ElevCat Landscape properties Mean elevation within catchment StreamCat
PctUrbLo2006Cat Land use % Developed, low intensity land use within catchment StreamCat
OmCat Underlying soil properties Mean organic matter of soils within catchment StreamCat
MgOCat Underlying soil properties Mean lithological magnesium oxide (MgO) content in StreamCat
surface geology within catchment
BFICat Landscape properties Ratio of baseflow to total flow within catchment StreamCat
PctGlacLakeCrsWs Underlying soil properties % of watershed classified as coarse-textured glacial out- StreamCat
wash and glacial lake sediment
Al2O3Cat Underlying soil properties Mean lithological aluminum oxide content in surface geol- StreamCat
ogy within catchment
aws0_30 Underlying soil properties Mean available water storage at 0–30 cm depth for gSSURGO
gSSURGO map unit
soc150_999 Underlying soil properties Mean soil organic carbon stock from 150 cm to max gSSURGO
reported depth of the soil profile for gSSURGO map unit
AgKffactCat Underlying soil properties Mean soil erodibility factor on ag land within catchment StreamCat
WetIndexWs Underlying soil properties Mean composite topographic (wetness) index within StreamCat
watershed
nccpi3sg Underlying soil properties National commodity crop productivity index for sorghum gSSURGO
in gSSURGO map unit
FertWs Inputs Mean rate of synthetic N fertilizer application to ag land StreamCat
within watershed
aws0_999 Underlying soil properties Available water storage in total soil profile in gSSURGO gSSURGO
map unit
Al2O3Ws Underlying soil properties Mean lithological aluminum oxide content in surface geol- StreamCat
ogy within watershed

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 Biogeochemistry

Table 1  (continued)
Abbreviation Category Short description Source layer

aws0_20 Underlying soil propertiesAvailable water storage estimate at 0–20 cm depth in gSSURGO
gSSURGO map unit
PctUrbLo2006CatRp100 Land use % Developed, low intensity land use in riparian zones StreamCat
within catchment
WtDepWs Underlying soil properties Mean seasonal water table depth of soils within watershed StreamCat
StreamType Landscape properties Whether soil samples were collected within riparian buffer NHDv2Plus
of stream network
SN_2008Ws Inputs Mean wet deposition for average sulfur and nitrogen within StreamCat
watershed
nccpi3all Underlying soil properties National commodity crop productivity index for all crops gSSURGO
in gSSURGO map unit
nccpi3soy Underlying soil properties National commodity crop productivity index for soybean in gSSURGO
gSSURGO map unit
Fe2O3Ws Underlying soil properties Mean lithological ferric oxide content in surface geology StreamCat
within catchment
aws0_150 Underlying soil properties Mean available water storage in top 150 cm of soil depth in gSSURGO
gSSURGO map unit
PctOw2006Cat Land use/landscape properties % Open water within catchment StreamCat
RdCrsCat Land use Road crossings in catchment StreamCat
PermCat Underlying soil properties Mean permeability of soils within catchment StreamCat
aws50_100 Underlyings soil properties Available water storage in 50–100 cm depth in ssurgo map gSSURGO
unit
CaOWs Underlying soil properties Mean lithological calcium oxide content in surface geology StreamCat
within watershed
PctHay2006WsRp100 Land use % Hay in riparian zones within watershed StreamCat
TmaxCat Climate 30 year normal max temperature, 1981–2010, within catch- StreamCat
ment
PctEolFineWs Underlying soil properties % of catchment area classified as eolian sediment, fine- StreamCat
textured (glacial loess)
PrecipWs Climate PRISM climate data—Mean precipitation (mm) within the StreamCat
watershed. Period: 2008
PctCrop2006WsRp100 Land use % Crop land use in riparian zones within watershed StreamCat
ElevWs Landscape properties Mean watershed elevation (m) StreamCat
BFICat Landscape properties Ratio of baseflow to total flow within catchment StreamCat
SN_2008Cat Inputs StreamCat
RunoffWs Landscape properties/climate Mean runoff (mm) within watershed StreamCat
CompStrgthWs Underlying soil properties Mean lithological uniaxial compressive strength content in StreamCat
surface geology within watershed
ManureCat Inputs Mean rate of manure application to ag land from CAFOs StreamCat
within catchment
PctImp2006Ws Land use % Impervious surfaces within watershed StreamCat
claytotal_r Underlying soil properties % Clay for soils in gSSURGO map unit gSSURGO
Na2OCat Underlying soil properties Mean lithological sodium oxide content in surface geology StreamCat
within catchment
Na2OWs Underlying soil properties Mean lithological sodium oxide content in surface geology StreamCat
within watershed
FertCat Inputs Mean rate of synthetic nitrogen fertilizer application to ag StreamCat
land within catchment
PctUrbHi2006CatRp100 Land use % developed, high-intensity land use within catchment StreamCat

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Biogeochemistry

Table 1  (continued)
Abbreviation Category Short description Source layer

NH4_2008Cat Inputs Mean wet deposition for ammonium ion concentration StreamCat
2008 within catchment
PermWs Underlying soil properties Mean permeability of soils within watershed StreamCat
PctUrbOp2006Ws Land use % Developed, open space land use within watershed StreamCat
Attributes are designated by major categories including ‘land use’, ‘underlying soil properties’, landscape properties’, ‘inputs’, and
‘climate’. More detailed descriptions of each attribute are available in SI Table S1. ‘Riparian zones’ refers to the 100 m buffer sur-
rounding the NHD stream network

Fig. 6  Predicted total soil P

(mg/kg) for the soil surface
(max soil depth = 30 cm)
at the 100 m grid scale for
the Upper Mississippi River
Basin

Wisconsin, and in southern Illinois and southern Discussion

Missouri.
Soil P across the study region

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Here, we have assembled a large dataset of total
P concentrations for soils across the Midwestern
United States from publicly available datasets and
used them to predict total soil P at fine resolution
across the UMRB, as well as to identify predic-
tors that were comparatively important to model
accuracy. These soil datasets, collected by federal
agencies over relatively long time periods and large
spatial extents, have great potential utility in the
analysis of dynamics in soil and water chemistry,
but the availability of these datasets is not widely
known and they are not uniformly organized (and
require considerable pre-processing), possibly
leading to their underutilization in the study of soil
nutrient dynamics. Our study highlights the poten-
tial of existing publicly-funded datasets to support
ongoing studies and management design related to
soil and water health. For this reason, we provide
the collated dataset together with the metadata and
code in an open science framework available in the
open access Github repository (https://​github.​com/​
cldol​ph/​SoilP).
The range of total P concentrations reported
here for soils of the Midwestern United States
(mean = 580 mg/kg, range = 17–4370 mg/kg) is
similar to that reported by Schilling et al. (2021)
for riparian soils across Iowa (mean = 460 mg/kg;
range = 109–1569 mg/kg; though it should be noted
that the latter study used the aqua regia digestion
method for measuring total P which can sometimes
result in slightly lower measured P concentrations
(J. Kovar, personal communication), rather than
the HCl digestion method used for the samples
in this study. Riparian soils in our study averaged
slightly higher total P (646 mg/kg) compared to
those measured by Schilling et al. (2021). Ringeval
et al. (2017) developed models to simulate total P
for cropland soils globally and estimated the global
average for total P in cropland soils to be 567 mg/
kg; however, their simulated total P values for soils
in North America ranged considerably higher, typi-
cally above 1000 mg/kg.
Model performance
Heterogeneity in total soil P is the outcome of
potentially complex interacting drivers including
geology, hydrology, climate, biogeochemical pro-
cesses, and specific land use practices. Given this
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complexity, we view the predictive accuracy of our
random forest model as relatively high ­ (R2 = 0.58
and RMSE = 129.3 for an independent validation
dataset). The RMSE for our model represents 24%
of mean soil P for the validation dataset, which is
comparatively more accurate than P prediction mod-
els developed at smaller scales in Europe and Russia
(Matos-Moreira et al. 2017 and references therein;
Sahabiev et al. 2021). Our model performance is also
considerably stronger than that for continental-scale
predictive models developed using similar methods
for soil organic carbon and total nitrogen by Ram-
charan et al. (2018). However, the model developed
here underpredicts total soil P for samples with very
high soil P (> 1000 mg/kg). Although such samples
comprised a relatively small proportion of our total
dataset (~ 5%), underestimating soil P content for
these samples may be substantively important if they
represent hotspots for P accumulation and ultimately
transport. Understanding the drivers of very high soil
P samples in this study region is an important area for
future research. Knowledge of specific land use prac-
tices at finer scales than those used in our study (e.g.,
fertilizer or manure application at field scales smaller
than the catchment or watershed scales available for
land use practices in the StreamCat dataset), could
also potentially help with predictive accuracy. Inten-
sive animal agriculture (e.g., CAFOs) and associated
manure inputs in particular have been shown to coin-
cide with areas of P accumulation (Stackpoole et al.
2019). Future research could also explore whether a
classification-based approach (i.e., applying expert
judgment to group numeric soil P estimates into bio-
chemically meaningful categories such as ‘very high’,
‘high’, moderate’, ‘low’ etc.) rather than the regres-
sion approach used here might enable random forest
models to more accurately identify hotspots or areas
of very high soil P.
Predictive variable importance
Our analysis indicates that, at the regional scale rep-
resented by our model, the variables with the greatest
comparative importance for predicting soil P included
sample depth, land use, underlying soil properties,
landscape properties, P inputs, and climate. Soil sam-
ple depth was the most comparatively important vari-
able to model performance, with soil P tending lower
with increased depth (Figure S3). This finding echoes
Biogeochemistry
Ramcharan et al. (2018), who found depth to be con-
sistently ranked as one of the most important predic-
tors for random forest models developed for soil prop-
erties including total nitrogen and soil organic carbon.
Land use in the immediate areas (30 m grid) where
soil samples were collected was the second most
important variable to model accuracy, according to
the conditional permutation importance measure we
used. The comparatively high ranking of land use/
land cover differs somewhat from that of Ringeval
et al. (2017), who found, using a different modeling
approach, that the main driver of variability for total
soil P at a global scale was the soil biogeochemical
background corresponding to P inherited from natu-
ral soils. However, at smaller (continental) scales,
Ringeval et al. (2017) found farming practices were
also important in driving heterogeneity in total soil P,
though still less important than native soil properties.
At a smaller scale, Kaya and Başayiğit (2022) found
that for an alluvial plain (~ 100 ­km2) characterized
by intensive agriculture, land cover classes were the
most important attributes to predicting soil P. For a
small watershed in Brittany, France, Matos-Moreira
et al. (2017) found that information about agricultural
practices contributed more to machine learning mod-
els for extractable P than for total P, whereas mod-
els for total P relied more strongly on soil and parent
material attributes.
In our study, land use in the immediate area of a
soil sample was more important to accurately pre-
dicting soil P than soil properties at the gSSURGO
map unit scale and more important than measures
of land use at catchment or watershed scales. Given
this finding, a question for future research would
be whether more specificity in soil properties and
land use practices at the hyper local scale (e.g., on-
field practices such as fertilizer and manure input,
specific crop type, tillage practices at the field or
30 m grid scale, etc.) could lead to improvements
in models for predicting soil P across the Midwest.
Matos-Moreira et al. (2017) suggested that detailed
information about crop rotation in particular may
improve the accuracy of soil P prediction models,
as it correlates with a number of agricultural prac-
tices, including fertilizer and pesticide application
and soil tillage.
Model variables associated with urban or high-
density areas, including extent of impervious sur-
faces, urban land use, and road density, were all
ranked as relatively important to model performance.
This finding suggests that soil P in urban or high-
density areas may be distinct from other landscapes.
However, several ranked “urban” attributes describe
the extent of low density or “open” urban land use,
which are indicative of suburban and exurban land-
scapes and may indicate that these landscapes are also
distinct in terms of soil P. Although soil P dynamics
in urban areas are relatively under-studied, they have
been identified as hotspots for P cycling, with dis-
tinct drivers that influence P stocks and flows (Met-
son et al. 2015). For example, Hobbie et al. (2017)
observed that urban watersheds in our study region
retained comparatively little of their P inputs, and
that the majority of annual P inputs were exported via
stormwater flows. Additional research is needed to
understand drivers of total soil P in urban and subur-
ban landscapes and how these may differ from those
in agricultural settings.
Riparian attributes summarized at the catchment
or watershed scale (e.g., the % of crop, hay or urban
land use cover in catchment or watershed-scale ripar-
ian zones) were also identified as relatively impor-
tant to model prediction accuracy. This finding could
result from the fact that land use in riparian zones
may be indicative of a particularly intensive form of
land use—i.e., if riparian zones are used for crops,
hay or dominated by urban land use, this may indi-
cate particularly intensive landscapes for these uses
in a way that affects soil P. Conversely, these driv-
ers may be strongly affecting soil P in riparian areas,
and therefore could have been important for model
accuracy for riparian samples. A categorical attrib-
ute (‘StreamType’) describing whether a sample was
collected in the riparian buffer of the stream network
(and which kind of stream reach it was adjacent to
such as a ditch, stream, river etc.) also appeared in
the list of important variables to model performance.
Post hoc analysis indicated that riparian areas (soils
within 100 m of the stream network) had significantly
higher total P (646 mg/kg) compared to non-riparian
areas (580 mg/kg). This echoes the finding by previ-
ous studies which have noted riparian and wetland
areas as potential sinks, and ultimately sources, of P
in agricultural landscapes (Kleinman et al. 2022).
Soil properties that were ranked as important to
model performance included the native P content
(as phosphorus oxide) and mineral content (alu-
minum, iron, calcium, and sodium oxides) of soils,
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along with aspects of soil texture, water storage and
depth, soil organic carbon/organic matter, glacial his-
tory, hydraulic conductivity, erodibility, and suitabil-
ity of soils for growth of various crop types. Exten-
sive research has documented the importance of soil
compounds such as iron and aluminum oxides and
calcium carbonate on soil P retention and release
(Records et al. 2016). Likewise, soil organic mat-
ter content has been shown to have direct and indi-
rect effects on P sorption capacity (e.g., Kang et al.
2009). And as documented recently by Plach et al.
(2018), the parental origins of soil and their glacial
history have a potentially strong effect on the physical
and geochemical properties of soil which can subse-
quently affect P retention and transport. Our findings
likewise indicate that many of these properties are
important for accurately predicting soil P across Mid-
western landscapes.
Nitrate and ammonium deposition at the catch-
ment scale, as well as fertilizer and manure inputs at
the catchment scale, were all identified as important
to model performance. Atmospheric deposition of
nitrogen could be an indicator of the proximity of fos-
sil fuel combustion, fertilizer or manure application
or livestock emissions (Russell et al. 1998), which
may also affect soil P.
Predictors summarizing aspects of climate, land-
scape properties, and their interaction—including
precipitation, temperature, runoff, slope, and the con-
tribution of groundwater to baseflow—also appeared
to affect model performance. Recent work has shown
that both temperature and precipitation are important
to soil P availability at a global scale and may have
contrasting effects (Hou et al. 2018). Slope and result-
ing erosional processes (whether driven by human
land use, climate, or other factors) also have a pro-
found effect on erosional and subsequent biogeo-
chemical processes that may affect soil P (Berhe et al.
2018).
In addition to land cover, a major driver of hydrol-
ogy and water-soil interactions in the UMRB is the
vast network of subsurface tile drainage that charac-
terizes much of the region (Schottler et al. 2013). The
predictor datasets we used did not include informa-
tion about subsurface drainage. Although tile drain-
age has important ramifications for downstream
transport of P (Smith et al. 2015), it may have less
of an impact on total soil P. For example, based on
soil P data assembled here, average total soil P in the
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Biogeochemistry
UMRB is 580 mg/kg. If we assume a soil bulk den-
sity of 1.4 (Jacobson et al. 2011), this average soil
P concentration equates to ~ 8,120 kg/ha of P in the
top meter of the soil. By comparison, previous stud-
ies have shown yearly P losses from tile drains to
be ~ 0.01% of this amount (e.g., 0.5—1.0 kg/ha/yr;
King et al. 2015; Dialameh and Ghane 2022). Mean-
while, P inputs may be ~ 12–25 kg/ha/yr, depending
on the crop rotation (Potter et al. 2010). Thus, while
accounting for tile drainage impacts is critical to
understanding losses of P to downstream water bod-
ies, it may be less important to accurately estimating
total soil P. In addition, it is likely that the presence
and density of tile drainage co-varies with other pre-
dictors already included in our model. For example,
attributes included in the model that relate to land
use, slope, soil texture and soil drainage class corre-
late with tile drainage (Valayamkunnath et al. 2020).
Future research in this area may consider using tile
drainage as a proxy for a more complex suite of soil
and management parameters if detailed soils data are
not available.
It is important to note that methods for the esti-
mation of variable importance within random for-
est models is an active area of research (Debeer and
Strobl 2020), with rapid development of prospective
improvements to “opening up” the black box of ran-
dom forest models. We applied a recently developed
approach that is aimed at examining the conditional
importance of predictors, which may give differ-
ent results than more commonly applied importance
measures. Care should be taken when interpreting
these results relative to other modeling approaches if
different methods for importance estimation are used.
Limitations and future directions
Our initial goal in developing the machine learning
model described here was to determine if we could
make accurate predictions for soil P across a broad
geographic area, for use in future biophysical mod-
eling and conservation planning applications in the
UMRB. Because the UMRB contains considerable
variation in underlying soil properties, land cover and
soil P values, we included a large number of potential
predictor variables in our machine learning frame-
work to improve model accuracy as much as possible.
Complex models often perform more accurately than
Biogeochemistry
simpler ones (Wadoux et al. 2020). Indeed, our model
performed relatively highly in terms of accuracy com-
pared with other machine learning models for soil
attributes, possibly because of the large number of
predictors included. The downsides of this approach
include the considerable time and effort required to
assemble and curate such a large dataset of predic-
tors, as well as increased difficulty in interpreting
the role of so many variables in predicting soil P. A
third challenge stemming from the use of hundreds
of heterogeneous predictors is the way it complicates
predictions for soil P at unknown locations. Because
we assembled predictors from existing disparate
public datasets, these variables were not summa-
rized at consistent spatial resolution and extent. For
example, data from the StreamCat dataset was sum-
marized at catchment and watershed scales, whereas
gSSURGO data is summarized at the SSURGO map
unit scale, etc. This variability presents an obstacle
to the application of recently developed approaches
to spatial prediction; e.g., where machine learning
is performed using stacks of raster data organized
at the same spatial extent and resolution (Hengl and
MacMillan 2019). We chose to predict soil P at the
scale of a 100 m grid to provide fairly fine resolution
data for a large geographic extent given the hundreds
of heterogeneous predictors we had access to. How-
ever, the disadvantage of this approach is that impor-
tant fine scale spatial variation in soil P could still
be obscured. Future work could further investigate a
soil P model in the context of parsimonious model
design and evaluate whether simpler machine learn-
ing models with fewer predicting variables could per-
form as well as the more complex one developed here
(Wadoux et al. 2020).
Conclusion
Here we have used existing, large public soil chem-
istry and geospatial datasets together with a random
forest model to generate predictions of total soil P at
fine spatial resolution across the Upper Mississippi
River Basin in an open science framework. Predicted
soil P values are publicly available as a raster data
layer at https://​github.​com/​cldol​ph/​SoilP. The combi-
nation of large existing datasets with powerful analyt-
ical tools like machine learning in a high-performance
computing environment offers new possibilities for
understanding and predicting complex biophysical
phenomena such as soil P at fine scales. Such pre-
dictions could be useful when combined with water-
shed models to improve estimates of P loss from this
largely agricultural landscape. Improved knowledge
of critical source areas of soil P to include under-
sampled locations is necessary to develop effective
regional conservation plans and prioritize resources
such that they can reduce the accumulation and trans-
port of P across landscapes.
Acknowledgements We would like to thank Zhen Xu for
alerting us to the availability of the USGS soil dataset. Ran-
dom forest model tuning and predictions were performed on
the High Performance Cluster at the University of Minne-
sota’s Supercomputing Institute, https://​www.​msi.​umn.​edu/.
This project was funded by a U.S. Department of Agricul-
ture Conservation Effects Assessment Project (CEAP) grant
#NR203A750023C023
Author contributions All authors contributed to the study
conception and design. Material preparation, data collection
and analysis were performed by CD. R script quality control
was performed by SJC, S.Cho also designed Fig. 2. The first
draft of the manuscript was written by CD and all authors com-
mented on previous versions of the manuscript. All authors
read and approved the final manuscript.
Funding This project was funded by a U.S. Department of
Agriculture Conservation Effects Assessment Project (CEAP)
Grant #NR203A750023C023.
Data availability The datasets and R scripts generated dur-
ing and/or analysed during the current study are available in the
Soil P repository, https://​github.​com/​cldol​ph/​SoilP.
Declarations
Competing interests The authors have no relevant financial
or non-financial interests to disclose.
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