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A physical explanation for the development of redox microzones in hyporheic flow

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Recent observations reveal a paradox of anaerobic respiration occurring in seemingly oxic‐saturated sediments. Here we demonstrate a residence time‐based explanation for this paradox. Specifically, we show how microzones favorable to anaerobic respiration processes (e.g., denitrification, metal reduction, and methanogenesis) can develop in the embedded less mobile porosity of bulk‐oxic hyporheic zones. Anoxic microzones develop when transport time from the streambed to the pore center exceeds a characteristic uptake time of oxygen. A two‐dimensional pore‐network model was used to quantify how anoxic microzones develop across a range of hyporheic flow and oxygen uptake conditions. Two types of microzones develop: flow invariant and flow dependent. The former is stable across variable hydrologic conditions, whereas the formation and extent of the latter are sensitive to flow rate and orientation. Therefore, pore‐scale residence time heterogeneity, which can now be evaluated in situ, offers a simple explanation for anaerobic signals occurring in oxic pore waters. Denitrification occurs in anoxic microzones of bulk oxic hyporheic sedimentsMicrozones develop in less mobile porosity due to increased local residence timeGeophysical methods have potential to evaluate hyporheic less mobile porosity
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A physical explanation for the development
of redox microzones in hyporheic ow
Martin A. Briggs
1
, Frederick D. Day-Lewis
1
, Jay P. Zarnetske
2
, and Judson W. Harvey
3
1
Ofce of Groundwater, Branch of Geophysics, U.S. Geological Survey, Storrs, Connecticut, USA,
2
Department of Geological
Sciences, Michigan State University, East Lansing, Michigan, USA,
3
National Research Program, U.S. Geological Survey,
Reston, Virginia, USA
Abstract Recent observations reveal a paradox of anaerobic respiration occurring in seemingly oxic-saturated
sediments. Here we demonstrate a residence time-based explanation for this paradox. Specically, we
show how microzones favorable to anaerobic respiration processes (e.g., denitrication, metal reduction,
and methanogenesis) can develop in the embedded less mobile porosity of bulk-oxic hyporheic zones.
Anoxic microzones develop when transport time from the streambed to the pore center exceeds a
characteristic uptake time of oxygen. A two-dimensional pore-network model was used to quantify how
anoxic microzones develop across a range of hyporheic ow and oxygen uptake conditions. Two types of
microzones develop: ow invariant and ow dependent. The former is stable across variable hydrologic
conditions, whereas the formation and extent of the latter are sensitive to ow rate and orientation.
Therefore, pore-scale residence time heterogeneity, which can now be evaluated in situ, offers a simple
explanation for anaerobic signals occurring in oxic pore waters.
1. Introduction
In stream systems, a substantial portion of total metabolic activity occurs at the interface of ground and
stream waters due to a favorable combination of physical and chemical conditions [Grimm and Fisher,
1984]. This interface is known as the hyporheic zone (HZ). The bidirectional exchange between surface
water and the surrounding sediments is crucial to conservative and reactive mass transport in streams.
When stream water enters a hyporheic ow path, it is typically rich in dissolved oxygen (O
2
), nitrate
(NO
3
), and organic carbon. These reactants are delivered to the microbially colonized sediment matrix
[Baker et al., 2000], creating a bioreactor that is more efcient per time than the stream water column,
especially for anaerobic processes [Duff and Triska, 1990]. As O
2
is consumed through aerobic respiration,
other terminal electron acceptors are utilized, leading to the zonation of redox processes in sediments
[Vroblesky and Chapelle, 1994; Hedin et al., 1998]. As the movement of water controls solute availability,
water residence time is recognized as a rst-order control on HZ redox zonation [Valett et al., 1996; Morrice
et al., 2000; Zarnetske et al., 2011; Briggs et al., 2013a]. However, residence time is typically conceptualized
and evaluated at the mean ow path scale, without specic regard to exchange between sediment pores
of varying connectivity. Further, there is growing evidence for mixed or overlapping redox zones. This is a
paradox because nonfavorableanaerobic reactions are proceeding within bulk oxic HZ pore waters. Here
we illustrate that heterogeneous pore-scale connectivity creates sediment microzones that explain
this paradox.
The process of denitrication is a well-studied coupling of O
2
uptake dynamics and anaerobic metabolic
processes because denitrication directly follows depletion of pore water O
2
[Duff and Triska, 2000;
Zarnetske et al., 2012]. Certain by-products of denitrication, namely, nitrous-oxide (N
2
O) and nitrogen (N
2
)
gases, are useful rst indicators of anoxic processes occurring in the HZ. Decades of N
2
O and N
2
evidence
collected in bulk-oxic hyporheic zones supports the hypothesis of embedded anoxic microzones [e.g.,
Holmes et al., 1996; Zarnetske et al., 2011; Harvey et al., 2013]; however, the mechanisms of HZ microzone
formation remain speculative. The microzone concept has also been discussed for unsaturated soils [e.g.,
Parkin, 1987], groundwater [Sawyer, 2015], and marine sediments [e.g., Sakita and Kusuda, 2000; Lehto
et al., 2014]. In each of these subsurface environments, spatial and temporal availability in particulate
carbon as reaction substrate has been found to drive local anoxic conditions due to increased reaction
rates. However, pore-scale residence time of water is just as fundamental to governing net transformation
BRIGGS ET AL. LESS-MOBILE POROSITY CREATES MICROZONES 1
PUBLICATION
S
Geophysical Research Letters
RESEARCH LETTER
10.1002/2015GL064200
Key Points:
Denitrication occurs in anoxic
microzones of bulk oxic hyporheic
sediments
Microzones develop in less mobile
porosity due to increased local
residence time
Geophysical methods have potential
to evaluate hyporheic less mobile
porosity
Supporting Information:
Text S1
Correspondence to:
M. A. Briggs,
mbriggs@usgs.gov
Citation:
Briggs,M.A.,F.D.Day-Lewis,J.P.Zarnetske,
and J. W. Harvey (2015), A physical
explanation for the development of
redox microzones in hyporheic ow,
Geophys.Res.Lett.,42, doi:10.1002/
2015GL064200.
Received 9 APR 2015
Accepted 8 MAY 2015
Accepted article online 14 MAY 2015
©2015. American Geophysical Union. All
Rights Reserved.
of redox sensitive solutes but is less
well characterized than biogeochemical
substrate explanations. For example,
when similar O
2
uptake dynamics are
found throughout the saturated matrix,
variability in sediment pore variability
pore size and connectivity alone can
drive anoxic microzones [Boulton et al.,
1998]; however, this straightforward
concept has essentially been neglected
from quantitative HZ research.
From a Lagrangian mass transport per-
spective, a parcel of stream water con-
taining O
2
and NO
3
moves through
mobile pores of a HZ where metabolic
reactions consume O
2
creating a redox
gradient within the mobile porous
domain (Figure 1a). The nature of this
gradient fundamentally depends on the
coupling of processes regulating both
net O
2
uptake rate and mean ow path
residence time [Boano et al., 2010;
Zarnetske et al., 2011, 2012; Gomez et al.,
2012; Briggs et al., 2013a]. Therefore, a
rst-order, Lagrangian approximation of
NO
3
reactive transport can be used to
dene a threshold transition time (τ
lim
)
from aerobic to anaerobic respiration,
which delineates bulk redox zonation
[Marzadri et al., 2011] (Figure 1a). One
method of predicting bulk τ
lim
is to com-
pare characteristic water residence time
to the characteristic reaction time of O
2
,
expressed as a dimensionless Damköhler number (Da
O2
; Figure 2) [Zarnetske et al., 2012]. The Da
O2
enables
the prediction and comparison of anaerobic respiration potential across many different systems and condi-
tions and has been successfully applied to eld and model data which relate pore water NO
3
concentration
to bulk ow path residence time [Zarnetske et al., 2012; Briggs et al., 2014b]. A Da
O2
of 1 indicates a balance
between O
2
supply and demand and therefore the predicted transition residence time to anaerobic-
dominated processes. By determining the required residence time to yield a Da
O2
of 1 (τ
A
in T, time of anoxia)
over a range of O
2
uptake rates (v
O2
in T
1
), physical residence time alone can be used as a predictor for
anoxic microsite formation [Zarnetske et al., 2012]:
τA¼
1
vO2
(1)
Some of the most striking evidence for embedded microzones comes from isotopically labeled
15
NO
3
eld
injections across disparate hyporheic systems; denitrication products (
15
N
2
) have been found within bulk
oxic pore water samples, upgradient to the predicted (ow path τ
lim
) transition to bulk anoxic conditions
based on the uptake rate of O
2
in the mobile domain (Figure 2) [Zarnetske et al., 2011; Harvey et al., 2013].
Further, pore water sampling in the bulk-oxic HZ has on many occasions shown low-level concentrations
of reduced metals, another anaerobic signal [e.g., Briggs et al., 2013a; Harvey et al., 2013].
Studies of solute transport have demonstrated the role the HZ plays in creating a spectrum of residence
times, commonly with power law behavior [Haggerty et al., 2002; Gooseff et al., 2003; Cardenas et al., 2008;
Aubeneau et al., 2014]. Advanced numerical models that predict the spectrum of ow paths through various
Figure 1. (a) The overarching conceptual model which shows dissolved
reactants in oxic stream water being carried into the hyporheic pore
network. As O
2
is consumed, a bulk transition to anaerobic respiration
occurs if mean ow path residence times exceed τ
lim
. (b) A hypothetical
ow path is simulated with a 2-D pore-network model that incorporates
pore-scale heterogeneity in pore throat size, creating microzones of
anoxic conditions. (c) Anoxic microzones (red) are classied based on
center-of-pore arrival times relative to the threshold time for anoxia, τ
A
.
(d) Microzone designation can be further rened into ow-dependent
(yellow) and ow-invariant (red) microzones.
Geophysical Research Letters 10.1002/2015GL064200
BRIGGS ET AL. LESS-MOBILE POROSITY CREATES MICROZONES 2
channel morphologic features (e.g., bedforms and
meanders) are useful for evaluating residence time
distributions (RTDs) and bulk biogeochemical zona-
tion; however, they still commonly represent hypor-
heic ow paths as individual pipesthat transmit
water in one direction. In reality, hyporheic
exchange does not occur along a series of indivi-
dual pipes but rather along more connected,
mobile porosity domains that exchange with
embedded and adjacent less mobile porosity
domains created by streambed heterogeneities
[Briggs et al., 2014a]. These less mobile porosity
domains represent potentially important localized
pockets of anomalously large residence time that
affect the biogeochemical importance of hyporheic
exchange. Therefore, numerical pore-network
models (PNMs) are a useful approach to include
the pore-scale heterogeneity in connectivity that
leads to dual-domain transport in hyporheic zones.
The PNM approach has been used for decades by
the groundwater research community (as reviewed
by Blunt et al. [2002]) but has not been broadly
applied to the hyporheic domain.
The concept of dual-domain porosity is applied to many groundwater systems to explain observed transport
behavior [Siegel, 2014]. Seminal studies of aquifer solute transport observed late-time skewing of RTDs, not
predicted by the processes of advection and dispersion alone, and therefore attributed these RTD
characteristics to less mobile exchange [Harvey et al., 1994; Harvey and Gorelick, 2000]. This less mobile
porosity is now known to affect elemental and biogeochemical cycling (e.g., coupling of uranium and
NO
3
[Luo et al., 2005]) and subsequent groundwater quality. Jørgensen [1977] provides an early example
of how a dual-porosity system, created by partially decomposed fecal pellets of benthic invertebrates in
shallow marine sediments, may contribute to chemical patterns not predicted by the bulk redox
conditions. However, characterization and sampling of less mobile pore space and associated reactive
processes have been historically problematic [Jørgensen, 1977; Harvey et al., 1995; Dentz et al., 2011]. These
issues are primarily attributed to traditional uid sampling of the saturated subsurface preferentially
drawing water from mobile porosity [Harvey, 1993; Harvey and Gorelick, 2000; Singha et al., 2007]. If
variability in carbon availability alone was responsible for redox zonation (e.g., microzones have similar
hydraulic connectivity to bulk HZ sediments), we would expect stronger signals regarding embedded
redox zones when collecting pore water samples. Holmes et al. [1996] hypothesized that microzones may
be particularly difcult to capture with pore water sampling or laboratory column experiments, because of
the potential disturbance by existing measurement techniques. Consequently, we are left with a
conundrum: strong evidence of anaerobic processes occurring in bulk oxic zones (e.g., Figure 2), without
techniques to observe and isolate the mechanisms that create them.
The goal of this study is to provide a physically based explanation for anoxic microzones across a range of
physical transport and oxygen uptake time scales observed in HZs. While there are many complex
biological and reaction substrate limitations on metabolic processes that lead to anoxic environments, we
illustrate here that there is also a simple physical explanation for the development of anoxic microzones
embedded within the bulk oxic streambed. Emerging geoelectrical techniques useful in directly evaluating
exchange with less mobile porosity in situ are also detailed.
2. Numerical Model
We use a pore-network model (PNM) to simulate advective-diffusive transport at the microscale where
microzones may form (e.g., submillimeter). PNMs have been used for decades to understand multiphase
Figure 2. .Hyporheic zone eld data from paired conservative
tracer (Cl
or Br
) and reactive (
15
NO
3
) tracer additions
across a cobbly gravel bar at Drift Creek, OR, USA [Zarnetske
et al., 2011] and the sand and gravel streambed of Sugar
Creek, IN, USA [Harvey et al., 2013]. The isotopic enrichment of
N
2
above the background concentration (δ
15
N
2
1.0)
indicates that denitrication has occurred; theoretically
anaerobic respiration, including denitrication, should only
occur when oxygen demand exceeds supply (Da
O2
>1
[Zarnetske et al., 2012]).
Geophysical Research Letters 10.1002/2015GL064200
BRIGGS ET AL. LESS-MOBILE POROSITY CREATES MICROZONES 3
ow and solute transport in porous media [Blunt et al., 2002] and to develop associated constitutive relations
between network characteristics and effective physical properties. Here we use a simple PNM developed in
MATLAB (Mathworks, Inc., Natick, MA) to calculate solute arrival and residence times through a two-
dimensional (2-D) lattice network (Figure 1c); for extensive detail on the modeling approach, see Text (S1)
in the supporting information. Similar to Bijeljic and Blunt [2007], we use a 2-D square lattice composed of
pipes with square cross section and pore-body width w, pore-throat width w
T
, and uniform length l.
Hydraulic conductances between pores are based on Hagen-Poiseuille ow for pipes of square cross
section; diffusive conductance is based on Ficks law assuming a molecular diffusion coefcient of
2×10
9
m
2
/s; and advective conductance is mass ux based on ow rate and concentration. The network
ow problem is solved for heads where the interpore ows are calculated for use in the transport solution.
Adapting the approach of Harvey and Gorelick [1995] for a network rather than continuum, we directly
solve for the arrival and residence time rather than concentration history by solving the steady state
network transport equations for the moments of concentration. To calculate arrival times at each pore, we
solve for the zeroth and rst moments of concentration for initial unit concentration at the input boundary
(left side in Figure 1b). To calculate residence times, we solve again for the zeroth and rst moments
placing unit concentration now at the pore rather than the boundary.
We randomly assigned the spatial distribution of two classes of pores in the PNM, where Class 1 represents
small, tight pores and Class 2 represents larger, more open pores. The two classes share the same pore body
width (w= 0.344 mm) and pore length (l= 1 mm), but Class 1 pores have tighter pore throats
(w
T
= 0.0053 mm) than Class 2 pores (w
T
= 0.344 mm), and Class 1 pores comprise 30% of the total model
pore volume (total porosity is 26% of bulk matrix). The Da
O2
can be used in downscaling from the ow
path scale to the pore scale to evaluate dominant redox condition based on the arrival time at the pore
center from the streambed interface, which combines the time scales of ow path transport and local
pore-scale exchange. This is related to, but a distinct concept from, the mean residence time within a
given pore, which is also evaluated here. Arrival time at the pore center is used to predict whether anoxic
processes are expected to dominate at the pore scale for any given O
2
uptake rate; we refer to the τ
lim
predicted by this localDa
O2
as τ
A
(time of anoxia) (Figure 1b). We evaluate the development of
microzones over a range of typical hyporheic conditions by examining ow rates, q(0.13 to1.67 m d
1
),
and observed oxygen (mg L
1
) uptake rates (0.1 to 0.6 h
1
), expressed in terms of τ
A
(1.7 to 10 h).
3. Results and Discussion
The PNM demonstrates the potential for the development of both ow-dependent and ow-invariant anoxic
microzones across a range of ow rates and oxygen uptake time scales.
3.1. Numerical Simulations
Our PNM framework tests a residence time-based explanation for evidence of anaerobic respiration
occurring in bulk oxic streambed sediments where anaerobic respiration should be inhibited. For
simplicity, we represent O
2
uptake kinetics using an approach based on pore-scale residence time,
assuming that anaerobic conditions dominate locally when the arrival time at the pore center exceeds the
threshold, τ
A
, corresponding to Da
O2
= 1. The example numerical model simulation in Figure 1b shows that
when less mobile porosity is included within the pore network, anoxic microzones form upgradient of the
general transitional front to bulk anoxic conditions (τ
lim
). Here a pore is classied as belonging to a
microzone if (1) the mean arrival time within the pore body exceeds τ
A
(local Da
O2
), a denition that
inherently includes both the travel time to, and exchange into, a singular pore of interest, and (2) the pore
is located in the domain upgradient of the anoxic/oxic transition based on the bulk redox zonation τ
lim
(Figures 1b and 1c).
As expected, most Class 1 (small throat) pores in the PNM form microzones, because their internal residence
time commonly exceeds τ
A
; however, a subset of the Class 2 (large throat) pores also form microzones,
particularly where adjacent to Class 1 pores and just upgradient of τ
lim
(Figure 1d). Based on these
observations, it is useful to delineate two distinct types of microzones: (1) ow-invariant microzones
created when diffusive exchange time scales through small pores exceeds τ
A
and (2) ow-dependent
microzones created where pore volume exchange is on time scales less than τ
A
. While arrival time to the
Geophysical Research Letters 10.1002/2015GL064200
BRIGGS ET AL. LESS-MOBILE POROSITY CREATES MICROZONES 4
pore center is used to predict microzone formation, it is mean residence time within the pore of interest that
indicates whether the pore is expected to form a ow-invariant or ow-dependent microzone; pores with a
mean residence time greater than the expected range of τ
A
(based on O
2
uptake dynamics) will be ow
invariant. Our denition of ow-invariant microzones is consistent with the numerical modeling study of
Kessler et al. [2013], who predicted that marine carbonate sand grains with high intragranular porosity
would only act as microzones if uptake kinetics within the grain are diffusion limited (e.g., τ
A
is exceeded).
In our HZ PNM, pores with internal residence time less than τ
A
may or may not belong to microzones
depending on the arrival time from the upgradient boundary. An example of this classication is depicted
in Figure 1d, where the general microzonecategory (Figure 1c) is rened to indicate which microzones
are expected to transition to oxic under different (high versus low) ow rate conditions.
The development of anoxic conditions in pores with large throats is more context dependent, as their
location relative to tight-throated pores and overall location along the ow paths control microzone
formation. If embedded within, or immediately adjacent to, the tight pores of Class 1, the Class 2 pores
often form microzones; otherwise, their arrival times indicate they would primarily contribute to bulk
mobileadvective ow. These particular ow-dependent microzones are therefore most sensitive to ow
magnitude and direction. Figure 3 shows how varying ow rate affects travel time across the model
domain and arrival time within discrete clusters of pores; these changes in RTD yield a reduced assemblage
of microzones at high ow. Although most of the microzones that transition to oxic conditions under high
ow are Class 2 pores, some of the tight Class 1 pores also become oxic, particularly near the upstream
boundary. General microzone density increases just upgradient of the bulk domain transition to anoxic
conditions (τ
lim
), a transition that is approached in Figure 3a (right edge of model domain). The difference
Figure 3. A comparison between pore -network models with low (0.45 m d
1
) and higher (1.7 m d
1
) advective uxes from
left to right across the domain, with identical structure and O
2
uptake time scale (τ
A
= 3 h): (a) center-of-pore arrival times in
the low-ux model and associated microzone designations, (b) center-of-pore arrival times in the high-ux model and
associated microzone designations, (c) the difference in pore arrival times and microzone designation from low-ux to
high-ux models, and (d) microzone internal pore residence times delineated between tight (Class 1) and larger (Class 2)
pores in high- and low-ux models.
Geophysical Research Letters 10.1002/2015GL064200
BRIGGS ET AL. LESS-MOBILE POROSITY CREATES MICROZONES 5
map in Figure 3c shows that most microzones that disappear at higher ow are near this transition and these
ow-dependent zones are dominated by larger pores.
RTDs within pores classied as microzones show key distinctions between Class 1 and Class 2 pores (Figure 3d).
Class 1 pores belonging to microzones have an internal-pore RTD centered around 25 h for most ow
rates. Although this distribution is shifted slightly toward shorter residence times at high ow rates, the
internal tight-throated pore residence time generally exceeds τ
A
and the microzones are ow invariant.
Class2poresbelongingtomicrozonesaremuchless numerous (Figure 3d) and display internal
residence times centered around 2.7 h, ranging down to minutes. This result indicates that the
biogeochemical functionality of ow-dependent microzones is quite different than longer residence
time ow-invariant microzones. Although anoxic reactions may begin in large pores, they could be
interrupted as water is quickly exchanged back into the bulk-oxic zone.
Heterogeneity of in situ carbon availability has been proposed to inuence microzone formation along
groundwater ow paths and within marine sediments [e.g., Sakita and Kusuda, 2000; Sawyer, 2015]. For
most simulations here we assume consistent reaction rates throughout the pore network to most clearly
investigate the underlying control of local hydraulic connectivity. However, we expand this analysis to
include variable O
2
uptake for the networks and advective elds presented in Figure 3. As suggested by
Briggs et al. [2014a] and Sawyer [2015], carbon aggregates, such as the fecal pellets observed by Jørgensen
[1977], may act to both locally increase reaction rates and decrease connectivity; the lower connectivity of
Class 1 pores are assumed to be formed by particulate organic carbon with anomalously high O
2
uptake.
When a constant τ
A
of 3 h (v
O2
= 0.3 h
1
) is applied across the domain at low and high advective uxes,
over 99% of Class 1 pores function as microzones. As the τ
A
approaches 0.1 h, or the upper limit on v
O2
observed in stream sediments [Zarnetske et al., 2012], 100% of Class 1 pores become anoxic and the tight
porosity is truly composed of ow-invariant microzones. This result supports the idea that carbon
aggregates may be particularly well suited to house redox microzones [e.g., Sawyer, 2015].
Under consistent O
2
uptake (τ
A
of 3 h), 13.7 and 7.8% of better connected Class 2 pores form microsites at low
and high ow, respectively (Figure 3). If reaction rates are allowed to vary randomly throughout the bulk Class
2 matrix across the entire τ
A
range depicted in Figure 4 (τ
A
of 2.510 h), these microsite frac tions drop to 7.8%
and 5.9% for low and high advective uxes, respectively. The slight reduction in microsite fraction is due to
the original τ
A
value of 3 h being at the lower end (high O
2
uptake) of the considered range, but the general
similarity between constant and variable uptake scenarios emphasizes the importance of hydraulic
connectivity as a control on microsite formation. As mentioned above, in some highly reactive streambed
domains, mean O
2
uptake rate has been observed to approach 0.1 h
1
. In systems with similar physical
pore-scale connectivity, it is conceivable that pore-scale reactivity may vary over a larger range than
explored above and microzone formation may be dominated by reaction substrates.
A hot spot of microzone formation is predicted to occur at the combination of low τ
A
and low advective uid
ux (Figure 4). The same pore lattice was used for all simulations, with a consistent makeup of 30% tight Class
1 pores. In the observed hot spot of low ux, up to 36% of pore space is classied as microzone, indicating
that approximately 6% of larger Class 2 pores embedded in the bulk-oxic zone become anoxic. Conversely,
at the combination of high ow rates and τ
A
, there is a large swath of model outcomes where microzones
make up less than 30% of pore space, indicating that some of the Class 1 pores may act as ow-
dependent microzones across the range of ows considered here (Figure 4). Uptake kinetics, summarized
by τ
A
, are more dominant than ow rate as the control on microsite formation. Even at low ow, less than
30% of the model pore spaces are classied as microzone when τ
A
exceeds 9 h; at low τ
A
(e.g., <5.5 h) the
model domain is greater than 30% microzones even at the highest ow rate. The concepts of ow-
invariant and ow-dependent microzones are most clear for a particular τ
A
, as the relationship of O
2
uptake kinetics to residence time is ultimately what drives pore-scale anoxia and the fate of NO
3
, while
advective ow rate is just a component of this residence time.
3.2. Relevance of Microzones and Paths Forward
Patchy distributions of resources and habitat have been shown to greatly increase overall system productivity
of ecosystems compared to predictions based on the average or bulkcondition [Grunbaum, 2012]; this
Geophysical Research Letters 10.1002/2015GL064200
BRIGGS ET AL. LESS-MOBILE POROSITY CREATES MICROZONES 6
general theory is directly relevant to anoxic microzones. Below, we illustrate how microzones affect
important N cycling processes that control ecosystem productivity and water quality.
It is hypothesized that the highest rates of denitrication, which is the one true removal pathway for NO
3
in
ecosystems, will occur at the threshold interface between bulk oxic and anoxic conditions in HZs [Sheibley
et al., 2003; Zarnetske et al., 2011; Harvey et al., 2013]. If this hypothesis is valid, the interfaces between less
mobile pore space and the oxic mobile zone at the pore scale may host microhot spots for N cycling
and NO
3
pollution mitigation. Denitrication in microzones of shallow sediment in streams is likely to be
stimulated by rapid replenishment in the adjacent mobile porosity domain of bioavailable organic carbon
from the readily connected stream sources [Jones et al., 1995; Holmes et al., 1996]; also, microzones formed
directly by in situ carbon-rich aggregates [e.g., Lehto et al., 2014] would augment those formed by physical
residence time heterogeneity. However, as Findlay [1995] illustrated, the cross system heterogeneity of
stream sediments leads to far greater variability in physical residence time controls than it does reaction
substrate (e.g., organic carbon or nitrogen) controls. Therefore, the physical microzone formation
explanation presented in this study is likely a dominant and ubiquitous control for groundwater-stream
water microzone distributions, in addition to pore-scale reaction-rate variability.
Denitrication rates in microzones could be increased via NO
3
production resulting from nitrication of
ammonium (i.e., an oxygen-dependent reaction that converts NH
4+
NO
3
) occurring in the adjacent
mobile domain. Further, the predicted relatively short water residence time at ow-dependent microzone
interfaces of the larger pores (e.g., here approximately 2.7 h; Figure 1d) may be particularly suited to
enable incomplete denitrication. Incomplete denitrication can result in the formation of N
2
O as the
end-product (instead of inert N
2
), and N
2
O is a powerful greenhouse gas the global production of which is
now thought to derive from streams [Beaulieu et al., 2011]. Slow diffusive exchange with extremely tight
porosity (upper end of Figure 3d; Class 1 residence times) would likely have less effect on net HZ chemistry
as mass ux would be relatively low even though local chemical change may be high. Interestingly, recent
microbiology research has shown that there are lamentous bacteria capable of accessing dissolved
resources across redox gradients occurring at the scales of our PNM (mm to cm) [Pfefferetal., 2012], offering
the possibility of resource exchange across microzone interfaces.
While we are not yet able to model or measure all biological and physical factors within the heterogeneous
HZ, and we may never be able to, recent methodological advancements may allow us to capture the primary
physical control of HZ function and microzone development. Traditional pore water sampling techniques
Figure 4. The fraction of pore space, f
A
, predicted to form anoxic microzones across a range of O
2
uptake, τ
A
, and
advective-ux time scales (controlled by q), using pore-network models with similar pore size distributions. The side
plots show the specicf
A
proles at specicO
2
uptake and uid-ux conditions (dashed lines) in the main summary plot.
Geophysical Research Letters 10.1002/2015GL064200
BRIGGS ET AL. LESS-MOBILE POROSITY CREATES MICROZONES 7
primarily reect mobile uid biogeochemical conditions and therefore miss or diminish the inuence of less
connected porosity [Harvey et al., 1995; Harvey and Gorelick, 1995]. Even the most careful sampling
techniques (e.g., very low ow MINIPOINT piezometers [Harvey and Fuller, 1998]) inherently subsample the
pore network and may alter the uid ow rate and direction, including accessing the ow-dependent
microzones of larger pores but not the smaller pores of the ow-invariant microzones. Fortunately,
emerging microscale and eld-scale techniques have potential to better characterize less mobile porosity.
For example, measurement of uid conductivity (σ
f
) and co-located bulk conductivity (σ
b
) during ionic
tracer tests provide information on mobile-immobile exchange [Singha et al., 2007; Briggs et al., 2013b].
Relatively tight pores that connect through pockets of ne-grained or organic material are expected to
contribute to the bulk conductivity signal; therefore, electrical data can be collected in situ to directly
describe less mobile exchange characteristics. Larger-scale groundwater application of these geoelectrical
methods was recently rened to the hyporheic scale to target small discrete volumes (e.g., cm
3
)[Briggs et al.,
2014a]. Briggs et al. [2014a] developed a method of graphical analysis and curve tting to determine less
mobile characteristics directly from the shape and timing of σ
b
versus σ
f
hysteresis patterns. This is an
important advancement from previous tracer-based methods that rely on simulating the cumulative effect
of assumed less mobile exchange on the mobile tracer breakthrough curve (e.g., tracer tailing), because
less mobile porosity is directly sensed. Larger ow path-scale tracer methods are also not well suited for
determining parameters in discrete matrix volumes where many microzones can form, such as the upper few
centimeters of a streambed, that have been observed to facilitate strong denitrication [e.g., Harvey et al., 2013].
4. Conclusions
Pore-scale heterogeneity leads to mobile and less mobile porosity domains in hyporheic systems. Here we
illustrate how anoxic microzones develop in less mobile porosity based on a combination of O
2
uptake
and prolonged local water residence times. The existence of physical structure-controlled local anoxic
zones adds to the more commonly invoked carbon-substrate-based explanations for microzone formation,
and it can reconcile the seemingly paradoxical observations of previous studies that nd clear anaerobic
respiration signals in bulk-oxic sediments of HZs. It is also important to be aware that certain pore water
sampling techniques used in HZ studies preferentially sample the mobile porosity and may be missing
much of the less mobile microzone water and its inuence on solute transport. Fortunately, there are new
geoelectrical techniques that have the potential to isolate and characterize microzone phenomena in HZs.
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BRIGGS ET AL. LESS-MOBILE POROSITY CREATES MICROZONES 8
Acknowledgments
The synthetic data created for this study
can be accessed at the Branch of
Geophysics website at http://water.
usgs.gov/ogw/bgas/. Funding for this
study was provided by the National
Science Foundation grants EAR-
1446300 and EAR-1446328, the U.S.
Geological Survey (USGS) Ofce of
Groundwater, USGS National Research
Program, and Groundwater Resources
Program and Toxic SubstancesHydrology
Program, and The Leverhulme Trust.
Development of the pore-network
model was supported by Department
of Energy Environmental Remediation
Science Program grant DE-SC0001773.
Any use of trade, rm, or product
namesisfordescriptivepurposesonly
and does not imply endorsement by
the U.S. Government.
The Editor thanks two anonymous
reviewers for their assistance in
evaluating this paper.
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BRIGGS ET AL. LESS-MOBILE POROSITY CREATES MICROZONES 9
... Nevertheless, it is important to highlight that, even if the bulk conditions indicate aerobic conditions (DO>2 mg/l), anoxic microsites (DADO<1) may develop at pore scale within the sediments, and denitrification may occur at substantial rates (Briggs et al., 2015;. ...
... With this formulation, denitrification can still occur (however at much lower rates) even if bulk DO concentrations indicate aerobic conditions. Completely disregarding denitrification under aerobic conditions would be an oversimplified assumption, since it can still take place within redox microzones of oxic-saturated sediments (e.g., Briggs et al., 2015;. Furthermore, we only analysed fully-saturated flow paths. ...
... influenced by different factors, such as stream stage, aquifer properties, and hydraulic connectivity(Kurz et al., 2017;, leading to significant changes in water quality. Both short-term and seasonal stream stage fluctuations modify water and solute exchange fluxes and affect short-and long term biogeochemical responses in the riparian zone(Boutt and Fleming, 2009;Chen et al., 2020;Jensen et al., 2017;Liang et al., 2018;Liao et al., 2014;Liu et al., 2019;.Several studies have illustrated the importance of aerobic respiration (AR) and the resulting dissolved oxygen (DO) depletion in regulating the redox conditions of near stream environments, affecting the turnover of redox-sensitive compounds like nitrate (NO3 -) via denitrification (DN)Briggs et al., 2015;Frei et al., 2012;Shuai et al., 2017;. DO consumption and the subsequent redox reactions are jointly governed by hydrologic dynamics (e.g., changes in water transit-times) and the reaction rates that are temperature dependent, both of which are subject to short-term (event scale) and long-term (seasonal scale) fluctuations.A rising stream stage will increase the hydraulic gradients between the stream and local groundwater (GW) ...
Full-text available
Thesis
The stream water (SW) and groundwater (GW) domains are two parts of one hydrologic continuum. The riparian zone (RZ) is a transition zone between both domains, which connects the aquatic and terrestrial ecosystems. The RZ has been shown to have a potential for regulating water quality in stream-corridors. This potential is mainly related to SW-GW interactions and the associated hydrological and biogeochemical processes occurring at different spatio-temporal scales within RZ. Mixing of different solutes, and high microbial activities are only some of the factors responsible for the high potential for contaminant attenuation and general solutes turnover within RZ. However, an adequate representation of these coupled processes, and their variations in space and time is challenging due to the multiple interactions between the hydrological and biogeochemical processes. This PhD addresses this challenge by aiming at an evaluation of the effects of flow dynamics on riparian reactive potential at different scales. The three consecutive studies comprising this thesis were carried out in a well-instrumented RZ located at the low-land portion of the Selke River catchment, a 4th-order stream, central Germany. The location is well suited for this type of research since it is well instrumented and has a long history of agricultural activity within the riparian corridor with associated inputs of nitrate (NO3-) into the riparian aquifer. This thesis combines data-driven and numerical modelling in order to explore and disentangle the different factors and processes shaping water quality at the different scales within the RZ. As dissolved oxygen (DO) is a key-component regulating the redox state of the system, in the data-driven analyses (Study 1), a suite of tracer-tests were carried out and combined with high-resolution hydrological and chemical data to characterize the near stream system (appx. 20m from stream bank) for aerobic respiration. For that, Damköhler numbers for DO (DADO) were employed. Results showed that seasonal and short-term variations in temperature are major controls shaping the reactive state of the system. Seasonal temperature variations in GW induce a shift on reactive state from transport-limited (DADO>1) in summer to reaction-limited conditions (DADO<1) in winter. On the other hand, short-term events had only minor impacts on the system, resulting in slightly less transport-limited conditions due to decreasing temperature and transit-times associated with the events. The study also shows that assuming a constant water temperature along a SW infiltration flowpath could lead to an over- or underestimation of reaction rates by a factor of 2-3 due to different infiltrating water temperature at the SW-GW interface. Also assuming constant water transit-times throughout the hydrological year results in an underestimation of NO3- removal (40%-50% difference). The numerical modelling of Study 2 focused on the simulation of water flow and mass (DO and NO3-) transport using the measured data from Study 1 but extended the spatial scale. The modelling concept combined a fully-integrated 3D transient numerical flow model with a temperature-dependent reactive transport along subsurface flow paths. Results revealed that temperature variations shift the reactive zone for NO3-, whereas this zone is near the stream under warmer conditions. Even under limited carbon availability (as an electron donor) and low-temperatures, NO3- removal fractions (RNO3) were greater further from the stream than along short hyporheic flow paths (RNO3=0.4 and RNO3=0.1, respectively). Conversely, transit-times and DO concentrations constrained nitrate removal at the near stream region. Additionally, with increasing temperature, the effects of stream flow and solute concentrations on biogeochemical turnover and the redox zonation around the stream strongly decreased. The modelling concept of this study provides an adaptive framework to quantify reach-scale biogeochemical turnover around hydrological dynamic streams. In Study 3, the flow model is coupled with a Hydraulic Mixing Cell method for mapping the source composition of water and tracking their spatio-temporal evolution within RZ. This allowed the identification of mixing hotspots which can be defined to have nearly equal fractions of SW and GW per aquifer volume. These mixing hotspots can facilitate mixing-dependent reactions and solute turnover. Only about 9% of the total simulated domain could be identified as mixing hot-spots (mainly at the fringe of the geochemical hyporheic zone), but this value could be 1.5x higher following large discharge events. Such events increase mixing further away from the stream, whereas near the stream the rapid increase of SW influx shifts the ratio between the water fractions to SW, reducing the potential for mixing and the associated reactions. The study also provides an easy-to-transfer approach to assess spatio-temporal patterns of mixing processes and mixing-dependent turnover reactions in riparian zones. In summary, findings from the three studies elucidated the relationships and controls among hydrology and biogeochemistry at different scales in the RZ. By combining innovative methods and using coupled, mechanistic models, this thesis advanced the understanding of reactive potentials within the RZ, which can be useful to devise further research and actions for integrated aquatic ecosystem management and recovery.
... The hyporheic zone (HZ) is well known as the hotspots of biogeochemical cycling and water exchange between stream and groundwater (Boano et al., 2014;Boulton et al., 1998). Stream water is typically rich with dissolved oxygen (DO) and nutrients, such as organic carbon and nitrate (NO 3 − ) (Briggs et al., 2015). When stream water enters hyporheic flow paths, these chemicals are delivered to contact with the microbially colonized streambed sediment (Baveye et al., 1998) and a series of redox reactions in which organic carbon is utilized as an electron donor would take place (Bardini et al., 2012;Boano et al., 2010). ...
... Exploring the formations mechanisms of the HZ microzones is of special interest because of their important functions for enhancing removal of NO 3 − (Sawyer, 2015) and production of greenhouse gas N 2 O that has almost 300 times the ability for heating the atmosphere of carbon dioxide per molecule (Reeder et al., 2018;Quick et al., 2019). In principle, water residence time and consumption rate of DO determine the microzones formations (Briggs et al., 2015). The former depends on flow fields of HZs, and the latter is closely related to microbial metabolic activity and nutrients availability. ...
... Accurate quantifications of these factors are critical for understanding the formations mechanisms of the microzones. At present, the microzones formations were attributed to partial small pores prolonging local residence time (Briggs et al., 2015) or partial low permeability silt structures with higher organic carbon content increasing local consumption rate of DO and residence time (Sawyer, 2015). However, the average flow pattern and concentrations of biomass and nutrients over representative elementary volumes (e.g., Sawyer, 2015) or synthetic pores in pore-network models (e.g., Briggs et al., 2015;Chowdhury et al., 2020) were typically conceptualized and adopted for evaluating residence and reaction times. ...
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Article
Plain Language Summary Stream water is typically rich in oxygen and nutrients such as organic carbon, nitrate. Some proportion of stream water enters streambed at an upstream location of the water‐sediment interface and then exits at a downstream location. Along the subsurface flow path, oxygen concentration gradually decreases due to microbial consumption, and thus the subsurface flow zone can often be divided as generally oxic and anoxic zones. Recent studies have indicated that anoxic microzones can form within the generally oxic zone, and the microzones are the hotspots of enhanced removal of nitrate and production of greenhouse gas nitrous oxide. Here, from the microscopic view, we apply computer model to investigate how the microzones develop and change over time and space. As microbial biomass grows and streambeds are progressively clogged, the microzones can form and change following two distinct patterns depending on the streambed biofilms in which the microbes reside. Specifically, the microzones can be perennial for well permeable biofilms, whereas the microzones are ephemeral for low permeability biofilms because the microzones would disappear and an anoxic macrozone forms across the streambed.
... In contrast, the patches of fine sediments, peat and clay lenses usually have higher potential for denitrification (Barnes et al., 2019;Hampton et al., 2020;Krause et al., 2013). This is because the combinations of a long residence time and a high organic matter content in fine sediments facilitate the development of local anoxic microzones and provide ample organic carbon for denitrification, and thus promoting nitrate removal (Briggs et al., 2015(Briggs et al., , 2018Hampton et al., 2020;Harvey et al., 2013;Wallace et al., 2020). For example, Sawyer (2015) indicated that the total or efficiency of nitrate removal can be consistently much higher in heterogeneous than homogeneous sediments under upwelling groundwater flow conditions. ...
Full-text available
Article
The transport of sediments induced by river flow leads to the formation and movement of bedforms like ripples, and the exchange flux caused by the interaction between stream and bedforms significantly influences nitrogen dynamics. Previous studies have studied the role of bedform migration on nitrogen cycling in homogeneous sediments, however, how bedform migration affects nitrate reduction in heterogeneous streambeds is still unknown. In this study, we established a series of two‐dimensional numerical models to investigate the role of bedform migration on nitrate removal in physically (permeability) and chemically (particulate organic carbon; POC) heterogeneous sediments. Results from mobile bedforms were compared with matching immobile bedforms and equivalently homogeneous mobile ones. Mobile bedforms create periodic exchange flux fluctuations, reduce solutes penetration depths and residence time, and result in decreased denitrification rate. Both a larger bedform celerity and a smaller silt fraction lead to a lower NO3⁻ removal efficiency. Thus, the bedforms are typically assumed to be immobile potentially making an overestimation of NO3⁻ removal. Moreover, sediment heterogeneity cannot enhance NO3⁻ removal in mobile bedforms, where the penetration depth and the residence timescale of NO3⁻ are suppressed, and the formation of anoxic microzone is inhibited. The finding is significantly different from the previous understanding about sediment heterogeneity that can obviously enhance NO3⁻ removal. This study is useful for understanding nitrate processing in streambed sediments and benefits to the management of watershed nutrients.
... /frwa. . cycles, with potentially important shifts in redox conditions and associated biochemical cycles (e.g., denitrification), including changes in the speciation of solutes mobilization of greenhouse gases, accumulation of silica, reduction of manganese, iron, phosphorous, and sulfate, and altered lability of exported dissolved organic and inorganic carbon stocks (Lautz and Fanelli, 2008;Navel et al., 2010;Zarnetske et al., 2011Zarnetske et al., , 2012Harvey et al., 2013;Briggs et al., 2015;Sherson et al., 2015;Bicknell et al., 2020;Regier et al., 2021). Since our sensors did not capture the dynamics of anaerobic processes, and the winter ecology of streams remains understudied, we call for studies to focus on how winter driven anoxia activates biogeochemical cycles that influence stream metabolism and ecologic function through the rest of the year, paradoxically turning previously assumed winter "cold-spots" and "cold-moments" into hot-spots and hot-moments for biogeochemical processing. ...
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Article
Climate change is causing pronounced shifts during winter in the US, including shortening the snow season, reducing snowpack, and altering the timing and volume of snowmelt-related runoff. These changes in winter precipitation patterns affect in-stream freeze-thaw cycles, including ice and snow cover, and can trigger direct and indirect effects on in-stream physical, chemical, and biological processes in ~60% of river basins in the Northern Hemisphere. We used high-resolution, multi-parameter data collected in a headwater stream and its local environment (climate and soil) to determine interannual variability in physical, chemical, and biological signals in a montane stream during the winter of an El Niño and a La Niña year. We observed ~77% greater snow accumulation during the El Niño year, which caused the formation of an ice dam that shifted the system from a primarily lotic to a lentic environment. Water chemistry and stream metabolism parameters varied widely between years. They featured anoxic conditions lasting over a month, with no observable gross primary production (GPP) occurring under the ice and snow cover in the El Niño year. In contrast, dissolved oxygen and GPP remained relatively high during the winter months of the La Niña year. These redox and metabolic changes driven by changes in winter precipitation have significant implications for water chemistry and biological functioning beyond the winter. Our study suggests that as snow accumulation and hydrologic conditions shift during the winter due to climate change, hot-spots and hot-moments for biogeochemical processing may be reduced, with implications for the downstream movement of nutrients and transported materials.
... This could be used to explain the anoxic microzones in the observed DO plume and required to validated in future studies. In recent hyporheic studies (Briggs et al., 2015;Roy Chowdhury et al., 2020), microzones, that is, sediment pores depleted in oxygen (i.e., O2 concentration less than 2.0 mg/L), are also found and embedded within an oxygen-rich porous domain. On the other hand, the response of microbial communities to the river salinization were also ignored. ...
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... For example, small (1 to 10% total porous volume) inclusions of anoxic sediments in an oxic aquifer can act as sources or sinks for redox-sensitive contaminants like nitrates (Dwivedi et al., 2018;Wallace et al., 2020), heavy metal(loid)s (Engel et al., 2021;Kumar et al., 2020), or radionuclides (Janot et al., 2016). Anoxic conditions in these sediments typically result from an interplay between physical and biogeochemical processes, where lower flow velocities, increased availability of electron donors, or a combination of both enable microbial respiration to outpace oxygen transfer rates (Briggs et al., 2015;Sawyer, 2015;Wainwright et al., 2016). Due to their comparatively high reactivity, these biogeochemical hotspots are often contrasted with the less reactive aquifer material they exchange with (Campbell et al., 2012;Dwivedi et al., 2018;McClain et al., 2003). ...
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Exceedences of health-based benchmarks were primarily caused by nitrate and coliform bacteria, which were associated with recharge from diverted surface water used primarily for irrigation. Exceedences of aesthetic-based benchmarks were primarily caused by iron, managanese, and hardness, which were associated with geologic factors. Regional irrigation practices and aquifer lithology can affect groundwater quality in fractured-rock aquifers in the northern Sierra Nevada foothills used for domestic drinking-water supply.
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