Alagal Bloom Analysis

240
ARTICLE
Hyperspectral analysis of algal biomass

in northern lakes, Churchill, MB, Canada
Kimisha Ghunowa, Andrew Scott Medeiros, and Richard Bello
Arctic Science Downloaded from cdnsciencepub.com by 103.27.167.24 on 05/30/22
Abstract: A hyperspectral approach to quantify algal biomass was studied across 30 shallow
ponds in the Hudson Bay Lowlands near Churchill, MB. Normalized difference algal indices
(NDAI) were calculated based on hyperspectral measurements of the reflectance collected
on shore with a hand-held spectrometer in parallel to estimations of biomass with an in
vivo fluorometer designed for benthic algae. Algal biomass and coarse assemblages were
differentiated through their spectral reflectance as a demonstration of concept for future
upscaling that would be necessary for regional monitoring using remote sensing technol-
ogy. Results indicated strong agreements between the calculated NDAI for measured
reflectance from each pond and that of the isolated benthic zone. Cyanobacteria were the
dominant component of the algal community for most ponds. As such, measures of reflec-
tance and use of simple NDAIs may be able to characterize the total biomass of northern
For personal use only.
ponds. However, the distinction between algal groups may require independent validation
of algal assemblages for estimations beyond total biomass. Nonetheless, hyperspectral
analysis could provide a strong potential for monitoring northern freshwater systems at a
regional scale.
Key words: hyperspectral monitoring, aquatic monitoring, algal biomass, subarctic.
Résumé : Une approche hyperspectrale visant à quantifier la biomasse algale a été utilisée
sur 30 étangs peu profonds des basses terres de la Baie d’Hudson près de Churchill au
Manitoba. Les indices différentiels normalisés de la présence d’algues (IDNA) ont été
calculés à partir des mesures hyperspectrales de la réflectance recueillies sur le rivage à
l’aide d’un spectromètre portable, parallèlement aux estimations de la biomasse avec un
fluorimètre in vivo conçu pour les algues benthiques. La biomasse algale et les assemblages
grossiers ont été différenciés par leur réflectance spectrale comme une preuve de concept
d’une future mise à l’échelle supérieure qui serait nécessaire au suivi régional par
télédétection. Les résultats indiquaient une forte concordance entre les IDNA calculés pour
la réflectance mesurée pour chaque étang et ceux des zones benthiques isolées. Les
cyanobactéries constituaient la composante dominante de la communauté algale de la plu-
part des étangs. De ce fait, les mesures de la réflectance et l’utilisation de simples IDNA
pourraient permettre de caractériser la biomasse totale des étangs du Nord. Cependant, la
distinction entre les groupes d’algues peut nécessiter une validation indépendante des
assemblages d’algues pour des estimations allant au-delà de la biomasse totale. Malgré tout,
l’analyse hyperspectrale offrirait un fort potentiel pour le suivi des systèmes d’eau douce du
Nord à une échelle régionale. [Traduit par la Rédaction]
Mots-clés : suivi hyperspectral, suivi aquatique, biomasse algale, subarctique.
Received 20 November 2018. Accepted 27 August 2019.

K. Ghunowa and R. Bello. Department of Geography, York University, Toronto, ON M3J 1P3, Canada.
A.S. Medeiros. School for Resource and Environmental Studies, College of Sustainability, Dalhousie University, Halifax,
NS B3H 4R2, Canada.
Corresponding author: Andrew Scott Medeiros (e-mail: andrew.medeiros@dal.ca).
This article is open access. This work is licensed under a Creative Commons Attribution 4.0 International License
(CC BY 4.0). http://creativecommons.org/licenses/by/4.0/deed.en_GB.
Arctic Science 5: 240–256 (2019) dx.doi.org/10.1139/as-2018-0030 Published at www.nrcresearchpress.com/as on 10 September 2019.

Ghunowa et al. 241
Introduction
The ability to monitor the productivity of northern freshwater systems is essential for
understanding how environmental change may influence aquatic trophic systems in a
warming future. Freshwater systems of high latitudes are typically oligotrophic, dominated
by benthic primary production due to shallow depths (Rautio et al. 2011; Bos and Pellatt
2012; Symons et al. 2012). These high surface area to volume ecosystems have become
particularly susceptible and responsive to evaporative stress due to warming (Bouchard
et al. 2013; Bakaic and Medeiros 2017). The magnitude and extent of changes in hydrologi-
cal, thermal, and biogeochemical regimes in response to environmental change are likely
to modify algal production at the landscape level and, in turn, aquatic trophic status and
biodiversity (Reist et al. 2006). Therefore, changes in algal biomass are an important indica-
tor of ecological changes and, consequently, ecosystem resilience and vulnerability.
Benthic algae are important contributors to primary production and can be responsible
for 65%–98% of total primary production of shallow northern ponds (Rautio and Vincent
2006) because of their ability to rapidly proliferate at the interface of water and nutrient-
rich bottom sediments in a high-ultraviolet environment (Joint 1978; Hansson 1992).
Cyanobacteria are the most dominant benthic community in northern ponds due to their
high tolerance to cold temperatures (Tang et al. 1997), often forming benthic mats along
the bottom sediments (Jungblut et al. 2010). The colonization of the bottom sediments by
benthic algal communities can stabilize sediments from resuspension in the water column
resulting from the secretion of mucilaginous films (Holland et al. 1974) and can become
sinks of carbon dioxide and methane (Macrae et al. 2004; Reist et al. 2006). Moreover, as sig-
nificant energy sources for the aquatic food web (McCormick and Cairns 1994), benthic
cyanobacteria are an essential component of total ecosystem productivity (Hawes and
Schwarz 1999; Vincent 2000).
Benthic algal communities are routinely monitored using conventional methods such as
point sampling, point-intersect transects, photographic quadrants, and visual assessments
(Bohnsack 1979; Meese and Tomich 1992). However, these methods are intrusive, and
require extensive time, labour, and cost (Werdell and Roesler 2003). Remote sensing has
shown potential as a cost efficient monitoring tool for benthic algae at large scales with
high resolution data acquisition and automated data processing (Malthus and Mumby
2003). Algae absorb light energy using photosynthetic and photoprotective pigments: chlo-
rophylls, carotenoids, and phycobilin. The pigments are taxonomic and phylogenetic mark-
ers with unique absorbance and, thus, reflectance signatures detectable by remote sensors
(Richardson 1996). Algal biomass can be quantified because they produce graded responses
in reflectance at specific wavelengths, which are related to the abundance of their pigments
(Richardson 1996). Remotely sensed reflectance has been successfully used for quantitative
analyses of benthic communities in optically clear shallow coastal and coral reef waters
(Louchard et al. 2003; Bertels et al. 2008), intertidal flats (Carrère et al. 2004; Murphy et al.
2005; Forster and Jesus 2006; Jesus et al. 2008; Tuominen and Lipping 2014), and fluvial sys-
tems (Legleiter et al. 2016).
Developments in hyperspectral sensors offer further possibilities for quantifying algal
pigments and for implementing new algorithms to classify remotely sensed data for moni-
toring aquatic systems at large spatial scales (Hunter et al. 2010; Dörnhöfer and Oppelt
2016). Improvements in spectral and spatial resolution provide a potential for assessments
of water column properties and benthic sediments at shallow depths (Dierssen 2013).
However, limited algorithms exist for monitoring benthic algae (Paterson et al. 1998;
Méléder et al. 2003; Murphy et al. 2005; Kromkamp et al. 2006) and few algorithms use
Published by NRC Research Press

242 Arctic Science Vol. 5, 2019
simple derivative-based methods that have been tested to estimate benthic algae
(e.g., Carrère et al. 2004; Murphy et al. 2005; Jesus et al. 2006a).
Benthic algae are often estimated using empirical spectral ratio indices (e.g., the
normalized difference vegetation index, the soil-adjusted vegetation index, the ratio vegeta-
tion index) developed from terrestrial systems, but Murphy et al. (2005) showed weak
correlations between terrestrial indices and benthic algae. Poor performance of empirical
terrestrial-based algorithms can be to the result of smaller amounts of pigments in benthic
algae compared with terrestrial vegetation, and episodic events resulting in variable
bottom sediment characteristics (Kühl and Jorgensen 1994; Rainey et al. 2000). More impor-
tantly, remote sensing of benthic algae can be challenging because of the composition and
distribution of optically active constituents in the water column (Moore 1980). This includes
solar-induced fluorescence (Serôdio et al. 2009) and specular reflection, which depend on
the angular distribution of photons governed by latitude and time of the day for the data
acquisition. Likewise, coloured dissolved materials, suspended solids, and pelagic algae
partially influence remotely sensed spectral reflectance of bottom sediments due to absorp-
tion and scattering properties of the water column itself (Moore 1980). Consequently, the
unique reflectance signatures of benthic algal pigments can be masked or altered, requir-
ing the application of water column correction algorithms (Zoffoli et al. 2014). Thus, remote
sensing relies on the development and validation of algorithms using in-situ data collec-
tion, and an understanding of the influence of the water column on reflectance of benthic
algae for proper implementation and for scalability to airborne or satellite sensors.
Despite the suitability of remote sensing for providing comprehensive synoptic datasets
for isolated locations, to our knowledge there have not been any studies to monitor benthic
algal communities in northern ecosystems. As such, we investigate the use of hyperspectral
analysis in quantifying benthic algal primary production in shallow ponds of the Hudson
Bay Lowlands (HBL), northern MB, Canada. The HBL is the second largest subarctic peatland
in the world (Gorham 1991). Shallow ponds dominate its landscape and play a key role in
global biogeochemical cycles (Rouse et al. 1997). Because of recent warming (Kaufman
et al. 2009; Hochheim and Barber 2010), they have become particularly susceptible to evapo-
rative stress in the dry summer (Bouchard et al. 2013), which may have a large influence on
their productivity in the future (MacDonald et al. 2015). To assess the application of hyper-
spectral remote sensing to quantify the benthic production of northern landscapes, we
address (1) whether absorption by algal pigments can be detected from ground-based hyper-
spectral measurements, (2) how the water column may influence the spectral reflectance of
bottom sediments, and (3) whether simple indices can be derived to quantify different algal
groups. Our objective is to elucidate the potential for using a hyperspectral approach to
monitor northern ecosystems and for upscaling ground and remotely sensed data to air-
borne platforms.
Materials and methods

Study site
The Hudson Bay Lowlands (HBL), Churchill, MB (58°44′N, 94°49′W) (Fig. 1) is character-
ized by low relief terrain dominated by tundra vegetation, spruce forests, meadows, and
shrubs (Ritchie 1957). Its surficial geology is composed of silt and clay deposits with poor
drainage, and is underlain by Paleozoic dolomite and limestone (Dredge and Nixon 1992).
The climate regime is highly influenced by strong onshore winds generated by Hudson
Bay, and a coastal land–sea breeze (Rouse 1991). The total annual precipitation is dominated
by snow (40%–80%), and the region experiences continuous and discontinuous permafrost
(Rouse et al. 1997). The climate normal for nearby Churchill is −6.9 °C (1971–2010) and

Ghunowa et al. 243
Fig. 1. The location of 30 ponds that were sampled in the Hudson Bay Lowlands, Churchill, MB, Canada, the
location of which is indicated in the inset. Names and coordinates corresponding to numbers are provided in
Supplementary Table S11. Map produced from CanVec digital cartographic reference data produced by Natural
Resources Canada under the Open Government Licence of Canada.
average total precipitation is 431 mm. Shallow ponds occupy approximately 25%–40% of the
surface area (Macrae et al. 2004).
Field measurements
A field survey was conducted in July 2013 between 1100 and 1500 under cloudless
weather conditions to collect ground-based measurements of hyperspectral reflectance
and benthic algal biomass for 30 ponds (Fig. 1; Supplementary Table S11). A sample location
was selected near the shore in each of the cardinal compass directions at each pond.
Reflectance (R) is calculated as the ratio of incident to reflected radiance (L) from an
object or an area over a specified wavelength. A hyperspectral spectroradiometer
(FieldSpec® HandHeld 2, ASD Inc., Longmont, CO, USA) and its spectralon target (which
1
Supplementary material is available with the article through the journal Web site at http://nrcresearchpress.com/doi/
suppl/10.1139/as-2018-0030.

Fig. 2. Schematic diagram showing the path of light as it travels from the atmosphere and is reflected through the
sediment–water continuum (A) and the water column only (B). LdO is the incident radiance below the water–air
interface that is not reflected by the water–air interface, L dA is the incoming ambient radiance, L uR is the
radiance reflected by the water–air interface, L dB is the incident radiance on bottom sediments, L uB is the
reflected radiance from the bottom sediments, LuOB is the reflected radiance from the bottom sediments that is
not reflected by the air–water interface, LuOW is the outgoing radiance from the water column only that is not
reflected by the air–water interface, L uW is the reflected light from the submerged white target, L dW is the
incident radiance on the submerged white target, ZB is the depth of the pond, ZW is the depth of water column
only, L uAW is the outgoing radiance from only the water column measured by the sensor, and L uAB is the
outgoing radiance from the continuum measured by the sensor.
A B
has a near-perfect reflectance = 100%) were used to obtain measurements of radiance at

each sample location (Fig. 2). This instrument’s wavelength range is from 325 to 1075 nm
(±1 nm) with a spectral resolution of 1 nm. It has a fibre optic cable with a sensor that is
pointed directly at the target of interest to obtain a measurement of radiance (which is an
average of three sequential automatic measurements). An L-shaped rod was attached to it
to ensure a 90° field of view and to prevent shadows because the cable was not rigid
(Supplementary Fig. S11). At each sample location, the spectroradiometer was calibrated
and a measurement was taken for the pond’s continuum and the pond’s isolated water col-
umn, respectively. The instrument was calibrated by taking a measurement of incoming
radiance from the atmosphere using the spectralon target (white reference) followed by a
measurement with the sensor closed (dark reference) to correct for instrument response
variables. The measurement for the pond’s continuum was taken at 10 cm above the water
surface to capture radiance leaving both the pond’s bottom sediments and water column.
The measurement for the pond’s water column was also taken at 10 cm above the water
surface using a rectangular white target with near-perfect reflectance submerged at 10 cm
depth (Supplementary Fig. S21). The white target allowed radiance entering the water col-
umn to be reflected to the water surface and prevented radiance from the bottom sedi-
ments to travel through the water column. The use of a white target accounts for higher
reflectance values of the isolated water column than expected in natural waters. A measur-
ing stick was used to ensure that the depth of the water at each location was more than
12 cm to allow the white target to be suspended, and the depth was recorded. The minimum
depth of 12 cm was chosen to prevent disturbance of the bottom sediments by the white
target. Radiance measurements were converted to reflectance using eq. (1). The mean
reflectance of each pond’s continuum and water column was calculated as the average of
the four sample locations’ respective calculated reflectance:
Radiance
(1) ReflectanceðRÞ =
White Reference

Ghunowa et al. 245
In-situ measurements of benthic algal concentrations were taken using a portable fluor-
ometer (BenthoTorch, BBE-Moldaenke, Schwentinental, Germany) at the same sample
locations as the radiance measurements. The fluorometer was submerged under water
and positioned on the substrate to take a measurement of chlorophyll-a concentration
(μg cm−2). Three measurements were taken at each sample location. Concentration of total
algae, concentration of each algal class (cyanobacteria, green algae, and diatoms), and GPS
coordinates were recorded. The mean concentration for each benthic algal biomass variable
(total algae, cyanobacteria, green algae, and diatoms) at each pond was calculated using the
three replicates from the four sample locations. Planktonic biomass was not assessed.
We note that the BenthoTorch does not account for dinoflagellate biomass and (or) the
signal for dinoflagellate biomass may be incorporated in the diatom signal.
Light transmissivity model

According to the Beer–Lambert Law, radiance, Ld(λ;z), at wavelength λ (nm) decreases
exponentially with depth, z (m) once it penetrates the water surface:
(2) Ld ðλ; zÞ = Ld ðλ; 0Þe−K d ðλÞz
where Ld(λ;0) is the radiance at wavelength λ (nm) and at depth 0 m and Kd(λ) is the vertical
attenuation coefficient of radiance in the water column.
A light transmissivity model (as further outlined in the Supplementary Material1) was
developed using the Beer–Lambert Law to calculate the vertical attenuation coefficient of
the water column and the reflectance of bottom sediments (Fig. 2). The equation for esti-
mating vertical attenuation coefficient of the water column was defined as:
0 1
L − ε L
(3) K d = −5 ln@ uAW 1 dA A
ð1 − ε2 Þð1 − ε1 ÞLdA
Using the calculated vertical attenuation coefficient, Kd, the reflectance of the bottom
sediments was estimated as:
LuAB
(4) RB =
ð1 − ε2 Þð1 − ε1 ÞLdA e−ZB K d + ε1 LdA
Indices
A normalized difference algal index (NDAI) was calculated for each algal biomass varia-
ble: total algae, cyanobacteria, green algae, and diatom concentrations, where
ReflectanceλA and ReflectanceλB are the reflectance at wavelengths A and B, respectively;
ReflectanceλA − ReflectanceλB
NDAI =
ReflectanceλA + ReflectanceλB
A normalized approach was used to isolate the spectral reflectance signature of algal
pigments independent of measurement conditions. To determine the best pair of wave-
lengths (A and B) for the index for each algal biomass variable, all possible combinations
of two different 1 nm wavelengths ranging from 420 to 900 nm were generated using
Python software. Thus, NDAIc for every pond was calculated for each pair of wavelengths
using their respective calculated continuum’s reflectance. A linear regression analysis was
performed for each pair of wavelengths to assess the relationship between each algal bio-
mass variable and the calculated NDAI c for the 30 sampled ponds. The pair of

wavelengths whose NDAIc had the highest correlation with each algal biomass variable was
determined to be the optimal pair of wavelengths for the corresponding algal biomass var-
iable’s NDAI c . We chose to present the most significant pairs of wavelengths using
their respective calculated continuum reflectance. Other combinations of wavelengths are
also important and could be adjusted for taxonomic differences with in-situ validation.
An index (NDAIB) for every pond was calculated using bottom sediments’ reflectance for
the same pair of wavelengths (A and B) of the optimal NDAIc. Paired t test statistics were
calculated to determine if there was a difference between the indices derived from
the reflectance of ponds (NDAI c ) and indices using reflectance of their bottom
sediments (NDAIB).
Results
The spectral reflectance of 30 sampled ponds was characterized from 420 to 900 nm by a
continuum of magnitude that incorporated the radiance leaving both the pond’s bottom
sediments and water column (Fig. 3A, Supplementary Fig. S31). The mean reflectance of this
continuum increased from 2.6% to 4.8% from 420 to 520 nm, and further from 4.8% to 7.7%
from 520 to 580 nm. Decreasing reflectance troughs of 7.15% at 625 nm and 5.73% at
678 nm preceded a peak of 9.5% at 710 nm. This was followed by a decrease to 6.2% reflec-
tance at 743 nm, an increase to 7.55% at 815 nm, and decreasing magnitudes from 815 to
900 nm to 3.5% reflectance.
The estimated reflectance of the bottom sediments for the 30 ponds was characterized
by a low, but increasing, reflectance of 1.2%–2.3% from 420 to 600 nm (Fig. 3B). Small peaks
of 2.6% and 3.0% occurred at 605 and 660 nm, respectively. A small trough at 678 of 2.9% pre-
ceded a large increase in reflectance to 8.7% at 730 nm. High, and variable, reflectance of the
bottom sediments continued from 680 to 820 nm, which then declined to 3.3% at 900 nm.
The isolated mean reflectance of the water column estimated from the spectralon target
increased from 34.0 to a high of 53.6% reflectance from 420 to 580 nm (Fig. 3C). A small
trough at 605 nm of 52.8% and 51.6% at 678 nm preceded a decrease in reflectance from
52.1% to 35.6% from 700 to 740 nm. A reflectance peak at 810 nm of 39.1% was followed by
a decline from 39.1% to 20.5% to 900 nm. The resulting estimated attenuation coefficient
calculated decreased from 4.7 to 0.2 cm −1 from 420 to 580 nm (Fig. 3D). From 580 to
700 nm the attenuation coefficient remained from 0.20 to 0.32 cm−1 prior to increasing to
2.35–2.45 cm−1 at 740–760 nm, respectively. A small decline in the attenuation coefficient
to 1.8 cm−1 was estimated at 810 nm, followed by an increase to 5.8 cm−1 to 900 nm.
The total algal concentration (1.07 ± 0.53 μg cm−2) as determined by portable fluorome-
ter was found to be dominated by cyanobacteria (0.73 ± 0.30 μg cm−2) (Fig. 4). Green algae
had a lower mean concentration (0.27 ± 0.32 μg cm−2) but had the highest range in variabil-
ity (0.02–1.64 μg cm−2), with much of the variation from high concentrations found in two
lakes. Among the three algal classes, diatoms had a consistently low mean concentration
across all 30 ponds (0.08 ± 0.08 μg cm−2). Cyanobacteria, green algae, and diatom concentra-
tions were not found to be correlated with each other (Supplementary Table S21). Mean
concentrations for each individual pond can be found in Supplementary Fig. S41.
From all possible combinations of reflectance at wavelengths from 420 to 900 nm, a
normalized difference algal index (NDAI) was calculated. Wavelength pairs with the best
relationship (highest R 2 ) for measured algal concentrations were chosen (Table 1;
Supplementary Table S3 1 ). A statistically significant relationship (p < 0.01) was found
between each measured algal biomass variable (total algae, cyanobacteria, green algae,
and diatoms) and the associated index generated from the sediment–water continuum
(NDAIc; Fig. 5). A positive relationship was found for total algal biomass, cyanobacteria,
and green algae, whereas there was a negative correlation between NDAI c and diatom

Ghunowa et al. 247
Fig. 3. Mean reflectance (%) of 30 sampled ponds in the Hudson Bay Lowlands. Reflectance of the sediment–water
continuum (A), reflectance of the estimated bottom reflectance (B), reflectance of the estimation of the isolated
water column (C), and the calculated attenuation coefficient (D). Shaded zones indicate range of values for each.
Fig. 4. Mean concentration of total algae, cyanobacteria, green algae, and diatoms for 30 sampled ponds in the
Hudson Bay Lowlands sampled using a portable fluorometer (BenthoTorch, BBE-Moldaenke).
concentrations (Table 1, Fig. 5). The difference between indices derived from reflectance
of ponds and indices calculated using reflectance of bottom sediments (NDAI B ) at
the same wavelengths was significant (p < 0.01) for only diatoms and green algae
(Table 2, Fig. 6).

Table 1. Linear regression between derived indices from

reflectance of ponds (NDAIc) and measured algal biomass.
NDAIc and algal biomass
λA λB R2 SE p
Total algae 691 663 0.87 0.01 <0.01
Cyanobacteria 697 695 0.82 0.004 <0.01
Green algae 569 567 0.84 0.004 <0.01
Diatoms 540 546 0.45 0.01 <0.01
Fig. 5. Linear regression between derived indices from reflectance of ponds (NDAIc) and biomass for total algae (A),
cyanobacteria (B), green algae (C), and diatoms (D).
Table 2. Correlation and paired t test showing

the differences between indices derived from
reflectance of ponds (NDAI c ) and indices
calculated using reflectance of bottom
sediments (NDAI B ) at the same wavelengths
(A and B).
NDAIB and NDAIc
R2 p
Total algae 0.38 0.84
Cyanobacteria 0.51 0.88
Green algae 0 0.01
Diatoms 0.17 0.04

Ghunowa et al. 249
Fig. 6. Relationship between indices derived from reflectance of ponds (NDAIc) and indices calculated using
reflectance of bottom sediments (NDAIB) at the same wavelengths for total algae (A), cyanobacteria (B), green
algae (C), and diatoms (D).
Discussion
Although the absorption and scattering properties of lakes and ponds can be affected by
properties of water molecules, coloured dissolved organic matter, detritic and inorganic
suspended particles, pelagic algae, and other planktonic organisms (Moore 1980), our
results show that for 30 shallow ponds near Churchill, MB, reflectance was characterized
by distinctive absorption characteristics of benthic algae. Here, we outline (1) the reflec-
tance properties of the sampled ponds, (2) the optical properties of the water column, and
(3) the optimal wavelengths of indices that could allow this approach to be used for quanti-
fying benthic algal biomass without requiring water column correction. We note that esti-
mates of algal biomass and community composition made in this study rely on
measurements from the BBE-Moldaenke BenthoTorch rather than in-situ measures of algal
groups. In a study of 24 subarctic oligotrophic Swedish streams, Kahlert and McKie (2014)
demonstrated that biomass did not significantly differ between conventional laboratory
methods and measures from a BenthoTorch. Harris and Graham (2015) also showed that
the BenthoTorch compared reasonably well with laboratory measurements for relative
measures of chlorophyll-a, but differences in absolute concentrations and periphyton bio-
mass existed due to thick filamentous algal systems. However, the BenthoTorch does not
account for variability in cell size and the presence of non-chlorophyll biomass in estimat-
ing the proportion of different algal groups, and is, therefore, unable to distinguish red-
fluorescing algal chlorophyll from that of other algal groups (Kahlert and McKie 2014).
Echenique-Subiabre et al. (2016) also note that although significant correlations between
chlorophyll-a measured using the BenthoTorch and spectrophotometry were found for thin
biofilms, bias existed in estimates of community composition for thicker algal mats. Thus,
although the hyperspectral approach used in this study enabled the determination of total

benthic biomass (Fig. 4), the distinction between algal groups may require independent val-
idation of algal assemblages for estimations beyond total biomass.
Reflectance of bottom sediments
Remote sensing using high spatial and spectral resolution may be able to detect and
quantify algal assemblages as they contain taxonomically and phylogenetically significant
pigments that can be discriminated by their unique light absorption characteristics at
specific wavelengths of light. The amount of light absorbed by algal pigments is related to
their abundance and can be quantified as a composite reflectance by remote sensors
(Richardson 1996). We found that the reflectance of bottom sediments of 30 sampled ponds
in the HBL showed unique reflectance characteristics of algal pigments below 720 nm. The
prominent reflectance trough (678 nm) in the red wavelengths’ range indicates possible
absorption by chlorophyll-a pigments (Hunter et al. 2008; Mao et al. 2010; Tuominen and
Lipping 2014). Low reflectance between 600 and 680 nm could indicate absorption by
phycobilins (phycocyanin and phycoerythrin) found in freshwater cyanobacteria and by
chlorophyll-c (638 nm) found in diatoms (Mao et al. 2010). We note that the BenthoTorch
has been shown to underestimate the biomass of phycoerythrin-containing cyanobacteria
(Echenique-Subiabre et al. 2016). Low reflectance in the blue and blue–green wavelengths
range (<600 nm) could be a result of strong absorption of chlorophylls and carotenoids
(Gitelson et al. 1999). The reflectance peak in the near infra-red wavelengths range
(720 nm) indicates possible absorption by chlorophylls (Datt 1999) and algal cell surface scat-
tering (Schalles et al. 1998). Beyond this peak, reflectance in the near infra-red wavelengths
range (>750 nm) is insensitive to algal pigments (Han et al. 1994).
Influence of the water column

The magnitude and shape of reflected light by bottom sediments are partially influenced
by water, pelagic algae, coloured dissolved organic matter (CDOM), and suspended solids
(Richardson and LeDrew 2006). Despite differing magnitudes, reflectance of the water col-
umn among the 30 sampled ponds of this study showed similar optical properties, which
were comparable with the shape of reflectance of turbid water (Moore 1980). Reflectance
was also inversely related to the estimated attenuation coefficient. An increase in attenua-
tion coefficients led to a decrease in reflectance in the blue and near-infrared wavelengths
(<520 and >700 nm, respectively) due to the absorbance of light by suspended solids
(Schiebe et al. 1992; Sváb et al. 2005), CDOM (Curran and Novo 1988; Menken et al. 2006),
and water (Smith and Baker 1981). Suspended solids can also lead to a constant and low
attenuation coefficient between the green and red wavelengths (570–700 nm) and conse-
quently, a constant and high reflectance (Schiebe et al. 1992; Sváb et al. 2005).
Reflectance of pelagic algae have absorption peaks at 650 and 690 nm (Sváb et al. 2005),
and can be detectable with varying concentrations of dissolved organic matter and high
suspended solids (Han et al. 1994; Karabulut and Ceylan 2005). However, substantial absorp-
tion peaks were not present in the reflectance of the water column from 570 to 700 nm for
any sampled ponds. The attenuation coefficient was also near constant and the lowest
within this range. Therefore, the influence of pelagic algae, which can mask the reflectance
of benthic algae, was not evident for the reflectance of the water column. This is consistent
with the findings of Watanabe et al. (2011) on the negligible role of pelagic algae on the
reflectance of northern ponds and the contribution of CDOM and suspended solids on
absorption and scattering.
Although there is an absence of substantial absorption of pelagic algal pigments from
570 to 700 nm, other optically active constituents in the water column and the water itself
could still present challenges to detecting reflectance of bottom sediments and

Ghunowa et al. 251
consequently, benthic algal pigments (Zoffoli et al. 2014). The reflectance of the ponds’
bottom sediments continuously decreased below 720 nm, whereas the reflectance of the
ponds’ continuum showed an increase in reflectance between 580 and 680 nm.
Suspended solids in the water column could have increased reflectance in the green and
red wavelengths’ ranges (Binding et al. 2010). Secondly, light was highly absorbed by water
in the near-infrared wavelengths’ range (>700 nm) because the reflectance of the ponds’
continuum decreased compared with the reflectance of the ponds’ bottom sediments
(Smith and Baker 1981). Despite the influence of the water column on the ranges of the
shorter and longer wavelengths, a trough at 680 nm was discernible in the reflectance of
both the ponds’ continuum and bottom sediments. It is evident that absorption of light
by benthic algal pigments in the red wavelengths’ range was detectable with the presence
of the water column. This is due to the constant and low attenuation coefficient of the
water column of all the ponds between 500 and 720 nm.
To assess the difference between the reflectance of ponds and reflectance of their
bottom sediments, algorithms using two different wavelengths were developed as normal-
ized difference algal indices using the reflectance of ponds (NDAIc), and the same indices
were applied to the reflectance of bottom sediments to calculate normalized difference
algal indices for bottom sediments (NDAIB). The NDAI was based on a statistical process
where the best wavelength pair for the generated index was statistically chosen based on
the region of algal absorption with as little influence of the water column as possible.
However, there were many indices that were found in that area to predict algae
(Supplementary Material1). A significant difference between the indices using reflectance

of ponds’ continuum and bottom sediments was found for diatoms and green algae. This
could be due to an increase in reflectance of the ponds’ bottom sediments by suspended
solid particles such as silt as the wavelengths of their indices were within the green wave-
lengths’ range (Moore 1980). There was not a significant difference between both indices
for total algae and cyanobacteria even though wavelengths of the indices were near the
absorption peaks of pelagic algae (Sváb et al. 2005). More importantly, their wavelengths
were within 680 and 700 nm whereby there was a negligible influence of the water column
and a constant and low attenuation coefficient. Therefore, it is evident that in addition to
pelagic algae, other optically active constituents of the water column and water did not
cause significant interference to the reflectance of bottom sediments at both wavelengths
used by their indices.
Optimal indices
At high latitudes, aquatic ecosystems are characterized by productive benthic algal com-
munities attached to bottom sediments (Björk-Ramberg and Ånell 1985; Bonilla et al. 2005)
and variable pelagic algal production in the water column (Rautio et al. 2011; Bos and Pellatt
2012; Symons et al. 2012). Benthic algal measurements among the 30 sampled ponds of this
study showed that cyanobacteria were the dominant benthic algal community. Bonilla et al.
(2005) similarly found that cyanobacteria represented 92.1% of benthic production, and that
cyanobacteria contributed to 98% of the total pigment stocks at Ward Hunt Lake in the
High Arctic. Green algae and diatoms were also found in basal layers of benthic algal mats
(Bonilla et al. 2005; de los Ríos et al. 2015), similar to the benthic measurements of green
algae and diatoms in this study. The high variability observed for green algae could be due
to their preference for different structures of benthic mats and ecological conditions
(de los Ríos et al. 2015), although our results are skewed by high concentrations observed
in only two of the 30 ponds.
Algal biomass is often estimated using empirical algorithms developed for terrestrial
vegetation, which may not be accurate for aquatic systems and are rarely validated

(Murphy et al. 2005). Algorithms for benthic algal monitoring at the ecosystem level using
remote sensing are currently limited (Paterson et al. 1998; Méléder et al. 2003; Murphy
et al. 2005; Jesus et al. 2006a; Kromkamp et al. 2006). Spectral indices based on ratios of
reflectance and derivative-based algorithms have been successfully tested for estimating
benthic algal biomass (e.g., Carrère et al. 2004; Murphy et al. 2005; Jesus et al. 2006a). Our
approach used simple spectral normalized ratio indices, and found optimal wavelengths
of indices in the red and near-infrared wavelengths for estimating total algal biomass,
primarily comprised of cyanobacteria. The red and near-infrared wavelengths range is
favourable for detecting chlorophyll-a absorption because of the minimal contribution of
accessory pigments and reduced absorption of dissolved organic carbon (Richardson and
LeDrew 2006). Reflectance of chlorophyll-a has been widely used to estimate algal blooms
and terrestrial vegetation (Gitelson 1992; Schalles et al. 1998; Gitelson et al. 1999).
The derived indices for total algae and cyanobacteria of this study were found to be
accurate indicators of their corresponding biomass. Our results also found a weak negative
relationship between diatoms and our biomass index; however, the estimated biomass of
diatoms was extremely low compared with other groups. The dominant presence of the
absorption of phycobilin for cyanobacteria could have influenced the absorption
wavelength of chlorophyll-c of diatoms (Barillé et al. 2007). During high light conditions,
xanthophylls may also become an important absorption mechanism because they provide
photo-protection by regulating the excitation states of chlorophyll (Lohr and Wilhelm
2001; Jesus et al. 2008). Consequently, chlorophyll-a pigment composition is decreased by
pigment dilution (Post et al. 1984). Therefore, measurements of chlorophyll-a concentra-

tions for diatom biomass in shallow ponds may not be accurate in the summer season
and can be limiting in quantifying diatom biomass at high concentrations due to reflec-
tance saturation (Lichtenthaler et al. 1996; Blackburn 1998; Méléder et al. 2003). Diatoms
can also migrate vertically in substrates at greater depths as a response to changes in light
intensities (Paterson 1986; Hay et al. 1993; Jesus et al. 2006b), which was observed by Bonilla
et al. (2005) at higher depths of benthic mats of Ward Hunt Lake. Therefore, estimating
diatom biomass from the surface of substrates may not have provided accurate estimations
of total benthic diatom biomass.
The possibility of monitoring ecosystem biomass at a regional scale is likely possible
with high resolution reflectance spectra. Improvements in the spatial resolution of air-
borne optical instruments can easily extend the scope and application of these methods.
This includes the potential for satellite remote sensing of northern aquatic production at
a circumpolar scale. At a time when environmental change is influencing aquatic produc-
tivity across all scales, the need for accurate monitoring of small northern ponds is
essential for understanding carbon flux and associated feedback mechanisms that could
exacerbate warming. The prohibitive cost associated with monitoring small northern
ponds limits our ability to understand the effects of environmental change at local scales,
as well as predict their influence in the global carbon cycle.
Conclusions
A hyperspectral approach to measuring benthic algal pigments in shallow ponds of the
Hudson Bay Lowlands allowed for estimates of total algal biomass. We found that for
30 sampled ponds, unique reflectance characteristics of algal pigments were present
below 720 nm. Likewise, absorption peaks were not present in the reflectance of the water
column from 570 to 700 nm. Thus, we were able to quantify the relative biomass of benthic
algal communities without interference by pelagic algae. Strong relationships were
observed between measured biomass and an index created for quantifying the sediment–
water continuum for total algae, cyanobacteria, and to a lesser extent, green algae.

Ghunowa et al. 253
Derived indices for total algae and cyanobacteria in this study were found to be accurate
indicators of their corresponding biomass. In addition, there was good correspondence
when indices derived from reflectance of the ponds were applied to reflectance of their
bottom sediments. Reflectance was also inversely related to the estimated attenuation coef-
ficient used to correct for measures across the water–sediment continuum. Our results indi-
cate that optically active constituents of the water column and water did not cause
significant interference to the reflectance of bottom sediments at both wavelengths used
by their indices. Thus, with simple measures of reflectance and use of a NDAI index, total
biomass of northern ponds could potentially be characterized. Our demonstration of
simple indices for the characterization of total algal biomass in northern ponds will reduce
barriers for monitoring aquatic biomass at regional and potentially global scales.
Acknowledgements
Financial assistance for this research was provided by the Northern Scientific Training
Program (NSTP), Polar Knowledge Canada, Dalhousie University, and York University.
Logistic support was provided by Churchill Northern Studies Centre, Churchill, MB. We
are very thankful to Dr. Suzanne Tank for her support in funding acquisition, and Patrick
Shuman and Ryan Ivan Rimas for field data collection and technical support. We are also
very grateful for the comments and insight from two anonymous reviewers that greatly
improved our manuscript.
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Alagal Bloom Analysis

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Alagal Bloom Analysis

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Hyperspectral analysis of algal biomass

Received 20 November 2018. Accepted 27 August 2019.

Arctic Science 5: 240–256 (2019) dx.doi.org/10.1139/as-2018-0030 Published at www.nrcresearchpress.com/as on 10 September 2019.

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Materials and methods

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has a near-perfect reflectance = 100%) were used to obtain measurements of radiance at

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signal for dinoflagellate biomass may be incorporated in the diatom signal.

Light transmissivity model

(2) Ld ðλ; zÞ = Ld ðλ; 0Þe−K d ðλÞz

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Table 1. Linear regression between derived indices from

Table 2. Correlation and paired t test showing

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Influence of the water column

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(Supplementary Material1). A significant difference between the indices using reflectance

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pigment dilution (Post et al. 1984). Therefore, measurements of chlorophyll-a concentra-

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Published by NRC Research Press

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Published by NRC Research Press

hyperspectral remote sensing. J. Coastal Res. 298: 1131–1139. doi: 10.2112/JCOASTRES-D-12-00240.1.

Published by NRC Research Press

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