Journal of Hydrology 624 (2023) 129863

Contents lists available at ScienceDirect

Journal of Hydrology
journal homepage: www.elsevier.com/locate/jhydrol

Research papers

Multirate mass transfer simulation of denitrification in a

woodchip bioreactor
Jingjing Wang a, b, c, d, *, Jesús Carrera c, d, Cristina Valhondo c, d, Maarten W. Saaltink b, d,
Jordi Petchamé Guerrero b, c, d, Fengshou Zhang a, Roger B. Herbert e
a
Department of Geotechnical Engineering, College of Civil Engineering, Tongji University, Shanghai 200092, China
b
Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya (UPC), Jordi Girona 1-3, 08034 Barcelona, Spain
c
Geosciences Department, Institute of Environmental Assessment and Water Research (IDAEA), Severo Ochoa Excellence Center, Spanish Scientific Research Council
(CSIC), Jordi Girona, 18-26, 08034 Barcelona, Spain
d
Associated Unit—Hydrogeology Group (UPC-CSIC), Spain
e
Department of Earth Sciences, Uppsala University, Villavägen 16, 752 36 Uppsala, Sweden

A R T I C L E I N F O A B S T R A C T

This manuscript was handled by Huaming Guo, Denitrifying woodchip bioreactors (DWBs) have proven to be an efficient nature-based solution for nitrate
Editor-in-Chief. removal. Modeling DWBs is required for improving their design and operation, but is hindered by the complexity
of the modeled system where numerous chemical species and model parameters are needed. Reactions inside the
Keywords: woodchips are different from those at the edges, causing chemical localization (i.e., apparent simultaneous
Multi-rate mass transfer
occurrence of incompatible reactions). We used the Multi Rate Mass Transfer (MRMT) approach to overcome
Reactive transport
these problems when simulating reactive transport processes in a DWB located at Kiruna, Sweden. Besides
Biomass growth
Denitrification denitrification, other nitrogen-cycling processes (e.g., nitrification, dissimilatory nitrate reduction to ammonium,
Denitrifying woodchips bioreactor anammox) and alternative electron donors (e.g. oxygen, sulfate) were also considered. Biomass concentration is
incorporated into the biochemical reaction rates, including growth and decay, to characterize microbial catalysis.
We found that the MRMT model: 1) can account for the heterogeneity of the porous woodchips; 2) was capable of
reproducing the nitrogen species evolution in the DWB with kinetic parameters from the literature; and 3) allows
reproducing localized biochemical reactions (e.g., aerobic reactions on the woodchip edges, near the DWB
entrance and anaerobic reactions inside); and 4) reproduces the full denitrification reactions sequence, but with
the different reactions occurring in different portions of the woodchip (e.g., nitrate to nitrite near the edges and
nitrite to nitrous oxide further inside). The latter observation suggests that increasing woodchip size may reduce
the outflow of these undesired species.

1. Introduction Denitrifying woodchip bioreactors (DWBs) are a nature-based tech­

Nitrogen (N) pollution is a problem that threatens surface and
groundwater resources globally, to the point that a global joint action
has been demanded (Basu et al., 2022). In fact, billions of dollars have
been invested in conservation measures worldwide, but their water
quality impact has been minimal (Basu et al., 2022). The situation is
especially severe in the Baltic Sea, which has suffered from eutrophi­
cation for many decades. In order to reduce nitrogen releases to rivers
that discharge to the Baltic Sea, an iron ore mine in Kiruna (northern
Sweden) has built several woodchip bioreactors (Nordström and Her­
bert, 2018; Storm and Smeds, 2021).
nology to reduce nitrate releases by passing the water through a trench
filled with woodchips (cf. Nordström and Herbert, 2018). DWBs are
widely used to remove nitrate from agriculture and surface water (see
reviews by Grießmeier et al., 2019; Lopez-Ponnada et al., 2017; Schipper
et al., 2010). In fact, Valhondo et al. (2015, 2020) used a similar concept
to enhance Soil Aquifer Treatment to remove recalcitrant emerging
contaminants by creating a sequence of redox states including, but not
limited to, nitrate reduction. The technology has proven to be efficient
for the treatment of mine drainage under temperatures characteristic of
subarctic environments, such as in Kiruna (Herbert et al., 2014;
Nordström and Herbert, 2018).

* Corresponding author at: Department of Geotechnical Engineering, College of Civil Engineering, Tongji University, Shanghai 200092, China.
E-mail address: jingjingwangxiang@126.com (J. Wang).

https://doi.org/10.1016/j.jhydrol.2023.129863
Received 10 April 2023; Received in revised form 20 June 2023; Accepted 22 June 2023
Available online 26 June 2023
0022-1694/© 2023 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-
nc-nd/4.0/).
J. Wang et al.
The performance of DWBs is highly variable, both within the DWB
from one site to another (Christianson et al., 2012) and, for a given site,
with time (Nordström and Herbert, 2019). This variability depends on
many microbial factors (e.g., distribution of microbial community, ge­
netic diversity, bacterial abundance) as well as various abiotic factors
such as pH, temperature, dissolved organic carbon (DOC) concentra­
tions, and presence of dissolved oxygen (DO) (Fan et al., 2022). This has
motivated numerous models of DWB treatment (Halaburka et al., 2017;
Kouanda and Hua, 2021; Störiko et al., 2022), which reflects the
complexity of reactive transport in DWBs.
Modeling bioreactors is complex for several reasons. First, numerous
reactions are involved (see Fig. 1a). Second, most of the involved re­
actions are microbially mediated, so their dynamics should be linked to
microbial growth. Third, the wood is porous and solutes may diffuse into
the woodchips, which act as an immobile but porous matrix. In fact,
since the woodchips yield DOC, woodchips provide ideal, cost-efficient
support material for microorganisms. Fourth, presumably incompatible
reactions (e.g., aerobic degradation and anaerobic denitrification) occur
simultaneously, which we attribute to chemical localization (i.e.,
different reactions take place in different portions of the medium within
any realistic representative elementary volume, Fig. 1b).
Given this complexity, modeling has followed different avenues.
Some modelers have acknowledged that reproducing the above pro­
cesses may lead to ungranted complexity and simply adopt zero order
kinetic models (Halaburka et al., 2017; Kouanda and Hua, 2021). These
kinds of models are useful and simple, typical nitrate removal rates
range between 2 and 20 g N d− 1 m− 3 reactor, which allows a preliminary
estimate of the required bioreactor volume. Further insight into the
functioning of the system can be gained by modeling the participating
individual species, which is typically achieved by means of Michelis-
Menten kinetics. The problem with this approach is two-fold. On the
one hand, it requires numerous parameters. On the other, it does not
recognize the growth of the microorganisms catalyzing the reactions.
Hence, it is not surprising that both Halaburka et al. (2017) and Kouanda
and Hua (2021) ended up preferring zero order kinetics. This is some­
what disheartening, given the efforts at characterizing microbial pop­
ulations in bioreactors (Hellman et al., 2021; Herbert et al., 2014; Jang
et al., 2019; Nordström et al., 2021). Microbial community character­
ization has been useful for gaining insight into the evolution of DWBs
and for suggesting improved designs, but has not been used for modeling
purposes. Worse, Störiko et al. (2022) ask for “caution against the use of
concentrations of functional-gene transcripts and enzymes as direct
proxies of microbial reaction rates”.
Beyond biochemical issues, problems may also arise from the
Fig. 1. a) N species and important reactions in DWBs. Note that N species may act both as electron acceptors (reactions represented by warm color arrows) or donors
(blue arrows); b) schematic view of woodchip bioreactor, including chemical variability (red more oxidizing than blue) both along the reactor and within each
woodchip. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
2
Journal of Hydrology 624 (2023) 129863
representation of physical transport. Transport is usually represented
using the Advection-Dispersion Equation (ADE), which is known to work
poorly for reactive transport (see discussion by Carrera et al., 2022). In
essence, the problem is that the ADE equates dispersion (spreading of
solutes caused by the spatial variability of velocity) with mixing (dilu­
tion caused by molecular diffusion). But mixing controls the rate of fast
reactions by controlling how reactants reach reaction sites (Rezaei et al.,
2005) and, specifically, how electron acceptors and donors reach the
microorganisms (Cirpka and Valocchi, 2007). This is illustrated by
Fig. 1b, which suggests that indeed the rate-limiting step for reactions
inside the woodchips may be diffusion across the woodchip. It is clear
that the modeler would have to use an artificially slow kinetic rate
parameter to compensate the fact that the ADE ignores this step. Obvi­
ously, these parameters depend on the specific experimental conditions
and the specific reaction rate, which may explain the broad range of
published parameters. We conjecture that properly modeling transport
limitations is a necessary step to the use of parameters that do not
depend on the model, but on the reaction conditions.
Numerous transport approaches have been developed to overcome
the limitations of the ADE (see the review of Carrera et al., 2022) to
represent the effect of heterogeneity. The majority can be considered
variants of Multi Rate Mass Transfer (MRMT), which treats the medium
as consisting of mobile and immobile zones. One such variant (the dual
porosity model) was explored by Jaynes et al. (2016), who represented
woodchips as an immobile zone, just as implied by Fig. 1b. They ob­
tained good fits with consistent parameters over two years, but they
assumed that reactions occurred both in the mobile and immobile re­
gions using zero and first order kinetic rates for denitrification. We
conjecture that it is possible to go one step forward and use not one but a
suite of immobile zones to represent a broad range of residence times
within the woodchips.
The objective of this paper is to explore the possibility of using
MRMT models to simulate the DWBs using reaction rates from well
controlled experiments; that is, without the need for calibration of
geochemical parameters. To do so, we designed a MRMT model for one
of the DWBs built in Kiruna, compared its results with experimental
data, and analyzed chemical localization to gain insight on the vari­
ability of chemical processes occurring at the woodchip scale, which
cannot be easily sampled.
J. Wang et al.
2. Materials and methods
2.1. Kiruna woodchip bioreactor description
The objective of the woodchip bioreactor was to remove nitrogen (in
the form of nitrate, NO−3 ) from waste rock drainage, where nitrogen was
derived from spillage and the incomplete detonation of explosives in the
underground Kiruna mine (Nordström and Herbert, 2018). Waste rock
from the excavation of tunnels in the mine is deposited on the ground
surface in large waste rock dumps; nitrogen compounds weakly bind to
the surfaces of the waste rock, and precipitation and snowmelt infiltrate
into the dumps and slowly leach out the nitrogen compounds (e.g.,
Bailey et al., 2013). At the Kiruna site, NO−3 was the only N compound
commonly occurring above detection limits in the leachate, and it was
decided that DWBs would be evaluated for the removal of NO−3 from the
waste rock drainage. Three full-scale DWBs were constructed in 2018 as
part of the EIT RawMaterials project NITREM. Data used in this study
are from bioreactor 3, DWB-3, and were collected during the summer
2019 sampling campaign.
The DWB-3 consisted of an excavation that was 44 m long and 7 m
wide at the ground surface, and tapered to a width of 2 m at the bottom
that was located at 2.1 m depth (see Fig. S1 in Supplementary materials).
The excavation was covered with an impermeable geomembrane (HDPE
plastic) and filled with pine woodchips (dimensions approximately 30
mm × 30 mm × 10 mm thickness) amended with a small amount of
activated sewage sludge. The purpose of the sewage sludge was to
introduce an active culture of denitrifying bacteria to the bioreactor. The
main idea with the use of woodchips was that the dissolved organic
carbon released from the woodchips would function as a carbon and
energy source for heterotrophic denitrifying bacteria. As the availability
of dissolved oxygen limits/inhibits the denitrification reaction, the
surface of the bioreactor was covered with 0.4 m glacial till (large rocks
removed), limiting oxygen diffusion from the atmosphere, and two inner
walls were constructed to induce the influent to flow through the deeper
section of the bioreactor. Finally, the bioreactor was covered with 1 m
peat for insulation.
Water was pumped (average flow rate 0.21 L/s during 2019) to the
bioreactor and entered through a perforated pipe that was located 1.6 m
above the bottom. Water then flowed by gravity through the bioreactor
until it reached the outlet at the other end (outlet situated 1.6 m above
the bottom). The outlet compartment was filled with crushed rock
(16–32 mm) so as to distribute the flow over the width of the bioreactor
and prevent channeling. The outlet pipe led water to a monitoring
chamber that was equipped with an H-flume for discharge measure­
ments. Five piezometer pairs at two different depths (screen interval 0 –
0.5 m and 1.0 – 1.5 m over bottom) were installed along the bioreactor
at 3.8, 11.4, 20.5, 29.2, and 37.5 m from the inlet for water monitoring.
Each piezometer (2 cm inner diameter) was purged of at least three tube
volumes prior to sampling, and there was no indication that oxygen
intrusion into the piezometer tubes affected denitrification in the DWB.
During the operation of the bioreactor in 2019 (from April to
November), temperature and flow rate were continuously measured,
and nitrate, nitrite, ammonium, alkalinity (as bicarbonate, HCO−3 ), sul­
fate (SO2−
4 ) and pH were determined weekly in the influent and effluent
to assess the performance of DWB-3. Additionally, 11 samples were
collected from each monitoring point (including piezometers) from 16
June to 17 September 2019 to characterize the evolution of the N species
along the DWB flow path.
A tracer test was conducted to determine the residence time distri­
bution of conservative compounds in DWB-3. Bromide (Br− ) was
injected at the bioreactor inlet and Br− concentrations were measured at
the outlet over a period of 30 days and a flow rate of 0.31 L/s.
Since data was not available for this study on the abundance of
microbiological groups with the genetic capacity to carry out N-cycle
reactions, data has been used from Nordström et al. (2021). In a DWB
3
Journal of Hydrology 624 (2023) 129863
that was comparable with the DWB modeled in this study (i.e. same
climate, dimensions, flow rate, woodchip source and similar water
quality), Nordström et al. (2021) quantified the genes encoding for ni­
trite reduction (nirS and nirK) and nitrous oxide reduction (nosZI and
nosZII), as well as the dhd and nrfA genes that were proxies for the mi­
crobial community performing anammox and DNRA reactions, respec­
tively. We used these genetic data as input in the MRMT model to set the
initial biomass in the immobile zones capable of performing the
biochemical reactions of the N-cycle.
2.2. MRMT model
The MRMT approach consists of viewing the medium as consisting of
a mobile zone and a suite of immobile zones, each with a characteristic
residence time, that exchange mass diffusively. The set of immobile
zones yields a residence time distribution. The mass balance equations
for reactive species (including microorganisms) in mobile and immobile
zones are expressed, respectively, as
∑N
( )
∂cm
ϕm = Lt [cm ] − ϕim,j αj cm − cim,j + ϕm Rm (1)
∂t
j=1
and
∂cim,j ( )
ϕim,j = ϕim,j αj cm − cim,j + ϕim,j Rim,j j = 1, ⋯, N (2)
∂t
where ϕm [-], and ϕim [-] are the porosity of the mobile and immobile
zones, denoting the volume fraction of the mobile zone and immobile
zones over the total volume, respectively. The total porosity of the
medium ϕ, a measured parameter (Nordström and Herbert, 2017), is
equal to ϕm + ϕim . N is the number of immobile zones. cm [ML− 3] and
cim,j [ML− 3], arrays of concentrations of all aqueous species in the mobile
and j th immobile zone, respectively. These two arrays consist of two
sub-arrays: cam , containing the concentrations of all aqueous (i.e.,
flowing) species, and csm , non-flowing species (we assume here that
microbes are not transported). Lt [cm ] is the transport operator. Thus,
Lt [csm ] = 0, whereas Lt [cam ] = − q∇cam + ∇ • (ϕm D∇cam ), where q
[LT− 1] is Darcy flux, and D [L2T− 1] is the hydrodynamic dispersion
tensor. The second term on the right-hand side of equation (1) describes
the mass transfer of aqueous species between mobile and immobile
zones. αj [T− 1] is a first-order mass transfer rate coefficient between the
mobile and j th immobile zone. The inverse of the mass transfer rate,
ταj = 1/αj , is used to characterize the residence time in the j th immobile
zone (it is indeed the mean residence time of inert aqueous species).
ϕim,j = ϕim pj , where pj is the probability of the j th immobile zone (i.e., its
volumetric fraction of water). Therefore, the sum of pj of all immobile
∑
zones should equal one, that is, Nj=1 pj = 1.0. Rm and Rim,j [ML− 3T− 1]
are the sink-source terms due to chemical reactions in the mobile and the
j th immobile zones, respectively. These terms express the mass of the
array of species removed (R < 0) or added (R > 0) by all reactions per
unit volume of water and per unit of time. It is a function of reaction
rates (Saaltink et al., 1998; Steefel and MacQuarrie, 1996)
r = STe re + STk rk (3)
where Se is the stoichiometric matrix for equilibrium reactions, and Sk is
the stoichiometric matrix for kinetic reactions, re and rk represent the
vectors of reaction rates for equilibrium and kinetic reactions, respec­
tively. Note that stoichiometric matrices contain the full description of
the biochemical system, as every row contains the stoichiometric co­
efficients of all species (columns) participating in the reactions (rows).
Immobile zones are connected “in parallel” (i.e., every immobile
zone is connected to the mobile zone) in the MRMT model of Eqs. (1) and
(2), but other configurations are also possible (Babey et al., 2015; De
Dreuzy et al., 2013). It can be shown that they are equivalent for inert
J. Wang et al. Journal of Hydrology 624 (2023) 129863

tracers, equilibrium reactions, or linear kinetics, provided that they have
the same residence time distribution, but not necessarily for non-linear
kinetics. We have chosen the configuration of Eqs. (1) and (2) for nu­
merical efficiency and conceptual simplicity, as the residence time dis­
( )
tribution is approximated discretely by the set of pairs αj , pj ,j = 1,⋯,
N.
It should be noticed that MRMT adds a dimension to the geometrical
dimensions of the problem. That is, concentrations, c, vary not only in
space, x, and time, t, but also along immobile zones c = c(x, t, α). This
allows us to represent the physical and chemical heterogeneity induced
by woodchips without having to represent them explicitly. The medium
can be seen as represented by several overlapping continua (hence, this
kind of models are often referred to as multicontinuum models).
different for each microorganism, and its decay or death, which is the
same for all. Woodchips are hydrolyzed in a similar way. Note that for
the formulation of the growth reactions, yield coefficients (mass of
biomass/mass of DOC) are required, which were taken from the litera­
ture (see Table S2 in Supplementary materials).
Kinetic reactions require a rate law, expressing the rate of the reac­
tion as a function of concentrations. For the biomass growth reactions,
we use a Monod equation (Rittmann and McCarty, 2001), multiplied by
the concentration of microorganisms, as discussed by Carrera et al.
(2022), but without a logistic factor. For the two reactions that use O2 as
electron acceptor (aerobic oxidation and nitrification) this gives:
rk,im,j,k = μk
cD,im,j cA,im,j
cim,j,k j = 1, ⋯, N k = 1, 2 (4)
KD,k + cD,im,j KA,k + cA,im,j

For the other biomass growth reactions an inhibition factor is added,

2.3. Biochemical system to take into account that O2 inhibits the reactions, because it is the
preferred electron acceptor in terms of Gibbs free energy.
Several biochemical reactions affect the chemical composition and
cD,im,j cA,im,j IA,k
the growth of microorganisms. Table 1 shows all reactions considered rk,im,j,k = μk cim,j,k j = 1, ⋯, N k
KD,k + cD,im,j KA,k + cA,im,j IA,k + cI,im,j
here. We represent dissolved organic carbon by the chemical formula
CH2 O, microbial biomass by C5 H7 O2 N and woodchips by = 3, ⋯, 8 (5)
C6 H12.012 O6 N0.004 . There are four inorganic acid base reactions, assumed
in equilibrium. We assume, for conceptual simplicity, that every redox where subscript k refers to the microorganism and μ [T− 1] is the
reaction is mediated by a specific microorganism that grows on the maximum growth rate, cim,j,k = ρb fk [ML− 3] is the concentration of
∑
energy released by that reaction. Therefore, our chemical system in­ microorganism k, ρb = k cim,j,k [ML− 3] is the biomass density (biomass
∑
cludes eight microorganisms with the genetic capacity for a certain type per unit volume of immobile zone), fk = ϕim,j,k / k ϕim,j,k [-] is the vol­
of reaction (recall that only six were identified in section 2.1). We as­ ume fraction of the k th microorganism, cD,im,j [ML− 3], cA,im,j [ML− 3], and
sume that they exist only in immobile zones, to acknowledge the fact cI,im,j [ML− 3] are the concentrations of electron donor, electron acceptor
that they constitute biofilm microbial communities and that aqueous and inhibitor in the j th immobile zone, respectively. KD [ML− 3], KA
species need to diffuse into the biofilm to react. Each of these microor­ [ML− 3], and IA [ML− 3] are the half-maximum rate concentrations for
ganisms is associated to a reaction related to its growth, which is electron donor, electron acceptor and inhibitor, respectively. The hy­
drolysis rate of biomass is simpler and follows first-order kinetics:
Table 1 rk,im,j,k = dk cim,j,k j = 1, ⋯, N k = 1, ⋯, 8 (6)
Equilibrium and kinetically-controlled reactions used for DWB-3 reactive
transport simulations.
where d [T− 1] is the decay rate constant. The rate of woodchip hydro­
Reaction Formulation Equilibrium Constant K at lysis is assumed constant.
25℃ The model has got 40 parameters, which would lead to an unstable
Equilibrium reactions and uncertain calibration. In fact, one of the motivations behind this
14
Water dissociation H2 O = H+ + OH− 10− work is to show that using a MRMT model allows us to adopt model
6.35
Carbonic acid dissociation H2 CO3 = H+ + 10−
independent parameters derived from well stirred reactors or waste­
HCO−3
Bicarbonate dissociation HCO−3 = H+ + CO2− 10− 10.33 water treatment plants, where transport is not a limiting factor. Rate
3
Hydrolysis of ammonium NH+ 10− 9.252 laws parameters are given in Table S2 (see Supplementary materials).
4 = H + NH3
+

Most of them are referenced from the literature, or when not available
from the most similar reaction.
Kinetic reactions for biomass growth

Aerobic oxidation of DOC 0.25CH2 O + 0.005NH+ 4 + 0.225O2 =

0.005C5 H7 O2 N + 0.23H+ + 0.225HCO−3 + 0.015H2 O 2.4. Numerical method
Nitrification 0.128NH+4 + 0.235O2 + 0.015HCO3 =
−

0.003C5 H7 O2 N + 0.238H+ + 0.125NO−3 + 0.134H2 O
Denitrification 0.25CH2 O + 0.24NO−3 = 0.02C5 H7 O2 N + 0.22NO−2 +
(NO−3 →NO−2 ) 0.15HCO−3 + 0.13H+ + 0.04H2 O
Denitrification 0.25CH2 O + 0.26NO−2 + 0.11H+ = 0.02C5 H7 O2 N +
(NO−2 →N2 O) 0.12N2 O + 0.15HCO−3 + 0.16H2 O
Denitrification (N2 O→N2 ) 0.25CH2 O + 0.27N2 O = 0.02C5 H7 O2 N + 0.26N2 +
0.15HCO−3 + 0.15H+ + 0.03H2 O
DNRA 0.25CH2 O + 0.0625NO−3 = 0.025C5 H7 O2 N +
0.0375NH+ 4 + 0.125HCO3 + 0.025H + 0.0125H2 O
−
+
The model was calculated by the code RT_MRMT_DSA_BG (https:
//github.com/Jingjingwangxiang/RT_MRMT_DSA_BG.git) developed
based on our preliminary code RT_MRMT_DSA (Wang et al., 2022a). It is
an object-oriented FORTRAN2003 code based on the finite element
method and capable of simulating reactive transport and biomass
growth in a heterogeneous porous medium with MRMT. The Direct
Substitution Approach is applied to solve the coupled and highly
nonlinear transport and biochemical reactions simultaneously, enabling

Anammox 0.29NH+4 + 0.3683NO2 + 0.029HCO3 + 0.0336H

− − +
=
0.0058C5 H7 O2 N + 0.2894N2 + 0.0736NO−3 +
a robust and fast convergence (Saaltink et al., 1998, 2001).
0.5911H2 O
Sulfammox 0.3433NH+ 2−
4 + 0.1SO4 + 0.05HCO3 = 2.5. Modelling setup and sequence
−

0.01C5 H7 O2 N + 0.1667N2 + 0.0933H+ + 0.1H2 S +

0.53H2 O
First, we interpreted the tracer test using a 1D model to obtain
transport parameters: porosities, longitudinal dispersion, mass transfer
Kinetic reactions for biomass decay
rates and probabilities. Models with and without MRMT were calibrated
Microbial biomass decay 0.05C5 H7 O2 N + 0.05H+ + 0.15H2 O = 0.25CH2 O + to reproduce the measured bromide breakthrough curve (BTC). A con­
0.05NH+ 4 stant flow rate was applied during the simulation, which is the average
Hydrolysis of woodchips C6 H12.012 O6 N0.004 + 0.004H+ = 6CH2 O + 0.004NH+
4
flow rate (i.e. 0.31 L/s) of the DWB-3 during the tracer test. The initial

4
J. Wang et al. Journal of Hydrology 624 (2023) 129863

concentrations of bromide were set to zero for both mobile and immo­
bile nodes, except for the first mobile node which has a concentration of
one. A Cauchy boundary condition was set at the inlet and an open
boundary condition was given at the outlet.
Then, we performed 1D reactive transport simulation of denitrifi­
cation reactions and compared the results with experimental sample
data collected and analyzed by the LKAB chemical laboratory. A con­
stant flow rate (i.e. 0.21 L/s) along the 1D domain was set, corre­
sponding to the average during 2019 with a mean residence time of 8.1
days and with a total porosity of 0.61. A Cauchy boundary condition was
used at the inlet, and a free boundary condition was imposed at the
outlet. Boundary concentrations of primary species at the inlet were set
as the average concentration measured at the entrance of DWB-3 during
the whole operation in 2019 and are given in Table S1 (see Supple­
mentary materials). Initial concentrations of primary species in the
mobile and immobile zones were the same as those at the inlet.
Parameter values for all kinetic rates are listed in Table S2 (see Sup­
plementary materials). The gene abundance was referenced to the
sample data of Nordström et al. (2021) in woodchips. The order-of-
magnitude differences in genes were used to quantify the volume frac­
tions of microorganisms. The nir gene abundance is two orders of
magnitude higher than nosZ, and nrfA genes abundance is half an order
of magnitude higher than nosZ (see Table S2 in Supplementary
materials).
To avoid numerical instability, the size of Δx and Δt were chosen
Δx2 /D
according to the criteria of Péclet (Pe = Δx/v = Δx
αL ≤ 2, which implies
qΔt
Δx ≤ 2αL ) and Courant (Cr = vΔt
Δx = ϕm Δx ≤ 1, which implies Δt ≤ ϕmqΔx),
respectively. Moreover, in reactive transport simulations with
biochemical kinetic reactions, the choice of Δt is also constrained by the
reaction rates. For example, if cD,im,j ≪KD , cA,im,j ≫KA , and cI,im,j ≪IA , in
μcim,j,k
Eq. (5), then rk,im,j ≈ KD cD,im,j , and therefore, Δt ≤ μcKim,j,k
D
. In the reactive
transport simulations, the following conditions were applied: total
length L = 41 m, total time T = 10 days, Δx = 0.5 m, Δt = 0.001 day,
q = 2.1 m/day, and αL = 0.3 m.

3. Results and discussion

3.1. Tracer test interpretation

The bromide tracer test revealed a 50% breakthrough after 7.0 days
(Fig. 2a). The mean arrival time, which usually a bit larger than the 50%
recovery time, should have been 4.8 days if transport had occurred in a
single porosity medium with a porosity of 0.54, which had been the
mobile porosity measured in laboratory experiments (Nordström and
Herbert, 2017). This observed retardation of the conservative bromide
tracer suggests that mass transfer is occurring between mobile and
immobile water in the bioreactor.
Parameters of the MRMT model obtained from the tracer test cali­
Fig. 2. MRMT model results of tracer test data with (a) narrow and (b) broad
brations are given in Table 2. The results show that the distribution of
mass transfer rate distribution, respectively. To compare the consistency be­
mass transfer rates that can fit the data is not unique (see Table 2 and
tween the numerical results and the experimental data, concentrations are
Fig. 2). We initially fitted the BTC with the narrow range of mass transfer normalized with respect to their maximum values. To highlight the BTCs tailing
rates, but we felt that the mean residence time in immobile zones caused by woodchip heterogeneity, results are also plotted on log–log scale (c).
∑
( pj ταj = 2.5 days) might be too small (the mean residence time in a
woodchip with 0.5 cm radius would be r2 /D ≅ 1 day, with molecular cannot reproduce well the tails of the observed BTC.
diffusion coefficient in the wood-biofilm of D = 3.0 × 10− 6 cm2/s). But The effect of MRMT can be observed by comparing the BTCs
woodchip sizes are non-uniform and, more importantly, some lumping computed with and without MRMT (Fig. 2a and b). In the narrow range
and clogging is too be expected. For example, if biofilms lump several model, peak arrivals coincide for MRMT and the single porosity (with ϕ
woodchips for an aggregate radius of 5 cm, the corresponding residence equal to MRMT ϕm ) models (Fig. 2a). In the broad range model, the peak
time would be some 100 days. Therefore, we also tried a model with a arrival is delayed. This type of behavior is discussed by Carrera et al.
much broader range of transfer rates. As it turns out, models with nar­ (1998). In all cases, the mean arrival time of the BTC is given by the fluid
row and broad ranges of mass transfer rates can fit the experimental data volume divided by the flow rate, but the peak reflects the porosity fully
equally well. Differences only become relevant for the very low con­ accessed by the tracer. Therefore, the model with a broad range of mass
centrations toward the end of the tracer test, best observed using a log transfer rates is more reasonable due to the higher volume fraction ratio
scale (Fig. 2c). In contrast, single porosity models (i.e., without MRMT) between the immobile and mobile zone (0.18/0.43 versus 0.08/0.52 for

5
J. Wang et al. Journal of Hydrology 624 (2023) 129863

Table 2 3.2. Simulation of denitrification

Model setup for tracer tests.
Parameters Symbols Units Values Fig. 3 compares the model results with experimental data collected in
DWB-3 during the summer campaign of 2019. Results show that the
MRMT with MRMT with
narrow αj broad αj MRMT model with the broad range of mass transfer rates fits the
distribution distribution experimental data well and reproduces the evolution of nitrate, nitrite,
and ammonium along DWB-3 better than the one with narrow mass
Porosity of mobile ϕm [-] 0.52 0.43
zone transfer rates. So, contrary to the behavior of conservative tracer, the
Porosity of ϕim [-] 0.08 0.18 narrow and broad MRMT provide different fits for the reactive species.
immobile zone Moreover, oxygen is consumed quickly in the MRMT model with broad
− 1
Mass transfer rates [day ] 0.3, 0.5, 0.8, 0.01, 0.1, 1, 10,
αj
mass transfer rate distribution, while oxygen consumption is slow in the
of the j th 1.0, 3.0 100
immobile zone MRMT model with the narrow one, which limits the denitrification re­
Probabilities of the pj [-] 0.6, 0.2, 0.1, 0.0709, 0.1222, actions and hampers the fit. This indicates that a proportion of immobile
j th immobile 0.06, 0.04 0.3530, 0.4539, zones with small mass transfer rates (long residence times) is important
zone 3.2207e-05 for the creation of anaerobic conditions at the downstream fraction of
Length of L [m] 41
the bioreactor (recall Fig. 1). The gene abundance did not evolve much
simulation
domain over 10 days due to the slow growth rates (not shown).
Darcy flux q [m/ 3.22 We must add that, if we modify reaction rate parameters, the model
day] with narrow distribution of residence times could yield similar fittings to
Longitudinal [m] 0.3
αL
the one with a broad distribution. In fact, we also obtained similar re­
dispersivity
Element size Δx [m] 0.5
sults with the traditional single porosity model by modifying the re­
Time increment Δt [day] 0.05 actions rates. But, as stated, the goal was to reproduce observations
Total time T [day] 500 without having to calibrate for kinetic parameters. Bearing this in mind,
the results of Fig. 3 are satisfactory.

the broad and narrow distributions, respectively, see Fig. 2c). Most
importantly, we know that MRMT model is needed to account for the
data tailing caused by the heterogeneity of woodchips in the bioreactor.

Fig. 3. Concentration of primary species in mobile zone versus distance at 10 days. Two other primary species, SO2− 4 and H2 S, are presented in Fig. S2 (see Sup­
plementary materials). The light blue bars represent the averaged sample data measured at the five piezometer pairs along DWB-3 in the 2019 summer campaign, the
red squares represent the mean and the red error bars represent the standard deviation of the sample data at the inlet and outlet during the same period. The solid
blue and orange-red lines represent the MRMT results with narrow and broad mass transfer rate distribution, respectively. (For interpretation of the references to
color in this figure legend, the reader is referred to the web version of this article.)

6
J. Wang et al.
3.3. Biochemical localization in woodchips
Figs. 4 and 5 illustrate biochemical localization favored by the
porous nature of woodchips. Reactions are localized in that, different
reactions occur at every point, only in different immobile zones. For
example, dissolved oxygen is rapidly consumed but also rapidly
replenished in fast immobile zones near the inlet of DWB-3 (see O2
concentrations in Fig. 4 and aerobic oxidation rates in Fig. 5). Nitrifi­
cation is also important near the inlet. The various stages of denitrifi­
cation occur in different immobile zones, nitrate is reduced to nitrite at
intermediate τα zones near the entrance, but at fast τα zones further
downstream, once O2 has been exhausted. Instead, nitrite is reduced to
N2 O, at longer τα and further downstream. Overall, this sequence of
denitrification reactions is the main terminal electron-accepting process
relative to nitrification, DNRA and anammox (cf. reaction rates in
Fig. 5).
In very fast immobile zones (i.e., those τα ≪10− 1 days, much smaller
than transport time), concentrations reach equilibrium between mobile
and immobile zones because of the fast mass exchange rates. On the
other hand, mass exchange is small between mobile and slow immobile
zones (i.e., τα > 10 days, greater than transport time). Thus, concen­
trations in these zones are mainly controlled by kinetics. This confirms
that reactive transport in heterogeneous media is jointly controlled by
the reaction times and residence times in immobile zones, relative to
transport time (Wang et al., 2022b).
Aerobic reactions (e.g., oxidation and nitrification) and anaerobic
reactions (e.g., denitrifications, DNRA, anammox, and sulfammox)
occur simultaneously along the woodchips bioreactor (see Fig. 5) in time
but only apparently in space, as the porous woodchips create a broad
range of redox conditions that allows aerobic and anaerobic reactions to
occur simultaneously in the different portions of the porous structure, at
scales below the usual sampling scale. This finding is consistent with the
general, though not unanimous, view that soft wood is more efficient
Fig. 4. Concentrations of primary species (mol/L, color scale) in immobile zones versus distance along the bioreactor after 10 days for the MRMT model with broad
mass transfer rates distribution. Two other primary species, SO2−
4 and H2 S, are presented in Fig. S3 (see Supplementary materials). For each point (x coordinate), the
vertical coordinate represents the distribution of concentrations in the immobile zone with residence time τα . Note that the most reduced species (CH2 O, H2 S, N2 O
and N2 but not ammonium) become localized in immobile zones with longest residence time (i.e., highest concentrations occur at longest residence times).
7
Journal of Hydrology 624 (2023) 129863
than hardwood in terms of overall denitrification (Lopez-Ponnada et al.,
2017).
These results invite for further conjectures. Our results make it clear
that the distribution of the residence times in immobile zones is
fundamental for the functioning of the bioreactor. Surprisingly, limited
research has gone into the impact of woodchip size. Some researchers
have studied its effect on durability (Ghane et al., 2018), or woodchip
degradation and subsidence (Schaefer et al., 2021). Some have studied
denitrification efficiency, but results are ambiguous (Cameron and
Schipper, 2010; Subramaniam et al., 2016). What our results suggest is
that the outflow of polluting byproducts, such a nitrite or nitrous oxide,
may be reduced by using large woodchips.
4. Conclusions
We built a MRMT model to explore denitrification processes and
biochemical localization in a DWB at Kiruna. MRMT requires the dis­
tribution of residence times in the immobile zones, as well as the mobile
and immobile porosities. These parameters were obtained by calibration
to a conservative tracer test, which confirmed that the MRMT model is
needed to reproduce the breakthrough curve tail caused by diffusion
into the porous woodchips. While the fit was non-unique, the resulting
parameters were consistent with the woodchip sizes, so that an
approximate distribution of residence times could have been obtained
based solely on the size of woodchips.
This MRMT transport model was coupled to a biochemical reaction
module, based on Monod kinetics. The model accounts for microbial
catalyzation, biomass growth and decay, represented by changing vol­
ume fractions of the immobile zones. The last feature is not relevant for
the Kiruna case, because biomass does not change significantly over the
duration of the simulation. Two MRMT models were used to reflect non-
uniqueness of the transport calibration: one with a broad and one with a
narrow distribution of mass transfer rates. Contrary to the conservative
J. Wang et al. Journal of Hydrology 624 (2023) 129863

Fig. 5. Biochemical reaction rates (mol/L/day, color scale) in immobile zones versus distance along the bioreactor. As in Fig. 4, the vertical coordinate represents
residence time τα , of immobile zones connected to each point. Different reactions dominate different immobile zones at every point of the 1D domain.

tracer, the two models yield different fits for the reactive species. It is
important to note that parameters for kinetic rate laws were taken from
wastewater treatment plants and well-mixed experiments, where, unlike
our MRMT model, kinetic rates are not limited by transport. Despite
that, our MRMT model satisfactorily reproduces measured concentra­
tions. It suggests that: 1) It is reasonable to assume that biochemical
reactions mediated by microbes occur mainly in the immobile zones of
woodchips. 2) The porous structure of woodchips allows localized
biochemical reactions and provides the possibility that aerobic and
anaerobic reactions occur simultaneously. 3) Compared to other
nitrogen-cycling processes (e.g., nitrification, DNRA, anammox), deni­
trification is the main processes occurring in the woodchip bioreactor.
An implication of our model results is that the distribution of resi­
dence times, controlled by the size of woodchips, is relevant to the
simulated reactions. In fact, the ultimate N reduction reactions (those
responsible for reducing nitrite and nitrous oxide) are localized in the
zones with long residence times (representative of the innermost portion
of woodchips). Therefore, we anticipate that increasing the size of
woodchips will contribute to reduce the outflow of these undesired
species.
Declaration of Competing Interest
The authors declare that they have no known competing financial
interests or personal relationships that could have appeared to influence
the work reported in this paper.
Data availability
Data will be made available on request.
Acknowledgements
The authors acknowledge the financial support of projects NITREM,
RESTORA (Agència Catalana de l’Aigua, ACA210/18/0040), and Con­
Mimo (Spanish Research Agency, AEI, number TED2021-131188B-

8
J. Wang et al. Journal of Hydrology 624 (2023) 129863

C31). NITREM (project number 17013) has received funding from the temperature conditions. Front. Microbiol. 10 (APR) https://doi.org/10.3389/
fmicb.2019.00635.
European Institute of Innovation and Technology (EIT). This body of the
Jaynes, D.B., Moorman, T.B., Parkin, T.B., Kaspar, T.C., 2016. Simulating woodchip
European Union received support from the European Union’s Horizon bioreactor performance using a dual-porosity model. J. Environ. Qual. 45 (3),
2020 research and innovation programme. Additional funding was ob­ 830–838.
tained from the Generalitat de Catalunya (2017 SGR1485) and the Kouanda, A., Hua, G., 2021. Determination of nitrate removal kinetics model parameters
in woodchip bioreactors. Water Res. 195, 116974.
Spanish Ministry of Science and Innovation (Centre of Excellence Lopez-Ponnada, E.V., Lynn, T.J., Peterson, M., Ergas, S.J., Mihelcic, J.R., 2017.
Severo-Ochoa, CSIC-IDAEA, CEX2018-000794-S). Application of denitrifying wood chip bioreactors for management of residential
non-point sources of nitrogen. In. J. Biol. Eng. 11 (1) https://doi.org/10.1186/
s13036-017-0057-4.
Appendix A. Supplementary data Nordström, A., Hellman, M., Hallin, S., Herbert, R.B., 2021. Microbial controls on net
production of nitrous oxide in a denitrifying woodchip bioreactor. J. Environ. Qual.
Supplementary data to this article can be found online at https://doi. 50 (1), 228–240.
Nordström, A., Herbert, R.B., 2017. Denitrification in a low-temperature bioreactor
org/10.1016/j.jhydrol.2023.129863. system at two different hydraulic residence times: laboratory column studies.
Environm. Technol. (United Kingdom) 38 (11), 1362–1375.
References Nordström, A., Herbert, R.B., 2018. Determination of major biogeochemical processes in
a denitrifying woodchip bioreactor for treating mine drainage. Ecol. Eng. 110,
54–66.
Babey, T., de Dreuzy, J.-R., Casenave, C., 2015. Multi-Rate Mass Transfer (MRMT)
Nordström, A., Herbert, R.B., 2019. Identification of the temporal control on nitrate
models for general diffusive porosity structures. Adv. Water Resour. 76, 146–156.
removal rate variability in a denitrifying woodchip bioreactor. Ecol. Eng. 127,
Bailey, B.L., Smith, L.J.D., Blowes, D.W., Ptacek, C.J., Smith, L., Sego, D.C., 2013. The
88–95.
Diavik waste rock project: persistence of contaminants from blasting agents in waste
Rezaei, M., Sanz, E., Raeisi, E., Ayora, C., Vázquez-Suñé, E., Carrera, J., 2005. Reactive
rock effluent. Appl. Geochem. 36, 256–270.
transport modeling of calcite dissolution in the fresh-salt water mixing zone.
Basu, N.B., Van Meter, K.J., Byrnes, D.K., Van Cappellen, P., Brouwer, R., Jacobsen, B.H.,
J. Hydrol. 311 (1-4), 282–298.
Jarsjö, J., Rudolph, D.L., Cunha, M.C., Nelson, N., Bhattacharya, R., Destouni, G.,
Rittmann, B.E., McCarty, P.L., 2001. Environmental biotechnology: principles and
Olsen, S.B., 2022. Managing nitrogen legacies to accelerate water quality
applications. Curr. Opin. Biotechnol. 7 (3).
improvement. Nat. Geosci. 15 (2), 97–105. https://doi.org/10.1038/s41561-021-
Saaltink, M.W., Ayora, C., Carrera, J., 1998. A mathematical formulation for reactive
00889-9.
transport that eliminates mineral concentrations. Water Resour. Res. 34 (7),
Cameron, S.G., Schipper, L.A., 2010. Nitrate removal and hydraulic performance of
1649–1656.
organic carbon for use in denitrification beds. Ecol. Eng. 36 (11), 1588–1595.
Saaltink, M.W., Carrera, J., Ayora, C., 2001. On the behavior of approaches to simulate
https://doi.org/10.1016/J.ECOLENG.2010.03.010.
reactive transport. J. Contam. Hydrol. 48 (3-4), 213–235.
Carrera, J., Sánchez-Vila, X., Benet, I., Medina, A., Galarza, G., Guimerà, J., 1998. On
Schaefer, A., Werning, K., Hoover, N., Tschirner, U., Feyereisen, G., Moorman, T.B.,
matrix diffusion: formulations, solution methods and qualitative effects. Hydrgeol. J.
Howe, A.C., Soupir, M.L., 2021. Impact of flow on woodchip properties and
6 (1), 178–190.
subsidence in denitrifying bioreactors. Agrosystems, Geosci. Environ. 4 (1) https://
Carrera, J., Saaltink, M.W., Soler-Sagarra, J., Jingjing, W., Valhondo, C., 2022. Reactive
doi.org/10.1002/agg2.20149.
Transport: A Review of Basic Concepts with Emphasis on Biochemical Processes.
Schipper, L.A., Robertson, W.D., Gold, A.J., Jaynes, D.B., Cameron, S.C., 2010.
Energies 15 (3). https://doi.org/10.3390/en15030925.
Denitrifying bioreactors—An approach for reducing nitrate loads to receiving
Christianson, L., Bhandari, A., Helmers, M., Kult, K., Sutphin, T., Wolf, R., 2012.
waters. Ecol. Eng. 36 (11), 1532–1543.
Performance evaluation of four field-scale agricultural drainage denitrification
Steefel, C.I., MacQuarrie, K.T.B., 1996. Approaches to modeling of reactive transport in
bioreactors in Iowa. Trans. ASABE 55 (6).
porous media. Rev. Mineral. 34.
Cirpka, O.A., Valocchi, A.J., 2007. Two-dimensional concentration distribution for
Störiko, A., Pagel, H., Mellage, A., Van Cappellen, P., Cirpka, O.A., 2022. Denitrification-
mixing-controlled bioreactive transport in steady state. Adv. Water Resour. 30 (6-7),
driven transcription and enzyme production at the river-groundwater interface:
1668–1679.
insights from reactive-transport modeling. Water Resour. Res. 58 (8) https://doi.
de Dreuzy, J.-R., Rapaport, A., Babey, T., Harmand, J., 2013. Influence of porosity
org/10.1029/2021WR031584.
structures on mixing-induced reactivity at chemical equilibrium in mobile/immobile
Storm, P., Smeds, M., 2021. Two successful projects from EIT RawMaterials on
Multi-Rate Mass Transfer (MRMT) and Multiple INteracting Continua (MINC)
digitalization and responsible mineral exploration. Mineral Econ. 34 (1), 169–171.
models. Water Resour. Res. 49 (12), 8511–8530.
Subramaniam, D., Mather, P., Russell, S., Rajapakse, J., 2016. Dynamics of nitrate-
Fan, Y., Essington, M., Jagadamma, S., Zhuang, J., Schwartz, J., Lee, J., 2022. The global
nitrogen removal in experimental stormwater biofilters under intermittent wetting
significance of abiotic factors affecting nitrate removal in woodchip bioreactors. Sci.
and drying. J. Environ. Eng. 142 (3) https://doi.org/10.1061/(asce)ee.1943-
Total Environ. 848, 157739.
7870.0001043.
Ghane, E., Feyereisen, G.W., Rosen, C.J., Tschirner, U.W., 2018. Carbon quality of four-
Valhondo, C., Carrera, J., Ayora, C., Tubau, I., Martinez-Landa, L., Nödler, K., Licha, T.,
year-old woodchips in a denitrification bed treating agricultural drainage water.
2015. Characterizing redox conditions and monitoring attenuation of selected
Trans. ASABE 61 (3). https://doi.org/10.13031/trans.12642.
pharmaceuticals during artificial recharge through a reactive layer. Sci. Total
Grießmeier, V., Leberecht, K., Gescher, J., 2019. NO3− removal efficiency in field
Environ. 512–513 (C), 240–250. https://doi.org/10.1016/J.
denitrification beds: key controlling factors and main implications. Environ.
SCITOTENV.2015.01.030.
Microbiol. Rep. 11 (3), 316–329.
Valhondo, C., Carrera, J., Martínez-Landa, L., Wang, J., Amalfitano, S., Levantesi, C.,
Halaburka, B.J., LeFevre, G.H., Luthy, R.G., 2017. Evaluation of mechanistic models for
Diaz-Cruz, M.S., 2020. Reactive barriers for renaturalization of reclaimed water
nitrate removal in woodchip bioreactors. Environ. Sci. Tech. 51 (9), 5156–5164.
during soil aquifer treatment. Water (Switzerland). https://doi.org/10.3390/
Hellman, M., Hubalek, V., Juhanson, J., Almstrand, R., Peura, S., Hallin, S., 2021.
W12041012.
Substrate type determines microbial activity and community composition in
Wang, J., Carrera, J., Saaltink, M.W., Valhondo, C., 2022a. A general and efficient
bioreactors for nitrate removal by denitrification at low temperature. Sci. Total
numerical solution of reactive transport with multirate mass transfer. Comput.
Environ. 755, 143023.
Geosci. 158, 104953 https://doi.org/10.1016/j.cageo.2021.104953.
Herbert, R.B., Winbjörk, H., Hellman, M., Hallin, S., 2014. Nitrogen removal and spatial
Wang, J., Carrera, J., Saaltink, M.W., Valhondo, C., 2022b. On the localization of
distribution of denitrifier and anammox communities in a bioreactor for mine
chemical reactions in multicontinuum media. Adv. Water Resour. 167, 104286
drainage treatment. Water Res. 66, 350–360. https://doi.org/10.1016/J.
https://doi.org/10.1016/J.ADVWATRES.2022.104286.
WATRES.2014.08.038.
Jang, J., Anderson, E.L., Venterea, R.T., Sadowsky, M.J., Rosen, C.J., Feyereisen, G.W.,
Ishii, S., 2019. Denitrifying bacteria active in woodchip bioreactors at low-