Ecological Modelling 354 (2017) 104–114

Contents lists available at ScienceDirect

Ecological Modelling
journal homepage: www.elsevier.com/locate/ecolmodel

An integrated ecological modeling system for assessing impacts of

multiple stressors on stream and riverine ecosystem services within
river basins
John M. Johnston ∗ , M. Craig Barber, Kurt Wolfe, Mike Galvin, Mike Cyterski,
Rajbir Parmar
USEPA/ORD/NERL, 960 College Station Rd., Athens, GA 30605, United States

a r t i c l e i n f o a b s t r a c t

Article history: We demonstrate a novel, spatially explicit assessment of the current condition of aquatic ecosystem
Received 16 September 2016 services, with limited sensitivity analysis for the atmospheric contaminant mercury. The Integrated Eco-
Received in revised form 21 March 2017 logical Modeling System (IEMS) forecasts water quality and quantity, habitat suitability for aquatic biota,
Accepted 21 March 2017
fish biomasses, population densities, productivities, and contamination by methylmercury across head-
Available online 14 April 2017
water watersheds. We applied this IEMS to the Coal River Basin (CRB), West Virginia (USA), an 8-digit
hydrologic unit watershed, by simulating a network of 97 stream segments using the SWAT watershed
Keywords:
model, a watershed mercury loading model, the WASP water quality model, the PiSCES fish community
Spatially explicit exposure
Forecasting
estimation model, a fish habitat suitability model, the BASS fish community and bioaccumulation model,
Freshwater provisioning and an ecoservices post-processer. Model application was facilitated by automated data retrieval and
Fisheries model setup and updated model wrappers and interfaces for data transfers between these models from a
prior study. This companion study evaluates baseline predictions of ecoservices provided for 1990–2010
for the population of streams in the CRB and serves as a foundation for future model development.
Published by Elsevier B.V. This is an open access article under the CC BY license (http://
creativecommons.org/licenses/by/4.0/).

1. Introduction Vidal-Abarca et al., 2014). Reduction in the quality of water, includ-

Watersheds, streams and river basins provide multiple ecosys-
tem services, or ecoservices, that benefit human health and
well-being and contribute to the sustainability of our economic
and social systems (Costanza et al., 2012; MEA, 2005). Aquatic
ecoservices include the provisioning of water in sufficient qual-
ity and quantity for agricultural, industrial, and residential uses;
habitat provisioning for aquatic and riparian biota; a trophic base
for aquatic, riparian, and migratory biota; and fisheries for human
consumption and recreation whose biomasses, population den-
sities, productivities, and contaminant levels can be used safely
in a sustainable manner (Limburg, 2009). Land use and regional
development affect stream and riverine ecoservices through water
withdrawals for agricultural, industrial, and residential uses; inputs
of sewage effluents, increased nonpoint source pollution from
urban and agricultural runoff; atmospheric deposition of contam-
inants; and alteration of hydrologic cycles (Auerbach et al., 2014;
∗ Corresponding author.
E-mail addresses: johnston.johnm@epa.gov (J.M. Johnston), wolfe.kurt@epa.gov
(K. Wolfe), galvin.mike@epa.gov (M. Galvin).
ing its temperature, contaminant concentrations (both suspended
and dissolved) and aquatic habitat availability (including depth and
velocity) are primary stressors from human activity and climate
change. Regional atmospheric pollutant transport (e.g., mercury) is
an interdependent process, affecting multiple spatial and tempo-
ral scales and piggybacking on the hydrologic cycle as wet and dry
deposition (Knightes et al., 2009).
The assessment of the impacts of multiple stressors poses a sig-
nificant challenge to environmental decision making and requires
modeling approaches beyond single media (e.g., soil, surface water,
atmosphere, etc.) that unifies expert knowledge across modeling
domains, namely an Integrated Ecological Modeling System (IEMS)
(Johnston et al., 2000; USEPA, 2008). No one model can supply all
of these aspects, and an IEMS embraces system complexity to sup-
port holistic and effective decision making for a diverse stakeholder
audience (Laniak et al., 2013; USEPA, 2008). The ultimate goal is
to support environmental decisions with quantifiable estimates of
uncertainty and variability, as a necessary evolution of quantitative
process-based modeling for prediction and long term forecasting
of alternative future scenarios. Although sustainability assessment
requires the integration of social, economic and environmental

http://dx.doi.org/10.1016/j.ecolmodel.2017.03.021
0304-3800/Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
 J.M. Johnston et al. / Ecological Modelling 354 (2017) 104–114
systems, this study focuses on environmental system integration
of biological, ecological, physical and chemical processes of lotic,
freshwater ecoservices to develop system understanding and facil-
itate experimentation (Kiker et al., 2005).
Environmental assessments generally need to address two con-
trasting but complementary scales of resolution. On one hand what
is needed is an overall characterization of condition for the entire
region of interest, including the location of areas of concern (i.e.,
hotspots). On the other hand, there is also the need for more spa-
tially and temporally refined assessments at prioritized locations
of interest. That is, after a decision maker is informed about the
overall status of regional environmental resources, the question
of where and what management actions to implement (e.g., best
management practices for sediment control and when and how
to manipulate fisheries stocking and harvest) applies at specific
locations. The Watershed Health Assessment Tools Investigating
Fisheries (WHAT IF) decision support tool is an early example of
this methodology for fisheries management (USEPA, 2006). WHAT
IF includes an open-source GIS tool to address fisheries stocking
and harvest and stream habitat restoration, but it lacks the full
complement of multidisciplinary process models for assessment
of landuse and climate change and regional pollutant transport.
As such it represents an effective integration of scales of consid-
eration for stakeholders; however, it is not a coupled component
model useful for hydrologic and water quality process prediction,
forecasting and system understanding (Kelly et al., 2013).
Consequently, the US Environmental Protection Agency (USEPA)
developed a fully functional IEMS to simulate environmental
stressor-response relationships for a stratified, random sample of
headwater subwatersheds in the Albemarle-Pamlico river basin
of North Carolina and Virginia, US (Johnston et al., 2011), which
is an 8-digit Hydrologic Unit (HU) watershed as defined by the
U.S. Geological Survey National Hydrologic Unit Map (Seaber et al.,
1987). Each subwatershed corresponded to a 12-digit HU water-
shed defined by the same mapping system. Using a collection
of existing environmental and ecological models, this IEMS was
configured to forecast multiple ecoservices provided by the head-
water subwatersheds of the river basin. A similar approach has also
been applied to the assessment of watershed-based human health
risks from pathogen exposure to human and animal fecal microbial
sources (Whelan et al., 2014).
In contrast to our previous probabilistic assessment of the
ecoservices provided by 12-digit HU headwater subwatersheds
(Johnston et al., 2011), regional condition assessment requires
treatment of the spatial network of small stream and river seg-
ments, including non-headwater streams. Because assessment
scales include watershed (regional) and stream segment endpoints
(local), it was necessary to extend our previous IEMS beyond a head-
water subwatershed pour-point analysis. To do so, we expanded
the capabilities of our IEMS in this companion study to address
the requirement for spatially explicit assessment of streams and
rivers and applied our expanded IEMS to a new geography to test
its reusability, a key attribute of sophisticated and cost-effective
IEMSs (Laniak et al., 2013).
Mountaintop removal mining (MTR) is an example of a
watershed-based assessment problem that requires integration of
multiple stressors for assessment, including land use and climate
change, but also the ability to target streams of interest for reme-
diation and field monitoring. The Coal River Basin (CRB) is within
the central Appalachian coal field region, an area of substantial MTR
activity, and a tributary of the Kanawha River which drains a portion
of the Cumberland Mountains in south central and southwestern
West Virginia (WV) (Fig. 1). Although many of the environmental
and cultural resources are protected on the lower river for pub-
lic recreation (http://wvexplorer.com/attractions/rivers-streams/
coal-river/), these coal field watersheds also support the highest
105
levels of biodiversity and endemism in the temperate zone. The
upper Kanawha contains seven “at risk” species of fish and mus-
sels (Master et al., 1998). The CRB has also been the subject of a
prior USEPA study regarding its potential for recreational fisheries
as an alternate economic strategy and renewable resource, using
a macroecological modeling approach to estimate abundances of
the two most popular sport fish, smallmouth bass (Micropertus
dolomieu) and eastern brook trout (Salvelinus fontinalis) (McGarvey
and Johnston, 2013).
The primary purpose of this study was to demonstrate a spa-
tially explicit, watershed assessment of current condition of aquatic
ecoservices, with a limited sensitivity analysis for the atmospheric
contaminant mercury. Our objective in developing and applying
the IEMS to the CRB is to provide a foundation for watershed con-
dition assessment, though not addressing MTR stressors explicitly
at this time. Although the current study does not include MTR
sources and related stressors (e.g., metals, salts and pH), it pro-
vides a foundation for future work. Requirements of the IEMS are
developed with the MTR problem statement in mind; however, this
study is intended to demonstrate and verify the functionality of the
IEMS. Next steps regarding its application to MTR are addressed in
the Summary and conclusions. Application of the IEMS to a new
geography and problem also provides an opportunity to address
resources and time needed for its reuse (Laniak et al., 2013). We
include a discussion of reuse as appropriate to the application of
this IEMS. Model predictions are provided for 97 stream segments
for the period 1991–2010 for flow, water quality, habitat quality,
fishery production (game and non-game), and fish contamination
by methylmercury. This baseline assessment extends our previous
analysis from a stratified, random sampling approach of repre-
sentative subwatersheds and pour point segments to a spatially
explicit treatment of an entire headwater 8-digit HU that includes
networked, downstream responses and increased system variabil-
ity. We also perform sensitivity analysis of the IEMS with respect
to rates of atmospheric deposition of mercury and on the transport
and bioaccumulation of methylmercury in selected game fish.
2. Materials and methods
2.1. Study area
The study area is the CRB, 8-digit HU code 05050009, located in
southwestern WV (Fig. 1) and a tributary of the Kanawha River. It
is a headwater watershed located in the central Appalachian coal
field region with drainage area of approximately 2300 km2 . The CRB
intersects the Central Appalachian Mountains and the Allegheny
Plateau, and MTR activity is extensive, with 20% of the watershed
surface area affected by current and expired mines (McGarvey and
Johnston, 2013).
2.2. IEMS configuration and initialization
The IEMS was configured to generate annual outputs for the
simulation period (1990–2010) (Fig. 2). This simulation time frame
included approximately 10 years to remove the effects of initial
conditions. Hydrologic inputs were time varying for the IEMS spin-
up, with precipitation input corresponding to weather data for
the period 2000–2010. Dissipation of the IEMS transient behav-
iors occurred after the longest lived fish species reached dynamic
steady state. Summary statistics for annual mean, median and stan-
dard deviation were calculated for all 97 stream segments for each
20-year simulation.
The Charleston, WV, Yeager airport weather station
(ID WV461570, http://www.nws.noaa.gov/climate/probability.
php?wfo=rlx&site=461570&lead=8) located in Kanawha County
was used for precipitation and related weather data, and land
use data were from the 2010 National Land Cover Database
106 J.M. Johnston et al. / Ecological Modelling 354 (2017) 104–114
Fig. 1. Coal River Basin (CRB) study area 8-digit HU code 05050009 located in southwestern West Virginia, including the network of 97 stream and river segments.
(http://www.mrlc.gov/). The CRB stream network was derived
from the U.S. National Hydrography Dataset (NHD), scale 1:24
000 (http://nhd.usgs.gov/). The primary purpose of this study
was to demonstrate a spatially explicit watershed assessment of
current condition of aquatic ecoservices, with a limited sensitivity
analysis for the atmospheric contaminant mercury. Because of
this focus, Monte Carlo analysis performed in the previous study
was not included. The IEMS utilized only the components D4EM
and FRAMES for automated data retrieval, model input and model
execution.
2.3. IEMS interoperability and reuse
Interoperability is a case of model reuse and involves mod-
ifications to a model or the modeling framework for use in a
different problem statement or study location (Laniak et al., 2013).
In this study, we reused the IEMS from the Albemarle-Pamlico
watershed to model the CRB. We did not change either the mod-
eling infrastructure (FRAMES v.2, Framework for Risk Assessment
in Multimedia Environmental Systems) nor the science models
SWAT (Soil Water Assessment Tool), WASP (Water Quality Analysis
Simulation Program), MLM (Mercury Loading Model), HSI (Habi-
tat Suitability Index), BASS (Bioaccumulation and Aquatic System
Simulator) or the ESP (Ecosystem Services Processor) which are
described in detail elsewhere (Johnston et al., 2011). A new model
was developed, PiSCES (Piscine Stream Community Estimation Sys-
tem), to more flexibly estimate fish community composition for
streams and rivers. The primary differences from the prior study
were that all models were executed on all stream segments, requir-
ing changes to all science model wrappers to enable reading and
writing of input and output, and modification to FRAMES input and
output dictionaries to read and write data indexed by stream seg-
ment. Models downstream of the WASP model (PiSCES, HSI, BASS
and ESP) were affected, requiring indices for stream segment and
fish species. In this study, for example, the HSI model wrapper
read the PiSCES output dictionary for fish community diversity and
biomass data, iterating over all stream segments.
2.4. PiSCES model description
PiSCES provides an expected species-specific fish assemblage
for each stream segment as well as initial species biomasses nec-
essary for simulating community dynamics (i.e., inputs to the BASS
model). PiSCES filters the expected distributions of all species (i.e.,
known and historic ranges) based on watershed and stream prop-
erties (e.g., drainage area, stream slope, stream temperature, etc.). A
detailed description of PiSCES and its design is addressed separately
(Cyterski et al., 2017). PiSCES represents a substantial enhance-
ment to our previous IEMS which utilized statistical approaches
to determine probable fish communities from field datasets. It is
often the case that fisheries data are not available for waterbod-
ies of interest, including within the CRB, nor are these data easily
accessible through the Internet (McGarvey and Johnston, 2013). As
such, characterization of regional fisheries can be a limiting step
requiring additional time and effort and is not easily automated
(e.g., as a Data for Environmental Modeling, or D4EM, external data
retrieval and model input use case). This can be a significant barrier
to model reuse (Laniak et al., 2013). To overcome the reliance on
field data and the resources needed to compile, quality assure and
statistically analyze the data, an alternative approach formulated in
the novel PiSCES model was developed. Historic and current geo-
graphic range data and species habitat preferences (described as
 J.M. Johnston et al. / Ecological Modelling 354 (2017) 104–114
Fig. 2. CRB integrated modeling study within IEMS interface with linked models and system service (top panel), excerpt from FRAMES simulation diagram within the
Simulation Editor.
occurrence envelopes) were used to derive probable fish commu-
nities. Occurrence envelopes were statistically derived from field
data for quantities such as stream width, watershed drainage area
and stream temperature (to name a few examples), with the expec-
tation that these envelopes are useful filters to superimpose on
raw distributional data for improved accuracy of predicting fish
communities for locations lacking field data (Cyterski et al., 2017).
PiSCES filters used in this study included stream width and depth,
watershed drainage area, dissolved oxygen (as % saturation), and
total suspended solids. PiSCES filters not used were conductivity,
pH and slope.
2.5. IEMS stream network delineation and parameterization to
the CRB study area
The Simulation Data Manager (SDM, Fig. 2) is internal to
FRAMES and interfaces with D4EM-derived data. The SDM is a
FRAMES service that bridges FRAMES models and D4EM data
retrieved from the external data sources and was developed for
our Albemarle-Pamlico ecoservices study (Johnston et al., 2011).
The SDM generated a stream network with minimum stream seg-
ment length of 6 km and a minimum slope of 0.0001. This resulted
in a stream network of 97 segments that are co-referenced by IEMS
107
models PiSCES, HSI, BASS and ESP. Segments with low relief near
the CRB outlet (Fig. 1) were set to the minimum slope to provide
nonzero water flow. NHD-defined stream segments were merged
consistent with the prior study (Johnston et al., 2011) to correct
known issues with NHD stream segmentation. That is, NHD is use-
ful for identifying stream locations but includes stream segments
on the order of meters that would dominate the WASP numerical
solution scheme. Inputs moving through extremely small WASP
segments force the entire system into smaller time steps, possibly
resulting in numerical dispersion.
BASS model input and output dictionaries and wrapper modi-
fications included the addition of indices for stream segments and
fish species; however, cohort variables were not written to file
to conserve system resources (e.g., RAM) and decrease runtimes.
Changes to the BASS wrapper included generation of BASS input
files (BASS project, community and fish files) for all stream seg-
ments and generation of a command file for execution on all stream
segments. The BASS output dictionary still contains the cohort vari-
ables, but the wrapper code was modified to not write the data for
this study. Only annual data by stream segment were written to
file, resulting in a decrease of 80MB per stream segment across
all years of simulation. This was necessary to successfully model
all CRB segments for the entire simulation period. Lastly, the ESP
108 J.M. Johnston et al. / Ecological Modelling 354 (2017) 104–114
Table 1
Wet and dry atmospheric mercury (Hg) deposition values used in the sensitivity analysis.
Value Total Wet Hg Deposition (␮g m −2 yr −1 )
Hg Baseline 11.26
Hg Low 8.24
Hg High 20.07
output dictionary was changed to provide annual average data by
stream segment.
Parameterization for the CRB included assignment of Manning’s
N for channel roughness and stream channel width and depth
ratios. Manning’s N was assigned using a polynomial curve for
each stream segment, varying from 0 to 1, with slopes(s) above
15% assigned a maximum value of 1. The Manning’s N used in
the CRB can be approximated by the following cubic regression,
N = 0.02 + 3.29*s – 72.8*s2 + 986*s3 . Stream width and depth rela-
tionships were used from bankfull channel width regressions for
wadeable streams developed for the conterminous US (Faustini
et al., 2009). Other than these parameters set at the beginning of
the study (and not revisited), no further changes were made to any
of the models compared with the prior study (Johnston et al., 2011).
As such the results represent an uncalibrated baseline simulation
comparable to the prior study.
2.6. Sensitivity analysis
A limited sensitivity analysis was conducted via changes to
atmospheric mercury deposition inputs from baseline. Both high
and low inputs were modeled by the IEMS through watershed
runoff, instream fate, transport and bioaccumulation in game fish.
Three total IEMS simulations were conducted for baseline, low and
high deposition (Table 1). Because modeled deposition data were
unavailable for this region as in the prior study, atmospheric mer-
cury deposition data were obtained from the Mercury Deposition
Network of the National Atmospheric Deposition Program (http://
nadp.sws.uiuc.edu/). Station numbers WV99, OH02 and TN11 were
selected for their proximity to the CRB, comprising data from 2002
through 2012. Baseline and low deposition values were developed
from each site’s annual average and minimum value. The high depo-
sition value was chosen as the maximum deposition of any station
value for wet deposition, using a factor of 1.3 X wet deposition for
dry deposition (Risch et al., 2012).
This study is not a traditional parameter sensitivity analysis
experiment but rather a model structural analysis that compares
differences in average annual means, standard deviations, and
medians for a suite of ecoservices across all stream segments for the
last ten years of simulation. The suite includes flow, water quality
standards violations, water depth and temperature (as aspects of
habitat suitability), mercury residues, and fish biomass, abundance
and productivity (total fish and game fish).
3. Results and discussion
The following sections summarize and discuss the spatially and
temporally averaged ecoservices provide by the CRB during the last
10 years of baseline simulation (from 2001 to 2010) when these
ecoservices have approximately attained their dynamic steady-
state trajectories. By this we mean the IEMS is not in equilibrium
and reaches nominal system behavior after transient dynamics
resolve around simulation year 10. These transient dynamics are
typically due to assumed initial conditions. Figs. 3–5 include the
last 10 years of period for all stream segments (n = 97). The sample
size for all of reported statistics is n = 970.
Total Dry Hg Deposition (ug m −2 yr −1 )
11.26
8.24
26.09
3.1. Water quantity and quality
Although segment streamflows (Q m3 /s) averaged 4.61 m3 /s
[median (X50 ) = 0.531; standard deviation (SD) = 9.78], the expected
streamflow from any given segment is strongly determined by its
cumulative drainage area (CDA km2 ) (Leopold and Maddock, 1953).
In this study, this interdependence is described by the simple log
linear model,
log Q = −1.70 + 1.00 log CDA (1)
The adjusted r2 and standard error of this regression are 0.979
and 0.101, respectively, and its coefficients are significant for P < 10
−6 . This regression agrees well with a similar hydraulic regres-
sion that we calculated for the three USGS gauging stations located
within the CRB (i.e., USGS 03198350 Clear Fork at Whitesville WV,
USGS 03198500 Big Coal River at Ashford WV, and USGS 03200500
Coal River at Tornado WV). In particular, using the complete period
of record for these sites, we calculated the regression,
log Q = −1.90 + 1.09 log CDA (2)
The adjusted r2
and standard error of this regression are 0.870
and 0.128, respectively, and its coefficients are also significant for
P < 10 −6 . The simulated hydraulic regression also agrees well with
the hydraulic regression,
log Q = −1.37 + 0.85 log CDA (3)
reported for 25 USGS gauging stations within the Appalachian
Plateau of the Mid-Atlantic Region (Mohamoud and Parmar,
2006). In particular, when the simulated CRB regression and the
Mohamoud and Parmar regression are evaluated for the aver-
age CDA of our study (i.e., 224 km2 ), the resulting streamflows
are within 5% of one another. Using the hydraulic regression for
bankfull streamflow in Appalachian Plateau rivers reported by
Messinger (Messinger, 2009), simulated streamflows average 4.98
percent of their predicted bankfull values (X50 = 4.51; SD = 1.77).
Predicted streamflows across the population of river and stream
segments fall into what appear to be three classes, from head-
waters with relatively lower flows to wadeable streams and
mainstem river segments with largest flows (Fig. 3). The majority
of streams are small streams with median flow near the minimum
(flow < 10 m3 /s, n = 83). Also note the period of increased stream-
flows from years 13–16 related to a period of increased rainfall with
corresponding increase in HSI values for this same period (Fig. 4).
Descriptive statistics are provided for the total number of occur-
rences per year that various drinking water standards (DWS) and
wildlife water quality criteria (WWQC) are exceeded in the base-
line CRB simulations (Table 2). This demonstrated the capability
of the IEMS to track events such as criteria exceedances over the
simulation period. Because of the spatially explicit implementation
of the IEMS, these predictions could be used to identify potential
hotspots to guide field sampling efforts. Although these simulations
predict that there would be no violations of DWSs for inorganic Hg
and ammonia or of WWQCs for dissolved oxygen, they do predict
minor to major violations of the nitrate DWS and all of ammonia
WWQCs. Minor violations (i.e., less than 2% of the year) are pre-
dicted for the nitrate DWS and the 4-day Non-Mussel WWQC. The
30-day Mussel WWQC, however, is predicted to be violated essen-
tially all year since there is a maximum of 335 or 336 consecutive
 J.M. Johnston et al. / Ecological Modelling 354 (2017) 104–114 109

Fig. 3. Average annual streamflow (m3 /s) across all river and stream segments (n = 97) for the final ten years of simulation period. Insets depict a) small streams (in blue)
with flow <10 m3 /s (n = 83), b) medium sized streams (in green) with flow between 10 and 35 m3 /s (n = 11), and c) large streams (in black) with flow >35 m3 /s (n = 3). For
each inset, solid lines represent median values and dashed lines the minimum and maximum values. Note y-axis difference in insets. (For interpretation of the references to
colour in this figure legend, the reader is referred to the web version of this article.)

Table 2
Statistics for the number of exceedances per year of drinking water standards (DWS) and wildlife water quality criteria (WWQC) across all segments in baseline CRB
simulations.

Standard, Criteria or Concentration Mean Median Standard Deviation Minimum Maximum

DWS Hg inorganic 0 0 0 0 0
DWS NH4 (taste) 0 0 0 0 0
DWS NO3 6.83 5.00 7.67 0 42.0
NH4 mg/L 1.22 1.10 0.630 0.401 3.83
NO3 mg/L 2.30 2.21 0.589 1.31 5.73
Total N mg/L 4.41 4.40 0.847 2.67 8.96
WWQC DO 1-day Fish 0 0 0 0 0
WWQC DO 30-day Fish 0 0 0 0 0
WWQC NH4 30-day Mussel 332 336 11.7 228 337
WWQC NH4 30-day Non-Mussel 54.4 0 100 0 337
WWQC NH4 4-day Mussel 16.4 0 54.9 0 320
WWQC NH4 4-day Non-Mussel 0.0619 0 0.929 0 26.0
110 J.M. Johnston et al. / Ecological Modelling 354 (2017) 104–114

Fig. 4. Average annual game fish habitat suitability index (HSI, unitless) across all river and stream segments (n = 97) for the final ten years of simulation period. Insets depict
a) streams (in blue) with HSI <0.3 (n = 60), b) streams (in green) with HSI between 0.3 and 0.5 (n = 33), and c) streams (in black) with HSI >0.5 (n = 4). For each inset, solid lines
represent median values and dashed lines the minimum and maximum values. Note y-axis difference in insets. (For interpretation of the references to colour in this figure
legend, the reader is referred to the web version of this article.)

30-day intervals within any year depending on whether that year
is a leap year or not.
3.2. Fishery habitat suitability
Habitat Suitability Indices (HSI) for CRB game fish and indi-
cator species average 0.279 (X50 = 0.279; SD = 0.120) and 0.887
(X50 = 0.997; SD = 0.141), respectively. Predicted HSI values across
all river and stream segments show the disappearance of transient
conditions around year 10, as well as dynamics between simula-
tion years 13–16 for larger segments related to increased periods
of streamflow (Figs. 3 and 4). It is important to note that although
a dynamic steady state was reached, the system was driven by
a continuous precipitation input and consequently reflected that
pattern rather than a cyclical or repeating time series. The high HSI
for indicator species, however, is artificially inflated by designating
all sucker species (Catostomidae) as indicator species regardless of
their relative environmental tolerances. For example, white suckers
(Catostomus commersonii), are a dominant fish species in the CRB
and considered to be environmentally tolerant. As such, this species
was assigned an HSI equal to 1. Consequently, average indicator
species HSI is strongly influenced by this species’ assumed HSI.
Two of the most important HSI variables used in our study are
the segment’s daily depth and temperature (Rashleigh et al., 2005).
Annual averaged stream depths and temperatures were 0.299 m
(X50 = 0.197; SD = 0.221) and 12.1 Celsius (X50 = 12.1; SD = 0.535),
respectively. These stream depths, however, are dependent on seg-
ment streamflow (Mohamoud and Parmar, 2006). When we fitted
the simulated segment depths (D m) to their simulated stream-
flows (Q m3/s) using a standard log linear model, we obtained the
following hydraulic geometry regression:
log D = −0.614 + 0.366 log Q (4)
The adjusted r2 and standard error of this regression are 0.993
and 0.0212, respectively, and its coefficients are also significant
 J.M. Johnston et al. / Ecological Modelling 354 (2017) 104–114 111

Fig. 5. Average annual total fish biomass (kg wet wt/ha) across all river and stream segments (n = 97) for the final ten years of simulation period. Insets depict a) streams
(in blue) with biomass <30 kg/ha (n = 54), b) streams (in green) with biomass between 30 and 60 kg/ha (n = 34), and c) streams (in black) with biomass >60 kg/ha (n = 9). For
each inset, solid lines represent median values and dashed lines the minimum and maximum values. Note y-axis difference in insets. (For interpretation of the references to
colour in this figure legend, the reader is referred to the web version of this article.)

for P < 10 −6 . Importantly, this regression agrees well with the
hydraulic regression,
log D = −0.538 + 0.24 log Q
reported by Mohamoud and Parmar (Mohamoud and Parmar, 2006)
for 25 USGS gauging stations within the Appalachian Plateau of the
Mid-Atlantic Region. In particular, when the simulated CRB regres-
sion and the Mohamoud and Parmar regression are evaluated for
the average streamflow of our study (i.e., 4.61 m3 /s), the resulting
stream depths are within 2% of one another.
Using the hydraulic regression for bankfull stream depth in
Appalachian Plateau rivers reported by Messinger (Messinger,
2009), simulated stream depths average 29.9 percent of their pre-
dicted bankfull values (X50 = 29.2; SD = 4.14).
3.3. Fishery biomass, population density, and production
Simulated total fish biomasses averaged 30.3 kg wet wt/ha
(X50 = 22.2; SD = 21.9), and our simulated total fish population
densities averaged 3720 fish/ha (X50 = 3740; SD = 713). Model pre-
(5)
dictions across all stream and river segments demonstrated a fairly
uniform distribution of fish biomass (Fig. 5). The annual produc-
tion of these fisheries averaged 42.5 kg wet wt ha−1 yr−1 (X50 = 27.3;
SD = 36.7), and their average production-to-biomass ratio was esti-
mated to be 1.30 yr −1 (X50 = 1.24; SD = 0.194). Whereas the average
percent biomasses of these fisheries that were game fish was 14.8
(X50 = 11.0; SD = 0.14.2), the average percent biomasses that were
indicator species (i.e., darters, suckers, etc.) was 37.6 (X50 = 29.2;
SD = 26.3).
These results agree well with those from impacted and refer-
ence streams in the MTM regions of Kentucky and West Virginia, US
(Stauffer and Ferreri, 2002). Using data reported by these authors,
we calculated an expected average total fish biomass of 32.3 kg
112 J.M. Johnston et al. / Ecological Modelling 354 (2017) 104–114

wet wt/ha (X50 = 22.1; SD = 48.5; n = 91) and an expected average
total fish population density of 6050 fish/ha (X50 = 3630; SD = 6520;
n = 91). Although Stauffer and Ferreri did not estimate the annual
productions of their study sites, we used the widely cited regres-
sion for estimating the fish production in lakes and rivers (Randall
et al., 1995). Using this regression, we estimated the average annual
production of Stauffer’s and Ferreri’s fish communities to be 37.7 kg
wet wt ha−1 yr−1 (X50 = 28.8; SD = 33.1; n = 91).
Even though the coefficients of this regression are significant for
P < 10 −6 , its adjusted r2 and standard error are 0.175 and 0.201,
respectively. Thus, even a 50% reduction in the high end deposition
rate would be expected to decrease dissolved mercury concentra-
tions only by 10% (i.e., 0.50.152 ), assuming no other mercury sources.
4. Summary and conclusions

We demonstrated and verified a spatially explicit, watershed-

3.4. Fishery mercury contamination
scale capability of the IEMS for a baseline, uncalibrated simulation
in the CRB in support of the problem statement forecasting
For baseline mercury deposition rates, whole-body MeHg con-
alternative future states of aquatic ecoservices in response to
centrations of game fish averaged 0.133 ␮g/g wet wt (X50 = 0.174;
changing landuse and climate. Nominal system behavior was veri-
SD = 0.0672) while whole-body MeHg concentrations of indicator
fied through comparison to available field data and independent
species averaged 0.0279 ␮g/g wet wt (X50 = 0.0242; SD = 0.0206).
models for average annual quantities of water flow, hydraulic
These results are consistent with results of a study involving
geometry, fish biomass, abundance and productivity (total fish),
mercury bioaccumulation in nongame fish in randomly sam-
and mercury residue for game fish and indicator species. A suite
pled wadeable streams across the US Mid-Atlantic Region, which
of predictive, process-based legacy models was used to simulate
encompasses the study area (Lazorchak et al., 2003). These authors
cause-and-effect relationships for multiple stressors and receptors,
estimated that 78.2–84.4% of this region’s wadeable stream lengths
and the IEMS has potential to be used across multiple spatial and
held nongame fish with whole-body concentrations of mercury
temporal scales. The addition of stream segment level detail has
which exceeded their detection limit of 0.025 ␮g/g wet wt. Reanal-
increased the utility of the approach to address the cumulative
ysis of the data used by Lazorchak et al. suggest that whole-body
impacts of multiple stressors, which more fully supports the assess-
MeHg concentrations of nongame fish in this region averages
ment of multiple stressors on stream networks. Specifically, stream
0.0600 ␮g/g wet wt (X50 = 0.0403; SD = 0.0867; n = 401).
segments now have unique combinations of slope, channel rough-
Simulated whole-body MeHg concentrations in game fish and
ness and width-to-depth ratio, and 8-digit HU stream segmentation
indicator species suggest possible ecological and human health
is used throughout the entire CRB. To accomplish this we esti-
concerns. In particular, Lazorchak et al. (Lazorchak et al., 2003)
mate approximately 80–90% of the IEMS was reused from a prior
estimated that kingfisher (Ceryle alcyon), mink (Mustela vison), and
study, with modifications limited to the science model wrappers
otter (Lutra canadensis) populations could be adversely impacted
and input and output dictionaries (the science models themselves
by the consumption of fish whose whole-body mercury concen-
remain unchanged). This estimate represents the collective judge-
trations exceeded 0.10, 0.07, and 0.03 ␮g/g wet wt, respectively.
ment of the development team, involving contributions from three
Similarly, using data on 626 western U.S. streams and rivers,
individuals for two months. Because CRB data are derived from
Peterson et al. (Peterson et al., 2007) proposed that the USEPA’s cri-
an automated D4EM process they were not included in the reuse
terion for the safe consumption of mercury contaminated fish [i.e.,
estimate. The new fish community estimator PiSCES is also not
0.30 ␮g/g wet wt fillet (USEPA, 2010)] was equivalent to a whole-
included in the estimate.
body criterion of 0.185 ␮g/g wet wt which is extremely close to the
A general class of watershed-based condition assessments exists
simulated median game fish value of 0.174 ␮g/g wet wt.
that includes landscape and climate change stressors on the hydro-
When we assumed the high and low end mercury deposition
logic cycle as fundamental drivers of ecosystem change. Further
rates (␮g m−2 yr−1 ) (Table 1), whole-body mercury concentrations
extension of this IEMS to other watersheds east of the Mississippi
in game fish and indicator species demonstrated no significant
River and above the Coastal Plain would involve a comparable or
increase and decrease, respectively. Although these results were
greater level of reuse, minimizing the need for new software devel-
surprising, the explanation is an outcome of averaging the mod-
opment. The addition of the new PiSCES model also facilitates a
eled data. Because mercury concentrations in fish within any given
greater degree of reuse by reducing the reliance on monitoring data
segment depend on their body weight, trophic position, mercury
for fish species and densities (Cyterski et al., 2017). Use of the IEMS
concentration in its prey and surrounding water, they lack the stan-
outside of the eastern US is therefore still constrained by data avail-
dardization typically used when presenting residues, such as by
ability for fisheries, provided assessments are watershed-based and
length of top predatory species (Knightes et al., 2009). For exam-
consistent with the process science of the peer reviewed models
ple, when the whole-body mercury concentrations (Cf ␮g/g wet wt)
(SWAT, WASP, MLM, HSI and BASS). The IEMS has the potential to
for all age classes of all fish species are fitted to a log-linear model
bring multi-disciplinary science to bear on a priority Agency need
of the segment’s dissolved mercury concentration (Cw ␮g/ml), the
at a fraction of the original development effort. And the extension
fish body weight (W g wet wt/fish), and the fish’s trophic position
of this IEMS from a stratified, random sample of study watersheds
(TP) for the last year of simulation assuming the high end mercury
(i.e., probabilistic assessment) to a spatially explicit, networked one
deposition rates, we calculated following regression:
is a necessary evolution of the approach.
log Cf = 5.67 + 1.18 log Cw + 0.0337 log W + 0.773 TP (6) A priority Agency headwater-to-riverine assessment need not
fully addressed by the IEMS, nor any other integrated model-
The adjusted r2 , standard error, and sample size of this regression ing approach to our knowledge, is MTR (USEPA, 2011). Surface
are 0.635, 0.298, and 4868 respectively, and all of its coefficients are coal mining is the major source of landcover change in central
significant for P < 10 −6 . Mercury dissolved water concentrations, Appalachia, and MTR and valley fill are responsible for damage to
however, are only weakly depended on the segment’s CDA which ecosystems, reduction and potential elimination of their aquatic
is directly proportional to the total potential mercury loading that ecoservices and also potential human health impacts (Ahern et al.,
can be processed by any given segment. In particular, for the above 2011; Bernhardt et al., 2012; Griffith et al., 2012; Palmer et al.,
dataset 2010). Waste mining material disposal buries headwater streams
and increases salinity and trace metal concentrations downstream
log Cw = −8.24 + 0.152 log CDA (7) of mined landscapes. The threshold for landuse change leading to
 J.M. Johnston et al. / Ecological Modelling 354 (2017) 104–114
aquatic biological impairment is surprisingly low, reached when
surface mining comprises greater than 5.4% of the watershed con-
tributing area (Bernhardt et al., 2012), and mining activity is only
expected to increase in the region. Biological impairment gener-
ally refers to changes in aquatic community structure or function,
or both. In their study Bernhardt et al. utilized state biocriteria
of impairment and macroinvertebrate data. Another field study
of MTR impacts in the Mud River watershed in southwestern WV
revealed reductions of fish species by one half and fish abundance
by one third (Hitt and Chambers, 2014). Streams and rivers in
mined lands therefore face threats from climate change and lan-
duse change in addition to MTR stressors that include pH, metals
and salts modeling not currently supported by the IEMS. MTR
source terms, loadings and dose-response relationships for bio-
logical assessment endpoints (e.g., macrobenthos, mussels, and
sport fish) would need to be incorporated into the suite of sci-
ence models. An additional requirement is the inclusion of first and
second order perennial streams needed to capture the footprint
of MTR and valley fill operations. The CRB is a headwater 8-digit
HU that includes 24 12-digit HU’s. A preliminary assessment of the
total number of streams within each 12-digit HU subwatershed
indicated on average 40–50 segments, well within the capabil-
ity of the IEMS. Non-headwater 12-digit HU subwatersheds, of
which there are 12 in the CRB, will require a further change to the
WASP wrapper and dictionaries to connect upstream and down-
stream streamflows and constituents. These modifications would
provide increased stream segment resolution needed to address
small streams throughout a watershed such as the CRB.
With respect to the simulation of MTR-related instream pro-
cesses such as metals and salt chemistry, there is the option to
develop new science models or utilize science contained within
the current IEMS (WASP-Toxics). That is, the necessary WASP mod-
ules could be integrated into FRAMES, requiring further changes
to the model wrapper and dictionaries. Similarly, the PiSCES con-
ductivity filter could also be utilized in a future study. Habitat
suitability relationships could also be developed for conductivity,
pH or metals to be incorporated into the HSI model, wrappers and
FRAMES dictionaries. Reductions in fish abundance and diversity
were associated with conductivity and aqueous selenium concen-
trations rather than physical habitat variables (Hitt and Chambers,
2014).
As a coupled, component modeling system, the IEMS is a valu-
able research tool for system understanding. Its strength is the
ability to simulate a complex, integrated system using existing
models of system components for cumulative impacts and aggre-
gate effects, while at the same time providing depth of process
representation using quantitative data for prediction and forecast-
ing (Kelly et al., 2013). Its use for decision making under uncertainty
is in its infancy, with research needed as to what quantities should
be utilized for decision support and how these quantities are sum-
marized in space and time. Multi-criteria analysis is a promising
decision analysis approach that could be integrated with the IEMS
(Kiker et al., 2005; Stahl and Cimorelli, 2013; Suedel et al., 2011;
von Stackelberg, 2013). The relationship between the IEMS and
decision making must be adequately constrained by the problem
statement though and not result in an over-parameterized sys-
tem and inability to fully explore uncertainties associated with
datasets, models and related methodologies (Kelly et al., 2013). The
USEPA has committed to integrated environmental modeling for
the assessment of complex problems, namely “a systems analysis-
based approach to environmental assessment. . . [that] includes a
set of interdependent science-based components (models, data,
and assessment methods). . . [and] is capable of simulating the
environmental stressor-response relationships relevant to a well
specified problem statement” (USEPA, 2008). We believe the IEMS
113
provides a suitable foundation for lotic system problem solving and
with continued development could meet MTR assessment needs.
We would like to make a final point with respect to the role of
field data in integrated modeling research and development. Mon-
itoring data provide necessary information on the state of a system
at the time those data were collected, but data have limitations and
do not always provide sufficient system understanding for decision
making. The interplay of data and modeling is well known, with
data serving multiple purposes as input to model parameters, ini-
tial conditions of state variables, and verification of model output
when independent from model parameterization. However, it is
through integrated modeling and IEMS development that system
understanding is possible, connecting discrete instances of data
collected with process understanding that represents our best sci-
entific description of system behavior. Without models we are at
a loss as to the status and, more importantly, the trajectory of sys-
tems and their ecoservices until after the fact. Lacking monitoring
data, an IEMS also provides a valuable experimental system suitable
for exploring a range of alternative future scenarios including lan-
duse change, regional atmospheric pollutant transport and climate
change. Even as an uncalibrated and partially verified approach,
the IEMS is a robust research tool to test hypotheses regarding sys-
tem state and the nature of various stressor-receptor relationships.
We also have testable hypotheses regarding water quality viola-
tions that could be investigated further. Ultimately, integration of
IEMS science within a decision context such as the assessment of
the cumulative impacts of landuse and climate change on mined
lands provides a science basis for decision making, enabling the
forecasting of alternative futures and filling data gaps where moni-
toring data are unavailable. This study captures a greater degree of
system variability and dynamics across the population of streams,
both of which are of value for decision making under uncertainty.
Conflict of interest
Authors declare no conflict of interest.
Acknowledgements
Gerry Laniak (USEPA) is thanked for review and feedback on the
development of the manuscript. Lourdes Prieto (USEPA) provided
GIS and database support for the study and created Figs. 3–5. Chris
Knightes (USEPA) is acknowledged for WASP model support and
mercury sensitivity analysis guidance. Justin Babendreier (USEPA)
is acknowledged for his contributions to team discussions. Cyn-
thia Stahl and Janet Kremer (USEPA) are thanked for their support
of integrated modeling. Jim Evans (SRA International) is cred-
ited with providing publication ready figures. Three anonymous
reviewers and the guest editor are thanked for their constructive
comments that improved the manuscript. Although this document
has been reviewed in accordance with USEPA policy and approved
for publication, it may not necessarily reflect official Agency policy.
Mention of trade names or commercial products does not consti-
tute endorsement or recommendation for use.
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